User:Anthony Lazzaro / SANDBOX
Fooling around with columns
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Modelling DumpPrevious workOverall our modelling for this project will take the form of [math]\displaystyle{ \frac{dFP}{dt}=k(t)-\delta_{FP}[FP] }[/math]
For each experiment we will do the following
Construct Specific ModellingModelled by 2006 Imperial Team, as part of their prey-sensing module of the molecular predation oscillator: The major problem with last year's derivation is that they assumed LuxR concentration to be constant and they didn't look into the co-operativity of the Plux Promoter e.g. the threshold of quorum.
LuxR will be constituitively expressed in our system, this means that the older our system is the more LuxR present and so the less sensitive our system will be to the amount of AHL around. We can model this by having a initial condition or history of our system in addition to last year's path way. [math]\displaystyle{ [LuxR]_{0}\; at\; t=t_{0} }[/math] [math]\displaystyle{ LuxR+AHL\rightarrow A }[/math] [math]\displaystyle{ A+P\leftarrow\rightarrow\;PA\;\rightarrow\;GFP }[/math] [math]\displaystyle{ \frac{d[LuxR]}{dt}=k-d_{LuxR}[LuxR]-k_{1}[LuxR][AHL]+k_{2}[A] }[/math] We will first consider the concentration of LuxR to be constant as per last year. Following this we will consider the history of the system and so the initial concentration of LuxR when AHL is detected.
We do not know what the cooperativity of the Plux Promoter is and in effect we do not know what exactly the threshold of our system will be. [math]\displaystyle{ \frac{d[GFP]}{dt}=\frac{X^a}{1+X^a} }[/math] [math]\displaystyle{ X=[LuxR][AHL]\;complex }[/math] [math]\displaystyle{ a\gt 1 }[/math] : initial gradient is zero and we see a step response
The threshold for biofilm detection, via AHL quorum sensing molecule is approximately 0.1nM. Feedback from MattyOverview of modelling this construct:
Breakdown of specific sections: Experiment 1:
Analysis 1:
[math]\displaystyle{ \frac{d[GFP]}{dt}=k_{5}\left\{\frac{[AHL][LuxR][P]_{0}}{K+[AHL][LuxR]}\right\}-\delta_{GFP}[GFP] }[/math]
Experiment 2:
Analysis 2:
Considerations
Diffusion coefficient of HSL in water - 4.9*10-6 Daq cm2/s Case1Case 1 : Both initial concentrations of LuxR and AHl are controllled [math]\displaystyle{ [A]=K_{\alpha}[AHL]_{0}[LuxR]_{0} }[/math] [math]\displaystyle{ [AP]=\frac{K_{\alpha}K_{\beta}[AHL]_{0}[LuxR]_{0}[P]_{0}}{1+K_{\alpha}K_{\beta}[AHL]_{0}[LuxR]_{0}}
}[/math] [math]\displaystyle{ R_{y}(x)=\frac{[AP]}{[P]_{0}}=\frac{K_{\alpha}K_{\beta}xy}{1+K_{\alpha}K_{\beta}xy} }[/math] [math]\displaystyle{ R_{y}(x)=1-\frac{1}{1+K_{\alpha}K_{\beta}xy} }[/math] [math]\displaystyle{ R_{y}'(x)=\frac{K_{\alpha}K_{\beta}y}{\left(1+K_{\alpha}K_{\beta}xy\right)^2} }[/math] Case2Case 3 : Only y is controlled [math]\displaystyle{ x=[AHL]_{0}=[AHL]+[A] }[/math] [math]\displaystyle{ [A]=x-[AHL] }[/math] but [math]\displaystyle{ [A]=K_{\alpha}[AHL]y }[/math] therefore [math]\displaystyle{ x-[AHL]=K_{\alpha}y }[/math] therefore [math]\displaystyle{ [AHL]=\frac{x}{1+K_{\alpha}y} }[/math] [math]\displaystyle{ [A]=K_{\alpha}\left(\frac{xy}{1+K_{\alpha}y}\right) }[/math] Now [math]\displaystyle{ Ry(x)=\frac{K_{\alpha}K_{\beta}xy}{1+yK_{\alpha}+K_{\alpha}K_{\beta}xy} }[/math] Construct 1 : IntroWith the chemical pathway below for construct 1 we can make form some initial equations about the system.
