1、A bioinformatics simulation of a mutant workup from a model genetic organism,Christopher 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
2、“stare and compare” informatics and reverse geneticsWhile 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 d
3、oing 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:,St
4、udents in a sophomore genetics classAdvanced 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 informati
5、cs toolsFlow chart ,Flow chart of the project,Give 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
6、 clone the gene (here is where corners would have to be cut) e.g. positional cloninge.g. P-element cloning by complementation etc.,Instructor provides the DNA sequence data,Students do bioinformatic analysis,Informatics phase,cDNA and application,The gene of interest would likely be eukaryotic and t
7、herefore possess intronsTherefore obtaining the cDNA is vitalUse the cDNA to identify open reading frames and translation tools to infer the amino acid sequence of the protein,Blast applications,BLAST,Use the sequence to find orthologs in other organismsAsk questions regarding conservation of functi
8、onWork up to human, if applicable, to find cognate genes,Clustal Analysis,Once orthologs are obtained, students could establish a database and compare related gene productsDiscuss evolution of function,Protein analysis,Go to Protein Data Bank to find orthologs or a protein (s) in the same gene famil
9、yIf 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 interestStudents could then analyze the orthologous human geneAt this point they would have access to a tremend
10、ous wealth of information,Discussion of future applications,Reverse genetic approaches in mouse models (knock outs, knock ins)Biotech applicationsGene therapy,Summary,This activity will expose students to an authentic research simulation while preserving the traditional discussion of geneticsCurriculum evolution,Wishes,It wouldve 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,
