Jeff Tabor

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== Background ==
== Background ==
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*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.   
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*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 also 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 rational design and directed 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].   
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====Bacterial Photography====
====Bacterial Photography====
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I was involved with a group that 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].  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]
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I was involved with a group that 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.  This work was enabled by the design of a chimeric light responsive protein from the [http://www.voigtlab.ucsf.edu/ Voigt lab].  Anselm Levskaya and Chris Voigt rewired a phytochrome protein from ''Synechocystis'' which changes conformation in response to red light to control an osmo-responsive genetic regulatory system in ''E.coli''.  To retain the functionality of the phytochrome protein, the metabolism of ''E.coli'' also 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 650nm (red) range.  Also, check out Nature's [http://openwetware.org/images/9/9d/Year_in_photos_2005.pdf 2005 Year in Pictures]
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====Edge Detector====
====Edge Detector====
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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.
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We are using bacterial photography as a platform for the construction of a biological edge detector.  In this system, each bacterium on detects 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 facile parallel information processing abilities inherent to Biological systems, a feature which is taken advantage of in natural systems such as metazoan development and neural networks.
    
    
==Publications==
==Publications==

Revision as of 14:49, 4 February 2009

Contents

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.

Jtabor.jpg

Research Interests

Synthetic Biology

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

Real intelligent designers use evolution.     Bacterial photo: Aaron Chevalier
Real intelligent designers use evolution. Bacterial photo: Aaron Chevalier

Bacterial Photography

I was involved with a group that 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. This work was enabled by the design of a chimeric light responsive protein from the Voigt lab. Anselm Levskaya and Chris Voigt rewired a phytochrome protein from Synechocystis which changes conformation in response to red light to control an osmo-responsive genetic regulatory system in E.coli. To retain the functionality of the phytochrome protein, the metabolism of E.coli also 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 650nm (red) range. Also, check out Nature's 2005 Year in Pictures


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 using bacterial photography as a platform for the construction of a biological edge detector. In this system, each bacterium on detects 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 facile parallel information processing abilities inherent to Biological systems, a feature which is taken advantage of in natural systems such as metazoan development and neural networks.

Publications

  • Jeffrey J. Tabor, Eli Groban and Christopher A. Voigt. Performance Characteristics for Sensors and Circuits Used to Program E.coli. In Systems Biology and Biotechnology of E.coli, ed. S.Y.Lee, Springer (In press).
  • 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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