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  • 1
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    dbPTM 2016: 10-year anniversary of a resource for post-translational modification of proteins (2016)
    Oxford University Press
    Details
    Publication Date: 2016-01-07
    Description: Owing to the importance of the post-translational modifications (PTMs) of proteins in regulating biological processes, the dbPTM ( http://dbPTM.mbc.nctu.edu.tw/ ) was developed as a comprehensive database of experimentally verified PTMs from several databases with annotations of potential PTMs for all UniProtKB protein entries. For this 10th anniversary of dbPTM, the updated resource provides not only a comprehensive dataset of experimentally verified PTMs, supported by the literature, but also an integrative interface for accessing all available databases and tools that are associated with PTM analysis. As well as collecting experimental PTM data from 14 public databases, this update manually curates over 12 000 modified peptides, including the emerging S -nitrosylation, S -glutathionylation and succinylation, from approximately 500 research articles, which were retrieved by text mining. As the number of available PTM prediction methods increases, this work compiles a non-homologous benchmark dataset to evaluate the predictive power of online PTM prediction tools. An increasing interest in the structural investigation of PTM substrate sites motivated the mapping of all experimental PTM peptides to protein entries of Protein Data Bank (PDB) based on database identifier and sequence identity, which enables users to examine spatially neighboring amino acids, solvent-accessible surface area and side-chain orientations for PTM substrate sites on tertiary structures. Since drug binding in PDB is annotated, this update identified over 1100 PTM sites that are associated with drug binding. The update also integrates metabolic pathways and protein–protein interactions to support the PTM network analysis for a group of proteins. Finally, the web interface is redesigned and enhanced to facilitate access to this resource.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    Direct activation of human and mouse Oct4 genes using engineered TALE and Cas9 transcription factors (2014)
    Oxford University Press
    Details
    Publication Date: 2014-04-15
    Description: The newly developed transcription activator-like effector protein (TALE) and clustered regularly interspaced short palindromic repeats/Cas9 transcription factors (TF) offered a powerful and precise approach for modulating gene expression. In this article, we systematically investigated the potential of these new tools in activating the stringently silenced pluripotency gene Oct4 ( Pou5f1 ) in mouse and human somatic cells. First, with a number of TALEs and sgRNAs targeting various regions in the mouse and human Oct4 promoters, we found that the most efficient TALE-VP64s bound around –120 to –80 bp, while highly effective sgRNAs targeted from –147 to –89-bp upstream of the transcription start sites to induce high activity of luciferase reporters. In addition, we observed significant transcriptional synergy when multiple TFs were applied simultaneously. Although individual TFs exhibited marginal activity to up-regulate endogenous gene expression, optimized combinations of TALE-VP64s could enhance endogenous Oct4 transcription up to 30-fold in mouse NIH3T3 cells and 20-fold in human HEK293T cells. More importantly, the enhancement of OCT4 transcription ultimately generated OCT4 proteins. Furthermore, examination of different epigenetic modifiers showed that histone acetyltransferase p300 could enhance both TALE-VP64 and sgRNA/dCas9-VP64 induced transcription of endogenous OCT4 . Taken together, our study suggested that engineered TALE-TF and dCas9-TF are useful tools for modulating gene expression in mammalian cells.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    Joint stage recognition and anatomical annotation of drosophila gene expression patterns (2012)
    Oxford University Press
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    Publication Date: 2012-06-12
    Description: Motivation: Staining the mRNA of a gene via in situ hybridization (ISH) during the development of a Drosophila melanogaster embryo delivers the detailed spatio-temporal patterns of the gene expression. Many related biological problems such as the detection of co-expressed genes, co-regulated genes and transcription factor binding motifs rely heavily on the analysis of these image patterns. To provide the text-based pattern searching for facilitating related biological studies, the images in the Berkeley Drosophila Genome Project (BDGP) study are annotated with developmental stage term and anatomical ontology terms manually by domain experts. Due to the rapid increase in the number of such images and the inevitable bias annotations by human curators, it is necessary to develop an automatic method to recognize the developmental stage and annotate anatomical terms. Results: In this article, we propose a novel computational model for jointly stage classification and anatomical terms annotation of Drosophila gene expression patterns. We propose a novel Tri - Relational Graph (TG) model that comprises the data graph, anatomical term graph, developmental stage term graph, and connect them by two additional graphs induced from stage or annotation label assignments. Upon the TG model, we introduce a Preferential Random Walk (PRW) method to jointly recognize developmental stage and annotate anatomical terms by utilizing the interrelations between two tasks. The experimental results on two refined BDGP datasets demonstrate that our joint learning method can achieve superior prediction results on both tasks than the state-of-the-art methods. Availability: http://ranger.uta.edu/%7eheng/Drosophila/ Contact: heng@uta.edu
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 4
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    Performance and defrosting effect study on the air-to-water heat pump with heat storage device (2014)
    Oxford University Press
    Details
    Publication Date: 2014-05-15
    Description: The heat storage device is proposed to avoid the frequent on–off state under partial load, large variation of the supply and return water temperature and long defrosting time of air-to-water heat pump with plate heat exchanger for heating. The heat storage device is composed of a water tank, the inner double-pipe heat exchanger, appendages and the electric heater. The energy storage can reduce on–off times of the compressor. The energy storage and the electric heater can make up the shortage of heating during defrosting. Performance test shows that on–off times for the heat storage device unit compressor under partial load is about four times per hour compared six times per hour for the plate heat exchange unit. Defrosting time is reduced by 78 s by heat storage device unit and 84 s by heat storage device with electric heater unit. More steady running parameters, inlet heating water temperature of heat storage device or heat storage device with electric heater unit is about 35°C, while that of plate heat exchanger reduces to 30.73°C. Therefore, the designed heat storage device can improve the unit performance and is suitable for the new projects with air-to-water heat pumps.
