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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
book
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
what is biotechnology?
cell and molecular biology microbiology genetics anatomy and physiology biochemistry engineering computer Science
what is biotechnology?
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 shel
ter; Includes domestication Classical biotechnology- built on ancient biotechnology; Ferme
ntation promoted food production, and medicine Modern biotechnology- manipulates genetic information in orga
nism; 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 sede
ntary 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)
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 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
sizes
viruses proteins involved in DNA, RNA, prot
ein 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, prot
ein 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 tis
sues 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
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
tools
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
recombination and crossover
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
cloning DNA
electrophoresis
electrophoresis
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
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
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