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Lecture 1 (2, 3)

Lecture 1 (2, 3). course mechanics Intro to biotechnology and molecular biotechnology Intro to life ….cells chemistry, biochemistry. Molecular Biotechnology. Don Seto, PhD Department of Bioinformatics and Computational Biology/ College of Science George Mason University @Manassas, VA USA

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Lecture 1 (2, 3)

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  1. Lecture 1 (2, 3) • course mechanics • Intro to biotechnology and molecular biotechnology • Intro to life • ….cells • chemistry, biochemistry

  2. Molecular Biotechnology Don Seto, PhD Department of Bioinformatics and Computational Biology/ College of Science George Mason University @Manassas, VA USA dseto@gmu.edu; (703) 993-8403. Occoquan Bldg, Rm 325 Ofc hours: T/Th and by request Website TBA Text: Molecular Biotechnology: Principles and Applications of Recombinant DNA. BR Glick and JJ Pasternak. ASM. 5th edition (2003) Format: 16 meetings 12 x 3hrs: lecture 2hr, discussion and student oral pres 0.5hr/class >three exams @100pts ea >two student oral presentations @12.5pts ea >three homework @25pts ea, question format from exam >total =400pts Grading structure: 85%A, 70%B, 55%C **Strict adherence to the George Mason University Honor Code expected. ***email contact as per GMU e-addresses, unless you tell me otherwise. Purpose: Advanced course in Biotechnology and Molecular Biotechnology, reinforcing molecular and cellular biology concepts in the context of Biotechnology. Develop skills for analysis, understanding and presentation of scientific information.

  3. Syllabus WeekTuesdayNote 1. Aug 28 Chapt. 1: 3-13; 2: 14-22; 3: 23-46; Chapt. 1-2, Lodish, et al. “Mol Cell Biol.” Introduction to the course, text, and course procedures; Brief review of the foundations of molecular biotechnology (bio, chem., biochem.) 2. Sept 04 Chapt. 4: 47-89; Chapt. 3, 5, Lodish, et al. “Mol Cell Biol.” Technology: protein-based, molecular biology-based (recombinant DNA technology) 3. Sept 11 Chapt. 5: 91-120 Molecular technology; microorganisms; genomics 4. Sept 18 Chapt. 6: 121-162 Gene expression in prokaryotes 5. Sept 25 (Lectures 1-4) Exam 1 6. Oct 02 Chapt. 7: 163-189; Chapt. 4: 481-509 Gene expression in eukaryotes;Large-scale production of proteins from recombinants 7. Oct 09 Oct 08 Columbus Day, no Tues Class 8. Oct 16 Chapt. 1: 3-13; Chapt. 9: 227-255 Molecular biotechnology: academia, biotech, pharma, ag; Molecular diagnostics, environmental surveillance 9. Oct 23 Chapt. 8: 190-223 Directed mutagenesis and protein engineering 10. Oct 30 (Lectures 5-7) Exam 2 11. Nov 06 Chapt. 10: 256-308; Chapt. 20: 633-670, 688-693; Chapt. 11: 309-339; Therapeutic agents; vaccines; human molec genetics; gene therapy 12. Nov 13 above (cont.) 13. Nov 20 Nov 21-25 Thanksgiving, no classes 14. Nov 27 Topics in Agriculture* 15. Dec 04 Topics in Agriculture* 16. Dec 11 (Lectures 8-11) Exam 3 *Topics may include Plant growth-promoting bacteria Chapt 14: 416-454 Microbial insecticides Chapt 15: 455-480 Herbicides? Genetic engineering of plants Chapt 17: 513-593 and Chapt 18

  4. Escaping superstition • Humans have always looked towards understanding… • Flammarion Woodcut, 18th cent.? (1888 reference) • “A medieval missionary....found the point where heaven and Earth meet” • heliocentrism • flat earth • gravity • creationism

  5. ….sometimes falling short, or backwards! CPurrington (Swarthmore)

  6. Who should be interested in biology (science) and why • Feb 14, 2006 Alan Leschner. CEO, AAAS • on Earth & Sky Radio program (Deborah Byrd and Joel Block) • “A new tension between science and people?” • Last 4-5 yrs, the relationship between science and society has seemingly deteriorated. • Encroachment or abutment of scientific findings onto issues of either core human moral values or issues of economic values. • For the scientific community, there’s a feeling of greater disengagement between science and society. • Rising tide of fundamentalism that is an overlay to their (the public’s) views of science. • Scientists believe that scientific truths have value. • “If the purpose of science is to tell us about the natural world and the way it actually is, we shouldn’t be saying, tell us about the nature of the world as long as we agree with it and so long as it doesn’t make us uncomfortable.” earthsky.org sciencedaily.com

