Team:KULeuven/Model/Kinetic Constants

From 2008.igem.org

(Difference between revisions)

Revision as of 10:25, 11 September 2008

dock/undock dropdown

[1]	“IGEM:Tsinghua/2007/Projects/RAP - OpenWetWare”; http://www.openwetware.org/wiki/IGEM:Tsinghua/2007/Projects/RAP.

[2]	R. Ikeda, A. Lin, and J. Clarke, “Initiation of transcription by T7 RNA polymerase as its natural promoters,” J. Biol. Chem., vol. 267, Feb. 1992, pp. 2640-2649.

[3]	R. Bandwar et al., “Kinetic and Thermodynamic Basis of Promoter Strength: Multiple Steps of Transcription Initiation by T7 RNA Polymerase Are Modulated by the Promoter Sequence,” Biochemistry, vol. 41, Mar. 2002, pp. 3586-3595.

[4]	G.M. Skinner et al., “Promoter Binding, Initiation, and Elongation By Bacteriophage T7 RNA Polymerase: A SINGLE-MOLECULE VIEW OF THE TRANSCRIPTION CYCLE,” J. Biol. Chem., vol. 279, Jan. 2004, pp. 3239-3244.

[5]	V.S. Anand and S.S. Patel, “Transient State Kinetics of Transcription Elongation by T7 RNA Polymerase,” J. Biol. Chem., vol. 281, Nov. 2006, pp. 35677-35685.

LacI - LuxI

Bibliography

[1]	M.B. Elowitz and S. Leibler, “A synthetic oscillatory network of transcriptional regulators,” Nature, vol. 403, Jan. 2000, pp. 335-338.

[2]	“Modeling a synthetic multicellular clock: Repressilators coupled by quorum sensing,” Jul. 2004; http://www.pnas.org/content/101/30/10955.full.

LuxI, LuxR, mRNALuxI, mRNALuxR decay

Bibliography

[1]	“Generation of cell-to-cell signals in quorum sensing: acyl homoserine lactone synthase activity of a purified Vibrio fischeri LuxI protein,” Sep. 1996; http://www.pnas.org/content/93/18/9505.

[2]	L. Chen et al., “Noise-induced cooperative behavior in a multicell system,” Bioinformatics, vol. 21, Jun. 2005, pp. 2722-2729.

HSL stuff

Bibliography

[1]	“Acyl homoserine-lactone quorum-sensing signal generation,” Apr. 1999; http://www.pnas.org/content/96/8/4360.full.

[2]	P. Nilsson et al., “Kinetics of the AHL Regulatory System in a Model Biofilm System: How Many Bacteria Constitute a "Quorum"?,” Journal of Molecular Biology, vol. 309, Jun. 2001, pp. 631-640.

[3]	Y. Wang and J.R. Leadbetter, “Rapid Acyl-Homoserine Lactone Quorum Signal Biodegradation in Diverse Soils,” Appl. Environ. Microbiol., vol. 71, Mar. 2005, pp. 1291-1299.

[4]	L. Wang et al., “Specificity and Enzyme Kinetics of the Quorum-quenching N-Acyl Homoserine Lactone Lactonase (AHL-lactonase),” J. Biol. Chem., vol. 279, Apr. 2004, pp. 13645-13651.

Diffusion

Bibliography

[1]	P.S. Stewart, “Diffusion in Biofilms,” J. Bacteriol., vol. 185, Mar. 2003, pp. 1485-1491.

OmpR, OmpF

Bibliography

[1]	K.J. Huang, J.L. Schieberl, and M.M. Igo, “A distant upstream site involved in the negative regulation of the Escherichia coli ompF gene.,” Journal of Bacteriology, vol. 176, Mar. 1994, pp. 1309–1315.

[2]	K.V. Srividhya and S. Krishnaswamy, “A simulation model of Escherichia coli osmoregulatory switch using E-CELL system,” BMC Microbiology, vol. 4, 2004, p. 44.

[3]	S.A. Forst, J. Delgado, and M. Inouye, “DNA-binding properties of the transcription activator (OmpR) for the upstream sequences of ompF in Escherichia coli are altered by envZ mutations and medium osmolarity.,” Journal of Bacteriology, vol. 171, Jun. 1989, pp. 2949–2955.

[4]	N. Ramani, M. Hedeshian, and M. Freundlich, “micF antisense RNA has a major role in osmoregulation of OmpF in Escherichia coli.,” Journal of Bacteriology, vol. 176, Aug. 1994, pp. 5005–5010.

[5]	T. Yoshida et al., “Transcription Regulation of ompF and ompC by a Single Transcription Factor, OmpR,” J. Biol. Chem., vol. 281, Jun. 2006, pp. 17114-17123.

