McGill University 2006

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=''Name: Fousion''=
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<center>[[Image:Banner.gif]]</center>
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= News =
 
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* '''2006-04-14''' Discussion page created
 
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* '''2006-03-16''' First kick-off meeting and team selection
 
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If there is a specific task that we need the bacteria to do (e.g. change colour on cue, aggregate...) list it here.
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'''Welcome to the McGill Wiki!'''
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We have a TON of composite bricks, and can plan custom ones.
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Basically, we're a team of 12 undergrads, 1 grad student, and 1 professor who like to have fun and clone things in our spare time. McGill University is located in Montreal, Quebec, which has given us wonderful opportunities to balance lab work with festivals and general craziness. iGEM has been a great opportunity to get lab experience while having the freedom to be creative, and we look forward to meeting the other teams at the jamboree!
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BUT I need to know what U want... I am going nuts looking at the list
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Your Dyslexic Dinosaur
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[[Image:Clip_image002.jpg]][[Image:Good_2.jpg]]
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= Organisation =
 
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== People ==
 
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=== Students ===
 
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{| width=700
 
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|[[Catie Lichten (Center for Nonlinear Dynamics)]]
 
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|[[Octavio Mondragon (Physics)]]
 
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|[[Belinda Kong (Microbiology and Immunology)]]
 
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|[[Adrian Kaats (Biomedical Engineering)]]
 
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|[[Jamie Schafer (Microbiology and Immunology)]]
 
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|[[Horia Vulpe (Physiology)]]
 
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|[[Ashwini Bapat (Biochemistry)]]
 
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|[[Aaron Lapierre (Anatomy & Cell Biology)]]
 
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|[[Josh Wright (Chemistry)]]
 
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|[[Jieun Kim(Biology)]]
 
