What kind of project would you devise?

Daniel Mcgoldrick ez005139 at chip.ucdavis.edu
Mon Sep 4 13:13:07 EST 1995

I think I can respond to that challenge given a more realistic starting
point. Let's say I isolate a protein and have some amino acids sequenced. 
Say it is known to be associated with a certain biological function say
heat shock response (you know the process by which living organisms are
able to survive stress when they normally wouldn't due to the protection
from protein denaturation). Let's say I have no idea what my protein is.
Could alternatively be an interesting mRNA or genomic DNA or a candidate
gene in a QTL region - doesn't matter - just something that I know is
associated with a process of interest.
	Let's say I get this protein sequence data, and probe a cDNA
library (or do a northern or southern in the other cases) now I have the
DNA sequence from which my gene/sequence is transcribed from. I may know
how many copies the gene has etc...Lastly, I do a database search and get a 
set of homologous genes and their alignment. 

1) I now know what species the gene is most closely related to, so I can
determine if the sequence was really derived from my study organism 
rather than, say, a virus, a lab tech. or my cloning vector.

2) I know a researcher/s who is/are studying something similar.

3) I can associate (inductively) the information about all homologous genes 
to help focus future hypotheses e.g. I can address comparative structural 
functional hypotheses.

4) I can address hypotheses about expression pattern and chromosomal linkage 

5) Oh yes, I can map my genes onto a phylogeny concordantly with 
associated phenotypes.

I think a lot of progress has been made in associating, for example, 
proteins that have DNA binding domains such as zinc finger, helix turn helix,
leucine zipper etc. with developmental patterning (the literature is 
over-whelming). Also in the identification of heat shock genes (again the 
literature is massive). All of this is based on comparative sequence data
and classic experimentalism. 

Daniel J. McGoldrick				(707) 875-2076 Lab
U.C. Davis, Bodega Marine Laboratory 		(707) 875-2089 Fax me
P.O. Box 247
Bodega Bay, Ca. USA 94923

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