User:Cheuk Ka Tong/Sandbox

MIT
--Anthony Lazzaro 07:24, 8 August 2007 (EDT) I know there's already one on MIT wiki but i think this is much better not finished yet but will be in 10mins

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.

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
VesoCops - Imperial College iGEM 2007 Team

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 Bactocops will be combat-ready.

Revised Project Description
Engineering biology 'in-veso' - Imperial College iGEM 2007 team

The Imperial College iGEM 2007 team consists of ten undergraduate students, as well as a number of graduate students and faculty supervisors. The aim of our project is to characterise new chassis with the hope of unlocking new potential in simple constructs. To date, work on synthetic biology has been done using the chassis of bacterial cells. However the use of living, replicating engineered bacteria has severe limitations : in terms of the range of applications possible due to health risk bacteria pose, in terms of the fidelity of systems due to mutations and in terms of the quality of our system response due to poor signal to noise ratio. We plan to compare and characterise the traditional E. coli chassis with several alternatives : in-vitro chassis composed of E. coli cytoplasmic extracts and 'in-veso' chassis (E. coli cytoplasmic extracts encapsulated in phospholipid vesicles) in the hope that they will be less limiting. To illustrate the benefits of these new non-living cell-free chassis we have two exciting applications in mind. Firstly Cell By Date, a device that determines when food is spoilt more accurately than estimates used to construct printed sell by dates. It acts as a thermal exposure device exploiting the thermal dependence of the rate of expression of a simple reporter system. Our Second application is Infector Detector, a system that detects biofilms on catheters and produces a fluorescent output. Biofilms are a critical problem in hospitals as they cause infections and are resistant to antibiotics. Our Infector Detector makes use of the Lux quorum sensing system to detect AHL secreted by the bacteria constituting a biofilm. This is analogous to eavesdropping on the communication between biofilm-forming bacteria. Through our two applications : Cell By Date and Infector Detector we hope to show that using non-living Cell-Free Chassis we can take a step forward in terms of integrating synthetic biology with our everyday lives in a meaningful, safe way. 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 different chassis for our two fantastic applications.

Project Description
Engineering biology 'in-veso' - Imperial College iGEM 2007 team

The Imperial College iGEM 2007 team consists of ten undergraduate students, as well as a number of graduate students and faculty supervisors. The aim of our project is to investigate the use of cell-free chassis to realise new potentials for simple constructs. To date, work on synthetic biology has been done using the chassis of bacterial cells. However the use of living, replicating engineered bacteria poses a huge limitation for applications in the medicine and food industries for reasons of public safety. To solve this problem, our team decided to introduce cell-free expression systems as a new chassis to the field of synthetic biology. For comparison, we are going to use the same DNA constructs in three different chassis. The first chassis is the traditional E. coli cells. Second, we will use in-vitro systems composed of E. coli cytoplasmic extracts. Third, the E. coli cytoplasmic extracts will be encapsulated in phospholipid vesicles to form in-veso systems. Using vesicles to compartmentalize the transcription-translation of plasmid genes can potentially prolong the lifespan of the systems by allowing exchange of nutrients and waste materials between the expression machineries and the surrounding feeding solution.

To illustrate the feasibility of cell-free chassis, we aim to assemble genetic circuits in-veso for two exciting applications. One of the applications is Cell By Date, a device that determines when food is spoilt more accurately than estimates used to construct the printed sell by date. It exploits the thermal dependence of the rate of expression of a simple reporter system. The other application is Infector Detector, a system that detects biofilms on catheters and produces a fluorescent output. Biofilms are a serious problem in hospitals as they cause infections and are resistant to antibiotics. Our Infector Detector makes use of the Lux quorum sensing system to detect AHL secreted by the bacteria constituting a biofilm. This is analogous to eavesdropping on the communication between biofilm-forming bacteria. Engineering biological systems in veso eliminates the need for bacterial contact with either food or medical devices, this demonstrates the advantages of our cell-free chassis over the conventional E. coli cells. 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 different chassis for our two applications.

Feedback 1

 * 1) Need to break up into paragraphs
 * 2) Need to elaborate on drawbacks of ecoli
 * 3) Need to make it interesting why should someone care about what we are doing ?
 * 4) Name is boring aswell