    Keywords: Other low-carbon energy technologies
    Print ISSN: 1748-1317
    Electronic ISSN: 1748-1325
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Published by Oxford University Press
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  • 5
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    PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants (2016)
    Oxford University Press
    Details
    Publication Date: 2016-01-07
    Description: Transcription factors (TFs) are sequence-specific DNA-binding proteins acting as critical regulators of gene expression. The Plant P romoter A nalysis N avigator (PlantPAN; http://PlantPAN2.itps.ncku.edu.tw ) provides an informative resource for detecting transcription factor binding sites (TFBSs), corresponding TFs, and other important regulatory elements (CpG islands and tandem repeats) in a promoter or a set of plant promoters. Additionally, TFBSs, CpG islands, and tandem repeats in the conserve regions between similar gene promoters are also identified. The current PlantPAN release (version 2.0) contains 16 960 TFs and 1143 TF binding site matrices among 76 plant species. In addition to updating of the annotation information, adding experimentally verified TF matrices, and making improvements in the visualization of transcriptional regulatory networks, several new features and functions are incorporated. These features include: (i) comprehensive curation of TF information (response conditions, target genes, and sequence logos of binding motifs, etc.), (ii) co-expression profiles of TFs and their target genes under various conditions, (iii) protein-protein interactions among TFs and their co-factors, (iv) TF-target networks, and (v) downstream promoter elements. Furthermore, a dynamic transcriptional regulatory network under various conditions is provided in PlantPAN 2.0. The PlantPAN 2.0 is a systematic platform for plant promoter analysis and reconstructing transcriptional regulatory networks.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 6
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    InterPro in 2017--beyond protein family and domain annotations (2017)
    Oxford University Press
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    Publication Date: 2017-01-05
    Description: InterPro ( http://www.ebi.ac.uk/interpro/ ) is a freely available database used to classify protein sequences into families and to predict the presence of important domains and sites. InterProScan is the underlying software that allows both protein and nucleic acid sequences to be searched against InterPro's predictive models, which are provided by its member databases. Here, we report recent developments with InterPro and its associated software, including the addition of two new databases (SFLD and CDD), and the functionality to include residue-level annotation and prediction of intrinsic disorder. These developments enrich the annotations provided by InterPro, increase the overall number of residues annotated and allow more specific functional inferences.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    Functional interplay between NTP leaving group and base pair recognition during RNA polymerase II nucleotide incorporation revealed by methylene substitution (2016)
    Oxford University Press
    Details
    Publication Date: 2016-05-06
    Description: RNA polymerase II (pol II) utilizes a complex interaction network to select and incorporate correct nucleoside triphosphate (NTP) substrates with high efficiency and fidelity. Our previous ‘synthetic nucleic acid substitution’ strategy has been successfully applied in dissecting the function of nucleic acid moieties in pol II transcription. However, how the triphosphate moiety of substrate influences the rate of P-O bond cleavage and formation during nucleotide incorporation is still unclear. Here, by employing β, -bridging atom-‘substituted’ NTPs, we elucidate how the methylene substitution in the pyrophosphate leaving group affects cognate and non-cognate nucleotide incorporation. Intriguingly, the effect of the β, -methylene substitution on the non-cognate UTP/dT scaffold (~3-fold decrease in k pol ) is significantly different from that of the cognate ATP/dT scaffold (~130-fold decrease in k pol ). Removal of the wobble hydrogen bonds in U:dT recovers a strong response to methylene substitution of UTP. Our kinetic and modeling studies are consistent with a unique altered transition state for bond formation and cleavage for UTP/dT incorporation compared with ATP/dT incorporation. Collectively, our data reveals the functional interplay between NTP triphosphate moiety and base pair hydrogen bonding recognition during nucleotide incorporation.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    On the shear estimation bias induced by the spatial variation of colour across galaxy profiles (2013)
    Oxford University Press
    Details
    Publication Date: 2013-06-09
