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| - | <center> <FONT size=5> '''All the parameters we might have to introduce in our models''' </FONT> <BR> </center> | + | <center> <FONT size=5> '''References''' </FONT> <BR> </center> |
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| - | [[Image:Diag_expr_time.jpg]] | + | <br> |
| - | expression of the fl-genes observed in [[Team:Paris/Modeling/Bibliography#References|[1]]]
| + | * [1] Shiraz Kalir, Uri Alon. Using quantitative blueprint to reprogram the dynamics of the flagella network. Cell, June 11, 2004, Vol.117, 713-720. |
| | + | * [2] Jordi Garcia-Ojalvo, Michael B. Elowitz, Steven H. Strogratz. Modeling a synthetic multicellular clock : repressilators coupled by quorum sensing. PNAS, July 27, 204, Vol. 101, no. 30. |
| | + | * [3] Nitzan Rosenfeld, Uri Alon. Response delays and the structure of transcription networks. JMB, 2003, 329, 645-654. |
| | + | * [4] Nitzan Rosenfeld, Michael B. Elowitz, Uri Alon. Negative autoregulation speeds the response times of transcription networks. JMB, 2003, 323, 785-793. |
| | + | * [5] S.Kalir, J. McClure, K. Pabbaraju, C. Southward, M. Ronen, S. Leibler, M. G. Surette, U. Alon. Ordering genes in a flagella pathway by analysis of expression kinetics from living bacteria. Science, June 2001, Vol 292. |
| | + | * [6] http://partsregistry.org/Part:BBa_E0040 |
| | + | * [7] M. Schuster, M. L. Urbanowski, and E. P. Greenberg. Promoter specificity in Pseudomonas aeruginosa quorum sensing revealed by DNA binding of purified LasR. |
| | + | * [8] Sheng Jian Cai and Masayori Inouye. EnvZ-OmpR Interaction and Osmoregulation in ''Escherichia coli''. The journal of biochemical chemistry Vol. 277, No. 27, Issue of July 5, pp. 24155–24161, 2002. |
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| - | == <FONT size=5> flhDC + fliA → pfliA → fliA → ∅ </FONT> <BR> ==
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| - | * is the contribution of flhDC and fliA on pfliA a SUM gate
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| - | [[Team:Paris/Modeling/Bibliography#flhDC_.2B_fliA_.E2.86.92_pfliL_.E2.86.92_Z1_.E2.86.92_.E2.88.85|(see fliL)]] ?
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| - | * It seems that the FlhDC complex is an hexamere, as FlhD4-FlhC2.
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| - | == <FONT size=5> flhDC + fliA → pfliL → Z1 → ∅ </FONT> <BR> ==
| + | <center>[[Image:Diag_expr_time.jpg]]</center> |
| - | | + | <center> ''expression of the fl-genes observed in'' [[Team:Paris/Modeling/Bibliography|[5]]] </center> |
| - | | + | |
| - | the contributions of flhDC and fliA in the activity of pfliL appear to be a SUM
| + | |
| - | [[Team:Paris/Modeling/Bibliography#References|[2]]] : <br> | + | |
| - | <FONT size=3> <center> act_pfliL(flhDC,fliA) = act_pfliL(flhDC,0)+act_pfliL(0,fliA) </center> </FONT> <BR> <br>
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| - | is it the same for the other promoters under the influence of both flhDC and fliA ?
