Title: Biotechnology
1Biotechnology
- bios life technos tool logos study of
- Biotechnology The Study of Living Tools
21. Timeline
- 4000 BC Egyptians use yeasts for bread and wine
- 1750 BC Sumerians brew beer
- 1500 AD Aztecs make cakes from Spirulina algae
- 1917 Biotechnology term coined
- 1972 Hamilton Smith discovers first restriction
enzyme - 1973 Stanley Cohen made first transgenic organism
with gene from African clawed toad into
bacteria - 1978 Louise Brown, first test tube baby born
- 1981 PCR Invented by Kary Mullis
- Genentech releases (Humulin?) human insulin
- 1984 PCR used by Alec Jeffries in DNA
fingerprinting - EPA approves release of genetically engineered
tobacco - 1990 Pfizer introduces Chymosin (Rennin)
- Michael Crichtons Jurassic Park published
- 1993 FDA approval of Monsantos rBGH/rBST
- 1994 Calgene introduces Flavr-Savr? Tomato
- 1995 O.J. Simpson Trial
- 1996 Sequence completed for S. cervisiae
- 1997 Cloning of Dolly at Roslin Institute
- 1998 First animal genome sequenced C. elegans
3Selective Breeding
- a. Luther Burbank
- disease resistant Burbank potato
- fight blight, etc in Ireland
- b. Norman Borlaug of International Maize
- Wheat Research Center in Mexico
- (received Nobel Prize)
- Crossed short-stemmed wheat with
- Mexicos best wheat
- Govt of India requested seeds,
- as tall wheat plants falling over
- Increased wheat production from 12 million metric
tons in 1965, to 20 million in 1970, 37 million
in 1982 - c. Hybridization
- Dissimilar individuals mate to hope to get
desired traits - Burbank Popular Shasta Daisies
- d. Inbreeding
- Keep desired traits
- Brings recessive traits too (joints in golden
retrievers)
4Increasing Variation
- a. Inducing mutations in bacteria
- Radiation, chemicals, r-strategists
- Can clean up oil spills (bioremediation)
- b. Polyploidy (extra chromosomes)
- Usually fatal in animals
- Bigger, stronger, sexier plants (bananas, citrus
fruits, day lilies)
5DNA Manipulation
- 1. Cutting Separating
- a. Restriction Enzymes
- Proteins from bacteria that cut DNA at specific
points - Cut at palindromes
- Evolved as viral defenses
- Can have blunt or sticky ends
- Can be spliced into DNA cut with same RE
Naming of EcoR1 E from genus of organism where
found (Escheria) co first 2 letters of species
name (coli) R Strain (RY13) 1 Order discovered
6Restriction Enzymes
7(Cutting Separating, Contd)
- b. Gel Electrophoresis
- Migration of charged particles under electric
field - DNA has negatively charged phosphate ends
- (-) electrode repels DNA, () electrode attracts
DNA - 1 agarose gel (natural colloid from seaweed)
- agarose is convoluted like a sieve
- TBE solution is electrolytic solution
- Migration of DNA molecules move through gel at
different rates (bigger slower, smaller
faster) - DNA is stained to see bands (Ethidium Bromide)
- Usually a marker is used (of known fragment sizes)
8Equipment
9Digest Separation
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11(Cutting Separating, Contd)
- c. Restriction Mapping
- Use of various restriction enzymes
- Gel digests show size of fragments
- Patterns of digests can create restriction map
- pUK 1 plasmid
Gel Digest Restriction Map
12- Restriction digest of plasmid DNA from
Escherichia coli - run on a 1 agarose gel and stained with ethidium
bromide - Lane 1 (far left) is a kilobase DNA ladder
- Lane 2 is the uncut plasmid DNA
- Lane 3 is a single digestion of the plasmid with
the EcoRI - Lane 4 is also a single digestion, but with XhoI
- Lane 5 (far right) is a double digestion - both
EcoRI and XhoI
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14DNA Manipulation, Contd
- 2. Identifying Genes - Southern Blot (named after
Ed Southern) - a. DNA cut with REs
- b. Separated by Gel Electrophoresis
