Team:BU Wellesley Software/Notebook/ShannonNotebook

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included a boot camp.
different topics were discussed (i.e. biobricks, gene regulation, differences between eukaryotes and prokaryotes).
boot camp also included a computer science component (focused on Clotho).
miniprepes were done on previously transformed BFP2. After minipreps, the Nanodrop was used to quantify the DNA. Minipreps did not have high DNA concentration, but were run on a gel (to show presence of DNA). Most lanes appeared empty (bands of DNA were not visible).
transformations of Pbad was conducted.
- The following day, transformations appeared to be contaminated. They looked significantly different than usual, but were still were used to produce plasmid preps.
- To ensure that E.coli was present gram staining was performed. Staining showed that no E.coli was present in the cultures. Minipreps and Nanodrop were used to quantify the DNA from the plasmid preps.
  - The results from the Miniprep/Nanodrop varied (some plasmid preps had a decent DNA concentration, others didn’t). Even though yields were not great the samples were run on a gel. However no bands were visible.

6/13/2011-6/17/2011

plasmid preps were made from the previous week’s transformations.
- this was done to improve the Nanodrop quantification values.
- plasmid preps didn’t grow properly (only UV plasmid).
an issue with the plates was discovered. All previous cultures were done on Ampicillian plates, and most were not growing well. We switched to a different antibiotic (Kanamycin) and all proceeding cultures grew well.
new Ampicillian plates were made.
a side project involved ligating GFP (Bba_J52625) and terminator (Bba_B0015) together for future use.
transformations were completed (involved transforming seven different biobrick parts).
- two seemed to look pinkish, especially towards the center of each colony.
- successful transformations were then used to produce more plasmid preps.

this week plasmid preps were done on the following: Bba_B0015.1, Bba_B0015.2, Bba_B0015.3, Bba_B0015.4, Bba_R0040.1, Bba_R0040.2, Bba_J52028.1, Bba_J52028.2, Bba_J52028.3,and Bba_J52028.4.
Nanodrop was also conducted. Chart below shows values from 6/23/2011.

Sample #	ng/uL	260/280	260/230
Bba_E0240	2.70	3.54	0.01
Bba_E0430	1.5	-32.2	0.01
Bba_B0015	4.5	2.69	0.03
Bba_I14033.1	3.7	4.41	0.02
Bba_I14033.2	6.3	1.81	0.04
Bba_I13453.1	2.3	3.71	0.01
Bba_I13453.2	1.8	29.53	0.02
Bba_I13453.3	1.9	1.93	0.01

Ligation was also performed. I tried ligating BFP (Bba_K156010) with terminator (Bba_B0015.2.2). Transformation was done of this ligation later that night. The following morning the transformation plates did not have any colonies on them.
Minipreps were conducted on 6/23/2011’s plasmid preps and Nanodrop quantification was then performed. Results are shown below in the following chart:

Sample #	ng/uL	260/280	260/230
Bba_B0015.1,	24.5	1.80	1.78
Bba_B0015.2	20.8	1.72	1.74
Bba_B0015.3	25.0	1.74	1.60
Bba_B0015.4	23.2	1.86	1.95
Bba_R0040.1	20.4	1.75	1.46
Bba_R0040.2	14.5	1.62	0.80
Bba_J52028.1	42.0	1.89	1.98
Bba_J52028.2	54.1	1.77	1.35
Bba_J52028.3	42.5	1.80	2.12
Bba_J52028.4	41.5	1.91	2.03

plasmid preps were done on the following: Bba_J23100, Bba_J23101, Bba_E0240, Bba_E0430, Bba_R2000, Bba_I13453, Bba_R4000, and Bba_I14033.
restriction digest was done on the following: Bba_R2000.1, Bba_R2000.2, Bba_R0040.1, Bba_E0240.1, Bba_E0240.2, and Bba_J52028.3.
transformation was also performed on the following ligations:
- Bba_E0240.1 + Bba_R2000.1
- Bba_E0240.1 + Bba_R2000.2
- Bba_E0240.2 + Bba_R2000.1
- Bba_R0240.2 + Bba_R2000.2
- Bba_E0240.1 + Bba_R0040.1
- Bba_E0240.2 + Bba_R0040.1
Minipreps and Nanodrop were done on the previous day’s plasmid preps. Results are shown below.

Sample #	ng/uL	260/280	260/230
Bba_I13453.1	16.8	1.9	1.98
Bba_I13453.2	17.8	2.19	1.10
Bba_R0040.1	15.4	Missing value	Missing value
Bba_R0040.2	20.1	1.58	1.61
Bba_E0240.1	27.9	1.89	1.69
Bba_E0240.2	36.2	2.07	1.85
Bba_J23100.1	49.7	Missing Value	Missing Value
Bba_J23100.2	47.8	1.95	1.86
Bba_E0430.1	22.9	1.98	1.76
Bba_E0430.2	39.4	1.90	1.80

Minipreps and Nanodrop were done on the ligations that were transformed earlier in the week. Results of Nanodrop are shown in the following chart.

Sample #	ng/uL	260/280	260/230
Bba_J23100 + Bba_I14033 2.5A	27.3	1.80	1.60
Bba_J23100 + Bba_I14033 2.5B	18.1	1.82	1.55
Bba_J23100 + Bba_I14033 2.5C	26.5	1.91	1.78
Bba_J23100 + Bba_I14033 1A	327.7	1.89	2.31
Bba_J23100 + Bba_I14033 1A (2nd try)	323.9	1.90	2.34
Bba_J23100 + Bba_I14033 1B	32.0	1.76	1.86
Bba_J23100 + Bba_I14033 5A	22.6	1.97	1.65

The 2.5A, B, and C all refer to various samples that were ligated with 2.5 uL of ligase. For example, sample 1A was ligated with 1 uL of ligase.
Glycerol stocks were also made from the following plasmid preps(two tubes were made for each, one went in the -90C and another in the -20 C):

Sample #	uL of ligase	Sample letter (A,B, or C)
row 1	row 1, cell 2	row 1, cell 3
row 2, cell 1	row 2, cell 2	row 2, cell 3
row 3, cell 1	row 3, cell 2	row 3, cell 3