biotechnology

c o u r s e l a y o u t
introduction
molecular biology
biotechnology
bioMEMS
bioinformatics
bio-modeling
cells and e-cells
transcription and regulation
cell communication
neural networks
dna computing
fractals and patterns
the birds and the bees .. and ants
book
introduction
biotech lab
what is biotechnology?

using scientific methods with organisms to produce new

products or new forms of organisms
any technique that uses living organisms or substances
from those organisms to make or modify a product, to
improve plants or animals, or to develop micro-
organisms for specific uses
what is biotechnology?

manipulation of genes is called genetic engineering or

recombinant DNA technology
genetic engineering involves taking one or more genes
from a location in one organism and either
Transferring them to another organism
Putting them back into the original organism in different
combinations
what is biotechnology?

cell and molecular biology

microbiology
genetics
anatomy and physiology
biochemistry
engineering
computer Science
applications

virus-resistant crop plants and livestock

diagnostics for detecting genetic diseases and acquired
diseases
therapies that use genes to cure diseases
recombinant vaccines to prevent disease
biotechnology can also aid the environment
computers in biotechnology

computer simulations with virtual reality and other uses

help in biotechnology.
computer modeling may be done before it is tested with
animals.
goals of biotechnology

To understand more about the processes of inheritance

and gene expression
To provide better understanding & treatment of various
diseases, particularly genetic disorders
To generate economic benefits, including improved
plants and animals for agriculture and efficient
production of valuable biological molecules
Example: Vitamin A fortified engineered rice
biotechnology terms

Genome or Genomics
DNA
Transcriptome
RNA or portion of genome transcribed
Proteome or Proteomics
Proteins
types of biotechnology

Recombinant, R protein, R DNA

Genetically Modified Organism (GMO)
Antibody (monoclonal antibody)
Transgenic
Gene therapy, Immunotherapy
Risks and advantages of biotech
h i s t o r y
biotechnology development

Ancient biotechnology- early history as related to food

and shelter; Includes domestication
Classical biotechnology- built on ancient biotechnology;
Fermentation promoted food production, and medicine
Modern biotechnology- manipulates genetic information
in organism; Genetic engineering
biotechnology

any technique that uses living organisms or substances to

make or modify a product, to improve plants, animals, or
microorganisms for specific uses
evolving corn
ancient biotech

History of Domestication and Agriculture

Paleolithic peoples began to settle and develop
agrarian societies about 10,000 years ago
Early farmers in the Near East cultivated wheat, barley,
and possibly rye
7,000 years ago, pastoralists roamed the Sahara region
of Africa with sheep, goats, cattle, and also hunted and
used grinding stones in food preparation
Early farmers arrived in Egypt 6,000 years ago with cattle,
sheep, goats, and crops such as barley, emmer, and
chick-pea
Archaeologists have found ancient farming sites in the
Americas, the Far East, and Europe
ancient biotech

Not sure why peoples began to settle down and

become sedentary
May be in response to population increases and the
increasing demand for food
Shifts in climate
The dwindling of the herds of migratory animals
Early Farmers could control their environment when
previous peoples could not
People collected the seeds of wild plants for cultivation
and domesticated some species of wild animals living
around them, performing selective breeding
s t one s heep , 2 9 0 0 BC
ancient plant germplasm

The ancient Egyptians saved seeds and tubers, thus

saved genetic stocks for future seasons

Nikolai Vavilov, a plant geneticist, came up with first real

plan for crop genetic resource management

National Seed Storage Laboratory in Fort Collins,

Colorado is a center for germplasm storage in the U.S.

