IGEM:MIT/2008

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<b>This page will soon host the website of the MIT team for iGEM 2008</b>
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<div id="mainpage">
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For now it is being used for planning the following (please edit!):
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<hr class=divider>
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<div id="about">
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{|
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| rowspan=2 | [[Image:team-logo.jpg|218px]]
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[[Image:Mit-blackred-header2.gif|194px http://web.mit.edu]]
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|
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'''Welcome to the MIT team Wiki for iGEM 2008'''
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*FOR OUR MORE UP-TO-DATE WIKI, PLEASE REFER TO OUR NEW WIKI [http://2008.igem.org/Team:MIT]
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*'''iGEM''' is the international genetically engineered machines competition.
 +
*The objective of the competition is to design and build an engineered biological system using [http://en.wikipedia.org/wiki/DNA DNA].
 +
*To see examples of the '''amazing possibilities''' of iGEM, check out last years [http://parts.mit.edu/igem07/index.php/Main_Page iGEM page]
 +
*Read our '''promotional brochure''' to learn about synthetic biology at MIT ([[media:mit_igem2008_brochure_front.gif|front]] and [[media:mit_igem2008_brochure_back.gif|back]]).
 +
*iGEM at MIT is possible because of '''outside support''', contact Tom Knight (tk [at] mit.edu) to help out!
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|}
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</div>
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<hr class=divider>
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# Scheduling interviews and finalizing the undergrad team
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{| cellspacing="5"
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<!-- # Preparing the UROP application
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|width="250px" class="green3" |
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#* Deadline = 4/10. See [http://web.mit.edu/urop/paperwork/ UROP paperwork].
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<!-- RESOURCES HEADER with edit link-->
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#* Submit application online at [http://web.mit.edu/urop/apply/mit_cme.html http://web.mit.edu/urop/apply/mit_cme.html]
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<h3><html>
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#* UROP office: The undergrads must apply individually. No specific project proposal is needed; the sample applications from Brian are great examples. 
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<img src="http://openwetware.org/images/b/b9/Icon_board.png" alt="Resources">
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#* We are also exploring additional UROP funding from BE, CE and Bio departments. -->
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</html>Resources</h3>
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# Brainstorming initial project ideas
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<hr/>
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# Creating a website for the 2008 team (probably based on 2007 page [[IGEM:MIT/2007]])
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<!-- END RESOURCES HEADER-->
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#* For help setting up a team lab notebook, please contact [[User: Ricardo Vidal]]. He's working with OpenWetWare at MIT this year, and could help you all get familiar with some new tools that update the notebook since [[IGEM:MIT/2007/Notebook|last year's iGEM notebooks]]. - [[User:Jason R. Kelly|Jason R. Kelly]]
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Interested in learning more about iGEM 2008? Explore below for an example of what's possible.
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# Should we schedule a regular meeting? Chia: Feedback from last year's advisers: regular meetings among grads are recommended. During summer, weekly lab meetings with the undergrads would be important. Perhaps let them rotate to be the team leader and lab meeting presenter so everyone gets a chance to practice their leadership skills.
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# iGEM requirements and relevant dates:
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#* Team registration deadline is '''May 9'''; need to specify instructors, students, lab space, and funding. Registration fee $1000/team.
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#* Jamboree: November 8-9, 2008 at MIT; $100 per undergrad and $250 for others.
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== Brainstorming Project Ideas ==
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For more info on this year's iGEM please see [http://2008.igem.org 2008.igem.org].
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iGEM research project tracks:
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# Foundational Research - basic science and engineering research
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# Information Processing - genetically encoded control, logic, and memory
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# Energy - biological fuels, feedstocks, and other energy projects
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# Environment - sensing or remediation of environmental state
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# Health & Medicine - applied projects with the goal of directly improving the human condition
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# (new track this year) - software tools to facilitate use of standard biological parts
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Many more valuable links and helpful tidbits are available at the [http://parts.mit.edu/wiki/index.php/Resources iGEM Resources page]