[6]	S. Tokishita et al., “Transmembrane signal transduction and osmoregulation in Escherichia coli. Functional importance of the periplasmic domain of the membrane- located protein kinase, EnvZ,” J. Biol. Chem., vol. 266, Apr. 1991, pp. 6780-6785.

Psid met P2ogr promotor

Bibliography

[1]	B. Julien and R. Calendar, “Bacteriophage PSP3 and phiR73 activator proteins: analysis of promoter specificities.,” Journal of Bacteriology, vol. 178, Oct. 1996, pp. 5668–5675.

[2]	“Cambridge/Amplifier project - IGEM07”; http://parts.mit.edu/igem07/index.php/Cambridge/Amplifier_project.

Constitutive promoters

Estimated transcription rate for J23105:[http://parts.mit.edu/igem07/index.php?title=ETHZ/Parameters]
Scale other transcription rate with table in parts registry.

Estimate the rate of transcription from a constitutive promotor family member.

Estimates for the rate of transcription from the constitutive promotor family members. X is the GFP fluorescence in arbitrary units according to the Registry. Y is the number of mRNA's produced per second from that promotor

E. coli transcription rates

Bibliography

[1]	M. Bon, S.J. McGowan, and P.R. Cook, “Many expressed genes in bacteria and yeast are transcribed only once per cell cycle,” FASEB J., vol. 20, Aug. 2006, pp. 1721-1723.