| + | |
| - | | + | |
| - | == <FONT size=5> flhDC + fliA → pflgA → Z2 → ∅ </FONT> <BR> ==
| + | |
| - | is the contribution of flhDC and fliA on pflgA a SUM gate
| + | |
| - | [[Team:Paris/Modeling/Bibliography#flhDC_.2B_fliA_.E2.86.92_pfliL_.E2.86.92_Z1_.E2.86.92_.E2.88.85|(see fliL)]] ? | + | |
| - | | + | |
| - | == <FONT size=5> flhDC + fliA → pflgB → Z2 → ∅ </FONT> <BR> ==
| + | |
| - | is the contribution of flhDC and fliA on pflgB a SUM gate
| + | |
| - | [[Team:Paris/Modeling/Bibliography#flhDC_.2B_fliA_.E2.86.92_pfliL_.E2.86.92_Z1_.E2.86.92_.E2.88.85|(see fliL)]] ? | + | |
| - | | + | |
| - | == <FONT size=5> flhDC + fliA → pflhB → Z3 → ∅ </FONT> <BR> ==
| + | |
| - | is the contribution of flhDC and fliA on pflhB a SUM gate
| + | |
| - | [[Team:Paris/Modeling/Bibliography#flhDC_.2B_fliA_.E2.86.92_pfliL_.E2.86.92_Z1_.E2.86.92_.E2.88.85|(see fliL)]] ?
| + | |
| - | | + | |
| - | == <FONT size=5> lasI → 3OC12HSL → ∅ </FONT> <BR> ==
| + | |
| - | | + | |
| - | == <FONT size=5> d[HSL]/dt = -D * Grad²([HSL]) </FONT> <BR> ==
| + | |
| - | | + | |
| - | == <FONT size=5> lasR → Rec → ∅ </FONT> <BR> ==
| + | |
| - | | + | |
| - | == <FONT size=5> 3OC12HSL + Rec → HSL-Rec → ∅ </FONT> <BR> ==
| + | |
| - | | + | |
| - | == <FONT size=5> HSL-Rec + pRep → TetR → ∅ </FONT> <BR> ==
| + | |
| - | | + | |
| - | == <FONT size=5> ∅ → aTc → ∅ </FONT> <BR> ==
| + | |
| - | | + | |
| - | == <FONT size=5> TetR + aTc → pTet → flhDC → ∅ </FONT> <BR> ==
| + | |
| - | | + | |
| - | == <FONT size=5> OmpR* → pflhDC → flhDC → ∅ </FONT> <BR> ==
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| - | | + | |
| - | == <center> '''References''' </center> ==
| + | |
| - | | + | |
| - | [1] ''Ordering Genes in a Flagella Pathway by Analysis of Expression Kinetics from Living Bacteria'' <br>
| + | |
| - | S. Kalir, J. McClure, K. Pabbaraju, C. Southward, M. Ronen, S. Leibler, M. G. Surette, U. Alon, <br>
| + | |
| - | [2] ''Using a Quantitative Blueprint to Reprogram the Dynamics of the Flagella Gene Network' <br>'
| + | |
| - | Shiraz Kalir and Uri Alon
| + | |
References
- [1] Shiraz Kalir, Uri Alon. Using quantitative blueprint to reprogram the dynamics of the flagella network. Cell, June 11, 2004, Vol.117, 713-720.
- [2] Jordi Garcia-Ojalvo, Michael B. Elowitz, Steven H. Strogratz. Modeling a synthetic multicellular clock : repressilators coupled by quorum sensing. PNAS, July 27, 204, Vol. 101, no. 30.
- [3] Nitzan Rosenfeld, Uri Alon. Response delays and the structure of transcription networks. JMB, 2003, 329, 645-654.
- [4] Nitzan Rosenfeld, Michael B. Elowitz, Uri Alon. Negative autoregulation speeds the response times of transcription networks. JMB, 2003, 323, 785-793.
- [5] S.Kalir, J. McClure, K. Pabbaraju, C. Southward, M. Ronen, S. Leibler, M. G. Surette, U. Alon. Ordering genes in a flagella pathway by analysis of expression kinetics from living bacteria. Science, June 2001, Vol 292.
- [6] http://partsregistry.org/Part:BBa_E0040
- [7] M. Schuster, M. L. Urbanowski, and E. P. Greenberg. Promoter specificity in Pseudomonas aeruginosa quorum sensing revealed by DNA binding of purified LasR.
- [8] Sheng Jian Cai and Masayori Inouye. EnvZ-OmpR Interaction and Osmoregulation in Escherichia coli. The journal of biochemical chemistry Vol. 277, No. 27, Issue of July 5, pp. 24155–24161, 2002.
expression of the fl-genes observed in [5]
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