IGEM:MIT/2006/Notebook/2006-8-2

to do

 * 1) LC B0030
 * 2) LC R0040
 * 3) LC B0015
 * 4) LC ATF1.B0015 variants
 * 5) LC R0040.E0840


 * 1) analyze 42 sequence results using prepared contigs in VectorNTI -'''done. unfortunately our analysis shows that nothing seems to have inserted. Perhaps digests are not being run long enough? also, pchBA mutagenesis was unsuccessful.
 * 2) start isoamyl alcohol generating device work
 * 3) *PCR BAT2 and THI3 again to get higher DNA concentrations for digesting/ligating on 8/3 -done
 * 4) (3 pm) meeting with advisors -done
 * 5) run gel of PCR products/PCR cleanup and nanodrop BAT2 and THI3
 * 6) colony PCRs -done
 * 7) make liquid cultures from each potentially useful transformant plate and glycerol stocks for assembly on 8/3

meeting topics

 * 1) troubleshoot pchBA primers
 * 2) troubleshoot pchBA mutagenesis
 * 3) troubleshoot digests/failed assemblies
 * 4) timeline of assembly work (best case scenario)

liquid cultures from potentially useful plates

 * 1) 7/31 plates: 4, 5, 6, 7, 8
 * 2) *4/5/6/7 = maybe ATF1mut-Term (colony PCR to check first)
 * 3) *8 = maybe ROO40-E0840
 * 4) 8/1 plates: 7, 8, 9
 * 5) *7/8/9 = maybe ATF1mut-Term (colony PCR to check first)

primers

 * 1) design/order THI3 mutagenesis primers
 * 2) order new (add 2 more annealing bases) pchA reverse primer

team meeting: assembly plan

 * 1) current status of parts:
 * 2) *WGGD: BSMT+Terminator
 * 3) *SAGD: still trying to PCR pchBA
 * 4) *BSGD: (?) ATF1mut+Term (?)
 * 5) *IAGD: PCRed both coding regions
 * 6) *osmY: pcr product