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 Metabolic Profiling: Metabolite Formulas from Isotopic Fine Structures in Heterogeneous Plant Cell Populations.
Laith Z. Samarah,Rikkita Khattar,Tina H Tran,Sylwia A. Stopka,Christine A. Brantner,Paola Parlanti,Dušan Veličković,Jared B. Shaw,Beverly J. Agtuca,Gary Stacey,Ljiljana Paša-Tolić,Nikola Tolić,Christopher R. Anderton,Akos Vertes +13 more
TL;DR: The combination of fiber-based laser ablation electrospray ionization (f-LAESI) with 21 tesla Fourier transform ion cyclotron reso-nance mass spectrometry (21TFTICR-MS) for in situ single-cell metabolic profiling in plant tissue enables the simultaneous capture of isotop-ic fine structures (IFSs) for 47 known and 11 unknown compounds, thus elucidating their elemental compositions from single cells.
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Is central dogma a global property of cellular information flow
TL;DR: High-throughput mRNA and protein expression data of Escherichia coli, Saccharomyces cerevisiae, and several mammalian cells are reviewed to suggest that the organizing structure guiding cellular processes is observed at omics-wide scale, and not at single molecule level.
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Are gene loops the cause of transcriptional noise
TL;DR: It is argued that gene loops are a likely cause of transcriptional bursting and, thus, biological noise and the most recent findings related to these subjects are discussed.
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Probabilistic and Piecewise Deterministic models in Biology
Bertrand Cloez,Renaud Dessalles,Alexandre Genadot,Florent Malrieu,Aline Marguet,Romain Yvinec +5 more
TL;DR: Piecewise Deterministic Markov Processes, first introduced in the probabilistic literature by Davis (1984), are a very general class of Markov processes and are being increasingly popular in biological applications and give new interesting challenges from the theoretical point of view.
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The shape-shifting quasispecies of RNA: one sequence, many functional folds.
TL;DR: Embracing that one sequence can give rise to multiple native folds, it is hypothesize that this phenomenon imparts adaptive advantages on any functionally evolving RNA quasispecies.
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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.