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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Phenotypic Heterogeneity in Bacterial Quorum Sensing Systems
Vera Bettenworth,Benedikt Steinfeld,Benedikt Steinfeld,Hilke Duin,Katrin Petersen,Wolfgang R. Streit,Ilka B. Bischofs,Ilka B. Bischofs,Anke Becker +8 more
TL;DR: Looking into potential origins of these incidences, and into how initial cell-to-cell variations might be amplified to establish distinct phenotypic heterogeneity therein, discusses potential functions heterogeneity in bacterial quorum sensing systems could serve.
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Single molecule photobleaching (SMPB) technology for counting of RNA, DNA, protein and other molecules in nanoparticles and biological complexes by TIRF instrumentation.
Hui Zhang,Peixuan Guo +1 more
TL;DR: The method described here can be applied to the single molecule counting of other molecules in other systems and the process of statistical modeling to reveal the true copy number of the biomolecules based on binomial distribution is described.
Journal ArticleDOI
Exploiting Natural Fluctuations to Identify Kinetic Mechanisms in Sparsely Characterized Systems
TL;DR: The approach is illustrated by revisiting systematic single-cell gene expression data and it is shown that the observed fluctuations contradict the assumptions made in most published models of stochastic gene expression, even when accounting for the possibility of systematic experimental artifacts.
Journal ArticleDOI
Transcription factor binding kinetics constrain noise suppression via negative feedback
TL;DR: The results demonstrate that a binding site's strength may be uncorrelated to its functional importance and that high-copy number transcription factors should bind weakly to their operators, which is observed for transcription factors in Escherichia coli.
Journal ArticleDOI
Direct comparison of small RNA and transcription factor signaling
Razika Hussein,Han N. Lim +1 more
TL;DR: The abilities of sRNAs to act on existing target mRNAs and, without needing to be first translated, have surprisingly little impact on the dynamics of synthetic circuits are shown.
References
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TL;DR: PfPMP1)与感染红细胞、树突状组胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作�ly.
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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.