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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Contributions of Cell Growth and Biochemical Reactions to Nongenetic Variability of Cells
Anne Schwabe,Frank J. Bruggeman +1 more
TL;DR: A widely-applicable theory on the influence of biochemical reactions and cellular growth on the phenotypic variability of growing, isogenic cells is offered and aids the design and interpretation of experiments involving single-molecule counting or real-time imaging of fluorescent reporter constructs.
Journal ArticleDOI
Mosaic patterns of B-vitamin synthesis and utilization in a natural marine microbial community.
Laura Gómez-Consarnau,Rohan Sachdeva,Scott M. Gifford,Lynda S. Cutter,Jed A. Fuhrman,Sergio A. Sañudo-Wilhelmy,Mary Ann Moran +6 more
TL;DR: The hypothesis that the mosaic of metabolic interdependencies through B-vitamin synthesis and exchange are key processes that contribute to shaping microbial communities in nature is supported.
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Automated single-molecule imaging in living cells
TL;DR: An artificial intelligence-assisted TIRF microscope with automated cell searching and focusing is presented and used for high-throughput single-molecule imaging of EGFR dynamics in response to various stimuli.
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Measuring transcription at a single gene copy reveals hidden drivers of bacterial individuality.
TL;DR: The combination of single-molecule quantification of mRNA and gene loci in single Escherichiacoli cells with mathematical models of mRNA dynamics reveals additional factors governing transcription, including contributions from the transcriptional state of another copy of the same gene present in the cell and from gene-replication events.
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mRNA modifications: Dynamic regulators of gene expression?
TL;DR: Results implicate that mRNA modifications are a powerful mechanism to post-transcriptionally regulate gene expression.
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.