Science - 07 October 2011

7 October 2011
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CONTENTS Volume 334 Issue 6052
page 41
www.sciencemag.org SCIENCE VOL 334 7 OCTOBER 2011 5
COVER
Scanning electron microscope image of a strand of hair
(about 80 micrometers wide) from the Aboriginal Australian
whose genome was sequenced. The genomic sequence provides
evidence for multiple dispersals into Asia of modern humans.
See page 94.
Courtesy of Timothy P. Topper, Natural History Museum of Denmark
DEPARTMENTS
11 This Week in Science
17 Editors Choice
21 Science Staff
113 New Products
114 Science Careers
page 32
EDITORIAL
15 Genomics Is Not Enough
Aravinda Chakravarti
NEWS OF THE WEEK
22 A roundup of the weeks top stories
NEWS & ANALYSIS
26 Human Cells ClonedAlmost
Where Do Human Eggs Come From?
28 Sifting Medical Records to Determine
Which Therapies Work Best
29 Gene Therapists Celebrate a
Decade of Progress
30 Curious Cosmic Speed-Up
Nabs Nobel Prize
31 Immunology Prize Overshadowed
by Untimely Death of Awardee
NEWS FOCUS
32 An Epoch Debate
A Global Perspective on the Anthropocene
A Sign of Our Times
>> Science Podcast
LETTERS
38 Strategic Success for Hydropower in Laos
G. Guerrier et al.
Justiable Changes to Indicators Survey
C. Toumey and T. Guterbock
NextGenVOICES: Future of a Generation
Exxon-Mobil Funding Overstated
J. L. Bast et al.
39 CORRECTIONS AND CLARIFICATIONS
BOOKS ET AL.
41 Out of This World
M. Ashley
POLICY FORUM
42 Paleolithic Art in Peril:
Policy and Science Collide
at Altamira Cave
C. Saiz-Jimenez et al.
PERSPECTIVES
45 The Guts of Dietary Habits
U. Gophna
>> Report p. 105
46 Resilience to Blooms
J. D. Brookes and C. C. Carey
47 Neuroimmune Communication
E. F. Trakhtenberg and J. L. Goldberg
>> Reports pp. 98 and 101
49 The Genomic Basis of
Local Climatic Adaptation
O. Savolainen
>> Reports pp. 83 and 86
50 Toward Control of Large-Scale
Quantum Computing
D. P. DiVincenzo
>> Report p. 57
51 Diamond Window into the Lower Mantle
B. Harte
>> Research Article p. 54
CONTENTS continued >>
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CONTENTS
pages 49, 83, & 86
pages 47, 98, & 101
page 79
RESEARCH ARTICLE
54 Deep Mantle Cycling of Oceanic Crust:
Evidence from Diamonds and
Their Mineral Inclusions
M. J. Walter et al.
Tiny minerals trapped inside Brazilian
diamonds show that Earths carbon cycle
extends down to the lower mantle.
>> Perspective p. 51
REPORTS
57 Universal Digital Quantum Simulation
with Trapped Ions
B. P. Lanyon et al.
A series of trapped calcium ions was used
to simulate the complex dynamics of an
interacting spin system.
61 Implementing the Quantum von Neumann
Architecture with Superconducting Circuits
M. Mariantoni et al.
A quantum version of a central processing
unit was created with superconducting circuits
and elements.
66 Three-Dimensional Anderson Localization
of Ultracold Matter
S. S. Kondov et al.
A localized and a propagating component
appear when an ultracold atomic gas expands
in a disordered optical potential.
69 Detection of Pulsed Gamma Rays
Above 100 GeV from the Crab Pulsar
The VERITAS Collaboration
This detection constrains the mechanism
and emission region of gamma-ray radiation
in the pulsars magnetosphere.
>> Science Podcast
72 Dispersible Exfoliated Zeolite
Nanosheets and Their Application
as a Selective Membrane
K. Varoon et al.
Thin zeolite lms prepared through a
polymer exfoliation method were used
as selective membranes.
75 A Major Constituent of Brown Algae
for Use in High-Capacity Li-Ion Batteries
I. Kovalenko et al.
Alginate extracts help stabilize silicon
nanoparticles used in a high-capacity
lithium-silicon battery.
79 A Self-Quenched Defect Glass in a
Colloid-Nematic Liquid Crystal Composite
T. A. Wood et al.
A high concentration of colloidal particles
stabilizes a defect network in a liquid crystal
and creates a gel-like material.
83 Adaptation to Climate Across the
Arabidopsis thaliana Genome
A. M. Hancock et al.
Alleles that are under selection in Arabidopsis
serve as genetic markers that can be used to
predict local adaptation.
86 A Map of Local Adaptation in
Arabidopsis thaliana
A. Fournier-Level et al.
Field experiments identify loci associated with
tness and local adaptation in Arabidopsis.
89 The Shaping of Modern Human Immune
Systems by Multiregional Admixture with
Archaic Humans
L. Abi-Rached et al.
Viral defense and embryo implantation
mechanisms have been shaped by
contributions from Neandertal and
Denisovan genes.
94 An Aboriginal Australian Genome Reveals
Separate Human Dispersals into Asia
M. Rasmussen et al.
Whole-genome data indicate that early
modern humans expanded into Australia
62,000 to 75,000 years ago.
98 Acetylcholine-Synthesizing T Cells Relay
Neural Signals in a Vagus Nerve Circuit
M. Rosas-Ballina et al.
A neural circuit that involves a specialized
population of memory T cells regulates
the immune response.
101 Functional Innervation of Hepatic
iNKT Cells Is Immunosuppressive
Following Stroke
C. H. Y. Wong et al.
Neurotransmitters relay immunosuppressive
signals to natural killer T cells after stroke.
105 Linking Long-Term Dietary Patterns
with Gut Microbial Enterotypes
G. D. Wu et al.
The basic composition of the human gut
microbiome is inuenced by long-term diet:
high fat and protein versus high ber.
CONTENTS continued >>
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CONTENTS
SCIENCEXPRESS
www.sciencexpress.org
An Activating Mutation of AKT2
and Human Hypoglycemia
K. Hussain et al.
A key kinase in the insulin signaling pathway
is constitutively activated in humans with
a severe form of hypoglycemia.
10.1126/science.1210878
Stochastic Pulse Regulation in
Bacterial Stress Response
J. C. W. Locke et al.
Energy stress activates an alternative sigma factor
in stochastic pulses and modulates pulse frequency
to control activity.
10.1126/science.1208144
The Inuence of Late Quaternary Climate-Change
Velocity on Species Endemism
B. Sandel et al.
Regions with low glacial-interglacial climate-change
velocity were essential refuges for many small-ranged
species.
10.1126/science.1210173
>> Science Podcast
Hot CarrierAssisted Intrinsic Photoresponse
in Graphene
N. M. Gabor et al.
Photoexcited electrons in graphene remain thermally
excited because they cannot transfer this energy
to lattice vibrations.
10.1126/science.1211384
Lithospheric Thinning Beneath Rifted Regions
of Southern California
V. Lekic et al.
Seismic imaging reveals the degree to which
extensional forces can pull apart the lithosphere.
10.1126/science.1208898
Editorial Expression of Concern
on Puneet et al. Report
B. Alberts
10.1126/science.1214735
SCIENCENOW
www.sciencenow.org
Highlights From Our Daily News Coverage
Ig Nobels Honor Bladder Control,
Beer Bottle Mating
Annual awards recognize the humorous side
of science.
http://scim.ag/_IgNobels
Got War? Blame the Weather
Study argues that climate shifts are behind
most of humankinds maladies.
http://scim.ag/war-weather
Beam Me Up, Ratty
Teleportation study shows that spatial memories
are stored in 125-millisecond packages.
http://scim.ag/rat-beams
SCIENCEONLINE
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SCIENCESIGNALING
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The Signal Transduction Knowledge Environment
4 October issue: http://scim.ag/ss100411
RESEARCH ARTICLE: Genome-Wide Analysis
of a Wnt1-Regulated Transcriptional Network
Implicates Neurodegenerative Pathways
E. M. Wexler et al.
A systems biology approach identies connections
between Wnt1 signaling and neurodegenerative
diseases.
RESEARCH ARTICLE: Itk Controls the Spatiotemporal
Organization of T Cell Activation
K. L. Singleton et al.
Loss of the kinase Itk in activated T cells disrupts
actin accumulation at the immunological synapse,
compromising T cell activation.
PERSPECTIVE: A WNTer Revisit: New Faces
of -Catenin and TCFs in Pluripotency
K. Watanabe and X. Dai
Wnt-stabilized -catenin may enable embryonic
stem cells to resist differentiation by balancing
transcriptional repression and activation.
PODCAST: Science Signaling Podcast: 4 October
2011
A. Levchenko and A. M. VanHook
By working together, cells can overcome
the loss of information as it ows through
a signaling network.
ST NETWATCH: E-RNAi
Get online help designing and evaluating
RNAi reagents.
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Access published proteomics data sets and
contribute your own mass spectrometry data
to an online public repository.
SCIENCETRANSLATIONAL MEDICINE
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Integrating Medicine and Science
5 October issue: http://scim.ag/stm100511
COMMENTARY: The Changing Burden
of Infectious Disease in Europe
R. Fears et al.
Opportunities and challenges are described for
improving disease surveillance and healthcare
innovation to tackle the growing threats of infection.
PERSPECTIVE: Striking a Balance Between
Feasible and Realistic Biological Models
A. Califano
A simple yet elegant quantitative modeling of
oncogene addiction advances our predictive
understanding of this physiological phenomenon.
RESEARCH ARTICLE: Increased Gene Dosage
of Ube3a Results in Autism Traits and Decreased
Glutamate Synaptic Transmission in Mice
S. E. P. Smith et al.
Tripling the dosage of an autism- and Angelman
syndromerelated gene in mice results in reduced
glutamatergic synaptic transmission and autism
behavioral traits.
RESEARCH ARTICLE: Neutrophil-Derived
Cathelicidin Protects from Neointimal Hyperplasia
O. Soehnlein et al.
Cathelicidin-coated stents limit neointima formation.
RESEARCH ARTICLE: Survival and Death Signals
Can Predict Tumor Response to Therapy After
Oncogene Inactivation
P. T. Tran et al.
Modeling survival and death signaling in tumors
by combining quantitative imaging and in situ
biomarker analysis can be used to predict responses
to therapy after oncogene inactivation.
SCIENCECAREERS
www.sciencecareers.org/career_magazine
Free Career Resources for Scientists
Scientists as Competitive-Intelligence Analysts
S. Lout
Scientic training gives applicants most of the skills
companies need to keep track of the competition.
http://scim.ag/Competitive_Intelligence
Taken for Granted: A Way to Improve
Lab-Safety Culture?
B. L. Benderly
A former lab manager argues that modern information
systems hold the key to safer academic labs.
http://scim.ag/rbuDBl
Content Collection: Science Writing and Editing
J. Austin
A collection of the best Science Careers articles
on this popular career path for scientists.
http://scim.ag/CC_Writing
SCIENCEPODCAST
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Free Weekly Show
On the 7 October Science Podcast: climate change and
species distributions, pulsar gamma ray emissions,
the case for the Anthropocene, and more.
SCIENCEINSIDER
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11
EDITED BY STELLA HURTLEY
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Continued on page 13
www.sciencemag.org SCIENCE VOL 334 7 OCTOBER 2011
Rolling in the Deep
The global carbon cycle involves a constant
exchange between oceans, biota, and the
atmosphere. A large portion of the carbon
cycle, however, extends deep into Earths solid
interior, and exchange occurs over much longer
time scales. Walter et al. (p. 54, published
online 15 September; see the Perspective by
Harte) show evidence, through the analysis of a
unique set of Brazilian diamonds, that the deep
carbon cycle extends further into Earth than
previously anticipated. The isotopic signature
of diamonds suggests that they formed from
carbon that originated from subducted oceanic
crust, but tiny mineral inclusions trapped within
the diamonds reveal that they must have passed
through the lower mantle before being sent
back up to Earths surface.
3D Ultracold Anderson
Localization
Random scatterers in a disordered medium may
scatter a propagating wave in such a way that
destructive interference occurs, effectively stop-
ping the propagation; this phenomenon, known
as Anderson localization (AL), has been observed
for light, acoustic, and matter waves. In one and
two dimensions (1D and 2D), AL may occur no
matter how weak the disorder, whereas in 3D, an
energy scale called the mobility edge separates
the states that are localized from those that con-
tinue to propagate. Ultracold atomic gases offer
the opportunity to vary the amount of disorder
systematically and to observe the effects of that
variation on AL. AL has been observed in 1D cold
atom systems; now, Kondov et al. (p. 66) ob-
serve AL in a 3D system and extract the behavior
of the mobility edge and localization length as a
function of disorder.
Looking into the Crab
The Crab pulsar is a spinning neutron star
located in the Crab Nebula, the remnant of a
supernova explosion recorded on Earth in 1054
CE. It is one of the most widely studied objects in
astronomy; yet the origin of its pulsed emission
is not completely understood, particularly at the
highest energies. The VERITAS Collaboration
(p. 69) reports the detection of pulsed emission
above 100 gigaelectron volts from the Crab
pulsar. This result challenges current pulsar
models, which do not predict pulsed emission at
these energies.
Reworking Zeolites
While zeolites have been used as
membranes and catalysts, there
are still substantial challenges
in processing zeolitic materi-
als into extended sheets.
Varoon et al. (p. 72)
show that a polymer
can be used to exfoli-
ate zeolite particles into akes and control their
deposition onto a substrate. Packing of the exfoli-
ated sheets allows the production of membranes
with enhanced ltration properties, compared with
a mixture of isotropically oriented nanoparticles.
Algae to the Rescue
A number of new battery chemistries may al-
low for greater charge storage beyond what is
currently possible with lithium-metal systems.
However, during charge-discharge cycles,
volume changes can degrade the anode. Previ-
ous attempts to create a Li-Si battery have used
a high fraction of binder material to stabilize
Si. Kovalenko et al. (p. 75, published online
8 September) show that alginate, a natural
polysaccharide extracted from brown algae,
works as an excellent binder and can stabilize
nanometer-sized Si powders.
Liquid Crystal Gels
In liquid crystals, the weak interactions between
the anisotropic molecules can give rise to long-
range ordering and inuence the optical and
rheological properties. The orientation of the mol-
ecules can be further biased by the addition of a
second material to the liquid crystal. Wood et al.
(p. 79) now describe gels or soft solids that form
in concentrated colloid-liquid crystal composites.
The mechanical properties of the gels arise
from the formation of particle-stabilized
defects, which form a percolated network
throughout the liquid crystal.
Local Adaptation Revealed
As climate changes, it is important to understand
how species have adapted to their current envi-
ronment at the genetic level (see the Perspective
by Savolainen). Fournier-Level et al. (p. 86)
examined local adaptation of single-nucleotide
polymorphisms in Arabidopsis thaliana, by map-
ping tness as a phenotype for the plant
A. thaliana in a number of different populations,
and provide insights into the process of local ad-
aptation. Hancock et al. (p. 83) take a comple-
A digital quantum simulator is a device that can be programmed and repro-
grammed to simulate any other quantum system efciently (see the Perspec-
tive by DiVincenzo). Lanyon et al. (p. 57, published online 1 September)
show that the ability to control and manipulate the interactions between
a series of trapped ions has the potential to create a powerful quantum
simulator. A series of six trapped and laser-cooled calcium ions were used
to simulate complex dynamics associated with interacting spin systems.
Quantum computers offer the possibility of solving problems that cannot be
tackled by classical computers. Mariantoni et al. (p. 61, published online 1
September) integrated a series of superconducting circuits and elements to
construct a rudimentary machine where quantum information travels back
and forth between storage elements and processing elements.
<< Quantum Simulation and Computers
Perform an Apples-to-Apples
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including Therma-Base; (b): 384-well plate on
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Data generated at Roche Applied Science.
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Roche Applied Science
Indianapolis, Indiana
This Week in Science
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mentary approach by using genome scans to identify local adaptation and predict tness in the eld.
The work suggests that populations of A. thaliana are best adapted to their locations on a continental
scale via adaptation of specic genetic loci.
Genomic Antiquities
It is likely that many human populations are the descendants of modern and archaic hominids.
Abi-Rached et al. (p. 89, published online 25 August) examined the HLA-A, HLA-B, and HLA-C genes
(which play central roles in immune defense and placental reproduction) of archaic Denisovan and
Neandertal individuals and modern humans. Population genetic evidence suggests that interbreeding
between archaic and modern hominids introduced an allele of HLA-B that subsequently reached appre-
ciable frequency in some modern human populations. Thus, admixture probably introduced advanta-
geous genetic alleles that may have been involved in shaping the immune system of modern humans.
Locks Open Up Human Migration
There has been much speculation on how early modern humans dispersed after leaving Africa and
how they moved across Asia. To address this question, Rasmussen et al. (p. 94, published online
22 September; see the cover) sequenced the genome of an Aboriginal Australian from a 100-year-
old lock of hair. The sequence would suggest that eastern Asians were the rst to populate Australia
and that modern Australian Aborigines are descended from that early dispersal. Furthermore, the ge-
nomes of three Han Chinese were sequenced and compared with the previously sequenced genomes
of Europeans and Africans, to infer the history and dispersal patterns associated with the more recent
origins of modern east Asians and Europeans. Aboriginal Australians probably arose from the same
ancestral population as Eurasians, at a time before the Asian and European populations diverged.
Nerves and T Cells Connect
Links between the nervous system and the immune system are becoming better understood (see the
Perspective by Trakhtenberg and Goldberg). The vagus nerve, which originates in the brainstem and
innervates major organs, including the spleen and the gut, regulates physiological responses to stress,
injury, and infection. Electrical stimulation
of the vagus nerve reduces the production of
inammatory cytokines and inammation-
associated pathology, primarily by acting
on cytokine-producing macrophages in the
spleen. Working in mice, Rosas-Ballina et
al. (p. 98, published online 15 September) found that a subpopulation of helper T cells produced
acetylcholine in the spleen and were necessary and sufcient for vagus-nervemediated inhibition of
proinammatory cytokine production. In order to prevent immune-related pathology that is induced
by tissue damage, the poststroke brain produces signals that result in immunosuppression. In a mouse
model of stroke, Wong et al. (p. 101, published online 15 September) found that stroke induced
changes in natural killer T cell movement in the liver and altered the range of cytokines they secrete
toward a more immunoregulatory prole. These changes were dependent on noradrenergic signaling.
You Are What You Eat
Different members of the human gut microbiota have distinct and characteristic inuences on health
and disease. Wu et al. (p. 105, published online 1 September; see the Perspective by Gophna)
attempted to characterize the dietary and environmental variables that affect the microbiota in a
pair of studies on humans. In one study, stool samples were taken for microbial sequencing from
99 volunteers whose long-term dietary preferences were known and dened. In another study, 10
people were segregated and put on controlled diets, and their stools were sampled at 1 and 10
days after recruitment. In the long-term study, three distinct microbiomes were apparent, which had
characteristic signature organisms: A Bacteroides-dominated community was associated with people
who ate animal protein and saturated fats, Ruminococcus tended to be linked with alcohol intake
and polyunsaturated fat consumption, andnallyPrevotella was found in people who enjoyed
a carbohydrate-based diet. Although dietary perturbation in the short-term study caused a transient
change in the respective enterotype, there were no marked shifts from one enterotype to another.
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Continued from page 11
Genomics Is Not Enough
NEXT WEEK, THE INTERNATIONAL CONGRESS OF HUMAN GENETICS CONVENES IN MONTREAL, WHERE
genomic science, its technologies, genetic disease, and personalized medicine will be dis-
cussed. Translating current knowledge into medical practice is an important goal for the
public who support medical research, and for the scientists and clinicians who articulate the
critical research needs of our time. However, despite innumerable successful gene discov-
eries through genomics, a major impediment is our lack of knowledge of how these genes
affect the fundamental biological mechanisms that are dysregulated in disease. If genomic
medicine is to prosper, we need to turn our attention to this gaping hole.
Advances in biomedical research have raised high expectations for translating research into
medical applications, including individualizing treatment and prevention. The concept of indi-
vidualized medicine is not new to genetics. The identication of numerous inborn errors of
metabolism and the discovery of their associated enzyme deciencies
paved the way for their specic genetic diagnosis and treatment. How-
ever, understanding their biological mechanisms was key. For example,
severe mental retardation can arise from the effects of systemic phenyl-
alanine accumulation on the brain, a condition called phenylketonuria.
It was determining the underlying cause as a recessive genetic defect
in the liver enzyme phenylalanine hydroxylase that led to individual-
ized treatment and public health screening of newborns for the disorder.
Today, genomics technologies can routinely scan the human
genome for genetic alterations in any disorder: More than 2000
single-gene Mendelian diseases have been elucidated in this way.
Finding the genetic changes that cause the remaining 2000 Mende-
lian diseases appears within reach. But despite many efforts, attaining
a similar understanding of common, chronic, complex diseases has
been disappointing. Here, to bring major medical benet, biomedical
research must move beyond simple gene discovery by mapping, sequencing, or genome-wide
association studies to focus on understanding human disease mechanisms. We need to answer
not only which DNA variants in which genes lead to disease, but how they do so.
The lessons from genome biology are quite clear. Genes and their products almost never
act alone, but in networks with other genes and proteins and in context of the environment.
The corollary to this is that compromising the activity of one gene need not cripple an entire
network. This is consistent with the observations that most traits involve multiple genes,
common complex disorders arise from an accumulation of genetic defects in many genes,
and Mendelian diseases are rare. Moreover, variation in the regulatory machinery of genes is
much more frequent than that in the structure of gene products. Genome biology now needs
to move to cell biology and physiology (systems biology) to understand how genetic pertur-
bations lead to downstream dysregulation of proteins, their networks, and cells in disease.
Our evolving knowledge of genetic variation complicates this understanding. Each indi-
vidual is genomically unique, with the DNA variation in our genomes serving as markers
of our ancestries. Are each individuals biology and disease also unique? Or does the exten-
sive sequence diversity in any disease coalesce into a smaller set of common functional
deciencies? By focusing on a mechanistic understanding of disease, genomic science has
much to offer and can provide concrete suggestions about when medical treatment needs to
be individualized and when made universal. These answers will themselves evolve as the
science evolves. Consider the simple example of blood typing for everyday transfusions.
This is individualized treatment that ignores widespread differences in type frequency
between different populations because the focus of treatment is the individual, not the group.
Recent research offers the future possibility of enzymatic treatment of any blood type to
make it the universal type O, thus making a once successful individualized treatment univer-
sal. As this example shows, for genomic medicine there is no time with a more acute need
for science than now.
10.1126/science.1214458
15
EDITORIAL
C
R
E
D
I
T
S
:

(
L
E
F
T
)

J
O
H
N
S

H
O
P
K
I
N
S

U
N
I
V
E
R
S
I
T
Y

S
C
H
O
O
L

O
F

M
E
D
I
C
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E
;

(
R
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T
)

T
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K

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M
A
G
E
/
S
C
I
E
N
C
E

P
H
O
T
O

L
I
B
R
A
R
Y
is a professor at the
McKusick-Nathans
Institute of Genetic
Medicine at the Johns
Hopkins University of
Medicine, Baltimore,
MD. E-mail: aravinda@
jhmi.edu.
Risk-free
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17
EDITORSCHOICE
EDITED BY KRISTEN MUELLER AND PHILLIP SZUROMI
C
R
E
D
I
T
:

A
G
G
A
R
W
A
L

E
T

A
L
.
,

D
E
V
.

C
E
L
L

2
1
,

4
4
5

(
2
0
1
1
)
involved in the sorting of lipids and membrane
proteins to the apical plasma membrane and
were key to the expansion of the apical domains
required for intestinal lumen formation. SMH
Nat. Cell Biol. 13, 10.1038/ncb2328 (2011).
B I O C H E MI S T R Y
Synchronized Stepping
Inside the cell, ensembles of different myosin
proteins attached to a single cargo molecule
allow for bidirectional transport along actin
tracks. To gain insight into the coordination
that must be required to deliver the cargo to its
destination, Ali et al. labeled myosin V (myoV)
and myosin VI (myoVI), which move in opposite
directions, with different colored quantum
dots. They coupled the motors through a third
quantum dot cargo and used total internal
uorescence microscopy to determine the
stepping dynamics of each individual motor.
Though the motors have similar stall forces,
myoV dominated ~80% of the time, prob-
ably because it has a higher unbinding force
than myoVI. Regardless of which motor won,
its movement was signicantly slowed by the
losing motor which, interestingly, took continu-
ous backward steps coincident with the forward
steps of the winning motor. In the presence of
micromolar concentrations of ADP, myoVI domi-
nated by acting as an anchor that prevented
myoV from stepping forward. The dominant
motor could also be shifted by varying the
myoV:myoVI:cargo conjugation ratio, consistent
with regulation by varying the ratio of motor
types bound to cargo. Such approaches that
provide a mechanochemical understanding of
motor coupling will be valuable in efforts to
model the regulatory mechanisms that govern
intracellular transport. VV
Proc. Natl. Acad. Sci. U.S.A. 108, E535 (2011).
A P P L I E D P H Y S I C S
Directing Single Photons
Photons are ideal carriers of bits of informa-
tionthey are fast, robust, and can travel
long distances. For secure applications such
as quantum key distribution for cryptography,
the information is conveyed by single photons.
Compared with classical keys, an attack on the
communication channel by an eavesdropper
that uses a quantum key is readily detected.
Quantum dots are useful sources of single
photons and can be integrated into on-chip
waveguides that direct where the single
C E L L B I O L O G Y
Going Tubular
Lipids provide the building blocks for cell
membranes but can also play a role in intracel-
lular membrane trafcking and signaling. In
nematodes, the gut develops from a tubular epi-
thelium that has very distinct apical membranes
that will be exposed to materials originating
outside the organism, as compared with the ba-
solateral membranes that communicate with the
interior of the organism. Zhang et al. wanted to
understand the role of lipids during the process
of organ formation in C. elegans. By systemati-
cally targeting lipid biosynthetic pathways and
examining changes in intestinal tubulogenesis,
the authors conrmed an essential role for gly-
cosphingolipids in maintaining epithelial polarity
and thereby the integrity of the central lumen
of the developing gut. Glycosphingolipids were
The myelin membrane that wraps around axons is essential for the speedy transmission of elec-
trical signals in the nervous system. Myelin is produced by oligodendrocytes and differs from
most cellular membranes because of its unusually high lipid content and exclusion of large
proteins: a composition that is optimized for the transmission of nerve impulses. Using an
in vitro culture system, Aggarwal et al. studied how oligodendrocytes are able to create these
specialized membranes. The membrane sheets are so thin that most cellular organelles cannot
encroach, keeping them restricted to the fatter parts of the cell body. With vesicle transport
excluded as a mechanism, the authors found that the composition of the membranes is regu-
lated within the membrane domain, by myelin basic protein (MBP), which acts as a regulator
of diffusion. In the absence of MBP, the exclusion of proteins with an overlarge cytoplasmic
domain from the membrane was disrupted. Thus MBP, which appears to be spread throughout
the myelin sheet, is critical for restricting access so that only a few, primarily small proteins
are integrated into the myelin sheet. PJH
Dev. Cell 21, 445 (2011).
i get data faster with 20x more assay choices
i amTaqMan
*Certain terms and conditions apply. To obtain a copy of the full terms and conditions of the guarantee, visit www.appliedbiosystems.com/taqmanguarantee.
For Research Use Only. Not intended for any animal or human therapeutic or diagnostic use. 2011 Life Technologies Corporation. All rights reserved. The trademarks mentioned herein are the
property of Life Technologies Corporation or their respective owners. TaqMan
is a registered trademark of Roche Molecular Systems, Inc., used under permission and license. CO23566 0711
The TaqMan
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Speed through samples with the largest collection of pre-optimized assays
EDITORSCHOICE
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A
photons go. However, extracting the photons
from the waveguide into an external commu-
nication channel (such as an optical ber) is
often inefcient because the photons undergo
internal reection at the waveguides interfaces.
Davanco et al. have designed a system whereby
a tapered ber waveguide is coupled to a
semiconductor waveguide that contains quan-
tum dots. The geometry of the semiconductor
waveguide is designed so that the properties of
the generated single photons can be selected
and matched to that of the tapered ber. This
matching enhances the extraction of the single
photons from the semiconductor waveguide
into the tapered ber. ISO
Appl. Phys. Lett. 99, 121101 (2011).
C H E MI S T R Y
Controlling Cluster Color
Strongly photoluminescent materials that
respond to changes in their environment, such
as mechanical stress or chemical solvation, are
useful in sensing applications. Lasanta et al.
synthesized gold-silver clusters by reacting gold
bearing a halogenated phenyl ligand (2-C
6
F
4
I,
R
II
) with silver triuoroacetate [Ag(tfa)]. Crystal-
lographic analysis revealed that the resulting
anionic compound, [Au
2
Ag
2
(2-C
6
F
4
I)
4
(tfa)
2
]
2
,
forms through metallophilic interactionsthe
bridging silver atoms each bear a tfa ligand and
coordinate to two gold atomsand through
halogen bonds between iodine and gold atoms.
This compound has strong green luminescence,
but the addition of a coordinating solvent such
as acetonitrile initially creates a dimeric form of
the compound through gold bridging inter-
actions. In this yellow luminescent material, the
silver atoms bear no coordinating solvent. After
a few minutes, the nal polymeric form, a red
emitter, forms through additional gold bridges
and coordinates acetonitrile at the silver atoms.
The monomeric form could be recovered by
aging for several hours or by grinding the
polymer in excess tfa. PDS
J. Am. Chem. Soc. 131, 10.1021/
ja206845s (2011).
MAT E R I A L S S C I E N C E
Mining for Pores
Porous networks within coal can determine its
value as a fuel; porosity helps dene how well
certain types of coal burn and whether methane
in the pores can be extracted efciently from
coal beds as an additional source of energy.
Determining the porosity of complex natural ma-
terials such as coal is difcult, because a sample
may contain many networks of pores that can be
often disconnected from each other and from the
surface of samples. Although several techniques
for measuring porosity exist, Melnichenko et al.
used small-angle neutron scattering to examine
the interconnectivity of pores within coal samples
as a function of pore size in a noninvasive and
quantitative manner. They compared the scat-
tering proles of a coal sample in a vacuum
and the same sample saturated with contrast-
matching gases that ll accessible pores and
make them invisible to the neutron beam. The
analysis conrms that the proportion of isolated
and accessible pores varies widely based on coal
type, but also shows that pore accessibility varies
with gas overpressure. These results may eventu-
ally help determine the feasibility of enhanced
methane recovery from coal beds by injecting
CO
2
gas at high pressure. NW
Fuel 90, 10.1016/j.fuel.2011.06.026 (2011).
B I O ME D I C I N E
Targeting Asthma
Asthma is a major public health problem. There
are a variety of causes of asthma, and the
pathogenesis of the disease is quite heteroge-
neous. Despite this, most patients are treated
with broadly immunosuppressive glucocorti-
coids, which do not always control disease. Thus,
there is substantial interest in developing more
targeted therapies that may be used to treat
specic clinical subtypes of patients.
Interleukin-13 (IL-13) is a cytokine that is
associated with the T helper 2 type responses
seen in many asthma patients and in a subset
of patients remains elevated even in the face of
glucocorticoid treatment. In a placebo-controlled
phase II clinical trial, Corren et al. now show that
treatment of adult asthma patients on gluco-
corticoid therapy with a monoclonal antibody
against IL-13 signicantly improved lung func-
tion. Patients with higher IL-13 levels showed
the greatest effect. Although the trend toward
reduced disease exacerbations in treated patients
did not reach statistical signicance, this study
does suggest that a targeted approach to asthma
therapy is worth pursuing. KLM
N. Engl. J. Med. 365, 1088 (2011).
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respective owners. TaqMan
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21
www.sciencemag.org
SENIOR EDITORIAL BOARD
A. Paul Alivisatos, Lawrence Berkeley Nat'l. Laboratory
Cori Bargmann, The Rockefeller Univ.
Ernst Fehr, Univ. of Zurich
Richard Losick, Harvard Univ.
Michael S. Turner, University of Chicago
BOARD OF REVIEWING EDITORS
Adriano Aguzzi, Univ. Hospital Zrich
Takuzo Aida, Univ. of Tokyo
Sonia Altizer, Univ. of Georgia
Sebastian Amigorena, Institut Curie
Angelika Amon, MIT
Kathryn Anderson, Memorial Sloan-Kettering Cancer Center
Siv G. E. Andersson, Uppsala Univ.
Peter Andolfatto, Princeton Univ.
Meinrat O. Andreae, Max Planck Inst., Mainz
John A. Bargh, Yale Univ.
Ben Barres, Stanford Medical School
Jordi Bascompte, Estacin Biolgica de Doana, CSIC
Facundo Batista, London Research Inst.
Ray H. Baughman, Univ. of Texas, Dallas
David Baum, Univ. of Wisconsin
Yasmine Belkaid, NIAID, NIH
Philip Benfey, Duke Univ.
Stephen J. Benkovic, Penn State Univ.
Gregory C. Beroza, Stanford Univ.
Peer Bork, EMBL
Bernard Bourdon, Ecole Normale Superieure de Lyon
Ian Boyd, Univ. of St. Andrews
Paul M. Brakeeld, Univ. of Cambridge
Christian Bchel, Universittsklinikum Hamburg-Eppendorf
Joseph A. Burns, Cornell Univ.
William P. Butz, Population Reference Bureau
Gyorgy Buzsaki, Rutgers Univ.
Mats Carlsson, Univ. of Oslo
Mildred Cho, Stanford Univ.
David Clapham, Childrens Hospital, Boston
David Clary, Univ. of Oxford
J. M. Claverie, CNRS, Marseille
Jonathan D. Cohen, Princeton Univ.
Robert Cook-Deegan, Duke Univ.
Alan Cowman, Walter & Eliza Hall Inst.
Robert H. Crabtree, Yale Univ.
Wolfgang Cramer, Medit. Inst. for Ecology & Paleoecology
F. Fleming Crim, Univ. of Wisconsin
Jeff L. Dangl, Univ. of North Carolina
Tom Daniel, Univ. of Washington
Stanislas Dehaene, Collge de France
Emmanouil T. Dermitzakis, Univ. of Geneva Medical School
Robert Desimone, MIT
Claude Desplan, New York Univ.
Ap Dijksterhuis, Radboud Univ. of Nijmegen
Dennis Discher, Univ. of Pennsylvania
Jennifer A. Doudna, Univ. of California, Berkeley
Julian Downward, Cancer Research UK
Bruce Dunn, Univ. of California, Los Angeles
Christopher Dye, WHO
David Ehrhardt, Carnegie Inst. of Washington
Michael B. Elowitz, Calif. Inst. of Technology
Tim Elston, Univ. of North Carolina at Chapel Hill
Gerhard Ertl, Fritz-Haber-Institut, Berlin
Barry Everitt, Univ. of Cambridge
Paul G. Falkowski, Rutgers Univ.
Ernst Fehr, Univ. of Zurich
Tom Fenchel, Univ. of Copenhagen
Alain Fischer, INSERM
Wulfram Gerstner, EPFL Lausanne
Karl-Heinz Glassmeier, TU Braunschweig
Diane Grifn, Johns Hopkins Bloomberg School of
Public Health
Elizabeth Grove, Univ. of Chicago
Taekjip Ha, Univ. of Illinois at Urbana-Champaign
Christian Haass, Ludwig Maximilians Univ.
Steven Hahn, Fred Hutchinson Cancer Research Center
Gregory J. Hannon, Cold Spring Harbor Lab.
Martin Heimann, Max Planck Inst., Jena
Isaac Held, NOAA
James A. Hendler, Rensselaer Polytechnic Inst.
Janet G. Hering, Swiss Fed. Inst. of Aquatic
Science & Technology
Ray Hilborn, Univ. of Washington
Michael E. Himmel, National Renewable Energy Lab.
Kai-Uwe Hinrichs, Univ. of Bremen
Kei Hirose, Tokyo Inst. of Technology
David Hodell, Univ. of Cambridge
Ove Hoegh-Guldberg, Univ. of Queensland
David Holden, Imperial College
Lora Hooper, UT Southwestern Medical Ctr at Dallas
Jeffrey A. Hubbell, EPFL Lausanne
Steven Jacobsen, Univ. of California, Los Angeles
Kai Johnsson, EPFL Lausanne
Peter Jonas, Universitt Freiburg
William Kaelin, Dana-Farber Cancer Inst.
Barbara B. Kahn, Harvard Medical School
Daniel Kahne, Harvard Univ.
Bernhard Keimer, Max Planck Inst., Stuttgart
Joel Kingsolver, Univ. of North Carolina at Chapel Hill
Robert Kingston, Harvard Medical School
Alberto R. Kornblihtt, Univ. of Buenos Aires
Leonid Kruglyak, Princeton Univ.
Mitchell A. Lazar, Univ. of Pennsylvania
David Lazer, Harvard Univ.
Virginia Lee, Univ. of Pennsylvania
Ottoline Leyser, Cambridge Univ.
Olle Lindvall, Univ. Hospital, Lund
Marcia C. Linn, Univ. of California, Berkeley
John Lis, Cornell Univ.
Jianguo Liu, Michigan State Univ.
Richard Losick, Harvard Univ.
Jonathan Losos, Harvard Univ.
Ke Lu, Chinese Acad. of Sciences
Laura Machesky, CRUK Beatson Inst. for Cancer Research
Andrew P. MacKenzie, Univ. of St Andrews
Anne Magurran, Univ. of St Andrews
Oscar Marin, CSIC & Univ. Miguel Hernndez
Charles Marshall, Univ. of California, Berkeley
Martin M. Matzuk, Baylor College of Medicine
Graham Medley, Univ. of Warwick
Yasushi Miyashita, Univ. of Tokyo
Richard Morris, Univ. of Edinburgh
Edvard Moser, Norwegian Univ. of Science and Technology
Sean Munro, MRC Lab. of Molecular Biology
Thomas Murray, The Hastings Center
Naoto Nagaosa, Univ. of Tokyo
James Nelson, Stanford Univ. School of Med.
Timothy W. Nilsen, Case Western Reserve Univ.
Pr Nordlund, Karolinska Inst.
Helga Nowotny, European Research Advisory Board
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Stuart H. Orkin, Dana-Farber Cancer Inst.
Christine Ortiz, MIT
Elinor Ostrom, Indiana Univ.
Andrew Oswald, Univ. of Warwick
Jane Parker, Max-Planck Inst. of Plant Breeding Research
Donald R. Paul, Univ. of Texas at Austin
P. David Pearson, Univ. of California, Berkeley
Reginald M. Penner, Univ. of California, Irvine
John H. J. Petrini, Memorial Sloan-Kettering Cancer Center
Simon Phillpot, Univ. of Florida
Philippe Poulin, CNRS
Colin Renfrew, Univ. of Cambridge
Trevor Robbins, Univ. of Cambridge
Barbara A. Romanowicz, Univ. of California, Berkeley
Jens Rostrup-Nielsen, Haldor Topsoe
Edward M. Rubin, Lawrence Berkeley National Lab
Mike Ryan, Univ. of Texas, Austin
Shimon Sakaguchi, Kyoto Univ.
Miquel Salmeron, Lawrence Berkeley National Lab
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Joseph Silk, Univ. of Oxford
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Alison Smith, John Innes Centre
Davor Solter, Inst. of Medical Biology, Singapore
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Allan C. Spradling, Carnegie Institution of Washington
Jonathan Sprent, Garvan Inst. of Medical Research
Elsbeth Stern, ETH Zrich
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Bert Vogelstein, Johns Hopkins Univ.
Cynthia Volkert, Univ. of Gottingen
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Jonathan Weissman, Univ. of California, San Francisco
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Ian A. Wilson, The Scripps Res. Inst.
Timothy D. Wilson, Univ. of Virginia
Jan Zaanen, Leiden Univ.
Kenneth Zaret, Univ. of Penn. School of Medicine
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Jonathan Zehr, Univ. of California, Santa Cruz
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7 OCTOBER 2011 VOL 334 SCIENCE www.sciencemag.org 22
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from that time. We accept that, and would
like to ask for forgiveness.
http://scim.ag/Namibianskulls
Ottawa 2
Canadas Top Court Keeps
Injecting Drug Use Site Open
The Supreme Court of Canada has ruled that
a safe injection site in Vancouver that aims
to thwart the spread of HIV can continue
to operate, providing a place for people to
inject drugs under medical supervision and
without the threat of arrest.
The federal government, including the
minister of health, had argued that the facil-
ity, called Insite, should close because it
violated the countrys laws about posses-
sion and trafcking of controlled substances.
The effect of denying the services of Insite
to the population it serves and the correlative
increase in the risk of death and disease to
injection drug users is grossly disproportion-
ate to any benet that Canada might derive
from presenting a uniform stance on the pos-
session of narcotics, the court wrote in its
unanimous decision.
Studies have shown that Insite has
reduced overdose deaths and the risk of
becoming infected with HIV and also led
to increased use of addiction treatment pro-
grams. Insite kept its doors open during the
court challenge and for now will continue to
operate under an exemption to the federal
substance control laws.
Tokyo 3
Nuclear Power Takes Hit
As Science Spending Rises
Japans ministry of education wants to boost
overall science-related spending next year
by 5.8%, to $14.7 billion. But spending on
nuclear-related research will drop 9.8%, to
$2.3 billion.
The ruling Democratic Party has pro-
posed $918 million in new programs to
accelerate the efforts of renewable and alter-
native energy schemes. Work on induced
pluripotent stem cells and regenerative
medicine will jump by 40%, to $69 million,
and space-related research, including Earth
observation, which will go up by 36%, to
$631 million. Rank-and-le researchers will
benet from a 6% increase, to $3 billion, in
competitively reviewed grants, including
substantial growth in a multi-year grant cat-
egory created last year.
Although increasing reliance on nuclear
power remains ofcial government policy,
the radiation release from the damaged
Fukushima Daiichi Nuclear Power Plant
has turned many politicians and the public
against that energy source. Japans troubled
experimental fast breeder reactor, Monju,
would receive a maintenance budget pend-
ing a review of the nations energy policy
http://scim.ag/Japanbudget
Faroe Islands 4
Project to Sequence Entire
Population Announced
The inhabitants of the Faroe Islands could
become the worlds rst fully sequenced
population, researchers announced at a
meeting on personal genomes at Cold
Spring Harbor Laboratory last week. The
project, dubbed FarGen, aims to sequence
the entire genome of every citizen and to
use the information for health care and
research in the self-governing Danish
dependency. A pilot project sequencing the
genomes of 100 individuals is under way.
If all goes according to plan, the rest of the
50,000 Faroe Islanders will follow in the
next 5 years, scientists said.
Namibia 1
Germany Returns Colonial-Era
Skulls to Namibia
The skulls of 20 Namibians killed by Ger-
man colonists a century ago returned to
Namibia on 4 October. The skulls have been
part of the anatomy collection at the Charit
University Hospital in Berlin and the Berlin
Medical Historical Museum for more than
a century. Namibian leaders asked in 2008
that they be returned. In a project launched
last year, researchers have been working to
identify where the estimated 7000 skulls in
the hospitals collections came from, and
which ones should be repatriated.
The scientists studied inscriptions on the
skulls referring to catalogs or publications,
says Charit anatomist Andreas Winkelmann,
one of the projects leaders. They also looked
for indicators of sex, age of death, and traces
of disease such as scurvy, which was rampant
at a prison camp on Namibias Shark Island
where many of the skulls came from.
The project is ongoing, Winkelmann
says. We also want to nd out more about
the scientic historical context. We have not
yet looked at who was involved in the col-
lecting and why they did what they did.
Museum director Thomas Shnalke noted
at a press conference last week in Berlin that
German science carries a burden of guilt
3
4
1
6
7
AROUND THE WORLD
>Its tough getting older, but this is
one birthday were happy to celebrate.
Sciences daily online news site Science-
NOW turns 15 today. In the past decade-
and-a-half, ScienceNOW has covered the
hottestand some of the most bizarre
stories in science, from early claims for
martian life to fellatio among fruit bats.
Check out our full coverage (http://scim.
ag/ScienceNOW15) and share your favor-
ite ScienceNOW stories.
NOTED
One of 20
skulls that
were returned
to Namibia
this week.
2
5
NEWS
Roses Are Red,
Roses Are Bluish
A 25-year struggle to sell genetically-
engineered blue roses in the United
States took a big step forward last week.
The U.S. Department of Agri culture
wont regulate U.S. efforts to grow and
sell the owers after concluding that
two mauve hybrids created by Austra-
lia-based Florigene dont pose a risk
to ecosystems or the economy. In the
1990s, an Australian offshoot of U.S.-
based biotech pioneer Calgene Inc. won
the race to nd and patent blue genes
to create roses of an unnatural hue
(Science, 1 June 1990, p. 1074). Suc-
cess, however, came slowly: The com-
pany didnt unveil its blue roses until
the mid-2000s, and started selling
them in Japan in 2009. Next month,
Florigene hopes to begin growing
3 million to 6 million blue roses annu-
ally in the United States for the cut-
ower market. But there are no plans to
sell whole plants to home gardeners.
Washington, D.C. 6
House Bill Would Boost
NIHs 2012 Budget by 3.3%
A House of Representatives sub-
committee last week released
a 2012 draft spending bill with
surprisingly good news for the
National Institutes of Health
(NIH): The agencys budget
would increase by $1 billion to
$31.7 billion, a 3.3% increase
compared to this years level.
The proposed spending boost matches
the presidents request and reverses a
$190 million cut approved by a Senate
committee on 21 September. The bill does
not mention NIHs plan to create a National
Center for Advancing Translational Sci-
ences and to abolish the National Center
for Research Resources. (The Senate bill
would make these changes.)
Although the House appropriations sub-
committee isnt expected to meet to approve
the bill, the draft gives the panel a marker
for upcoming negotiations with its Senate
counterpart on an omnibus measure that
would fund most, if not all, of the federal
government. http://scim.ag/HouseNIH
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Researchers in other countries, such as
Iceland, Estonia, and the United Kingdom,
are building national genetic biobanks, but
this is the rst project aimed at compiling
whole genomes for everyone. The cost for
the project would be roughly $50 million, if
sequencing prices keep falling at the current
rate. Full funding has not yet been secured,
however. And its scientic value will depend
on how many citizens sign up for it, cautions
geneticist Markus Nthen of the University
of Bonn in Germany. This is a brave step,
but it will only be successful if enough peo-
ple take part, he says. http://scim.ag/Faroes
Farmington, Connecticut 5
Jackson Lab Branch Comes
To Connecticut
Connecticut is offering $291 million to
help open a new offshoot of the Jackson
Laboratory (JAX), a genetics research
institute best known as a leading breeder of
research mice. On 30 September, Connect-
icut Governor Dannel Malloy announced
the collaboration, which aims to make
Farmington a hub of genetically custom-
ized personalized medicine.
The state made a compelling case, said
Edison Liu, JAXs president and CEO. He
calls the locationwithin a short drive of
bioscience hubs in Boston, New York City,
and New Havenideal.
The deal calls for constructing 16,000
square meters of new lab space for 30
senior scientists on the campus of the Uni-
versity of Connecticut, Farmington. Plan-
ners forecast that the research center could
employ 600 employees within 20 years.
Before ground can be broken, however,
the Connecticut Legislature will need to
sign off on bonds to oat the project, with
a review expected to start next month. JAX
estimates that, over the next 20 years, it will
add another $809 million from grants, gifts
and business income to the state money.
http://scim.ag/JacksonLab
Marshall Islands 7
Giant Sanctuary for Sharks
The lions of the sea just got additional safe
haven in the Pacic. Last week, the Repub-
lic of the Marshall Islands declared its
waters1.9 million square kilometers
off-limits to shark shing and banned the
import and export of shark products. The
island nation joins ve other countries in
setting up shark sanctuaries, and this one is
expected to eventually expand to 4 million
square kilometers.
As the oceans top predator, sharks help
keep the marine food chain in balance
and maintain healthy sheries, says Matt
Rand, director of global shark conserva-
tion at the Pew Charitable Trusts in
Far out. The entire Faroese population
may have its genome sequenced.
>>
An oceanic white tip shark.
NEWS OF THE WEEK
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Worlds Smallest Periodic Table,
Engraved on a Human Hair
Its not quite angels dancing on the head of
a pin, but scientists have squeezed a repro-
duction of the entire periodic table onto a
human hairand the 2012 Guinness World
Records book has acknowledged that repro-
duction to be the smallest in the world.
The hair initially belonged to chemist
Martyn Poliakoff at the University of Not-
tingham in the
United Kingdom.
During a visit to
the Nottingham
Nanotechnology
and Nanoscience
Centre, Poliakoff
contributed a hair
for the creation
of a special ver-
sion of the peri-
odic table. The
researchers engraved the hair by irradiating
it with gallium ions at high speeds, break-
ing off tiny akes in the shape of the table.
When completed, the table was about
90 micrometers long and almost 50 micro-
meters tall (including the actinides and
lanthanides). The engraved hair earned the
title of smallest periodic tableand the
hair itself was returned to Poliakoff as a
birthday gift.
NEWSMAKERS
Ig Nobels Honor Bladder Control,
Beer Bottle Mating
Full bladders affect short-term memory
and attention spanbut can aid in impulse
control. Tortoise yawning is not conta-
gious. How do you rouse a
deaf person in the event of
a re? Wasabi. These are a
few of the research ndings
honored at Harvard Univer-
sity on 29 September as part
of the 2011 Ig Nobel Prizes.
Most Ig Nobel awards go to
recently published work, but a 1983 study
of why male Buprestid beetles try to mate
with a certain brand of Australian beer
bottle netted the Ig Nobel biology prize for
Darryl Gwynne and David Rentz, entomol-
ogists with the Commonwealth Scientic
and Industrial Research Organisation in
Canberra. The color and shape of the bottle
is a turn-on for the beetles, they found, and
a series of bumps on the glass seal the deal.
The ceremony had a somber moment,
as two longtime Ig Nobel participants were
memorialized. Mathematician and pioneer
of fractal geometry Benot Mandelbrot, 85,
and Harvard University chemist William
Lipscomb, 91 (who also won a real Nobel
Prize), both passed away within the last
year. They were frequent participants in
the traditional Ig Nobel Win a Date With
a Nobel Laureate contest. This year, the
prize was a date with Lou Ignarro (Nobel
Prize for physiology or medicine 1998).
http://scim.ag/_IgNobels
Wasabi.
Finger Drawings From a Prehistoric Preschool
Among the prolic paintings and other art in the 8-kilometer-long Roufgnac cave
system in southwestern France are a number of unusual markings known as nger
utings, which were made by people dragging their hands through the soft silt that
lines the caves walls. By analyzing the nger utings of modern humans, researchers
discovered that the ratio of the distance between the three middle ngers indicates
that many of the cave artists were very young children, one as young as 2 or 3 years
old, the researchers reported 2 October at the archaeology of childhood conference in
Cambridge, U.K. Some of these utings were too steady for a toddler, they found, sug-
gesting that an adult guided the childs hand. Since the childrens drawings seemed
to be concentrated in one chamber, the researchers believe that the alcove may have
been a sort of art school. And some of the drawings were high on the walls and on the
ceiling, suggesting that the children were lifted.
Washington, D.C. They also boost the local
economy by serving as tourist attractions.
About 30% of shark species are threatened,
and not enough is known about many of the
rest to determine their conservation status,
says Rand, but some at-risk species, like
the oceanic white tip, will get a reprieve
thanks to the new Marshall Islands law.
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BY THE NUMBERS
23,000 Air miles (and carbon
footprint) the average astronomer
logs each year traveling to meet-
ings and observatories, according to
astrophysicist Philip Marshall of the
University of Oxford.
100 meters Estimated thick-
ness of snow on parts of Saturns
moon Enceladus, according to data
presented last week at a planetary
sciences meeting.
Random Sample
Following Berlusconis Risqu Gaze
If Silvio Berlusconi leers at someone to his right, Italys conservative voters will tend to glance
in that direction, too, as if to see what hes looking at. Right-wing Italians seem to naturally
track the gaze of those in power, says Marco Tullio Liuzza, a social neuroscientist at the Sapienza
University of Rome.
Liuzza and colleagues organized
28 subjects into right- and left-leaning
voters, and sat them in front of a com-
puter screen displaying a range of Ital-
ian politicians. The images included
Prime Minister Berlusconi and left-
leaning Antonio Di Pietro. The subjects
were instructed to pay attention to the
color of a square positioned between
the politicians eyes, and to look left or
right, depending on its color. But while
the subjects waited for the square to
change, the team also quickly shifted
the gaze of the politican in the image,
making the image appear to glance
right or left.
Right-wing voters were more likely
to follow the direction of Berlusconis
gaze than Di Pietros and would fol-
low Berlusconis gaze even when the
box color instructed the voters to look
in the opposite direction, the team
reported in a study published online in
PLoS ONE last month. That result, they
suggested, is similar to behavior observed in monkeys in which subordinate primates follow the
gaze of dominant monkeys much more than those big cheeses returned the favor. Left-leaning
voters, however, were less inclined to follow Di Pietros gaze, Liuzza says.
But theres an important caveat: This study was conducted in 2009, long before Berlusconi
became embroiled in numerous sex scandals, Liuzza notes. It would be interesting to see if this
effect would disappear now that the condence in Berlusconis coalition has drastically dropped.
FINDINGS
CFS Researcher Fired
Judy Mikovits, who for 2 years has champi-
oned the controversial theory that XMRV,
a mouse retrovirus, has links to chronic
fatigue syndrome (CFS),
was red on 29 Septem-
ber. The next day, a blog-
ger raised questions about a
slide Mikovits presented at a
scientic meeting, triggering
a probe by Science of a g-
ure in a paper it published by
Mikovits and colleagues in October 2009.
The Whittemore Peterson Institute for
Neuro-Immune Disease (WPI), a private
organization in Reno, Nevada, devoted to
CFS research and treatment, said it red
Mikovits for withholding a cell line from
a co-worker. In a termination letter dated
30 September, Annette Whittemore, CEO of
WPI, charged Mikovits with being insub-
ordinate and insolent. Mikovits, who was
immediately locked out of her lab, responded
that she withheld the cell line because the co-
worker failed to take her direction.
That same day, a blog written by gradu-
ate student Abbie Smith at the University of
Oklahoma, Oklahoma City, noted that Miko-
vits had presented a slide at a recent CFS
meeting that looked identical to an image in
the 2009 Science paper. But the slide had dif-
ferent patient numbers and unique experi-
mental conditions. Science Executive Editor
Monica Bradford said the journal was con-
tacting the authors to review the description
of the slide in the original paper.
Mikovits and collaborator Francis Rus-
cetti of the National Cancer Institute in Fred-
erick, Maryland, say patient numbers were
changed to protect privacy and no wrong-
doing occurred. http://scim.ag/_Mikovits Full color. Vestas myriad minerals.
Berlusconi
Di Pietro
Asteroid Vesta Exceeds
Expectations
The 529-kilometer-diameter asteroid Vesta is
revealing even more geologic diversity than
scientists had expected. They knew that a col-
lision with another asteroid had splashed off
three kinds of rock that still land on Earth as
meteorites. And Vestas overall spectral color,
as returned by NASAs orbiting Dawn space-
craft, matches that of these Vesta meteorites,
Dawn team members reported 3 October at a
planetary science meeting in Nantes, France.
But rather than a monotonously uniform sur-
face homogenized by impact cratering over
the eons, the rst up-close look at the aster-
oid reveals a full palette of mineral colors
(mapped in false color reecting
the wide range of rock composi-
tions). Researchers will now have
to sort out how more than 4 billion
years of impactsincluding one at
the south pole that nearly destroyed
the asteroidreshaped Vesta after
it developed a crust, mantle, and
core much like Earths.
Mikovits
NEWS & ANALYSIS
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Its a result many have hoped forand
some have fearedfor more than a decade:
Researchers have found a way to use human
oocytes to reprogram adult cells, allowing
them to form early embryos that can give
rise to embryonic stem (ES) cells. The result-
ing stem cells are not normal, however. They
carry the genomes of both the adult cell and
the oocyte, so they have three copies of each
chromosome instead of the usual two. But
they can still form a variety of tissues in the
lab, and they seem, in initial tests, to act like
other pluripotent stem cells, cells that can
form all of the bodys tissue types.
The work for the rst time demonstrates
that the human egg has the ability to turn a dif-
ferentiated cell into a stem cell, says Dieter
Egli of the New York Stem Cell Foundation
laboratory in New York City. Egli led the
work, which is published this week in Nature.
Thats good news for the scientists who have
been hoping to use oocytes to reprogram
cells from patients suffering from a variety
of hard-to-treat diseasesa technique that
could enable them to better understand dis-
ease and perhaps someday treat it. Scientists
did the proof-of-principle experiment with
mouse cells in 2002, but success in primates
has been elusive.
At the same time many have dreaded such
a result, fearing it will prompt demand for
human oocytes (see sidebar). Others oppose
the work because it involves creating a human
embryo and then destroying it. And some
worry that if human nuclear transfer works
in the lab, someone could eventually use it to
clone a human being.
In the near term, at least, the fact that
Eglis technique produces abnormal triploid
cells should dampen some of those concerns.
The resulting embryos developed for about
a week but would likely not be viable much
beyond that point.
Because the cells are abnormal, they
wont be useful as disease models. Even so,
the advance could bring scientists closer to
understanding how the oocyte pulls off its
reprogramming feat and how this process dif-
fers from another technique, called induced
reprogramming, that can transform a mature
cell into an embryolike one. In 2006, a team
led by Shinya Yamanaka of Kyoto University
in Japan reported that by adding a handful of
genes to a skin cell, they could turn it into an
induced pluripotent stem (iPS) cell.
That technique seemed to offer a way
around the difcult and controversial research
on human nuclear transfer, but the question
has remained: Are iPS cells equivalent to ES
cells? There is some evidence, for example,
that mouse ES cells produced via nuclear
transfer may be more thoroughly repro-
grammed than iPS cells, some of which retain
traces of the adult tissue type they came from.
Many researchers argue that to fully under-
stand reprogramming, they need to be able to
study human cells reprogrammed by oocytes.
But nuclear programming using primate
oocytes has proved surprisingly difficult.
More than a decade of research in many labs
has yielded just a handful of reports of suc-
cessful nuclear transfer using monkey or
human oocytes. Most famously, Woo Suk
Hwang at Seoul National University in South
Korea claimed to have made a dozen stem cell
lines from nuclear transferderived embryos.
Those claims turned out to be fraudulent.
In the vast majority of attempts, the nuclear
transfer embryos seem to hit a wall and stop
developing after about 3 days, when they
have just six to eight cells.
At rst, Egli and colleagues ran into the
same roadblock. When they removed the
oocyte nucleus, fused the enucleated oocyte
with a skin cell, and triggered cell division,
the oocytes divided once or twice. But after
2 or 3 days, the cells stopped dividing and
ultimately died.
The researchers noticed that develop-
ment stopped at the time when the embry-
onic nucleus would usually start expressing
genes. And they saw that the green uores-
cent protein (GFP) that marked the donor
skin cells was not expressed in the arrested
cells. When they looked more closely, they
found several lines of evidence that, for
some reason, the new nucleus wasnt able to
turn on any of its genes.
As a control experiment, the researchers
fused a GFP-tagged donor skin cell with an
intact oocytewithout removing the oocyte
nucleusand triggered the cell to divide.
Immediately, they saw a difference. On day
4, the embryos started to express the GFP.
And, out of 63 tries, the researchers produced
13 blastocysts, the hollow ball of cells that
forms around day 5 of development. From
those 13 blastocysts, the researchers were
able to derive two stem cell lines. One car-
ries the genome of a male who has type 1 dia-
betes, and the other carries the genome of a
healthy male adult. Despite their extra chro-
mosomes, the cells expressed genes typical
of pluripotent cells, and they were able to
form tissues from all three embryonic germ
layersa basic test of pluripotency. In their
overall gene expression, they resembled both
iPS and ES cells.
To test how thoroughly the donor genome
had been reprogrammed, Egli and colleagues
sequenced parts of the oocyte genome and the
donor cell genome so they could distinguish
whether genes were being expressed prefer-
entially from one or the other. If the skin cell
genome were incompletely reprogrammed,
they reasoned, those chromosomes would
express relatively more skin-type genes and
the oocyte chromosomes more embryonic
genes. Their initial analysis suggests the skin
cell memory had been erased.
The authors are to be congratulated. Its
very systematically done, says Ian Wilmut
Human Cells ClonedAlmost
STEM CELLS
Some assistance required. Without the oocytes
nucleus, human embryos formed by nuclear transfer
stop developing by day 3.
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of the University of Edinburgh in
the United Kingdom, who with his
colleagues cloned Dolly the sheep
in 1996, the rst mammal cloned by
somatic cell nuclear transfer. The
experiments take researchers much
closer to understanding the obsta-
cles in primate nuclear transfer
experimentsand ultimately over-
coming them, he says. There is
clearly something missing that you
have to have at the start of transcrip-
tion, he says. It should be possible
to a), identify it, and, b), supply it.
Kevin Eggan, a stem cell
researcher at Harvard University
who was Eglis postdoctoral super-
visor, agrees. There is a gene or
genes which cannot be expressed
on the somatic chromosomes that are needed
to get transcription started, he says. He, with
Egli and other colleagues, published this
week in Nature Communications an account
of their attempts to use fertilized human eggs
in place of oocytes in nuclear transfer experi-
ments. (The fertilized eggs were left over
after fertility treatments; patients donated
them for research.) The technique works
with mouse cells, but with human cells the
embryos stopped dividing at the six- or eight-
cell stage. These experiments also suggest
that the problem is a failure to turn on tran-
scription in the donor genome.
The missing factorwhatever it isis
absolutely required, says Eggan, who sus-
pects that other reported successes
with human nuclear transfer may
have been accidents. Having
done hundreds of experiments
in zygotesand Dieter has done
hundreds with oocytesmy view
is that everyone who made a blas-
tocyst probably messed up and left
a chromosome in, he says.
Egli and his team are now
looking for the missing factor,
he says, as well as testing to see
whether using a different kind of
adult cellperhaps a stem cell
from blood or neural tissue
might get around the problem.
They will also continue to char-
acterize the nuclear transfer stem
cell lines, he says, to see how they
compare with ES and iPS cells.
Despite the ethical, legal, and practical
hurdles that complicate his work, Egli says
the effort is worth it. Its not about deter-
mining which is the easier approach, he
says. It is about determining which is the
better approach.
GRETCHEN VOGEL
Turn it on. A fused oocyte and somatic cell form an early embryo that turns
on the somatic cells green uorescent protein on day 4 of development and
forms a blastocyst by day 6.
Where Do Human Eggs Come From?
A key limitation for human nuclear transfer research has been the difculty
and ethical questions about obtaining oocytes from young, fertile women.
A combination of factors in New York enabled Dieter Eglis lab to receive
a steady supply of healthy human oocytes from a cooperating assisted-
reproduction clinic. Ultimately, over the course of 19 months, 16 women
donated 270 oocytes to the research program. Egli and his colleagues used
this unusual resource to set up a systematic study of human nuclear transfer,
which has now brought scientists signicantly closer to understanding why
most attempts have so far failed (see main text).
Egli started working on cloning in the lab of Kevin Eggan at Harvard
University, who, with several colleagues at the Harvard Stem Cell Insti-
tute, had private funding to work on human nuclear transfer. But just as
the project was getting under way, Massachusetts passed a law making it
illegal to compensate women beyond direct expenses for donating eggs
for research purposes. Eggan, Egli, and colleagues spent 2 years attempt-
ing to recruit donors, advertising in newspapers, magazines, on public
transportation, and online. Although 239 women contacted the program
and 79 met all eligibility criteria, only one woman ended up donating.
The scientists describe their experience this week in Cell Stem Cell. We
had a feeling it wasnt going to work, but we had to try, Eggan says. And
try we did, really hard, for a long time. We beat every bush. We learned
that we cant get women to donate oocytes without compensation.
In 2008, Egli set up his own lab at the privately funded New York
Stem Cell Foundation laboratory. New York law allows compensation for
oocyte donors, and the Empire State Stem Cell Board has endorsed the
practice. In New York, Egli started working with Mark Sauer, a reproduc-
tive endocrinologist and program director for assisted reproduction at
Columbia University Medical Center in New York. Sauer had surveyed
women who came to the clinic with the intention of donating eggs to the
assisted-reproduction program, which pays its donors $8000. After the
women received information on the risks and discomforts of egg dona-
tion, he asked them whether they would prefer to donate to assisted
reproduction or research. Many of them said they would prefer research.
Sixteen such donorswho were each paid the standard $8000 fee
ultimately provided Egli and his colleagues with 270 oocytes for the
study published this week. Sauer says he continues to provide Eglis lab
with oocytes from one or two donors a month without impacting our
assisted-reproduction program.
Many top stem cell researchers, however, wont be able to follow up
on Eglis work. The California Institute for Regenerative Medicine, which
funds leading researchers in California and beyond, prohibits research-
ers from paying oocyte donors. Massachusetts, which hosts top stem cell
labs at Harvard and the Massachusetts Institute of Technology, also pro-
hibits donor payment. In the United Kingdom, authorities have allowed
only egg sharing, in which women who are undergoing assisted repro-
duction can donate some of their excess oocytes to research and receive
a discount on the costs of the procedure.
Such regulations are intended to prevent women from being unduly
coerced into donating eggs. Eggan says that worry is legitimate, but a
ban on any payment goes too far. Now that I know what is involved, it
just seems right to me that women should be compensated fairlynot
overly, but fairly. G.V.
NEWS&ANALYSIS
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Tucked away in a temporary office close
to the White House in Washington, D.C.,
Joe Selby is preparing to launch the best-
funded new medical research institute you
may never have heard of. Its namePCORI,
the Patient-Centered Outcomes Research
Instituteis not a household word. But it
already has a few assets that would make
any agency head salivate: a mandate from
Congress to scale up, a trust partly nanced
by insurance fees that will provide about
$500 million a year, independent status, and
an almost open agenda. Its task is mind-
bogglingly broad, though: to discover what
kinds of therapies work best for patients.
Selby, 64, a family physician and epide-
miologist, has been on the job as PCORIs
rst executive director for only 3 months.
He was recruited from Kaiser Permanente
of Northern California, where he spent
27 years as a doctor-investigator and then
head of research. His main interest in recent
years has been type 2 diabetes, and he led
studies that helped establish the value of the
drug metformin to prevent or slow the dis-
ease. Early use of metformin is accepted
everywhere now, Selby says, but it took a
decade of research to prove that it was safer
and more effective than the sulfonylurea
drugs used for more than 3 decadesand to
persuade doctors to switch.
PCORI was created by the 2010 Patient
Protection and Affordable Care Act. But
even before that health reform bill was
enacted, the Obama Administration and
Congress steered $1.1 billion of economic
stimulus money into the eld Selby special-
izes in, known as comparative effective-
ness research. Its practitioners aim to sift
data from medical records to discover which
treatments benet large numbers of patients.
The eld blossomed with the advent of elec-
tronic records; Kaiser Permanente was an
early convert.
During the debate over health care
reform, advocates said that comparative
effectiveness studies could help promote the
best medicine and even slow medical cost
inflation. Heated confrontations ensued;
opponents charged that the Administra-
tion would create death panels to allo-
cate medicine and regulate when Granny
should be pulled off life support. Mindful
of that furor, Congress eventually agreed
to fund comparative effectiveness research
in the 2010 health bill but only through a
new, self-governing, independent patient
centered agency: PCORI. And Congress
said that PCORI absolutely may not study
cost effectiveness. Stakeholders from every
medical constituency now sit on PCORIs
board of governors and set policy.
Selby met with Science last week to talk
about PCORIs agenda, the tension in its
mandate, and plans to involve patients in
designing and reviewing research. The com-
ments have been edited.
ELIOT MARSHALL
Q: What is the main goal of this research?
J.S.: We think it starts by listening to the
patients, that the research agenda is driven
by what patients say is important. Patient-
centeredoutcomes research is putting use-
ful, practical information in the hands of
patients and their clinicians.
Q: Why cant clinical trials do this?
J.S.: I think a lot of comparative effective-
ness research will be done with randomized
trials. But a lot of clinical trials have been
driven in substantial part by a desire to better
understand the biology, sometimes to the
de-emphasis of the importance of outcomes.
Trials of using estrogens in postmenopausal
women showed very nicely that estrogens
improved the lipid prole, but a large out-
comes study came along and proved that
estrogens denitely didnt have a benecial
effect on cardiovascular disease.
Q: How will stakeholders set the agenda?
J.S.: Over the next 2 to 3 months we will be
going out to patient organizations, conven-
ing meetings of patients, conducting focus
groups. We will very likely be using some
sort of crowd sourcing, so we will be using
social media to reach people. We expect
[the process will lead to] 10 priorities [to
guide research grant and contract awards].
Q: How will patients be involved in reviews?
J.S.: We will add an additional criterion to the
list that reviewers [use to] evaluate the grants
or contract proposals. That is, what is the
evidence that the researchers have engaged
patients and other stakeholders in the planning
and design of the study? Whats the evidence
that they have experience in doing that? And
patients will be among the members of the
study sections. I cant tell you the exact num-
ber per study section, but it will be more than
a token patient. We will take patients through
training to get them ready to participate.
Q: Will PCORI studies look at cost?
J.S.: We are funded and have a mandate to
measure clinical outcomes. One thing we
very clearly wont do is do cost-effectiveness
studies. It is very clear that the framers of the
legislation do not want us to go near that.
Q: Who will conduct this research?
J.S.: PCORI hopes to fund a broader spectrum
of researchers; it hopes to pull new players
who are close to patients, close to communi-
ties, closer to usual care. We have to do this
while preserving the rigor of research. One
way that could happen is by fostering partner-
ships between patients, or community-based
clinicians, or patient groups, or hospital
groups, and researchers.
Q: Whats the advantage of being indepen-
dent?
J.S.: We can fund a wider range of applicants.
As one example, we can give grants to for-
prot entities as well as nonprots. Its easier
for us to conduct large surveys. If a topic
arises suddenly and theres a need to learn
how patients feel about it, we can solicit
information quickly.

Q: How soon will the substantive work begin?
J.S.: I dont think it will take long after the
research agenda is specied and put out for
comment [a few months]. We are all anxious
to get started. But we are trying something
new and different, and weve got to put the
foundation in place. Be sure to come back
in 6 months.
Sifting Medical Records to Determine
Which Therapies Work Best
NEWSMAKER I NTERVI EW: JOE SELBY
NEWS&ANALYSIS
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8
)
;

N
A
T
U
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E

4
6
7
,

3
1
8

(
2
0
1
0
)
It has taken many years, but researchers may
have reached a prized goal in gene therapy:
lowering the risk of uncontrolled bleeding in
patients with hemophilia. At a meeting last
week, researchers reported that six patients
who received a virus engineered to carry a
gene for a blood-clotting protein called fac-
tor IX needed fewer transfusions of the pro-
tein for as long as 18 months; some didnt
require any transfusions. One patient devel-
oped an immune response to the viral vector,
but this side effect was successfully treated
with drugs.
Some researchers say these results mark a
watershed for the long-struggling eld. At the
meeting at the U.S. National Insti-
tutes of Health (NIH) in Bethesda,
Maryland, gene therapy research-
ers summarized progress on several
fronts. They said they have proved
that they can treat at least a half-
dozen rare genetic diseases (see
table), and that early trials are begin-
ning to find benefits for common
diseases as well, including HIV, leu-
kemia, and heart disease.
Most important, gene therapy
seems to have overcome a reputa-
tion for recklessness it acquired a
decade ago after an 18-year-old,
Jesse Gelsinger, died in a trial. Its
a different day now, says meeting
attendee Theodore Friedmann of
the University of California (UC),
San Diego, who has followed the
field since the 1970s: People recognize
that it really is the right thing to do for
some diseases.
To be sure, enthusiasm is not what it was
20 years ago when NIH last held a simi-
lar symposium. That event attracted nearly
twice as many speakers and attendees (21
speakers and about 400 registrants came
this time), noted R. Jude Samulski of the
University of North Carolina, Chapel Hill,
president of the American Society of Gene
and Cell Therapy (ASGCT), a meeting co-
sponsor. Back then, excitement clearly
exceeded any of the data, Samulski said at
the meeting. After the Gelsinger incident,
U.S. regulators put many trials on hold; oth-
ers were canceled.
But in the early 2000s, teams in Paris and
Milan demonstrated the rst clear-cut ben-
efits from gene therapy, treating children
with two different forms of severe combined
immunodeciency disorder (SCID), which
make the patient highly vulnerable to infec-
tion. Last year, researchers reported success
in two patients with another immune dis-
order, Wiskott-Aldrich syndrome; like SCID
patients, they were treated by adding a cura-
tive gene to blood stem cells. By now, about
86 patients with these immune deciencies
have been helped this way, Donald Kohn of
UC Los Angeles said at the NIH meeting.
Last year also brought good news in a
new area: Gene therapy researchers pub-
lished the rst success in treating a patient
with -thalassemia, a blood disorder that
is relatively common in South Asia and the
Mediterranean region. Eight centers are
now setting out to expand on this result,
noted Michel Sadelain of Memorial Sloan-
Kettering Cancer Center in New York City.
These trials were not without problems,
however. In some the viral vector, a retro-
virus, which can insert unpredictably in
DNA, turned on an oncogene, increasing the
risk of cancer. Nine patients, including three
with chronic granulomatous disease, another
immune disorder, who initially seemed cured
by gene therapy later developed a leuke-
mia-like disease, Kohn noted. In response,
a U.S.-European consortium has developed
alternative self-inactivating retroviral vec-
tors that are less likely to turn on other genes.
All new trials treating blood cells are using
these vectors.
Its a sign of the elds overall health that
researchers are going beyond safety test-
ing now. The San Raffaele Telethon Insti-
tute for Gene Therapy in Milan, for example,
will soon apply to European regulators to
conduct a phase III trial needed for regula-
tory approval of a plan for treating adenos-
ine deaminase deciencySCID. Last year,
that institute struck a deal with pharmaceu-
tical giant GlaxoSmithKline to commercial-
ize gene therapies for seven disorders. Gene
therapy for rare genetic diseases is really a
mature eld now, Telethon Institute immu-
nologist Maria-Grazia Roncarolo said at the
NIH meeting.
Eye diseases are another success story.
In three trials that are kind of biblical in
impact, Friedmann says, eyesight improved,
sometimes dramatically, in 28 of 30 patients
with Lebers congenital amaurosis, a type of
inherited blindness, after gene ther-
apy using an adeno-associated virus
(AAV) to deliver a curative gene to
the retina. The Childrens Hospital of
Philadelphia (CHOP) plans to apply
this fall to the U.S. Food and Drug
Administration to conduct a phase
III trial for this treatment. Gene
therapy trials for two other blind-
ness diseases are under way. In the
next year and a half, theres going
to be a boatload coming out, says
Stephen Rose, chief research ofcer
for Foundation Fighting Blindness.
Gene therapy is working for
neuro logic diseases, too. The San
Raffaele Telethon Institute has
treated four patients with a devas-
tating brain disorder called meta-
chromatic leukodystrophy, following
a report published in 2009 from a team in
France that used a similar strategy to halt the
progression of a related disease, adrenoleuko-
dystrophy. So far the treatment seems safe and
the patients blood cells are producing the cor-
rected enzyme, Roncarolo reported.
The path to better health has been long
and winding for hemophilia B patients. A
trial in the early 2000s led by Katherine High
of CHOP and Stanford Universitys Mark
Kay resulted in only brief gene expression;
patients developed an immune response that
destroyed cells with the corrected gene. This
trial used AAV to deliver a factor-IX clotting
factor gene to the liver. But a new trial led by
Amit Nathwani of University College London
and Andrew Davidoff of St. Jude Childrens
Research Hospital in Memphis, Tennes-
see, has overcome earlier immune problems.
These researchers used a different AAV that
can be delivered intravenously and may be
less likely to trigger an immune reaction. As
Gene Therapists Celebrate a Decade of Progress
CLI NI CAL RESEARCH
Disorder Disease Patients First
type beneting publication
X-SCID Immunodeciency 17/20 2000

ADA-SCID Immunodeciency 26/37 2002

Adrenoleukodystrophy Neurologic 2/4* 2009

Lebers congenital
Blindness 28/30 2008
amaurosis

Wiskott-Aldrich
Immunodeciency 8/10 2010
syndrome

-thalassemia Hemoglobinopathy 1/1 2010

Hemophilia Coagulation 6/6 2011?

