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TLM-Quant : an open-source pipeline for visualization and quantification of gene expression heterogeneity in growing microbial cells
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Piersma, Sjouke, Denham, Emma, Drulhe, Samuel, Tonk, Rudi H. J., Schwikowski, Benno and Dijl, Jan Maarten van (2013) TLM-Quant : an open-source pipeline for visualization and quantification of gene expression heterogeneity in growing microbial cells. PLoS One, Volume 8 (Number 7). Article number e68696. doi:10.1371/journal.pone.0068696 ISSN 1932-6203.
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WRAP_journal.pone.0068696.pdf - Published Version Available under License Creative Commons Attribution. Download (1954Kb) | Preview |
Official URL: http://dx.doi.org/10.1371/journal.pone.0068696
Abstract
Gene expression heterogeneity is a key driver for microbial adaptation to fluctuating environmental conditions, cell differentiation and the evolution of species. This phenomenon has therefore enormous implications, not only for life in general, but also for biotechnological applications where unwanted subpopulations of non-producing cells can emerge in large-scale fermentations. Only time-lapse fluorescence microscopy allows real-time measurements of gene expression heterogeneity. A major limitation in the analysis of time-lapse microscopy data is the lack of fast, cost-effective, open, simple and adaptable protocols. Here we describe TLM-Quant, a semi-automatic pipeline for the analysis of time-lapse fluorescence microscopy data that enables the user to visualize and quantify gene expression heterogeneity. Importantly, our pipeline builds on the open-source packages ImageJ and R. To validate TLM-Quant, we selected three possible scenarios, namely homogeneous expression, highly ‘noisy’ heterogeneous expression, and bistable heterogeneous expression in the Gram-positive bacterium Bacillus subtilis. This bacterium is both a paradigm for systems-level studies on gene expression and a highly appreciated biotechnological ‘cell factory’. We conclude that the temporal resolution of such analyses with TLM-Quant is only limited by the numbers of recorded images.
| Item Type: | Journal Article | ||||
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| Subjects: | Q Science > QH Natural history > QH301 Biology Q Science > QH Natural history > QH426 Genetics Q Science > QR Microbiology |
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| Divisions: | Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School > Biomedical Sciences > Microbiology & Infection Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School |
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| Library of Congress Subject Headings (LCSH): | Bacillus subtilis -- Genetics, Gene expression, Microscopy -- Technique, Bacterial genetics | ||||
| Journal or Publication Title: | PLoS One | ||||
| Publisher: | Public Library of Science | ||||
| ISSN: | 1932-6203 | ||||
| Official Date: | 2013 | ||||
| Dates: |
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| Volume: | Volume 8 | ||||
| Number: | Number 7 | ||||
| Page Range: | Article number e68696 | ||||
| DOI: | 10.1371/journal.pone.0068696 | ||||
| Status: | Peer Reviewed | ||||
| Publication Status: | Published | ||||
| Access rights to Published version: | Restricted or Subscription Access | ||||
| Date of first compliant deposit: | 26 December 2015 | ||||
| Date of first compliant Open Access: | 26 December 2015 | ||||
| Funder: | European Commission (EC), Nederlandse Organisatie voor Wetenschappelijk Onderzoek [Netherlands Organisation for Scientific Research] (NWO), Systems Biology of Microorganisms (SysMO) | ||||
| Grant number: | LSHG-CT-2006-037469, PITN-GA-2008-215524, 244093 (EC) |
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