Josh Michener

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__NOTOC__
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=Josh Michener=
=Josh Michener=
==Education==
==Education==
[[Image:JKMpic.jpg|right|thumb]]
[[Image:JKMpic.jpg|right|thumb]]
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*3rd year Bioengineering PhD candidate at Caltech
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*PhD, 2012, Bioengineering at Caltech
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**Currently on detached duty at Stanford
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*S.B. 2006, Chemical Engineering and Biology at MIT
*S.B. 2006, Chemical Engineering and Biology at MIT
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==Lab history==
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==Research Experience==
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*Grad student in the [[Smolke]] Lab ([http://bioengineering.stanford.edu/ Stanford Bioengineering]) and [[Arnold]] Lab ([http://be.caltech.edu Caltech Bioengineering]).
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*NRSA Postdoctoral Fellow in the Marx Lab, Harvard Department of Organismic and Evolutionary Biology
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*Rotated in the Smolke, Arnold, and Elowitz labs at Caltech
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*Nordic Research Fellow in the Nielsen Lab, Chalmers Institute of Technology (Gothenburg, Sweden)
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*UROP in the [[Endy Lab]] at [http://web.mit.edu/ MIT], January 2005 - January 2006.
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*NSF Graduate Research Fellow in the Smolke Lab, Caltech/Stanford Bioengineering
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*UROP in the Endy Lab at MIT
==Contact Info==
==Contact Info==
Josh Michener<br>
Josh Michener<br>
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Bioengineering - Smolke Lab<br>
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16 Divinity Ave Room 3082<br>
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Y2E2-B07, MC 4200<br>
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Cambridge, MA, 02138<br>
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473 Via Ortega<br>
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Stanford, CA 94305<br>
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[[Image:Michener-email.png]]
[[Image:Michener-email.png]]
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==Research==
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==Research Interests==
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My research focuses on applying RNA switches, developed elsewhere in the lab, to provide dynamic control of enzymatic pathways. Specifically, I am using those switches to construct feedback control systems, with the goal of producing a predictable output despite variations in reaction conditions. These control systems can then be used in metabolic engineering to change both the transient and equilibrium responses of a pathway.
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No gene exists in isolation. To be useful, a gene must be functionally expressed and its host must be able to deal with any resulting stresses. Most genes have had sufficient time in their current host that the gene and host have co-evolved to minimize deleterious interactions. However, while this type of coexistence might be the rule, the exceptions can be both interesting and extremely consequential. When, for example, a microbe acquires new genetic material through horizontal gene transfer or synthetic biology, genes must function in an environment with which they did not co-evolve. Efficient use of a new ability will require careful integration into the existing metabolic and regulatory networks of the host. The interactions between gene and host, as well as their evolutionary outcomes, will determine whether a microbe can become pathogenic, remediate a polluted site, or produce a biofuel. Understanding these interactions and the strategies by which evolution optimizes them will allow us to better anticipate the emergence of new microbial phenotypes.
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==Publications==
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===Research Articles===
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*'''Michener JK''', Vuilleumier S, Bringel F, and Marx CJ. Phylogeny poorly predicts the utility of a challenging horizontally-transferred gene in ''Methylobacterium'' strains. J Bacteriol. June 2014 196:2101-2107. [http://jb.asm.org/content/196/11/2101.abstract]
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*'''Michener JK''', Nielsen J, and Smolke CD. Identification and treatment of heme depletion due to over-expression of a lineage of evolved P450 monooxygenases. PNAS. 2012; 109(47):19504-9. [http://www.pnas.org/content/109/47/19504.abstract]
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*'''Michener JK''' and Smolke CD. High-throughput enzyme evolution in ''Saccharomyces cerevisiae'' using a synthetic RNA switch. Metab Eng. 2012 Jul; 14(4):306-16. [http://www.sciencedirect.com/science/article/pii/S109671761200047X]
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==Past Projects==
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===Methods and Reviews===
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*Development of an ''in vivo'' screen for synthetic riboswitches.
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*'''Michener JK''' and Smolke CD. Synthetic RNA switches for yeast metabolic engineering. 2014 .Valeria Mapelli (ed.), Yeast Metabolic Engineering: Methods and Protocols, Methods in Molecular Biology, 1152:125-36. [http://link.springer.com/protocol/10.1007/978-1-4939-0563-8_7]
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*Design and construction of a [[Endy:Screening plasmid|screening plasmid]] to measure the PoPS transfer curve of a [http://parts.mit.edu BioBricks] device.
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*'''Michener JK''', Thodey K, Liang JC, Smolke CD. Applications of genetically-encoded biosensors for the construction and control of biosynthetic pathways. Metab Eng. 2012 May; 14(3):212-22. [http://www.sciencedirect.com/science/article/pii/S1096717611000942]
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==Interesting papers==
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*[[User:Jkm/Feedback|Metabolic control]]
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*[[User:Jkm/Caffeine|Caffeine metabolism]]
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==Random pages==
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*[http://dx.doi.org/10.1016/S0009-2509(03)00183-0d53c2e392aa18 Chemical and Biological Engineering]
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*[http://brodylab.eng.uci.edu/~jpbrody/reynolds/lowpurcell.html Edward Purcell: Life at Low Reynold's Number]
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*[http://www.cs.virginia.edu/~robins/YouAndYourResearch.html Richard Hamming: You and Your Research]
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*[[User:Jkm/Alternate_protocols|Alternate page design]]
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*[[User:Jkm/sidebar|My sidebar]]
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*[[User:Jkm/What not to do|Cautionary tales]]
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Current revision

