Make a new vial of food. Remember, the new recipe is 2 grams of dry food plus 10 ml of water. Put a few grains of yeast on the food, like 5 or 6, not a whole pinchful.
Transfer your mixture of mutant and wild-type flies to the new vial. Keep the old vial for now, in case the new one doesn't work. If some of the adults don't get transferred, because they're stuck in the food or because they fly away, make a note of it, and think about how it might influence the population.
Make a couple more new vials of food and transfer the adults from your pure stock vials to them. This way, if you need virgins of the pure stock in a few weeks for your individual experiment, you'll have several vials to collect them from.
Go back to Flybase and find your gene (not the allele). Get the "Decorated FASTA" sequence and save it to a file. How many exons does your gene have? How long are the introns? Do all of the introns begin with GT and end in AG? Is the first translated codon ATG, or something else?
From Flybase, get the FASTA translation of the gene and save it to a file. How many amino acids long is it? Are there more than one translation; if so, how do they differ from each other?
If you and your partner have the same gene, one of you should look at a gene located near it in the genome--ask me for help picking one.
Go to BLAST. This is a tool that searches the genome databases for sequences similar to the one you enter. Under "Basic BLAST," choose "Protein BLAST." Copy the protein sequence you got from Flybase into the box, choose the "non-redundant protein sequences database", and hit BLAST. The program will find similar protein sequences to the one you entered, and list them from most similar on down. Make a note of the first few listings--what organism are they? Does the gene in them have the same name?
Do the BLAST search again, only this time, instead of using the non-redundant protein database, limit the search to humans. In the box labelled "Organism (optional)," enter "homo sapiens." Find the best match and get some of the information about it--gene name, function, etc. Save the protein sequence in FASTA format.
Do the BLAST search again, only tihis time limit the search to "Homo sapiens neanderthalensis". If you find the same gene as in H. sapiens, save the protein sequence to a file.
Do the BLAST search again, limiting yourself to Pan troglodytes (common chimpanzee) and Gorilla gorilla. The goal is to have sequences from human, neanderthal, chimp and gorilla. You'll analyze them on Thursday.
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This page was last revised September 15, 2009. Its URL is http://udel.edu/~mcdonald/geneticslab5.html