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  • 1
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    Systematic measurement of TF-DNA interactions [Systems Biology] (2013)
    National Academy of Sciences
    Details
    Publication Date: 2013-02-27
    Description: Regulation of gene expression involves the orchestrated interaction of a large number of proteins with transcriptional regulatory elements in the context of chromatin. Our understanding of gene regulation is limited by the lack of a protein measurement technology that can systematically detect and quantify the ensemble of proteins associated with...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 2
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    Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-07-31
    Description: 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.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2922915/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2922915/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Taniguchi, Yuichi -- Choi, Paul J -- Li, Gene-Wei -- Chen, Huiyi -- Babu, Mohan -- Hearn, Jeremy -- Emili, Andrew -- Xie, X Sunney -- DP1 OD000277/OD/NIH HHS/ -- DP1 OD000277-03/OD/NIH HHS/ -- DP1 OD000277-04/OD/NIH HHS/ -- DP1 OD000277-05/OD/NIH HHS/ -- MOP-77639/Canadian Institutes of Health Research/Canada -- New York, N.Y. -- Science. 2010 Jul 30;329(5991):533-8. doi: 10.1126/science.1188308.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20671182" target="_blank"〉PubMed〈/a〉
    Keywords: Escherichia coli/chemistry/*genetics/metabolism ; Escherichia coli Proteins/*analysis/metabolism ; *Gene Expression ; *Gene Expression Profiling ; Gene Library ; In Situ Hybridization, Fluorescence ; Luminescent Proteins ; Microfluidic Analytical Techniques ; Microscopy, Fluorescence ; Protein Biosynthesis ; Proteome/*analysis ; RNA Stability ; RNA, Bacterial/analysis/genetics/metabolism ; RNA, Messenger/*analysis/genetics ; Saccharomyces cerevisiae/chemistry/genetics/metabolism ; Transcription, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    Chromosome organization by a nucleoid-associated protein in live bacteria (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-09-10
    Description: Bacterial chromosomes are confined in submicrometer-sized nucleoids. Chromosome organization is facilitated by nucleoid-associated proteins (NAPs), but the mechanisms of action remain elusive. In this work, we used super-resolution fluorescence microscopy, in combination with a chromosome-conformation capture assay, to study the distributions of major NAPs in live Escherichia coli cells. Four NAPs--HU, Fis, IHF, and StpA--were largely scattered throughout the nucleoid. In contrast, H-NS, a global transcriptional silencer, formed two compact clusters per chromosome, driven by oligomerization of DNA-bound H-NS through interactions mediated by the amino-terminal domain of the protein. H-NS sequestered the regulated operons into these clusters and juxtaposed numerous DNA segments broadly distributed throughout the chromosome. Deleting H-NS led to substantial chromosome reorganization. These observations demonstrate that H-NS plays a key role in global chromosome organization in bacteria.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3329943/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3329943/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, Wenqin -- Li, Gene-Wei -- Chen, Chongyi -- Xie, X Sunney -- Zhuang, Xiaowei -- GM 096450/GM/NIGMS NIH HHS/ -- R01 GM096450/GM/NIGMS NIH HHS/ -- R01 GM096450-03/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Sep 9;333(6048):1445-9. doi: 10.1126/science.1204697.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physics, Harvard University, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21903814" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Cell Division ; Chromosomes, Bacterial/*metabolism/*ultrastructure ; DNA, Bacterial/chemistry/*metabolism ; DNA-Binding Proteins/metabolism ; Escherichia coli K12/genetics/metabolism/*ultrastructure ; Escherichia coli Proteins/chemistry/genetics/*metabolism ; Factor For Inversion Stimulation Protein/metabolism ; Fimbriae Proteins/chemistry/genetics/*metabolism ; Gene Expression Regulation, Bacterial ; Genetic Loci ; Genome, Bacterial ; Integration Host Factors/metabolism ; Molecular Chaperones/metabolism ; Nucleic Acid Conformation ; Operon ; Protein Multimerization ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/metabolism ; Repressor Proteins/chemistry/genetics/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 4
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    The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria (2012)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2012-03-30
