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Jackson State University Mississippi E Center June 5, 6, 7 & 8, 2007

Bioinformatics for High School and College Instructors Funded by the National Science Foundation EPSCoR (05-589) Innovations through Computational Sciences. Jackson State University Mississippi E Center June 5, 6, 7 & 8, 2007. Contributing Scientists. Barbara Wilson, Ph.D., Biology, JSU

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Jackson State University Mississippi E Center June 5, 6, 7 & 8, 2007

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  1. Bioinformatics for High School and College InstructorsFunded by the National Science Foundation EPSCoR (05-589)Innovations through Computational Sciences Jackson State University Mississippi E Center June 5, 6, 7 & 8, 2007

  2. Contributing Scientists • Barbara Wilson, Ph.D., Biology, JSU • Susan Bridges, Ph.D., Computer Science and Engineering, MSU • data mining and knowledge discovery • Robert Hester, Ph.D., Department of Physiology & Biophysics, University Medical Center • in vivo venular perfusions include arteriolar diameter, red cell velocity, and hemoglobin saturation. In vitro techniques include intracellular measurements of calcium and hydrogen ions of endothelial cells. • Raphael Isokpehi, Ph.D. Biology JSU • Bindu Nanduri, Ph.D., Computational Science, MSU • Sherry Herron, Ph.D., Biology Education, USM

  3. Personnel • Selvi Gopal, Graduate Asst. USM • Bianca Jefferson, Graduate Asst. MSU • Pamela Heard, Grant Specialist, JSU • Dois Bradley, Registrar, JSU • Giselle Thibideaux Munn, MS EPSCoR Education Coordinator, MSU • Pseudo personnel: Dr. Aleta Sullivan, MSTA

  4. Bioinformatics for High School and College Instructors • $400.00 stipend provided • Lodging and travel reimbursed up to $300.00 • 9:00 – 5:00 p.m. daily with continental breakfast and lunch provided • May apply for CEUs or graduate credit in biology. Attending the workshop and giving a presentation to your co-workers or at a conference would give you 3 hours of credit (BSC 692)

  5. Day One Agenda • Day One A.M. • Dr. Barbara Wilson • Day One P.M. • Dr. Susan Bridges • Dr. Raphael Isokpehi

  6. Presenter: Dr. Barbara WilsonJSU • DNA chemistry, transcription, translation • DNA isolation • Restriction enzyme digestion • Gel electrophoresis • Bacteria selection and resistance on antibiotic plates.

  7. Day Two Agenda Dr. Herron • Alu Insertion Polymorphisms • in vitro experiment: hair follicle DNA extraction, PCR, gel electrophoresis • in silico experiments: DNALC.org/bioinformatics/PV92 • DNA manipulatives

  8. Protein Synthesis Manipulatives Kit DNA Manipulatives & Recombinant DNA Using Manipulatives

  9. Cold Spring Harbor’s Dolan DNA Learning Center Website and Instructional Modules Provide Free DNA Sequencing for Educational Purposes

  10. Day Three Agenda Dr. Herron • HDA Amplification • Helicase-Dependent Amplification (HDA) for diagnosis of Sickle-Cell Anemia • Human Genetic Variation • Bioinformatics and the Human Genome Project

  11. Helicase-Dependent Amplification (HDA) for diagnosis of Sickle-Cell Anemia • Isothermic – no PCR required! • Helicase, primer, restriction enzyme, and DNA polymerase provide the mechanics to amplify target DNA • What are the genotypes of the father, mother, and their newborn child?

  12. helicase B1 B2 B3 Keep on ice Mineral oil B1 B2 B3 Incubate 1 hr at 65 degrees C1 C2 C3 Restriction enzyme Digest by DdeI (cuts CTNAG from Desulfovibrio desulfuricans)

  13. Electrophorese • Enzyme will cut 160 bp wild type amplicon into two 80 bp fragments; will not cut mutated amplicon. • Measure against a 100 bp ladder • What are the genotypes of the father, mother, and their newborn child?

