|CCL 06.07.02 Fundamentals of Genomics and Proteomics, U Puerto Rico, Med Sci Campus|
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To: chemistry-request at ccl.net
Date: Wed Feb 1 10:14:16 2006
Subject: 06.07.02 Fundamentals of Genomics and Proteomics, U Puerto Rico, Med Sci Campus
Fundamentals of Genomics and Proteomics University of Puerto Rico Medical Sciences Campus in University of Puerto Rico July 2-7, 2006 Emie Breyer (Georgia State University) http://chemistry.gsu.edu/CWCS/genetics.html Tentative Workshop Outline The "Evolutionary Genetics Techniques and Statistical Analyses" portion of the workshop introduces participants to a variety of topics in biotechnology and molecular genetics, with a particular emphasis on modern techniques for DNA sequencing, genotyping and the statistical analyses for the evolution of populations and species. The "Protein Structure and Function" portion of the workshop emphasizes molecular visualization of protein structures and an introduction to topics from current research in protein structure/function relationships and protein engineering. In addition to the lectures and lab exercises presented by the workshop instructors, there will be an invited lecturer, Dr. Rebecca Cann of University of Hawaii-Manoa. Day 1: Lecture - "Introduction to Molecular Biology and Cloning". The workshop begins with an overview of the central dogma of Biology: transcription and translation of genes. Discussion will include DNA replication, types and implications of mutations, in vitro cloning, and basics of DNA extraction, PCR, DNA genotyping and sequencing. Day 2: Lecture - "Phylogenetic Analysis and DNA genotyping and sequencing". Topics include: DNA analysis to examine evolution of populations and species, type of data used for phylogenetic analyses including RFLP, AFLP, RAPD, microsatellite and DNA sequencing techniques, introduction to phylogenetic statistical analyses. Day 3: Lecture - "Bioinformatics: Data mining and analysis". Topics include: RFLP mapping, genotyping using AFLP, RAPD or microsatellite, DNA sequence alignment, and analysis of DNA variation for population and species comparisons. Day 4: Lecture - "Protein Structure". The structure-function relationships of proteins will be explored, using the galactose/glucose binding protein as a primary example. Topics include: The hierarchy of protein structure (primary, secondary and super-secondary, tertiary, quaternary) and the relationship of the primary amino acid sequence to protein structure and function ("intrinsic" secondary structure propensities of amino acids, hydrophobic periodicity, non-covalent interactions between amino acids and between proteins and bound ligands). Computer-based molecular visualization of proteins and protein complexes that can be incorporated into lecture and lab will be described, and experimental methods for secondary structural analysis of proteins will be discussed. Day 5: Lecture - "Current Research in Protein Structure/Function Relationships and Protein Engineering". Topics could include: proteomics, drug design, protein splicing (inteins), design of structure/function relationship studies. The laboratory component of the workshop includes experiments that illustrate concepts and methods from throughout the lecture material. The experiments can be incorporated in the undergraduate curriculum at a diversity of institutions. Experiment 1: "DNA Extraction and PCR". Participants are introduced to the fundamentals of molecular biology. Participants will extract DNA from a variety of organisms including genetically modified food products, laboratory and wild species. Participants will also amplify DNA markers that are known to be diagnostic of genetic modification in food, and will be used for DNA and phylogenetic analyses. Experiment 2: "Gel purification and Restriction of PCR products". This laboratory exercise involves electrophoresis of amplified DNA products. One procedure will examine the presence or absence of the amplified DNA marker. Another procedure will include restriction digest of the DNA marker as a gross measure of DNA sequence differences. The final procedure will lead to the direct examination of DNA sequences differences to be complete in experiment 3. Experiment 3: "DNA Sequence and Phylogenetic Analysis". This is a two-day experiment covering the assembly of an RFLP map, DNA sequencing on an automatic DNA sequencer, sequence alignment, and the statistical analyses for phylogenetic comparisons. Participants will learn methods for constructing RFLP maps, the use of automatic DNA sequencers, phylogenetic data analysis using PAUP, data mining using BLAST searches on Genbank. Experiment 4: "Computer-Based Exploration of Protein Structure". This is a tutorial and hands-on lab using PDB and other databases to find and download protein structures. RasMol, Protein Explorer, and/or other software programs will be used to examine the 3-D structure of proteins and the covalent and non-covalent interactions that stabilize protein folding. Experiment 5: "Techniques in the Conformational Analysis of Proteins". This laboratory will involve the use of fluorescence and circular dichroism spectroscopies for analysis of protein structure under native and denaturing conditions.NOTE THAT E-MAIL ADDRESSES HAVE BEEN MODIFIED!!!
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