From OpenWetWare
Jump to navigationJump to search

<html><style type='text/css'> .tabs {

 width: 100%;
 color: #FFFFFF;
 background:#FFFFFF url("/images/5/54/DarkgreenTab-bg.gif") repeat-x bottom;


.tabs li {

 background:url("/images/3/36/DarkgeenTab-left.gif") no-repeat left top;


.tabs a,.tabs strong {

 background:url("/images/d/d3/DarkgreenTab-right.gif") no-repeat right top;
 padding: 3px 10px 3px 4px;


.tabs strong{



.tabs a:hover{




DNA Synthesis Companies

  1. Blue Heron Biotechnology, Inc.
    • Advertised as 2-4 weeks, but teams have had problems getting sequences on time in the past.
  2. Codon Devices, Inc.
  3. DNA 2.0, Inc.
  5. CODA Genomics Synthetic Expression

Add more links here. Additional information would be useful.

Important people to contact

  1. Prof. Alexander van Oudenaarden MIT
    • Emailed, we can meet up with him when he gets back from Woods Hole first week of July
    • May have many of the genes we want already on plasmids
  2. Jeffrey Chabot
    • Post Doc who wrote the PhD thesis on cyanobacteria
    • We have his email address
  3. Prof. Susan Golden Texas A&M
    • Is working on pretty much the same stuff we are looking at
    • Have emailed
    • Have talked to on phone-- see here
  4. Peter Weigele MIT
    • Post Doc who works with cyanobacteria
    • Have emailed correspondance (see Peng); can get PCC7942 strains
    • Have contacted and obtained PCC7942 and PCC6803 (a glucose-digesting strain)
  5. Prof. Andrew Knoll Harvard OEB
    • Worked with evolutionary cyanobacteria
    • Called; gave references to other experts around the area
  6. Prof. Stjepko Golubic BU
    • Prof. Knoll said he knew a lot about cyanobacteria
  7. Prof. Colleen Cavanaugh Harvard OEB
  8. Prof. Woodland Hastings Harvard OEB
    • Corresponded with a Japanese lab group which works with cyanobacteria
    • Specializes in circadian rhythms

Questions that we need to ask

  1. If we put a reporter downstream of kaiBC what happens to it
    • It oscillates in cyanobacteria, but won't in E. coli b/c transcription isn't controlled
  2. What happens when we put a plasmid in cyanobacteria? Does it replicate?
    • Only if it is based on an endogenous plasmid. Paper from 20 yrs back...
    • There are endogenous plasmids (2)
    • PCC7942 has homologous recombination
      • But we don't know if a plasmid will be maintained
      • new: hybrid plasmid possible on this paper
      • Another hybrid plasmid developed by Professor Golden in 1983: link here
  3. Do we know what the sigma factor is in Kondo et al
    • We can put in alot
  4. Possible ways for reporting if oscillation works
  5. Any other mechanisms?
  6. How bad is the codon bias problem / would we need to actually mutate parts of the genome to move to E. coli?
  7. Is there any feasible reporter we can have in E. coli?
  8. How to grow WH8102?
  9. Difference in circadian clock b/t PCC7942 and PCC6903?
  10. Growth conditions in liquid: use thiiosulfate? Hours light/dark? General streaking?
  1. Ask Professor Golden about the plasmids pAM1579 and pAM1303.