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  • Oxford University Press  (7)
  • Paleontological Society  (1)
  • 2010-2014  (8)
  • 1980-1984
  • 1965-1969
  • 1
    Publication Date: 2014-08-27
    Description: Motivation: Time-evolving differential protein–protein interaction (PPI) networks are essential to understand serial activation of differentially regulated (up- or downregulated) cellular processes (DRPs) and their interplays over time. Despite developments in the network inference, current methods are still limited in identifying temporal transition of structures of PPI networks, DRPs associated with the structural transition and the interplays among the DRPs over time. Results: Here, we present a probabilistic model for estimating Time-Evolving differential PPI networks with MultiPle Information (TEMPI). This model describes probabilistic relationships among network structures, time-course gene expression data and Gene Ontology biological processes (GOBPs). By maximizing the likelihood of the probabilistic model, TEMPI estimates jointly the time-evolving differential PPI networks (TDNs) describing temporal transition of PPI network structures together with serial activation of DRPs associated with transiting networks. This joint estimation enables us to interpret the TDNs in terms of temporal transition of the DRPs. To demonstrate the utility of TEMPI, we applied it to two time-course datasets. TEMPI identified the TDNs that correctly delineated temporal transition of DRPs and time-dependent associations between the DRPs. These TDNs provide hypotheses for mechanisms underlying serial activation of key DRPs and their temporal associations. Availability and implementation: Source code and sample data files are available at http://sbm.postech.ac.kr/tempi/sources.zip . Contact: seungjin@postech.ac.kr or dhwang@dgist.ac.kr Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 2
    Publication Date: 2013-11-15
    Description: A bstract The Sesong Formation is a member of the Taebaek Group, Korea, which extends from late Cambrian Series 3 to middle Furongian in age. Recent studies on the trilobites of the Sesong Formation have contributed significantly to the revision of the biostratigraphy. However, trilobites in the lower part of the formation, which may include the " Stephanocare Zone", have remained essentially overlooked since the establishment of the biozone, making it difficult to correlate with the equivalent biozones of North China. Here we report trilobite faunas from the lower part of the Sesong Formation in two different sections, the Seokgaejae and the Jikdong sections, which yield two species of Jiulongshania among other species. Species of Jiulongshania have been known to occur successively in North China, so are useful for detailed correlation. Specimens of Stephanocare richthofeni are fragmentary and rarely occur in association with Jiulongshania regularis , while Jiulongshania species occur throughout the studied intervals. Accordingly, it is reasonable to extend the previously established Jiulongshania Zone of the uppermost part of the underlying Daegi Formation into the lower part of the Sesong Formation. By doing so, the Jiulongshania Zone is correlated with the Blackwelderia Zone of North China with confidence. The lowermost part of the Sesong Formation in the Jikdong section yields a fauna including J. regularis , which implies that the boundary between the Daegi and Sesong formations is diachronous within the Taebaeksan Basin. The Daegi/Sesong formation boundary in Korea is comparable to the Zhangxia/Gushan boundary in North China in that it displays an abrupt change from a carbonate-dominant facies to a shale-dominant facies. The correlation employing the Jiulongshania species indicates that the facies shift occurred significantly earlier in Shandong, North China than in the Taebaeksan Basin, Korea.
    Print ISSN: 0022-3360
    Electronic ISSN: 1937-2337
    Topics: Geosciences
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  • 3
    Publication Date: 2014-02-28
    Description: The nucleotide excision repair pathway removes ultraviolet (UV) photoproducts from the human genome in the form of short oligonucleotides ~30 nt in length. Because there are limitations to many of the currently available methods for investigating UV photoproduct repair in vivo , we developed a convenient non-radioisotopic method to directly detect DNA excision repair events in human cells. The approach involves extraction of oligonucleotides from UV-irradiated cells, DNA end-labeling with biotin and streptavidin-mediated chemiluminescent detection of the excised UV photoproduct-containing oligonucleotides that are released from the genome during excision repair. Our novel approach is robust, with essentially no signal in the absence of UV or a functional excision repair system. Furthermore, our non-radioisotopic methodology allows for the sensitive detection of excision products within minutes following UV irradiation and does not require additional enrichment steps such as immunoprecipitation. Finally, this technique allows for quantitative measurements of excision repair in human cells. We suggest that the new techniques presented here will be a useful and powerful approach for studying the mechanism of human nucleotide excision repair in vivo .