@@ Line 16: / Line 16: @@
 ===mRNA decay===
-*[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays]
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/>
+<title>Bibliography</title>
+</head>
+<body>
+<table style="border-collapse:collapse;line-height:1.1em;">
+<tr style="vertical-align:top;"><td>[1]</td><td style="padding-left:4pt;">J.A. Bernstein et al., “Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays,” <span style="font-style:italic;">Proceedings of the National Academy of Sciences of the United States of America</span>,  vol. 99, Jul. 2002, pp. 9697–9702. <span class="Z3988" title="url_ver=Z39.88-2004&amp;ctx_ver=Z39.88-2004&amp;rft_id=info%3Adoi/10.1073/pnas.112318199&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=Global%20analysis%20of%20mRNA%20decay%20and%20abundance%20in%20Escherichia%20coli%20at%20single-gene%20resolution%20using%20two-color%20fluorescent%20DNA%20microarrays&amp;rft.jtitle=Proceedings%20of%20the%20National%20Academy%20of%20Sciences%20of%20the%20United%20States%20of%20America&amp;rft.stitle=Proc%20Natl%20Acad%20Sci%20U%20S%20A.%20&amp;rft.volume=99&amp;rft.issue=15&amp;rft.aufirst=Jonathan%20A.&amp;rft.aulast=Bernstein&amp;rft.au=Jonathan%20A.%20Bernstein&amp;rft.au=Arkady%20B.%20Khodursky&amp;rft.au=Pei-Hsun%20Lin&amp;rft.au=Sue%20Lin-Chao&amp;rft.au=Stanley%20N.%20Cohen&amp;rft.date=2002-07-23&amp;rft.pages=9697%E2%80%939702"></span></td></tr>
+<tr><td colspan="2">&nbsp;</td></tr>
+</table></body>
+</html>
 ===T7 RNAP===
-*[http://www.jbc.org/cgi/reprint/267/4/2640 Initiation of Transcription by T7 RNA Polymerase at Its Natural Promoters]
-*[http://pubs.acs.org/cgi-bin/article.cgi/bichaw/2002/41/i11/pdf/bi0158472.pdf Kinetic and Thermodynamic Basis of Promoter Strength: Multiple Steps of Transcription Initiation by T7 RNA Polymerase Are Modulated by the Promoter Sequence]
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en">
-*[http://www.openwetware.org/wiki/IGEM:Tsinghua/2007/Projects/RAP data T7 team Tsinghua 2007]
+<head>
-*[http://www.jbc.org/cgi/reprint/281/47/35677 Transient State Kinetics of Transcription Elongation by T7 RNA Polymerase]
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/>
-*[http://www.jbc.org/cgi/content/full/279/5/3239#FIG2 Single molecule studies of T7 RNA polymerase]
+<title>Bibliography</title>
+</head>
+<body>
+<table style="border-collapse:collapse;line-height:1.1em;">
+<tr style="vertical-align:top;"><td>[1]</td><td style="padding-left:4pt;">“IGEM:Tsinghua/2007/Projects/RAP - OpenWetWare”; http://www.openwetware.org/wiki/IGEM:Tsinghua/2007/Projects/RAP.</td></tr>
+<tr><td colspan="2">&nbsp;</td></tr>
+<tr style="vertical-align:top;"><td>[2]</td><td style="padding-left:4pt;">R. Ikeda, A. Lin, and J. Clarke, “Initiation of transcription by T7 RNA polymerase as its natural promoters,” <span style="font-style:italic;">J. Biol. Chem.</span>,  vol. 267, Feb. 1992, pp. 2640-2649. <span class="Z3988" title="url_ver=Z39.88-2004&amp;ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=Initiation%20of%20transcription%20by%20T7%20RNA%20polymerase%20as%20its%20natural%20promoters&amp;rft.jtitle=J.%20Biol.%20Chem.&amp;rft.volume=267&amp;rft.issue=4&amp;rft.aufirst=RA&amp;rft.aulast=Ikeda&amp;rft.au=RA%20Ikeda&amp;rft.au=AC%20Lin&amp;rft.au=J%20Clarke&amp;rft.date=1992-02-05&amp;rft.pages=2640-2649"></span></td></tr>
+<tr><td colspan="2">&nbsp;</td></tr>
+<tr style="vertical-align:top;"><td>[3]</td><td style="padding-left:4pt;">R. Bandwar et al., “Kinetic and Thermodynamic Basis of Promoter Strength: Multiple Steps of Transcription Initiation by T7 RNA Polymerase Are Modulated by the Promoter Sequence,” <span style="font-style:italic;">Biochemistry</span>,  vol. 41, Mar. 2002, pp. 3586-3595. <span class="Z3988" title="url_ver=Z39.88-2004&amp;ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=Kinetic%20and%20Thermodynamic%20Basis%20of%20Promoter%20Strength%3A%20Multiple%20Steps%20of%20Transcription%20Initiation%20by%20T7%20RNA%20Polymerase%20Are%20Modulated%20by%20the%20Promoter%20Sequence&amp;rft.jtitle=Biochemistry&amp;rft.stitle=Biochemistry&amp;rft.volume=41&amp;rft.issue=11&amp;rft.aufirst=R.P.&amp;rft.aulast=Bandwar&amp;rft.au=R.P.%20Bandwar&amp;rft.au=Y.%20Jia&amp;rft.au=N.M.%20Stano&amp;rft.au=S.S.%20Patel&amp;rft.date=2002-03-19&amp;rft.pages=3586-3595&amp;rft.issn=0006-2960"></span></td></tr>