*Includes a patient treated too recently to see benet
Some Gene Therapy Successes
NEWS&ANALYSIS
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Thirteen years ago, two teams of astrono-
mers and physicists independently made the
same stark discovery: Not only is the universe
expanding like a vast inating balloon, but its
expansion is speeding up. At the time, many
scientists expected that the gravitational pull
of the galaxies ought to slow the expansion
down. Today, researchers from both teams
shared the Nobel Prize in physics for that dra-
matic observation,
which has changed
the conceptual land-
scape in cosmology,
astronomy, and par-
ticle physics.
Half of the $1.45
million prize will go
to Saul Perlmutter of
Lawrence Berkeley
National Laboratory
and the University of California, Berkeley,
who led the Supernova Cosmology Proj-
ect. The other half will be shared by Brian
Schmidt of the Australian National University
in Weston Creek, who led the High-z Super-
nova Search Team, and Adam Riess of Johns
Hopkins University and the Space Telescope
Science Institute in Baltimore, Maryland,
who worked on High-z. Im really happy for
them, says Yannick Mellier of the Institute
for Astrophysics in Paris. Its a huge discov-
ery that has impact in all of physics.
Both teams traced the expansion of
the universe back through time using stel-
lar explosions called type Ia supernovae.
Because all such supernovae explode with
essentially the same brightness, astrono-
mers can use them as standard candles:
They can tell how far away a supernova is
by measuring its apparent brightness from
Earth. They can also tell how long ago the
stellar bomb went off by measuring how
much its light has been stretched to lon-
ger, redder wavelengths by the expansion
of space. Using different supernovae, both
teams found that the expansion of the uni-
verse is accelerating. We thought we must
be making some mistake, Schmidt says.
But the mistake refused to go away.
Other evidence soon bolstered the case
for the accelerating expansion and some sort
of dark energy to power it. A few years
later, measurements of the afterglow of the
big bangthe so-called cosmic micro-
wave backgroundindicated that 70%
of the stuff in the universe had to be dark
energy. Studies of clusters of galaxies show
that their growth has slowed over the 14-
billion-year age of the universe, as if space-
stretching dark energy were impeding it.
Exactly how surprising the discovery of
the accelerating expansion was remains a
matter of debate. By the late 1990s, cosmolo-
gists had begun to suspect that the universe
contained a large amount of dark energy and
only a little matter, says Simon White, a the-
orist at the Max Planck Institute for Astro-
physics in Garching, Germany. In contrast,
Schmidt recalls that the debate was between
theorists who claimed the universes expan-
sion should be slowing a lot and observers
who found no evidence for that.
Cosmologists, astrophysicists, and par-
ticle physicists must still explain what dark
energy is. Much effort focuses on how the
density of dark energy changes as space
expands. If dark energy is an inherent part
of space, the density should remain constant.
If dark energy is something in space, then
it should become more dilute. The question
comes down to using
further astronomi-
cal observations to
determine whether
a single parameter
in the cosmological
equation of state is
exactly 1, indicating
dark energy is part of
space, or something
like 0.93, indicating
that dark energy is something in space. Cur-
rently the value of this parameter is consistent
with 1 with an uncertainty of about 10%.
Will scientists ever know what dark
energy is? Thats not a sure thing, White
says. The problem is that you cant prove
by observations that a parameter is exactly
minus one.
Each team comprised about 20 scientists.
This is another example of what a shame
it is that the Nobels cant recognize teams,
says Martin Rees of the University of Cam-
bridge in the United Kingdom. It sends
the wrong signal. White notes that Robert
Kirshner of Harvard University was the the-
sis adviser for Schmidt and Riess and got
them started on the prize-winning project.
Oddly, Edwin Hubble, who in the 1920s
discovered that the universe is expanding,
never won a Nobel Prize. ADRIAN CHO
With reporting by Daniel Clery.
Curious Cosmic Speed-Up Nabs Nobel Prize
NOBEL PRI ZE I N PHYSI CS
Ulrike Reiss of St. Jude reported at the meet-
ing, levels of factor IX reached 1% to 8% of
normal levels in the six patients, high enough
that two patients could cut back on their twice-
or thrice-weekly infusions of factor IX, and
four could go off infusions altogether.
Even so, one patient who got the highest
dose did experience immune effects: As in
the previous trial, the patients T cells targeted
the capsid, or protein coat, of the viral vector,
causing liver enzymes to rise. But this time,
researchers controlled the reaction by giv-
ing the patient prednisolone, a widely used
steroid, for several weeks until the capsids
degraded and cleared. However, prednisolone
may not be acceptable for hemophilia patients
with hepatitis, says High, a trial collaborator.
The treatment also wont work for the 30% of
patients with preexisting immunity to AAV8.
And gene therapy will be more challenging
for the more common form of the disease,
hemophilia A, which involves a larger gene
that cannot be delivered as easily with AAV.
Still, this trial and the eye studies show
the promise of AAV vectors for gene ther-
apy, High says. To have achieved success
with hemophilia feels great, she says. Its
much more fun to think about obstacles to
treating more patients rather than how to
get it to work, High says.
Researchers at the meeting pointed to
many hurdles that still lie ahead: the morass
of multistage reviews these protocols face,
particularly in the United States; long time-
lines for some patients to show benets; and
scarce funding for rare diseases. But research-
ers are optimistic enough that the ASGCT is
working on a list of 10 diseases that it hopes
will be successfully treated with gene ther-
apy within the next 7 years. Says Samulski,
Now were where everyone wanted to be
10 years ago. JOCELYN KAISER
BRIAN P. SCHMIDT SAUL PERLMUTTER ADAM G. RIESS
N BEL
PRIZE
2011
PHYSI CS
NEWS&ANALYSIS
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Nobel Prizes typically trigger immense cel-
ebration, by the individual winners and by
members of the scientic elds they repre-
sent. But the celebrations for this years Nobel
Prize in physiology or medicine, which hon-
ored three scientists who unraveled key details
of how the immune system becomes activated,
were muted by the death of one of the winners.
The Nobel Assembly at the Karolinska
Institute in Stockholm awarded one-half of
the $1.45 million prize to Bruce Beutler of
the Scripps Research Institute in San Diego,
California, and Jules Hoffmann of the Uni-
versity of Strasbourg in France for their
work on toll-like receptors (TLRs), the cell
surface proteins that help provide a broad,
rst-line defense against microbial patho-
gens. While that selection generated some
debate among immunologists, a tragic twist
involving the third winner, Ralph Steinman
of Rockefeller University in New York City,
grabbed most of the attention.
Unbeknownst to the Nobel Assembly
and most scientistsSteinman had died a few
days before the Nobel Prize was announced on
Monday morning. The assembly recognized
Steinman for his discovery of so-called den-
dritic cells and the role they play in the activa-
tion of other immune cellsknowledge used
to design treatments for him during his 4-year
battle with pancreatic cancer. We were all
stunned. Its a real shame, says immunologist
Luke ONeill of Trinity College Dublin.
Once Rockefeller University learned of
Steinmans death and informed the Nobel
Assembly, the Board of the Nobel Founda-
tion hurriedly gathered on Monday to delib-
erate; the statutes governing the prizes say
that they must go to living scientists. By
the end of the day, the foundation released
a statement calling the situation unprec-
edented but conrming that the award to
Steinman would stand.
Steinmans battle with cancer represents a
sign of how far the dendritic eld he launched
has progressed. Steinman discovered this new
immune cell type in 1973. He later showed
that it can activate the immune systems T and
B cells and helped unravel the mechanisms by
which the so-called adaptive immune system,
the arm that targets microbes with specic
killer cells and antibodies, decides whether
to mount a response. Cancer vaccines either
using or targeting dendritic cells are now the
subject of numerous clinical trials, and one tar-
geting prostate cancer was recently approved
for use in the United States.
When Steinman was diagnosed with
pancreatic cancer back in 2007, he knew he
wanted to marshal his own dendritic cells
in the ght. He had great faith in dendritic
cells, says Sarah Schlesinger, a physician and
immunologist at Rockefeller University. He
believed they would establish immunity, and
that would cure him.
Steinman tried three dendritic cell thera-
pies. A company, Argos Therapeutics in Dur-
ham, North Carolina, had a dendritic cell
vaccine in trials for kidney cancer and per-
sonalized the vaccine for Steinman, even
though his cancer was a different type; scien-
tists at Baylor College of Medicine in Texas
did something similar for another dendritic
cell vaccine, which they were testing against
melanoma. Both clinical trials were closely
vetted by the U.S. Food and Drug Adminis-
tration. Steinman also tried a therapy called
GVAX, which aims to recruit dendritic cells
in the body. There were dozens of colleagues
around the country who helped, Schlesinger
says. (For more details on Steinmans treat-
ments, see http://scim.ag/Steinman.)
There is an intimate connection between
Steinmans work and that of his co-winners,
as TLRs are molecular sensors by which den-
dritic cells, and some other cells, recognize
general features of pathogens, such as viral
DNA or bacterial wall components. TLRs
power the rst line of immune defense, the so-
called innate immune response that involves
inammation and cells such as neutrophils;
TLRs, acting through dendritic cells, also
kick-start the adaptive response involving
T and B cells.
In 1996, Hoffmann, who was born in Lux-
embourg but has spent his career in France
and chaired the French Academy of Sciences,
showed that the gene called Toll, at the time
known primarily to be involved in embryo
development, plays a key role in mounting
an innate immune defense against bacteria
and fungi in fruit ies; mutants without Toll,
which encodes the original TLR, died more
readily from fungal infections, he and his co-
workers reported in a paper in Cell.
In a paper published in Science 2 years
later, Beutler and his colleagues won a erce
race that solidly linked TLRs to mammalian
immunity. Immunologists had been looking
for the receptor that binds a bacterial com-
pound called lipopolysaccharide, which can
cause septic shock, a dangerous overreac-
tion of the immune system. Beutlers team
proved it was a specic TLR. These proteins
are able to detect almost any kind of infec-
tion. If you dont have TLR signaling, you
are severely immunocompromised, says
Beutler, who is soon returning to the Uni-
versity of Texas Southwestern Medical Cen-
ter at Dallas, where he did much of the early
TLR research.
Many companies are now developing
drugs that either inhibit or activate TLRs in
order to treat conditions including asthma,
lupus, cancer, and transplant organ rejec-
tion (Science, 14 April 2006, p. 184). And
although some TLR-based treatments have
failed in testing, a drug approved to treat gen-
ital warts was found to work by stimulating
one of the receptors.
Research on TLRs has long been very
competitive, and while no one is challeng-
ing the quality of Beutler and Hoffmanns
work, some grumblings have emerged over
who did not get chosen. For example, Ruslan
Medzhitov, a Russian immunologist at Yale
University who worked on TLRs, recently
shared a major award with Beutler and
Hoffmann. Nobel Prize rules limit the award
to three people, and ONeill conrmed to
Science that in 2009 he was asked by the
Nobel Assembly to prepare a condential
report on the history of the eld to help guide
the panels prize deliberations. I struggled
with it, he says, noting that there are at
least ve or six key people who could have
been honored. JOHN TRAVIS
With reporting by Jennifer Couzin-Frankel, Sara Reardon,
Elizabeth Pennisi, and Martin Enserink.
JULES A. HOFFMANN BRUCE A. BEUTLER RALPH M. STEINMAN
N BEL
PRIZE
2011
PHYSI OLOGY
Immunology Prize Overshadowed by
Untimely Death of Awardee
NOBEL PRI ZE I N PHYSI OLOGY OR MEDI CI NE
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Eon
Era
Epoch
Period
Proterozoic | 2.5 billion years ago
Phanerozoic | 542 million years ago
Archean | 3.8 billion
years ago
Hadean | 4.6 billion years ago Anthropocene Since 150 years ago?
Each time I see it, its dramatic; the equiv-
alent of listening to a particularly impres-
sive bit of Mozartlike the opening of
Don Giovanni, or the bit where Don gets
dragged down to the pits, says geologist Jan
Zalasiewicz of the University of Leicester in
the United Kingdom.
The object of his awestruck tone seems
unremarkable: a stripe of black rock abut-
ting a pale gray section of cliff in Dobs Linn
gorge in the United Kingdom. But to geol-
ogists, this slice of shale represents one of
the major transitions in Earths history. It is
the location for a golden spike, an interna-
tionally agreed-on marker for the boundary
between two different geological periods,
eras, or epochs. In this case, the golden spike
marks the boundary between the Ordovician
and Silurian periods, two planetary states so
different from each other that, to geologists,
the rocky evidence for each is clearly dis-
tinguishable. The Ordovician ended some
445 million years ago as rapid glaciation and
other global changes triggered the planets
fth mass extinction event, wiping out more
than 60% of marine life.
Now, scientists say, the planet has crossed
another geological boundary, a transforma-
tion that will leave its own signature stripe
in the rocksand humans are the change-
makers. An inuential group of geologists,
ecologists, and biologists argue that humans
have so changed the planet that it is entering
another phase of geological time, called the
Anthropocene, the Age of Man. Human-
ity, they contend, can be considered a
An Epoch Debate
Theres no dispute that humans are leaving their mark on the planet,
but geologists and other scientists are debating whether this imprint is
distinctive and enduring enough to designate a new epoch: the Anthropocene
NEWSFOCUS
NEWSFOCUS
geophysical force on a par with supervolca-
noes, asteroid impacts, or the kinds of tec-
tonic shift that led to the massive glaciation
of the Ordovician.
The Dobs Linn golden spike marks a
revolutionary period in the Earths history,
Zalasiewicz says. I feel quite the same
sense of awe when I think about the kinds
of large-scale geological changes that we are
making to our planet now.
From the invention of agriculture and
domestication of animals to the creation of
cities, humans have been altering the land-
scape ever since the Holocene epoch began
11,500 years ago at the end of the last ice
age. But, until recently, people have only
changed their local environments. The
industrial revolution increased the extent
and reach of our impact, making it truly
global. And after World War II, the system-
wide human effect on our planet accelerated
dramatically to the extent that the human-
wrought changes may be considered com-
parable, many scientists say, to geological
transformations of the past, like that of the
Ordovician to the Silurian.
It was Nobel laureate Paul Crutzen
who rst came up with the term Anthro-
pocene. In an article in Nature in 2002,
Crutzen argued that human changes have
moved the planet out of the Holocene into a
much less climatically stable age. The notion
took hold. A wide range of scientists have
used the term to describe our unprecedented,
planetwide environmental effects, some of
which are immediately obvious from satel-
lite images of Earth. But formally accepting
the Anthropocene as a geological term is a
more controversial matter. After all, changes
that appear vast from our human perspec-
tive might be invisible on a geological time
scale. And debates over designating a new
epoch, era, or period can take decades
even centuriesto resolve.
In 2009, the International Commission
on Stratigraphy, the body charged with for-
mally designating geological time periods,
decided the Anthropocene concept has
some merit. It set up the Anthropocene
Working Group, chaired by Zalasiewicz,
to investigate the proposed age and report
back. This February, members of the group
published their initial ndings in a special
issue of the Philosophical Transactions of
the Royal Society A. The group reported a
wide range of human impacts on the planet
that will leave a stratigraphically signicant
mark on the geological record.
Although he may often sound like an
Anthropocene convert, Zalasiewicz says he
hasnt ofcially made up his mind. What
were trying to do is to ask how different is
our current world from that of a prehuman
equivalent. And to what extent is the present
state of the planet and its various changes
in biology, chemistry, geography converted
into geology? he says.
The Anthropocene debate is continuing
next week at the 2011 Geological Society
of America conference in a session chaired
by Stanley Finney, a geologist at California
State University, Long Beach, who is the
current chair of the International Commis-
sion on Stratigraphy. Finney is one of the
most outspoken skeptics of the Anthropo-
cene designation. He agrees that humans are
changing the planet but questions how much
of a mark will be left in the strata. Many
of our visible impacts could be removed
through erosion, he says.
The writing in the rocks
Erle Ellis, an ecologist at the University of
Maryland, Baltimore County, comes down
firmly on the side of designating a new
epoch, a view colored by his investigations
into how humans have altered the plan-
ets land covering. Ellis, a member of the
Anthropocene Working Group, calculates
that 80% of Earths land surface has been
modied by humans, with about 40% cur-
rently being used to produce fooda gure
that doesnt include
land used for tim-
ber pl ant at i ons.
Such deforestation
and conversion to
cropland or savanna
leaves clear signs
in the geological record; palynologists, who
study pollen paleontology, can date human-
kinds ancient agricultural forays with great
accuracy. The current unprecedented rate of
deforestation80,000 km
2
per yearwill
also be easy to spot in the rock record, Ellis
says. There are now more trees in agricul-
tural land than in forests.
The human impact on biodiversity will
inuence the types and dispersal of fossil
remains. Biostratigraphy is a very effec-
tive way of recognizing ones place in deep
time, Zalasiewicz says. Consider that more
than 90% of total vertebrate biomass today
is made up of humans and domesticated
animals, up from 0.1% 10,000 years ago.
And if the prediction of some biologists
comes true, Earth will experience the sixth
mass extinction event in its 4.5-billion-year
history because of hunting, overshing, hab-
itat loss, pollution, and climate change; that
would offer another, sobering piece of evi-
dence for the Anthropocene.
Although humans have changed Earths
biota and its hydrology through damming
rivers, creating reservoirs, sucking dry aqui-
fers, and melting glaciers, the geologists
who will ultimately judge the Anthropocene
case may end up focusing more on altera-
tion of the planets lithosphere, its rocky
shape. Some suggest that humanmade infra-
structure will fashion a unique and endur-
ing strata. In the eyes of a geologist, were
making really quite interesting patterns out
of our raw materials, Zalasiewicz says.
Wherever a road was buried, it would look
like a rather strange and distinctive fossil
river channel, but one which is quite rectan-
gular in shape and with a particular pattern
of gravel and other materials like concrete
that are not typical of river channels. Mil-
lions of years from now, a geologist would
see this and raise an eyebrow. A lot that
were producing is distinctive.
Cities, too, would leave their marks.
Some may erode away, but others, particu-
larly those like Amsterdam or New Orleans
that are in low-lying coastal zones and could
become fossilized as sediments accumu-
late over them, would leave their signatures
of foundations, plumbing, and rubble in the
lithostrata. Peel back the pavements and
the human interventions are already writ in
the rocks, says Simon Price, an urban geo-
scientist with the British Geological Survey.
Were witnessing a geological process, but
its by our hands, not by glaciers or rivers.
Humans are changing the lithostratig-
raphy in now easily visible ways. Mining
and other excavations remove four times as
much sediment as the worlds glaciers and
rivers move each year, and massive land-
forming projects have created entire islands
in the United Arab Emirates and elsewhere.
Other anthropogenic changes are not
obvious from Google Earth but will leave
an enduring legacy. Long-lasting alterations
to the planets chemistry are already evi-
dent: The world is currently being ooded
with light carbon (the C-12 isotope rather
than C-13) due to fossil-fuel burning, and
there is now a measurable differencecon-
sistent around the worldin the carbon
composition of biological specimens such
as sea shells, coral, and the shells of plank-
ton foraminifera, which will be preserved
in the strata. Chemostratigraphy will also
reveal the appearance of novel chemicals,
such as PCBs, plastics, radioactive isotopes
like cesium from atomic tests (see sidebar,
p. 37), and newly common materials, from
metals such as aluminum (which doesnt nat-
urally appear in its elemental state) to nitrates
Online
sciencemag.org
Podcast interview
with author
Gaia Vince.
NEWSFOCUS
A Global Perspective on the Anthropocene
AIR
1 2 3 4 5
Aragonite saturation state Getting More Acidic
CO
2
280 PPM CO
2
450 PPM
SOURCE: O. HOEGH-GULDBERG ET AL., SCIENCE 318, 5857 (14 DECEMBER 2007)
3000 5000 500 1000 B.C.E.
Year
1 500 1000 C.E. 1500 2000
0
1
2
3
4
5
6
H
u
m
a
n

p
o
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t
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(
b
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o
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s
)
240
260
280
300
320
340
360
380
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t
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o
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i
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C
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2

c
o
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c
e
n
t
r
a
t
i
o
n

(
p
p
m
)
Atmospheric CO
2
Concentration vs. Human Population
SOURCE: JED O. KAPLAN ET AL., THE HOLOCENE 21, 5 (AUGUST 2011)
Atmospheric N
2
O Concentration PPMV % Ozone Depletion Over Antarctica
60
70
1750 1800 1850 1900 1950 2000 1750 1800 1850 1900 1950 2000 1750 1800 1850 1900 1950 2000
50
40
30
20
10
0
310
300
290
280
270
1750
1500
1250
1000
750
Atmospheric CH
4
Concentration PPMV
SOURCE: WILL STEFFEN ET AL., PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A 369 (2011)
Humans are increasingly exerting
control over Earths fresh water,
through reservoirs, dams, and canals.
And as atmospheric carbon dioxide
(currently at 392 ppm) increases, the
ocean is becoming more acidic, as shown
by the decreasing saturation state of
aragonite (right). Aragonite is a type
of calcium carbonate that many ocean
creatures use to build their shells.
We cant directly see many of the
changes weve made to our atmosphere,
although we can measure the chemical pol-
lutants and isotopic changes. Indirectly,
though, we can feel the global warming
effect of releasing increasing amounts of
carbon dioxide into the air.
WATER
1850 1900
1950 2000
Growth of U.S. Dams and Reservoirs
SOURCE: JAMES P. M. SYVITSKI ET AL., PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A 369, (2011)
Ever since humans launched Sputnik
into space, weve been able to observe
our planet and its changes from a
truly global perspective. Satellites and
improved data collection and analysis
have allowed scientists to measure the
anthropogenic inuence on a range of
Earth systems, enabling researchers to
track rates of deforestation in the Ama-
zon, Arctic ice melt, trails of air pollu-
tion, the extent of sea-level rise, and
many other regional and global phenom-
ena. These tools are enabling scientists
to look at human changes to the planets
atmosphere, hydrology, lithosphere, and
biotaand infer which changes are pro-
found enough to be measurable millions
of years hence.
NEWSFOCUS
Terrestrial species
Freshwater species
All vertebrate species
Marine species
2000 1970
120
100
80
60
40
S
p
e
c
i
e
s

a
b
u
n
d
a
n
c
e
1975 1980 1985 1990 1995
The Fall of the Wild
SOURCE: WORLD WIDE FUND FOR NATURE AND UNEP WORLD CONSERV. MONITORING CENTER
50008000
30005000
20003000
10002000
5001000
250500
100250
< 100
Moderate use (>500 years)
Woodlands
Grasslands & steppe
Shrublands
Desert & tundra
>8000 years
YEARS OF
Intensive Use
Anthropogenic Transformation of the Terrestrial Biosphere
Wild NO HISTORY OF USE
Seminatural NO HISTORY OF USE
CREDIT: ERLE ELLIS, ADAPTED FROM E. ELLIS, PROCEEDINGS OF THE ROYAL SOCIETY A, 369:1010 (2011)
LAND
LIFE
T
o
n
n
e
s

o
f

a
n
n
u
a
l

l
o
s
s

(
b
i
l
l
i
o
n
s
)
1000
1000 100 10
100
10
1.0
0.1
0.01
Deep Time, Deep Erosion: Who Erodes Land Faster?
Mean rate of erosion
from natural processes
Human-induced erosion
Years before present (C.E. 2000)
7.2 billion tons/ year
SOURCE: BRUCE H. WILKINSON, GEOLOGY 33, 3 (MARCH 2005)
% Worldwide Fisheries Fully Exploited
100
1950 1960 1970 1980 1990 2000
80
60
40
20
0
SOURCE: WILL STEFFEN ET AL., PHILOSOPHICAL TRANSACTIONS
OF THE ROYAL SOCIETY A 369 (2011)
Domesticating the Planet
Consider that 90%
of total mammalian
biomass is made up
of humans and
domesticated
animals
up from
0.1% 10,000
years ago.
VACLAV SMIL, THE EARTHS BIOSPHERE: EVOLUTION,
DYNAMICS, AND CHANGE. MIT PRESS (2002)
Perhaps the most obvious mark weve
made to the planet is in land-use
changes. For millennia, humans have
chopped down forests and moved rock and
soil for agriculture and pasturelandand
more recently, for construction.
Humans have boosted numbers of
useful species such as cattle while
depleting others through hunting, oversh-
ing, habitat loss, or invasive competition.
Some scientists believe humans will cause the
planets sixth mass extinction: Average species
abundance of 3000 wild populations
declined 40% between 1970 and 2000.
NanoDrop
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learn about our free trial program www.thermoscientic.com/nanodrop
2
0
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NEWSFOCUS
C
R
E
D
I
T
S

(
T
O
P

T
O

B
O
T
T
O
M
)
:

Y
O
S
H
I
T
A
K
A

K
A
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U
W
A
;

D
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L
I
M
I
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/
C
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(
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)
;

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E
S
(which humans have made abundant through
fertilizer production and fossil-fuel burning).
The nitrates in agricultural runoff also
cause the massive dead zones that currently
affect 250,000 km
2
of the worlds oceans.
Similar zones have been recorded in the
planets paleontological record, and the
current ones likely will be as well. Ocean
acidification, too, is a measurable result
of anthropogenic carbon emissions being
dissolved in the oceansthey are now
more acidic than at any time in the past
800,000 years or more.
Challenging tradition
The working group is still gathering evi-
dence that human changes such as these
will leave an enduring legacy, then they will
assess it and decide whether the Anthropo-
cene should be formalized on the geological
time scale, and if so, at what level: an age,
epoch, era, or a period.
Finney questions how relevant the geo-
logical time scale is to the Anthropocene.
In 100,000 years from now, people will not be
digging the strata to nd out about the world
as it was in 2011, he argues; there are far better
tools for that. Geologists now and in the future
will use the human calendar and the many
cultural records that are kept in order to look
back to this time. The Anthropocene may be a
useful general term, Finney says, but it has no
place on the ofcial stratigraphic time scale.
Ellis disagrees. Its really helpful and rel-
evant to think like a geologist, even though
Im not one. It frames our impacts on a big-
ger planetary perspective. To be able to look
back at the rocks and say, Something hap-
pened here that cannot be explained by any-
thing other than human impact is really
powerful, Ellis says.
I think were challenging the traditional
view that geology always looks backwards.
Geology is happening all around us now at a
rate that we can certainly discern, says Will
Steffen, executive director of the Australian
National Universitys Climate Change Insti-
tute in Canberra. Different eras and epochs
in the past have been dened by changes
in climate and biodiversity. Were already
experiencing both of these, and for the rst
time we are aware of doing so and actually
driving these changes.
Zalasiewiczs working group is aiming
to deliver a final report at the 2016 Inter-
national Geological Congress in South
Africa. But theres unlikely to be a quick
vote then on whether the Anthropocene
deserves the title of epochor period or age.
The Ordovician-Silurian boundary at Dobs
Linn was finally agreed on in 1986, more
than a century after its proposal by geolo-
gist Charles Lapworth. Only about half of
the major boundaries in the Phanerozoic
our current geological eon covering the past
542 million yearshave been xed; the rest
are still being argued over. Geologists, like
their subject, are resistant to rapid change.
GAIA VINCE
Gaia Vince writes on environmental issues in the devel-
oping world at wanderinggaia.com.
A Sign of Our Times
If we are living in a new geological phase called the Anthropocene, when did
it begin? In other words, where does its golden spike belong?
Many human-driven planetary changes have their roots in the indus-
trial revolution, when the human population reached 1 billion. Atmo-
spheric carbon dioxide from fossil fuels started to build from around
1800, although it probably took 50 to 100 years before new concen-
trations of light carbon accumulated in measurable levels in marine
shells. That change could be the marker for the golden spike designat-
ing the beginning of the Anthropocene. There is a precedent: The bound-
ary between the Paleocene and the Eocene epochs of the Cenozoic era is
based on a change of carbon isotope chemistry.
But the scale of our impact accelerated rapidly after 1945 when popu-
lation doubled (from 3 billion in 1950 to 6 billion by 2000). As a result,
some think the golden spikeofcially known as a Global Boundary Stra-
totype Section and Pointshould
be set around 1945, which hand-
ily provides a marker thats sud-
den, distinctive, and global:
the introduction of radioactive
nuclei into the environment from
the first atomic-bomb tests in
Alamogordo, New Mexico. The
golden spike could be put into a
layer of accumulating lake sedi-
ments in which the radioactive
cesium rst appears, geologist
Jan Zalasiewicz of the University
of Leicester in the United King-
dom says.
From a geological perspec-
tive, it doesnt matter whether the
spike is at 1800, 1945, or 2050,
Zalasiewicz says, because millions of years
in the future, with error bars of thousands
of years, that kind of distinction will be impossible to perceive. Events that
look abrupt in the strata may have taken millions of years to occur, and
many changes take time to reveal themselves. For example, the tempera-
ture rise at the beginning of the Holocene was fairly abrupt, but it still took
some 5000 years for sea-level rise to catch up.
The golden spike we choose would be a time boundary that we use
with full knowledge that most changes on Earth are happening in different
places at different times, Zalasiewicz says. Its useful and instructive to
think of [the Anthropocene] from the far future perspective, but in practice
were dealing with it today. So we have to adopt as precise a time scale as
we can. G.V.
Reading the rocks. A geologist marks the
golden spike of the Ordovician-Silurian
boundary at Dobs Linn, Scotland, where a
darker stripe in the shale reveals the rst
appearance of graptolite fossils (inset).
Explosive signal. The atomic bomb
tests of 1945 produced a sudden
dispersal of radioactive dust that can
be measured globally.
LETTERS
edited by Jennifer Sills
LETTERS I BOOKS I POLICY FORUM I EDUCATION FORUM I PERSPECTIVES
41
Yesterdays tomorrows Diet-microbe
proles
45
COMMENTARY
C
R
E
D
I
T
:

N
T
P
C
/
V
I
N
C
E
N
T

G
A
U
T
I
E
R
Strategic Success for Hydropower in Laos
IN HIS NEWS FOCUS STORY MAYHEM ON THE MEKONG (12 AUGUST, P. 814), R. STONE REPORTS
concerns about hydropower development projects on the lower Mekong River and its trib-
utaries. The ecological transformations induced by water resource development are espe-
cially critical in tropical areas, where favorable conditions are created for the transmission of
vector-borne diseases. With regard to large hydroelectric projects, there has been a miscon-
ception that public health pre-
vention measures are too costly;
thus, they have been neglected or
enacted at a minimal level (1).
Water projects have been
shown to have direct and indi-
rect effects on diseases such as
malaria (2, 3), schistosomiasis
(4, 5), and hepatitis C (6). How-
ever, there is a paucity of com-
prehensive, in-depth assessment
of the global health and environ-
mental burden attributable to the
development and operation of
large dams. One exception is the
1070-MW Nam Theun 2 hydro-
power station in Laos. The com-
pany that operates the dam, along
with its partners and stakehold-
ers, has developed policies that balance hydroelectric production with responsible and coher-
ent social and environmental programs, including the strengthening of the provincial public
health infrastructure. This strategy could serve as a model for others. As part of this approach,
increased resources have been provided for local mother and child care, curative and preventa-
tive medicine, and psychosocial well-being. Adequate water supplies and sanitation have been
provided, mosquito and gastropod vector populations responsible for disease transmission are
monitored, and targeted vector control strategies have been implemented (7). To cope with the
occurrence of potential infectious hazards, the company has developed a tailored outbreak
response preparedness plan to be used in conjunction with the national plan. Surprisingly, the
implementation of such measures has been proven feasible at an acceptable cost ratio (0.2% of
the overall project development budget) (8).
Twenty-ve years after Chernobyl, the Fukushima incident will undoubtedly make hydro-
power an increasingly attractive renewable energy resource for countries facing urgently
rising needs for electricity to fuel their economies. A systematic, durable evaluation of the
health status of dam-affected populations is vital to improve our understanding of the impact of
dams and to develop appropriate mitigation strategies. Lending agencies and power companies
constructing and operating these dams need to reevaluate their responsibilities concerning the
public health impact on affected populations.
GILLES GUERRIER,
1
* RICHARD PAUL,
2
PANY SANANIKHOM,
3
SURINDER KAUL,
3
RUEDI LUTHI,
3

JEAN-PIERRE KATZ,
3
MICHEL ROBINO,
3
PHASOUK KHAMMANITHONG,
4
PAUL T. BREY
1
1
Institut Pasteur du Laos, 1 rue Louis Pasteur, Post Ofce
Box 3560, Vientiane, Lao PDR.
2
Unit de Gntique Fonc-
tionnelle des Maladies Infectieuses, Institut Pasteur, 25
rue du Docteur Roux, 75724 Paris Cedex 15, France.
3
Nam
Theun Power Company Limited, 23 Singha Road, Nong
Bone Village, Post Ofce Box 5862, Vientiane, Lao PDR.
4
Khammouane Provincial Health Service, rue no. 13 B, Lao-
phoxay Village, Thakhek Khammouane Province, Lao PDR.
*To whom correspondence should be addressed. E-mail:
guerriergilles@gmail.com
References
1. World Commission on Dams, Dams and Development:
A New Framework for Decision-Making (Earthscan
Publications, London, 2000).
2. J. Keiser et al., Am. J. Trop. Med. Hyg. 72, 392 (2005).
3. D. Yewhalaw et al., Malar. J. 8, 21 (2009).
4. P. Steinmann, J. Keiser, R. Bos, M. Tanner, J. Utzinger,
Lancet Infect. Dis. 6, 411 (2006).
5. H. M. Zhu, S. Xiang, K. Yang, X. H. Wu, X. N. Zhou,
Ecohealth 5, 137 (2008).
6. C. Frank et al., Lancet 355, 887 (2000).
7. E. T. Sayasone et al., Asian Pac. J. Trop. Med. 2, 63 (2009).
8. Nam Theun 2 Hydroelectric Project, Project Implementa-
tion Plan (http://www.namtheun2.com/images/stories/
PIP/PIP%20Final%20-%20Part%20B%
20Chapter%202_Health_050527.pdf).
Justiable Changes
to Indicators Survey
THE NEWS & ANALYSIS STORY NEW NSF SUR-
vey tries to separate knowledge and belief
(Y. Bhattacharjee, 22 July, p. 394) discussed
the National Science Board (NSB) and the
National Science Foundations (NSFs) call
for a reevaluation of the conceptual frame-
work for public knowledge of science as
reported in the NSB Science and Engineering
Indicators. We led the two workshops men-
tioned, which provided suggestions for revis-
ing the survey. In the story, Jon Miller from
the University of Michigan alleges that the
workshops recommended that the Indicators
should downplay the truth about public
knowledge of evolution. We disagree with
this characterization.
The report of the workshop convened by
Toumey says: The workshop participants
strongly feel that the NSB, the NSF, and the
Nakai Dam in central Laos.
47 49
Neuroimmune
crosstalk
Local adaptation
Indicators cannot retreat from controversies
about important scientic concepts. Evolu-
tion is a cornerstone of Biology. Measures
and reports of public knowledge of science in
the Indicators and elsewhere need to explore
knowledge of evolution (1).
The next paragraph recommends that
measures of public knowledge of evolu-
tion be improved by including such topics
as adaptation, natural selection, and specia-
tion, and by broadening the topic of evolu-
tion beyond human evolution. The evolution
of plants is germane to questions of genet-
ically modified organisms, for example,
and microbial evolution is relevant to our
use of antibiotics and vaccines. The public
must know the basics of evolution to under-
stand the important policy questions in these
areas. These recommendations do not down-
play evolution, as Miller suggests. Just the
oppositethey enhance and expand mea-
sures of public knowledge of evolution.
The workshop convened by Guterbock
(2) used its participants expertise in sur-
vey design and methods to develop ways to
implement the recommendations of the rst
workshop and to allow deeper understand-
ing of what the public knows and believes
about science.
The News story also quotes Miller as say-
ing that the question of human evolution is
being altered for religious reasons, and that
the workshop participants recommended
those changes because Americans are not
scoring high enough. We see no evidence
that the NSB members were motivated by
religious reasons. We organized the two work-
shops, and each of us participated in both.
There is no truth to the allegation that we and
our colleagues made those recommendations
because Americans are not scoring high
enough. We hope that readers will refer to
the two workshop reports rather than trusting
the allegations made in the News story.
CHRIS TOUMEY
1
* AND TOM GUTERBOCK
2
1
USC NanoCenter, University of South Carolina, Columbia,
SC 29208, USA.
2
Center for Survey Research, Weldon Cooper
Center for Public Service, University of Virginia, Charlottes-
ville, VA 22903, USA.
Toumey@mailbox.sc.edu
References
1. C. Toumey et al., Science in the service of citizens and
consumers (USC NanoCenter, Columbia, SC, 2010);
www.nano.sc.edu/resources/publications.aspx.
2. T. M. Guterbock et al., Measurement and operationaliza-
tion of the Science in the service of citizens and consum-
ers framework (Center for Survey Research, University
of Virginia, Charlottesville, VA, 2011); www.coopercenter.
org/csr/publications/measurement-and-operationalization-
science-service-citizens-and-consumers-framework.
Exxon-Mobil Funding
Overstated
IN HER NEWS FOCUS STORY CLIMATE CHANGE
sparks battles in classroom (5 August,
p. 688), S. Reardon writes that my organiza-
tion, The Heartland Institute, has received
signicant funding from Exxon-Mobil. The
story did not clarify that the amount of support
we received never exceeded 5% of our budget.
Nor did the story make clear that we havent
received Exxon-Mobil funding since 2006,
3 years before we began mailing research
material to school board presidents.
JOSEPH L. BAST
President, The Heartland Institute, Chicago, IL 60607, USA.
E-mail: jbast@heartland.org
CORRECTIONS AND CLARIFICATIONS
Reports: Impacts of shing lowtrophic level species on
marine ecosystems by A. D. M. Smith et al. (26 August, p.
1147). A note should have been included indicating that
after the rst author, all authors are listed alphabetically.
Reports: Ribosomal protein S6 kinase 1 signaling regulates
mammalian life span by C. Selman et al. (2 October 2009, p.
140). The authors reported that, in Caenorhabditis elegans,
effects of the rsks-1(ok1255) mutation on development, body
size, fertility, and life span require the presence of a wild-type
allele of the gene aak-2, which encodes an adenosine mono-
phosphate (AMP) kinase alpha subunit (see Fig. 3). Because
the rsks-1;aak-2 strain described in the Report did not actu-
ally contain the rsks-1 allele, initially noted by D. Z. Korta
and E. J. Hubbard, the authors have now performed epistasis
tests using a newly constructed rsks-1(ok1255);aak-2(ok524)
strain. The new trials conrm the original nding that muta-
tion of aak-2 suppresses the longevity of rsks-1(ok1255)
mutants. However, the small size, reduced brood size, and
delayed reproduction associated with rsks-1(ok1255) proved
to be aak-2 independent. This means that the effects of rsks-1
on life span require AMP kinase, but those on growth and
reproduction do not. Together with the data derived from the
S6K1
/
mice, these ndings implicate AMP kinase in the lon-
gevity phenotype produced by loss of S6K1. The authors have
now sent the new rsks-1(ok1255);aak-2(ok524) strain to the
Caenorhabditis Genetics Center.
Reports: A silent polymorphism in the MDR1 gene changes
substrate specicity by C. Kimchi-Sarfaty et al. (26 January
2007, p. 525). Figure 1, D to F, shows the effect of plasmid
DNA concentration during infection/transfection on Rh123
efux (0.5 M) in the presence of an inhibitor, 10 M CsA;
the amounts of infected/transfected DNA were represented
as 3 g, 10 g, and 15 g, respectively, in panels D to F.
Because of an error in overlaying the data, the histograms for
the 3x haplotype (C1236T-G2677T-C3435T) in panels E and F
are identical; they both depict cells infected/transfected with
10 g of DNA, whereas Fig. 1F should have shown the histo-
gram for cells infected/transfected with 15 g of DNA. The g-
ure above shows the histogram originally published in Fig. 1F
(red) overlaid with the correct histogram (blue). The original
conclusions are not affected. The authors thank A. Malcolm
Campbell and his students at Davidson College for analyzing
the report and noting this error.
Letters to the Editor
Letters (~300 words) discuss material published in
Science in the past 3 months or matters of gen-
eral interest. Letters are not acknowledged upon
receipt. Whether published in full or in part, Let-
ters are subject to editing for clarity and space.
Letters submitted, published, or posted elsewhere,
in print or online, will be disqualied. To submit a
Letter, go to www.submit2science.org.
Future of a Generation
What will the future of science look like?
How will your generation mold the way
science is practiced? Have ideas? We want
to hear from you! Add your voice to the
pages of Science by answering this question:
How will the practice of science change in
your lifetime? What will improve and what
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BOOKS ET AL.
41
W
hen did an enemy nation last use
a military strategy taken from
a story predicting the very war
being fought (with the added irony that the
future history in question should have
been written by a citizen of the nation under
attack)? Or a writer imagine a revolution that
subsequently completely transformed the
way you and I work, communicate, and play?
In Out of This World: Science Fiction: But
Not As You Know It, bibliographer and author
Mike Ashley relates both the impact and
the predictive powers of the broad literary
genre that is science ction. In the rst case
above, the story was Arthur Conan Doyles
Danger! (1914) and the enemy, Germany
in World War I; in the second case, Will F.
Jenkins (aka Murray Leinster)
envisioned both home comput-
ers and the Internet in his 1946
story A Logic Named Joe.
Out of This World offers a
sumptuously illustrated sur-
vey of the themes and ideas
that underpin science f ic-
tion. If you are interested in
machines that evolve faster
than humans to the point where
humans become subservient to
machines, there is Samuel But-
lers novel Erewhon (1872). For
considerations of beings that
live in different dimensions,
see Edwin A. Abbotts classic
Flatland (1884). The dangers
of atomic energy? Robert Cro-
mie was already foreseeing the
dangers of atomic energy in
his novel The Crack of Doom
(which appeared in 1895, the
year before Henri Becquerel
discovered radioactivity).
These ideas, and many more
recycled with such enthusiasm
that they have become science-
ction tropeswere conceived
even before the phrase science
ction was coined (in 1929,
by science-fiction magazine
editor Hugo Gernsback).
But, as Out of This World
documents, more than modern
science ction is the warmed-
over imaginings of earlier
generations. New ideas con-
tinued to emerge throughout
the past century: The word robot comes
from Karel apek in his 1920 play Ros-
sums Universal Robots. Terra forming,
engineering a planet to Earth-
like conditions, rst appeared
in Jack Williamsons story
Collision Orbit (1942),
where he applied it to an aster-
oid. Fredric Browns vignette
Answer (1954) presages
the technological singular-
ity, when computers become
superintelligent. For Burn-
ing Chrome (1982), William
Gibson drew on Norbert Wieners cyber-
netics to coin cyberspace, the milieu of
electronic and computer-based communica-
tion. And science ction has expanded into
new subgenres: steampunk, cyberpunk, and
the New Weird.
The lusciously presented illustrations
form an integral part of Ashleys narrative.
That is no surprise, as the book accompa-
nies an exhibition of the same name at the
British Library (which closed 25 September
2011). Readers will nd a
wonderfully eclectic mix of
book and magazine covers,
art taken from stories and
graphic novels, stills from
films and plays, and even
authors annotated man-
uscript pages. Although
some of the artists who
helped dene the visual his-
tory of science fiction get
a name check, it is a pity that others could
not have also been includedfor example,
the iconic book-cover art by Chris F. Foss,
Bruce Pennington, and Alan
Aldridge or the movie art of
Hans Rudolf Giger. Perhaps
those could be covered in a
future exhibition and book.
The text should, however,
come with a warning: Ash-
ley delivers a history of ideas
and not an exercise in literary
criticism. He mentions astron-
omer Fred Hoyles The Black
Cloud (1957) but not that it
has dated badly nor that Fifth
Planet (1963), cowritten with
son Geoffrey, offers a consider-
ably more persuasive portrayal
of the interaction between
humans and a vastly superior
intelligence. Ashley might
have noted that director Ridley
Scotts 1982 lm Blade Runner
is a more satisfyingly crafted
story than the book it is based
on, Philip K. Dicks awkward
Do Androids Dream of Electric
Sheep (1968). And his exem-
plar of the New Weird, China
Mivilles novel Perdido Street
Station (2000), strikes me as
simply daft in places.
Still, these are no more than
minor quibbles. I would recom-
mend Out of This World to any-
one with an interest in explor-
ing science ction far beyond
the limits of Dune, Starship
Troopers, and I, Robot.
Picture Perfect Future Past
SCIENCE FICTION
Out of This World
Science Fiction:
But Not As You Know It
by Mike Ashley
The British Library, London,
2011. 144 pp. Paper, $29.95,
16.95. ISBN 9780712358354.
10.1126/science.1213758
Well represented. The book includes ten examples of Frank R. Pauls work, including
this cover illustration for the short story City of the Living Dead by Laurence Manning
and Fletcher Pratt (from the May 1930 issue of Science Wonder Stories). C
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Guy Riddihough
POLICYFORUM
Paleolithic Art in Peril: Policy and
Science Collide at Altamira Cave
CONSERVATION
Cesareo Saiz-Jimenez,
1
* Soledad Cuezva,
2
Valme Jurado,
1
Angel Fernandez-Cortes,
3

Estefania Porca,
1
David Benavente,
2
Juan C. Caaveras,
2
Sergio Sanchez-Moral
3

Despite evidence of damaging human impacts,
cave paintings may again be threatened if
visitors are allowed access.
I
n the last decade, considerable atten-
tion has been paid to the deteriora-
tion of the caves that house the worlds
most prominent Paleolithic rock art. This is
exemplied by the caves of Lascaux (Dor-
dogne, France) ( 1) and Altamira (Canta-
bria, Spain), both declared World Heritage
Sites. The Altamira Cave has been closed
to visitors since 2002. Since 2010, reopen-
ing the Altamira Cave has been under con-
sideration. We argue that research indicates
the need to preserve the cave by keeping it
closed in the near future.
In the 1970s, Altamira Cave sparked a
political dispute between local and regional
administrations and the state and received
a great deal of public attention. In October
1977, Altamira had to be closed to the public
because of severe deterioration of the paint-
ings after decades of visits (e.g., 175,000
visitors in 1973). In 1978, the Spanish gov-
ernment took over ownership of the cave,
which today belongs to the Spanish Ministry
of Culture and is managed by the National
Museum of Altamira ( 2).
In 1982, after a microclimatic sur-
vey, Altamira reopened to the public with
a limit of 11,000 people per year ( 3) or, in
another document, 8500 visitors per year,
excluding guides ( 4). However, in Septem-
ber 2002, Altamira had to be closed to the
public because of the presence of photo-
trophic microorganisms on the paintings ( 5)
(see the gure and g. S1), a phenomenon
similar to that suffered by Lascaux 50 years
before. Colonization by these microorgan-
isms was a consequence of decades of use of
articial lighting in the famous Polychrome
Hall and was accompanied by development
of white microbial colonizations directly on
the red paintings ( 6) (see the gure and g.
S3). This showed that Altamira Cave might
be mimicking the deterioration processes
at Lascaux.
Harmful Impacts of Visitors
The current status of the cave is the result of
the accumulation of multiple microenviron-
mental changes and impacts suffered from
the time of its discovery in 1879 ( 2) (gs. S1
to S6). In its natural state, the cave should
be an oligotrophic (nutrient-poor) environ-
ment with very little connection to the out-
side atmosphere. The numerous condition-
ing projects, changes in the top soil and cave
sediments, archaeological digs, and massive
amounts of visitors transformed the pristine
ecosystem into one with an abundance of
available nutrients.
Preservation of a large part of the Poly-
chrome Hall ceiling paintings from their
creation more than 14,000 years ago until
their discovery was aided by several factors:
absence of light; low rates of water inltra-
tion, precipitation of speleothems (mineral
deposits) and exchange with the external
atmosphere; and the maintenance of very sta-
ble microenvironmental conditions because
of limited airow in the Polychrome Hall.
The Spanish National Resource Council
(Consejo Superior de Investigaciones Cient-
cas, CSIC) studied the cave between 1996
and 1999. The studies focused on determin-
ing the impact of visitors on the micro-envi-
ronmental conditions of the Polychrome Hall
and highlighted the need to revise the criteria
used by the University of Cantabria to design
the 1982 visitation schedule ( 7) because
deterioration processes had not stopped.
Sanchez-Moral et al. ( 3) concluded that cor-
rosion caused by visitors under the 1982 visi-
tation schedule would be up to 78 times that
arising from natural processes.
Phototrophic microorganisms were
observed in 2000 in the Polychrome Hall, as
resting forms or with their metabolic activ-
ity reduced to a minimum. Caaveras et al.
( 8) predicted that in the event of a change
in the lighting conditionssuch as perma-
nent or extensive lighting, as subsequently
occurredgrowth of these communities
would take place. This did indeed occur
in 2002 (fig. S1A) and led to the second
cave closure.
Once the cave was closed in 2002, the
Ministry of Culture appointed the CSIC team
to survey and control the cave from 2003
to 2005 and from 2007 to 2009. Thereaf-
ter, CSIC is controlling cave microclimate
through successive contracts, the last ending
on March 2012. Research focused on the cave
as an ecosystem dependent both on micro-
environmental and geochemical characteris-
tics of the underground environment and an
energy-matter exchange with the external
atmosphere. The conclusions of the research
were against the reopening of the cave to
visitors ( 9 11). This was supported by envi-
ronmental, geochemical, hydrological, and
microbiological data put at the disposal of the
Ministry of Culture.
Progress, but Persistent Problems
The 2002 closing represented a clear benet
for conservation of the paintings: The green
phototrophic colonizations did not continue
to progress; however, small patches are still
evident (g. S1B), and the corrosion rate
of the paintings host rock decreased. A
decrease was also noted in the content of
organic matter and nitrogen compounds in
the inltration waters after the elimination
of cattle activities in the land above the cave
and regular mowing and removal of grasses.
Installation of a new access door in 2007,
equipped with a thermal insulation sys-
tem, followed 20 m after by a second door,
reduced the entry of airborne particles, the
condensation rate in the entrance area, and
the metabolic activity of the main visible
microbial colonies ( 10 12) [see supporting
online material (SOM)].
These preventive conservation actions
were quite different from steps taken in Las-
caux, where chemical products and antibiot-
ics were used ( 1). However, in Altamira the
conservation problems are still far from being
solved. Evidence of microbial colonies con-
sisting of different-colored patches are mainly
located in the area near the cave entrance (g.
S2) but have already reached the Polychrome
Hall ( 10) (see the figure and fig. S3). The
objective of the corrective measures imple-
mented in recent years was depriving the eco-
system of carbon in order to inhibit bacterial
growth and to reduce exchange between the
cave atmosphere and exterior.
1
Institute for Natural Resources and Agrobiology, Spanish
National Research Council (IRNAS-CSIC), 41012 Sevilla,
Spain.
2
Universidad de Alicante, 03080 Alicante, Spain.
3
National Museum of Natural Sciences, Spanish National
Research Council (MNCN-CSIC), 28006 Madrid, Spain.
*Author for correspondence. E-Mail: saiz@irnase.csic.es
POLICYFORUM
Our team has modeled
the impact of visitors on
the cave and gathered data
from hundreds of visits
monitored between 1996
and 1999 (fig. S5). If the
cave reopens to the pub-
lic, continued entry of visi-
tors would cause increases
in temperature, humidity,
and CO
2
in Polychrome
Hall, reactivating conden-
sation and host-rock corro-
sion ( 3). Air warming and
the inevitable turbulence
caused by visitors favor an
air exchange between Poly-
chrome Hall and areas clos-
est to the entrance, where
there are microbial coloni-
zations on walls and ceil-
ings ( 10) (see the figure).
In addition, visitors walk-
ing will cause f ine par-
ticle resuspension from
ground sediments. Air cur-
rents caused by visitors
will erode wall and sedi-
ment surfaces, provoking microparticle
detachment (releasing bacterial and fungal
spores). Additionally, new nutrient sources
will be supplied to the ecosystem by tourists
and guides. This could lead to a new stage
of proliferation of microorganisms whose
current trend appears to be moving toward
a stationary state.
In addition to bacterial colonization,
fungi have been observed in Altamira Cave
( 11, 12), as in Lascaux (g. S4 and table
S1). These fungi have three well-defined
origins: plant saprophytes introduced from
the exterior, entomopathogenic fungi intro-
duced by arthropoda, and coprophilous
fungi growing on rodent feces (g. S4A).
In 2007, the scientic instruments control-
ling cave environment were repeatedly col-
onized by fungi (g. S4B) after an archae-
ological excavation was carried out within
the cave in October 2006, despite the rec-
ommendations of CSIC. Periodic cleanings
of instruments were required using envi-
ronmentally friendly methods and com-
pounds. For example, periodic mechanical
removal of the ground sediments adjacent
to the instruments, which were colonized by
fungi, and treatment with hydrogen perox-
ide. Biocides have not been used because
the experience of Lascaux showed that ben-
zalkonium chloride applied between 2001
and 2004 is being used by microorganisms
as a carbon and nitrogen source ( 1).
Politics and Uncertainty
Since 2010, reopening the cave to visi-
tors has been seriously considered, with
the belief that this will boost the local tour-
ism economy ( 13). In December 2010, the
Board of Directors of the cave called for a
new international scientic commission to
prepare a report deciding whether cave con-
servation is compatible with visits.
Although our recommendations, based
on data collected over the past 15 years, do
not support reopening of the cave, as sci-
entists, we are in favor of the possibility
of evaluating our data with other special-
ists. We are hopeful that the international
scientific commission to be appointed by
the Board of Directors, which has declared
that this cave is one of the best scientically
studied in the world ( 14), will consider the
data we have collected.
Tourist visits to many caves and other
subterranean sites should be looked upon
as a potential risk for the conservation of
cultural heritage. Archaeologists, environ-
mentalists, and microbiologists agree on
the benecial effect of closing subterranean
sites for their conservation, as shown by
the recent announcement that some Egyp-
tian tombs including Tutankhamuns will be
closed to visits, with the tourists rerouted to
a replica ( 15). Altamira Cave, although cur-
rently closed, is at real risk. Whether or not
this cave follows the dangerous path of Las-
caux Cave with continued fungal outbreaks
is in the hands of the Ministry of Culture to
keep the cave closed to visits.
References
1. F. Bastian, V. Jurado, A. Novkov, C. Alabouvette,
C. Saiz-Jimenez, Microbiology 156, 644 (2010).
2. J. A. Lasheras, C. de las Heras, Coalition 12, 7 (2006);
www.rtphc.csic.es/PDF/NL12.pdf.
3. S. Snchez-Moral et al., Sci. Total Environ. 243-244, 67
(1999).
4. Museum of Altamira, http://museodealtamira.mcu.es/
ingles/historia_museo.html.
5. C. Holden, Science 297, 47 (2002).
6. C. Schabereiter-Gurtner, C. Saiz-Jimenez, G. Piar, W.
Lubitz, S. Rlleke, FEMS Microbiol. Lett. 211, 7 (2002).
7. E. Villar et al., in Estudios Fsico-Qumicos de la Sala
de Polcromos. Inuencia de la Presencia Humana
y Criterios de Conservacin (Ministerio de Cultura,
Madrid, 1984), pp. 95110.
8. J. C. Caaveras, S. Sanchez-Moral, V. Soler, C. Saiz-Jimenez,
Geomicrobiol. J. 18, 223 (2001).
9. S. Sanchez-Moral et al., in Redescubrir Altamira (Grupo
Santander, Madrid, 2002), pp. 245257.
10. S. Cuezva, S. Sanchez-Moral, C. Saiz-Jimenez, J. C.
Caaveras, Int. J. Speleol. 38, 83 (2009).
11. V. Jurado et al., Naturwissenschaften 96, 1027 (2009).
12. E. Porca et al., Ecol. Indic. 11, 1594 (2011).
13. T. Constenla, El Pais, 21 December 2010,
www.elpais.com/articulo/english/The/prehistoric/art/that/
won/t/be/seen/elpepueng/20101221elpeng_4/Ten.
14. Ministry of Culture, Spain, www.mcu.es/
archivoswebmcu/gabineteprensa/notas/23952010/
altamira.pdf.
15. M. Pitts, The Guardian, 17 January 2011, p. G2;
www.guardian.co.uk/culture/2011/jan/17/tutankhamun-
tomb-to-close.
Supporting Online Material
www.sciencemag.org/cgi/content/full/334/6052/42/DC1
10.1126/science.1206788
1
st
door (entrance)
2
nd
door
Polychrome Hall
Microbial colonies
Microenvironmental
monitoring system
Conduit through the wall
N
0 5 10
Meters
Conduit through the wall
Corridor
Crossing
Yellow colonies
Gray colonies
White colonies
Cyanobacteria
Entrance Hall
Spatial distribution of the visible microbial colonies on the ceiling at Altamira Cave. The Polychrome Hall features
dozens of paintings of bison, deer, and other animals, spread across 150 square meters of cave ceiling that were painted more
than 14,000 years ago. [Figure modified from (10)]
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PERSPECTIVES
T
here is a multimillion-dollar industry
based on the concept that introduc-
ing benecial bacteria into the human
intestines will improve our health. The tril-
lions of symbionts in the large intestine pro-
foundly affect our metabolism and immunity.
Accordingly, abnormal bacterial communi-
ties have been identied in several human
diseases such as inammatory bowel diseases
( 1 3), colon cancer ( 4, 5), irritable bowel syn-
drome ( 6), and nonalcoholic fatty liver dis-
ease ( 7). The composition of microbial com-
munities is generally stable within each indi-
vidual. Past studies of the gut microbiota
emphasized the huge impact of nutrition ( 8),
which is likely to outweigh that of the host
genotype ( 9). On page 105 of this issue. Wu
et al. ( 10) further explore how dietary factors
can inuence the prole and stability of intes-
tinal microbes.
The dissimilarity in gut bacterial com-
position between individuals is huge, even
between identical twins ( 11), complicating
the extraction of clinically relevant generaliza-
tions from studies of the microbiota. Recent
analysis shows that it is possible to simplify
matters, because all people, including those
with chronic intestinal disease, can be classi-
ed into just three broad enterotypes dom-
inated by three different genera: Bacteroides
and Prevotella (both belonging to the phylum
Bacteroidetes), and Ruminococcus ( 12). More
surprisingly, these enterotypes were indepen-
dent not just of sex and body mass index but
also of nationality, despite the profound dif-
ferences in long-term dietary habits between
western nations and east Asian countries.
By combining detailed nutritional analy-
sis and microbiome determination in 98 indi-
viduals, Wu et al. sought to identify nutrients
that substantially affect abundances of micro-
bial species. They found that higher fat intake
and lower ber intake are associated with par-
ticular bacterial groups. Intriguingly, entero-
types appeared to be determined by long-
term diet: The Bacteroides enterotype was
positively associated with animal protein and
saturated fats, whereas the Prevotella entero-
type was associated with a predominantly
plant-based nutrition with high carbohy-
drates and low meat and dairy consumption.
These ndings are in agreement with a previ-
ous study comparing children from Italy and
Burkina-Faso, which showed that the African
children, who have practically no animal fat
and protein in their diets, are colonized by
members of Prevotella (or Xylanibacter, a
closely related genus), whereas their Euro-
pean counterparts have high Bacteroides lev-
els ( 13). The third enterotype, Ruminococcus,
previously shown to be the most commonly
encountered ( 12), was not well separated and
often merged with the Bacteroides entero-
type. This is perhaps unsurprising given that
the abundance of the Ruminococcus genus in
that cluster was relatively low to begin with,
resulting in more egalitarian microbial com-
munities with no dominant genus. Thus, it
may be that this definition by exclusion
enterotype may not represent a stable state.
Wu et al. then performed a dietary inter-
vention with 10 individuals, all with a Bac-
teroides enterotype, to examine the short-
term (10 days) effects of nutrition on bacte-
rial communities and enterotypes (see the
gure). In agreement with a previous study
in mice, changes were detectable within the
rst 24 hours, testifying to the rapid effects
that diet can have on quickly dividing bacte-
ria. Remarkably, however, no stable changes
to the Prevotella enterotype were observed in
the ve individuals who were switched to a
high-ber/low-fat diet, although one showed
a temporary 1-day switch. Thus, enterotypes
appear to reect long-term nutritional hab-
its, and altering them may require a more
prolonged dietary intervention, unless it is
preceded by antibiotic treatment, which is
usually undesirable. Is the goal of switch-
ing enterotypes really desirable, even if one
enterotype should be shown to correlate with
increased disease risk? Establishing causa-
The Guts of Dietary Habits
MICROBIOLOGY
Uri Gophna
Can dietary intervention change an individuals
gut microbiome composition?
Long- and short-term effects. Nutrients affect the composition of the intestinal microbiota. Two different
long-term diets are associated with a distinct gut microbe population (enterotypes). These microbial proles
are stable, and short-term dietary changes are not sufcient to alter them. C
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Molecular Microbiology and Biotechnology, George S. Wise
Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel
Aviv 69000, Israel. E-mail: urigo@tauex.tau.ac.il
PERSPECTIVES
tion from microbiota-disease associations is
difcult. Moreover, bacteria to which health
benets have been attributed, such as Faeca-
libacterium prausnitzii ( 14), have not been
associated with a particular enterotype. Thus,
although the enterotypes represent a useful
framework for the study of the gut micro-
biota, the clinical value of knowing ones
enterotype remains to be determined.
Wu et al. also show that several dietary
factors that have an impact on gut bacteria,
such as red wine and the articial sweetener
aspartame, are not correlated with entero-
types. That an articial sweetener can mod-
ify bacterial communities is surprising.
How even minor concentrations of such a
sweetener are sufcient to cause substantial
changes in some gut inhabitants warrants fur-
ther study. Undoubtedly, consumers of these
food additives, which are otherwise perceived
as safe, are unaware that these substances
may inuence their gut bacteria. This may be
of particular importance to patients with dis-
eases correlated with modications of the gut
microbiota, such as irritable bowel syndrome
and inammatory bowel diseases. These indi-
viduals often adhere to self-imposed diets
that they have empirically found to reduce
symptoms such as diarrhea, but are unlikely
to anticipate that an articial sweetener may
affect their indigenous microbiota and possi-
bly their well-being.
It is anticipated that the study by Wu et al.
will be followed up by larger diet-microbi-
ome association studies that will help rene
the picture of nutrients that affect the com-
position of the intestinal microbiota. Follow-
up work is important because the large num-
ber of dietary parameters forced the authors
to use a relatively lenient false discovery rate,
and thus it is possible that a small number
of links that they discovered are the product
of chance. Further insights into diet-micro-
biome relationships could eventually have
an impact on nutritional guidelines for both
healthy individuals and patients with chronic
intestinal diseases and metabolic diseases
such as obesity and diabetes. We are still
only at the beginning stages of considering
microbiomes as a diagnostic and engineering
microbiome structure as treatment.
References
1. U. Gophna, K. Sommerfeld, S. Gophna, W. F. Doolittle,
S. J. Veldhuyzen van Zanten, J. Clin. Microbiol. 44, 4136
(2006).
2. C. Manichanh et al., Gut 55, 205 (2006).
3. D. N. Frank et al., Proc. Natl. Acad. Sci. U.S.A. 104,
13780 (2007).
4. P. D. Scanlan et al., Environ. Microbiol. 10, 789 (2008).
5. T. Wang et al., ISME J. 10.1038/ismej.2011.109 (2011).
6. A. Kassinen et al., Gastroenterology 133, 24 (2007).
7. M. D. Spencer et al., Gastroenterology 140, 976 (2011).
8. P. J. Turnbaugh et al., Sci. Transl. Med. 1, 6ra14 (2009).
9. A. Kovacs et al., Microb. Ecol. 61, 423 (2011).
10. G. D. Wu et al., Science 334, 105 (2011).
11. P. J. Turnbaugh et al., Nature 457, 480 (2009).
12. M. Arumugam et al., Nature 473, 174 (2011).
13. C. De Filippo et al., Proc. Natl. Acad. Sci. U.S.A. 107,
14691 (2010).
14. H. Sokol et al., Proc. Natl. Acad. Sci. U.S.A. 105, 16731
(2008).
10.1126/science.1213799
Resilience to Blooms
ECOLOGY
Justin D. Brookes
1
and Cayelan C. Carey
2

Managing nitrogen and phosphorus pollution
of fresh water may decrease the risk of
cyanobacterial blooms, even in the face
of warming temperatures.
C
yanobacterial blooms (see the fig-
ure) present health risks worldwide
for humans and livestock that drink
or use contaminated water, and also repre-
sent substantial economic costs to commu-
nities due to water treatment, lost tourism
and recreation revenue, and declining prop-
erty values ( 1). These explosive growths
occur in fresh and marine water, and may be
increasing globally. One recommendation is
that water managers must address the effects
of climate change when combating cyano-
bacterial blooms ( 2). However, recent stud-
ies suggest that controlling nutrients may be
more important in increasing aquatic eco-
system resilience to these blooms.
A number of factors may potentially con-
tribute to an increase in blooms, primar-
ily climate change and changing land use.
Most climate change modeling scenarios
predict that aquatic systems will experience
increases in temperature, thermal strati-
cation ( 2), and water column stability, all
factors that favor cyanobacteria over other
phytoplankton ( 2, 3). Thermal stratication
leads to a greater propensity for cyanobac-
terial blooms, as many cyanobacteria have
gas-lled vesicles that enable them to rise to
the water surface and form dense blooms ( 2,
4). In addition to climate change, deforesta-
tion, human and commercial animal waste,
and agricultural fertilization have increased
nutrient runoff into aquatic systems ( 5), also
favoring cyanobacterial blooms.
What is the relative importance of warm-
ing temperature versus nutrient (nitrogen
and phosphorus) loading in driving cya-
nobacterial dynamics? Many modeling
studies ( 6, 7), historical data analyses ( 4,
8), and experimental studies ( 9, 10) show
increased nutrient concentrations as a con-
sistently more important driver of blooms
than warming temperatures. For example,
in Lake Mggel (Mggelsee), Germany,
cyanobacteria did not directly benet from
increased water temperatures; rather, blooms
decreased as nutrient loading was reduced
( 4, 11). Whereas some studies indicate that
increasing nutrients and temperatures may
exert a synergistic effect on cyanobacterial
dominance ( 4, 6, 7), nutrient loading, nota-
bly nitrogen and phosphorus, is the primary
factor in the expansion of blooms ( 12).
There are several mechanisms by which
increased nutrients lead to the dominance of
1
School of Earth and Environmental Science, University of
Adelaide, Adelaide 5005, Australia.
2
Department of Ecol-
ogy and Evolutionary Biology, Cornell University, Ithaca,
NY 14853, USA. E-mail: justin.brookes@adelaide.edu.au,
ccc99@cornell.edu
Big bloom. A cyanobacterial bloom in Lake Winder-
mere, England, in June 2007. See SOM text for sug-
gested resources related to cyanobacerial blooms. P
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Neuroimmune Communication
IMMUNOLOGY
Ephraim F. Trakhtenberg and Jeffrey L. Goldberg
Neurotransmitters link the nervous system to immune responses associated with inammation
and poststroke infections.
O
ur immune and nervous systems
inuence each other, both locally
and at a distance ( 1 4). Locally,
immune responses in the central nervous
system (CNS) include activation of resi-
dent glia cells and macrophages ( 3 6), and
inltration of circulating immune cells ( 5).
Many responses rely on cytokines secreted
by immune cells for communicating not
only to immune cells but also to neurons
and glia to control synaptic pruning ( 7),
neuroplasticity ( 8), and neuroprotection ( 3).
Molecules important in the immune system,
such as major histocompatibility complex
(MHC) proteins, are also expressed by neu-
rons and glia and likely contribute to neu-
ral function. Can the nervous system com-
municate with the immune system through
neurotransmitterschemicals that relay
signals from neurons to target cellsto reg-
ulate inammation and immunity, or even to
feed back and regulate the nervous system
itself? Two papers in this issue, by Rosas-
Ballina et al. on page 98 ( 9) and Wong et
al. on page 101 ( 10), demonstrate how neu-
rotransmitters directly modulate specific
cells and cellular responses in the immune
system at a distance.
Previous work pointed to pathways of
direct, long-distance neuroimmune cross-
talk. For example, stimulation of the vagus
nerve, which originates in the brainstem and
innervates visceral organs, inhibits cytokine
release and attenuates inammatory damage
in endotoxemia and sepsis. The vagus nerve
stimulates celiac ganglion adrenergic neurons
that innervate the spleen, leading to release
of the neurotransmitter acetylcholine (ACh)
and activation of the nicotinic ACh recep-
tor (nAChR) on splenic macrophages. This
blocks production of the proinflammatory
cytokine tumor necrosis factor (TNF-).
Bascom Palmer Eye Institute, Interdisciplinary Stem Cell
Institute, Neuroscience Program, University of Miami
Miller School of Medicine, Miami, FL 33136, USA. E-mail:
jgoldberg@med.miami.edu
cyanobacteria. Enclosure experiments have
demonstrated that nutrient addition can
increase water column thermal stratication
without directly affecting water tempera-
tures ( 13, 14). The increased cyanobacte-
rial and algal biomass resulting from nutri-
ent loading increases light attenuation and
modies the vertical distribution of short-
wave radiation. This promotes thermal
stratication and creates a more stable envi-
ronment for cyanobacterial growth ( 13).
Such an effect was demonstrated in Lake
Constance, Germany, with both historical
data analyses and modeling ( 15). Buoyant
cyanobacteria can outcompete phytoplank-
ton by reducing available light for nonbuoy-
ant phytoplankton competitors ( 2). Hence,
increased nutrients can create the stratica-
tion conditions suitable for cyanobacterial
blooms in the absence of increased water
temperatures ( 13).
Cyanobacterial biomass can indeed be
decreased substantially by lowering nutri-
ent inputs, despite warming temperatures,
as observed in lakes Constance, Germany
( 8); Veluwe, Netherlands ( 16); and Mg-
gel, Germany ( 4, 11). Although decreasing
nutrient loading may not completely stop
the incidence of cyanobacterial blooms, it
decreases cyanobacterial dominance. In
addition to lowering external nutrient loads,
lake managers must also take into account
other factorstrophic structure, and the
seasonal life cycles of planktonthat will
be affected by changing climate ( 17). In par-
ticular, the altered magnitude and timing of
precipitation and consequent runoff events
(overland ow of water from saturated soil
into aquatic ecosystems) may increase nutri-
ent loading ( 18). Lowering nutrient inputs
to soils should reduce nutrient loads to
lake ecosystems, which would buffer both
increased temperature and altered precipi-
tation effects, and decrease the maximum
phytoplankton biomass ( 19), the incidence
of problematic cyanobacterial blooms ( 12),
and the subsequent heat capture by phyto-
plankton within the surface layer of lakes.
Returning aquatic systems to lower nutrient
status will ultimately make them less vul-
nerable to the predicted negative impacts
of global warming, particularly more cya-
nobacterial blooms, because phytoplankton
biomass in low-nutrient lakes will generally
not respond to the increased water tempera-
tures expected from climate change ( 20, 21).
Nutrient reduction is a long-term invest-
ment. Decreased cyanobacterial biomass
would be delayed due to nutrient recycling
from the lake sediments and lengthy hydrau-
lic residence time in large water-bodies ( 16).
Regardless, nutrient loading is far easier to
remediate at the decadal and regional scale
than warming temperatures, which must be
regulated on the global scale and will con-
tinue to increase through year 2100, even
if greenhouse gases stabilize at year 2000
concentrations ( 22). Alternatively, nutri-
ent remediation can be implemented at the
watershed scale, for which many successful
engineering and policy options are available
( 23). Increased temperatures, even under
the best scenarios, are inevitable. However,
it is not necessarily inevitable that cyano-
bacteria will grow to bloom proportions
in aquatic ecosystems.
References and Notes
1. W. K. Dodds et al., Environ. Sci. Technol. 43, 12 (2009).
2. H. W. Paerl, J. Huisman, Science 320, 57 (2008).
3. K. D. Jhnk et al., Glob. Change Biol. 14, 495 (2008).
4. C. Wagner, R. Adrian, Limnol. Oceanogr. 54, 2460 (2009).
5. V. H. Smith, G. D. Tilman, J. C. Nekola, Environ. Pollut.
100, 179 (1999).
6. J. A. Elliott, Glob. Change Biol. 16, 864 (2010).
7. H. Markensten, K. Moore, I. Persson, Ecol. Appl. 20, 752
(2010).
8. H. B. Stich, A. Brinker, Glob. Change Biol. 16, 877 (2010).
9. B. Moss et al., J. Appl. Ecol. 40, 782 (2003).
10. D. McKee et al., Limnol. Oceanogr. 48, 707 (2003).
11. J. Khler et al., Freshw. Biol. 50, 1639 (2005).
12. D. J. Conley et al., Science 323, 1014 (2009).
13. M. Kumagai et al., Limnology 1, 1 (2000).
14. I. Jones, G. George, C. Reynolds, Freshw. Biol. 50, 1239
(2005).
15. K. Rinke, P. Yeates, K. O. Rothkaupt, Freshw. Biol. 55,
1674 (2010).
16. B. W. Ibelings et al., Ecosystems 10, 4 (2007).
17. S. R. Carpenter, J. F. Kitchell, The Trophic Cascade in
Lakes (Cambridge Univ. Press, Cambridge, 1993).
18. E. Jeppesen et al., J. Environ. Qual. 38, 1930 (2009).
19. E. Jeppesen, J. P. Jensen, M. Sondergaard, Ecosyst. Health
5, 3 (2002).
20. S. E. Arnott et al., Environ. Monit. Assess. 88, 365 (2003).
21. D. P. Hamilton, C. Spillman, K. Prescott, T. K. Kratz,
J. Magnuson, Verh. Internat. Verein. Limnol. 28, 467
(2002).
22. G. A. Meehl et al., in IPCC Climate Change 2007:
The Physical Science Basis, S. Solomon et al., Eds.
(Cambridge Univ. Press, New York, 2007), pp. 747845.
23. G. D. Cooke, E. B. Welch, S. Peterson, S. A. Nichols, Res-
toration and Management of Lakes and Reservoirs (CRC
Press, Boca Raton, FL, ed. 3, 2005).
24. We thank N. G. Hairston Jr., D. P. Hamilton, G. E. Likens,
and J. M. Melack for helpful comments and GLEON
(Global Lakes Ecological Observatory Network) for nan-
cial support.
Suppporting Online Material
SOM text
10.1126/science.1207349
PERSPECTIVES
How does stimulation of adrenergic neurons
induce ACh release in the spleen? Rosas-
Ballina et al. show that a splenic T cell capable
of synthesizing and secreting ACh fullls this
role (see the gure). The authors identied
a subpopulation of CD4
+
T cells that secrete
ACh, express -adrenergic receptors, and are
located adjacent to adrenergic nerve endings
in the spleen. Transplanting these T cells into
mutant mice devoid of T cells and with endo-
toxemia rescued the attenuation of TNF-
by vagus nerve stimulation. Furthermore,
reducing expression by small interfering
RNA of choline acetyltransferase, an enzyme
required for ACh biosynthesis, in these
T cells before transplantation blocked rescue
of TNF- attenuation after vagus nerve stimu-
lation. Thus, ACh secretion by these T cells is
required in this inammatory reex. Consid-
ering the roles of TNF- in CNS inamma-
tion ( 11), this pathway should also be explored
with CNS injury and disease models.
Long-distance neuroimmune communi-
cation also occurs in poststroke immuno-
suppression, which protects the brain from
inammatory damage ( 12) but leaves the
body prone to infection, a major cause of
stroke-related death ( 13). Although the fun-
damental mechanism of this immunosup-
pression is not known, Wong et al. focused
on stroke-activated hepatic invariant natural
killer T (iNKT) cells to address how stroke
modulates immunosuppression. Using a
mouse stroke model, they observed that mice
decient in iNKT cells developed periph-
eral infection earlier and had higher mor-
tality, suggesting that iNKT cells normally
attenuate stroke-induced immunosuppres-
sion. They then found that noradrenergic
innervation in the liver, rather than a circu-
lating molecule, signals hepatic iNKT cells
after stroke to promote systemic immuno-
suppression. Either depletion of noradren-
ergic nerve terminals in the liver or block-
ade of -adrenergic receptors with propran-
olol altered the cytokines secreted by iNKT
cells, thereby attenuating immunosuppres-
sion, bacterial infection, and mortality in
wild-type mice. Conversely, noradrenaline
injected directly into the liver activated
iNKT cells and increased immunosuppres-
sion and infection. Unexpectedly, Wong
et al. found that another iNKT cell activator,
the glycolipid antigen -galactoceramide
(-GalCer), which acts through MHC
proteins, also reduced bacterial infection
after stroke. Together, these data suggest
that the determining factor in iNKT cell-
mediated immunosuppression after stroke
may not simply be their activation, but
adrenergic regulation of a shift from proin-
ammatory T helper cell 1 (T
H
1)type cyto-
kines [such as interferon- (IFN-)] to anti-
inammatory T
H
2-type cytokines [such as
interleukin-10 (IL-10)]. Pretreatment of
mice with IL-10 led to increased lung infec-
tions, whereas administration of proprano-
lol and -GalCer reversed cytokine produc-
tion from IL-10 back to IFN- after stroke.
Demonstrating stroke-induced increase in
noradrenergic signaling in the liver would
bolster this hypothesis.
The ndings of Rosas-Ballina et al. and
Wong et al. raise the possibility of leverag-
ing specic pathways to extinguish dam-
aging neuroinammation without compro-
mising the ability to fight infectionfor
example, by activating nAChR in the spleen
and blocking -adrenergic receptors and
activating MHC receptors in the liver. Fur-
thermore, these ndings raise several ques-
tions: Are T cells and noradrenaline special-
ized for mediating long-distance cross-talk
between the immune and nervous systems,
or do other subpopulations of immune cells
participate? Various brain insults and neu-
rodegenerative diseases may range from
subclinical involvement to primary or sec-
ondary damage from inflammationare
these regulated by long-distance feedback
loops between the CNS and peripheral
immune organs, in addition to local interac-
tions within the nervous system? For exam-
ple, although noradrenaline in the spleen
increased damaging neuroinflammation,
and noradrenaline as well as IL-10 in the
liver increased infection, both are neuro-
protective in the CNS ( 5, 6). Neuroactivated
immune cells and their cytokine signals
may enter the CNS and modulate neuronal
and/or glial function, prompting investiga-
tion of immunoneurobiology pathways in
which the peripheral immune system may
regulate neural plasticity and behavior.
1. H. O. Besedovsky, A. del Rey, Nat. Immunol. 7, 537
(2006).
2. E. C. Trakhtenberg, Int. J. Neurosci. 118, 839 (2008).
3. C. Farina, F. Aloisi, E. Meinl, Trends Immunol. 28, 138
(2007).
4. D. R. Wilson, L. Warise, Perspect. Psychiatr. Care 44, 285
(2008).
5. A. London et al., J. Exp. Med. 208, 23 (2011).
6. J. L. Madrigal, J. C. Leza, P. Polak, S. Kalinin,
D. L. Feinstein, J. Neurosci. 29, 263 (2009).
7. B. Stevens et al., Cell 131, 1164 (2007).
8. G. S. Huh et al., Science 290, 2155 (2000).
9. M. Rosas-Ballina et al., Science 334, 98 (2011).
10. C. H. Y. Wong, C. N. Jenne, W.-Y. Lee, C. Lger,
P. Kubes, Science 334, 101 (2011); 10.1126/
science.1210301.
11. L. Probert et al., J. Neuroimmunol. 72, 137 (1997).
12. A. Chamorro, X. Urra, A. M. Planas, Stroke 38, 1097
(2007).
13. K. Kimura, K. Minematsu, S. Kazui, T. Yamaguchi, Japan
Multicenter Stroke Investigators Collaboration (J-MUSIC),
Cerebrovasc. Dis. 19, 171 (2005).
14. We acknowledge support from the American Heart
Association (grant 11PRE7310069 to E.F.T.), NIH (grants
EY020913, EY020297, NS061348, and NS074490
to J.L.G.; grant P30-EY014081 from the University of
Miami), and an unrestricted grant from Research to
Prevent Blindness (University of Miami).
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Liver Spleen
Spleen
Liver
Neuroimmune cross-talk. Noradrenaline-secreted from peripheral nerve terminals in the spleen and liver
regulates pro- and anti-inammatory cytokine secretion by stimulating specialized T cells. These immune
cells and cytokines, in turn, could feed back into the nervous system and regulate neuroinammation and
neural function. APC, antigen-presenting cell.
PERSPECTIVES
M
any plant populations are locally
adapted and genetically differenti-
ated for traits related to tness, but
the genetic basis of this adaptation remains
poorly known. The best genomic resources
for plants are available either for model spe-
cies such as Arabidopsis thaliana, or for crop
plants such as maize. In contrast, studies of
fitness variation in natural conditions are
spread over a large number of species with
poorly understood genomes. Two reports in
this issue, by Fournier-Level et al. on page 86
( 1) and Hancock et al. on page 83 ( 2), report
a major advance toward nding
the genomic sites related to cli-
matic adaptation in A. thaliana
by combining genome-wide
analysis of single-nucleotide
polymorphism (SNP) and fit-
ness estimates. Such informa-
tion may eventually be used to
better predict and manage cli-
mate change responses.
Reciprocal transplant exper-
iments can verify that at each
geographic site, the native pop-
ulation has higher tness than
any introduced population of
that same species. Such experi-
ments have detected strong sig-
nals of local adaptation, espe-
cially in species with large pop-
ulations ( 3), such as forest trees
( 4), and in relatives of A. thali-
ana ( 5, 6). These ndings imply
that natural selection has been
strong relative to genetic drift,
and has caused genetic differ-
entiation with respect to traits
related to tness. In small pop-
ulations natural selection may
be too weak, relative to genetic
drift, for local adaptation to
evolve ( 3).
In A. thaliana itself, the clas-
sical evidence for local adapta-
tion is weaker. There are few
reciprocal transplant experi-
ments, and correlations of putative adaptive
phenotypes with latitude are lower ( 7) than
in many other species (see the gure). DNA
sequence variation analysis ( 8) and associa-
tion studies ( 9) have provided some evidence
of local adaptation. Range expansions, recol-
onizations, and bottlenecks can, however, also
give rise to patterns suggestive of adaptation.
Scientists have previously searched for
genetic variants for local adaptations in sev-
eral plant species, but not with truly genome-
wide approaches ( 5). The two studies in this
issue relate SNP variations in extensive col-
lections of A. thaliana to the climate at the
location where each genotype was collected.
Both studies also examine how the environ-
mentally correlated SNPs relate to fitness
data from the eld experiments.
Fournier-Level et al. analyze data from
eld experiments in which about 150 dis-
tinct samples from different locations (acces-
sions) were grown at four different eld sites
across Europe ( 10), and both survival and
reproductive tness were estimated. Among
more than 200,000 genotyped SNPs, the
authors identify SNPs that account for tness
variation in the different eld
sites. In most cases, SNP vari-
ants favorable in one environ-
ment did not have deleterious
effects in other environments
the SNPs associated with fit-
ness occurred at different loci
in different environments. This
suggests that the mechanism
of adaptation differs for differ-
ent environments. Thus, natural
selection (or plant breeders) can
benet from exible responses
based on different mechanisms
across environments.
Hancock et al. examine cli-
mate associations of SNPs in
a different set of accessions.
They have correlated the geno-
typic data of more than 200,000
SNPs of nearly 1000 A. thali-
ana lines with the climatic data
of the location where these
plants were originally collected.
Similar approaches have earlier
detected loci related to climatic
adaptation in humans ( 11) and
forest trees ( 12). To confirm
that the correlations of SNPs
with climate variables are due to
natural selection and not popu-
lation history, Hancock et al.
use two approaches. First, they
show that nonsynonymous (that
is, amino acidchanging) SNPs
are enriched among the cli-
mate-correlated ones. Second,
they demonstrate that the cli-
mate-related SNPs can account
The Genomic Basis
of Local Climatic Adaptation
EVOLUTION
Outi Savolainen
Studies of Arabidopsis thaliana help to identify
the genomic sites associated with adaptation
to local climatic conditions.
Department of Biology, FIN-90014, Uni-
versity of Oulu, Finland. E-mail: outi.
savolainen@oulu.
Northern latitude (degrees)
G
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h

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e
s
s
a
t
i
o
n

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a
y

l
e
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t
h

(
h
o
u
r
s
)
22
21.5
20.5
19.5
21
20
19
18.5
18
35 40 45 50 55 60 70 65
Northern latitude (degrees)
A. thaliana
Norway spruce
F
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o
w
e
r
i
n
g

t
i
m
e

(
d
a
y
s
)
140
120
100
80
60
40
20
0
35 40 45 50 55 60 70 65
A
B
Adaptation with latitude. (A) The day length below which seedlings of Norway spruce
(Picea abies) will set bud in preparation for winter depends on latitude. Based on popu-
lation data of Dormling ( 4). (B) The latitude dependence of how many days it takes after
4-week cold treatment for A. thaliana to ower is much less pronounced. Data on Euro-
pean accessions from ( 9), binned in groups of ve based on latitude. P
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;

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.

