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  • 1
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    Electronic structure of Ca_{10}(Pt_{4}As_{8})(Fe_{2−x}Pt_{x}As_{2})_{5} with metallic Pt_{4}As_{8} layers: An angle-resolved photoemission spectroscopy study (2013)
    American Physical Society (APS)
    Details
    Publication Date: 2013-09-14
    Description: Author(s): X. P. Shen, S. D. Chen, Q. Q. Ge, Z. R. Ye, F. Chen, H. C. Xu, S. Y. Tan, X. H. Niu, Q. Fan, B. P. Xie, and D. L. Feng We studied the low-lying electronic structure of the newly discovered iron-platinum-arsenide superconductor, Ca 10 (Pt 4 As 8 )(Fe 2− x Pt x As 2 ) 5 ( T c =22 K) with angle-resolved photoemission spectroscopy. We found that the Pt 4 As 8 layer contributes to a small electronlike Fermi surface, indicative of metallic c... [Phys. Rev. B 88, 115124] Published Fri Sep 13, 2013
    Keywords: Electronic structure and strongly correlated systems
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
    Published by American Physical Society (APS)
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  • 2
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    Phase diagram and physical properties of NaFe_{1−x}Cu_{x}As single crystals (2013)
    American Physical Society (APS)
    Details
    Publication Date: 2013-09-26
    Description: Author(s): A. F. Wang, J. J. Lin, P. Cheng, G. J. Ye, F. Chen, J. Q. Ma, X. F. Lu, B. Lei, X. G. Luo, and X. H. Chen A series of high-quality NaFe 1− x Cu x As single crystals have been grown with the self-flux technique, which were systematically characterized via structural, transport, thermodynamic, and high-pressure measurements. Both the structural and magnetic transitions are suppressed by Cu doping, and bulk sup... [Phys. Rev. B 88, 094516] Published Wed Sep 25, 2013
    Keywords: Superfluidity and superconductivity
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
    Published by American Physical Society (APS)
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  • 3
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    Alternative splicing creates two new architectures for human tyrosyl-tRNA synthetase (2016)
    Oxford University Press
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    Publication Date: 2016-02-20
    Description: Many human tRNA synthetases evolved alternative functions outside of protein synthesis. These functions are associated with over 200 splice variants (SVs), most of which are catalytic nulls that engender new biology. While known to regulate non-translational activities, little is known about structures resulting from natural internal ablations of any protein. Here, we report analysis of two closely related, internally deleted, SVs of homodimeric human tyrosyl-tRNA synthetase (TyrRS). In spite of both variants ablating a portion of the catalytic core and dimer-interface contacts of native TyrRS, each folded into a distinct stable structure. Biochemical and nuclear magnetic resonance (NMR) analysis showed that the internal deletion of TyrRSE2–4 SV gave an alternative, neomorphic dimer interface ‘orthogonal’ to that of native TyrRS. In contrast, the internal C-terminal splice site of TyrRSE2–3 prevented either dimerization interface from forming, and yielded a predominantly monomeric protein. Unlike ubiquitous TyrRS, the neomorphs showed clear tissue preferences, which were distinct from each other. The results demonstrate a sophisticated structural plasticity of a human tRNA synthetase for architectural reorganizations that are preferentially elicited in specific tissues.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 4
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    Probing the spatial distribution of high-angular-momentum Rydberg wave packets (2011)
    American Physical Society (APS)
    Details
    Publication Date: 2011-10-12
    Description: Author(s): B. Wyker, S. Ye, F. B. Dunning, S. Yoshida, C. O. Reinhold, and J. Burgdörfer [Phys. Rev. A 84, 043412] Published Tue Oct 11, 2011
    Keywords: Atomic and molecular processes in external fields, including interactions with strong fields and short pulses
    Print ISSN: 1050-2947
    Electronic ISSN: 1094-1622
    Topics: Physics
    Published by American Physical Society (APS)
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  • 5
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    Creating and Transporting Trojan Wave Packets (2012)
    American Physical Society (APS)
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    Publication Date: 2012-01-25
    Description: Author(s): B. Wyker, S. Ye, F. B. Dunning, S. Yoshida, C. O. Reinhold, and J. Burgdörfer Nondispersive localized Trojan wave packets with n i ∼305 moving in near-circular Bohr-like orbits are created and transported to localized near-circular Trojan states of higher n , n f ∼600 , by driving with a linearly polarized sinusoidal electric field whose period is slowly increased. The protocol is ... [Phys. Rev. Lett. 108, 043001] Published Tue Jan 24, 2012
    Keywords: Atomic, Molecular, and Optical Physics
    Print ISSN: 0031-9007
    Electronic ISSN: 1079-7114
    Topics: Physics
    Published by American Physical Society (APS)
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  • 6
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    ExpTreeDB: Web-based query and visualization of manually annotated gene expression profiling experiments of human and mouse from GEO (2014)
    Oxford University Press
    Details
    Publication Date: 2014-11-26
    Description: Motivation: Numerous public microarray datasets are valuable resources for the scientific communities. Several online tools have made great steps to use these data by querying related datasets with users’ own gene signatures or expression profiles. However, dataset annotation and result exhibition still need to be improved. Results: ExpTreeDB is a database that allows for queries on human and mouse microarray experiments from Gene Expression Omnibus with gene signatures or profiles. Compared with similar applications, ExpTreeDB pays more attention to dataset annotations and result visualization. We introduced a multiple-level annotation system to depict and organize original experiments. For example, a tamoxifen-treated cell line experiment is hierarchically annotated as ‘agent-〉drug-〉estrogen receptor antagonist-〉tamoxifen’. Consequently, retrieved results are exhibited by an interactive tree-structured graphics, which provide an overview for related experiments and might enlighten users on key items of interest. Availability and implementation: The database is freely available at http://biotech.bmi.ac.cn/ExpTreeDB . Web site is implemented in Perl, PHP, R, MySQL and Apache. Contact: boxc@bmi.ac.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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  • 7
