Team:Paris

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<center>'''Welcome to iGEM08 Paris' wiki page'''</center>
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<html><div style="text-align:justify; background: url(https://static.igem.org/mediawiki/2008/f/fc/IGEM_PARIS_2008_fond4.jpg); background-repeat:no-repeat; margin=0;"></html>
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<center><html><div style="color:#275D96; font-size:4em;">The BacteriO'Clock</div></html>
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<div style="font-size: 2em;">by the <html><a alt="Team" title="Discover our team !" style="text-decoration: underline;" href="https://2008.igem.org/Team:Paris/Team">Paris iGEM Team</a></html></div>
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<embed  width="320" height="240"  src="http://biosynthetique.free.fr/videos/flv_player/flvplayer.swf?autostart=true&amp;repeat&amp;file=http://biosynthetique.free.fr/videos/out2.flv" quality="high" type="application/x-shockwave-flash"  allowfullscreen="true" />
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==Where and when iGEM08 Paris took place ?==
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[[Image:IGEM_paris_logo_bleu_dernier_copy.jpg|right|200px|iGEM Paris]]
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The Center for Research and Interdisciplinarity (CRI) is a structure hosted in the medicine faculty of Cochin-Port Royal in cooperation with the universities Paris V (Paris Descartes), Paris VII (Paris Diderot) and the Ecole Normale Supérieure (ENS). It proposes to students and researchers from different backgrounds to create multidisciplinary projects. Synthetic biology is a promising subject for the development of such projects as it tries to put into practice the concepts of engineering into biology.
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Have you ever dreamed of a new way of thinking everyday life objects? Be sure, this could one day become true, under the form of our '''BacteriO'Clock !''' A simple test tube containing our modified bacteria might give you the time, directly from living organisms, the hours of the day being '''color-coded''', and '''oscillations''' ensuring the repeated periodic behavior. Inspired by the flagellar motor machine, our clock at this stage of developpement serves as a '''chassis''' to be used in building future modular molecular machines in an optimized and coordinated manner. It may serve as well to control in an optimized fashion '''multi-reaction pathways'''.
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The CRI is a structure in the heart of which students animate scientific clubs, where they meet to read scientific articles, share ideas and receive guests. The club SYNBIOSYS for Synthetic and Systems Biology was created in November 2006. This initiative was truly a hit, and, quite understandably, the students heard about iGEM and decided to participate in 2007, supported by several teachers and scientists.
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To achieve this incredible project, we relied on a well characterized genetic structure that allows a specific sequence of fluorescent proteins expression to occur in a First In - First Out order. This '''FIFO''' behavior enables us to define a rich color encoding of day time. An additional negative feedback loop generates clock oscillations!
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Based on in-depth studies and experimentally measured parameters we developed predictive models that suggest that this core system is not likely to demonstrate stable oscillations due to damping phenomenon leading to a stationary steady-state. Importantly, our modeling approach provided us with alternative improved designs that should lead in principle to an optimized '''BacteriO'Clock'''. In particular, this is achieved through '''synchronization at the population level''' by adopting a quorum sensing feedback mediated by HSL production that enforces a necessary delay and provides an elegant cellular synchronization mechanism :
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<center><html><a href="https://2008.igem.org/Team:Paris/Project" alt="Project" title="Learn more about our project !"><img width=350px src="https://static.igem.org/mediawiki/2008/5/58/Unimo.png" /></a></html></center>
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Thanks to its original project of Multicellular Synthetic Bacteria, able to optimize the production of a useful substance for men, the Parisian iGEM team managed to reach the Finale where the students won a Gold Medal as well as the prestigious Grand Prize for Foundational Research. Quite understandably, the SYNBIOSYS club created another iGEM team for the 2008 edition.
 
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''If you want to know more about us, visit our [[Team:Paris/Team|team]] page !''
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In a nutshell, the new trendy item which will make every biologist in your lab jealous will soon be available. Through a long-cloning period, '''we now have all biobricks needed and much of the final constructions'''. Furthermore, we initiated an extensive characterization plan of these parts. If you manage to wait for the updates, you might even get the version that automatically reacts to daylight saving time ;)
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==About our project==
 
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After several months of deep reflexion, our project took shape !
 
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Our project aims at biologically devising a “oscillating FIFO behaviour, synchronized at population level”. Such a setup will trigger periodic events and,therefore, can be considered as a “biological clock”. To completely deserve this appellation, the system has to fulfill the following specifications :
 
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* Oscillatory system : It will consist in providing a periodic output for the duration of the experiment. To do so, we will use a genetic cascade, initiated by a specific inducer which last step will inhibit the previously mentioned inducer.
 
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* FIFO System : The period of the oscillation is even more interesting if fit allows the sequential switching on and off of several genes. Our setup involves three genes which will get activated and desactivated successively as a “FIFO : First In, First Out”. This sequence is monitored by a logic structure called Feed-Forward Loop (FFL).
 
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* Synchronization : Yet, being able to control this sequential activation within a single cell can be seen as a “first step” in biological clock devising. In order to amplify this phenomenon (to observe it in an easier way or even to find future applications), it has to be extended to a whole population of bacteria. Here comes the synchronization issue: we will use methods based on the “quorum sensing” phenomenon.
 
