A bioinformatics simulation of a mutant workup from a model genetic organism Christopher J. Harendza...
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Transcript of A bioinformatics simulation of a mutant workup from a model genetic organism Christopher J. Harendza...
A bioinformatics simulation of a mutant workup from a model genetic organismChristopher J. Harendza – Montgomery County Community College
Importance Students are losing the appreciation for the
power of traditional “forward genetic” approaches and a situation is arising where most everything is mass “stare and compare” informatics and reverse genetics
While the new approaches are very powerful, full scale mutant screens have and should continue to be important
Example Nusslein Volhard, who did a full scale
saturation mutagenesis to identify developmentally important genes in Drosophila, is now doing similar work with Zebrafish
“Genetics (mutant analysis) is the window to the unknown”
-Christopher Harendza, not a famous person. Ha ha
Objective
Introduce students to the power of traditional genetic analysis of mutants and extrapolate this to bioinformatics tools on the web
Target Audience:
Students in a sophomore genetics class
Advanced freshman biology majors
Overview
Give students model data on a real mutant using, Drosophila, C. elegans, etc.
This data could parallel a wet lab, or series of wet labs, where students learn the techniques, but can then do concordant studies with informatics tools
Flow chart
Flow chart of the projectGive students a collection of mutants
Allow groups to choose a mutant of interest
↓
Groups perform a series of crosses to establish linkage-use Virtual Fly to obtain real data
↓
↓
Students design appropriate 3 point cross to map the gene
Go over strategies to clone the gene (here is where corners would have to be cut)
e.g. positional cloning e.g. P-element cloning by complementation
etc.↓
Instructor provides the DNA sequence data
↓
Students do bioinformatic analysis
Informatics phase
DNA SEQUENCE
Find homologs in fly cDNA library database
BLAST
Generate restriction enzyme map (do this backwards)
cDNA and application
The gene of interest would likely be eukaryotic and therefore possess introns
Therefore obtaining the cDNA is vital
Use the cDNA to identify open reading frames and translation tools to infer the amino acid sequence of the protein
Blast applications
BLAST
Find orthologs
Go to OMIM to find information on human ortholog
Do Clustal analysis to compare to known proteins
BLAST
Use the sequence to find orthologs in other organisms
Ask questions regarding conservation of function
Work up to human, if applicable, to find cognate genes
Clustal Analysis
Once orthologs are obtained, students could establish a database and compare related gene products
Discuss evolution of function
Protein analysis
Go to Protein Data Bank to find orthologs or a protein (s) in the same gene family
If someone has solved the structure of this or some related protein, structural analysis could be performed
OMIM Application
Human applications would be the ultimate “hook” to draw in the interest
Students could then analyze the orthologous human gene
At this point they would have access to a tremendous wealth of information
Discussion of future applications Reverse genetic approaches in mouse
models (knock outs, knock ins)
Biotech applications
Gene therapy
Summary This activity will expose students to an
authentic research simulation while preserving the traditional discussion of genetics
Curriculum evolution
Wishes It would’ve been nice if others at the
workshop had interest in this project and I could stay for the last session; lack of interest makes me think it may not be such a good idea!
A trial run this term with my newfound tools will allow assessment of its efficacy