Agricultural expansion and the use of herbicides has put

germplasm in danger and led to a global effort to
salvage germplasm for gene banks
fermented food, 1500 BC

Yeast - fruit juice wine

Brewing beer - CO2
Baking bread, alcohol
Egyptians used yeast in 1500 B.C.
1915-1920 Bakers Yeast
fermented food, 1500 BC
fermentation

Fermentation: microbial process in which enzymatically

controlled transformations of organic compounds occur
Fermentation has been practiced for years and has
resulted in foods such as bread, wine, and beer
9000 B.C. - Drawing of cow being milked Yogurt - 4000
B.C. Chinese Cheese curd from milk - 5000-9000 years
ago
Fermented dough was discovered by accident when
dough was not baked immediately
fermentation

Modern cheese manufacturing involves:

inoculating milk with lactic acid
bacteria
adding enzymes such as rennet to
curdle casein
heating
separating curd from whey
draining the whey
salting
pressing the curd
ripening
fermented beverages

Beer making began as early as

6000-5000 B.C.
Egypt ~5000 B.C made wine from
grapes
Barley malt earthenware
Yeast found in ancient beer urns
Monasteries - major brewers
1680 - Leeuwenhoek observed
yeast under microscope
Between 1866 and 1876 - Pasteur
established that yeast and other
microbes were responsible for
fermentation.
classical biotech
Describes the development that fermentation has taken place
from ancient times to the present

Top fermentation - developed first, yeast rise to top

1833 - Bottom fermentation - yeast remain on bottom

1886 Brewing equipment made by E.C. Hansen and still used

today

World War I fermentation of organic solvents for explosives

(glycerol)

World War II bioreactor or fermenter:

Antibiotics
Cholesterol Steroids
Amino acids
classical biotech

large quantities of vinegar

are produced by
Acetobacter on a substrate
of wood chips
fermented fruit juice is
introduced at the top of the
column and the column is
oxygenated from the
bottom
classical biotech advances

In the 1950s, cholesterol was converted to cortisol and

sex hormones by reactions such as microbial
hydroxylation (addition of -OH group)

By the mid-1950s, amino acids and other primary

metabolites (needed for cell growth) were produced, as
well as enzymes and vitamins

By the 1960s, microbes were being used as sources of

protein and other molecules called secondary
metabolites (not needed for cell growth)
classical biotech advances

Today many things are produced:

Pharmaceutical compounds such as antibiotics
Amino Acids
Many chemicals, hormones, and pigments
Enzymes with a large variety of uses
Biomass for commercial and animal consumption (such as
single-cell protein)
amino acids and their uses
old biotech meets new

Fermentation and genetic engineering have been used

in food production since the 1980s
Genetically engineered organisms are cultured in
fermenters and are modified to produce large quantities
of desirable enzymes, which are extracted and purified
Enzymes are used in the production of milk, cheese, beer,
wine, candy, vitamins, and mineral supplements
Genetic engineering has been used to increase the
amount and purity of enzymes, to improved an enzymes
function, and to provide a more cost-efficient method to
produce enzymes.
Chymosin, used in cheese production, was one of the first
produced
foundations of modern biotech

1590 - Zacharias Janssen - First two lens

microscope (30x)

1665 - Robert Hooke - Cork Cellulae

(Small Chambers)

Anthony van Leeuwenhoek (200x)

1676 - animalcules (in pond water)
1684 - protozoa/fungi
microscopy

van Leeuwenhoeks microscope (200x)

van Leeuwenhoeks drawing of yeast

published in 1684
foundations of modern biotechnology

1838, Matthias Schleiden, determined that all plant tissue

was composed of cells and that each plant arose from a
single cell
1839, Theodor Schwann, came to a similar determination
as Schleiden, for animals
1858, Rudolf Virchow, concluded that all cells arise from
cells and the cell is the basic unit of life
Before cell theory the main belief was vitalism: whole
organism, not individual parts, posses life
By the early 1880s, microscopes, tissue preservation
technology, and stains allowed scientists to better
understand cell structure and function
transforming principle

1928 - Fred Griffith performed

experiments using Streptococcus
pneumonia
Two strains:
Smooth (S) - Virulent (gel coat)
Rough (R) - Less Virulent
Injected R and heat-killed S - mice
died and contained S bacteria
Unsure of what changed R to S, which
he called the Transforming principle
transforming principle
1 9 5 2 A lf r e d H e r s h e y a n d Ma rt ha C ha s e