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|}
 
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=== Supervisors ===
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{| width=650
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|-valign="top"
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|[[Jay Nadeau]]
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|}
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EDITED BY ASHWIN. If you want to change it, feel free :)-->
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== Timeline ==
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<center><h2><font face="broadway,verdana">Projects</font></h2></center>
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* [[Meetings]]
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== Tasks ==
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<table cellpadding="5" border="0"><tr>
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* [[Task Assignment]]
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<td valign="top" width="50%">
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<h3><ul><li>'''Team 1: Split YFP'''</ul></h3>
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This project on fluorescence complementation involves the joining of two proteins, Jun and Fos, each fused to a half terminus of YFP. Both of these chimeric proteins were fused to a beta gene that codes for a membrane protein. Then, two cell populations - one expressing Jun-beta-YFPN and the other Fos-beta-YFPC - were combined, ideally resulting in the fusion of the Jun and Fos proteins on the cell membrane. The two halves of the YFP protein would bind as well, giving rise to fluorescence.
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== Parts shopping list==
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[[Background|Background]]
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Composite bricks - these are the best to use as less cloning is required.
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[[Methods and Materials|Methods and Materials]]
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'''All these bricks express YFP and downregulate it in response to a signal'''
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[[Results|Results]]
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YELLOW
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[[Future Prospects|Conclusions and Future Work]]
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ARABINOSE RESPONSE.
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</td>
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BBa_E0610: Arabinose turns on lac repressor which in turn shuts down Yellow fluorescent protein.
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<td valign="top" width="50%">
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<h3><ul><li>''' Team 2: Repressilator'''</ul></h3>
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BBa_E0600: like BBa_E0610 but YFP is destabilized - slow degradation. Not listed as available.
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Our project is based on the repressilator system coupled to quorum sensing as described by Jordi Garcia-Ojalvo, Michael B. Elowitz and Steven H. Strogatz in "Modeling a synthetic multicellular clock: Repressilators coupled by quorum sensing" (PNAS). We attempt to visualize the synchronization of the oscillatory phase between cells by the addition of the CFP reporter gene. We expand on this theory by placing cI under the control of pLac, hoping that this would assist in synchronizing the oscillations.
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BBa_E0611: Arabinose turns on destabilized TetR repressor which shuts down yellow fluorescent protein. Addition of Tetracyline blocks TetR repressor allowing yellow fluorescent protein to be turned back on.
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[[Theory Behind the Oscillator|Theory Behind the Oscillator]]
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BBa_E0601: Like BBa_E0611 but YFP is destabilized - slow degradation. Not listed as available
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[[McGill_Repressilator_M_and_M|Methods and Materials]]
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BBa_E0613: Arabinose turns on destabilized lambda repressor which shuts down yellow fluorescent protein.
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[[McGill_Repressilator_Results|Results]]
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</td>
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BBa_E0602: Like BBa_E0613 but YFP is destabilized - slow degradation. Not listed as available
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</tr></table>
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BBa_E0603: Like BBa_E0602 but baseline expression of YFP is higher. Not listed as available
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<center><h2><font face="broadway,verdana">Lab Procedures</font></h2></center>
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<table border="0"><tr><td valign="top" width="85%">
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* [[Protocols]]
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* [[Lab Notebook]]
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</td>
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<td>[[Image:Test_tubes.jpg]]</td></tr></table>
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BBa_E0604: Arabinose turns on destabilized 434 cl epressor which in turn shuts down destabilized (slow) Yellow fluorescent protein. Not listed as available
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{| cellspacing="2px" cellpadding="0" border="0" style="padding: 0px; width: 750px; color: #000000; background-color: #ffffff;"
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|-valign="top"
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BBa_E0614: Like BBa_E0604 but YFP is not destabilized (hangs around forever). Not listed as available
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<center><h2><font face="broadway,verdana">Club</font></h2></center>
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* [[News]]
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* [[Team Members]]
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* [[Executive Council|Executive Council]]
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* [[Journal Club Meetings]]
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* [[Journal Club Papers]]
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BBa_E0605: Arabinose turns on destabilized p22 repressor which in turn shuts down destabilized (slow) Yellow fluorescent protein. Not listed as available
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<center><h2><font face="broadway,verdana">Just for Fun</font></h2></center>
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* [[iGEM Party Pictures]]
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* [[ahessel:montreal|Ambassador Visit]] [http://www.flickr.com/search/?q=igem+montreal&m=text Photos]
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* [[iGEM Soundtrack]]
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<Center>[[Image:Poutine.gif]]</Center>
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BBa_E0615: Like BBa_E0605, but YFP is not destabilized, hangs around forever.
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__NOTOC__
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Lac I REGULATED
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BBa_I12026: Produces YFP (not destabilized). Controlled by Lac I
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MULTIPLE REGULATORS
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BBa_I12051: Lactose induces lambda repressor. Arabinose induces 434 repressor. Lambda repressor activates YFP, 434 represses YFP. YFP is destabilized (AAV, fast).
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BBa_I12052: Like BBa_I12051 but promoter for YFP has double binding sites for better control.
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CYAN
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TET response
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BBa_I0401: Expresses CFP and lux from the Tet-OFF promoter. Neither is destabilized. Not listed as available
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BBa_I0402: Like BBa_I0401 but lux is destabilized (LVA, slow)
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BBa_I0404: Produces rhlR and CFP, downregulated by Tet. rhlR binds with N-butyryl-HSL, regulates transcription. rhlR but not CFP is destabilized.
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BBa_I0405: same as BBa_I0404, but produces rhIl which produces N-butyryl-HSL.
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BBa_I0406: produces CFP and lasR, which accepts chemical signal AI-1. Downregulated by Tet. LasR but not CFP are destabilized.
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BBa_I0407. Like BBa_I0406 but produces lasI (destabilized LVA slow) which generates the chemical signal Al-1.
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BBa_I0408: produces CFP and CinR, repressed by Tetracycline. Cin R is LVA (slow) destabilized. Cin R binds O3-C14:1-HSL and activates the Cin promoter.
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BBa_I0409: Like BBa_I0408 but produces cinL (destabilized LVA slow) which generates the chemical signal O3-C14:1-HSL.
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ARABINOSE response:
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BBa_I0403 Expresses CFP and aiiA from an arabinose promoter. aiiA degrades  N-acyl homoserine lactones (quorum sensing autoinducers). aiiA but not CFP is destabilized (LVA, slow).
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GREEN
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ARABINOSE
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BBa_I13540: Arabinose turns on green fluorescent protein.
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RED:
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BBa_I13507: Basic red fluorescent protein: ribosome binding site, red, stop. B.Y.O. promoter.
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ARABINOSE
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BBa_I13520: Arabinose turns on mRFP. This think was actually shown to work.
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BBa_I13517: Like BBa_I13520 but weaker ribosome binding site.
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SIGNALING
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BBa_I0460 aiiA cassette. Produces enzyme which degrades N-acyl homoserine lactones (quorum sensing autoinducers. Destabilized with LVA (slow) B.Y.O.P (Bring your own promoter).
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BBa_I10100: Produces adhesin, makes bacteria stick to each other. B.Y.O.P (Bring your own promoter)
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BBa_I12002: Lambda promoter driving expression of 434 repressor. Not destabilized.
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BBa_I12054: same as BBa_I12002, lambda promoter is modified to be activated by lac repressor cI
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BBa_I12055: Hybrid lambda promoter activated by lambda and repressed by 434, driving expression of destablized lambda (LVA slow degradation). This was used as part of an oscillator.
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BBa_I12056: Like BBa_I12055:but the promoter has duplicate sites for better control.
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BBa_I12011: Lambda promoter driving expression of p22 repressor. LVA (slow) destabilized.
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BBa_I13271: Cassette: rhiR upstream of rhi promoter. rhiR with butyl-homoserine lactone activates rhi promoter. rhiR needs a promoter, not included.
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BBa_I13303: Like BBa_I13271 but controlled by lac promoter.
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BBa_I13309: like BBa_I13303
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BBa_I13310: like BBa_I13303 but controlled by TetR
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BBa_I13312: like BBa_I13303 but controlled by TetR
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BBa_I13305: Lac I induces LasR, LasR with homoserine lactone activates Las promoter (downstream). Can add your own gene after Las promoter.
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ARABINOSE responsive:
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BBa_I13016: Arabinose induces LVA (slow) destabilized TetR protein.
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BBa_I13017: Expression of LVA(slow) destabilized TetR protein controlled by lactose (Lac I promoter).
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CHAIN REACTION PREMADE:
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BBa_I13036: Arabinose induces TetR. TetR induces LuxR. LuxR induces YFP if a homoserine lactone signal is received.
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BBa_I13037: Lactose induces TetR. TetR induces LuxR. Arabinose induces LuxL which produces homoserine lactone. LuxR and homoserine lactone activate YFP.
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BBa_I13038: Arabinose induces TetR, and also luxL which makes homoserine lactone. TetR induces LuxR. LuxL and LuxR together activate YFP.
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BBa_I13920: Lux pL makes Lux R protein. Lux R protein + homoserine lactone shuts off Lux pL (no more lux R) and activates Lux pR which makes LacI. Lac I shuts off homoserine lactone which shuts down lac I and HSL production, Lux pL is free to start over.
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MOTILITY
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TetR control
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BBa_I13710: TetR induces CheY, which is a phosphorylation target for motility.
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BBa_I13711: TetR induces CheB. CheB can be phosphorylated and will demethylate Aspartate receptors.
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BBa_I13712: TetR induces CheR. CheR opposes Che B.
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LACTOSE control
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BBa_I13721: Lactose induces CheB. (lac promoter)
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MULTI-COMPONENT
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BBa_I13730: Lac I controls Che B, TetR controls Che R. Che B opposes Che R (chemosensing)
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BASIC TOOLS
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BBa_I13800: ampicillin resistance
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BBa_I13801: kanamycin resistance
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=Introduction= Our brainstorming meeting on 3-16 gave us several preliminary ideas which we will explore via modeling and research
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Latest revision as of 20:19, 31 October 2006