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We will base our project on an already existing structure, partly fulfilling the evoked specifications: the system that leads to the production of ''E. coli'' flagella.
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<center><html><a title="Discover our team !" href="https://2008.igem.org/Team:Paris/Team"><img style="padding: 5px; border: orange dashed 1px;" src="https://static.igem.org/mediawiki/2008/1/19/ParisTeam.jpg" width="300px" /></a></html>
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''For more information, have a look to our [[Team:Paris/Project|project]] page !''
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[[Team:Paris/Notebook/Freezer|Freezer]] || [[Team:Paris/Notebook|Notebook]]
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{{Paris/Header|We are extremely grateful to the organizations that support our project:}}
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{|
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|width=25%| [[Image:bettencourt.png]]
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Bettencourt-Schueller Foundation
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[http://www.fondationbs.org/ www.fondationbs.org]
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|width=25%| [[Image:Logocri.jpg|115px]]
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Centre de Recherches Interdisciplinaires
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[http://www.cri-paris.org/fr/cri/ www.cri-paris.org/fr/cri/]
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|width=25%| [[Image:LogoPCU1.jpg|100px]]
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Paris Centre universités
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[http://www.pariscentreuniversites.fr/ www.pariscentreuniversites.fr]
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|-
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|[[Image:Embassy.png|250px]]
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Embassy of France in the United States
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[http://www.ambafrance-us.org/ www.ambafrance-us.org]
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|[[Image:FacMed.png|140px]]
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Faculté de Médecine Université Paris Descartes
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[http://www.medecine.univ-paris5.fr/ www.medecine.univ-paris5.fr]
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|[[Image:Qiagen.GIF|60px]]
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Qiagen
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[http://www.qiagen.com/ www.qiagen.com/]
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|[[Image:Ibisc.jpeg|100px]]
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Ibisc Laboratory
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[http://www.ibisc.univ-evry.fr/ www.ibisc.univ-evry.fr]
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|[[Image:Gdrbim.jpg|100px]]
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GdR BiM
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[http://www.gdr-bim.u-psud.fr/ www.gdr-bim.u-psud.fr]
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|[[Image:Logo INRIA.jpg|180px]]
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INRIA
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[http://www.inria.fr/ www.inria.fr]
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[[Team:Paris/Museum|Have fun visiting our old wiki!]]</center>

Latest revision as of 12:24, 2 April 2009


The BacteriO'Clock





Have you ever dreamed of a new way of thinking everyday life objects? Be sure, this could one day become true, under the form of our BacteriO'Clock ! A simple test tube containing our modified bacteria might give you the time, directly from living organisms, the hours of the day being color-coded, and oscillations ensuring the repeated periodic behavior. Inspired by the flagellar motor machine, our clock at this stage of developpement serves as a chassis to be used in building future modular molecular machines in an optimized and coordinated manner. It may serve as well to control in an optimized fashion multi-reaction pathways.


To achieve this incredible project, we relied on a well characterized genetic structure that allows a specific sequence of fluorescent proteins expression to occur in a First In - First Out order. This FIFO behavior enables us to define a rich color encoding of day time. An additional negative feedback loop generates clock oscillations!

Based on in-depth studies and experimentally measured parameters we developed predictive models that suggest that this core system is not likely to demonstrate stable oscillations due to damping phenomenon leading to a stationary steady-state. Importantly, our modeling approach provided us with alternative improved designs that should lead in principle to an optimized BacteriO'Clock. In particular, this is achieved through synchronization at the population level by adopting a quorum sensing feedback mediated by HSL production that enforces a necessary delay and provides an elegant cellular synchronization mechanism :


In a nutshell, the new trendy item which will make every biologist in your lab jealous will soon be available. Through a long-cloning period, we now have all biobricks needed and much of the final constructions. Furthermore, we initiated an extensive characterization plan of these parts. If you manage to wait for the updates, you might even get the version that automatically reacts to daylight saving time ;)



Freezer || Notebook


We are extremely grateful to the organizations that support our project:


Bettencourt.png

Bettencourt-Schueller Foundation

[http://www.fondationbs.org/ www.fondationbs.org]

Logocri.jpg

Centre de Recherches Interdisciplinaires

[http://www.cri-paris.org/fr/cri/ www.cri-paris.org/fr/cri/]

LogoPCU1.jpg

Paris Centre universités

[http://www.pariscentreuniversites.fr/ www.pariscentreuniversites.fr]

Embassy.png

Embassy of France in the United States

[http://www.ambafrance-us.org/ www.ambafrance-us.org]

FacMed.png

Faculté de Médecine Université Paris Descartes

[http://www.medecine.univ-paris5.fr/ www.medecine.univ-paris5.fr]

Qiagen.GIF

Qiagen

[http://www.qiagen.com/ www.qiagen.com/]

Ibisc.jpeg

Ibisc Laboratory

[http://www.ibisc.univ-evry.fr/ www.ibisc.univ-evry.fr]


Gdrbim.jpg

GdR BiM

[http://www.gdr-bim.u-psud.fr/ www.gdr-bim.u-psud.fr]

Logo INRIA.jpg

INRIA

[http://www.inria.fr/ www.inria.fr]




Have fun visiting our old wiki!