    Description: Protein synthesis by ribosomes takes place on a linear substrate but at non-uniform speeds. Transient pausing of ribosomes can affect a variety of co-translational processes, including protein targeting and folding. These pauses are influenced by the sequence of the messenger RNA. Thus, redundancy in the genetic code allows the same protein to be translated at different rates. However, our knowledge of both the position and the mechanism of translational pausing in vivo is highly limited. Here we present a genome-wide analysis of translational pausing in bacteria by ribosome profiling--deep sequencing of ribosome-protected mRNA fragments. This approach enables the high-resolution measurement of ribosome density profiles along most transcripts at unperturbed, endogenous expression levels. Unexpectedly, we found that codons decoded by rare transfer RNAs do not lead to slow translation under nutrient-rich conditions. Instead, Shine-Dalgarno-(SD)-like features within coding sequences cause pervasive translational pausing. Using an orthogonal ribosome possessing an altered anti-SD sequence, we show that pausing is due to hybridization between the mRNA and 16S ribosomal RNA of the translating ribosome. In protein-coding sequences, internal SD sequences are disfavoured, which leads to biased usage, avoiding codons and codon pairs that resemble canonical SD sites. Our results indicate that internal SD-like sequences are a major determinant of translation rates and a global driving force for the coding of bacterial genomes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3338875/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3338875/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Li, Gene-Wei -- Oh, Eugene -- Weissman, Jonathan S -- Howard Hughes Medical Institute/ -- England -- Nature. 2012 Mar 28;484(7395):538-41. doi: 10.1038/nature10965.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, California 94158, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22456704" target="_blank"〉PubMed〈/a〉
    Keywords: Bacillus subtilis/*genetics ; Base Sequence ; Codon/*genetics/metabolism ; Escherichia coli/*genetics ; Genome, Bacterial/genetics ; Models, Genetic ; Peptide Chain Termination, Translational/genetics ; Protein Biosynthesis/*genetics ; RNA, Bacterial/genetics/metabolism ; RNA, Ribosomal, 16S/genetics/metabolism ; Ribosomes/*metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 5
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    Central dogma at the single-molecule level in living cells (2011)
    Nature Publishing Group (NPG)
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    Publication Date: 2011-07-22
    Description: Gene expression originates from individual DNA molecules within living cells. Like many single-molecule processes, gene expression and regulation are stochastic, that is, sporadic in time. This leads to heterogeneity in the messenger-RNA and protein copy numbers in a population of cells with identical genomes. With advanced single-cell fluorescence microscopy, it is now possible to quantify transcriptomes and proteomes with single-molecule sensitivity. Dynamic processes such as transcription-factor binding, transcription and translation can be monitored in real time, providing quantitative descriptions of the central dogma of molecular biology and the demonstration that a stochastic single-molecule event can determine the phenotype of a cell.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3600414/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3600414/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Li, Gene-Wei -- Xie, X Sunney -- DP1 OD000277/OD/NIH HHS/ -- England -- Nature. 2011 Jul 20;475(7356):308-15. doi: 10.1038/nature10315.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21776076" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Survival ; Cells/*metabolism ; Gene Expression Profiling ; Gene Expression Regulation ; Humans ; Molecular Imaging/*methods ; Transcription Factors/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 6
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    Probing transcription factor dynamics at the single-molecule level in a living cell (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-05-26
    Description: Transcription factors regulate gene expression through their binding to DNA. In a living Escherichia coli cell, we directly observed specific binding of a lac repressor, labeled with a fluorescent protein, to a chromosomal lac operator. Using single-molecule detection techniques, we measured the kinetics of binding and dissociation of the repressor in response to metabolic signals. Furthermore, we characterized the nonspecific binding to DNA, one-dimensional (1D) diffusion along DNA segments, and 3D translocation among segments through cytoplasm at the single-molecule level. In searching for the operator, a lac repressor spends approximately 90% of time nonspecifically bound to and diffusing along DNA with a residence time of 〈5 milliseconds. The methods and findings can be generalized to other nucleic acid binding proteins.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2853898/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2853898/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Elf, Johan -- Li, Gene-Wei -- Xie, X Sunney -- DP1 OD000277/OD/NIH HHS/ -- DP1 OD000277-02/OD/NIH HHS/ -- New York, N.Y. -- Science. 2007 May 25;316(5828):1191-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17525339" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/genetics/*metabolism ; DNA, Bacterial/*metabolism ; Diffusion ; Escherichia coli/*genetics ; Escherichia coli Proteins/*metabolism ; Kinetics ; *Lac Operon ; Lac Repressors ; Luminescent Proteins/genetics/metabolism ; Microscopy, Fluorescence ; Operator Regions, Genetic ; Protein Binding ; Repressor Proteins/*metabolism ; Signal Transduction
