Team:MIT

From 2008.igem.org

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<!--- The Mission, Experiments --->
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{|
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'''Welcome to the MIT team Wiki for iGEM 2008'''
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*'''iGEM''' is the international genetically engineered machines competition.
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*The objective of the competition is to design and build an engineered biological system using [http://en.wikipedia.org/wiki/DNA DNA].
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*To see examples of the '''amazing possibilities''' of iGEM, check out last years [http://parts.mit.edu/igem07/index.php/Main_Page iGEM page]
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*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]]).
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*iGEM at MIT is possible because of '''outside support''', contact Tom Knight (tk [at] mit.edu) to help out!
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Interested in learning more about iGEM 2008?  Explore below for an example of what's possible.
 
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For more info on this year's iGEM please see [https://2008.igem.org 2008.igem.org].
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{| style="color:#1b2c8a;background-color:#CCCCCC;" cellpadding="3" cellspacing="1" border="1" bordercolor="#green" width="62%" align="center"
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!align="center"|[[Team:MIT|Home]]
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!align="center"|[[Team:MIT/Team|The Team]]
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!align="center"|[[Team:MIT/Project|The Project]]
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!align="center"|[[Team:MIT/Experiments|Experiments]]
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!align="center"|[[Team:MIT/Parts|Parts Submitted to the Registry]]
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!align="center"|[[Team:MIT/Modeling|Results]]
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!align="center"|[[Team:MIT/Notebook|Notebook]]
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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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===For visitors===
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<hr class=divider>
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*Read more about [[Synthetic Biology|engineering biology]].
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<div id="about">
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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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===External links===
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==Biogurt: A Sustainable and Savory Drug Delivery System==
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*[[iGEM|iGEM on OpenWetWare]]
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'''
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*[http://parts.mit.edu/registry BioBricks Parts registry]
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Streptococcus mutans, the main cause of dental caries, binds to glycoproteins on the teeth. A clinical study (Kelly CG et al.; Nature Biotechnol. 1999) isolated the 20aa functional segment (p1025) that S.mutans uses to attach to the teeth. p1025 competitively inhibits the binding of S.mutans, causing unharmful bacteria to grow in its place, preventing the recolonization of S.mutans for 90 days.
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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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===Internal links===
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We are engineering Lactobacillus bulgaricus, a bacteria commonly found in yogurt, to produce and secrete this peptide under a promoter activated by lactose.
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*'''[[../2008/Notebook/Yogurt|Team Notebook]]'''
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===Protocols===
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The peptide p1025 could simply be added to any food. But production of this peptide by L. bulgaricus is an independent process, so inserting the gene into live bacteria in yogurt will enable continuous production. Since a new batch of yogurt can be made using the bacteria from a small  amount of the old batch, a continuous supply of teeth-cleaning yogurt will be available from the first successfully engineered batch. This could be the key to providing effective dental health care in underdeveloped rural communities, especially if yogurt is already an integral part of the diet.
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*[http://openwetware.org/wiki/Endy:DNA_ligation_using_T4_DNA_ligase T4 ligation]
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*[http://openwetware.org/wiki/TOP10_chemically_competent_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/Knight:Restriction_Digest Restriction Digests]
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===Good Lab Citizenship===
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Also, the p1025 gene could be replaced by any other gene, so this same expression system could be used to produce other useful peptides.  Yogurt with modified bacteria will provide a cheap, efficient, and delicious way to distribute vitamins, vaccines and more.
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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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'''
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===Wiki editing resources===
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==Results==
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*[[Simple_wiki_editing_examples| Simple wiki editing examples]]
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====Characterization====
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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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*plasmid pTG262 - Last year's Edinburgh team worked with the plasmid pTG262 in trying to transform it into different gram-positive bacteria. They had not transformed it into ''Lactobacillus'' but were optimistic that it could be, since pTG262 is known to be able to replicate in strains of ''Lactobacillus''. Dr. Chris French was very helpful and graciously supplied us with this plasmid. Working extensively with this plasmid with all of our strains of bacteria, we were unable to successfully transform pTG262 into ''Lactobacillus'', and we have concluded that it is our opinion that pTG262 '''cannot''' be electroporated into ''Lactobacillus delbruckii''. We have added '''characterization''' to this part's main page and user review page, [http://partsregistry.org/wiki/index.php?title=Part:BBa_I742103 '''here'''].
