User:ClarkeS

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
(Potential research topics)
(Bio)
(26 intermediate revisions not shown.)
Line 1: Line 1:
==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 a first-year [http://web.mit.edu/be/ Biological Engineering] (BE, course 20) graduate student who worked in the [[Endy Lab]] this past summer 2005.  This semester I am taking classes, and looking for a lab I would like to join.  The Endy lab is one possibility.  I naively expected to be able to continue some lab work, but classes and other demands of the first year have made that practically impossible.
+
==Past life and credentials==
 +
 
 +
My background is in mechanical engineering and design, but not of things quite as small as [[BioBricks]].
*B.S.M.E., [http://www.utexas.edu University of Texas at Austin], biomedical technical area
*B.S.M.E., [http://www.utexas.edu University of Texas at Austin], biomedical technical area
-
*B.A., [http://www.utexas.edu University of Texas at Austin], Plan II Liberal Arts Honors Program
+
*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]
*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]
-
My background is in mechanical engineering and design, but not of things quite as small as [[BioBricks]].
+
==Other research interests==
-
 
+
*Food microbiology
-
==Potential research topics==
+
*Microbiomes of the built environment
-
*Scaling of engineered biology
+
*How bacteria move and live in cities
-
*Replicating biological machines
+
*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
*Technologies/vocabularies to make biological engineering easier
 +
*Ethics and philosophy of science instruction for scientists/engineers
*Biomimicry, bioscaffolds for material processing
*Biomimicry, bioscaffolds for material processing
*Recycling/"cradle to cradle" design of biological systems
*Recycling/"cradle to cradle" design of biological systems
-
*Usability of biological design software or methods
+
*Usability of biological design software and equipment
*Biomineralization
*Biomineralization
==Classes==
==Classes==
 +
*BE.400
 +
*BE.410
*BE.420
*BE.420
*BE.430
*BE.430
-
*[http://web.mit.edu/biophysics/sbio/ 7.81 Systems Biology]
+
*[http://web.mit.edu/5.95J/ 5.95] Teaching College-Level Science and Engineering
-
*[http://math.mit.edu/18085 18.085 Applied Math for Engineers]
+
*[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
-
==Projects==
+
==Past Projects==
-
*My first project was the [[Orthogonal cloning of clpXP]] from ''E. coli'' into yeast. So far I've been more successful at learning molecular biology and techniques by making mistakes than at cloning into yeast.  My work is documented in a lab notebook, but I would like to move to a wiki or other on-line lab notebook for searching, organization, and linking.  
+
*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.
-
*Another useful project would be 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''.
+
[[Sean Clarke/Notes|Notes]]

Revision as of 21:44, 27 October 2011

Contents

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

Personal tools