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'''Project Idea: Use of a Virus-injected Vector to Create Serotonin-Creating Biodevices'''
Stephen T. Payne
spayne@mit.edu
(412) 716-4001
________________________________________


We will use a virus to inject into mice brains a vector containing serotonin-creating biodevices.  The biodevices will consist of a genetic circuit which is sensitive to the serotonin levels present in the brain. If a sufficiently low level of serotonin is being made, expression of a part of the genetic circuit will allow for the production of serotonin.
Education Massachusetts Institute of Technology Class of 2008
Degree name: Bachelor of Science in Biological Engineering
GPA: 4.5 on a 5.0 Scale
Fox Chapel Area High School, Pittsburgh, PA Class of 2004
Senior Scholar, Awarded to seniors graduating with a 4.0 (on a 4 point scale) for all four
years of high school.


The vector will consist of a serotonin-sensing receptor coding region (specified by Dr. Hellinga in the article available at http://www.dukemednews.org/news/article.php?id=6549), which will be able to sense the levels of serotonin in the environment. This would be connected to a constitutive promoter in order for the protein to be synthesized continuously.  The receptor coding region will then be connected to an inverter which will create a high PoPs signal when serotonin levels are low.  This inverter will lead to the coding regions of two enzymes, both responsible for the conversion of tryptophan to serotonin (see the biochemistry section of http://en.wikipedia.org/wiki/Serotonin).  Since excess tryptophan is available in the brain, such a system should be feasible.
Work Experience Member of MIT’s International Genetically Engineered Machine Competition Team (Massachusetts Institute of Technology- Professor Drew Endy’s Biological Engineering Laboratory), Synthetic Biological Engineer, developed a synthetic biological system using various pieces of DNA dubbed Biobricks. Along with four other MIT undergraduates, I competed against forty biological engineering teams from universities around the world. In our project, we were able to successfully engineer strains of E. coli to smell like banana and mint by making genetic circuits consisting of specific promoters, ribosome binding sites, coding regions, terminators, and inverters in various plasmids.  The final goal of the project is to have the E. coli produce a mint scent during exponential phase and a banana scent during stationary phase.  This project is ongoing.  The project website can be accessed at http://openwetware.org/wiki/IGEM:MIT/2006.  Our work was noted on Forbes.com, in Technology Review, in Medgadget, in the Boston Globe, and in the German magazine, der Spiegel. Summer 2006, Fall 2006, January 2007, Summer 2007, Fall 2007 


The reason why such a system would be useful is that many mental disorders, including depression and obsessive-compulsive disorder, result from abnormal serotonin production in the brain.  This system would allow for increased production of serotonin when serotonin levels are low in the mouse brain, which would certainly be a substantial step in the development of therapies for these mental disorders in humans. 
Professor Tom Knight’s Biological Engineering Laboratory (Massachusetts Institute of Technology), Lab Assistant/Researcher, conducted various experiments involving construction plasmids, including DNA ligations and restriction enzymes, examined the growth of bacteria containing different construction plasmids, developed picker instruments for plates containing wells for DNA samples using a laser cutter machine and shop tools, managed and maintained the refrigerator stock of synthetic DNA in the lab, Summer 2005


If everything goes according to plan, such a goal would be accomplished, and we could then try to move to working with the human brain.  The challenge in accomplishing this goal is the following.  Although viruses have been used to carry vectors to neurons in the brain before (most notably, Larry Young used viruses to transfect prairie voles' brain cells with a gene that made the animals monogamous, see http://www.nature.com/news/2001/010927/full/010927-4.html;jsessionid=D8FFD24796C542BBDC34656E498280DD), the feasibility of such a feat in mouse brains is uncertain.  The making of the genetic circuit will probably be the easiest step as genetic circuits have become increasingly easy to manufacture with the advent of DNA synthesis technology.  The worst case scenario would be that the viruses are unable to transfect the cells with the vector.  Thus, the worst possible outcome will probably be entail an additional search for another model organism, such as the prairie vole, or to find another way of transfecting mouse brain cells.
Professor Elizabeth Jones’ Biology Laboratory (Carnegie Mellon University), Lab Assistant, prepared solutions for experiments, cleaned and sterilized lab equipment, and observed cell reproduction, Summers 2003 and 2004, Fox Chapel High School credit for professional experience, Grade 12


The above resources will be integral to the accomplishment of a research goals.
Apprenticeship in Meteorology, Selected to participate in the 2002-2003 Meteorology Apprenticeship sponsored by the Allegheny Intermediate Unit’s Gifted Program, Grade 11


'''Applications of Scent in Yeast'''
Mandi Foods, Inc., Food preparation worker, packed cheese, worked on an assembly line, and made boxes, Summers 2001 and 2002.  Developed statistical analyses of sales and production data, Fox Chapel High School credit for work experience, Grade 12
If the genes encoding the enzymes responsible for producing scents can be successfully transfected into yeast, these mutated yeast have many applications. 


