Team:KULeuven/Modeling

From 2008.igem.org

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{|style="font color="#000000"; background-color:#ffffff; border-spacing:6px; text-align:center" width="960px"
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{{:Team:KULeuven/Tools/Navigation_Bar}}
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!style="text-align:center; background-color:#003E81; border-width:0px; padding:3px;"|[[Team:KULeuven|<font color="#ffffff">Home</font>]]
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!style="text-align:center; background-color:#003E81; border-width:0px; padding:3px;"|[[Team:KULeuven/Team|<font color="#ffffff">The Team</font>]]
+
= Modeling =
-
!style="text-align:center; background-color:#003E81; border-width:0px; padding:3px;"|[[Team:KULeuven/Road Map|<font color="#ffffff">Road Map</font>]]
+
 
-
!style="text-align:center; background-color:#003E81; border-width:0px; padding:3px;"|[[Team:KULeuven/Project|<font color="#ffffff">The Project</font>]]
+
* [https://static.igem.org/mediawiki/2008/1/19/Numbers.xls Numbers.xls]
-
!style="text-align:center; background-color:#003E81; border-width:0px; padding:3px;"|[[Team:KULeuven/Parts|<font color="#ffffff">Parts Submitted to the Registry</font>]]
+
 
-
!style="text-align:center; background-color:#003E81; border-width:0px; padding:3px;"|[[Team:KULeuven/Modeling|<font color="#ffffff">Modeling</font>]]
+
* [http://www.nature.com/nature/journal/v438/n7067/full/nature04405.html Synthetic biology: Engineering Escherichia coli to see light]
-
!style="text-align:center; background-color:#003E81; border-width:0px; padding:3px;"|[[Team:KULeuven/Notebook|<font color="#ffffff">Notebook</font>]]
+
 
 +
== CellDesigner ==
 +
 
 +
=== [https://static.igem.org/mediawiki/2008/d/d9/Output_v2.zip Output] ===
 +
 
 +
[[Image:output_v2.png|500px|center|Output]]
 +
 
 +
{| border="1"
 +
|+ Parameter values Output
 +
! Name !! Value !! Reference
 +
|-
 +
! Degradation
 +
|  ||
 +
|-
 +
| CFP (protein) || 1.05E-4 /s || [https://2007.igem.org/ETHZ/Parameters link]
 +
|-
 +
| CFP (mRNA) || 0.0023 /s || [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
 +
|-
 +
! Transcription Rate
 +
|-
 +
| CFP || OmpF dependent ||
 +
|-
 +
! Translation Rate
 +
|-
 +
| CFP || 0.167 /s || Based on effenciency RBS
|}
|}
-
=Modeling=
+
[[Image:Sim_output_1.png|500px|center|Output]]
 +
[[Image:Sim_output_2.png|500px|center|Output]]
 +
[[Image:Sim_output_3.png|500px|center|Output]]
 +
 
 +
===[https://static.igem.org/mediawiki/2008/4/47/Celldeath.zip Cell Death]===
 +
 
 +
[[Image:celldeath.png|800px|center|Cell Death]]
 +
 
 +
{| border="1"
 +
|+ 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<sub>a</sub> (HSL+LuxR) || 1E6 /s || chosen to be relatively (to the other rate constants) high and such that K<sub>d</sub> equals 1E-6
 +
|-
 +
| k<sub>d</sub> (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_1*K_m^n/(K_m^n + [LuxR]^n) = 0.025*1E-9/(1E-9^1+[LuxR]) ||
 +
|-
 +
|}
 +
 
 +
===[https://static.igem.org/mediawiki/2008/1/11/Inverter_v4.zip Inverter]===
 +
 
