Team:BU Wellesley Software/Notebook/ShannonNotebook

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Contents


WEEK 1: 6/06-6/10/2011
  • 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 were conducted.
    • The following day, transformations appeared to be contaminated. They looked significantly different than usual, but were still were used to produce overnight cultures.
    • To ensure that E.coli was present gram staining was performed. Staining showed that no E.coli was present in the cultures. Nanodrop was used to quantify the DNA from the overnight cultures.
      • The results from the Miniprep/Nanodrop varied (some overnight cultures 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.
WEEK 2: 6/13-6/17/2011
  • Overnight cultures were made from the previous week’s transformations.
    • cultures 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 several different biobrick parts).
    • Two seemed to look pinkish, especially towards the center of each colony.
    • Successful transformations were then used to produce more overnight cultures.
WEEK 3: 6/20-6/24/2011
  • Overnight cultures were made for 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 day. The following morning the transformation plates did not have any colonies on them.
  • Minipreps were conducted on 6/23/2011’s overnight cultures 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
WEEK 4: 6/27-7/01/2011
  • Overnight cultures made using the following parts: 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.
  • transformations were done using 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 overnight cultures. 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 overnight cultures that were done the previous day. 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 overnight cultures(two tubes were made for each, one went in the -90C and another in the -20 C):
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