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  • 1
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    Increased genome instability in human DNA segments with self-chains: homology-induced structural variations via replicative mechanisms (2013)
    Oxford University Press
    Details
    Publication Date: 2013-06-07
    Description: Environmental factors including ionizing radiation and chemical agents have been known to be able to induce DNA rearrangements and cause genomic structural variations (SVs); however, the roles of intrinsic characteristics of the human genome, such as regional genome architecture, in SV formation and the potential mechanisms underlying genomic instability remain to be further elucidated. Recently, locus-specific observations showed that ‘self-chain’ (SC), a group of short low-copy repeats (LCRs) in the human genome, can induce autism-associated SV mutations of the MECP2 and NRXN1 genes. In this study, we conducted a genome-wide analysis to investigate SCs and their potential roles in genomic SV formation. Utilizing a vast amount of human SV data, we observed a significant biased distribution of human germline SV breakpoints to SC regions. Notably, the breakpoint distribution pattern is different between SV types across deletion, duplication, inversion and insertion. Our observations were coincident with a mechanism of SC-induced DNA replicative errors, whereas SC may sporadically be used as substrates of nonallelic homologous recombination (NAHR). This contention was further supported by our consistent findings in somatic SV mutations of cancer genomes, suggesting a general mechanism of SC-induced genome instability in human germ and somatic cells.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 2
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    Human Fis1 regulates mitochondrial dynamics through inhibition of the fusion machinery (2019)
    Springer Nature
    Details
    Publication Date: 2019
    Description: 〈sec〉〈st〉Synopsis〈/st〉〈p〉〈textbox textbox-type="graphic"〉〈p〉〈inline-fig〉〈/inline-fig〉〈/p〉〈/textbox〉〈/p〉 〈p〉Yeast Fis1 regulates mitochondrial dynamics by recruiting dynamin-related fission factors, but the role of mammalian Fis1 has remained elusive. Human Fis1 (hFis) promotes Drp1- and Dyn2-independent mitochondrial fragmentation by inhibiting mitofusins and OPA1 GTPase activity, revealing evolutionary divergence.〈/p〉 〈p〉 〈l type="unord"〉〈li〉〈p〉Fission factors Drp1 and Dyn2 are dispensable for hFis1-mediated mitochondrial fragmentation.〈/p〉〈/li〉 〈li〉〈p〉hFis1 binds pro-fusion mitofusins Mfn1 and Mfn2, and OPA1.〈/p〉〈/li〉 〈li〉〈p〉hFis1 inhibits the GTPase activities of Mfn1, Mfn2, and OPA1, but not of Drp1 and Dyn2.〈/p〉〈/li〉 〈li〉〈p〉Overexpression of hFis1 reduces mitochondrial fusion, whereas knockdown of hFis1 enhances mitochondrial fusion.〈/p〉〈/li〉〈/l〉 〈/p〉〈/sec〉
    Print ISSN: 0261-4189
    Electronic ISSN: 1460-2075
    Topics: Biology , Medicine
    Published by Springer Nature on behalf of The European Molecular Biology Organization (EMBO).