    Description: The spatial variation of the colour of a galaxy may introduce a bias in the measurement of its shape if the point spread function (PSF) profile depends on wavelength. We study how this bias depends on the properties of the PSF and the galaxies themselves. The bias depends on the scales used to estimate the shape, which may be used to optimize methods to reduce the bias. Here, we develop a general approach to quantify the bias. Although applicable to any weak lensing survey, we focus on the implications for the ESA Euclid mission. Based on our study of synthetic galaxies, we find that the bias is a few times 10 –3 for a typical galaxy observed by Euclid . Consequently, it cannot be neglected and needs to be accounted for. We demonstrate how one can do so using spatially resolved observations of galaxies in two filters. We show that Hubble Space Telescope ( HST ) observations in the F606W and F814W filters allow us to model and reduce the bias by an order of magnitude, sufficient to meet Euclid ’s scientific requirements. The precision of the correction is ultimately determined by the number of galaxies for which spatially resolved observations in at least two filters are available. We use results from the Millennium simulation to demonstrate that archival HST data will be sufficient for the tomographic cosmic shear analysis with the Euclid data set.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 9
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    Information Diffusion Model Based on Privacy Setting in Online Social Networking Services (2015)
    Oxford University Press
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    Publication Date: 2015-03-27
    Description: Social networking service (SNS) is one of the major technological applications based on Web 2.0, which can help users to express their views and share information with others. How to describe the information diffusion process in online SNS accurately has attracted considerable interest recently. However, almost all existing models focus on a single online SNS tool and face many challenges with multiple online SNS tools. In this paper, we turn to users’ privacy setting policies and propose a general stochastic model with multiple diffusion mechanisms in online SNS, called DMPS. Specifically, we first define a privacy protection mechanism based on information sharing in online SNS and classify nodes according to different privacy setting policies; then, we define the states of the nodes and information dissemination rules with dynamics of infectious disease; finally, we describe the evolution process of different nodes by dynamic evolution equations. Detailed simulations and analysis show that the DMPS can precisely describe the diffusion process with multiple diffusion mechanisms and have the same characteristics as a diffusion process in real online SNS. As a result, DMPS can be used to identify the underlying diffusion mechanism of information and forecast its trend in online SNS.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
    Published by Oxford University Press
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  • 10
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    Phylogenetic and climatic constraints drive flowering phenological patterns in a subtropical nature reserve (2015)
    Oxford University Press
    Details
    Publication Date: 2015-03-28
    Description: Aims Exploring flowering patterns and detecting processes are essential when probing into the nature of reproductive traits during the life history and the interactions among different evolutionary clades. Such patterns are believed to be influenced by many factors, but quantifying these impacts at the community-level remains poorly understood. Methods We investigated the flowering patterns based on long-term herbarium records in a given area from subtropical forest regions in southern China. We obtained 5258 herbarium voucher specimens collected from the Dinghushan National Nature Reserve (DNNR) belonging to 166 families, 943 genera and 2059 species and examined the month when each species was flowering during the period 1920–2007. Important Findings The results showed that plants flowered sequentially almost throughout the whole year, showing the characteristics of subtropical evergreen broad-leaved forests. Flowering spectrums of the entire flora and the four life forms exhibited a clear unimodality that is probably typical of subtropical forest communities. Flowering patterns of the DNNR were positively correlated with mean rainfall, mean air temperature and mean sunshine duration. Median flowering dates of the 38 large species-rich families ranged from early April to late August; 25 families exhibited significant unimodal distribution patterns, whereas the remaining families were unclear or bimodal. Median flowering dates of the 10 most species-rich genera ranged from middle May to later July. While the results are consistent with climatic factors playing a general role in flowering patterns, median flowering dates varied significantly among species-rich families and genera, suggesting that phylogenies could provide specific constraints in subtropical forests.
    Print ISSN: 1752-993X
    Electronic ISSN: 1752-9921
    Topics: Biology
    Published by Oxford University Press
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