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  • 1
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    Exome-based analysis for RNA epigenome sequencing data (2013)
    Oxford University Press
    Details
    Publication Date: 2013-06-06
    Description: Motivation: Fragmented RNA immunoprecipitation combined with RNA sequencing enabled the unbiased study of RNA epigenome at a near single-base resolution; however, unique features of this new type of data call for novel computational techniques. Result: Through examining the connections of RNA epigenome sequencing data with two well-studied data types, ChIP-Seq and RNA-Seq, we unveiled the salient characteristics of this new data type. The computational strategies were discussed accordingly, and a novel data processing pipeline was proposed that combines several existing tools with a newly developed exome-based approach ‘exomePeak’ for detecting, representing and visualizing the post-transcriptional RNA modification sites on the transcriptome. Availability: The MATLAB package ‘exomePeak’ and additional details are available at http://compgenomics.utsa.edu/exomePeak/ . Contact: yufei.huang@utsa.edu or jmeng@mit.edu Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 2
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    LuxGLM: a probabilistic covariate model for quantification of DNA methylation modifications with complex experimental designs (2016)
    Oxford University Press
    Details
    Publication Date: 2016-09-02
    Description: Motivation: 5-methylcytosine (5mC) is a widely studied epigenetic modification of DNA. The ten-eleven translocation (TET) dioxygenases oxidize 5mC into oxidized methylcytosines (oxi-mCs): 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). DNA methylation modifications have multiple functions. For example, 5mC is shown to be associated with diseases and oxi-mC species are reported to have a role in active DNA demethylation through 5mC oxidation and DNA repair, among others, but the detailed mechanisms are poorly understood. Bisulphite sequencing and its various derivatives can be used to gain information about all methylation modifications at single nucleotide resolution. Analysis of bisulphite based sequencing data is complicated due to the convoluted read-outs and experiment-specific variation in biochemistry. Moreover, statistical analysis is often complicated by various confounding effects. How to analyse 5mC and oxi-mC data sets with arbitrary and complex experimental designs is an open and important problem. Results: We propose the first method to quantify oxi-mC species with arbitrary covariate structures from bisulphite based sequencing data. Our probabilistic modeling framework combines a previously proposed hierarchical generative model for oxi-mC-seq data and a general linear model component to account for confounding effects. We show that our method provides accurate methylation level estimates and accurate detection of differential methylation when compared with existing methods. Analysis of novel and published data gave insights into to the demethylation of the forkhead box P3 ( Foxp3) locus during the induced T regulatory cell differentiation. We also demonstrate how our covariate model accurately predicts methylation levels of the Foxp3 locus. Collectively, LuxGLM method improves the analysis of DNA methylation modifications, particularly for oxi-mC species. Availability and Implementation: An implementation of the proposed method is available under MIT license at https://github.org/tare/LuxGLM/ Contact: taijo@simonsfoundation.org or harri.lahdesmaki@aalto.fi Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 3
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    Human CD1d knock-in mouse [Immunology] (2013)
    National Academy of Sciences
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    Publication Date: 2013-02-20
    Description: Despite a high degree of conservation, subtle but important differences exist between the CD1d antigen presentation pathways of humans and mice. These differences may account for the minimal success of natural killer T (NKT) cell-based antitumor therapies in human clinical trials, which contrast strongly with the powerful antitumor effects in...