Banner.gif


Welcome to the McGill Wiki! Basically, we're a team of 12 undergrads, 1 grad student, and 1 professor who like to have fun and clone things in our spare time. McGill University is located in Montreal, Quebec, which has given us wonderful opportunities to balance lab work with festivals and general craziness. iGEM has been a great opportunity to get lab experience while having the freedom to be creative, and we look forward to meeting the other teams at the jamboree!

Clip image002.jpgGood 2.jpg



Projects

  • Team 1: Split YFP

This project on fluorescence complementation involves the joining of two proteins, Jun and Fos, each fused to a half terminus of YFP. Both of these chimeric proteins were fused to a beta gene that codes for a membrane protein. Then, two cell populations - one expressing Jun-beta-YFPN and the other Fos-beta-YFPC - were combined, ideally resulting in the fusion of the Jun and Fos proteins on the cell membrane. The two halves of the YFP protein would bind as well, giving rise to fluorescence.

Background

Methods and Materials

Results

Conclusions and Future Work

  • Team 2: Repressilator

Our project is based on the repressilator system coupled to quorum sensing as described by Jordi Garcia-Ojalvo, Michael B. Elowitz and Steven H. Strogatz in "Modeling a synthetic multicellular clock: Repressilators coupled by quorum sensing" (PNAS). We attempt to visualize the synchronization of the oscillatory phase between cells by the addition of the CFP reporter gene. We expand on this theory by placing cI under the control of pLac, hoping that this would assist in synchronizing the oscillations.

Theory Behind the Oscillator

Methods and Materials

Results

Lab Procedures

Test tubes.jpg

Club

Just for Fun

Poutine.gif
Retrieved from "http://2006.igem.org/wiki/index.php/McGill_University_2006"
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