McGill University 2006

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<center>[[Image:Banner.gif]]</center>
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= News =
 
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* '''2006-05-31''' [[iGEM Party Pictures!]]
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'''Welcome to the McGill Wiki!'''  
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* '''2006-05-15''' Lab Notebook page created
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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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* '''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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[[Image:Clip_image002.jpg]][[Image:Good_2.jpg]]
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We have a TON of composite bricks, and can plan custom ones.
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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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= Organisation =
 
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== People ==
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<!--{| cellspacing="2px" cellpadding="0" border="0" style="padding: 0px; width: 750px; color: #000000; background-color: #ffffff;"
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=== Students ===
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|-valign="top"
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{| width=700
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|width=179.25px style="padding: 5px; background-color: #fffaf0; border: 2px solid #20b2aa;" |
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|[[Catie Lichten (Center for Nonlinear Dynamics)]]
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EDITED BY ASHWIN. If you want to change it, feel free :)-->
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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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|[[Brock Dumville (Biomedical Sciences)]]
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|}
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{| width=700
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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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|[[Julia Ishak (Biomedical Sciences)]]
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|[[Ashwin Dixit (Microbiology and Immunology)]]
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|[[Adam Katolik (Biochemistry)]]
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|[[Alexandre David (Physiology)]]
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|}
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=== Supervisors ===
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<center><h2><font face="broadway,verdana">Projects</font></h2></center>
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|[[Jay Nadeau]]
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|}
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== Timeline ==
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<table cellpadding="5" border="0"><tr>
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* [[Meetings]]
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<td valign="top" width="50%">
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* [[Lab Notebook]]
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<h3><ul><li>'''Team 1: Split YFP'''</ul></h3>
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* [[file registry]]
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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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== Tasks ==
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[[Background|Background]]
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* [[Task Assignment]]
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Modelling people: check out these bricks: BBa_I13920, BBa_I13921, BBa_I13922.
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[[Methods and Materials|Methods and Materials]]
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What happens if you plug these into your computer simulation?
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Also try this: BBa_J11002 and BBa_J06913. What happens if you substitute an AAV-degradation-tagged GFP?
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[[Results|Results]]
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Test EcoMscL to see if it does anything cool
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[[Future Prospects|Conclusions and Future Work]]
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How many vials of competent Mscl(-) E. coli do we have?  *make more*
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Do we have a luciferase reporter? What is its selection marker
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Amplify the Eco MscL plasmid
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==Useful papers==
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</td>
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A synthetic gene–metabolic
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oscillator
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Eileen Fung1,2, Wilson W. Wong1, Jason K. Suen1, Thomas Bulter1,
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Sun-gu Lee1 & James C. Liao1,2
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NATURE | VOL 435 | 5 MAY 2005
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http://www.nature.com/nature/journal/v435/n7038/abs/nature03508.html
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Proc Natl Acad Sci U S A. 2002 Jan 22;99(2):679-84.
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<td valign="top" width="50%">
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Synchronizing genetic relaxation oscillators by intercell signaling.
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<h3><ul><li>''' Team 2: Repressilator'''</ul></h3>
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McMillen D, Kopell N, Hasty J, Collins JJ.
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http://www.pnas.org/cgi/content/full/99/2/679
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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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Cell Mol Life Sci. 2006 May
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[[Theory Behind the Oscillator|Theory Behind the Oscillator]]
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The design of intracellular oscillators that interact with metabolism.
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Wong WW, Liao JC.
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== Parts shopping list==
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[[McGill_Repressilator_M_and_M|Methods and Materials]]
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[[Parts Shopping List]]
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[[McGill_Repressilator_Results|Results]]
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</td>
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[[Example for oscillator]]
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</tr></table>
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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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<center><h2><font face="broadway,verdana">Lab Procedures</font></h2></center>
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Things I learned at the teach the teachers meeting
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<table border="0"><tr><td valign="top" width="85%">
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* [[Protocols]]
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Standard plasmids: pSB1AK3 ("ampicillin kanamycin")
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* [[Lab Notebook]]
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                  pSB1AT3 ("amplicillin tetracycline)
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</td>
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                  pSB1AC3 ("ampicillin chloramphenicol)
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<td>[[Image:Test_tubes.jpg]]</td></tr></table>
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all of these are high copy number, if inappropriate, also provided are inducible plasmids:
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                  pSB2K3 (IPTG inducible)
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the "3" refers to the MCS and the transcriptional terminator
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We will be provided with a plate with dried DNA samples, we can amplify the ones that we want
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There are standard cloning protocols that use specific sites; products are checked by sequencing with promoter sequences VF ("verification forward") and VR ("verification reverse")
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They often use 3-way ligations selected with 2 antibiotics to create composites
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{| cellspacing="2px" cellpadding="0" border="0" style="padding: 0px; width: 750px; color: #000000; background-color: #ffffff;"
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You can put > 1 plasmid in a cell; chose according to copy number desired (eg, you might want GFP at high copy and AraC at low...)
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|-valign="top"
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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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EVERYONE should have a BioBrick account with their real name
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<center><h2><font face="broadway,verdana">Just for Fun</font></h2></center>
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go here:
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* [[iGEM Party Pictures]]
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http://partsregistry.org/Help:Create_a_Registry_Account
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* [[ahessel:montreal|Ambassador Visit]] [http://www.flickr.com/search/?q=igem+montreal&m=text Photos]
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It is important to document parts every time we create them
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* [[iGEM Soundtrack]]
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They should have the "BioBrick ends" what does this mean?
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<Center>[[Image:Poutine.gif]]</Center>
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We will get 2 384-well plates with the DNA; pierce the foil, dissolve in 30-50 microliters, and transform
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__NOTOC__
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it's colour-coded with food coloring: KANAMYCIN = red; TET = yellow; CHLOR = green; AMP = orange
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the key to what's in each well will be provided on the registry
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fill out address on Group pages next week!
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when we send parts, they should be sent as stabs labeled w/ part name, plasmid, cell (on Help page)
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(or foreign schools can send dried DNA)
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as soon as a part is Available, it will be sent to EVERYONE, that way they don't worry about shopping lists
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The letters on the plates are very small, so watch out
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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
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