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,

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PERSPECTIVES
for some tness variation in a eld experi-
ment in Lille, France.
Changing climates may require rapid
adaptation. Adaptation based on selection on
new mutations (species-wide or regionally
limited selective sweeps) can be slowed down
by the lack of suitable mutations, whereas
selection on existing low- or intermediate
frequency variants can be faster. Only selec-
tion on new mutations leaves a footprint of
long tracks of correlated variants around the
selected sites. Fournier et al. did not find
such a signal, and conclude that selection has
mostly been on existing variation. In con-
trast, Hancock et al. did identify this signal
of selection on new mutations. These differ-
ent ndings remain to be explained. Recent
genome-wide resequencing studies have
shown that such selection on new mutations
has been common in Drosophila ( 13) but not
in the human lineage ( 14).
In addition to selection on individual
loci, phenotypic data suggest that selection
on quantitative traits is also important for
local adaptation. Suitable methods need to be
developed for nding the signals of this kind
of selection in the genome ( 15).
Perhaps surprisingly, none of the top
climate adaptation SNPs identied in ( 1)
were close to the intensively studied ower-
ing-time genes FRI and FLC ( 9). The role of
these loci in governing tness variation mer-
its further study.
SNP-based studies cannot be used to
examine all polymorphisms. The effects of
the polymorphisms related to climate are
only detected if they are correlated with the
SNPs that were genotyped. As the Arabi-
dopsis resequencing project ( 16) advances,
these problems will be avoided. Improving
genomic resources will also allow genome-
wide studies of species with very strong sig-
nals of local adaptation.
1. A. Fournier-Level et al., Science 334, 86 (2011).
2. A. M. Hancock et al., Science 334, 83 (2011).
3. R. Leimu, M. Fischer, PLoS ONE 3, e4010 (2008).
4. O. Savolainen, T. Pyhjrvi, T. Knrr, Annu. Rev. Ecol.
Evol. Syst. 38, 595 (2007).
5. J. T. Anderson, J. H. Willis, T. Mitchell-Olds, Trends Genet.
27, 258 (2011).
6. P. H. Leinonen, D. L. Remington, O. Savolainen,
Evolution 65, 90 (2011).
7. A. Giakountis et al., Plant Physiol. 152, 177 (2010).
8. V. Le Corre, F. Roux, X. Reboud, Mol. Biol. Evol. 19,
1261 (2002).
9. S. Atwell et al., Nature 465, 627 (2010).
10. A. M. Wilczek et al., Science 323, 930 (2009).
11. A. M. Hancock et al., PLoS Genet. 7, e1001375 (2011).
12. A. J. Eckert et al., Genetics 185, 969 (2010).
13. S. Sattath, E. Elyashiv, O. Kolodny, Y. Rinott, G. Sella,
PLoS Genet. 7, e1001302 (2011).
14. R. D. Hernandez et al., 1000 Genomes Project, Science
331, 920 (2011).
15. L. M. Chevin, F. Hospital, Genetics 180, 1645 (2008).
16. See http://1001genomes.org/.
10.1126/science.1213788
D
uring the past decade, a wide array
of physical systemsatoms, semi-
conductors, and superconductors
have been used in experiments to create the
basic components of quantum-information
processing. Precision control over elemen-
tary quantum two-state systems (qubits) is
now well advanced, and it is now possible
to ask how a complete, functioning quantum
computer with many qubits would really
work. In this issue, two very different steps
in this direction have been taken. On page
61, Mariantoni et al. ( 1) examine how the
basic architectural elements of a stored-pro-
gram computer, as articulated originally by
von Neumann, can be achieved in the quan-
tum setting. On page 57, Lanyon et al. ( 2)
explore how a quantum computer can be
programmed. Although the physical qubits
used in each study are extremely different,
both attack a device-independent question
of system functionality.
A vision of the possible approaches to
programming a quantum computer has
emerged only very tentatively in the past
decade. Quantum computers will unques-
tionably be able someday to solve arithme-
tic problems that are so difcult that they
are intractable for digital computing, most
notably nding the prime number factors of
large numbers. However, the scale of these
problems in their interesting form (that is,
exceeding what supercomputers could do),
and the high precision of operation needed
to solve them, points toward a machine con-
taining millions of qubits.
Such large machines are many years
away, so attention has focused in the near
term on other problems, more directly con-
nected to quantum physics, for which much
smaller machines can be programmed to
solve problems. Lanyon et al. present results
on digital quantum simulation, as distinct
from the less powerful technique of analog
quantum simulation. The analog approach
implies a direct emulation of the system to
be simulated; the quantum processor is tai-
lored to have, up to a scale, the same intra-
and interqubit forces (i.e., described theoret-
ically by the same type of Hamiltonian func-
tion) as the simulated system.
In the digital approach, the qubit Hamil-
tonian is xed to be one of two (or several)
optimized forms. The simulated Hamilto-
nian is approximated by switching rapidly
between these qubit Hamiltonians, so that
the average effect is correct. Parallel park-
ing provides a good analogy of the enhanced
capability of this machine. An analog sim-
ulation that emulates moving forward and
backward to park on the right can do only
that operation. Digital simulation implies
programmability; the car can also be parked
to the left with a modied application of the
same basic actions. Lanyon et al. used up to
six qubits in an ion trap, with only one type
of physical coupling between them medi-
ated by quanta of collective ion vibrations.
By successive alternation of interactions,
they simulated the dynamical creation of
entangled quantum states in small magnetic
clusters with a variety of spin interactions.
Mariantoni et al. attacked the very dif-
ferent problem of machine architecture. The
superconducting device toolkit has grown
in recent years to include qubits of a wide
variety of constructions and characteristics,
and a quantum version of computer bus-
ses (a classical bus transfers data between
computer components; quantum busses can
be created from harmonic quantum systems
based on superconducting electrical resona-
tors). Can these devices be combined to take
Toward Control of Large-Scale
Quantum Computing
PHYSICS
David P. DiVincenzo
Basic quantum computing elements are
combined to improve quantum simulations
and to create a quantum version of a central
processing unit.
Rheinisch-Westfaelische Technische Hochschule Aachen,
Forschungszentrum Juelich, Juelich 52425 Germany.
E-mail: d.divincenzo@fz-juelich.de
PERSPECTIVES
Diamond Window into
the Lower Mantle
GEOCHEMISTRY
Ben Harte
Tiny inclusions in diamonds reveal subduction of oceanic crust to depths of at least 700 km.
advantage of their individual strengths in a
processing system?
Mariantoni et al. used, without modica-
tion, a two-qubit structure used in previous
studies ( 3) but created a new architectural
interpretation of its parts. The two qubits
were coupled via a resonator in such a way
as to allow for rapid application of quan-
tum operations; this is the quantum central
processing unit, or quCPU, of the structure.
Each qubit was also coupled separately to
another resonator that was good at receiv-
ing and retaining information received
from the qubits to form a quantum random-
access memory element, or quRAM. The
superconducting devices contained other
microscopic two-level systems suitable for
dumping information from the qubits so
they could be reset. These systems function
as reset registers, although they were not
designed for that purpose. Mariantoni et al.
used these basic circuit elements to demon-
strate three-qubit operations using retrieved
and re-stored data.
There is not, and there should not be,
any reason that architecture is the exclu-
sive domain of superconducting structures
or that programming for digital simulation
is conned to ion systems. These very basic
computer engineering problems should be
solvable independent of the hardware plat-
form. Indeed, the roles have been reversed
in previous studies; Mariantoni et al.s hard-
ware was previously used to demonstrate a
crude quantum algorithm ( 3), and a vision
for a scaled-up ion-trap quantum proces-
sor was already proposed several years ago
( 4) (see the figure). In
this proposal, there is a
central processor area,
cooling ions, which
perform the resetting
function, and side traps
with a shuttling sys-
tem for storing quantum
information. Slow prog-
ress has been made in the
experimental realization
of this vision ( 5).
Before much more
progress is made on
these design problems,
basic device metrics
must be developed both in the atomic and
the solid-state areas. Such metrics will eval-
uate coherence (how long quantum states
survive) and delity of quantum operations
(how well quantum states are being prepared
and measured). Improved designs that attain
an order of magnitude greater coherence
times for superconducting qubits ( 6) must
be adopted, and the technical limits imposed
by laser intensity uctuations in the ion sys-
tem must be overcome. Only then will we
start seeing quantum processors of respect-
able complexity and power.
References
1. M. Mariantoni et al., Science 334, 61 (2011).
2. B. P. Lanyon et al., Science 334, 57 (2011).
3. M. Mariantoni et al., Nat. Phys. 7, 287 (2011).
4. D. Kielpinski, C. R. Monroe, D. J. Wineland, Nature 417,
709 (2002).
5. R. B. Blakestad et al., arXiv:1106.5005 (2011).
6. L. DiCarlo et al., Nature 460, 240 (2009).
10.1126/science.1211284
N
atures secrets are often well hid-
den, but painstaking investigation
of minute quantities of material may
unravel complex histories of mineral forma-
tion and provide major insights into Earths
evolution. On page 54 of this issue, Walter
et al. ( 1) illustrate this point by revealing
the extent of the subduction of oceanic crust
into Earths interior. They found that natu-
ral diamonds, carried to the surface by kim-
berlite volcanoes 92 to 95 million years ago
in Juina (Brazil), contained minute (0.015
to 0.040 mm long) inclusions composed
of several minerals such as nepheline, Na-
kalsilite, and MgFe-spinel. These miner-
als are expected to form at depths of less
than 200 km. However, careful investigation
showed that these minerals had formed by
the breakdown of other minerals known to
form only at very high pressures and depths
in excess of 700 km.
The principal rock compositions expected
in Earths mantle are those of basic and ultra-
basic rocks. Many diamonds contain inclu-
sions of minerals (e.g., olivine, pyroxene,
garnet) formed in such rock compositions
at depths of less than 200 km in continen-
tal lithosphere; but, rarely, distinct groups
of other minerals are found that formed at
much greater depths. The Juina kimber-
lite province in Brazil has been prominent
in yielding such deep diamonds, includ-
ing a suite indicating minerals expected
in ultrabasic rocks at lower-mantle depths
(>660 km). These ultrabasic inclusions are
thought to have formed in slabs of oceanic
Centre for Science at Extreme Conditions, School of GeoSci-
ences, University of Edinburgh, Edinburgh EH9 3JW, Scot-
land, UK. E-mail: ben.harte@ed.ac.uk
Electrode segments
Memory region
Interaction region
Harnessing ion-trap qubits. The ideas explored in Mariantoni et al.creating the
elements of a quantum computing architecture using superconducting circuit ele-
mentshave been previously articulated (4) for qubits like the ones used by Lanyon
et al. based on trapped ions. In this vision of a quantum computer, arrays of radio-
frequency electrodes trap ions. These ions (blue circles) can be moved from a memory
region to an interaction region (the central processor) by changing the operating volt-
ages on the electrodes (shown as gray bars). Slow progress has been made in realizing
this vision. [Adapted from ( 4)]
PERSPECTIVES
lithosphere that had been carried down to
lower-mantle depths via subduction zones
at the margins of Earths tectonic plates ( 2,
3). However, it is known that oceanic lith-
osphere includes a crust of basic composi-
tion as well as a thicker layer of ultrabasic
rocks, and up to now it has been puzzling
that inclusions of basic origin with denite
lower-mantle minerals have not been found.
The observations of Walter et al. provide
unequivocal identication of basic mineral
inclusions formed at lower-mantle depths.
They also provide the rst recognition in
nature of two minerals (NAL, a new alu-
minum silicate phase; CF, a calcium ferrite
phase) previously only known from labora-
tory experiments at very high pressures and
temperatures ( 4, 5). Moreover, the diamonds
containing the inclusions show highly neg-
ative carbon isotope ratios (
13
C down to
24); this feature is associated with ocean
crust and thereby implies the recycling of
carbon from Earths crust down to lower
mantle depths and back again.
In the wider perspective, Walter et al.
note that it is appropriate to consider the dia-
mond evidence in conjunction with studies
of distant earthquake waves. In the past 20
years, such seismic studies have provided
tomographic images of slabs of oceanic lith-
osphere descending to near the upper man-
tlelower mantle boundary, where they at-
ten out to form so-called stagnant slabs
( 6, 7). These slabs have been found world-
wide to take up a variety of subhorizontal
positions from just above to below the upper
mantlelower mantle boundary (the com-
mon range of depths is indicated by the two
cases shown in the gure), although such
positions are temporary and the slabs even-
tually sink through the lower mantle.
With the relatively simple stagnant slab
shapes shown in the gure, it is evident from
the ndings of Walter et al. that in order to
give rise to the Juina basic inclusions, the
slab must have resided at the lower level
illustrated. However, more complex struc-
tures are possible, and a slab might undergo
buckling and penetrate the lower man-
tle before assuming a subhorizontal posi-
tion along the upper mantlelower mantle
boundary ( 6 8). It is also possible that basic
and ultrabasic portions of the slab become
detached as a consequence of density differ-
ences ( 6, 9). Lower-mantle diamonds might
form at various locations within the sub-
ducted slabs, before eventually being trans-
ported toward Earths surface in a plume of
rising mantle material and eventually erupt-
ing in a kimberlite. It is during this upward
transport that the lower-mantle minerals are
broken down to the lower-pressure minerals
that were actually found in the inclusions.
The Juina deep diamonds may be fur-
ther placed in the context of geological his-
tory. Throughout much of the Paleozoic
and Mesozoic geological eras, slabs of oce-
anic lithosphere forming the protoPacic
Ocean were repeatedly subducted beneath
the Gondwanaland supercontinent that
included South America ( 10, 11). Among
the Juina diamonds are some with majoritic
inclusions formed from basic compositions
at depths of 300 to 450 km. The Nd and Sr
isotope compositions of these majorites are
those expected for oceanic crust of Meso-
zoic or younger age ( 8). Assuming that all
the Juina deep diamonds are derived from
a single subducted slab, then its subduction
must have occurred in the approximately
100-million-year interval from the start of
the Mesozoic to the 92- to 95-million-year
age given by the kimberlites containing the
diamonds ( 8).
The results presented by Walter et al.
add to the plate tectonic histories provided
by both conventional geological/geochemi-
cal studies and the results of modern seismic
tomography. Given further discoveries of
diamonds with mineral inclusions from the
deep upper mantle and from the uppermost
lower mantle, one may expect the emergence
of a much clearer picture of the behavior of
subducted slabs. Aligned with further labo-
ratory experimental studies on mineral struc-
ture and composition, the pressures and tem-
peratures of formation of inclusions in deep
diamonds will become better dened; and
with seismic tomographic data the shapes
of slabs, including their basic and ultraba-
sic portions, may become rened. Key ques-
tions of wide interest may be addressed, such
as the potential liberation of hydrous uids
from subducted slabs during their descent
and stagnation ( 3, 7, 12 14), with conse-
quent formation of melts. Further nds of
deep diamonds in Juina and other kimberlite
provinces around the world will give momen-
tum to these advances in understanding.
References
1. M. J. Walter et al., Science 334, 54 (2011).
2. T. Stachel, G. P. Brey, J. W. Harris, Elements 1, 73 (2005).
3. B. Harte, Mineral. Mag. 74, 189 (2010).
4. K. Hirose, N. Takafuji, N. Sata, Y. Ohishi, Earth Planet.
Sci. Lett. 237, 239 (2005).
5. A. Ricolleau et al., J. Geophys. Res. 115, B08202 (2010).
6. Y. Fukao, M. Obayashi, T. Nakakuki, Annu. Rev. Earth
Planet. Sci. 37, 19 (2009).
7. D. Zhao, S. Yu, E. Ohtani, J. Asian Earth Sci. 40, 689
(2011).
8. B. Harte, S. Richardson, Gondwana Res.
10.1016/j.gr.2011.07.001 (2011).
9. T. Irifune, A. E. Ringwood, Earth Planet. Sci. Lett. 117,
101 (1993).
10. B. C. Storey, Nature 377, 301 (1995).
11. P. A. Cawood, Earth Sci. Rev. 69, 249 (2005).
12. T. Komabayashi, S. Omori, Phys. Earth Planet. Inter. 156,
89 (2006).
13. K. D. Litasov, E. Ohtani, A. Sano, Geophys. Monogr. 168,
95 (2006).
14. H. Keppler, J. R. Smyth, Eds., Water in Nominally
Anhydrous Minerals (Mineralogical Society of America,
Chantilly, VA, 2006).
Continental lithosphere
Plume
Higher-level
stagnant slab
Lower-level
stagnant slab
Basic crust Lower mantle
Transition
zone
D
e
p
t
h

(
k
m
)
200
400
600
800
0
O
c
e
a
n
i
c

l
i
t
h
o
s
p
h
e
r
e
Stagnant slabs. Illustration of some different positions of stagnant slabs formed of subducted oceanic litho-
sphere. The two cases shown illustrate the range of levels from above to below the upper mantlelower man-
tle boundary found in worldwide tomographic seismic images ( 6). The data from Walter et al. for the Juina
(Brazil) situation clearly imply a case like the lower slab illustrated, with extensive penetration into the lower
mantle. Possible formation points of diamonds with basic and ultrabasic lower-mantle mineral inclusions are
indicated by red and green diamonds, respectively.
10.1126/science.1213012
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Deep Mantle Cycling of Oceanic Crust:
Evidence from Diamonds and Their
Mineral Inclusions
M. J. Walter,
1
* S.C. Kohn,
1
D. Araujo,
2
G. P. Bulanova,
1
C. B. Smith,
1
E. Gaillou,
3
J. Wang,
3
A. Steele,
4
S. B. Shirey
3
A primary consequence of plate tectonics is that basaltic oceanic crust subducts with lithospheric
slabs into the mantle. Seismological studies extend this process to the lower mantle, and
geochemical observations indicate return of oceanic crust to the upper mantle in plumes. There
has been no direct petrologic evidence, however, of the return of subducted oceanic crustal
components from the lower mantle. We analyzed superdeep diamonds from Juina-5 kimberlite,
Brazil, which host inclusions with compositions comprising the entire phase assemblage expected
to crystallize from basalt under lower-mantle conditions. The inclusion mineralogies require
exhumation from the lower to upper mantle. Because the diamond hosts have carbon isotope
signatures consistent with surface-derived carbon, we conclude that the deep carbon cycle
extends into the lower mantle.
D
iamonds and the mineral inclusions that
they trap during growth provide samples
of materials from deep within Earth. On
the basis of inclusion mineralogy, most diamonds
sampled at the surface originated in continental
lithospheric mantle at depths of <200 km (1).
Several localities, however, yield rare superdeep
diamonds with inclusion compositions that re-
quire a sublithospheric origin in the deep upper
mantle and even the lower mantle (1, 2). Inclu-
sions of majorite garnet that formed in the deep
upper mantle (~200 to 500 km) commonly have
compositions linking them to basaltic oceanic
crust (18), and aluminous inclusions have been
identified with compositions indicative of sili-
ceous sediments (3). The diamonds that host these
inclusions have carbon isotopic compositions
that are atypical of normal mantle (d
13
C 5),
instead displaying a large isotopic range (~ 1to
24) with a clear tendency toward isotopically
light (<10) compositions (13, 9). Although
there is debate regarding the origin of light car-
bon in diamonds (10), a leading hypothesis is
the subduction of the isotopically light organic
carbon fraction of altered oceanic crust.
The rarest diamonds are those containing in-
clusions with compositions indicating an origin
in the lower mantle (>660 km). Inclusions in-
terpreted as representing the lower-mantle phases
Mg-perovskite and Ca-perovskite have major el-
ement compositions that indicate an origin in
mantle peridotite (2, 1113). No lower-mantle
inclusions have previously been identified with
major element compositions consistent with an
origin in subducted basalt. Furthermore, the car-
bon isotopic compositions of diamonds with
lower-mantle inclusions are typically all mantle-
like (~ 4 to 6) (2), which suggests that
surface-derived carbon may not survive into
the lower mantle. Oceanic lithosphere clearly
enters the lower mantle (14, 15), so the rarity
of lower-mantle diamonds with inclusions of
high-pressure phases that would occur in sub-
ducted basalt suggests that once oceanic crust
enters the lower mantle, it usually remains there,
possibly as a result of intrinsic high density and
negative buoyancy (1618).
Here, we describe a suite of mineral inclu-
sions in low-nitrogen (type IIa) diamonds from
the Juina-5 kimberlite pipe in the Juina kimberlite
field (92 to 95 million years old) (19) located in
the Proterozoic Rio NegroJuruena Mobile Belt
southwest of the Amazon Craton, Brazil (20). In-
clusions in sublithospheric diamonds common-
ly show mineralogical evidence of exsolution
from originally homogeneous silicate phases into
composite assemblages, and these are interpreted
to have formed during ascent in the mantle un-
related to kimberlite eruption (25, 8, 12, 21, 22).
Inclusion unmixing provides compelling evidence
that some superdeep diamonds were transported
upward by hundreds of kilometers in the upper
mantle, presumably by upwelling of solid mate-
rial (3, 4, 13). For example, the bulk composi-
tions of composite garnet plus clinopyroxene
inclusions in diamonds from the Juina region in-
dicate a deep upper-mantle origin as majorite, with
inclusion unmixing to garnet plus clinopyroxene
occurring during transport to shallower levels
beneath the lithosphere (24). Each of the in-
clusions presented here is composed of a multi-
phase mineral assemblage (Fig. 1). We interpret
RESEARCHARTICLE
1
School of Earth Sciences, University of Bristol, Bristol BS8 1RJ,
UK.
2
Instituto de Geocincias, Universidade de Braslia, CEP
70910-900 Braslia, DF, Brazil.
3
Department of Terrestrial Mag-
netism, Carnegie Institution, Washington, DC 20015, USA.
4
Geophysical Laboratory, Carnegie Institution, Washington,
DC 20015, USA.
m.j.walter@bristol.ac.uk
Fig. 1. Backscattered electron micrographs showing composite inclusions in diamonds from Juina-5. (A)
An inclusion in diamond Ju5-20 composed of a mixture of spinel (Mg,Fe)Al
2
O
4
(Sp) and nepheline
NaAlSiO
4
(Ne) (fig. S1 and table S5), together with a small sulfide (Sf) in one corner that we interpret as an
originally distinct phase from the composite silicate; sulfide can participate in diamond crystallization
reactions as a melt phase that is immiscible in silicate (33). (B) An inclusion in diamond Ju5-67 that is
composed of phases with the compositions of spinel and a nepheline-kalsilite (Ka) phase, (Na,K)AlSiO
4
(table S5). (C) An inclusion in diamond Ju5-89 containing spinel and a mixture of micrometer-sized
Na-rich (Na) and K-rich (K) silicate regions, with a bulk composition similar to Ju5-67 (fig. S2 and table
S5). (D) An inclusion in diamond Ju5-47 that consists of orthopyroxene (Opx), ulvospinel (Ulv), and olivine
(Ol) (fig. S3 and table S5). (E) An inclusion in diamond Ju5-43 that consists of a complex mixture of
orthopyroxene and a Ti-, Al-, and Fe-rich phase similar to tetragonal almandine pyrope phase (TAPP)
(table S5). (F) An inclusion in diamond Ju5-104 composed of CaSiO
3
plus micrometer-sized Ti-rich phases
(e.g., CaTiO
3
) and a small sulfide (table S5).
the composite silicate and oxide phases as ex-
solution products from originally homogeneous
silicate phases that were trapped during diamond
growth.
Inclusion compositions and the depth of
formation. The inclusions range from about 15
to 40 mm in their longest dimension. Individual
phases within the composite inclusions were iden-
tified by Raman spectroscopy and spot electron
microprobe analysis, and homogeneous bulk in-
clusion compositions were obtained using wide-
beam microprobe analysis (Fig. 1, Table 1, and
tables S1 to S5) (20). There is close correspon-
dence between the inclusion bulk compositions
and the individual phases that coexist in experi-
ments on basaltic compositions under lower-mantle
conditions. We ascribe the composite inclusions
to the following lower-mantle phases: (i) cal-
cium ferrite (CF) phase (Ju5-20); (ii) new alu-
minum silicate (NAL) phase, also known as
the hexagonal phase (Ju5-67 and Ju5-89); (iii)
Al-, Ti-, and Fe-rich Mg-perovskite (Ju5-43 and
Ju5-47); and (iv) Ti-rich Ca-perovskite (Ju5-104).
The CF and NAL phases, as well as Al-, Ti-, and
Fe-rich Mg-perovskite compositions, have not
been identified before as inclusions in diamond,
but have previously been observed in experi-
ments on basaltic bulk compositions at lower-
mantle pressures and temperatures (1618). The
sums of the cations and cation fractions in the
bulk inclusion compositions closely correspond
to the ideal stoichiometries of the experimentally
synthesized phases (Table 1 and tables S1 to S4).
It is unlikely that randomly trapped mineral ag-
gregates at upper-mantle pressures could, by co-
incidence, have the correct stoichiometry of all
four lower-mantle phases.
Each of the Juina-5 composite inclusions has
a bulk composition that can be linked to a spe-
cific phase that would crystallize in a basaltic
composition only in the lower mantle (Fig. 2).
The composite inclusion in diamond Ju5-20
would form a homogeneous CF phase, and in-
clusions Ju5-67 and Ju5-89 would formthe NAL
phase at lower-mantle conditions (Fig. 2A). Al-
though these two phases are compositionally
similar to each other, a distinguishing feature is
the considerable potassium solubility in experi-
mental NAL phases, whereas experimental CF
phases are potassium-free (Table 1 and tables S1
and S2). The bulk compositions of the composite
inclusions in diamonds Ju5-43 and Ju5-47 are
very similar to Mg-perovskites produced in ex-
periments on basaltic compositions (Fig. 2B,
Table 1, and table S3). They are much richer in
Ti, Al, and Fe than is Mg-perovskite that forms
in experiments on mantle peridotite (23) or in
previously reported Mg-perovskite inclusions in
Table 1. Summary of the bulk major element chemistry of Juina-5 mineral
inclusions and phases produced in high-PT experiments on basaltic com-
positions (cation fraction per formula unit), with carbon isotopic compositions
of host diamonds. Isotopic values represent range observed in three or more
analyses in different growth zones, as revealed in CL images. See tables S1 to
S4 for experimental data and references.
Ju5-43 Ju5-47 MgPv in Exp Ju5-104 CaPv in Exp Ju5-20 CF in Exp Ju5-67 Ju5-89 NAL in Exp
Si 0.69 0.81 0.470.87 0.94 0.880.99 1.71 1.742.30 1.25 1.61 0.832.03
Ti 0.10 0.06 0.020.23 0.04 0.010.09 0.03 <0.10 0.05 0.07 0.020.10
Al 0.43 0.17 0.260.50 0.01 0.020.11 4.21 2.983.95 4.45 3.77 3.235.06
Fe 0.32 0.35 0.150.60 0.01 0.010.06 0.88 0.351.04 0.75 0.93 0.411.07
Mg 0.42 0.63 0.360.62 0.01 0.010.07 0.88 1.431.82 1.58 1.55 0.931.78
Ca 0.01 0.01 0.010.07 1.01 0.800.96 0.02 <0.18 0.03 0.08 0.050.19
Na 0.01 0.02 0.010.08 0.00 0.000.03 1.36 1.141.99 0.29 0.55 0.710.92
K 0.00 0.00 <0.01 0.00 <0.01 0.00 <0.01 0.42 0.21 0.010.22
Sum 1.99 2.06 1.982.13 2.02 1.962.05 9.09 8.59.5 8.83 8.79 8.679.29
Ideal 2 2 2 2 2 9 9 9 9 9
O 3 3 3 3 3 12 12 12 12 12
Mg/(Mg+Fe) 0.57 0.64 0.540.88 0.50 0.320.78 0.50 0.540.79 0.68 0.63 0.520.81
Al/(Al+Si+Ti) 0.35 0.16 0.240.43 0.01 0.020.11 0.71 0.580.69 0.77 0.69 0.620.82
Ti/(Ti+Si) 0.13 0.07 0.030.33 0.04 0.010.10 0.02 0.00.04 0.04 0.04 0.020.07
d
13
C () 15.4 to
21.6
23.4 to
24.1
4.9 to
5.7
0.9 to
6.3
21.1 to
21.7
18.1 to
19.0
Fig. 2. Portions of three ter-

nary diagrams (cation fraction)
illustrating the composition-
al correspondence between
bulk composite mineral inclu-
sions in diamonds from Juina-
5 and phases produced in
experiments at lower-mantle
pressures. (A) Shaded fields
represent CF and NAL phases
synthesized in experiments on
basaltic bulk compositions
(tables S1 and S2). (B) Shaded
fields represent Mg-perovskite
phases synthesized in experi-
ments on basaltic (table S3)
and peridotitic bulk compo-
sitions (23). (C) The shaded
field represents the composi-
tions of Ca-perovskites that
coexist with Mg-perovskite, as
synthesized in experiments
on basaltic bulk compositions
(table S4). In (A) and (B), Fe
3+
and Fe
2+
are calculated from
mineral formulae to satisfy site
occupancy constraints (tables
S1 to S3).
RESEARCH ARTICLE
diamonds (2, 11). The composite inclusion in
diamond Ju5-104 has the bulk composition and
stoichiometry of a CaSiO
3
phase, but with a mod-
erate Ti component [~3 weight % (wt %) TiO
2
]
not previously observed in other CaSiO
3
inclu-
sions in sublithospheric diamonds. The inclusion
composition is a close match to Ca-perovskite
that coexists with Mg-perovskite in experiments
on basaltic compositions (Fig. 2C, Table 1, and
table S4).
Experimentally estimated changes in miner-
alogy with depth for typical mid-ocean ridge
basalts (17, 18) indicate that, as a group, the in-
clusions constitute a phase assemblage that co-
exists in basaltic compositions at depths between
about 700 and 1400 km (Fig. 3A); an SiO
2
in-
clusion has been identified in our Juina-5 collec-
tion as well, which likely originated as stishovite.
We suggest that the inclusions must have orig-
inated when diamond-forming fluids incorpo-
rated basaltic components fromoceanic lithosphere
subducted into the lower mantle. To trap these
specific inclusion compositions as homogeneous
phases, the diamonds must have grown in the
upper part of the lower mantle, and cannot simply
be diamonds derived from shallower depths in
the upper mantle but subducted into the lower
mantle. For example, there are no known phases
stable in the upper mantle with the bulk com-
positions of CF and NAL phases, and majorite
garnets included in diamond in the deep upper
mantle have far more calcium (e.g., 5 to 15 wt %
CaO) (3, 6) and less titanium than observed in
Mg-perovskite synthesized experimentally in ba-
saltic compositions.
Diamond isotopic signatures and the origin
of carbon. If the above hypothesis is correct, then
the carbon from which the diamonds formed
may have been deposited originally within oce-
anic crust at the seafloor. We measured the car-
bon isotopic composition (d
13
C values) of the
Juina-5 diamonds and found a range from about
1 to 24, with four of the six diamonds hav-
ing values less than 15 (Fig. 4 and Table 1).
These light isotopic values possibly indicate a
recycled organic source of carbon (10). In con-
trast, all previously analyzed diamonds hosting
ultramafic inclusions of lower-mantle origin have
heavier, typical mantle carbon isotopic compo-
sitions around 5 (2).
The origin of light carbon isotopic values
(< ~ 10) in mantle-derived samples is a mat-
ter of ongoing debate, with plausible explana-
tions including intramantle isotopic fractionation,
a primordial carbon reservoir with a light compo-
nent, and subducted organic carbon (10, 24). Ray-
leigh fractionation in an open system involving
phase separation can generate considerable iso-
topic fractionation and may account for much of
the variation in d
13
C in the range of 8 to 2
seen in lithospheric diamonds (10). However, it
has yet to be demonstrated that this is a viable
process for producing the isotopically light sig-
natures (~ 10 to 25) commonly associated
with sublithospheric diamonds of basaltic affin-
ity, and an explanation would be needed for the
correspondence of isotopically light carbon sig-
natures with specific inclusion mineralogies. A
primordial light carbon reservoir also appears un-
likely, as the light component must have survived
vigorous mantle mixing in an early magma ocean
and billions of years of solid-state mantle convec-
tion to appear in the composition of these dia-
monds (24). Juina superdeep diamonds are likely
only about 100 million years old, on the basis
of a dated sublithospheric inclusion from the
Collier-4 kimberlite 30 kmto the north of Juina-5
(3), and so these young diamonds are very un-
likely to have formed from an ancient, isotopic-
ally light primordial carbon component.
In contrast, a burgeoning body of evidence
supports a subducted carbon source for many
superdeep diamonds. The Juina-5 composite in-
clusions and many other inclusions in sublitho-
spheric diamonds require an origin involving
oceanic crust and sediments, and these com-
monly have light carbon isotopic compositions
(2, 3, 6, 7, 9). Recent measurements of the carbon
isotopic compositions in altered oceanic crust
as deep as 2 km beneath the seafloor indicate
mixing between an organic component (d
13
C
27) and a carbonate component (d
13
C
0) (25). As a group, sublithospheric diamonds
with inclusions showing affinity with subducted
oceanic crustal materials have carbon isotopic
compositions that effectively span the entire iso-
topic range measured in altered oceanic crust. Our
results suggest that subducted organic carbon can
retain its isotopic signature even into the lower
mantle. Experimental data indicate that subducted
carbon, regardless of its original form in carbo-
nates or organic compounds, can become fixed as
either elemental carbon (graphite or diamond) or
carbonate at high pressures in oceanic crust, de-
pending on the redox state (26). Because the in-
clusions require that the diamonds grew in the
lower mantle, we suggest that carbon was trans-
ported as carbonate, some of which would have
been isotopically light, having originated as or-
ganic carbon (Fig. 4).
Implications for a deep carbon cycle. The
diamonds and their inclusions may have grown
Fig. 3. (A) Estimated modal mineralogy in subducted basaltic oceanic crust as a function of depth in the
mantle (17, 18). MgPv, Mg-perovskite; CaPv, Ca-perovskite; CF, CF phase; NAL, NAL phase; St, stishovite;
Gt, garnet; Cpx, clinopyroxene. The inclusion mineralogy in diamonds from Juina-5, including MgPv,
CaPv, CF phase, NAL phase, and stishovite, is stable at depths of ~700 to 1400 kmin the lower mantle. (B)
A schematic model for diamond formation and ascent beneath the Brazilian lithosphere. We suggest that
the diamonds and inclusions initially formed from subducted oceanic crustal components in the upper
part of the lower mantle and were transported in an upwelling plume to the upper mantle, where they
unmixed into composite inclusions according to lower-pressure phase relations.
Fig. 4. Carbon isotopic compositions of diamonds in
this study compared to some possible carbon sources.
White rectangles represent the range observed in
each diamond on the basis of multiple spot measure-
ments in different growth zones revealed by cathodo-
luminescence images (20). The isotopic compositions
of several possible carbon sources are drawn sche-
matically on the basis of ranges given in (10). Organic
carbon denotes either biogenic or abiogenic noncar-
bonate carbon originating in surface or near-surface
environments; mantle carbon denotes a carbon com-
ponent that is typical of primitive ultramafic mantle
rocks and peridotitic lithospheric diamonds; car-
bonate denotes surface-derived carbon deposited
as carbonate from seawater.
RESEARCH ARTICLE
when subducted lithosphere entered the shallow
lower mantle and stagnated because of density
inversion and increased mantle viscosity (14, 27)
(Fig. 3B). If heated to ambient mantle tempera-
tures, carbonated basaltic lithologies form carbo-
nated melts, which can then be reduced to diamond
during reactions with surrounding mantle (8, 28).
Our results also indicate that the diamonds were
transported by convection from the lower to the
upper mantle, where the originally homogeneous
inclusions unmixed. For example, phase relations
along the NaAlSiO
4
-MgAl
2
O
4
boundary (29) in-
dicate that the bulk composition of inclusion
Ju5-20 would yield the observed assemblage of
nepheline plus spinel (Fig. 1A and fig. S1B) at
depths of ~150 km; other inclusions in diamonds
from the Juina region (3, 4, 8) also suggest equil-
ibration near the base of the Brazilian lithosphere
(~150 to 200 km). Thus, the diamonds record a
history of upward transport on the order of 500
to 1000 km or more before being sampled by a
Cretaceous kimberlite and brought to the surface.
On the basis of seismological and petrological
evidence, previous workers have argued for a man-
tle plume beneath Brazil during the Cretaceous
(30, 31). Furthermore, paleo-plate reconstruc-
tions show that the Juina region of Brazil was lo-
cated at the margin of the African large lowshear
velocity provinces during the Cretaceous, which
may be indicative of the presence of deep mantle
plumes (32). We suggest that some portion of
stagnated subducted lithosphere in which the di-
amonds grew was transported from the lower
mantle to the base of the Brazilian lithosphere in
a rising mantle plume (Fig. 3B). The Juina-5 di-
amonds and their inclusions provide compelling
evidence for deep cycling of oceanic crust and
surface carbon into the lower mantle and, ulti-
mately, exhumation back to the upper mantle and
Earths surface.
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mantle zircon ages for kimberlites from the Juina and
Paranatinga Provinces, Brazil. Extended Abstracts, 7th
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L. R. M. Daniels, Appl. Geochem. 6, 477 (1991).
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A. P. Dickin, G. J. Mitchell, J. Petrol. 36, 89 (1995).
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L. D. Ashwal, Nature 466, 352 (2010).
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Acknowledgments: We thank I. Buisman and S. Kearns
for assisting in the collection of electron microprobe
data and L. Gobbo on behalf of Rio Tinto for providing
samples. Supported by UK Natural Environment Research
Council grant NE/H011242/1 (M.J.W.) and NSF grant
EAR-1049992 (S.B.S. and J.W.). See (20) for additional
compositional data on inclusion phases, experimental run
products, and Raman spectroscopy.
www.sciencemag.org/cgi/content/full/science.1209300/DC1
Materials and Methods
SOM Text
Figs. S1 to S3
Tables S1 to S5
References (3445)
3 June 2011; accepted 22 August 2011
Published online 15 September 2011;
10.1126/science.1209300
REPORTS
Universal Digital Quantum Simulation
with Trapped Ions
B. P. Lanyon,
1,2
* C. Hempel,
1,2
D. Nigg,
2
M. Mller,
1,3
R. Gerritsma,
1,2
F. Zhringer,
1,2
P. Schindler,
2
J. T. Barreiro,
2
M. Rambach,
1,2
G. Kirchmair,
1,2
M. Hennrich,
2
P. Zoller,
1,3
R. Blatt,
1,2
C. F. Roos
1,2
A digital quantum simulator is an envisioned quantum device that can be programmed to efficiently
simulate any other local system. We demonstrate and investigate the digital approach to quantum
simulation in a system of trapped ions. With sequences of up to 100 gates and 6 qubits, the full
time dynamics of a range of spin systems are digitally simulated. Interactions beyond those naturally
present in our simulator are accurately reproduced, and quantitative bounds are provided for the
overall simulation quality. Our results demonstrate the key principles of digital quantum simulation and
provide evidence that the level of control required for a full-scale device is within reach.
A
lthough many natural phenomena are ac-
curately described by the laws of quan-
tum mechanics, solving the associated
equations to calculate properties of physical sys-
tems, i.e., simulating quantum physics, is in gen-
eral thought to be very difficult (1). Both the
number of parameters and differential equations
that describe a quantum state and its dynamics
grow exponentially with the number of particles
involved. One proposed solution is to build a
highly controllable quantum system that can ef-
ficiently perform the simulations (2). Recently,
quantum simulations have been performed in
several different systems (313), largely follow-
ing the analog approach (2) whereby an analo-
gous model is built, with a direct mapping between
the state and dynamics of the simulated system
and those of the simulator. An analog simulator
is dedicated to a particular problem, or class of
problems.
A digital quantum simulator (2, 1416) is a
precisely controllable many-body quantum sys-
temon which a universal set of quantumoperations
(gates) can be performed, i.e., a quantum computer
(17). The simulated state is encoded in a register
1
Institut fr Quantenoptik und Quanteninformation, ster-
reichische Akademie der Wissenschaften, Otto-Hittmair-Platz 1,
A-6020 Innsbruck, Austria.
2
Institut fr Experimentalphysik, Uni-
versity of Innsbruck, Technikerstr. 25, A-6020 Innsbruck,
Austria.
3
Institut fr Theoretische Physik, University of
Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria.
ben.lanyon@uibk.ac.at
of quantuminformation carriers, and the dynamics
are approximated with a stroboscopic sequence of
quantumgates. Inprinciple, it canbe reprogrammed
to efficiently simulate any local quantum system
(14) and is therefore referred to as a universal
quantumsimulator. Furthermore, there are known
methods to efficiently correct for and quantita-
tively bound experimental error in large-scale
digital simulations (18).
We report on digital simulations using a sys-
tem of trapped ions. We focus on simulating the
full time evolution of networks of interacting
spin-1/2 particles, which are models of magnet-
ism (19) and exhibit rich dynamics. We do not
use error correction, which has been demon-
strated separately in our system (20) and must
be included in a full-scale fault-tolerant digital
quantum simulator.
The central goal of a quantumsimulation is to
calculate the time-evolved state of a quantum
system y(t). In the case of a time-independent
Hamiltonian H, the form of the solution is y(t) =
e
iHt/
y(0) = Uy(0). A digital quantum simulator
can solve this equation efficiently for any local
quantum system (14), i.e., where H contains a
sum of terms H
k
that operate on a finite number
of particles, owing to interaction strengths that
fall off with distance, for example. In this case the
local evolution operators U
k
= e
iH
k
t/
can be ap-
proximated with a fixed number of operations
from a universal set. However, these terms do
not generally commute U
k
e
iH
k
t/
. This
can be overcome with the Trotter approximation
(14, 21), e
iHt=
lim
n
k
e
iHk t=n
n
, for inte-
ger n, which is at the heart of the digital quan-
tumsimulation algorithm. For finite n, the Trotter
error is bounded and can be made arbitrarily small.
The global evolution of a quantum system can
therefore be approximated by a stroboscopic se-
quence of many small time-steps of evolution,
generated by the local interactions present in the
system. The digital algorithm can also be applied
to time-dependent Hamiltonians and open quan-
tum systems (14, 16, 17, 22).
Our simulator is based on a string of electri-
cally trapped and laser-cooled calcium ions (23).
The |S
1/2
= |1 and |D
5/2
= |0 Zeeman states en-
code a qubit in each ion. Simulated states are
encoded in these qubits and manipulated by laser
pulses that implement the operation set: O
1
(q, j) =
exp(iqs
j
z
); O
2
(q) = exp(iq
i
s
z
i
); O
3
(q,f) =
exp(iq
i
s
f
i
); O
4
(q,f) = exp(iq
i<j
s
i
f
s
j
f
).
Here s
f
= cosfs
x
+ sinfs
y
and s
j
k
denotes the
k-th Pauli matrix acting on the j-th qubit. O
4
is an
effective qubit-qubit interaction mediated by a
common vibrational mode of the ion string (24).
Recent advances have seen the quality of these
operations increase appreciably (25). For our sim-
ulations, we define dimensionless Hamiltonians
1
H, i.e., H E

H such that U e
i

HEt=
and the
systemevolution is quantified by a unitless phase
q = Et/.
We begin by simulating an Ising system of
two interacting spin-1/2 particles, which is an
elementary building block of larger and more
complex spin models and was one of the first
systems to be simulated with trapped ions follow-
ing an analog approach (6, 26). The Hamiltonian
is given by H
Ising
Bs
1
z
s
2
z
Js
1
x
s
2
x
.
The first bracketed termrepresents the interaction
of each spin with a uniform magnetic field in the
z direction and the second an interaction between
the spins in an orthogonal direction. The interactions
do not commute, giving rise to nontrivial dynamics
and entangled eigenstates. Each spin is mapped
directly to an ionic qubit (|1 = |, |0 = |). The
dynamics are implemented with a stroboscopic
sequence of O
2
and O
4
gates, representing the
magnetic field and spin-spin evolution operators,
respectively. We first simulate a time-independent
case J = 2B, which couples the initial state | to
a maximally entangled superposition of |
and | (Fig. 1A). The simulated dynamics con-
verge closer to the exact dynamics as the digital
resolution is increased. The overall simulation
quality is quantified by quantum process to-
mography (QPT) (27), yielding a process fidelity
of 91(1)% at the finest digital resolution used. In
(23), we show how higher-order Trotter decom-
positions can be used to achieve more accurate
digital approximations with fewer operations.
We now consider a time-dependent case
where J increases linearly from 0 to 4B during a
total evolution q
t
. In the limit q
t
, spins initial-
ly prepared in the paramagnetic ground state of
the magnetic field (|) will evolve adiabatically
into the antiferromagnetic ground state of the
final Hamiltonian: an entangled superposition of
the
j
s
x
j
eigenstates |
x
and |
x
. As a
demonstration, we approximate the continuous
dynamics, for q
t
= p/2, using a stroboscopic
sequence of 24 O
2
and O
4
gates and measure the
populations in the s
x
basis (Fig. 1B). The evo-
lution closely follows the exact case, and an
entangled state is created [63(6)% tangle (28)].
Full quantum state reconstructions are performed
after each digital step, yielding fidelities between
the ideal digitized and measured state of at least
91(2)% and overlaps with the instantaneous
ground state of no less than 91(2)%. The observed
oscillation in expectation values is a diabatic ef-
fect, as excited states become populated.
More complex systems with additional spin-
spin interactions in the y (XY model) and z
Fig. 1. Digital simulations of a two-spin Ising system. Dynamics of
initial state | for two cases. (A) A time-independent system ( J = 2B)
and increasing levels of digital resolution (iiv). A single digital step is
D.C = O
4
(q
a
/n,0).O
2
(q
a
/2n), where q
a
= p / 2
2
p
and n = 1,2,3,4 (for
panels i to iv, respectively). Quantum process fidelities between the
measured and exact simulation at q
a
are (i) 61(1)% and (iv) 91(1)%
(ideally 61% and 98%, respectively) (23). (B) A time-dependent sys-
tem. J increases linearly from 0 to 4B. Percentages: fidelities between
measured and exact states with uncertainties less than 2%. The initial
and final state have entanglement 0(1)% and 63(6)% [tangle (28)],
respectively. The digitized linear ramp is shown at the bottom: c = O
2
(p/16), d = O
4
(p/16,0). For more details, see (23). Lines; exact dynamics. Unfilled
shapes: ideal digitized; filled shapes: data (
x).
REPORTS
(XYZ model) directions can be simulated by
reprogramming the operation sequence. The dy-
namics due to an additional spin-spin interaction
in the y direction is simulated by adding another
O
4
operation to each step of the Ising stroboscopic
sequence (with f = p/2). A third spin-spin in-
teraction in the z direction is realized by adding
an O
4
gate sandwiched between a pair of O
3
operations set to rotate the reference frame of the
qubits. Dynamics of the initial state |
x
are
simulated for each model, with a fixed digital
resolution of q/n = p/16 and up to 12 Trotter
steps (Fig. 2). Up to 24, 48, and 84 gates are used
for the Ising, XY, and XYZ simulations, re-
spectively. This particular initial state is chosen
because the ideal evolution is different for each
model. The results show close agreement with
the exact dynamics and results from QPT after
four digital steps yield process fidelities, with
the exact unitary evolution, of 88(1), 85(1), and
79(1)%for the Ising, XY, and XYZ, respectively.
With perfect operations, the Trotter error would
be less than 1% in each case. Although analog
simulations of Ising models have previously been
demonstrated in ion traps (6, 8), XY and XYZ
models have not.
The digital approach allows arbitrary interac-
tion distributions between spins to be programmed.
For three-spin systems, we realize various inter-
actions that give rise to the dynamical evolutions
of the initial state | (Fig. 3). Figure 3Ashows
a system supporting interactions between all spin
pairs with equal strength, and between each spin
and a transverse field. The initial state couples
equally to |, |, and |, while the
strength of the field determines the amplitude and
frequency of the dynamics. For the case shown
(J = 2B), an equal superposition of the coupled
states is periodically created [an entangled W
state (29)]. Figure 3B shows how nonsymmetric
interaction distributions can be programmed, with
sequences of O
4
and O
1
to add spin-selective
interactions. The interaction between one spin
pair is dominant. Owing to this broken symmetry,
one coupled state (|) is populated faster than
the others, yielding more complex dynamics than
in the symmetric case. Figure 3C demonstrates
the ability to simulate n-body interactions; spe-
cifically, s
z
1
s
x
2
s
x
3
. Aclear signature is observed:
direct coupling between
j
s
y
j
eigenstates
|
y
and |
y
, periodically producing
an entangled GHZ state (29). Many-body spin
interactions of this kind are an important ingre-
dient in the simulation of systems with strict
symmetry requirements (30) or spin models ex-
hibiting topological order (31). Measurements in
other bases and simulations of nearest-neighbor
and many-body interactions with a transverse field
using more than 100 gates are presented in (23).
Figure 4A shows the observed dynamics of
the four-spin state | under a long-range
Ising-type interaction. The rich structure of the
dynamics reflects the increased complexity of the
underlying Hamiltonian: Oscillation frequencies
correspond to the energy gaps in the spectrum.
This information can be extracted via a Fourier
transform of the data (23). Specific energy gaps
could be targeted by preparing superpositions of
eigenstates via an initial quasi-adiabatic digital
evolution (10). Figure 4B shows the observed
dynamics for our largest simulation: a six-spin
many-body interaction, which directly couples
the states | and |, periodically
producing a maximally entangled GHZ state.
Direct quantification of simulation quality for
more than two qubits is impractical via QPT: For
three qubits, expectation values must be mea-
sured for 1728 experimental configurations, and
this increases exponentially with qubit number
(3 10
6
for six qubits). However, the average
process fidelity (F
p
) can be bounded more effi-
ciently (32). We demonstrate this for the three-
and six-spin simulations of Figs. 3C and 4B,
respectively. Bounds of 85(1)% F
p
91(1)%
(three spins) and 56(1)% F
p
77(1)% (six
spins) are obtained at f = 0.25 p, with 40 and
512 experimental configurations, respectively
(23). The largest system for which a process
fidelity has previously been measured is three
qubits (33). A different measure of process
quality is given by the worst-case fidelity, over all
input states, and may be better used to assess
errors in future full-scale fault-tolerant simula-
tions. Regardless of the measure used, the error in
large-scale digital simulations built from finite-
sized operations can be efficiently estimated.
Each operation can be characterized with a finite
number of measurements, then the error in any
combination can be chained (34). To exploit this,
the number of ionic qubits on which our many-
qubit operators O
24
can act must be restricted.
The dominant effect of experimental error can
be seen in Figs. 3Band 4B: The dynamics damps
as a result of decoherence processes. Laser
frequency and ambient magnetic field fluctua-
tions are far from the leading error source: In the
absence of coherent operations, qubit lifetimes
are more than an order of magnitude longer
(coherence times 30 ms) than the duration of
Fig. 2. (A to C) Digital simulations of increasingly complex two-spin systems. Dynamics of the initial
state |
x
with a fixed digital resolution of p/16. The graphic in each panel shows how a single digital
step is built: C = O
2
(p/16), D = O
4
(p/16,0), E = O
4
(p/16,p), F = O
3
(p/4,0). Quantum process fidelities
between the measured and exact simulation after one and four digital steps are shown with gray arrows
[uncertainties 1% (23)]. Lines; exact dynamics. Unfilled shapes: ideal digitized; filled shapes: data
(
x

x
x or
x
).
REPORTS
experiments (1 to 2 ms). The current leading
sources of error, which limit both the simulation
complexity and size, are thought to be laser
intensity fluctuations (23). This is not currently
a fundamental limitation and, once properly ad-
dressed, should enable an increase in simulation
capabilities.
The digital approach can be combined with
existing tools and techniques for analog simu-
lations to expand the range of systems that can be
simulated. In light of the present work, and cur-
rent ion trap development (35), digital quantum
simulations involving many tens of qubits and
hundreds of high-fidelity gates seems feasible in
coming years.
1. R. P. Feynman, Int. J. Theor. Phys. 21, 467 (1982).
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Dynamics of the initial state | in three cases.
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field. C = O
2
(p/32), D = O
4
(p/16,0). (B) Inhomog-
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posed into an equal-strength interaction and
another with twice the strength between one pair.
E = O
1
(p/2,1). (C) Three-body interaction, which
couples the
j
s
y
j
eigenstates |
y
and |
y
.
An O
3
(p/4,0) operation before measurement
rotates the state into the logical s
z
basis. F =
O
1
(q,1), 4D = O
4
(p/4,0). Any point in the phase
evolution is simulated by varying the phase q of
operation F. Inequalities bound the quantum pro-
cess fidelity F
p
[see (23) for details].
Fig. 4. Digital simulations of four and six spin sys-
tems. Dynamics of the initial state where all spins
point up. (A) Four spin long-range Ising system.
Each digital step is D.C = O
4
(p/16,0).O
2
(p/32).
Error bars are smaller than point size. (B) Six spin
six-body interaction. F = O
1
(q,1), 4D = O
4
(p/4,0).
The inequality at f = 0.25 p bounds the quantum
process fidelity F
p
at q = 0.25 p [see (23) for details].
Lines; exact dynamics. Unfilled shapes: ideal digitized;
filled shapes: data (P
0
P
1
P
2 P
3 P
4 P
5 P
6
,
where P
i
is the total probability of finding i spins
pointing down).
REPORTS
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Acknowledgments: We thank W. Dr, A. Aspuru-Guzik, and
M. Brownnutt for discussions. We acknowledge financial
support by the Austrian Science Fund (FWF) [SFB F40
FOQUS], the Institut fr Quanteninformation GmbH,
Intelligence Advanced Research Projects Activity, and the
European Commission for support via the integrated
project AQUTE, two Marie Curie International Incoming
Fellowships, and the ERC advanced grant CRYTERION.
SOM Text
Figs. S1 to S9
Tables S1 to S6
References
6 May 2011; accepted 14 July 2011
10.1126/science.1208001
Implementing the Quantum
von Neumann Architecture with
Superconducting Circuits
Matteo Mariantoni,
1,4
* H. Wang,
1
T. Yamamoto,
1,2
M. Neeley,
1
Radoslaw C. Bialczak,
1
Y. Chen,
1
M. Lenander,
1
Erik Lucero,
1
A. D. OConnell,
1
D. Sank,
1
M. Weides,
1
J. Wenner,
1
Y. Yin,
1
J. Zhao,
1
A. N. Korotkov,
3
A. N. Cleland,
1,4
John M. Martinis
1,4
*
The von Neumann architecture for a classical computer comprises a central processing unit
and a memory holding instructions and data. We demonstrate a quantum central processing
unit that exchanges data with a quantum random-access memory integrated on a chip, with
instructions stored on a classical computer. We test our quantum machine by executing codes
that involve seven quantum elements: Two superconducting qubits coupled through a quantum
bus, two quantum memories, and two zeroing registers. Two vital algorithms for quantum
computing are demonstrated, the quantum Fourier transform, with 66% process fidelity, and
the three-qubit Toffoli-class OR phase gate, with 98% phase fidelity. Our results, in combination
especially with longer qubit coherence, illustrate a potentially viable approach to factoring
numbers and implementing simple quantum error correction codes.
Q
uantum processors (14) based on nu-
clear magnetic resonance (57), trapped
ions (810), and semiconducting devices
(11) were used to realize Shors quantum
factoring algorithm (5) and quantum error correc-
tion (6, 8). The quantum operations underlying
these algorithms include two-qubit gates (2, 3), the
quantum Fourier transform (7, 9), and three-qubit
Toffoli gates (10, 12). In addition to a quantum
processor, a second critical element for a quan-
tum machine is a quantum memory, which has
been demonstrated, for example, using optical
systems to map photonic entanglement into and
out of atomic ensembles (13).
Superconducting quantum circuits (14) have
met a number of milestones, including demonstra-
tions of two-qubit gates (1520) and the advanced
control of both qubit and photonic quantum states
(1922). We demonstrate a superconducting
integrated circuit that combines a processor
executing the quantum Fourier transform and a
three-qubit Toffoli-class OR phase gatewith a
memory and a zeroing register in a single device.
This combination of a quantum central process-
ing unit (quCPU) and a quantum random-access
memory (quRAM), which comprise two key ele-
ments of a classical von Neumann architecture,
defines our quantum von Neumann architecture.
In our architecture (Fig. 1A), the quCPU per-
forms one-, two-, and three-qubit gates that process
quantum information, and the adjacent quRAM
allows quantuminformation to be written, read out,
and zeroed. The quCPU includes two supercon-
ducting phase qubits (18, 19, 21, 22), Q
1
and Q
2
,
connected through a coupling bus provided by
a superconducting microwave resonator B. The
quRAM comprises two superconducting resona-
tors M
1
and M
2
that serve as quantum memories,
as well as a pair of zeroing registers Z
1
and Z
2
,
two-level systems that are used to dump quan-
tum information. The chip geometry is similar
to that in (21, 22), with the addition of the two
zeroing registers. Figure 1B shows the character-
ization of the device by means of swap spec-
troscopy (21).
The computational capability of our archi-
tecture is displayed in Fig. 2A, where a seven-
channel quantumcircuit, yieldinga 128-dimensional
Hilbert space, executes a prototypical algorithm.
First, we create a Bell state between Q
1
and Q
2
using a series of p-pulse,
iSWAP
p
(entangling
state), and iSWAP (exchanging state) operations
(step I, a to c) (22). The corresponding density
matrix r
%
(I)
[Fig. 2C (I)] is measured by quantum
state tomography. The Bell state is then written
into the quantum memories M
1
and M
2
by an
iSWAP pulse (step II) (22), leaving the qubits
in their ground states |g, with density matrix
1 r
%
(II)
[Fig. 2C(II)]. While storing the first Bell state
in M
1
and M
2
, a second Bell state with density
matrix r
%
(III)
[Fig. 2C (III)] is created between the
qubits, using a sequence similar to the first op-
eration (step III, a to c).
To reuse the qubits Q
1
and Q
2
, for example to
read out the quantum information stored in the
memories M
1
and M
2
, the second Bell state has to
be dumped (23). This is accomplished using two
zeroing gates, by bringing Q
1
on resonance with Z
1
and Q
2
with Z
2
for a zeroing time t
z
, corresponding
to a full iSWAP (step IV). Figure 2B shows the
corresponding dynamics, where each qubit, initially
in the excited state |e, is measured in the ground
state |g after 30 ns. The density matrixr
%
(IV)
of the
zeroed two-qubit system is shown in Fig. 2C (IV).
Once zeroed, the qubits can be used to read the
memories (step V), allowing us to verify that, at
the end of the algorithm, the stored state is still
entangled. This is clearly demonstrated by the
density matrix shown in Fig. 2C (V).
The ability to store entanglement in the mem-
ories, which are characterized by much longer
coherence times than the qubits, is key to the
quantum von Neumann architecture. We demon-
strate this capability in Fig. 2, Dand E, where the
fidelity and concurrence metrics (24) of the Bell
states stored in M
1
and M
2
are compared with
1
Department of Physics, University of California, Santa Barbara,
CA 931069530, USA.
2
Green Innovation Research Labora-
tories, NEC Corporation, Tsukuba, Ibaraki 305-8501, Japan.
3
Department of Electrical Engineering, University of California,
Riverside, CA 92521, USA.
4
California NanoSystems Institute,
University of California, Santa Barbara, CA 931069530, USA.
matmar@physics.ucsb.edu (M.M.); martinis@physics.ucsb.
edu (J.M.M.)
Present address: Department of Physics, Zhejiang University,
Hangzhou 310027, China.
Present address: Lincoln Laboratory, Massachusetts Institute
of Technology, 244 Wood Street, Lexington, MA 024209108,
USA.
Present address: National Institute of Standards and Tech-
nology, Boulder, CO 80305, USA.
REPORTS
those for the same states stored in Q
1
and Q
2
. The
experiment is performed as in Fig. 2A, but elim-
inating steps (III) and (IV) for memory storage,
and steps (II) to (V) for qubit storage. For the
qubits, the storage time t
st
is defined as the wait
time at the end of step (I), before measuring the
qubit states, whereas for the resonators the wait
time is that between the write and read steps. The
fidelity of the qubit states decays to below0.2 after
400 ns, whereas for the states stored in the mem-
ories it remains above 0.4 up to 1.5 ms. Most
important, after only 100 ns the state stored in the
qubits does not preserve any entanglement, as in-
dicated by a zero concurrence, whereas the mem-
ories retain their entanglement for at least 1.5 ms
(Fig. 2E). We expect to take advantage of our ar-
chitecture in long computations, where qubit states
can be protected and reused by writing them into,
and reading them out of, the long-lived quRAM.
Two-qubit gates are a vital resource for the
operation of the quCPU (2, 3). Avariety of such
gates have been implemented in superconducting
circuits (1520), with some recent demonstra-
tions of quantum algorithms (16, 18). Control
Z-p (CZ-p) gates are readily realizable with su-
perconducting qubits, due to easy access to the
third energy state of the qubit, effectively operat-
ing the qubit as a qutrit (16, 18, 20, 25). However,
CZ-p gates are just a subset of the more general
class of CZ-f gates, obtained for the special case
where the phase f = p. In our architecture, the
full class of CZ-f gates, with f from 0 to p,
can be generated by coupling a qutrit close to
resonance with a bus resonator.
Figure 3A shows the quantum logic circuit
that generates the CZ-f gate (left) and a short-
hand symbol for the gate (right). The logic circuit
demonstrates the nontrivial case where qubits
Q
1
and Q
2
are brought from their initial ground
state to |Q
1
Q
2
= |ee by applying a p-pulse to
each qubit. The excitation in Q
2
is then trans-
ferred into bus resonator B, and Q
1
s |e |f
transition is brought close to resonance with Bfor
the time required for a 2p rotation, where the
states |Q
1
B = |e1 and |f0 are detuned by a fre-
quency d
Q
1
B
, which we term a semiresonant con-
dition. In this process, Q
1
acquires the phase (26)
f = p p
d
Q
1
B
d
2
Q
1
B
g
2
Q
1
B
q 1
where g
Q
1
B
is the coupling frequency between
|e1 and |f0. The final step is to move the ex-
citation from B back into Q
2
.
The time-domain swaps of |Q
1
B between
the states |e1 and |f0 are shown in Fig. 3B, where
the solid black line indicates the detunings and
corresponding interaction times used to gener-
ate any phase 0 f p (ideally f 0 when
d
Q
1
B
). These phases are measured by per-
forming two Ramsey experiments on Q
1
for each
value of the detuning d
Q
1
B
, one with B in the |0
state, and the other with B in the |1 state. The
relative phase between the Ramsey fringes cor-
responds to the value of f for the CZ-f gate (26),
as shown in Fig. 3C.
A more sophisticated version of this experi-
ment is performed by initializing Q
1
and Q
2
each
in the superposition state |g + |e. We move Q
2
s
state into B, performa CZ-f gate with0 f p,
move the state in B back into Q
2
, rotate Q
1
s
resulting state by p/2 about the y axis, and per-
form a joint measurement of Q
1
and Q
2
. Ideally,
this protocol permits the creation of two-qubit
states ranging from a product state for f = 0 to a
maximally entangled state for f = p. In the two-
qubit basis set M
2
= {|gg, |eg, |ge, |ee}, the gen-
eral density matrix of such two-qubit states reads
r
%
f
=
0 0 0 0
0 1=2 1 e
if
=4 1 e
if
=4
0 1 e
if
=4 1 cosf=4 i sin f=4
0 1 e
if
=4 i sin f=4 1 cosf=4
2
Figure 3D shows the fidelity and entanglement of
formation (EOF) (24) of two-qubit states generated
Fig. 1. The quantum von Neumann architecture. (A) The quCPU (blue box)
includes two qubits Q
1
and Q
2
and the bus resonator B. The quRAM (magenta
boxes) comprises two memories M
1
and M
2
and two zeroing registers Z
1
and
Z
2
. The horizontal dotted lines indicate connections between computational
elements. The vertical direction represents frequency, where the memory and
zeroing registers are fixed in frequency, whereas the qubit transition fre-
quencies can be tuned by z-pulses (gray dashed double arrows). (B) Swap
spectroscopy (21) for Q
1
(left) and Q
2
(right): Qubit excited state |e probability
P
e
(color scale) versus z-pulse amplitude (vertical axis) and delay time Dt
(horizontal axis), after exciting the qubit with a p-pulse. At zero z-pulse
amplitude the qubits are at their idle points, where they have an energy
relaxation time T
rel
400 ns. A separate Ramsey experiment yields the qubits
dephasing time T
deph
200 ns. By tuning the z-pulse amplitude, the qubit
transition frequencies f
Q1
andf
Q2
can be varied between 5.5 and 8 GHz. For
z-pulse amplitudes indicated by B and M
1
for Q
1
, and by B and M
2
for Q
2
, the
chevron pattern of a qubit-resonator interaction is observed (21). The transition
frequencies of B, M
1
, and M
2
are f
B
= 6.82 GHz, f
M1
=6.29 GHz, andf
M2
= 6.34
GHz, respectively. From the chevron oscillation, we obtain the qubit-resonator
coupling strengths, which for both the resonator bus and the memories are
20 MHz (splitting) for the |g |e qubit transition, and
2
p
faster for the
|e |f transition (|g, |e, and |f are the three lowest qubit states) (22). For
all resonators, T
rel
4 ms. Swap spectroscopy also reveals that the qubits
interact with several modes associated with spurious two-level systems. Two of
them, Z
1
and Z
2
, are used as zeroing registers. Their transition frequencies are
f
Z1
= 6.08 GHz and f
Z2
= 7.51 GHz, respectively, with coupling strength to the
qubits of 17 MHz.
REPORTS
using 70 values of f. Figure 3E shows three
examples of r
%
f
for f = 0.28, f = p/2, and f = p,
respectively.
The state generated using f = p/2 plays a
central role in the implementation of the two-
qubit quantum Fourier transform. Neglecting bit-
order reversal, the quantumFourier transformcan
be realized by applying a Hadamard gate to Q
2
,
followed by a CZ-p/2 gate between Q
1
and Q
2
,
and finally a Hadamard on Q
1
(2, 7, 9), as sketched
in Fig. 3F (top left). Representing the input state
of the transform as |x (position) and the output
as | p (momentum), assuming | x M
2
and the
indexes x and p are integers, with p {0, 1, 2, 3},
the output state is jp
3
x0
e
i2pxp=4
jx=2, cor-
responding to a 4 4 unitary operator. This op-
erator can be fully characterized by means of
quantum process tomography (2, 18), which al-
lows us to obtain the c
p
m
matrix (2, 18) shown in
Fig. 3F (bottom).
Finally, by combining the CZ-f and zeroing
gates, we can implement a Toffoli-class gate
(10, 12, 27), the three-qubit OR phase gate. This
gate, combined with single-qubit rotations, is suf-
ficient for universal computation. AToffoli gate
is a doubly controlled quantumoperation, where
a unitary operation is applied to a target qubit
subject to the state of two control qubits. The
canonical Toffoli is a doubly controlled NOT
gate; here, we consider a doubly controlled phase
gate, which is equivalent through a change of
basis of the target qubit. In the canonical Toffoli
gate, the control gate is applied if both control
qubits, Q
1
AND Q
2
, are in state |e. In our case,
the control gate is applied conditionally if the
controls Q
1
OR Q
2
are in |e. Additionally, we
have implemented a three-qubit gate for the
logical function exclusive OR (XOR), which,
even though not a Toffoli-class gate, helps to
understand the more complex OR gate.
The quantum logic circuits for the XOR and
OR gates are drawn in Fig. 4, A and D. The
control qubits are Q
1
and Q
2
, and the target is the
bus resonator B, effectively acting as the third
qubit (as only the states |0 and |1 of B are used).
The XOR gate is realized as a series of two CZ-p
gates between the controls and the target, and the
ORgate as the series CZ-p, CZ-p, and CZ-p,
in an M-shaped configuration.
The truth table for the XOR gate is dis-
played in Fig. 4B (top). The control qubits Q
1
and Q
2
are assumed to be in one of the states
in M
2
, whereas the target B is in |0 + |1. The
target acquires a phase p, corresponding to a
true result, only when the controls are in the
state |Q
1
Q
2
= |ge or |eg. For the other non-
trivial case |Q
1
Q
2
= |ee, the target acquires 0
phase, corresponding to a false result. This
is due to the action of the two CZ-p gates, giv-
ing a global phase p when either of the controls
Fig. 2. Programming the quantum von
Neumann architecture. (A) Quantum algo-
rithm comprising seven independent chan-
nels interacting through five computational
steps. Dotted and solid lines represent chan-
nels in the ground and excited/superposition
states, respectively. A black rectangle rep-
resents a p-pulse; two crosses connected by
a solid line a
iSWAP
p
; an open and a closed
circle connected by a single arrow an iSWAP;
oblique arrows indicate decay froma zeroing
register. (B) Calibration of the zeroing gates.
Each qubit is prepared in |e, interacts on resonance with its zeroing register for a time t
z
, and its probability P
e
measured, with P
e
plotted versus t
z
(large
and small blue circles). The solid green line is a decaying cosine fit to the data. The black arrows indicate the zeroing time for each qubit. (C) Density matrices
r%
(I)
, r%
(II)
, , r%
(V)
of the Q
1
-Q
2
state for each step in (A) (scale key on bottomleft). Gray arrows, ideal state. Red and black arrows and black dots, measured state
(black arrows indicate errors). The off-diagonal elements of r%
(I)
, r%
(III)
, and r%
(V)
have different angles because of dynamic phases (26). Fidelities: F
(I)
= 0.772 T
0.003, F
(II)
= 0.916 T 0.002, F
(III)
= 0.689 T 0.003, F
(IV)
= 0.913 T 0.002, and F
(V)
= 0.606 T 0.003. Concurrences: C
(I)
= 0.593 T 0.006, C
(II)
= 0.029 T
0.005, C
(III)
= 0.436 T 0.007, C
(IV)
= 0.019 T 0.005, and C
(V)
= 0.345 T 0.008. (D) Comparison of fidelity Fas a function of storage time t
st
for a Bell state
stored in Q
1
and Q
2
(blue circles) versus that stored in M
1
and M
2
(magenta squares; error bars smaller than symbols). The solid lines are exponential fits to
data. (E) As in (D), but for the concurrence C. In (D) and (E), the vertical black dotted line indicates the time delay ( 59 ns) associated with memory
storage, with respect to storage in the qubits, due to the writing and reading operations (II) and (V) in (A).
REPORTS
is in |e and a phase 2p (equivalent to a 0 phase)
when both are in |e.
The truth table can be experimentally mea-
sured by performing Ramsey experiments on the
target, one for each pair of control states. The
experiments are realized by (i) preparing Q
2
in
the superposition state |g + |e by means of a p/2-
pulse; (ii) moving the state from Q
2
into B, thus
creating a |0 + |1 state in B; (iii) preparing Q
1
and Q
2
in each possible pair of control states in
M
2
by means of p-pulses; (iv) performing the
XORgate; (v) zeroing Q
2
into Z
2
at the end of the
XOR gate; (vi) moving the final target state from
B into the zeroed Q
2
; and (vii) completing the
Ramsey sequence on Q
2
with a second p/2-pulse
with variable rotation axis relative to the pulse
in (i). The measurement outcomes are dis-
played in Fig. 4B (bottom), together with the
least-squares fits used to extract the phase in-
formation associated with each value of the
truth table. The Ramsey fringes for the two con-
trol states |ge and |eg are inverted relative to the
reference state |gg, as expected from the XOR
gate truth table.
In general, given the Q
1
-Q
2
-B basis set M
3
=
{|gg0, |gg1, |ge0, |ge1, |eg0, |eg1, |ee0, |ee1},
the vector t
XOR
of the diagonal elements as-
sociated with the ideal unitary matrix of the XOR
gate reads
t
XOR
= (1, 1, 1, 1, 1, 1, 1, 1) 3
whereas all off-diagonal elements of the matrix
are zero. Each element t
XOR
k
can be expressed as
a complex exponential e
if
jlmn
, with |lmn M
3
.
The phase f
|lmn
can be either 0, when t
XOR
k
= 1,
or p, when t
XOR
k
= 1. Among the eight values
of f
|lmn
, only seven are physically independent,
as the element e
if
jgg0
can be factored, reducing
the set of possible phases to f
|lmn
f
|gg0
, with
|lmn M
3
{|gg0}.
In analogy to the truth table for the target
B, a table with four phase differences can also
be obtained for the controls Q
1
and Q
2
, resulting
in a total of 12 phase differences. These differ-
ences can be measured by performing Ramsey
experiments both on the target and the control
qubits. It can be shown that from the 12 phase
differences, one can obtain the seven indepen-
dent phases associated with the diagonal ele-
ments t
XOR
k
(26), thus realizing a quantum phase
tomography of the Toffoli gate (28). Figure
4C displays the phase tomography results for
our experimental implementation of the XOR
gate.
The truth table associated with the M gate is
reported in Fig. 4E (top), where the only dif-
ference from the XOR gate is the phase p ac-
quired by the target B when the controls Q
1
and
Fig. 3. The quantum Fourier transform. (A) (Left) Quantum logic circuit of a CZ-f gate
(enclosed in a gray box) for |Q
1
Q
2
= |ee. The |f state of Q
1
is indicated by a dashed
line. The process where Q
1
acquires the phase f is represented by a pair of open/closed
circles, connected by a single arrow in an arc shape. All other symbols are as in Fig. 2A.
(Right) Shorthand symbol for the CZ-f gate. Although the gate unitary matrix is sym-
metric, the symbol shows the asymmetric implementation of the gate. (B) Time-domain
swaps between the states |Q
1
B = |e1 and |f0, where we plot the probability P
e
(color
scale) versus interaction time Dt and detuning d
Q1B
. The solid black line indicates
combinations of interaction time and detuning that completely depopulate the non-
computational |f state. The three black dots on this line correspond to a CZ-p, CZ-p/2, and CZ-0.28 gate (see far right). The fourth black dot (outside
the line) corresponds to a CZ-p gate (see bottom left), where the |e state has been shelved to the noncomputational |f state. (C) Phase f acquired
by Q
1
as a function of d
Q1B
. The blue dots indicate experimental data and the solid green line the theory of Eq. 1 (26). (D) Fidelity F (blue + symbols)
and EOFE (magenta symbols) of measured density matrices r%
f
versus d
Q1B
. (E) (Left to right) Density matrices r%
f
= r%
0:28
, r%
p=2
, and r%
p
, obtained when
f = 0.28, f = p/2, and f = p rad in Eq. 2 (scale key on bottom left). The arrows are color coded as in Fig. 2C. The measured fidelities are F
0.28
= 0.751 T
0.064, F
p/2
= 0.735 T 0.017, and F
p
= 0.741 T 0.030; and EOFs are E
0.28
= 0.020 T 0.055 (lower bound E
0.28
= 0), E
p/2
= 0.106 T 0.031, and E
p
=
0.401 T 0.062. (F) (Top left) Logic circuit for a two-qubit quantum Fourier transform. (Bottom) Real part of the corresponding c
m
p
matrix (2, 18). The
process fidelity for the real and imaginary (not shown) part of c
m
p
is F
c
= 0.657 T 0.014. The confidence intervals are estimated from 10 measurements
for r%
0:28
, 6 for r%
p=2
and r%
p
, and 15 for c
m
p
.
REPORTS
Q
2
are loaded in state |Q
1
Q
2
= |ee. In this case,
the action of the first CZ-p gate between Q
1
and B shelves the |1 state from B to the non-
computational state |f in Q
1
, where it remains
until the second CZ-p gate. Moving the state
of Q
1
outside the computational space during
the intermediate CZ-p gate between Q
2
and B
effectively turns off the CZ-p gate (12, 29). The
target B thus only acquires a total phase p due
to the combined action of the two CZ-p gates
(see Figure 4D). The experimental truth table ob-
tained from Ramsey fringes is shown in Fig. 4E
(bottom).
The vector t
M
of the diagonal elements as-
sociated with the ideal unitary matrix of the M
gate is t
M
= (1, 1, 1, 1, 1, 1, 1, 1). A similar
procedure as for the XOR gate allows us to
obtain the quantum phase tomography of the M
gate (Fig. 4F).
Quantum phase tomography makes it possi-
ble to define the phase fidelity of the XOR and
M gate,
F
1
e
p
4
where e
is the gate root-mean-square phase

error, with an upper bound of p. For the XOR
gate we find that F
= 0.954 T 0.004, and for

the M gate F
= 0.979 T 0.003.
Our results provide optimism for the near-
term implementation of a larger-scale quantum
processor (13) based on superconducting cir-
cuits. Our architecture shows that proof-of-
concept factorization algorithms (2, 3, 5) and
simple quantum error correction codes (2, 3, 6, 8)
might be achievable using this approach.
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Introduction (Cambridge Univ. Press, Cambridge,
2007).
4. H. M. Wiseman, G. J. Milburn, Quantum Measurement
and Control (Cambridge Univ. Press, Cambridge,
2010).
5. L. M. K. Vandersypen et al., Nature 414, 883 (2001).
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28. A full gate characterization by quantum process
tomography was not possible because we could only
simultaneously measure two qubits, with the resonator
acting as the third qubit.
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022313 (2007).
Acknowledgments: This work was supported by Intelligence
Advanced Research Projects Activity (IARPA) under
ARO award W911NF-08-1-0336 and under Army Research
Office (ARO) award W911NF-09-1-0375. M. M. acknowledges
support from an Elings Postdoctoral Fellowship. Devices
were made at the University of California Santa Barbara
Nanofabrication Facility, a part of the NSF-funded
National Nanotechnology Infrastructure Network. The
authors thank A. G. Fowler for useful comments on
scalability, and M. H. Devoret and R. J. Schoelkopf for
discussions on Toffoli gates. M.M. performed the
experiments and analyzed the data. M.M. and H.W.
fabricated the sample. T.Y., H.W., and Y.Y. helped with
the Fourier transform, and M.N. with three-qubit
gates. M.M., A.N.C., and J.M.M. conceived the experiment
and cowrote the manuscript.
Supporting Online Materials
Figs. S1 to S12
Tables S1 to S3
References
10.1126/science.1208517
Fig. 4. Three-qubit gates: The XOR phase gate and the Toffoli-class M gate. (A) Quantum logic circuit for
the XOR phase gate. (B) (Top) XOR gate truth table. (Bottom) Ramsey fringes associated with the truth
table, showing the probability P
e
of measuring Q
2
in |e, versus the Ramsey phase , for the control input
states in M
2
. Black and magenta dots, 0 phase. Blue and green dots, p phase. The solid lines are least-
squares fits to the data used to extract the truth-table phases. (C) Quantumphase tomography for the XOR
gate. Phase f
|lmn
f
|gg0
for each state |lmn M
3
. Black open boxes, ideal values. Pink areas, measured
values with corresponding confidence intervals (black lines). (D) Quantum logic circuit for the M gate,
implemented as a
1
/
2
CZ-p gate (see Fig. 3B) between Q
1
and B (half-dot/half-open circle connected by
solid line), followed by a CZ-p gate between Q
2
and B, and a second
1
/
2
CZ-p gate between Q
1
and B. The
dotted black lines connecting the two CZ-p gates indicate qubit shelving to the |f state. (E) As in (B),
but for the M gate. (F) As in (C), but for the M gate.
REPORTS
Three-Dimensional Anderson
Localization of Ultracold Matter
S. S. Kondov, W. R. McGehee, J. J. Zirbel, B. DeMarco*
Anderson localization (AL) is a ubiquitous interference phenomenon in which waves fail to
propagate in a disordered medium. We observe three-dimensional AL of noninteracting
ultracold matter by allowing a spin-polarized atomic Fermi gas to expand into a disordered
potential. A two-component density distribution emerges consisting of an expanding mobile
component and a nondiffusing localized component. We extract a mobility edge that increases
with the disorder strength, whereas the thermally averaged localization length is shown to
decrease with disorder strength and increase with particle energy. These measurements provide
a benchmark for more sophisticated theories of AL.
W
ave propagation in disordered media
is affected by scattering from random
impurities. When those scattered waves
self-interfere destructively, a phenomenon known
as Anderson localization (AL) can arise (1). AL
occurs in a wide variety of classical and quantum
materials, affecting the transport of light (2, 3),
acoustic (4), and matter (5, 6) waves. Localiza-
tion is known to affect electrical conductivity in
solids as a result of scattering fromimpurities and
defects (7), which is relevant to technological
applications. We investigate three-dimensional
(3D) AL of a noninteracting ultracold atomic
Fermi gas in a disordered potential created with
the use of optical speckle. The behavior of the gas
is qualitatively consistent with several features
of 3D AL and is shown to be incompatible with
simple trapping and classical diffusion. Where-
as in sufficiently large 1D and 2D systems par-
ticles can be localized no matter how weak the
disorder, AL is not inevitable in 3D (8). This
distinctive feature of 3D ALthat the disorder
strength sets a critical energy, the mobility
edge, below which states are localizedis re-
flected here in measurements of the fraction of
localized particles. We perform a direct measure-
ment of how the mobility edge depends on dis-
order strength by smoothly tuning the speckle
intensity.
We use standard techniques to create trapped,
ultracold gases of fermionic
40
K atoms (911).
The atoms are confined in an optical dipole trap,
cooled to between 170 and 1500 nK, and then
spin polarized (12). Quantumstatistics do not play
a major role in the measurements discussed here,
because the lowest temperature we sample cor-
responds to roughly one-half of the Fermi tem-
perature of the gas. A focused optical speckle
field (Fig. 1A), created by 532-nm light scat-
tered through a diffuser and consisting of ran-
domly distributed light and dark regions, is
superimposed on the trapped gas [as in (13)].
The atoms experience a repulsive potential pro-
portional to the speckle intensity, resulting in a
disordered potential characterized by an ap-
proximately Gaussian autocorrelation function
with z
x
= 270-nm and z
z
= 1600-nm root mean
square (RMS) radii. The laser beam creating
the speckle propagates in the vertical z direc-
tion; we refer to the transverse directions (resid-
ing in the focal plane of the speckle) as x. The
speckle intensity varies somewhat across the
gas because it has a Gaussian envelope with a
170-mm 1/e
2
radius along x and y and a 400-mm
Rayleigh range along z. The disorder strength
D, which is the potential energy averaged over
z
x
and z
z
at the center of the speckle field, can
be continuously varied from 0 to k
B
1000 nK
by adjusting the 532-nm laser power (k
B
is
Boltzmanns constant). After the speckle field
is slowly turned on over 200 ms, the trap is
suddenly turned off, and the gas is allowed to
expand in the disordered potential while sup-
ported against gravity by a magnetic field gradient.
Until the expansion, the Gaussian momentum
distribution of the trapped gas is unchanged by
the presence of the speckle potential (12).
Our experiments are distinguished from pre-
vious work on AL of ultracold atoms in pri-
marily two ways. First, we work in 3D, where
AL relies on small-angle scattering rather than
partial back reflections as in 1D (14). Also, we
eliminate interparticle interactions by using a
spin-polarized gas of fermionic atoms at tem-
peratures far belowthe ~150 mKp-wave collision
threshold (15). In previous experiments, bosonic
atoms were employed, and the effects of inter-
actions were suppressed or eliminated by using
a Feshbach resonance (6) or by reducing the
density (5).
AL in 3D is conditional on the Ioffe-Regel
criterion, which is equivalent to the quantum
wavelengthof the particle exceedingthe Boltzmann
transport mean-free path l
B
. For the maximum
D we achieve and the range of particle ener-
gies we sample, l
B
reaches a lower limit set
by the speckle correlation length (16). With
l
B
z
2
x
z
z
1=3
and the thermal deBroglie wave-
length L
dB
h=
2pmk
B
T
p
, the Ioffe-Regel cri-
terion corresponds to T 300 nK (here, h is
Plancks constant, T is temperature, and m is the
atomic mass). Because a spread of particle wave-
lengths is present in the gas and the Ioffe-Regel
criterion is not a precise constraint, localization is
possible even for temperatures somewhat above
this limit.
We probe localization by imaging the den-
sity profile after the gas has expanded for a
variable time in the speckle potential. As ob-
served for the typical absorption image (Fig.
Department of Physics, University of Illinois at Urbana
Champaign, Urbana, IL 61801, USA.
bdemarco@illinois.edu
Fig. 1. (A) Ultracold
gas expanding into
an optical speckle field
(green) and separat-
ing into localized (blue)
andmobile(red) compo-
nents. (B) The measured
optical depth, propor-
tional to the atomic den-
sity integrated through
y, is shown in false col-
or. The image depicts a
480-nK gas that has
expanded for 20 ms
through the disordered
potential with D =
k
B
240 nK. All images
shown in this manuscript
are averaged over at
least five experimental
realizations. Slices are
shown through the image
along x (C) and z (D).
The filled curves are
fits to independent mo-
bile (red) and localized
(blue) components.
X
Z
Y
A
D
C
B
Optical Depth
0.2 0.4 0.6
0.2
0.4
0.6
O
p
t
i
c
a
l