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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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*  p1025-This sequence codes for a short peptide, found to competitively inhibit binding of S.mutans to the tooth surface (CG et al.; Nature Biotechnol. 1999). S.mutans takes in sugars and secretes lactic acid, causing dental cavities, so introduction of this peptide into the mouth prevents colonies. This part uses the modified Silver BioBrick prefix and suffix to allow for protein construction.
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====Models====
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[[Team:MIT/Competitive Binding Model|Competitive Binding Model]]
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[[Image:Competitve binding.jpg]]
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*This model shows that p1025 inhibits binding of s. mutans to the salivary receptors on the tooth surface. p1025 serves as the competitive peptide inhibitor of bacterial adhesion in this model. Our team is the first to not only invent a tooth binding assay but characterize p1025 as a competitive inhibitor.
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=== Want to help out the iGEM team? ===
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====New Methods====
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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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*''S.mutans'' Binding Assay
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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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*p1025 Competitive Binding Assay
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*'''Read more''' about our team on our '''[[/Notebook/Fundraise|fundraising notebook]]'''.
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* [[Team:MIT/Tooth_binding_assay_protocol|Novel Tooth Binding Assay]]
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* [[Team:MIT/Transforming_Lactococcus lactis|''Lactococcus lactis'' Transformation Protocol]]
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* [http://openwetware.org/wiki/L._acidophilus_transformation ''Lactobacillus acidophilus'' Transformation Protocol]
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* [http://openwetware.org/wiki/Lactobacillus_transformation ''Lactobacillus delbruckii'' Transformation Protocol]
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* [http://openwetware.org/wiki/Lactobacillus_culture Culturing ''Lactobacillus'']
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* [http://openwetware.org/wiki/Lactobacillus_miniprep ''Lactobacillus delbruckii'' Miniprep protocol'']
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* [http://openwetware.org/wiki/Lactobacillus_planarum_miniprep ''Lactobacillus plantarum'' Miniprep protocol'']
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====Lactobacillus Work====
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*We '''successfully transformed Lactobacillus delbruckii subsp. bulgaricus and Lactobacillus delbruckii subsp. lactis''' with a modified version of Serror et al's electrotransformation procedure.  Our [http://openwetware.org/wiki/Lactobacillus_transformation '''transformation protocols'''] are found here. We also plan to submit these plasmids, with biobrick sites inserted in them, to the registry. These plasmids are [http://partsregistry.org/wiki/index.php?title=Part:BBa_K128008 '''pJK650'''] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K128007 '''pLEM415'''].
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=== Want to join the iGEM team? ===
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*We are currently working on a method to effectively miniprep plasmid DNA from our ''Lactobacillus''. For information about our protocol for doing so, please click [http://openwetware.org/wiki/Lactobacillus_miniprep '''here'''].
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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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*We have built an expression system for Lactobacillus to secrete protein, including individual biobricked parts of a Lactobacillus [http://partsregistry.org/wiki/index.php?title=Part:BBa_K128006 '''promoter'''] and a Lactobacillus [http://partsregistry.org/Part:BBa_K128004 '''signal sequence'''].
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*Please visit the results page and experiments page of this wiki for full report of all our results and team-generated protocols!!!!
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===Schedule===
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==Acknowledgements==
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*April 10 - UROP funding deadline
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=====Graduate Advisers=====
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*April 18 - iGEM registration opens
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Scott Carlson, Felix Moser, Chia-Yung Wu, Lav Varshney, Vikramaditya Yadav, Woo Chung, Rachel Hilmer, Robbier Barbero, Brian Cook, Jyoti Goda, Laure-Anne Ventouras
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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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=====Faculty Advisors:=====
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Drew Endy, Tom Knight
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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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=====Others=====
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Isadora Deese,
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Dr. Pascale Serror at L'Institut National de la Recherche Agronomique,
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Dr. Bernhard Heinrich at the University of Kaiserslautern,
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Dr. Chris French at the University of Edinburgh,
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Dr. Daniel Smith at the Forsyth Institute,
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Joey Davis at the Sauer Lab at MIT,
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The Fink Lab at the Whitehead Institute,
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Emiko Bare at the Keating Lab at MIT,
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Jennifer Hou at the Baker Lab at MIT,
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The UROP office and Biological Engineering Department for financial support
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===Brainstorming===
 
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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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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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'''[[Picture of MIT iGEM 2008 (coming soon!)]]'''
 
