From 2008.igem.org

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Revision as of 17:47, 16 July 2008

Result:

Home
The Team
Research Labs and Groups Students Instructors Advisors Pictures
The Project
Summary Components
Input Output Filter Invertimer Reset Cell Death Memory
End Evaluation Literature Brainstorm
Ethics
Submitted Parts
Listing Sandbox
Modeling
Overview Kinetic Constants Components
Output Filter Invertimer Reset Cell Death Memory
Full Model Sensitivity Analysis Multi-cell Model Diffusion
Data Analysis
Overview New Parts
GFP (LVA-tag) T7 (UmuD-tag) Antisense LuxI Celldeath (ccdB) Hybrid Promotor
Components
Input Output Filter Invertimer Reset Cell Death Memory
Full Model
Software
Multi-cell Toolbox Simbiology2LaTeX Toolbox
Notebook
Calendar Summer Holidays Reports
Daily Weekly
Lab Data
Freezer Primers Ligation
Tools Press Guestbook

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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<div id="ddnav" align="center">
<ul>
	<li>
		<a href="https://2008.igem.org/Team:KULeuven">Home</a>
	</li>
	<li>
		<a>The Team</a>
		<div>
			<a href="https://2008.igem.org/Team:KULeuven/Team/LabsandGroups">Research Labs and Groups</a>
			<a href="https://2008.igem.org/Team:KULeuven/Team/Students">Students</a>
			<a href="https://2008.igem.org/Team:KULeuven/Team/Instructors">Instructors</a>
			<a href="https://2008.igem.org/Team:KULeuven/Team/Advisors">Advisors</a>
                        <a href="https://2008.igem.org/Team:KULeuven/Team/Pictures">Pictures</a>
		</div>
	</li>
	<li>
		<a>The Project</a>
		<div>
			<a href="https://2008.igem.org/Team:KULeuven/Project">Summary</a>
			<span>
				<a>Components</a>
				<div>
					<a href="https://2008.igem.org/Team:KULeuven/Project/Input">Input</a>
					<a href="https://2008.igem.org/Team:KULeuven/Project/Output">Output</a>
					<a href="https://2008.igem.org/Team:KULeuven/Project/Filter">Filter</a>
					<a href="https://2008.igem.org/Team:KULeuven/Project/Inverter">Invertimer</a>
					<a href="https://2008.igem.org/Team:KULeuven/Project/Reset">Reset</a>
					<a href="https://2008.igem.org/Team:KULeuven/Project/CellDeath">Cell Death</a>
					<a href="https://2008.igem.org/Team:KULeuven/Project/Memory">Memory</a>
				</div>
			</span>
                        <a href="https://2008.igem.org/Team:KULeuven/Evaluation">End Evaluation</a>
			<a href="https://2008.igem.org/Team:KULeuven/Literature">Literature</a>
                        <a href="https://2008.igem.org/Team:KULeuven/Brainstorm">Brainstorm</a>
		</div>
	</li>
        <li>
		<a>Ethics</a>
		<div>

