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biotechnology. course layout. 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.

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slide2

course layout

  • 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
slide6

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
slide7

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
slide8

what is biotechnology?

  • cell and molecular biology
  • microbiology
  • genetics
  • anatomy and physiology
  • biochemistry
  • engineering
  • computer Science
slide9

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
slide10

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
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
biotechnology terms
  • Genome or Genomics
    • DNA
  • Transcriptome
    • RNA or portion of genome transcribed
  • Proteome or Proteomics
    • Proteins
types of biotechnology
types of biotechnology
  • Recombinant, R protein, R DNA
  • Genetically Modified Organism (GMO)
  • Antibody (monoclonal antibody)
  • Transgenic
  • Gene therapy, Immunotherapy
  • Risks and advantages of biotech
biotechnology development
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
biotechnology
  • any technique that uses living organisms or substances to make or modify a product, to improve plants, animals, or microorganisms for specific uses”
slide18

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
slide19

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
slide21

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
slide22

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
slide24

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
slide25

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
slide26

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.
slide27

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
slide28

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
slide29

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)
slide30

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)
slide32

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
slide33

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
slide34

microscopy

van Leeuwenhoek’s microscope (200x)

slide36

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
slide37

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”
slide39

1952 – Alfred Hershey and Martha Chase

  • 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
slide41

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
slide42

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)
slide43

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
slide45

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
slide46

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
slide47

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
slide48

public reaction

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
slide50

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
biotechnology52
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
biotechnology53
biotechnology
  • Using scientific processes to get new organisms or new products from organisms.
biotechnology54
biotechnology
  • Large area
  • Includes many approaches and methods in science and technology
official definition
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
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
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 biotech58
organismic biotech
  • Study and use natural genetic variations
  • Cloning is an example of organismic biotech
cloning
cloning
  • Process of producing a new organism from cells or tissues of existing organism.
  • 1997 cloned sheep –“Dolly” in Edinburgh Scotland
molecular biotech
molecular biotech
  • Changing the genetic make-up of an organism
  • Altering the structure and parts of cells
  • Complex!
molecular biotech61
molecular biotech
  • Uses genetic engineering, molecular mapping and similar processes
genetic engineering
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
transgenic
  • Results of Gen. Eng. Are said to be “transgenic”
  • Genetic material in an organism has been altered
slide66

viruses

  • 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
slide67

bacteria

  • proteins involved in DNA, RNA, protein synthesis, metabolism
  • gene regulation
  • targets for new antibiotics
  • cell cycle
  • signaling
slide68

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
slide69

roundworm

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
slide70

fruit fly

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
slide72

fruit fly

EMBRYO

Body segments

LARVA

Gene expression

ADULT FLY

Head end

Tail end

slide73

zebrafish

  • development of vertebrate body tissue
  • formation and function of brain and nervous system
  • birth defect
  • cancer
slide75

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
slide76

homeotic genes

Fly chromosomes

Mouse chromosomes

  • The order of homeotic genes is the same
  • The gene ordercorresponds toanalogous bodyregions

Fruit fly embryo (10 hours)

Mouse embryo (12 days)

Adult fruit fly

Adult mouse

slide78

plants

  • development and patterning of tissues
  • genetics of cell biology
  • agricultural applications
  • physiology
  • gene regulation
  • immunity
  • infectious disease
slide84

applications

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
slide85

applications

Medicine

  • Development of novel therapeutic molecules for medical treatments
  • Diagnostics
  • Drug delivery systems
  • Tissue engineering of replacement organs
  • Gene therapy
slide86

applications

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
slide87

applications

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
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
slide89

the promise of biotech

protein

DNA

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

slide93

recombination and crossover

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

cloning dna
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 dna96
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.

control
control
  • so where are the computers?
convergence of biotech and information technology
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
control111
control
  • molecular modelling
  • simulation
  • bioinformatics
  • monitoring
  • expert systems
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
information flow
information flow

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

distributed bioprocessing
distributed bioprocessing

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

distributed bioprocessing117
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
synthetic biology120
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 biology121
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
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