genomics (research help plz)

nike04211 · Post by **nike04211** » Tue Dec 20, 2005 3:58 pm

Ok, I am doing a genomics project to use computational means to find the function of a protein......I am comparing the amino acid sequences in different and distinctly related species to figure out the protein's function....does anyone know of any genetic/protein similarities in distinctly related organisms?????

HELP!!!!

carolinethorn · Post by **carolinethorn** » Wed Dec 21, 2005 11:02 am

If a protein is similar, or "conserved" between distantly related organisms it usually means it has a very important or basic function.
Do you already have a protein or gene you are testing or are you looking for one to test?

What kinds of functions are you interested in as then it would make doing the background research more fun - are you interested in blood? or how a body defends itself against infection? or how cells in an embryo develop into a head or a body? or how cells die?
or are you interested in a particular disease like cancer or diabetes?

Are you trying use knowledge about a protein in one organism to suggest functions in another organism?
Or are you trying to pick 2 proteins with the same function and show how similar they are in 2 different organisms?

nike04211 · Post by **nike04211** » Wed Dec 21, 2005 3:38 pm

Currently, I am testing a Hemoglobin S protein and a specific ribosomal protein...I am studying these proteins for comparison within the animalia kingdom, but I am looking for AT LEAST one protein which is common across the kingdoms...

I am trying t compare the amino acid sequences of the same protein in two (or more) different proteins to find common sequences between them...this way, I will try to conclude the dominant function of the protein indirectly.

nike04211 · Post by **nike04211** » Wed Dec 21, 2005 3:39 pm

I am specifically interested in the proteins affected by genetic diseases.

nike04211 · Post by **nike04211** » Wed Dec 21, 2005 3:45 pm

I got my idea from:

https://www.sciencebuddies.org/mentorin ... ?from=Home

Any genes/proteins that you know that are ubiquitous throughout the species would be helpful in my studies

carolinethorn · Post by **carolinethorn** » Wed Dec 21, 2005 5:03 pm

You could try looking at some homeobox genes/proteins. These were first discovered in flies (drosophila)and are involved in development. Mistakes in these genes in humans can lead to extra ribs or different numbers of fingers, or sometimes more severe skeletal malformations.

There are a set of genes that were first examined in C. elegans worms that control when cells die. In the worm they have the gene prefix ced and a number. When these genes malfunction in humans they can cause cancer.

Some of the fundamental metabolic processes in cells, like how glucose is metabolized are conserved through evolution. There are some severe genetics diseases known as glycogen storage diseases that occur in this pathway.

You should be able to find the genes and proteins for these by searching keywords on OMIM

If you want to look at something that is hot in the news right now but not disease related - there was a paper in science magazine about a gene that determines skin colour in zebrafish that has a homologue in humans.

phamlinh · Post by **phamlinh** » Wed Dec 21, 2005 11:42 pm

Hi,

This sounds like an interesting project. In addition to the homeobox genes that Caroline suggested, there are a few others that will be conserved across all different species of organisms. One of them you have already suggested: ribosomal proteins will be conserved among all organisms. Another example is actin, a protein involved in cell structure, movement, and transport.

When you're looking at proteins that are conserved across many different species, you usually have a control (something you know that is conserved) and something you're interested in (such as a gene related to disease). That way, you can tell how much the gene has diverged between two different species.

Let me give you a hypothetical example. Let's say you look at the amino acid sequence of a ribosomal protein and compare the sequence between humans, mice, and frogs (I list frogs as an outgroup). Because it's highly conserved, you would expect that any changes are due to evolutionary drift and are not that functional (since every species needs this particular ribosomal protein to synthesize proteins). Let's say that if you're looking at percent identity, the human is 100% (because this is what you're comparing things to), mouse is 95% identical, and frog is 80% identical. Now you look at your favorite protein sequence (it could be the gene associated with disease like you mentioned). If you compare the sequence identities, and then the differences versus your controls, you may be able to come up with interesting hypotheses. For example, if you look at the homeobox genes for all three different organisms, humans would be 100%, mouse may be 95%, and frog may be 80% (I stress that this is a hypothetical example). What would this suggest to you? In other words, why do you think the percentages are so close to the ones derived from your ribosomal protein?

I hope this helps. I think you can find plenty of genes for which you can compare sequences using the OMIM link that Caroline provided. If you're interested in a particular gene, you can also always google or post the question here.

I hope this was helpful.

Best of luck,

Linh

nike04211 · Post by **nike04211** » Fri Dec 23, 2005 6:30 pm

Thanks for all the help....I have started researching the postaxial polydactyly and the genes/proteins associated with it...perhaps I can incorporate the drosophila fly as my difference and humans as my control.

I see how (if I use more than two species) I can draw a hypothetical phylogenetic tree using the results. Thanks for the idea!