User:ClarkeS: Difference between revisions

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==Bio==
==Bio==
Sean Clarke
Sean Clarke<br>
saclarke at mit<br>
48-208<br>
[[BE_Board:Sean_Clarke | directory info]]


saclarke at MIT
I am a [http://web.mit.edu/be/ Biological Engineering] (BE, MIT Course XX) graduate student in the [[Alm_Lab|Alm lab]] (48-324).  Our focus is on microbial ecology and the evolution of microbial genomes. My work is on engineering genetic diversity and stress tolerance in ''Vibrio splendidus''.  I hope to determine what alleles and loci contribute to environmental stress tolerance using experimental evolution and resequencing.


I am an incoming BE graduate student working in the Endy lab this summer.
==Past life and credentials==


My background is in mechanical engineering and design, but not of things quite as small as BioBricks.  Please forgive the questions about methods that might seem routine.  I'm still trying to suss out the techniques for the line between the mundane and the not yet possible.
My background is in mechanical engineering and design, but not of things quite as small as [[BioBricks]].


==Projects==
*B.S.M.E., [http://www.utexas.edu University of Texas at Austin], biomedical technical area
*My first project is [[Orthogonal cloning of clpXP]] system from ''E. coli'' into yeast. After background reading and conversations, my first task is [[Primer design|primer design]].
*B.A., [http://www.utexas.edu University of Texas at Austin], [http://www.utexas.edu/cola/progs/plan2/ Plan II] Liberal Arts Honors Program
*Fulbright grant, Milan, Italy, independent study of industrial and engineering design methods, and classes in biomaterials at the [http://www.polimi.it Politecnico di Milano]


*Another possible project is the construction of a low copy number plasmid for use with BioBricks. It might be  based on the F or mini-F plasmid from ''E. coli''.
==Other research interests==
*Food microbiology
*Microbiomes of the built environment
*How bacteria move and live in cities
*Engineering microbial stress tolerance
*Relating stress tolerance to genetic loci
*Resequencing evolved microbes
*Scaling of engineered biology to industrial purposes
*Design and use of replicating biological machines
*Technologies/vocabularies to make biological engineering easier
*Ethics and philosophy of science instruction for scientists/engineers
*Biomimicry, bioscaffolds for material processing
*Recycling/"cradle to cradle" design of biological systems
*Usability of biological design software and equipment
*Biomineralization
 
==Classes==
*BE.400
*BE.410
*BE.420
*BE.430
*[http://web.mit.edu/5.95J/ 5.95] Teaching College-Level Science and Engineering
*[http://web.mit.edu/biophysics/sbio/ 7.81 Systems Biology] Excellent class, Alex van Oudenaarden
*[http://math.mit.edu/18085 18.085 Applied Math for Engineers] with the indefatigable Gil Strang, who might have taught your parents and is still revising his book daily.
*[http://web.mit.edu/7.56 7.56 Graduate Cell Biology], with an emphasis on yeast, Profs. Stephen Bell and Frank Solomon
*1.89 Environmental Microbiology with Martin Polz
*OEB.192 Microbial Evolution with Chris Marx, a great subject that is not taught enough
*directed evolution seminar
 
==Past Projects==
*My first project at MIT was during the summer of 2005 when I tried the [[Orthogonal cloning of clpXP]] from ''E. coli'' into yeast.  I was more successful at learning molecular biology techniques by making mistakes than at cloning into yeast.  This work is continuing in someone else's more capable hands.
 
[[Sean Clarke/Notes|Notes]]

Revision as of 19:44, 27 October 2011

Bio

Sean Clarke
saclarke at mit
48-208
directory info

I am a Biological Engineering (BE, MIT Course XX) graduate student in the Alm lab (48-324). Our focus is on microbial ecology and the evolution of microbial genomes. My work is on engineering genetic diversity and stress tolerance in Vibrio splendidus. I hope to determine what alleles and loci contribute to environmental stress tolerance using experimental evolution and resequencing.

Past life and credentials

My background is in mechanical engineering and design, but not of things quite as small as BioBricks.

Other research interests

  • Food microbiology
  • Microbiomes of the built environment
  • How bacteria move and live in cities
  • Engineering microbial stress tolerance
  • Relating stress tolerance to genetic loci
  • Resequencing evolved microbes
  • Scaling of engineered biology to industrial purposes
  • Design and use of replicating biological machines
  • Technologies/vocabularies to make biological engineering easier
  • Ethics and philosophy of science instruction for scientists/engineers
  • Biomimicry, bioscaffolds for material processing
  • Recycling/"cradle to cradle" design of biological systems
  • Usability of biological design software and equipment
  • Biomineralization

Classes

  • BE.400
  • BE.410
  • BE.420
  • BE.430
  • 5.95 Teaching College-Level Science and Engineering
  • 7.81 Systems Biology Excellent class, Alex van Oudenaarden
  • 18.085 Applied Math for Engineers with the indefatigable Gil Strang, who might have taught your parents and is still revising his book daily.
  • 7.56 Graduate Cell Biology, with an emphasis on yeast, Profs. Stephen Bell and Frank Solomon
  • 1.89 Environmental Microbiology with Martin Polz
  • OEB.192 Microbial Evolution with Chris Marx, a great subject that is not taught enough
  • directed evolution seminar

Past Projects

  • My first project at MIT was during the summer of 2005 when I tried the Orthogonal cloning of clpXP from E. coli into yeast. I was more successful at learning molecular biology techniques by making mistakes than at cloning into yeast. This work is continuing in someone else's more capable hands.

Notes

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