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  • 3
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    High-precision evaluation of Wigner's d matrix by exact diagonalization (2015)
    American Physical Society (APS)
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    Publication Date: 2015-10-20
    Description: Author(s): X. M. Feng, P. Wang, W. Yang, and G. R. Jin The precise calculations of Wigner's d matrix are important in various research fields. Due to the presence of large numbers, direct calculations of the matrix using Wigner's formula suffer from a loss of precision. We present a simple method to avoid this problem by expanding the d matrix into a co… [Phys. Rev. E 92, 043307] Published Mon Oct 19, 2015
    Keywords: Computational Physics
    Print ISSN: 1539-3755
    Electronic ISSN: 1550-2376
    Topics: Physics
    Published by American Physical Society (APS)
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  • 4
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    Pyruvate carboxylase is required for glutamine-independent growth of tumor cells [Cell Biology] (2011)
    National Academy of Sciences
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    Publication Date: 2011-05-25
    Description: Tumor cells require a constant supply of macromolecular precursors, and interrupting this supply has been proposed as a therapeutic strategy in cancer. Precursors for lipids, nucleic acids, and proteins are generated in the tricarboxylic acid (TCA) cycle and removed from the mitochondria to participate in biosynthetic reactions. Refilling the pool of precursor molecules (anaplerosis) is therefore crucial to maintain cell growth. Many tumor cells use glutamine to feed anaplerosis. Here we studied how “glutamine-addicted” cells react to interruptions of glutamine metabolism. Silencing of glutaminase (GLS), which catalyzes the first step in glutamine-dependent anaplerosis, suppressed but did not eliminate the growth of glioblastoma cells in culture and in vivo. Profiling metabolic fluxes in GLS-suppressed cells revealed induction of a compensatory anaplerotic mechanism catalyzed by pyruvate carboxylase (PC), allowing the cells to use glucose-derived pyruvate rather than glutamine for anaplerosis. Although PC was dispensable when glutamine was available, forcing cells to adapt to low-glutamine conditions rendered them absolutely dependent on PC for growth. Furthermore, in other cell lines, measuring PC activity in nutrient-replete conditions predicted dependence on specific anaplerotic enzymes. Cells with high PC activity were resistant to GLS silencing and did not require glutamine for survival or growth, but displayed suppressed growth when PC was silenced. Thus, PC-mediated, glucose-dependent anaplerosis allows cells to achieve glutamine independence. Induction of PC during chronic suppression of glutamine metabolism may prove to be a mechanism of resistance to therapies targeting glutaminolysis.
    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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  • 5
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    Competing magnetic states, disorder, and the magnetic character of Fe_{3}Ga_{4} (2015)
    American Physical Society (APS)
    Details
    Publication Date: 2015-04-14
    Description: Author(s): J. H. Mendez, C. E. Ekuma, Y. Wu, B. W. Fulfer, J. C. Prestigiacomo, W. A. Shelton, M. Jarrell, J. Moreno, D. P. Young, P. W. Adams, A. Karki, R. Jin, Julia Y. Chan, and J. F. DiTusa The physical properties of metamagnetic Fe 3 Ga 4 single crystals are investigated to explore the sensitivity of the magnetic states to temperature, magnetic field, and sample history. The data reveal a moderate anisotropy in the magnetization and the metamagnetic critical field along with features in ... [Phys. Rev. B 91, 144409] Published Mon Apr 13, 2015
    Keywords: Magnetism
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
    Published by American Physical Society (APS)
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  • 6
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    Correlation between frequency of non-allelic homologous recombination and homology properties: evidence from homology-mediated CNV mutations in the human genome (2015)
    Oxford University Press
    Details
    Publication Date: 2015-02-10
    Description: Non-allelic homologous recombination (NAHR) is one of the key mechanisms of DNA rearrangement. NAHR occurring between direct homologous repeats can generate genomic copy number variation (CNV) and make significant contributions to both genome evolution and human diseases such as cancer. Intriguingly, previous observations on the rare CNVs at certain genomic disorder loci suggested that NAHR frequency could be dependent on homology properties. However, such a correlation remains unclear at the other NAHR-mediated CNV loci, especially the common CNVs in human populations. Different from the rare CNVs associated with genomic disorders, it is challenging to identify de novo NAHR events at common CNV loci. Therefore, our previously proposed statistic M was employed in estimating relative mutation rate for the NAHR-mediated CNVs in human populations. By utilizing generalized regression neural network and principal component analysis in studying 4330 CNVs ascertained in 3 HapMap populations, we identified the CNVs mediated by NAHR between paired segmental duplications (SDs) and further revealed the correlations between SD properties and NAHR probability. SD length and inter-SD distance were shown to make major contributions to the occurrence of NAHR, whereas chromosomal position and sequence similarity of paired SDs are also involved in NAHR. An integrated effect of SD properties on NAHR frequency was revealed for the common CNVs in human populations. These observations can be well explained by ectopic synapsis in NAHR together with our proposed model of chromosomal compression/extension/looping (CCEL) for homology mis-pairing. Our findings showed the important roles of SDs in NAHR and human genomic evolution.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 7
