User:Pakpoom Subsoontorn

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(Current Research Projects)
(Current Research Projects)
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** Starting in spring 2009, I started a new project in Endy's lab on how to reliably store multiple bits of information in a living cell using genetically encoded devices. I designed and computationally analyzed the performance of genetically encoded combinatorial counters as a study case for high-order genetically encoded information storage systems.  Our counters can take an input from arbitrary genetically encoded system and transition from one state to the next state depending on the number of input pulses it receives. Unlike earlier work in genetically encoded counters which can count up to only N states using N bits and which are sensitive to input pulse width, our counter designs could count up to 2^N-1 states and are predicted to operated robustly with respect to input pulse width. In addition, our counter architecture is highly modular at three functional levels: set-reset latches, toggle flip-flops and counters. A set-reset latch can be implemented from DNA Inversion controlled by bacteriosphage integrases-excisionase, two mutually inhibiting repressors, or single positively autoregulating activator. A toggle flip-flop can be implemented from two set-reset latches or a single set-reset latch and a relay unit with switching delay. A counter can be implemented as an asynchronous counter or a synchronous counter. Different designs at each level can readily be composed together into the next level devices, resulting in at least 12 possible ways to build counters. The performances for different choices of device implementations and kinetic parameters ranges are compared. I am now preparing the manuscript to publish. In addition, I am also working closely with Jerome Bonnet, a postdoctoral fellow in Endy's lab, on implementing DNA inversion-based set-reset latches in E.coli. We have demonstrated that the latches can be set, reset and hold state. We are now working on improving the reliability of the latch operation and possible ways to scale up the number of latches that can be engineered into a cell.  
** Starting in spring 2009, I started a new project in Endy's lab on how to reliably store multiple bits of information in a living cell using genetically encoded devices. I designed and computationally analyzed the performance of genetically encoded combinatorial counters as a study case for high-order genetically encoded information storage systems.  Our counters can take an input from arbitrary genetically encoded system and transition from one state to the next state depending on the number of input pulses it receives. Unlike earlier work in genetically encoded counters which can count up to only N states using N bits and which are sensitive to input pulse width, our counter designs could count up to 2^N-1 states and are predicted to operated robustly with respect to input pulse width. In addition, our counter architecture is highly modular at three functional levels: set-reset latches, toggle flip-flops and counters. A set-reset latch can be implemented from DNA Inversion controlled by bacteriosphage integrases-excisionase, two mutually inhibiting repressors, or single positively autoregulating activator. A toggle flip-flop can be implemented from two set-reset latches or a single set-reset latch and a relay unit with switching delay. A counter can be implemented as an asynchronous counter or a synchronous counter. Different designs at each level can readily be composed together into the next level devices, resulting in at least 12 possible ways to build counters. The performances for different choices of device implementations and kinetic parameters ranges are compared. I am now preparing the manuscript to publish. In addition, I am also working closely with Jerome Bonnet, a postdoctoral fellow in Endy's lab, on implementing DNA inversion-based set-reset latches in E.coli. We have demonstrated that the latches can be set, reset and hold state. We are now working on improving the reliability of the latch operation and possible ways to scale up the number of latches that can be engineered into a cell.  
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Revision as of 03:07, 11 October 2010

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Contents

Contact Info

Pakpoom Subsoontorn
Pakpoom Subsoontorn
  • Pakpoom (Ton) Subsoontorn
  • Ph.D student, Bioengineering Stanford
  • Address: 73 Barnes Apartment 106 Stanford CA 94305
  • Phone: (626)-375-2764
  • Email: tons[at]stanford.edu, pakpoomTon[at]gmail.com
  • Official Website
  • I'm on facebook and hi5, just search my full name. There is only one pakpoom subsoontorn!
  • Email me through OpenWetWare

Education

  • 2008-, MS/PhD, Bioengineering, Stanford University
  • 2004-2008, BS (Biology and Computer Science), California Institute of Technology

Research interests

Past Research Projects

  • In vitro self-activating Switch (at Winfree Lab, Caltech)
  • Single-cell studies of bacterial transcriptional regulation (at | Phillips Lab, Caltech)
  • Biophysics of bacterial cell shapes (at | Haung Lab, Stanford)
    • In fall 2008, as a rotation student, I helped prof. KC Huang set up a new at Stanford. I started pilot projects related to biophysics of bacterial cell shape. The projects include 1) using light microscope and quantitative image analysis to study how E.coli cells convert between rod shape and nearly spherical shape during the transition between exponential growth phase and stationery phase, 2) studying the mechanics of E.coli cell wall cracking induced by antibiotic vancomysin, 3) designing a microfluidic device for culturing and imaging the lineage of rod-shape bacteria.
  • Protein structural determination with mulitple FRET distance constraints (at |Quake Lab, Stanford)
    • In winter 2009, as a rotation student, I worked on project to develop a new techniques for determining protein structure by measuring intramolecular distances using FRET. The idea is to label different pairs of amino acid residues on a protein with fluorescent donor an acceptor, measure FRET efficiency and infer the distances between each pair. The measured distances will be used as constraints to reconstruct the shape of the protein

Current Research Projects

  • Designs and performance analysis of genetically encoded combinatorial counter . (at | Endy Lab, Stanford)
    • Starting in spring 2009, I started a new project in Endy's lab on how to reliably store multiple bits of information in a living cell using genetically encoded devices. I designed and computationally analyzed the performance of genetically encoded combinatorial counters as a study case for high-order genetically encoded information storage systems. Our counters can take an input from arbitrary genetically encoded system and transition from one state to the next state depending on the number of input pulses it receives. Unlike earlier work in genetically encoded counters which can count up to only N states using N bits and which are sensitive to input pulse width, our counter designs could count up to 2^N-1 states and are predicted to operated robustly with respect to input pulse width. In addition, our counter architecture is highly modular at three functional levels: set-reset latches, toggle flip-flops and counters. A set-reset latch can be implemented from DNA Inversion controlled by bacteriosphage integrases-excisionase, two mutually inhibiting repressors, or single positively autoregulating activator. A toggle flip-flop can be implemented from two set-reset latches or a single set-reset latch and a relay unit with switching delay. A counter can be implemented as an asynchronous counter or a synchronous counter. Different designs at each level can readily be composed together into the next level devices, resulting in at least 12 possible ways to build counters. The performances for different choices of device implementations and kinetic parameters ranges are compared. I am now preparing the manuscript to publish. In addition, I am also working closely with Jerome Bonnet, a postdoctoral fellow in Endy's lab, on implementing DNA inversion-based set-reset latches in E.coli. We have demonstrated that the latches can be set, reset and hold state. We are now working on improving the reliability of the latch operation and possible ways to scale up the number of latches that can be engineered into a cell.

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