D
e
p
t
h
200 m
REPORTS
1B), a two-component profile emerges for any
finite disorder energy. The mobile component
has a Gaussian profile similar to that of a freely
expanding gas, but it expands (at a constant
velocity) more rapidly than a thermal gas. In
stark contrast, the stationary localized compo-
nent has a profile along z that is approximately
exponential and a distribution along x that is
described well by a Gaussian. Although strongly
localized single particles are known to gener-
ally possess exponential density profiles (7)
with localization lengths x that depend on the
particle energy E, D, and the microscopic dis-
order parameters (16), a theoretical distribution
applicable to our experiment (for example, ac-
counting for a thermal average over particle
energies and localization lengths) is unresolved.
Density profiles are therefore analyzed using a
heuristic fit that reproduces their basic features
(12). The dynamics of the localized component
are measured [after subtracting the mobile com-
ponent from images (12)] using a fit to a distri-
bution proportional to e
x
2
=2s
2
x
jzj=x
z
with an
exponential localization length x
z
and an RMS
radius s
x
along x (Fig. 1, C and D).
As shown in Fig. 2, the size of the localized
component becomes fixed after it rapidly ex-
pands along z for ~25 ms; the transverse size is
approximately constant at the in-trap size. This
apparent lack of diffusion cannot be explained
classically. In a 3D speckle field, there are no
local intensity minima that can trap and classi-
cally localize particles, in contrast to 1D (17, 18)
and 2D (19, 20). Rather, a 3D speckle field con-
sists of a rich collection of topological features,
such as dark optical vortex rings and lines that do
not propagate in a single direction but instead
wander in all three directions on the length scales
associated with z
x
and z
z
(21). Though the vortex
rings can trap particles in a finite volume,
calculations of the percolation threshold for a
3D speckle field establish that less than 0.2% of
the particles are classically trapped for all of the
data presented here (22). The expansion of the
localized component is also inconsistent with
classical dynamics. We numerically simulated clas-
sical trajectories in a 3D speckle potential for a
thermal ensemble of particles under the conditions
used for the data in Fig. 2C (12). The simulated
sizes after expansion (solid lines) are incom-
patible with the observed dynamics of the local-
ized component.
Based on the expansion dynamics, we inter-
pret the localized component as being composed
of particles with energies below the mobility
edge E
c
and atoms with higher energy constitut-
ing the mobile component. The density profile of
the localized component after expansion can be
clearly understood in this context. The Gaussian
distribution along x is stationary because the
transverse localization lengths are much smaller
than the initial size of the gas; the observed pro-
file cannot be explained by diffusion strongly
suppressed via localization solely in z (12). The
profile along z results from a thermal average of
exponentially localized wave functions with
much longer localization lengths, distributed
such that the overall profile is approximately
exponential. A disparity in localization lengths
between x and z is expected because l
B
, which
controls the localization length and the range of
energies over which it diverges when E ~ E
c
,
strongly depends on the disordered potential cor-
relation length. At low energies, l
B
z
2
, and at
high energies, l
B
z
5
(in the weak scattering
limit) (16); thus, the typical localization length
should be at least 36 times larger along z.
Fig. 2. Dynamics of the localized com-
ponent for a 390-nK gas with D =
k
B
600 nK. Slices through an image
taken before release from the trap
(black) and after the gas has ex-
panded for 40 ms (red) and 140 ms
(blue) along the x (A) and z (B)
directions. The wavelength of the
imaging laser was changed to
reduce the optical depth of the
in-trap image by a factor of 15.
The decrease in optical depth be-
tween 40 and 140 ms is a conse-
quence of atoms slowly decaying
from the localized component. (C)
The measured localization length
x
z
(red circles) and RMS size s
x
(black squares) of the localized
component for variable hold time
in the speckle potential. Each point
is determined from an average of
six images; the error bars (not visi-
ble for every point) in all figures
are the standard error unless other-
wise specified. The simulated classi-
cal expansion (solid lines) ignores rapid ballistic motion at short times, which lasts for several milliseconds
along z.
O
p
t
i
c
a
l

D
e
p
t
h
Hold Time (ms)
C
A
B
X Z
m
)
z
m
)
x
200 m
Fig. 3. (A) Fraction of atoms in the
localized component measured af-
ter 20 ms of expansion into the
disordered potential for varying D
and T = 240 T 20 nK (blue circles),
480 T 20 nK (green squares), 1130 T
60 nK (orange triangles), and 1470 T
230 nK (red diamonds). Each point is
determined from fits to five images.
The growing localized fraction with
increasing D is evident in the insets
to (B), which are images (with a false-
color logarithmic scale) taken at T =
480 nK and D = k
B
0 (i), 80 (ii), 160
(iii), and 320 nK (iv). (B) Using the
data in (A), the mobility edge E
c
is
determined at each D. Each point is a
weighted average of E
c
, accounting
for the uncertainty in T and localized
fraction. The error bars are the range
of E
c
for the different temperatures
that contribute to each point.
L
o
c
a
l
i
z
e
d

F
r
a
c
t
i
o
n
A
B
B
/k (nK)
E

/
k

(
n
K
)
B
c
i ii iii iv
REPORTS
By measuring the fraction of localized par-
ticles, we determine the mobility edge that sep-
arates localized from extended states. The mobility
edge we observe is unrelated to a similar quantity
in 1D (5) that results from correlations in the dis-
ordered potential (23). In 1D, an effective mobility
edge arises because the quantum scattering gen-
erating back reflections becomes higher-order
above a momentum cutoff determined by the
Fourier spectrum of the speckle potential. We
measure the localized fraction after the atoms are
held in the speckle potential for 20 ms to resolve
the mobile component and to minimize the impact
of decay of atoms from the localized component
(evident in Fig. 2, A and B). This decay to finite
localized fraction at long times is characterized by
a 30- to 50-ms exponential time constant, does not
strongly depend on temperature, and may partly
arise from the atoms sampling lower-intensity
regions away fromthe center of the speckle field.
Figure 3A shows the fraction of localized atoms
determined from fits to density profiles (12) for
temperatures spanning 200 to 1500 nK and across
the full range of accessible disorder energy. More
particles are localized as D is increased and E
c
correspondingly grows, or as T is decreased and
fewer particles are thermally excited above E
c
.
The mobility edge is determined from each
point in Fig. 3A by calculating the momentum
cutoff
2mE
c
p
required to achieve the measured
fraction of localized particles for a 3D spherically
symmetric Gaussian momentum distribution
consistent with the temperature (12). Figure 3B
shows E
c
averaged across data taken at different
temperatures for a fixed D. Whereas E
c
increases
with D, it does not follow the prediction that
E
c
D
2
from the self-consistent Born approx-
imation (24) and weak-scattering theory (16);
for D k
B
80 nK, the data fit well to a power
law with E
c
D
0.59 T 0.02
(dashed line in Fig.
3B). Although these approaches are broadly ap-
plied to localization, this disagreement is prob-
ably a result of their failure, precisely in the
regime of AL. How D affects E
c
has not been
predicted for the strongly localized regime that
we probe here.
The dependence of the measured localization
length on the disorder strength and particle en-
ergy (controlled by changing temperature) is
shown in Fig. 4. Although data are only shown
for a limited range of D and T, the observed qual-
itative behaviorthat x
z
increases with T and
decreases with Dis characteristic of the entire
range of parameters explored here. Extracting
universal parameters from the data shown in
Fig. 4 is difficult in the absence of theory, be-
cause the measured quantities are averaged across
all particle energies present in the gas. The general
monotonic trends, however, are consistent with a
weak-scattering picture, in which the localization
length is controlled by I
B
E
p
=D
2
(16) at low
energy.
The variation of the speckle intensity across
the gas is a complication that may affect the
interpretation of the data shown in Figs. 3 and
4. Though we have used the central speckle
intensity D as a single parameter to character-
ize the disorder strength in Figs. 3 and 4, the
speckle envelope causes a range of speckle
intensities to be sampled by the atoms. The ef-
fect of the transverse speckle envelope is minor,
because s
x
35 mm, which is small compared
with the Gaussian waist. However, the maxi-
mum localization length in z is ~270 mm, which
leads to the disorder energy averaged across
the atomic density distribution being reduced
to ~70% of D; for smaller x
z
, the disorder en-
ergy averaged in this way is closer to D. Al-
though we have determined that this averaging
does not directly affect the measured scaling
of the mobility edge with disorder strength (12),
the effect of the speckle envelope will probably
be important to future comparisons between the-
ory and our data.
In the future, the exquisite control that is
possible over ultracold disordered gases may en-
able measurements to shed new light on aspects
of 3D localization that are not well understood or
are complicated by interparticle interactions or
dissipation in other systems [see (25) for a review].
An important issue that may be addressed if
the single-particle states can be resolved [using
Bragg spectroscopy, for example (26)] is the
critical exponent that controls how the local-
ization length diverges for energies near the
mobility edge. The influence of interparticle
interactions on the localization of fermions, an-
other crucial question, can be studied by the
controlled introduction of a second spin species
of particular interest is the impact of disorder on
the Bose-Einstein condensateBardeen-Cooper-
Schrieffer crossover [see (27, 28) and references
therein]. Finally, the impact of finite correla-
tions in the disordered potential may be inves-
tigated with the use of simple Gaussian or more
complex holographic optics (29).
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Acknowledgments: We thank L. Sanchez-Palencia for
stimulating discussions and M. White and P. Koehring for
technical assistance. We acknowledge funding from the
Defense Advanced Research Projects Agency Optical
Lattice Emulator program, the Office of Naval Research
(award N000140911023), and the NSF (award
0855027). The data presented in this paper are available
for download at www.illinois.edu/~bdemarco.
27 May 2011; accepted 15 August 2011
10.1126/science.1209019
Fig. 4. Dependence of the measured local-
ization length x
z
on disorder strength D at
fixed temperature T =480 nK(green squares)
and on T at fixed D = k
B
480 nK (open
circles). The green points are from the same
data set as in Fig. 3A, and the black points are
an average of 10 experimental realizations.
The error bars in T are fromthe uncertainty in
the thermal-expansion velocity.
T (nK)
/k (nK)
B
m
)
z
REPORTS
Detection of Pulsed Gamma Rays
Above 100 GeV from the Crab Pulsar
The VERITAS Collaboration; E. Aliu,
1
T. Arlen,
2
T. Aune,
3
M. Beilicke,
4
W. Benbow,
5
A. Bouvier,
3
S. M. Bradbury,
6
J. H. Buckley,
4
V. Bugaev,
4
K. Byrum,
7
A. Cannon,
8
A. Cesarini,
9
J. L. Christiansen,
10
L. Ciupik,
11
E. Collins-Hughes,
8
M. P. Connolly,
9
W. Cui,
12
R. Dickherber,
4
C. Duke,
13
M. Errando,
1
A. Falcone,
14
J. P. Finley,
12
G. Finnegan,
15
L. Fortson,
16
A. Furniss,
3
N. Galante,
5
D. Gall,
22
K. Gibbs,
5
G. H. Gillanders,
9
S. Godambe,
15
S. Griffin,
17
J. Grube,
11
R. Guenette,
17
G. Gyuk,
11
D. Hanna,
17
J. Holder,
18
H. Huan,
19
G. Hughes,
20
C. M. Hui,
15
T. B. Humensky,
19
A. Imran,
21
P. Kaaret,
22
N. Karlsson,
16
M. Kertzman,
23
D. Kieda,
15
H. Krawczynski,
4
F. Krennrich,
21
M. J. Lang,
9
M. Lyutikov,
12
A. S Madhavan,
21
G. Maier,
20
P. Majumdar,
2
S. McArthur,
4
A. McCann,
17
* M. McCutcheon,
17
P. Moriarty,
24
R. Mukherjee,
1
P. Nuez,
15
R. A. Ong,
2
M. Orr,
21
A. N. Otte,
3
* N. Park,
19
J. S. Perkins,
5
F. Pizlo,
12
M. Pohl,
20,25
H. Prokoph,
20
J. Quinn,
8
K. Ragan,
17
L. C. Reyes,
19
P. T. Reynolds,
26
E. Roache,
5
H. J. Rose,
6
J. Ruppel,
25
D. B. Saxon,
18
M. Schroedter,
5
* G. H. Sembroski,
12
G. D. entrk,
27
A. W. Smith,
7
D. Staszak,
17
G. Tei,
17
M. Theiling,
12
S. Thibadeau,
4
K. Tsurusaki,
22
J. Tyler,
17
A. Varlotta,
12
V. V. Vassiliev,
2
S. Vincent,
15
M. Vivier,
18
S. P. Wakely,
19
J. E. Ward,
8
T. C. Weekes,
5
A. Weinstein,
21
T. Weisgarber,
19
D. A. Williams,
3
B. Zitzer
7
We report the detection of pulsed gamma rays from the Crab pulsar at energies above
100 gigaelectron volts (GeV) with the Very Energetic Radiation Imaging Telescope Array
System (VERITAS) array of atmospheric Cherenkov telescopes. The detection cannot be explained
on the basis of current pulsar models. The photon spectrum of pulsed emission between
100 megaelectron volts and 400 GeV is described by a broken power law that is statistically
preferred over a power law with an exponential cutoff. It is unlikely that the observation can
be explained by invoking curvature radiation as the origin of the observed gamma rays above
100 GeV. Our findings require that these gamma rays be produced more than 10 stellar radii
from the neutron star.
P
ulsars were first discovered more than 40
years ago (1) and are now believed to be
rapidly rotating, magnetized neutron stars.
Within the corotating magnetosphere, charged
particles are accelerated to relativistic energies
and emit nonthermal radiation from radio waves
through gamma rays. Although this picture re-
flects the broad scientific consensus, the details are
still very much a mystery. For example, a number
of models exist that can be distinguished from
each other on the basis of the location of the ac-
celeration zone. Popular examples include the outer-
gap model (25), the slot-gap model (6, 7), and
the pair-starved polar-cap model (810). One way
to better understand the dynamics within the mag-
netosphere is through observation of gamma rays
emitted by the accelerated particles.
All of the detected gamma-ray pulsars in (11)
exhibit a break in the spectrum between a few
hundred MeVand a few GeV, with a rapidly fad-
ing flux above the break. The break energy is re-
lated to the maximum energy of the particles and
to the efficiency of the pair production. Mapping
the cutoff can help to constrain the geometry of
the acceleration region, the gamma-ray radiation
mechanisms, and the attenuation of gamma rays.
Previous measurements of the spectral break are
statistically compatible with an exponential or sub-
exponential cutoff, which is currently the most
favored shape for the spectral break.
One of the most powerful pulsars in gamma
rays is the Crab pulsar (12, 13), PSRJ0534 +2200,
which is the remnant of a historical supernova
that was observed in the year 1054. It is located
at a distance of 6500 T 1600 light-years (1 light-
year = 9.46 10
15
m) and has a rotation period
of ~33 ms, a spin-down power of 4.6 10
38
erg s
1
, and a surface magnetic field of 3.8
10
12
G (14, 15). Attempts to detect pulsed gam-
ma rays above 100 GeV from the Crab pulsar
began decades ago (16). Before the work re-
ported here, the highest energy detection was at
25 GeV (17). At higher energies, near 60 GeV,
only hints of pulsed emission have been reported
in two independent observations (17, 18). Al-
though Fermi-LAT measurements of the Crab
pulsar spectrum are consistent, within the errors
of the measurements, with a power law with an
exponential cutoff at about 6 GeV (13), the flux
measurements above 10 GeVare systematically
higher than the fit with an exponential cutoff,
which hints that the spectrum is indeed harder
than a power law with an exponential cutoff
(13, 17). However, the sensitivity of the previous
data was insufficient to allow a definite conclu-
sion about the spectral shape.
We observed the Crab pulsar with the Very
Energetic Radiation Imaging Telescope Array
System (VERITAS) for 107 hours between Sep-
tember 2007 and March 2011. VERITAS is a
ground-based gamma-ray observatory composed
of an array of four atmospheric Cherenkov tel-
escopes located in southern Arizona, USA (19).
VERITAS has a trigger threshold of 100 GeV.
Most of the data, 77.7 hours, were recorded af-
ter the relocation in summer 2009 of one of
the VERITAS telescopes, which resulted in a
lower energy threshold and better sensitivity of
the array. We processed the recorded atmospheric
shower images with a standard moment anal-
ysis (20) and calculated the energy and arrival
direction of the primary particles (21). We then
rejected events caused by charged cosmic-ray
events. For gamma rays, the distribution of the
remaining, or selected, events as a function of
energy peaks at 120 GeV. In the pulsar analysis,
for each selected event, we first transformed the
arrival time to the barycenter of the solar system
and then calculated the spin phase of the Crab
pulsar from the barycentered time using con-
temporaneously measured spin-down parame-
ters (22, 23). All steps in the analysis have been
cross-checked by an independent software pack-
age and are explained in detail in the supporting
online material (SOM). We applied the H test
(24) to evaluate periodic emission at the frequen-
cy of the Crab pulsar (SOM). This yielded a test
value of 50, which corresponded to a significance
of 6.0 SD that pulsed emission is present in
the data.
The phase-folded event distribution, hereafter
pulse profile, of the selected VERITAS events is
shown in Fig. 1. The most significant structures
are two pulses with peak amplitudes at phase 0.0
and phase 0.4. These coincide with the locations
1
Department of Physics and Astronomy, Barnard College,
Columbia University, NY 10027, USA.
2
Department of Physics
and Astronomy, University of California, Los Angeles, CA
90095, USA.
3
Santa Cruz Institute for Particle Physics and
Department of Physics, University of California, Santa Cruz,
Santa Cruz, CA 95064, USA.
4
Department of Physics, Washing-
ton University, St. Louis, MO 63130, USA.
5
Fred Lawrence
Whipple Observatory, Harvard-Smithsonian Center for Astrophysics,
Amado, AZ 85645, USA.
6
School of Physics and Astronomy,
University of Leeds, Leeds LS2 9JT, UK.
7
Argonne National Labo-
ratory, 9700SouthCass Avenue, Argonne, IL 60439, USA.
8
School
of Physics, University College Dublin, Belfield, Dublin 4, Ireland.
9
School of Physics, National University of Ireland Galway, Uni-
versity Road, Galway, Ireland.
10
Physics Department, California
Polytechnic State University, San Luis Obispo, CA 94307, USA.
11
Astronomy Department, Adler Planetarium and Astronomy
Museum, Chicago, IL 60605, USA.
12
Department of Physics,
Purdue University, West Lafayette, IN 47907, USA.
13
Department
of Physics, Grinnell College, Grinnell, IA 501121690, USA.
14
Department of Astronomy and Astrophysics, 525 Davey Lab,
Pennsylvania State University, University Park, PA 16802, USA.
15
Department of Physics and Astronomy, University of Utah,
Salt Lake City, UT 84112, USA.
16
School of Physics and Astron-
omy, University of Minnesota, Minneapolis, MN 55455, USA.
17
Physics Department, McGill University, Montreal, Quebec H3A
2T8, Canada.
18
Department of Physics and Astronomy and the
Bartol Research Institute, University of Delaware, Newark, DE
19716, USA.
19
Enrico Fermi Institute, University of Chicago,
Chicago, IL 60637, USA.
20
Deutsches Elektronen Synchrotron,
Platanenallee 6, 15738 Zeuthen, Germany.
21
Department of Phys-
ics andAstronomy, Iowa State University, Ames, IA 50011, USA.
22
Department of Physics and Astronomy, University of Iowa,
Van Allen Hall, Iowa City, IA 52242, USA.
23
andAstronomy, DePauwUniversity, Greencastle, IN461350037,
USA.
24
Department of Life and Physical Sciences, Galway-Mayo
Institute of Technology, DublinRoad, Galway, Ireland.
25
Institut fr
PhysikundAstronomie, Universitt Potsdam, 14476Potsdam-Golm,
Germany.
26
Department of Applied Physics and Instrumentation,
Cork Institute of Technology, Bishopstown, Cork, Ireland.
27
Depart-
ment of Physics, Columbia University, New York, NY 10027.
nepomuk.otte@gmail.com (A.N.O.); mccann@hep.physics.
mcgill.ca (A.M.); schroedter@veritas.sao.arizona.edu (M.S.)
REPORTS
of the main pulse and interpulse, hereafter P1 and
P2, which are the two main features in the pulse
profile of the Crab pulsar throughout the electro-
magnetic spectrum. We characterized the pulse
profile using an unbinned maximum-likelihood
fit (SOM). In the fit, the pulses were modeled
with Gaussian functions, and the background
was determined from the events that fell between
phases 0.43 and 0.94 in the pulse profile (re-
ferred to as the off-pulse region). The positions
of P1 and P2 in the VERITAS data thus lie at
the phase values 0.0026 T 0.0028 and 0.3978 T
0.0020, respectively, and are shown by the ver-
tical lines (Fig. 1). The full widths at half max-
imum (FWHM) of the fitted pulses are 0.0122 T
0.0035 and 0.0267 T 0.0052, respectively. The
pulses are narrower by a factor of two to three
than those measured by the Fermi Large Area
Telescope (Fermi LAT) at 100 MeV (13) (Fig. 1).
If gamma rays observed at the same phase are
emitted by particles that propagate along the same
magnetic field line (25) and if the electric field in
the acceleration region is homogeneous, then a
possible explanation of the observed narrowing
Phase
-1 -0.5 0 0.5 1
C
o
u
n
t
s

p
e
r

B
i
n
3100
3200
3300
3400
3500
3600
3700
Phase
-1 -0.5 0 0.5 1
C
o
u
n
t
s

p
e
r

B
i
n
3100
3200
3300
3400
3500
3600
3700
VERITAS > 120 GeV
Phase
-1 -0.5 0 0.5 1
0
500
1000
1500
2000
Fermi > 100 MeV
C
o
u
n
t
s

p
e
r

B
i
n
Phase
-0.1 -0.05 0 0.05 0.1
C
o
u
n
t
s

p
e
r

B
i
n
1500
1550
1600
1650
1700
1750
1800
1850
1900
1950
P1
VERITAS > 120 GeV
Phase
-0.1 -0.05 0 0.05 0.1
0
500
1000
1500
2000
C
o
u
n
t
s

p
e
r

B
i
n
Fermi > 100 MeV
Phase
0.3 0.35 0.4 0.45 0.5
C
o
u
n
t
s

p
e
r

B
i
n
1500
1550
1600
1650
1700
1750
1800
1850
1900
1950
P2
VERITAS > 120 GeV
Phase
0.3 0.35 0.4 0.45 0.5
0
200
400
600
C
o
u
n
t
s

p
e
r

B
i
n
Fermi > 100 MeV
A
B C
Fig. 1. Pulse profile of the Crab pulsar. Phase 0 is the position of P1 in radio.
The shaded histograms show the VERITAS data. The pulse profile in (A) is
shown twice for clarity. The dashed horizontal line shows the background level
estimated from data in the phase region between 0.43 and 0.94. (B and C)
Expanded views of the pulse profile with a finer binning than in (A) and are
centered at P1 and P2, which are the two dominant features in the pulse profile
of the Crab pulsar. The data above 100 MeV from the Fermi LAT (13, 30) are
shown beneath the VERITAS profile. The vertical dashed lines in the panels (B)
and (C) mark the best-fit peak positions of P1 and P2 in the VERITAS data. The
solid black line shows the result of an unbinned maximum-likelihood fit of
Gaussian functions to the VERITAS pulse profile (described in text). The peak
positions for the Fermi-LAT and the VERITAS data agree within uncertainties.
REPORTS
is that the region where acceleration occurs tapers.
However, detailed calculations are necessary to
explain fully the observed pulse profile.
Along with the observed differences in the
pulse width, the amplitude of P2 is larger than
P1 in the profile measured with VERITAS, in
contrast to what is observed at lower gamma-ray
energies where P1 dominates (Fig. 1). It is known
that the ratio of the pulse amplitudes changes as
a function of energy above 1 GeV (13) and be-
comes near unity for the pulse profile integrated
above 25 GeV (17). To quantify the relative in-
tensity of the two peaks above 120 GeV, we in-
tegrated the pulsed excess between phase 0.013
and 0.009 for P1 and between 0.375 and 0.421
for P2. This is the T2 SD interval of each pulse
as determined from the maximum-likelihood fit.
The ratio of the excess events and thus the inten-
sity ratio of P2/P1 is 2.4 T 0.6. If one assumes
that the differential energy spectra of P1 and P2
above 25 GeV can each be described with a
power law, F(E) ~ E
a
and that the intensity
ratio is exactly unity at 25 GeV (17), then the
spectral index a of P1 must be smaller than the
spectral index of P2 by a
P2
a
P1
= 0.56 T 0.16.
We measured the gamma-ray spectrum above
100 GeV by combining the pulsed excess in the
phase regions around P1 and P2. This can be
considered a good approximation of the phase-
averaged spectrum because no bridge emis-
sion, which is observed at lower energies, is seen
between P1 and P2 in the VERITAS data. How-
ever, the existence of a constant flux component
that originates in the magnetosphere cannot be
excluded and would be indistinguishable from
the gamma-ray flux from the nebula. Figure 2
shows the VERITAS phase-averaged spectrum
together with measurements made with Fermi
LAT and the Major Atmospheric Gamma-ray Im-
aging Cherenkov telescope (MAGIC). In the en-
ergy range between 100 GeV and 400 GeV
measured by VERITAS, the energy spectrum
is well described by a power law F(E) = A(E/150
GeV)
a
, with A = (4.2 T 0.6
stat
+ 2.4
syst
1.4
syst
)
10
11
TeV
1
cm
2
s
1
and a = 3.8 T 0.5
stat
T
0.2
syst
. At 150 GeV, the flux from the pulsar is
~1% of the flux from the nebula. The detection
of pulsed gamma-ray emission between 200 GeV
and 400 GeV, the highest energy flux point, is
only possible if the emission region is at least
10 stellar radii from the stars surface (26). Using
calculations from (27), the emission region can even
be constrained to be at least 30 to 40 stellar radii.
Combining the VERITAS data with the Fermi-
LAT data we can place a stringent constraint on
the shape of the spectral turnover. The previ-
ously favored spectral shape of the Crab pulsar
above 1 GeV was an exponential cutoff F(E) =
A(E/E
0
)
a
exp(E/E
c
), which is a good parame-
terization of the Fermi LAT (13) and MAGIC
(17) data. The Fermi-LAT and MAGIC data can
be equally well parameterized by a broken power
law, but those data are not sufficient to signif-
icantly distinguish between a broken power law
and an exponential cutoff. The VERITAS data,
on the other hand, clearly favor a broken power
law as a parameterization of the spectral shape.
The fit of the VERITAS and Fermi-LAT data
with a broken power law of the form A(E/E
0
)
a
/
[1 + (E/E
0
)
a-b
] results in a c
2
value of 13.5 for
15 degrees of freedom with the fit parameters
A= (1.45 T 0.15
stat
) 10
5
TeV
1
cm
2
s
1
, E
0
=
4.0 T 0.5
stat
GeV, a = 1.96 T 0.02
stat
and b =
3.52 T 0.04
stat
(Fig. 2). A corresponding fit with
a power law and an exponential cutoff yields a
c
2
value of 66.8 for 16 degrees of freedom. The
fit probability of 3.6 10
8
derived from the c
2
value excludes the exponential cutoff as a viable
parameterization of the Crab pulsar spectrum.
The detection of gamma-ray emission above
100 GeV provides strong constraints on the
gamma-ray radiation mechanisms. If one assumes
a balance between acceleration gains and radia-
tive losses by curvature radiation, the break in
the gamma-ray spectrumis expected to be at E
br
=
150 GeV h
3/4
sqrt(x), where h is the acceleration
efficiency (h < 1) and x is the radius of curvature
in units of the light-cylinder radius (28) (SOM).
Only in the extreme case of an acceleration field
that is close to the maximumallowed value and a
radius of curvature that is close to the light-cylinder
radius would it be possible to produce gamma-ray
emission above 100 GeVwith curvature radiation.
It is, therefore, unlikely that curvature radiation is
the dominant production mechanism of the ob-
served gamma-ray emission above 100 GeV. A
plausible different radiation mechanismis inverse-
Compton scattering that has motivated previous
searches for pulsed very high energy emission, e.g.,
(29). With regard to the overall gamma-ray produc-
tion, two possible interpretations are that a single
emission mechanism alternative from curvature
radiation dominates at all gamma-ray energies or
that a second mechanismbecomes dominant above
the spectral break energy. It might be possible to
distinguish between the two scenarios with higher-
resolution spectral measurements above 10 GeV.
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Energy (MeV)
3
10
4
10
5
10
6
10
)
-
1

s
-
2

d
F
/
d
E

(
M
e
V

c
m
2
E
-7
10
-6
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-4
10
-3
10
VERITAS, this work
Fermi (Abdo et al, 2010)
MAGIC (Aliu et al. 2008)
MAGIC (Albert et al. 2008)
CELESTE (De Naurois et al. 2002)
STACEE (Oser et al. 2001)
HEGRA (Aharonian et al. 2004)
Whipple (Lessard et al. 2000)
Broken power law fit
Exponential cutoff fit
Energy (MeV)
3
10
4
10
5
10
6
10
2
0
5
10
15
20
Power law with exponential cutoff
Broken power law
Fig. 2. Spectral energy distribution (SED) of the Crab pulsar in gamma rays. VERITAS flux measurements
are shown by the bowtie. The dotted line enclosed by the bow tie gives the best-fit power-law spectrum and
the statistical uncertainties, respectively, for the VERITAS data using a forward-folding method. The solid
red circles show VERITAS flux measurements using a different spectral reconstruction method (SOM). Fermi-
LAT data (13) are given by green squares, and the MAGIC flux point (17) by the solid reddish triangle. The
open symbols are upper limits from the CErenkov Low-Energy Sampling and Timing Experiment (CELESTE)
(31), the High-Energy-Gamma-Ray Astronomy (HEGRA) experiment (32), MAGIC (18), Solar Tower At-
mospheric Cherenkov Effect Experiment (STACEE) (33), and Whipple (29). The result of a fit of the VERITAS
and Fermi-LAT data with a broken power law is given by the solid line, and the result of a fit with a
power-law spectrum multiplied with an exponential cutoff is given by the dashed line. Below the SED,
we plot c
2
values to visualize the deviations of the best-fit parameterization from the Fermi-LAT and
VERITAS flux measurements.
REPORTS
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Cosmic Ray Conference, Mrida, Mexico, 3 to 7 July
2007, vol. 3, p. 1385 (ICRC, Mrida, 2008).
22. A. G. Lyne et al., Mon. Not. R. Astron. Soc. 265, 1003 (1993).
23. Jodrell Bank Crab Pulsar Monthly Ephemeris,
www.jb.man.ac.uk/~pulsar/crab.html.
24. O. C. de Jager, Astrophys. J. 436, 239 (1994).
25. X.-N. Bai, A. Spitkovsky, Astrophys. J. 715, 1282 (2010).
26. M. G. Baring, Adv. Space Res. 33, 552 (2004).
27. K. J. Lee et al., Mon. Notic. Roy. Astron. Soc. 405, 2103
(2010).
28. M. Lyutikov, A. N. Otte, A. McCann, arXiv:1108.3824
(2011).
29. R. W. Lessard et al., Astrophys. J. 531, 942 (2000).
30. The Fermi-LAT pulse profile of the Crab pulsar above
100 MeV that is shown in Fig. 1 is not the original one
from reference (13) but one that has been calculated
with an updated ephemerides that corrects for a small
phase offset that has been introduced in the original
analysis http://fermi.gsfc.nasa.gov/ssc/data/access/lat/
ephems/0534+2200/README.
31. M. de Naurois et al., Astrophys. J. 566, 343 (2002).
32. F. Aharonian et al., Astrophys. J. 614, 897 (2004).
33. S. Oser et al., Astrophys. J. 547, 949 (2001).
Acknowledgments: This research is supported by grants from
the U.S. Department of Energy, NSF, and the Smithsonian
Institution; by Natural Sciences and Engineering Research
Council of Canada; by Science Foundation Ireland (SFI
10/RFP/AST2748); and by the Science and Technology
Facilities Council in the United Kingdom. We acknowledge
the excellent work of the technical support staff at the
Fred Lawrence Whipple Observatory and at the collaborating
institutions in the construction and operation of the
instrument. A.N.O. was supported in part by a Feodor-Lynen
fellowship of the Alexander von Humboldt Foundation.
We are grateful to M. Roberts and A. Lyne for providing us
with Crab-pulsar ephemerides before the public ones
became available.
SOM Text
Figs. S1 to S4
References (3436)
10.1126/science.1208192
Dispersible Exfoliated Zeolite
Nanosheets and Their Application
as a Selective Membrane
Kumar Varoon,* Xueyi Zhang,* Bahman Elyassi, Damien D. Brewer, Melissa Gettel,
Sandeep Kumar, J. Alex Lee, Sudeep Maheshwari,|| Anudha Mittal, Chun-Yi Sung,
Matteo Cococcioni, Lorraine F. Francis, Alon V. McCormick, K. Andre Mkhoyan, Michael Tsapatsis
Thin zeolite films are attractive for a wide range of applications, including molecular sieve
membranes, catalytic membrane reactors, permeation barriers, and low-dielectric-constant
materials. Synthesis of thin zeolite films using high-aspect-ratio zeolite nanosheets is desirable
because of the packing and processing advantages of the nanosheets over isotropic zeolite
nanoparticles. Attempts to obtain a dispersed suspension of zeolite nanosheets via exfoliation
of their lamellar precursors have been hampered because of their structure deterioration and
morphological damage (fragmentation, curling, and aggregation). We demonstrated the synthesis
and structure determination of highly crystalline nanosheets of zeolite frameworks MWW and MFI.
The purity and morphological integrity of these nanosheets allow them to pack well on porous
supports, facilitating the fabrication of molecular sieve membranes.
H
igh-aspect-ratio zeolite single crystals
with thickness in the nanometer range
(zeolite nanosheets) are desirable for ap-
plications including building blocks for hetero-
geneous catalysts (13) and the fabrication of
thin molecular sieve films and nanocomposites
for energy-efficient separations (4). They could
also be of fundamental importance in probing
the mechanical, electronic, transport, and catalytic
properties of microporous networks at the nano-
scale (5, 6). Despite steady advances in the prep-
aration and characterization of layered materials
containing microporous layers and of their pil-
lared and swollen analogs (13, 717), the syn-
thesis of suspensions containing discrete, intact,
nonaggregated zeolite nanosheets has proven
elusive because of structural deterioration and/or
aggregation (18) of the lamellae upon exfoliation.
Here, we report the isolation and structure deter-
mination of highly crystalline zeolite nanosheets
of the MWW and MFI structure types, and we
demonstrated the use of their suspensions in the
fabrication of zeolite membranes.
MWW and MFI nanosheets were prepared
starting fromtheir corresponding layered precursors
ITQ-1 (1) and multilamellar silicalite-1 (3), respec-
tively. Before exfoliation by melt blending with
polystyrene (weight-average molecular weight =
45000 g/mol), ITQ-1 was swollen according to a
previously reported procedure (18); multilamellar
silicalite-1 was used as made. Melt blending was
performed under a nitrogen environment in a co-
rotating twin screw extruder with a recirculation
channel (19). The polystyrene nanocomposites
obtained by melt blending were characterized by
x-ray diffraction (XRD), and microtomed sections
were imaged by transmission electron micros-
copy (TEM) to reveal the presence of exfoliated
MWW and MFI nanosheets embedded in the
polymer matrix (figs. S1 and S2).
To obtain a dispersion of these nanosheets,
the nanosheet-polystyrene nanocomposites were
placed in toluene and sonicated. After polymer
dissolution and removal of the larger particles
by centrifugation, the dispersions, containing ap-
proximately 1.25%w/wpolymer and 0.01%w/w
nanosheets, were used to prepare samples for
TEM and atomic force microscopy (AFM) exam-
ination, by drying a droplet on TEM grids and
freshly cleaved mica surfaces, respectively (the
AFM sample was calcined in air at 540C to
remove polymer). Low-magnification TEM im-
ages of high-aspect-ratio MWW and MFI nano-
sheets reveal their flakelike morphology (Fig. 1,
A and B). The uniform contrast from isolated
nanosheets suggests uniform thickness, whereas
the darker areas can be attributed to overlapping
of neighboring nanosheets. Although lattice fringes
are not easily visible in the high-resolution TEM
(HRTEM) images of the nanosheets (figs. S3A
and B), they do exist, as confirmed by their fast
Fourier transform (FFT) (figs. S3C and D). In
addition, electron diffraction (ED) from single
MWWand MFI nanosheets (Fig. 1, Cto E, and G)
and XRD data obtained from calcined powders
of MWWand MFI nanosheets (Fig. 2, A and B)
confirm that the nanosheets are highly crystal-
line materials of the MWW and MFI type, re-
spectively. The thin dimensions of MWW and
MFI nanosheets, as expected, are along the c
and b axes, respectively, as indicated from the
FFT of the HRTEM images and the ED data.
AFM measurements, calibrated using steps
formed on freshly cleaved mica (20), revealed
Department of Chemical Engineering and Materials Science,
University of Minnesota, 151 Amundson Hall, 421 Washington
Avenue Southeast, Minneapolis, MN 55455, USA.
*These authors contributed equally to this work.
Present address: Department of Chemical and Environmental
Engineering, University of California, Riverside, 1175 West
Blaine Street, Riverside, CA 92507, USA.
Present address: Material Analysis Laboratory, Intel Corpora-
tion, Hillsboro, OR 97124, USA.
Present address: Department of Chemical and Biomolecular
Engineering, Rice University, MS-362, 6100 Main Street,
Houston, TX 77005, USA.
||Present address: Schlumberger Doll-Research, Schlumberger
Limited, 1 Hampshire Street, Cambridge, MA 02139, USA.
To whom correspondence should be addressed. E-mail:
tsapatsis@umn.edu
REPORTS
remarkable uniformity in nanosheet thickness:
2.6 T 0.3 and 3.4 T 0.3 nm for the MWW and
MFI nanosheets, respectively (Fig. 2, C to E,
and F). The MWW nanosheet thickness is close
to the one expected from the thickness of the
ITQ-1 layers (2). Figure 3, A and B, show side
and top views of the proposed MWW nano-
sheet structure that are consistent with the AFM
measurements and MWW layer structure. The
MFI nanosheet thickness, determined by AFM,
is consistent with 1.5 unit cells along the b axis.
Further examination of the HRTEM images col-
lected here (fig. S4) and of the images given in
(3), in conjunction with the thickness deter-
mined by AFM, suggests the presence of three
complete pentasil chains running along the nano-
sheets. The proposed structure of MFI nano-
sheets based on these data is shown in Fig. 3C
(side viewalong c axis) and Fig. 3D (top view).
A Q
3
/(Q
3
+ Q
4
) ratio of 11% is calculated from
this model, which is in agreement with the
29
Si
magic angle spinning nuclear magnetic reso-
nance data (fig. S5).
The proposed structures of the MWW and
MFI nanosheets are consistent with all the TEM,
ED, and AFM data and the structures of their
precursors (Fig. 3). Optimization of nanosheet
structures using damped-dynamics simulation
by the Car-Parrinello molecular dynamics code
in the Quantum ESPRESSO package (21) [see
details in the supporting online material (SOM)
(22)] led to minor changes (fig. S6) when com-
pared to those obtained by simple termination
of the MWW and MFI structures. More specifi-
cally, the calculated MWW and MFI nanosheet
thicknesses are slightly different as compared to
the ones obtained from the MWW and MFI
frameworks (2.63 nmversus 2.49 nmand 3.20 nm
versus 3.21 nm, respectively), and both are in
agreement with the AFM measurements. The
corresponding ED and XRD patterns from the
optimized structures were simulated [see details
in (22)] and compared to the experimental data.
The ED pattern simulations (Fig. 1, F and H), per-
formed with the Multislice method (23, 24), are in
agreement with the experimental ED patterns
(Fig. 1, E and G). Moreover, XRD simulations
[using the powder pattern theorem, implemented
with the UDSKIP algorithm (25, 26)] are also in
good agreement with the experimental XRDdata
(Fig. 2, Aand B). The positions of the broad peaks
at low angles are very sensitive to the layer thick-
ness and confirm the thickness suggested by
AFM. More specifically, simulations using MFI
nanosheet thicknesses of 1, 1.5, 2.5, and 3.5 unit
cells (fig. S7) showed that the best agreement with
the experimental data is obtained for the 1.5-
unit-cell thickness, whereas the MWW simula-
tions indicated 1-unit-cell thickness. The position
of the sharper peaks at higher angles is insensitive
to the layer thickness. Theyindicate long-range order
preservation upon exfoliation. The XRD analysis
of MFI nanosheets shows sharper reflections as
compared to those of MWW nanosheets, prob-
ably due to the differences in thicknesses and the
Fig. 2. Powder XRD pattern fromMWW nanosheets (A) and MFI nanosheets (B). a.u., arbitrary units. The
bottom traces show experimental XRD patterns (Cu Ka source, wavelength = 1.5418 ) of the powder
obtained by calcination of the nanosheet-polystyrene nanocomposite at 540C. The top traces are the
simulated XRD patterns (powder pattern theorem, implemented with UDSKIP) of the proposed structure of
the nanosheets. AFM(tapping mode) topographical images of MWW and MFI nanosheets are shown in (C)
and (D), respectively. The average step-height (h) data of the area highlighted in (C) and (D) are plotted in
(E) (MWW nanosheet) and (F) (MFI nanosheet). The height data are calibrated using steps formed on
freshly cleaved mica. Scale bars in (C) and (D), 200 nm.
Fig. 1. Low-magnification TEM im-
ages of c-oriented MWW (A) and
b-oriented MFI nanosheets (B).
TEM images of single MWW and
MFI nanosheets are shown in (C)
and (D), respectively. (E) and (G)
are the corresponding ED patterns
of the same particles shown in (C)
and (D), respectively. Simulations
of the ED patterns of proposed
structures of nanosheets down the
c axis (MWW) and b axis (MFI)
are shown in (F) and (H), respec-
tively. Scale bars in (A) to (C),
200 nm; in (D), 50 nm; in (E) and
(G), 1 nm
1
.
REPORTS
better structural preservation of MFI nanosheets.
The latter could be attributed to the absence of
the swelling step in their processing.
Previous attempts to obtain exfoliated nano-
sheets of MWW have had only partial success
because of the fragmentation, aggregation, and
curling of the lamellae (13, 19, 27), whereas
exfoliation of lamellar silicalite-1 has not been
reported before. Our attempts to remove the
polystyrene by methods that include calcination
or other thermal treatments of the nanosheet-
polymer nanocomposite resulted in particles
that exhibited significant curling (fig. S8, A and
B). The presence of curled particles is detrimental
to the quality of coatings, because the curled par-
ticles neither pack nor orient themselves in their
coatings (fig. S8, C and D). However, the disso-
lution and purification process reported here
was sufficient to obtain flat, crystalline, exfoliated
nanosheets capable of producing a highly packed
and oriented coating.
The presence of microporosity (fig. S9) with-
in the MWW and MFI layers imparts molec-
ular sieving and hosting capabilities and thus
expands the list of available nanosheets amena-
ble to layer-by-layer assembly (28, 29) for the
fabrication of nanocomposites. Moreover, be-
cause of their large lateral area and small thick-
ness, the zeolite nanosheets can coat porous
substrates to form well-packed thin deposits. As
a result, these nanosheets are attractive materials
for the fabrication of thin zeolite membranes. For
example, simple filtration of the MFI nanosheet
suspension through an anodized alumina mem-
brane (Anopore, pore size 200 nm) followed by
calcination for polymer removal resulted in a
uniform, well-packed deposit consisting of high-
ly oriented, overlapping, flat nanosheets (Fig. 4A).
Even rough porous substrates, such as homemade
a-alumina supports with ~200-nm pores, can be
coated by filtration to obtain smooth films (Fig. 4,
B to D, and E). Figure 4B is a top-view scanning
electron microscope (SEM) image of an MFI
nanosheet coating on a-alumina, indicating uni-
form surface coverage. Because the nanosheets
are very thin, secondary electrons from the un-
derlying nanosheets can be observed marking
their morphology and underscoring the overlap.
Cross sections cut by focused ion beam (FIB)
were observed by ion-beam microscopy (Fig. 4C)
and TEM (Fig. 4, D and E). We observed no
penetration of the nanosheets in the interior of
the substrate. This is a desirable feature for
forming thin zeolite films to achieve high-flux
membranes. The nanosheets conform to the sub-
strate surface roughness because of their high
aspect ratio and nanometer-range thickness. As
a result, neither masking of the support pores (30)
nor use of smoothened multilayered (asymmetric)
membranes (31) or functionalization (32) is nec-
essary, as in the case of coating from isotropic
zeolite nanoparticles or nonisotropic micro-
particles. However, these films do not show any
selectivity for p-/o-xylene [a typical mixture that
is widely used to assess the molecular sieving
capability of MFI films (33, 34)]. It is evident
from Fig. 4D and the HRTEM image in Fig. 4E
that nanometer-sized gaps exist between the
nanosheets. After a single hydrothermal treat-
ment for 4.5 hours at 90C under conditions
that in the absence of nanosheet coating do not
result in an observable deposit (molar composi-
tion, 60 SiO
2
: 9 tetrapropylammoniumhydroxide:
8100 H
2
O: 240 ethanol; aged at 90Cfor 6 hours),
the MFI nanosheet film thickness remained un-
changed (fig. S10, A to D), whereas the gaps
between the nanosheets were reduced, as sug-
gested by the TEM images of the film cross-
section (figs. S10, D and E) and an improved
separation performance. Five membranes pre-
pared by this method separated xylene isomers
Fig. 3. Relaxed surface structures of the MWW and MFI nanosheets obtained by structure optimization
of the 1-unit-cell-thick MWW and 1.5-unit-cell-thick MFI structures with Car-Parrinello molecular
dynamics. Si, O, and H atoms are colored in yellow, red, and white, respectively. (A and B) MWW
nanosheet viewed along the a (or b) axis (A) and along the c axis (B). (C and D) MFI nanosheet viewed
along the c axis (C) and along the b axis (D).
Fig. 4. Images of the
MFI nanosheet coating
on porous supports. (A)
SEM image (top view)
of the coating of MFI
nanosheets on an Ano-
pore disk. The top half
of the image shows the
bare Anopore support,
whereas the bottom half
shows a uniform coat-
ing of nanosheet on the
200-nmpores of the sup-
port. (B) SEM image (top
view) of the coating of an
MFI nanosheet onahome-
made porous a-alumina
support. (C) FIB image of
the cross section of the
coating in (B). The image
was taken by a Ga ion
source (30 kV) at a tilt
angle of 52. The nano-
sheet coating is sand-
wiched between the
FIB-deposited platinum
(to protect the coating from milling) and the alumina support. (D) TEM image of the cross section of
the coating in (B). The dark layer on top of the coating is FIB-deposited platinum. (E) HRTEM image of the
coating cross section. Scale bars in (A) to (D), 200 nm; in (E), 20 nm.
REPORTS
( p-xylene fromo-xylene) with a p-xylene/o-xylene
separation factor of 40 to 70 and p-xylene per-
meance of 3 10
7
mol m
2
s
1
Pa
1
at 150C
(fig. S11). Preliminary findings fromMWWnano-
sheet coatings show that a seed layer of similar
quality to that of MFI nanosheets can be obtained
(fig. S12A), which, after secondary growth (fig.
S12B), leads to membranes exhibiting molecular
sieving properties (fig. S12, C and D) with ideal
selectivies for He/H
2
and He/N
2
up to 3 and 17,
respectively, which are different from the values
expected from Knudsen diffusion and consist-
ent with the small transport-limited aperture of
MWWalong the c axis.
These findings indicate that the films fab-
ricated using exfoliated zeolite nanosheets exhibit
the expected molecular sieving properties and are
appropriate to be used as membranes. The exfolia-
tion and purification process described here may
also be applicable to other microporous layered
materials to obtain high-aspect-ratio crystalline
nanosheets with high purity and uniformity of
thickness. Moreover, the simple film formation
method introduced, based only on filtration of
the nanosheet suspensions, is likely to be easily
scalable for large-scale membrane formation on
low-cost, commercially available porous supports
with large pores and rough surfaces.
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Acknowledgments: We acknowledge support from the
U.S. Department of Energy (DOE) (grant DE-09FE0001322),
the Petroleum Institute of Abu Dhabi through the ADMIRE
partnership, NSF (grant NSF-NIRT CMMI 0707610),
and the Industrial Partnership for Research in Interfacial
and Material Engineering and Minnesota Supercomputing
Institute at the University of Minnesota. Aspects of this work
(MFI nanosheet synthesis and imaging by TEM) were
supported as part of the Catalysis Center for Energy
Innovation, an Energy Frontier Research Center funded by
DOEs Office of Science, Office of Basic Energy Sciences
under Award Number DESC0001004. Portions of it were
conducted at the University of Minnesota Characterization
Facility, which receives partial support from NSF through
the National Nanotechnology Infrastructure Network.
SOM Text
Figs. S1 to S12
References (3544)
10.1126/science.1208891
A Major Constituent of Brown Algae for
Use in High-Capacity Li-Ion Batteries
Igor Kovalenko,
1
Bogdan Zdyrko,
2
Alexandre Magasinski,
1
Benjamin Hertzberg,
1
Zoran Milicev,
1
Ruslan Burtovyy,
2
Igor Luzinov,
2
* Gleb Yushin
1
*
The identification of similarities in the material requirements for applications of interest and those of living
organisms provides opportunities to use renewable natural resources to develop better materials and design
better devices. In our work, we harness this strategy to build high-capacity silicon (Si) nanopowderbased
lithium (Li)ion batteries with improved performance characteristics. Si offers more than one order of
magnitude higher capacity than graphite, but it exhibits dramatic volume changes during electrochemical
alloying and de-alloying with Li, which typically leads to rapid anode degradation. We show that mixing Si
nanopowder with alginate, a natural polysaccharide extracted from brown algae, yields a stable battery
anode possessing reversible capacity eight times higher than that of the state-of-the-art graphitic anodes.
A
typical procedure for the preparation of
Li-ion battery electrodes includes mixing
electroactive powder with conductive
carbon additives and a polymeric binder dis-
solved in a solvent. The produced slurry is then
cast on metal foil current collectors and dried.
Traditionally, most research has been focused
on synthesis of active powders with improved
properties, and less attention was devoted to the
advancement of the electrically inactive compo-
nents of battery electrodes, such as binders. Yet
recent studies have shown that many important
battery characteristics, including stability and irre-
versible capacity losses, are critically dependent
on the binders properties (14). High-capacity
electrochemically active particles that exhibit
substantial volume changes during insertion and
extraction of Li require improved binder charac-
teristics to ensure electrode integrity during use.
Si, in particular, exhibits the largest volume
changes during Li-ion battery operation. The in-
terest in Si-based anodes (1, 511) stems fromthe
abundance of Si in nature, its low cost, and its
high theoretical capacity, which is an order of
magnitude higher than that of the conventionally
used graphite.
Recent studies have shown that synthetic and
bio-derived polymers that contain carboxy groups,
such as polyacrylic acid (PAA) and carboxy-
methyl cellulose (CMC), demonstrate promising
characteristics as binders for Si-based anodes
(1, 9, 12). Low binder extensibility did not dem-
onstrate a negative effect on the battery perform-
ance (12). Reasonably stable anode performance,
however, could only be achieved when Si vol-
ume changes were minimized by incomplete Li
insertion in the tests (9) or accommodated by the
use of extra-large binder content (1, 13), which
lowers the resulting anode capacity. The polar
hydrogen bonds between the carboxy groups of
the binder and the SiO
2
on the Si surface were
proposed to exhibit a self-healing effect and re-
form if locally broken (1). An alternative expla-
nation for the observed stability of the rigid binders
with lower extensibility could be that Si nano-
particles deform plastically during electrochem-
ical alloying with Li (8), expanding toward the
existing pores between the particles.
Here, we report that alginate, a high-modulus
natural polysaccharide extracted from brown
algae, yields a remarkably stable battery anode.
Unlike many polysaccharides commonly found
1
School of Materials Science and Engineering, Georgia Insti-
tute of Technology, Atlanta, GA 30332, USA.
2
School of
Material Science and Engineering and Center for Optical
Materials Science and Engineering Technologies, Clemson
University, Clemson, SC 29634, USA.
luzinov@clemson.edu (I.L.); yushin@gatech.edu (G.Y.)
REPORTS
in terrestrial plants, alginates, a major constituent
of brown algae (Fig. 1A) and many aquatic mi-
croorganisms, contain carboxylic groups in each
of the polymers monomeric units (Fig. 1A). A
higher content of carboxylic group in the binder
should lead to a larger number of possible binder-
Si bonds and, thus, better Si electrode stability
(1). The extraction of alginates (commonly in a Na
salt form) from algae proceeds by heating algae
in a hot soda (Na
2
CO
3
) solution, which results in
the dissolution of its alginate component. From
a chemical standpoint, alginate (also called al-
ginic acid) is a copolymer of 14 linked b-D-
mannuronic acid (M) and a-L-guluronic acid (G)
residues (Fig. 1A). Different compositions and
sequences of M and G monoblocks in alginates
yield a plethora of physical and biological prop-
erties, optimized in brown algae for a given en-
vironment. For example, algae growing in coastal
areas have higher G content than the same algae
growing in streaming waters (14). Ahigh content
of G makes alginate gels more rigid (14). Mul-
tivalent ions from seawater can cross-link the
matrix, also increasing the rigidity of the plant
body (15).
The ratio of M-to-G monoblocks in alginates
may range from 0.3 to 9, with a typical value in
commercial samples being ~1 (16). Nuclear mag-
netic resonance (NMR) spectroscopy measure-
ments (Fig. 1B) revealed that the ratio of M-to-G
monoblocks in the Na alginate sample used in
this study was 1.13. This ratio was calculated on
the basis of integration of the peaks at 4.7, 5.3,
and 5.7 parts per million (Fig. 1B). Atomic force
microscopy indentation studies showed that in
a dry state, films made of the Na alginate exhib-
ited ~6.7 times higher stiffness than dry films of
polyvinylidene difluoride (PVDF), a common
commercial binder used in Li-ion battery elec-
trodes (Fig. 1, C and E). Interestingly, when im-
mersed into the electrolyte solvent, the stiffness
of alginate did not change appreciably (Fig. 1D),
whereas the PVDF films became nearly 50 times
softer (Fig. 1F). Ellipsometry studies show no
detectable swelling of thin (~70-nm) Na-alginate
films in the electrolyte solvent vapors. In con-
trast, PVDF films of similar thickness attract sub-
stantial amounts of carbonates from the vapor,
demonstrating changes in thicknesses of ~20%.
The negligibly small swellability of the alginate
indicates a low level of polymer/electrolyte inter-
action. This property may prevent undesirable
access of the electrolyte liquid to the binder/Si
interface. The similar behavior of Na-CMCbind-
ers (fig. S1) probably explains their promising
performance with Si anodes as well (1, 9, 17).
Scanning electron microscopy (SEM) studies
showed the majority of Si nanoparticles used in
our studies to be of elliptical or spherical shape
with diameter in the range of 20 to 100 nm (fig.
S2A). X-ray diffraction (XRD) (fig. S2B) studies
revealed no impurities in the nanopowder. The
average Si crystal size was calculated from the
XRD data to be ~37 nm. The shape of the N
2
adsorption/desorption isotherms collected on
the Si nanopowder (type II, according to the
Brunauer classification) is typical for macropo-
rous (>50-nm) solids with unrestricted multi-
layer adsorption (fig. S2C). The specific surface
area of the Si nanopowder calculated with the
Brunauer-Emmett-Teller equation is 96 m
2
/g,
which is much higher than 0.5 to 10 m
2
/g found
in graphites used in Li-ion batteries. Assuming
the density of Si nanoparticles to be 2.3 g/cm
3
,
the average Si particle size can be calculated to
be ~27 nm, which is close to what we observed
with SEM and estimated using XRD measure-
ments. The electrodes prepared using Si nano-
powder, conducive C additives, and Na-alginate
show a uniform structure and a smooth surface
(fig. S2D) with small (<100-nm) pores visible be-
tween the nanoparticles. We estimated the elec-
trode density to be 0.50 g/cm
3
. Assuming the
theoretical density of graphite, Si, and alginate
to be accurate, one can estimate the remaining
pore volume of the electrode to be ~five times the
volume of Si particles. In recent studies on electro-
chemical alloying of Si in a nanoconfined space,
we demonstrated that nano-Si may undergo the
Fig. 1. Alginate origin and
characterization. (A) Giant kelp
forest (Macrocystis pyrifera al-
gae) inthe Pacific Ocean, pho-
tographed near the coast of
California, USA. Theinsets show
the chemical structure of man-
nuronic (left) and guluronic
(right) acids. (B)
1
HNMRspec-
trumof Na-alginate. The num-
bers above the peaks marked
as (a), (b), and (c) correspond
to their integrated intensities.
ppm, parts per million; a.u.,
arbitrary units. (C to F) Com-
parisonbetweenYoungs mod-
ulus of Na-alginate and PVDF
and in a dry [(C) and (E)] and
wet [impregnated with elec-
trolyte solvent, (D) and (F)]
state.
Fig. 2. Spectroscopic characterization of the nano-Si Na-alginate and electrodes prepared by mixing
nano-Si with Na-alginate binder. (A and B) XPS spectra of alginate, Si nanopowder, nano-Si electrode,
and Si nanopowder extracted from the electrode after extensive purification. (C) FTIR spectra of alginate,
Si nanopowder, and nano-Si electrode.
REPORTS
irreversible shape changes upon the initial Li
insertion, adapting to the restricted shape of the
rigid pore (8). In subsequent cycles, however,
the Si-Li alloy may exhibit fully reversible shape
changes (8). Therefore, even if the rigidity of the
alginate binder would prevent electrode expan-
sion upon the first Li insertion, the initial electrode
porosity could offer space to accommodate the
volume changes in Si during cycling.
To evaluate the interactions of Na-alginate
with Si and C particles, we have prepared elec-
trodes consisting of pure Si/alginate and pure
C/alginate mixtures. After drying the electrodes
in vacuum (0.01 Torr) at 105C for 4 hours, we
have immersed pieces of the electrodes in large
beakers filled with deionized (DI) water (alginate
solvent) and stirred for 4 hours. After filtering and
drying in air, the Si (or C) particles were collected,
immersed in DI water, stirred for 4 hours, and fil-
tered. We repeated this procedure five times. Be-
fore spectroscopy measurements, all samples were
dried in a vacuum at 105C for at least 8 hours.
The C
1s
core-level x-ray photoelectron spectros-
copy (XPS) spectra of the alginate and Si-alginate
films showthree characteristic peaks correspond-
ing to ether, hydroxyl, and carboxylate functional
groups (Fig. 2A). As expected, the initial Si pow-
der does not show any signs of C atoms on the
surface. In spite of the extensive purification of
the Si powder after mixing with alginate, the
powder retains substantial content of alginate
residues on the surface (Fig. 2A, top). A com-
parison of the C
1s
spectra of DI water-cleaned
Si nanopowder before and after mixing with Na-
alginate suggests formation of strong hydrogen
bonding between the hydroxylated Si surface
and alginate carboxylic moieties. Somewhat sim-
ilar conclusions could be made by analyzing the
Si
2p
core-level peaks. Before mixing with algi-
nate, the Si nanopowder surface shows a strong
bulk Si peak at ~99.2 eVand a peak correspond-
ing to hydroxyl functional groups at ~103 eV
(Fig. 2B). However, an additional peak corre-
sponding to R(O)-O-Si at 103.9 eV(9) is observed
after mixing Si with Na-alginate and vacuum an-
nealing to form an electrode (Fig. 2B). This peak
is mostly retained after the extensive cleaning
of the Si nanopowder described above (Fig. 2B,
top). Analogous XPS experiments with C addi-
tives (fig. S3) suggest rather similar interactions
between the polar groups and defects on the
carbon surface and alginate moieties.
Fourier transform infrared (FTIR) spectros-
copy studies provide further support for the strong
bonding between the alginate and Si powder. A
Na-alginate filmexhibits a broad absorption band
at ~3320 cm
1
related to hydrogen-bonded O-H
stretching vibrations, a peak at ~1598 cm
1
cor-
responding to O-C-O (carboxylate) asymmetric
vibrations, a peak at ~1410 cm
1
corresponding
to O-C-Osymmetric vibrations, a peak at ~1300
cm
1
related to the C-C-H and O-C-H defor-
mation of pyranose rings, and a peak at ~1028
cm
1
related to C-O-C asymmetric vibrations,
among others (Fig. 2C) (18). After electrode for-
mation, the relative intensity of the 1300 cm
1
peak
related to pyranose-ring deformation vibrations
decreases considerably when compared with pure
Na-alginate. This decrease provides evidence of
a chemical interaction between the alginate and
Si nanoparticles (19). The strong interactions be-
tween the binder and the Si surface have been pre-
viously identified as one of the most critical factors
affecting the stability of Si-based electrodes (1, 9).
Coin cells with metallic Li counter electrode
were employed to evaluate the electrochemical
performance of all of the electrodes. In contrast to
earlier studies on CMC binders, which often
required low Si [33 weight percent (wt %)] and
high binder and carbon-additive (33 wt % each)
content (1, 13), we used a high ratio of Si to C
(Si:C = 3:1) and a considerably smaller amount
of binder (15 wt %) for our tests.
Charge-discharge cycling performed with Li
insertion capacity limited to 1200 mAhour/g Si
showed stable anode performance for more than
1300 cycles (Fig. 3A). In real-life applications,
however, a noticeable variation in the degree of
lithiation of individual Si particles may take place.
Therefore, it is important to test the ability of Si
anodes and Si-binder interface to withstand the
largest volume changes taking place during full
lithiation. In our additional tests (Fig. 3, B to D,
and fig. S4), we inserted Li to nearly 100% depth
of discharge (to 0.01 mV versus Li/Li
+
) and
additionally held the anode at this potential for
more than 10 min. Because the average time of
full Li insertion into 100-nm diameter Si nano-
particles is 6 min (20) and average Si particles in
our electrode are only 27 nm, this procedure
warranted that a large portion of the Si particles
(close to a Cu foil) be fully lithiated. In spite of
the severe testing conditions, an alginate binder
allowed for a stable performance of Si electrodes
(Fig. 3B and fig. S4). This is in contrast to Si
anodes with PVDF and Na-CMC, which demon-
strated poor stability (Fig. 3B). At a current density
of 4200 mA/g, the reversible Li extraction specific
capacity of an alginate-based Si anode is in the
range of 1700 to 2000 mAhour/g (Fig. 3, B and
C, and fig. S4), which is ~five times higher than
the theoretical capacity of graphite and 9 to 23
times higher than the experimentally determined
capacity of graphites (85 to 190 mAhour/g) at
such a high current density. At a smaller current
density of 140 mA/g (Fig. 3C and fig. S4), the
specific capacity of the Si anode reaches 3040
mAhour/g, which is more than 8 times higher
than the theoretical specific capacity of graphite
(372 mAhour/g). The contribution of Si nano-
powder alone could be calculated as ~4000
mAhour/g, which is consistent with observations
on other nano-Si materials (1, 7, 8) but is notice-
ably higher than what was previously observed
for micron-size Si (21). The volumetric anode ca-
pacity was determined to be ~1520 mAhour/cm
3
at 140 mA/g current density, which is 2.5 times
higher than ~620 mAhour/cm
3
for graphitic
anodes.
We propose that a stable binder for Si anodes
needs to posses several critical properties. First, a
very weak binder-electrolyte interaction is needed
for the long-termanode stability. All of the binders
Fig. 3. Electrochemical performance of alginate-based nano-Si electrodes (electrode density = 0.50 g/cm
3
,
weight ratio of Si:C = 3:1). (A) Reversible Li-extraction capacity and CE of the nano-Si electrodes versus cycle
number for Li insertion level fixed to 1200 mAhour/g Si (Ah, ampere hour). (B) Reversible Li-extraction
capacity of nano-Si electrodes with alginate, CMC, and PVDF binders versus cycle number collected for the
current density of 4200 mA/g for cells cycled in the potential window of 0.01 to 1 V versus Li/Li
+
. (C)
Galvanostatic discharge profiles of the nano-Si electrode at different current densities between 0 and 1 V.
(D) Differential capacity curves of the nano-Si electrode in the potential window of 0 to 1 V versus Li/Li
+
collected at the rate of 0.025 mV/s after the first galvanostatic charge-discharge cycle. Q/m, specific capacity;
V, voltage. All electrochemical measurements were performed at room temperature in two-electrode 2016
coin-type half-cells. In (A), the capacity is reported for the Si contribution only. In (B) to (D), the capacity is
normalized by the total weight of Si and C additives.
REPORTS
that provide at least satisfactory performance in
Si anodes (including CMC and PAA) experience
virtually no swelling in commonly used electro-
lytes (Fig. 1 and fig. S1) (12). If a solvent reaches
the Si electrode surface by permeating through a
binder layer, it decomposes (2224). The solvent-
decomposition products deposited in the region
between the binder and the Si would substantially
weaken the Si-binder bond strength and lead to
rapid anode degradation (PVDFinFig. 3B). There-
fore, little-to-no interaction between the binder
and the solvent is needed to prevent access of
the solvent molecules to the Si-binder boundary.
Another property of an ideal Si binder is to
provide access of Li ions to the Si surface. There-
fore, if a binder is not permeable to solvent elec-
trolyte molecules, it should either cover only a
portion of the Si surface or remain permeable to
Li ions. Due to the small size of Si nanopowder
and its resultant high surface curvature, the num-
ber of anchor points between binder polymeric
chains and Si particles is limited, suggesting
that a portion of the Si surface should indeed
be directly exposed to the electrolyte. Our XPS
studies on alginate-coated Si particles showthat a
portion of Si surface is alginate-free (Fig. 2B). To
identify the conductivity of Li-ions through Na-
alginate, we deposited a thin (1-mm) layer on
Cu foil and performed cyclic voltammetry and
electrochemical-impedance spectroscopy tests
with Li foil as a counter electrode (fig. S5). Both
tests revealed small but sufficient ionic conduct-
ance. From the impedance data, we determined
the Warburg constant and estimated the diffusion
coefficient of Li in Na-alginate to be ~10
8
S/cm.
Although this is four orders of magnitude smaller
than the diffusion coefficient of Li in solid elec-
trolytes (25), the nanometer-level thickness of
a Na-alginate layer compensates for its limited
diffusivity. The proposed mechanismof ion trans-
port through the alginate film is via hopping of
Li ions between the adjacent carboxylic cites,
similarly to alginates function for the ion trans-
port in the algae cells (15).
Third, an ideal binder should assist in build-
ing a deformable and stable solid-electrolyte in-
terphase (SEI) on the Si surface. High Coulombic
efficiency (CE) is critical for practical applica-
tions and is challenging to achieve in Si-based
anodes because of the need to maintain a stable
SEI layer, in spite of the large changes in particle
volume (and, therefore, surface area) during the
battery operation. In ultrathin Si films, high sta-
bility is achieved (26) because the film surface
area does not change during cycling, and the
volume changes are accommodated largely via
variation in film thickness. Thus, maintaining a
stable SEI is not a challenge. In thicker films that
exhibit cracks at the current collector-Si interface
and, thus, experience some surface-area changes,
electrolyte additives are needed to achieve a
stable SEI. In free-standing Si nanowires that do
not need a binder but experience much more
substantial surface-area changes upon cycling,
the unprotected Si fails to maintain a stable SEI,
causing continuous Li consumption, increasing
Si surface roughness, and decreasing CE with
every cycle (27). Si nanowires commonly dem-
onstrate CE of only 93 to 97% (5). In contrast,
our electrodes show improving CE with every
cycle approaching 99.9% (fig. S4A), suggesting
that the alginate binder contributes to building a
stable passivating SEI layer. To test our hypoth-
esis that Na-alginate assists in building a stable
SEI, we performed XPS studies on our electrodes
before and after cycling (Fig. 4). The surface
chemistry of the SEI did not noticeably change
between the 10th and 200th cycle, suggesting
excellent SEI stability and fully supporting our
hypothesis. Earlier studies performed on graphit-
ic anodes also suggested that interactions be-
tween the functional groups of Na-CMC and
electrolyte may contribute to the SEI formation
and explain Na-CMCs good performance (28).
Its positive impact on improving CE of Si anodes
was observed as well (1), but only when the
relative amount of Na-CMC was several times
higher than that of Na-alginate (13). The com-
plex interactions between Na cations, Si, and var-
ious electrolytes deserve a separate study.
Even if the stability of the SEI and binder-Si
interface is achieved, binders that show low ex-
tensibility under stress require the Si electrode to
possess sufficient pore volume, which is needed
for Si expansion. Increasing the pore volume of
CMC-based Si electrodes markedly improved
their stability (29). The lack of sufficient pore
volume may cause sealing of the interparticle
pores (and, thus, a dramatic reduction in the ion
transport) and mechanical failure of the electrode
during operation. The smallest sufficient pore
volume should be larger than the total volume of
Si expansion for several reasons. First, the shape
of the Si particles and the shape of the pores are
different. Therefore, at the fully expanded state
some pore volume will remain unfilled. Note that
plastic deformation of lithiated Si nanoparticles
may take place (8), thereby reducing the strict-
ness of the requirements on local pore shape and
size. However, strong bonding of the binder to Si
particles (Fig. 2) and high binder stiffness (Fig.
1D) is needed, because the endurance limit of the
binder and the binder-Si interface must exceed
the internal stresses in the electrode caused by the
volume expansion of Si nanoparticles. Second,
the SEI formation requires some available vol-
ume as well. Furthermore, at the expanded state
Si particles could be pressed against each other,
inducing highly undesirable damage in the SEI.
Finally, open pores not filled with any electrolyte
decomposition products are needed for the rap-
id transport of Li ions within the electrode. Too
large a pore volume, however, will lead to a de-
crease in the volumetric capacity of the anode.
Because the considerations discussed above make
it difficult to precisely predict the minimumpore
volume, we performed additional experiments to
intentionally densify our electrodes. We noticed
that when the electrode density was increased
to ~0.75 g/cm
3
(and the total pore volume equal
to 2.7 times the volume occupied by Si particles),
the electrodes showed noticeably worse perform-
ance (fig. S6). Therefore, we estimate that the ide-
al pore volume should be somewhere between
three and six times the volume of Si component
of the electrode, provided that the binder has
properties similar to that of alginate or CMC.
Because both CMC and alginate exhibit sim-
ilar mechanical properties (Fig. 1, C and D, and
fig. S1, A and B) and show no interaction with
electrolyte, we conclude that the differences in
their chemical properties explain the considerable
difference in their performance in Si electrodes of
similar porosity levels (Fig. 3B). In alginate, car-
boxylic groups are naturally present and evenly
distributed in the polymer chain, whereas in
CMC they are synthetically induced and their
Fig. 4. Stability of the SEI layer in an alginate-based Si anode. (A to C) XPS spectra on the anode surface before and after cycling in the potential range 0.01
to 1 V versus Li/Li
+
. No major changes in the chemistry of the SEI of the anode cycled for 10 or 200 cycles are visible.
REPORTS
distribution is random, where some monomeric
units may have more than one carboxylic group
and other have none. The higher concentration
and a more uniformdistribution of the carboxylic
groups along the chain in alginate (Fig. 1A) could
be responsible for the better transport of Li ions
in the vicinity of Si particles, more uniform
coverage, and more efficient assistance in the
formation of a stable SEI layer on the Si surface
(Fig. 4). Alginate macromolecules are also much
more polar than the CMC polymer chains, which
can ensure better interfacial interaction between
the polymer binder and the particles, as well as
stronger adhesion between the electrode layer
and Cu substrate. This large difference in chem-
istry of CMC and alginate results in major dif-
ferences in their behavior. For example, the
alginate solution in water has dramatically higher
viscosity than CMC (fig. S7). This high viscosity
prevents Si particles from sedimentation and
aggregation during the electrode formation, as
water is evaporating, resulting in high slurry
uniformity. This uniformity is known to be crit-
ical for obtaining uniform distribution of active
materials within the anode needed for the long-
term electrode stability. Alginate solution also
exhibits a much higher degree of shear-thinning
behavior (fig. S8), which offers an opportunity to
lower a slurry viscosity needed for fast homog-
enization by increasing the mixing rate and an
opportunity to increase a slurry viscosity for po-
rosity and uniformity control during the electrode
formation by lowering the mixing rate. To achieve
viscosity comparable to alginate solutions, sub-
stantially higher CMC content is needed. Sim-
ilarly, to get a remotely comparable performance
with a CMC binder, one needs to increase the
binder:Si ratio by a factor of 4 (1, 13). The high
binder content decreases the electrical conductiv-
ity of the electrode and necessitates the use of a
higher content of the conductive carbon additives
(increasing the C:Si ratio by a factor of 3) (1),
which inevitably lowers the electrode specific
capacity.
To further characterize the behavior of the
alginate-based electrode, we performed cyclic
voltammetry experiments. The differential capac-
ity curves show one broad Li insertion (cathodic)
peak at ~0.21 V and two Li extraction (anodic)
peaks at 0.33 and 0.51 V (Fig. 3D). The origin of
the potential difference between the correspond-
ing peaks in the cathodic and anodic directions is
commonly modeled by a thermodynamic (rate-
independent) hysteresis (30). The first 0.33-V
anodic peak is not always observed. In some Si-C
nanocomposite particles, for example, only one
Li extraction peak at ~0.5 Vappears (6). There-
fore, the 0.33-V peak could be related to the
surface properties of Si. A small Li-extraction
peak observed at ~0.17 V corresponds to Li dein-
tercalation from C additives. The five cyclic vol-
tammetry cycles (Fig. 3D) demonstrate high
reproducibility, indicative of good anode stability.
The shapes of the galvanostatic Li insertion
and extraction profiles for the produced Si anodes
(Fig. 3C and fig. S4B) are similar to the profiles
previously reported in literature for other Si elec-
trodes (6, 9, 13). In contrast to intercalation-type
electrode materials, these profiles do not exhibit
strictly horizontal plateaus and cover a larger
potential range. The Li-extraction profiles be-
come more horizontal and exhibit slightly smaller
overpotential with cycling (fig. S4B), suggesting
a gradual improvement in the discharge kinet-
ics (20). The current-dependent overpotential in-
creases the Li-extraction potential when current
density is increased from 140 to 4200 mA/g (20)
(Fig. 3C). By comparing the Li-extraction ca-
pacities achieved at different current densities
(Fig. 3C), we can conclude that these electrodes
possess moderate rate capability, inferior to that
achieved in Si-C composite anodes with hierar-
chical porosity (6) or in nanowires (5, 10). The
advantage of this traditional battery technology,
however, is higher volumetric capacity, higher
CE, and compatibility with existing manufacturing
techniques. Further electrode optimization and
introduction of additional pores is expected to
substantially increase the rate performance, be-
cause the diffusion of Li into or out of Si nano-
particles can be achieved within minutes (20).
In addition to improving performance of Si
anodes, the alginate properties may provide ad-
vantages to other electrodes, such as traditional
graphitic anodes. For example, replacing PVDF
with lower-cost, environmentally friendly algi-
nate was found to improve the first-cycle CE and
cycle stability (fig. S9).
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Material and Methods
Figs. S1 to S9
10.1126/science.1209150
A Self-Quenched Defect Glass
in a Colloid-Nematic Liquid
Crystal Composite
T. A. Wood, J. S. Lintuvuori, A. B. Schofield, D. Marenduzzo, W. C. K. Poon*
Colloidal particles immersed in liquid crystals frustrate orientational order. This generates defect
lines known as disclinations. At the core of these defects, the orientational order drops sharply.
We have discovered a class of soft solids, with shear moduli up to 10
4
pascals, containing high
concentrations of colloidal particles (volume fraction f 20%) directly dispersed into a nematic
liquid crystal. Confocal microscopy and computer simulations show that the mechanical strength
derives from a percolated network of defect lines entangled with the particles in three dimensions.
Such a self-quenched glass of defect lines and particles can be considered a self-organized
analog of the vortex glass state in type II superconductors.
I
n a typical colloidal suspension, particles are
dispersed in a simple, isotropic liquid that
acts as a passive, homogeneous background
medium. But it is also possible to disperse par-
ticles in a liquid that itself has complex proper-
ties. For example, particles in a demixing binary
REPORTS
liquid mixture may gather at and arrest the bi-
continuous interface separating the two phases
(1). Another class of dispersions with complex
suspending media is particles in liquid crystals
(LCs) (2, 3), in which upon cooling, the dis-
persing mediumcan undergo a succession of phase
transitions from an isotropic liquid to a nematic
or other ordered mesophase (4). The competition
between ordering in the bulk of a mesophase and
on the surface of particles gives rise to the pos-
sibility of new microstructures and functions,
e.g., as biosensors (5, 6), but also to barriers
against dispersing the particles in the first place.
The latter feature means that, to date, there have
been few successful attempts at dispersing high
concentrations of particles into LCs. But analogy
with dispersions in simple liquids suggests that
constructing a colloid-LC composite at high par-
ticle volume fraction, f, may pay rich dividends
both in terms of applications (for instance, better
mechanical stability) and fundamental science
(for example, understanding glassy arrest).
We have synthesized a soft solid (Fig. 1) by
dispersing a high concentration (f 50%) of
particles directly into a nematic LC. This con-
trasts with the majority of previous work where
f 0, and the particles were initially dispersed
into the isotropic phase. Computer simulations
show that the rigidity (Fig. 2) of our new colloid-
LC gel (Fig. 3) is due to particle-entangled defect
lines percolating in three dimensions (Fig. 4).
Rigidity is important because LCs are increas-
ingly being used as biomedical sensors (7), for
which materials able to support their own weight
(5) and the weight of embedded living cells (6)
are needed. Our findings are also of fundamental
interest to a larger audience interested in in-
teracting line defects, from LCs in porous media
(8) through vortices in superconductors (9) to
cosmic strings (10).
In a (thermotropic) nematic LC, the aniso-
tropic molecules align, on average, along a di-
rector, n. The physics of single particles in
nematic LCs is reasonably well known in broad
outline only in the f 0 limit (11). A particle
(radius a) anchors the LC molecules to its sur-
face, either in parallel or perpendicularly (ho-
meotropic), with energy Wa
2
(where W is the
anchoring strength), giving rise to an inhomog-
eneous director field n(r) and stored elastic en-
ergy Ka (where K is an average Frank elastic
constant). For weak anchoring, Wa/K << 1, n(r)
is continuous. As Wa/Kincreases, topological sin-
gularities appear: first, an equatorial ring on the
particle surface, and then a ring away from the
surface (a Saturn ring), either of which gener-
ates an n(r) with quadrupolar symmetry. But at
the highest value of Wa/K, a defect pattern with a
totally different (dipolar) symmetry appears.
Although the conditions under which these
defects occur are still open to debate (12), it is
clear that the elastic distortion associated with
any of these defects around a particle induces an
anisotropic interparticle attraction. In a confined,
two-dimensional (2D) environment where the ne-
matic LC is aligned parallel to the confining
planes (a 2D planar nematic cell), such elasticity-
mediated interparticle interaction gives rise to
straight chains (for dipoles) (2) and zigzag lines
(for Saturn rings) (13) when f is vanishingly small
(f 0). In these multiparticle structures, the de-
fect around each particle retains its individual
character. Recent simulations and experiments
(1416) have revealed that multiparticle struc-
tures can also form when particle-mediated de-
fects become entangled. Again, in a 2D planar
nematic cell, different entangled-defect configu-
rations around particles can give rise to various
multiparticle clusters (chains, etc.), as well as 2D
crystals (13). A simulation study (15) of 3D self-
assembly of particles in a nematic LC at finite f
8% showed a more or less random dispersion
of planar clusters.
Experimental study of such defect-mediated
colloidal self-assembly is challenging for kinet-
ic reasons. The calculated phase diagram of a
colloid-LC mixture (17) shows that below the
isotropic-nematic transition temperature (T
IN
), a
practically particle-free nematic phase should co-
exist with particles at f 64%. Thus, we expect
all space-filling defect-mediated particle struc-
tures to be metastable. Simply quenching a particle-
laden isotropic LCbelowT
IN
in the bulk does not
produce such structures. Instead, particles are
swept along by fast nematic-isotropic fronts and
Scottish Universities Physics Alliance and School of Physics
and Astronomy, The University of Edinburgh, James Clerk
Maxwell Building, Kings Buildings, Mayfield Road, Edinburgh,
EH9 3JZ, UK.
w.poon@ed.ac.uk
Fig. 1. (A) A quadrupolar
birefringencepatternaround
a 2-mm-diameter particle
in a uniformly aligned ne-
matic cell. (B) A colloid-
nematic composite at f =
49% can be sculpted as a
solid at roomtemperature.
(C) The sculpture melts at
the isotropic-nematic tran-
sition temperature. Scale
bars, 1 cm.
A B C
Fig. 2. (A) Measured storage (G, black circles) and loss (G, open circles)
moduli as a function of strain amplitude (g) at f = 28%. (B) Maximumstorage
modulus as a function of volume fraction f. Particle diameters are 0.7 mm
(black squares), 1.2 mm (red circles), and 2.0 mm (blue triangles); the line is a
guide for the eye. (C) Storage and loss moduli measured before and after a
f = 28% sample is sheared at 200 s
1
for 150 s, with the shear history shown
by the continuous line. (D) Plot of G(t)* = [G
max
G(t)]/(G
max
G
0
),
versus the time elapsed (t ) since the cessation of shear. Here, G
max
is the
maximum modulus attained during our experimental period, and G
0
is the
modulus at t = 0.
REPORTS
eventually become trapped between nematic do-
mains, giving rise to a cellular solid (17). (A bulk
simulation that is smaller than the size of a typical
nematic domain does not face this constraint.) In
2D experiments (16), well-defined boundary con-
ditions (hence, the planar nematic cell) and local
laser preheating are necessary to observe defect-
entangled particle clusters.
We generated extended defect-mediated par-
ticle structures by dispersing sterically stabilized
polymethylmethacrylate (PMMA) particles (2a =
0.7, 1.2, 2 mm) directly into the bulk nematic
phase of 4-cyanobiphenyl (5CB) (T
IN
= 35.2C)
in untreated 2-cm
3
sample bottles at room tem-
perature (19C). (Note that, as in other similar
systems (17), no measurable shift in T
IN
due to
particle dispersion was found.) The core of the
particles includes the dye 7-nitrobenzo-2-oxa-1,3-
diazolemethylmethacrylate chemically linked to
the PMMA polymer. Polarized optical micros-
copy shows that single particles are surrounded
by a quadrupolar director field (Fig. 1A), con-
sistent with either a surface or Saturn-ring de-
fect. From this, we estimate an upper bound for
our anchoring strength: A quadrupolar director
field should only occur if Wa=K 25 for par-
ticles in 5CB (11).
Attempts to disperse dried PMMA particles
into nematic 5CB by hand-shaking failed; large
clumps of undispersed particles, presumably held
together by entangled defects, sedimented. Our
simulations suggest that it takes 10
2
k
B
T (k
B
, the
Boltzmann constant; T, temperature) to break
such clumps. We used vigorous mechanical agi-
tation on a whirly mixer to input this energy
and produce well-dispersed samples. We estimate
that our shaking induces maximum velocities
on the order of v 10
2
m s
1
, and the viscosity
of 5CBat roomtemperature is h 20 mPa s
1
(18),
so that a typical force at the particle level is F
hva 200 pN. The work done by this force over
a distance on the order of a disclination core, l
c
5 nm (19), is Fl
c
200k
B
T, consistent with our
estimate of the energy barrier for dispersion.
Here, we focus on samples with f 5%.
Macroscopically, none of our samples sedimented
over long times (up to many months); that is,
particles remain dispersed throughout the whole
volume of the LC. All samples were solid enough
to be scooped out of their vials. Within the range
5% f 20%, samples had a curdlike ap-
pearance. As f increased above 8%, larger ag-
gregates became visible within the curdlike sample,
and the aggregate size increased with volume
fraction until the samples adopted a homoge-
neous appearance at f 23%. At the highest
concentrations reached, f 50%, samples were
found to be highly malleable. Asculpture molded
by a metal spatula is shown in Fig. 1B. When
heated to above T
IN
, this sculpture melted into a
liquid (Fig. 1C), demonstrating that the rigidity is
provided by the nematic order.
We probed the mechanical properties of these
arrested states using oscillatory rheometry in a
cone-plate stress-controlled rheometer (TA In-
struments, New Castle, DE, AR2000; 40 mm, 1
cone) at a frequency of 1 Hz. The cone and plate
presented rough boundary conditions and home-
otropic anchoring to the LC molecules. All
samples with f 5% exhibited solidlike re-
sponses at lowstrain amplitudes (g) with plateaus
in both the storage (G) and loss (G) moduli
that are g-independent. The plateau moduli sat-
isfy G
max
=G
max
0:5; the behavior of the sam-
ple shown in Fig. 2A is typical. At f 10%, the
plateau storage modulus (G
max
) is essentially
constant (Fig. 2B), staying at G
max
G
0
10
2
Pa. Beyond f 10%, G
max
(f) increases rapidly
with f, with a functional form that is consistent
with G
max
(f) G
0
(f f
c
)
n
with n = 2.5 T 0.5
and f
c
= 0.12 T 0.01; data for three different
particle sizes collapse onto the same curve.
As the strain amplitude increases, both G
and G begin to drop, with the former dropping
faster than the latter so that they eventually cross.
Again, the behavior shown in Fig. 2A is typical.
The crossing may be taken as the point at which
a solidlike (G > G) colloid-nematic composite
yields into a liquidlike state (G < G). It was dif-
ficult to obtain reliable values of the yield strain
(g
c
) at low f. Above f 0.1, g
c
settles down to
values well below1%(Fig. 2A), reaching g
c
0.2%
at f 60%.
We also used rheometry to probe the kinetics
of network formation. We shear-melted the gel
structure at a steady shear rate of 200 s
1
, then
switched off the steady shear and monitored
the recovery of G and G as a function of time
(Fig. 2C). Plotting G(t) against the logarithm of
elapsed time since the cessation of shear (Fig.
2D) shows a two-staged recovery of solidlike
behavior. Half of the recovery is fast, complete in
10 s, then the process dramatically slows down,
with the rest of the recovery not complete for
another 10
3
s. Both stages of the recovery, es-
pecially the much slower second stage, are linear
in this representation.
The rheology data in Fig. 2B suggest that
there are two regimes of gel behavior: below and
above f 15%. To make sense of these two re-
gimes, we turn to confocal microscopy (performed
with the use of a Nikon TE300 inverted micro-
scope and a BioRad Radiance 2100 scanner at an
incident wavelength of 488 nm). The thickness of
the sample was 100 mm. Due to turbidity, we
could only image 10 mm into each sample.
We show images typical of the two regimes,
5% f 10% and f 20%; respectively. A sam-
ple at f = 6% shows disconnected clusters of
particles (Fig. 3A). These clusters do not show
any visible thermal fluctuations (Brownian mo-
tion). On the other hand, the sample at f = 33%
shows a connected particle structure (Fig. 3B).
This qualitative change in the microstructure
presumably lies behind the change from approx-
imately constant G to a regime in which G in-
creases strongly with f.
To understand this transition fromsingle clus-
ters to a space-filling network, we need to know
how the defect lines interact with the particles.
We performed extensive simulations of the be-
havior of defect lines interacting with multiple
particles (radius a) in a 3D box of volume (12a)
3
with periodic boundary conditions [see supporting
online material (SOM) for all algorithmic details].
We used a Landau-de Gennes model (4) at two
anchoring strengths, Wa/K 15 and 30, brack-
eting our estimate of the upper bound of the
anchoring strength in our systemWa/K 25. We
also studied a range of finite particle volume
fractions: 3% < f < 30%. Particles move ac-
cording to a molecular-dynamics algorithm de-
fined on the basis of the elastic forces calculated
by integrating the LC stress tensor over their
surfaces. Thermal noise is also included, although
elastic forces dominate. The LC order parameter
relaxes to minimize the Landau-de Gennes free
energy, which consists of: (i) a bulk term favor-
ing nematic ordering in the bulk; (ii) a distortion
term penalizing splay, twist, and bend defor-
mations in n(r); and (iii) an anchoring energy
that favors normal anchoring of n at the particle
surface. The time scale of the relaxational dy-
namics is given by the rotational viscosity of the
LC. We typically started simulations from an
isotropic configuration quenched to the nematic
phase. We identify defect lines as regions where
the order parameter drops below 60% of its max-
imum bulk value.
The size of particle clusters that are entan-
gled by a single defect line increases with f. We
A B
Fig. 3. (A) Confocal micrograph at f = 6%: Colloids aggregate in loosely connected clusters within large
expanses of a nematic LC. (B) At f = 33%, the colloid structure is densely knitted around small nematic
domains. Scale bars, 20 mm.
REPORTS
quantify this by plotting the volume of defect
lines associated with the largest defect-entangled,
system-spanning cluster (normalized by the total
defect volume) as a function of f (Fig. 4A). At
low volume fractions, f 5%, we see some iso-
lated particles supporting Saturn-ring defects.
Even at such f, the Saturn-ring defects on neigh-
boring particles can already merge to form en-
tangled point defects, giving rise to clusters of a
few particles, some of which can be linear or
planar (see Fig. 4Bfor an example). In the steady-
state configuration, clusters interact and hold each
other in place through long-range elastic dis-
tortions in the LC. This is confirmed by an inverse
quench into the isotropic phase, which releases
elastic forces and quickly leads to the dissolution
of the clusters.
A fully percolated defect structure emerges at
f 15 to 20% (Fig. 4C, see also fig. S3 for
versions with the particles removed). Interesting-
ly, the volume fraction at which this occurs does
not depend much on anchoring strength for the
range we simulated. What is crucial is the nature
of the anchoring: We find that entangled defect
structures are not observed with planar anchoring
of the LC at particle surfaces.
These simulations throw light on our bulk
observations, rheological measurements, and mi-
croscopy images. First, our simulations allow us
to estimate typical energy barriers between states.
In particular, we find that an energy on the order
of 10
2
to 10
3
k
B
T is needed to form a dimer held
together by a defect line starting from separated
colloidal particles (see SOM). This is consistent
with our earlier estimate of an input of 10
2
k
B
T
in vigorous shaking to mix particles into nematic
5CB to prepare our samples.
Visually, both confocal microscopy and sim-
ulations find two aggregation regimes: isolated
clusters (Figs. 3A and 4B) and space-spanning
clusters (Figs. 3B and 4C). Our simulations sug-
gest that these clusters are held together by en-
tangled defects. In the simulations, the isolated
clusters at low f hold each other in place by the
elastic interaction mediated by the LC, which we
take to be the origins of the finite storage mod-
ulus, G
0
10
2
Pa, in our samples at f 10%
(Fig. 2B). The curdlike appearance of our sam-
ples in the range 5% f 20% is presumably
due to the presence of large clusters of this kind.
We associate the sharp change in rheological
properties observed at f 20% (Fig. 2B) with
the emergence of a system-spanning cluster held
together by percolated defect lines seen in simu-
lations at around the same particle concentration
(Fig. 4A). It has been known for some time that a
dense network of defect lines in a nematic LC
displays considerable elasticity (20), but without
permanent pinning centers, this elasticity decays
in a matter of days. In our case, the percolated
network pins the defects, and the elasticity lasts
indefinitely (years).
Quantitatively, we find that the measured
storage modulus for all particle sizes is given by
G
max
f G
0
Gf f
c
v
1
with the prefactor G 10
5
Pa K=l
2
c
[when K
10
11
N (21)]. A full theory for this behavior is
not yet available, but the relevant physics is
reasonably clear. First, note that the form of the
f scaling is ubiquitous in percolated systems,
which typically display a nonuniversal elasticity
exponent in the range 1:5 v 3:5 (22). Next,
to understand the prefactor, we first recall that
the elasticity of a network of defect lines with
mesh size x can be estimated by K/x
2
(23). Thus,
it appears that the scale of elasticity in our system
G is set by defect lines packed at close to maxi-
mum possible density (one per l
2
c
). We expect
this to occur in the space between two particles
entangled by disclinations (Fig. 4, B and C). A
geometric argument (see SOM) then suggests
that in a close packed systemof defect-entangled
particles (f 0.64), the scale of the modulus is
indeed set by K=l
2
c
, independent of particle
size.
Finally, we turn to the kinetics of formation of
our gel. Figure 2C shows that the recovery of the
storage modulus is a two-staged process. Be-
cause our simulations show that this new form of
soft matter is dominated by disclinations, we sug-
gest that the kinetics of the initial, fast process are
controlled by the relaxation of stretched disclina-
tion lines, which is dependent logarithmically on
system size (24). Disclinations in a nematic LC
with properties very similar to 5CB confined to
10
2
mm, which is the order of magnitude of the
gap size in our cone-plate rheometer, relax with a
characteristic time of 10 s (24), in good agree-
ment with the location of the cross-over to a
second process in our data (Fig. 2D). The latter is
presumably due to the much slower relaxation of
entangled disclination line in a disordered particle
environment (8). It is known that the motion of
defects in systems where they can be pinned into
favorable metastable configurations by frozen-in
disorder generically gives rise to kinetics with
log(t) scaling (25). More interestingly, dynamics
controlled by log(t) were also found in a model of
a self-quenched glass (26).
Particles can also organize defects in 3D in
other LC mesophases; for example, in a choles-
teric, particles can act as nodes in a network of
disclinations, even at f 0 (23). But in the ne-
matic, which is the least ordered of all meso-
phases, we never observed isolated clusters linked
by long defect lines in our simulations. Arrested
states due to 3D entangled defects associated
with particles in other mesophases remain to be
discovered and characterized. Our entangled-
defect colloidal gel (Fig. 1A) should also be care-
fully distinguished fromthe kind of foamlike soft
solids previously made by quenching a disper-
sion of PMMA particles in the isotropic phase of
5CBto belowT
IN
(17). The latter relies on totally
different physics: particles being jammed at (and
therefore stabilizing) the interfaces between ne-
matic domains, and a near analog being the
bijel (1, 27) (though the fact that the relevant
order parameters are nonconserved and conserved,
respectively, in LCs and binary liquids imposes
interesting differences).
To summarize, we have dispersed hard-
sphere colloids in thermotropic liquid crystals
over a wide range of volume fractions. We find
that beyond some critical volume fractions, f
c