Dead Sexy - Imperial College's iGEM 2007 Team

The aim of our project is to characterise new chassis with the hope of unlocking new potential in simple constructs. To date, work on synthetic biology has been done using the chassis of bacterial cells. However the use of living, replicating engineered bacteria has severe limitations : in terms of the range of applications possible due to health risk bacteria pose, in terms of the fidelity of systems due to mutations and in terms of the quality of our system response due to poor signal to noise ratio. We Plan to compare and characterise the traditional E. coli chassis with several alternatives : in-vitro chassis composed of E. coli cytoplasmic extracts and 'in-veso' chassis (E. coli cytoplasmic extracts encapsulated in phospholipid vesicles) in the hope that they will be less limiting. To illustrate the benefits of these new non-living cell-free chassis we have two exciting applications in mind. Firstly Cell By Date, a device that determines when food is spoilt more accurately than estimates used to construct printed sell by dates. It acts as a thermal exposure device exploiting the thermal dependence of the rate of expression of a simple reporter system. Our Second application is Infector Detector, a system that detects biofilms on catheters and produces a fluorescent output. Biofilms are a critical problem in hospitals as they cause infections and are resistant to antibiotics. Our Infector Detector makes use of the Lux quorum sensing system to detect AHL secreted by the bacteria constituting a biofilm. This is analogous to eavesdropping on the communication between biofilm-forming bacteria. Through our two applications : Cell By Date and Infector Detector we hope to show that using non-living Cell-Free Chassis we can take a step forward in terms of integrating synthetic biology with our everyday lives in a meaningful, safe way.

''In terms of progress we know the chassis and have investigated the preparation of them. In addition have the idea of an engineering cycle for the applications. So we have specifications, have a design (although it is lacking a chassis so far) and are developing a modeling (this week) and testing. Next stage would be to build and characterize the chassis in terms of our simple construct and then apply them to the applications.''

Anthony Lazzaro 05:27, 7 August 2007 (EDT) Hope these changes are alright progress section needs major work get back with feedback plz

Cheuk Ka Tong 05:47, 7 August 2007 (EDT) Hey Ant, thanks for the changes! It sounds much more interesting, I don't think we can use 'dead sexy' for a name though.

Anthony Lazzaro 06:14, 7 August 2007 (EDT) Why not? Dead becuase we are using non-living chassis and sexy because it's exciting, more interesting than e.coli and just becuase what else can you have after Dead ???

Cheuk Ka Tong 06:21, 7 August 2007 (EDT) Haha, I didn't think of that reasoning, I've sent the supervisors the 'revised project description' already. I didn't put the name 'Dead sexy' though. We could ask the team abt it later. =)

Feedback 2
Very good job so far, I think the content is good and it is well worded. Two suggestions: Although i think you have talked about all of these except the last, maybe restructure in terms of these key points. In terms of what to write for 'how far the projects are', could say, we've know the chassis and have investigated the preparation of them. In addition have the idea of an engineering cycle for the applications. So we have specifications, have a design (although it is lacking a chassis so far) and are developing a modeling (this week) and testing. Next stage would be to build and characterize the chassis in terms of our simple construct and then apply them to the applications. Only a suggestion and may not be exactly what we want to put, but overall top job so far!!!!! Oh also the team logo is very good as well!
 * 1) try to break it down into paragraphs as suggested above.
 * 2) Try to apply the following structure of:
 * Information about the team
 * Projects
 * How far into projects,

Alternate Angle
The Imperial College iGEM 2007 project is being carried out by ten undergraduate biologists and engineers, under the supervision of graduate students and faculty. We will build two systems: Cell by Date, which determines when food is spoilt more accurately than current printed methods; and Infector Detector, an easy to use visual indicator of the presence of E.coli biofilms.

Both Cell by Date and Infector Detector are very simple DNA constrtucts, inside a common chassis. The response of these systems exploits different and unrelated natural phenomena: cumulative temperature variations in one, and presence of bacterial signalling molecules in the other. We are comparing the performance of these constructs in E.coli, in vitro, and in veso. We aim to show that the vesicle chassis has several advantages, such as its suitability for use in areas where infection must be avoided, and can be easily applied to many other different applications.

So far, we have defined the constructs to be used for each system, and are working on the comparison of chassis and the development of the in veso technique.

To Do: A diagram showing both application systems, and perhaps the different chassis. Aything else? Project cycle? Progress bars?

Feedback (Vincent)

 * Good summary of the project, however by giving such a detailed description you are loosing the impact.
 * In terms of the project, I would suggest to focus first on the 2 applications you are targeting (problem addressed and solution proposed).
 * I would put all the rest (cell-free stuff) in a section related to 'Our contributions to the Synthetic Biology Community', where you would describe the common/standard platform used for the 2 applications.
 * Visual content would be helpful.
 * Links to some tidy sections of our OpenWetWare wiki could be useful.

Feedback (Matthieu)

 * I agree with Vincent that your description of Cell by Date and the Infector Detector needs expanding
 * A picture is worth a 1000 words : Make diagrams to explain what your projects are about
 * If you can link the pictures to the appropriate sections of OWW it is a bonus (see what was done last year with the engineering cycle )
 * As for the structure of the summary, why not detail the applications first and then introduce the cell-free component of your project?
 * It would reinforce the fact that your cell-free solution can be used in many other applications
 * Local=> global (Generalisation, Abstraction)