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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Ubiquitin-mediated control of plant hormone signaling.
Dior R. Kelley,Mark Estelle +1 more
TL;DR: The ubiquitin-proteasome system plays a role in nearly every aspect of plant biology and rivals the well-studied area of transcriptional regulation for importance in cellular regulation.
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Promoter sequence determines the relationship between expression level and noise
Lucas B. Carey,David van Dijk,David van Dijk,Peter M. A. Sloot,Peter M. A. Sloot,Jaap A. Kaandorp,Eran Segal +6 more
TL;DR: A single transcription factor can activate or repress expression by three different mechanisms: one that increases cell-to-cell variability in target gene expression (noise) and two that decrease noise.
Journal ArticleDOI
Mapping the environmental fitness landscape of a synthetic gene circuit
TL;DR: It is found that knowing the fitness and nongenetic memory associated with specific gene expression states were necessary for predicting the overall fitness of cell populations in combined environments, and may have important implications for phenotypic variability of drug resistance in natural settings.
Journal ArticleDOI
Measurements of translation initiation from all 64 codons in E. coli
Ariel Hecht,Ariel Hecht,Jeff E. Glasgow,Jeff E. Glasgow,Paul R. Jaschke,Paul R. Jaschke,Lukmaan A. Bawazer,Lukmaan A. Bawazer,Matthew S. Munson,Matthew S. Munson,Jennifer R. Cochran,Drew Endy,Marc L. Salit,Marc L. Salit +13 more
TL;DR: In this article, the authors quantified translation initiation of green fluorescent protein and nanoluciferase in E. coli from all 64 triplet codons and across a range of DNA copy number.
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Single cell-resolution western blotting
TL;DR: This protocol describes how to perform western blotting on individual cells to measure cell-to-cell variation in protein expression levels and protein state and describes an optional gel de-cross-linking protocol for more effective introduction of antibodies into the gel layer.
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.