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 microorganisms 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 Baker’s 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 1950’s, cholesterol was converted to cortisol and
sex hormones by reactions such as microbial
hydroxylation (addition of -OH group)
 By the mid-1950’s, amino acids and other primary
metabolites (needed for cell growth) were produced, as
well as enzymes and vitamins
 By the 1960’s, 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 enzyme’s
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 Leeuwenhoek’s microscope (200x)
van Leeuwenhoek’s 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 1980’s 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 herbicideresistant
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
environmental management
and
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)
Adult fruit fly
Mouse embryo (12 days)
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)
some #
Genome Size
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
medical treatments
 Diagnostics
 Drug delivery systems
 Tissue engineering of replacement organs
 Gene therapy
for
a p p l i c a t i o n s
Food Industry
 Production of bakers' yeast, cheese, yogurt
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
and
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, Knight’s 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