IGEM:Cambridge/2008

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<h1> Welcome to the Cambridge iGEM 2008 Wiki!</h1>
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This year, Cambridge is working on three different projects! (could someone please edit this part to something of a more general introduction of our team?)
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==[[iGEM:Cambridge/2008/Notebook/Turing_Pattern_Formation|Turing Pattern Formation]]==
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[[Image:Struktur-e.gif|thumb|left|Turing Patterns]]
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We plan to implement a simple two-component Reaction-Diffusion system in the gram-positive model organism Bacillus subtilis. In 1952, Alan Turing famously described this system and suggested it as the basis for self-organization and pattern formation in biological systems. The simplest of these patterns, which we are planning to model in bacteria, mimic the spots and stripes seen on animal coats.
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We intend to use two well-characterized bacterial communication systems to generate this behavior.  The agr peptide signalling system from S. aureus will serve as our activatory signal (pictured), while the lux system from V. fischeri will serve as our inhibitor. Bacillus subtilis serves as an excellent chassis for this project because of the ease with which chromosomal integration can be performed. This project will focus on a tight integration of modeling and experiment; we will test different promoter strengths and other variables, feed these system parameters into our multi-cell models, and then use those models to tweak the regulatory machinery that will control signal production.
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==[[iGEM:Cambridge/2008/Notebook/Voltage|Voltage Output]]==
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[[Image:800px-Cambridge_2008_voltage.jpg|thumb|right|Schematic]]
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The aim of this project is to work towards an interface between biological and electric systems. We hope to do this by measuring a voltage change due to the presence of a certain substance.
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In the first instance, this substance will be glutamate, as it acts as a ligand for a prokaryotic gated potassium channel.
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Our idea is to sequester K+ inside E.coli cells by using leak channel knock-out mutants, and over-expressing K+ influx pumps. Then, when glutamate is present it will open K+ channels, allowing an efflux of potassium and causing a small but measureable change in voltage in the medium.
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==[[IGEM:Cambridge/2008/Notebook/Magnetic_Bacteria|Magnetic Bacteria]]==
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We are investigating the formation of magnetosomes (membrane bound magnetite particles) in magnetotactic bacteria. This process is believed to take place in the following steps: i) production of invaginations along the inner membrane ii) uptake of iron into these invaginations iii) biomineralisation of the iron into magnetite crystals of a specific size and shape iv) axial alignment of the magnetosomes
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<h2>Subprojects:</h2><br/>
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<td class="tdboxes"><a href="http://openwetware.org/wiki/iGEM:Cambridge/2008/Notebook/Voltage"><img border="0" src="http://openwetware.org/images/0/00/Vol_logo.JPG" width="256" height="201"></a></td>
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<td class="tdboxes"><a href="http://openwetware.org/wiki/iGEM:Cambridge/2008/Notebook/Magnetic_Bacteria"><img border="0" src="http://openwetware.org/images/d/d1/Mag_logo.JPG" width="210" height="201"></a></td>
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<td class="tdboxes"><a href="http://openwetware.org/wiki/iGEM:Cambridge/2008/Notebook/Turing_Pattern_Formation"><img border="0" src="http://openwetware.org/images/f/fe/Tur_logo.JPG" width="201" height="201"></a></td>
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This mechanism gives the bacteria the ability to align itself like a compass needle along geomagnetic field lines. We are attempting to engineer the uptake of soluble iron into membrane invaginations in E.coli, and stimulate formation of magnetite using genes from Magnetospirillum.
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<h2>Wiki</h2>
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* [[/Wiki Discussions/]]
 
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<h2>Photos</h2>
 
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* [[/Photos from the first day/]]
 
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<td width="37%"> <h2>Work</h2>
 
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*[[/Organisation/]]
 
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*[[/Brainstorming/]]
 
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*[[/Protocols/]]
 
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<h2>Lectures</h2>
 
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* Links to .pdf and other good stuff.
 