 +
[[Image:inverter_v4.png|400px|center|Inverter]]
 +
 
 +
{| border="1"
 +
|+ Parameter values Inverter
 +
! Name !! Value !! Reference
 +
|-
 +
! Degradation
 +
|  ||
 +
|-
 +
| LuxI (protein) || 0.00231 /s ||
 +
|-
 +
| LuxI (mRNA) || 0.0025 /s || [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
 +
|-
 +
| LuxI (complex) || 0.00125 /s ||
 +
|-
 +
| LacI (protein) || 0.00231 /s ||
 +
|-
 +
| LacI (gesloten mRNA) || 0.0046209812 /s ||
 +
|-
 +
| LacI (open mRNA) || 0.0023104906 /s ||
 +
|-
 +
| open mRNA LacI complex || 0.0023104906 /s ||
 +
|-
 +
| HSL || 1.02E-6 /s || [http://aem.asm.org/cgi/content/abstract/71/3/1291 link]
 +
|-
 +
! Dissociation Rate
 +
|-
 +
! Transcription Rate
 +
|-
 +
| LacI || 0.0011 /s ||
 +
|-
 +
| LuxI || 0.0025 /s ||
 +
|-
 +
| K_m || 1.0E-10 /s ||
 +
|-
 +
! Translation Rate
 +
|-
 +
| LuxI (RBS B0034) || 0.5 /s ||
 +
|-
 +
| LacI (RBS ?) || 0.16667 /s ||
 +
|-
 +
! Equilibrium Constant
 +
|-
 +
| closed and open mRNA LacI || 0.015 ||
 +
|-
 +
| closed and complex mRNA LacI || 0.0212 /M ||
 +
|-
 +
! Hill coëfficiënt
 +
|-
 +
| n || 2 ||
 +
|-
 +
! Others
 +
|-
 +
| LuxI --> HSL || 0.16 ||
 +
|-
 +
| LuxI (mRNA) + anti sense <-> complex LuxI || 4.22E14 ||
 +
|-
 +
|
 +
|}
 +
 
 +
===[https://static.igem.org/mediawiki/2008/0/05/Memory.zip Memory]===
 +
 
 +
[[Image:Memory.png|400px|center|Memory]]
 +
 
 +
{| border="1"
 +
|+ Parameter values Memory
 +
! Name !! Value !! Reference
 +
|-
 +
! Degradation
 +
|-
 +
| P2ogr (protein) || 0.002265 /s ||
 +
|-
 +
| P2ogr (mRNA) || 0.002265 /s || [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
 +
|-
 +
| P22CII (protein) || 0.002311 /s ||
 +
|-
 +
| P22CII (mRNA)|| 0,0022651 /s || [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
 +
|-
 +
| antimRNA_luxI  || 0.0045303/s ||
 +
|-
 +
! Transcription rate
 +
|-
 +
| P2ogr || 0.0125 || 
 +
|-
 +
| P22CII || 0.0125 ||
 +
|-
 +
| AntimRNA || 0.0094 ||
 +
|-
 +
! Dissociation Constant
 +
|-
 +
| P2-ogr || 4.2156 M || [http://www.jbc.org/cgi/content/abstract/258/17/10536?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=P22+c2+repressor&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=258&resourcetype=HWCIT link]
 +
|-
 +
| R0053-P22CII || 0.1099 M ||
 +
|-
 +
! Hill coëfficiënt
 +
|-
 +
| n || 2 ||
 +
|-
 +
|}
 +
 
 +
===[https://static.igem.org/mediawiki/2008/8/8b/Filter_Final.zip Filter]===
 +
 
 +
[[Image:FilterCellD.png|800px|center|filter]]
 +
 
 +
{| border="1"
 +
|+ 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 ||
 +
|}
 +
 
 +
===[https://static.igem.org/mediawiki/2008/8/8c/PulseGenerator.zip Pulse Generator]===
 +
 
 +
[[Image:PulseGenerator.png|400px|center|Pulse Generator]]
 +
 
 +
===Constant Lactonase production===
 +
 
 +
===[https://static.igem.org/mediawiki/2008/c/c0/FilterLactonaseCelldeathInverter.zip Partial Model]===
 +
 
 +
[[Image:Model.png|950px|center|Model]]
 +
 
 +
==Kinetic Constants==
 +
 
 +
===ETHZ list of parameters===
 +
* [https://2007.igem.org/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===
 +
*[https://2007.igem.org/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]
-
''This is the modeling section''
+
===Constitutive promoters===
 +
*Estimated transcription rate for J23105:[https://2007.igem.org/title=ETHZ/Parameters]
 +
*Scale other transcription rate with table in parts registry.
-
===Note===
+
* Estimate the rate of transcription from a constitutive promotor family member.
 +
[[Image:Const_pro_strength.png|center|400px|thumb|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]]
-
If you choose to include a '''Modeling''' page, please write about your modeling adventures here. This is not necessary but it may be a nice list to include.
+
===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>
 +
[http://users.path.ox.ac.uk/~pcook/data/catalogs.html Tables with the calculated transcription rates for every E.coli ORF]

Latest revision as of 15:17, 22 July 2008

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. 

