User:Jec105

From 2008.igem.org

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=== Summer Summary ===
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{{Imperial/Box2||
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This page will include...
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[[Image:Imperial_2008_Logo.png|center|400px|Bad name, I know... But half the fun of iGEM is poor punning!]]
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Genetic diagrams, engineering cycle, overview of modelling, overview of major results, contributions etc.
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Basically just an overview of our project progress and results, with a section detailing how we achieved a Gold medal!|}}
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<hr>
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{{Imperial/Box1|Our Approach|
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<center>Welcome to the Imperial 2008 iGEM team's main project page. It's {{CURRENTDAYNAME}}, {{CURRENTMONTHNAME}} {{CURRENTDAY}} and a great day to read about an awesome iGEM project!</center>
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[[Image:Imperial_2008_Basic_Circuit.png|300px|right]]
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Our basic approach was to constitutively upregulate a light-sensitive pathway in ''B. subtilis'', then use a downstream product from that pathway to selectively regulate expression of our clutch and biomaterial. This overview is shown on the right. To do this we need to produce at least one constitutive promoter to precede our light-sensing mechanism, as well as a 'light-inducible' promoter in front of our clutch and biomaterial. Additionally, we'll need to make all the other standard parts such as ribosome binding sites (RBS) and terminators.
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The local weather is ''hot hot hot'' with an 80% chance of ''passion''...
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The diagram below shows our theoretical final construct once it's all put together - as you can see, it's a little more complex than the one on the right!
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<html><center><img width=750px src="http://s59.photobucket.com/albums/g305/Timpski/S1L.png"></center></html>
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| For the 2008 iGEM competition, the Imperial College team is working on the foundations for a bioprinter. We are using the Gram-positive ''Bacillus subtilis'' bacterium as a chassis (for a variety of reasons) and hope to be able to exert fine control over its movement via a recently-discovered clutch mechanism. Using light as a stimulus to localise the bacteria, we then intend to trigger production and secretion of a biomaterial in a set pattern. The project was inspired by 3D printers used in fabrication of prototypes for manufacturing, and our "blue-sky" aim is to make a 3D bioprinter!
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Here, AB is our antibiotic resistance cassette, ''ytvA'' is the gene controlling the light-sensing pathway, ''SB'' is the biomaterial, ''epsE'' the clutch and the 5' and 3' sections are integration sites. Light-inducible promoters are labelled with an 'L'.
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{| border=0 cellspacing=0 cellpadding=5 width=500px style="background:#3366FF" align=right
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! align=left colspan=1 |The Team || rowspan=2 |[[Image:Imperial_2008_Big_Team_Photo.jpg|216px|Prudence is taking the picture... Click for larger image!]] || bgcolor="#3344DD" rowspan=2|
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{{Imperial/Box1|Dry Lab Overview|
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| colspan=1 valign=top |The Imperial College 2008 iGEM team is made up of 9 students (5 undergraduate bioengineers, 3 graduate biochemists and 1 graduate biologist), 5 advisors and two professors. You can find out more about the team members at the [[Team:Imperial_College/Team | team page]].
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Basically our dry lab team concentrated on characterising the chassis. In the dry lab section you'll find pages on the genetic circuit, growth curve and motility analysis from our project; this section will give a brief brief overview of each area (no pictures?). It will also include (in the motility analysis part) a movie (y/n?) of the motility response of ''B. subtilis'' with an inducible ''epsE'' gene BioBricked in.
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====== Growth Curve ======
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The growth curve of ''B. subtilis'' was modelled by superposition of three more basic ODE models, which were constructed and simulated in MATLAB. The lag, exponential and stationary phases are modelled and combined to produce the curve on the right (Image here?).
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====== Genetic Circuit ======
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We feel accurate modelling of the genetic circuit contributes greatly to the characterisation of synthetic systems. As part of the project, the behaviours of constitutive and inducible promoters were modelled for comparison with our experimental data.
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====== Motility Analysis ======
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| [[Image:Imperial_2008_Bioprinter_Cartoon.png |450px| Overview of our planned system]]
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A major component of the system is the motility and shift between a motile and arrested state with the expression of EpsE.
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| valign="top" |This diagram gives a basic overview of how we intend our system to work. In the starting phase, ''B. subtilis'' are motile and are not producing our desired product - they swim freely in the medium. If we want to print a serif "I" shape of product, we shine light of the correct wavelength (red is used as an arbitrary example here) in the desired shape onto the plate. <br>Bacteria within this area will sense that light, and production of a clutch molecule (EpsE) will be triggered. This should disengage the flagella from the motor quite quickly, rendering the ''subtilis'' stationary - coupled with EpsE is a gene for expression of our desired product, so they will start producing it when in the area. We had considered also causing them to release a chemoattractant to bring in "reinforcements" and improve localisation, but this may be beyond the scope of our project. <br>Should any individuals stray from the correct area, the clutch should disengage and material synthesis should stop. Thus, we hope to build up material in the defined area only - the basis of our bioprinter.
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{{Imperial/Box1|Wet Lab Overview|
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[[Team:Imperial_College/Test_Page | '''''Test page and storage for random parts - Also see here for intro to editing the Imperial Wiki''''']]
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The wet lab team was responsible for designing the constructs and setting up the cloning strategy to get us from the starting parts to the finished system. We were also responsible for designing and BioBricking the starting parts, of course, and designing and implementing the integration brick technique. This section shows some of the major results that came from the wet lab over the summer. Motility results can go in the dry lab overview above.
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{{Imperial/EndPage}}
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====== Transformation ======
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Transformation stuff goes here...
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====== Calibration Curve ======
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Calibration curve results go here...
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|Stuff}}
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{{Imperial/Box1|Achievements|
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*Helped Bristol by sending them a mini-iGEM project: ''Chemotactic dot-to-dot'' with information on quorum sensing and directed movement
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*Helped Bristol by sending them a part (BBa_J37015) from our 2007 stock which was an empty vector in the Registry
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*Developed integration bricks, to allow devices to be constructed that can then be excised and planted into ''B. subtilis''
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*Layed the groundwork for future teams to work with ''B. subtilis'' by BioBricking promoters, RBSs, terminators and so on and characterising them
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*Showed that expansion into other organisms is a definite possibility!
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|<html><align="right"><img width="100px" src="http://i59.photobucket.com/albums/g305/Timpski/Gold_Medal.png"></align></html>}}
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<hr><br>
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{{Imperial/Box2||Of course, that's a very simplified description of our project. We expanded upon our project by looking into possible areas for real-world application; for a case-study of such an implementation check out how our project fits in with [[Team:Imperial_College/Biocouture | '''>>> Biocouture >>>''']]}}
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{{Imperial/EndPage|Chassis_2|Biocouture}}

