IGEM:IMPERIAL/2007/Projects/Cell by date/Modelling: Difference between revisions

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==Summary:==


In the design section we outlined which variants of Cell By Date we would like to implement in different Chassis, as shown in the table below. <br>
{| style="background:#FAF5FF; border:1px solid #FFDAB9; color:#000000"
|- style="background:#FFA07A"
|| '''Chassis''' || Level 1 || Level 2 || Level 3
|- style="background:#FFDAB9"
|style="background:#FFA07A" |  E.coli || X ||  || ||
|- style="background:#FFDAB9"
| style="background:#FFA07A" | In-Vitro|| X || X || X ||
|- style="background:#FFDAB9"
| style="background:#FFA07A" | In-Veso|| X || X || X ||
|}
In this section we modify the variants of Cell by Date so that they can be implemented advantageously in each chassis.  We also model these modified variants in order to understand the behaviour we expect or to tune the system to realise a particular behaviour.  This leads us to write up experiments to determine if our system behaves the way our models predict.
Ant - Think about using Arrhenius Equation to model temperature response of system


==Overview of Modelling ==
==Overview of Modelling ==


Overall our modelling for this project will take for form of  
Welcome to our portal page for the modelling of Cell By Date


<math>\frac{dFP}{dt}=k(t)-d_{FP}[GFP] </math>
Cell by date tries to improve on printed cell by date as acting as a thermal exposure device, exploiting the thermal dependance of the rate of expression of a simple reporter system.  We are looking at a variety of constructs to realise this behaviour.


# k : Function of Temperature.  k is based on the promoter used as promoters take time to turn on.
===Constructs to be Used ===
# dFP : Function of System.  May be considered to be a function of temperature as proteins may degrade at high temperatures.


{|
|-
|GFP Based
|[[IMAGE:ICGEMS_dvc_Ptet_gfp.png|left|frame]]
|[[IMAGE:ICGEMS_dvc_PT7_gfp.png|left|frame]]
|[[IMAGE:PcI_construct.PNG|left|frame]]
|-
|RFP Based
|[[IMAGE:ICGEMS_dvc_Ptet_rfp.PNG|left|frame]]
|[[IMAGE:ICGEMS_dvc_PT7_rfp.PNG|left|frame]]
|[[IMAGE:ICGEMS_dvc_PcI_rfp.PNG|left|frame]]
|-
|}


Two graphs of k vs. time (special pt is ko.) and [FP] vs. time key point is [FP]ss
As can be seen in the above table all of our constructs have the same general form of a promoter upstream of a reporter. Looking at the rate of Fluorescent Protein (FP) produced :


* Our major problem at the moment is estimating the errosrs involved with our fluorometer and Pipette we hope to address these through calibration curves.
<math>\frac{d[FP]}{dt}=k_{FP}(t)-d_{FP}[FP] </math>


For each experiment we will do the following
# kFP : Function of Temperature.  k is based on the promoter used as promoters take time to turn on.
# dFP : Function of System.  May be considered to be a function of temperature as proteins degrade faster at higher temperatures.


#Calibration curve to determine error in Fluorometer
{| cellspacing="5"
#Decay Experiment @ Varying temperatures
|-valign="top"
#Plug Together to find transient response and k
|width=50%|
#Find these parameters as a function of Temperature


===Construct Specific modelling (Do not Edit Anthony is working on this now !)===


[[IMAGE:ICGEMS_dvc_Ptet_gfp.png|left|frame|Picture5]]<br clear = "all">
<!--ROW 2-->
|-valign="top"
||


Apply the above general equation to this specific construct.
===Transient Response of System===


<math>\frac{d[GFP]}{dt}=k_{Ptet}(t)-d_{GFP}[GFP] </math>
Image needs to be changed to matlab plot of system


==E.coli==
[[Image:ConstantTempCBDresponseC.png|left|500px]]<br clear = "all">


===Level 1===
||


Calibration:
===Transfer Function of System===


The process criteria for minced meat and mechanically separated meat are:
Image needs to be changed to matlab plot of system


5 samples per sampling session
[[Image: CellByDate_tf.jpg|thumb|left|500px|Construct 2 - LuxR not expressed]]<br clear = "all">


Aerobic Plate Count (APC) and E. coli (EC) specified limits per gram
|}
 
APC all 5 samples must be less than 5 x 106 cfu/g and 3 samples must be less than 5 x 10 5 cfu/g.
 
EC all 5 samples must be less than 500 cfu/g and 3 samples must be less than 50 cfu/g.
[http://www.ukmeat.org/Assessment.htm Info obtained here]


==In-Vitro==
===Feedback from Protocols/"Manufacturing"===


===Level 1===
====Construct to be pursued====
===Level 2===
*pTet           
===Level 3===


==In-Veso==
Refer to the [[IGEM:IMPERIAL/2007/DNA_Constructs|constructs]] page for more information.


===Level 1===
===Performance Specifications===
===Level 2===
===Level 3===

Latest revision as of 08:56, 30 August 2007

Cell by Date: Modelling




Overview of Modelling

Welcome to our portal page for the modelling of Cell By Date

Cell by date tries to improve on printed cell by date as acting as a thermal exposure device, exploiting the thermal dependance of the rate of expression of a simple reporter system. We are looking at a variety of constructs to realise this behaviour.

Constructs to be Used

GFP Based
RFP Based

As can be seen in the above table all of our constructs have the same general form of a promoter upstream of a reporter. Looking at the rate of Fluorescent Protein (FP) produced :

[math]\displaystyle{ \frac{d[FP]}{dt}=k_{FP}(t)-d_{FP}[FP] }[/math]

  1. kFP : Function of Temperature. k is based on the promoter used as promoters take time to turn on.
  2. dFP : Function of System. May be considered to be a function of temperature as proteins degrade faster at higher temperatures.


Transient Response of System

Image needs to be changed to matlab plot of system


Transfer Function of System

Image needs to be changed to matlab plot of system

Construct 2 - LuxR not expressed

Feedback from Protocols/"Manufacturing"

Construct to be pursued

  • pTet

Refer to the constructs page for more information.

Performance Specifications

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