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-	=Model Development for Infector Detector <font color = red> ''(page population in progress)''</font>=	+	<center>'''Welcome to the Modelling Sub-Portal Page'''</center><br><br>
		+	<center>This page serves as a shuttle to the modelling phase of each project:Infector Detector and Cell-by-Date. </center>
		+	----
-	==Formulation of the problem==	+	<center>Select one of the following links to be transferred to the modelling of the relevant project.</center>
-	As described earlier, catheter-associated urinary tract infection (CAUTI) in the clinical setting is a prevalent problem with extensive economic impact. The underlying cause of many such infections can be attributed to the formation of biofilm, by aggregating-bacteria on the surface of urinary catheters.	+
-	[[Image: IC07_QS.png|right|thumb|500px| Role of AHL (HSL) quorum-sensing in biofilm formation]]
-	Infector Detector (ID) is a simple biological detector, which serves to expose bacterial biofilm. It functions by exploiting the inherent AHL (Acetyl Homoserine Lactone)  production employed by certain types of quorum-sensing bacteria, in the formation of such structures.<br>	+	{| border="0" width="80%" align="center"
-		+	|- align="center"
-	Our project attempts to improve where previous methods of biofilm detection have proven ineffective: first and foremost, by focussing on the sensitivity of the system, to markers of biofilm: in this case, low levels of AHL production (which represents the bacterial "chatter" of such aggregating bacteria).	+	||
-		+	{{Click || image = ID ModelPage.jpg| link = Imperial/Infector_Detector/Modelling | width = 200px | height = 198px }}
-	In doing so, a complete investigation of the level of sensitivity to AHL concentration needs to be performed - in other words, what is the minimal AHL concentration for appreciable expression of a chosen reporter protein. Furthermore, establish a functional range for possible AHL detection. How does increased AHL concentration impact on the maximal output of reporter protein?<br>	+	<br> [[Imperial/Infector_Detector/Modelling| '''Infector Detector''']]
-	Finally, how can the system performance be tailored, by exploiting possible state variables (e.g. varying initial LuxR concentration and/or concentration of pLux promoters).	+	||
-		+	{{Click || image = ThermoDA.jpg| link = Imperial/Cell_by_Date/Modelling | width = 200px | height = 200px }}<br>
-	The system performance here revolves most importantly around AHL sensitivity; however, the effect on the maximal output of fluorescent reporter protein and response time is, likewise, of great importance.	+	[[Imperial/Cell_by_Date/Modelling| '''Cell-by-Date''']]
-		+
-	==Selection of Model Design and Structure==	+
-		+
-	Since the novelty of our solution revolves around the use of cell-free systems as a "bacterial-free" solution in the clinical setting, a simple system is selected. Our approach involves a modified version of the bioluminescence machinery employed by the bacterium ''Vibrio Fischeri''.	+
-		+
-	In fact, the characterization of this machinery, forms the setting for the first detailed description of the above-mentioned quorum-sensing phenomenon (Engebrecht and Silverman, 1984 and Engebrecht et al., 1983).	+
-	A system which employs two regulatory proteins LuxR and LuxI, which, together with the autoinducer protein, AHL, control the expression of the in-house reporter (luciferase).	+
-		+
-	Our system maintains the general flavour of this configuration; involving a marginally-varied sensor and reporter element.	+
-	In fact, an already present system is utilized, for its simplicity and good definition - [http://partsregistry.org/Part:BBa_T9002 T9002]. This forms our construct 1.	+
-		+
-	One of the questions posed in the formulation of the model, involved exploring means of "tweaking" the system to achieve improved performance (sensitivity/maximal output/response time). A possible solution could involve introducing purified LuxR into the system, and in this way impose steady-state far sooner than for construct 1. Theoretically, this should shorten response time. It is for this reason, that a second construct will be investigated. Construct 2 thus differs only w.r.t the elimination of the constitutive promoter pTET. (here, LuxR is introduced directly).	+
-		+
-	<font color = red>~~Insert diagram illustrating both constructs </font><br>	+
-		+
-	<font color = red>~~Insert diagram illustrating both interaction of molecules </font><br>	+
-		+
-	<font color = red>~~Insert diagram illustrating sensor and reporter elements </font><br>	+
-		+
-	==Establishing a model==	+
-	Duis autem vel eum iriure dolor in hendrerit in vulputate velit esse molestie consequat, vel illum dolore eu feugiat nulla facilisis at vero eros et accumsan et iusto odio dignissim qui blandit praesent luptatum zzril delenit augue duis dolore te feugait nulla facilisi	+