+<tr><td colspan="2">&nbsp;</td></tr>
+<tr style="vertical-align:top;"><td>[4]</td><td style="padding-left:4pt;">G.M. Skinner et al., “Promoter Binding, Initiation, and Elongation By Bacteriophage T7 RNA Polymerase: A SINGLE-MOLECULE VIEW OF THE TRANSCRIPTION CYCLE,” <span style="font-style:italic;">J. Biol. Chem.</span>,  vol. 279, Jan. 2004, pp. 3239-3244. <span class="Z3988" title="url_ver=Z39.88-2004&amp;ctx_ver=Z39.88-2004&amp;rft_id=info%3Adoi/10.1074/jbc.M310471200&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=Promoter%20Binding%2C%20Initiation%2C%20and%20Elongation%20By%20Bacteriophage%20T7%20RNA%20Polymerase%3A%20A%20SINGLE-MOLECULE%20VIEW%20OF%20THE%20TRANSCRIPTION%20CYCLE&amp;rft.jtitle=J.%20Biol.%20Chem.&amp;rft.volume=279&amp;rft.issue=5&amp;rft.aufirst=Gary%20M.&amp;rft.aulast=Skinner&amp;rft.au=Gary%20M.%20Skinner&amp;rft.au=Christoph%20G.%20Baumann&amp;rft.au=Diana%20M.%20Quinn&amp;rft.au=Justin%20E.%20Molloy&amp;rft.au=James%20G.%20Hoggett&amp;rft.date=2004&amp;rft.pages=3239-3244"></span></td></tr>
+<tr><td colspan="2">&nbsp;</td></tr>
+<tr style="vertical-align:top;"><td>[5]</td><td style="padding-left:4pt;">V.S. Anand and S.S. Patel, “Transient State Kinetics of Transcription Elongation by T7 RNA Polymerase,” <span style="font-style:italic;">J. Biol. Chem.</span>,  vol. 281, Nov. 2006, pp. 35677-35685. <span class="Z3988" title="url_ver=Z39.88-2004&amp;ctx_ver=Z39.88-2004&amp;rft_id=info%3Adoi/10.1074/jbc.M608180200&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=Transient%20State%20Kinetics%20of%20Transcription%20Elongation%20by%20T7%20RNA%20Polymerase&amp;rft.jtitle=J.%20Biol.%20Chem.&amp;rft.volume=281&amp;rft.issue=47&amp;rft.aufirst=Vasanti%20Subramanian&amp;rft.aulast=Anand&amp;rft.au=Vasanti%20Subramanian%20Anand&amp;rft.au=Smita%20S.%20Patel&amp;rft.date=2006-11-24&amp;rft.pages=35677-35685"></span></td></tr>
+<tr><td colspan="2">&nbsp;</td></tr>
+</table></body>
+</html>
 ===LacI - LuxI===
-* [http://www.tam.cornell.edu/tam/cms/manage/upload/Strogatz_20coupled_repressilators_PNAS.pdf Coupled repressilators]
-* [http://www.nature.com/nature/journal/v403/n6767/full/403335a0.html A synthetic oscillatory network of transcriptional regulators]
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/>
+<title>Bibliography</title>
+</head>
+<body>
+<table style="border-collapse:collapse;line-height:1.1em;">
+<tr style="vertical-align:top;"><td>[1]</td><td style="padding-left:4pt;">M.B. Elowitz and S. Leibler, “A synthetic oscillatory network of transcriptional regulators,” <span style="font-style:italic;">Nature</span>,  vol. 403, Jan. 2000, pp. 335-338. <span class="Z3988" title="url_ver=Z39.88-2004&amp;ctx_ver=Z39.88-2004&amp;rft_id=info%3Adoi/10.1038/35002125&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=A%20synthetic%20oscillatory%20network%20of%20transcriptional%20regulators&amp;rft.jtitle=Nature&amp;rft.stitle=Nature&amp;rft.volume=403&amp;rft.issue=6767&amp;rft.aufirst=Michael%20B.&amp;rft.aulast=Elowitz&amp;rft.au=Michael%20B.%20Elowitz&amp;rft.au=Stanislas%20Leibler&amp;rft.date=2000&amp;rft.pages=335-338&amp;rft.issn=0028-0836"></span></td></tr>
+<tr><td colspan="2">&nbsp;</td></tr>
+<tr style="vertical-align:top;"><td>[2]</td><td style="padding-left:4pt;">“Modeling a synthetic multicellular clock: Repressilators coupled by quorum sensing,” Jul. 2004; http://www.pnas.org/content/101/30/10955.full.</td></tr>
+<tr><td colspan="2">&nbsp;</td></tr>
+</table></body>
+</html>
 ===LuxI, LuxR, mRNALuxI, mRNALuxR decay===
-*[http://bioinformatics.oxfordjournals.org/cgi/content/full/21/11/2722#E11 Noise-induced cooperative behavior in a multicell system]
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/>
+<title>Bibliography</title>
+</head>
+<body>
+<table style="border-collapse:collapse;line-height:1.1em;">
+<tr style="vertical-align:top;"><td>[1]</td><td style="padding-left:4pt;">“Generation of cell-to-cell signals in quorum sensing: acyl homoserine lactone synthase activity of a purified Vibrio fischeri LuxI protein,” Sep. 1996; http://www.pnas.org/content/93/18/9505.</td></tr>