Our aim in modelling Infector Detector is to determine the concentration of biofilm we can detect such that we report a visible signal. Therefore we want to relate the GFP concentration to the concentration of AHL. Starting that the rate of change in GFP concentration: [math]\displaystyle{ \frac{d[GFP]}{dt}=k_{6}[AP]-\delta_{GFP}[GFP] }[/math] Aussume : [AP] reaches a constant level [math]\displaystyle{ \therefore\frac{d[AP]}{dt}=0=k_{4}[A][P]-k_{5}[AP] }[/math] we can infer that [math]\displaystyle{ [AP]=\frac{k_{4}}{k_{5}}[A][P] }[/math] Assume : Conservation of Plux Promoters Reason : no damage to Promoters will occour eg. no DNA damage due to old age or cell defence mechanisms attacking the DNA [math]\displaystyle{ [P]_{0}=[P]+[AP] }[/math] [math]\displaystyle{ Insert formula here }[/math] Construct 1 : Case 1 (Previously called case 4)Construct 2 : IntroConstruct 2 : Case1Case 1 : Both initial concentrations of LuxR and AHL are controllled [math]\displaystyle{ \displaystyle[A]=K_{\alpha}[AHL]_{0}[LuxR]_{0} }[/math] [math]\displaystyle{ [AP]=\frac{K_{\alpha}K_{\beta}[AHL]_{0}[LuxR]_{0}[P]_{0}}{1+K_{\alpha}K_{\beta}[AHL]_{0}[LuxR]_{0}}
}[/math] [math]\displaystyle{ R_{y}(x)=\frac{[AP]}{[P]_{0}}=\frac{K_{\alpha}K_{\beta}xy}{1+K_{\alpha}K_{\beta}xy} }[/math] [math]\displaystyle{ R_{y}(x)=1-\frac{1}{1+K_{\alpha}K_{\beta}xy} }[/math] [math]\displaystyle{ R_{y}'(x)=\frac{K_{\alpha}K_{\beta}y}{\left(1+K_{\alpha}K_{\beta}xy\right)^2} }[/math] Construct 2 : Case 2Jerry Has this in his sandbox Construct 2 : Case3Case 3 : Only y is controlled [math]\displaystyle{ x=[AHL]_{0}=[AHL]+[A] }[/math] [math]\displaystyle{ [A]=x-[AHL] }[/math] but [math]\displaystyle{ [A]=K_{\alpha}[AHL]y }[/math] therefore [math]\displaystyle{ x-[AHL]=K_{\alpha}y }[/math] therefore [math]\displaystyle{ [AHL]=\frac{x}{1+K_{\alpha}y} }[/math] [math]\displaystyle{ [A]=K_{\alpha}\left(\frac{xy}{1+K_{\alpha}y}\right) }[/math] Now [math]\displaystyle{ Ry(x)=\frac{K_{\alpha}K_{\beta}xy}{1+yK_{\alpha}+K_{\alpha}K_{\beta}xy} }[/math] Construct 2 : Case 4(Previously called case 5)Construct 2 : Case 5(Previously called case 6)Milestones for PR on week basis
Imperial's 2007 iGEM Project DefinitionVesoCops - Imperial College iGEM 2007 Team ** Work in Progress We're making VesoCop!!! **The Imperial College iGEM 2007 team consists of ten undergraduate bioengineering and bioscience students. This year, we are engineering VesoCops, biological systems that report the presence of nasty bacteria. Under the Cell-Free Intelligence (CFI), we have two divisions. First, a surveillance team called Cell By Date that determines when food is spoilt more accurately than printed sell by dates. It exploits the thermal dependence of the rate of expression of a simple reporter system. The second division consists of an undercover team - Infector Detector, which detects biofilms that are antibiotic-resistant and a major source of infection in hospitals. This system makes use of Lux quorum sensing to eavesdrop on the communication between biofilm-forming bacteria. Our contributions to the synthetic biology community will be the characterization of Cell-Free Chassis, the common platform on which Cell By Date and Infector Detector will be built. The cell-free approach is particularly useful for VesoCops to operate in the food and medical industries. We believe this new chassis will unlock fresh potential in simple constructs. Our project strategy is based on the Engineering Cycle, of which we have completed specification and design of the systems. We are starting on modelling and implementation and we aim to test our final constructs in the new chassis. By the end of the summer, the VesoCops will be combat-ready. The Story: We approach synthetic biology with a view of making bacteria help us. The media is rife with stories of Synthetic Biology being a threat as it could make the next super weapon and how bacteria are bad and make us sick. We want bacteria that serve us, to inspire confidence in Synthetic biology, and that protect us from these daily threats to show that bacteria can be well behaved. The idea of to protect & serve leads us to the idea of a cop , a bactocop of you will. The Project: BactoCops, Imperial College’s iGEM 2007 project, delivers a new breed of grime fighting officers. The current state of affairs is that only the run of the mill BactoCops are in operation, the make up the BAPD is you will. These BactoCops can’t do a lot because they use E.Coli as a chassis – they can’t be near open wounds or near our food for example. We are focusing on bringing a new type of agency to the BactoCop world consisting of SuperBactocops – we call it the CIA : the Cell Free Intelligence Agency. This new agency has unbelievable potential and to demonstrate this we have two amazing teams. Firstly, a surveillance team called Cell By Date that determines when food is spoilt more accurately than printed sell by dates. It exploits the thermal dependence of the rate of expression of a simple reporter system. Our second team goes undercover, codename - Infector Detector, it detects biofilms that are antibiotic-resistant and a major source of infection in hospitals. This system makes use of Lux quorum sensing to eavesdrop on the communication between biofilm-forming bacteria.