    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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  • 4
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    MeT-DB: a database of transcriptome methylation in mammalian cells (2015)
    Oxford University Press
    Details
    Publication Date: 2015-01-16
    Description: Methyltranscriptome is an exciting new area that studies the mechanisms and functions of methylation in transcripts. The MethylTranscriptome DataBase (MeT-DB, http://compgenomics.utsa.edu/methylation/ ) is the first comprehensive resource for N6-methyladenosine (m 6 A) in mammalian transcriptome. It includes a database that records publicaly available data sets from methylated RNA immunoprecipitation sequencing (MeRIP-Seq), a recently developed technology for interrogating m 6 A methyltranscriptome. MeT-DB includes ~300k m 6 A methylation sites in 74 MeRIP-Seq samples from 22 different experimental conditions predicted by exomePeak and MACS2 algorithms. To explore this rich information, MeT-DB also provides a genome browser to query and visualize context-specific m 6 A methylation under different conditions. MeT-DB also includes the binding site data of microRNA, splicing factor and RNA binding proteins in the browser window for comparison with m 6 A sites and for exploring the potential functions of m 6 A. Analysis of differential m 6 A methylation and the related differential gene expression under two conditions is also available in the browser. A global perspective of the genome-wide distribution of m 6 A methylation in all the data is provided in circular ideograms, which also act as a navigation portal. The query results and the entire data set can be exported to assist publication and additional analysis.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 5
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    The Measurement And Comparison Of Antarctic Krill Capacity Utilization In 48.1, 48.2 And 58.4 Subareas (2018)
    Institute of Physics (IOP)
    Details
    Publication Date: 2018-12-20
    Description: In this paper, the fishing data of Longteng vessel in 48.1, 48.2 and 58.4 subareas in 2018 are analyzed by the DEA method. Taking times of operation, operating time and wrap tension as input factors, the catch as output factor for the analysis. The capacity utilization and target input are obtained, pure technology efficiency and scale efficiency are summarized in time series, no-deflection capacity utilization are calculated, the rationality of input allocation and the input impact on capacity utilization are evaluated. It is conducted by comparison analysis: in 58.4 subarea, the pure technology efficiency fluctuates obviously and has no growth trend, the production scale is on the rise, but the capacity utilization does not increases proportional to the growth of scale efficiency. There exists a large proportion of input waste, the scale needs to be optimized continually. In 48.1 subarea, capacity utilization and the scale efficiency trend gradually decreases, and the technica...
    Print ISSN: 1755-1307
    Electronic ISSN: 1755-1315
    Topics: Geography , Geosciences , Physics
    Published by Institute of Physics (IOP)
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  • 6
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    Specific inhibition of Stat3 signal transduction by PIAS3 (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-12-31
    Description: The signal transducer and activator of transcription-3 (Stat3) protein is activated by the interleukin 6 (IL-6) family of cytokines, epidermal growth factor, and leptin. A protein named PIAS3 (protein inhibitor of activated STAT) that binds to Stat3 was isolated and characterized. The association of PIAS3 with Stat3 in vivo was only observed in cells stimulated with ligands that cause the activation of Stat3. PIAS3 blocked the DNA-binding activity of Stat3 and inhibited Stat3-mediated gene activation. Although Stat1 is also phosphorylated in response to IL-6, PIAS3 did not interact with Stat1 or affect its DNA-binding or transcriptional activity. The results indicate that PIAS3 is a specific inhibitor of Stat3.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chung, C D -- Liao, J -- Liu, B -- Rao, X -- Jay, P -- Berta, P -- Shuai, K -- AI39612/AI/NIAID NIH HHS/ -- T32CA09056/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1997 Dec 5;278(5344):1803-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Chemistry, University of California, Los Angeles, CA 90095, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9388184" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Carrier Proteins/chemistry/genetics/*metabolism/pharmacology ; Cell Line ; DNA/metabolism ; DNA-Binding Proteins/genetics/*metabolism ; Gene Expression Regulation ; Humans ; Interferon Regulatory Factor-1 ; Interferon-alpha/pharmacology ; Interleukin-6/pharmacology ; *Intracellular Signaling Peptides and Proteins ; Mice ; Molecular Sequence Data ; NF-kappa B/metabolism ; Phosphoproteins/genetics ; Phosphorylation ; Phosphotyrosine/metabolism ; Protein Inhibitors of Activated STAT ; Recombinant Fusion Proteins/pharmacology ; STAT1 Transcription Factor ; STAT3 Transcription Factor ; *Signal Transduction ; Trans-Activators/*metabolism ; Transcriptional Activation ; Transfection ; Tumor Cells, Cultured ; Tumor Necrosis Factor-alpha/pharmacology