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===Information Storage Device===
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===For visitors===
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*Read more about [[Synthetic Biology|engineering biology]].
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*[http://stellar.mit.edu/S/course/20/sp08/20.020/ 20.020: MIT's introduction to bioengineering design]
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I was thinking a bit about information storage. There have been a whole slew of papers that suggest storing artificial messages in DNA. A few representative examples are
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===External links===
 +
*[[iGEM|iGEM on OpenWetWare]]
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*[http://parts.mit.edu/registry BioBricks Parts registry]
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*[http://parts.mit.edu/igem07/index.php/Main_Page Official iGEM 2007 wiki]
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*[http://parts.mit.edu/igem Official iGEM 2006 wiki]
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*[http://openwetware.org/wiki/IGEM:MIT/2007 MIT 2007 Wiki]
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*[http://parts.mit.edu/wiki/index.php/MIT_2006 MIT 2006 Wiki]
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*BioBricks parts contributed by MIT:
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**[http://parts.mit.edu/registry/index.php/Part:BBa_I728005 OmpC Surface Display]
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**[http://parts.mit.edu/registry/index.php/Part:BBa_I728004 CPX Surface Display]
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*[http://openwetware.org/wiki/20.109(S08) 20.109 instructions (2008)]
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* C. Bancroft, T. Bowler, B. Bloom, and C. T. Clelland, "[http://dx.doi.org/10.1126/science.293.5536.1763c Long-Term Storage of Information in DNA]," <i>Science</i>, vol. 293, no. 5536, pp. 1763-1765, Sept. 2001.
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===Internal links===
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*'''[[../2008/Notebook/Yogurt|Team Notebook]]'''
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* P. C. Wong, K.-K. Wong, and H. Foote, "[http://doi.acm.org/10.1145/602421.602426 Organic data memory using the DNA approach]," <i>Commun. ACM</i>, vol. 46, no. 1, pp. 95–98, Jan. 2003.
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===Protocols===
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*[[General Cloning Protocol]]
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*[http://openwetware.org/wiki/MIT_iGEM_T4_and_Quick_Ligation DNA Ligations]
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*[http://openwetware.org/wiki/MIT_iGEM_Top10_ChemComp_Ecoli_transformation_protocol#Regular_Transformation_protocol_for_Top10_cells Top10 chem competent cell transformation]
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*[http://web.mit.edu/biopolymers/www/DNA.html DNA sequencing]
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*[http://openwetware.org/wiki/Endy_pcr PCR]
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*[http://openwetware.org/wiki/MIT_iGEM_Agarose_Gels Running DNA Gels]
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*[http://openwetware.org/wiki/MIT_iGEM_Restriction_Digests Restriction Digests]
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*[http://openwetware.org/wiki/Endy:Preparing_Antibiotic_Stocks Preparing Antibiotic Stocks]
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*[http://openwetware.org/wiki/Endy:_DNA_sequencing DNA sequencing]
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* J. P. L. Cox, "[http://dx.doi.org/10.1016/S0167-7799(01)01671-7 Long-term data storage in DNA]," <i>Trends in Biotechnology</i>, vol. 19, no. 7, pp. 247-250, July 2001.
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===Good Lab Citizenship===
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*Go over the [[DOs_and_DONTs_of_Good_Lab_Citizenship|Do's and Dont's of Good Lab Citizenship]]
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===Wiki editing resources===
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*[[Simple_wiki_editing_examples| Simple wiki editing examples]]
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*[http://en.wikipedia.org/wiki/Wikipedia:How_to_edit_a_page How to edit a page (extended - wikipedia)]
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*[http://www.mediawiki.org/wiki/Help:Images Help with images (wikipedia)]
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*[http://en.wikipedia.org/wiki/Help:Table Help with tables (wikipedia)]
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All of these works envision long-term storage where complicated cloning techniques with restriction enzymes, oligonucleotide synthesis or PCR, and ligation would be used for storage.  I don't know much at all about this, but are there ways of making a storage device where it is moderately easy to change what is written in the memory?  Basically designing some kind of encoder and decoder that makes DNA more of a rewritable medium rather than just a long-term storage medium. A related question is whether there might be a way to introduce an error-correcting circuit along the lines of
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|width="350px" class="green2" |
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<!-- INFORMATION HEADER with edit link-->
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<h3><html>
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<img src="http://openwetware.org/images/e/e2/Icon_info.png" alt="INFORMATION" border="0">
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</html>Information</h3>
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<hr/>
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<!-- END INFORMATION HEADER with edit link-->
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* M. G. Taylor, "Reliable information storage in memories designed from unreliable components," <i>Bell Syst. Tech. J.</i>, vol. 47, no. 10, pp. 2299–2337, Dec. 1968.
 
