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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Effects of σ factor competition are promoter initiation kinetics dependent.
TL;DR: A promoter's responsiveness to indirect regulation by σ factor competition is determined by the sequence-dependent kinetics of the rate limiting steps of transcription initiation, and it is concluded that, in E. coli, the smaller is the time-scale of the closed complex formation relative to the open complex formation, the weaker is a promoters' responsiveness to changes in σ(38) numbers.
Journal ArticleDOI
Bacterial responses to antibiotics and their combinations.
Karin Mitosch,Tobias Bollenbach +1 more
TL;DR: Recent progress in the understanding of bacterial responses to antibiotics and their combinations is reviewed, focusing on effects at the levels of growth rate and gene expression.
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Quantification of very low-abundant proteins in bacteria using the HaloTag and epi-fluorescence microscopy
Alessia Lepore,Hannah Taylor,Dirk Landgraf,Burak Okumus,Sebastián Jaramillo-Riveri,Lorna McLaren,Somenath Bakshi,Somenath Bakshi,Johan Paulsson,Meriem El Karoui,Meriem El Karoui +10 more
TL;DR: The use of the self-labelling protein tag called HaloTag, in conjunction with an organic fluorescent dye, to label and accurately count endogenous proteins present in very low numbers (<7) in individual Escherichia coli cells is characterized.
Journal ArticleDOI
Method for physiologic phenotype characterization at the single-cell level in non-interacting and interacting cells.
Laimonas Kelbauskas,S.P. Ashili,Jeff Houkal,Dean Smith,Aida Mohammadreza,Kristen Lee,Jessica Forrester,Ashok Kumar,Yasser H. Anis,Thomas G. Paulson,Cody Youngbull,Yanqing Tian,Mark R. Holl,Roger H. Johnson,Deirdre R. Meldrum +14 more
TL;DR: A measurement platform that features the capability to quantify oxygen consumption rates of individual, non-interacting and interacting cells under normoxic and hypoxic conditions is presented and the effects of cell-to-cell interactions by using the system's capability to isolate two and three cells in a single well are measured.
Journal ArticleDOI
Kinetic Foundation of the Zero-Inflated Negative Binomial Model for Single-Cell RNA Sequencing Data
TL;DR: Single-cell RNA sequencing data have complex features such as dropout events, overdispersion, and high-magnitude outliers, resulting in complicated probability distributions of mRNA abundances that...
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.
Journal ArticleDOI
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.
Journal ArticleDOI
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.