Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells.
Yuichi Taniguchi,Paul J. Choi,Gene-Wei Li,Huiyi Chen,Mohan Babu,Jeremy Hearn,Andrew Emili,X. Sunney Xie +7 more
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TLDR
System-wide analyses of protein and mRNA expression in individual cells with single-molecule sensitivity using a newly constructed yellow fluorescent protein fusion library for Escherichia coli found that almost all protein number distributions can be described by the gamma distribution with two fitting parameters which, at low expression levels, have clear physical interpretations as the transcription rate and protein burst size.Abstract:
Protein and messenger RNA (mRNA) copy numbers vary from cell to cell in isogenic bacterial populations. However, these molecules often exist in low copy numbers and are difficult to detect in single cells. We carried out quantitative system-wide analyses of protein and mRNA expression in individual cells with single-molecule sensitivity using a newly constructed yellow fluorescent protein fusion library for Escherichia coli. We found that almost all protein number distributions can be described by the gamma distribution with two fitting parameters which, at low expression levels, have clear physical interpretations as the transcription rate and protein burst size. At high expression levels, the distributions are dominated by extrinsic noise. We found that a single cell's protein and mRNA copy numbers for any given gene are uncorrelated.read more
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Steady-state fluctuations of a genetic feedback loop: an exact solution.
TL;DR: In this article, an exact solution of the steady-state master equation for arbitrary values of the parameters, and simplified solutions for a number of special cases, are presented for a gene regulatory feedback loop.
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Live imaging of nascent RNA dynamics reveals distinct types of transcriptional pulse regulation
Tetsuya Muramoto,Danielle Cannon,Marek Gierlinski,Adam M. Corrigan,Geoffrey J. Barton,Jonathan R. Chubb +5 more
TL;DR: In this article, the authors compared the pulsing of five housekeeping and five developmentally induced genes by direct imaging of single gene transcriptional events in individual living Dictyostelium cells.
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Division of labor by dual feedback regulators controls JAK2/STAT5 signaling over broad ligand range
Julie Bachmann,Andreas Raue,Marcel Schilling,Martin Böhm,Clemens Kreutz,Daniel Kaschek,Hauke Busch,Norbert Gretz,Wolf D. Lehmann,Jens Timmer,Jens Timmer,Ursula Klingmüller +11 more
TL;DR: A dynamic pathway model is established to dissect the roles of the two transcriptional negative feedback regulators of the suppressor of cytokine signaling (SOCS) family, CIS and SOCS3, in JAK2/STAT5 signaling and reveals dose‐dependent feedback control as key property to regulate STAT5‐mediated survival decisions over a broad range of ligand concentrations.
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Investigating the physiology of viable but non-culturable bacteria by microfluidics and time-lapse microscopy.
Rosemary A. Bamford,Ashley Smith,Jeremy Metz,Georgina Glover,Richard W. Titball,Stefano Pagliara +5 more
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Transcriptomic responses to environmental temperature in eurythermal and stenothermal fishes
TL;DR: Comparative transcriptomics is rapidly accelerating the authors' understanding of how fish respond to thermal stress; this review summarizes and synthesizes gene expression patterns from stenothermal and eurythermal species responding to acute and long-term exposure to temperature.
References
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Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection.
Tomoya Baba,Takeshi Ara,Miki Hasegawa,Yuki Takai,Yoshiko Okumura,Miki Baba,Kirill A. Datsenko,Masaru Tomita,Barry L. Wanner,Hirotada Mori,Hirotada Mori +10 more
TL;DR: These mutants—the ‘Keio collection’—provide a new resource not only for systematic analyses of unknown gene functions and gene regulatory networks but also for genome‐wide testing of mutational effects in a common strain background, E. coli K‐12 BW25113.
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Stochastic Gene Expression in a Single Cell
TL;DR: This work constructed strains of Escherichia coli that enable detection of noise and discrimination between the two mechanisms by which it is generated and reveals how low intracellular copy numbers of molecules can fundamentally limit the precision of gene regulation.
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Global analysis of protein localization in budding yeast
Won-Ki Huh,James V. Falvo,Luke C. Gerke,Adam S. Carroll,Russell W. Howson,Jonathan S. Weissman,Erin K. O'Shea +6 more
TL;DR: The construction and analysis of a collection of yeast strains expressing full-length, chromosomally tagged green fluorescent protein fusion proteins helps reveal the logic of transcriptional co-regulation, and provides a comprehensive view of interactions within and between organelles in eukaryotic cells.
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Fabrication of microfluidic systems in poly(dimethylsiloxane)
J.C. McDonald,David C. Duffy,Janelle R. Anderson,Daniel T. Chiu,Hongkai Wu,Olivier Schueller,George M. Whitesides +6 more
TL;DR: Fabrication of microfluidic devices in poly(dimethylsiloxane) (PDMS) by soft lithography provides faster, less expensive routes to devices that handle aqueous solutions.