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There are probably more easily editable means of biological information storage that are more worthy of exploration.
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=== Want to help out the iGEM team? ===
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*iGEM at MIT is partly supported by the [http://web.mit.edu/urop/basicinfo/ Undergraduate Research Opportunity Program] and faculty including Drew Endy and Tom Knight.
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*We guarantee UROP funding for undergrads.  We need help to continue supporting undergrads, paying registration fees, and supplying lab reagents, contact [[Tom Knight]] to help out!
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*'''Read more''' about our team on our '''[[/Notebook/Fundraise|fundraising notebook]]'''.
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*'''cookb''': Hmm, that's an interesting idea and quite original for iGEM! I'm getting an image of some sort of simple physical signal (e.g., exposure to light) being converted into DNA information, sort of like a Morse code encoding words into DNA. I wonder what possible mechanisms one could use to facilitate that... But even encoding something simple like "Hello world" would be a huge deal, and have big ramifications on areas such as commercial gene synthesis.
 
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====Recombination-based tools to alter DNA sequences====
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=== Want to join the iGEM team? ===
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*'''Graduate''' students interested in advising the team should email '''grads [AT] igem.mit.edu'''
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*'''Undergraduate''' students should get in touch during IAP or Spring of 2009!
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* High frequency deletion of a DNA region: Flank the region with two identical target sequences recognized by a DNA recominase (Cre or Flp) [http://en.wikipedia.org/wiki/Site-specific_recombinase_technology diagram]
 
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* Inversion of a DNA region (low reversion rate): Flank the region with two mutant loxP sequences, lox66 and lox71. (both are in the registry)[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=137435 Reference]
 
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* Reversible inversion of a DNA region: Flank with target sequences of the Hin recombinase. See [http://parts.mit.edu/wiki/index.php/Davidson_2006 2006 Davidson team page]
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===Schedule===
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*April 10 - UROP funding deadline
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*April 18 - iGEM registration opens
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*May 3 - Teachers Workshop, MIT, USA
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*May 9 - Registration closes
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*June 9 - Summer term, lab work begins
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*June 15 - Team rosters due
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*July 1 - Registration fee due
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*August 1 - Team project descriptions due
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*August 19 - Summer term ends
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*September 1 - Final team roster due
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*October 1 - Jamboree attendance fees due
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*October 15 - Project Summary form due
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*October 29 - Project and part documentation due
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*October 29 - BioBrick Part DNA received by the Registry
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*November 8-9 - iGEM competition Jamboree, MIT, USA
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* Transposons:
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<html>
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** Sleeping Beauty (transposon from fish) [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-418PXHC-C&_user=501045&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000022659&_version=1&_urlVersion=0&_userid=501045&md5=6075fd72a8fcc1e7628afe2ff0661d21 Molecular Reconstruction of Sleeping Beauty]
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<script language="JAVASCRIPT"><!-- update your browser, silly-->
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Today = new Date();
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Jamboree = new Date("November 8, 2008");
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msInADay = 1000 * 60 * 60 * 24;
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display = Math.floor((Jamboree.getTime() - Today.getTime())/msInADay);
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document.write("There are " + display +" days left until the Jamboree!");
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// </script>
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</html>
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====Write-Once Memory Information Theory====
 
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*'''[[User:Lav R. Varshney|Lav R. Varshney]] 23:55, 17 April 2008 (EDT)''': A couple of basic papers on write-once memories are:
 
