Matt Gethers/CRI, Thailand/Labwork/HmgR Binding Assay/Week of 8.3.08

=8.4.08=

To Do:
 * Photocopy the info for the HmgR Probe and the GpxR probe that arrived on Friday.
 * Add the information to their profiles on the wiki
 * Align second round of sequencing for pIs001.P1 to see if G insertion still remains when it arrives.

=8.5.08=

To Do:
 * Photocopy the info for the HmgR Probe and the GpxR probe that arrived on Friday.
 * Add the information to their profiles on the wiki
 * Align second round of sequencing for pIs001.P1 to see if G insertion still remains when it arrives.

Summary:

Sequencing came in. I wrote a script, Sequencing_flags.m, to help me with cataloging disputed bases. Will finish tomorrow.

=8.6.08=

To Do:
 * Photocopy the info for the HmgR Probe and the GpxR probe that arrived on Friday.
 * Add the information to their profiles on the wiki
 * Finish aligning second round of sequencing.

=8.7.08=

To Do:
 * Run FA on GpxR today
 * Check the concentration of probe used in FA protocol
 * Reconstitute probe primers to 100 &mu;M
 * Anneal 10 &mu;l of each primer (add 80 &mu;l water) - 100 degrees C for 5 minutes, then cool.
 * Get more GpxR from p'So
 * Get reaction buffer or protocol to make buffer from p'So.
 * Recheck concentration of GpxR aliquots with Bradford.
 * Photocopy the info for the HmgR Probe and the GpxR probe that arrived on Friday.
 * Add the information to their profiles on the wiki
 * Finish aligning second round of sequencing.

Summary:

I completed my first run of the binding assay using GpxR and both Gpx1 and HmgA promoters. Results were not too promising. Tomorrow I will try the assay with the HmgR that I have.

=8.8.08=

Summary:

I did a second run of the binding assay using the "special" HmgR that I purified. Encouraging results - will place on wiki in morning.