Used T2 bacteriophage, a virus that infects bacteria

Radiolabeled the bacteriophage with S35 (Protein) and
P32 (DNA)
Bacterial cells were infected and put in a blender to
remove phage particles
Analysis showed labeled DNA inside the bacteria and
was the genetic material
1 9 5 2 A lf r e d H e r s h e y a n d Ma rt ha C ha s e
1953 watson and crick

Determined the structure of

DNA
Rosalind Franklin and Maurice
Wilkins provided X-ray
diffraction data
Erwin Chargaff determined
the ratios of nitrogen bases in
DNA
DNA replication model - 1953
DNA bases made up of purine
and pyrimidine
Nobel Prize - 1962
first recombinant DNA experiments

1971 scientists manipulated

DNA and placed them into
bacteria

1972 scientists joined two DNA

molecules from different
sources using the endonuclease
EcoRI (to cut) and DNA ligase
(to reseal)
first recombinant DNA experiments

Herbert Boyer later went to Cold Spring Harbor

Laboratories and discovered a new technique
called gel electrophoresis to separate DNA
fragments
A current is applied so that the negative
charged DNA molecules migrate towards
the positive electrode and is separated by
fragment size
first recombinant DNA experiments
biotech revolution: cracking the code

1961, Nirenberg and Mattei made the

first attempt to break the genetic code,
using synthetic messenger RNA (mRNA)
Nirenberg and Leder developed a
binding assay that allowed them to
determine which triplet codons
specified which amino acids by using
RNA sequences of specific codons
first DNA cloning

Boyer, Helling Cohen, and Chang

joined DNA fragments in a vector, and
transformed an E. coli cell

Cohen and Chang found they could

place bacterial DNA into an unrelated
bacterial species

In 1980 Boyer and Cohen received a

patent for the basic methods of DNA
cloning and transformation
p u b l i c r e a c t i o n

Recombinant DNA technology sparked debates more

than 30 years ago among scientists, ethicists, the media,
lawyers, and others
In the 1980s it was concluded that the technology had
not caused any disasters and does not pose a threat to
human health or the environment
p u b l i c r e a c t i o n

However, concerns have focused on both applications and

ethical implications:
Gene therapy experiments have raised the question of
eugenics (artificial human selection) as well as testing
for diseases currently without a cure
Animal clones have been developed, and fears have
been expressed that this may lead to human cloning
In agriculture, there is concern about gene
containment and the creation of super weeds
(herbicide and/or pesticide resistant weeds)
Today, fears have focused on genetically engineered
foods in the marketplace and has resulted in the rapid
growth of the organic food industry
p u b l i c r e a c t i o n
progress continues

Many genetically modified disease, pest, and herbicide-

resistant plants are awaiting approval for
commercialization
Genes involved in disease are being identified
New medical treatments are being developed
Molecular pharming, where plants are being used to
produce pharmaceuticals (biopharmaceuticals), is
being developed
biotechnology
biotechnology

Biotechnology helps to meet our basic needs.

Food, clothing, shelter, health and safety

Improvements by using science

Science helps in production plants, animals and other
organisms

Also used in maintaining a good environment that

promotes our well being
biotechnology

Using scientific processes to get new organisms or new

products from organisms.
biotechnology

Large area
Includes many approaches and methods in science and
technology
official definition

Any technique that uses living organisms or substances

from those organisms to make or modify a product, to
improve plants or animals.
Or to develop microorganisms for specific uses.
agricultural view

All of the applied science based operations in producing

food, fiber, shelter, and related products

Milk production
New horticultural and ornamental plants
Wildlife, aquaculture, natural resources and
environmental management
organismic biotech

Working with complete, intact organisms or their cells

Organisms are not genetically changed with artificial
means

Help the organism live better or be more productive

Goal improve organisms and the conditions in which
they grow
organismic biotech

Study and use natural genetic variations

Cloning is an example of organismic biotech
c l o n i n g

Process of producing a new organism from cells or tissues

of existing organism.
1997 cloned sheep Dolly in Edinburgh Scotland
molecular biotech

