User:Reshma P. Shetty

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==Bio==
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[[Image:ReshmaShettyPhoto.jpg|right|thumb]]
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Ph.D. Candidate in [http://web.mit.edu/be Biological Engineering] at [http://web.mit.edu MIT].  I am advised by [[User:Tk|Tom Knight]] and [[User:Endy | Drew Endy]].
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B.S. in [http://www.cs.utah.edu/ Computer Science] from the [http://www.utah.edu/ University of Utah], 2002
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I am a co-founder of [http://ginkgobioworks.com Ginkgo BioWorks, Inc.].
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==Thesis project==
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===Education===
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'''My goal is to engineer transcription-based combinational digital logic in ''Escherichia coli'' cells.'''
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Synthetic Biology seeks to intentionally design, fabricate and operate biological systems. There are three primary areas in which synthetic biological systems are of immediate utility: chemical energy, materials and information. To harness these systems to either generate new energy sources or synthesize new materials, it is necessary to develop the necessary infrastructure such that cells can be engineered to sense information, process that information using some form of logic and effect a response. Ideally, the parts and devices used to carry out information processing ''in vivo'' would have the following characteristics:
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*Ph.D. in [http://web.mit.edu/be Biological Engineering] from [http://web.mit.edu MIT], 2008.
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*B.S. in [http://www.cs.utah.edu/ Computer Science] from the [http://www.utah.edu/ University of Utah], 2002.
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#Well-characterized:  Device behavior should be quantitatively measured under standard operating conditions.
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===Current research===
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#Composable:  Devices should be designed such that the output of one device can drive the input of another device.  In other words, devices should be well-matched.
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#Engineerable: It is difficult to imagine every context in which a device might be used.  Therefore it is helpful if devices can be tuned such that they work well in larger systems.
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#Numerous:  Currently the size of the systems we can construct is severely limited by the lack of well-characterized devices.  Therefore, it will be important to develop libraries of devices such that more complicated systems can be assembled.
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My thesis work seeks to address these goals by developing a new type of transcription-based logic that uses modular, synthetic transcription factors.  I derive the DNA binding domains of these transcription factors from zinc finger domains so that arbitrary DNA recognition sites may be used.  I use leucine zippers as the dimerization domain so that these repressors are also capable of heterodimerizing increasing both the number and functionality of available dimerization domains.  This implementation change adds modularity to the repressors so that domains are interchangeable and may be fine-tuned independently.  Also, since there are large sets of both of these domains kinds available, this design enhances the scalability of transcription-based logic.  Another key benefit of my proposed transcription-based logic is that by changing the fundamental event that occurs in the device from a single protein dimerizing on the DNA and repressing transcription to two proteins heterodimerizing on the DNA and repressing transcription, faster and more compact logic may be developed.
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'''My current work is in the area of synthetic biology.'''
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===Open questions===
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*[http://hdl.handle.net/1721.1/41843 Applying engineering principles to the design and construction of transcriptional devices] (Ph.D. thesis)
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Some of the questions that I am interested in addressing as a part of my thesis work include the following.
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*[[Reshma Shetty/FAQ and thoughts | FAQ and thoughts]]: my own answers to frequently asked questions and objections to the field as well as thoughts on related experimental issues.
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# How do you evaluate device performance?  When is the performance of a device good enough?  What does good enough mean?
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# How do you engineer a device to deliver good performance?
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# How should device behavior be characterized and quantified?  How little work can we get away with and call a device characterized?
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and more.
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===But life isn't digital!===
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'''Other related discussions and projects in which I am involved.'''
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The most common question I receive when talking about my work with others is "Biology isn't digital, so why concentrate on digital logic"?  There's an answer on the [[SB:FAQ | Synthetic Biology FAQ]] but I'll give my own two cents here.  In my mind, there are two valid responses to this question.
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====Maybe not, but we are better at thinking digitally.====
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*[[BioBricks]]: a one stop shop for all BioBricks related information and projects.
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This is the answer I usually give.  After thinking about this question a fair amount and talking with others in the MIT Synthetic Biology Working Group (especially Tom Knight), I came to the conclusion that the first "digital" devices in electrical engineering probably weren't very digital either. In fact, even today's devices aren't 100% digital. Calling a device "digital" is really an abstraction we place upon a physical object that behaves according to certain specifications.  By carefully determining those behavior requirements and carefully engineering the device, the digital abstraction holds up sufficiently well for the device to work as desired. A lot of work has already been done in electrical engineering in terms of engineering digital circuits from analog electrical components.  We should be able to leverage this expertise to design digital devices from analog, biological components.
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*[[Synthetic Biology:Abstraction hierarchy | Abstraction hierarchy]]: thinking about a framework within which to engineer synthetic biological systems.
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*[[Synthetic Biology:Vectors/pSB**5 design | A new BioBricks vector design]]: designing a new, extensible BioBricks vector scaffold.
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*[[Standard_E._coli_Strain_for_BioBricks | A standard strain for BioBricks]]: specifying a standard strain in which BioBricks parts, devices and systems would operate.