1) Bread.  Yeast acts as a leavener in the production of bread.  The organisms feed on the sugars in flour and release carbon dioxide as a product.  The carbon dioxide produced from yeast gives bread its air-bubble structure. There are two types of yeast used for bread production.  The first is active dry yeast, which requires the organisms to be submerged in water before using at high temperatures.  The second is instant yeast.  These seem the most desirable for our purposes since it is added directly to the bread ingredients and then heated just once since the bread production process takes place in one rising.
Papers Eau d’e coli, manuscript in process to be submitted for publication.  Co-authors: Kate
Broadbent, Andre Green, Veena Venkatachalam, Boyuan Zhu, Barry Canton, Austin Che, Jason Kelly, Reshma P. Shetty, Samantha Sutton, Drew Endy, Tom Knight


http://whatscookingamerica.net/Bread/yeastbreadtip.htm
What in Coal Causes Coal Workers Pneumoconiosis?, manuscript in process to be submitted for publication.  Co-author: Robert J. McCunney


2) Beer.  Yeast serves two purposes in beer brewing.  From sugar, yeast produces both carbon dioxide and alcohol during the fermentation process.  I am assuming that since we are in a lab setting, we would use S. cerevisiae, which are the type of yeast used in top fermentation (also known as ale fermentation).  Ale fermentation should occur between 55-75 degrees Fahrenheit and involves a large number of yeast staying on the surface via dispersion. This fermentation process lasts for roughly ten days after malt is converted to a sweetened liquid using water and heat processes.  Secondary fermentation and filtering can be implemented after the initial fermentation process.
Honors 15th Annual International Conference on Microbial Genomics, Speaker and Attendee, The University of Maryland, College Park, MD, September 16- September 20, 2007
http://www.alabev.com/brew.htm


http://www.rpi.edu/dept/chem-eng/Biotech-Environ/beer/yeast/yeast1.htm
2007 MIT Amgen-UROP Scholar, Selected to receive a stipend to conduct undergraduate research in biological engineering under my faculty mentor, Professor Drew Endy.  Attended lectures featuring MIT faculty, attended a mid-summer symposium in Lake Tahoe, California on biotechnology with Amgen Scholars from ten institutions across the United States, presented at a poster session as a capstone to the summer.  The program website can be accessed at http://www.amgenscholars.com/, Summer 2007


*- An important note is that in bread production, the yeast are killed, while in brewing, the yeast are not killed.  Thus, scented bread would be a more likely application of scented yeast since it does not contain living, recombinant organisms unapproved by the FDA.
2007 Annual Meeting of the Institute for Biological Engineering (IBE), Speaker and Attendee, St. Louis, MO, March 30- April 1, 2007
 
2006 iGEM Competition, First Place for ‘Best System’, Third Place for ‘Best Presentation,’ November 4, 2006
 
National Honor Society, Inducted for Scholarship, Leadership, Service, and Character, Grades 10, 11, and 12
 
AP Scholar with Distinction, Designated for earning a 5 on the Calculus BC Exam (a 5 on the Calculus AB subscore), a 5 on the Statistics Exam, a 5 on the US Government Exam, a 4 on the English Literature Exam, and a 4 on the US History Exam, Fall 2004
 
National Student Leadership Conference, Invited to attend the National Student Leadership Conference “in recognition of academic excellence, extracurricular involvement, and demonstrated leadership potential,” Summer 2003
 
Activities MIT Hockey Club, Defenseman, Varsity, 2005-2006, 2006-2007, 2007-2008 Seasons
 
MIT Rugby Club, Hooker, 2005 Spring Season
 
Fox Chapel Area Hockey Club, Defenseman, Varsity, Grade 12, Junior varsity, Grades 9, 10, and 11, Captain, Grade 11, Voted as junior varsity’s “Player’s Player,” awarded for respect among one’s teammates; voted by teammates, Grade 11, Awarded “Best Defenseman” by coach, Grade 11
 
Young Foxes Hockey Club, Assistant Coach, Grade 12
 
Fox Chapel Area Rugby, Hooker, Varsity, Grades 9, 10, 11, and 12, Regular season champions, Grades 9, 10, 11, and 12
 
Tapestry (Fox Chapel Student Literary Magazine), Poetry Contributor, Grades 11 and 12

Revision as of 12:22, 10 December 2007

Stephen T. Payne spayne@mit.edu (412) 716-4001 ________________________________________

Education Massachusetts Institute of Technology Class of 2008 Degree name: Bachelor of Science in Biological Engineering GPA: 4.5 on a 5.0 Scale Fox Chapel Area High School, Pittsburgh, PA Class of 2004 Senior Scholar, Awarded to seniors graduating with a 4.0 (on a 4 point scale) for all four years of high school.

