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

• 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)
  • UC Santa Barbara (JH Waite -- Organic Chemistry -- Marine Biotechnology Building --http://www.chem.ucsb.edu/people/faculty/waite/index.shtml)
  • Prairie View
  • Pohang University, Korea (will ask my dad about Korean research culture)
• 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