  7. Policies and attitudes affect you more than you know; ex., Cervical cancer can be caused by a common virus • http://tell-someone.hpv.com/ (Merck; 2006) • Human papillomavirus (HPV) • One of most common STI; >100 different types • CDC estimates 20 million Americans have HPV ‘06 • NIH: 5.5 million new cases reported every year • Cervical cancer- kills 3,500 US women every year • Genital warts • Cancer of the vagina, vulva, penis and anus • ACS (‘06) estimates 2,420 new cases of vaginal cancer in US; 3,740 vulvar cancer; 4,660 anal cancer • Recurrent respiratory papillomatosis (RRP) • (noncancerous tumors in throat) • Abnormal Pap tests

  8. ....not required to follow the recommendations of its panel of outside experts, but... • Intentional eradication of a species -smallpox, ~polio, papilloma virus • Merck • Developed HPV vaccine • Gardasil against four HPVs • Two responsible for cervical cancer • Two responsible for 90% genital warts • Under FDA review • Conservative groups opposed on the grounds that it would encouragepromiscuity. • FDA panel of outside experts met 5/18/06 to recommend to FDA; recommended approval, but • FDA is not required to follow the recommendation, “but usually does.” • June 2006, approved by FDA • SC Harrison, EMBO J ‘02 • ‘Structure and Function of Macromolecular • Assemblies” • Hybrid technique of EM and X-ray crys data • Generates atomic model • Spatial relationships of coat proteins affect • host immunological response • Vaccine development

  9. Life....... • Chemistry/Biology • Cell Biology/Biochemistry/Genetics • Molecular Biology • Genomics • “Bioinformatics”/ “Computational Biology” • Systems Biology > all lead to and contribute to biotechnology, molecular biotechnology • “nothing is really new.....” ……limited by imagination and background • “There is grandeur in this view of life..... most beautiful and most wonderful have been, and are being, evolved.” -Darwin

  10. Basic versus applied research -signal transduction field

  11. What is biotechnology? • Karl Ereky- “biotechnology” • sugar beets [raw materials] • pigs [biotransformation] • pork [downstream processing]

  12. What is molecular biotechnology? • Yeast to beer, bread; bacteria to yogurt • 1917 Karl Ereky- “biotechnology” • to describe pig farming • “products from raw materials with aid of living things • 1940 A. Jost “genetic engineering” • Industrial fermentation • [Ergonomics] • 1943 penicillin produced on industrial scale • New research field ca late ‘70s • Molecular biology and bacterial genetics • Recombinant DNA technology driven • Object is to create a useful product or • a commercial process • Pushed biotechnology out of the edges

  13. What is the outcome of molecular biotechnology? What are products resulting? • Proteins • Pharmaceuticals • Medical protocols • Molecular diagnostics • Agricultural • ‘Better living’/enhancement of life • Bioremediation • Industrial What are concerns?

  14. What is the outcome of molecular biotechnology? What are products resulting? • Proteins • Pharmaceuticals • Medical protocols • Molecular diagnostics • Agricultural • ‘Better living’/enhancement of life • Bioremediation • Industrial What are concerns? • genetically engineered organisms- safe to ecosystem? • genetically engineered organisms- reduce natural diversity? • should humans and ? be genetically engineered? • will diagnostic procedures undermine individual privacy? • will financial resources be diverted to the exclusion of other developments? • will the entire world share in the benefits? • what impact is there on traditional agriculture? • will older but effective medical practices be superceded? • will there be free exchange of ideas?

