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


 * Paper Research

Notes from Evening Meeting

 * 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