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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The slow-scale linear noise approximation: an accurate, reduced stochastic description of biochemical networks under timescale separation conditions
TL;DR: A new general method is derived and shown to correctly describe the statistics of intrinsic noise about the macroscopic concentrations under timescale separation conditions, which is expected to be of widespread utility in studying the dynamics of large noisy reaction networks.
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Biophysical principles predict fitness landscapes of drug resistance
João V. Rodrigues,Shimon Bershtein,Annabel Li,Elena R. Lozovsky,Daniel L. Hartl,Eugene I. Shakhnovich +5 more
TL;DR: It is shown that IC50 of trimethoprim resistance of Escherichia coli can be predicted, with high accuracy, from a unique combination of molecular properties of stepwise-resistant DHFR variants, and a comprehensive quantitative genotype–phenotype map for the essential enzyme that serves as an important target of antibiotic and anticancer therapies.
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Transcription Dynamics in Living Cells
TL;DR: The techniques allowing for single-cell transcription measurements are presented, evidence from different organisms is reviewed, and how these experiments have broadened the mechanistic understanding of transcription regulation is discussed.
Journal ArticleDOI
Escherichia coli achieves faster growth by increasing catalytic and translation rates of proteins
TL;DR: Co-regulation analysis of enzymatic capacities revealed tightly coupled regulatory dependencies of protein synthesis and RNA precursor synthesis, substrate utilization, biosynthetic and energy generation pathways carrying the highest flux, which contributes to the much needed quantitative understanding of coordinated gene expression regulation and metabolic flux control.
Journal ArticleDOI
Deterministic and Stochastic Allele Specific Gene Expression in Single Mouse Blastomeres
Fuchou Tang,Catalin Barbacioru,Ellen Nordman,Siqin Bao,Caroline Lee,Xiaohui Wang,Brian B. Tuch,Edith Heard,Kaiqin Lao,M. Azim Surani +9 more
TL;DR: It is demonstrated that ASE is both deterministic and stochastic in early blastomeres, and 1,718 genes express two isoforms with different lengths of 3′UTRs, suggesting that microRNA mediated regulation of gene expression acquires increasing importance as development progresses.
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.