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 tone 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

f o u n d a ti o n s o f m o d e r n b i o t e c h
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 He r s h e y a n d Ma rt ha Cha 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 He r s h e y a n d Ma rt ha Cha 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 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
EMBRYO

f l y
Body segments

LARVA ADULT FLY Head end

Gene expression

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
The order of homeotic genes is the same The gene order corresponds to analogous body regions

genes
Fly chromosomes Mouse chromosomes

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
Organism

specification
Type Chromo Gene # (bp) some # Genome Size

Hepatitus B E. coli S.cerevisiae D. melanogaster C. elegans A. thaliana M.musculus H. sapiens

virus bacterium yeast fruit fly nematode plant mouse human

1 1 16 4 6 5 20 23

4 4,394 6,183 14,000 19,000 25,000 35,000 35,000

3215 4,639,221 12,000,000 140,000,000 90,000,000 125,000,000 3,000,000,000 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, 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