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

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

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

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)

Day One Agenda

Day One A.M. Dr. Barbara Wilson

Day One P.M. Dr. Susan Bridges Dr. Raphael Isokpehi

Presenter: Dr. Barbara WilsonJSU

DNA chemistry, transcription, translation

DNA isolation Restriction enzyme digestion Gel electrophoresis Bacteria selection and resistance

on antibiotic plates.

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

Using Manipulatives Protein

Synthesis Manipulatives Kit

DNA Manipulatives &

Recombinant DNA

/wcsstore/

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

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

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?

B1 B2 B3

helicase

C1 C2 C3

B1 B2 B3

Mineral oil

Incubate 1 hr at 65 degrees

Keep on ice

Restriction enzymeDigest by DdeI(cuts CTNAGfrom Desulfovibrio desulfuricans)

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?

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

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 abundant5’--- ε---Gγ--Aγ---β1—δ---β---3’

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’

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.

The Evolution of Hemoglobin is a story of…

Duplications Mutations Transpositions Over billions of years through

plants and all animals (see color page)

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

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.

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

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

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

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

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/

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

Day Four Agenda

Dr. Robert Hester, Mathematical Modeling of Human Physiology

Dr. Bindu Nanduri, Mining Biological Information for function