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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Quantifying post-transcriptional regulation in the development of Drosophila melanogaster
Kolja Becker,Alina Bluhm,Nuria Casas-Vila,Nadja Dinges,Mario Dejung,Sergi Sayols,Clemens Kreutz,Jean-Yves Roignant,Falk Butter,Stefan Legewie +9 more
TL;DR: A systems biology framework for the identification of post-transcriptional gene regulation from large-scale, time-resolved transcriptome and proteome data is presented and basic mathematical models describing the temporal regulation of most protein-RNA pairs are presented.
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Revealing physical interaction networks from statistics of collective dynamics.
TL;DR: This work exploits changes in invariant measures, in particular distributions of sampled states of the system in response to driving signals, and uses compressed sensing to reveal physical interaction networks in complex synthetic and natural systems.
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Single-molecule enzymology à la Michaelis-Menten.
TL;DR: Both experimental and theoretical techniques that enable single‐molecule analysis are reviewed, with particular emphasis on the major developments in the field of theoretical stochastic enzyme kinetics, from its inception in the mid‐20th century to its modern‐day status.
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Combined Model of Intrinsic and Extrinsic Variability for Computational Network Design with Application to Synthetic Biology
Tina Toni,Bruce Tidor +1 more
TL;DR: It was shown that transcriptional autoregulation was more successful than post-transcriptional in suppressing variability across a wide range of intrinsic and extrinsic magnitudes and sources, and that variability in transient states did not necessarily follow the same principles as variability in the steady state.
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Experimental approaches for addressing fundamental biological questions in living, functioning cells with single molecule precision
Tchern Lenn,Mark C. Leake +1 more
TL;DR: The impact that the application of single molecule bioscience experimentation has had on the understanding of various cellular systems and processes is demonstrated, and the potential that this approach has for the future to really address very challenging and fundamental questions in the life sciences is demonstrated.
References
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疟原虫var基因转换速率变化导致抗原变异[英]/Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A
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.