Jeff Tabor: Difference between revisions

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== Background ==
== Background ==
*I received my B.A. studying Biology and [http://www.cm.utexas.edu/ Biochemistry] from the [http://www.utexas.edu/ University of Texas] in 2001.  I studied evolutionary biology in the lab of [http://www.zo.utexas.edu/faculty/antisense/ Jim Bull] for two years during that time.   
*I received my B.A. studying Biology and [http://www.cm.utexas.edu/ Biochemistry] from the [http://www.utexas.edu/ University of Texas] in 2001.  I studied Evolutionary Biology in the laboratory of [http://www.zo.utexas.edu/faculty/antisense/ Jim Bull] for two years during that time.   


*I received my Ph.D. in May 2006 from the University of Texas, studying the design and evolution of synthetic biological systems under [http://ellingtonlab.org/ Andy Ellington].   
*I received my Ph.D. in May 2006 from the University of Texas, studying the rational design and directed evolution of Synthetic Biological systems under [http://ellingtonlab.org/ Andy Ellington].   


*I am currently a postdoc in the [http://www.voigtlab.ucsf.edu/ Voigt lab] at [http://www.ucsf.edu/ UCSF].
*I am currently a Postdoctoral Scholar in the [http://www.voigtlab.ucsf.edu/ Voigt lab] at [http://www.ucsf.edu/ UCSF].




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===Synthetic Biology===
===Synthetic Biology===
My primary interests include the forward design and programming of novel cellular behaviors ([http://en.wikipedia.org/wiki/Synthetic_biology synthetic biology]) using genetic regulation strategies at both the canonical protein/DNA interaction level (e.g. controlling [http://openwetware.org/wiki/Adventures POPS]; Endy, ''Nature'', 2005) and at the level of riboregulation (e.g. [http://openwetware.org/images/b/b7/Bayer.pdf Bayer and Smolke], ''Nature Biotechnology'' 2005).
I am primarily interested in programming multicellular behaviors using synthetic genetic circuits.


====Bacterial Photography====
====Bacterial Photography====
I was involved with a group at the University of Texas designed a "[http://www.nature.com/nature/journal/v438/n7067/abs/nature04405.html bacterial photography]" system in which a community of ''E.coli'' act as a biological film capable of capturing and permanently recapitulating an image of light (see figure below).  This work was enabled by the design of an incredible chimeric light responsive genetic element from the [http://www.voigtlab.ucsf.edu/ Voigt lab] at [http://www.ucsf.edu/ UCSF].  Basically, Anselm Levskaya and Chris Voigt rewired a phytochrome protein from ''Synechocystis'' which changes conformation in response to light and transduces this into a change in gene expression in that organism to control an osmo-responsive genetic regulatory system in ''E.coli''.  In order to retain the functionality of the phytochrome protein, the metabolism of ''E.coli'' had to be re-engineered to produce a ringed organic compound, phycocyanobilin (PCB).  This work had previously been done in the [http://www.mcb.ucdavis.edu/faculty-labs/lagarias/main.html Lagarias lab] at [http://www.ucdavis.edu/index.html UC-Davis] (Gambetta and Lagarias, ''PNAS'', 2001).  The result is a synthetic genetic signal transduction cascade in E.coli that responds to light in the 660nm (red) range.  There are many interesting applications that may be enabled by high resolution photoregulatory methods.  Also, check out Nature's [http://openwetware.org/images/9/9d/Year_in_photos_2005.pdf 2005 Year in Pictures]
I was involved with a group at the University of Texas designed a "[http://www.nature.com/nature/journal/v438/n7067/abs/nature04405.html bacterial photography]" system in which a community of ''E.coli'' act as a biological film capable of capturing and permanently recapitulating an image of light (see figure below).  This work was enabled by the design of an incredible chimeric light responsive genetic element from the [http://www.voigtlab.ucsf.edu/ Voigt lab] at [http://www.ucsf.edu/ UCSF].  Basically, Anselm Levskaya and Chris Voigt rewired a phytochrome protein from ''Synechocystis'' which changes conformation in response to light and transduces this into a change in gene expression in that organism to control an osmo-responsive genetic regulatory system in ''E.coli''.  In order to retain the functionality of the phytochrome protein, the metabolism of ''E.coli'' had to be re-engineered to produce a ringed organic compound, phycocyanobilin (PCB).  This work had previously been done in the [http://www.mcb.ucdavis.edu/faculty-labs/lagarias/main.html Lagarias lab] at [http://www.ucdavis.edu/index.html UC-Davis] (Gambetta and Lagarias, ''PNAS'', 2001).  The result is a synthetic signal transduction cascade in ''E.coli'' that responds to light in the 660nm (red) range.  There are many interesting applications that may be enabled by high resolution photoregulatory methods.  Also, check out Nature's [http://openwetware.org/images/9/9d/Year_in_photos_2005.pdf 2005 Year in Pictures]
 
 
If you'd like to take your own pictures, check out the page on [http://openwetware.org/wiki/LightCannon how to build a light cannon].


