TOP MODELS

- IN BIOLOGY





RAVIKUMAR

09M51A2304
In any field of study, it is prudent to
learn processes in a simple setting,
understand the basis for these
processes and then progress onto more
complex settings to see if the same
apply there as well.
WHAT IS MODEL ORGANISM?
Over the last century, research on a small number
of organisms has played a pivotal role in
advancing our understanding of numerous
biological processes.
This is because many aspects of biology are
similar in most or all organisms, but it is
frequently much easier to study a particular
aspect in one organism than in others.
These much-studied organisms are commonly
referred to as model organisms, because each
has one or more characteristics that make it
suitable for laboratory study.


HOW to choose a model organism?
It depends on what question is
being asked. When studying
fundamental issues of molecular
biology, simpler unicellular
organisms or viruses are
convenient. For developmental
questions, more complicated
organisms should be used.
MAMMALIAN MODELS
MOUSE
RAT
RABBIT
PIG

NON-MAMMALIAN MODELS
S. cerevisiae (budding yeast)
S. pombe (fission yeast)
Neurospora (filamentous fungus)
D. discoideum (social amoeabae)
C. elegans (round worm)
Daphnia (water flea)
D. melanogaster (fruit fly)
D. rerio (zebrafish)
Xenopus (frog)
Gallus (chicken)
Other MODEL ORGANISMS
ARABIDOPSIS
ZEA MAYS
PISUM SATIVUM
Schizosaccharomyces pombe
This image shows vegetatively
growing fission yeast cells stained
with DAPI to visualize the nucleus.
micro-
mammal
Schizosaccharomyces pombe, or fission yeast, is an
African brewing yeast originally isolated from millet
beer. This species has a distinguished research
history in studies of the cell cycle and mitosis,
chromosome dynamics, and epigenetics.
With a doubling time of 2-4 hours and simple
culture conditions, S. pombe is easily adapted to any
molecular biology laboratory.
Investigators from non-genetic systems are frequent
recruits to the fission yeast community, using S.
pombe as a genetic adjunct in their laboratories,
which has led to S. pombe being nicknamed
the micro-mammal.
Schizosaccharomyces pombe
Neurospora crassa
This image shows a rosette
of maturing asci (meiotic
cells) of Neurospora crassa,
from Wild type x histone H1-
GFP. Histone H1 being a
chromosomal protein, the
GFP-tagged nuclei (two per
spore at this stage) glow in
four of the eight ascospores
of each ascus; the remaining
four ascospores carry the
untagged nuclei from the
wild-type parent.
Neurospora crassa
Neurospora crassa is a eukaryotic multicellular
fungus with a sequenced 43 mb genome that
contains 10,620 predicted genes a
complexity comparable to that of animal
model systems such as Drosophila.
Neurospora offers numerous advantages for
basic research in genetics, molecular, cell, and
evolutionary biology.
Genetic analysis is readily accomplished. Haploid
progeny are easily obtained as random isolates by
manual isolation of ascospores or by ascospore plating.
Tetrad analysis employs ordered or unordered asci to
obtain the four products of individual meiotic events.
Among other pioneering contributions, Neurospora
was used to demonstrate the one-gene-one-enzyme
hypothesis and has provided novel examples of genetic
and epigenetic gene silencing. Study of rhythmic
vegetative sporulation in Neurospora has resulted in
major advances toward understanding the mechanism
of circadian rhythms.
Neurospora crassa
Daphnia
The microcrustacean Daphnia, commonly
referred to as the water flea, has been
subject to intense biological investigations
for over a century.
The development of genomic infrastructure
coupled with a wide range of phenotypic
diversity make Daphnia a versatile model
system to investigate fundamental
mechanisms of inheritance and
development, cellular function,
physiological systems, immunity response,
disease, macromolecular
structure/function relationships, and the
genetic basis of complex phenotypic traits.
Daphnia are an exceptional
model for studying
developmental and disease
processes. Daphnia are
transparent throughout
lifeallowing for studies of tissue-
specific gene expression at any
life stage and direct observation
of parasites and pathogens.
. Dictyostelium discoideum (Slime
Mold)
Dictyostelium discoideum: Model
System in Motion
The ameboid protozoan Dictyostelium discoideum is a
powerful system for genetic and functional analysis of gene
function.
The 34 Mb genome contains many genes that are
homologous to those in higher eukaryotes and are missing
in Saccharomyces cerevisiae.
The organism is uniquely suited for studing cytokinesis, cell
motility, phagocytosis, chemotaxis, signal transduction, and
cell differentiation during development.
Many of these processes, which play important roles in
health and disease, are either absent or are less accessible
in other model organisms.

