BioControl:Week4: Difference between revisions
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During the Engineering Principles in Bio conference at Cold Springs (which a few of us were at back in December), Uri Alon's name came up quite a bit, so it seems appropriate to do one of his papers. Here is an interesting one on the connection between fitness and regulatory mechanism, though if anyone has any other favorites, go ahead and post them here too. | During the Engineering Principles in Bio conference at Cold Springs (which a few of us were at back in December), Uri Alon's name came up quite a bit, so it seems appropriate to do one of his papers. Here is an interesting one on the connection between fitness and regulatory mechanism, though if anyone has any other favorites, go ahead and post them here too. | ||
<biblio> | <biblio> | ||
# | #Shinar pmid=16537475 | ||
#Milo pmid=12399590 | #Milo pmid=12399590 | ||
#Shen-Orr pmid=11967538 | #Shen-Orr pmid=11967538 | ||
#Dekel pmid=16049495 | |||
</biblio> | </biblio> | ||
===Discussion Points=== | ===Discussion Points=== | ||
* | ====Eric==== | ||
*I really like how the first paper makes a clear connection between noise minimization, fitness and regulatory mechanism. There are additional consequences of noise/error levels, and some of them are demonstrated through the modular construction of regulatory proteins (for transcriptional regulation these would have separate domains for binding the DNA and for recruiting the polymerase.) | |||
*The paper shows how variation in the time a protein is required can cause changes in the regulatory scheme (for instance, to change a repressor to an activator). There are additional environmental factors that may change independently, for instance: the number of proteins required for a metabolic process. | |||
** let <math>N</math> be the number of proteins required for <math>p</math> percent of the time the protein is required. <math>p</math> is controlled by a combination of the DNA binding energy and the number of regulatory proteins (remember the Phillips paper from [[BioControl:Week1|week1]]. So while it would be possible to change <math>N</math> via a change in <math>p</math>, it might have negative effect due to an increased sensitivity to errors. It would be best to change <math>N</math> independently of <math>p</math>, hence the usefulness of modular domains for DNA-binding and Polymerase recuitment. | |||
** There are certainly other uses for modularity in proteins, but I think this is interesting on a short term scale. The forth paper discusses the level of a protein is tuned fairly quickly to optimum via evolution, so I wonder if something like this might be in effect. | |||
** what other independent environmental parameters have corresponding functional parts? can anyone think of one for the time scale over which an environment switches between conditions? | |||
* Last year I went hear Alon talk about the development of modular logic networks under variable and modular fitness landscapes, and modular protein structures seems a direct correlary: functional separation allows for the independent tuning and error-optimization of the different signal transfer steps of a cellular circuit. | |||
** I've known how modularity is important to engineering and programming, but this error-minimization was an additional constraint that I hadn't considered previously. What other seemingly equivalent tradeoffs are affected by noise propogation? | |||
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Latest revision as of 23:17, 11 January 2007
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ReadingDuring the Engineering Principles in Bio conference at Cold Springs (which a few of us were at back in December), Uri Alon's name came up quite a bit, so it seems appropriate to do one of his papers. Here is an interesting one on the connection between fitness and regulatory mechanism, though if anyone has any other favorites, go ahead and post them here too.
Discussion PointsEric
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