- c. DNA blotted to filter paper and probe is
added - d. Only DNA fragments with identified gene bind
to probe
15Southern Blot
16DNA Manipulation, Contd
- 3. Nucleotide Sequencing (fluorescent
dye-terminator cycle sequencing) - a. Unknown Single Stranded DNA put in test tube
- b. DNA polymerase and nucleotide bases (dNTPs)
added - c. Small number of bases with flourescent dye
attached (ddNTPs) - d. Each time dye-labeled nucleotide binds to
fragment, synthesis stops - e. Ultimately yields DNA strands of different
lengths - f. Separated (by gel electrophoresis)
- g. Color of bands tells sequence (read by laser
detector, computer software analyzes)
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19Laser Readout
20ABI Prism
21DNA Manipulation, Contd
- 4. Making Copies (Polymerase Chain Reaction or
PCR) - a. Small amount of double stranded DNA
- b. Heated to separate, then cooled
- c. Add DNA polymerase, primers (short pieces of
artificial DNA), and free nucleotides - Taq polymerase (from Thermophilus aquaticus)
- Isolated from hot springs in Yellowstone
- Can withstand hot temperatures
- d. DNA poly attaches nucleotides to primers
- e. REPEATED many times (5 minute cycles)
- f. Use of a thermal cycler
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24DNA Manipulation, Contd
- 5. Recombinant DNA
- a. Use REs to cut out gene
- b. Cut host DNA with same RE
- c. Need a vector to incorporate into host
- d. Screen for effective transfer
- e. If successful, then results in Transgenic
Organism - f. First done by Steven Howell by inserting
luciferase gene (for glowing) from firefly into
tobacco plant - g. Transgenic Organisms
- 1. Bacteria
- Transformation with plasmid
- Plasmid ring of DNA used to transfer genes
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27- 2. Plants
- Bacterium
- Has small DNA plasmid causes tumors
- Inactivation of tumor gene
- Insertion of foreign DNA
- May uptake DNA if cell walls removed
- Gene gun!
- 3. Animals
- Viral vectors
28- 4. Nuclear Transfer
- Can inject DNA into large egg nuclei
- Enzymes used to repair and recombine DNA in cell
help insert foreign DNA
29- 5. Scientists may also insert marker gene to tell
if procedure worked - ampicillin resistance (bacteria then grown on
nutrient medium with ampicillin) - glowing gene from jellyfish (produces GFP)
To determine what turns on color in wings,
University of Buffalo (NY) biologists inserted a
marker gene from jellyfish into African
butterflies resulting in fluorescent green eyes
30Using Glowing Markers
Fruit Fly Embryo
Glowing Tobacco!!
31- 6. Knockout Mice
- Scientists transfer a defective version of a gene
they want to study into stem cells - The defective gene knocks out the normal gene,
and scientists can examine the effects of the
disabled gene on the resulting young mouse. - Using gene targeting, researchers can transfer
human disease genes into embryonic stem cells to
make mouse models of many human ailments -
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34- 7. Whole Genome Analysis
- Allows analysis of multiple genes in various
conditions - Complexity does not come from the number of
genes, but from the way in which they are used
(Gerald Rubin, HHMI VP) - Gene Chips (Affymetrix)
- ½ square inch glass with short DNA fragments
- 200,000 each
- Microarrayer
- Robot designed by Patrick Brown _at_ Stanford
- Can analyze 6,000 genes in yeast simultaneously
- Make your own for 25,000
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36A Microarrayer Shows How Genes in a Yeast Cell
Respond to Different Types of Stress
http//www.hhmi.org/genesweshare/a110.html
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38US GOV vs. Celera Genomics
39Uses
- 1. Human Genome Project
- a. Attempt to map all of human genome!