Though we may not appear to have much in
common with a slime mold, scientists have
discovered that many of its genes are close copies
of our own. Because of its unusual properties and
ability to live alone or in a group, the slime mold
intrigues researchers who study cell division,
movement and various aspects of organ and tissue
development.
Drosophila melanogaster
In 1908, Thomas Hunt Morgan and his
research associates at Columbia University
placed rotting fruit on the window ledge of
their laboratory. Among the menagerie of
creatures that were captured, the fruit fly
emerged as the animal of choice.

There is disks for appendages, eyes, antennae, the
mouthparts, and genitalia.
Disks are composed of fewer than 100 cells in the
embryo but thousands of cells in mature larvae.
The wing imaginal disk has become an important
model system for the control of complex
patterning processes by gradients of secreted
signaling molecules.
Arabidopsis thaliana (the cress in
stress)
A small flowering plant related to cabbage and
mustard, Arabidopsis the most popular
model for studying plant genetics is
appealing to biologists because ithas almost
all of the same genes as other flowering plants
and has relatively little DNA that doesn't
encode for proteins. It also grows quickly,
going from seed to mature plant in only 6
weeks.
ZEAMAYS
Maize (Zea mays)

Zea mays ssp. mays is one of the worlds most
important crop plants, boasting a multibillion dollar
annual revenue. In addition to its agronomic
importance, maize has been a keystone model
organism for basic research for nearly a century. Within
the cereals, which include other plant model species
such as rice (Oryza sativa), sorghum (Sorghum bicolor),
wheat (Triticum spp.),
Advantages
large flowers and inflorescences
important crop plant

Pisum sativum

This model was built with a rule-based computer modelling
system using the information from the crystal structures of
the photosynthetic reaction centres of Rhodopseudomonas
viridis and Rhodobacter sphaeroides. An alignment of the
primary sequences of twenty three D1, nine D2, eight
bacterial L and eight bacterial M subunits predicts strong
similarity between bacterial and higher plant reaction
centres, especially in the transmembrane region where the
cofactors responsible for electron transport are located.
The ancestral relationship between the bacteria and higher
plant sequences allowed both the L and M subunits to be
used as structural templates as they were equally related to
the higher plant polypeptides. The regions with the highest
predicted structural homology were used as a framework
for the construction of the structurally conserved regions.
E. COLI
E.COLI
Gram-negative rod
Facultative anaerobe

Named for Theodor Escherich
German physician (ca. 1885)
Demonstrated that particular strains were responsible
for infant diarrhea and gastroenteritis

Normal flora of the mouth and intestine
Protects the intestinal tract from bacterial infection
Assists in digestion
Produces small amounts of vitamins B
12
and K




Colonizes newborns GI tract within hours after
birth

There are more than 700 different serotypes of E.
coli
Distinguished by different surface proteins and
polysaccharides

Escherichia coli
coli- large intestine, colon
Mammalian large intestine
Escherichia blattae
blattae. L. n. blatta cockroach
Hindgut of cockroach Blatta orientalis

Mus musculus (the mouse from your
warehouse)
The predominance of the
mouse model

The mouse is an excellent model for human development
and disease, although, the life cycle of the mouse is slow by
the standard of the nematode worm and fruit fly.
The mouse provides the link between the basic principles,
discovered in simpler creatures like worms and flies, and
human disease.
The chromosome complement is similar between the mouse
and human (autosomomes and X,Y sex chromosomes)
Extended regions of a given mouse chromosome contain
homologous regions of the corresponding human
chromosomes. (more than 85% of the mouse genes are
correspond to human genes.)



Mice are the premier model organism
for human disease
Saccharomyces cerevisiae (aka, Baker's
yeast)

BAKERS YEAST
Saccharomyces cerevisiae
Features of S. cerevisiae
Have small genomes
Can be grown rapidly in the lab
Central characteristics:
they contain a discrete nucleus with
multiple linear chromosomes packaged
into chromatin;
their cytoplasm includes a full spectrum
of intracellular organelles and
cytoskeletal structures.


