IGEM:IMPERIAL/2007/Projects: Difference between revisions

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[[Image:Icgems_project-matrix.jpg|center]]
===VesoCops - Imperial College iGEM 2007 Team===
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===Summary===
[[image:IC07_biofilm.png|thumb|right|330px|Infector Detector]]
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 traditional E. coli cells.
The Imperial College iGEM 2007 team consists of ten 2nd year undergraduates from Bioengineering and Bioscience. 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.
 
 
[[image:IC07_cellbydate.png|thumb|left|340px|Cell By Date]]
Our contribution to the synthetic biology community will be the investigation of a '''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 medical and food industries. We believe that the characterization of this cell-free chassis will unlock fresh potential in simple constructs. Our project strategy is based on the '''Engineering Cycle''', of which we have completed specifications and design of the systems. We are starting on modelling and implementation, and we aim to test our final constructs in the new chassis. We hope that by the end of the summer, the VesoCops will be ready to start their investigations.
 


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==Chassis characterisation==
===[[IGEM:IMPERIAL/2007/Projects/chassis|Chassis]]===


===In-vivo===
==Projects==
===In-vitro===
===[[IGEM:IMPERIAL/2007/Projects/In-Veso|In-Veso Gene Expression]]===
 
==Applications==
===[[IGEM:IMPERIAL/2007/Projects/Hrp System|Hrp System]]===
===[[IGEM:IMPERIAL/2007/Projects/Cell By Date|Cell By Date]]===
===[[IGEM:IMPERIAL/2007/Projects/Cell By Date|Cell By Date]]===
===[[IGEM:IMPERIAL/2007/Biofilm Detector|Biofilm Detector]]===
===[[IGEM:IMPERIAL/2007/Biofilm Detector|Infector Detector]]===


==DNA Consructs==
==Chassis characterisation==
====[[IGEM:IMPERIAL/2007/DNA Constructs|DNA Constructs]]====
===[[IGEM:IMPERIAL/2007/Projects/In-Veso|In-Veso Gene Expression]]===
DNA constructs for all our projects.
 
==[[IGEM:IMPERIAL/2007/Projects/Lab Notebook|Lab Notebook]]==
Follow the link above to the team's lab notebook


===[[IGEM:IMPERIAL/2007/Projects/General Protocols | General Protocols]]===
==Resources==
===[[IGEM:IMPERIAL/2007/Experimental Design| Experimental Design]]===
===[[IGEM:IMPERIAL/2007/DNA Constructs|DNA Constructs]]===
===[[IGEM:IMPERIAL/2007/Notebook/General Protocols | General Protocols]]===
Protocols being used by all projects. Examples:
Protocols being used by all projects. Examples:
* Plasmid preparation
* Plasmid preparation
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* Restriction digest
* Restriction digest
* Ligation
* Ligation
 
===[[IGEM:IMPERIAL/2007/Projects/Lab Notebook|Lab Notebook]]===
A notebook of the daily activities in the lab
===[[IGEM:IMPERIAL/2007/Projects/Reporters | Reporters]]===
===[[IGEM:IMPERIAL/2007/Projects/Reporters | Reporters]]===
Any reporters that might be used for the projects
Any reporters that might be used for the projects
===Equipments needed===
<br>1. LB media
<br>2. LB+ Amplicillin plate                                  x 30
<br>3. LB+ Kanamycin plate                                    x 30
<br>4. LB+ Amp+ Kn                                            x 15
<br>5. 37oC shaking incubator                                x 1
<br>6. 4oC freezer                                            x 1
<br>7. Table top centrifuge                                  x 3
<br>8. 4oC table top centrifuge/ cold room/ fridge
<br>9. UV Spectrometer                                        x 2
<br>10. Gilson pipettes (1000, 200, 20, 10, 2)                x5 each
<br>11. Tips (yellow and blue)                                x 20 boxes each
<br>12. Small tips                                            x 5 boxes
<br>13. Eppendorf tubes
<br>14. Centrifuge tubes
<br>15. Machine to check for purity of DNA (260/280)
<br>16. 37oC water bath
<br>17. Metal block incubator
<br>18. Innoculation loops                                    x 10 packets
<br>19. 15oC water bath
<br>20. Agarose gel equipments                                x 3
<br>21. TBE x 1 litre of 50x TBE
<br>22. Microwave oven
<br>23. Camera
<br>24. Blades (for cutting agarose gel)                      x 3
<br>25. Band detection machine
<br>26. EB buffer (Tris-Cl + EDTA)
<br>27. Gloves
<br>28. Whiteboard markers
<br>29. Paper towels
<br>30. 10ml pipettes                                        x 50
<br>31. Pipette fillers                                      x 5

Latest revision as of 01:58, 14 August 2007


VesoCops - Imperial College iGEM 2007 Team

Infector Detector

The Imperial College iGEM 2007 team consists of ten 2nd year undergraduates from Bioengineering and Bioscience. 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.


Cell By Date

Our contribution to the synthetic biology community will be the investigation of a 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 medical and food industries. We believe that the characterization of this cell-free chassis will unlock fresh potential in simple constructs. Our project strategy is based on the Engineering Cycle, of which we have completed specifications and design of the systems. We are starting on modelling and implementation, and we aim to test our final constructs in the new chassis. We hope that by the end of the summer, the VesoCops will be ready to start their investigations.



Projects

Cell By Date

Infector Detector

Chassis characterisation

In-Veso Gene Expression

Resources

Experimental Design

DNA Constructs

General Protocols

Protocols being used by all projects. Examples:

  • Plasmid preparation
  • Plasmid extraction
  • Restriction digest
  • Ligation

Lab Notebook

A notebook of the daily activities in the lab

Reporters

Any reporters that might be used for the projects

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