Team:Edinburgh/Notebook

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Lab Book Day1 19.6.12

Experiment 1: Gel analysis of Magic Dust (fluorescent fusion proteins, project unrelated to iGEM 2012)

Agarose gel was prepared following OpenWetWare AGE protocol by Dr Chris French. Prepared TAE buffer was of 1x strength (as suggested by protocol) rather than 0,5x strength commonly used in the lab; further preparations should use 0,5x strength buffer in order to allow electrophoresis at higher speed. 2 ul of AGE buffer were added to samples 1E,2E,3E,4E and E (10 ul each). The samples were briefly centrifuged (short pulse spin at max speed) in order to mix the content. The samples were then loaded on the gel along with molecular marker and electrophoresis was performed at 100V and 50mA for 30 minutes. Following the electrophoresis, the gel was incubated with SYBR-green stain for 30 minutes. Following the incubation, gel was visualised with blue light. Gel was then destained in order to obtain high quality photo with results that will be posted along with this report at later date.

Experiment 2: Transformation of competent cells and sugar degradation selective marker test

a) Agar plates preparation At first M9 base agar was prepared by adding 250 ul of trace elements (buffer with Mg and Ca ions) to molten agar (containing phosphate buffer and NH4Cl as nitrogen source). The base agar was then poured into petri dishes to form 12 plates labelled iGEM 19.6.12 M9 base. 6 of these plates were taken for further use and the rest was sealed using parafilm. Following plates were prepared: 2 NO SUGAR plates - control with no sugars, 2 GLUCOSE plates - plates with 200 mg glucose solubilised in water, 2 SUCROSE plates - 200 mg sucrose solubilised in water, 2 CML plates - with chloramphenicol and 2 XGAL plates for white-blue selection.

b) Competent cells transformation Samples J7 and J9 (with competent cells prepared on 18.6.12) were takend from the freezer and transfered to ice water to thaw. 15 ul DNA sample were added to sample J9 100 ul of J7 sample were taken into a fresh tube marker control cell 5 ul of LIGN DNA were added to remaining 100 ul of J7 sample. following 30 minutes ice incubation all three tubes were subjected to heat shock by 90 seconds water bath at 40 degrees C. Following the heat shock, cells were returned to ice for 90 seconds and then incubated in order to let them express resistance to chloramphenicol. It was noted that with non-antibiotic resistance selection, this incubation step will no longer be necessary, expediting the process. After incubation, LB (from 18.6.12) was added to all three samples to reach 1ml volume.

c) Plating of transformed cells The samples were plated as follows (using spreader sterilised with alcohol): 100 ul of J9 was plated on plates NO SUGAR DNA+, SUCROSE DNA+, GLUCOSE DNA+ and CML DNA+; 100 ul of control cell sample was plated on plates NO SUGAR NO DNA, SUCROSE NO DNA, GLUCOSE NO DNA and CML NO DNA; 100 ul of J7 was plated on first XGAL plate, then the rest of J7 was centrifuged; the pellet was resuspended in 100 ul LB and plated on second XGAL plate. The plates were left overnight for incubation.

Lab Book Day2 20.6.12

1) Results from day1 - experiment 2

CML plate with transformed cells ( +DNA sample) resulted in multiple colonies while CML plate with control cells ( NO DNA sample) didnt result in growth, indicating that the cells used for experiment are competent and readily transform. GLUCOSE plates (both +DNA and NO DNA) showed little growth while SUCROSE and NO SUGAR plates resulted in no growth. Plates were returned for further incubation. Lack of growth may be attributed to low metabolic rate with single sugars as sole carbon source.

2) Shewanella oneidensis MR-1 cell revival

A sample of S. oneidensis MR-1 culture was plated on nutrient agar and incubated at room temperature in order to revive the cells and examine whether the culture is still viable.

3) Magic Dust (fluorescent fusion protein, project unrelated to iGEM 2012) plasmid DNA preparation

Plasmid DNA minipreps were prepared following OpenWetWare minipreps1 protocol by Dr Chris French.