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  • 1
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    Structural heterogeneity and functional diversity of topologically associating domains in mammalian genomes (2015)
    Oxford University Press
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    Publication Date: 2015-08-29
    Description: Recent chromosome conformation capture (3C) derived techniques have revealed that topologically associating domain (TAD) is a pervasive element in chromatin three-dimensional (3D) organization. However, there is currently no parameter to quantitatively measure the structural characteristics of TADs, thus obscuring our understanding on the structural and functional differences among TADs. Based on our finding that there exist intrinsic chromatin interaction patterns in TADs, we define a theoretical parameter, called aggregation preference (AP), to characterize TAD structures by capturing the interaction aggregation degree. Applying this defined parameter to 11 Hi-C data sets generated by both traditional and in situ Hi-C experimental pipelines, our analyses reveal that heterogeneous structures exist among TADs, and this structural heterogeneity is significantly correlated to DNA sequences, epigenomic signals and gene expressions. Although TADs can be stable in genomic positions across cell lines, structural comparisons show that a considerable number of stable TADs undergo significantly structural rearrangements during cell changes. Moreover, the structural change of TAD is tightly associated with its transcription remodeling. Altogether, the theoretical parameter defined in this work provides a quantitative method to link structural characteristics and biological functions of TADs, and this linkage implies that chromatin interaction pattern has the potential to mark transcription activity in TADs.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    Spatial Colocalization of Human Ohnolog Pairs Acts to Maintain Dosage-Balance (2016)
    Oxford University Press
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    Publication Date: 2016-08-19
    Description: Ohnologs –paralogous gene pairs generated by whole genome duplication– are enriched for dosage sensitive genes, that is, genes that have a phenotype due to copy number changes. Dosage sensitive genes frequently occur in the same metabolic pathway and in physically interacting proteins. Accumulating evidence reveals that functionally related genes tend to co-localize in the three-dimensional (3D) arrangement of chromosomes. We query whether the spatial distribution of ohnologs has implications for their dosage balance. We analyzed the colocalization frequency of ohnologs based on chromatin interaction datasets of seven human cell lines and found that ohnolog pairs exhibit higher spatial proximity in 3D nuclear organization than other paralog pairs and than randomly chosen ohnologs in the genome. We also found that colocalized ohnologs are more resistant to copy number variations and more likely to be disease-associated genes, which indicates a stronger dosage balance in ohnologs with high spatial proximity. This phenomenon is further supported by the stronger similarity of gene co-expression and of gene ontology terms of colocalized ohnologs. In addition, for a large fraction of ohnologs, the spatial colocalization is conserved in mouse cells, suggestive of functional constraint on their 3D positioning in the nucleus.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    Numerical analysis of the interactions of sheet cavitation and cloud cavitation around a hydrofoil (2015)
    Institute of Physics (IOP)
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    Publication Date: 2015-01-16
    Description: Partial cavitation and cloud cavitation on NACA66(MOD) was studied based on PANS turbulence model combined with the Zwart cavitation model. The results agree well with the data from the experimental results. The existence of a kind of unsteady characteristics of cloud cavitation is analysed in details. The reasons for the inhibition mechanism of the sheet cavitation are discussed. Pressure shock wave occurs near the tailing edge of the hydrofoil when the collapse of cloud is so large leading to great influence on the cavity closed to the leading edge. The evolution of the pressure peak and its propagation toward the leading edge were investigated through the study of the time domain signal of the monitor points along the streamline of flow. Finally, the propagation of the pressure wave on the suction side was further investigated through analysing the spatial-time history of wall pressure.
    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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  • 4
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    Digitization and reduction of old astronomical plates of natural satellites (2016)
    Oxford University Press
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    Publication Date: 2016-02-20
    Description: Old astrophotographic plates are precious sources of historical data for astronomical studies, especially regarding the improvement of natural satellite orbits. Today, with the advent of new, accurate techniques, these old data can be re-processed so as to give positions that are much more accurate than those initially obtained. Various recent projects, including our Chinese project, have involved measuring and reducing these old plates again. Here we present a method for measurement and reduction that involves the digitization of plates using an advanced commercial scanner, namely the EPSON 10000 XL. We selected a set of 27 plates of the satellites of Jupiter, Saturn and Uranus taken from 1987 to 1990. A total of 125 satellite positions were derived from the new measurement and reduction of these plates using the UCAC4 catalogue. A comparison of the new observed positions with recent ephemerides has shown a general consistency with satellite theory of about 100 mas. The new positions present an accuracy equivalent to the most recent CCD observations, and better than the original positions. Moreover, nearly 30 per cent of the 125 positions obtained in this work are published for the first time here. This paper is a preliminary contribution to the larger project of new measurements and reductions of all the old Chinese plates of natural satellites, which should allow further improvements in the knowledge of the orbits of these satellites.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 5
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    Dissecting the chromatin interactome of microRNA genes (2014)
    Oxford University Press
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    Publication Date: 2014-03-13
