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Team:LCG-UNAM-Mexico/Notebook/2008-May
From 2008.igem.org
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Discussion of Papers & Ideas <br> | Discussion of Papers & Ideas <br> | ||
Sprinzak & Elowitz, 2005. <br> | Sprinzak & Elowitz, 2005. <br> | ||
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Combinatorial experiment.<br> | Combinatorial experiment.<br> | ||
Three TF and 5 binding sites.<br> | Three TF and 5 binding sites.<br> | ||
Combinatorial and phenotypes analysis.<br> | Combinatorial and phenotypes analysis.<br> | ||
With a few well characterized elements much can be done.<br> | With a few well characterized elements much can be done.<br> | ||
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Experimental Technique: Promoters recombination.<br> | Experimental Technique: Promoters recombination.<br> | ||
Suggestion: PCR to avoid direct recombination.<br> | Suggestion: PCR to avoid direct recombination.<br> | ||
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It is not enough to have the network topology, the context also influences the outcome. <br> | It is not enough to have the network topology, the context also influences the outcome. <br> | ||
We need to check whether the module works in the desired conditions. Two modules working separately doesn't mean that they will work when joined together.<br> | We need to check whether the module works in the desired conditions. Two modules working separately doesn't mean that they will work when joined together.<br> | ||
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Next steps, future models:<br> | Next steps, future models:<br> | ||
-Protein level phosphorylation (example: Phytocrome found in cyanobacteria that get phosphorylated when activated with a specific wavelength and eventually trigger the activation of TF.<br> | -Protein level phosphorylation (example: Phytocrome found in cyanobacteria that get phosphorylated when activated with a specific wavelength and eventually trigger the activation of TF.<br> | ||
-miRNA (only in eukaryotes, not found in yeast)<br> | -miRNA (only in eukaryotes, not found in yeast)<br> | ||
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Sequence-specific Ribosomes. (few well characterized)<br> | Sequence-specific Ribosomes. (few well characterized)<br> | ||
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Repressilator: Three genes that are repressed among them.<br> | Repressilator: Three genes that are repressed among them.<br> | ||
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Signaling cascades not exploited yet. Response time delay. It is mentioned as the simplest system. The noise is accumulated in these systems.<br> | Signaling cascades not exploited yet. Response time delay. It is mentioned as the simplest system. The noise is accumulated in these systems.<br> | ||
Design a signaling cascade and see how noise affects and speads throughout the system. Compare the noise of a two element cascade with the one of a three-element cascade.<br> | Design a signaling cascade and see how noise affects and speads throughout the system. Compare the noise of a two element cascade with the one of a three-element cascade.<br> | ||
Evidence that a noisy system, to reduce noise introduces noise into the noise, and as a result the system become ordered. | Evidence that a noisy system, to reduce noise introduces noise into the noise, and as a result the system become ordered. | ||
Increase copies of the elements and see how does the noise is affected. Theory says that noise should decrease, see if this system converges to a deterministic system.<br> | Increase copies of the elements and see how does the noise is affected. Theory says that noise should decrease, see if this system converges to a deterministic system.<br> | ||
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Compare strains with different protein production ratios. EXPLOIT MORE THIS POINT. See if it is easy to do. However in this system it is very unlikely to find multi-stationary states.<br> | Compare strains with different protein production ratios. EXPLOIT MORE THIS POINT. See if it is easy to do. However in this system it is very unlikely to find multi-stationary states.<br> | ||
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Measuring noise is a potential problem, Do we have access to technology to measure it?<br> | Measuring noise is a potential problem, Do we have access to technology to measure it?<br> | ||
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Investigate the difficulty to study the competition between the two enzymes for | Investigate the difficulty to study the competition between the two enzymes for | ||
same metabolite in a metabolic pathway.<br> | same metabolite in a metabolic pathway.<br> | ||
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In positive circuits it is possible to see multiple states.<br> | In positive circuits it is possible to see multiple states.<br> | ||
</p> | </p> | ||
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