Brown:iGEM proposal


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The iGEM competition: Where engineering meets biology

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 expertice in biology, chemistry, computer science, engineering, mathematics, neuroscience and physics.

Synthetic Biology: A new 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.

Hypothesis: standard interchangable parts can 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 contruct 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 lef 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 international 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."[Knight 2005]

Student led research at Brown

The main competition 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. Here at Brown we already have support and offers of lab space from Gary Wessel in Molecular-Cellular Biology (MCB), Marc Tatar in Ecology and Evolutionary Biology (EEB) and offers from a number of faculty ranging from engineering, computer science and physics to join a multidisciplinary cross-campus faculty advisory board. This mentoring board will meet each week in order for students to report progress and to discuss ideas. The project gives students the opportunity to become directly involved with research at Brown. Previous entries in the iGEM competition have been published in Nature. [Engineering E.Coli to see light, 2005]

Table of needs

We hope to get departmental and university sponsorship to cover the following 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 acquire specific genetic material necessary for participating in the competition.
Lab Reagents expenses will enable the team maintain a well 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 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. We hope to find industry sponsorship to support the competition.

Cross campus faculty support and mentoring

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 Soloman, 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

Potential support (TBC)
Nicola Neretti, Assistant Professor of Physics

(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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