12%, the elasticity of the samples increases rap-
idly, and the storage modulus exhibits power-law
behavior G (f f
c
)
2.5
. At high f, the mate-
rial yields at a strain of 0.1%. Simulations sug-
gest that we have prepared a defect-entangled
gel in which the rigidity is due to a percolating
network of disclination lines entangled with the
particles.
Our material has conceptual similarities with
vortex glasses in type II superconductors (9),
where preexisting, static impurities pin vortex
lines. Liquid crystals in random porous media (8)
forma soft matter analog of such vortex glasses.
However, in our case, the particles (pinning cen-
ters) generate the defects, and the collective mo-
tion of the defects and particles spontaneously
organize each other into a jammed percolating
network. Such a self-quenched glass of line de-
fects, where the dynamical arrest does not orig-
inate from any intrinsic (quenched) disorder but
arises from geometric constraints on the coupled
motions of the interacting particle-disclination sys-
tem(28), invites comparison with more tradition-
al self-quenched glasses (29), especially structural
Fig. 4. (A) Fraction of percolated defects as a function of the colloid-packing fraction from simulations:
weak homeotropic anchoring (blue circles), Wa/K 15; strong homeotropic anchoring (red squares),
Wa/K 30; and planar anchoring (green triangles). The dotted lines denote a typical uncertainty (TSD).
(B) Snapshot of a configuration with a nonpercolated defect line at f = 4%. (C) Snapshot of a con-
figuration with percolated defect lines at f = 16%. In the snapshots, blue ribbons are defects, and
oranges spheres are particles.
REPORTS
glasses of various kinds. Finally, we note that the
very slow log(t) long-time aging of the storage
modulus is reminiscent of similar stretched dy-
namics in systems with quenched (9) or self-
induced (26, 28) disorder.
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SOM Text
Figs. S1 to S4
References (3038)
10.1126/science.1209997
Adaptation to Climate Across the
Arabidopsis thaliana Genome
Angela M. Hancock,
1
Benjamin Brachi,
2
Nathalie Faure,
2
Matthew W. Horton,
1
Lucien B. Jarymowycz,
1
F. Gianluca Sperone,
1
Chris Toomajian,
3
Fabrice Roux,
2
Joy Bergelson
1
*
Understanding the genetic bases and modes of adaptation to current climatic conditions is essential
to accurately predict responses to future environmental change. We conducted a genome-wide scan
to identify climate-adaptive genetic loci and pathways in the plant Arabidopsis thaliana. Amino
acidchanging variants were significantly enriched among the loci strongly correlated with climate,
suggesting that our scan effectively detects adaptive alleles. Moreover, from our results, we successfully
predicted relative fitness among a set of geographically diverse A. thaliana accessions when grown
together in a common environment. Our results provide a set of candidates for dissecting the molecular
bases of climate adaptations, as well as insights about the prevalence of selective sweeps, which has
implications for predicting the rate of adaptation.
C
limate change has already led to altered
distributions of species, phenotypic vari-
ation, and allele frequencies (15), and
the impact of changing climates is expected to
intensify. The capacity to respond to changing
climate is likely to vary widely as a consequence
of variation among species in their degree of
phenotypic plasticity and their potential for ge-
netic adaptation (6), which in turn depends on the
amount of standing genetic variation and the rate
at which newgenetic variation arises. Arabidopsis
thaliana is an excellent model for investigating
the genetic basis and mode of adaptation to cli-
mate owing to the extensive climatic variation
across its native range, as well as the availability
of genome-wide single-nucleotide polymorphism
(SNP) data among a geographically diverse col-
lection. We examined the correlations between
107ecologicallyimportant phenotypes inA. thaliana
(7) and 13 climate variables that represent extremes
and seasonality of temperature and precipitation,
photosynthetically active radiation (PAR), rela-
tive humidity, season lengths, and aridity (figs. S1
to S4). We observed strong correlations between
1
Department of Ecology and Evolution, University of Chicago,
1101 East 57th Street, Chicago, IL 60637, USA.
2
Laboratoire
Gntique et Evolution des Populations Vgtales, FRE CNRS
3268, Universit des Sciences et Technologies de Lille 1,
Villeneuve d'Ascq, France.
3
Department of Plant Pathology,
Kansas State University, Manhattan, KS 66502, USA.
jbergels@uchicago.edu
Fig. 1. Enrichment of amino
acidchanging SNPs (red), syn-
onymous SNPs (green), and in-
tergenic SNPs (yellow) in the
1% tails of the distributions for
(A) climate overall (using a rank
statistic based on the minimum
rank across climate variables) and
(B) for each individual climate
variable. Enrichments shown are
relative to the proportion of each
class of SNPs in the genome
overall. Gray dots show the dis-
tribution of results of 1000 per-
mutations. The gray line shows
the expected enrichment under
the null hypothesis of no en-
richment. Enrichments that are
significant relative to permuta-
tions are denoted by asterisks.
c
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.
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.
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.
8
1
1
.
2
1
.
4
1
.
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o
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* * * * * * * * * * * * * * * *
* *
* * * * * * *
REPORTS
day length and phenotypes related to de-
velopment time and flowering, supporting the
observation that flowering time in the field is
modulated by complex environmental cues that
are difficult to simulate under controlled growth
conditions (810). Correlations were also found
between leaf yellowing (chlorosis) and temper-
ature (11), as well as between dormancy-related
traits and those related to temperature and mois-
ture (12), consistent with the role for both ver-
nalization and moisture in breaking dormancy.
These results provide evidence for a genetic basis
for climate adaptations in A. thaliana.
We conducted genome-wide scans to detect
climate associations for ~215,000 SNPs geno-
typed across 948 A. thaliana accessions distrib-
uted throughout the native range of the species
(fig. S5) (13). Because we cannot be certain that
our model completely accounts for the effects of
population history (13), we tested whether our
results detect true signals of adaptations by as-
sessing enrichment of likely functional [i.e., non-
synonymous (NS)] variants relative to putative
neutrally evolving [i.e., synonymous (S) and in-
tergenic] variants in the 1% tail of the combined
climate correlation distributions (14). We found
that intergenic SNPs show deficits and NS SNPs
show strong and significant enrichments in the
tail relative to their proportions in the genome as
a whole for climate overall (Fig. 1A), as well as
for all but 1 of the 13 individual climate variables
(precipitation seasonality; Fig. 1B). The pattern
was similar when we controlled for allele fre-
quency but contrasts sharply to climate correla-
tions that did not control for population history
(13) (fig. S6).
Notably, for climate overall and for many
individual variables, S variants are also signifi-
cantly enriched in the tail (Fig. 1). The tendency
toward enrichment of S variants is expected be-
cause of linkage disequilibrium under neutral pro-
cesses but may be intensified by background
selection (15) and/or hitchhiking (16). NS SNPs
were slightly enriched relative to S SNPs (ratio of
NS to S = 1.146, P = 0.036) for climate overall.
In addition, precipitation in the wettest and driest
months, relative humidity, length of the growing
season, and PARwere enriched for NS relative to
S variants (ratios ranging from 1.137 to 1.361
and P values ranging from 0.025 to 1 10
4
).
Given that we do not have data for all individual
SNPs, but rather use SNPs to represent variation
in the genome, these results are surprisingly
strong.
We examined which biological processes are
overrepresented among strong climate correlations,
focusing in particular on climate variables for
which we observed a significant NS-to-S enrich-
ment (Table 1 and table S2). PARshows the largest
number of enriched categories, including photo-
synthesis, auxin biosynthesis, and gravitropism.
In addition, we found enrichment of processes
related to energy metabolism (i.e., starch metab-
olism and mitochondrial electron transport) with
both precipitation extremes. These links between
energy metabolism and water availability likely
result from variation in photosynthetic capac-
ity across precipitation gradients due to differ-
ences in the proportion of time when stomata are
open (17).
Although pleiotropic gene functions may in-
fluence the rate of adaptation (18, 19), we have
an incomplete understanding of the extent and
magnitude of their effects on adaptation (20). We
find substantial overlap in the 1% tails of climate
variables, with pairwise combinations sharing 0
to 70% of top SNPs (fig. S7), suggesting that
pleiotropy is common among adaptive alleles.
However, some of these results may be due to
correlations among the climate variables them-
selves, rather than pleiotropy per se. Indeed, a
significant positive correlation was observed be-
tween the matrix of pairwise correlation coef-
ficients among climate variables and the matrix
of their proportional overlap of SNPs (Mantel
r
2
= 0.59, P = 2 10
4
). Hence, outliers that are
compared to the variable correlation matrix are
particularly interesting (e.g., fig. S8).
It would be difficult to confirmthe candidates
from climate-related genome scans, even if it
were possible to predict climate with absolute
certainty, because of the scale of such tests. We
thus validated our model by reasoning that if we
are observing true signals, then they should be
able to predict the relative fitness of genotypes
grown in a particular climate. We tested our abil-
ity to predict the relative fitness of 147 A. thaliana
accessions planted in the fall in a common garden
in Lille, France (Fig. 2A). In particular, we se-
lected all SNPs in the 0.01% tail of correlations
with any climate variable and pruned this set of
SNPs to include only one per chromosomal re-
gion on the basis of patterns of linkage dis-
equilibrium. We identified alleles that are more
common within a window of climate similar to
Lilles. Then, we asked whether the count of
these alleles could predict relative fitness, as mea-
sured by total silique length (21) among the
accessions. We created a null distribution by con-
ducting the same analysis on resampled sets of
SNPs. We found a strong and significant corre-
Table 1. Enrichment of biological processes (BPs) in the 1%tail (P < 1 10
3
) for climate variables with
significant NS relative to S enrichments.
Biological process Enrichment P value
Photosynthetically active radiation
Maintenance of root meristem identity 31.42 1.0 10
5
*
Indoleacetic acid biosynthetic process 28.94 1.0 10
5
*
Cellular response to water deprivation 27.26 6.0 10
5
*
Regulation of defense response 24.24 2.8 10
4
Gynoecium development 22.44 2.0 10
5
*
Red light signaling pathway 21.62 1.1 10
4
Stomatal complex development 21.62 1.1 10
4
Cotyledon vascular tissue pattern formation 18.96 5.0 10
5
*
Positive gravitropism 15.47 1.0 10
5
*
Cotyledon development 10.34 2.1 10
4
Phloem or xylem histogenesis 9.09 3.1 10
4
Jasmonic acid mediated signaling pathway 7.57 1.0 10
3
Photosynthesis 4.59 1.0 10
3
Response to cold 2.98 6.9 10
4
Precipitation in the wettest month
Pyridine nucleotide biosynthetic process 17.39 6.8 10
4
Base-excision repair 13.59 9.0 10
5
Root hair cell tip growth 11.68 1.0 10
3
Stomatal complex morphogenesis 11.11 7.4 10
4
Starch metabolic process 9.72 1.0 10
3
Protein catabolic process 6.42 2.9 10
4
Cell division 5.75 3.0 10
4
Precipitation in the driest month
Maintenance of root meristem identity 22.85 3.6 10
4
Indoleacetic acid biosynthetic process 21.05 1.0 10
4
Mitochondrial electron transport, succinate to ubiquinone 20.68 1.0 10
3
Length of the growing season
Mitochondrial electron transport, NADH to ubiquinone 24.99 5.0 10
4
Base-excision repair 13.59 8.0 10
5
Epidermal cell differentiation 13.11 3.0 10
4
Embryonic development ending in seed dormancy 2.25 2.2 10
4
Relative humidity
Synapsis 12.30 5.0 10
4
Regulation of signal transduction 29.99 1.0 10
3
*Significance with P < 0.05 with Bonferroni correction across BP categories (P < 6.83 10
5
).
REPORTS
lation between the number of favored alleles and
fitness (Spearmans rho = 0.48, P= 0.003; Fig. 2,
B and C), demonstrating that our climate scan is
picking up a true signal. As no accessions from
within 100 km of Lille were included in the
analysis, the correlation between relative fitness
and the number of favorable alleles is robust to
home versus away effects. Further, additional
analyses support this conclusion (13).
The geographic extent of climate-correlated
SNPs provides at least an initial picture of how
climate shapes patterns of genetic variation in
A. thaliana. Geographic extents varied widely
across climate variables, with day length and rel-
ative humidity representing the extremes (Fig.
3A); SNPs correlated with day length tended to
be localized, whereas SNPs correlated with rel-
ative humidity tended to be widespread (Fig. 3B
and fig. S9). These results, at least in part, can be
understood in relation to the geographic distri-
bution of the climate variables themselves.
Narrow SNP distributions may correspond to
hard selective sweeps, or situations in which a
new variant was driven quickly to high frequen-
cy in the population. A scan for hard selective
sweeps based on extended pairwise haplotype
homozygosity (PHS) (22) identified partial se-
lective sweeps throughout the genome and ex-
amined the geographic extents of these genomic
regions (Fig. 3A). SNPs identified as candidates
for selective sweeps were, indeed, shifted toward
narrow geographic distributions, consistent with
the idea that hard sweeps result in narrow geo-
graphic distributions. To quantify the generality of
these results, we examined overlap between the 1%
tails of the overall climate correlation distributions
100 110 120 130
0
2
0
0
0
4
0
0
0
6
0
0
0
Number of favorable alleles
S
i
l
i
q
u
e

L
e
n
g
t
h

(
m
m
)
r = 0.48
Spearmans rho
F
r
e
q
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n
c
y
0 0.1 0.2 0.3 0.4 0.5
5
0
1
0
0
1
5
0
2
0
0
0
A
B C
Fig. 2. The SNPs with strongest climate correlations predict ranks
in reproductive success (fitness) in Lille, France. (A) Red dots show
the locations where accessions included in the experiment were
collected, and the green cross shows the location where plants
were grown. (B) The relation between total silique length (a mea-
sure of reproductive success) and the number of alleles expected
to be favorable based on the climate analysis. (C) Observed
Spearman correlation coefficient between total silique length
and number of favorable alleles (red line) compared to the
distribution of correlation coefficients from permutations.
0.0 0.5 1.0
0
.
0
0
.
5
1
.
0
1
.
5
2
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.
5
3
.
0
Percent Rank of Area
D
e
n
s
i
t
y
daylength
relative humidity
all climate
phs
all SNPs
A B
Fig. 3. Geographic distributions of SNPs with the strongest climate cor-
relations. (A) Distributions of SNP extents for all SNPs and for SNPs in the 1%
tail for climate overall, day length, relative humidity, and PHS. SNPs rep-
resented in the plot were filtered to remove redundant information resulting
from linkage disequilibrium between SNPs. (B) Distributions of the top five regions for day length overlaid on a map of the distribution of this variable (with
values ranging from12.3 to 16.6 hours). The central panel contains polygons showing the geographic extents of all five SNPs, and other panels show the central
feature and extent of each individual SNP.
REPORTS
and the PHS results and found overlap threefold
greater than expected by chance if the two var-
iables were independent. This increased to nearly
10-fold enrichment when we examined overlap
among the 10% of climate-related SNPs with the
smallest geographic extents; enrichments were
strongest for aridity, maximum temperature, pre-
cipitation in the driest month, and length of the
growing season. Although selection on standing
variation also plays a role, these results reveal
that selective sweeps are likely an important mode
of adaptation in A. thaliana. The central role of
selective sweeps here suggests that species like
A. thaliana may reach adaptive limits under rapid
climate change, owing to the constraints imposed
by waiting for new mutations.
1. W. E. Bradshaw, C. M. Holzapfel, Proc. Natl. Acad.
Sci. U.S.A. 98, 14509 (2001).
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Sci. U.S.A. 104, 1278 (2007).
3. D. B. Lobell, W. Schlenker, J. Costa-Roberts, Science 333,
616 (2011).
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Change, P. M. Kareiva, J. G. Kingsolver, R. B. Huey,
Eds. (Sinauer Associates, Sunderland, MA, 1993),
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5. P. A. Umina, A. R. Weeks, M. R. Kearney, S. W. McKechnie,
A. A. Hoffmann, Science 308, 691 (2005).
6. A. A. Hoffmann, C. M. Sgr, Nature 470, 479 (2011).
8. J. Bergelson, F. Roux, Nat. Rev. Genet. 11, 867 (2010).
9. B. Brachi et al., PLoS Genet. 6, e1000940 (2010).
10. C. Weinig et al., Genetics 162, 1875 (2002).
11. D. H. Kim, M. R. Doyle, S. Sung, R. M. Amasino,
Annu. Rev. Cell Dev. Biol. 25, 277 (2009).
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(1985).
13. See supporting material in Science Online.
14. A. M. Hancock et al., PLoS Genet. 7, e1001375 (2011).
15. B. Charlesworth, M. T. Morgan, D. Charlesworth,
Genetics 134, 1289 (1993).
16. J. H. Gillespie, Genetics 155, 909 (2000).
17. H.-u, -R. Athar, M. Ashraf, in Handbook of
Photosynthesis, M. Pessarakli, Ed. (CRC Press, Boca
Raton, FL, 2005), p. 928.
18. H. A. Orr, Evolution 54, 13 (2000).
19. Z. Wang, B. Y. Liao, J. Zhang, Proc. Natl. Acad. Sci. U.S.A.
107, 18034 (2010).
20. G. P. Wagner, J. Zhang, Nat. Rev. Genet. 12, 204 (2011).
21. F. Roux, J. Gasquez, X. Reboud, Genetics 166, 449 (2004).
22. C. Toomajian et al., PLoS Biol. 4, e137 (2006).
Acknowledgments: Funded by NIH GM083068 and
NSF DEB0519961 to J.B. A.M.H. was supported by a
V. Dropkin Postdoctoral Fellowship, and M.W.H. was
supported by an NSF Predoctoral Fellowship and a
Graduate Assistance in Areas of National Need (GAANN)
training grant. F.R. was supported by a Bonus Qualit
Reserche (BQR) grant from the University of Lille, and
B.B. received funding from a Ph.D. fellowship from
the French Research Ministry and a mobility grant from
the Collge Doctoral Europen. This is contribution
11-389-J from the Kansas Agricultural Experiment
Station. We thank J. Borevitz, A. Fournier-Level,
M. Nordborg, A. Platt, J. Schmitt, members of the
Bergelson laboratory, and two anonymous reviewers
for helpful input. Climate data for the 948 accessions
used in these analyses, result files for the correlation
analyses, and a browser that allows for viewing the
results in their genomic context are available at
http://bergelson.uchicago.edu/regmap-data/
climate-genome-scan/. The genotype data used for
these analyses resulted from the RegMap project
(http://regmap.uchicago.edu).
Figs. S1 to S10
Table S1
References (2335)
10.1126/science.1209244
A Map of Local Adaptation
in Arabidopsis thaliana
A. Fournier-Level,
1
A. Korte,
2
M. D. Cooper,
1
M. Nordborg,
2
J. Schmitt,
1
* A. M. Wilczek
1,3
Local adaptation is critical for species persistence in the face of rapid environmental change,
but its genetic basis is not well understood. Growing the model plant Arabidopsis thaliana in field
experiments in four sites across the species native range, we identified candidate loci for local
adaptation from a genome-wide association study of lifetime fitness in geographically diverse
accessions. Fitness-associated loci exhibited both geographic and climatic signatures of local
adaptation. Relative to genomic controls, high-fitness alleles were generally distributed closer
to the site where they increased fitness, occupying specific and distinct climate spaces. Independent
loci with different molecular functions contributed most strongly to fitness variation in each
site. Independent local adaptation by distinct genetic mechanisms may facilitate a flexible
evolutionary response to changing environment across a species range.
A
daptation to local environments has been
observed experimentally in many or-
ganisms (1) and may critically limit a
given species capacity to evolve in the face of
rapid environmental change (24). However,
the molecular basis of local adaptation remains
largely unexplored (5, 6). Understanding the ge-
netic mechanisms of adaptation requires under-
standing the genetic basis of fitness variation
within and across natural environments (7, 8).
Although genome scans for signatures of past
selection have identified candidate loci show-
ing high levels of environmental differentiation
(9, 10), few studies have directly connected fit-
ness variation measured in the natural environment
of the species to the corresponding molecular
variation (11, 12). Determining the extent of lo-
cal adaptation requires identification of the loci
associated with individual fitness in different nat-
ural environments, as well as characterization of
the distribution pattern of adaptive variants, their
environment specificity, and the type of genes
involved.
To identify loci associated with fitness in the
annual plant Arabidopsis thaliana, we grew a geo-
graphically diverse set of ecotypes (inbred lines
derived from natural populations) across their
native range, in replicated common garden ex-
periments in four European field sites (fig. S1).
Sites in Oulu (Finland) and Valencia (Spain)
spanned the species climate range limits from
Nordic to Mediterranean environments; sites in
Halle (Germany) and Norwich (UK) represented
continental and oceanic climates at similar mid-
range latitude (13). Mean survival and lifetime
fruit (silique) production differed markedly among
ecotypes within each planting site, indicating
heritable variation among source populations in
viability and fecundity (table S1). We carried out
a genome-wide association study (GWAS) for
survival and silique number using 213,248 single-
nucleotide polymorphisms (SNPs) in a mixed-
model approach to eliminate confounding due to
genomic background (14, 15). For each fitness
trait in each of the four field sites, we defined
a set of associated SNPs corresponding to the
0.05% of the SNPs that explained the most var-
iance (around 100 per GWAS; figs. S2 and S3).
Individual SNPs explained a substantial amount
of variation in lifetime fitness, with R
2
in GWAS
models ranging on average from 9% for the SNP
set associated with survival in England to 24% for
the SNP set associated with survival in Finland
(fig. S1).
We tested whether alleles associated with
high fitness in a given site were more locally abun-
dant than genomic controls, as expected if they
contributed to the local adaptation of that pop-
ulation (16). Indeed, the geographic centroids of
the alleles associated with higher survival in En-
gland and Spain and silique number in Germany,
England, and Spain were significantly closer to
the planting sites in Germany, England, and Spain,
respectively, relative to genomic controls; this con-
stitutes evidence of local adaptation for specific
loci (Fig. 1). Similar analyses excluding low-
frequency polymorphisms provided similar re-
sults, demonstrating that the result was not biased
as a result of the presence of rare alleles (table
S2). In contrast, we found no evidence that the
alleles conferring high fitness in Finland were
locally abundant. However, our ability to detect
1
Department of Ecology and Evolutionary Biology, Brown
University, Providence, RI 02912, USA.
2
Gregor Mendel Insti-
tute, Austrian Academy of Sciences, 1030 Vienna, Austria.
3
Deep Springs College, Big Pine, CA 93513, USA.
johanna_schmitt@brown.edu
REPORTS
locally adapted alleles near the species northern
and southern range limits may have been limited
by sample size in Finland (16) as well as by the
sparse sample of local ecotypes available for
our sites in Finland and Spain (fig. S1).
We next examined whether local alleles as-
sociated with fitness are associated with specific
climatic factors, as expected if climate variation
has strongly contributed to adaptation. We used
maximum entropy models [MaxEnt (17)] to in-
fer the contributions of 11 bioclimatic varia-
bles to the distribution of each SNP allele (table
S3) (16) and tested whether fitness-associated al-
leles occupy specific climate spaces relative to
genomic controls. We then used a random re-
sampling procedure to compare climate spec-
ificity scores for each fitness-associated SNP for
each climate variable to genomic controls. Ex-
cluding rare alleles (frequency <5%; table S4)
had little effect on the results. The distribution
of alleles associated with survival was particu-
larly limited by temperature variables (fig. S4 and
table S3). In some cases, the alleles associated
with high fitness exhibited greater climate spec-
ificity (e.g., temperature of the coolest quarter for
survival in Germany, Finland, and Spain; table
S4). However, more often alleles associated with
low fitness exhibited greater climate specializa-
tion (e.g., to precipitation in the coolest quarter
for survival and to temperature in the warmest
quarter for silique number) (Fig. 2 and table S3).
Such alleles may be effectively neutral within the
specific climate conditions where they occur, but
deleterious when transplanted to field sites with
different climates.
We also investigated whether locally adapt-
ive alleles tended to be rare or common rela-
tive to the overall genome. If selection favors
specific alleles in restricted geographic regions,
we expect those variants to be common only
in those regions and otherwise rare. On the
other hand, if local adaptation acts largely by
culling locally deleterious alleles that are neu-
tral elsewhere in the range, then we might ex-
pect high-fitness alleles to occur at relatively high
frequency. We therefore tested whether the glob-
al frequency of the alleles associated with high
fitness was different relative to genomic con-
trols. Alleles associated with increased silique
number were significantly rarer than genomic
controls (table S5), which suggests that their
advantage was local for all sites except Finland
(where no evidence of local adaptation was found).
In contrast, alleles improving survival were high-
frequency alleles, which suggests that viability
selection keeps deleterious alleles rare, confining
their genetic load to environments where they
have no effects (i.e., are neutral; fig. S5). We also
tested whether fitness-associated SNPs were in-
volved in recent selective sweeps by computing
the integrated extended haplotype homozygos-
ity (iEH) around each SNP (18, 19), both in the
global sample and in the local population for
each field site (16). With the exception of sur-
vival in Germany and marginally in Finland, we
found no evidence that loci associated with fit-
ness had significantly greater iEH than genomic
Fig. 1. Locations of the centroids of alleles associated with increased
silique number for the 0.05% most strongly associated SNPs in Spain or
Finland (left) and in England or Germany (right). Large squares represent
the location of the planting site; small squares represent the centroid of the
allele increasing the fitness in the planting site of similar color. The
higher-fitness alleles in a particular environment are distributed signif-
icantly closer to that location than are genomic controls, as tested by 10,000
random draws.
Fig. 2. Influence of temperature and precipitation on the distribution of alleles linked to fitness variation.
(A) Variation in temperature during the warmest quarter of the year. (B) Variation in precipitation
during the coolest quarter of the year. (C to F) Box plots of the difference in climatic contribution
between pairs of SNP alleles significantly associated with fitness in Germany, England, Finland, and
Spain. Negative values indicate when the deleterious alleles are more correlated with the climate
variable; positive values indicate when the beneficial alleles are more correlated with the climate
variable. Light and dark shades represent the 25% and 50% quantile statistics of genome-wide neutral
expectation obtained through permutation (16). *P < 0.004, **P < 0.0001. All test statistics are reported
in table S2.
REPORTS
controls (table S5), which suggests that no re-
cent selective sweeps have occurred at these loci.
Thus, environment-specific fitness may depend
more on standing variation than on recent pos-
itive selection at specific loci, as recently observed
in aspen (20).
We examined the genetic architecture of lo-
cal adaptation by determining whether local selec-
tion in different environments more commonly
acted upon alternate alleles of the same loci, or
if entirely different loci were found among dif-
ferent environments. Individual SNP additive
effects for survival were weakly negatively cor-
related between Finland and England or Spain,
which suggests cross-environment tradeoffs at
specific loci (fig. S6) (16). In contrast, SNP ef-
fects on survival were weakly positively correlated
between England and Spain, which suggests
that they share a similar genetic basis for fitness.
However, all the observed correlations across sites
were relatively weak, and loci associated with
fruit production in England showed little to no
effect on fitness in either Finland or Spain; such
findings suggest an environment-specific genet-
ic basis. Overall, among the 797 top SNPs, only
12 SNPs were associated with fitness in more
than one environment; loci with major genetic
effects were largely independent across sites.
This result suggests that local adaptation relies
on different loci in each environment. Such in-
dependent local adaptation by different genetic
mechanisms may facilitate flexible evolutionary
response to changing environments across the
species range.
We sought insight into the molecular func-
tions of the genes contributing to local adap-
tation by testing whether the candidate genes
present in 10,000base pair (10-kbp) windows
surrounding the associated SNPs were enriched
for a particular subset of the Gene Ontology (GO
slim) annotations relative to 1000 genomic per-
mutations (16). The loci associated with fitness
displayed significant enrichment for specific mo-
lecular functions in all sites (fig. S7). However,
no molecular function was significantly over- or
underrepresented in all sets of candidate genes
(table S6). Typically, only transcription factor
and protein binding activities showed significantly
different enrichment for the same trait in more
than one site. Protein binding was overrepresented
in genes associated with survival in Germany
and underrepresented in England, whereas tran-
scription factor activity was underrepresented
in both England and Spain. Overall, those mo-
lecular functions that were significantly over- or
underrepresented relative to the whole genome
always differed among field sites. This result sug-
gests that local selection acts not only on different
target loci but also on different molecular processes
in different environments across the species cli-
mate range.
To identify potential candidate genes for lo-
cal adaptation, we searched for fitness-associated
SNPs in the top 0.05% (with minor allele fre-
quency >8% to exclude rare deleterious muta-
tions) that also appeared in the top 0.5% of allele
Fig. 3. Geographic distribution probability
of the survival-associated alleles located
within the SAG21 gene (left) and the CHR8
gene (right). Probabilities were calculated
with MaxEnt models as described (16). For
both genes, the minor allele is distributed
at the species range margin following a par-
ticular climate space and shows signs of
recent positive selection. They correspond to
the best candidate genes for local adapta-
tion reported in this study.
Table 1. List of candidate genes associated with fitness in field condition.
Chromosome Position Site
Climate
variable
Trait Rank P SNP position Locus Gene name
Molecular function
(biological process)
Ref.
1 6235221 GER Temperature
seasonality
Silique number 41 3.80 10
4
In the gene AT1G18140 LAC1 Laccase (lignin catabolic
process)
(21)
Within 10 kbp AT1G18130 ATP binding (threonyl-tRNA
aminoacylation)
2 8132698 GER Precipitation
during the
warmest
quarter of
the year
Survival 33 1.08 10
4
In the gene AT2G18770 CHR8 Signal recognition particle
binding
(22)
Within 10 kbp AT2G18780 F-box domaincontaining
protein
AT2G18790 PHYB G proteincoupled
photoreceptor (abscisic
acid metabolism)
(25)
3 5510910 FIN Precipitation
during the
coolest
quarter of
the year
Survival 26 1.12 10
4
In the gene AT3G16240 D-TIP Ammonia transmembrane
transporter
4
Within 10 kbp AT3G16250 NDF4 Electron carrier activity
(photosystem I)
AT3G16260 TRZ4 3-tRNA processing
endoribonuclease
AT3G16270 (Intracellular protein
transport)
4 1046738 FIN Isothermality Survival 4 2.69 10
6
In the gene AT4G02380 SAG21 (Response to water
deprivation)
(23, 24)
4
Within 10 kbp AT4G02370
AT4G02390 PARP1 NAD
+
ADP-ribosyltransferase
(protein amino acid
ADP-ribosylation)
REPORTS
climate differentiation and in the top 5% of glob-
al iEH (Table 1). This screen identified four SNPs
within four candidate genes, and linked within
10 kbp to eight additional candidate genes. The
three most interesting candidate genes with the
associated SNP situated in the coding region
were the LAC1 gene (AT1G18140), involved in
the response to necrotrophs (21), associated with
silique number in Germany; CHR8 (AT2G18770),
involved in DNA repair after viral infection (22),
associated with survival in Germany; and SAG21
(AT4G02380), involved in water stress tolerance
(23, 24) and associated with survival in Finland.
Note that for both CHR8 and SAG21, the allele
showing iEH evidence of a selective sweep cor-
responds to the minor and geographically re-
stricted allele. The CHR8 allele associated with
low survival in Germany is established in the
species northern range, and the SAG21 allele
associated with low survival in Finland is re-
stricted to the southern part of the species range
(Fig. 3). Recent positive selection may have fa-
vored these alleles locally, but their geographic
range may be restricted by negative pleiotropic
effects on fitness in other environments, such as
our field sites.
This study provides robust molecular evidence
for broad scale local adaptation in A. thaliana.
By investigating SNPs linked to loci experienc-
ing real-time selection in different natural en-
vironments, we found that the genetic basis of
fitness differs dramatically across sites. More-
over, alleles associated with high fitness within
sites tend to be local alleles linked to partic-
ular climatic factors, providing evidence of lo-
cal adaptation in A. thaliana at the scale of the
European continent. Our finding that loci as-
sociated with fitness in natural environments
display geographic and climatic signatures of
adaptation complements recent observations
of candidate loci associated with climate (10).
GWAS of fitness traits measured in multiple
natural environments, combined with geograph-
ic and climatic analyses, constitutes a powerful
approach to identify environment-specific can-
didate genes for local adaptation.
1. J. Hereford, Am. Nat. 173, 579 (2009).
2. S. N. Aitken, S. Yeaman, J. A. Holliday, T. L. Wang,
S. Curtis-McLane, Evol. Appl. 1, 95 (2008).
3. J. R. Bridle, T. H. Vines, Trends Ecol. Evol. 22, 140
(2007).
4. A. S. Jump, J. Peuelas, Ecol. Lett. 8, 1010 (2005).
5. D. H. Reed, R. Frankham, Evolution 55, 1095
(2001).
6. I. M. Ehrenreich, M. D. Purugganan, Am. J. Bot. 93,
953 (2006).
7. J. Bergelson, F. Roux, Nat. Rev. Genet. 11, 867
(2010).
8. J. Stapley et al., Trends Ecol. Evol. 25, 705 (2010).
9. I. Baxter et al., PLoS Genet. 6, e1001193 (2010).
10. A. J. Eckert et al., Mol. Ecol. 19, 3789 (2010).
11. M. C. Hall, D. B. Lowry, J. H. Willis, Mol. Ecol. 19, 2739
(2010).
12. C. Mariac et al., Mol. Ecol. 20, 80 (2011).
13. A. M. Wilczek et al., Science 323, 930 (2009).
15. H. M. Kang et al., Nat. Genet. 42, 348 (2010).
17. S. J. Phillips, R. P. Anderson, R. E. Schapire, Ecol. Modell.
190, 231 (2006).
18. P. C. Sabeti et al., Nature 419, 832 (2002).
19. K. Tang, K. R. Thornton, M. Stoneking, PLoS Biol. 5, e171
(2007).
20. D. De Carvalho et al., Mol. Ecol. 19, 1638 (2010).
21. L. Pourcel et al., Plant Cell 17, 2966 (2005).
22. J. Molinier, E. J. Oakeley, O. Niederhauser, I. Kovalchuk,
B. Hohn, Mutat. Res. 571, 235 (2005).
23. L. M. Weaver, S. S. Gan, B. Quirino, R. M. Amasino,
Plant Mol. Biol. 37, 455 (1998).
24. S. B. Mowla et al., Plant J. 48, 743 (2006).
25. A. C. McCormac, G. C. Whitelam, M. T. Boylan, P. H. Quail,
H. Smith, J. Plant Physiol. 140, 707 (1992).
Acknowledgments: We thank M. Blzquez, C. Dean,
M. Hoffmann, H. Kuittinen, and O. Savolainen for
hosting the experiments; J. Anderson, D. Eaton, J. F. Egan,
C. Lopez-Gallego, L. J. Martin, C. D. Muir, R. Petipas, J. Roe,
and R. N. Schaeffer for managing the field experiments;
Brown undergraduates for fruit counts; and J. Bergelson,
A. Hancock, and J. Mossman for comments on the
manuscript. Supported by NSF grant EF-0425759
and an Alexander von Humboldt Research Award.
Supplemental data for the phenotypes and the associated
SNPs are available at http://dx.doi.org/10.5061/
dryad.37f9t. Genotype data for the SNPs used in this study
are available at http://regmap.uchicago.edu.
Figs. S1 to S7
Tables S1 to S6
References
10.1126/science.1209271
The Shaping of Modern Human
Immune Systems by Multiregional
Admixture with Archaic Humans
Laurent Abi-Rached,
1
Matthew J. Jobin,
2,3
Subhash Kulkarni,
1
Alasdair McWhinnie,
4
Klara Dalva,
5
Loren Gragert,
6
Farbod Babrzadeh,
7
Baback Gharizadeh,
7
Ma Luo,
8,9
Francis A. Plummer,
8,9
Joshua Kimani,
10
Mary Carrington,
11,12
Derek Middleton,
13
Raja Rajalingam,
14
Meral Beksac,
5
Steven G. E. Marsh,
4,15
Martin Maiers,
6
Lisbeth A. Guethlein,
1
Sofia Tavoularis,
16
Ann-Margaret Little,
4,15
Richard E. Green,
17
Paul J. Norman,
1
Peter Parham
1
*
Whole genome comparisons identified introgression from archaic to modern humans. Our analysis of
highly polymorphic human leukocyte antigen (HLA) class I, vital immune system components subject to
strong balancing selection, shows how modern humans acquired the HLA-B*73 allele in west Asia through
admixture with archaic humans called Denisovans, a likely sister group to the Neandertals. Virtual
genotyping of Denisovan and Neandertal genomes identified archaic HLA haplotypes carrying functionally
distinctive alleles that have introgressed into modern Eurasian and Oceanian populations. These alleles,
of which several encode unique or strong ligands for natural killer cell receptors, now represent more than
half the HLA alleles of modern Eurasians and also appear to have been later introduced into Africans.
Thus, adaptive introgression of archaic alleles has significantly shaped modern human immune systems.
W
hether or not interbreeding occurred
between archaic and modern humans
has long been debated (1, 2). Recent
estimates suggest that Neandertals contributed
1 to 4% to modern Eurasian genomes (3), and
Denisovans, a likely sister group to the Neander-
tals, contributed 4 to 6% to modern Melanesian
genomes (4). These studies, based on statistical
genome-wide comparisons, did not address if
there was selected introgression of functionally
advantageous genes (5). We explored whether the
highly polymorphic HLA class I genes (HLA-A,
-B, and -C) (fig. S1) of the human major histo-
compatibility complex (MHC) are sensitive probes
for such admixture. Because of their vital func-
tions in immune defense and reproduction, as
ligands for T cell and natural killer (NK) cell re-
1
Department of Structural Biology and Department of Mi-
crobiology and Immunology, Stanford University School of
Medicine, Stanford, CA 94305, USA.
2
Department of An-
thropology, Santa Clara University, Santa Clara, 95050, USA.
3
Department of Anthropology, Stanford University, Stanford,
CA 94305, USA.
4
Anthony Nolan Research Institute, Royal Free
Hospital, London NW3 2QG, UK.
5
Department of Hematology,
Ankara University, 06520 Ankara, Turkey.
6
National Marrow
Donor Program, Minneapolis, MN 55413, USA.
7
Stanford Ge-
nome Technology Center, Stanford University School of Medi-
cine, Palo Alto, CA 94304, USA.
8
Public Health Agency of
Canada, National Microbiology Laboratory, Winnipeg, Manitoba
R3E 3R2, Canada.
9
Department of Medical Microbiology, Uni-
versity of Manitoba, Winnipeg, Manitoba R3E 0J9, Canada.
10
Department of Medical Microbiology, University of Nairobi,
Nairobi 00202, Kenya.
11
Cancer and Inflammation Program,
Laboratory of Experimental Immunology, SAIC-Frederick, Inc.,
National Cancer Institute-Frederick, Frederick, MD 21702,
USA.
12
Ragon Institute of MGH, MIT and Harvard, Boston, MA
02129, USA.
13
Division of Immunology, School of Infection
and Host Defense, University of Liverpool, Transplant Immu-
nology, Royal Liverpool University Hospital, Liverpool L7 8XP,
UK.
14
UCLA Immunogenetics Center, Department of Pathology
and Laboratory Medicine, David Geffen School of Medicine at
UCLA, University of California at Los Angeles, Los Angeles, CA
90095, USA.
15
UCL Cancer Institute, University College London,
Royal Free Campus, London WC1E 6BT, UK.
16
Canadian Blood
Services, Head Office, HLA Laboratory, Ottawa, Ontario KIG 4J5,
Canada.
17
Department of Biomolecular Engineering, University
of California Santa Cruz, Santa Cruz, CA 95064, USA.
peropa@stanford.edu
REPORTS
ceptors, maintaining a variety of HLA-A, -B, and
-C proteins is critical for long-term human sur-
vival (6). Thus, HLA-A, -B, and -C are subject to
strong multiallelic balancing selection, which,
with recombination, imbues human populations
with diverse HLA alleles and haplotypes of dis-
tinctive structures and frequencies (7).
An exceptionally divergent HLA-B allele is
HLA-B*73:01 (8, 9). Comparison with the other
>2000 (10) HLA-B alleles and chimpanzee and
gorilla alleles from the same locus (MHC-B)
shows that HLA-B*73:01 is most closely related
to subsets of chimpanzee and gorilla MHC-B
alleles (11) (figs. S2 to S4). This relation extends
throughout a ~9-kilobase (kb) region of the
B*73:01 haplotype (Fig. 1A) and defines a deep-
ly divergent allelic lineage (MHC-BII ), distinct
from the MHC-BI lineage to which other human
HLA-B alleles belong. These two lineages diverged
~16 million years ago (Fig. 1B), well before the
split between humans and gorillas, but whereas
MHC-BI comprises numerous types and subtypes,
MHC-BII is only represented in modern humans
by B*73:01 (fig. S5). HLA-B*73:01 combines an-
cient sequence divergence with modern sequence
homogeneity, properties compatible with modern
humans having recently acquired HLA-B*73:01
through introgression.
In modern humans, HLA-B*73 is concentrated
in west Asia and is rare or absent in other regions
(12) (Fig. 1C and fig. S6). This distribution is
consistent with introgression of HLA-B*73 in
west Asia, a site of admixture between modern
and archaic humans (3). Also consistent with in-
trogression is the linkage disequilibrium (LD) be-
tween B*73:01 and HLA-C*15:05 (13), an allele
having wider distribution than B*73, but con-
centrated in west and southeast Asia (Fig. 1D).
Worldwide, ~98% of people carrying B*73
also carry C*15:05 (Fig. 1E and fig. S7). In Af-
ricans, the LD reaches 100%, but in west Asians,
it is weaker (~90%). These data are all consist-
ent with introgression in west Asia of an archaic
B*73:01-C*15:05 haplotype that expanded in
frequency there, before spreading to Africa and
elsewhere. HLA-B*73 is absent from Khoisan-
speaking and pygmy populations who likely
diverged from other Africans before the Out-of-
Africa migration (14) (fig. S8). That Khoisan
and pygmies uniquely retain ancient mitochon-
drial and Y-chromosome lineages (14, 15), as
well as MHC-BI diversity (fig. S8), suggests that
B*73 was probably not present in any African
population at the time of the migration. These
data argue for models in which modern humans
acquired B*73 by archaic admixture in west
Asia and against models in which B*73 arose in
F
HLA-C*15:05
E
D
4.9
4.0
3.0
2.0
1.0
0.0
C
Modern/archaic homo split
Admixture
Out-of-Africa migration
Back-to-Africa
migration
Africa West Asia
Models
67.5kya
270-440kya
50kya
B*73+
C*15+
B*73+
C*15-
10kya
Emergence
of C*15:05
65kya
B*73-
C*15+
B*73+
C*15-
b a
HLA-B*73:01
4.0
3.0
2.0
1.0
0.0
4.5
af
(%)
A
20kb 30kb 38kb 10kb 1
HLA-B*73
E1 E2 E3 E4 E5 E6-7
1 2 3 4 5 14 13 11 12
10
6
7
8
9
af
(%)
ARCHAIC
M
O
D
E
R
N
Eurasia
B
30kya
Gene
duplication
Formation of
two lineages
MHC-BI
MHC-BII
Gene loss
MHC-B
16.3 MYA
[13.8-19.9 MYA]
Inter-locus
recombination
Human
Gorilla
HLA-B*73
Chimpanzee
Preservation of two lineages at the same locus
Europe 2,677 98.4 0.3 0.4 0.9
Europe
#
2,907 98.5 0.3 0.3 0.9
Africa 39 100 0.0 0.0 0.0
Africa
##
90 97.8 2.2 0.0 0.0
W Asia 128 89.8 5.5 0.8 3.9
N/S/E Asia 53 92.5 5.7 1.9 0.0
Other 498 99.0 0.0 0.4 0.6
Total 3,676 98.2 0.5 0.4 0.9
Geographic
region
N
B*73 individuals
+
C*15
not
15:05
15:05
Associated
HLA-C alleles
(%)
Not C*15
12:02
not
12:02
Disappear
Fig. 1. Modern humans acquired HLA-B*73 from archaic humans. (A) The B*73 haplotype contains
segments most closely related to chimpanzee and gorilla MHC-B alleles (green) and flanking segments
highly related to other HLA-B (blue) (brown segment is related to HLA-C) (fig. S4). (B) B*73s divergent
core has its roots in a gene duplication that occurred >16 million years ago (MYA on figure). (Left to
right) MHC-B duplicated and diverged to form the MHC-BI and BII loci. One allele of BII recombined to
the BI locus, giving rise to the ancestor of B*73 and its gorilla and chimpanzee equivalents. B*73 is
thus the only remnant in modern humans of a deeply divergent allelic lineage. Mean and 95% credibility interval. (C to E) B*73:01 is predominantly found
outside Africa (C) as is C*15:05 (D), which is strongly associated with B*73 in 3676 individuals worldwide (E). (C and D) Color scale bars give allele frequency
(af) categories (top number, highest tick mark). Individuals with the B*73 haplotype were categorized on the basis of their geographic origin and the status of
the most commonly linked (C*15) and second-most commonly linked (C*12:02) HLA-C alleles (fig. S24). Number sign (#) includes Hispanic-Americans, double
number sign (##) includes African-Americans. (F) Archaic admixture (model a) or African origin (model b) could explain the distribution and association of
B*73 with C*15:05; simulations favor the former (a = 0.01 to 0.001) (figs. S9 to S11) (11). The large dotted box indicates the part of the models examined
by simulation; kya, thousand years ago.
REPORTS
Africa and was carried to other continents in the
Out-of-Africa migration (Fig. 1F), as do the re-
sults of coalescence simulations that implement
rejection-based approximate Bayesian inference
(16) (a = 0.01 to 0.001) (figs. S9 to S11).
Byreanalyzinggenomic sequence data (3, 4, 11),
we characterized archaic HLAclass I content froma
Denisovan and three Neandertals. The Denisovans
two HLA-Aand two HLA-Callotypes are identi-
cal to common modern allotypes, whereas one
HLA-B allotype corresponds to a rare modern
recombinant allotype, and the other has never
been seen in modern humans (Fig. 2B and fig.
S12). The Denisovans HLA type is thus consist-
ent with an archaic origin and the known propen-
sity for HLA-B to evolve faster than HLA-A and
HLA-C (17, 18).
Not knowing the haplotype phase, we ex-
amined all possible combinations of Denisovan
HLA-A and HLA-C for their current distribution
worldwide. All four combinations are present in
Asia and Oceania, but absent from sub-Saharan
Africa, and uncommon in Europe (Fig. 2, C and D,
and fig. S13). Genome-wide comparisons showed
that modern and archaic non-African genomes
share only 10 long, deeply divergent haplotypes (3),
which are all considerably shorter (100 to 160 kb)
than the ~1.3-megabase (Mb) HLA-A-C haplotype
(Fig. 2A). Because modern HLA haplotypes di-
versify rapidly by recombination (1719), it is im-
probable that the HLA-A-C haplotypes shared
by modern humans and Denisovans were pre-
served on both lines since modern and Denisovan
ancestors separated >250 thousand years ago
(kya) [~10,000 generations (4)]. More likely is
that modern humans acquired these haplotypes
by recent introgression from Denisovans [note
II.6 in (11)]. Both alternative haplotype pairs are
common in Melanesians and reach 20% frequen-
cy in Papua New Guinea (PNG), consistent with
genome-wide assessment of Denisovan admix-
ture in Melanesians (4). The current distribution
Fig. 2. Effect of adaptive introgression of Denisovan
HLA class I alleles on modern Asian and Oceanian
populations. (A) Simplified map of the HLA class I
region showing the positions of the HLA-A, -B,
and -C genes. (B) Five of the six Denisovan HLA-A,
-B, and -C alleles are identical to modern counter-
parts. Shown at the left for each allele is the num-
ber of sequence reads (4) specific to that allele and
their coverage of the ~3.5-kb HLA class I gene. Cen-
ter columns give the modern-human allele (HLA type)
that has the lowest number of single-nucleotide
polymorphism (SNP) mismatches to the Denisovan
allele. The next most similar modern allele and the
number of SNP differences are shown in the columns on the right. A recombinant allele with 5 segments originating from B*40. The coding sequence is
identical to C*15:05:02. (C and D) Worldwide distributions of the two possible Denisovan HLA-A to -C haplotype combinations. Both are present in modern
Asians and Oceanians but absent from sub-Saharan Africans. (E to G) The distribution of three Denisovan alleles: HLA-A*11 (E), C*15 (F), and C*12:02 (G), in
modern human populations shows they are common in Asians but absent or rare in sub-Saharan Africans. (H) Estimation of divergence times shows that A*11,
C*15, and C*12:02 were formed before the Out-of-Africa migration. Shown on the left are the alleles they diverged from, on the right are the divergence time
estimates: median, mean, and range.
REPORTS
of the Denisovan haplotypes (Fig. 2, C and D,
and fig. S13) shows, however, that Denisovan ad-
mixture widely influenced the HLA system of
Asians and Amerindians.
Of the two Denisovan HLA-A alleles (Fig. 2B),
A*02 is widespread in modern humans, whereas
A*11 is characteristically found in Asians (Fig.
2E) and reaches 50 to 60% frequency in PNG and
China, is less common in Europe, and is absent
from Africa (fig. S14). This distribution cou-
pled with the sharing of long HLA-A-C haplo-
types between Denisovans and modern Asians,
particularly Papuans (fig. S13), indicates that
Denisovan admixture minimally contributed the
A*11:01-C*12 or A*11:01-C*15 haplotype to mod-
ern Asians. A*11:01, which is carried by both these
archaic haplotypes, is by far the most common
A*11 subtype (12). Because HLA alleles evolve
subtype diversity rapidly (17, 18), it is highly im-
probable that A*11:01 was preserved indepen-
dently in Denisovan and modern humans through-
out >250,000 years (4), as would be required if the
Out-of-Africa migration contributed any signif-
icant amount of A*11. The more parsimonious
interpretation is that all modern A*11 is derived
from Denisovan A*11 and that, after introgres-
sion, it increased in frequency to ~20% to become
almost as common in Asia as A*02 at ~24% (11).
Denisovan HLA-C*15 and HLA-C*12:02 are
also characteristic alleles of modern Asian popula-
tions (Fig. 2, F and G, and fig. S14). At high fre-
quency in PNG, their distribution in continental
Asia extends further west than A*11 does, and in
Africa, their frequencies are low. C*12:02 and C*15
were formed before the Out-of-Africa migration
(Fig. 2H and fig. S15) and exhibit much higher
haplotype diversity in Asia than in Africa (fig. S16),
contrasting with the usually higher African genetic
diversity (20). These properties fit with C*12:02
and C*15 having been introduced to modern
humans through admixture with Denisovans in
west Asia, with later spreading to Africa (21, 22)
(Fig. 1F and fig. S11 for C*15). Given our min-
imal sampling of the Denisovan population, it is
remarkable that C*15:05 and C*12:02 are the
two modern HLA-C alleles in strongest LD with
B*73 (Fig. 1E). Although B*73 was not carried by
the Denisovan individual studied, the presence of
these two associated HLA-Calleles provides strong
circumstantial evidence that B*73 was passed
from Denisovans to modern humans.
Genome-wide analysis showing that three
Vindija Neandertals exhibited limited genetic di-
versity (3) is reflected in our HLA analysis: Each
individual has the same HLA class I alleles (fig.
S17). Because these HLA identities could not be
the consequence of modern human DNA con-
tamination of Neandertal samples, which is <1%
(3), they indicate that these individuals likely
belonged to a small and isolated population (fig.
Fig. 3. Effect of adaptive introgression of Nean-
dertal HLA class I alleles on modern human pop-
ulations. (A) All six Neandertal HLA-A, -B, and -C
alleles are identical to modern HLA class I alleles.
Shown at the left for each allele is the number of
allele-specific sequence reads (3) and their cover-
age of the ~3.5-kb HLA gene. Center columns give
the modern-human allele (HLA type) having the
lowest number of SNP differences from the Nean-
dertal allele. The next most similar modern allele
and the number of SNP differences are shown in
the columns on the right. Alleles marked with include additional rare alleles. (B and C) Worldwide distributions of the two possible Neandertal HLA-A to -C
haplotype combinations. Both are present in modern Eurasians, but absent from sub-Saharan Africans. (D to G) Distribution of four Neandertal alleles: HLA-
B*07:02/03/06 (D), B*51:01/08 (E), C*07:02 (F), and C*16:02 (G), in modern human populations.
REPORTS
S18). Clearly identified in each individual were
HLA-A*02, C*07:02, and C*16; pooling the three
sequence data sets allowed identification of HLA-
B*07, -B*51 and either HLA-A*26 or its close
relative A*66 as the other alleles (Fig. 3A). As
done for the Denisovan, we examined all combi-
nations of Neandertal HLA-A and HLA-C for their
current distribution worldwide. All four combi-
nations have highest frequencies in Eurasia and
are absent in Africa (Fig. 3, B and C, and fig. S19).
Such conservation and distribution strongly sup-
port introgression of these haplotypes into mod-
ern humans by admixture with Neandertals in
Eurasia. The Neandertal HLA-B and -C alleles were
sufficiently resolved for us to study their distribution
in modern human populations (fig. S20); their
frequencies are high in Eurasia and low in Africa
(Fig. 3, D to G, and fig. S21). Our simulations of
HLA allele introgression predicted the increased
frequency and haplotype diversity in Eurasia that
we observed (Fig. 1 and fig. S11) and was particu-
larly strong for B*51 and C*07:02 (fig. S22), and
the presence of such alleles in Africa was due to
back-migrations. Thus, Neandertal admixture con-
tributed B*07-, B*51-, C*07:02-, and C*16:02-
bearing haplotypes to modern humans and was
likely the sole source of these allele groups. Un-
like the distributions of Denisovan alleles, which
center in Asia (Fig. 2, E to G), Neandertal alleles
display broader distributions peaking in different
regions of Eurasia (Fig. 3, D to G).
Modern populations with substantial levels of
archaic ancestry are predicted to have decreased
LD (23). From analysis of HapMap populations
(20), we find that HLA class I recombination rates
are greater in Europeans (1.7- to 2.5-fold) and
Asians (2.9- to 7.7-fold) than in Africans, con-
sistent with their higher frequencies of archaic
HLA class I alleles (Fig. 4A). Enhanced LD de-
cay correlates with the presence of archaic alleles
(Fig. 4B and fig. S23), and the strongest correla-
tion was with HLA-A, for which the six haplo-
types exhibiting enhanced LD decay are restricted
to non-Africans. These haplotypes include A*24:02
and A*31:01, along with the four archaic allele
groups we characterized (A*11, A*26, and two
A*02 groups). A*24:02 and A*31:01 are common
in non-Africans and thus likely also introgressed
from archaic to modern humans. From the com-
bined frequencies of these six alleles, we estimate
the putative archaic HLA-A ancestry to be >50%
in Europe, >70% in Asia, and >95% in parts of
PNG (Fig. 4, C and D). These estimates for HLA-A
are much higher than the genome-wide estimates
of introgression (1 to 6%), which shows how
limited interbreeding with archaic humans has,
in combination with natural selection, substan-
tially shaped the HLA system in modern human
populations outside of Africa. Our results demon-
strate how highly polymorphic HLA genes can
be sensitive probes of introgression, and we pre-
dict that the same will apply to other polymorphic
immune-system genes, for example, those encod-
ing the killer-cell immunoglobulin-like receptors
(KIR) of NK cells. Present in the Denisovan ge-
nome (11), a candidate KIR for introgression is
KIR3DS1*013 (Fig. 4E), rare in sub-Saharan Af-
ricans, but the most common KIR3DL1/S1 allele
outside Africa (24).
On migrating out of Africa, modern humans
encountered archaic humans, residents of Eurasia
for more than 200,000 years, who had immune
systems better adapted to local pathogens (25).
Such adaptations almost certainly involved changes
in HLA class I, as exemplified by the modern hu-
man populations who first colonized the Americas
(17, 18). For small migrating populations, admix-
ture with archaic humans could restore HLA di-
versity after population bottleneck and also provide
a rapid way to acquire new, advantageous HLA
variants already adapted to local pathogens. For
example, HLA-A*11, an abundant archaic allo-
type in modern Asian populations, provides T
cellmediated protection against some strains of
Epstein-Barr virus (EBV) (26), and in combina-
tion with a peptide derived from EBV, is one of
only two HLA ligands for the KIR3DL2 NK cell
receptor (27). HLA*A11 is also the strongest lig-
and for KIR2DS4 (28). Other prominent intro-
gressed HLA class I proteins are good KIR ligands.
HLA-B*73 is one of only two HLA-B allotypes
carrying the C1 epitope, the ligand for KIR2DL3
(29). Prominent in Amerindians, C*07:02 is a
strong C1 ligand for KIR2DL2/3 and both B*51
and A*24 are strong Bw4 ligands for KIR3DL1
(30). Such properties suggest that adaptive intro-
gression of these HLA alleles was driven by their
role in controlling NK cells, lymphocytes essential
for immune defense and reproduction (6). Con-
versely, adaptive introgression of HLA-A*26,
-A*31, and -B*07, which are not KIR ligands,
was likely driven by their role in Tcell immunity.
Adaptive introgression provides a mechanism for
A
C
D E
Putative archaic ancestry at HLA-A
30.0
0.0
98.2
60.0
90.0
af
(%)
15.0
0.0
52.3
30.0
45.0
af
(%)
KIR3DS1*013
B
Mean SD
African 0.33 0.02
European 0.57 0.05
Japanese 0.98 0.11
Chinese 1.07 0.11
African 0.32 0.03
European 0.57 0.06
Japanese 0.92 0.09
Chinese 0.95 0.10
African 0.51 0.10
European 1.72 0.39
Japanese 2.52 0.52
Chinese 3.94 0.81
Genomic
region
Population
Recombination
rate (cM/Mb)
HLA-A-B
(~1.4Mb)
HLA-A-C
(~1.3Mb)
HLA-C-B
(~85kb)
Population Putative archaic ancestry at HLA-A
African 6.7%
European 51.7%
Chinese 72.2%
Japanese 80.7%
Papua New Guinea 82.3% [65.9% - 95.3%]
African European Chinese Japanese
22 17 14 11
Number 0 5 3 5
02:01 02:01 02:01
02:06 02:06
---
11:01 11:01
---
24:02 24:02 24:02
26:01 26:01
---
31:01
Allele-specific
haplotypes
with
enhanced
LD decay
Population
Distinct alleles
HLA-A
Defining
allele
name
(A* )
Fig. 4. LD decay patterns of modern HLA haplotypes identify putative archaic HLA alleles. (A) HLA class I
recombination rates in Eurasia exceed those observed in Africa. We focused on the three intergenic
regions between HLA-A, -B, and -C (left-most column) in the four HapMap populations (center column)
(20). Recombination rates were corrected for effective population size (11). (B) Enhanced HLA class I LD
decay significantly correlates with archaic ancestry (a = 0.0042) (11). Shown for each HapMap
population are (top row) the number of distinct HLA-A alleles present and (second row) the number
exhibiting enhanced LD decay [all allele-defining SNPs (correlation coefficient r
2
> 0.2) are within 500
kb of HLA-A (31)]. The allele names are listed (rows 3 to 8) and colored green when observed in archaic
humans (Figs. 2 and 3) or associated with archaic-origin haplotypes (fig. S25). HLA-B and -C are shown in
fig. S23. Dashed line indicates absent in the population. (C) Predicted archaic ancestry at HLA-A [on the
basis of the six alleles of panel (B)] for the four HapMap populations and six populations from PNG; for the
latter, mean and extreme values are given. (Dand E) Worldwide distribution in modern human populations
of putative archaic HLA-A alleles (D) and KIR3DS1*013, a putative archaic NK cell receptor (E).
REPORTS
rapid evolution, a signature property of the extra-
ordinarily plastic interactions between MHC class
I ligands and lymphocyte receptors (6).
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2. V. Yotova et al., Mol. Biol. Evol. 28, 1957 (2011).
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PLoS Genet. 4, e1000168 (2008).
6. P. Parham, Nat. Rev. Immunol. 5, 201 (2005).
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15. O. Semino, A. S. Santachiara-Benerecetti, F. Falaschi,
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18. D. I. Watkins et al., Nature 357, 329 (1992).
19. M. L. Petzl-Erler, R. Luz, V. S. Sotomaior, Tissue Antigens
41, 227 (1993).
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1299 (2005).
21. F. Cruciani et al., Am. J. Hum. Genet. 70, 1197 (2002).
22. Y. Moodley et al., Science 323, 527 (2009).
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Acad. Sci. U.S.A. 106, 16057 (2009).
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(2008).
26. P. O. de Campos-Lima et al., Science 260, 98 (1993).
27. P. Hansasuta et al., Eur. J. Immunol. 34, 1673 (2004).
28. T. Graef et al., J. Exp. Med. 206, 2557 (2009).
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31. P. I. de Bakker et al., Nat. Genet. 38, 1166 (2006).
Acknowledgments: We thank individual investigators and the
Bone Marrow Donors Worldwide (BMDW) organization
for kindly providing HLA class I typing data, as well as
bone marrow registries from Australia, Austria, Belgium,
Canada, Cyprus, Czech Republic, France, Ireland, Israel,
Italy, Lithuania, Norway, Poland, Portugal, Singapore,
Spain, Sweden, Switzerland, Turkey, United Kingdom,
and United States for contributing typing data through
BMDW. We thank E. Watkin for technical support. We are
indebted to the large genome sequencing centers for
early access to the gorilla genome data. We used
sequence reads generated at the Wellcome Trust Sanger
Institute as part of the gorilla reference genome
sequencing project. These data can be obtained from
the National Center for Biotechnology Information (NCBI)
Trace Archive (www.ncbi.nlm.nih.gov/Traces). We also
used reads generated by Washington University School of
Medicine; these data were produced by the Genome
Institute at Washington University School of Medicine in
St. Louis and can be obtained from the NCBI Trace
Archive (www.ncbi.nlm.nih.gov/Traces/). Funded by NIH
grant AI031168, Yerkes Center base grant RR000165,
NSF awards (CNS-0619926, TG-DBS100006), by federal
funds from the National Cancer Institute (NCI), NIH
(contract HHSN261200800001E), and by the Intramural
Research Program of the NCI, NIH, Center for Cancer
Research. The content of this publication does not
necessarily reflect the views or policies of the Department
of Health and Human Services, nor does mention of
trade names, commercial products, or organizations
imply endorsement by the U.S. government. Sequence
data have been deposited in GenBank under accession
nos. JF974053 to 70.
Figs. S1 to S26
References (3287)
Published online 25 August 2011;
10.1126/science.1209202
An Aboriginal Australian Genome
Reveals Separate Human
Dispersals into Asia
Morten Rasmussen,
1,2
* Xiaosen Guo,
2,3
* Yong Wang,
4
* Kirk E. Lohmueller,
4
* Simon Rasmussen,
5
Anders Albrechtsen,
6
Line Skotte,
6
Stinus Lindgreen,
1,6
Mait Metspalu,
7
Thibaut Jombart,
8
Toomas Kivisild,
9
Weiwei Zhai,
10
Anders Eriksson,
11
Andrea Manica,
11
Ludovic Orlando,
1
Francisco M. De La Vega,
12
Silvana Tridico,
13
Ene Metspalu,
7
Kasper Nielsen,
5
Mara C. vila-Arcos,
1
J. Vctor Moreno-Mayar,
1,14
Craig Muller,
15
Joe Dortch,
16
M. Thomas P. Gilbert,
1,2
Ole Lund,
5
Agata Wesolowska,
5
Monika Karmin,
7
Lucy A. Weinert,
8
Bo Wang,
3
Jun Li,
3
Shuaishuai Tai,
3
Fei Xiao,
3
Tsunehiko Hanihara,
17
George van Driem,
18
Aashish R. Jha,
19
Franois-Xavier Ricaut,
20
Peter de Knijff,
21
Andrea B Migliano,
9,22
Irene Gallego Romero,
19
Karsten Kristiansen,
2,3,6
David M. Lambert,
23
Sren Brunak,
5,24
Peter Forster,
25,26
Bernd Brinkmann,
26
Olaf Nehlich,
27
Michael Bunce,
13
Michael Richards,
27,28
Ramneek Gupta,
5
Carlos D. Bustamante,
12
Anders Krogh,
1,6
Robert A. Foley,
9
Marta M. Lahr,
9
Francois Balloux,
8
Thomas Sicheritz-Pontn,
5,29
Richard Villems,
7,30
Rasmus Nielsen,
4,6
Jun Wang,
2,3,6,31
Eske Willerslev
1,2
We present an Aboriginal Australian genomic sequence obtained from a 100-year-old lock of