Josh Michener

Education

  • PhD, 2012, Bioengineering at Caltech
  • S.B. 2006, Chemical Engineering and Biology at MIT

Research Experience

  • NRSA Postdoctoral Fellow in the Marx Lab, Harvard Department of Organismic and Evolutionary Biology
  • Nordic Research Fellow in the Nielsen Lab, Chalmers Institute of Technology (Gothenburg, Sweden)
  • NSF Graduate Research Fellow in the Smolke Lab, Caltech/Stanford Bioengineering
  • UROP in the Endy Lab at MIT

Contact Info

Josh Michener
16 Divinity Ave Room 3082
Cambridge, MA, 02138

Image:Michener-email.png

Research Interests

No gene exists in isolation. To be useful, a gene must be functionally expressed and its host must be able to deal with any resulting stresses. Most genes have had sufficient time in their current host that the gene and host have co-evolved to minimize deleterious interactions. However, while this type of coexistence might be the rule, the exceptions can be both interesting and extremely consequential. When, for example, a microbe acquires new genetic material through horizontal gene transfer or synthetic biology, genes must function in an environment with which they did not co-evolve. Efficient use of a new ability will require careful integration into the existing metabolic and regulatory networks of the host. The interactions between gene and host, as well as their evolutionary outcomes, will determine whether a microbe can become pathogenic, remediate a polluted site, or produce a biofuel. Understanding these interactions and the strategies by which evolution optimizes them will allow us to better anticipate the emergence of new microbial phenotypes.

Publications

Research Articles

  • Michener JK, Vuilleumier S, Bringel F, and Marx CJ. Phylogeny poorly predicts the utility of a challenging horizontally-transferred gene in Methylobacterium strains. J Bacteriol. June 2014 196:2101-2107. [1]
  • Michener JK, Nielsen J, and Smolke CD. Identification and treatment of heme depletion due to over-expression of a lineage of evolved P450 monooxygenases. PNAS. 2012; 109(47):19504-9. [2]
  • Michener JK and Smolke CD. High-throughput enzyme evolution in Saccharomyces cerevisiae using a synthetic RNA switch. Metab Eng. 2012 Jul; 14(4):306-16. [3]

Methods and Reviews

  • Michener JK and Smolke CD. Synthetic RNA switches for yeast metabolic engineering. 2014 .Valeria Mapelli (ed.), Yeast Metabolic Engineering: Methods and Protocols, Methods in Molecular Biology, 1152:125-36. [4]
  • Michener JK, Thodey K, Liang JC, Smolke CD. Applications of genetically-encoded biosensors for the construction and control of biosynthetic pathways. Metab Eng. 2012 May; 14(3):212-22. [5]
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