Science Buddies: "Ask an Expert"

Hi

I'm doing my project about zebrafishes' regeneration.
I'm trying to look for genes in heart,retina,fin regeneration and find what they are really doing.
I mean if there are unknown genes, I'm trying to figure out a function of it and see how it works.

I'm also planning to see whether these genes only work in zebrafish or also in other animals.

Till now I found several genes like mps1, sly1, hsp60,and fgf20a.
But I don't know yet whether their roles are already found out.
Anyway, if I want to find out the function of those genes, what kind of technics can I use here?
Or you can give me a website of procedure of the technics.



Thank you,
Ryan

Hi Ryan,

I think a basic answer to your question is on these sites:

http://www.ornl.gov/sci/techresources/H ... hromosome/

https://www.sciencebuddies.org/science- ... p002.shtml

https://www.sciencebuddies.org/science- ... rces.shtml

Have you checked ou the Science Buddies Project Idea tool? It has a number of genomic projects that intoduce you to the tools you seek:

https://www.sciencebuddies.org/science- ... Genom&dl=9


One basic tool is BLAST, whose usage is described in this project writeeup:
https://www.sciencebuddies.org/science- ... p017.shtml

We havve had a number of similar questions in the past, whose answers might prove useful:

https://www.sciencebuddies.org/science- ... =14&t=2118

https://www.sciencebuddies.org/science- ... f=3&t=2124

https://www.sciencebuddies.org/science- ... p003.shtml

https://www.sciencebuddies.org/science- ... p023.shtml

I think this will give you a fair sampling of the Science Buddies Resources for the information you seek.
You can also find information by searching with Google for the keywords or questions of interest to you(and do not be shy about reviewing the first 5 to 10 pages of hits - often the item you will find most helpful is not on the first one or two pages of search results.

This kind of project is always an adventure. Have fun with it!!!

Best regards,

Barrett L Tomlinson

Hi Ryan,

This is of course a very interesting question. It still seems very broad at this point (which is not a bad thing), but focusing on maybe a few genes in one organ or comparing between a few organs might be simpler.

One way to start would be to isolate genes that differ in expression between different organs (eg regenerating and non-regenerating ones). DNA microarrays (http://en.wikipedia.org/wiki/DNA_microarray) would be very useful for something like this. Along with the genes that you have researched, you could (and yes you would likely need to be in a research lab to do this) run a microarray to check the gene expression levels for say, 100 or so genes that could be of interest in the heart, retina, fin (all regenerating) as well as non-regenerating ones. Between these two groups (regenerating and non-regenerating organs), you would compare which genes were up or downregulated, and this provides you with some targets as to genes that may be responsible for the regeneration.

You would then want to find a way to test just a few of those genes. Imaginably, one way would be to culture some zebrafish heart tissue and then apply a heat (or some other type) of shock to damage the cells. You test for the presence of the gene products of those genes of interest before and after the shock to see if they are upregulated during stress. Then you could create knockouts (cells without the genes of interest) of those cells and then apply a stress to determine whether or not the genes of interest were responsible for the regeneration.

Sorry I didn't include too much of the detail. Feel free to ask for more.

Hope this helps!
Aaron Lin

kyhekm wrote:Hi

I'm doing my project about zebrafishes' regeneration.
I'm trying to look for genes in heart,retina,fin regeneration and find what they are really doing.
I mean if there are unknown genes, I'm trying to figure out a function of it and see how it works.

I'm also planning to see whether these genes only work in zebrafish or also in other animals.

Till now I found several genes like mps1, sly1, hsp60,and fgf20a.
But I don't know yet whether their roles are already found out.
Anyway, if I want to find out the function of those genes, what kind of technics can I use here?
Or you can give me a website of procedure of the technics.



Thank you,
Ryan

Dear Ryan,

I found this zebrafish gene database, which I think may be helpful http://www.ensembl.org/Danio_rerio/Info/Index
A way to hypothesize gene function without doing experimentation is to look at other genes that interact with the ones that you study and see the functions of those genes. Odds are, the interacting genes will have a similar function as the one you are studying. As stated by Aaron Lin, the procedures for studying gene function are really only found in a lab, so I would suggest contacting a professor at a local college or university that does the type of research that you are interesting in doing. For the past two summers I studied gene function with a professor and the experience was very rewarding. If you have any more questions let me know.

good luck,
scienceexpert123

Hi!

I really appreciate to all three of you guys for replying on mine.
Now, I'm currently working with graduate student and I just got tons of information from him.
I guess it is time to read all through the papers
Thank you for telling me many websites which they are really helpful.
I will post further question after I have some reading exercises !

Best,
Ryan