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*[[Parts characterization | Standards for parts characterization]]: thinking about what BioBricks characterization standards might look like.
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*[[Synthetic Biology:Vectors/Barcode | Barcodes for synthetic biological systems]]
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====Sure it is.====
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===Teaching===
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Information in biology is encoded by DNA which consists of strings of 4 kinds of nucleotides. Therefore life is fundamentally digital. I first heard this argument in a talk given by [http://www.systemsbiology.org/Scientists_and_Research/Faculty_Groups/Hood_Group Leroy Hood] at MIT in 2003 but I am sure that others use it as wellIf biology at its core is digital, then it is no longer so unreasonable to design digital devices from biological parts.
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*[[iGEM:MIT/2006|MIT iGEM]]: I served as an advisor to the 2006 MIT iGEM team.  (iGEM is an acronym for international Genetically Engineering Machines competition.)  The team won [http://igem2006.com/results.htm "Best System"] for engineering bacteria to smell like wintergreen and banana over the course of a single summer. 
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*[[BE.109|BE.109: Laboratory fundamentals of biological engineering]]: I was a teaching assistant for BE.109 in Spring 2006.  [[Natalie Kuldell]] and I experimented with the integration of BE.109 and OpenWetWare.
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*[http://stellar.mit.edu/S/course/7/sp04/7.91/index.html BE.490: Foundations of Computational & Systems Biology]: In Spring 2004, I was a teaching assistant for BE.490.
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===Previous research===
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*Prior to coming to MIT, I spent a few months in [http://www-cryst.bioc.cam.ac.uk/ Tom Blundell's lab] at the [http://www.cam.ac.uk/ University of Cambridge] working on [http://raven.bioc.cam.ac.uk/ RAPPER]: ''ab initio'' conformational search algorithm for restraint-based protein structure modeling.
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*Before that, I worked as an undergrad research assistant for several years in [http://www.biology.utah.edu/faculty2.php?inum=7 Baldomero Olivera's] lab at the [http://www.utah.edu/ University of Utah].  I worked on a few different projects during that time including the identification of the post-translational modification enzyme γ-glutamyl carboxylase in ''Conus'' and ''Drosophila''.  Also, I helped to discover two novel superfamilies of neurotoxins from the venom of the molluscs ''Conus''.
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See [[Reshma Shetty/Publications | my publications]].
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===Honors===
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*National Science Foundation Graduate Research Fellowship, 2005-2007.
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*Whitaker Graduate Fellowship in Biomedical Engineering, 2002-2004.
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*Andrew and Edna Viterbi Fellowship in Computational Biology, 2002-2003.
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===Activities===
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'''Some non-research but still important discussions and projects in which I am participating.'''
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*[[Main Page | OpenWetWare]]: a wiki for researchers in biological science and engineering to enable more sharing and collaboration in the research community.  I serve on the [[OpenWetWare steering committee]].  Here are [[Special:Contributions/Rshetty | my contributions]] to the site.
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*[http://igem2006.com iGEM]: I served as a part-time iGEM 2006 ambassador to Asia.
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*[[Publishing Group | Publishing]]: can we improve the publishing system in synthetic biology?  
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**To this end, I helped set up the MIT DSpace synthetic biology publishing archive.  Check out the archive [https://dspace.mit.edu/handle/1721.1/18185/browse-date by date] [https://dspace.mit.edu/handle/1721.1/18185/browse-author by author]
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*[[Synthetic Society | Synthetic Society Working Group]]: a working group exploring societal issues around synthetic biology.
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*Previously, I also helped to organize [http://syntheticbiology.org/Synthetic_Biology_1.0.html Synthetic Biology 1.0]: The First International Meeting on Synthetic Biology.
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===Contact===
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Reshma Shetty<br>
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rshetty AT ginkgobioworks DOT com
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===Bookmarks===
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http://del.icio.us/rss/rpshetty/research
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===Miscellaneous===
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*[[Reshma Shetty/blog]] <-- trying out a blog
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*[http://science.slashdot.org/science/06/11/06/1913228.shtml We made Slashdot!]
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*[http://money.cnn.com/ CNN Money] has an [http://money.cnn.com/2005/08/15/pf/training_pay/index.htm article] called "Big jobs that pay badly."  The three examples they cite: architect, chef and academic research scientist.
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*The other kind of [http://www.newscientist.com/article.ns?id=dn2731 biobricks].
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*[http://www.washingtonpost.com/wp-dyn/content/article/2005/11/11/AR2005111100674.html Google, Venter and genomics ... oh my!]
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*[http://www.quarter-life-crisis.com Quarter-Life-Crisis]: outlet for the artistically inclined twenty-something. (Shameless plug for a friend's website.)
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*The [http://aimediaserver.com/studiodaily/videoplayer/?src=harvard/harvard.swf&width=640&height=520 Mechanome]
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[[Category:Steering Committee member]]

Current revision

I am a co-founder of Ginkgo BioWorks, Inc..

Education

Current research

My current work is in the area of synthetic biology.

Other related discussions and projects in which I am involved.

Teaching

Previous research

  • Prior to coming to MIT, I spent a few months in Tom Blundell's lab at the University of Cambridge working on RAPPER: ab initio conformational search algorithm for restraint-based protein structure modeling.
  • Before that, I worked as an undergrad research assistant for several years in Baldomero Olivera's lab at the University of Utah. I worked on a few different projects during that time including the identification of the post-translational modification enzyme γ-glutamyl carboxylase in Conus and Drosophila. Also, I helped to discover two novel superfamilies of neurotoxins from the venom of the molluscs Conus.

See my publications.

Honors

  • National Science Foundation Graduate Research Fellowship, 2005-2007.
  • Whitaker Graduate Fellowship in Biomedical Engineering, 2002-2004.
  • Andrew and Edna Viterbi Fellowship in Computational Biology, 2002-2003.

Activities

Some non-research but still important discussions and projects in which I am participating.

Contact

Reshma Shetty
rshetty AT ginkgobioworks DOT com

Bookmarks

Miscellaneous

Personal tools