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Bioinformatics Workshop Summer 2006

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1 Bioinformatics Workshop Summer 2006
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 NSF EPSCoR Herron

2 Contributing Scientists
Bioinformatics Workshop Summer 2006 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 NSF EPSCoR Herron

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
Bioinformatics Workshop Summer 2006 Bioinformatics for High School and College Instructors $ 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) NSF EPSCoR Herron

5 Bioinformatics Workshop Summer 2006
Day One Agenda Day One A.M. Dr. Barbara Wilson Day One P.M. Dr. Susan Bridges Dr. Raphael Isokpehi NSF EPSCoR Herron

6 Presenter: Dr. Barbara Wilson JSU
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 Bioinformatics Workshop Summer 2006
Using Manipulatives Protein Synthesis Manipulatives Kit DNA Manipulatives & Recombinant DNA NSF EPSCoR Herron

9 Bioinformatics Workshop Summer 2006
Cold Spring Harbor’s Dolan DNA Learning Center Website and Instructional Modules Provide Free DNA Sequencing for Educational Purposes NSF EPSCoR Herron

10 Day Three Agenda Dr. Herron HDA Amplification Human Genetic Variation
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 Mineral oil Keep on ice 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 α globin: gene on chromosome 16 2 β globin: 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

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 Bioinformatics Workshop Summer 2006
Research-based Instructional Modules for High School and College-age Students Funded by NIH NSF EPSCoR Herron

22 Bioinformatics Workshop Summer 2006
Research-based Instructional Modules for High School and College-age Students Funded by DOE NSF EPSCoR Herron

23 Bioinformatics Workshop Summer 2006
Contig assemblies, multiple alignments, BLAST searches, taxonomic trees, molecular clocks, and more… NSF EPSCoR Herron

24 Bioinformatics Workshop Summer 2006
NSF EPSCoR Herron

25 Bioinformatics Workshop Summer 2006
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 NSF EPSCoR Herron

26 Bioinformatics Workshop Summer 2006
Web Resources NSF EPSCoR Herron

27 DNA Today The 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: Vodcasts and podcasts: Copy this URL into a podcasting tool:

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


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