+<tr><td colspan="2">&nbsp;</td></tr>
+<tr style="vertical-align:top;"><td>[2]</td><td style="padding-left:4pt;">L. Chen et al., “Noise-induced cooperative behavior in a multicell system,” <span style="font-style:italic;">Bioinformatics</span>,  vol. 21, Jun. 2005, pp. 2722-2729. <span class="Z3988" title="url_ver=Z39.88-2004&amp;ctx_ver=Z39.88-2004&amp;rft_id=info%3Adoi/10.1093/bioinformatics/bti392&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=Noise-induced%20cooperative%20behavior%20in%20a%20multicell%20system&amp;rft.jtitle=Bioinformatics&amp;rft.volume=21&amp;rft.issue=11&amp;rft.aufirst=Luonan&amp;rft.aulast=Chen&amp;rft.au=Luonan%20Chen&amp;rft.au=Ruiqi%20Wang&amp;rft.au=Tianshou%20Zhou&amp;rft.au=Kazuyuki%20Aihara&amp;rft.date=2005-06-01&amp;rft.pages=2722-2729"></span></td></tr>
-*[http://www.pnas.org/content/93/18/9505 LuxI kinetics]
+<tr><td colspan="2">&nbsp;</td></tr>
+</table></body>
+</html>
 ===HSL stuff===
-*[http://aem.asm.org/cgi/content/abstract/71/3/1291 Rapid Acyl-Homoserine Lactone Quorum Signal Biodegradation in Diverse Soils] Fig 6: half-life 185 h ==> decay rate 1.02 * 10^-6 s^-1 ==> 0.00889 nM/h
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/>
+<title>Bibliography</title>
+</head>
+<body>
+<table style="border-collapse:collapse;line-height:1.1em;">
+<tr style="vertical-align:top;"><td>[1]</td><td style="padding-left:4pt;">“Acyl homoserine-lactone quorum-sensing signal generation,” Apr. 1999; http://www.pnas.org/content/96/8/4360.full.</td></tr>
+<tr><td colspan="2">&nbsp;</td></tr>
+<tr style="vertical-align:top;"><td>[2]</td><td style="padding-left:4pt;">P. Nilsson et al., “Kinetics of the AHL Regulatory System in a Model Biofilm System: How Many Bacteria Constitute a "Quorum"?,” <span style="font-style:italic;">Journal of Molecular Biology</span>,  vol. 309, Jun. 2001, pp. 631-640. <span class="Z3988" title="url_ver=Z39.88-2004&amp;ctx_ver=Z39.88-2004&amp;rft_id=info%3Adoi/10.1006/jmbi.2001.4697&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=Kinetics%20of%20the%20AHL%20Regulatory%20System%20in%20a%20Model%20Biofilm%20System%3A%20How%20Many%20Bacteria%20Constitute%20a%20%22Quorum%22%3F&amp;rft.jtitle=Journal%20of%20Molecular%20Biology&amp;rft.volume=309&amp;rft.issue=3&amp;rft.aufirst=Patric&amp;rft.aulast=Nilsson&amp;rft.au=Patric%20Nilsson&amp;rft.au=Anna%20Olofsson&amp;rft.au=Magnus%20Fagerlind&amp;rft.au=Torbj%EF%BF%BDrn%20Fagerstr%EF%BF%BDm&amp;rft.au=Scott%20Rice&amp;rft.au=Staffan%20Kjelleberg&amp;rft.au=Peter%20Steinberg&amp;rft.date=2001-06-08&amp;rft.pages=631-640"></span></td></tr>
-*[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-457D0X9-9&_user=877992&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000047079&_version=1&_urlVersion=0&_userid=877992&md5=36d07f326b2c2e55c4de05a1ab426e09 Kinetics of the AHL Regulatory System in a Model Biofilm System]
+<tr><td colspan="2">&nbsp;</td></tr>
+<tr style="vertical-align:top;"><td>[3]</td><td style="padding-left:4pt;">Y. Wang and J.R. Leadbetter, “Rapid Acyl-Homoserine Lactone Quorum Signal Biodegradation in Diverse Soils,” <span style="font-style:italic;">Appl. Environ. Microbiol.</span>,  vol. 71, Mar. 2005, pp. 1291-1299. <span class="Z3988" title="url_ver=Z39.88-2004&amp;ctx_ver=Z39.88-2004&amp;rft_id=info%3Adoi/10.1128/AEM.71.3.1291-1299.2005&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=Rapid%20Acyl-Homoserine%20Lactone%20Quorum%20Signal%20Biodegradation%20in%20Diverse%20Soils&amp;rft.jtitle=Appl.%20Environ.%20Microbiol.&amp;rft.volume=71&amp;rft.issue=3&amp;rft.aufirst=Ya-Juan&amp;rft.aulast=Wang&amp;rft.au=Ya-Juan%20Wang&amp;rft.au=Jared%20Renton%20Leadbetter&amp;rft.date=2005-03-01&amp;rft.pages=1291-1299"></span></td></tr>
+<tr><td colspan="2">&nbsp;</td></tr>
