Team:KULeuven/Model/Kinetic Constants
From 2008.igem.org
Result:
To have a dropdown for your own team copy over all of the content below. It might be needed to adjust a thing or two. Comments have been added throughout the code what must be changed.
Inspirational websites:
- [http://javascript-array.com/scripts/simple_drop_down_menu/ Most basic dropdown menu, with no submenu's]
- [http://jquery.com/ The javascript library used to add effects and optimise the dropdown]
- [http://www.tyssendesign.com.au/articles/css/centering-a-dropdown-menu/ How to center a ul list effectively]
The dropdown has been created and developed by the KULeuven team.
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href="https://2008.igem.org/Team:KULeuven/Data/HybridProm">Hybrid Promotor</a> </div> </span> <span> <a>Components</a> <div> <a href="https://2008.igem.org/Team:KULeuven/Data/Input">Input</a> <a href="https://2008.igem.org/Team:KULeuven/Data/Output">Output</a> <a href="https://2008.igem.org/Team:KULeuven/Data/Filter">Filter</a> <a href="https://2008.igem.org/Team:KULeuven/Data/Inverter">Invertimer</a> <a href="https://2008.igem.org/Team:KULeuven/Data/Reset">Reset</a> <a href="https://2008.igem.org/Team:KULeuven/Data/CellDeath">Cell Death</a> <a href="https://2008.igem.org/Team:KULeuven/Data/Memory">Memory</a> </div> </span> <a href="https://2008.igem.org/Team:KULeuven/Data/FullModel">Full Model</a> </div> </li> <li> <a>Software</a> <div> <a href="https://2008.igem.org/Team:KULeuven/Software/MultiCell">Multi-cell Toolbox</a> <a href="https://2008.igem.org/Team:KULeuven/Software/Simbiology2LaTeX">Simbiology2LaTeX Toolbox</a> </div> </li> <li> <a>Notebook</a> <div> <a href="https://2008.igem.org/Team:KULeuven/Meeting_Calendar">Calendar</a> <a href="https://2008.igem.org/Team:KULeuven/SummerHolidays">Summer Holidays</a> <span> <a>Reports</a> <div> <a href="https://2008.igem.org/Team:KULeuven/Meeting Reports">Daily</a> <a href="https://2008.igem.org/Team:KULeuven/Weekly Meetings">Weekly</a> </div> </span> <span> <a>Lab Data</a> <div> <a href="https://2008.igem.org/Team:KULeuven/Freezer">Freezer</a> <a href="https://2008.igem.org/Team:KULeuven/Primers">Primers</a> <a href="https://2008.igem.org/Team:KULeuven/Ligation">Ligation</a> </div> </span> <a href="https://2008.igem.org/Team:KULeuven/Tools">Tools</a> <a href="https://2008.igem.org/Team:KULeuven/Press">Press</a> <a href="https://2008.igem.org/Team:KULeuven/Guestbook">Guestbook</a> </div> </li> </ul> </div> </div> </html>
Contents[hide] |
Kinetic Constants
ETHZ list of parameters
- [http://parts.mit.edu/igem07/index.php/ETHZ/Parameters ETHZ list of parameters]
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]
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]
- [http://www.openwetware.org/wiki/IGEM:Tsinghua/2007/Projects/RAP data T7 team Tsinghua 2007]
- [http://www.jbc.org/cgi/reprint/281/47/35677 Transient State Kinetics of Transcription Elongation by T7 RNA Polymerase]
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]
LuxI, LuxR, mRNALuxI, mRNALuxR decay
- [http://bioinformatics.oxfordjournals.org/cgi/content/full/21/11/2722#E11 Noise-induced cooperative behavior in a multicell system]
- [http://www.pnas.org/content/93/18/9505 LuxI kinetics]
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
- [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]
- [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)]
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)
- [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
- [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)
- [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
- [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...
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 Psid promotor with different activators]
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.
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]
[http://users.path.ox.ac.uk/~pcook/data/catalogs.html Tables with the calculated transcription rates for every E.coli ORF]