User:Pakpoom Subsoontorn

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(Past Research Projects)
(Past Research Projects)
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* '''''In vitro'' self-activating Switch''' (at [http://dna.caltech.edu/| Winfree Lab], Caltech)
* '''''In vitro'' self-activating Switch''' (at [http://dna.caltech.edu/| Winfree Lab], Caltech)
** From winter 2004 to summer 2006, I was working as an undergraduate researcher at Winfree's lab on developing new functional modules for ''in vitro'' transcirptional networks. ''In vitro'' transcriptional switches were originally developed by Jongmin Kim, a former graduate student in Winfree lab, as a stripped-down version of genetic switches in the cell. A switch consists of only DNA template, RNA polymerase and RNase. Signals are carried by the concentrations of specific RNA transcripts. RNA transcript from one switch can be used to regulate the production of RNA transcript from another switch, allowing us to build up a complex regulatory network from collections of simple switches. The original version of ''in vitro'' transcriptional switches can only be negatively regulated by RNA transcript. My contribution was to design and characterize a new version of switches which can be positively regulated. I have shown that a simple bistable bistable can be implemented using a single transcriptional switch positively regulated itself. The switch was also later used by Jongmin to construct the first ''in vitro'' transcriptional oscillator. We are now preparing the manuscript for publication.   
** From winter 2004 to summer 2006, I was working as an undergraduate researcher at Winfree's lab on developing new functional modules for ''in vitro'' transcirptional networks. ''In vitro'' transcriptional switches were originally developed by Jongmin Kim, a former graduate student in Winfree lab, as a stripped-down version of genetic switches in the cell. A switch consists of only DNA template, RNA polymerase and RNase. Signals are carried by the concentrations of specific RNA transcripts. RNA transcript from one switch can be used to regulate the production of RNA transcript from another switch, allowing us to build up a complex regulatory network from collections of simple switches. The original version of ''in vitro'' transcriptional switches can only be negatively regulated by RNA transcript. My contribution was to design and characterize a new version of switches which can be positively regulated. I have shown that a simple bistable bistable can be implemented using a single transcriptional switch positively regulated itself. The switch was also later used by Jongmin to construct the first ''in vitro'' transcriptional oscillator. We are now preparing the manuscript for publication.   
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* '''Single-cell studies of bacterial transcriptional regulation''' (at [http://www.rpgroup.caltech.edu/ | Phillips Lab], Caltech)
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* '''Single-cell studies of bacterial transcriptional regulation''' (at [http://www.rpgroup.caltech.edu/| Phillips Lab], Caltech)
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** From winter 2007 to spring 2008, I was working as an undergraduate researcher at Phillips lab on the analysis of transcriptional regulation at single cell level. In winter and spring 2007, I designed and tested microfluidic device for high throughput single cell microscope imaging. In summer 2007, I developed a plug-in for image-based autofocus using [http://www.micro-manager.org/ |<math>\mu</math>Manager] software as part to the tool for automated microscopy. From summer 2007 to spring 2008, as part of my senior thesis, I constructed synthetic gene circuits that allow the calibration for the absolute concentration of transcription factor in a single bacterial cell (based on system developed by Rosenfeld et. al. 2005). In parallel, I worked in collaboration with [http://www.vision.caltech.edu/ | prof. Pietro Perona] on developing software from automated analysis of fluorescence microscopy images to be used for my data analysis. This project is still an on-going research at Phillips lab after I left Caltech.     
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** From winter 2007 to spring 2008, I was working as an undergraduate researcher at Phillips lab on the analysis of transcriptional regulation at single cell level. In winter and spring 2007, I designed and tested microfluidic device for high throughput single cell microscope imaging. In summer 2007, I developed a plug-in for image-based autofocus using [http://www.micro-manager.org/| <math>\mu</math>Manager] software as part to the tool for automated microscopy. From summer 2007 to spring 2008, as part of my senior thesis, I constructed synthetic gene circuits that allow the calibration for the absolute concentration of transcription factor in a single bacterial cell (based on system developed by Rosenfeld et. al. 2005). In parallel, I worked in collaboration with [http://www.vision.caltech.edu/| prof. Pietro Perona] on developing software from automated analysis of fluorescence microscopy images to be used for my data analysis. This project is still an on-going research at Phillips lab after I left Caltech.     
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* '''Biophysics of bacterial cell shapes''' (at [http://whatislife.stanford.edu/Homepage/LoCo.html | Haung Lab], Stanford)
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* '''Biophysics of bacterial cell shapes''' (at [http://whatislife.stanford.edu/Homepage/LoCo.html| 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.  
**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.  
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* '''Protein structural determination with mulitple FRET distance constraints''' (at [http://thebigone.stanford.edu/ |Quake Lab], Stanford)
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* '''Protein structural determination with mulitple FRET distance constraints''' (at [http://thebigone.stanford.edu/| 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
**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

Revision as of 09:57, 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)
    • From winter 2004 to summer 2006, I was working as an undergraduate researcher at Winfree's lab on developing new functional modules for in vitro transcirptional networks. In vitro transcriptional switches were originally developed by Jongmin Kim, a former graduate student in Winfree lab, as a stripped-down version of genetic switches in the cell. A switch consists of only DNA template, RNA polymerase and RNase. Signals are carried by the concentrations of specific RNA transcripts. RNA transcript from one switch can be used to regulate the production of RNA transcript from another switch, allowing us to build up a complex regulatory network from collections of simple switches. The original version of in vitro transcriptional switches can only be negatively regulated by RNA transcript. My contribution was to design and characterize a new version of switches which can be positively regulated. I have shown that a simple bistable bistable can be implemented using a single transcriptional switch positively regulated itself. The switch was also later used by Jongmin to construct the first in vitro transcriptional oscillator. We are now preparing the manuscript for publication.
  • Single-cell studies of bacterial transcriptional regulation (at Phillips Lab, Caltech)
    • From winter 2007 to spring 2008, I was working as an undergraduate researcher at Phillips lab on the analysis of transcriptional regulation at single cell level. In winter and spring 2007, I designed and tested microfluidic device for high throughput single cell microscope imaging. In summer 2007, I developed a plug-in for image-based autofocus using μManager software as part to the tool for automated microscopy. From summer 2007 to spring 2008, as part of my senior thesis, I constructed synthetic gene circuits that allow the calibration for the absolute concentration of transcription factor in a single bacterial cell (based on system developed by Rosenfeld et. al. 2005). In parallel, I worked in collaboration with prof. Pietro Perona on developing software from automated analysis of fluorescence microscopy images to be used for my data analysis. This project is still an on-going research at Phillips lab after I left 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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