+<tr style="vertical-align:top;"><td>[4]</td><td style="padding-left:4pt;">L. Wang et al., “Specificity and Enzyme Kinetics of the Quorum-quenching N-Acyl Homoserine Lactone Lactonase (AHL-lactonase),” <span style="font-style:italic;">J. Biol. Chem.</span>,  vol. 279, Apr. 2004, pp. 13645-13651. <span class="Z3988" title="url_ver=Z39.88-2004&amp;ctx_ver=Z39.88-2004&amp;rft_id=info%3Adoi/10.1074/jbc.M311194200&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=Specificity%20and%20Enzyme%20Kinetics%20of%20the%20Quorum-quenching%20N-Acyl%20Homoserine%20Lactone%20Lactonase%20(AHL-lactonase)&amp;rft.jtitle=J.%20Biol.%20Chem.&amp;rft.volume=279&amp;rft.issue=14&amp;rft.aufirst=Lian-Hui&amp;rft.aulast=Wang&amp;rft.au=Lian-Hui%20Wang&amp;rft.au=Li-Xing%20Weng&amp;rft.au=Yi-Hu%20Dong&amp;rft.au=Lian-Hui%20Zhang&amp;rft.date=2004-04-02&amp;rft.pages=13645-13651"></span></td></tr>
+<tr><td colspan="2">&nbsp;</td></tr>
+</table></body>
+</html>
-*[http://www.pnas.org/content/96/8/4360.full HSL lactone synthesis kinetics by a LuxI-related enzyme]
-*[http://www.jbc.org/cgi/content/full/279/14/13645#TBL2 Lactonase mediated HSL degradation (hydrolysis)]
 ====Diffusion====
-*[http://jb.asm.org/cgi/content/full/185/5/1485 AHL diffusion model]
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en">
+<head>
-*[http://jb.asm.org/cgi/content/full/185/5/1485 AHL diffusion constants & stuff]
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/>
+<title>Bibliography</title>
+</head>
+<body>
+<table style="border-collapse:collapse;line-height:1.1em;">
+<tr style="vertical-align:top;"><td>[1]</td><td style="padding-left:4pt;">P.S. Stewart, “Diffusion in Biofilms,” <span style="font-style:italic;">J. Bacteriol.</span>,  vol. 185, Mar. 2003, pp. 1485-1491. <span class="Z3988" title="url_ver=Z39.88-2004&amp;ctx_ver=Z39.88-2004&amp;rft_id=info%3Adoi/10.1128/JB.185.5.1485-1491.2003&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=Diffusion%20in%20Biofilms&amp;rft.jtitle=J.%20Bacteriol.&amp;rft.volume=185&amp;rft.issue=5&amp;rft.aufirst=Philip%20S.&amp;rft.aulast=Stewart&amp;rft.au=Philip%20S.%20Stewart&amp;rft.date=2003-03-01&amp;rft.pages=1485-1491"></span></td></tr>
+<tr><td colspan="2">&nbsp;</td></tr>
+</table></body>
+</html>
 ===OmpR, OmpF===
-*[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=543474&blobtype=pdf A simulation model of Escherichia coli osmoregulatory switch using E-CELL system] (Relevance: High), bekijk pg.11/13
-*[http://www.jbc.org/cgi/reprint/281/25/17114 Transcription Regulation of ompF and ompC by a Single Transcription Factor, OmpR] (Relevance: Medium)
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en">
-*[http://jb.oxfordjournals.org/cgi/reprint/111/6/707.pdf Transmembrane Signal Transduction and Osmoregulation in Escherichia coli: Functional Importance of the Transmembrane Regions of Membrane-Located Protein Kinase, EnvZ] (Relevance:?), geen toegang tenzij account
+<head>
-*[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=209999 DNA-Binding Properties of the Transcription Activator (OmpR) for the Upstream Sequences of ompF in Escherichia coli Are Altered by envZ Mutations and Medium Osmolarity] (Relevance: Low)
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/>
-*[http://jb.asm.org/cgi/reprint/176/5/1309 A Distant Upstream Site Involved in the Negative Regulation of the Escherichia coli ompF Gene] (Relevance: ?), voor repressor regulatie van OmpF door OmpR
+<title>Bibliography</title>
-*[http://jb.asm.org/cgi/reprint/176/16/5005.pdf micF Antisense RNA Has a Major Role in Osmoregulation of OmpF in Escherichia coli] (Relevance: Low), invloed ''''Antisense RNA'''' op OmpF regulatie, hmm...
+</head>
+<body>
+<table style="border-collapse:collapse;line-height:1.1em;">
+<tr style="vertical-align:top;"><td>[1]</td><td style="padding-left:4pt;">K.J. Huang, J.L. Schieberl, and M.M. Igo, “A distant upstream site involved in the negative regulation of the Escherichia coli ompF gene.,” <span style="font-style:italic;">Journal of Bacteriology</span>,  vol. 176, Mar. 1994, pp. 1309–1315. <span class="Z3988" title="url_ver=Z39.88-2004&amp;ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=A%20distant%20upstream%20site%20involved%20in%20the%20negative%20regulation%20of%20the%20Escherichia%20coli%20ompF%20gene.&amp;rft.jtitle=Journal%20of%20Bacteriology&amp;rft.stitle=J%20Bacteriol.%20&amp;rft.volume=176&amp;rft.issue=5&amp;rft.aufirst=K%20J&amp;rft.aulast=Huang&amp;rft.au=K%20J%20Huang&amp;rft.au=J%20L%20Schieberl&amp;rft.au=M%20M%20Igo&amp;rft.date=1994-03&amp;rft.pages=1309%E2%80%931315"></span></td></tr>
