Science fair help

[aicatn]

Hi, I have to do school science fair.
I am interested in an idea at sciencebuddies.org/science-fair-projects/recommender_nav.php?GoTo=Genom_p003.shtml&isb=c2lkOjEsaWE6R2Vub20scDoyLHJpZDozMTYwNDEz&fave=no&from=TSW

However, for science fair i need variables and graph.

I want to compare if types of flu mutate at the same regions and make a pie chart of that.

Here are the variables I have so far:
Independent: type of flu
Dependent: region of mutating protein
Constant: type of BLAST program

Is this correct?

If you're feeling really helpful, look at the questions i posted on the Science Buddies Ask An Expert Forum. Attempt to answer the questions on the 2nd page...
Here's the link (my user name is swimmy)
http://www.sciencebuddies.org/science-f ... 1858847a4b

Thanks,
aicatn

[JackBean]

I'm not sure, whether you wish to compare the flu sequences or the vaccines, but I think, more likely than a pie chart you could use column graph, where on x you will have position (from some multiple sequence alignment) and on y you will get something like mutation probability or frequence, ltes say number of mutations on this position on 100 mutations in whole sequence. Here you should see nicely pathes of conserved regions (with low columns) and highly mutable regions (with high columns)

[aicatn]

If I compared the regions where flu from different year/strain mutate, what would be the motive behind it?
Would it give scientists an idea of how to make a vaccine?

[JackBean]

To my knowledge, antivirotics against flu (like Tamiflu) are small organic molecules. By vaccines you mean antibodies or proteins resembling flu proteins and making up the immunity?

[aicatn]

This is how the science fair application is like and how i think im going to enter it:

Student Participants: (I will not put my name in the forum)

Title of Project: Do flu viruses from different years change at the same regions of protein?

List your procedures/steps you'll complete:*
1) Go to the Flu Activity & Surveillance page at The U.S. Centers for Disease Control and Prevention (CDC) website: http://www.cdc.gov/flu/weekly/fluactivity.htm.

2) Click on "Go" next to the year 2008-2009 “Current Weekly Influenza Report”.

3) Read the information on the page. In particular, find the paragraph with the heading "Antigenic Characterization." It will tell you the name of the virus strains that are candidates as vaccines.

4) You can obtain the sequences for these strains from the NCBI GenBank website: http://www.ncbi.nlm.nih.gov/Genbank/.

5) Select "Protein" with the “Search” drop-down menu. Type in the name of the flu strain (use A/California/07/2009 (H1N1) in the search box.

6) Full-length HA is 566 amino acids. In order to retrieve full length-entries, add this text to the search box AND 566[SLEN]. Click "Go."

7) Click on the active link for the HA protein page.

Copy the accession number for the full-length HA protein. Click on the "BLAST Sequence" link (column on right side of page).

9) The BLAST page will pop up. The database should be set automatically to "non-redundant protein" and the algorithm should be "blastp." Click the BLAST button.

10) The BLAST report contains alignments of your search sequence against sequences in the database. The regions of the protein that is most likely to change show up as lowercase letters in the alignment.

11) Repeat Steps 1-10 with past flu seasons (2000-2008) and compare.

List the materials you will use: computer with high speed internet

Independent Variables: type of flu

Dependent Variables: region where protein is likely to mutate

Controlled Variables: same kind of BLAST search

Hypothesis:** My hypothesis is that viruses from different flu seasons do not mutate in the same regions of protein.

What research will you do before experimenting?:*** I will research BLAST (internet tool that I will be using), flu virus, flu vaccine, and the seasons of flu.

How will you display your results? (Create a table/graph/chart):****

*Please give me feedback for my hypothesis.
**In the application, I don't need to explain my hypothesis (as I was not supposed to conduct any experiment. I wanted to try this in case there was a problem...)
***Whoops... I did my research already. Have any suggestions for any other research?
****What should I make a table/graph/chart for?


Ok, I don't really get how I can get one mutation from all those strains of flu?


If I compared mutations in types of flu by year, would it make more sense to limit it to only 2009 mutations (if I'm doing 2009) or just BLAST without specifying?


The way I see it, if I do the year specified mutations, i get mutations for the flu that year, and if i don't i have to do the different types of strains.
Is this right?


Ok, so when I did the swine flu BLAST without specifying the year of mutations, I got the following:
Mutations by strain
H1N1 (2009)
-212 (4)
-101 (74)
-217
-333 (73)
-410 (2)
-443 (2)
-385
-166
-520
-8 (2)
-544 (2)
-467 (2)
-240 (4)
-225 (23)
-48 (3)
-476 (4)
-286 (4)
-75

The most common mutation is at 101/566

Is this how I would say the results?

And did I do the right thing by looking at the whole blast search for the mutations?

ok, i don't really get how you can see which number protein the mutation is. Is it 1-20 or the numbers such as 141?
also, what does more conservative mean?

[JackBean]

* your hypothasis is actually wrong If want to know why, I might answer you, if you want to find out by yourself, I will keep it for myself
*** your pre-experiment might be to look, what strains have there been in each year, is it changing or stuff like that ( :-/ )
**** make the graph I told you about already, something as you did the table, but for all the positions in the aligment And do multiple alignment, do not align only two sequences, as that won't tell you anything
(e.g. find some ClustalW application, I'm not currently on my PC, so I can't give you some working link, but search on Google;)

[aicatn]

how about this:
what could you tell if the question "do flu viruses from different seasons mutate in the same regions of protein" is true? what if its false?

[JackBean]

I will tell you one thing: the proteins have some regions called catalyzation center or binding center, which are responsible for their function (whatever it is) and changing amino acids in this region, you might get useless rope of amino acids. Of course, you can get something with new binding/catalyzing properties, but that is more less likely, but also, this is responsible for evolution and for resistance (e.g. of the flu).
Try to think about it

[aicatn]

here is a graph i have made,
i will make another graph because I don't think this is clear...
and its not a legit graph

[aicatn]

Also, how would I include "swine flu" in my title?

[JackBean]

How can you pick up only one mutation per year? There aren't more mutations?