[[Image:Darwin.JPG|thumb|left|250px|Real intelligent designers use evolution.    Bacterial photo: Aaron Chevalier]]
[[Image:Darwin.JPG|thumb|left|250px|Real intelligent designers use evolution.    Bacterial photo: Aaron Chevalier]]
If you'd like to take your own bacterial photographs, check out the page on [http://openwetware.org/wiki/LightCannon how to build a light cannon].


====Edge Detector====
====Edge Detector====
We are advancing using bacterial photography as a platform for the construction of a biological edge detector.  In this design, each ''E.coli'' on the lawn would compute whether it were in the light, the dark, or at the boundary of light and dark.  Those cells at boundary will express a reporter, and the result would not be a recapitulated image, but the outline of the image.  Interestingly, edge detection is an expensive serial computational problem, wherein the computation time increases quadratically with the size of the image.  In the parallel ''E.coli'' edge detector, the problem is solved in constant time regardless of image size.   
We are advancing using bacterial photography as a platform for the construction of a biological edge detector.  In this system, each bacterium on the lawn senses whether it is located in the light, the dark, or at the boundary of light and dark.  Those cells at boundary express a visible reporter gene, and the result is not a positive of the projected image, but the outline of the image.  Edge detection is a well studied serial algorithm where computation time increases linearly with the number of pixels (approximately as the square of image size).  In the massively parallel Biological edge detector, the algorithm runs in constant time regardless of image size.  This bottom-up approach highlights the unique parallel information processing abilities inherent to Biological systems, a feature which is highlighted in nature in areas such as developmental biology and neural networks.
    
    
===Noise===
I am also interested in the quantitative characteristics of natural mechanisms of gene regulation and expression.  Uncontrollable fluctuations in gene expression in populations of genetically identical individuals can lead to diverse (even opposite) phenotypes within that population.  It is becoming more and more obvious that biology, being evolutionarily adept as it is, has taken advantage of the noise inherent in gene expression to encode complex population level behaviors using simple genetic level specifications.  For example, the virus HIV encodes a genetic amplifier in its genome, wherein a protein product of a gene results in higher transcription levels of that gene.  Upon infection of a host cell, the levels of that protein product usually tend about some mean.  Uncontrollable fluctuations below that mean at some critical time point result in the HIV genomes in that invaded cell going lysogenic.  Fluctuations above that mean at some critical time point result in the HIV genomes in that cell going lytic.  There are fitness advantages to such a bifuracted reproductive strategy, and this virus has used noise as opposed to hard-wired genetics to encode this behavior.  Clearly, noise can sometimes be detrimental to cellular survival, and in certain instances biology has evolved ways to insulate, buffer or engineer away noise in gene expression as well.  Check out my [http://esmane.physics.lsa.umich.edu/wl/external/ICSB/2005/20051020-umwlap001-04-tabor/real/f001.htm talk] from [http://csbi.mit.edu/icsb-2005/program/program.htm ICSB 2005].
==Publications==
==Publications==
*Jeffrey J. Tabor, Matthew Levy, Zachary B. Simpson and Andrew D. Ellington (In press). Parasitism and protocells: The tragedy of the molecular commons. In ''Protocells: Bridging Nonliving and Living Matter'', eds. S. Rasmussen, M.A. Bedau, L.Chen, D.Deamer, D.C. Krakauer, N. Packer and P.F. Stadler, MIT Press, 11/2008. <br>
*Jeffrey J. Tabor, Matthew Levy, Zachary B. Simpson and Andrew D. Ellington. Parasitism and protocells: The tragedy of the molecular commons. In ''Protocells: Bridging Nonliving and Living Matter'', eds. S. Rasmussen, M.A. Bedau, L.Chen, D.Deamer, D.C. Krakauer, N. Packer and P.F. Stadler, MIT Press, 11/2008. <br>


*Jeffrey J. Tabor, Travis S. Bayer, Zachary B. Simpson, Matthew Levy and Andrew D. Ellington.  Engineering Stochasticity in Gene Expression (2008).  ''Molecular Biosystems'', '''4''' (7) 754-61. [http://openwetware.org/images/5/56/Tabor_2008.pdf pdf] <br>
*Jeffrey J. Tabor, Travis S. Bayer, Zachary B. Simpson, Matthew Levy and Andrew D. Ellington.  Engineering Stochasticity in Gene Expression (2008).  ''Molecular Biosystems'', '''4''' (7) 754-61. [http://openwetware.org/images/5/56/Tabor_2008.pdf pdf] <br>

Revision as of 18:10, 10 October 2008

Background

  • I received my Ph.D. in May 2006 from the University of Texas, studying the rational design and directed evolution of Synthetic Biological systems under Andy Ellington.


