User:Aram Kang/Notebook/Analysis of biofilm gene expression

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(Project Description/Abstract)
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==Project Description/Abstract==
==Project Description/Abstract==
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* Place short description of project or notes regarding this project
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* Purpose: Studies of gene expression in E. coli biofilms: Comparison of two population living in a heterogeneous environment using FACS
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* Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Donec porta commodo tellus. Nam a est eget libero mollis tincidunt. Aliquam purus. Quisque nulla ligula, facilisis in, pulvinar sed, molestie a, quam. Vestibulum at pede. In in sem eget odio eleifend placerat. Phasellus ultricies felis quis sapien. Etiam molestie volutpat quam. Praesent pulvinar scelerisque mi. Nam mi urna, fringilla eu, mattis sed, venenatis id, nunc. Maecenas velit eros, congue ut, placerat in, ornare vel, sem. Aenean porta enim sit amet felis gravida posuere. Phasellus faucibus nibh et orci.
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* Assumptions and underlying hypothesis
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** An oxygen gradient in chemically heterogeneous biofilm may affect cells’ gene expression profiles
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** Maturation of GFP needs oxygen molecule, so if one cell has fluorescence intensity we can assume this cell has lived in aerobic environment and thus access to oxygen (even including microaerobic environments).
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** Sorting according to microbial individual cells’ accessibility to oxygen molecule and                              diffusion of oxygen molecules into cells
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** Maybe not related to aerobic/anaerobic metabolic status
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** oxygen can penetrate only 1/3 depth of colony biofilm, about 50µm of 150 µm (Werner, Roe et al. 2004), but most of them are viable cells and only 10.1% are dead cells(Rani, Pitts et al. 2007)
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** Then how about 50% of cells? Under Anaerobic metabolism or like persister cells?
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** And how does phenomenon related with the dispersion mechanism and quorum sensing?
==Notes==
==Notes==

Revision as of 04:09, 25 December 2008

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Project Description/Abstract

  • Purpose: Studies of gene expression in E. coli biofilms: Comparison of two population living in a heterogeneous environment using FACS
  • Assumptions and underlying hypothesis
    • An oxygen gradient in chemically heterogeneous biofilm may affect cells’ gene expression profiles
    • Maturation of GFP needs oxygen molecule, so if one cell has fluorescence intensity we can assume this cell has lived in aerobic environment and thus access to oxygen (even including microaerobic environments).
    • Sorting according to microbial individual cells’ accessibility to oxygen molecule and diffusion of oxygen molecules into cells
    • Maybe not related to aerobic/anaerobic metabolic status
    • oxygen can penetrate only 1/3 depth of colony biofilm, about 50µm of 150 µm (Werner, Roe et al. 2004), but most of them are viable cells and only 10.1% are dead cells(Rani, Pitts et al. 2007)
    • Then how about 50% of cells? Under Anaerobic metabolism or like persister cells?
    • And how does phenomenon related with the dispersion mechanism and quorum sensing?

Notes

  • Now I am doing preparation of E.coli W3110 pNgFP


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