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 7
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    Adeno-associated viral transfer of opioid receptor gene to primary sensory neurons: A strategy to increase opioid antinociception (2003)
    National Academy of Sciences
    Details
    Publication Date: 2003-04-28
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 8
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    Measurement of Charged-Particle Stopping in Warm Dense Plasma (2015)
    American Physical Society (APS)
    Details
    Publication Date: 2015-05-29
    Description: Author(s): A. B. Zylstra, J. A. Frenje, P. E. Grabowski, C. K. Li, G. W. Collins, P. Fitzsimmons, S. Glenzer, F. Graziani, S. B. Hansen, S. X. Hu, M. Gatu Johnson, P. Keiter, H. Reynolds, J. R. Rygg, F. H. Séguin, and R. D. Petrasso Charged particle energy loss and stopping power in warm dense matter (a moderately-coupled plasma at high density and moderate temperature) have been measured at the percent level by the OMEGA laser facility. [Phys. Rev. Lett. 114, 215002] Published Wed May 27, 2015
    Keywords: Plasma and Beam Physics
    Print ISSN: 0031-9007
    Electronic ISSN: 1079-7114
    Topics: Physics
    Published by American Physical Society (APS)
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  • 9
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    rRNA:mRNA pairing alters the length and the symmetry of mRNA-protected fragments in ribosome profiling experiments (2013)
    Oxford University Press
    Details
    Publication Date: 2013-06-06
    Description: Motivation: Ribosome profiling is a new technique that allows monitoring locations of translating ribosomes on mRNA at a whole transcriptome level. A recent ribosome profiling study demonstrated that internal Shine–Dalgarno (SD) sequences have a major global effect on translation rates in bacteria: ribosomes pause at SD sites in mRNA. Therefore, it is important to understand how SD sites effect mRNA movement through the ribosome and generation of ribosome footprints. Results: Here, we provide evidence that in addition to pausing effect, internal SD sequences induce a caterpillar-like movement of mRNA through the ribosome cavity. Once an SD site binds to the ribosome, it remains attached to it while the ribosome decodes a few subsequent codons. This leads to asymmetric progressive elongation of ribosome footprints at the 3'-end. It is likely that internal SD sequences induce a pause not on a single, but on several adjacent codons. This finding is important for our understanding of mRNA movement through the ribosome and also should facilitate interpretation of ribosome profiling data. Contact: brave.oval.pan@gmail.com
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 10
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    The Relationship Between the Plasmapause and Outer Belt Electrons (2016)
    Wiley
    Details
    Publication Date: 2016-08-17
    Description: We quantify the spatial relationship between the plasmapause and outer belt electrons for a five-day period, 15–20 January 2013, by comparing locations of relativistic electron flux peaks to the plasmapause. A peak-finding algorithm is applied to 1.8–7.7 MeV relativistic electron flux data. A plasmapause gradient-finder is applied to wave-derived electron number densities 〉10 cm −3 . We identify two outer belts. Outer belt 1 is a stable zone of 〉3 MeV electrons located 1–2  R E inside the plasmapause. Outer belt 2 is a dynamic zone of 〈3 MeV electrons within 0.5  R E of the moving plasmapause. Electron fluxes earthward of each belt's peak are anti-correlated with cold plasma density. Belt 1 decayed on hiss timescales prior to a disturbance on 17 January, and suffered only a modest dropout, perhaps owing to shielding by the plasmasphere. Afterward, the partially-depleted belt 1 continued to decay at the initial rate. Belt 2 was emptied out by strong disturbance-time losses, but restored within 24 hours. For global context we use a plasmapause test particle (PTP) simulation, and derive a new plasmaspheric index F p , the fraction of a circular drift orbit inside the plasmapause. We find that the locally-measured plasmapause is (for this event) a good proxy for the globally-integrated opportunity for losses in cold plasma. Our analysis of the 15–20 January 2013 time interval confirms that high-energy electron storage rings can persist for weeks or even months if prolonged quiet conditions prevail. This case study must be followed up by more general study (not limited to a five-day period).
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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