Research Interests

Synthetic Biology

I am primarily interested in programming multicellular behaviors using synthetic genetic circuits.

Bacterial Photography

I was involved with a group at the University of Texas designed a "bacterial photography" system in which a community of E.coli act as a biological film capable of capturing and permanently recapitulating an image of light (see figure below). This work was enabled by the design of an incredible chimeric light responsive genetic element from the Voigt lab at UCSF. Basically, Anselm Levskaya and Chris Voigt rewired a phytochrome protein from Synechocystis which changes conformation in response to light and transduces this into a change in gene expression in that organism to control an osmo-responsive genetic regulatory system in E.coli. In order to retain the functionality of the phytochrome protein, the metabolism of E.coli had to be re-engineered to produce a ringed organic compound, phycocyanobilin (PCB). This work had previously been done in the Lagarias lab at UC-Davis (Gambetta and Lagarias, PNAS, 2001). The result is a synthetic signal transduction cascade in E.coli that responds to light in the 660nm (red) range. There are many interesting applications that may be enabled by high resolution photoregulatory methods. Also, check out Nature's 2005 Year in Pictures

Real intelligent designers use evolution. Bacterial photo: Aaron Chevalier

If you'd like to take your own bacterial photographs, check out the page on how to build a light cannon.

Edge Detector

We are advancing using bacterial photography as a platform for the construction of a biological edge detector. In this system, each bacterium on the lawn senses whether it is located in the light, the dark, or at the boundary of light and dark. Those cells at boundary express a visible reporter gene, and the result is not a positive of the projected image, but the outline of the image. Edge detection is a well studied serial algorithm where computation time increases linearly with the number of pixels (approximately as the square of image size). In the massively parallel Biological edge detector, the algorithm runs in constant time regardless of image size. This bottom-up approach highlights the unique parallel information processing abilities inherent to Biological systems, a feature which is highlighted in nature in areas such as developmental biology and neural networks.

Publications

  • Jeffrey J. Tabor, Matthew Levy, Zachary B. Simpson and Andrew D. Ellington. Parasitism and protocells: The tragedy of the molecular commons. In Protocells: Bridging Nonliving and Living Matter, eds. S. Rasmussen, M.A. Bedau, L.Chen, D.Deamer, D.C. Krakauer, N. Packer and P.F. Stadler, MIT Press, 11/2008.
  • Jeffrey J. Tabor, Travis S. Bayer, Zachary B. Simpson, Matthew Levy and Andrew D. Ellington. Engineering Stochasticity in Gene Expression (2008). Molecular Biosystems, 4 (7) 754-61. pdf
  • Matthew Levy, Jeffrey J. Tabor and Stephen Wong. Taking pictures with E.coli: Signal processing using synthetic biology (2006). IEEE Signal Processing Magazine, 23 (3), 142-144. pdf
  • Jeffrey J. Tabor, Matthew Levy, and Andrew D. Ellington (2006). Deoxyribozymes that recode sequence information. Nucleic Acids Research, 34 (8):2166-2172. pdf
  • Jeffrey J. Tabor, Eric A. Davidson and Andrew D. Ellington (2006). Developing RNA tools for engineered regulatory systems. In Biotechnology and Genetic Engineering Reviews, ed. S.E. Harding, Intercept, Ltd., 22, 21-44. pdf
  • A. Levskaya, A.A. Chevalier, J.J. Tabor, Z.B. Simpson, L.A. Lavery, M.Levy, E.A. Davidson, A.Scouras, A.D. Ellington, E.M. Marcotte, and C.A. Voigt (2005). Engineering Escherichia coli to see light. Nature, 438 (7067), 441-442. pdf
  • Jeffrey J. Tabor and Andrew D. Ellington (2003). Playing to Win at DNA computation. Nature Biotechnology, 21(9):1013-5. pdf


Contact

email:
account: jeff.tabor
server: gmail.com

Shipping and mailing address:
Byer's Hall Room 409
1700 4th Street
San Francisco, CA 94158-2330

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Synthetic Biology Team Challenge

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