User:Jec105

From 2008.igem.org

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__NOTOC__
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=== Summer Summary ===
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{{Imperial/Box2|Our Approach|[[Image:Cycle.PNG|center|500px]]|}}
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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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{{Imperial/Box1|Design|
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In order to achieve our specifications of design previously described, we require the following constructs;
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*'''Light sensing device''' - Converting a light input into an output of PoPS,
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*'''Biomaterial production device'''- Converting a PoPS input into an output of biomaterial,
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*'''Motility Control device''' - Converting a PoPS input into an output of motility arrest,
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*'''Integration device''' - To allow integration and selection of our genetic constructs,
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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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[[Image:Genetic circuit.PNG|750px|center]]
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<hr>
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|}}
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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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The local weather is ''hot hot hot'' with an 80% chance of ''passion''...
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{{Imperial/Box1|Modeling - Overview|
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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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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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{{Imperial/Box1|Implementation|
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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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Think what we can refer to implementation as 1)the construction of the parts ,2) the work with B.subtilis integration3)growth curve if we want to. Idea is to have three sub boxes with a large picture and brief text underneath. Last week Kirsten had the idea that we could make a big gel with the digests from all our parts, I will look into this week to get an image. \We could use this then put some stuff about no. of parts etc. Think}}
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{| border=0 cellspacing=0 cellpadding=5 width=500px style="background:#3366FF" align=right
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{{Imperial/Box1|Testing|
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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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Results from the B.subtilis motility and maybe the part characterisation
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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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{{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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<br clear="all">
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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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| [[Image:Imperial_2008_Bioprinter_Cartoon.png |450px| Overview of our planned system]]
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*Showed that expansion into other organisms is a definite possibility!
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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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|<html><align="right"><img width="100px" src="http://i59.photobucket.com/albums/g305/Timpski/Gold_Medal.png"></align></html>}}
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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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{{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}}
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{{Imperial/EndPage|Chassis_2|Biocouture}}

Latest revision as of 08:16, 21 October 2008

Summer Summary

Our Approach
Cycle.PNG

Design

In order to achieve our specifications of design previously described, we require the following constructs;

  • Light sensing device - Converting a light input into an output of PoPS,
  • Biomaterial production device- Converting a PoPS input into an output of biomaterial,
  • Motility Control device - Converting a PoPS input into an output of motility arrest,
  • Integration device - To allow integration and selection of our genetic constructs,

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'.

Genetic circuit.PNG

Modeling - 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.


Implementation

Think what we can refer to implementation as 1)the construction of the parts ,2) the work with B.subtilis integration3)growth curve if we want to. Idea is to have three sub boxes with a large picture and brief text underneath. Last week Kirsten had the idea that we could make a big gel with the digests from all our parts, I will look into this week to get an image. \We could use this then put some stuff about no. of parts etc. Think


Testing

Results from the B.subtilis motility and maybe the part characterisation


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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