Changing the genetic make-up of an organism

Altering the structure and parts of cells
Complex!
molecular biotech

Uses genetic engineering, molecular mapping and

similar processes
genetic engineering

Changing the genetic information in a cell

Specific trait of one organism may be isolated,cut, and
moved into the cell of another organism
t r a n s g e n i c

Results of Gen. Eng. Are said to be transgenic

Genetic material in an organism has been altered
m o d e l o r g a n i s m
sizes
v i r u s e s

proteins involved in DNA, RNA,

protein synthesis
gene regulation
cancer and control of cell
proliferation
transport of proteins and
organelles inside cells
infection and immunity
possible gene therapy
approaches
bacteria

proteins involved in DNA, RNA,

protein synthesis, metabolism
gene regulation
targets for new antibiotics
cell cycle
signaling
yeast

Saccharomyces cerevisiae
control of cell cycle and cell
division
protein secretion and
membrane biogenesis
function of the cytoskeleton
cell differentiation
aging
gene regulation and
chromosome structure
r o u n d w o r m

Caenorhabditis elegans
development of the body
plane
cell lineage
formation and function of the
nervous system
control of programmed cell
death
cell proliferation and cancer
genes
aging
behaviour
gene regulation and
chromosome structure
f r u i t f l y

Drosophila melanogaster
development of the body plan
generation of differentiated cell
lineages
formation of the nervous system,
heart and musculature
programmed cell death
genetic control of behaviour
cancer genes and control of
cell proliferation
control of cell polarisation
effect of drugs, alcohol and
pesticides
f r u i t f l y
f r u i t f l y
EMBRYO
Body segments

LARVA Gene expression

ADULT FLY

Head end
Tail end
zebrafish

development of vertebrate
body tissue
formation and function of
brain and nervous system
birth defect
cancer
zebrafish
mice

development of body tissues

function of mammalian
immune system
formation and function of
brain and nervous system
models of cancer and other
human diseases
gene regulation and
inheritance
infectious disease
homeotic genes
Fly chromosomes Mouse chromosomes
The order of
homeotic genes
is the same
The gene order
corresponds to
analogous body
regions

Fruit fly embryo (10 hours) Mouse embryo (12 days)

Adult fruit fly Adult mouse

mouse with human ear
p l a n t s

development and patterning

of tissues
genetics of cell biology
agricultural applications
physiology
gene regulation
immunity
infectious disease
genome specification
Organism Type Chromo Gene # (bp) Genome Size
some #

Hepatitus B virus 1 4 3215

E. coli bacterium 1 4,394 4,639,221

S.cerevisiae yeast 16 6,183 12,000,000

D. melanogaster fruit fly 4 14,000 140,000,000

C. elegans nematode 6 19,000 90,000,000

A. thaliana plant 5 25,000 125,000,000

M.musculus mouse 20 35,000 3,000,000,000

H. sapiens human 23 35,000 3,000,000,000

genome specification
p r o d u c t i o n
products of biotech
products of biotech
a p p l i c a t i o n s

Agriculture
Plant breeding to improve resistance to pests, diseases,
drought and salt conditions
Mass propagation of plant clones Bioinsecticide
development modification of plants to improve
nutritional and processing characteristics

Chemical Industry
Production of bulk chemicals and solvents such as
ethanol, citric acid, acetone and butanol
Synthesis of fine specialty chemicals such as enzymes,
amino acids, alkaloids and antibiotics
a p p l i c a t i o n s

Medicine
Development of novel therapeutic molecules for
medical treatments
Diagnostics
Drug delivery systems
Tissue engineering of replacement organs
Gene therapy
a p p l i c a t i o n s

Food Industry
Production of bakers' yeast, cheese, yogurt and
fermented foods such as vinegar and soy sauce
Brewing and wine making
Production of flavors and coloring agents

Veterinary Practice
Vaccine production
Fertility control
Livestock breeding
a p p l i c a t i o n s