  15. What is the outcome of molecular biotechnology? What are products resulting? • Proteins • Pharmaceuticals • Medical protocols • Molecular diagnostics • Agricultural • ‘Better living’/enhancement of life • Bioremediation • Industrial What are concerns? • genetically engineered organisms- safe to ecosystem? • genetically engineered organisms- reduce natural diversity? • should humans and ? be genetically engineered? • will diagnostic procedures undermine individual privacy? • will financial resources be diverted to the exclusion of other developments? • will the entire world share in the benefits? • what impact is there on traditional agriculture? • will older but effective medical practices be superceded? • will there be free exchange of ideas? -> Knowledge! -design life

  16. Driven by and commercialization via DNA • 1944 Avery, MacLeod and McCarty • 1953 Watson and Crick • 1970 First Restriction enzyme • 1973 Boyer and Cohen establish recombinant DNA technology • 1976 DNA sequencing • 1978 Genentech produces human insulin in E. coli • 1980 US Supreme Court rules genetically manipulated microbes • can be patented (Chakrabarty) • 1981 Commercial automated sequencer • 1981 mAb-based diagnostic kit • 1988 PCR method • 1990 Recombinant chymosin used for cheese making in US • 1996 First recombinant protein, erythropoietin, exceeds $1B annual sales • 1996 Commercial planting of genetically modified crops • 1997 Nuclear cloning of a mammal- Dolly • 1998 FDA approves first antisense drug • 1999 FDA approves recombinant fusion protein for T-cell lymphoma • 2000 mAbs exceed $2B in annual sales • 2000 ‘Golden rice’ • [2001] Human genome sequenced • 2002 complete human gene microarray commercially available • 1002 FDA approves first nucleic acid system to screen HIV and HCV • 2006 Human genome ‘really’ sequenced -Nanopedia

  17. Genetic Engineering DNA Sequencing Human Genome Project Genetic Fingerprinting H. Influenzae C. elegans Human Genome auto DNA seq 1975 1980 PCR 1990 2000 recomb DNA Chromosome 1 1972 March 2006 DNA Chips Growth of Genome Databases Sped up by DNA analysis technologies • Biology is continuing its accelerate as a data-rich science • New Fields: • Genomics • Bioinformatics • Systems Biology

  18. Application of basic science discovery -> recombinant DNA technology • Nov 1972 Honolulu Meeting on plasmids • Boyer- bacterial enzymes which cut DNA at specific sites • Cohen- collaboration • 1973- series of expts resulting in method to select and replicate specific foreign genes in bacteria • Feb 1975 Asilomar in Pacific Grove, CA; goal to estimate risk of biohazard and formulate guidelines • Dec 1980 First of three patents on gene cloning to Stanford and UC • April 1976 Genentech incorporated (Boyer) • 1977 Rutter et al cloned rat insulin gene • 1981 Founded Chiron • 1986 First recomb vaccine to receive FDA approval; • Chiron-Merck hepB vaccine • [retrospect, first cancer vaccine] • http://bancroft.berkeley.edu/Exhibits/Biotech/25

  19. What does this represent? • 1980 founded as AMgen (Applied molecular genetics) • based on recombinant DNA and molecular biology • 1983 Amgen • 1983 F-K Lin clones human erythropoietin • recombinant as Epogen (epoetin alfa) • 1985 LM Souza clones human granulocyte colony- • stimulating factor G-CSF • recombinant as Neupogen (filgrastim) • 1987 First epo patent; 1989 First neupo patent • 1992 Sales > $1B; 1996 Sales > $2B; 1999 Sales > $3B

  20. Intro to life • ….cells

  21. Cells come in all shapes, sizes, functions…

  22. Prokaryotes vs eukaryotes

  23. But, single cellular does not mean ‘simple’

  24. Multicellular • Systems biology

  25. Jaenisch, R.Nat. Genet. 2001 27: 327-331

  26. Cells [and the world] are divided into two types • …..exception!

  27. Exception- What is a virus? • Mimi virus • LaScola, B......Raoult, D. Science 299: 2033 (03). • 1992 “influenza” outbreak • 1.2Mb • 1260 genes • 50 not seen in viruses previously

  28. To make sense of it, need reductionism tools imagination

  29. What is life? [how is life] [molecules of life]

  30. metabolism centered around ATP

  31. What is life? [sorta...]

  32. “Simple” structures

  33. “Complex” structures

  34. Cell biology • Genetics • Developmental biology • Molecular biology • Genomics • Bioinformatics • New applications…… (molecular biotechnology)

  35. Developmental biology......

  36. Genomics: Structure and consequences of genomes Bioinformatics: Making sense of data, predictions….

  37. Genomics/bioinformatics and Developmental biology Convergence of fly genetics and developmental biology, ca. 1900s with molecular biology, ca. 1977 and with genomics and bioinformatics, ca. 1990s • Developmental patterns and homeostasis genes

  38. Fly mutation “eyeless” ‘The fly and you are not much different.”

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