    Description: Our knowledge of the role of higher-order chromatin structures in transcription of microRNA genes ( MIRs ) is evolving rapidly. Here we investigate the effect of 3D architecture of chromatin on the transcriptional regulation of MIRs . We demonstrate that MIRs have transcriptional features that are similar to protein-coding genes. RNA polymerase II–associated ChIA-PET data reveal that many groups of MIRs and protein-coding genes are organized into functionally compartmentalized chromatin communities and undergo coordinated expression when their genomic loci are spatially colocated. We observe that MIRs display widespread communication in those transcriptionally active communities. Moreover, miRNA–target interactions are significantly enriched among communities with functional homogeneity while depleted from the same community from which they originated, suggesting MIRs coordinating function-related pathways at posttranscriptional level. Further investigation demonstrates the existence of spatial MIR–MIR chromatin interacting networks. We show that groups of spatially coordinated MIRs are frequently from the same family and involved in the same disease category. The spatial interaction network possesses both common and cell-specific subnetwork modules that result from the spatial organization of chromatin within different cell types. Together, our study unveils an entirely unexplored layer of MIR regulation throughout the human genome that links the spatial coordination of MIRs to their co-expression and function.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 6
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    New astrometric observations of Triton in 2007-2009 (2014)
    Oxford University Press
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    Publication Date: 2014-04-20
    Description: Astrometric positions of the Neptunian satellite Triton with a visual magnitude of 13.5 were obtained during three successive oppositions in 2007, 2008 and 2009. A total of 1095 new observed positions of Triton were collected during 46 nights of observations, involving eight missions and three telescopes. We compared our observations to the best ephemerides of Triton available now. This comparison has shown that our observations present a high level of accuracy as they provide standard deviations of residuals hardly higher than 50 mas and mean residuals lower than 30 mas, corresponding to about only 500 km in the position of the very distant satellite Triton. Moreover, we have compared most of the different planetary ephemerides of Neptune available now as well as two recent orbit models of Triton. These new comparisons have clearly shown the differences between all of these ephemerides which can be significant and that are presented in this work.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 7
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    The sequencing bias relaxed characteristics of Hi-C derived data and implications for chromatin 3D modeling (2013)
    Oxford University Press
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    Publication Date: 2013-10-19
    Description: The 3D chromatin structure modeling by chromatin interactions derived from Hi-C experiments is significantly challenged by the intrinsic sequencing biases in these experiments. Conventional modeling methods only focus on the bias among different chromatin regions within the same experiment but neglect the bias arising from different experimental sequencing depth. We now show that the regional interaction bias is tightly coupled with the sequencing depth, and we further identify a chromatin structure parameter as the inherent characteristics of Hi-C derived data for chromatin regions. Then we present an approach for chromatin structure prediction capable of relaxing both kinds of sequencing biases by using this identified parameter. This method is validated by intra and inter cell-line comparisons among various chromatin regions for four human cell-lines (K562, GM12878, IMR90 and H1hESC), which shows that the openness of chromatin region is well correlated with chromatin function. This method has been executed by an automatic pipeline (AutoChrom3D) and thus can be conveniently used.
    Keywords: Computational Methods, Massively Parallel (Deep) Sequencing, Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    Analysis of physical composition and heavy metals pollution of municipal solid waste (MSW) in Beijing (2018)
    Institute of Physics (IOP)
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    Publication Date: 2018-03-25
    Description: By using on-site sampling and physical-chemical analysis, the physical composition and the contents of heavy metals in Beijing MSW were researched. The result showed that the main components of MSW in Beijing are mainly kitchen waste, the average content of kitchen waste are more than 60% and 50% in summer and in winter, respectively. The pollution of Cu, Hg and Cr are all more serious for MSW in Haidian and Dongcheng district. The heavy metal pollution of MSW in summer is higher than that in winter in Beijing. Seasonal impacts should be taken into consideration when dealing with MSW. The content of heavy metals in MSW exceeded the background value of soil in Haidian and Dongcheng districts. In order to reduce heavy metal pollution, the MSW should be separated collection and treated.
    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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    Identification of transcription factors for drug-associated gene modules and biomedical implications (2014)
    Oxford University Press
    Details
    Publication Date: 2014-01-29
    Description: Motivation:  One of the major findings in systems biomedicine is that both pathogenesis of diseases and drug mode of action have a module basis. However, the transcription factors (TFs) regulating the modules remain largely unknown. Results:  In this study, by using biclustering approach FABIA (factor analysis for bicluster acquisition), we generate 49 modules for gene expression profiles on 1309 agent treatments. These modules are of biological relevance in terms of functional enrichment, drug–drug interactions and 3D proximity in chromatins. By using the information of drug targets (some of which are TFs) and biological regulation, the links between 28 modules and 12 specific TFs, such as estrogen receptors (ERs), nuclear factor-like 2 and peroxisome proliferator-activated receptor gamma, can be established. Some of the links are supported by 3D transcriptional regulation data [derived from ChIA-PET (chromatin interaction analysis using paired-end tags) experiments] and drug mode of action as well. The relationships between modules and TFs provide new clues to interpreting biological regulation mechanisms, in particular, the lipid metabolism regulation by ERα. In addition, the links between natural products (e.g. polyphenols) and their associated modules and TFs are helpful to elucidate their polypharmacological effects in terms of activating specific TFs, such as ERs, nuclear factor-like 2 and peroxisome proliferator-activated receptor gamma. Contact: zhy630@mail.hzau.edu.cn 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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  • 10
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    An orbital determination of Triton with the use of a revised pole model (2014)
    Oxford University Press
    Details
    Publication Date: 2014-01-29
    Description: In this paper, we used the 3108 Earth-based astrometric observations from the Natural Satellite Data Center over more than 30 yr time span from 1975 to 2006 for determining the epoch state vectors of the Neptunian largest satellite Triton. These observations almost contain all modern photo and CCD observations available. In integrating perturbation equation, the barycentric frame of Neptune–Triton system is adopted, and in considering the oblateness perturbation due to Neptune, a revised pole model describing the precession of the Neptune's pole is used in our calculation.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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