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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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===Grad Advisors===
 
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*[[User:Barbero|Robbie Barbero]]
 
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*[[User:Scottmc|Scott Carlson]]
 
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*[[Tom Knight]]
 
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*[[Drew Endy]]
 
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Email grads: '''grads [AT] igem.mit.edu'''
 
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Email undergrads: '''team [AT] igem.mit.edu'''
 
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''    * Our goal is to engineer a common yogurt bacteria, Lactobacillus bulgaricus, so that it will express the 20aa peptide p1025. A clinical study (Kelly CG et al.; Nature Biotechnol. 1999) reports that p1025 is good for your teeth. p1025 reduces oral colonization of Streptococcus mutans, a tooth-decaying bacterium.
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          o Stage 1: Construction of p1025 fusion peptide and expression of gene in E. coli. This is an intermediate step to evaluate gene function and protein secretion/efficacy.
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          o Stage 2: Binding Assay - see if the p1025 produced by E.coli inhibits binding of S. mutants to hydroxyapatite (HA) beads.
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          o Stage 3: Expression of p1025 in Lactobacillus.
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          o Stage 4: Make yogurt with modified Lactobacillus and test for inhibition of S. mutants binding.
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|align="center"|[[Team:MIT | Team Example 2]]
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<!--- The Mission, Experiments --->
<!--- The Mission, Experiments --->
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{| style="color:#1b2c8a;background-color:#CCCCCC;" cellpadding="3" cellspacing="1" border="1" bordercolor="#green" width="62%" align="center"
!align="center"|[[Team:MIT|Home]]
!align="center"|[[Team:MIT|Home]]
!align="center"|[[Team:MIT/Team|The Team]]
!align="center"|[[Team:MIT/Team|The Team]]
!align="center"|[[Team:MIT/Project|The Project]]
!align="center"|[[Team:MIT/Project|The Project]]
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!align="center"|[[Team:MIT/Experiments|Experiments]]
!align="center"|[[Team:MIT/Parts|Parts Submitted to the Registry]]
!align="center"|[[Team:MIT/Parts|Parts Submitted to the Registry]]
!align="center"|[[Team:MIT/Modeling|Modeling]]
!align="center"|[[Team:MIT/Modeling|Modeling]]
!align="center"|[[Team:MIT/Notebook|Notebook]]
!align="center"|[[Team:MIT/Notebook|Notebook]]
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(''Or you can choose different headings.  But you must have a team page, a project page, and a notebook page.'')
 

Latest revision as of 09:46, 30 October 2008


MitBanner.jpg


Home The Team The Project Experiments Parts Submitted to the Registry Results Notebook


Contents

Biogurt: A Sustainable and Savory Drug Delivery System

Streptococcus mutans, the main cause of dental caries, binds to glycoproteins on the teeth. A clinical study (Kelly CG et al.; Nature Biotechnol. 1999) isolated the 20aa functional segment (p1025) that S.mutans uses to attach to the teeth. p1025 competitively inhibits the binding of S.mutans, causing unharmful bacteria to grow in its place, preventing the recolonization of S.mutans for 90 days.

We are engineering Lactobacillus bulgaricus, a bacteria commonly found in yogurt, to produce and secrete this peptide under a promoter activated by lactose.

The peptide p1025 could simply be added to any food. But production of this peptide by L. bulgaricus is an independent process, so inserting the gene into live bacteria in yogurt will enable continuous production. Since a new batch of yogurt can be made using the bacteria from a small amount of the old batch, a continuous supply of teeth-cleaning yogurt will be available from the first successfully engineered batch. This could be the key to providing effective dental health care in underdeveloped rural communities, especially if yogurt is already an integral part of the diet.

Also, the p1025 gene could be replaced by any other gene, so this same expression system could be used to produce other useful peptides. Yogurt with modified bacteria will provide a cheap, efficient, and delicious way to distribute vitamins, vaccines and more.

