Team:Caltech/Week 6

July 18

Colonies 1-6 from Gibson plates; 7 and 8 are reswabs of two colonies. From left to right: DNA ladder,(PNT001; colony 1; vector), P2v, P3v, P4v, P5v, P6v, P7v, P8v, (PNT001; colony 1; insert), P3i, P4i, P5i, P6i

from left to right: DNA ladder, (PNT001; reswab 7; insert), P8i, (16s; colony A; vector), 16Bv, 16Cv, (16s; A; insert), 16Bi, 16Ci

Colony PCR of 16s plasmids, for vector and insert
Gel of short PCR parts to confirm they are being amplified
Pulsed field gel with a larger amount of soil sample DNA
Retransform pSB3K5 into Xl-10s

Results

Gels show mostly expected single bands

July 19

PCR parts for Gibson assembly of pNT001, pNT003 and Joe's positive GFP control

Results

pSB3K5 plate had 0 colonies.
PFGE of soil-extracted DNA shows a smear; will do gel extraction of ~40kbp sequences for fosmid kit.

lane 1 lambda mono-cut ladder, 2 blank, 3 40 kb control DNA, 4 LA River sample 9, 5 LA-River sample 10

Gibson PCR concentrations

July 20

Pulse field gel of soil-extracted DNA, in preparation for fosmid insertion
PCR parts for Gibson assembly of pNT001, pNT003 and positive control
Redo Gibson assembly of pNT001 using a smaller total mass of DNA. Gibson assemble GFP from Joe that is known to have worked before as a positive control
Try transforming pSB3K5 with less DNA and as a liquid culture

Results

PCR concentrations

July 21

Gel extraction of 40kb LA River sample DNA from pulse field gel
Transform pSB3K3 into competent cells, since the pSB3K5 transform is not working

Results

Gibson Plates