+<tr><td colspan="2">&nbsp;</td></tr>
+<tr style="vertical-align:top;"><td>[2]</td><td style="padding-left:4pt;">K.V. Srividhya and S. Krishnaswamy, “A simulation model of Escherichia coli osmoregulatory switch using E-CELL system,” <span style="font-style:italic;">BMC Microbiology</span>,  vol. 4, 2004, p. 44. <span class="Z3988" title="url_ver=Z39.88-2004&amp;ctx_ver=Z39.88-2004&amp;rft_id=info%3Adoi/10.1186/1471-2180-4-44&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=A%20simulation%20model%20of%20Escherichia%20coli%20osmoregulatory%20switch%20using%20E-CELL%20system&amp;rft.jtitle=BMC%20Microbiology&amp;rft.stitle=BMC%20Microbiol.%20&amp;rft.volume=4&amp;rft.aufirst=K.%20V.&amp;rft.aulast=Srividhya&amp;rft.au=K.%20V.%20Srividhya&amp;rft.au=Sankaran%20Krishnaswamy&amp;rft.date=2004&amp;rft.pages=44"></span></td></tr>
+<tr><td colspan="2">&nbsp;</td></tr>
+<tr style="vertical-align:top;"><td>[3]</td><td style="padding-left:4pt;">S.A. Forst, J. Delgado, and M. Inouye, “DNA-binding properties of the transcription activator (OmpR) for the upstream sequences of ompF in Escherichia coli are altered by envZ mutations and medium osmolarity.,” <span style="font-style:italic;">Journal of Bacteriology</span>,  vol. 171, Jun. 1989, pp. 2949–2955. <span class="Z3988" title="url_ver=Z39.88-2004&amp;ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=DNA-binding%20properties%20of%20the%20transcription%20activator%20(OmpR)%20for%20the%20upstream%20sequences%20of%20ompF%20in%20Escherichia%20coli%20are%20altered%20by%20envZ%20mutations%20and%20medium%20osmolarity.&amp;rft.jtitle=Journal%20of%20Bacteriology&amp;rft.stitle=J%20Bacteriol.%20&amp;rft.volume=171&amp;rft.issue=6&amp;rft.aufirst=S%20A&amp;rft.aulast=Forst&amp;rft.au=S%20A%20Forst&amp;rft.au=J.%20Delgado&amp;rft.au=M.%20Inouye&amp;rft.date=1989-06&amp;rft.pages=2949%E2%80%932955"></span></td></tr>
+<tr><td colspan="2">&nbsp;</td></tr>
+<tr style="vertical-align:top;"><td>[4]</td><td style="padding-left:4pt;">N. Ramani, M. Hedeshian, and M. Freundlich, “micF antisense RNA has a major role in osmoregulation of OmpF in Escherichia coli.,” <span style="font-style:italic;">Journal of Bacteriology</span>,  vol. 176, Aug. 1994, pp. 5005–5010. <span class="Z3988" title="url_ver=Z39.88-2004&amp;ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=micF%20antisense%20RNA%20has%20a%20major%20role%20in%20osmoregulation%20of%20OmpF%20in%20Escherichia%20coli.&amp;rft.jtitle=Journal%20of%20Bacteriology&amp;rft.stitle=J%20Bacteriol.%20&amp;rft.volume=176&amp;rft.issue=16&amp;rft.aufirst=N.&amp;rft.aulast=Ramani&amp;rft.au=N.%20Ramani&amp;rft.au=M.%20Hedeshian&amp;rft.au=M.%20Freundlich&amp;rft.date=1994-08&amp;rft.pages=5005%E2%80%935010"></span></td></tr>
+<tr><td colspan="2">&nbsp;</td></tr>
+<tr style="vertical-align:top;"><td>[5]</td><td style="padding-left:4pt;">T. Yoshida et al., “Transcription Regulation of ompF and ompC by a Single Transcription Factor, OmpR,” <span style="font-style:italic;">J. Biol. Chem.</span>,  vol. 281, Jun. 2006, pp. 17114-17123. <span class="Z3988" title="url_ver=Z39.88-2004&amp;ctx_ver=Z39.88-2004&amp;rft_id=info%3Adoi/10.1074/jbc.M602112200&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=Transcription%20Regulation%20of%20ompF%20and%20ompC%20by%20a%20Single%20Transcription%20Factor%2C%20OmpR&amp;rft.jtitle=J.%20Biol.%20Chem.&amp;rft.volume=281&amp;rft.issue=25&amp;rft.aufirst=Takeshi&amp;rft.aulast=Yoshida&amp;rft.au=Takeshi%20Yoshida&amp;rft.au=Ling%20Qin&amp;rft.au=Linda%20A.%20Egger&amp;rft.au=Masayori%20Inouye&amp;rft.date=2006-06-23&amp;rft.pages=17114-17123"></span></td></tr>
+<tr><td colspan="2">&nbsp;</td></tr>
+<tr style="vertical-align:top;"><td>[6]</td><td style="padding-left:4pt;">S. Tokishita et al., “Transmembrane signal transduction and osmoregulation in Escherichia coli. Functional importance of the periplasmic domain of the membrane- located protein kinase, EnvZ,” <span style="font-style:italic;">J. Biol. Chem.</span>,  vol. 266, Apr. 1991, pp. 6780-6785. <span class="Z3988" title="url_ver=Z39.88-2004&amp;ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=Transmembrane%20signal%20transduction%20and%20osmoregulation%20in%20Escherichia%20coli.%20Functional%20importance%20of%20the%20periplasmic%20domain%20of%20the%20membrane-%20located%20protein%20kinase%2C%20EnvZ&amp;rft.jtitle=J.%20Biol.%20Chem.&amp;rft.volume=266&amp;rft.issue=11&amp;rft.aufirst=S&amp;rft.aulast=Tokishita&amp;rft.au=S%20Tokishita&amp;rft.au=A%20Kojima&amp;rft.au=H%20Aiba&amp;rft.au=T%20Mizuno&amp;rft.date=1991-04-15&amp;rft.pages=6780-6785"></span></td></tr>
