Presentation on theme: "Bioinformatics Workshop Summer 2006"— Presentation transcript:
1 Bioinformatics Workshop Summer 2006 Bioinformatics for High School and College Instructors Funded by the National Science Foundation EPSCoR (05-589) Innovations through Computational SciencesJackson State UniversityMississippi E CenterJune 5, 6, 7 & 8, 2007NSF EPSCoR Herron
2 Contributing Scientists Bioinformatics Workshop Summer 2006Contributing ScientistsBarbara Wilson, Ph.D., Biology, JSUSusan Bridges, Ph.D., Computer Science and Engineering, MSUdata mining and knowledge discoveryRobert Hester, Ph.D., Department of Physiology & Biophysics, University Medical Centerin 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 JSUBindu Nanduri, Ph.D., Computational Science, MSUSherry Herron, Ph.D., Biology Education, USMNSF EPSCoR Herron
4 Bioinformatics for High School and College Instructors Bioinformatics Workshop Summer 2006Bioinformatics for High School and College Instructors$ stipend providedLodging and travel reimbursed up to $300.009:00 – 5:00 p.m. daily with continental breakfast and lunch providedMay 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 AgendaDay One A.M.Dr. Barbara WilsonDay One P.M.Dr. Susan BridgesDr. Raphael IsokpehiNSF EPSCoR Herron
6 Presenter: Dr. Barbara Wilson JSU DNA chemistry, transcription, translationDNA isolationRestriction enzyme digestionGel electrophoresisBacteria selection and resistance on antibiotic plates.
7 Day Two Agenda Dr. Herron Alu Insertion Polymorphisms in vitro experiment: hair follicle DNA extraction, PCR, gel electrophoresisin silico experiments: DNALC.org/bioinformatics/PV92DNA manipulatives
9 Bioinformatics Workshop Summer 2006 Cold Spring Harbor’s Dolan DNA Learning Center Website and Instructional Modules Provide Free DNA Sequencing for Educational PurposesNSF EPSCoR Herron
10 Day Three Agenda Dr. Herron HDA Amplification Human Genetic Variation Helicase-Dependent Amplification (HDA) for diagnosis of Sickle-Cell AnemiaHuman Genetic VariationBioinformatics 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 DNAWhat are the genotypes of the father, mother, and their newborn child?
12 helicaseB1B2B3Mineral oilKeep on iceB1B2B3Incubate 1 hr at 65 degreesC1C2C3Restriction enzymeDigest by DdeI(cuts CTNAGfrom Desulfovibrio desulfuricans)
13 ElectrophoreseEnzyme will cut 160 bp wild type amplicon into two 80 bp fragments; will not cut mutated amplicon.Measure against a 100 bp ladderWhat are the genotypes of the father, mother, and their newborn child?
14 Adult Human Hemoglobin: 4 polypeptides 2 α globin: gene on chromosome 162 β globin: gene on chromosome 11Each 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 bpYields a 626 bp mRNA transcriptTranslated into a 147 amino acid polypeptideEpsilon ε – expressed during first trimesterGamma γ – “ during fetal developmentDelta δ - “ in small quantitiesBeta β – most abundant5’--- ε---Gγ--Aγ---β1—δ---β---3’
16 Alpha Globin (HbA) Gene Locus Chromosome 162 ζ genes expressed only first few weeks of development2 α genes expressed thereafter5’----ζ2--ζ1--α1--α2--α1----3’
17 Human hemoglobins Embryonic: 2ζ, 2ε; 2α, 2ε Fetal (HbF): 2α, 2γ Adult (HbA2): 2α, 2δAdult (HbA): 2α, 2βHbF 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… DuplicationsMutationsTranspositionsOver 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 TCTLeu 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 NIHNSF EPSCoR Herron
22 Bioinformatics Workshop Summer 2006 Research-based Instructional Modules for High School and College-age Students Funded by DOENSF EPSCoR Herron
25 Bioinformatics Workshop Summer 2006 ResourcesFREE – Award-winning multimedia DVDs & related materials from Howard Hughes Medical Institute – Holiday Lectures on ScienceVideo: The Biological Revolution: 100 Years of Science at Cold Spring HarborNSF EPSCoR Herron
26 Bioinformatics Workshop Summer 2006 Web ResourcesNSF 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 BirdsIn 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 dogAll 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 AgendaDr. Robert Hester, Mathematical Modeling of Human PhysiologyDr. Bindu Nanduri, Mining Biological Information for function