Revision as of 20:44, 20 October 2008

Summer Summary

This page will include...

Genetic diagrams, engineering cycle, overview of modelling, overview of major results, contributions etc.

Basically just an overview of our project progress and results, with a section detailing how we achieved a Gold medal!


Our Approach
Imperial 2008 Basic Circuit.png

Our basic approach was to constitutively upregulate a light-sensitive pathway in B. subtilis, then use a downstream product from that pathway to selectively regulate expression of our clutch and biomaterial. This overview is shown on the right. To do this we need to produce at least one constitutive promoter to precede our light-sensing mechanism, as well as a 'light-inducible' promoter in front of our clutch and biomaterial. Additionally, we'll need to make all the other standard parts such as ribosome binding sites (RBS) and terminators.

The diagram below shows our theoretical final construct once it's all put together - as you can see, it's a little more complex than the one on the right!

Here, AB is our antibiotic resistance cassette, ytvA is the gene controlling the light-sensing pathway, SB is the biomaterial, epsE the clutch and the 5' and 3' sections are integration sites. Light-inducible promoters are labelled with an 'L'.


Dry Lab Overview

Basically our dry lab team concentrated on characterising the chassis. In the dry lab section you'll find pages on the genetic circuit, growth curve and motility analysis from our project; this section will give a brief brief overview of each area (no pictures?). It will also include (in the motility analysis part) a movie (y/n?) of the motility response of B. subtilis with an inducible epsE gene BioBricked in.

Growth Curve

The growth curve of B. subtilis was modelled by superposition of three more basic ODE models, which were constructed and simulated in MATLAB. The lag, exponential and stationary phases are modelled and combined to produce the curve on the right (Image here?).

Genetic Circuit

We feel accurate modelling of the genetic circuit contributes greatly to the characterisation of synthetic systems. As part of the project, the behaviours of constitutive and inducible promoters were modelled for comparison with our experimental data.

Motility Analysis

A major component of the system is the motility and shift between a motile and arrested state with the expression of EpsE.


Wet Lab Overview

The wet lab team was responsible for designing the constructs and setting up the cloning strategy to get us from the starting parts to the finished system. We were also responsible for designing and BioBricking the starting parts, of course, and designing and implementing the integration brick technique. This section shows some of the major results that came from the wet lab over the summer. Motility results can go in the dry lab overview above.

Transformation

Transformation stuff goes here...

Calibration Curve

Calibration curve results go here...

Stuff


Achievements
  • Helped Bristol by sending them a mini-iGEM project: Chemotactic dot-to-dot with information on quorum sensing and directed movement
  • Helped Bristol by sending them a part (BBa_J37015) from our 2007 stock which was an empty vector in the Registry
  • Developed integration bricks, to allow devices to be constructed that can then be excised and planted into B. subtilis
  • Layed the groundwork for future teams to work with B. subtilis by BioBricking promoters, RBSs, terminators and so on and characterising them
  • Showed that expansion into other organisms is a definite possibility!



Of course, that's a very simplified description of our project. We expanded upon our project by looking into possible areas for real-world application; for a case-study of such an implementation check out how our project fits in with >>> Biocouture >>>



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