- b. Begun in 1999, working draft Feb. 2001,
finished 2003 (3 years ahead of schedule!) - c. Collaboration of 20 labs in 6 countries
- d. Competition with Craig Ventnor, Celera
Genomics - e. Discoveries
- 3.2 billion base pairs
- only 30-40,000 genes
- over 120,000 unique mRNA molecules
- only 1-1.5 of human DNA codes for proteins
- Each cell has 6 ft of DNA 1 inch of exons to be
transcribed - Most of genome is Junk DNA
- Genes not evenly distributed
- Chromosome 19 packed with genes
- Large chromosomes 4 8 have few transcribed genes
40Types of Genetic Maps
41pGLO Plasmid Map
42- pGLO Sequence
- ATCGATGCATAATGTGCCTGTCAAATGGACGAAGCAGGGATTCTGCAAA
CCCTATGCTACTCCGTCAAGCCGTCAATTGTCTGATTCGTTACCAATTAT
GACAACTTGACGGCTACATCATTCACTTTTTCTTCACAACCGGCACGGAA
CTCGCTCGGGCTGGCCCCGGTGCATTTTTTAAATACCCGCGAGAAATAGA
GTTGATCGTCAAAACCAACATTGCGACCGACGGTGGCGATAGGCATCCGG
GTGGTGCTCAAAAGCAGCTTCGCCTGGCTGATACGTTGGTCCTCGCGCCA
GCTTAAGACGCTAATCCCTAACTGCTGGCGGAAAAGATGTGACAGACGCG
ACGGCGACAAGCAAACATGCTGTGCGACGCTGGCGATATCAAAATTGCTG
TCTGCCAGGTGATCGCTGATGTACTGACAAGCCTCGCGTACCCGATTATC
CATCGGTGGATGGAGCGACTCGTTAATCGCTTCCATGCGCCGCAGTAACA
ATTGCTCAAGCAGATTTATCGCCAGCAGCTCCGAATAGCGCCCTTCCCCT
TGCCCGGCGTTAATGATTTGCCCAAACAGGTCGCTGAAATGCGGCTGGTG
CGCTTCATCCGGGCGAAAGAACCCCGTATTGGCAAATATTGACGGCCAGT
TAAGCCATTCATGCCAGTAGGCGCGCGGACGAAAGTAAACCCACTGGTGA
TACCATTCGCGAGCCTCCGGATGACGACCGTAGTGATGAATCTCTCCTGG
CGGGAACAGCAAAATATCACCCGGTCGGCAAACAAATTCTCGTCCCTGAT
TTTTCACCACCCCCTGACCGCGAATGGTGAGATTGAGAATATAACCTTTC
ATTCCCAGCGGTCGGTCGATAAAAAAATCGAGATAACCGTTGGCCTCAAT
CGGCGTTAAACCCGCCACCAGATGGGCATTAAACGAGTATCCCGGCAGCA
GGGGATCATTTTGCGCTTCAGCCATACTTTTCATACTCCCGCCATTCAGA
GAAGAAACCAATTGTCCATATTGCATCAGACATTGCCGTCACTGCGTCTT
TTACTGGCTCTTCTCGCTAACCAAACCGGTAACCCCGCTTATTAAAAGCA
TTCTGTAACAAAGCGGGACCAAAGCCATGACAAAAACGCGTAACAAAAGT
GTCTATAATCACGGCAGAAAAGTCCACATTGATTATTTGCACGGCGTCAC
ACTTTGCTATGCCATAGCATTTTTATCCATAAGATTAGCGGATCCTACCT
GACGCTTTTTATCGCAACTCTCTACTGTTTCTCCATACCCGTTTTTTTGG
GCTAGAAATAATTTTGTTTAACTTTAAGAAGGAGATATACATATGGCTAG
CAAAGGAGAAGAACTTTTCACTGGAGTTGTCCCAATTCTTGTTGAATTAG
ATGGTGATGTTAATGGGCACAAATTTTCTGTCAGTGGAGAGGGTGAAGGT
GATGCTACATACGGAAAGCTTACCCTTAAATTTATTTGCACTACTGGAAA
ACTACCTGTTCCATGGCCAACACTTGTCACTACTTTCTCTTATGGTGTTC
AATGCTTTTCCCGTTATCCGGATCATATGAAACGGCATGACTTTTTCAAG
AGTGCCATGCCCGAAGGTTATGTACAGGAACGCACTATATCTTTCAAAGA
TGACGGGAACTACAAGACGCGTGCTGAAGTCAAGTTTGAAGGTGATACCC
TTGTTAATCGTATCGAGTTAAAAGGTATTGATTTTAAAGAAGATGGAAAC
ATTCTCGGACACAAACTCGAGTACAACTATAACTCACACAATGTATACAT
CACGGCAGACAAACAAAAGAATGGAATCAAAGCTAACTTCAAAATTCGCC
ACAACATTGAAGATGGATCCGTTCAACTAGCAGACCATTATCAACAAAAT
ACTCCAATTGGCGATGGCCCTGTCCTTTTACCAGACAACCATTACCTGTC
GACACAATCTGCCCTTTCGAAAGATCCCAACGAAAAGCGTGACCACATGG
TCCTTCTTGAGTTTGTAACTGCTGCTGGGATTACACATGGCATGGATGAG
CTCTACAAATAATGAATTCGAGCTCGGTACCCGGGGATCCTCTAGAGTCG
ACCTGCAGGCATGCAAGCTTGGCTGTTTTGGCGGATGAGAGAAGATTTTC
AGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATAAAACAGAA
TTTGCCTGGCGGCAGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACT
CAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCCCCCATGCGA
GAGTAGGGAACTGCCAGGCATCAAATAAAACGAAAGGCTCAGTGCAAAGA
CTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCCTGAGTA
GGACAAATCCGCCGGGAGCGGATTTGAACGTTGCGAAGCAACGGCCCGGA
GGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCA
GAAGGCCATCCTGACGGATGGCCTTTTTGCGTTTCTACAAACTCTTTGTT
TATTTTTCTAAATACATTCAAATATGTATCCGCTCATGAGACAATAACCC
TGATAAATGCTTCAATAATATTGAAAAAGGAAGAGTATGAGTATTCAACA
TTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTT
TTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTG
GGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCT
TGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAG
TTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAA
CTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACC
AGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCA
GTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACA
ACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGA
TCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATAC
CAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTG
CGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATT
AATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGG
CCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGT
GGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCG
TATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAA
ATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAACTG
TCAGACCAAGTTTACTCATATATACTTTAGATTGATTTACGCGCCCTGTA
GCGGCGCATTAAGCGCGGCGGGTGTGGTGGTTACGCGCAGCGTGACCGCT
ACACTTGCCAGCGCCCTAGCGCCCGCTCCTTTCGCTTTCTTCCCTTCCTT
TCTCGCCACGTTCGCCGGCTTTCCCCGTCAAGCTCTAAATCGGGGGCTCC
CTTTAGGGTTCCGATTTAGTGCTTTACGGCACCTCGACCCCAAAAAACTT
GATTTGGGTGATGGTTCACGTAGTGGGCCATCGCCCTGATAGACGGTTTT
TCGCCCTTTGACGTTGGAGTCCACGTTCTTTAATAGTGGACTCTTGTTCC
AAACTGGAACAACACTCAACCCTATCTCGGGCTATTCTTTTGATTTATAA
GGGATTTTGCCGATTTCGGCCTATTGGTTAAAAAATGAGCTGATTTAACA
AAAATTTAACGCGAATTTTAACAAAATATTAACGTTTACAATTTAAAAGG
ATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACG
TGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGAT
CTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAA
AAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAAC
TCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTG
TCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCA
CCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAG
TGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGG
ATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGC
TTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCATTG
AGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAA
GCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAAC
GCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCG
TCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCA
GCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCAC
ATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGC
CTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCG
AGTCAGTGAGCGAGGAAGCGGAAGAGCGCCTGATGCGGTATTTTCTCCTT
ACGCATCTGTGCGGTATTTCACACCGCATATGGTGCACTCTCAGTACAAT
CTGCTCTGATGCCGCATAGTTAAGCCAGTATACACTCCGCTATCGCTACG
TGACTGGGTCATGGCTGCGCCCCGACACCCGCCAACACCCGCTGACGCGC
CCTGACGGGCTTGTCTGCTCCCGGCATCCGCTTACAGACAAGCTGTGACC
GTCTCCGGGAGCTGCATGTGTCAGAGGTTTTCACCGTCATCACCGAAACG
CGCGAGGCAGCAAGGAGATGGCGCCCAACAGTCCCCCGGCCACGGGGCCT
GCCACCATACCCACGCCGAAACAAGCGCTCATGAGCCCGAAGTGGCGAGC
CCGATCTTCCCCATCGGTGATGTCGGCGATATAGGCGCCAGCAACCGCAC
CTGTGGCGCCGGTGATGCCGGCCACGATGCGTCCGGCGTAGAGGATCTAA
TTCTCATGTTTGACAGCTTATC
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45- 2. DNA Fingerprinting
- a. History
- Lynda Mann in England
- Raped and Murdered, Nov. 22, 1983
- Local dishwasher questioned pleads guilty to
similar case - Alec Jeffries uses new method of PCR for
identification, exonerates dishwasher of both
crimes - Every man in area fingerprinted by DNA, no
matches - Colin Pitchfork finally caught and tested
positive (friend went in to fake test for him) - Plant Witness
- Murder case in Phoenix, Arizona
- Pager found at crime scene led police to suspect
(said that victim had robbed him) - Palo Verde pods in truck yielded DNA that matched
with trees at crime scene
46- b. Uses
- Identification and exoneration of rapists,
criminals - Paternity cases (Jefferson/Sally Hemmings)
- Identification of body parts
- Supposed heart of Louis XVIII (child king who
