Tracing E. coli Contamination in Cores

Approximately 2.8 × 10⁷ cells/ml of E. coli strain DH10B harboring a pBAD vector (Thermofisher Scientific, Canada), suspended in a total of 50 ml 1 × PBS, was sprayed from a spray bottle on the core catcher, diamond bits, and the surface of the frozen cores^{45 (link)–47 (link)}. pBAD is an expression vector that codes for the mNeonGreen protein. This vector and its product was targeted as the main contamination tracer in this study via PCR of vector sequences and macro-photography of the mNeonGreen protein fluorescence under 470 nm wavelength using a xenon arc lamp (Sutter Instruments, USA).

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Saidi-Mehrabad A., Neuberger P., Cavaco M., Froese D, & Lanoil B. (2020). Optimization of subsampling, decontamination, and DNA extraction of difficult peat and silt permafrost samples. Scientific Reports, 10, 14295.

Publication 2020

pBAD vector xenon arc lamp

Cells strain Diamond E coli Fluorescence Frozen Protein Vector Xenon

Corresponding Organization : University of Alberta

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Variable analysis

independent variables

Spray bottle used to apply E. coli strain DH10B harboring pBAD vector (Thermofisher Scientific, Canada) to the core catcher, diamond bits, and the surface of the frozen cores

dependent variables

Presence and quantification of pBAD vector sequences via PCR
Fluorescence of mNeonGreen protein under 470 nm wavelength using a xenon arc lamp (Sutter Instruments, USA)

control variables

Concentration of E. coli strain DH10B harboring pBAD vector (approximately 2.8 × 10^7 cells/ml)
Volume of 1 × PBS used to suspend the E. coli cells (50 ml)

positive controls

Not explicitly mentioned

negative controls

Not explicitly mentioned

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