Environment
Biological recovery of heavy metals from mine tailings
and other industrial sources
Bioremediation of soil and water polluted with toxic
chemicals
Sewage and other organic waste treatment
future of medicine

smart drugs for cancer and autoimmune diseases

(arthritis, psoriasis, diabetes)
gene-based diagnostics and therapies
pharmaco-genomics and personalised medicine
stem cells and regenerative medicine
health and longevity
the promise of biotech

DNA protein

drugs are so complex they can only be synthesized in a living system

tools
recombination and crossover
recombination and crossover
recombination and crossover
If no exchange of genes (i.e.
phenotypic marker) occurs,
recombination event can not
be detected
recombination and crossover
cloning DNA

Insert the DNA into plasmids

Gene of interest is inserted into small DNA molecules known as
plasmids, which are self-replicating, extrachromosomal genetic
elements originally isolated from the bacterium, Escherichia coli. The
circular plasmid DNA is opened using the same endonuclease that
was used to cleave the genomic DNA.

Join the ends of DNA with the enzyme, DNA ligase.

The inserted DNA is joined to the plasmid DNA using another enzyme,
DNA ligase, to give a recombinant DNA molecule. The new plasmid
vector contains the original genetic information for replication of the
plasmid in a host cell plus the inserted DNA.
cloning DNA

Introduce the new vector into host

The new vector is inserted back into a host where many copies of
the genetic sequence are made as the cell grows and divide with
the replicating vector inside.

Isolate the newly-synthesized DNA or the protein coded for by the

inserted gene.
The host may even transcribe and translate the gene and obligingly
produce product of the inserted gene. Alternatively, many copies of
the DNA gene itself may be isolated for sequencing the nucleic acid
or for other biochemical studies.
cloning DNA
cloning DNA
cloning DNA
cloning DNA
electrophoresis
electrophoresis
electrophoresis
If DNA is too large for conventional electrophoresis.
electrophoresis
b i o p r o c e s s c o n t r o l
c o n t r o l

so where are the computers?

convergence of biotech and information technology

automated sequencing (Celera)

gene chips and microarrays
high throughput screening
data visualisation and data mining
web-based clinical trials and FDA submission
in silico simulations of biological systems
c o n t r o l
c o n t r o l
c o n t r o l
c o n t r o l

molecular modelling
simulation
bioinformatics
monitoring
expert systems
e x p e r t s y s t e m s

Automate the Implicit Understanding

Heuristic Reasoning

More than Rule Based

Reason over events

Events -- Qualitative Description

Sensors
Empirical Models
Lab Data
Historical Data
Human
e x p e r t s y s t e m s
e x p e r t s y s t e m s
 information flow

Christian Cimander and Carl-Fredrik Mandenius. Adaptive bioprocess control from multivariate process trajectories
 distributed bioprocessing

Christian Cimander and Carl-Fredrik Mandenius. Adaptive bioprocess control from multivariate process trajectories
 distributed bioprocessing

http://www.amershambiosciences.com/APTRIX/upp01077.nsf/Content/Products?OpenDocument&parentid=5179&
moduleid=6016&zone=Labsep
sy n t h e ti c bi o l o gy
synthetic biology

Creating lifelike characteristics through the use of

chemicals
Based on creating structures similar to those found in
living organisms
synthetic biology

Is important because it brings science closer to creating

life in the lab
Cells and tissues may be developed to treat human
injury and disease
synthetic biology

Synthetic biology hopes to bring engineering practices

common in other engineering disciplines to the field of
molecular genetics and thus create a novel nanoscale
computational substrate
Advantages
Tightly integrated biological inputs and outputs
Easily grow thousands of computational engines
Natural use of directed evolution

Disadvantages
Speed is on the order of millihertz (tens of seconds)
Modest computational capability of each engine

at MIT, Knights group

 synthetic biology applications

Autonomous biochemical sensors

Biomaterial manufacturing
Programmed therapeutics
Smart agriculture
Engineered experimental systems for biologists

M. Elowitz and S. Leibler, A synthetic oscillatory network of transcriptional regulators. Nature, January 2000
biotechnology?
the end