Koeris/Notebook/2006-12-27

Strategic planning for 2007

Mike Kohanski and I talked about which experiments we were both planning to do in order to answer the most pertinent questions in the two main thrusts/focuses for the lab.

Antibiotic mechanism of killing

Mike-2 will start by focusing exclusively on the mechanism of killing until the end of February? During that time he will work on getting the ICL mutants straightened out (and other 18 mutants...), i.e. see if the results are replicable.

Persistence

Mike-3 will start after 1/13 full-time on the ChIP-chip experiment involving yneL, hipA and hipB.

Chromatin immunoprecipitation

To do for the month of January:

1. Sequence all constructs containing [his]6
2. Establish expression in E. coli
3. Verify detection in a western blot system
   1. Buy anti-[His]6 antibody (mAB) from Sigma [1] cat. no.: H1029
4. Fine-tune parameters for chromatin shearing

Microarrays

There are several microarrays that need to be run and CAN be run prior to the ChIP-chip arrays. Triplicates are not necessary as per Boris' analysis.

1. LB media baseline
2. M9 media baseline
3. The following strains:
   1. wt
   2. ΔhipBA
   3. ΔydeUΔhipBA
   4. ΔyneL
   5. wt+accC overexpression (lower priority)

For a total of at least 8 microarrays that span the space of interest for our experiments. All arrays will be run on mRNA isolated from deep-stationary cells, i.e. 16h growth post-innoculation.