<html>

<style type="text/css">
#content {z-index:4;}
#ddwrapper * {z-index:8 !important;}

div#ddwrapper {
	margin:0;
	padding:0;
	height:28px;
	width:945px;				/* change to adjust imperfections in width */
}
div#ddnav {
	margin:0 auto;				/* needed to center the dropdown */
	padding:0;
	top:5px;
	/* width: 965px */
	visibility:hidden;			/* dropdown is hidden until properly initalised by javascript */
}
div#ddtoggle {
	margin:0;
	position:fixed;
	right:2px;
	top:15px;
	height:10px;
	width:10px;
	z-index:100;
}

#ddnav ul {
	display:table-row;			/* works only for firefox, later adjusted by javascript for IE */
	margin:0 auto;
	padding:0;
}
#ddnav ul li {
	display:table-cell;			/* works only for firefox, later adjusted by javascript for IE */
	list-style:none;
	margin:0;
	padding:0 !important;
	border-right:1px solid #FFF;		/* creates illusion of spacing between tabs */
}
#ddnav ul li:last-child{border-right:none;}
#ddnav a{
	display:block;
	margin:0;
	padding:4px 14px;			/* play with dimensions for size of tabs */
	background-color:#075A90;		/* background color for tabs */
	color:#FFF !important;			/* font color for text in tabs */
	text-align:center;			/* aligning for text in tabs */
	text-decoration:none !important;
	font:bold 10pt Trebuchet MS;		/* font properties for text in tabs */
	outline:0;
}
#ddnav ul li a:hover {background-color:#99CCFF;}/* background color for tabs on mouseover */
#ddnav li a:active {outline:none;}		/* remove standard dotted border for links when clicked (IE) */
#ddnav li a:focus {-moz-outline-style:none;}	/* remove standard dotted border for links when clicked (FF) */
#ddnav div {
	display:none;
	position:absolute;
	width:9em;
	background-color:#000;			/* bug solution, do not change ! */
	border:1px solid #5970B2;		/* border color for dropdown menus */
	opacity:0.9;				/* transparancy of the dropdown menus (FF) */
	filter:alpha(opacity=90);		/* transparancy of the dropdown menus (IE) */
}
#ddnav div a {
	display:block;
	padding:5px 10px;			/* play with dimensions of block element in dropdown menus */
	position:relative;
	font:normal 8pt arial;			/* font properties for text in dropdown menus */
	text-align:left;			/* aligning of text in dropdown menus */
	cursor:pointer;
}
#ddnav div a:hover, #ddnav span a:hover {color:#000 !important;}	/* text color on mouseover */
#ddnav span div {
	position:relative;
	border:none;
	border-bottom:2px groove #5970B2;	/* separator for submenus, groove does not work in FF */
	opacity:1.0;				/* avoid stacking transparancy for submenus (FF) */
	filter:alpha(opacity=100);		/* avoid stacking transparancy for submenus (IE) */
}

/* may want to upload the following pictures to a new location */
.expand {background: url('https://static.igem.org/mediawiki/2008/e/ef/Icon-expand.png') no-repeat 95% 50%;}
.collapse {background: url('https://static.igem.org/mediawiki/2008/c/cd/Icon-collapse.png') no-repeat 95% 50%;}

.docked {background: #99ccff url("https://static.igem.org/mediawiki/2008/6/62/Ddnavundock.png") no-repeat 50% 50%;}
.undocked {background: #99ccff url("https://static.igem.org/mediawiki/2008/e/e4/Ddnavdock.png") no-repeat 50% 50%;}
</style>

<!-- IMPORTANT: save following script under a personalized webspace or download the library at www.jquery.com -->
<script type="text/javascript" src="http://student.kuleuven.be/~s0173901/wiki/js/jquery.js"></script>
<script type="text/javascript">
	function ddnav() {
		$('#ddnav ul li').hover(
			function () {
				$(this).find('div:first').css('display','block');},
			function () {
				$(this).find('div:first').css('display','none');}
		);
	}
			
	function ddnavsub() {
		$('#ddnav span > a').toggle(
			function () {
				$(this).removeClass("#ddnav expand").addClass("#ddnav collapse");
				$(this).parent().find('div:first').slideDown('fast');
				$(this).hover(
					function (){$(this).css('background-color','#99AAFF');},
					function (){$(this).css('background-color','#99AAFF');});},
			function () {
				$(this).removeClass("#ddnav collapse").addClass("#ddnav expand");
				$(this).parent().find('div:first').css('display','none');
				$(this).hover(
					function (){$(this).css('background-color','#99CCFF');},
					function (){$(this).css('background-color','#075A90');});}
		).addClass("#ddnav expand");
	}
	