-		+
-	===Approach===	+
-	At reasonably high molecular concentrations of the state variables, a continuous model can be adopted, which is represented by a system of ordinary differential equations.	+
-		+
-	It is for this reason that our approach to modelling the system follows a deterministic, continuous approximation. In developing this model, we were interested in the behaviour at steady-state, that is when the system has equilibrated and the concentrations of the state variables remain constant.	+
-		+
-	We can condition the system in various manners, but for the purposes of our project, we will seek a formulation which is valid for both constructs considered, i.e. the governing equations are a represenation of both constructs.	+
-		+
-	The only difference is with regards to the parameter k<sub>1</sub>, the maximum transcription rate of the constitutive promoter (pTET) in Construct 1. <br> Thus k<sub>1</sub> = 0 for construct 2 (which lacks pTET).	+
-		+
-	Furthermore, we generate two models based upon the available system energy:	+
-		+
-	'''Model 1''':  Infinite Energy<br>	+
-	'''Model 2''':  Limited Energy<br>	+
-		+
-	The system kinetics are determined by the following coupled-ODEs. For a derivation of the governing equations,  please access	+
-	[https://2007.igem.org/wiki/index.php?title=Imperial/Dry_Lab/Modelling/Model_Derivation Model Derivation]	+
-		+
-	===Model 1===	+
-	Our initial approach assumed that energy would be in unlimited supply, and that our system would eventually reach steady-state.	+
-	[[Image: IC07 Model1.png|600px]]	+
-		+
-	===Model 2===	+
-		+
-	Experimentation suggested otherwise; our system needed to be amended. This lead to the development of model 2, an energy-dependent network, where the dependence on energy assumes Hill-like dynamics:<br>	+
-		+
-	[[Image: IC07 Model2.png|600px]]	+
-		+
-	====''Model Parameters''====	+
-		+
-	{| class="wikitable" border="1" cellspacing="0" cellpadding="2" style="text-align:left; margin: 1em 1em 1em 0; background: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;"	+
-	! Parameter	+
-	! Description	+
-	|-	+
-	|<font color = blue>''Kinetic <br> Constants'' </font>	+
-	|	+
-	|-	+
-	| k<sub>1</sub>	+
-	| Maximal constitutive transcription of LuxR by pTET	+
-	|-	+
-	|k<sub>2</sub>	+
-	|Binding between LuxR and AHL	+
-	|-	+
-	|k<sub>3</sub>	+
-	|Dissociation of protein complex LuxR-AHL (A)	+
-	|-	+
-	|k<sub>4</sub>	+
-	|Binding between A and pLux promoter	+
-	|-	+
-	|k<sub>5</sub>	+
-	|Dissociaton of A-pLux complex	+
-	|-	+
-	|k<sub>6</sub>	+
-	|Transcription of FP	+
-	|-	+
-	|<font color = blue>''Degradation <br> Rates'' </font>	+
-	|	+
-	|-	+
-	|&delta;<sub>LuxR</sub>	+
-	|Degradation rate of LuxR	+
-	|-	+
-	|&delta;<sub>AHL</sub>	+
-	|Degradation rate of AHL	+
-	|-	+
-	|&delta;<sub>GFP</sub>	+
-	|Degradation rate of GFP	+
-	|-	+
-	|<font color = blue>''Hill Co-operativity''</font>	+
-	|	+
-	|-	+
-	|n	+
-	|Co-operativity coefficient describing the degree of energy dependence, which follows Hill-like dynamics	+
-	|-	+
-	|<font color = blue>''Energy consumption <br> of transcription''</font>	+
-		+
-	|	+
-	|-	+
-	|&alpha;<sub>1</sub>	+
-	|Energy consumption due to constitutive transcription of LuxR	+
-	|-	+
-	|&alpha;<sub>2</sub>	+
-	|Energy consumption due to transcription of ''gfp'' gene	+
	|}		|}
-	<br>	+	<br clear="all">
-		+
-	==Simulations==	+
-	[https://2007.igem.org/wiki/index.php?title=Imperial/Dry_Lab/Modelling/ID_Simulations Simulations]	+
-	==References==
-	==Log==	+	<center> | [[Imperial/Dry_Lab | Dry Lab >>]]</center>
-	*Images - black borders, pastel backgrounds (pale) - see QS image; stretch to fill gaps - no white spaces	+
-	*Equations - bordered	+
-	*Improve appearance of eqns - presentation? symmetry?	+
-	*LaTeX on MIT wiki?	+

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Latest revision as of 02:10, 27 October 2007

• Home
  • Site Map
  • Meet the Team
  • Fun with iGEM
  • IcGEMs@OpenWetware
  • Acknowledgements
• Infector Detector
  • Introduction
  • Specification
  • Design
  • Modelling
  • Implementation
  • Testing/Validation
  • F2620 Comparison
  • Conclusion
• Cell by Date
  • Introduction
  • Specification
  • Design
  • Modelling
  • Implementation
  • Testing/Validation
  • Conclusion
• Cell-Free
  • What is Cell-Free?
  • Cell-Free Vs. Cell
  • Our Contributions
  • Characterisation
  • Applications
• Wet Lab
  • Lab Notebook
  • Protocols & Results
  • DNA Constructs
• Dry Lab
  • Modelling
  • Data Analysis
  • Software

Welcome to the Modelling Sub-Portal Page

This page serves as a shuttle to the modelling phase of each project:Infector Detector and Cell-by-Date.

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Select one of the following links to be transferred to the modelling of the relevant project.

Infector Detector

Cell-by-Date

| Dry Lab >>