The Existence of Haploid and Diploid
Cells Facilitate Genetic Analysis of S.
cerevisiae

S. Cerevisiae can grow in either a haploid state
(one copy of each chromosome) or diploid
state (two copies of each chromosome).
Conversion between the two states is
mediated by mating (haploid to diploid) and
sporulation (diploid to haploid).

Figure 21-10
S. Cerevisiae
exist in
three forms:
two haploid
cell types, a
and , and
the diploid
product of
mating
between
these two.
S. Cerevisiae Has a Small, Well-
Characterized Genome

S. Cerevisiae was the first eukaryotic
organism to have its genome entirely
sequenced. (1996)
1.3X10
6
bp, approximately 6,000 genes.
The availability of the complete genome
sequence has allowed genome-wide
approaches to studies of this organism.

THE NEMATODE WORM,
Caenorhabditis elegans

The nematode worm, C. elegans is used extensively
in the fields of genetics and developmental biology.
The suitability of this organism for research in these
fields was first identified by Sydney Brenner and
through his and other scientists work, the complete
wiring diagram of C. elegans showing the
developmental fate of each cell of the adult organism
is now known. This incredible knowledge makes C.
elegans a real favourite among geneticists and
developmental biologists worldwide.

Suitable characteristics:
Rapid generation time
Hermaphrodite reproduction
producing large numbers of self-
progeny
Sexual reproduction so that genetic
stocks could be constructed
A small number of transparent cells
so that development could be
followed directly




Figure 21-14 b The body plan of the
wrom
Mutations that disrupt the formation
of the vulva form a bag of worms
(the hatched worms devour their
mother The genes are components of
a highly conserved receptor tyrosine
kinase signaling pathway that
controls cell proliferation.
and become trapped inside her skin).
Mutations that inactivate this pathway
eliminate vulva development.
Mutations that activate this pathway cause
overproliferation of the vulva precursor
cells.
The cell Death Pathway Was Discovered
in C. elegans
Cell death is under genetic control (a
mutated ced gene).
Analysis of the ced mutants showed
that the cell commits suicide. In males,
a cell known as the linker cell is killed
by its neighbor.
C
a
e
n
o
r
h
a
b
d
i
t
i
s

e
l
e
g
a
n
s

Zebrafish in
genome research
What is zebrafish?
Danio rerio
Small freshwater fish from South Asia.
4 cm long when fully grown.
Common aquarium fish.
Very easy to look after.

Why use zebrafish?
Small size.
All major organs present
within 5 days post fertilisation.
Short generation time
(3-4 months).
Produces 300-400 eggs every
2 weeks.
Translucent embryos.
Lots of genome resources available.




The zebrafish embryo
~3.5 mm
eye heart
swim
bladder
muscle
block
segments
ear
brain
notochord
Zebrafish and human disease
Zebrafish mutants have been produced to
model human diseases such as:
Alzheimer's disease
congenital heart disease
polycystic kidney disease
Duchenne muscular dystrophy
malignant melanoma
leukaemia

Chicken (Gallus gallus)

The domesticated chicken is a modern descendant of
dinosaurs. It is the premier non-mammalian model
organism with a large international research community
dedicated to developing and sharing information. The
chicken provides a new perspective on vertebrate genome
evolution. Its genome is composed of approximately one
billion base pairs and approximately 20,000-23,000 genes
organized in 39 chromosome pairs. Although it shares a
similar number of genes, the chickens genome is only
about a third the size of mammalian genomes. This
reflects a reduction in interspersed repeat content,
pseudogenes and duplications. There are hundreds of
mutant chicken stocks and inbred lines available for study.
Research using the chicken as a model organism has
resulted in important discoveries in virology, immunology,
oncology, vertebrate development, genetics and evolution.

XENOPUS
Xenopus

Model organisms are often assumed to be representative
of some more inclusive taxon of which the species is a part.
This assumption leads to mistaken generalizations about
the evolutionary and comparative significance of the data
gathered. This paper reviews comparative and evolutionary
studies of Xenopus laevis and its relatives. Phylogenetic
analysis of data from DNA sequences and morphology
indicate that Xenopus is monophyletic and that Silurana is
its sister group. The most basal lineages of Pipidae diverged
prior to the breakup of Gondwana. The bizarre morphology
of Xenopus is in part due to changes in the mode of
metamorphosis. Speciation in Xenopus is unique among
Anura in being associated with various levels of polyploidy
owing to allopolyploidy.
THANK YOU