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I would appreciate suggestions for my year-long AP Biology project. Such a project would consists of a standard experiment, to be done over the period of a year, so it would have >to be fairly substantial.

I'm interested in anything cell/DNA/molebio related with a mathematical connection. I >would prefer something other than mere statistical analysis, maybe something like >differential equations.

I have access to standard undergraduate lab equipment; assume that I'm able to procure all necessary materials and that I'm capable of performing the experiment. Thank you for the help.

As per the suggestion of shigeta below, I leafed through the links, and found gene circuits interesting. So, what exactly is a gene circuit, how are they modeled, and what are they used for?

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closed as primarily opinion-based by WYSIWYG, MattDMo, Damien, terdon, Mad Scientist Aug 21 '13 at 17:13

Many good questions generate some degree of opinion based on expert experience, but answers to this question will tend to be almost entirely based on opinions, rather than facts, references, or specific expertise.If this question can be reworded to fit the rules in the help center, please edit the question.

    
systems biology.. do a cell bio experiment and develop a mathematical model for the system. you can validate the model using the experiments.. –  WYSIWYG Aug 21 '13 at 3:22
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You really need to narrow this down. We don't know your competences, the materials you have available, the fields of the various labs you may have access to, there is no way of answering this question without a much more specific scope. –  terdon Aug 21 '13 at 12:23
    
Yes, I probably should have been more specific about that; it'll be edited. I'll look into systems biology. –  Ayesha Aug 21 '13 at 13:06
    
Still going to need a little more on the equipment side. I consider tissue culture standard undergrad work because that's what I did a lot of the time in undergrad. I also have been doing Westerns since high school. You mention cells, do you have a way to culture them, you mention DNA, do you have gel rigs and the means to isolate DNA, and molebio is so broad it's not really limiting. –  Atl LED Aug 21 '13 at 13:12
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I'm still not certain that this is a good question for SE, because I'm not sure it can be answered, but I would look into a forward genetics experiment. You can do predictive and analytical modeling, and push the forward genetics over a whole year easily. –  Atl LED Aug 21 '13 at 13:57
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1 Answer

This is a bit hard - most possible answers you still aren't going to like, but I'll give you three suggestions.

It sounds like you want to take something with a mathematical model and try to modulate it with molecular biology.

It seems unlikely that I can really give you a specific project, but there are four sources I will recommend you look at.

I think I'd suggest the further limiting assumptions:

  1. you want to work with E coli - its the easiest and most readily available organism to work with.
  2. you want to work with a system that is self contained within a single plasmid - so it relies only upon 2 genes to act, 3 at the outside or you will have issues getting it all to work.
  3. you want a mathematical system that already has a well fit model that you will peturb. building a new model might be a bit of a big first off project. (but who am I to tell you what to do - these are just suggestions).

The First suggestion I have is Jeff Hasty at UCSD. He has focused a lot on oscillating gene circuits. He has simple systems that might be reproducible with a small lab, most recent work that combines a GFP oscillator with LUX is pretty cool. Both oscillators and LUX are independently good systems to work with. . I've been a science fair judge and I can tell you, just reproducing one of his systems would be an impressive lot of work

Another body of work to look at is Adam Arkin. He has looked at lots of circuitry component candidates. Articles such as "The hunt for the biological transistor" might get you thinking. This is a broader body of work, and so it might take a while to get an idea from it.

Third, if this is boring to you and you want to look more broadly, you can look through the iGEM competitions. These are projects with oscillators and bio synthesis systems which sometimes have mathematical models associated with them. The big advantage here is that you might be able to start or join an iGEM team and then some or all the plasmids will be made already - mol bio gets very expensive if someone doesn't gift you some materials.

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