		</div>
	</li>
	<li>
		<a>Submitted Parts</a>
		<div>
			<a href="https://2008.igem.org/Team:KULeuven/Parts">Listing</a>
			<a href="http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2008&group=KULeuven">Sandbox</a>
		</div>
	</li>
	<li>
		<a>Modeling</a>
		<div>
			<a href="https://2008.igem.org/Team:KULeuven/Model/Overview">Overview</a>
			<a href="https://2008.igem.org/Team:KULeuven/Model/KineticConstants">Kinetic Constants</a>
			<span>
				<a>Components</a>
				<div>
					<a href="https://2008.igem.org/Team:KULeuven/Model/Output">Output</a>
					<a href="https://2008.igem.org/Team:KULeuven/Model/Filter">Filter</a>
					<a href="https://2008.igem.org/Team:KULeuven/Model/Inverter">Invertimer</a>
					<a href="https://2008.igem.org/Team:KULeuven/Model/Reset">Reset</a>
					<a href="https://2008.igem.org/Team:KULeuven/Model/CellDeath">Cell Death</a>
					<a href="https://2008.igem.org/Team:KULeuven/Model/Memory">Memory</a>
				</div>
			</span>
			<a href="https://2008.igem.org/Team:KULeuven/Model/FullModel">Full Model</a>
                        <a href="https://2008.igem.org/Team:KULeuven/Model/Sensitivity">Sensitivity Analysis</a>
			<a href="https://2008.igem.org/Team:KULeuven/Model/MultiCell">Multi-cell Model</a>
			<a href="https://2008.igem.org/Team:KULeuven/Model/Diffusion">Diffusion</a>
		</div>
	</li>
	<li>
		<a>Data Analysis</a>
		<div>
			<a href="https://2008.igem.org/Team:KULeuven/Data/Overview">Overview</a>
			<span>
				<a>New Parts</a>
				<div>
					<a href="https://2008.igem.org/Team:KULeuven/Data/GFP">GFP (LVA-tag)</a>
					<a href="https://2008.igem.org/Team:KULeuven/Data/T7">T7 (UmuD-tag)</a>
					<a href="https://2008.igem.org/Team:KULeuven/Data/Antisense">Antisense LuxI</a>
					<a href="https://2008.igem.org/Team:KULeuven/Data/ccdB">Celldeath (ccdB)</a>
					<a 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>

Modeling

Numbers.xls

[http://www.nature.com/nature/journal/v438/n7067/full/nature04405.html Synthetic biology: Engineering Escherichia coli to see light]

CellDesigner

Output

Parameter values Cell Death
Name	Value	Reference
Degradation
CFP (protein)	1.05E-4 /s	[http://parts.mit.edu/igem07/index.php/ETHZ/Parameters link]
CFP (mRNA)	0.0023 /s	[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
Transcription Rate
CFP	OmpF dependend
Translation Rate
CFP	0.5 /s	Based on effenciency RBS

Cell Death

Parameter values Cell Death
Name	Value	Reference
Degradation
LuxR (protein)	0.0010 /s
LuxR (mRNA)	0.00227 /s	[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
CcdB (protein)	7.7E-5 /s	[http://www.ncbi.nlm.nih.gov/pubmed/8022284?dopt=abstract link]
CcdB (mRNA)	0.00231 /s	[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
HSL	1.02E-6/s	[http://aem.asm.org/cgi/content/abstract/71/3/1291 link]
Dissociation Rate
K_a (HSL+LuxR)	1E6 /s
K_d (HSL+LuxR)	1 /s
Dissociation Constant
HSL-LuxR	1E-6 M/L	[http://jb.asm.org/cgi/content/full/189/11/4127?view=long&pmid=17400743 link]
Binding LuxR on LuxPromotor	1E-9 M/L	[http://jb.asm.org/cgi/content/full/189/11/4127?view=long&pmid=17400743 link]
Transcription Rate
LuxR (constitutive promotor)	0.025 mRNA/s	see sections on Constitutive Promotors & E. coli transcription Rates
CcdB (LuxR repressor)	k_1K_m^n/(K_m^n + [LuxR]^n) = 0.0251E-9/(1E-9^1+[LuxR])

Filter

Parameter values Filter
Name	Value	Reference
Degradation
pT7_tag(protein)	0.00155/s
mRNA_RIBOKEY (RNA)	0.00462 /s	[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
gesloten_mRNA_T7 (RNA)	0.00462 /s	[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
open_mRNA_T7 (RNA)	0.00231 / s	[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
open_mRNA_T7_complex (RNA)	0.00231 /s	[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
Equilibrium Constant
closed and open mRNA	0,015
closed and key complex mRNA	0.0212 /M
Transcription Rate
mRNA_RIBOKEY	Input dependent
mRNA_T7	0,0011 mRNA/s

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]

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]

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]

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

[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]

@@ Line 5: / Line 5: @@
 =Modeling=
-* [[Image:Numbers.xls]]
+* [https://static.igem.org/mediawiki/2008/1/19/Numbers.xls Numbers.xls]
 * [http://www.nature.com/nature/journal/v438/n7067/full/nature04405.html Synthetic biology: Engineering Escherichia coli to see light]

Team:KULeuven/Modeling