Brown:iGEM proposal


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iGEM -Cross disciplinary student competition June-August 2006

This summer a cross-disciplinary team of Brown students will enter the MIT-based iGEM competition. The challenge is to design and implement a genetically engineered machine and students are set to draw on Brown's cross disciplinary expertise in biology, chemistry, computer science, engineering, mathematics, neuroscience and physics.

Synthetic Biology: A novel field

In the last decade, a revolution in genomics has shown us how the power of the human genome can be harnessed to find, understand and combat mutations that cause the human molecular machinery to breakdown (3). Synthetic Biology is a new cross-disciplinary field that allows us to not only decipher how DNA holds and translates information, but to use this understanding to produce novel biological machines to start to repair this damage, increase product yields(4) or deliver cancer drugs to targeted cells in the body(5). To this end, the field calls upon the knowledge and accomplishments of related disciplines. The November 24th 2005 issue of Nature magazine highlighted the growing field of Synthetic Biology indicating that through the combined intellectual resources of the hard science, research in this field will be at the forefront in the coming decade.

Can standard interchangeable parts be constructed in vivo?

The Genetically Engineered Machine competition (iGEM) is designed to test the hypothesis that "Simple biological systems can be built from standard interchangeable parts and operated in living cells?" (1). The Brown team wants to test this hypothesis by working over the summer to design and construct such a machine. The competition challenges students to implement a machine capable of performing an engineered task. Unlike other engineering challenges, the machines produced by the competitors are transcribed from DNA sequences, rather than blue prints, and the constituent parts are RNA, proteins and cells, instead of steel, nuts and bolts. This student led initiative has backing from some of Brown's best researchers, bringing together faculty in this cross disciplinary field which demonstrates the essential nature of an interdisciplinary approach to hard scientific research.

High-profile intercollegiate competition

"Started in 2003, MIT students created biological oscillators coupled to fluorescent reporters. The summer of 2004 brought the first Synthetic Biology Competition. Student teams from five schools (Princeton, MIT, Caltech, UT Austin, and Boston University) and competed to build cellular state machines and counters. The teams gathered in early November to compare their results. The most graphic project was "photographic biofilm" that could capture an image.

In the summer of 2005, student teams from thirteen schools (Berkeley, Caltech, Cambridge UK, Davidson, ETH Zurich, Harvard, MIT, Oklahoma, Penn State, Princeton, Toronto, UCSF, and UT Austin) participated in the 2005 International Genetically Engineered Machine (iGEM) competition. Later, during the first weekend of November, over 150 of these students, instructors, and PIs came together to share and celebrate their work.

The iGEM 2005 student projects displayed the designs of chemotaxis regulation systems, cell-cell genetic communications systems, cellular/biological wires, thermometers, biological sketch pads (drawing systems), cellular relay races, a digital counter, and many more.

At the core of these activities is the notion of a standard biological part that is well specified and able to be paired with other parts into subassemblies and whole systems. Once the parameters of these parts are determined and standardized, simulation and design of genetic systems will become easier and more reliable." (1)

Student led research at Brown

The competition give students the chance to spend 12 weeks developing ground breaking research in Synthetic Biology. It takes place over the summer with students spending their time designing novel engineered parts, modeling biochemical reactions and then implementing these designs in the lab. The team already has support, lab space and supervision from Professor Gary Wessel in Molecular-Cellular Biology (MCB) and Professor Marc Tatar in Ecology and Evolutionary Biology (EEB). This will then be combined with other offers from a number of cross-campus faculty to advise, support and mentor the team. The mentoring board will meet each week in order for students to report progress and to discuss new ideas. the outcome of the project will be advances in current research in synthetic biology. Previous entries in the iGEM competition have been published by students in the journal Nature (2). Whatever the field, the competition provides a great opportunity for science students at Brown to develop their own ideas and to start publishing research for a future career in science.

Table of needs

We aim to raise departmental, university and industrial sponsorship to cover the following team costs.

DNA Synthesis $ 4,000
Lab Reagents $ 7,000
Travel expenses $ 1,000
8 undergraduate summer support stipends ($3500 x 8) $ 28,000
Total $ 40,000

DNA synthesis funding will allow the Brown iGEM team to acquire specific genetic material necessary for participating in the competition. Lab reagents expenses will enable the team to maintain a stocked laboratory environment in which it could conduct novel biosynthetic research. Funding for travel expenses would allow the team and faculty mentoring board to travel to MIT in November 2006 to participate in the iGEM jamboree. Support stipends will be used to accomplish two goals. First, a portion of the money will be used to provide housing to undergraduates without lodging in or near Providence. Second, the remainder of the money will be allocated to ensure that team members can participate in research full time, rather than maintaining other employment. Stipend recipients will be selected by the faculty advisory panel.

The future of iGEM

We hope that in coming years the Brown iGEM team can continue to grow, taking on new students and continuing research in synthetic biology at Brown. Research could also continue by establishing Group Independent Study Projects (GISPs) and by continuing the synthetic biology journal club during the semester.

Cross campus faculty support and mentoring

There are currently 12 undergraduates interested in taking part in the competition. The final number of funded places on the team will be 8 undergraduates. A synthetic biology journal club has been started in order to start the preliminary research into ideas for the competition. The 8 funded students will be chosen by the faculty advisory board from students applications and participation in the journal club.

Marc Tatar * Associate Professor of Ecology and Evolutionary Biology
Gary Wessel * Professor of Biology
Alex Brodsky * Assistant Professor in MCB, Ship Street
Karen Marie Haberstroh Assistant Professor of Engineering
Sorin Istrail Professor of Computer Science
Tayha Palmore Associate Professor of Engineering
Art Salomon Assistant Professor of Biology/Proteomics/Biochemistry
David Targan Dean for Science Programs
Marjorie Thompson Associate Dean of Biological Sciences
Jim Valles Professor of Physics
Herman Vandenburgh Professor of Pathobiology

* - indicates offer of wet lab facilities

Students currently interested in forming an iGEM team

John Cumbers - Graduate Student Computational Biology
Annie Gao
Peter Goldstein - Undergraduate Student Computational Biology
Smita Gupta
Nicholas Halden
Elena Helman - Undergraduate Student Computational Biology
Julia Heneghan
Brendan Hickey - Undergraduate Student Computational Biology
Victoria Lattanzi- Undergraduate Student Biochemistry and French Studies
Jamie Lemon - Undergraduate Student Biology
Kara Neergaard
Peter Rosenthal
Megan Schmidt - Undergraduate Student Human Biology
Julie Spector - Undergraduate Student Neuroscience
Elaine Tran


iGEM is a high profile international biotech competition. A Brown team would highlight the university as a liberal arts college with a strong multidisciplinary faculty encouraging student participation in cutting edge scientific research. To take part in the competition, we require funding to support the team with undergraduate stipends, lab reagent costs and travel expenses.

(1) Tom Knight 2005, iGEM: International Genetically Engineered Machine competition.
(2) Chris Voigt 2005, Synthetic biology: Engineering Escherichia coli to see light, Nature 438, 441-442 (24 November 2005)
(3) The International HapMap Consortium. A haplotype map of the human genome. Nature 437, 1299-1320. 2005. (4) Jay D Keasling, Engineering a mevalonate pathway in Escherichia coli for production of terpenoids, Nature Biotechnology 21, 796 - 802 (2003) (5) Anderson, J. C., Clarke, E. J., Arkin, A. P., & Voigt, C. A. (2005) Environmentally Controlled Invasion of Cancer Cells by Engineered Bacteria, Journal of Molecular Biology, in press.

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