The Progress: Our project strategy is based on the Engineering Cycle, of which we have completed specification and design of the systems. We are starting on modelling and implementation and we aim to test our final constructs in the new chassis. By the end of the summer, the BactoCops will be combat-ready.
Re-Revised Project dEscription corrections: 1. Remove BactoCops 2. Make Biofilm Detector Picture look more medical My Project Description Corrections: 1. Story needs to be re-written it paints syn bioin a very negative light 2. Cell by date doesn't report the presence of nasty bacteria 3. BactoCops is misleading because we are not using bacteria Possible way forward is to extend the RoboCop / VesoCop Idea
Potentials for Motifs
Mr. BeanJames BondWe'll be Q-Branch 1. Bond as human get new gadget which is our project cell by date / infector detector 2. Bond is a cell : he goes through transformation and becomes a super agent
Projects are missions 1. Cell by Date :
James Bond 007 : Licence to Glow Vesper Vesicle - Bond's no. 57 on the bang list. Pussy Galore - Lipids Galore Octopussy - Spherical Pussy - Pleasure from all angles Revised VesoCop Story
The Story: Current state of affairs is that syn. Bio has made tremendous progress in terms of making Bacteria Do wonderful things for us protecting us in Variety of situations, they behave like the police men around us they are if you will BactoCops. But these bactocops can't do everything, with E.Coli as a Chassis they are ineffective in certain situation. There is a need now for a new breed of BactoCop that can go to these places, further than any BactoCop before him : we can him VesoCop The Project: The Progress:
Austin Veso Story
The Story: Mission 2: A lot of Biofilm's Penthouse Through Veso Powers our contributions to the synthetic biology community will be the characterization of Cell-Free Chassis, the common platform on which Cell By Date and Infector Detector will be built. The cell-free approach is particularly useful for Veso Powers to operate in the food and medical industries. We believe this new chassis will unlock fresh potential in simple constructs. The Progress:
Sherlock Veso Story
The Story:
Current state of affairs is that syn. Bio has made tremendous progress in terms of making Bacteria Do wonderful things for us protecting us in Variety of situations, they behave like the police men around us they are if you will BactoCops. But these bactocops can't do everything, with E.Coli as a Chassis they are ineffective in certain situation. There is a need now for a new breed of BactoCop that can go to these places, further than any BactoCop before him : we can him VesoCop
Pictures: asdfasdfasdf
text below picture Download Link : Anchoring Citations for PubMed Links Internal : internal External : ign Time Stamp Anthony Lazzaro 11:23, 12 July 2007 (EDT) Google specific search Search Term site :openwetware.org Well Characterised Part in Registry: Recievers: BBa_F2620 :
Summary of Brainstorming 18th July: Hrp has promise as a black box feedback loop mechanism
Hrp has promise as a very specific switch Other Promising Ideas: Lucas: Bacteria that move away from a source
Density flow receptor:
Not only detect presence of bacteria but also how much of it there is a particular location
Uses for Hrp System: (Blood testing) Immediate blood-test results can mean the difference between life and death in medical situations such as poisonings and infectious diseases. In many cases, by the time the test results are analyzed and a diagnosis made, the patient is in critical condition or beyond treatment Blood poisoning is an illness due to an infectious agent or its toxin spreading through the bloodstream. The presence of bacteria in the blood is called bacteremia. Short bursts of low levels of bacteria in the blood usually do not cause problems. For example, mild bacteremia typically occurs during a dental cleaning or when brushing your teeth. Your body's immune system fights off these bacteria. If bacteria persist in the blood, however, they may cause sepsis, a serious, life-threatening condition.
20th July Further Brainstorming for new ideas:All my ideas have been rejected so far Avenues to explore for new ideas: 1.Pre-2006 iGEMs
2.Registry 3.New Parts in Papers (start with reviews) Focus on Adhesion:1.Easy Application-Make Bacteria Bind to something when told to do so
mammalian surface carbohydrates [2]
(eg. simple promoter activation)
2.Technical Use-Determine how many bacteria are attached to target 3.Real World Application-Determine A certain concentraion of a species on a surf 4.Modular Real World ApplicationFocus on Biofilm:1.Easy ApplicationSecrete Biofilm when inducer given:
2.Technical Use
3.Real World Application4.Modular Real World Application22nd July Last Minute Susan TimeMajor Focus on Biofilm 1.Easy ApplicationSecrete Biofilm when inducer given:
2.Technical Use3.Real World Application4.Modular Real World ApplicationPapers:
Quick note on Noise reduction in iGEMI think one way to reduce noise & cross talk in iGEM projects is to have 'comm channels' 'Channels' used by the chassis should be chara |