    Keywords: Repair
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 4
    Publication Date: 2014-03-21
    Description: Recent observations have indicated the existence of dust in high-redshift galaxies, however, the dust properties in them are still unknown. Here we present theoretical constraints on dust properties in Lyman-break galaxies (LBGs) at z  = 3 by post-processing a cosmological smoothed particle hydrodynamics simulation with radiative transfer calculations. We calculate the dust extinction in 2800 dark matter haloes using the metallicity information of individual gas particles in our simulation. We use only bright galaxies with rest-frame ultraviolet (UV) magnitude M 1700  〈 –20 mag, and study the dust size, dust-to-metal mass ratio, and dust composition. From the comparison of calculated colour excess between B and V band [i.e. E ( B  –  V )] and the observations, we constrain the typical dust size, and show that the best-fitting dust grain size is ~ 0.05 μm, which is consistent with the results of theoretical dust models for Type II supernova. Our simulation with the dust extinction effect can naturally reproduce the observed rest-frame UV luminosity function of LBGs at z  = 3 without assuming an ad hoc constant extinction value. In addition, in order to reproduce the observed mean E ( B  –  V ), we find that the dust-to-metal mass ratio needs to be similar to that of the local galaxies, and that the graphite dust is dominant or at least occupy half of dust mass.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 5
    Publication Date: 2014-04-03
    Description: In the present study, we investigated the 3' untranslated region (UTR) of the mouse core clock gene cryptochrome 1 ( Cry1 ) at the post-transcriptional level, particularly its translational regulation. Interestingly, the 3'UTR of Cry1 mRNA decreased its mRNA levels but increased protein amounts. The 3'UTR is widely known to function as a cis -acting element of mRNA degradation. The 3'UTR also provides a binding site for microRNA and mainly suppresses translation of target mRNAs. We found that AU-rich element RNA binding protein 1 (AUF1) directly binds to the Cry1 3'UTR and regulates translation of Cry1 mRNA. AUF1 interacted with eukaryotic translation initiation factor 3 subunit B and also directly associated with ribosomal protein S3 or ribosomal protein S14, resulting in translation of Cry1 mRNA in a 3'UTR-dependent manner. Expression of cytoplasmic AUF1 and binding of AUF1 to the Cry1 3'UTR were parallel to the circadian CRY1 protein profile. Our results suggest that the 3'UTR of Cry1 is important for its rhythmic translation, and AUF1 bound to the 3'UTR facilitates interaction with the 5' end of mRNA by interacting with translation initiation factors and recruiting the 40S ribosomal subunit to initiate translation of Cry1 mRNA.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 6
    Publication Date: 2012-05-22
    Description: Motivation: Gene clusters are arrangements of functionally related genes on a chromosome. In bacteria, it is expected that evolutionary pressures would conserve these arrangements due to the functional advantages they provide. Visualization of conserved gene clusters across multiple genomes provides key insights into their evolutionary histories. Therefore, a software tool that enables visualization and functional analyses of gene clusters would be a great asset to the biological research community. Results: We have developed GeneclusterViz, a Java-based tool that allows for the visualization, exploration and downstream analyses of conserved gene clusters across multiple genomes. GeneclusterViz combines an easy-to-use exploration interface for gene clusters with a host of other analysis features such as multiple sequence alignments, phylogenetic analyses and integration with the KEGG pathway database. Availability: http://biohealth.snu.ac.kr/GeneclusterViz/ ; http://microbial.informatics.indiana.edu/GeneclusterViz/ Contact: sunkim.bioinfo@snu.ac.kr ; ybrun@indiana.edu Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 7
    Publication Date: 2012-04-11
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 8
    Publication Date: 2012-12-21
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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