  14. Adult Human Hemoglobin: 4 polypeptides • 2 αglobin: gene on chromosome 16 • 2 βglobin: gene on chromosome 11 • Each globin consists of 8 alpha helices folded together into an identical shape and containing an identical heme group

  15. Beta Globin (HbB) Locus: multiple genes arranged sequentially from 5’ to 3’ • Locus: 11p 15.5 (near tip) • 3 exons scattered over 1600 bp • Yields a 626 bp mRNA transcript • Translated into a 147 amino acid polypeptide • Epsilon ε – expressed during first trimester • Gamma γ – “ during fetal development • Delta δ - “ in small quantities • Beta β– most abundant 5’--- ε---Gγ--Aγ---β1—δ---β---3’

  16. Alpha Globin (HbA) Gene Locus • Chromosome 16 • 2 ζ genes expressed only first few weeks of development • 2 α genes expressed thereafter 5’----ζ2--ζ1--α1--α2--α1----3’

  17. Human hemoglobins • Embryonic: 2ζ, 2ε; 2α, 2ε • Fetal (HbF): 2α, 2γ • Adult (HbA2): 2α, 2δ • Adult (HbA): 2α, 2β HbF has a much higher affinity for oxygen than HbA. A significant amount of HbF persists for ~8 months after birth.

  18. The Evolution of Hemoglobin is a story of… • Duplications • Mutations • Transpositions • Over billions of years through plants and all animals (see color page)

  19. HbA HbS • CTG ACT CCT GAG GAG AAG TCT • Leu Thr Pro Glu Glu Lys Ser • 3 6 9 • CTG ACT CCT GTG GAG AAG TCT • Leu Thr Pro Val Glu Lys Ser • 3 6 9

  20. HbS: different charge • Glutamic acid is acidic • Valine is neutral • Therefore, HbS has 2 fewer negative charges that HbA – which changes the pH, pI, tertiary structure, quaternary structure, and oxygen affinity (function) of hemoglobin. Polymerizes when deoxygenated.

  21. Research-based Instructional Modules for High School and College-age Students Funded by NIH

  22. Research-based Instructional Modules for High School and College-age Students Funded by DOE

  23. Contig assemblies, multiple alignments, BLAST searches, taxonomic trees, molecular clocks, and more…

  24. Resources • FREE – Award-winning multimedia DVDs & related materials from Howard Hughes Medical Institute – Holiday Lectures on Science • Video: The Biological Revolution: 100 Years of Science at Cold Spring Harbor

  25. Web Resources • http://nsdl.org/ • http://www.scinfo.org/ • http://www.mrw.interscience.wiley.com/cp/cpbi/cpbi_contents_fs.html • http://www.dnalc.org/home.html • http://www.ncbi.nlm.nih.gov/

  26. DNA TodayThe Dolan DNA Learning Center • Join commentators Dave Micklos and Jan Witkowski for a series of topical video podcasts . Dave is executive director of the Dolan DNA Learning Center, the world.s first science center devoted entirely to genetics education. Jan is executive director of Cold Spring Harbor Laboratory's Banbury Center. • Episode 1: Dino Protein is for the Birds • In echoes of Jurassic Park, organic material has for the first time been recovered from a dinosaur fossil. Protein fragments from a 68 million year old T. rex bone most closely match samples from a chicken, providing further evidence of the evolutionary relationship between dinosaurs and birds. • Episode 2: BIG DOG, little dog • All dogs are members of the same species, and each characteristic breed is a result of selective breeding by humans. Now, scientists have found that the extreme differences in dog size - between say a Chihuahua and Great Dane - are largely determined by a single change in a single gene. • DNA Today videos can be found at the Gene Almanac Internet site: www.dnalc.org • Vodcasts and podcasts: Copy this URL into a podcasting tool: http://www.dnalc.org/ddnalc/dna_today/dna_today.xml

  27. Day Four Agenda • Dr. Robert Hester, Mathematical Modeling of Human Physiology • Dr. Bindu Nanduri, Mining Biological Information for function

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