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* Ronald L. Rivest and Adi Shamir, "[http://dx.doi.org/10.1016/S0019-9958(82)90344-8 How to Reuse a 'Write-Once' Memory]," <i>Inf. Control</i>, vol. 55, no. 1-3, pp. 1-19, Oct.-Dec. 1982.
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----
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* Gilles Zemor and Gerard D. Cohen, "[http://dx.doi.org/10.1109/18.79943  Error-correcting WOM-codes]," <i>IEEE Trans. Inf. Theory</i>, vol. 37, no. 3, pp. 730-734, May 1991.
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===Brainstorming===
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* Amos Fiat and Adi Shamir, "[http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1056918  Generalized 'write-once' memories]," <i>IEEE Trans. Inf. Theory</i>, vol. IT-30, no. 3, pp. 470-480, May 1984.
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*'''[[/Notebook/Yogurt/Brainstorming|Brainstorming]]
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===Meeting Logistics===
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*'''[[/Room Reservations|Room Reservations]]'''
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*'''[[/Onduty|Gradvisor "On Duty" Shifts]]'''
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*'''[[Technical Overseers|Technical Overseers]]'''
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The following paper that I am working on is also rather related, so if anyone wants to take a look at the unsubmitted draft, let me know:
 
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* Lav R. Varshney and Julius Kusuma, "Malleable Compression," in preparation.
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|width="250px" class="green3" |
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<!-- PEOPLE HEADER with edit link-->
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<h3><html>
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<img src="http://openwetware.org/images/3/39/Icon_groups.png" alt="People">
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</html>People</h3>
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<hr/>
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<!-- END PEOPLE HEADER with edit link-->
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The MIT iGEM team consists of six undergraduate students working full-time during summer 2008 on engineering a biological system.  In addition, we have a number of graduate student and faculty advisers.
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===Synthetic Taxis===
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'''[[Picture of MIT iGEM 2008 (coming soon!)]]'''
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Develop some sort of Kalman filter-like circuit or some other signal processing circuit to detect or track pathogens.  The [http://www.qb3.org/cpl/ UCSF/UCB Center for Engineering Cellular Control Systems] has started to look at some similar problems.
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===Students===
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*[[User:Prarthna_Desai|Prarthna Desai]]
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*[[User:Derek_Ju|Derek Ju]]
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*[[User:John_Kucharczyk|John Kucharczyk]]
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*[[User:Asad_Moten|Asad Moten]]
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*[[User:Sara_Mouradian|Sara Mouradian]]
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*[[User:Allin_Resposo|Allin Resposo]]
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*[[User:Andrew_Ang|Andrew Ang]]
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===Bacterial lava lamp===
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===Grad Advisors===
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*'''[[User:Reshma P. Shetty|Reshma]] 10:16, 19 March 2008 (CDT)''': I've been wanting to make a bacterial lava lamp for a long time. The U. of Melbourne 2007 team engineered this super cool part that enables bacteria to float (used in natural systems to maintain marine bacteria at a particular depth).  By combining this floatation part with a luciferase, I think you could make some nice lighting for the home!  :)
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*[[User:Barbero|Robbie Barbero]]
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(from Melbourne 07 team) - they just sink more slowly atm ;)
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*[[User:Scottmc|Scott Carlson]]
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*[[User:Cookb|Brian Cook]]
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*[[User:Rachel_A._Hillmer|Rachel Hillmer]]
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*[[User:Lav_R._Varshney|Lav Varshney]]
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*[[User:Lventouras|Laure-Anne Ventouras]]
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*[[User:Chia-Yung_Wu|Chia-Yung Wu]]
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*[[User:Vikram Yadav|Vikramaditya Yadav]]
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*[[User:Fmoser|Felix Moser]]
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*[[User:Jyoti_Goda|Jyoti Goda]]
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*[[User:Woo Chung|Woo Chung]]
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If we did this, we would want the cells to clump together so that it looks lava lamp like.
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==Faculty Advisors==
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*[[Tom Knight]]
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*[[Drew Endy]]
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How is this combo:
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Email grads: '''grads [AT] igem.mit.edu'''
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Flocculating E. coli + increased buoyancy + GFP or luciferase on cell surface + self-made tube-flipping device (mechanical or manual) + blue excitation light or luciferin?  A name for this GEM suggested by Brian: E.GloLite
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*[http://www.ncbi.nlm.nih.gov/pubmed/11118595 Display of green fluorescent protein on Escherichia coli cell surface.]
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Email undergrads: '''team [AT] igem.mit.edu'''
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**'''[[User:Jason R. Kelly|Jason R. Kelly]] 16:46, 4 April 2008 (EDT):'''You probably don't need to get it on the surface, they glow pretty well if you just make a bunch of GFP inside the cell (also easier to do).
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*'''Chia''':  A microbe-based lava lamp - cute! We can make budding yeast cells clump as well. There is a family of cell surface glyco-proteins that confer cell-cell adhesion (flocculation) and/or adhesion to hydrophobic substratum [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=17311]. Flocculation mediated by the protein Flo1p can be altered by adding certain sugar or EDTA.  Yeast cell density can be altered by mutations in secretory pathways such as sec1.
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alternative address: '''igem2008-all [AT] mit.edu'''
