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| | <tr> | | <tr> |
| - | <td class="bodyText"><p>May 7th(summary)- -- -- -- -- -- -- -- - ------ -----. --- ------ --- ---- -- --- ----- -- -- -- ------ ---- ---- - -- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ---- ----- --- --- ----- ---- ----- ------ ---- -- -- --- ------- - ----- --- ---- --- --- -- - ------ -- ---- --- --- --- -- -- ----- ---, --- - - --- -- -- -- -- -- -- -- - ------ -----. | + | <td class="bodyText"><p>Preliminary Projects Group Presentation (2nd Round)<br> |
| - | --- ------ --- ---- -- --- ----- -- -- -- ------ ---- ---- - -- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ---- ----- --- --- ----- ---- ----- ------ ---- -- -- --- ------- - ----- --- ----. </p>
| + | Discussion of Papers & Ideas <br> |
| | + | Sprinzak & Elowitz, 2005. <br> |
| | + | |
| | + | Combinatorial experiment.<br> |
| | + | Three TF and 5 binding sites.<br> |
| | + | Combinatorial and phenotypes analysis.<br> |
| | + | With a few well characterized elements much can be done.<br> |
| | + | |
| | + | Experimental Technique: Promoters recombination.<br> |
| | + | Suggestion: PCR to avoid direct recombination.<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> |
| | + | |
| | + | 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> |
| | + | -miRNA (only in eukaryotes, not found in yeast)<br> |
| | + | |
| | + | Sequence-specific Ribosomes. (few well characterized)<br> |
| | + | |
| | + | Repressilator: Three genes that are repressed among them.<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> |
| | + | 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> |
| | + | |
| | + | 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> |
| | + | |
| | + | Measuring noise is a potential problem, Do we have access to technology to measure it?<br> |
| | + | |
| | + | Investigate the difficulty to study the competition between the two enzymes for |
| | + | same metabolite in a metabolic pathway.<br> |
| | + | |
| | + | In positive circuits it is possible to see multiple states.<br> |
| | + | </p> |
| | </td> | | </td> |
| | </tr> | | </tr> |
 |
LCG-UNAM-Mexico |
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| iGEM 2008 TEAM |
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| May |
May's summary:--- ---- - --- ---
|
Preliminary Projects Group Presentation (2nd Round)
Discussion of Papers & Ideas
Sprinzak & Elowitz, 2005.
Combinatorial experiment.
Three TF and 5 binding sites.
Combinatorial and phenotypes analysis.
With a few well characterized elements much can be done.
Experimental Technique: Promoters recombination.
Suggestion: PCR to avoid direct recombination.
It is not enough to have the network topology, the context also influences the outcome.
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.
Next steps, future models:
-Protein level phosphorylation (example: Phytocrome found in cyanobacteria that get phosphorylated when activated with a specific wavelength and eventually trigger the activation of TF.
-miRNA (only in eukaryotes, not found in yeast)
Sequence-specific Ribosomes. (few well characterized)
Repressilator: Three genes that are repressed among them.
Signaling cascades not exploited yet. Response time delay. It is mentioned as the simplest system. The noise is accumulated in these systems.
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.
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.
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.
Measuring noise is a potential problem, Do we have access to technology to measure it?
Investigate the difficulty to study the competition between the two enzymes for
same metabolite in a metabolic pathway.
In positive circuits it is possible to see multiple states.
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May 11th(summary)- -- -- -- -- -- -- -- - ------ -----. --- ------ --- ---- -- --- ----- -- -- -- ------ ---- ---- - -- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ---- ----- --- --- ----- ---- ----- ------ ---- -- -- --- ------- - ----- --- ---- --- --- -- - ------ -- ---- --- --- --- -- -- ----- ---, --- - - --- -- -- -- -- -- -- -- - ------ -----.
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May 12th(summary)- -- -- -- -- -- -- -- - ------ -----. --- ------ --- ---- -- --- ----- -- -- -- ------ ---- ---- - -- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ---- ----- --- --- ----- ---- ----- ------ ---- -- -- --- ------- - ----- --- ---- --- --- -- - ------ -- ---- --- --- --- -- -- ----- ---, --- - - --- -- -- -- -- -- -- -- - ------ -----.
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May 21st(summary)- -- -- -- -- -- -- -- - ------ -----. --- ------ --- ---- -- --- ----- -- -- -- ------ ---- ---- - -- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ---- ----- --- --- ----- ---- ----- ------ ---- -- -- --- ------- - ----- --- ---- --- --- -- - ------ -- ---- --- --- --- -- -- ----- ---, --- - - --- -- -- -- -- -- -- -- - ------ -----.
--- ------ --- ---- -- --- ----- -- -- -- ------ ---- ---- - -- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ---- ----- --- --- ----- ---- ----- ------ ---- -- -- --- ------- - ----- --- ----.
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May 28th(summary)- -- -- -- -- -- -- -- - ------ -----. --- ------ --- ---- -- --- ----- -- -- -- ------ ---- ---- - -- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ---- ----- --- --- ----- ---- ----- ------ ---- -- -- --- ------- - ----- --- ---- --- --- -- - ------ -- ---- --- --- --- -- -- ----- ---, --- - - --- -- -- -- -- -- -- -- - ------ -----.
--- ------ --- ---- -- --- ----- -- -- -- ------ ---- ---- - -- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ---- ----- --- --- ----- ---- ----- ------ ---- -- -- --- ------- - ----- --- ----.
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