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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Single-cell microscopy of suspension cultures using a microfluidics-assisted cell screening platform.
Burak Okumus,Charles James Baker,Juan Carlos Arias-Castro,Juan Carlos Arias-Castro,Ghee Chuan Lai,Emanuele Leoncini,Somenath Bakshi,Scott Luro,Dirk Landgraf,Johan Paulsson +9 more
TL;DR: A platform for microfluidics-assisted cell screening (MACS), which enables high-throughput and automated single-cell microscopy for a wide range of cell types and sizes and can be used to impart mechanical pressure for assessing the structural integrity of individual cells and their response to mechanical perturbations.
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A GFP promoter fusion library for the study of Salmonella biofilm formation and the mode of action of biofilm inhibitors.
Stijn Robijns,Stefanie Roberfroid,S Van Puyvelde,B. De Pauw,E. Uceda Santamaría,A De Weerdt,D. De Coster,Kim Hermans,S C J De Keersmaecker,Jozef Vanderleyden,Hans Steenackers +10 more
TL;DR: A GFP-promoter fusion library with 79 important Salmonella biofilm genes was developed, which is a fast, inexpensive, and easy-to-use tool, and can be conducted in different experimental setups in a time-dependent manner.
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Interindividual variation in response to xenobiotic exposure established in precision-cut human liver slices.
Marlon J. Jetten,Sandra M.H. Claessen,Cornelis H. C. Dejong,Agustín Lahoz,José V. Castell,Joost H.M. van Delft,Jos C. S. Kleinjans +6 more
TL;DR: GSTM1, known to be highly polymorphic within the human population, but so far could not be linked to toxicity in acetaminophen-poisoned patients, is suggested to cause interindividual variability in acetamophen-metabolism, dependent on the individual's gene expression-responses of CYP-enzymes.
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Protein Melting Temperature Cannot Fully Assess Whether Protein Folding Free Energy Underlies the Universal Abundance–Evolutionary Rate Correlation Seen in Proteins
TL;DR: It is found that the nontrivial relationship between Tm and ΔG and inaccuracy in Tm measurements by Leuenberger et al. 2017 can be responsible for not observing strong positive abundance-Tm and strong negative Tm-evolutionary rate correlations.
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Advancements and Potential Applications of Microfluidic Approaches—A Review
TL;DR: Various integrations of microfluidic technologies into biotechnology and its paradigmatic significance in bio-research, supporting mechanical and chemical in vitro cellular microenvironment and specific innovations related to the application ofmicrofluidics to advance microbial life, solitary and co-cultures along with a multiple-type cell culturing, cellular communications, cellular interactions, and population dynamics are discussed.
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.
Journal ArticleDOI
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.