+<tr><td colspan="2">&nbsp;</td></tr>
+</table></body>
+</html>
 ===Psid met P2ogr promotor===
-*[http://parts.mit.edu/igem07/index.php/Cambridge/Amplifier_project Cambridge amplifier project, combinatie van verschillende promotoren met verschillende activatoren, experimenteel amplification factor bepaald met GFP reporter]
-*[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=178405 P<sub>sid</sub> promotor with different activators]
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/>
+<title>Bibliography</title>
+</head>
+<body>
+<table style="border-collapse:collapse;line-height:1.1em;">
+<tr style="vertical-align:top;"><td>[1]</td><td style="padding-left:4pt;">B. Julien and R. Calendar, “Bacteriophage PSP3 and phiR73 activator proteins: analysis of promoter specificities.,” <span style="font-style:italic;">Journal of Bacteriology</span>,  vol. 178, Oct. 1996, pp. 5668–5675. <span class="Z3988" title="url_ver=Z39.88-2004&amp;ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=Bacteriophage%20PSP3%20and%20phiR73%20activator%20proteins%3A%20analysis%20of%20promoter%20specificities.&amp;rft.jtitle=Journal%20of%20Bacteriology&amp;rft.stitle=J%20Bacteriol.%20&amp;rft.volume=178&amp;rft.issue=19&amp;rft.aufirst=B.&amp;rft.aulast=Julien&amp;rft.au=B.%20Julien&amp;rft.au=R.%20Calendar&amp;rft.date=1996-10&amp;rft.pages=5668%E2%80%935675"></span></td></tr>
+<tr><td colspan="2">&nbsp;</td></tr>
+<tr style="vertical-align:top;"><td>[2]</td><td style="padding-left:4pt;">“Cambridge/Amplifier project - IGEM07”; http://parts.mit.edu/igem07/index.php/Cambridge/Amplifier_project.</td></tr>
+<tr><td colspan="2">&nbsp;</td></tr>
+</table></body>
+</html>
 ===Constitutive promoters===
@@ Line 73: / Line 176: @@
 ===E. coli transcription rates===
-[http://www.fasebj.org/cgi/content/summary/20/10/1721 Paper about the calculated transcription rates for every E.coli ORF] <br>
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en">
-[http://users.path.ox.ac.uk/~pcook/data/catalogs.html Tables with the calculated transcription rates for every E.coli ORF]
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/>
+<title>Bibliography</title>
+</head>
+<body>
+<table style="border-collapse:collapse;line-height:1.1em;">
+<tr style="vertical-align:top;"><td>[1]</td><td style="padding-left:4pt;">M. Bon, S.J. McGowan, and P.R. Cook, “Many expressed genes in bacteria and yeast are transcribed only once per cell cycle,” <span style="font-style:italic;">FASEB J.</span>,  vol. 20, Aug. 2006, pp. 1721-1723. <span class="Z3988" title="url_ver=Z39.88-2004&amp;ctx_ver=Z39.88-2004&amp;rft_id=info%3Adoi/10.1096/fj.06-6087fje&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=Many%20expressed%20genes%20in%20bacteria%20and%20yeast%20are%20transcribed%20only%20once%20per%20cell%20cycle&amp;rft.jtitle=FASEB%20J.&amp;rft.volume=20&amp;rft.issue=10&amp;rft.aufirst=Michael&amp;rft.aulast=Bon&amp;rft.au=Michael%20Bon&amp;rft.au=Simon%20J.%20McGowan&amp;rft.au=Peter%20R.%20Cook&amp;rft.date=2006-08-01&amp;rft.pages=1721-1723"></span></td></tr>
+<tr><td colspan="2">&nbsp;</td></tr>
+</table></body>
+</html>

Team:KULeuven/Model/Kinetic Constants

From 2008.igem.org

Revision as of 10:25, 11 September 2008

Contents

ETHZ list of parameters

mRNA decay

T7 RNAP

LacI - LuxI

LuxI, LuxR, mRNALuxI, mRNALuxR decay

HSL stuff

Diffusion

OmpR, OmpF

Psid met P2ogr promotor

Constitutive promoters

E. coli transcription rates

[1]	“ETHZ/Parameters - IGEM07”; http://parts.mit.edu/igem07/index.php/ETHZ/Parameters.

[1]	J.A. Bernstein et al., “Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays,” Proceedings of the National Academy of Sciences of the United States of America, vol. 99, Jul. 2002, pp. 9697–9702.