	/* If you wish to omit the docking feature, remove following function ddtoggle() */	
	function ddtoggle() {
		$('#ddtoggle').toggle(
			function () {
				$(this).removeClass('undocked').addClass('docked');
				$('#ddnav').css('position','fixed');},
			function () {
				$(this).removeClass('docked').addClass('undocked');
				$('#ddnav').css('position','static');}
		);
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	function ddalign() {
		var _windowWidth = $(window).width();
		var _leftOffset = (_windowWidth - 965)/2;

		$('div#ddnav').css('left',_leftOffset);
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	function ddmsie() {
		$('#ddnav a').hover(
			function () {$(this).css('background-color','#99ccff');},
			function () {$(this).css('background-color','#075a90');}
		);
				
		/* toggle doesn't work yet */
		$('#ddtoggle').css('display','none');
				
		$('#ddnav ul').css('display','inline-block');
		$('#ddnav ul li').css('display','inline');
		$('#ddnav ul li').css('position','relative');
		$('#ddnav ul li>a').css('display','inline-block');
		$('#ddnav ul li>a').css('margin-right','-4px');
				
		$('#ddnav div').css('left','0');
		$('#ddnav div').css('top','100%');
		$('#ddnav span div').css('top','0');
	}
			
	function ddmozilla() {
		ddtoggle();
		$(window).bind('resize', function() {ddalign();});
	}

	$(function () {
		ddnav();
		ddnavsub();

		if(jQuery.browser.msie) ddmsie();
		if(jQuery.browser.mozilla) ddmozilla();

		$('#ddnav').css('visibility','visible');
	});
</script>

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					<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>
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					<a href="https://2008.igem.org/Team:KULeuven/Data/Input">Input</a>
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					<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>
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			<a href="https://2008.igem.org/Team:KULeuven/Data/FullModel">Full Model</a>
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					<a href="https://2008.igem.org/Team:KULeuven/Freezer">Freezer</a>
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Contents

Modeling

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

CellDesigner

Output

Output
Parameter values Output
Name Value Reference
Degradation
CFP (protein) 1.05E-4 /s link
CFP (mRNA) 0.0023 /s [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
Transcription Rate
CFP OmpF dependent
Translation Rate
CFP 0.167 /s Based on effenciency RBS
Output
Output
Output

Cell Death

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
ka (HSL+LuxR) 1E6 /s chosen to be relatively (to the other rate constants) high and such that Kd equals 1E-6
kd (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_1*K_m^n/(K_m^n + [LuxR]^n) = 0.025*1E-9/(1E-9^1+[LuxR])

Inverter

Inverter
Parameter values Inverter
Name Value Reference
Degradation
LuxI (protein) 0.00231 /s
LuxI (mRNA) 0.0025 /s [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
LuxI (complex) 0.00125 /s
LacI (protein) 0.00231 /s
LacI (gesloten mRNA) 0.0046209812 /s
LacI (open mRNA) 0.0023104906 /s
open mRNA LacI complex 0.0023104906 /s
HSL 1.02E-6 /s [http://aem.asm.org/cgi/content/abstract/71/3/1291 link]
Dissociation Rate
Transcription Rate
LacI 0.0011 /s
LuxI 0.0025 /s
K_m 1.0E-10 /s
Translation Rate
LuxI (RBS B0034) 0.5 /s
LacI (RBS ?) 0.16667 /s
Equilibrium Constant
closed and open mRNA LacI 0.015
closed and complex mRNA LacI 0.0212 /M
Hill coëfficiënt
n 2
Others
LuxI --> HSL 0.16
LuxI (mRNA) + anti sense <-> complex LuxI 4.22E14

Memory

Memory
Parameter values Memory
Name Value Reference
Degradation
P2ogr (protein) 0.002265 /s
P2ogr (mRNA) 0.002265 /s [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
P22CII (protein) 0.002311 /s
P22CII (mRNA) 0,0022651 /s [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
antimRNA_luxI 0.0045303/s
Transcription rate
P2ogr 0.0125
P22CII 0.0125
AntimRNA 0.0094
Dissociation Constant
P2-ogr 4.2156 M [http://www.jbc.org/cgi/content/abstract/258/17/10536?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=P22+c2+repressor&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=258&resourcetype=HWCIT link]
R0053-P22CII 0.1099 M
Hill coëfficiënt
n 2

Filter

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

Pulse Generator

Pulse Generator

Constant Lactonase production

Partial Model

Model

Kinetic Constants

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://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=178405 Psid promotor with different activators]

Constitutive promoters

  • Estimated transcription rate for J23105:[1]
  • 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]

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