Work Experience Member of MIT’s International Genetically Engineered Machine Competition Team (Massachusetts Institute of Technology- Professor Drew Endy’s Biological Engineering Laboratory), Synthetic Biological Engineer, developed a synthetic biological system using various pieces of DNA dubbed Biobricks. Along with four other MIT undergraduates, I competed against forty biological engineering teams from universities around the world. In our project, we were able to successfully engineer strains of E. coli to smell like banana and mint by making genetic circuits consisting of specific promoters, ribosome binding sites, coding regions, terminators, and inverters in various plasmids. The final goal of the project is to have the E. coli produce a mint scent during exponential phase and a banana scent during stationary phase. This project is ongoing. The project website can be accessed at http://openwetware.org/wiki/IGEM:MIT/2006. Our work was noted on Forbes.com, in Technology Review, in Medgadget, in the Boston Globe, and in the German magazine, der Spiegel. Summer 2006, Fall 2006, January 2007, Summer 2007, Fall 2007

Professor Tom Knight’s Biological Engineering Laboratory (Massachusetts Institute of Technology), Lab Assistant/Researcher, conducted various experiments involving construction plasmids, including DNA ligations and restriction enzymes, examined the growth of bacteria containing different construction plasmids, developed picker instruments for plates containing wells for DNA samples using a laser cutter machine and shop tools, managed and maintained the refrigerator stock of synthetic DNA in the lab, Summer 2005

Professor Elizabeth Jones’ Biology Laboratory (Carnegie Mellon University), Lab Assistant, prepared solutions for experiments, cleaned and sterilized lab equipment, and observed cell reproduction, Summers 2003 and 2004, Fox Chapel High School credit for professional experience, Grade 12

Apprenticeship in Meteorology, Selected to participate in the 2002-2003 Meteorology Apprenticeship sponsored by the Allegheny Intermediate Unit’s Gifted Program, Grade 11

Mandi Foods, Inc., Food preparation worker, packed cheese, worked on an assembly line, and made boxes, Summers 2001 and 2002. Developed statistical analyses of sales and production data, Fox Chapel High School credit for work experience, Grade 12

Papers Eau d’e coli, manuscript in process to be submitted for publication. Co-authors: Kate Broadbent, Andre Green, Veena Venkatachalam, Boyuan Zhu, Barry Canton, Austin Che, Jason Kelly, Reshma P. Shetty, Samantha Sutton, Drew Endy, Tom Knight

What in Coal Causes Coal Workers Pneumoconiosis?, manuscript in process to be submitted for publication. Co-author: Robert J. McCunney

Honors 15th Annual International Conference on Microbial Genomics, Speaker and Attendee, The University of Maryland, College Park, MD, September 16- September 20, 2007

2007 MIT Amgen-UROP Scholar, Selected to receive a stipend to conduct undergraduate research in biological engineering under my faculty mentor, Professor Drew Endy. Attended lectures featuring MIT faculty, attended a mid-summer symposium in Lake Tahoe, California on biotechnology with Amgen Scholars from ten institutions across the United States, presented at a poster session as a capstone to the summer. The program website can be accessed at http://www.amgenscholars.com/, Summer 2007

2007 Annual Meeting of the Institute for Biological Engineering (IBE), Speaker and Attendee, St. Louis, MO, March 30- April 1, 2007

2006 iGEM Competition, First Place for ‘Best System’, Third Place for ‘Best Presentation,’ November 4, 2006

National Honor Society, Inducted for Scholarship, Leadership, Service, and Character, Grades 10, 11, and 12

AP Scholar with Distinction, Designated for earning a 5 on the Calculus BC Exam (a 5 on the Calculus AB subscore), a 5 on the Statistics Exam, a 5 on the US Government Exam, a 4 on the English Literature Exam, and a 4 on the US History Exam, Fall 2004

National Student Leadership Conference, Invited to attend the National Student Leadership Conference “in recognition of academic excellence, extracurricular involvement, and demonstrated leadership potential,” Summer 2003

Activities MIT Hockey Club, Defenseman, Varsity, 2005-2006, 2006-2007, 2007-2008 Seasons

MIT Rugby Club, Hooker, 2005 Spring Season

Fox Chapel Area Hockey Club, Defenseman, Varsity, Grade 12, Junior varsity, Grades 9, 10, and 11, Captain, Grade 11, Voted as junior varsity’s “Player’s Player,” awarded for respect among one’s teammates; voted by teammates, Grade 11, Awarded “Best Defenseman” by coach, Grade 11

Young Foxes Hockey Club, Assistant Coach, Grade 12

Fox Chapel Area Rugby, Hooker, Varsity, Grades 9, 10, 11, and 12, Regular season champions, Grades 9, 10, 11, and 12

Tapestry (Fox Chapel Student Literary Magazine), Poetry Contributor, Grades 11 and 12

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