hair donated by an Aboriginal man from southern Western Australia in the early 20th century.
We detect no evidence of European admixture and estimate contamination levels to be below
0.5%. We show that Aboriginal Australians are descendants of an early human dispersal into
eastern Asia, possibly 62,000 to 75,000 years ago. This dispersal is separate from the one that
gave rise to modern Asians 25,000 to 38,000 years ago. We also find evidence of gene flow
between populations of the two dispersal waves prior to the divergence of Native Americans
from modern Asian ancestors. Our findings support the hypothesis that present-day Aboriginal
Australians descend from the earliest humans to occupy Australia, likely representing one of the
oldest continuous populations outside Africa.
T
he genetic history of Aboriginal Austra-
lians is contentious but highly important
for understanding the evolution of modern
humans. All living non-African populations like-
ly derived from a single dispersal of modern hu-
mans out of Africa, followed by subsequent serial
founder effects (1, 2). Accordingly, eastern Asia
is hypothesized to have been populated by a
single early migration wave rather than multiple
dispersals (3). In this single-dispersal model,
Aboriginal Australians are predicted to have di-
versified from within the Asian cluster [for defi-
nitions of human populations and groups, see (4)]
(Fig. 1A, top). Recent whole-genome studies re-
veal a split between Europeans and Asians dat-
ing to 17,000 to 43,000 years before the present
(B.P.) (5, 6). Because greater Australia (Australia
and Melanesia, including NewGuinea) has some
of the earliest archaeological evidence of ana-
tomically modern humans outside Africa, dating
back to ~50,000 years B.P. (7, 8), a divergence of
aboriginal Australasians from within the Asian
cluster is not compatible with population conti-
nuity in Australia. Alternatively, on the basis of
archaeological and fossil evidence, it has been
proposed that greater Australia was occupied by
an early, possibly independent out-of-Africa dis-
persal, before the population expansion giving
rise to the majority of present-day Eurasians (9, 10).
According to this multiple-dispersal model,
the descendants of the earlier migration became
assimilated or replaced by the later-dispersing
populations, with a few exceptions that include
Aboriginal Australians (10, 11) (Fig. 1A, bottom).
We sequenced the genome of an Aboriginal
Australian male from the early 20th century to
overcome problems of recent European admix-
ture and contamination (4). We used 0.6 g of hair
for DNA extraction (4, 12). Despite its relatively
young age, the genomic sequence showed a high
degree of fragmentation, with an average length
of 69 base pairs. The genome was sequenced to
an overall depth of 6.4; the ~60% of the ge-
nomic regions covered was sequenced to an av-
erage depth of 11 (4) [theoretical maximum is
~85% (12)]. Cytosine-to-thymine misincorpora-
tion levels typical of ancient DNA (13) were low
REPORTS
1
Centre for GeoGenetics, Natural History Museumof Denmark,
and Department of Biology, University of Copenhagen, ster
Voldgade 5-7, 1350 Copenhagen, Denmark.
2
Sino-Danish
Genomics Center, BGI-Shenzhen, Shenzhen 518083, China,
and University of Copenhagen, Denmark.
3
Shenzhen Key
Laboratory of Transomics Biotechnologies, BGI-Shenzhen,
Shenzhen 518083, China.
4
Departments of Integrative Biol-
ogy and Statistics, University of California, Berkeley, Berkeley,
CA 94720, USA.
5
Center for Biological Sequence Analysis,
Department of Systems Biology, Technical University of
Denmark, 2800 Lyngby, Denmark.
6
Department of Biology,
University of Copenhagen, 2200 Copenhagen, Denmark.
7
Department of Evolutionary Biology, Tartu University and
Estonian Biocentre, 23 Riia Street, 510101 Tartu, Estonia.
8
MRC Centre for Outbreak, Analysis and Modeling, Department
of Infectious Disease Epidemiology, Imperial College Faculty
of Medicine, London W2 1PG, UK.
9
Leverhulme Centre for
Human Evolutionary Studies, Department of Biological
Anthropology, University of Cambridge, Cambridge CB2
1QH, UK.
10
Beijing Institute of Genomics, Chinese Academy
of Sciences, No. 7 Beitucheng West Road, Chaoyang District,
Beijing 100029, China.
11
Evolutionary Ecology Group,
Department of Zoology, University of Cambridge, Cambridge
CB2 3EJ, UK
12
Department of Genetics, Stanford University
School of Medicine, Stanford, CA 94305, USA.
13
Ancient DNA
Lab, School of Biological Sciences and Biotechnology,
Murdoch University, Western Australia 6150, Australia.
14
Undergraduate Program on Genomic Sciences, National
Autonomous University of Mexico, Avenida Universidad s/n
Chamilpa 62210, Cuernavaca, Morelos, Mexico.
15
Goldfields
Land and Sea Council Aboriginal Corporation, 14 Throssell
Street, Kalgoorlie, Western Australia 6430, Australia.
16
Ar-
chaeology, University of Western Australia, Crawley, Western
Australia 6009, Australia.
17
Department of Anatomy, Kitasato
University School of Medicine, 1-15-1 Kitasato, Minami-ku,
Sagamihara 252-0374, Japan.
18
Institut fr Sprachwissenschaft,
Universitt Bern, 3000 Bern 9, Switzerland.
19
Department of
Human Genetics, University of Chicago, Chicago, IL 60637,
USA.
20
Laboratoire dAnthropologie Molculaire et Imagerie de
Synthse, Universit de Toulouse (Paul Sabatier)CNRS UMR
5288, 31073 Toulouse Cedex 3, France.
21
Department of Hu-
man and Clinical Genetics, Postzone S5-P, Leiden University
Medical Center, 2333 ZA Leiden, Netherlands.
22
Department
of Anthropology, University College London, London WC1E
6BT, UK.
23
Griffith School of Environment and School of
Biomolecular and Physical Sciences, Griffith University,
Nathan, Queensland 4111, Australia.
24
Novo Nordisk
Foundation Center for Protein Research, Faculty of Health
Sciences, University of Copenhagen, 2200 Copenhagen, Den-
mark.
25
Murray Edwards College, University of Cambridge,
Cambridge CB3 0DF, UK.
26
Institute for Forensic Genetics,
D-48161 Mnster, Germany.
27
Department of Human Evolu-
tion, Max Planck Institute for Evolutionary Anthropology,
04103 Leipzig, Germany.
28
Department of Anthropology,
University of British Columbia, Vancouver, British Columbia
V6T 1Z1, Canada.
29
Novo Nordisk Foundation Center for
Biosustainability, Technical University of Denmark, 2800
Lyngby, Denmark.
30
Estonian Academy of Sciences, 6 Kohtu
Street, 10130Tallinn, Estonia.
31
Novo Nordisk Foundation Center
for Basic Metabolic Research, University of Copenhagen, 2200
Copenhagen, Denmark.
ewillerslev@snm.ku.dk (E.W.); wangj@genomics.org.cn (W.J.);
rasmus_nielsen@berkeley.edu (R.N.)
Fig. 1. (A) The two models for early dispersal of modern humans into eastern
Asia. Top: Single-dispersal model predicting a single early dispersal of modern
humans into eastern Asia. Bottom: Multiple-dispersal model predicting sep-
arate dispersals into eastern Asia of aboriginal Australasians and the an-
cestors of most other present-day East Asians. AF, Africans; EU, Europeans;
ASN, Asians; ABR, Aboriginal Australians. Arrow symbolizes gene flow. (B) PCA
plot (PC1 versus PC2) of the studied populations and the ancient genome of
the Aboriginal Australian (marked with a cross). Inset shows the greater
Australia populations (4). (C) Ancestry proportions of the studied 1220 in-
dividuals from 79 populations and the ancient Aboriginal Australian as re-
vealed by the ADMIXTURE program (28) with K = 5, K = 11, and K = 20. A
stacked column of the K proportions represents each individual, with fractions
indicated on the y axis [see (4) for the choice of K]. The greater Australia pop-
ulations are shown in detail at the upper right.
REPORTS
(maximum3%of all cytosines) and were restricted
to a 5-nucleotide region at each read terminus.
For this reason, read termini were trimmed to im-
prove single-nucleotide polymorphism(SNP) call
quality (4).
The genome was mapped and genotyped,
identifying 2,782,401 SNPs, of which 449,115
were considered high-confidence, with a false-
positive rate of <2.4%, and were used in further
analyses (4). Of these, 28,395 (6.3%) have not
been previously reported (4). Despite extensive
handling of the hair by people of European an-
cestry, contamination levels based on the level of
X-chromosome heterozygosity were estimated
to be less than 0.5% (4). These findings are in
agreement with studies showing that ancient hu-
man hair can be decontaminated by pretreatment
(12, 14). Furthermore, no evidence of recent Eu-
ropean admixture or contamination could be de-
tected at the genotype level (4).
The Australian individuals mitochondrial ge-
nome (mtDNA) was sequenced to an average
depth of 338. It belongs to a new subclade of
haplogroup O (hg O) that we term hg O1a (4).
Haplogroup O is one of the four major lineage
groups specific to Australia and has been re-
ported from various parts of the Northern Terri-
tory (15 to 16%) (1517). From high-confidence
Y-chromosome SNPs, we assigned his Y chro-
mosome to the K-M526* macro-haplogroup (4).
Although the O and P branches of haplogroup
K-M526 account for the majority of East and
West Eurasian Y chromosomes, the unresolved
K-M526* lineages are more common (>5%) on-
ly among contemporary populations of Australasia
(15, 18). Both uniparental markers fall within the
known pattern found among contemporary Ab-
original Australians (15), providing further evi-
dence that the genomic sequence obtained is not
contaminated.
We compared our high-confidence SNPs with
Illumina SNP chip data from 1220 individuals
belonging to 79 populations (4). Among these
are individuals from the Kusunda and Aeta, two
populations of hunter-gatherers from Nepal and
the Philippines, respectively. Both groups have
been hypothesized to be possible relict popula-
tions from the proposed early wave of dispersal
across eastern Asia (19, 20).
Principal components analysis (PCA) results
illustrated genetic differentiation among Africans,
Asians, and populations of greater Australia. The
Australian genome clusters together with High-
land Papua New Guinea (PNG) samples and is
thus positioned roughly between South and East
Asians. Apart fromthe neighboring Bougainville
Papuans, the closest populations to the Aborig-
inal Australian are the Munda speakers of India
and the Aeta from the Philippines (Fig. 1B). This
pattern is confirmed from542 individuals from43
Asian and greater Australia populations (4) and by
including an additional 25 populations from India
(21) that all fall on the Eurasian axis, including
those of the Great Andamanese and Onge from
the Andaman Islands (21). The PCA and ad-
mixture results (Fig. 1C) further confirm the lack
of European contamination or recent admixture in
the genome sequence.
We used the D test (22, 23) on the SNP chip
data and genomes to look for shared ancestry
between Aboriginal Australians and other groups
(4). We found significantly larger proportions of
shared derived alleles between the Aboriginal
Australian and Asians (Cambodian, Japanese,
Han, and Dai) than between the Aboriginal Aus-
tralian and Europeans (French) (Table 1, rows
1 to 4). We also found a significantly larger pro-
portion of shared derived alleles between the
French and the Asians than between the French
and the Aboriginal Australian (Table 1, rows 5
to 8). These findings do not allow us to dis-
criminate between the two models of origin, but
they do rule out simple models of complete iso-
lation of populations since divergence. Our data
do not provide consistent evidence of gene flow
between populations of greater Australia (Ab-
original Australian/PNG Highlands) and Asian
ancestors after the latter split from Native Amer-
icans under various models (4) (there may still be
some gene flow between Bougainville and some
Asian ancestors after that time; Table 1). This sug-
gests that before European contact occurred, Ab-
original Australian and PNGHighlands ancestors
Table 1. Results of D test.
Ingroup 1 Ingroup 2 Outgroup Difference* Total D SD Z||
1 French Cambodian Australian 461 8,035 0.06 0.013 4.5
2 French Japanese Australian 463 8,107 0.06 0.013 4.5
3 French Han Australian 674 7,908 0.09 0.012 7.0
4 French Dai Australian 636 8,214 0.08 0.013 6.0
5 Australian Cambodian French 435 8,009 0.05 0.013 4.3
6 Australian Japanese French 357 7,991 0.04 0.012 3.6
7 Australian Han French 487 7,713 0.06 0.012 5.1
8 Australian Dai French 343 7,919 0.04 0.012 3.5
9 Surui Cambodian Australian 4 7,644 0.00 0.012 0.0
10 Surui Japanese Australian 1 7,477 0.00 0.013 0.0
11 Surui Han Australian 215 7,261 0.03 0.013 2.4
12 Surui Dai Australian 169 7,493 0.02 0.013 1.7
13 Surui Cambodian PNG Highlands 195 64,149 0.00 0.006 0.5
14 Surui Japanese PNG Highlands 288 62,364 0.00 0.006 0.7
15 Surui Han PNG Highlands 393 60,947 0.01 0.006 1.0
16 Surui Dai PNG Highlands 427 62,925 0.01 0.006 1.0
17 Surui Cambodian Bougainville 319 64,951 0.00 0.006 0.8
18 Surui Japanese Bougainville 1,543 63,063 0.02 0.007 3.6
19 Surui Han Bougainville 1,577 62,019 0.03 0.006 3.9
20 Surui Dai Bougainville 1,691 63,585 0.03 0.006 4.2
*Number of sites where a derived allele is shared between outgroup and ingroup 1 subtracted from sites where the derived allele is
shared between outgroup and ingroup 2. Number of sites where a derived allele is found in the outgroup and one of the
ingroups. D test statistics (difference divided by total). Standard deviation (found by block jackknife). ||Standardized
statistics (to determine significance).
Table 2. Results of the D
4P
test. The results are from NA19239 (for YRI), NA12891 (for CEU), HG00421
(for ASN), and the Aboriginal Australian genome (ABR). The two groups are patterns representing the two
ways in which eligible SNPs can partition the four genomes (they have not been polarized).
Group 1 Group 2
YRI 1 1
ABR 0 1
CEU 0 0
ASN 1 0
Observed number* 13,974 14,765
Observed proportion (95% CI) 48.6%
(47.8 to 49.4%)
51.4%
(50.6 to 52.2%)
Expected proportion under multiple-dispersal model 1 48.7% 51.3%
Expected proportion under multiple-dispersal model 2 48.0% 52.0%
Expected proportion under single-dispersal model|| 50.3% 49.7%
*Average number of eligible SNPs showing groups 1 and 2 across block bootstrap replicates. 95% confidence interval obtained
from a block bootstrap (4). Z test rejects the null hypothesis that this value is equal to 50% (Z = 3.3, P < 0.001). Expected
proportion from a multiple-dispersal model in which aboriginal Australasians split from Eurasian populations 2500 generations ago,
before the split of European and Asian populations. This split time was estimated using the Aboriginal, NA12891, and HG00421
sequences (4). These were the same individuals used for the D
4P
analysis. Expected proportion froma multiple-dispersal model in
which aboriginal Australasians split from Eurasian populations 2750 generations ago, before the split of European and Asian pop-
ulations. This split time was estimated using the Aboriginal Australian and all Eurasian sequences (4). ||Expected proportion from
coalescent simulations under a model in which aboriginal Australasians split from Asian populations 1500 generations ago. The other
parameters were those estimated by Schaffner et al. (27). See (4) for additional models.
REPORTS
had been genetically isolated from other pop-
ulations (except possibly each other) since at least
15,000 to 30,000 years B.P. (24).
To identify which model of human dispersal
best explains the data, we sequenced three Han
Chinese genomes to an average depth of 23 to
24 (4) and used a test comparing the patterns of
similarity between these or the Aboriginal Aus-
tralian to African and European individuals (4).
This test, which we call D
4P
, is closely related to
the D test (22, 23) but is far more robust to errors
and can detect subtle demographic signals in the
data that may be masked by large amounts of
secondary gene flow (4).
Taking those sites where the Aboriginal Aus-
tralian (ABR) differs from a Han Chinese repre-
senting eastern Asia (ASN), and comparing ABR
and ASN with the Centre dEtude du Polymor-
phisme Humain (CEPH) European sample (CEU)
representing Europe and the Yoruba represent-
ing Africa (YRI), the single-dispersal model (Fig.
1A, top) predicts an equal number of sites sup-
porting group 1 [(YRI, ASN), (CEU, ABR)] and
group 2 [(YRI, ABR), (CEU, ASN)]. In contrast,
the multiple-dispersal model (Fig. 1A, bottom)
predicts an excess of group 2. Indeed, we found
a statistically significant excess of sites (51.4%)
grouping the Yoruba and Australian genomes
together (group 2) relative to the Yoruba and East
Asian genomes together (group 1, 48.6%, P <
0.001), consistent with a basal divergence of Ab-
original Australians in relation to East Asians and
Europeans (Table 2). Another possible explana-
tion of our findings is that gene flow between
modern European and East Asian populations
caused these two populations to appear more sim-
ilar to each other, generating an excess of sites
showing group 2, even under the single-dispersal
model. However, simulations under such a model
show that the amount of gene flow between Eu-
ropeans and East Asians (5) cannot generate the
excess of sites showing group 2 unless Aborig-
inal Australian, East Asian, and European ances-
tral populations all split from each other around
the same time, with no subsequent migration be-
tween aboriginal Australasians and East Asians
(4). Such a model, however, would be incon-
sistent with our results from D test, PCA, and
discriminant analysis of principal components
(DAPC) (4), given that the Aboriginal Australian
is found to be genetically closer to East Asians
than to Europeans (Table 1 and Fig. 1B). Thus,
our findings suggest that a model in which Ab-
original Australians are directly derived from an-
cestral Asian populations, as proposed by the
single-dispersal model, is not compatible with
the genomic data. Instead, our results favor the
multiple-dispersal model in which the ancestors
of Aboriginal Australian and related popula-
tions split from the Eurasian population before
Asian and European populations split from each
other (4).
To estimate the times of divergence, we de-
veloped a population genetic method for esti-
mating demographic parameters from diploid
whole-genome data. The method uses patterns of
allele frequencies and linkage disequilibrium to
obtain joint estimates of migration rates and di-
vergence times between pairs of populations (4).
Using this method, we estimate that aboriginal
Australasians split from the ancestral Eurasian
population 62,000 to 75,000 years B.P. This es-
timate fits well with the mtDNA-based coales-
cent estimates of 45,000 to 75,000 years B.P. of
the non-African founder lineages (4, 15, 25, 26).
Furthermore, we find that the European and Asian
populations split from each other only 25,000 to
38,000 years B.P., in agreement with previous
estimates (5, 6). All three populations, however,
have a divergence time similar to the representa-
tive African sequence. Additionally, our esti-
mated split time between aboriginal Australasians
and the ancestral Eurasian population predicts the
observed excess of sites showing group 2 dis-
cussed above (Table 2). To obtain confidence
intervals and test hypotheses, we used a block
bootstrap approach. In 100 bootstrap samples, we
always obtained a longer divergence time be-
tween East Asians and the Aboriginal Australian
than between East Asians and Europeans, show-
ing that we can reject the null hypothesis of a
trichotomy in the population phylogeny with sta-
tistical significance of approximately P < 0.01. In
these analyses we have taken changes in popu-
lation sizes and the effect of gene flow after
divergence between populations into account.
However, our models are still relatively simple,
and the models we consider are only a subset of
all the possible models of human demography. In
addition, we have not attempted directly to model
the combined effects of demography and selec-
tion. The true history of human diversification is
likely to be more complex than the simple de-
mographic models considered here.
We used two approaches to test for admixture
in the genomic sequence of the Aboriginal Aus-
tralian with archaic humans [Neandertals and
Denisovans (22, 23)]. We asked whether previ-
ously identified high-confidence Neandertal ad-
mixture segments in Europeans and Asians (22)
could also be found in the Aboriginal Australian.
We found that the proportion of such segments
in the Aboriginal Australian closely matched that
observed in European and Asian sequences (4).
In the case of the Denisovans, we used a D test
(22, 23) to search for evidence of admixture with-
in the Aboriginal Australian genome. This test
compares the proportion of shared derived al-
leles between an outgroup sequence (Denisovan)
and two ingroup sequences. This test showed a
relative increase in allele sharing between the
Denisovan and the Aboriginal Australian genomes,
compared to other Eurasians and Africans includ-
ing Andaman Islanders (4), but slightly less allele
sharing than observed for Papuans. However, we
found that the D test is highly sensitive to errors
in the ingroup sequences (4), and shared errors
are of particular concern when the comparisons
involve both an ingroup and outgroup ancient
DNAsequence. Although we cannot exclude these
results being influenced by such errors, the latter
result is consistent with the hypothesis of in-
creased admixture between Denisovans or related
groups and the ancestors of the modern inhab-
itants of Melanesia (23). This admixture may
have occurred in Melanesia or, alternatively, in
Eurasia during the early migration wave.
The degree to which a single individual is
representative of the evolutionary history of Ab-
original Australians more generally is unclear.
Nonetheless, we conclude that the ancestors of
Fig. 2. Reconstruction of early spread of modern humans outside Africa. The tree shows the divergence of
the Aboriginal Australian (ABR) relative to the CEPH European (CEU) and the Han Chinese (HAN) with
gene flow between aboriginal Australasians and Asian ancestors. Purple arrow shows early spread of the
ancestors of Aboriginal Australians into eastern Asia ~62,000 to 75,000 years B.P. (ka BP), exchanging
genes with Denisovans, and reaching Australia ~50,000 years B.P. Black arrow shows spread of East Asians
~25,000 to 38,000 years B.P. and admixing with remnants of the early dispersal (red arrow) some time
before the split between Asians and Native American ancestors ~15,000 to 30,000 years B.P. YRI, Yoruba.
REPORTS
this Aboriginal Australian manand possibly of
all Aboriginal Australiansare as distant from
Africans as are other Eurasians, and that the Ab-
original ancestors split 62,000 to 75,000 years B.P.
from the gene pool that all contemporary non-
African populations appear to descend from.
Rather than supporting a single early human ex-
pansion into eastern Asia, our findings support
the alternative model of Aboriginal Australians
descending from an early Asian expansion wave
some 62,000 to 75,000 years B.P. The data also
fit this models prediction of substantial admix-
ture and replacement of populations fromthe first
wave by the second expansion wave, with a few
populations such as Aboriginal Australians, and
possibly PNG Highlands and Aeta, being rem-
nants of the early dispersal (Fig. 2). This is com-
patible with mtDNA data showing that although
all haplogroups observed in Australia are unique
to this region, they derive from the same few
founder haplogroups that are shared by all non-
African populations (4). Finally, our data are in
agreement with contemporary Aboriginal Aus-
tralians being the direct descendants from the
first humans to be found in Australia, dating to
~50,000 years B.P. (7, 8). This means that Ab-
original Australians likely have one of the oldest
continuous population histories outside sub-
Saharan Africa today.
1. S. Ramachandran et al., Proc. Natl. Acad. Sci. U.S.A.
102, 15942 (2005).
2. H. Liu, F. Prugnolle, A. Manica, F. Balloux, Am. J.
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3. HUGO Pan-Asian SNP Consortium, Science 326, 1541
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C. D. Bustamante, PLoS Genet. 5, e1000695 (2009).
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8726 (2007).
16. M. Ingman, U. Gyllensten, Genome Res. 13, 1600 (2003).
17. S. M. van Holst Pellekaan, M. Ingman, J. Roberts-Thomson,
R. M. Harding, Am. J. Phys. Anthropol. 131, 282 (2006).
18. T. M. Karafet et al., Mol. Biol. Evol. 27, 1833 (2010).
19. M. Lahr, The Evolution of Modern Human Diversity:
A Study of Cranial Variation (Cambridge Univ. Press,
Cambridge, 1996).
20. P. Whitehouse, T. Usher, M. Ruhlen, W. S.-Y. Wang,
Proc. Natl. Acad. Sci. U.S.A. 101, 5692 (2004).
21. D. Reich, K. Thangaraj, N. Patterson, A. L. Price, L. Singh,
Nature 461, 489 (2009).
22. R. E. Green et al., Science 328, 710 (2010).
23. D. Reich et al., Nature 468, 1053 (2010).
24. T. Goebel, M. R. Waters, D. H. ORourke, Science 319,
1497 (2008).
25. P. Endicott, S. Y. W. Ho, M. Metspalu, C. Stringer,
Trends Ecol. Evol. 24, 515 (2009).
26. P. Soares et al., Am. J. Hum. Genet. 84, 740 (2009).
27. S. F. Schaffner et al., Genome Res. 15, 1576 (2005).
28. D. H. Alexander, J. Novembre, K. Lange, Genome Res. 19,
1655 (2009).
Acknowledgments: Our work was endorsed by the Goldfields
Land and Sea Council, the organization representing
the Aboriginal Traditional Owners of the Goldfields
region, including the cultural (and possibly the
biological) descendents of the individual who provided
the hair sample. See (4) for letter. Data are accessible
through NCBI Sequence Read Archive SRA035301.1 or
through http://dx.doi.org/10.5524/100010. We note the
following additional affiliations: S.T. also works for the
Australian Federal Police; J.D. is a partner in Dortch &
Cuthbert Pty. Ltd.; P.F. is director of Genetic Ancestor Ltd.
and Fluxus Technology Ltd.; and C.D.B. serves as an
unpaid consultant for 23andMe. For author contributions
and extended acknowledgements, see (4).
SOM Text
Figs. S1 to S39
Tables S1 to S28
References
14 July 2011; accepted 13 September 2011
10.1126/science.1211177
Acetylcholine-Synthesizing
T Cells Relay Neural Signals
in a Vagus Nerve Circuit
Mauricio Rosas-Ballina,
1
* Peder S. Olofsson,
1
* Mahendar Ochani,
1
Sergio I. Valds-Ferrer,
1,2
Yaakov A. Levine,
1
Colin Reardon,
3
Michael W. Tusche,
3
Valentin A. Pavlov,
1
Ulf Andersson,
4
Sangeeta Chavan,
1
Tak W. Mak,
3
Kevin J. Tracey
1
Neural circuits regulate cytokine production to prevent potentially damaging inflammation. A

prototypical vagus nerve circuit, the inflammatory reflex, inhibits tumor necrosis factora production
in spleen by a mechanism requiring acetylcholine signaling through the a7 nicotinic acetylcholine
receptor expressed on cytokine-producing macrophages. Nerve fibers in spleen lack the enzymatic
machinery necessary for acetylcholine production; therefore, how does this neural circuit terminate in
cholinergic signaling? We identified an acetylcholine-producing, memory phenotype T cell population
in mice that is integral to the inflammatory reflex. These acetylcholine-producing T cells are required
for inhibition of cytokine production by vagus nerve stimulation. Thus, action potentials originating in the
vagus nerve regulate T cells, which in turn produce the neurotransmitter, acetylcholine, required to
control innate immune responses.
N
eural circuits regulate organ function in
order to maintain optimal physiological
stability, providing homeostasis to the
bodys internal environment. The vagus nerve,
named by the Latin word for wandering, is a
paired structure that arises in the brain stem and
travels to visceral organs, where it regulates phys-
iological responses to environmental changes, in-
jury, and infection. In the immune system, electrical
stimulation of the vagus nerve inhibits cytokine
release; attenuates tissue injury; and ameliorates
inflammation-mediated injury in endotoxemia,
sepsis, and other cytokine-dependent models of in-
flammatory disease (14). This neural circuit, termed
the inflammatory reflex, requires action poten-
tials arising in the vagus nerve, and acetylcholine
interacting with the a7 subunit of the nicotinic ace-
tylcholine receptor (nAChR) expressed oncytokine-
producing macrophages in spleen (5). Selective
cholinergic agonists significantly inhibit cytokine
production in spleen and improve outcome in ex-
perimental models of inflammatory disease (612).
Vagus nerve fibers terminate in the celiac gan-
glion, the location of neural cell bodies that project
axons in the splenic nerve to innervate the spleen
(13, 14). Electrical stimulation of either the vagus
nerve above the celiac ganglion or the splenic nerve
itself significantly inhibits tumor necrosis factora
(TNF-a) production by red pulp and marginal zone
macrophages, the principal cell source of TNF-a
released into the circulation during endotoxemia
(1517). Paradoxically, nerve fibers in spleen, orig-
inating in the celiac ganglion, are adrenergic, not
cholinergic, and utilize norepinephrine as the pri-
mary neurotransmitter (18). Thus, although the
spleen has been shown to contain acetylcholine
(19, 20), the cellular source of this terminal neuro-
transmitter in the inflammatory reflex is unknown.
Because lymphocytes can synthesize and release
acetylcholine (21, 22), we reasoned that they might
be the source of acetylcholine that relays functional
information transmitted by action potentials origi-
nating in the vagus nerve to the spleen.
To determine whether vagus nerve stimulation
induces increasedacetylcholine release inthe spleen,
1
Laboratory of Biomedical Science, The Feinstein Institute for
Medical Research, 350 Community Drive, Manhasset, New
York 11030, USA.
2
Elmezzi Graduate School of Molecular
Medicine, The Feinstein Institute for Medical Research, 350
Community Drive, Manhasset, New York 11030, USA.
3
The
Campbell Family Institute for Breast Cancer Research, Univer-
sity Health Network, Toronto, Ontario M5G 2C1, Canada.
4
Department of Womens and Childrens Health, Karolinska
Institutet, S-171 76 Stockholm, Sweden.
kjtracey@nshs.edu
REPORTS
we measured acetylcholine in perfusate samples col-
lected by microdialysis. Acetylcholine levels were
elevated within minutes after electrical vagus nerve
stimulation and reached peak levels within 20 min
(Fig. 1A). This indicates that action potentials orig-
inating in the vagus nerve can enhance acetylcho-
line release in the spleen. Previous work indicated
that adrenergic nerve endings in the spleen termi-
nate in the Tcell region of the white pulp and that
splenic nerve stimulation enhances norepinephrine
release fromspleen (23, 24). To determine the effect
of norepinephrine on acetylcholine release, we incu-
bated spleen lymphocytes in the presence of nor-
epinephrine. Norepinephrine significantly stimulated
acetylcholine release by spleen lymphocytes (Fig.
1B), which suggested that functional stimulation
of adrenergic splenic neurons can stimulate spleen
lymphocyte acetylcholine release.
Next, to evaluate the role of T cells in mediat-
ing the inflammatory reflex, we studied the effect
of vagus nerve stimulation in nude mice, which
are devoid of functional T cells. As expected,
vagus nerve stimulation in control BALB/c mice
significantly suppressed serum TNF-a produc-
tion during endotoxemia (Fig. 1C). Vagus nerve
stimulation failed to attenuate serum TNF-a in
nude mice, which indicated that Tcell deficiency
impairs the inflammatory reflex (Fig. 1D). To
identify acetylcholine-producing T cells required
for the integrity of the inflammatory reflex, we
Fig. 1. Vagus nerve stimulation increases acetylcholine levels in the spleen
and requires T lymphocytes to attenuate TNF-a in endotoxemia. (A) BALB/c
mice (n = 5) were subjected to vagus nerve stimulation (5 min), and spleen
acetylcholine levels were determined in dialysate samples by mass spectrom-
etry. Results are expressed as a percentage of the average levels of three
consecutive samples T SEM obtained before vagus nerve stimulation (basal).
P < 0.05 at 20 min compared with basal [repeated measures analysis of var-
iance (ANOVA) and the Dunnett post hoc test]. VNS, vagus nerve stimulation.
(B) Acetylcholine was measured by mass spectrometry in supernatants of
nonadherent spleen cells in the presence or absence of norepinephrine at
the indicated concentrations. Data were obtained from pooled cells stimulated
in duplicate. Results are expressed as the mean of two experiments. *P < 0.05
compared with unstimulated cells (two-tailed t test). (C) BALB/c mice (four or
five per group) and (D) BALB/c nude mice (five per group) were subjected to
sham surgery or vagus nerve stimulation followed by endotoxin injection. Serum
was obtained 90 min after endotoxin administration, and TNF-a was measured
by enzyme-linked immunosorbent assay (ELISA). Results are means T SEM.
*P < 0.05 compared with the sham group (two-tailed t test).
Fig. 2. Spleen acetylcholine-
synthesizing T cells express a
memory T cell phenotype. (A)
ChAT-EGFP expression in spleen
CD3
+
T cells of wild-type and
ChAT(BAC)-EGFP mice. (B) Ex-
pression of ChAT-EGFP in CD4
+
and CD8
+
spleen T cells. (C)
CD44 and CD62L expression in
spleen CD4
+
cells (left), and
ChAT-EGFP expression in CD4
+
CD44
high
CD62L
low
and CD4
+
CD44
low
CD62L
high
spleen cells
(middle and right, respectively).
(D) Percentage of ChAT-EGFP
and ChAT-EGFP
+
cells among
spleen CD4
+
CD44
high
CD62L
low
cells, n = 5. (E) Spleen CD4
+
CD44
high
CD62L
low
ChAT-EGFP
and CD4
+
CD44
high
CD62L
low
ChAT-EGFP
+
cells were obtained
by cell sorting. (F) Acetylcholine
concentration was determined
0 10
2
10
3
10
4
10
5
CD3
0
10
2
10
3
10
4
10
5
C
h
A
T
-
e
G
F
P
0 10
2
10
3
10
4
10
5
CD3
0
10
2
10
3
10
4
10
5
C
h
A
T
-
e
G
F
P
WT ChAT(BAC)eGFP
0
2.2
0 10
2
10
3
10
4
10
5
CD4
0
10
2
10
3
10
4
10
5
C
h
A
T
-
e
G
F
P
0 10
2
10
3
10
4
10
5
CD8
0
10
2
10
3
10
4
10
5
C
h
A
T
-
e
G
F
P
ChAT(BAC)eGFP ChAT(BAC)eGFP
3.6 0.1
CD44
low
CD62L
high
CD44
high
CD62L
low
CD4
+
CD4
+
CD4
+
0 10
2
10
3
10
4
10
5
CD44
0
10
2
10
3
10
4
10
5
C
D
6
2
L
0 10
2
10
3
10
4
10
5
CD4
0
10
2
10
3
10
4
10
5
C
h
A
T
-
e
G
F
P
0 10
2
10
3
10
4
10
5
CD4
0
10
2
10
3
10
4
10
5
C
h
A
T
-
e
G
F
P
9.4 0.04
ChAT-eGFP
-
ChAT-eGFP
+
0
25
50
75
100
*
%

o
f

C
D
4
+
C
D
4
4
h
i
g
h
C
D
6
2
L
l
o
w
A B
C
D
E
F
ChAT-eGFP
-
ChAT-eGFP
+
0
20
40
60
*
A
c
e
t
y
l
c
h
o
l
i
n
e
(
n
m
o
l
/
L
)
0 10
2
10
3
10
4
10
5
ChAT-eGFP
0
50
100
150
200
250
#

C
e
l
l
s
ChAT-eGFP
-
ChAT-eGFP
+
0.05 96
0 10
2
10
3
10
4
10
5
ChAT-eGFP
0
20
40
60
80
#

C
e
l
l
s
96
in supernatants of cells under resting conditions. Data were
obtained from pooled cells cultured in duplicate. Results are
the means of two experiments. *P < 0.05 compared with
CD4
+
CD44
high
CD62L
low
ChAT-EGFP
cells (two-tailed t test).

REPORTS
used ChAT(BAC)-EGFP mice, which express en-
hanced green fluorescent protein (EGFP) under
the control of transcriptional regulatory elements
for ChAT, the enzyme that catalyzes the biosyn-
thesis of acetylcholine (25). Flow cytometry re-
vealed that ChAT-EGFP
+
cells were 2.6 T 0.4%
of total spleen CD3
+
T cells (Fig. 2A), which in-
dicated that only a relatively small subset of total
spleen T cells express ChAT. ChAT-EGFP was
expressed in 4.4 T 0.7% of CD4
+
cells, but in
only a negligible number (0.2 T 0.1%) of CD8
+
T cells (Fig. 2B). When CD4
+
cells were further
divided into CD44
high
CD62L
low
memory and
CD44
low
CD62L
high
nave Tcell populations, ChAT-
EGFP
+
cells were predominantly observed in the
CD44
high
CD62L
low
population (Fig. 2C). Among
the total memory CD4
+
CD44
high
CD62L
low
cells,
10.5 T 2.1% were ChAT-EGFP
+
Tcells (Fig. 2D).
To examine the capacity for acetylcholine syn-
thesis by Tcells, spleen CD4
+
CD44
high
CD62L
low
ChAT-EGFP
+
and CD4
+
CD44
high
CD62L
low
ChAT-EGFP
cells were collected by cell sorting,

and acetylcholine was measured in supernatants
of these cells under basal conditions. Acetyl-
choline production was significantly elevated in
supernatants of CD4
+
CD44
high
CD62L
low
ChAT-
EGFP
+
cells, as compared with CD4
+
CD44
high
CD62L
low
ChAT-EGFP
(Fig. 2, E and F). To func-

tionally characterize these acetylcholine-producing
T cells, spleen CD4
+
CD44
high
CD62L
low
ChAT-
EGFP
+
cells were stimulated with plate-bound
CD3-specific antibody. Levels of interleukin-17A
(IL-17A), IL-10, and the T helper 1 cytokine
interferon-g (IFN-g) were significantly elevated
in supernatants 48 hours after stimulation (fig.
S1), whereas the T helper 2 cytokines IL-4 and
IL-6 were not significantly elevated (fig. S1). This
suggested that ChAT expression is not restricted
to a discrete functional Tcell subset and raised the
possibility that T cell acetylcholine-synthesizing
capacity might be linked to T cell activation
status. To examine this, ChAT-EGFP expression
was analyzed on CD4
+
CD44
high
CD62L
low
ChAT-
EGFP
Tcells after stimulation with CD3-specific

antibody. Flow cytometry analysis revealed a sig-
nificant increase in ChAT-EGFP expression with-
in 48 hours after Tcell stimulation (fig. S2), which
suggested that T cell activation enhances ex-
pression of ChAT and acetylcholine release.
The spatial relation between ChAT-EGFP
+
T
cells and splenic nerve fibers was explored by
immunofluorescence analysis of spleen sections
to reveal that ChAT-EGFP expression in T lym-
phocytes localized primarily in the white pulp
(Fig. 3, A and B). ChAT-EGFP
+
cells in the white
pulp were adjacent to splenic nerve fibers ex-
pressing tyrosine hydroxylase, the rate-limiting
enzyme in catecholamine synthesis (Fig. 3C).
As expected, splenic nerve fibers failed to express
ChAT-EGFP, in agreement with earlier results,
which indicated that splenic nerves are adrener-
gic and do not produce acetylcholine (15, 18).
Synaptophysin, a glycoprotein expressed at neu-
ral synapses, was localized adjacent to ChAT-
EGFP
+
cells in white pulp parenchyma (Fig. 3D).
Together with previous results indicating that
splenic nerve endings form synapse-like structures
on T lymphocytes (23), the termination of these
synaptophysin-positive nerve fibers on ChAT-
EGFP
+
T cells provides an anatomical basis for
splenic nerve fibers interacting with acetylcholine-
producing T cells. Extensive prior work has es-
tablished that splenic nerve signals modulate
T cell responses by signal transduction through
b-adrenergic receptors (2628). Analysis of mRNA
levels of adrenergic receptors b1, b2, and b3 in
CD4
+
CD44
high
CD62L
low
ChAT-EGFP
+
spleen
ChAT-eGFP
CD3
B
D
ChAT-eGFP
Synaptophysin
ChAT-eGFP
TH
CA
C
A ChAT-eGFP
CD3
CA
20 m 20 m
20 m 5 m
Fig. 3. Acetylcholine-synthesizing T cells in spleen are located in the proximity of catecholaminergic
nerve endings. (A and B) Immunofluorescent micrographs of ChAT-EGFP (green) expression by T cells in
spleen white pulp (CD3, red). (C) Immunofluorescent micrographs of ChAT-EGFP
+
cells (green) and nerve
fibers stained with tyrosine hydroxylase (TH, red). (D) Fluorescent micrographs of splenic nerve endings
(synaptophysin, red) juxtaposed (arrows) to ChAT-EGFP
+
(green) cells in the white pulp. CA, central artery.
(A) 400 magnification, (B) 630 magnification, (C) 400 magnification, (D) 630 magnification. Images
are representative of spleen sections (n = 3 to 5) from five experiments.
SHAM VNS
0
50
100
150
*
s
e
r
u
m

T
N
F
(
%

o
f

s
h
a
m
)
ChAT-eGFP
+
A
SHAM VNS
0
50
100
150
s
e
r
u
m

T
N
F
(
%

o
f

s
h
a
m
)
ChAT-eGFP
-
B
SHAM VNS
0
50
100
150
*
Scrambled siRNA
s
e
r
u
m

T
N
F
(
%

o
f

s
h
a
m
)
C
SHAM VNS
0
50
100
150
ChAT siRNA
s
e
r
u
m

T
N
F
(
%

o
f

s
h
a
m
)
D
Fig. 4. Vagus nerve stimulation requires acetylcholine-synthesizing T cells to
attenuate TNF-a in endotoxemia. Indicated groups of mice were subjected to
sham surgery or vagus nerve stimulation followed by endotoxin injection.
Serum was obtained 90 min after endotoxin administration, and TNF-a was
measured by ELISA. (A) BALB/c nude mice receiving spleen CD4
+
CD44
high
CD62L
low
ChAT-EGFP
+
cells, eight mice per group. (B) BALB/c nude mice re-
ceiving spleen CD4
+
CD44
high
CD62L
low
ChAT-EGFP
cells, six or seven mice

per group. (C) BALB/c nude mice receiving spleen CD4
+
cells transfected with
control scrambled siRNA, five or six mice per group. (D) BALB/c nude mice
receiving spleen CD4
+
cells transfected with ChAT siRNA, six or seven mice
per group. Results are means T SEM. *P < 0.05 compared with the respective
sham group (two-tailed t test).
REPORTS
cells revealed expression of adrenergic receptors
b1 and b2, but not b3 (fig. S3). This agrees with
previous work that b-adrenergic receptors on T
cells underlie the mechanism of adrenergic splenic
nerve signaling (2628).
In order to assess the role of acetylcholine-
producing T cells in the inflammatory reflex,
CD4
+
CD44
high
CD62L
low
ChAT-EGFP
+
cells ob-
tained by cell sorting were adoptively transferred
to nude mice. Vagus nerve stimulation significant-
ly decreased serum TNF-a levels in endotoxemic
nude mice reconstituted with CD4
+
CD44
high
CD62L
low
ChAT-EGFP
+
cells (Fig. 4A) but not
in controls reconstituted with CD4
+
CD44
high
CD62L
low
ChAT-EGFP
cells (Fig. 4B). The fate

of adoptively transferred CD4
+
CD44
high
CD62L
low
ChAT-EGFP
+
T cells in this nude mouse model
was examined by flow cytometry and histo-
logical analysis of spleen sections. We found
that CD4
+
CD44
high
CD62L
low
ChAT-EGFP
+
and CD4
+
CD44
high
CD62L
low
ChAT-EGFP
T
cells harvested from spleens of recipient nude
mice remained ChAT-EGFP
+
and ChAT-EGFP
,
respectively (fig. S4, A and B). We also ob-
served significant accumulation of ChAT-EGFP
+
cells in the vicinity of synaptophysin-positive nerve
fibers in white pulp (fig. S4C). The localization of
ChAT-EGFP
+
T cells in the white pulp of nude
mice after adoptive transfer was indistinguishable
fromthat of ChAT-EGFP
+
Tcells observed in trans-
genic ChAT(BAC)-EGFP mice (Fig. 2). Together,
these results indicate that acetylcholine-producing
T cells populate the spleen after adoptive transfer
and localize to the region of splenic neurons under
functional control of action potentials originating
in the vagus nerve.
It remained theoretically possible that some
other unanticipated effect of these cells not re-
lated to acetylcholine restored the inflammatory
reflex. Accordingly, we next utilized small inter-
fering RNA (siRNA) to deplete (knockdown)
ChAT in spleen CD4
+
T cells (fig. S5). Scram-
bled or ChAT siRNA-transfected CD4
+
T cells
were adoptively transferred into nude mice. Vagus
nerve stimulation attenuated serum TNF-a levels
in mice that received CD4
+
T cells transfected
with control siRNA (Fig. 4C), but failed to atten-
uate TNF-a in nude mice that received CD4
+
T cells transfected with ChAT siRNA (Fig. 4D).
Vagus nerve stimulation also significantly reduced
serum IL-6 and IL-10 levels in nude mice that
received CD4
+
T cells transfected with control
siRNA, but not in nude mice that received ChAT
siRNA-treated T cells (fig. S6). Together, these
data indicate that T cells with an intrinsic ca-
pacity to synthesize acetylcholine are required
for the integrity of the inflammatory reflex.
It had been previously established that the
inflammatory reflex requires an intact splenic
nerve (15) and a7 nAChR expression in effector
cytokine-producing cells in spleen (16). These
results were previously difficult to rectify with
observations that splenic nerves are adrenergic
and do not produce the neurotransmitter, acetyl-
choline, required to interact with a7 nAChR. As
early as 1965, investigators had observed that
electrical stimulation of the splenic nerve in-
duced acetylcholine release in spleen, but the
cell source of this acetylcholine had been con-
tested (2932). The present findings show that
vagus nerve stimulation also increases acetyl-
choline release from spleen and that spleen lym-
phocytes release acetylcholine in response to
norepinephrine. It is likely that the regulatory
effect of acetylcholine-synthesizing T cells de-
scribed here is not restricted to the spleen, because
CD4
+
CD44
high
CD62L
low
ChAT-EGFP
+
Tcells
are also present in lymph nodes and Peyers patches
(fig. S7), which are innervated by adrenergic neu-
rons (33). Further, polyclonal activation of Tcells
also up-regulates ChAT-EGFP expression (fig. S2)
(34) and augments acetylcholine production and
release (35), which together make plausible the
possibility that T cell activation status modulates
the activity of the inflammatory reflex.
A major finding of this study is the surpris-
ing functional role for acetylcholine-producing
memory T cells as integral components of a neu-
ral information system that controls innate im-
mune responses. It should be possible to target
these cells as therapeutic modalities for inflam-
matory and autoimmune diseases.
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T. van der Poll, Shock 28, 700 (2007).
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14. D. L. Bellinger, S. Y. Felten, D. Lorton, D. L. Felten,
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11008 (2008).
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17. M. G. Kees, G. Pongratz, F. Kees, J. Schlmerich,
R. H. Straub, J. Neuroimmunol. 145, 77 (2003).
18. D. L. Bellinger, D. Lorton, R. W. Hamill, S. Y. Felten,
D. L. Felten, Brain Behav. Immun. 7, 191 (1993).
19. H. H. Dale, H. W. Dudley, J. Physiol. 68, 97 (1929).
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22. I. Rinner, K. Schauenstein, J. Neurosci. Res. 35, 188 (1993).
23. S. Y. Felten, J. Olschowka, J. Neurosci. Res. 18, 37 (1987).
24. D. L. Bellinger, S. Y. Felten, T. J. Collier, D. L. Felten,
J. Neurosci. Res. 18, 55, 126 (1987).
25. Y. N. Tallini et al., Physiol. Genomics 27, 391 (2006).
26. R. D. Feldman, G. W. Hunninghake, W. L. McArdle,
J. Immunol. 139, 3355 (1987).
27. A. P. Kohm, V. M. Sanders, Pharmacol. Rev. 53, 487 (2001).
28. C. Riether et al., Brain Behav. Immun. 25, 59 (2011).
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Acknowledgments: This work was supported in part by
grants from National Institute of General Medical Sciences,
NIH, to K.J.T. and from the Wenner-Gren Foundations in
Stockholm to P.S.O. We thank B. Diamond for helpful
discussions, and H. Borrero and S. Matheravidathu for
technical support. The data reported in this paper are
tabulated in the main text and supporting online material.
Figs. S1 to S7
References
17 June 2011; accepted 26 July 2011
10.1126/science.1209985
Functional Innervation of Hepatic
iNKT Cells Is Immunosuppressive
Following Stroke
Connie H. Y. Wong,
1
Craig N. Jenne,
1,2
Woo-Yong Lee,
1
Caroline Lger,
2
Paul Kubes
1,2,3
*
Systemic immunosuppression has been associated with stroke for many years, but the underlying
mechanisms are poorly understood. In this study, we demonstrated that stroke induced profound
behavioral changes in hepatic invariant NKT (iNKT) cells in mice. Unexpectedly, these effects were
mediated by a noradrenergic neurotransmitter rather than a CD1d ligand or other well-characterized
danger signals. Blockade of this innervation was protective in wild-type mice after stroke but had no
effect in mice deficient in iNKT cells. Selective immunomodulation of iNKT cells with a specific activator
(a-galactosylceramide) promoted proinflammatory cytokine production and prevented infections after
stroke. Our results therefore identify a molecular mechanism that leads to immunosuppression after
stroke and suggest an attractive potential therapeutic alternative to antibiotics, namely,
immunomodulation of iNKT cells to prevent stroke-associated infections.
A
major cause of death resulting from
stroke is infection (1, 2). Immunosup-
pression, perhaps due to a systemic shift
from T helper cell (T
H
) 1type to T
H
2-type cy-
tokine production, has been proposed as a com-
pensatory response to protect the post-ischemic
REPORTS
brain from overwhelming inflammation (3). This
excessive activation of inhibitory pathways in-
creases the susceptibility to infections (46), al-
though the underlying mechanism has remained
elusive to date. Invariant natural killer T (iNKT)
cells have a highly restricted repertoire of T cell
receptors (TCRs) that recognize lipid antigens
presented by CD1d (7, 8). These antigens include
various bacterial glycolipids but also endogenous
moieties that could function as alarmins and alert
the immune system to danger. Because iNKT
cells reside in the vasculature of organs like the
liver, where circulating antigens can be captured
and presented, we proposed that iNKT cells in
this tissue are also able to respond to remote sites
of injury, such as the brain, and modulate sys-
temic immune responses.
iNKT cells primarily reside in the liver and
spleen (9). iNKT cells patrol the hepatic micro-
vasculature and can be tracked in Cxcr6
gfp/+
mice
(10). When activated with either CD1d ligands or
exogenous administration of interleukin (IL)12
and IL-18, iNKT cells showed altered behavior,
including cessation of intravascular crawling as-
sociated with activation and release of key cyto-
kines (11). We hypothesized that, on the basis of
their intravascular localization, iNKT cells are
well positioned to detect distant tissue injury and
participate in systemic immunomodulation. To
investigate this, we examined liver iNKTcell be-
havior in response to transient midcerebral artery
occlusion (MCAO)induced brain injury, a ro-
dent model of stroke. Using intravital spinning-
disk confocal microscopy, we observed that iNKT
cells crawl randomly within liver sinusoids under
control conditions (Fig. 1A; fig. S1, Aand B; and
movie S1) (12). The crawling velocities of iNKT
cells in control and sham-operated animals did
not differ (fig. S1C). In contrast, we observed
markedly restricted crawling of liver iNKT cells
after MCAO as reperfusion progressed (Fig. 1, B
and C, and fig. S1D). There was a significant
decrease in the number of crawling iNKT cells
and an increasing number of stationary iNKTcells
at 4, 8, and 24 hours after MCAO (Fig. 1D and
movie S2). Some of the arrested cells continued to
send out pseudopods, pirouetting or scanning in
a circular pattern (Fig. 1, Dand E, and movie S3).
These behaviors were particular to the ischemia-
reperfusion in the brain, as ischemia-reperfusion
injury of the hindlimb had no effect on the be-
havior of liver iNKT cells (fig. S1E).
Stroke induces major immune changes, in-
cluding severe lymphopenia in the peripheral
blood, thymus, and spleen (13, 14). Interestingly,
the number of iNKT cells did not decrease in
the peripheral blood, liver, spleen, thymus, and
lymph node of post-ischemic mice (fig. S2). How-
ever, increased expression of CD69 in iNKTcells
was observed in the peripheral blood and liver
(Fig. 1, F and G), which suggests regional iNKT
cell activation after stroke (Fig. 1G). Taken to-
gether, these data demonstrate that brain injury
has far-reaching effects, including the capacity to
induce profound behavioral changes in hepatic
iNKT cells.
Activated iNKT cells produce cytokines and
chemokines (15). After MCAO, systemic T
H
1-
type cytokines such as interferon-g (IFN-g) and
IL-12p70 decreased in wild-type mice (fig. S3, Ai
and Bi), reaching significance at 8 hours reper-
fusion. By contrast, T
H
2-type cytokines, includ-
ing IL-10 and IL-5, were increased at 4 hours
after MCAO (fig. S3, Ci and Di). We did not
detect IL-4 at any time. In the liver, iNKT cells
produced significantly increased amounts of
IL-10, but not IFN-g or IL-4, at 8 hours after
MCAO (Fig. 1H). The increased ratio of T
H
2-
type over T
H
1-type cytokines in post-ischemic
wild-type mice highlights a general switch in sys-
temic immunity fromT
H
1- to T
H
2-type in the early
stages of reperfusion after stroke (fig. S3E).
Consistent with the view that stroke triggers
an immunomodulatory response that decreases
the antimicrobial drive of the immune system in
humans (5), all of the wild-type mice developed
infection 24 hours after MCAO, detectable in
blood, lung, liver, and spleen (Fig. 2A and fig.
S4). These mice also displayed a significant in-
crease in neutrophilic infiltration into lungs, as
measured by myeloperoxidase (MPO) levels, and
pulmonary edema (Fig. 2, B and C), both hall-
mark features of pneumonia, the most common
infection in humans after stroke. Wild-type mice
always demonstrated some mortality after MCAO
throughout the study (Fig. 2D), nearly identical
to human mortality data of 12 to 14% (16, 17).
To investigate the role of iNKTcells in stroke
and the associated systemic bacterial infection
and tissue injury, mice deficient in iNKT cells
(Cd1d
/
) were also subjected to MCAO. Bacte-
rial cultures from blood and lungs were clearly
evident as early as 8 hours after MCAOin Cd1d
/
1
Calvin, Phoebe, and Joan Snyder Institute for Infection,
Immunity, and Inflammation, University of Calgary, Calgary,
Alberta, Canada.
2
Department of Critical Care Medicine, Uni-
versity of Calgary, Calgary, Alberta, Canada.
3
Department of
Physiology and Pharmacology, University of Calgary, Calgary,
Alberta, Canada.
pkubes@ucalgary.ca
Fig. 1. Stroke alters the behavior of hepatic iNKT
cells in vivo. The tracks of green fluorescent protein
positive (GFP
+
) cells within the liver during 10 min
of recording in sham-operated (A) and post-ischemic
Cxcr6
gfp/+
mice at 8 hours (B) and 24 hours (C). Paths
are normalized for their origins, and the dotted circle
denotes 10 mm radius from origin. N 4 individual
mice per group. (D) The percentage of crawling, sta-
tionary, and pirouetting GFP
+
cells in the liver of
sham-operated and post-ischemic Cxcr6
gfp/+
mice at
4, 8, and 24 hours after MCAO. Data are expressed
as the percentage of GFP
+
cells per field of view
(FOV). N 4 individual mice per group; error bars,
mean T SEM; ***P < 0.001, *P < 0.05 versus sham
by t test. (E) A representative pirouetting GFP
+
cell
showing cell surface ruffling and pseudopod pro-
trusion during 8 min of recording. The x denotes
stationary cell body, and the yellow arrow denotes
the direction of the cells pseudopod. Scale bar,
25 mm. (F) CD69 expression in the hepatic iNKT cells
of control (gray tint), positive control a-GalCer
treated (blue line), or post-ischemic Cxcr6
gfp/+
mice
at 24 hours after MCAO (red line). (G) The percent-
age of iNKT cells with CD69 expression in indicated
organs or peripheral blood (PBL) of sham-operated
and post-MCAO mice at 24 hours was determined by flow cytometry (LN, six
individual lymph nodes collected from the periphery). N 4 individual mice per
group; error bars, mean T SEM; ***P <0.001, *P <0.05 by t test. (H) Intracellular
hepatic iNKT cell production of IL-10, IFN-g, and IL-4 from sham-operated and
post-MCAO mice at 8 hours reperfusion was examined by flow cytometry. N 4
individual mice per group; error bars, mean T SEM; *P < 0.05 by t test.
REPORTS
mice (Fig. 2A and fig. S4A). Cd1d
/
mice de-
veloped even greater pulmonary damage as
early as 4 hours after MCAO, with more prom-
inent pulmonary neutrophil infiltration (Fig. 2B)
and edema (Fig. 2C), suggestive of even earlier
pneumonia-like symptoms. The majority of post-
ischemic Cd1d
/
mice did not survive past 12
hours of reperfusion (Fig. 2D); this occurred de-
spite the fact that both strains of mice showed
similar brain infarct size (Fig. 2E) (18).
We hypothesized that the high mortality rate
of post-ischemic Cd1d
/
mice was the result of
their increased susceptibility to post-stroke in-
fections. Indeed, prophylactic administration of
antibiotics in post-ischemic mice dramatically
improved the survival rate of both strains of mice
(Fig. 2D). Most striking was the increase in sur-
vival of post-ischemic Cd1d
/
mice. The antibi-
otic treatment did not affect the infarct size of the
brain lesion after MCAO but completely pre-
vented the infections in post-ischemic wild-type
and Cd1d
/
mice (fig. S5). Moreover, wild-type
mice pretreated with recombinant IL-10, a T
H
2-
type cytokine that iNKT cells were shown to
produce after MCAO (Fig. 1H), developed in-
creased stroke-induced lung infections (fig. S6).
Clearly, stroke-activated iNKTcells continued to
function and afforded some protection to the
host, whereas a complete absence of iNKT cells
rendered the animals even more susceptible to
post-stroke infections, consistent with the lower
T
H
1-type cytokine levels observed in these mice,
including no detectable IFN-g (fig. S3, Aii and E).
We next investigated where iNKT cells fit
into the previously described peripheral lympho-
cyte changes in post-stroke mice (14, 19, 20).
T cell activation (CD69 expression) was in-
creased in the peripheral blood and liver after
stroke in wild-type but not Cd1d
/
mice (Fig. 2F).
In fact, Cd1d
/
mice failed to activate CD4
+
T
cells in the peripheral blood (Fig. 2G) and CD8
+
Tcells in the liver after MCAO (Fig. 2H), tissues
where iNKT cells were observed to be activated
after stroke (Fig. 1G). These data suggest that the
immune regulation of post-ischemic iNKT cells
is upstream of CD4
+
and CD8
+
T cell activation
in the peripheral blood and liver, respectively,
and that iNKT cells function as the conductor of
immunity, whereby their acute responses modu-
late and facilitate the adaptive immune response.
Although a systematic assessment of numbers of
lymphocytes, NK cells, and granulocytes after
stroke revealed some additional changes in blood
and tissues, these were not affected by the presence
or absence of iNKT cells (fig. S7), suggesting
that not all changes to leukocyte cell numbers are
modulated by iNKT cells.
The manner in which iNKTcells detect tissue
damage after stroke could be through endoge-
nous glycolipids presented by CD1d, cytokines
like IL-12 and/or IL-18 released from other
sentinel cells (e.g., macrophages), or some other
as-yet-unknown mechanism. Antibody blockade
of CD1d had no effect on iNKT cell arrest in
response to MCAO(fig. S8, Ato C), whereas it
prevented cessation of iNKTcells caused by stim-
ulation with the CD1d ligand a-galactoceramide
(a-GalCer), a specific activator of iNKT cells
(fig. S8D) (21). Another inhibitor that blocks the
presentation of glycolipid ligands in the context
of CD1d, isolectin B (iB) 4, also did not alter
iNKT cell arrest after MCAO (fig. S8, A to C),
ruling out glycolipid presentation by CD1d as the
pathway alerting iNKTcells to distal tissue injury
in stroke. Furthermore, blockade of IL-12 and
IL-18, cytokines known to activate and arrest
iNKTcells (fig. S8E) (11), had no effect on iNKT
cell arrest in response to MCAO(fig. S8, Ato C).
Finally, apyrase, an inhibitor of ATP, a well-known
alarmin in the brain and liver (22), had no effect
on iNKTcell responses to MCAO(fig. S8, Ato C).
An as-yet-unidentified, long-distance path-
way was affecting the crawling behavior and ac-
tivation of iNKT cells in the liver after cerebral
ischemia. Previous literature suggested that the
nervous system may affect immune cells, includ-
ing iNKT cells, and alter their function (23, 24),
thereby potentially regulating the magnitude of
the host response to infection or injury (25, 26).
Administration of the nonspecific b-adrenergic
receptor blocker, propranolol, reversed the iNKT
cell phenotype induced by MCAO (Fig. 3, A to
C; fig. S9A; and movie S4). Furthermore, post-
ischemic cessation of iNKT cell crawling was
completely inhibited by specific chemical deple-
tion of peripheral neuronal terminals containing
noradrenaline with6-hydroxydopamine (6-OHDA),
suggesting a neural rather than humoral input
(Fig. 3, A, B, and D, and fig. S9A). Despite the
phenotypic changes of iNKTcells after systemic
administration of propranolol or 6-OHDA, these
treatments did not alter the blood flow (fig. S9B)
or infarct size in post-ischemic mice (fig. S9C).
Fig. 2. iNKT cells are critical in the defense against stroke-associated infections. (A) Bacteriological
analysis was carried out to investigate the bacterial load in the lungs of sham-operated and post-ischemic
wild-type and Cd1d
/
mice at 4, 8, and 24 hours of reperfusion. ND, not detectable; , mice did not
survive for analysis. Values represent the number of colony-forming units (CFU) per mg of tissue. N 4
individual mice per group; error bars, mean T SEM; *P < 0.05 by t test. The lungs of sham-operated and
post-ischemic wild-type and Cd1d
/
mice at 4, 8, and 24 hours of reperfusion were removed and assayed
for neutrophil infiltration, as measured by MPO activity (B) or analyzed for lung edema formation (C).
, mice did not survive for analysis. N 4 individual mice per group; error bars, mean T SEM; ***P <0.001,
**P < 0.01 Cd1d
/
versus corresponding wild-type counterparts;
###
P < 0.001,
##
P < 0.01 post-ischemic
wild-type versus sham-operated wild-type;
&&&
P < 0.001,
&&
P < 0.01,
&
P < 0.05 post-ischemic Cd1d
/
versus sham-operated Cd1d
/
, all by t test. (D) Survival rate of post-ischemic wild-type and Cd1d
/
mice
treated with or without antibiotics. N 15 mice per untreated group; N 5 mice per antibiotics-treated
group. (E) Infarct size of post-ischemic wild-type and Cd1d
/
mice assessed at 8 and 24 hours after MCAO.
ND, not detectable. N 4 individual mice per group; error bars, mean T SEM. The percentage of CD3
+
(F),
CD4
+
(G), or CD8
+
(H) T cells with CD69 expression in the indicated organs from sham-operated and post-
MCAO wild-type and Cd1d
/
mice at 24 hours reperfusion was determined by flow cytometry (LN, six
individual nodes collected from the periphery). NS, not statistically significant. N 3 individual mice per
group; error bars, mean T SEM; **P < 0.01, *P < 0.05 by t test.
REPORTS
Mortality at 24 hours of reperfusion was reduced
by 50% with 6-OHDA and completely inhibited
by propranolol (fig. S9D).
Localized noradrenaline administration direct-
ly mimicked the behavior of iNKT cells in the
liver of post-ischemic Cxcr6
gfp/+
mice in vivo.
Significantly fewer iNKTcells crawled, and more
cells adopted a pirouetting phenotype in the epi-
center of noradrenaline administration (Fig. 3, E
and F, and fig. S10). By contrast, in an area of
liver distant from the localized noradrenaline su-
perfusion, iNKTcells did not alter their crawling
behavior (Fig. 3, E and F, and fig. S10). In ad-
dition, when noradrenaline was applied to iNKT
cells in vitro, these cells acquired a flattened
and pseudopod protruding phenotype reminis-
cent of iNKT cell behavior after MCAO in vivo
(Fig. 3, G and H). In fact, pretreatment of iNKT
cells with propranolol inhibited this behavioral
change (Fig. 3I), suggesting that noradrenaline
directly induces the biology we observed in vivo.
Next, we examined whether direct immuno-
modulation of iNKTcells can reverse the stroke-
induced immunosuppression and infection.
Administration of a-GalCer in a therapeutically
relevant manner significantly increased systemic
levels of endogenous IFN-g (Fig. 4A) and re-
duced stroke-induced neutrophil pulmonary in-
flux, lung edema (Fig. 4, Band C), and infections
in post-ischemic mice (Fig. 4, D to G). a-GalCer
is an immunostimulant that could potentially have
deleterious effects on cerebral ischemia, but we
found no notable differences in infarct sizes (fig.
S11A). Furthermore, a-GalCer has been docu-
mented to induce liver damage, but we found no
significant difference in liver enzyme levels with-
in the blood of post-ischemic mice after the sin-
gle dose of a-GalCer (fig. S11B).
Interestingly, wild-type mice receiving pro-
pranolol or 6-OHDA also demonstrated signif-
icantly reduced bacterial infections at 24 hours
after MCAOin a manner similar to that observed
in a-GalCertreated mice (Fig. 4, D to G). Fur-
thermore, the effects of propranolol were entirely
dependent on iNKT cells, because the addition
of propranolol to Cd1d
/
mice provided no pro-
tection from infection or mortality (fig. S12). No-
tably, post-ischemic wild-type mice treated with
propranolol reversed the preference for intracel-
lular IL-10 production back to an intracellular
IFN-g dominant production and toward a T
H
1-
dominant phenotype (fig. S13). These data strongly
suggest that direct modulation of iNKTcells with
Fig. 3. iNKT cell crawling cessation after MCAO is dependent
on sympathetic innervation. The percentage of crawling (A)
and stationary (B) GFP
+
cells in the liver of sham-operated and
post-ischemic Cxcr6
gfp/+
mice treated with propranolol (PPL) or
6-hydroxydopamine (6-OHDA) at 24 hours after MCAO. Data
are expressed as percentage of GFP
+
cells per FOV. N 4 in-
dividual mice per group; error bars, mean T SEM; ***P < 0.001,
**P < 0.01 by t test. The tracks of GFP
+
cell within the liver
during 10 min of recording in post-ischemic Cxcr6
gfp/+
mice
treated with propranolol (C) or 6-OHDA (D) at 24 hours after
MCAO. Paths are normalized for their origins, and the dotted
circle denotes 10 mm radius from the origin. N 4 individual
mice per group. The percentage of crawling (E) and pirouetting
(F) GFP
+
cells within the liver of sham-operated and Cxcr6
gfp/+
mice treated with localized noradrenaline superfusion. Data are
expressed as percentage of GFP
+
cells per FOV. N 4 individual
mice per group; error bars, mean T SEM; ***P < 0.001, **P <
0.01 by t test. Representative photographs of isolated iNKT
cells for in vitro analysis in untreated (G) and noradrenaline-
treated conditions (H). Scale bar, 50 mm. N 4 individual experi-
ments per group. (I) The percentage of nonpolarized (nonactivated)
and polarized (activated) iNKT cells was determined in un-
treated, noradrenaline-treated, and propranolol-pretreated plus
noradrenaline-treated in vitro. Data are expressed as percentage
of iNKT cells per FOV. N 4 individual experiments per group;
error bars, mean T SEM; ***P < 0.001, *P < 0.05 by t test.
Fig. 4. Selective modulation of iNKT cells decreased stroke-induced lung injury and infectious
complications. (A) For determination of IFN-g production, blood samples were collected and cytokine
expression was analyzed as described in the supporting online material. N 5 individual mice per group;
**P < 0.01 by t test. The lung tissues were removed at 24 hours after MCAO and measured for neutrophil
infiltration by MPO activity (B) or lung edema (C). N 4 individual mice per group; error bars, mean T
SEM; ***P < 0.001, **P <0.01 by t test. Bacteriological analysis was performed to investigate the bacterial
culture from peripheral blood (D), lungs (E), livers (F), and spleens (G) in post-ischemic mice treated with
a-GalCer, propranolol, or 6-OHDA 24 hours after MCAO. ND, not detectable. Data are presented as
number of CFU per ml of blood or mg of tissue. N 4 individual mice per group; error bars, mean T SEM;
**P < 0.01, *P < 0.05 versus MCAO by one-way analysis of variance with Bonferronis post-test.
REPORTS
a-GalCer or through the blockade of noradrener-
gic neurotransmitters was sufficient to modulate
iNKT cells in a manner that results in reduced
infection and associated lung injury after stroke.
iNKTcells are emerging as an important pop-
ulation of cells crucial for the regulation of im-
munity. We have described an essential role of
the sympathetic nervous system and iNKT cells
in the defense against infectious complications
after stroke. Although aspiration pneumonia is
a contributing factor to increased infection in
stroke patients, it cannot explain the immuno-
suppression noted by us and others. Our data sug-
gest that a functional innervation of iNKTcells in
the liver contributes to this immunosuppression.
Our study also provides insights into the cross-
talk that occurs between the central nervous
system and the immune system, which is only
beginning to be understood, and may be a step
toward the development of an effective therapy
for the number one killer in stroke patients,
namely, infection. Although antibiotics may be
a viable option for treatment, with the ever-
increasing problem of antibiotic resistance, im-
munomodulation is an attractive alternative.
1. K. Kimura, K. Minematsu, S. Kazui, T. Yamaguchi; Japan
Multicenter Stroke Investigators Collaboration ( J-MUSIC),
Cerebrovasc. Dis. 19, 171 (2005).
2. P. Langhorne et al., Stroke 31, 1223 (2000).
3. A. Chamorro, X. Urra, A. M. Planas, Stroke 38, 1097
(2007).
4. C. Meisel et al., Stroke 35, 2 (2004).
5. A. Chamorro et al., J. Neurol. Neurosurg. Psychiatry 77,
1279 (2006).
6. R. J. Howard, R. L. Simmons, Surg. Gynecol. Obstet. 139,
771 (1974).
7. L. Brossay et al., J. Exp. Med. 188, 1521 (1998).
8. T. Kawano et al., Science 278, 1626 (1997).
9. A. Bendelac, P. B. Savage, L. Teyton, Annu. Rev.
Immunol. 25, 297 (2007).
10. F. Geissmann et al., PLoS Biol. 3, e113 (2005).
11. P. Velzquez et al., J. Immunol. 180, 2024
(2008).
12. W. Y. Lee et al., Nat. Immunol. 11, 295 (2010).
13. H. Offner, A. A. Vandenbark, P. D. Hurn, Neuroscience
158, 1098 (2009).
14. K. Prass et al., J. Exp. Med. 198, 725 (2003).
15. D. I. Godfrey, M. Kronenberg, J. Clin. Invest. 114, 1379
(2004).
16. J. H. Lichtman et al., Neurology 76, 1976 (2011).
17. V. L. Roger et al.; American Heart Association
Statistics Committee and Stroke Statistics
Subcommittee, Circulation 123, e18 (2011).
18. A. Liesz et al., Brain 134, 704 (2011).
19. H. Offner et al., J. Cereb. Blood Flow Metab. 26, 654
(2006).
20. H. Offner et al., J. Immunol. 176, 6523 (2006).
21. J. Mattner et al., Nature 434, 525 (2005).
22. B. McDonald et al., Science 330, 362 (2010).
23. M. Minagawa et al., Hepatology 31, 907 (2000).
24. H. Oya et al., Clin. Exp. Immunol. 121, 384 (2000).
25. L. Steinman, Nat. Immunol. 5, 575 (2004).
26. K. J. Tracey, Nat. Rev. Immunol. 9, 418 (2009).
Acknowledgments: We thank D. R. Littman (New York
University School of Medicine) for the Cxcr6
gfp/+
knock-in mice, and the Live Cell Imaging Facility
funded by the Canada Foundation for Innovation and
P. Colarusso for training and assistance related to
microscopy. We thank C. Badick for excellent technical
support. The NIH Tetramer Core Facility provided mouse
PBS57-loaded CD1d-tetramer for identification of
iNKT cells by flow cytometry. We also thank the
University of Calgary Flow Cytometry Facility and
L. Kennedy for their assistance with the flow cytometric
analysis. The work is supported by the Canadian
Association of Gastroenterology (C.H.Y.W), the Canadian
Institutes of Health Research (C.H.Y.W., W-Y.L., and P.K.),
the Canada Research Chairs Program (P.K.), the Alberta
Innovates Health Solutions (C.N.J and P.K.), and the
Calvin, Phoebe, and Joan Snyder Chair for Translational
Research in Critical Care Medicine (C.L.). The data
reported in this paper are tabulated in the supporting
online material. The authors declare no competing
financial interests. C.H.Y.W designed and did most of
the experiments, analyzed the results, and prepared
the manuscript; C.N.J. did some flow cytometry
experiments; W-Y.L. isolated iNKT cells for the in vitro
experiments; C.L. performed the multiplex mouse
cytokine/chemokine assay; and P.K. provided overall
supervision, helped design all of the experiments,
and prepared the manuscript.
Figs. S1 to S13
References (2732)
Movies S1 to S4
10.1126/science.1210301
Linking Long-Term Dietary Patterns
with Gut Microbial Enterotypes
Gary D. Wu,
1
* Jun Chen,
2,3
Christian Hoffmann,
4,5
Kyle Bittinger,
4
Ying-Yu Chen,
1
Sue A. Keilbaugh,
1
Meenakshi Bewtra,
1,2
Dan Knights,
6
William A. Walters,
7
Rob Knight,
8,9
Rohini Sinha,
4
Erin Gilroy,
2
Kernika Gupta,
10
Robert Baldassano,
10
Lisa Nessel,
2
Hongzhe Li,
2,3
Frederic D. Bushman,
4
* James D. Lewis
1,2,3
*
Diet strongly affects human health, partly by modulating gut microbiome composition. We used
diet inventories and 16S rDNA sequencing to characterize fecal samples from 98 individuals.
Fecal communities clustered into enterotypes distinguished primarily by levels of Bacteroides
and Prevotella. Enterotypes were strongly associated with long-term diets, particularly protein
and animal fat (Bacteroides) versus carbohydrates (Prevotella). A controlled-feeding study of
10 subjects showed that microbiome composition changed detectably within 24 hours of
initiating a high-fat/low-fiber or low-fat/high-fiber diet, but that enterotype identity remained
stable during the 10-day study. Thus, alternative enterotype states are associated with
long-term diet.
W
e coexist with our gut microbiota as
mutualists, but this relationship some-
times becomes pathological, as in obe-
sity, diabetes, atherosclerosis, and inflammatory
bowel diseases (1, 2). Factors including age,
genetics, and diet may influence microbiome com-
position (3). Of these, diet is easiest to modify
and presents the simplest route for therapeutic
intervention. Recently, an analysis of gut micro-
bial communities proposed three predominant
variants, or enterotypes, dominated by Bacte-
roides, Prevotella, and Ruminococcus, respec-
tively (4). The basis for enterotype clustering is
unknown but appears independent of nationality,
sex, age, or body mass index (BMI).
Here, we investigated the association of die-
tary and environmental variables with the gut mi-
crobiota. First, in a cross-sectional analysis of 98
healthy volunteers (abbreviated COMBO), we
collected diet information using two questionnaires
that queried recent diet (Recall) and habitual
long-term diet (food frequency questionnaire;
FFQ). Second, 10 individuals were sequestered
in a hospital environment in a controlled-feeding
study (abbreviated CAFE) to compare high-
fat/low-fiber and low-fat/high-fiber diets. Stool
samples were collected (5), and DNA samples
were analyzed by 454/Roche pyrosequencing (6)
of 16S rDNA gene segments and, for selected
samples, shotgun metagenomics (7). In CAFE,
rectal biopsy samples were also collected and
analyzed on days 1 and 10.
For COMBO, we used 16S ribosomal DNA
(rDNA) sequence information to calculate pair-
wise UniFrac distances (8) among the microbial
communities. We assessed both relative abundance
data (weighted analysis) and presence/absence in-
formation (unweighted analysis). Specific nutrients
associated with variation in the gut microbiome
for the 98 subjects were extracted, along with
1
Division of Gastroenterology, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, PA 19104, USA.
2
Center for Clinical Epidemiology and Biostatistics, Perelman
School of Medicine, University of Pennsylvania, Philadelphia,
PA 19104, USA.
3
Department of Biostatistics and Epidemiol-
ogy, Perelman School of Medicine, University of Pennsylvania,
Philadelphia, PA 19104, USA.
4
Department of Microbiology,
Perelman School of Medicine, University of Pennsylvania, Phil-
adelphia, PA 19104, USA.
5
Instituto de Cincias Biolgicas,
Universidade Federal de Gois Goiania, GO, 74001-970, Bra-
zil.
6
Department of Computer Science, University of Colorado,
Boulder, CO 80309, USA.
7
Department of Molecular, Cellular
and Developmental Biology, University of Colorado, Boulder,
CO 80309, USA.
8
Department of Chemistry and Biochemistry,
University of Colorado, Boulder, CO 80309, USA.
9
Howard
Hughes Medical Institute, University of Colorado, Boulder, CO
80309, USA.
10
Division of Gastroenterology, Childrens Hos-
pital of Philadelphia, Philadelphia, PA 19104, USA.
gdwu@mail.med.upenn.edu (G.D.W.); lewisjd@mail.med.
upenn.edu (J.D.L.); bushman@mail.med.upenn.edu (F.D.B.)
REPORTS
demographic factors (table S1). For each nu-
trient, we performed PERMANOVA (9) to test
for nutrient microbiome association, from which
we identified 72 and 97 microbiome-associated
nutrients in Recall and FFQ, respectively, at a
false discovery rate (FDR) of 25% (the relatively
high value was used so as not to miss possible
effects of diet on low-abundance bacteria). Both
weighted and unweighted UniFrac identified
similar nutrients, although the discrimination was
sharper with unweighted UniFrac, indicating that
change in community membership rather than
community composition was the main factor.
For each of these nutrients, we used Spearman
correlations to identify the associated bacterial
genera. We considered only the 78 taxa that had
abundance 0.2% in at least one sample and ap-
peared in more than 10% of the samples. Figure
1 shows a heat map summarizing Spearman cor-
relations between nutrients from the FFQ and
bacterial taxa. For a given taxon, individual nutri-
ents account for 3 to 20% of the between-subject
variation in abundance.
Nutrients of the same food groups from Recall
and FFQ tended to cluster together (fig. S1A).
The nutrients from fat versus plant products and
fiber showed inverse associations with microbial
taxa (Spearman r = 0.68, P < 0.0001). Inverse
associations were also seen with amino acids and
proteins versus carbohydrates (Spearman r =
0.73, P < 0.0001) and with fat versus carbo-
hydrates (Spearman r = 0.61, P = 0.0001).
Phyla positively associated with fat but neg-
atively associated with fiber were predominant-
ly Bacteroidetes and Actinobacteria, whereas
Firmicutes and Proteobacteria showed the op-
posite association. However, within each phylum,
not all lower-level taxa demonstrated similar cor-
relations with dietary components (fig. S1B).
Taxa correlated with BMI also correlated with
fat and percent calories from saturated fatty acids
(fig. S1B and table S1).
Following the suggestion by Arumugamet al.
(4) that the human gut microbiome can be parti-
tioned into enterotypes, we investigated whether
the 98 COMBO samples partitioned into clusters
that were detectably associated with dietary or
demographic data (Fig. 2). Several methods for
data processing and clustering were compared
(fig. S2). In one analytical approach (weighted
UniFrac, no lane masking; fig. S2), partitioning
around medoids (PAM) analysis favored parti-
tioning into three clusters, although with quite
low support (silhouette score 0.2) suggesting that
clustering could be due to chance. Comparison to
the three genera specified by Arumugamet al. (4)
showed that relatively high levels of the genera
Bacteroides and Prevotella distinguished two of
the clusters, whereas the third showed slightly
higher levels of Ruminococcus. However, most
methods showed two clusters, with stronger sup-
port (Fig. 2; Jensen-Shannon distance, silhouette
score 0.66), in which the Bacteroides enterotype
was fused with the less well distinguished
Ruminococcus enterotype. As described below,
Peonidin, anthocyanidin
Malvidin, anthocyanidin
Petunidin, anthocyanidin
Total anthocyanidins
Delphinidin, anthocyanidin
Pelargonidin, anthocyanidin
Potassium
Potassium w/o suppl.
Magnesium
Magnesium w/o suppl.
Free Choline, cholinecontrib. metabolite
Free Choline w/o suppl.
Natural Food Folate
AOAC fiber
Pantothenic Acid w/o suppl.
Naringenin, flavanone
Vitamin E w/o vit. suppl.
Proanthocyanidin, 46mers
Proanthocyanidin, trimers
Proanthocyanidin, 710mers
Cyanidin, anthocyanidin
Proanthocyanidin, polymers
Proanthocyanidin, dimers
Catechin, flavan3ol
Alcohol
Phenylalanine, Aspartame
Aspartic Acid, Aspartame
Aspartame
Caffeine
Retinol
Retinol Equivalents of Vit A
Total Folate post 1998
Folate Equivalents, suppl. & fort. foods
Riboflavin B2 w/o vit. pills
Histidine
Threonine
Methionine
Lysine
Leucine
Tyrosine
Valine
Isoleucine
Protein
Phenylalanine
Serine
Tryptophan
Glycine
Alanine
Arginine
Asparate
Choline, Phosphatidylcholine
Choline, Phosphatidylcholine w/o suppl.
Total Choline, no betaine
Choline w/o suppl.
Sum of Betaine & Choline
Cystine
Glutamate
Proline
Vitamin D w/o vit. pills
Choline, Glycerophosphocholine
Choline, Phosphocholine
Phosphorus
Phosphorus w/o suppl.
Calcium
Calcium w/o vit. pills
Dairy Protein
Dairy Calcium
Animal Protein
Choline, Sphingomyelin
Cholesterol
Taurine
Palmitoleic fatty acid
Hydroxyproline
Animal fat
c9,t11 conjug diene isomer 18:2 Linoleic
Palmitic fatty acid
Saturated fat
Stearic fatty acid
Palmitelaidic trans fatty acid
Sodium
Dihydrophylloquinone Vitamin K1
Trans Oleic fatty acid
Total Trans
Total Trans/Cis Trans Linoleic
Eicosenoic fatty acid
Gamma Linolenic fatty acid (2002)
Gamma linolenic fatty acid (2000)
Fructose
Glucose
Carbohydrates
Total Sugars
Sucrose
Glycemic Index
Maltose
Eriodictyol, flavonone
Added Germ from wheats
Vitamin E, Food Fortification
*
*
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*
*
*
*
*
*
*
*
*
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*
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Bacteroides Prevotella
0.2 0 0.2
Spearman Correlation
Phylum
Firmicutes
Bacteroidetes
Actinobacteria
Proteobacteria
Amino Acids
and
Choline
Fiber
and
Plant Derived
Compounds
Fats
Carbohydrates
Fig. 1. Correlation of diet and gut microbial taxa identified in the cross-sectional COMBO analysis. Columns
correspond to bacterial taxa quantified using 16S rDNA tags; rows correspond to nutrients measured by dietary
questionnaire. Red and blue denote positive and negative association, respectively. The intensity of the colors
represents the degree of association between the taxa abundances and nutrients as measured by the Spearmans
correlations. Bacterial phyla are summarized by the color code on the bottom; lower-level taxonomic assign-
ments specified are in fig. S1. The dots indicate the associations that are significant at an FDR of 25%. The FFQ
data were used for this comparison (both FFQ and Recall dietary data are shown together in fig. S1). Columns
and rows are clustered by Euclidean distance, with rows separated by the predominant nutrient category.
REPORTS
2004 2006 2009 2016 2019 2005 2008 2011 2012 2020
Day 1 to others
Between other days
Subject Number
W
e
i
g
h
t
e
d