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Two scientists made a microbial lava lamp. Not as fancy as what we want here but we might find their design useful.  Basically, brewer's yeast cells are immobilized in a mixture of glass beads, a carbohydrate polymer from seaweed and some dye to make colored "beads". Then the beads are placed in a sucrose solution allowing yeast cells to produce CO2, which is trapped in the beads and giving them buoyancy.  As the beads slowly rise to the surface, CO2 escapes and the beads drop. [http://www.csun.edu/~hcbio029/lavalamp/Lava_Lamp_Teachers.pdf PDF describing details]
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|}
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</div>
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===Multi-colored moss===
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__NOEDITSECTION__
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*'''[[User:Jason R. Kelly|Jason R. Kelly]] 12:23, 19 March 2008 (CDT):''' Austin and I went out and visited Magdalena Bezanilla's lab at [http://www.bio.umass.edu/biology/faculty/bezanilla.phtml Umass-Amhearst] that studies this [[Physcomitrella_patens|moss]] and found out that it's not too hard to grow and genetically manipulate it.  One idea was to express pigments from other plans (flowers) in the moss to make it in different colors.  Magdalena thought this might be possible, could follow up with her if it was an idea that folks thought was cool. Even if it didn't work, you could make the first BioBrick parts and vectors for engineering plants!
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__NOTOC__
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===Turing machine===
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===A counting device for plasmid copy number===
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===Bacteria with limited # of cell divisions, after flipping a switch===
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A neat idea initiated by Vikram. Such a GEM would have much less potential to contaminate the environment if accidentally released from the laboratory.
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This might be possible if the bacterial genome shortens gradually like linear eukaryotic chromosomes. A method to linearize the E. coli genome without affecting its stability has been reported [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17218953].
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If the chromosome ends were generated differently, one might be able to implement a replication dependent shortening mechanism.  (Brain power needed!)
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One way to visualize chromosome shortening (besides PCR or Southern blotting) could be insertion of a reporter at various locations of the linearized chromosome.  Ideally the presence/absence of the reporter would make E. coli colonies look different on a agar plate. (Say lacZ + X-gal as in blue/white screen?)  If the reporter is lost right after the first division (since it's inserted very close to the initial chromosome end), the colony would be one color.  If the reporter is inserted far away from chromosome ends and thus retained for many generations, the colony would be another color.
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- Chia
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=== Other ideas from dinner meeting on 3/31 ===
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(feel free to edit!)
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# modulation of heterocyst differentiation. See [http://aiche.confex.com/aiche/2005/techprogram/P31823.HTM Heterocyst Differentiation and H2 Production in N2-Fixing Cyanobacteria]
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# creative use of FLP recombinase for storing/removing DNA based information
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# modulation of com sensing in B. subtilis (model system in Alan Grossman's lab in the Bio Dept)
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# a bacterial diagnostic device for diabetes?
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=== Suggestions from the meeting on 4/4 ===
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# Various people are going to do background research on technical aspects of ideas listed above.  They plan to report back on 4/11.
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# Additional idea of making bacteria responsive to electrical stimuli.
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=== Suggestions from the meeting on 4/17 ===
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*'''cookb''': Use of inteins (protein introns) as switches / biosensors
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# Big advantage is their modular design which allows easy creation of new functional systems
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# Could use to switch on reporter/effector using temperature change or addition of ligand
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# Huge possibilities as a biosensor (pop in ligand binding domain of choice)
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#* Some ideas: glucose sensor (diabetes), pollutant detector (metal binding domains), cancer test (VEGF, other GFs), in vivo phosphotyrosine assay (SH2 domain), detection of biohazards/pesticides/organophosphate, drug testing (steroids)...
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Relevant papers:
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<biblio>
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# skretas05a pmid=15632292
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# skretas05b pmid=15878176
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# gillies08 pmid=18081307
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# skretas07 pmid=17569534
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# zeidler04 pmid=15184905
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# buskirk04 pmid=15247421
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# review pmid=16043448
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</biblio>
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=== Suggestions from the meeting on 4/24 ===
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* Fundraising! Potential donors = MIT alumni (Need to create an official web site, a brochure and a standard letter/budget for continuous fundraising for MIT's iGEM team every year
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* Meeting registration deadline = May 9th
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* Combinatorial use of Flp and Cre target sites (see "Recombination-based tools to alter DNA sequences" above) to store info in DNA
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* Couple recombinases to inteins to make novel a sensor/pathway
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* Talk to Prof. Penny Chisholm to learn the basics of handling Cynanobacteria. (Growth condition and doubling time? Any potential toxicity?)
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=== Notes from 5/1/ ===
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Still brainstorming:
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#still thinking about computation in cells
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#brian mentioned something about bacterial films on our teeth
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*yeast that makes a peptide that prevents bad streptococcus from binding from teeth. 
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#something for sensing
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#phosphotyrosine sensing (SH2 domain) coupled to
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Current revision