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    BswR controls bacterial motility and biofilm formation in Pseudomonas aeruginosa through modulation of the small RNA rsmZ (2014)
    Oxford University Press
    Details
    Publication Date: 2014-04-15
    Description: Pseudomonas aeruginosa relies on cell motility and ability to form biofilms to establish infections; however, the mechanism of regulation remains obscure. Here we report that BswR, a xenobiotic response element-type transcriptional regulator, plays a critical role in regulation of bacterial motility and biofilm formation in P. aeruginosa . Transcriptomic and biochemical analyses showed that BswR counteracts the repressor activity of MvaT, controls the transcription of small RNA rsmZ and regulates the biogenesis of bacterial flagella. The crystal structure of BswR was determined at 2.3 Å resolution; the monomer comprises a DNA-binding domain with a helix-turn-helix motif in the N terminus and two helices (α6 and α7) with a V-shaped arrangement in the C-terminus. In addition to the contacts between the parallel helices α5 of two monomers, the two helical extensions (α6 and α7) intertwine together to form a homodimer, which is the biological function unit. Based on the result of DNase I protection assay together with structural analysis of BswR homodimer, we proposed a BswR–DNA model, which suggests a molecular mechanism with which BswR could interact with DNA. Taken together, our results unveiled a novel regulatory mechanism, in which BswR controls the motility and biofilm formation of P. aeruginosa by modulating the transcription of small RNA rsmZ .
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    Suppression of subtelomeric VSG switching by Trypanosoma brucei TRF requires its TTAGGG repeat-binding activity (2014)
    Oxford University Press
    Details
    Publication Date: 2014-11-12
    Description: Trypanosoma brucei causes human African trypanosomiasis and regularly switches its major surface antigen, VSG, in the bloodstream of its mammalian host to evade the host immune response. VSGs are expressed exclusively from subtelomeric loci, and we have previously shown that telomere proteins Tb TIF2 and Tb RAP1 play important roles in VSG switching and VSG silencing regulation, respectively. We now discover that the telomere duplex DNA-binding factor, Tb TRF, also plays a critical role in VSG switching regulation, as a transient depletion of Tb TRF leads to significantly more VSG switching events. We solved the NMR structure of the DNA-binding Myb domain of Tb TRF, which folds into a canonical helix-loop-helix structure that is conserved to the Myb domains of mammalian TRF proteins. The Tb TRF Myb domain tolerates well the bulky J base in T. brucei telomere DNA, and the DNA-binding affinity of Tb TRF is not affected by the presence of J both in vitro and in vivo . In addition, we find that point mutations in Tb TRF Myb that significantly reduced its in vivo telomere DNA-binding affinity also led to significantly increased VSG switching frequencies, indicating that the telomere DNA-binding activity is critical for Tb TRF's role in VSG switching regulation.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 9
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    Three-stage quality control strategies for DNA re-sequencing data (2014)
    Oxford University Press
    Details
    Publication Date: 2014-11-20
    Description: Advances in next-generation sequencing (NGS) technologies have greatly improved our ability to detect genomic variants for biomedical research. In particular, NGS technologies have been recently applied with great success to the discovery of mutations associated with the growth of various tumours and in rare Mendelian diseases. The advance in NGS technologies has also created significant challenges in bioinformatics. One of the major challenges is quality control of the sequencing data. In this review, we discuss the proper quality control procedures and parameters for Illumina technology–based human DNA re-sequencing at three different stages of sequencing: raw data, alignment and variant calling. Monitoring quality control metrics at each of the three stages of NGS data provides unique and independent evaluations of data quality from differing perspectives. Properly conducting quality control protocols at all three stages and correctly interpreting the quality control results are crucial to ensure a successful and meaningful study.
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
    Published by Oxford University Press
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  • 10
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    Pif1 is a force-regulated helicase (2016)
    Oxford University Press
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    Publication Date: 2016-05-20
    Description: Pif1 is a prototypical member of the 5' to 3' DNA helicase family conserved from bacteria to human. It has a high binding affinity for DNA, but unwinds double-stranded DNA (dsDNA) with a low processivity. Efficient DNA unwinding has been observed only at high protein concentrations that favor dimerization of Pif1. In this research, we used single-molecule fluorescence resonance energy transfer (smFRET) and magnetic tweezers (MT) to study the DNA unwinding activity of Saccharomyces cerevisiae Pif1 (Pif1) under different forces exerted on the tails of a forked dsDNA. We found that Pif1 can unwind the forked DNA repetitively for many unwinding-rezipping cycles at zero force. However, Pif1 was found to have a very limited processivity in each cycle because it loosened its strong association with the tracking strand readily, which explains why Pif1 cannot be observed to unwind DNA efficiently in bulk assays at low protein concentrations. The force enhanced the unwinding rate and the total unwinding length of Pif1 significantly. With a force of 9 pN, the rate and length were enhanced by more than 3- and 20-fold, respectively. Our results imply that the DNA unwinding activity of Pif1 can be regulated by force. The relevance of this characteristic of Pif1 to its cellular functions is discussed.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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