U
n
i
F
r
a
c

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i
s
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a
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e
0
.
0
0
.
1
0
.
2
0
.
3
0
.
4
0
.
5
A B
Low Fat Diet High Fat Diet
Fig. 3. Changes in bacterial communities during controlled feeding. Ten
subjects were randomized to high-fat/low-fiber or low-fat/high-fiber diets, and
microbiome composition was monitored longitudinally for 10 days by sequenc-
ing 16S rDNA gene tags (CAFE study). (A) Cluster diagrambased principal
coordinates analysis using unweighted UniFrac. Colors indicate samples from
each individual. (B) Day 1 samples are outliers compared to all other days,
indicating change in the gut microbiome within 24 hours of initiating con-
trolled feeding. In this analysis, weighted UniFrac distances between samples
are compared within subjects in two groups. The first collection of distances
compares the day 1 samples to days 2 to 10; the second group compares
samples from all days to all others excluding day 1, indicating rapid change
(P = 0.0003, 10,000 permutations). Error bars indicate 1 SD of the distances.
5 10 15 20
0
.
0
0
.
1
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2
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3
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6
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k (# clusters)
A
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Color Key
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Enterotype 2
(Prevotella)
Enterotype 1
(Bacteroides)
Fig. 2. Clustering of gut microbial taxa into entero-
types is associated with long-term diet. (A) Clustering in
the COMBO cross-sectional study using Jensen-Shannon
distance. The left panel shows that the data are most
naturally separated into two clusters by the PAM method.
The x axis shows cluster number; the y axis shows sil-
houette width, a measure of cluster separation (12). The
right panel shows the clustering on the first two principal
components. (B) Proportions of bacterial taxa characteristic of each en-
terotype. Boxes represent the interquartile range (IQR) and the line inside
represents the median. Whiskers denote the lowest and highest values
within 1.5 IQR. (C) The association of dietary components with each
enterotype. The strength and direction of each association, as measured by
the means of the standardized nutrient measurements, is shown by the color
key at the lower right. Enterotype is shown at the right. Red indicates greater
amounts, blue lesser amounts of each nutrient in each enterotype (complete
lists of nutrients are in table S2). Columns were clustered by Euclidean
distance.
REPORTS
dietary effects primarily distinguish the Prevotella
enterotype from the Bacteroides enterotype.
At an FDR of 5%, six genera differed be-
tween the Prevotella and Bacteroides enterotypes
(fig. S3). The Bacteroides enterotype was distin-
guished by the additional presence of Alistipes
and Parabacteroides (phylumBacteroidetes). The
Prevotella enterotype was distinguished by the
additional presence of Paraprevotella (phylum
Bacteroidetes) and Catenibacterium (phylum
Firmicutes) (fig. S3). The enterotype clustering
was driven primarily by the ratio of the two dom-
inant genera, Prevotella to Bacteroides, which de-
fines a gradient across the two enterotypes (fig. S5).
At an FDR of 25%, nutrients from the long-
term FFQ but not the short-term Recall question-
naire were associated with enterotype composition,
indicating that long-term diet strongly correlates
with enterotype (the relatively high FDR was
used to avoid excessively strict filtering and to
visualize the full pattern). The Bacteroides entero-
type was highly associated with animal protein, a
variety of amino acids, and saturated fats (Fig.
2C), which suggests that meat consumption as in
a Western diet characterized this enterotype. The
Prevotella enterotype, in contrast, was associated
with low values for these groups but high values
for carbohydrates and simple sugars, indicat-
ing association with a carbohydrate-based diet
more typical of agrarian societies. Self-reported
vegetarians (n = 11) showed enrichment in the
Prevotella enterotype (27%Prevotella enterotype
versus 10%Bacteroides enterotype; P= 0.13). The
one self-reported vegan was in the Prevotella
enterotype. No significant associations were seen
with demographic data at this FDR.
A short-term controlled-feeding experiment
(CAFE) was carried out to test the stability of
the gut microbiome and the observed nutrient-
microbiome associations. Ten subjects were se-
questered and randomized to high-fat/low-fiber
or low-fat/high-fiber diets and were then sampled
over 10 days (Fig. 3). Analysis of 16S tag data
from stool samples showed that intersubject var-
iation was by far the predominant source of var-
iance in the data (10). Figure 3A shows sharp
clustering of the microbiome sequence data by
individual in unweighted UniFrac, emphasizing
that distinctive lineages are present in each sub-
ject. Over 10 days of controlled feeding, there
was no reduction in UniFrac distances for stool or
biopsy samples between individuals fed the same
diet, demonstrating that a short-term identical
diet does not overcome intersubject variation.
Remarkably, changes in microbiome compo-
sition were detectable within 24 hours of ini-
tiating controlled feeding. For each individual
sampled, the first sampling day represented an
outlier (Fig. 3B; P = 0.0003, 10,000 permuta-
tions), indicating rapid change. Similar results
were seen in the unweighted analysis (P= 0.0002).
The taxa affected differed among individuals.
The relationship of changes in microbiome com-
position to the transit time of material through the
gut was alsoinvestigated. Subjects swallowedx-ray
opaque markers at the start of the study, allowing
quantification of transit time by abdominal x-ray.
Transit time was faster with the high-fiber diet (2
to 4 days) than with the high-fat diet (2 to 7 days;
P= 0.02; two-sided Wilcoxon rank sum test), as ex-
pected. All patients retained at least one of the 24
markers 48 hours after the start of the experimental
diet. Thus, the changes in microbiome composi-
tion, which occurred within 24 hours, were faster
than clearance of residual material from the gut.
To probe metabolic functionality during the
CAFE study, we also analyzed changes in total
gene content using shotgun metagenomics. We
compared stool samples from day 1 and day 10
(1.05 10
6
sequence reads total). Sequence reads
were annotated for function using the KEGG
database (11), then interrogated to assess the
taxa and classes of genes present. No significant
changes in proportions among archaea, bacteria,
and eukaryotes were detected, and bacterial taxa
inferred from shotgun metagenomic data paral-
leled the 16S rDNA data (fig. S4). We investi-
gated gene groups that changed significantly
between day 1 and 10 and differed between the
high-fat and high-fiber groups. To control for
between-subject variability, we used the day
1 samples as within-subject controls, and sub-
tracted each subjects day 1 functional category
counts from day 10 samples from that same sub-
ject. Functional categories that differentiated diets
included bacterial secretion system (P = 0.01,
t test), protein export (P = 0.022), and lipoic acid
metabolism (P = 0.045), thus indicating bacterial
functions potentially involved in responding to
these dietary changes.
We next assessed the response of enterotypes
to the controlled feeding regimen. Each of the
samples from the 10 subjects was assigned to an
enterotype category on the basis of their micro-
biome distances to the medoids (12) of the en-
terotype clusters as defined in the COMBO data.
All subjects started in the Bacteroides enterotype
(high protein and fat). None switched stably to
the Prevotella (carbohydrate) enterotype over the
duration of the study. A single specimen scored
in the Prevotella (carbohydrate) enterotype but
reverted by the time of the next sample. Thus,
over the 10 days of the dietary intervention, we
did not see stable switching between the two
enterotype groups characterized by the dietary
extremes, despite feeding of a low-fat/high-fiber
diet to half the subjects.
Finally, several factors were significantly cor-
related with microbiome composition but not
with enterotype partitioning. Examples included
BMI, red wine, and aspartame consumption (7).
Thus, not all associations between host and mi-
crobiota are captured in the enterotype distinctions.
Comparison of long-term and short-term die-
tary data showed that only the long-termdiet was
correlated with enterotype clustering in the cross-
sectional study. In the interventional study, changes
were significant and rapid, but the magnitude of
the changes was modest and not sufficient to
switch individuals between the enterotype clus-
ters associated with protein/fat and carbohydrates.
Thus, our data indicate that long-term diet is par-
ticularly strongly associated with enterotype parti-
tioning. The dietary associations seen here parallel
a recent study comparing European children, who
eat a typical Western diet high in animal protein
and fat, to children in Burkina Faso, who eat
high-carbohydrate diets lowin animal protein (13).
The European microbiome was dominated by
taxa typical of the Bacteroides enterotype, where-
as the African microbiome was dominated by the
Prevotella enterotype, the same pattern seen here.
There are, of course, many differences between
Europe and Burkina Faso that might influence
the gut microbiome, but dietary differences pro-
vide an attractive potential explanation. Having
confirmed enterotype partitioning and established
the association with dietary patterns, it will be
important to determine whether individuals with
the Bacteroides enterotype have a higher inci-
dence of diseases associated with a Western diet,
and whether long-term dietary interventions can
stably switch individuals to the Prevotella entero-
type. If an enterotype is ultimately shown to be
causally related to disease, then long-termdietary
interventions may allow modulation of an in-
dividuals enterotype to improve health.
1. L. V. Hooper, J. I. Gordon, Science 292, 1115 (2001).
2. A. Emminger, E. Kahmann, D. S. Savage, Cancer Lett. 2,
273 (1977).
3. S. R. Gill et al., Science 312, 1355 (2006).
4. M. Arumugam et al., Nature 473, 174 (2011).
5. G. D. Wu et al., BMC Microbiol. 10, 206 (2010).
6. M. Margulies et al., Nature 437, 376 (2005).
8. C. Lozupone, M. Hamady, R. Knight, BMC Bioinformatics
7, 371 (2006).
9. B. H. McArdle, M. J. Anderson, Ecology 82, 290 (2001).
10. R. E. Ley, P. J. Turnbaugh, S. Klein, J. I. Gordon, Nature
444, 1022 (2006).
11. M. Kanehisa, S. Goto, S. Kawashima, Y. Okuno,
M. Hattori, Nucleic Acids Res. 32 (database issue), D277
(2004).
12. P. J. Rousseeuw, J. Comput. Appl. Math. 20, 53 (1987).
13. C. De Filippo et al., Proc. Natl. Acad. Sci. U.S.A. 107,
14691 (2010).
Acknowledgments: Supported by NIH grants UH2 DK083981
(F.D.B., J.D.L., and G.D.W.) and RO1 AI39368 (G.D.W.);
Penn Genome Frontiers Institute; Penn Digestive Disease
Center grant P30 DK050306; Joint Penn-CHOP Center
for Digestive, Liver, and Pancreatic Medicine grants
S10RR024525, UL1RR024134, and K24-DK078228; and
the Howard Hughes Medical Institute. The content is
solely the responsibility of the authors and does not
necessarily represent the official views of the National
Center for Research Resources, National Institutes of
Health, or Pennsylvania Department of Health. Accession
numbers (Sequence Read Archive): for the CAFE study,
SRX021237, SRX021236, SRX020587, SRX020379,
and SRX020378 (metagenomic); for the COMBO study,
SRX020773, SRX020770, and SRX089367.
Figs. S1 to S5
Tables S1 to S10
References (1421)
10.1126/science.1208344
REPORTS
membercentral.aaas.org
22
minutes and 58 seconds of
video on accelerated mass loss
from Antarcticas ice shelves.
One more data point on why you should spend
more time at membercentral.aaas.org. There
you can enjoy evidence-based videos, webinars,
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R

UPCOMING FEATURES
Genomics: Gene ExpressionNovember 4
Genomics: Building Clinically Relevant ModelsFebruary 24
Toxicology: Animal-Free TechniquesMarch 2
T
he Gene Quantification website is like a 7-Eleven
store for quantitative polymerase chain reaction
(qPCR): a one-stop shop for news, advice, and prod-
uct links. Its curator is Michael W. Pfaffl, a professor
in the physiology department at Technical University
of Munich, who has been developing qPCR methodology for
more than a decade. Pfaffl sees qPCR innovation in three areas:
platforms, technologies, and physiology.
Innovations in platforms are in high throughput and miniatur-
ization, says Pfaffl, and a major factor is microfluidics technol-
ogyrunning submicroliter reactions in submillimeter spaces.
The RainStorm platform in RainDance Technologies RDT 1000
produces picoliter droplets at a rate of 10 million per hour by
running aqueous samples through a stream of oil. Samples in
the droplets undergo PCR amplification on a disposable chip
that allows more than 2.5 million parallel reactions. Using com-
pletely different microfluidics technology, the Fluidigm BioMark
HD runs PCR reactions in soft rubber chips that control the
flow of picoliter reaction mixes with pressure-activated valves,
like a hose on a driveway that you drive across, says Fluidigm
Chief Executive Officer Gajus Worthington. The highest capacity
chip runs 96 reactions on 96 samples for 9,216 assays in just a
few hours.
You dont need microfluidics to run thousands of simultane-
ous assays, though. A more traditional high throughput option,
specialized for detection of cancer-related genes or microRNAs,
is the WaferGen SmartChip System. The systems metal-alloy
chips run as many as 5,184 qPCR reactions in about two hours,
with instruments and software for loading, amplifying, and an-
alyzing cDNA samples in SmartChip Panels. These come pre-
loaded with primers for expression profiling up to 1200 human
microRNAs or 1,250 human cancer-related genes, with controls.
Panels can also be made with custom configurations of Wafer-
Gen pre-validated or customer-specified primers.
A DIGITAL REVOLUTION
High throughput capability is driving the development of digi-
tal PCR, named for its binary outputa yes or no answer to
the question Did the reaction contain the target sequence?
Digital PCR allows absolute instead of relative quantification,
eliminating the need for standard curves or endogenous con-
trols. You partition samples to the point where a reaction either
has a template molecule or it doesnt, explains Ramesh Ramak-
rishnan, director of molecular biology and assay development
at Fluidigm. End-point PCR is conducted on an array of diluted
samples, then you figure out the starting concentration of the
sample by counting positives after the partitioning. Ramakrish-
nans group published a 2010 PLoS One proof-of-concept study
on haplotyping, or determining the sequence of alleles along a
chromosome. They found that digital PCR can be used to show
that specific alleles are linkedmeaning they are on the same
chromosomeif the alleles are co-amplified in a single-molecule
reaction. The alleles tested by the group included one that modi-
fies the severity of sickle cell anemia.
Another application of digital PCR is cell-free, noninvasive
fetal diagnostic assays using nucleic acids from maternal blood
samples. In 1997, Yuk Ming Dennis Lo, director of the Li Ka
Shing Institute of Health Sciences, Chinese University of
Hong Kong, found that fetal DNA could be detected in maternal
blood plasma, and surprisingly, about 510 percent of DNA from
the mothers plasma is fetal. We can easily detect the sex
of the baby using Y chromosomal DNA in the blood, he says.
Then, for a male fetus, his group established prenatal diagnosis
principles using single-molecule counting by digital PCR for
recessive, X-linked diseases such as hemophilia. If a woman
carries one normal and one affected allele for the hemophilia
gene, Los digital PCR assay will show a balance between the
normal allele on one X chromosome and the disease allele on
the other X. When she is carrying a male fetus, which has one X
qPCR Innovations and
Blueprints
Quantitative PCR users can rapidly generate large amounts
of high-quality data with new instruments and products made
possible by microfluidics and miniaturization technology. These
platforms are the tools for developing techniques that require
extremely high throughput and sensitivity such as digital PCR
and single-cell analysis. Researchers are adopting these meth-
ods to ask sophisticated questions about genetics and cancer
biology as well as to develop novel research and diagnostic
assays. As qPCR innovators explore new frontiers and everyday
users venture into more complicated workflows, international
groups of industry and academic partners are keeping us on the
path of best practices. Two consortia are generating guidelines
on the qPCR processfrom experimental design and pre-analy-
sis sample collection, to processing data and publishing results.
The guidelines are blueprints that ensure reproducibility, validity,
and transparency. By Chris Tachibana
One reason were excited about digital
now is because there are nally platforms
that can perform large numbers of
reactions with reasonable economics.
LIFE SCIENCE TECHNOLOGIES
qPCR
Produced by the Science/AAAS Custom Publishing Office
110
and one Y chromosome, the inherited allele for the hemophilia
genenormal or affected, will stand out as overrepresented
in the maternal plasma. The same principle can be applied to
Down syndrome (trisomy 21) detection for overrepresentation
of chromosome 21 sequences relative to sequences on other
chromosomes.
Digital PCR is a rapid and sensitive method for detecting chro-
mosome or gene copy number variations, says Ramakrishnan.
Another application is monitoring targeted drug treatments,
such as with the breast cancer drug herceptin, which targets the
HER2 receptor. Tumor cells become resistant to the drug as the
copy number of the HER2 gene increases. With microarrays,
youre doing well if you can see two-fold differences in copy
number, says Ramakrishnan. With real-time PCR, a two-fold
difference is easy, but seeing the difference between two- and
three-fold, or three- and four-fold is difficult. As long as enough
molecules are sampled for good statistics, he says, digital PCR
allows simple counting against a reference sequence, so subtle
differences in ratios can be detected, such as 3-to-1 versus 4-to-1.
Digital PCR is also a sensitive method for detecting low levels of
pathogens or contaminants in a dilute sample.
Paul Pickering, head of the Digital PCR Business Unit for Life
Technologies, says that digital PCR is not a new idea, but is
now feasible with the availability of high throughput instruments
like the OpenArray Real-Time PCR Platform, a system capable
of simultaneously running up to three plates, each with 3,072
wells of 33-nanoliter reaction size, for more than 36,000 data
points per day. Imagine trying to do that with 384-well plates,
says Pickering. One reason were excited about digital now is
because there are finally platforms that can perform large num-
bers of reactions with reasonable economics. Life Technologies
offers a kit of plates, software and a proprietary master mix op-
timized to facilitate digital PCR.
LOOKING AT INDIVIDUALS INSTEAD OF
POPULATIONS
New qPCR technologies let researchers ask increasingly sophis-
ticated physiological questions. Besides detecting nucleic acids
in blood or urine, a hot topic at qPCR meetings is single-cell
analysis. Fluidigms Worthington says that current gene profiling
methods for tissue or culture samples are like getting a com-
bined score for all kids and all subjects in a classroom, instead
of individual grades by subject. Many differences cant be seen
unless you test individuals instead of populations. Because it
enables this level of analysis, single-cell qPCR is gaining much
interest from the cancer biology community.
Tumors are not one kind of cell, says Mikael Kubista, chief
executive officer of the qPCR training and contract services com-
pany TATAA Biocenter, and head of the Department of Gene
Expression Profiling, Biotechnology Institute, Academy of
Sciences, Czech Republic. Single-cell qPCR promises a more
nuanced analysis of the genetics and gene expression of biopsy
cells, he says. Several systems can now collect individual cells
for analysis, including laser microdissection of cells from solid
tissue, or capturing single cells in suspension by fluorescence-
activated cell sorting or micromanipulation with glass capillaries
the width of an individual cell. The next step is addressing tech-
nical issues such as the best way to lyse a single cell and re-
verse transcribe its approximately one picogram of mRNA with
minimal loss and variability. New analysis methods are needed
to distinguish genuine cell-to-cell differences from technical vari-
ation and noise. With the right methods and markers, however,
Kubista says that single-cell expression profiling could detect
cancer stem cells, which have the potential for self-renewal and
differentiation and to cause relapse and metastasis. Expression
profiling on 10,000 cells wont pick up the signature of a few
tumor stem cells, he says. However, single-cell assays might
be able to detect cells undergoing an epithelial-to-mesenchymal
transition with a loss of cell-cell adhesion and increase in mobil-
ity that is associated with tumor invasiveness. Single-cell qPCR
requires an extremely careful workflow, though. You have such
tiny amounts, if you make a mistake, your sample is gone,
says Pfaffl.
qPCR GUIDELINES (THERES AN APP FOR THAT)
Attention to workflow, from experimental design to sample pro-
cessing to final analysis, is increasingly important as research-
ers push the boundaries of qPCR, yet strive to stay within the
lines of reliability, reproducibility, and validation. Years of discus-
sion on these issues are coalescing into universal guidelines for
qPCR best practices. Were entering a phase where standard-
ization is important for making more reliable, robust assays,
says Kubista.
An example is the four-year European Union Standardisation
and improvement of generic Pre-analytical tools and procedures
for In-vitro DIAgnostics (SPIDIA) initiative. This consortium of
academic and industry partners and the European Committee
for Standardization (CEN) is generating evidence-based guide-
lines and tools for standardizing the pre-analysis process, such
as ways to collect samples that preserve gene expression pro-
files as they were in vivo and to minimize ex vivo biomolecu-
lar synthesis, degradation, and modification. The project is co-
ordinated by Qiagen, and Uwe Oelmueller is Qiagens SPIDIA
coordinator and vice president of Research and Development,
Molecular Diagnostic Sample Preparation. Qiagen is in charge
of overall project management, coordinating the activities of
the 16 partners, he says, and we also do sciencedevelop-
ment and discovery work. Of the 13 million
FEATURED PARTICIPANTS
Barts and the London
School of Medicine and
Dentistry, University of
London
www.smd.qmul.ac.uk
Biogazelle
www.biogazelle.com
Department of Gene
Expression Proling,
Biotechnology Institute,
Academy of Sciences,
Czech Republic
www.img.cas.cz/ge
Fluidigm
www.uidigm.com
Ghent University
www.ugent.be/en
Life Technologies
www.lifetechnologies.com
Li Ka Shing Institute of
Health Sciences, The Chinese
University of Hong Kong
www.lihs.cuhk.edu.hk
QIAGEN
www.qiagen.com
RainDance Technologies
www.raindancetechnologies.
com
TATAA Biocenter
www.tataa.com
Technical University
of Munich
www.tum.de
Thermo Fisher Scientic
www.thermo.com
Wafergen
www.wafergen.com
continued

qPCR
111
budget, 4 million comes largely from the industry partners,
says Oelmueller. The project is a natural fit with Qiagens prod-
ucts for sample preparation that preserve bioanalyzable profiles,
and all consortium companies benefit from the networking and
product development opportunities. Guideline releases have
been ongoing, from the SPIDIA consortiums published recom-
mendations to standards that require approval by 31 European
countries, which will take several years to finalize.
In 2009, a set of qPCR best-practice guidelines was published
by an international consortium led by Stephen A. Bustin, pro-
fessor of molecular science, Barts and the London School of
Medicine and Dentistry, University of London. The minimum
information for publication of quantitative real-time PCR experi-
ments (MIQE, or mikey) guidelines are a blueprint for good
assay design, and they standardize the information submitted
with publications. Developed in part after considerable variability
was found in clinical qPCR assay results, the guidelines include
a checklist of items to include with any publication using qPCR,
and cover everything from sample collection and experimental
design, to data analysis and reporting results. Guideline devel-
opers are urging journals to include MIQE compliance in their
publication requirements. Some MIQE guidelines are simple,
for example, using the term RT-PCR for reverse transcription-
qPCR, and qPCR for quantitative real-time PCR, which might not
include reverse transcription. Others require more effort from
investigators, such as supplying primer or amplicon sequences.
Its worth it, though. A researcher following the guidelines is
virtually guaranteed to end up with an efficient PCR assay and is
encouraged to provide all assay details to enhance the transpar-
ency of experiments, says Bustin. And to make MIQE easy and
fun, theres an iPhone app with links to references and screens
to tick off checklist items.
DOI: 10.1126/science.opms.p1100058
Chris Tachibana is a science writer based in Seattle, USA, and
Copenhagen, Denmark.
Companies are now helping investigators follow MIQE guide-
lines. Ian Kavanagh, senior research and development manager
at Thermo Fisher Scientific says the Solaris qPCR gene expres-
sion assays were developed with input from the MIQE guideline
authors. The assays offer predesigned, optimized primers and
probes that detect all known splice variants of mRNAs in the
human and mouse genomes. An essential component of the
MIQE guidelines is knowing your amplicon, and Kavanagh says,
Solaris fully discloses all primer and probe sequences so cus-
tomers can do their own bioinformatics searches to see what
the amplicon looks like.
On the data-crunching end, MIQE compliance is a feature of
qbase
PLUS
, third-party qPCR data-analysis software that is com-
patible with more than 95 percent of qPCR instruments on the
market. It originated as freeware developed by Jan Hellemans
and Jo Vandesompele, researchers at Ghent University in Bel-
gium, who started the qPCR software and services company
Biogazelle in 2007. Vandesompele says qbase
PLUS
uses only
peer-reviewed quantification models for relative quantification,
efficiency correction, inter-run calibration and error propagation,
and stores and exports the assay information that is required for
MIQE guidelines. This information includes primer sequences,
target information, and PCR efficiency.
The MIQE guidelines are a work in progress. An update was
published in March 2011 and guideline developers are constantly
receiving feedback from researchers. Some find the checklist
daunting, but Kavanagh says, every scientist should have the
information it asks for in their laboratory notebooks anyway, if
theyve done their experiments correctly.
THE FUTURE: LEAVING IT TO THE PROS
Of course, one way to ensure high-quality qPCR is to let the
pros do it. Kubista predicts developments in qPCR similar to
oligonucleotide synthesis and sequencing, which were first set
up in academic labs, then in core labs. Today, its cheaper to send
samples to a specialized provider with high throughput instru-
mentation and quality control programs, so everything is accord-
ing to guidelines and best practices. Within five years I believe
we will have this change in qPCR. Kubista is banking on this
trend with the TATAA Biocenter. In addition to offering training
in basic qPCR, including hands-on workshops, and courses in
experimental design, sample preparation, standardization, qual-
ity control, data mining, and data analysis, the TATAA Biocenter
performs qPCR contract services, from study design to post-
PCR analysis. Biogazelle also provides contract services, includ-
ing expression profiling for human and mouse microRNAs and
long non-coding RNAs, and WaferGen offers proof-of-principle
expression profiling or single-nucleotide polymorphism genotyp-
ing on customer-supplied samples.
With the economies of scale and quality assurance that core
facilities or contract research organizations can provide, out-
sourcing qPCR work is tempting. Researchers still need to un-
derstand good data handling and experimental design, though,
says Kubista. The user doesnt need to be a statistician, but
has to understand the purpose of different controls and repli-
cates. Its a lot to keep track of, with technological advances
leading researchers in many directions; but a regular stop at the
Gene Quantification website will keep you stocked up on current
qPCR news and developments.
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A researcher following the guidelines is
virtually guaranteed to end up with an
efcient PCR assay.
qPCR
112
Gene Quantication Web Pages
www.gene-quantication.info
MIQE App
itunes.apple.com/app/miqe-qpcr/id423650002?mt=8
MIQE Guidelines
www.clinchem.org/cgi/content/full/55/4/611
SPIDIA
www.spidia.eu
ADDITIONAL RESOURCES
PORTABLE PCR SYSTEM
The Palm PCR system is an innovative portable polymerase chain
reaction (PCR) device that delivers high performance nucleic acid
amplication in a small handheld format. The palm-sized, battery-
powered Palm PCR thermocycler promises to extend the range
of applications of this well-established technology beyond its cur-
rent indoor limitations. Designed for simplicity and robustness,
the Palm PCR system delivers fast and efcient amplication of a
large variety of targets including very low copy number human ge-
nomic DNA. Its battery-powered automated operation (more than
four hours of continuous operation on a single battery charge),
extremely low power consumption (less than 5 W), and high ef-
ciency make it ideal for both indoor and outdoor applications. It
is designed to conform to the standard 9 mm spaced well format
to use with a disposable plastic sample tube. The Palm PCR deliv-
ers highly accurate and reproducible results with high temperature
uniformity (less than +/- 0.1 degrees Celsius).
Ahram Biosystems
For info: 408-400-0600 www.ahrambio.com
MICRORNA PCR PANELS
The highly exible Pick & Mix microRNA PCR Panels are for sensi-
tive and specic quantication of custom selected microRNAs in
both 96- and 384-well array formats. The Pick & Mix microRNA
Panel system allows customers to design a real-time polymerase
chain reaction (qPCR) array based on pre-validated LNA-enhanced
microRNA PCR primers via an online array conguration tool. In
simple, intuitive steps the array conguration tool guides custom-
ers through selections including choice of format: 96-well or 384-
well plate format, array layout, target organism, microRNA assays,
controls, and real-time PCR instrument of choice. These custom-
ized qPCR arrays are delivered ready-to-use. Reliable microRNA
proling can be achieved using only 1 pg of total RNA without
need for pre-amplication and can be performed on challenging
samples such plasma, including plasma from mouse and rat where
only very little sample material can be obtained.
Exiqon
For info: 888-647-2879 www.exiqon.com
STEM CELL PLURIPOTENCY KIT
The PluriPCR Kit has been designed as a quantitative and reliable
assay of ve genes strongly specic to pluripotency. These genes
(Oct-3/4, Nanog, DNMT3b, Dppa4, and Rex1) are expressed by
human embryonic stem cells and induced pluripotent stem (iPS)
cells, and are all sharply down regulated during differentiation.
Both simple and easy to use with existing real time quantitative
polymerase chain reaction (qRT-PCR) equipment, PluriPCR uses
these ve key genes in combination with a unique normalization
method to give a reliable and quantitative readout for a cell lines
pluripotency. This kit is ideally suited for all aspects of pluripotent
stem cell research: To measure if culture conditions result in the
loss of pluripotency, to assess the success of iPS cell nuclear re-
programming, and as a release assay in the manufacture and clini-
cal development of pluripotent stem cells. The PluriPCR kit is fully
optimized for routine quality control using either two-step or one-
step qRT-PCR methods.
AMS Biotechnology
For info: +44-(0)-1235-828200 www.amsbio.com
PCR TARGET ENRICHMENT KIT
The new HaloPlex Target Enrichment Kit revolutionizes next gener-
ation sequencing, reducing costs and saving up to 80% in sample
preparation time compared to many other kits. HaloPlex Target En-
richment Kit introduces a dramatically improved polymerase chain
reaction (PCR) technology that enables millions of PCR reactions in
a single tube. Following fragmentation using specically selected
restriction endonucleases, and denaturing of the DNA sample, a
Selector Probe library is added. Each probe, designed to hybridize
to both ends of a targeted DNA restriction fragment, guides the
targeted fragments to form circular DNA molecules. Only circular
DNA targets are amplied, ready for sequencing using any next
generation procedure, and results are highly reproducible. This
new Halo Genomics kit provides a lab-in-a-tube solution which
greatly simplies PCR workow, with no need for expensive in-
strumentation or automation.
Cambio
For info: +44-(0)-1954-210200 www.cambio.co.uk
Electronically submit your new product description or product literature information! Go to www.sciencemag.org/products/newproducts.dtl for more information.
Newly offered instrumentation, apparatus, and laboratory materials of interest to researchers in all disciplines in academic, industrial, and governmental organizations are
featured in this space. Emphasis is given to purpose, chief characteristics, and availability of products and materials. Endorsement by Science or AAAS of any products or
materials mentioned is not implied. Additional information may be obtained from the manufacturer or supplier.
PCR ARRAY SYSTEM
The qBiomarker Somatic Mutation PCR Array System is designed for rapid
and accurate mutation proling in basic research and drug discovery. The
assays consist of collections of pathway- or cancer-specic assays in 96-
or 384-well plate formats with a number of pathways (EGFR, ErbB2, etc.)
and cancer types. Laboratory experiments have shown that the PCR arrays
provide a sensitivity of as low as 12% mutant DNA in a background of
wild-type DNA. The pathway-focused approach also enables an in-depth
understanding of the mutations that are present in a specic tumor sample
in a short time frame. The experiments require approximately two hours
from sample to result and are easy to perform: The DNA is extracted from
the sample, amplied if needed, and then used for the PCR array with any
block-based real-time cycler.
Qiagen
For info: 888-503-3187 www.qiagen.com
113
NEW PRODUCTS: qPCR
BASIC SCIENCE RESEARCH
DIRECTOR, ASIA.
Estee Lauder Companies, a global innovator
in prestige skincare, is seeking an MD or
PhD with focus on dermatology or related
elds to manage its growing basic science
research program in Asia, headquartered
in Shanghai, China. The position includes
directing basic and clinical research,
collaborating with academic institutions,
supporting product development, representing
the companys research to the Asian press,
and communicating with and travel to the
companys research centers in Europe and
New York. The candidate should have 5+
years working in basic or clinical research,
preferably with time in the personal care
industry. The candidate should have strong
people management and networking skills,
and excellent communication in English and
Chinese. Estee Lauder provides a generous
and competitive compensation package.
Please submit a cover letter summarizing
goals and qualications together with resume
to Ms. Jing Cheng, jcheng@cn.estee.com.
Tracy Holmes
Worldwide Associate Director
Science Careers
Phone: +44 (0) 1223 326525
UNITED STATES & CANADA
E-mail: advertise@sciencecareers.org
Fax: 202-289-6742
Tina Burks
Midwest/West Coast/
South Central/Canada
Phone: 202-326-6577
Elizabeth Early
East Coast & Industry
Phone: 202-326-6578
Marci Gallun
Sales Administrator
Phone: 202-326-6582
Online Job Posting Questions
Phone: 202-312-6375
EUROPE & REST OF WORLD
E-mail: ads@science-int.co.uk
Fax: +44 (0) 1223 326532
Simone Jux
Phone: +44 (0)1223 326529
Alex Palmer
Phone: +44 (0) 1223 326527
Lisa Patterson
Phone: +44 (0) 1223 326528
JAPAN
Makiko Hara
Phone: +81 (0) 90-9853-9982
E-mail: mhara@aaas.org
Fax: +81 (0) 3-6369-4491
CHINA & TAIWAN
Ruolei Wu
Phone: +86-1367-1015-294
E-mail: rwu@aaas.org
For full advertising details, go to
ScienceCareers.org and click For Employers,
or call one of our representatives.
All ads submitted for publication must comply
with applicable U.S. and non-U.S. laws. Science
reserves the right to refuse any advertisement
at its sole discretion for any reason, including
without limitation for offensive language or
inappropriate content, and all advertising is
subject to publisher approval. Science encour-
ages our readers to alert us to any ads that
they feel may be discriminatory or offensive.
S
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Faculty Position
The Koch Institute for Integrative Cancer Research
at the Massachusetts Institute of Technology
(http://ki.mit.edu/) invites applications for a junior
or senior faculty appointment. The Koch Institute
is an NCI-designated Cancer Center which
features research across a wide range of areas in
cancer biology and cancer-oriented engineering.
This is an open search with regard to eld of
study and specic research focus, but clear cancer
relevance of the proposed research program is
essential. Areas of interest include, but are not
limited to: imaging, proteomics, single-cell
analysis, systems biology, metastasis, stem cell
biology, and novel approaches to detecting,
monitoring and treating cancer. The candidate(s)
will be expected to develop and lead an
internationally competitive research program as
well as participate in undergraduate and graduate
teaching. The successful candidate(s) will have
laboratory space in the recently opened Koch
Institute building and a faculty appointment in
an appropriate department at MIT.
The deadline for the complete application with
letters is November 1, 2011.
Please apply at
https://academicjobsonline.org/ajo/jobs/926
The David H. Koch Institute for Integrative Cancer Research
at MIT is an Equal Employment Opportunity/Afrmative
Action Employer.
Were Looking for World-Class Faculty.
Come Invent the Future with Us.
Virginia Tech plans to recruit 100
faculty members during
2011-12. Searches will focus on
faculty members who will contribute
to four discovery areas from the
universitys strategic plan:
Energy, Materials, and Environment
Health, Food, and Nutrition
Innovative Technologies and
Complex Systems
Social and Individual
Transformation
Faculty members will be recruited
across the eight colleges to promote
growth in these and other research
areas.
Please visit www.provost.vt.edu to
review faculty searches as they are
launched across the fall semester.
COLLEGES
http://www.vt.edu/academics/academic-departments.html
College of Agriculture and Life Sciences
College of Architecture and Urban Studies
Pamplin College of Business
College of Engineering
College of Liberal Arts and Human Sciences
College of Natural Resources and Environment
College of Science
College of Veterinary Medicine
RESEARCH INSTITUTES
http://www.research.vt.edu/institutes/index.php
Fralin Life Science Institute
Institute for Creativity, Arts, and Technology
Institute for Critical Technology and Applied Science
Institute for Society, Culture and Environment
Virginia Bioinformatics Institute
Virginia Tech Carilion Research Institute
Virginia Tech Transportation Institute
Virginia Tech is an AA/EEO employer; applications from
members of underrepresented groups are especially
encouraged.
............................................................................................................................................................
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TOP EMPLOYERS
www.sciencecareers.org 115 www.sciencecareers.org
T
he 2011 Science Careers Top Employers Survey was
designed to identify the 20 companies with the nest
reputations in the industry, as well as the characteris-
tics that most impact an employers status. The results
are based on 3,784 responses to a web-based sur-
vey (see Survey Methodology on p. 116).
Nearly half of the respondents are under 40 years old,
79 percent work in the United States, and 40 percent are
female.
Besides innovation and research, survey respondents
expect a leading company to be socially responsible,
treat its employees with respect, and inspire their loyalty.
This year, the #5 criteriahas a top leadership that suc-
cessfully makes changes needed to keep the organiza-
tion moving in the right directionreplaced 2010s has
a clear vision of where the organization is headed. (See
Driving Characteristics chart on p. 120.)
The 2011 results brought a new, rst-time #1 employer:
Vertex Pharmaceuticals Incorporated (#3 in 2010). In fact,
three of the highest-ranking companies are new to the top 20 list
(see Top 20 Employers chart on p. 116 for complete company listing).
These shifts arent surprising, because Its been an interesting time
in the industry, observes Alan Smith, Genzyme Corporations chief
scientic ofcer before its acquisition by Sano. For us, the past
year has been a period of upheaval, but weve regularly scored well
in this survey, he notes (Genzyme is #13 this year, #8 in 2010). Now
chief science advisor for Sano Global Research and Development,
he says, As part of Sano, well take the approach weve used at
Genzyme and apply it more generally.
Other top employers are entering new phases, too. Vertex re-
cently introduced their rst drug, Incivek, to the market, and began
building their rst commercial team. This [survey] recognition is
tied directly to the passion and creativity that our 1,800 employees
bring to Vertex each day, as we seek to change the lives of peo-
ple with devastating diseases, says Peter Mueller, Vertexs chief
science ofcer and executive vice president for global research
and development.
Regeneron Pharmaceuticals, Inc. (#2, and new to the top 20 list)
has a treatment for a major eye disease under FDA review. Later this
year, theyll seek FDA approval for a new cancer drug and request an
additional application for Arcalyst, their rst product on the market.
Since Arcalyst was created for a rare genetic condition, Regeneron
is now essentially developing a brand-new sales and marketing func-
tion. Explains Ross Grossman, human resources vice president,
Weve focused a great deal of energy on retaining a true biotech
culture[stressing] innovation and great scienceas weve grown
and matured as a company. Its especially gratifying to be recognized
UPCOMING FEATURES
Focus on EuropeOctober 21
Neuroscience: Emerging FieldsNovember 4
Focus on ChinaDecember 9
Innovation and
Research
The Human Factor
Continuous innovation and outstanding research are the most important attributes
to respondents choosing this years best biotech and pharma companiesyet to top
employers, their scientists ingenuity and enthusiasm are the real essentials for excellence.
By Carol Milano
li
"We choose people who
aren't afraid to take risks
by trying something new or
bringing a nontraditional idea
forwardand who are not
satised with the status quo."
Lisa Kelly-Croswell, senior
vice president, Vertex
h i ib
FOCUS ON CAREERS Produced by the Science/AAAS Custom Publishing Office
TOP EMPLOYERS SURVEY
by Science for our science-driven culture, and to come out so high
in our rst year.
Eight of this years top 20 companies are based in Europe. Global
collaborations and concerns are increasingly important to leading
biotech/pharma companies, which pay careful attention to their re-
search facilities and services in devel-
oping countries. Health care provid-
ers in less-developed areas may not
have access to the newest medical
procedures and pharmaceutical treat-
ments.
Denmark-based Novo Nordisk (#9
this year, and also new to the top 20
list) is one pharmaceutical company
that is addressing a specic interna-
tional need. Diabetes treatments ac-
count for about 75 percent of Novo
Nordisks business. They provide
training about best practices in dia-
betes care for thousands of physicians in China. Diabetes doesnt
get the attention it deserves there because of limited resources,
observes Steve Chinn, vice president for human resources. Were
striving to be a partner with the Chinese health care system, not
simply as just a maker of medicine, but by doing more to help
educate and inform patients and physicians about the severity of
the disease.
SELECTING THE SCIENTISTS
Being an innovative leader continues to be the most powerful
driver for selecting a company as a top employer. When asked to
describe what makes the best company, the best, survey respon-
dents specically mentioned supports a culture of innovation,
employee-driven curiosity, and innovative ideas of everyone are
considered.
How do top employers create an innovative and inspiring corporate
atmosphere? Among many highly qualied applicants, they search
for the exceptional scientists most likely to bring fresh, original ideas
to the company.
At Novo Nordisk, Chinn species one priority:
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continued
www.sciencecareers.org 116
Passion about diabetes and hemophilia, the two diseases for
which the company creates medications. We want people who are
very knowledgeable and educated about these disease states, and
who are known within their eld for the research theyve done or for
being thought leaders.
Bayers U.S. division seeks scientists with the ingenuity,
curiosity, and enthusiasm for working at an organization striving for
innovations that make a difference in the world, summarizes Bryan
Iams, director of external communications. In a global company
operating in every country, can they be respectful and understand
that in different cultures, different beliefs drive people? he asks.
With 108,000 employees worldwide, the Germany-based company
(#20; reappearing on the list since being #19 in 2006) looks for
versatility and the kind of entrepreneurial thinking encouraged at
Bayers innovation centers in China, Europe, and California. These
then hook into and get translated into our larger global organization,
explains Iams.
Its sometimes easy to hire someone just because they are an
exceptional scientist, but we spend ample time to nd a person
with the technical skills who also ts with our core values, says
Lisa Kelly-Croswell, Vertex's senior vice president of human
resources. We choose people who arent afraid to take risksby
trying something new or bringing a nontraditional idea forwardand
who are not satised with the status quo.
Their research and development group hires for what we
want to be, not what we are today, says Vertexs Mueller, who
looks for people with the scientic and technologic expertise
to take Vertex to the next frontier, and the courage to constantly
move the frontier forward. In science, experiments often have
unexpected outcomes. Some scientists have the willingness
and joy to deal with this uncertainty. Thats the phenotype
were looking for.
Mueller wants his scientists maximally integrated across all func-
tionsresearch, development, commercial, legal, human resources,
accountingso they can communicate and collaborate. Thats fun-
damental to our ultimate goal: Discovering and developing transfor-
mational medicines.
Genzyme prefers highly trained scientists, several years be-
yond their Ph.D.s. Our best hires, in a creative sense, have
about ve years of postdoc experience. Theyre really where the
excitement is in researchand theyre exciting to be around,
says Smith.
In 2008, needing several hundred additional employees for a new
collaboration with Sano-Aventis, Regeneron worked
The 20 companies with the best reputations as employers and the top three driving characteristics for each company, according to respondents in the 2011 survey
undertaken for the Science/AAAS Custom Publishing Ofce. The companies without a 2010 rank did not rank among the top 20 in the 2010 survey.
This web-based survey was
conducted from March 24 to
April 11, 2011 by Brighton Con-
sulting Group and Cell Associ-
ates. For this years survey, a
mixed methodology was again
used.
The rst part of this meth-
odology included e-mailed
invitations to roughly 46,000
individuals who were located
worldwide. These individuals
were Science website visitors
who have registered with AAAS
and past survey respondents.
This year Facebook, Twitter, and
online banner ads were also
used to promote participation in
this survey. Forty-two percent
of all surveys submitted were
from this rst effort.
The second part of the meth-
odology included an e-mail blast
to a list of about 500 human
resource contacts at industry
rms that were pulled from
the Science Careers sales data-
base. The remaining 58 percent
of the surveys were from this
second effort.
This report is based on a
total sample of 3,784 survey
respondents.
SURVEY
METHODOLOGY
Top
Twenty
Employers
FOCUS ON CAREERS
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2011
Rank
2010
Rank
Employer (Global Headquarters)
1 3 Vertex Pharmaceuticals Incorporated (Cambridge, MA)

2 Regeneron Pharmaceuticals, Inc. (Tarrytown, NY)

3 1 Genentech (South San Francisco, CA)

4 19 Pioneer Hi-Bred, a DuPont business (Johnston, IA)

5 4 Millennium: The Takeda Oncology Company (Cambridge, MA)

6 10 Amgen (Thousand Oaks, CA)

7 6 Boehringer Ingelheim (Ingelheim, Germany)

8 7 Syngenta (Basel, Switzerland)

9 Novo Nordisk (Bagsvaerd, Denmark)

10 15 Biogen Idec (Weston, MA)

11 13 Abbott (Abbott Park, IL)

12 9 Merck KGaA/Merck Serono/EMD Serono (Darmstadt, Germany)

13 8 Genzyme Corp. (Cambridge, MA)

14 11 Novartis (Basel, Switzerland)

15 5 Roche (Basel, Switzerland)

16 2 Monsanto Company (Creve Coeur, MO)

17 14 Eli Lilly and Company (Indianapolis, IN)

18 17 Gilead Sciences (Foster City, CA)

19 20 AstraZeneca PLC (London, UK)

20 Bayer (Leverkusen, Germany)

continued
THE SCIENCE of POSSIBILITY

Vertex creates new possibilities in medicine to cure
diseases and improve peoples lives.
Join us as we work with leading researchers, doctors, public health
experts and other collaborators who share our vision for transforming
the lives of people with serious diseases, their families and society.
Discover the possibilities. www.vrtx.com/careers
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new therapeutic areas have Bachelors or Masters degrees. Theyre
working alongside M.D.s and Ph.D.s.
This is such a diverse organization, we want people who bring a
different perspective and understanding, so we can expand globally,
explains Susan Bunz, human resources and corporate services vice
president at Pioneer Hi-Bred, a DuPont business, the plant genetics
company that ranked #4 this year (a big leap from #19 in 2010). The
Iowa-based companys 3,000 plus scientists work at 110 research
locations in 24 countries. Our culture is very collaborative. People
share a can do attitude, want to work in a very dynamic environ-
ment, and know how to complete a project.
RETAINING OUTSTANDING SCIENTISTS
The worlds best scientists are always on recruiters radar screens,
and employers know that people often change jobs. Its one thing to
attract new talent, another to retain them, says Bayers Iams.
You must provide an environment that recognizes accomplish-
ment and celebrates the entire team, Iams continues. Bayer offers
growth programs, such as internal education activities, so an em-
ployee always feels, Im learning here. Motivators include letters
of recognition, awards (some monetary), and performance-based
bonuses, which are sometimes reinvested into company shares.
However, many biotech/pharma companies are moving away from
broad eligibility for stock options, according to Grossman. Regen-
eron, though, remains absolutely committed to employee owner-
ship. Every new hire will be a shareholder. The company recently
introduced an on-site mini-MBA program with Rutgers University
professors presenting a broad view of the industrys business is-
sues. Beyond classrooms, we give scientists very challenging
roles, where they can contribute to the fullest extent of their abili-
ties, adds Grossman.
From microbiology to entomology to agronomy, Pioneer Hi-Bred
uses a diverse range of expertise. A scientists specic assignment
depends somewhat on his or her degree, explains Bunz. Ph.D.s are
at the senior scientist level; a B.S.-degree holder would be an as-
sociate or assistant researcher. Thanks to the educational support
Pioneer provides, employees can go back to school while theyre
here, when they see that additional education will increase their pro-
motional opportunities.
Novo Nordisk encourages scientists to focus on a specic job
aspect that will forward their research, and their personal develop-
ment, says Chinn. Every employee is required to prepare an Indi-
vidual Development Plan. They can opt to attend symposia, specic
educational programs, or other learning opportunities. The company
gladly provides tuition to further their employees education. We
hope its holisticnot just to help Novo Nordisk, but to improve their
own specialized skills, he explains.
Vertex holds weekly social hours where scientists and other
staff members share perspectives. The company also has unique
employee incentives, such as the Vertex Nobel Prize for outstand-
ing research and the recently introduced Science Technology Ex-
change Program (STEP), a sabbatical opportunity. Bench scientists
whose proposals are accepted get to STEP out of their usual roles
and pursue a new path for three months. The program was devel-
oped by seven Vertex scientists working in a focus group on improv-
ing career paths and recognition.
In many professions, accomplishments and recognition bring pro-
motion into management. For a scientist, that means moving away
from the bench, Smith observes, but you may not want to have a
hundred people reporting to you. Genzyme offers a popular, four-
level alternative track: fellow, senior fellow, distinguished fellow, and
one coveted slot as presidential fellow. If you want to stay at the
bench, a fellow here can be paid as much as a senior
with a recruitment and branding rm to attract the right people.
They launched an online ad campaign, highlighting what Grossman
calls their quirkiness and selectivity, by presenting their recently
formalized corporate values (The Regeneron 5), through reverse
psychology:
If science isnt your obsessionDONT APPLY
If youre content being the smartest person in the room
DONT APPLY
If youre afraid to failDONT APPLY
If you think good enough is good enoughDONT APPLY
If you need a routine to dene youDONT APPLY
By the years end, Regeneron met its goal of hiring 350 highly
qualied new employees.
Genentech, a member of the Roche group, (#3 in 2011; #1 in eight
of 10 previous surveys) is continuously recognized for its innovative
leadership, high-quality research, and talent pool. Genentechs deci-
sion makers are extremely respectful of the companys scientists.
Emphasizing excellent communication skills, Genentech screens
for a strong publication record, because they feel that it indicates
an ability to communicate well in writing. Everyone I interview is
very bright, motivated, and accomplished, especially on the biology
side, observes Andy Chan, senior vice president of research biol-
ogy. But they must really want to translate biology into medicine.
Thats the driving force behind who comes to Genentech, and why
were in the business. Some skilled scientic problem solvers, Chan
believes, are far better suited for academia. We want the ones who
want to make something happen that helps people.
At these top employers, research and development jobs arent
only for Ph.D.s. Throughout his organization, reports Novo Nordisks
Chinn, scientists work at many different levels. At their Seattle site,
for example, some of the scientists doing fundamental research on
FOCUS ON CAREERS
SURVEY
DEMOGRAPHICS

GENDER
57% Male, 40% Female, 3% No response
EXPERIENCE
64% have 10 years or more of work experience
HIGHEST DEGREE EARNED
42% Doctorate, 26% Master's, 27% Bachelor's,
5% Other
COMPANY TYPE
53% Biotech, 34% Pharma, 7% University,
6% Other; more than four out of ve work in
private industry
NATURE OF WORK
36% Development, 33% Applied Research, 27% Basic
Research, 13% Administrative/Executive, 11% QA/QC/
Regulatory Affairs, 19% Other (Respondents were able to
choose more than one response.)
GEOGRAPHY
80% from North America; 12% from Europe;
6% from Asia/Pacic Rim; 2% from rest of world
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THATS UNCOMMON. THATS REGENERON.