died in prison) compared to hair from Marie
Antoinette - ID of bodies in mass graves in Guatemala (from
civil war) - Genetic testing (blood stain on Lincolns jacket
tested for Marfans syndrome) - Migration patterns
- ID tags for children, pets
- ID of endangered/protected species
- Food authentication, such as in wine and caviar
- Authentication of official 2000 Summer Olympic
goods (sections of DNA taken from several unnamed
Australian athletes added to ink used to mark all
items)
47National Geographic March 2006
48- c. Use of RFLPs (restriction fragment length
polymorphisms) - Procedure
- Restriction enzymes cut DNA differently
- Fragments separated with GE
- Probed and exposed to X-ray film
- Screening for Sickle Cell Anemia
- Point mutation of CAG (betaA gene) to CTG (betaS
gene) SNP or single nucleotide polymorphism - Produces valine instead of glutamic acid in
hemoglobin molecule - REs cut DNA differently
- Probe attaches to specific sequence
- Affected large fragment
- Pedigree shows family son with sickle-cell
anemia - Electrophoresis pattern below each child
49RFLP
50- d. DNA Typing
- Small percentage of DNA different from person to
person (less than 1/10th of 1) - Variable regions used for comparison
Gel Lanes MARKERS VICTIM EVIDENCE 1 (semen stain
left on the victim's clothing) EVIDENCE 2
(semen from the vagina of the rape victim)
SUSPECT 1 SUSPECT 2 CONTROL (check to see if
probes are working)
- Results
- Suspect 2 can be clearly ruled out
- Suspect 1 MAY be guilty (probability that 6
alleles match is 1 in 4056) - Suspects NOT picked at random Evidence used in
conjunction with - More probes (alleles) the better 14 chance of
match is 1 in 268 million
51- 3. Transgenic Organisms
- a. Medicine
- 1. Isolate gene for protein needed for medicine
- 2. Inserted into bacteria, will make protein in
normal course of its life cultured in bioreactor
Humulin? (Human Insulin)
52Genetically Engineered Medicines
- Erythropoetin Anemia
- Growth Factors Burns, Ulcers
- Human Growth
- Hormone (HGH) Dwarfism
- Insulin Diabetes
- Interferons Viral Infections, Cancer
- Taxol Ovarian Cancer
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54- 3. Inserted into animals (livestock)
- Dolly cloned in 1997 by Ian Wilmut in Scotland
- Potential to produce protein in milk
- Cloning done once, then livestock reproduce
regularly to pass on gene FARMacy
55- b. Agriculture
- 1. Improving crops
- Crops resistant to biodegradable weedkiller
(glyphosate) - Kills only weeds
- Half of 72 million acres of Soybeans in 2000
- Flavr-Savr? tomato last longer
- Genetically enhanced rice with more Vitamin A
56- Concerns
- Natural resistance to enhancement
- Jumping genes
- Allergies
- 2. Improving livestock growth hormone added to
cow (bGH/bST) - c. Bioremediation - microorganisms engineered to
feed on toxic or hazardous materials - 1. Pseudomonas bacteria engineered to degrade
polyhalogentated compounds (pollutants) - 2. E. coli engineered to clean up mercury
57Bioremediation Cartoon
584. RNA interference (RNAi)
- post-transcriptional gene silencing
- double stranded RNA (dsRNA) causes
sequence-specific degradation of homogolous
mRNAsequences - First found in C. elegans
59The Future?
- Alternatives to antibiotics to protect livestock
against bacterial infections - 2nd Gen of GM crops is expected that could
eliminate of allergens in food, increase
nutritional content, and lower fat and oil levels - 3rd Gen GM crops may have properties like salt
tolerance, drought resistance, drugs and vaccines
within them, and plastic starter chemicals to
create bioplastics - http//www.biotechnologyonline.gov.au/foodag/timel
ine.cfm