194px http://web.mit.edu

Welcome to the MIT team Wiki for iGEM 2008

  • FOR OUR MORE UP-TO-DATE WIKI, PLEASE REFER TO OUR NEW WIKI [1]
  • iGEM is the international genetically engineered machines competition.
  • The objective of the competition is to design and build an engineered biological system using DNA.
  • To see examples of the amazing possibilities of iGEM, check out last years iGEM page
  • Read our promotional brochure to learn about synthetic biology at MIT (front and back).
  • iGEM at MIT is possible because of outside support, contact Tom Knight (tk [at] mit.edu) to help out!

Resources Resources


Interested in learning more about iGEM 2008? Explore below for an example of what's possible.

For more info on this year's iGEM please see 2008.igem.org.

Many more valuable links and helpful tidbits are available at the iGEM Resources page

For visitors

External links

Internal links

Protocols

Good Lab Citizenship

Wiki editing resources

INFORMATION Information



Want to help out the iGEM team?

  • iGEM at MIT is partly supported by the Undergraduate Research Opportunity Program and faculty including Drew Endy and Tom Knight.
  • We guarantee UROP funding for undergrads. We need help to continue supporting undergrads, paying registration fees, and supplying lab reagents, contact Tom Knight to help out!
  • Read more about our team on our fundraising notebook.


Want to join the iGEM team?

  • Graduate students interested in advising the team should email grads [AT] igem.mit.edu
  • Undergraduate students should get in touch during IAP or Spring of 2009!


Schedule

  • April 10 - UROP funding deadline
  • April 18 - iGEM registration opens
  • May 3 - Teachers Workshop, MIT, USA
  • May 9 - Registration closes
  • June 9 - Summer term, lab work begins
  • June 15 - Team rosters due
  • July 1 - Registration fee due
  • August 1 - Team project descriptions due
  • August 19 - Summer term ends
  • September 1 - Final team roster due
  • October 1 - Jamboree attendance fees due
  • October 15 - Project Summary form due
  • October 29 - Project and part documentation due
  • October 29 - BioBrick Part DNA received by the Registry
  • November 8-9 - iGEM competition Jamboree, MIT, USA



Brainstorming

Meeting Logistics


People People


The MIT iGEM team consists of six undergraduate students working full-time during summer 2008 on engineering a biological system. In addition, we have a number of graduate student and faculty advisers.

Picture of MIT iGEM 2008 (coming soon!)

Students

Grad Advisors

Faculty Advisors

Email grads: grads [AT] igem.mit.edu

Email undergrads: team [AT] igem.mit.edu

alternative address: igem2008-all [AT] mit.edu


Personal tools