REGENERON
regeneron.jobs
WEVE DISCOVERED
11 NEW DRUG CANDIDATES NOW IN CLINICAL DEVELOPMENT.
And there are many more in our labs. At Regeneron, we are dedicated to great science.
We take pride in overcoming challenges and searching for new and better ways to
do things. Were the rare company that discovers, develops and commercializes its
own products. Regeneron people work hard because we believe in what we do and
we enjoy the people we work with. We were voted one of the Best Places to Work
in our industry in 2008, 2009 and 2010 and were ranked in the 2010 Top 10 Most
Innovative Biotech Companies by Fast Company.
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vice president. Its a great way to keep people who may not want
management, but want to progress. Its very effectivethese are
such valuable people, he says.
Its easier to do well when things are going well, Smith reects,
and hard to do well when times are tough. Im very proud and
pleased that weve scored well this yearit says that people are
seeing and believing in new opportunity here. We pay a lot of atten-
tion to how we convince and keep convincing people that this is a
good place to work even during a rough period. Very few people have
left since the acquisition.
INNOVATION AND RESEARCH
Two of the surveys perennial top driversinnovative leadership and
quality researchare never taken for granted at excellent compa-
nies. Theyre carefully nurtured and cultivated.
Were highly committed to further strengthening our innovative
capabilitiesinnovation is key to maintaining or gaining a leading po-
sition in every market in which we operate, and also the foundation
for improving the lives of many millions of people, says Katharina
Jansen, director of global media relations and issues management
for Bayer Schering Pharma AG in Leverkusen, Germany. She consid-
ers Bayers research and development investments to be long-term:
Their pharmaceutical or agricultural research projects average 10
years before reaching the marketplace.
To encourage innovation, Regeneron labs operate like a hybrid of
academe and business, Grossman explains. We give researchers
a great deal of freedom, and encourage employees to suggest im-
provements at the implementation level. Anyone comfortable with a
scientic organizations give-and-take can be part of any discussion
here. Were not yet big enough to have lots of channels, formal
procedures, or hierarchies. The enemy is bureaucracy, he says.
Regeneron is continuously seeking new approaches, says Gross-
man, and asking at every stage, Whats the next generation of tech-
nology? He elaborates: When it wasnt fashionable, we invested
in building a technology that was then highly innovative, and brought
us to our rst marketable product. Then we invented a suite of tech-
niques that led to Arcalyst. Although Regeneron uses these suc-
cessful techniques to develop other drugs, theyre also committed
to ongoing innovation.
Genentech concentrates on innovations in transformative therapy.
Our strength is our patient focus, asserts Mike Varney, senior
vice president, small molecule drug discovery. We constantly work
with clinical groups to understand whats going on with a particular
disease, how its treated, and the limitations of existing therapies.
This proximity to the patient is rare. Even with portfolio reviews,
discussions center around the
patients, how to help them, and the
reality of improving a patients life.
Genentechs culture encourages
ambitious research. Genentech
values risk-taking, creativity, and sci-
entic exploration, which spur our
scientists to succeed, says Chan.
Once they make a breakthrough,
its a very addicting feeling. Their
success encourages more emphasis
on innovation.
With its incredibly strong com-
mitment to high-risk innovation, Ver-
tex starts with a disease and nds
a way to treat its underlying cause,
says Mueller. Were innovative in
the way we partner, how we set our-
selves up as an organization, how we reach out in the community,
and how we interact with patients and physicians. We balance risk
on several shoulders, increasing our chances for success, through
our network of global partners.
For Pioneer Hi-Bred, global interconnections are internal. Theyve
added 4,000 employees since 2007, in 95 locations. Research and
development (R&D) scientists in Europe, Asia/Pacic, Latin America,
and North America are in constant contact. They know where the
soils are similar and who should be collaborating. One strategy may
be applicable in North and South America, but the same products
dont work globally, explains Bunz.
Bayer takes a similar approach. Collaboration at our worldwide
locations is part of our model for success, Iams emphasizes. Shar-
ing information today is so much easier than even ve years ago.
Other scientists can access your les to further [distant] collabora-
tions. Now our high-growth regions are really learning from other
locations, allowing much faster development in China, India, and
Latin America. All 2,500 Bayer scientists, engineers, and chemists
in various labs are charged with driving innovation.
ECONOMIC IMPACT
Survey respondents indicated that the soft economy has led to lay-
offs, site closures, and outsourcing. When asked which key events
have had the greatest effect on the industry over the past year, re-
spondents named mergers and acquisitions, which have created
some instability and uncertainty. Yet, many top employers experi-
enced surprisingly few effects during the lengthy global recession.
Bayer takes adequate precautions that economic instabilities do
not impact R&D activities, a priority on our agenda, says Jansen.
Bayers R&D investments increased from 2.9 billion (US$4.06 bil-
lion) in 2009 to 3.1 billion (US$4.34 billion) in 2010 and 2011.
Another international rm, Novo Nordisk, has thrived, with 36
quarters of double-digit growth. We actually grew, added employ-
ees, and brought new products to market last year, says Chinn.
Regeneron also seems countercyclical, having hired two-thirds
of our employees since 2008, when we were under 700. Well soon
reach 1,800, says Grossman. At the end of 2010, 43 percent of
employees had been here one year or less.
Like Regeneron, Genentech has been expanding. Since 2008, as
cutbacks left talented professionals unemployed, the company has
been very lucky to hire some exceptionally qualied scientists,
says Varney. Our small molecule group, and research in general,
have been growing, while the rest of the industry is contracting. Be-
ing a little out of sync allowed us to cherry-pick the very best.
Weather, not economics, is the biggest variable
Black type indicates the characteristics in common for the two years.
FOCUS ON CAREERS
DRIVING CHARACTERISTICS
1. Innovative leader in the industry
2. Treats employees with respect
3. Loyal employees
4. Socially responsible
5. Clear vision
6. Does important quality research
7. Work and personal values are aligned
2010 2011
1. Innovative leader in the industry
2. Treats employees with respect
3. Socially responsible
4. Loyal employees
5. Makes changes needed
6. Does important quality research
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Were passionate and rigorous about our science. For more than 30 years, Genentech has been at the forefront of the biotechnology industry, using
innovative science to develop breakthrough medicines that improve the lives of people with serious or life-threatening diseases. Were also passionate
about our people, our most important asset. Thats why we offer Genentech employees:
The chance to make a difference in the lives of patients
Extraordinary colleagues
An inclusive environment that encourages diversity
Highly competitive benets
Now a member of the Roche Group, Genentech has multiple medicines on the market for cancer and other serious illnesses. We are an equal opportunity
employer and in 2011, we were named a top employer in the biopharmaceutical industry by Science magazine.
Join us as we continue to tackle medicines most challenging problems and live a life inspired. For complete position descriptions and to apply, please visit
careers.gene.com and enter the Requisition number in the keyword search eld.
Life
Inspired.
careers.gene.com
Sergio, Patient
Associate Director/Director, Antibody Engineering Req. #377081
The successful candidate will lead a group of 15-30 researchers in
developing innovative antibody technologies and therapeutics as well
as running their own lab. The ideal candidate will have a PhD and
10+ years of experience in engineering antibodies for human therapy,
including publications, patents, and generation of investigational
drugs. Candidates with strong leadership skills are particularly
encouraged to apply.
Associate Director, Immune Cell Signaling Req. #376671
This position will lead research efforts focused on discovering and
pursuing new drug targets and will be jointly appointed within the
departments of Discovery Immunology and Biochemical Pharmacology.
The ideal candidate has a PhD or equivalent in biological sciences
with extensive research as well as small molecule drug discovery
experience in immunology. Eight or more years experience as an
independent scientist in a biopharmaceutical and/or academic
environment is required.
Associate Director, Bioinformatics Req. #380051
As an Associate Director within the Bioinformatics department, this
position will focus on novel variant discovery, biomarker discovery,
and data integration. The ideal candidate should have well developed
research plans that will take advantage of newer technologies such as
DNA-seq, ChIP-seq, RNA-seq, proteomics and metabolomics. A PhD in
life sciences, computer sciences, mathematics or other relevant eld
is required.
Associate Director, Drug Metabolism and Pharmacokinetics
(DMPK) Req. #379896
The Associate Director will lead a team of more than 15 talented
ADME Scientists and work closely with colleagues in other
departments on advancing projects ranging from early to late
stage discovery and in the clinic up to approval. A PhD degree in
pharmacokinetics, drug metabolism or other relevant elds such
as pharmaceutical, biological or chemical sciences and at least 10
years industrial experience is required.
We have the following opportunities in Genentech Research and Early Development (gRED) in our South San Francisco, CA, headquarters:
Scientist/Senior Scientist, Antibody Engineering B-Cell Cloning
Req. #376466
Senior Scientist, X-ray Crystallography
Req. #377162
Senior Scientist, Antibody Drug Conjugates
Req. #380053
Scientist, Vascular and Lymph System Biology
Req. #379942
Passionate About Our Science and Our People
EMD Serono is the US biopharmaceutical division of Merck KGaA,
Darmstadt, Germany, a global pharmaceutical and chemical company.
As a leader in US biotechnology, we focus on reproductive health,
metabolic endocrinology, oncology and neurology. With more than
1,100 employees in the United States, EMD Serono is dedicated to
fostering the culture of the possible and recognizes that our
strength is our people. Our employees are intellectually curious,
thrive on new experiences, and welcome professional challenges.
We pride ourselves on rewarding our employees by offering
a rich, competitive array of benets and value-added programs
which support a healthy work/life balance.
EMD Serono is an Equal Employment Opportunity Employer. No employee or
applicant for employment will be discriminated against on the basis of race,
color, religion, age, sex, sexual orientation, national origin, ancestry, disability,
military or veteran status, genetic information, or any other classifcation
protected by applicable federal, state, and local law.
For more information on career opportunities at
EMD Serono, please visit:
www.emdserono.com/careers.
MAKE GREAT THINGS HAPPEN
Use your imagination
to transform lives
2011 Millennium Pharmaceuticals, Inc. All rights reserved.
Our achievements change lives. Our people inspire cures.
At Millennium: The Takeda Oncology Company located in Cambridge, MA, We Aspire to Cure Cancer. As a leading
biopharmaceutical company focused on oncology, Millennium combines the agility, ideals and camaraderie of a start-up
with the resources of Japans largest pharmaceutical company. The result is an entrepreneurial culture where the priorities
are quality science and making a diference in patients lives and the communities we serve.
Our people share a commitment to innovation in an environment where individual contributions are not just valued, but
rewarded. Here youll enjoy outstanding benefts, a friendly, respectful atmosphere and a culture that promotes fexibility
between your personal and professional life. Join Millenniumand improve the lives of others while living yours to the fullest.
To view our current career opportunities and apply online,
visit: joinmillennium.com/25
Image: colored scanning electron
micrograph (SEM) of a lung cancer cell.
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To learn more about Pioneer careers, visit www.Pioneer.com/Careers.
, TM, SM
Trademarks and service marks of Pioneer Hi-Bred. 2011 PHII 11-2922
The DuPont Oval Logo, DuPont and The miracles of science are trademarks of DuPont or its afliates.
Are you
ready to
meet the
challenge?
Are you ready to meet the challenge of
feeding and fueling a world population of
nine billion people by 2050?
Join the Pioneer team, where people are passionate
about moving science forward to serve our customers.
We are a respected leader in the agricultural industry,
with nearly 100 years of experience advancing
agricultural production. Pioneer provides seed that
contains the most highly developed technologies for
growing corn, soybeans, sorghum, sunower, alfalfa,
rice, canola and wheat, among others.
We use our unique germplasm with tools such as
biotechnology to create a rich pipeline of superior
products for our customers, who are located in 90
countries. While our reach is global, our commitment
to the best products, service, business partners and
employees remains constant.
Join our team and work on projects where the results
are used around the world. At Pioneer, were not on the
cutting edge of research, were pushing past it.
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DOI: 10.1126/science.opms.r1100109
Carol Milano is an independent journalist in New York City, covering
health care and science.
FOCUS ON CAREERS
O
To hear the Top Employers Podcast and read the extended
content about social responsibility, see the online version
at www.sciencecareers.org/TopEmployers2011
SOCIAL RESPONSIBILITY
Social responsibility is increasingly
signicant to both survey respon-
dents and excellent employers. Its
the #3 driver, up from #5 in 2010.
Thats a big part of who we are,
says Novo Nordisks Chinn. We
know we have a nancial responsi-
bility to shareholders, and we also
have a social and environmental
responsibility.
Chan praises Genentech for its
signicant infrastructure and phil-
anthropic funds to help patients
copay for medications. Since
1985, when their rst product
was approved, the company has
dispensed US$2.3 billion of free
medications in the United States.
Genentechs Access To Care
Foundation is based on the prin-
ciple that no patient should ever
go without a Genentech drug
because of inability to pay.
The top bio/pharma companies are also particularly proud of their
science education programs, both local and distant. Since the late
1990s, over two million students in Asia have participated in Bayers
youth environmental programs, which educate schoolchildren about
the science and technology that is available to help address current
environmental problems.
Regeneron cosponsors the Westchester County National Intel
Science and Engineering program, and sends its BioBus to local
schools. The rolling science lab is designed to introduce kids to what
makes science so exciting. We also have 75 high-school and col-
lege interns, says Grossman, and weve come full-circle. One of
our high school interns now is a patient who suffers from the condi-
tion that our rst drug treats.
In Vertexs STEM (Science, Technology, Engineering, and Mathe-
matics) Initiative, staff scientists volunteer in local schools in nearby
communities, and engage kids to become enthusiastic about sci-
ence. The company works with United Way to bring six-to-ten-year-
olds to Vertexs headquarters for hands-on science exploration.
Apart from their academic and motivational benets to students
(and strong appeal to staff scientists), science education efforts are
valuable for high-achieving bio/pharma companies. These types of
programs are mission-critical, Vertexs Mueller declares. Unfortu-
nately, in our society the science and technology track is no longer
the most wanted. We have to engage kids when theyre young, so
that science becomes understandable to them, and fun. As a com-
pany, but also as a society, we need to nurture and inspire future
scientists.
Top employers invest in developing a stream of eager, curious
future scientists because they recognize that, as Genzymes Alan
Smith attests, Your most precious resource is your people.
for Pioneer Hi-Bred. We continue to create products to deal with
weather factors, says Bunz. An innovative new drought-resistant
product, AQUAmax, is for areas with a dry climate or too little rainfall
for farming. New products have to be tested in-ground in a target-
type location, but uncooperative weather can prevent planting. In
areas with a single growing season, that can delay testing for an
entire year.
CORPORATE CULTURE
Three of this years top ve drivers reect workplace values and
environment. To survey respondents, outstanding employers are
socially responsible and have loyal employees whom they treat
with respect.
What we do to shape our culture comes from listening to em-
ployees, notes Vertex's Kelly-Croswell. We hold numerous focus
groups, often in-the-moment. We take what we hear and translate
it into action. Employees routinely tell us, Hey, thanks for asking.
Leading companies often codify their corporate values, as exempli-
ed by The Regeneron 5. Not only do we hire scientists who will
treat patients with respect, we also expect them to respect each
other, asserts Chinn. The recently revised Novo Nordisk Way
stresses accountability and responsibility. Our employees have a
right and a responsibility to say something if they see people not
treating someone else well. Being an organization focused on just
a few therapeutic areas, rather than many, makes us different, and
gives us a shared sense of commitment.
Bayer, too, recently updated its global corporate values statement,
choosing an acronym easily remembered in many languages: LIFE.
It stands for Leadership, Integrity, Flexibility, and Efciency. The
company seeks to keep its culture consistent throughout all loca-
tions. LIFE encourages individual employees to make decisions, to
take the lead whenever they see things they think could be changed
or adapted. The culture empowers our research scientists to think
independently, see ideas and solutions, and propose or just imple-
ment whatever helps the company move towards our larger vision,
Iams summarizes.
This is the only place Ive ever worked, declares Vertexs Kelly-
Croswell, where everyone can recite our core values, because we
all live them: Fearless pursuit of excellence; innovation is our life-
blood; and we wins.
Comparison of the top 10 companies on the basis of the top three drivers (scored out of 100): Socially responsible
(bubble width), Innovative leader (x-axis), and Treats employees with respect (y-axis).
Comparison of the top 10 companies on the basis of the top three drivers (scored out of 100): Socially responsible
Genentech
100
95
85
75
80
70
90
65
65 70 75 80 90 95 100 85
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P
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T
BUBBLE WIDTH = SOCIALLY RESPONSIBLE
Vertex
Regeneron
Pioneer Hi-Bred
Amgen
Millennium/ Takeda
Syngenta
Biogen
Idec
Boehringer
Ingelheim
Novo
Nordisk
60
60
INNOVATIVE
COMPARISON OF TOP TEN'S
TOP CHARACTERISTICS
Genzyme. Today.
For those eager to improve the lives of people with
debilitating medical conditions, there is no better place
to work than Genzyme. One of the worlds leading
biotechnology companies, Genzyme is dedicated to
making a major positive impact on the lives of people
with serious diseases.
Since its founding in 1981, the company has introduced
breakthrough treatments that have provided new hope
for patients. Genzyme focuses its efforts on well-defned
medical areas with serious, unmet needswhere
breakthrough therapies and services might signifcantly
improve patients lives. Genzymes research and
development efforts span a range of medical areas,
including rare genetic diseases, multiple sclerosis,
cardiovascular disease, and endocrinology.
Genzyme is continuing to grow and we are looking for
qualifed candidates to join us. If your passion for impact
matches your dedication to helping others, Genzyme
offers a workplace unrivaled in the industry.
Join us, and be a part of everything Genzyme is, today.
www.jobsatgenzyme.com
Genzyme is an EOE/AA employer.
LIFE CHANGING WORK @
Work fearlessly to remove the boundaries
caused by serious diseases in neurology,
immunology and hematology.
Feel that your work will truly matter to the
lives of patients
and change even your own life.
For more information about life changing work
opportunities at Biogen Idec, please contact
www.biogenidec.com/careers.
Biogen Idec is an equal opportunity employer.
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Division of Vision Science
TORONTO WESTERN RESEARCH
INSTITUTE
University Health Network
Donald K. Johnson Chair in Vision
Sciences
The Toronto Western Research Institute of the
University Health Network invites applicants
to apply for the endowed Donald K. Johnson
Chair in Vision Sciences. The ideal candidate
will hold a PhD degree (or equivalent) and
have an established record of excellence in
basic science areas that have relevance to
vision.
The successful candidate will have the ability
to establish an independent, well funded, pro-
gram of international prominence and to col-
laborate with other members of our research
and clinical staff. There will be the oppor-
tunity to build vision science at the UHN.
Qualied candidates will be appointed to the
Departments of Ophthalmology and Vision
Sciences at the University of Toronto, and an
appropriateAcademic Graduate Department at
a level commensurate with their experience.
Send applications (CV, statement of inter-
est, and contact information for three refer-
ees) by January 3rd, 2012 to Dr. Martin
Steinbach, Director of Vision Research,
UHN, by e-mail only c/o Ms Janet Wong,
(tang@uhnresearch.ca)
CLINICAL ASSISTANT PROFESSOR OF BIOLOGY
& ENVIRONMENTAL STUDIES
Department of Biology/Environmental Studies Program
ARTS AND SCIENCE
New York University invites applications for a full time, non tenure-track teaching
Clinical Assistant Professor appointment joint between the Department of Biology and
the Environmental Studies Program to start September 1, 2012, pending budgetary
and administrative approval. Responsibilities include developing and teaching
courses related to ecology and the environment to support the Biology Departments
undergraduate minor in Environmental Biology and the Environmental Science Track
within the related Environmental Studies Program, and to serve as a core faculty
member in Environmental Studies. Teaching duties will include six courses annually.
Applicants should be able to teach fundamental courses in ecology and environmental
science and more specialized skill-building courses that utilize the unique urban and
coastal environment of the New York City region. Previous teaching and research
experience is strongly preferred. The Department of Biology (http://biology.as.nyu.
edu) and the Environmental Studies Programs (http://environment.as.nyu.edu) offer
an outstanding and collegial environment.
Candidates should submit applications, including a CV, teaching statement and
three letters of reference, through the NYU Department of Biology website
(http://biology.as.nyu.edu), via the Faculty Recruitment link. You may use the following
address in the cover letter: Chair of the Environmental Biology Search Committee,
Department of Biology, New York University, 1009 Silver Center, 100 Washington
Square East, New York, NY 10003. Closing date is November 30, 2011.
NYU is an Equal Opportunity/Affirmative Action Employer.
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TOP EMPLOYERS
POSITIONS OPEN
The National Institutes of Health (NIH) . . . The center of medical and
behavioral research for the Nation.
Director
National Center for Advancing Translational Sciences, NIH
The National Institutes of Health is seeking candidates for the Director, National Center for Advancing
Translational Sciences (NCATS), a newly proposed Center of the NIH. NCATS, one of 27 NIHInstitutes
and Centers, is being established to catalyze the generation of innovative methods and technologies
that will enhance the development, testing, and implementation of diagnostics and therapeutics across a
wide range of human diseases and conditions. To accomplish its mission, NCATS supports and enables
research on the process of therapeutics discovery, development, testing, and implementation into patient
care. By studying the steps in the therapeutics development pipeline, identifying constriction points,
and testing novel approaches to circumvent those constriction points, NCATS works to advance the
entire discipline. In this way, NCATS catalyzes translational medicine and therapeutics research in
other NIH Institutes and Centers, academia, industry and other sectors. The Director, NCATS, offers
a unique and exciting opportunity for an exceptional leader to serve as the chief executive, leading
all aspects of this highly complex scientic organization: providing visionary leadership, executive
management, and strategic direction for streamlining the process for therapeutics development. As
Director, NCATS, s/he will be responsible for leading all NCATS initiatives, communicating with
various sectors and stakeholders, overseeing the Clinical and Translational Science Awards (CTSA)
program, and facilitating effective collaborations among government, academia, industry, venture
capitalists, non-prot and community organizations.
Applicants must possess an advanced degree (M.D., and/or Ph.D. or equivalent) in a eld related
to the mission of the NIH and have senior-level research experience and knowledge of research
programs in one or more scientic areas related to the broad elds of biomedical, clinical and
translational research. Applicants should be recognized by scientists, industry leaders, educators and
research administrators as individuals of outstanding scientic competence within their profession,
both nationally and internationally.
Salary is commensurate with experience and accomplishments. Afull package of Federal benets,
including leave, health and life insurance, retirement, and savings plan (401K equivalent) will be
provided.
Please access the detailed vacancy announcement for mandatory qualications requirements and
application procedures at http://www.jobs.nih.gov/ (under Executive Jobs). Applications will be
reviewed starting December 2, 2011, and will be accepted until the position is lled.
NCATS, NIH, AND DHHS ARE EQUAL OPPORTUNITY EMPLOYERS.
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Applications are invited for:-
Assistant Professors
(Ref. 1112/019(665)/2)
The Department invites applications for faculty positions at the level of
Assistant Professor with prospect for substantiation tenable from the academic
year 2012-2013. The Department anticipates that there will be a maximum of
three positions.
Applicants should have a relevant PhD degree with postdoctoral research
experience. Outstanding candidates in all areas of physics, particularly in the
elds of experimental condensed matter physics, theoretical and computational
materials physics, and theoretical or experimental biophysics, are welcome to
apply. Successful candidates are expected to demonstrate a strong record of
research accomplishments, potential for establishing a signicant externally
funded research programme, and a strong interest in teaching at undergraduate
and postgraduate levels. Appointments will normally be made on contract basis
for up to three years initially, which, subject to mutual agreement, may lead to
longer-term appointment or substantiation later (substantive appointment may
be considered during the second three-year contract). Applications will be
accepted until the positions are lled.
Salary and Fringe Benets
Salary will be highly competitive, commensurate with qualications and
experience. The University offers a comprehensive fringe benet package,
including medical care, a contract-end gratuity for appointments of two years or
longer, and housing benets for eligible appointees. Further information about
the University and the general terms of service for appointments is available at
http://www.cuhk.edu.hk/personnel. The terms mentioned herein are for reference
only and are subject to revision by the University.
Application Procedure
Applications (comprising a full curriculumvitae, a detailed publication list with
three selected published papers, a research plan, a teaching statement, and three
letters of recommendation) should be sent to Professor Ke-Qing Xia, Chairman,
Department of Physics, The Chinese University of Hong Kong, Shatin, Hong
Kong. (email: physics@cuhk.edu.hk; fax: (852) 2603 5204). The Personal
Information Collection Statement will be provided upon request. Please quote
the reference number and mark Application Condential on cover.
TRANSLATIONAL BIOMEDICAL RESEARCH OPPORTUNITY
Genomic Medicine/Bioinformatics
Sigfried and Janet Weis Center for Research is seeking outstanding independent
scientists for full-time research positions at ranks equivalent to Assistant, Associate
or Full Professor in the areas of Genomics and Bioinformatics. The Weis Center is
a basic and translational research facility of Geisinger Clinic located at Geisinger
Medical Center (GMC) in Danville, PA. Genomic Medicine is a strategic focus for
translational research at Geisinger.
Genomic Medicine is a strategic focus for translational research at Geisinger.
About the position:
Expertise in laboratory, computational, or statistical genetic approaches
Expand ongoing research on the genetic basis of disease
Proven records of innovative research with relevance to human disease
Collegial environment with collaborative research opportunities
Geisinger Health Systems advanced electronic medical record system and health
information technology infrastructure allows for electronic capture of clinical data
and large biorepository of patient specimens.
Technical resources include instrumentation for confocal,TIRF, and single cell
fluorescence imaging, microarray analysis, genotyping, DNA sequencing, and flow
cytometry, and an AAALAC-accredited animal facility. Substantial resources are
available for start-up, ongoing research support and salary.
Qualified individuals should submit curriculum vitae, statement of research interests
and three reference letters to Ms. Kristin Gaul, Weis Center for Research, Geisinger
Clinic, via email (kgaul@geisinger.edu). Please refer to position WCR-3638 in the
subject line. Applications will be accepted until the positions are filled.
For more information on research programs at Geisinger visit our website at
http://www.geisinger.org/professionals/research/wcr.
Geisinger Health System is an Affirmative Action/Equal Opportunity Employer
HE ALTH S YS TE M
REDEFINING THE BOUNDARIES OF MEDICINE
http://www.neu.edu
Assistant/Associate Professor
Pharmaceutics and Drug Delivery
The Department of Pharmaceutical Sciences at Northeastern University invites applications for a tenure-
track or tenured faculty position at the rank of Assistant or Associate Professor. Northeastern University
is located in the heart of Boston within close proximity to major biotech/pharma companies, academic
institutions, and medical centers.
The candidate should have demonstrated research productivity through a focused research program in
Pharmaceutics and Drug Delivery, and complement the Departments existing strengths in targeted drug
delivery and nanomedicine, drug discovery/medicinal chemistry, neuropharmacology, as well as in
inflammation and immunology. The successful candidate will be expected to establish an extramurally-funded
research program, participate in both professional PharmD and graduate (MS and PhD) teaching, and service.
Applicants with current transferable funding will be given a priority. The candidate must have experience in,
or commitment to, working with diverse student populations and/or in a culturally diverse work and
educational environment. The Department of Pharmaceutical Sciences houses the Center for Drug
Discovery, New England Inflammation and Tissue Protection Institute, the Center for Pharmaceutical
Biotechnology and Nanomedicine, and the Center for Translational Imaging. For additional information
about the Department, please visit the website: http://www.pharmsci.neu.edu.
Interdisciplinary appointments and highly competitive start-up packages are available to qualified
applicants. The candidate should send his/her curriculum vitae, statement of research interests, and
a list of three references to: Heather Clark, Ph.D., Associate Professor and Search Committee Chair,
Department of Pharmaceutical Sciences, Room 110, Mugar Life Sciences Building, 360 Huntington
Avenue, Boston, MA 02115. She can also be reached by telephone at 617-373-3091 or email at
h.clark@neu.edu.
Equal Employment Opportunity:
Northeastern University is an Equal Opportunity, Affirmative Action Educational Institution and
Employer, Title IX University. Northeastern University particularly welcomes applications from
minorities, women and persons with disabilities. Northeastern University is an E-Verify Employer.
Faculty Positions in Materials
Science and Engineering
The Department of Materials Science and Engineering at
the University of Pennsylvania (www.mse.seas.upenn.edu)
invites applications for a faculty position in the area of
theory and computational modeling of materials. Atenured
appointment at the Associate or Full Professor level is
strongly preferred, although extraordinary junior candidates
may apply at the Assistant Professor level.
In addition, we encourage appropriate candidates to apply
to the School of Engineering and Applied Sciences Penn
Nano Cluster-Hiring Initiative (www.seas.upenn.edu/nano)
in anticipation of the opening of the $100M Krishna P. Singh
Center for Nanotechnology.
Successful candidates for these positions must be
committed to excellence in undergraduate and graduate
teaching and conduct leading edge research programs
benefiting from Penns strong interdisciplinary tradition and
multi-school research institutes. These include two
NSF-funded centers, a Materials Research Science and
Engineering Center and a Nanoscale Science and
Engineering Center, the Nanotechnology Institute and the
Institute of Medicine and Engineering.
Applications (CV, statement of research and teaching
interests, and names of three references) should be
submitted online at www.mse.seas.upenn.edu/jobs.
Applications submitted by mail will not be accepted.
Applications will be evaluated on a rolling basis. Final
deadline for submission: December 15, 2011.
The University of Pennsylvania is an equal opportunity
employer. Minorities, women, individuals with disabilities
and veterans are encouraged to apply.
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Tenure-Track Group Leader Position
in RNA Biology
The Friedrich Miescher Institute for Biomedical Research (FMI) in Basel,
Switzerland invites applications for a tenure-track group leader position
(equivalent to an assistant professorship). We are seeking an outstanding
individual who will establish an ambitious research program on fundamental
questions in the field of RNA Biology.
Opportunities exist for collaborative interactions with the other FMI research
programs located within the focal areas of Epigenetics, Signaling & Cancer, and
Neurobiology. The Institute provides core facilities for advanced microscopy and
image analysis, cell sorting, genomics, protein crystallography, proteomics, and
bioinformatics. We also offer a highly competitive start-up package.
Applications, including a CV, the names and
email addresses of three referees, and a
concise description of research interests and
future plans should be submitted online at:
www.fmi.ch/gl_search
Informal inquiries can be sent to:
Dr. Helge Grosshans (helge.grosshans@fmi.ch)
or the Director of the FMI
Dr. Susan Gasser (susan.gasser@fmi.ch)
The closing date for applications is
November 1, 2011.
The Friedrich Miescher Institute for Biomedical Research (FMI) invites applications
for a tenure track group leader position (equivalent to an assistant professorship)
in Neurobiology. We are seeking an outstanding individual who will establish an
ambitious interdisciplinary research program focused on the function of neuronal
circuits. We are particularly interested in research investigating circuits in vivo
in behaving animals. This could for example involve combinations of neuronal
ensemble imaging, in vivo electrophysiological recordings, genetic targeting of
identified neurons, optogenetic strategies, virtual reality protocols and quantita-
tive analyses of behavior.
Neurobiology groups at FMI investigate the assembly, function and dysfunction of
identified neuronal circuits, using combinations of genetic, molecular, cellular,
anatomical, physiological, behavioral and computational approaches. Individual
groups currently focus on the circuits of vision, olfaction, proprioception, memory,
fear and motor control. Opportunities exist for collaborative interactions with other
FMI research groups in the areas of Epigenetics, Stem cells, Genome stability and
Cancer. A highly competitive start-up package will be provided.
Applications, including a CV, the names and
email addresses of three referees, and a
concise description of research interests and
future plans should be submitted online at:
www.fmi.ch/gl_search
Informal inquiries can be sent to:
Dr. Botond Roska (botond.roska@fmi.ch)
or the Director of the FMI
Dr. Susan Gasser (susan.gasser@fmi.ch)
The closing date for applications is
October 31, 2011.
Tenure-Track Group Leader Position in
Neurobiology: from Circuits to Behavior
The Friedrich Miescher Institute for Biomedical Research is an international biomedical research center with more than 300
members, including approximately 200 postdoctoral fellows and graduate students, dedicated to basic research in areas of
relevance to human health and disease. It is part of the Novartis Research Foundation and associated with the University of
Basel. The Institute runs a successful international PhD program. The FMI is situated in Basel, Switzerland, which offers an
outstanding scientific and cultural environment in the center of Europe. Institute core facilities include experimental mouse
genetics, high-end microscopy, single cell genomics, proteomics, histology, protein structure determination and bioinformatics.
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Arkansas State University invites nominations and applications for a dynamic, visionary individual to
serve as the Executive Director of the Arkansas Biosciences Institute (ABI) at Arkansas State University
(http://abi.astate.edu). The ABI currently supports several broad interdisciplinary research areas relat-
ed to health improvement. ASU is an Equal Opportunity Employer/Affirmative Action Employer with a
strong institutional commitment to the achievement of excellence and diversity among its administrators,
faculty, staff, and students.
The successful candidate will have a clear understanding of ABIs role and importance; a vision for
enhancing and expanding its contributions to scholarship, teaching, and economic development; a
demonstrable commitment to diversity; and a record of outstanding leadership and accomplishments in
a university or research setting. The candidate must hold an earned terminal degree in science, engineer-
ing, medicine or related field from an accredited institution of higher education, possess academic cre-
dentials and a record of scholarly accomplishments sufficient to merit a tenured appointment at senior
rank in one of the Universitys academic departments, and have a proven record of administrative expe-
rience that may include academic appointments as department chairperson, associate dean, and/or dean,
and must have a record of establishing and maintaining scholarly, interdisciplinary collaboration.
Please visit https://jobs.astate.edu for detailed information and to apply for position A00246.
Screening of completed applications will begin on October 24, 2011 and will continue until the position
is filled. Under the provisions of Arkansas Freedom of Information Act, applications are subject to pub-
lic inspection. Rent Consulting Group, LLC is assisting in the search and may be contacted for more
information at info@rentconsultinggroup.com or 704-366-2388. Nominations should be sent to the
Chair of the Search Committee, Dr. Andrew Sustich, ASU Graduate School, PO Box 60, State
University, AR 72467, 870-972-3029, or sustich@astate.edu.
Executive Director
Arkansas Biosciences Institute
ASU is committed to creating a productive workplace in which both persons and property are secure. To achieve
that goal, background investigations are conducted on all final applicants recommended for employment.
Cancer Biology Positions at
The Tisch Cancer Institute
The newly established Tisch Cancer Institute of Mount Sinai School
of Medicine invites applications from outstanding scientists for faculty
positions at the Assistant, Associate or Full Professor level. Our areas of
interest include: Cancer model systems, Cancer epigenetics, Cancer stem
cells, Cancer systems biology, Cancer therapeutics and Cancer immunol-
ogy. Disease areas that are presently the focus of the Tisch Cancer Institute
are: Hepatocellular carcinoma, Hematological malignancies, Head and
neck cancer, Prostate, Breast, and Lung cancer.
Applicants should have an M.D., and/or Ph.D. degree with an outstanding
record of publications. The successful candidate will receive generous
start-up resources with state-of-the-art laboratory space and institutional
shared resources to support their research activities.
The Tisch Cancer Institute members are working together to integrate
Mount Sinais expanding research capacity. Over the next several years,
the Cancer Institute will grow by 150,000 sq. ft. of research and clinical
space in the new Center for Science and Medicine building. The Center
for Science and Medicine is under construction with an expected occu-
pancy by mid-2012.
Mount Sinai School of Medicine and Mount Sinai Hospital are among the
worlds leading biomedical institutions. The Medical Center is in the midst
of a $1 billion capital campaign in support of our $2.25 billion strategic
plan, which has a primary focus on the delivery of outstanding clinical
care and translational research leading to therapeutic discoveries.
Candidates should send a CV, three letters of reference, and a summary
of their research to: Steven Burakoff, M.D., Chair of the Search Com-
mittee, c/o Chan-Bene Lin (tci.recruitment@mssm.edu) by October
31, 2011.
Mount Sinai Medical Center is an Equal Opportunity/Afrmative
Action Employer. We recognize the power and importance of a diverse
employee population and strongly encourage applicants with various
experiences and backgrounds.
Integrative Biologists in Cell Biology,
Physiology, or Ecology
As part of a long-termhiring plan, the Department of Biology expects to ll
multiple full-time tenure-trackAssistant or Associate Professor positions.
We encourage applications from candidates working in the broad areas
of cell biology, organismal physiology, or interdisciplinary ecology.
We are particularly interested in candidates appreciative of the breadth of
research encompassed within the Department of Biology and whose work
actually or potentially integrates perspectives from multiple disciplines.
Some of many examples include:
theoretical or empirical approaches to genotype phenotype
mapping
systems or engineering approaches to cell biology
ecological or evolutionary approaches to developmental biology,
physiology, or both
novel approaches to understanding interactions within or between
organisms, or between organisms and their environment
As a Department, we are looking for individuals with a record of outstand-
ing achievement or strong indications of outstanding future potential, rather
than specic research topics or study organisms. Priority will be given to
applications received by 15 October 2011 at: http://www.biology.wash
ington.edu/faculty/search/. Applicants must have earned a doctorate by
the date of appointment. All University of Washington faculty engage in
teaching, research, and service.
The University of Washington is an Afrmative Action, Equal
Opportunity Employer. The University is building a culturally diverse
faculty and staff and strongly encourages applications from women,
minorities, individuals with disabilities and covered veterans. The
University is the 2006 recipient of the Alfred P. Sloan award for Faculty
Career Flexibility, and is committed to supporting the work-life balance
of its faculty. Our NSF-supported ADVANCE program
http://advance.washington.edu/ is dedicated to increasing the
participation of women in STEM disciplines.
Tenure Track Position
Biophysics or Nanoscience
The Department of Physics invites applications for
an open rank tenure-track position in experimental
or theoretical areas of biophysics or nanoscience to
begin in the fall of 2012. The successful candidate
should have a Ph.D. in physics or in closely related
areas and will have, or high potential of, a vigorous
externally funded research program.
Requirements:
Interested candidates should submit an application
(in pdf format) consisting of (i) a cover letter
addressing the alignment of the candidates
research with the departments interests, (ii) a
curriculum vitae, (iii) a description of research
plans addressing the connection to the department
and WPI, (iv) a statement of teaching philosophy,
and (v) arrange for three to fve reference letters.
Send to Prof. Germano Iannacchione, Head,
Department of Physics at ph-search@wpi.edu.
Review of applications will be conducted on a
rolling basis but application materials should be
submitted by December 1st, 2011.
To apply, please visit: apptrkr.com/207070
To enrich education through
diversity, WPI is an affrmative action,
equal opportunity employer.
Worcester Polytechnic Institute
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COGNITIVE NEUROSCIENTIST
The GEORGEWASHINGTONUNIVERSITYseeks to ll a tenure-track
position for an ASSISTANT PROFESSOR of PSYCHOLOGY, to begin
in Fall, 2012. We seek an investigator with established expertise in the
molecular, genetic, cell biological, developmental and/or physiological
characterization of a distinctive brain circuit that mediates behaviors
whose performance can be measured and related back to the organiza-
tion of the circuit. We will focus on investigators working in mammalian
animal models, especially the mouse. This position is part of the recruit-
ment effort to expand neuroscience research across the campus with
appointments made in the College of Arts and Sciences, the School of
Medicine and Health Sciences, and the George Washington Institute for
Neuroscience. Basic
Qualications: Applicants must have a Ph.D. or equivalent degree in
neuroscience or a closely related eld, post-doctoral research training,
a strong publication record in peer-reviewed journals, and a planned or
ongoing research program with the potential for future external funding.
Competitive salary and startup funds are available commensurate with
experience.
Application Procedure: Only complete applications will be considered.
To be considered, please send electronic copies (pdfs preferred) of your
curriculum vitae, a statement of research and teaching interests, up to 3
representative reprints, and three letters of recommendation to: Cognitive
Neuroscience Search Committee, recruit2011@gwumc.edu. Review
of applications will begin on December 1, 2011, and will continue until
the position is lled.
The George Washington University is an Equal Opportunity/
Afrmative Action Employer.
APPLICATIONINSTRUCTIONS: Please apply to the Scholars Program through the BSSP website at:
(http://www.med.umich.edu/medschool/research/bssp/). A curriculum vitae (including bibliography), a three-
page research plan, an NIH biosketch, and three original letters of support should all be submitted through the BSSP
website. More information about the Scholars Program, instructions for applicants and those submitting letters of
recommendation, and how to contact us is located on the BSSP web site: (http://www.med.umich.edu/medschool/
research/bssp/). The deadline for applications is Friday, October 28, 2011.
BIOLOGICAL SCIENCES SCHOLARS PROGRAM
For Junior, Tenure-Track Faculty
The University of Michigan announces recruitment for the Biological Sciences Scholars Program (BSSP) to
continue to enhance its investigational strengths in the life sciences research programs.
Now entering its 15th year, this Program has led to the recruitment of outstanding young scientists in the
areas of genetics, microbiology, immunology, virology, structural biology, pharmacology, biochemistry,
molecular pharmacology, stemcell biology, cancer biology, physiology, cell and developmental biology, and
the neurosciences. The Program seeks individuals with PhD, MD, or MD/PhD degrees, at least two years
of postdoctoral research experience, and evidence of superlative scientifc accomplishment and scholarly
promise. Successful candidates will be expected to establish a vigorous, externally-funded research
program, and to become leaders in departmental and programactivities, including teaching at the medical,
graduate, and/or undergraduate levels. Primary college and department afliation will be determined
by the applicants qualifcations and by relevance of the applicants research program to departmental
initiatives and focus. All faculty recruited via the BSSP will be appointed at the Assistant Professor level.
The University of Michigan is an Afrmative Action/Equal Opportunity Employer.
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H O WA R D H U G H E S M E D I C A L I N S T I T U T E
J A N E L I A F A R M R E S E A R C H C A M P U S
Janelia Farm invites committed and gifted graduate
students to apply to a fully funded, collaborative Ph.D.
program with either the University of Cambridge or
the University of Chicago.
Find out more and apply: www.janelia.org/grad/sci
APPLICATION DEADLINES:
DEC. 1, 2011 (University of Chicago)
FEB. 1, 2012 (University of Cambridge)
DONT JUST STUDY GREAT
SCIENCE. LIVE IT.
The Howard Hughes Medical Institute
is an equal opportunity employer.
Director, Center for Immunology
The Director will lead the newCenter for Immunology with responsibility
to expand the existing Immunology research program in the Department
of Pathology and lead interdepartmental research and education programs
in Immunology. A substantial start-up package will be provided for the
Directors laboratory, and the Director will have responsibility to lead
recruitment of 3-4 additional faculty positions supported by start-up
packages.
The current Immunology programs strengths include fundamental
immunology (innate immunity, signaling, MHC molecules, APCs, T cell
biology), immunology of infectious diseases (particularly tuberculosis
and HIV), autoimmunity (e.g. IBD) and other topics. Annual research
funding in areas related to infectious disease immunology, pathogen-
esis and biology exceeds $100M at CWRU and afliated institutions.
Research training is focused on the Immunology Training Program(http:
//www.case.edu/med/pathology/training/itp.html).
Candidates should be established scientists with international stature and
successful and rigorous research programs. Leadership experience and a
successful track record as a scientic mentor are desired. Appointment
as Professor with tenure is anticipated.
Please send a cover letter, CV, and contact information for three references
to Clifford V. Harding, Chair, Department of Pathology, c/o Denise
Davis (dmd10@case.edu).
In employment and education, CWRU is committed to equal
opportunity and diversity. Women, veterans, members of
underrepresented minority groups, and individuals with disabilities are
encouraged to apply. Accommodations for application and hiring are
described at http://www.case.edu/diversity/faculty/writinganad.html.
The Molecular Biology Program of the Sloan-Kettering Institute, Memorial
Sloan-Kettering Cancer Center (www.ski.edu), has initiated a faculty search
at the Assistant Member level (equivalent to Assistant Professor). We are
interested in outstanding individuals who have demonstrated records of
significant accomplishment and the potential to make substantial contributions
to the biological sciences as independent investigators. Successful applicants
will have research interests that move the Program into exciting new areas that
complement and expand our existing strengths in the areas of maintenance
of genomic integrity, regulation of the cell cycle, and regulation of gene
expression. Faculty will be eligible to hold appointments in the Gerstner
Sloan-Kettering Graduate School of Biomedical Sciences, the Weill Cornell
Graduate School of Medical Sciences, as well as the Tri-Institutional MD/PhD
Training Program.
The deadline for applications is November 1, 2011. Interested candidates
should visit http://facultysearch.ski.edu to apply via the on-line faculty
application. Please visit the site as soon as possible, as it contains important
information on the required application materials, including deadlines for
submission of letters of reference.
Informal inquiries may be sent to Julie Kwan at kwanj@mskcc.org
or to Dr. Kenneth Marians, Chair, Molecular Biology Program at
kmarians@sloankettering.edu. MSKCC is an equal opportunity and affirmative
action employer committed to diversity and inclusion in all aspects of recruiting
and employment. All qualified individuals are encouraged to apply.
www.mskcc.org
Faculty Position
Molecular Biology
Sloan-Kettering Institute
EARTH AND ENVIRONMENTAL SCIENCE
Professorship in Earth and Environmental Science
The Department of Earth and Environmental Science at the University
of Pennsylvania invites applications for a tenured professorship at
the Associate or Full Professor level. We seek an individual with
research interests that complement or augment our existing strengths
in Earth history and surcial processes. The Department especially
invites applicants with research emphasis in: (1) the properties
and interactions of Earth materials, and their formative physical,
chemical and biological processes; and/or (2) the basic science of
natural hazards associated with geologic, hydrologic, climatic and
atmospheric processes.
The successful candidate is expected to have developed an
internationally recognized, externally funded, multi-disciplinary
research program, and will be required to actively participate in our
core undergraduate and graduate teaching and in the administration
of the Department. Individuals who can further increase interactions
with other departments within the School of Arts and Sciences
are strongly encouraged to apply. Further information about the
Department is available at www.sas.upenn.edu/earth/.
Applicants apply online at: https://facultysearches.provost.upenn.
edu/applicants/Central?quickFind=50979 with a cover letter, CV,
statements of research and teaching interests, and three publications.
The Search Committee will begin to evaluate applications on
January 6, 2012.
The University of Pennsylvania is an Afrmative Action/Equal
Opportunity Employer.
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Founded in 1944 and located in The World-Famous Historical
City Xian, Shaanxi Normal University (SNNU) is one of the key
insttutons of higher learning directly afliated to Ministry of
Educaton and 211 Project University in china. The university
is seeking individuals with outstanding scientfc credentals for
Recruitment Programof Global Experts, Thousand Young Talents
Program, Chang Jiang Scholars Program, Bai Ren Scholars Plan
of Shaanxi Province and Qu Jiang Scholars Program of Shaanxi
Normal University, which are designed for the recruitment at
the level of professors, associate professors and chair professors,
etc.
Qualifcatons
Applicants are expected to have remarkable academic
achievements andtodemonstrate capacity inleading anacademic
team to keep a compettve edge in fronter areas. Successful
candidates for the professorship will be expected to undertake
full-tme teaching and research in general, and those for the chair
professorship to work part-tme (two months minimum/year).
Applicants of Thousand Young Talents Program should be
under the age of 40, have obtained a doctoral degree in a world-
renowned university, and have no less than three years of post-
doctoral research experience. Applicants, who have obtained a
doctoral degree in Mainland of China, should have no less than
fve years of overseas research experience afer obtaining a
doctoral degree. Special ofers are granted to those who have
made distnguished research achievements in their doctoral
studies or in other areas. Successful candidates for Thousand
Young Talents Program will be expected to undertake full-tme
teaching and research at SNNU.
SNNU has a broad range of academic disciplines, positons are
available in all the relevant areas belowincluding but not limited
to: mathematcs, physics, chemistry, material science, biology,
computer science and technology, environmental science and
engineering, food science.
Salary and Housing Allowances
The university provides state-of-the-art research facilities
and strong supporting staffs. Internationally competitive
start-up support, salary and benefts will be ofered according
to qualifications and experience. Successful candidates of
the specially listed programs will receive supplementary
remuneraton, including newly renovated ofce and laboratory
spaces, and a highly collegial and interactve environment, as well
as assistance on the establishment of a delicate research team.
Applicaton Documents
Applicants are expected to submit a CV with cover leter which
is supported by such documents as photocopies of advanced
degrees, and three recommendation letters among other
things.
Applications of Thousand Young Talents Program should
include a rsum with a list of publicatons, a concise statement
of research and teaching interests, and the names and addresses
(including e-mail) of at least three referees.
You are welcome to click on the university website at htp://rsc.
snnu.edu.cn/zhaopin.asp for more informaton.
Please direct your applicatons and inquiries to:
Mrs. Wu Jinfeng or Mr. Yang Yuanzheng
Email address: rcb@snnu.edu.cn
Tel: 86-29-85310456, 86-29-85310455
Fax: 86-29-85310359
Professorships and Chair Professorships
at Shaanxi Normal University, China
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The Structural Biology Program of the Sloan-Kettering Institute (www.ski.
edu) invites applications for a tenure-track faculty position at the Assistant
Member level (equivalent to Assistant Professor). We are interested in
individuals who have an outstanding record of research accomplishments.
Areas of interest include x-ray crystallography, NMR spectroscopy, EM
and optical imaging, as well as the interface of structural, chemical
and computational biology. Faculty will be eligible to hold graduate
school appointments in the Gerstner Sloan-Kettering Graduate School
of Biomedical Sciences, the Weill Cornell Graduate School of Medical
Sciences, as well as the Tri-Institutional MD/PhD Training Program.
The deadline for applications is November 1, 2011. Interested
candidates should visit http://facultysearch.ski.edu to access the on-line
faculty application. Please visit the site as soon as possible, as it contains
important information on the required application materials, including
deadlines for submission of letters of reference.
Informal inquiries may be sent to Julie Kwan at kwanj@mskcc.org
or to Dr. Nikola Pavletich, Chair, Structural Biology Program at
palvletin@mskcc.org. MSKCC is an equal opportunity and affirmative
action employer committed to diversity and inclusion in all aspects of
recruiting and employment. All qualified individuals are encouraged
to apply.
www.mskcc.org
Faculty Position
Structural Biology Program
Sloan-Kettering Institute
The Department of Genetics and the Center for Genomics
and Personalized Medicine invites applications to ll
MULTIPLE TENURE-TRACK POSITIONS at the ASSISTANT,
ASSOCIATE, and/or FULL PROFESSOR level.
We are interested in outstanding scientists with innovative research
programs in any area of genetics and/or genomics. Candidates should have
a Ph.D. and/or M.D. degree and a clear record of creative achievement.
The predominant criteria for appointment in the University Tenure Line
are a major commitment to research and teaching.
The Department of Genetics and The Center for Genomics and
PersonalizedMedicine at the StanfordUniversitySchool of Medicine offer
a highly collegial and interdisciplinary environment that spans clinical
medicine, human genetics, model-organism genetics, and genome-scale
approaches. For more information, see http://genetics.stanford.edu.
Stanford University is an equal opportunity employer and is committed
to increasing the diversity of its faculty. It welcomes nominations of
and applications from women and members of minority groups, as well
as others who would bring additional dimensions to the Universitys
research, teaching, and clinical missions.
Candidates are encouraged to apply electronically by November 4,
2011 with curriculum vitae and a statement of research and teaching
interests, in one pdf le, with your last name in the subject line, to:
search-genetics@stanford.edu. Applicants for the position at theAssistant
Professor rank should also arrange to have three letters of evaluation
sent to:
Michael Snyder, Chair
Department of Genetics
300 Pasteur Drive, Alway M344
Stanford, CA94305-5120
search-genetics@stanford.edu
ASSISTANT PROFESSOR
The Department of Neuroscience at the University of Texas Southwestern
Medical Center at Dallas, under the leadership of Dr. Joseph Takahashi,
invites applications at the Assistant Professor level for a tenure-
track Faculty position in the broadly dened areas of neurogenetics,
electrophysiology and imaging. We seek outstanding scientists addressing
molecular and genetic mechanisms underlying behavior, neural circuits
and related neurological disorders. Our emphasis is on individuals using
forward genetic approaches to understand the nervous system and
behavior. Individuals using advanced functional approaches to study
neural circuits are also particularly encouraged to apply. Scientists within
the Department of Neuroscience participate in a vibrant, interdisciplinary,
interdepartmental, and highly collaborative research community within
the University, and enjoy access to state-of-art research cores in imaging,
mouse MRI imaging, metabolic phenotyping, behavioral phenotyping,
protein chemistry, structural biology, genomics, genetics and transgenic
technology.
Applicants should submit a curriculum vitae, two-page summary of
research accomplishments and future plans. Applicants should arrange
to have 3-5 letters of recommendation sent to the search committee.
Please e-mail application materials to: neurosciencesearch@utsout
hwestern.edu, Neuroscience Search Committee,The University of
Texas Southwestern Medical Center at Dallas, 5323 Harry Hines
Blvd., Dallas, TX 75390-9111. The deadline for receipt of applications
is November 15, 2011.
The University of Texas Southwestern Medical Center is an Afrmative
Action/Equal Opportunity Employer. Women and minority candidates
are encouraged to apply.
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Three Professorships in Biology and Ecology
and One Tenure-Track Lectureship in Biology
The School of Natural Sciences at the University of California, Merced
seeks applicants for four faculty positions: Ecology (Full or Associ-
ate with tenure or Assistant tenure-track), Systems Biology (Assistant
tenure-track), Biostatistics (Assistant tenure-track), and one tenure-
track Biology Lecturer. For the Ecology position, we seek outstand-
ing individuals with research interests in any ecological eld using
experimental, eld, computational, and/or theoretical approaches and
working at population to global scales. The Systems Biology position
includes research areas that use comprehensive datasets and multiple
types of analysis to relate overall biological function to underlying
biochemical or biophysical processes for predictive understanding. The
Biostatistics research areas of interest include statistical methods for
experimental design, epidemiology, medical informatics, evolutionary
biology, sequence bioinformatics, genomics, evolution of microbial
systems and pathogens, and systems biology. The Lecturer posi-
tion closely parallels a tenure-track Assistant Professor but with an
emphasis on undergraduate education. All applicants must be able to
teach effectively at both undergraduate and graduate levels. For more
information and to apply go to: http://jobs.ucmerced.edu/n/academic/
listings.jsf?seriesId=1.
Interested applicants should submit materials online. Applications will
be considered starting December 1, 2011.
UC Merced is an AA/EOP Employer.
Assistant Professor
Duke University School of Medicine
Applications are invited for a tenure track appointment as Assistant
Professor in the Department of Pharmacology and Cancer Biology
in the Duke University School of Medicine. The department faculty
members have diverse interests that include cell signaling and
regulation, cancer biology, gene regulation, chemical biology,
neuropharmacology and metabolism. Individuals using innovative
approaches or pioneering techniques to investigate fundamental
biological questions are particularly encouraged to apply.
Applicants should submit curriculumvitae, a brief statement of past
research accomplishments and future research interests, and a list
of three references as a single PDF. In addition, the applicant should
arrange for three letters of recommendation to be sent by email to
the Pharmacology and Cancer Biology Search Committee 2011 at:
PCBSearch@duke.edu
Applications and letters are due by December 1, 2011.
Make a Difference!
Invest your career where you can
Founded in 1901, Idaho State University (ISU) is a growing research institution with
dynamic research faculty, the largest number of graduate students in the state, and
$36 million in new research activity per year. ISU offers a wide range of certificates
and degree programs including: technical certificates; Associates, baccalaureate,
Masters, and doctoral degrees; post-doctoral certificates; and residency programs in
family medicine, dentistry, and pharmacy. ISU educates approximately 15,000 stu-
dents per year in more than 280 programs and has a statewide mission for education
in the health professions. The University has the Division of Health Sciences (College
of Pharmacy, Kasiska School of Health Professions, School of Nursing, Office of
Medical/Oral Health, School of Rehabilitation and Communication Sciences) and the
Colleges of: Arts and Letters, Business, Education, Science/Engineering, and
Technology. ISUs main campus is located in Pocatello, a community of approximate-
ly 60,000 nestled in a scenic mountain valley in southeastern Idaho. Described as
the last undiscovered mountain college town in the west, Pocatello is within a few
hours drive of Salt Lake City, Sun Valley, Yellowstone and Grand Teton National
Parks, and numerous world-class skiing, fishing, rafting, climbing, and mountain
biking opportunities. Through its outreach centers, early college programs, and dis-
tance education classrooms, ISU delivers a wide range of courses and programs
throughout Idaho which include campuses in Pocatello, Idaho Falls, Twin Falls and
the Boise area, all contributing to ISUs expanding research portfolio.
Position: Idaho State University is designated as a Carnegie Research University-High
institution and has a rapidly growing research agenda. The Office of the President is
seeking an innovative Vice President for Research and Economic Development (VPR)
with extensive research experience, strong interpersonal skills, creativity, vision, and
initiative to lead ISUs research and intellectual property portfolio. The Office of
Research coordinates all research activities at Idaho State University and works to facil-
itate research opportunities for faculty and students. Additionally, the Office of
Research oversees the Office of Sponsored Programs that facilitates the request and
acceptance of external funding. ISU also has a number of research centers, institutes,
and facilities, including: Boise Center Aerospace Laboratory (BCAL), Center for
Advanced Energy Studies (CAES), Center for Archaeology, Materials, and Applied
Spectroscopy (CAMAS), Center for Ecological Research and Education (CERE),
Family Medicine Clinical Research Center, GIS Teaching and Research Center (GIS
TReC), ISU Biomedical Research Institute (IBRI), Idaho Accelerator Center (IAC),
Informatics Research Institute (IRI), Institute of Nuclear Science & Engineering
(INSE), Institute of Rural Health (IRH), Intermountain Center for Education
Effectiveness (ICEE), Measurement and Control Engineering Research Center
(MCERC), and the Molecular Research Core Facility (MRCF). This position is a full-
time, 12-month appointment with faculty rank (as applicable).
Responsibilities: The VPR reports directly to the President and will be a member of
the Presidents cabinet. The VPR works closely with the various levels of administra-
tion (deans, chairs, principal investigators, and center/institute directors), faculty and
student governance, staff councils, regional centers, and national labs. The VPR will
have direct responsibility for creation and review of large interdisciplinary research
centers and institutes; faculty research startups and retention packages and seeding of
initiatives and internal research programs; institutional-wide research
affiliations/memberships; private/public partnerships that impact research; addressing
the federal and state research agenda; research compliance (including compliance
committees), policies, ethics and conflict of interest; management of research space;
material transfer and confidentiality agreements; liaison to sponsor negotiations and
export controls; intellectual property portfolio; sponsored programdata, contracts and
grants; institutional research marketing publications; institutional workshops on pro-
posal writing and funding opportunities; and other aspects of research administration.
Minimum Qualifications: Earned doctorate or equivalent in a relevant discipline;
demonstrated progressive leadership; experience in obtaining extramural funding;
publication record demonstrating research excellence within an academic or related
setting; outstanding communication skills; experience in budget management and
planning; ability to establish and maintain collaborative relationships with diverse
individuals, groups, and organizations across disciplines.
Preferred Qualifications: We seek a visionary leader with demonstrated success in
obtaining extramural funds and fundraising; an academic with an appreciation for a
broad range of research, scholarship, and creative activities; one who has experience
with research infrastructure, contract and grant administration, national and state
policies, and cyberinfrastructure and information systems; broad experience in
strategic planning, and research program and infrastructure development; skills in
staff and faculty management, consensus building, conflict resolution, and decision
making in complex environments; a history of fundraising, budgeting, and measures
of accountability; the ability to work closely with state and federal agencies, nation-
al and international research organizations, and national laboratories; and one who
can encourage business development and technology transfer through successful
interactions with corporate and community entities.
Salary: Commensurate with experience and qualifications; competitive benefits package.
Closing Date: Open until filled. Reviewof applications will begin on November 1, 2011.
Special Instructions to Applicants: Submit a cover letter describing your interest
in this position and experiences and qualifications that make you an
exceptional fit for ISU, your curriculum vita, and contact information
for five professional references.
Application Process: For full consideration, please apply through the
Idaho State University-Human Resources website (www.isujobs.net).
For information, contact Dr. Herbert Maschner, Chair, VPR Search
Committee, 208-282-5417, maschner@isu.edu.
Vice President for Research
and Economic Development
Pocatello, Idaho
ISU is an equal opportunity/affirmative action employer. We have an
institution-wide commitment to inclusion and diversity and encourage all
qualified individuals to apply. Veterans' preference.
Upon request, reasonable accommodations in the application process will be
provided to individuals with disabilities.
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Inrecognizing thevalueof creatveresearchinproviding intellectual assets
for the future, Nagoya University established the Insttute for Advanced
Research (IAR) in April 2002 as a research base for achieving the highest
level of academic research. IARs founding director is Dr Ryoji Noyori, the
2001 Nobel Laureate in Chemistry. IAR is the frst academic insttuton in
Japan that intensively promotes highly creatve research in all academic
disciplines. IARs Young Leaders CultvatonTenure-track (YLC-t) Program
has been selected as part of the Japanese Ministry of Educaton, Culture,
Sports, Science andTechnology (MEXT)s ProgramtoDisseminate Tenure
Tracking System. IARis invitng applicatons fromyoung researchers from
all over the world for 3 tenure-track positons in the following felds: (1)
Advanced Life Sciences (Graduate School of Science), (2) Basic Medical
Science or Clinical Medical Science (Graduate School of Medicine), (3)
Foundaton of Sofware Science, in partcular Rewritng Computaton
and its Applicaton (Graduate School of Informaton Science). Appointees
selected will be appointed as Designated Associate Professors/Lecturers
of Nagoya University. Appointees will be provided with an outstanding
research environment and will be expected to commit to the highest
standards of scholarship and professionalism.
Requirements: APhDdegree granted within the past 10 years (as of April
1, 2011). Closing date: November 8, 2011.
Interested candidates should apply online at: htp://www.iar.nagoya-u.
ac.jp/ylc-t/index.html. Additonal informatonabout IARandtheprogram
can be found at htp://www.iar.nagoya-u.ac.jp/. Inquiries are handled
by email only. Email Address: ylc-t@iar.nagoya-u.ac.jp.
Nagoya University is an Equal Opportunity Employer.
INSTITUTE FOR ADVANCED RESEARCH, NAGOYA UNIVERSITY
3 Tenure-Track Positons
(Designated Associate Professors/Lecturers)
Faculty Positions in Cancer Biology
The Solid Tumor Program at the Ohio State University Comprehensive
Cancer Center and the Department of Molecular Genetics in the College
of Arts and Sciences invites applications for tenure-track faculty posi-
tions at the levels of Assistant, Associate and Full Professor. Outstanding
individuals using and/or developing mouse models of cancer are encour-
aged to apply. At present, research in the programand department spans a
wide range of topics in cancer biology including genetics, signaling, cell
cycle, cell differentiation, DNA repair, transcription, DNA replication,
checkpoint control, cachexia, metabolism, aging, tumor microenviron-
ment. Additional information about the OSUCCC and the Department
of Molecular Genetics is available at http://cancer.osu.edu and http:
//molgen.osu.edu.
Applicants should email their curriculum vitae and a brief description of
their research interests to the attention of Dr. Gustavo Leone, Chair of
Search Committee, at siegman.1@osu.edu. Applicants should request
three letters of recommendation to be sent to the same address. Applica-
tions will be considered beginning on November 1, 2011. The deadline
for submission is December 15, 2011.
The Ohio State University is an Equal Opportunity Employer
committed to the recruitment of candidates traditionally
underrepresented on university faculties and encourages applications
from women, minorities, veterans, and individuals with disabilities.
Flexible work options are available. EEO/AA Employer.
Ohio State is an NSF Advance Institution.
Department of Biology
Assistant Professorship
California State University, Northridge invites applications for a tenure-
track position in the Department of Biology. Applicants must hold a
Ph.D. and have post-doctoral experience. The successful candidate
shall develop a vigorous research program involving undergraduate and
Masters students, seek extramural research funding, and demonstrate
teaching excellence.
Marine Biologist: Focused on the biology of early life stages of near-
shore organisms with interests in population connectivity and the biologi-
cal effects of climate change; expertise in mathematical modeling and the
capacity to develop a research program based in California is preferred.
Teaching options include a course on early life stages/bentho-pelagic
coupling, climate change and the marine environment, and introductory
biology. Contact information: marinebio@csun.edu.
Molecular Geneticist: Specialized research combining molecular genet-
ics and molecular cell biology approaches to study fundamental questions
of modern eukaryotic genetics/cell biology. Teaching responsibilities
include molecular genetics, molecular cell biology, and introductory
biology. Contact information: molsearch@csun.edu.
Applicants should submit a cover letter, CV, three letters of
recommendation, summary of teaching experience, statements of
teaching philosophy and research interests, and three publications.
Electronic submissions as a single PDF fle are strongly preferred.
For more information: www.csun.edu/facultyaffairs/openings/sm/.
Screening will begin on November 14, 2011.
The Department of Neuroscience at Columbia University
is now recruiting faculty in two broad areas of neuroscience.
We are interested in investigators who: (1) analyze motor and
cognitive processes in awake, nonhuman primates; or (2) use
molecular and cellular approaches to study the development
or function of neural circuitry in genetically tractable model
systems. We encourage applications for positions at all levels,
from Assistant to Full Professors.
Columbia University has an exceptionally strong and broad
program in the neurosciences and aims to enhance interac-
tions between basic and clinical research, and to link the
neurosciences with other scientific disciplines within the
University. New faculty will be affiliated with the Department of
Neuroscience and with the Doctoral Program in Neurobiology
and Behavior. There are many opportunities for interaction
with other scientific departments and programs at the Medical
Center and Morningside Heights campuses.
Applications must be received by November 30, 2011, and
should be submitted online at:
https://academicjobs.columbia.edu/applicants/
Central?quickFind=55356
Please include a curriculum vitae, cover letter, statement of
research interests, and three letters of reference.
Columbia University takes affirmative action
to ensure equal employment opportunity.
Neuroscience Faculty Recruitment
COLUMBIA UNIVERSITY
IN THE CITY OF NEW YORK
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TENURED AND TENURE-
TRACK FACULTY POSITIONS
Department of Biology
Johns Hopkins University
As part of a major, multi-year expansion,
the Department of Biology at JHU is seek-
ing two talented new faculty members at
the levels of Assistant, Associate, and/or
Full Professor. We especially invite appli-
cants who apply whole-genome, quantita-
tive approaches to investigate biological
problems in creative and innovative ways.
Areas of particular interest include, but are
not limited to, genome function and regula-
tion. Successful candidates will complement
and enrich our scientic research programs,
and will be expected to establish a vibrant
research programand to participate in under-
graduate and graduate teaching. Applications
from women and minority candidates are
especially encouraged.
Please submit a single pdf le with a cover
letter, CV, and statements of current and
planned research and teaching interests/
philosophy to bio-facsearch@jhu.edu.
Arrange to have three letters of recom-
mendation sent also to this email address,
or to: Chair, Search Committee, Dept. of
Biology, Krieger School of Arts and Sci-
ences, Johns Hopkins University, 3400
N. Charles St., Baltimore, MD 21218-
2608. Website: http://www.bio.jhu.edu.
The deadline for receipt of all materials is
November 15, 2011.
Three Faculty Positions
The Department of Biology at Northeastern University, Boston, Massachusetts invites applications for three
tenure-track positions in the following areas:
Developmental Neurobiology and/or Regenerative Biology: Specic areas of interest are adult
stem cells and their role in either behavioral plasticity or tissue regeneration; or development of axons
and/or axonal regeneration.
Microbial Genomics
Computational Biology/Bioinformatics
Although appointments at the assistant professor levels are preferred, applications at associate or full professor
levels will be considered for candidates with particularly strong track records. The anticipated start date is
the Fall Semester 2012. Acompetitive start up package will be provided.
Responsibilities: Responsibilities will include: teaching undergraduate and graduate courses; conducting an
independent, externally funded research program; and engaging in university, professional, and community
activities. The appointee in Computational Biology/Bioinformatics will also assume a leadership role in the
Professional Science Masters in Bioinformatics program. The department has 33 full-time faculty members
and administers programs in Biology, Biochemistry, and Behavioral Neuroscience for 1,200 undergraduates.
It hosts 150 students in Ph.D., Masters, and Professional Masters programs.
Qualications: Applicants should have a doctorate in Biology or a eld relevant to the position, at least
two years of postdoctoral experience, and a strong record of publications.
Additional Information: Acomplete application includes a cover letter, curriculumvitae, research statement,
teaching statement, and a list of three references. Letters of reference will be requested at a later stage.
Reviewof applications by the Search Committees will begin November 15, 2011; each search will continue
until the position is lled. For questions about the search, the Chair of the Department, Professor Gnther
K.H. Zupanc, can be contacted at (617) 373-2260.
Equal Employment Opportunity: Northeastern University is an Equal Opportunity, Afrmative Action
Educational Institution and Employer, Title IX University. Northeastern University particularly welcomes
applications from minorities, women and persons with disabilities. Northeastern University is an E-Verify
Employer.
How To Apply: To apply, visit Careers at Northeastern at: https://psoft.neu.edu/psc/neuhrprdpub/
EMPLOYEE/HRMS/c/NEU_HR.NEU_JOBS.GBL. Click on Faculty Positions and search for the
current position under the College of Science.
You can also apply by visiting the College of Science website at: http://www.northeastern.edu/cos/ and
clicking on the Faculty Positions button.
The Department of Chemistry
Is looking for a professor
Educational minimum requirements:
- MSc (and/or BSc) in Analytical Chemistry
- Doctorate in Science, preferentially on a
topic in phytochemistry
- International experience (e. g. Postdoc).
Job description: full time
We expect:
A. Research experience documented by
original publications in refereed journals
B. Willingness to teach in Analytical
Chemistry
Complete applications should be sent,
per email only, to:
wbaumann@uniandes.edu.co
Application deadline:
December 2
nd
, 2011
Address your application materials to:
MBARI, Human Resources
Job code: Postdocs-2012
7700 Sandholdt Road, Moss Landing, CA 95039-9644
Submit by e-mail to jobs_postdocs@mbari.org (preferred),
by mail, or fax to (831) 775-1620.
EOE MBARI Welcomes Diversity
Monterey Bay Aquarium Research Institute
2012 POSTDOCTORAL FELLOWSHIP PROGRAM
Applications for postdoctoral fellowship program at the Monterey Bay Aquarium Research Institute (MBARI)
are invited. MBARI is dedicated to the development of state-of-the-art instrumentation, systems, and methods
for scientic research in the oceans. Ongoing programs in marine robotics, ocean physics, chemistry, geology,
and biology, as well as information management and ocean instrumentation research and development exist at
MBARI. Located in Moss Landing, California at the head of Monterey Bay, MBARI enjoys convenient access to
diverse oceanographic environments. The institute operates research vessels equipped with remotely operated
vehicles, autonomous underwater vehicles, and diverse oceanographic equipment, operates the MARS seaoor
cabled observatory. MBARI is a non-prot oceanographic research institute supported by the David and Lucile
Packard Foundation.
Offers will be made to candidates from the elds of biological, chemical, and physical oceanography, marine
geology, and ocean engineering. Candidates must be awarded their Ph.D. degree prior to commencing the
two-year appointment and start during the 2012 calendar year. Applicants are encouraged to communicate
with potential research sponsors at MBARI for guidance on project feasibility, relevance to ongoing research
projects, and resource availability (http://www.mbari.org/about/postdoc_mentors.htm).
Application deadline: Wednesday, December 7, 2011
Selected candidates will be contacted in early March 2012.
Application requirements:
1. Curriculum vitae
2. At least three professional letters of recommendation
3. Succinct statement of the applicants doctoral research
4. Potential research goals at MBARI
5. Supplemental Information online form (http://www.mbari.org/oed/jobs/forms/postdoc_form_2012.htm)
Competitive compensation and benets package.
MBARI considers all applicants for employment without regard to race,
color, religion, sex, national origin, disability, or veteran status.
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POSITIONS OPEN
The University of South Florida_s (USF) Center for
Drug Discovery and Innovation (CDDI) and Depart-
ment of Chemistry are pleased to invite applications
for a tenure-track position in medicinal chemistry at
the ASSOCIATE/FULL PROFESSOR rank. CDDI
(website: http://www.cddi.usf.edu), established in
2007 as a State designated Florida Center of Excellence
on the USF campus is at the center of active efforts in
early phase drug discovery. CDDI supports drug dis-
covery through its center faculty and core laboratories in
structural biology (NMR, proteomics), protein produc-
tion, and small molecule diversity. USF has established
strengths in synthetic organic chemistry, computation-
al chemistry/molecular modeling, and disease target
identification and screening in the areas of infectious,
neurodegenerative, cancer, and metabolic diseases. The
joint appointment with Chemistry, together with col-
laborative opportunities with USF Health, the Moffitt
Cancer Center, and the Byrd Alzheimer_s Center pro-
vide a robust research environment. USF is the ninth
largest university in the United States. serving more
than 45,000 students and is one of three Research Tier
I universities in Florida with more than $380 million in
research funding. The USF campus has a diverse stu-
dent body reflecting the multicultural strength of the
Tampa Bay region. Successful applicants must possess
a Ph.D. in Chemistry or a closely related area, have a
vigorous, externally funded research program consist-
ent with the Center_s mission, and must be eminently
qualified to teach undergraduate and graduate courses
in Chemistry. Salary is negotiable. Applicants should
submit by 1 November 2011, curriculum vitae along
with a letter of application detailing their research plans
in the context of the center mission and a statement of
teaching philosophy. Three confidential letters of rec-
ommendation should also be arranged. Send mate-
rials to e-mail: cddisearches@usf.edu (preferred) or
to: Professor Bill Baker, Director, CDDI, 3720 Spec-
trumBoulevard, Suite 303, Tampa, FL 33612-9220.
PROFESSOR AND DIRECTOR
Center for Bioinformatics and
Computational Biology
University of Maryland, College Park
The University of Maryland invites applications for
Director of the Center for Bioinformatics and Com-
putational Biology (CBCB). Candidates are expected to
be prominent scholars with publications and research
experience at the interface of biological science and
computing. Their primary responsibility will be to lead
a nationally visible research program complementing ex-
isting strengths in computational genomics, proteomics,
and molecular evolution. They will also be expected to
promote the CBCB, and help build collaborative rela-
tionships, both on and off-campus. Information about
the Center can be found at website: http://www.cbcb.
umd.edu. Collectively, the CBCB faculty spans the fields
of computer science, mathematics and statistics, biology,
and biochemistry. The Center is housed in contiguous
space and has access to significant high-end computing
infrastructure through the University of Maryland In-
stitute for Advanced Computer Studies. CBCB faculty
members are also affiliated with at least one other cam-
pus academic unit appropriate to their interests. There
is ample potential for collaboration with other organi-
zations in the area, such as the NIH, the JCVI, and
the Smithsonian Institution. For more information,
contact the search chair, Thomas D. Kocher (e-mail:
tdk@umd.edu). To apply, send a letter of application,
curriculum vitae, and names of three references, fol-
lowing the instructions at website: http://cbcb.umd.
edu/hiring/. Review of applications will begin No-
vember 15, 2011.
The University of Maryland is an Affirmative Action/Equal
Opportunity Employer. Women and minorities are encouraged
to apply.
POSITIONS OPEN
FULL PROFESSOR in Physical Chemistry
Francis Crick Endowed Chair in
The Department of Chemistry and Biochemistry at
UC San Diego
The Department of Chemistry and Biochemistry
at UC San Diego (website: http://www-chem.ucsd.
edu) is playing a key role in a UCSD campus-wide
effort to build the preeminent program in quantita-
tive biosciences (q-Bio) research and teaching. To an-
chor this effort, the department invites applications
for a tenured Full Professorship in Physical Chemistry,
with a preferred focus on theoretical molecular bio-
physics. The successful candidate will hold the Francis
Crick Endowed Chair, and will help to steer future
development of the q-Bio initiative. This will include
collaborations with other departments including Math-
ematics and Physics, and such UCSD organizations
as the San Diego Supercomputer Center and the Cen-
ter for Theoretical Biological Physics. Candidates must
have a Ph.D. in one of the quantitative physical sciences
and a recognized program of excellence in both teach-
ing and research in theoretical molecular biophysics. A
successful candidate will be judged on teaching and
research accomplishments as well as on a demonstrated
commitment to diversity, equity, and inclusion in higher
education. Salary is commensurate with qualifications.
Candidates should submit online curriculum vitae, list
of publications, reprints of up to five representative
papers, and a personal statement that includes a sum-
mary of research plans as well as their past and/or po-
tential contributions to and leadership in promoting
equity, inclusion, and diversity at website: https://apol-
recruit.ucsd.edu/apply. Please select the following
recruitment: Chemistry and Biochemistry Full Pro-
fessor in Physical Chemistry (10-313). Candidates
should also arrange to have three letters of reference
addressing research, teaching and professional service
submitted at the above-mentioned URL. Prompt re-
sponse is recommended. Review of applications will
commence on November 1, 2011 until the position
is filled. UCSD is an Affirmative Action/Equal Opportunity
Employer with a strong institutional commitment to excellence
through diversity (website: http://diversity.ucsd.edu).
SYSTEMS BIOLOGIST
Loyola University Chicago (LUC), College of Arts
and Sciences, Department of Biology, invites applica-
tions for a full-time tenure-track position in Systems
Biology at the rank of ASSISTANT PROFESSOR,
beginning August 2012. For an overview of the de-
partment visit website http://www.luc.edu/biology.
Candidates must have a Ph.D. and postdoctoral expe-
rience, and will be expected to establish a vigorous,
externally funded research program involving under-
graduates and M.S. students. Preference will be given
to candidates with expertise in systems biology who
use bioinformatics approaches. Teaching responsibil-
ities will include Cell Biology, Developmental Biology,
and an advanced course in the candidate_s area of spe-
cialization that can contribute to the Bioinformatics pro-
gram (website: http://www.luc.edu/bioinformatics).
Candidates should complete the online application
in full at www.careers.luc.edu with cover letter, curric-
ulum vitae, research plan, teaching philosophy statement,
and names/contact information for three references.
Review of applications will begin November 1, 2011,
and continue until the position is filled. Inquiries about
the position can be sent to: Systems Biology Search
Committee, Department of Biology, Loyola Univer-
sity Chicago, 1032 West Sheridan Road, Chicago,
IL 60660. Loyola University Chicago is an Equal Opportunity/
Affirmative Action Employer with a strong commitment to diver-
sifying its faculty. Applications from women and minority candi-
dates are especially encouraged. For information about LUC,
visit website: http://www.luc.edu.
POSITIONS OPEN
ASSISTANT PROFESSORSHIP
IN CHEMISTRY
Harvard University
Candidates are invited to apply for a tenure-track
assistant professorship in chemistry. We are specifically
seeking individuals with research and teaching interests
in inorganic chemistry or associated fields. Candidates
should arrange to have three letters of recommendation
sent independently and provide curriculum vitae, state-
ment of teaching philosophy, list of publications, and
outline of their future research plans. A strong doc-
toral record is required. All applications and support-
ing materials must be submitted via website: http://
academicpositions.harvard.edu/postings/3694. The
deadline for receipt of applications and supporting
materials is October 15, 2011. Harvard University is an
Affirmative Action, Equal Opportunity Employer. Applications
from and nominations of women and minority candidates are strongly
encouraged.
NEUROBIOLOGIST
Loyola University Chicago (LUC), College of Arts
and Sciences, Department of Biology, invites applica-
tions for a full-time tenure-track position in Neuro-
biology at the rank of ASSISTANT PROFESSOR,
beginning August 2012. For an overview of the depart-
ment visit website: http://www.luc.edu/biology/.
Candidates must have a Ph.D. and postdoctoral ex-
perience, and will be expected to establish a vigorous,
externally funded research program involving under-
graduates and M.S. students. Preference will be given
to candidates with expertise in electrophysiogy and mo-
lecular biology and with research interests in adult stem
cells, neural plasticity, or vertebrate CNS development.
Teaching responsibilities will include Neurobiology,
Neuroscience Lab, and two or more other courses such
as Introductory Biology, Cell Biology, Genetics, Bio-
chemistry, Molecular Biology, or an advanced course in
the candidate_s area of specialization. Candidates should
complete the online application in full at website:
http://www.careers.luc.edu with cover letter, curric-
ulum vitae, research plan, teaching philosophy state-
ment, and names and contact information for three
references. Review of applications will begin on No-
vember 1, 2011, and continue until the position is filled.
Inquiries about the position can be sent to: Neuro-
biologist Search Committee, Department of Biolo-
gy, Loyola University Chicago, 1032 West Sheridan
Road, Chicago, IL 60660. Loyola University Chicago is
an Equal Opportunity/Affirmative Action Employer with a strong
commitment to diversifying its faculty. Applications from women
and minority candidates are especially encouraged. For informa-
tion about LUC, visit website: http://www.luc.edu.
TENURE-TRACK ASSISTANT PROFESSOR
in Human Physiology
The Department of Biology, University of Wisconsin
Stevens Point, offers a tenure-track, nine-month faculty
position in Human Physiology at the Assistant Profes-
sor level, beginning August 2012. Teaching includes
human physiology, introductory biology, senior sem-
inar, and opportunity for advanced course in specialty.
Research involving undergraduates, department ser-
vice, and student advising are expected. Ph.D. in mam-
malian physiology or equivalent required for tenure.
Teaching and research experience are highly desirable,
as defined by grants, publications, evidence of teaching
excellence, and/or postdoctoral work. Coursework or
research in neurobiology is desirable.
Include curriculum vitae, statements of teaching phi-
losophy and research interests, three letters of recom-
mendation, and undergraduate and graduate transcripts.
Send application materials to: Dr. C. Yahnke, Chair;
Biology Department, University of WisconsinStevens
Point; Stevens Point, WI 54481. Review begins 15
November 2011 and continues until filled. For more
information, telephone: 715-346-2455; fax: 715-
346-3624; e-mail: cyahnke@uwsp.edu. We are an Af-
firmative Action/Equal Opportunity Employer.
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7 OCTOBER 2011 VOL 334 SCIENCE www.sciencecareers.org 138
The Division of Hematology, Center for the Study of
Aging, and Duke Translational Research Institute are
jointly recruiting an established mid-career investigator actively
focusing on age-related aspects of non-malignant hematologic
problems (e.g. anemia of aging, coagulation, or stem cell
disorders). The Deans Biology of Aging initiative will support
translational and clinical investigations, along with laboratory-
based research, as appropriate to the candidate.
Duke Medicine strives to transform medicine and health
locally and globally through innovative scientic research,
rapid translation of breakthrough discoveries, educating
future clinical and scientic leaders, advocating and practicing
evidence-based medicine to improve community health, and
leading efforts to eliminate health inequalities.
Interested investigators should submit a full curriculum vitae
and current NIH Biosketch, along with a cover letter stating
relevant interests and activities, to:
Hematology and Aging Search Committee
c/o Marilyn Telen, MD
Wellcome Professor of Medicine
Box 2615 DUMC, Durham, NC 27710
Or by email to: Marilyn.telen@duke.edu
Duke University is an Afrmative Action and Equal Opportunity
Employer. Women and minorities are encouraged to apply.
Associate Professor Positons in Applied Physics,
The University of Tokyo
Applicatons are invited for two faculty positons in Department of Applied Physics, The University of
Tokyo. The rank of the two positons is that of associate professor. The University of Tokyo seeks for
individuals of the highest internatonal caliber who lead the research actvity in applied physics on
appointment. The successful applicant is expected to have a strong background in physical science and
excellent research actvites in experimental applied physics. The emphasis is put on the felds of sof-
mater science, condensed mater physics, quantum informaton and nanoscience, but other felds are
not excluded. The applicant is expected to teach at both Graduate School and College of Engineering in
The University of Tokyo. Salary will be commensurate with qualifcatons and experience, being subject
to the regulaton of The University of Tokyo. Medical insurance and other benefts are equivalent to
those of employees of Japan government.
Job type: Associate Professor
Rank: Full-tme (tenured)
Number of positons: Two
Qualifcatons: Applicants must have a Doctoral degree
Deadline for applicatons: December 15, 2011
Startng date: As soon as possible afer the completon of the selecton
Applicaton materials: 1. Curriculumvitae, 2. Summary of achievements and aspiraton for research (about
3000 words) and aspiraton for educaton (about 1000 words), 3. Publicaton list (items are classifed into
original paper, review, proceedings, book, patents, etc), 4. Reprints of three signifcant publicatons, 5. Two
recommendaton leters. Applicaton materials will not be returned.
Method of selecton: An interview will be conducted following inital selecton based on applicaton
materials.
Where to contact: For inquiries regarding this invitaton, please contact:
Professor Akira Furusawa, Department of Applied Physics,
School of Engineering, The University of Tokyo,
7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656 JAPAN
E-mail: akiraf@ap.t.u-tokyo.ac.jp
Tel: +81-3-5841-6857
Department URL: htp://www.ap.t.u-tokyo.ac.jp/e/index.html
Applicatons are welcome from women according to Declaraton of Gender Equality Acceleraton of The
University of Tokyo (3 March 2009).
Professor and Director of the
Mildred E. Mathias Botanical Garden
The University of California, Los Angeles (UCLA) Department of Ecol-
ogy and Evolutionary Biology seeks to ll an open-rank (tenure track
or tenured) faculty position in Plant Sciences. We are interested in all
subelds within organismal plant biology but especially in candidates
with strong interests in cross-disciplinary approaches to plant ecology,
plant evolutionary biology, conservation science, and biogeography. The
successful candidate is expected to establish an internationally recognized
and externally funded research programand will assume faculty director-
ship of the Mildred E. Mathias Botanical Garden, a seven-acre garden on
the UCLAcampus. We encourage applicants with experience relevant to
botanical garden administration and development but will consider appli-
cants with other leadership experience or potential. As a campus with a
diverse student body, individuals with a history of mentoring under-repre-
sented minorities in the sciences are encouraged to discuss their activities
in their cover letter. Applicants should submit application materials online
to www.eeb.ucla.edu/botgard including a cover letter, curriculumvitae,
statements of research, teaching and interdisciplinary interests, and the
names and contact information of four references by December 1, 2011.
Please use job number 0830-1112-01in all correspondence.
Additional information about the Botanical Garden and the Depart-
ment may be found at http://www.botgard.ucla.edu/ and http:
//www.eeb.ucla.edu/, respectively. Inquiries regarding the posi-
tion should be directed to Search Chair, Professor Philip Rundel,
rundel@ucla.edu.
Women and minority applicants are encouraged to apply.
UCLA is an Afrmative Action/Equal Opportunity Employer
with a strong institutional commitment to the achievement of
faculty and staff diversity.
Download your free copy today at
ScienceCareers.org/booklets
Brought to you by the
AAAS/Science Business Ofce
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POSITIONS OPEN
FACULTY POSITION
Pharmacology, Physiology and Neuroscience
University of South Carolina
School of Medicine-Columbia
The Department of Pharmacology, Physiology and
Neuroscience at the University of South Carolina
School of Medicine in Columbia, SC invites appli-
cations for a faculty position at the ASSISTANT or
ASSOCIATE PROFESSOR level. New faculty mem-
bers will join a collegial and collaborative department
at a university in the midst of an ambitious program
to achieve national prominence in research and edu-
cation. Candidates with research interests that com-
plement the departmental research programs that
focus on studying the molecular or cellular mecha-
nisms underlying physiological processes, complex
behaviors, or drug action are desirable, with priority
given to our neuroscience-based research focus. Suc-
cessful candidates will also be expected to participate
in medical and graduate teaching. Applicants must
have a doctoral degree and postdoctoral experience.
Preference will be given to individuals with experience
in medical education, funding success and potential,
and research interests that enhance departmental pro-
grams targeting neurological and neuropsychiatric
disorders. Substantial start-up funds and modern fa-
cilities will be provided. For junior investigators, the
initial appointment could be viewed as a non-tenure-
track position, with transition into a tenure-track follow-
ing establishment of a funded, independent research
program and demonstration of teaching competency.
Candidates with necessary credentials will be consid-
ered for immediate appointment on the tenure-track as
an Assistant or Associate Professor.
Qualified applicants may apply by submitting a sin-
gle electronic file (PDF or Word) that includes a cover
letter summarizing qualifications, curriculum vitae and
publication list, a statement of research plans and pro-
fessional goals, and contact information for four refer-
ences. The file should be attached to an e-mail message
sent to Dr. Marlene Wilson at e-mail: ppn.search@
uscmed.sc.edu with BPPN Faculty Search[ as the sub-
ject before January 15, 2012. For more information
about the department including our research programs,
please visit website: http://ppn.med.sc.edu/. The
University of South Carolina is an Affirmative Action/Equal
Opportunity Employer.
MEDICAL DIRECTOR
Physician, biomedical researcher, or other medical/
bioscience professional sought by Manhattan family
to research and coordinate family medical and health
care issues. This person will manage a small team of
professionals and interface with physicians, medical re-
searchers, and consultants (in academia and otherwise)
to ensure delivery of highest-quality medical care to
family members. Considerable weight will be given
to unusual academic distinction and other intellectu-
al achievements. Excellent communication skills are a
must, a Ph.D. or M.D. is strongly preferred, and clini-
cal experience is a plus. This is a full-time position
with a highly attractive compensation package and sig-
nificant upside potential. Resume to e-mail: mdrecr@
gmail.com.
POSTDOCTORAL RESEARCH ASSOCIATE in
Neurophysiology
The College of William & Mary seeks a postdoctoral
research associate to investigate the neural mechanisms
of breathing in mammals. Experience with patch-clamp
electrophysiology and fluorescence microscopy is de-
sirable. Applicants should have a Ph.D. or M.D. by the
time of the appointment. The position is available No-
vember 1. Review of applications will begin immediately
and continue until position is filled. Submit curriculum
vitae, statement of research interests, and contact in-
formation for three references at website: https://
jobs.wm.edu (position number F0685W). The Col-
lege of William & Mary is an Equal Employment Opportunity/
Affirmative Action Employer.
POSITIONS OPEN
University of Vermont-Department of Ani-
mal Science seeks two tenure-track ASSISTANT
PROFESSORS. Positions are in Ruminant Nu-
trition and Animal Genetics/Genomics. Evalua-
tion of applications begins November 15, 2011.
For full position descriptions, see website: http://
www.uvmjobs.com. The University of Vermont is
an Affirmative Action/Equal Opportunity Institution.
ENDOWED FACULTY POSITION in
Molecular, Cellular, Developmental, and
Quantitative Biology at the
University of California, Santa Barbara
The Department of Molecular, Cellular, and De-
velopmental Biology at the University of California,
Santa Barbara invites applications for a faculty posi-
tion at an open rank. A generous Endowed Chair is to
be filled at the advanced ASSISTANT, ASSOCIATE,
or FULL PROFESSOR rank with cross-appointments
available in the Department of Chemistry and Bio-
chemistry, the Biomolecular Science and Engineering
Program, and other departments as appropriate. We
seek an outstanding scholar with an internationally
recognized research program in any area of molecular,
cellular, and developmental biology and/or biochem-
istry, with particular preference toward candidates who
apply cross-disciplinary quantitative experimental or the-
oretical approaches to solving fundamental problems
in biology.
Applicants should submit curriculum vitae, selected
reprints, and a brief research plan, and, in the case of
junior faculty applicants, arrange for three letters of
reference to be sent to: Faculty Search Committee,
Department of Molecular, Cellular and Developmental
Biology, University of California, Santa Barbara, Santa
Barbara, CA 93106-9610. Send application documents
in PDF Format to c/o Maria Boschee, e-mail: mcdb-
search@lifesci.ucsb.edu. Review of applications will
begin on November 15, 2011, and will continue until
the positions are filled.
In addition to submitting your application, please
fill out the supplemental survey at website: https://
docs.google.com/spreadsheet/viewform?formkey=
dEFpeHJndVFLR2l1amNkOEEzYUZhYlE6MQ.
The department is especially interested in candidates who can
contribute to the diversity and excellence of the academic com-
munity through research, teaching, and service. UCSB is an Equal
Opportunity/Affirmative Action Employer.
FACULTY POSITION in
Ecological or Evolutionary Genomics
Saint Louis University, a Catholic, Jesuit institution
dedicated to student learning, research, health, and ser-
vice, is seeking applicants for a tenure-track faculty po-
sition in Ecological or Evolutionary Genetics/Genomics
in the Department of Biology. Competitive applicants
will have a Ph.D., postdoctoral experience, a record of
research productivity, and a commitment to undergrad-
uate and graduate student training. The successful can-
didate will be expected to establish an independent,
extramurally funded research program that applies
genetic and/or genomic approaches to fundamental
questions in ecology or evolutionary biology. The fac-
ulty member will contribute to an undergraduate course
in Genetics, a graduate course in the candidate_s area
of expertise, and/or a general biology course.
All applications must be made online at website:
http://jobs.slu.edu (Req ID 20110817) and include
a cover letter, curriculum vitae, a research statement,
and a statement of teaching experience and philoso-
phy. In addition, please have three letters of reference
sent to Dr. Robert Wood, Department of Biolo-
gy, Saint Louis University, 3507 Laclede Avenue,
St. Louis, MO, 63103. Review of applications will
begin on 1 November 2011 and continue until the
position is filled. Additional information on the De-
partment of Biology can be found at website: http://
www.slu.edu/x14762.xml.
Saint Louis University is an Affirmative Action/Equal Oppor-
tunity Employer (AA/EOE), and encourages nominations of and
applications from women and minorities.
POSITIONS OPEN
FACULTY POSITION
in Innate Immunology/Inflammation
Department Of Immunobiology
The University Of Arizona
The Department of Immunobiology at the Univer-
sity of Arizona College of Medicine is seeking inter-
active, well-qualified applicants for a Tenure-Track or
Tenured position at the ASSISTANT, ASSOCIATE,
or FULL PROFESSOR rank depending upon qual-
ifications, investigating the initiation and regulation
of innate and inflammatory responses. Successful ap-
plicants will be expected to bring novel expertise, de-
velop independent research programs, and contribute
to graduate (Ph.D.) and medical (M.D.) education.
In addition, the candidate will be expected to invest a
fraction of their effort to help build interactive and
collaborative programs within and outside the De-
partment to tackle larger biomedical problems rele-
vant to human health.
The University of Arizona is ranked amongst the
top 20 public research and education universities. It
boasts excellent core facilities and a rich scientific envi-
ronment that includes a number of strong, interactive
departments covering a broad range of molecular and
biomedical sciences. The University also offers a lively
campus with nationally recognized academic, sports,
and performing arts programs. It is located in sunny
Tucson, which is surrounded by the majestic Sonoran
Desert and bio-diverse sky islands that rise to more
than 9,000 feet above the desert floor. The city boasts
a vibrant multicultural population of approximately
900,000, and a strong, diverse economy.
Please complete an online application for Job
#48568 & 48571 at website: http://www.hr.arizona.
edu. Be prepared to attach your curriculum vitae.
The University of Arizona is an Equal Employment Oppor-
tunity/Affirmative Action Employer. Minorities/Women/Persons
with Disabilities/Veterans.
ASSISTANT OR ASSOCIATE PROFESSOR
Arthritis Center/Rheumatology
The Arthritis Center at the Boston University School
of Medicine invites applications for a position at the
rank of Assistant or Associate Professor in the areas
of immunology relevant to autoimmune disorders. Out-
standing candidates working in all areas of immunol-
ogy are invited to apply. We particularly encourage
applications from candidates working in the field of
innate immunity and lymphocyte function. Preference
will be given to applicants with research interest and
experience in areas that complement and enhance the
existing programs (website: http://www.bumc.bu.
edu/rheumatology/).
Successful candidates for this position are expected
to develop and maintain a competitively funded re-
search program. The minimum requirements for an
Assistant Professor position include a M.D., Ph.D., or
M.D.-Ph.D. with at least three years postdoctoral ex-
perience. Appointment at the Associate Professor level
requires a minimum of five years experience at the As-
sistant Professor level or equivalent, and a nationally
recognized and federally funded research program.
Arthritis Center offers competitive startup package,
excellent core facilities, and collegial atmosphere. Inter-
ested candidates should electronically submit curricu-
lum vitae, a brief summary of research interest and
plans, and the contact information for three references
to: Maria Trojanowska, Ph.D. (e-mail: trojanme@
bu.edu), Director, Arthritis Center, 72 East Con-
cord Street, E-5, Boston, MA 02118.
Boston University is an Equal Opportunity Employer and
actively seeks applications from women and underrepresented
groups.
POSTDOCTORAL POSITION
Germline Stem Cells
Studies include culture, differentiation, and gene ac-
tivity of male germline stem cells. See Science 316:404,
2007 and PNAS 106:21672, 2009. Send curriculum
vitae, names of three references, and a letter describing
research experience to: R. L. Brinster, School of Vet-
erinary Medicine, University of Pennsylvania. E-mail:
cpope@vet.upenn.edu.
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Assistant Professor in Human Genetics
The Center for Human Genetics (McDermott Center) at The University
of Texas Southwestern Medical Center at Dallas invites applications
for a tenure-track position of Assistant Professor. We are seeking
individuals with innovative experimental research programs in human
molecular genetics. Successful applicants will be expected to establish
a vigorous independent research program and to teach students at the
graduate level.
The individual should hold a graduate degree (MD, PhD or MD/PhD)
and have completed a post-doctoral fellowship. The appointment will
include a competitive salary, attractive start-up package, excellent labo-
ratory space in a dynamic research environment with access to genetic
core facilities. The faculty member will have a joint appointment in
a basic science or clinical department. Applicants should submit their
curriculum vitae containing a summary of past accomplishments, a
statement of future objectives, and three professional references to:
Faculty Search Committee
c/o Susan Hayes
Dept. Administrator
McDermott Center for Human Growth & Development
UT Southwestern Medical Center at Dallas
5323 Harry Hines Boulevard
Dallas, Texas 75390-8591
Or by email to: Susan.Hayes@UTSouthwestern.edu
UTSW is an Equal Opportunity Employer.
Women and Minorities are encouraged to apply.
Virologist - Tenure-Track Faculty Position
The Department of Infectious Diseases and Pathology at the
University of Florida College of Veterinary Medicine is seeking a
virologist to fill a tenure-accruing position, and strengthen ongoing
research programs to advance diagnosis, prevention and/or therapy
for viral pathogens. This search encompasses all academic ranks,
seeking an individual with the demonstrated skills needed to lead an
extramurally-funded research program on diseases of veterinary
and/or public health interest. The incumbent is expected to provide
expertise in viral pathogens of public health or veterinary interest and
teach veterinary virology to professional students. Applicants must
have a DVM/PhD, MD/PhD, PhD, or equivalent degrees, and a
record of NIH R01, or equivalent, extramural funding as an
independent investigator. The primary responsibility of the incumbent
will be to maintain a competitive research program that will form
the core of an expanding enterprise. The Department
(http://www.vetmed.ufl.edu/ college/departments/patho/) has strong
ties to the UF Emerging Pathogens Institute, as well as an active
graduate program in infectious diseases, and excellent research
facilities within a dynamic and expanding Health Science Center
comprised of six colleges and associated clinical facilities.
Applicants should submit a letter outlining professional goals, a
curriculum vitae, and a list of three professional referees to: Dr. John
B. Dame, Search Committee Chair, Department of Infectious
Diseases and Pathology, College of Veterinary Medicine, P.O. Box
110880, University of Florida, Gainesville FL 32611-0880; e-mail
damej@ufl.edu, fax: 352-392-9704. Review of applications will begin
November 15, 2011 and will continue until the position is filled.
The University of Florida is an equal employment opportunity employer.
SCIENTIFIC, ENGINEERING & TECHNICAL STAFF VACANCIES
King Abdullah University of Science and Technology {KAUST} located in Saudi
Arabia, is an international graduate level research university dedicated to
advancing science and technology through bold and collaborative research and
to addressing challenges of regional and global significance, thereby serving the
Kingdom, the region and the world. KAUST faculty are engaged in such globally
significant areas as Energy, Water, and Food. In addition, KAUST emphasizes
research on the Environment and Red Sea, and the discipline of Computational
Science serves as an enabling technology for all its research activities.
KAUST is located on the Red Sea in Thuwal (80 km north of Jeddah). Newly
opened in September 2009. KAUST is an independent merit-based university
which welcomes exceptional researchers, faculty and students from around the
world. KAUST offers attractive salaries and a wide range of benefits. Further
information about KAUST can be found at http://www.kaust.edu.sa
KAUST now recruiting SCIENTISTS, ENGINEERS, SPECIALISTS & TECHNICAL STAFF
who are needed to operate and engage in collaborative research using state of the art
facilities in its extensive Labs:
ANALYTICAL CHEMISTRY LAB
BIOSCIENCE LAB
NANOFABRICATION, IMAGING & CHARACTERIZATION LAB
MARINE OPERATIONS LAB
SUPERCOMPUTING LAB
VISUALIZATION LAB
Interested persons may visit KAUST website www.kaust.edu.sa to nd general information
about KAUST and to review the job requirements of Core Labs vacancies. Or may click on
the link under each of individual Lab. To apply: http://apptrkr.com/207836
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www.westernu.edu
Faculty Positions in Pharmacology
and other disciplines
available for 2012
Western University of Health Sciences, a thriving center for human health care
and veterinary medicine education is growing and along with our newly opened
site for the College of Osteopathic Medicine of the Pacic Northwest (COMP-
NW) in Lebanon, Oregon, we are further expanding our campus in Pomona, CA.
The Universitys 10 year plan and core values have propelled the Institution to be
a benchmark University for the development of interprofessional and graduate
medical education. The University values a diverse institutional community and
is committed to excellence in its faculty, staff and students. Western University
seeks applicants of distinguished academic accomplishments who possess a
passion for excellence and can illustrate a proven track record of educational
achievements.
The Department of Basic Medical Sciences provides the preclinical education
for the College of Osteopathic Medicine, and invites applications from highly
motivated individuals for a tenure-track faculty position in pharmacology. This
is a full-time, 12-month, tenure-track position at theAssistant Professor/Associate
Professor/Professor rank dependent upon qualications. Successful candidates
will be located at the COMPPomona, CAcampus. Applicants must have a Ph.D.
in pharmacology or equivalent eld and at least 2 years of postdoctoral experience.
Similar positions in physiology, biochemistry, and microbiology/immunology are
also available at both the Lebanon, OR and Pomona, CAcampuses. Preference
will be given to master educators who have demonstrated excellence in teach-
ing with signicant scholarly activity and/or those with a history of extramural
funding and a strong potential to obtain further grant support for their research
program. Submit a current curriculum vitae and a cover letter describing your
teaching experience and philosophy, your research activity and goals, and how
you meet the qualications for the position. Please include contact information for
at least three references. These positions will remain open until lled. NissarA.
Darmani, PhD, Assistant Dean for Basic Sciences and Research, Department
of Basic Medical Sciences, College of Osteopathic Medicine of the Pacic,
Western University of Health Sciences, 309 E. Second Street, Pomona, CA
91766-1854; Email Address: ndarmani@westernu.edu
Western University of Health Sciences is an Equal Opportunity Employer.
POSITIONS OPEN
CELL BIOLOGIST
The Biology Department at the University of the
South seeks a Cell Biologist for a position as Tenure-
Track ASSISTANT PROFESSOR in one of the na-
tion_s top liberal arts institutions. Primary teaching
responsibilities will be in Cell Biology and Biochem-
istry. The successful candidate will maintain an active
research program with opportunities for undergrad-
uate involvement. Candidates should be enthusiastic
about developing a teaching and research program in
the context of the liberal arts tradition in education. The
University of the South, familiarly known as Sewanee,
consists of a highly selective, 1,425-student College
of Arts and Sciences and a 70-student School of The-
ology. Located on a 13,000-acre campus on Tennes-
see_s Cumberland Plateau, it is an institution of the
Episcopal Church that welcomes individuals of all
backgrounds.
Review of applications will begin October 3, 2011,
and continue until the position is filled.
Eligibility for employment is contingent upon success-
ful completion of a pre-employment screening.
Send a letter of application, curriculum vitae, state-
ments of teaching and research interests, transcripts,
and three letters of reference to:
Ms. Tammy Elliott
Faculty Hiring Specialist
The University of the South
735 University Avenue
Sewanee, TN 37383-1000
Electronic submission is preferred e-mail: tmelliot@
sewanee.edu.
The University of the South is an Equal Opportunity Em-
ployer. Women and minorities are encouraged to apply.
ELECTRON MICROSCOPISTS
Center Director and Assistant Director
Indiana University, Bloomington
The Departments of Chemistry, Biology and Mo-
lecular and Cellular Biochemistry at Indiana Univer-
sity, Bloomington seek outstanding candidates for
leadership positions in the newly constituted Electron
Microscopy Imaging Center (EMIC). This Center cur-
rently houses a JEOL JSM-5800LV STEM and a JEOL
JEM-1010 TEM and a new state-of-the-art JEOL JEM
3200FS Cryo-TEM equipped for cryo-TEM, tomogra-
phy, STEM, EELS, and EDS, as well as ancillary equip-
ment (website: http://sites.bio.indiana.edu/cryo/).
We seek applicants for both the Director and Assistant
Director positions in EMIC, to be filled commensurate
with experience. Applicants with primary or exclusive
experience in materials chemistry applications or cryo-
TEM of biological samples are strongly encouraged
to apply. The primary responsibilities of these posi-
tions are data collection and processing, user training
and liaison, and scope maintenance. Opportunities for
collaboration, independent research, and some teach-
ing will also be made available. Applicants must have a
Ph.D. in a relevant field, with five years experience in
electron microscopy desirable. Review of applications
will begin on November 1, 2011 and the anticipated
start date is no later than July 1, 2012. Please submit a
cover letter, curriculum vitae, and a statement outlining
research experience with EM techniques/applications,
data processing, and image reconstruction and ar-
range to have three letters of recommendation sent to:
David P. Giedroc, Chair, Department of Chemis-
try, Indiana University, 800 E. Kirkwood Avenue,
Bloomington, IN 47405, preferably as a single PDF
to e-mail: cemchair@indiana.edu. Indiana University is
an Equal Opportunity/Affirmative Action Employer.
PLANT MOLECULAR BIOLOGIST. Tenure-
track ASSISTANT PROFESSOR to begin September
2012; Ph.D. required. Eckerd College, Saint Petersburg,
Florida. Teach seven course equivalents per academic
year, including botany, genetics, organisms and evolu-
tion, other courses in the biology major, and January
Term; participate in the general education program;
develop a research program that includes undergrad-
uates. Application deadline 7 November Full details
website: http://www.eckerd.edu/hr/employment.
php.
POSITIONS OPEN
RESEARCH ASSISTANT PROFESSOR
The Division of Metabolism, Endocrinology, and
Nutrition in the Department of Medicine at the Uni-
versity of Washington is recruiting a full-time faculty
member at the Research Assistant Professor level. The
appointment requires a Ph.D., M.D., or equivalent de-
gree and a record of research publications in the area
of lipid metabolism and the brain. The applicant is
expected to have expertise in the role of lipid transfer
proteins in the brain, lipid and lipoprotein metabolism
in health and disease, pathophysiology of neurode-
generative and neuroinflammatory diseases and other
neurological disorders and partial support for his/her
research. In order to be eligible for University sponsorship
for an H-1B visa, graduates of foreign (non-U.S.) med-
ical schools must show successful completion of all three
steps of the U.S. Medical Licensing Exam (USMLE),
or equivalent as determined by the Secretary of Health
and Human Services. Interested applicants should sub-
mit a letter of interest, curriculum vitae, and a brief sum-
mary of research capabilities and funding to: John
Albers, Ph.D., Search Committee Chair Northwest
Lipid Metabolism and Diabetes Research Labora-
tories, 401 Queen Anne Avenue North, Campus Box
359119, Seattle, WA 98109, telephone: 206-685-
3300, e-mail: jja@u.washington.edu. Review of ap-
plications will begin immediately and continue until
the position is filled. University of Washington faculty en-
gage in teaching, research, and service. The University of Washing-
ton is an Affirmative Action/Equal Opportunity Employer. The
University is building a culturally diverse faculty and staff and
strongly encourages applications from women, minorities, individ-
uals with disabilities, and protected veterans.
ASSISTANT PROFESSOR
Biological Chemistry
The Johns Hopkins University
School of Medicine
The Department of Biological Chemistry at The
Johns Hopkins University School of Medicine invites
applications for a new tenure-track faculty position at
the Assistant Professor level. The Department is seek-
ing candidates with an outstanding record in any area
of biochemistry, cellular, or molecular biology and a
commitment to excellence in research and teaching.
Applicants should submit (preferably, as a single PDF
file) curriculum vitae, list of publications, summary of
research accomplishments, and a description of their
future research plans by November 1, 2011. Electronic
files should be sent to e-mail: bcfacultyrecruitment@
jhu.edu. Applicants should also request that three let-
ters of recommendation be sent electronically or to
the address below:
Daniel M. Raben, Ph.D.
Faculty Search Committee Chair
C/O Ms. Angelina Hines
Department of Biological Chemistry
The Johns Hopkins University
School of Medicine
725 North Wolfe Street
Baltimore, M.D. 21205-2185
Equal Opportunity/Affirmative Action Employer
POSTDOCTORAL RESEARCHER in Analy-
sis and Modeling of Social Networks The Center for
Complex Networks and Systems Research (website:
http://CNetS.indiana.edu) at Indiana University
has an open postdoctoral position to study how ideas
propagate through complex online social networks
(website: http://www.jsmf.org/grants/2011022/).
The appointment starts in January 2012 for one year
and is renewable for up to three additional years.
The ideal candidate will have a Ph.D. in computing or
physical sciences; a strong background in analysis and
modeling of complex systems and networks; and solid
programming skills necessary to handle big data and
develop large scale simulations. To apply, send curric-
ulum vitae and e-mails of three references to CNetS
(e-mail: tgholbro@indiana.edu) or to: 919 E 10th
Street, Bloomington, IN 47408, USA. Applications
received by October 16, 2011 will be given full con-
sideration, but the position will remain open until filled.
Indiana University is an Equal Opportunity/Affirmative Action
Employer.
POSITIONS OPEN
ASSISTANT PROFESSOR (Tenured-Track)
Department of Pharmacology
Job Description. We seek an experienced research
scientist with strong expertise and a publication record
in drug abuse research involving bioinformatics, neuro-
pharmacology, and neurobehavioral approaches. This
individual will have a doctoral degree in a basic biomed-
ical science and completed rigorous postdoctoral train-
ing. Evidence of strong interpersonal skills and a proven
ability to manage a multi-dimensional laboratory while
directly maintaining an active laboratory research pro-
gram is essential. This individual will have a depth of
knowledge and practical expertise in the following areas:
(a) neurobehavior using operant self-administration and
social interactions; (b) neuroanatomy, including confocal
microscopy, laser capture microdissection, Golgi stain-
ing, and synaptic mapping; and (c) neurogenomic anal-
ysis of RNAseq data and text mining using Linux-based
programming.
Curriculum vitae, succinct statement of research in-
terests and accomplishments, and three letters of refer-
ence should be sent to:
Jeffery D. Steketee, Ph.D.,
Pharmacology Search Committee
Department of Pharmacology
University of Tennessee Health Science Center
874 Union Avenue; Suite 115
Memphis, Tennessee 38163
E-mail: jsteketee@uthsc.edu
The University of Tennessee is an Equal Employment Op-
portunity/Affirmative Action/Title VI/Title IX/Section 504/
ADA/ADEA Institution in the provision of its education and
employment programs and services.
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