    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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    Ferroelectricity of structural origin in the spin-chain compounds ${\mathrm{Ca}}_{3}{\mathrm{Co}}_{2−x}{\mathrm{Mn}}_{x}{\mathrm{O}}_{6}$ (2017)
    American Physical Society (APS)
    Details
    Publication Date: 2017-08-23
    Description: Author(s): J. Shi, J. D. Song, J. C. Wu, X. Rao, H. L. Che, Z. Y. Zhao, H. D. Zhou, J. Ma, R. R. Zhang, L. Zhang, X. G. Liu, X. Zhao, and X. F. Sun We report a systematic study of the structure, electric, and magnetic properties of Ca 3 Co 2 − x Mn x O 6 single crystals with x = 0.72 and 0.26. The dc and ac magnetic susceptibilities display anomalies with characteristic of the spin freezing. The crystals show ferroelectric transition at 40 and 35 K ( T FE ) ... [Phys. Rev. B 96, 064112] Published Mon Aug 21, 2017
    Keywords: Structure, structural phase transitions, mechanical properties, defects
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
    Published by American Physical Society (APS)
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  • 8
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    Hydrodynamic characteristics of the oval cambered double slotted otter board in bottom trawl fisheries (2017)
    Institute of Physics (IOP)
    Details
    Publication Date: 2017-07-26
    Description: The otter board is one of the main components of single boat trawl fisheries. An oval cambered double slotted otter board was developed for improving the expansion performance of trawl net in bottom trawl fisheries. A flume model experiment was conducted to measure the lift coefficient ( C L ), drag coefficient ( C D ), and lift to drag ratio ( K ) in different angles of attack ( α ). The experimental results are as follows : (1) The C L and K value show a trend of increasing at the beginning and then decreasing with the increase of angle of attack, the C D value reflects an upward trend as the angle of attack increases; (2) The D3 otter board (front flow deflector angle at 29 ° ) showed a better hydrodynamic performance. When α =30 ° , the max lift coefficient ( C Lmax ) was 1.464, in this case C D = 0.554 and K =2.643. When α
    Print ISSN: 1755-1307
    Electronic ISSN: 1755-1315
    Topics: Geography , Geosciences , Physics
    Published by Institute of Physics (IOP)
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  • 9
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    Unexpected evolutionary benefit to phages imparted by bacterial CRISPR-Cas9 (2018)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2018-02-15
    Description: Bacteria and bacteriophages arm themselves with various defensive and counterdefensive mechanisms to protect their own genome and degrade the other’s. CRISPR (clustered regularly interspaced short palindromic repeat)–Cas (CRISPR-associated) is an adaptive bacterial defense mechanism that recognizes short stretches of invading phage genome and destroys it by nuclease attack. Unexpectedly, we discovered that the CRISPR-Cas system might also accelerate phage evolution. When Escherichia coli bacteria containing CRISPR-Cas9 were infected with phage T4, its cytosine hydroxymethylated and glucosylated genome was cleaved poorly by Cas9 nuclease, but the continuing CRISPR-Cas9 pressure led to rapid evolution of mutants that accumulated even by the time a single plaque was formed. The mutation frequencies are, remarkably, approximately six orders of magnitude higher than the spontaneous mutation frequency in the absence of CRISPR pressure. Our findings lead to the hypothesis that the CRISPR-Cas might be a double-edged sword, providing survival advantages to both bacteria and phages, leading to their coevolution and abundance on Earth.
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
    Published by American Association for the Advancement of Science (AAAS)
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  • 10
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    Dependance of naphthenic acid corrosion of SA106B on temperature and turbulence (2018)
    Institute of Physics (IOP)
    Details
    Publication Date: 2018-02-03
    Description: Analysis about the kinetic mechanism of Naphthenic Acid Corrosion (NAC) indicated that the natural logarithm of corrosion rate (ln r ) was proportional to negative reciprocal of temperature(-1/T,K), linear regression on the corrosion data in API581 and experiments both proved the linear relationship between ln r -(-1/T,K) which could be applied to predicate the average corrosion rate under different temperature. Corrosion morphology observations proved the influence of turbulence on NAC, measurements on the maximum corrosion depth in different turbulence area indicated that in 7.5% turbulence area the corrosion depth could be 2-3 times of the corrosion depth in 2% turbulence area, existence of turbulence could lead to serious local NAC.
    Print ISSN: 1757-8981
    Electronic ISSN: 1757-899X
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Published by Institute of Physics (IOP)
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