IGEM:Stanford/2009/The Mud Room

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If you have a question that you just don't get, here is a great place to ask it.

If you have a question it is likely that other people also have that EXACT SAME QUESTION. So ask, ask, ask and ask some more!

Acromyns...
Could you go over a quick list of acronyms such as RBS, GFP, and some of the well-known promoter genes and promoters?


 * RBS = ribosome binding site
 * GFP = green fluorescent protein... things that end in "FP" are usually fluorescent proteins. Other examples:
 * CFP = cyan
 * RFP = red
 * YFP = yellow
 * sidenote: if you think fluorescent proteins are cool, check this out --Isis

Lab Procedures
I'm sure we'll go over these soon and many I have performed, but I think it may be helpful to go over ways to test your results and procedures in the lab and what they pertain to- such as northern blotting, PCR, assays... Just a handout or something would be nice to give a better idea of thinking of how to design projects...

My understanding is that synthetic biology is new field. Are we buying the tools we need? Sharing them with another lab?
As far as I understand it we will have to obtain consummables ourselves (i.e. nucleotides, reagents, assay materials) but we will share equipment such as PCR machines, hoods, and gel stations at the lab. -Mark

What are biobricks and how do they work?
For those who are still confused about the whole biobricks idea, this was taken from the biobricks.org website: "A BioBrick™ standard biological part is a standard biological part that meets the technical and legal standards set forth by the BioBricks™ Foundation (BBF). Each distinct BioBrick™ standard biological part is a nucleic acid-encoded molecular biological function (e.g., turn on/off gene expression), along with the associated information defining and describing the part." I likely to simply put it as a DNA part that has a purpose. If you are taking Dr. Endy's course, I assume you will go through abstraction hierarchy which is described here. In other words, Biobricks come in three forms, Parts, Devices and Systems. A part is a sequence of DNA that can be combined with other parts such as a promoter or an RBS or even a gene, etc. These parts combine and form devices. An example of a device could be a reporter plasmid containing a promoter, we'll use pLac, an RBS, GFP, and a terminator. This device is not of use by itself as it will only glow green in the presence of IPTG / Lactose, but when combined with other devices, it can form a system that accomplishes something useful. An example could be an synthetic oscillator and such as the one found in Michael Elowitz's Repressilator. Both the oscillator plasmid and reporter plasmid are useless alone, but when combined, they can accomplish something useful. I hope this gave a greater understanding! Add more information or ask further questions if needed!

Gene splicing
What can and can't be spliced? I suppose we will go through this in BIOE 144 but it would help a lot to see what has been done, what is possible to do, and what we should just forget about trying to do.