Detection of Specific mRNA Molecules in Hydrocarbon-Degrading Bacteria

Kim, Ju-Hyun; Lorenzo, Vı́ctor de

doi:10.1007/8623_2015_100

Cited by 1 publication

(1 citation statement)

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“…The blue‐colored cells, P. putida mt‐2 , have their chromosomal DNA stained by DAPI (4',6‐diamidino‐2‐phenylindole). Red spots from the same strain indicate mRNA signals of the TOL plasmid transcripts triggered by growth on toluene generated through in situ mRNA hybridization with fluorescent primers . In a separate set of experiments (correlation function) the green and red signals show, respectively RNA polymerase (β'‐subunit tagged with GFP) and ribosomes (L13 subunit tagged with mCherry) of P. putida KT2440.…”

Section: Methodsmentioning

confidence: 99%

CellShape: A user‐friendly image analysis tool for quantitative visualization of bacterial cell factories inside

Goñi-Moreno

Kim

2016

Biotechnology Journal

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Visualization of the intracellular constituents of individual bacteria while performing as live biocatalysts is in principle doable through more or less sophisticated fluorescence microscopy. Unfortunately, rigorous quantitation of the wealth of data embodied in the resulting images requires bioinformatic tools that are not widely extended within the community-let alone that they are often subject to licensing that impedes software reuse. In this context we have developed CellShape, a user-friendly platform for image analysis with subpixel precision and double-threshold segmentation system for quantification of fluorescent signals stemming from single-cells. CellShape is entirely coded in Python, a free, open-source programming language with widespread community support. For a developer, CellShape enhances extensibility (ease of software improvements) by acting as an interface to access and use existing Python modules; for an end-user, CellShape presents standalone executable files ready to open without installation. We have adopted this platform to analyse with an unprecedented detail the tridimensional distribution of the constituents of the gene expression flow (DNA, RNA polymerase, mRNA and ribosomal proteins) in individual cells of the industrial platform strain Pseudomonas putida KT2440. While the CellShape first release version (v0.8) is readily operational, users and/or developers are enabled to expand the platform further.

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Section: Methodsmentioning

confidence: 99%