Science Buddies: "Ask an Expert"

Hi,

I posted a topic before because I was wondering what sort of project I should pursue. I've now decided to investigate the origins of beta-lactamases; more specifically, the metallo-beta-lactamase NDM-1 (the recent "superbug"). I've run some BLAST searches, and I'm still doing searching for more links, but I had a few questions about the science fair procedure in general.

First, I have to turn in forms and a research plan soon. However, the "research" I'm doing is simply using gene database searches (that will hopefully include more than just BLAST soon). There's not a whole lot I can say for my procedure. Are BLAST searches and the like even considered data?
Another part of the research plan is asking me what methods of data analysis I'm using. I'm guessing these include graphs and visual representations of data, but I'm not sure how I would ultimately present my findings other than explanations. My goal is to get to a few likely descendants or genes, research them, and try to explain each evolutionary step up to NDM-1 (why/how they developed the drug resistance enzymes and such).
Finally, how would I structure a hypothesis?

If I have any more questions about this procedure stuff or my topic, I'll just post them here.
Thank you!

Hi,
Sounds like you're off to a good start. Typically, BLAST searches and the like are used for verification purposes and to support the data found -- they usually do not constitute the actual data itself. That being said, your data analysis seems to consist of mostly research based upon the results you get from the sequence alignment tools and databases. If you would like to be more involved in actual data collection, perhaps you can find a university lab or a professor who is working on this particular beta-lactamase and see if you can gather some data on this superbug yourself. What would be really interesting to look at is to see if there are empirical similarities and differences in the function of beta-lactamase and the proteins coded for by the supposed "parent sequences" that you are trying to verify. This way, you will be able to collect real data and analyze it using statistical significance tests and the like. Right now, it seems to me like your hypothesis is along the lines of: Genes X, Y, and Z are likely genetic precursors of NDM-1. What you are trying to figure out through your project will be, ultimately, whether or not the origins of NDM-1 can be found within these particular genes. This is a very interesting idea, best of luck!

Hi!
By now it's been a while. I talked to the staff who manages the science fair; they said that a research project like my project is acceptable. It doesn't give definitive, hard data or achieve conclusions by completely empirical means, but it's something I can pursue. At that time, anyway, I couldn't get hold of a researcher who is knowledgeable about that and would allow me to use a laboratory... (I want to do this with another science project next year/later this year sometime though!)
I plan to finish experimenting (or rather, BLASTing/researching) by next week. Right now I've got several "paths" I'm investigating and see if they lead me to a common sequence/gene.
The more interesting part of my project, I think, is when I actually analyze things and research WHY the evolutionary pathway progressed as it did.

In any case, my real question at this point is about sequence similarity and related tools. So far I'm using BLAST and KEGG as tools. Are there any other things I could use, such as other databases? One thing I was thinking about is a tool for comparing two sequences to one another.

I'd be happy to hear any suggestions.