Results

Characterization

  • plasmid pTG262 - Last year's Edinburgh team worked with the plasmid pTG262 in trying to transform it into different gram-positive bacteria. They had not transformed it into Lactobacillus but were optimistic that it could be, since pTG262 is known to be able to replicate in strains of Lactobacillus. Dr. Chris French was very helpful and graciously supplied us with this plasmid. Working extensively with this plasmid with all of our strains of bacteria, we were unable to successfully transform pTG262 into Lactobacillus, and we have concluded that it is our opinion that pTG262 cannot be electroporated into Lactobacillus delbruckii. We have added characterization to this part's main page and user review page, [http://partsregistry.org/wiki/index.php?title=Part:BBa_I742103 here].
  • p1025-This sequence codes for a short peptide, found to competitively inhibit binding of S.mutans to the tooth surface (CG et al.; Nature Biotechnol. 1999). S.mutans takes in sugars and secretes lactic acid, causing dental cavities, so introduction of this peptide into the mouth prevents colonies. This part uses the modified Silver BioBrick prefix and suffix to allow for protein construction.

Models

Competitive Binding Model Competitve binding.jpg

  • This model shows that p1025 inhibits binding of s. mutans to the salivary receptors on the tooth surface. p1025 serves as the competitive peptide inhibitor of bacterial adhesion in this model. Our team is the first to not only invent a tooth binding assay but characterize p1025 as a competitive inhibitor.

New Methods

  • S.mutans Binding Assay
  • p1025 Competitive Binding Assay
  • Novel Tooth Binding Assay
  • Lactococcus lactis Transformation Protocol
  • [http://openwetware.org/wiki/L._acidophilus_transformation Lactobacillus acidophilus Transformation Protocol]
  • [http://openwetware.org/wiki/Lactobacillus_transformation Lactobacillus delbruckii Transformation Protocol]
  • [http://openwetware.org/wiki/Lactobacillus_culture Culturing Lactobacillus]
  • [http://openwetware.org/wiki/Lactobacillus_miniprep Lactobacillus delbruckii Miniprep protocol]
  • [http://openwetware.org/wiki/Lactobacillus_planarum_miniprep Lactobacillus plantarum Miniprep protocol]

Lactobacillus Work

  • We successfully transformed Lactobacillus delbruckii subsp. bulgaricus and Lactobacillus delbruckii subsp. lactis with a modified version of Serror et al's electrotransformation procedure. Our [http://openwetware.org/wiki/Lactobacillus_transformation transformation protocols] are found here. We also plan to submit these plasmids, with biobrick sites inserted in them, to the registry. These plasmids are [http://partsregistry.org/wiki/index.php?title=Part:BBa_K128008 pJK650] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K128007 pLEM415].
  • We are currently working on a method to effectively miniprep plasmid DNA from our Lactobacillus. For information about our protocol for doing so, please click [http://openwetware.org/wiki/Lactobacillus_miniprep here].
  • We have built an expression system for Lactobacillus to secrete protein, including individual biobricked parts of a Lactobacillus [http://partsregistry.org/wiki/index.php?title=Part:BBa_K128006 promoter] and a Lactobacillus [http://partsregistry.org/Part:BBa_K128004 signal sequence].
  • Please visit the results page and experiments page of this wiki for full report of all our results and team-generated protocols!!!!

Acknowledgements

Graduate Advisers

Scott Carlson, Felix Moser, Chia-Yung Wu, Lav Varshney, Vikramaditya Yadav, Woo Chung, Rachel Hilmer, Robbier Barbero, Brian Cook, Jyoti Goda, Laure-Anne Ventouras

Faculty Advisors:

Drew Endy, Tom Knight

Others

Isadora Deese, Dr. Pascale Serror at L'Institut National de la Recherche Agronomique, Dr. Bernhard Heinrich at the University of Kaiserslautern, Dr. Chris French at the University of Edinburgh, Dr. Daniel Smith at the Forsyth Institute, Joey Davis at the Sauer Lab at MIT, The Fink Lab at the Whitehead Institute, Emiko Bare at the Keating Lab at MIT, Jennifer Hou at the Baker Lab at MIT, The UROP office and Biological Engineering Department for financial support


Home The Team The Project Experiments Parts Submitted to the Registry Modeling Notebook
Retrieved from "http://2008.igem.org/Team:MIT"