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.

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