pip00

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Hi does anyone know how to find data in the literature or to infer from the data, something that would answer the following questions: avg rate of transcription of a lac gene, when a repressor is bound to 0 operators, 1 operator, or 2 operator? The same with some other operon(for example NRI), wehre an activator is bound to the enhancer sites? Also i might have some idea on how to find data for this, but completely clueless on the following:

how many times/sec/conc of repressor does the repressor bind/unbind to a lac operator?
thanks!
 

solitude

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pip00 said:
Hi does anyone know how to find data in the literature or to infer from the data, something that would answer the following questions: avg rate of transcription of a lac gene, when a repressor is bound to 0 operators, 1 operator, or 2 operator? The same with some other operon(for example NRI), wehre an activator is bound to the enhancer sites? Also i might have some idea on how to find data for this, but completely clueless on the following:

how many times/sec/conc of repressor does the repressor bind/unbind to a lac operator?
thanks!

did you try pubmed?
 

acetonile

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It's unlikely you'll find information about transcription rates for the lac operon with those sorts of specifics in mind. Surprisingly there isn't much kinetic data out there (I only know this because my lab is working on a visualization system fit for obtaining kinetic info). :p
 
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pip00

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acetonile said:
It's unlikely you'll find information about transcription rates for the lac operon with those sorts of specifics in mind. Surprisingly there isn't much kinetic data out there (I only know this because my lab is working on a visualization system fit for obtaining kinetic info). :p
thanks. but actually i found some of the data. but right now i've got a whole new sets of ideas. i have 2 days to hand in the term project. and i probably wont have enough time to do all those stochastic models. but i think i only need them to verify certain theories that i've come up with.

i wonder if i could show the following things, if that would be publishable, or it's child's play?

1) intrinsic noise is actually important in regulating certain biological functions(i showed which in a specific circuit). in another paper they discussed how the intrinsic noise(fluctuations in transcription rates) is less in magnitude than extrinsic noise(fluctuations in translation or post-transcriptional controls), and so they concluded that intrinsic noise was just some useless artifact of nature.

2) i can show how certain circuits are very good!
 

tr

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pip00 said:
i wonder if i could show the following things, if that would be publishable, or it's child's play?

1) intrinsic noise is actually important in regulating certain biological functions(i showed which in a specific circuit). in another paper they discussed how the intrinsic noise(fluctuations in transcription rates) is less in magnitude than extrinsic noise(fluctuations in translation or post-transcriptional controls), and so they concluded that intrinsic noise was just some useless artifact of nature.
Are you referring to the PNAS paper by Thattai and Oudenaarden some years ago? If you have not had a look at the more recent literature, you should check out this paper:

Elowitz et al.
Stochastic Gene Expression in a Single Cell
http://www.sciencemag.org/cgi/content/full/297/5584/1183

It has some very cleverly obtained actual experimental data.
The group used a reporter system capable of discriminating intrinsic from extrinsic noise. I think their original purpose was to construct an artificial biological oscillator (they call it the Repressilator), but along the way they ran into some trouble because the intrinsic noise levels were derailing the synchrony of their system. It looks like they used that lemon to make lemonade though, because they published a Science paper demonstrating the importance of intrinsic noise. ;)


2) i can show how certain circuits are very good!
That is rather general!
What circuits are you interested in, and which specific functions do you find to be affected by intrinsic noise?
 

pip00

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tr said:
Are you referring to the PNAS paper by Thattai and Oudenaarden some years ago? If you have not had a look at the more recent literature, you should check out this paper:

Elowitz et al.
Stochastic Gene Expression in a Single Cell
http://www.sciencemag.org/cgi/content/full/297/5584/1183

It has some very cleverly obtained actual experimental data.
The group used a reporter system capable of discriminating intrinsic from extrinsic noise. I think their original purpose was to construct an artificial biological oscillator (they call it the Repressilator), but along the way they ran into some trouble because the intrinsic noise levels were derailing the synchrony of their system. It looks like they used that lemon to make lemonade though, because they published a Science paper demonstrating the importance of intrinsic noise. ;)




That is rather general!
What circuits are you interested in, and which specific functions do you find to be affected by intrinsic noise?
Hey, i read a few papers by all the authors that youve mentioned. but only a few of them carefully. For my project i was asked to critique this repressilator system by Elowitz and another one by another author that has a mixed-feedback system. I didnt read about noise much at all. I dont have time to read the article that you've posted above, but doesnt it say somewhere that extrinsic noise is actually more important for gene regulation than intrinsic noise? If so, i have prove that it's the other way around, or at least they both contribute significant large parts. But i dont have much time to read about "noise". All i know is that for the intrinsic component, the fluctuations in binding of the repressors/activators are very important to consider when doing the continuous model!

Yeah i dont have time to be specific now. I have this term paper due in 2 days and i havent started it yet. But the idea is to show how the mixed feedback system is so much better an oscillator and some other great features that it has compared to the original repressilator. But i talked about this with my partner and though we're doing this together and he's supposed to be enthusiastic about any ideas, he didnt seem to be. So i'm afraid professor will be even less enthusiastic. Thats why i need to compile the stochastic model in the next few hours(for the simplified version), so that he would believe that if i had time to compile the fuller version it would give much more interesting results.
 

pip00

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tr said:
That is rather general!
What circuits are you interested in, and which specific functions do you find to be affected by intrinsic noise?
oscillatory circuits. my results show that intrinsic noise switches between growing and damping amplitudes of oscillations, adding variety(perhaps at 1 amplitude of oscillations that a certain group of cells has 1 signal is sent, while the other cells showing a different amplitude produce a different signal), while promoter strength is what controls this level of noise, so that the cells arent too out of phase. of course this doesnt consider the extrinsic noise. extrinsic noise affects the initial conditions, which also adds to the variety of signals. also all of this shows that mixed feedback circuits have memory, while repressilator does not.
 
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