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    The co-regulation mechanism of transcription factors in the human gene regulatory network (2012)
    Oxford University Press
    Details
    Publication Date: 2012-10-10
    Description: The co-regulation of transcription factors (TFs) has been widely observed in various species. Why is such a co-regulation mechanism needed for transcriptional regulation? To answer this question, the following experiments and analyses were performed. First, examination of the human gene regulatory network (GRN) indicated that co-regulation was significantly enriched in the human GRN. Second, mathematical simulation of an artificial regulatory network showed that the co-regulation mechanism was related to the biphasic dose–response patterns of TFs. Third, the relationship between the co-regulation mechanism and the biphasic dose–response pattern was confirmed using microarray experiments examining different time points and different doses of the toxicant tetrachlorodibenzodioxin. Finally, two mathematical models were constructed to mimic highly co-regulated networks (HCNs) and little co-regulated networks (LCNs), and we found that HCNs were more robust to parameter perturbation than LCNs, whereas LCNs were faster in adaptation to environmental changes than HCNs.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    Chemical screen reveals small molecules suppressing fragile X premutation rCGG repeat-mediated neurodegeneration in Drosophila (2012)
    Oxford University Press
    Details
    Publication Date: 2012-04-12
    Description: Fragile X-associated tremor/ataxia syndrome (FXTAS) is a progressive neurodegenerative disorder recognized in fragile X premutation carriers. Using Drosophila , we previously identified elongated non-coding CGG repeats in FMR1 allele as the pathogenic cause of FXTAS. Here, we use this same FXTAS Drosophila model to conduct a chemical screen that reveals small molecules that can ameliorate the toxic effects of fragile X premutation ribo-CGG (rCGG) repeats, among them several known phospholipase A 2 (PLA 2 ) inhibitors. We show that specific inhibition of PLA 2 activity could mitigate the neuronal deficits caused by fragile X premutation rCGG repeats, including lethality and locomotion deficits. Furthermore, through a genetic screen, we identified a PLA 2 Drosophila ortholog that specifically modulates rCGG repeat-mediated neuronal toxicity. Our results demonstrate the utility of Drosophila models for unbiased small molecule screens and point to PLA 2 as a possible therapeutic target to treat FXTAS.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 9
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    Origin of the metal-insulator transition in ultrathin films of La_{2/3} Sr_{2/3} MnO_{3} (2015)
    American Physical Society (APS)
    Details
    Publication Date: 2015-09-15
    Description: Author(s): Zhaoliang Liao, Fengmiao Li, Peng Gao, Lin Li, Jiandong Guo, Xiaoqing Pan, R. Jin, E. W. Plummer, and Jiandi Zhang Many ultrathin films of transition metal oxides exhibit nonmetallic behavior, in contrast to their metallic bulk counterpart, thus displaying a metal-insulator transition (MIT) as the film thickness is reduced. The nature of this MIT has been a long-standing issue in the epitaxial oxide research com… [Phys. Rev. B 92, 125123] Published Mon Sep 14, 2015
    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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  • 10
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    Enhancement of Rashba interaction in GaAs/AlGaAs quantum wells due to the incorporation of bismuth (2015)
    American Institute of Physics (AIP)
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    Publication Date: 2015-10-06
    Description: This paper reports on the predicted increase in the Rashba interaction due to the incorporation of Bi in GaAs/AlGaAs heterostructures. Band structure parameters obtained from the band anti-crossing theory have been used in combination with self-consistent Schrödinger-Poisson calculations and k.p models to determine the electron spin-splitting caused by structural inversion asymmetry and increased spin-orbit interaction. A near linear seven fold increase in the strength of the Rashba interaction is predicted for a 10% concentration of Bi in a GaAsBi/AlGaAs quantum well heterostructure.
    Print ISSN: 0003-6951
    Electronic ISSN: 1077-3118
    Topics: Physics
    Published by American Institute of Physics (AIP)
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