IGEM:MIT/2006/Notebook/2006-6-20

To do

1. Possibly reconsider BAMT/SAMT primers
2. Reconsider ATF1 primers definitely
3. Get in touch with GC lab
   • • • • 3 pm: Stephen has meeting --- light sensor part!

WINTERGREEN!!!!!!! (and plating)

1. The liquid cultures from yesterday SMELLED LIKE WINTERGREEN!! SO EXCITING!!!! YAY!
2. The SAMT+SA and the BSMT+SA worked, in both LB and minimal media
   • Now it's time to optimize SA concentration :)
3. Plated liquid cultures onto M9 with 50, 100, 200 μL SA
   • 2 sets of 4 (BSMT M9, BSMT LB, SAMT M9, SAMT LB) with one set of 3 missing BSMT M9

Indole

1. Indole from [[../2006-6-19 |6-19-2006]] definitely was root of bad bacterial smell.

Repeat Smell Experiment

Control	BAMT/BA	SAMT/SA	BSMT/BA	BSMT/SA
10mL LB + 20μL BL21 cells + 8.2μL BA [in a tube]	10mL LB Kan + 20μL BAMT cells + 8.2μL BA [in a tube]	10mL LB Kan + 20μL SAMT cells + 6.2μL SA [in a tube]	10mL LB Kan + 20μL BSMT cells + 8.2μL BA [in a tube]	10mL LB Kan + 20μL BSMT cells + 6.2μL SA [in a tube]
10mL minimal media + 20μL BL21 cells + 8.2μL BA [in a tube]	10mL minimal media Kan + 20μL BAMT cells + 8.2μL BA [in a tube]	10mL minimal media Kan + 20μL SAMT cells + 6.2μL SA [in a tube]	10mL minimal media Kan + 20μL BSMT cells + 8.2μL BA [in a tube]	10mL minimal media Kan + 20μL BSMT cells + 6.2μL SA [in a tube]

Repeat BAMT/SAMT PCR and run PCR products on gels

1. 16 sample tubes, 6 controls (8, 3 of each)
   • (-): no template- just primers, (-): no primer- just plasmid, (+): new primer/template
2. Sample master mix 18x, control master mix 10x, [[../2006-6-15 | from here]]
3. Temperature gradient from 42-54

Repeat ATF1 PCR at higher temperature range

1. try 48 to 64 degrees
2. place most of tubes in center of PCR machine

BSMT PCR cleanup and digest

1. cut with ECOR1 and PST1