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<h2>Misc.</h2>
 
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* [http://www.flickr.com/groups/777370@N24/ Slides & Pictures]
 
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*[http://www.localendar.com/public/CamiGEM08 Team Calendar]
 
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* [http://2008.igem.org/Calendar_of_Events|iGEM Calendar of Events]
 
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<td width="26%"><h2>People</h2>
 
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<b>Students</b>
 
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* [[User:Linda_Boettger | Linda Boettger]]
 
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* [[User:Marie_Chapart | Marie Chapart]]
 
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* [[User:Kevin Cheng | Kevin Cheng]]
 
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* [[User:Kathryn_Chung | Kathryn Chung]]
 
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* [[User:Daniel_Goodman | Daniel Goodman]]
 
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* [[User:Chris_Hill | Chris Hill]]
 
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* [[User:Rebecca_Koenigsberg-Miles | Rebecca Koenigsberg-Miles]]
 
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* [[User:Arjun_Mehta | Arjun Mehta]]
 
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* [[User:Dmitriy_Myelnikov | Dmitriy Myelnikov]]
 
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* [[User:Ellis_O'Neill | Ellis O'Neill]]
 
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* [[User:Yee_Yen_Tang| Ian (Yee Yen) Tang]]
 
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* [[User:James_Wu | James Wu]]
 
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* [[User:Xiao-Hu_Yan | Xiao-Hu Yan]]
 
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<b>Advisors</b>
 
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* [[User:Stefan_Milde | Stefan Milde]]
 
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* [[User:James_Brown | James Brown]]
 
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<b>Faculty</b>
 
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* [[User:Jim_Ajioka | Jim Ajioka]]
 
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* [[User:Jim_Haseloff |Jim Haseloff]]
 
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* [[User:Duncan_Rowe | Duncan Rowe]]
 
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* [[User:Gos_Micklem | Gos Micklem]]
 
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Revision as of 11:28, 31 July 2008



This year, Cambridge is working on three different projects! (could someone please edit this part to something of a more general introduction of our team?)

Turing Pattern Formation

Turing Patterns
Turing Patterns

We plan to implement a simple two-component Reaction-Diffusion system in the gram-positive model organism Bacillus subtilis. In 1952, Alan Turing famously described this system and suggested it as the basis for self-organization and pattern formation in biological systems. The simplest of these patterns, which we are planning to model in bacteria, mimic the spots and stripes seen on animal coats. We intend to use two well-characterized bacterial communication systems to generate this behavior. The agr peptide signalling system from S. aureus will serve as our activatory signal (pictured), while the lux system from V. fischeri will serve as our inhibitor. Bacillus subtilis serves as an excellent chassis for this project because of the ease with which chromosomal integration can be performed. This project will focus on a tight integration of modeling and experiment; we will test different promoter strengths and other variables, feed these system parameters into our multi-cell models, and then use those models to tweak the regulatory machinery that will control signal production.


Voltage Output

Schematic
Schematic

The aim of this project is to work towards an interface between biological and electric systems. We hope to do this by measuring a voltage change due to the presence of a certain substance. In the first instance, this substance will be glutamate, as it acts as a ligand for a prokaryotic gated potassium channel. Our idea is to sequester K+ inside E.coli cells by using leak channel knock-out mutants, and over-expressing K+ influx pumps. Then, when glutamate is present it will open K+ channels, allowing an efflux of potassium and causing a small but measureable change in voltage in the medium.

Magnetic Bacteria

We are investigating the formation of magnetosomes (membrane bound magnetite particles) in magnetotactic bacteria. This process is believed to take place in the following steps: i) production of invaginations along the inner membrane ii) uptake of iron into these invaginations iii) biomineralisation of the iron into magnetite crystals of a specific size and shape iv) axial alignment of the magnetosomes

This mechanism gives the bacteria the ability to align itself like a compass needle along geomagnetic field lines. We are attempting to engineer the uptake of soluble iron into membrane invaginations in E.coli, and stimulate formation of magnetite using genes from Magnetospirillum.





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