biotechnology introduction molecular biology biotechnology bioMEMS bioinformatics bio-modeling...

biotechnology

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

course layout

introduction

biotech lab

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


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

computer simulations with virtual reality and other uses help in biotechnology.

computer modeling may be done before it is tested with animals.

computers in biotechnology

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

history

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 d

emand for food Shifts in climate The dwindling of the herds of migratory animals Early Farmers could control their environment when previous peo

ples could not People collected the seeds of wild plants for cultivation and d

omesticated some species of wild animals living around them, performing selective breeding

stone sheep, 2900 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 – earthenwareYeast found in ancient beer urns

Monasteries - major brewers 1680 - Leeuwenhoek observed yeast un

der microscope Between 1866 and 1876 - Pasteur esta

blished 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 produc

ed

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)

published in 1684

van Leeuwenhoek’s drawing of yeast

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 an

d contained S bacteria Unsure of what changed R to S, which he c

alled the “Transforming principle”

transforming principle

1952 – Alfred Hershey and Martha Chase

Used T2 bacteriophage, a virus that infects bacteria Radiolabeled the bacteriophage with S35 (Protein) and P32 (D

NA) Bacterial cells were infected and put in a blender to remove ph

age particles Analysis showed labeled DNA inside the bacteria and was the

genetic material

1952 – Alfred Hershey and Martha Chase

1953 watson and crick

Determined the structure of DNA Rosalind Franklin and Maurice Wil

kins 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 an

d 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)


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

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 b

acterial DNA into an unrelated bacterial species

In 1980 Boyer and Cohen received a patent for the basic methods of DNA cloning and transformation

public reaction

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

public reaction

However, concerns have focused on both applications and ethical implications: Gene therapy experiments have raised the question of eugeni

cs (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

public reaction

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

Using scientific processes to get new organisms or new products from organisms.

biotechnology

Large area Includes many approaches and methods in science

and technology

biotechnology

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

Study and use natural genetic variations Cloning is an example of organismic biotech

organismic biotech

cloning

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!

Uses genetic engineering, molecular mapping and similar processes

molecular biotech

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

transgenic

Results of Gen. Eng. Are said to be “transgenic” Genetic material in an organism has been altered

model organism

viruses

proteins involved in DNA, RNA, protein synthesis

gene regulation cancer and control of cell proliferati

on transport of proteins and organelle

s 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 divisio

n protein secretion and membrane bi

ogenesis function of the cytoskeleton cell differentiation aging gene regulation and chromosome s

tructure

Caenorhabditis elegans development of the body plane cell lineage formation and function of the nervo

us system control of programmed cell death cell proliferation and cancer genes aging behaviour gene regulation and chromosome s

tructure

roundworm

fruit fly

Drosophila melanogaster development of the body plan generation of differentiated cell line

ages formation of the nervous system, h

eart and musculature programmed cell death genetic control of behaviour cancer genes and control of cell pro

liferation control of cell polarisation effect of drugs, alcohol and pestici

des

fruit fly

fruit fly

Body segments

Gene expressionLARVA

ADULT FLY

Head endTail end

EMBRYO

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 s

ystem formation and function of brain an

d nervous system models of cancer and other huma

n diseases gene regulation and inheritance infectious disease

The order of homeotic genes is the same

The gene ordercorresponds toanalogous bodyregions

Mouse chromosomes

Mouse embryo (12 days)

Adult mouse

Fly chromosomes

Fruit fly embryo (10 hours)

Adult fruit fly

homeotic genes

mouse with human ear

plants

development and patterning of tissues

genetics of cell biology agricultural applications physiology gene regulation immunity infectious disease

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

genome specification

production

products of biotech

Agriculture Plant breeding to improve resistance to pests, diseases, droug

ht 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, cit

ric acid, acetone and butanol Synthesis of fine specialty chemicals such as enzymes, amino

acids, alkaloids and antibiotics

applications

Medicine Development of novel therapeutic molecules for medical treat

ments Diagnostics Drug delivery systems Tissue engineering of replacement organs Gene therapy

applications

applications

Food Industry Production of bakers' yeast, cheese, yogurt and fermented foo

ds such as vinegar and soy sauce Brewing and wine making Production of flavors and coloring agents

Veterinary Practice Vaccine production Fertility control Livestock breeding

applications

Environment Biological recovery of heavy metals from mine tailings and othe

r 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

DNA protein

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

the promise of biotech

recombination and crossover

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


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

electrophoresis

If DNA is too large for conventional electrophoresis….electrophoresis

bioprocess control

control

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

control

control

molecular modelling simulation bioinformatics monitoring expert systems

expert systems

Automate the Implicit Understanding Heuristic Reasoning

More than Rule Based Reason over ‘events’

Events -- Qualitative Description Sensors Empirical Models Lab Data Historical Data Human

expert systems

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

synthetic biology

synthetic biology

Creating lifelike characteristics through the use of chemicals

Based on creating structures similar to those found in living organisms

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

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

biotechnology introduction molecular biology biotechnology bioMEMS bioinformatics bio-modeling...

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