IGEM:MIT/2007/Notebook/2007-6-17

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*Paper Research
*Paper Research
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===Notes from Meeting at 8 pm===
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*Attendance:  SK, LBH, FL, DL, JH, AL, TTP
 +
*Univ. Latin America -- iron biosensors?
 +
*Cadmium surrounding bacteria
 +
*Our goal: to detect and capture (stick to) metal
 +
*Find papers for...
 +
**metal-induced detector/promoter
 +
**bacteria turned on by metal?  genes turned on by metal in surroundings?
 +
**similarly, glass/plastic-induced?
 +
*See the arsenic project for planning genes
 +
**Example = lactose -- binds to molecule in cell -- prevents/enhances transcription factor
 +
*Prairie View (Texas, 2005): trimetallic sensor, bound to GFP?
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**iron promoter
 +
**see References
 +
**did they get it to work? (Yes)
 +
**use their BB part (input)
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*Note on BB Registry: green/red color coding indicates usability
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*Possible contacts (to get parts/organisms)
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**UC Santa Barbara (JH Waite -- Organic Chemistry -- Marine Biotechnology Building --http://www.chem.ucsb.edu/people/faculty/waite/index.shtml)
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**Prairie View
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**Pohang University, Korea  (will ask my dad about Korean research culture)
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*Filters: if bacteria stick to wall of filter system, clean water will result
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**What is the state of the art water filtration system?
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*Specificity: what will the bacteria bind to?
 +
**Limitations -- peptide binds to certain things; have promoters?
 +
*Find bacteria engineered to recognize multiple things?
 +
*Are sticky peptides expressed on the surface of bacteria?
 +
*Linear surface protein; N and C termini both pointing outside on E. coli [Toan]
 +
*How to ensure all metal in whatever solution (water?) is, indeed, gone?
 +
===Further Research===
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*Stickiness; Detection and Capture; How are environmental problems solved today?  Also, what is a hard-to-capture metal?
 +
*Variations on systems
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**(1) Make bacteria take in/capture metal (ingest/engulf) --> become more sticky --> sticks to surface/wall/filter wall [dead cells will not matter]
 +
**(2) Proteins are expressed outside, stick to metal, stick to each other and clump -- the bacteria are always present, but only functional when metal is present
 +
*Input: metal?  light?  should be straightforward and logical
 +
**Metal promoter in existence? (Texas)
 +
**Will metal bind DNA directly or is there a middle man?
 +
*Output: see if bacteria sticks to metal
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===To research for a group meeting on Wednesday afternoon===
 +
*LBH = filtration, biosystems and current methods (biofiltration?)
 +
*AL, TTP, AK = Prairie View references list; promoters for glass/metal; gene expressed --> protein made?; downstream pathway -- what sticks to it best/easiest?  Done before?  Can we obtain it?; iron genes
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*JH, SK = stickiness, what sticky protein can bind to; how to carry out exactly; other organisms (vs. mussel) that have sticky genes; is the sticky peptide on E. coli (Pohang papers) expressed on the surface?; will the sticky peptide on E. coli bind to metal?; how to stickify without killing cell, if possible; how to trigger stickiness; specific protein [mfp 1/5/3?]
 +
*Each subgroup will have a wiki page to post links/resources/ideas/discussion

Revision as of 00:46, 18 June 2007

  • Paper Research

Notes from Meeting at 8 pm

  • Attendance: SK, LBH, FL, DL, JH, AL, TTP
  • Univ. Latin America -- iron biosensors?
  • Cadmium surrounding bacteria
  • Our goal: to detect and capture (stick to) metal
  • Find papers for...
    • metal-induced detector/promoter
    • bacteria turned on by metal? genes turned on by metal in surroundings?
    • similarly, glass/plastic-induced?
  • See the arsenic project for planning genes
    • Example = lactose -- binds to molecule in cell -- prevents/enhances transcription factor
  • Prairie View (Texas, 2005): trimetallic sensor, bound to GFP?
    • iron promoter
    • see References
    • did they get it to work? (Yes)
    • use their BB part (input)
  • Note on BB Registry: green/red color coding indicates usability
  • Possible contacts (to get parts/organisms)
  • Filters: if bacteria stick to wall of filter system, clean water will result
    • What is the state of the art water filtration system?
  • Specificity: what will the bacteria bind to?
    • Limitations -- peptide binds to certain things; have promoters?
  • Find bacteria engineered to recognize multiple things?
  • Are sticky peptides expressed on the surface of bacteria?
  • Linear surface protein; N and C termini both pointing outside on E. coli [Toan]
  • How to ensure all metal in whatever solution (water?) is, indeed, gone?

Further Research

  • Stickiness; Detection and Capture; How are environmental problems solved today? Also, what is a hard-to-capture metal?
  • Variations on systems
    • (1) Make bacteria take in/capture metal (ingest/engulf) --> become more sticky --> sticks to surface/wall/filter wall [dead cells will not matter]
    • (2) Proteins are expressed outside, stick to metal, stick to each other and clump -- the bacteria are always present, but only functional when metal is present
  • Input: metal? light? should be straightforward and logical
    • Metal promoter in existence? (Texas)
    • Will metal bind DNA directly or is there a middle man?
  • Output: see if bacteria sticks to metal

To research for a group meeting on Wednesday afternoon

  • LBH = filtration, biosystems and current methods (biofiltration?)
  • AL, TTP, AK = Prairie View references list; promoters for glass/metal; gene expressed --> protein made?; downstream pathway -- what sticks to it best/easiest? Done before? Can we obtain it?; iron genes
  • JH, SK = stickiness, what sticky protein can bind to; how to carry out exactly; other organisms (vs. mussel) that have sticky genes; is the sticky peptide on E. coli (Pohang papers) expressed on the surface?; will the sticky peptide on E. coli bind to metal?; how to stickify without killing cell, if possible; how to trigger stickiness; specific protein [mfp 1/5/3?]
  • Each subgroup will have a wiki page to post links/resources/ideas/discussion
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