User:Anthony Lazzaro
Anthony LazzaroDepartment of Bioengineering
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Anthony is a second year undergraduate student part of Imperial's 2007 iGEM team
MESSING AROUND
Modelling Dump
Intro : Construct 1
With the chemical pathway below for construct 1 we can make form some initial equations about the system.
- Picture of pathway for construct from Jerry
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 Reason : Treat 1st formation of AP complex as a black box - it just reaches steady state.
Therefore [math]\displaystyle{ \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 : Case1
Case 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]
Construct 2 : Case 2
Jerry Has this in his sandbox
Construct 2 : Case3
Case 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
- Motif
- Tshirt / Logo / Photo : Finalise Defn of Wiki / Russell Peters
- Slide Layout : Finalise Tshirt / Logo / Photo
- Contact Tom Millar
- Drinks
- Champange reception
Imperial's 2007 iGEM Project Definition
VesoCops - 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.
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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 BactoCops to operate in the food and medical industries. This is because living, replicating engineered bacteria pose major health risks. We believe this new chassis will unlock fresh potential in simple constructs.
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.Bean
- James Bond
- Dr.Who
- Austin Powers
- Sherlock Homes
- Robin Hood
- Alice in Wunderland
- The Queen
- MI6
- Scotland Yard
- Inspector Morse
- The Bill
- Bobbies
- Red Phone Box
- The Avengers
- Red Bus
- Royal Guards
- Bad Teeth
- Repressed Women
- The Beetles
- Oasis
- Spice Girls
- David Beckham
- Monty Python
- Billy Conelly
- Beer
- Drunkedness
- The InVesible Man
Mr. Bean
James Bond
We'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
Project Description:
Projects are missions
1. Cell by Date :
vehicle sounds like vesicle
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
- Back Story - how VesoCop came to be
- VesoCop in action - Project Definition
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:
- Potential as a motif - Look forward to slide layout / presentation / Logo / Tshirt Design
Austin Veso Story
- Feedback from Group on Austin Veso:
- Jerry likes big chicks
- Teeth need changing - make them whiter less crooked
- Colar needs fixing
- Consider 3/4 view
- Text is too bland - make it in crazy 60s theme
- Back Story - how Austin Veso came to be
- Austin Veso in action - Project Definition
The Story:
Synthetic Biology has amde awe inspiring Progress to date : it has helped to produce a malaria vacine and by the the looks of previous iGEM it will improve our lives in many other ways(Need more wow! milestones here). We feel that we can contribute to this amazing movement through the exploration of Cell Free Chasis. In Looking into Cell Free Chassis we think we've come up with something special we call him Veso Powers: International Bag Of Lipids
The Project:
Veso Powers: International Bag of Lipids is the ultimate spy, using his cell free mojo he can do amazing things. Check out two incredible missions that Veso Powers will be able to carry out by the end of summerof after he has completed our rigerous trainging programme in the ways of the Mojo at our super secret HQ in london.
Click here to find out more about how Austin Veso came to be (link to Austin Veso Back Story Page)
Mission 1: Thermal Steakout
Veso Powers' First mission involves our food. Using his special Cell By Date ability he can determine when food is spoilt more accurately than printed sell by dates. Veso Powers Cell By Date ability exploits the thermal dependence of the rate of expression of a simple reporter system.
Mission 2: A lot of Biofilm's Penthouse
Austin Veso Second Mission is to go undercover, using his Infector Detector ability. With this ability Veso Powers can detect biofilm that are antibiotic-resistant and a major source of infection in hospitals. The Infector Detector ability system makes use of Lux quorum sensing to eavesdrop on the communication between biofilm-forming bacteria.
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:
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, Veso Powers will have his mojo in full swing and will be mission ready - Yeah Baby !.
- Potential as a motif - Look forward to slide layout / presentation / Logo / Tshirt Design
Sherlock Veso Story
- Back Story - how VesoCop came to be
- VesoCop in action - Project Definition
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:
- Potential as a motif - Look forward to slide layout / presentation / Logo / Tshirt Design
