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  • 1
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    A search for eclipsing binaries that host discs (2014)
    Oxford University Press
    Details
    Publication Date: 2014-06-05
    Description: We search for systems hosting eclipsing discs using a complete sample of eclipsing binaries (EBs); those previously identified in the third phase of the Optical Gravitational Lensing Experiment (OGLE-III). Within a subsample of 2823 high-cadence, high-photometric precision and large eclipsing depth detached EBs previously identified in the Large Magellanic Cloud (LMC), we find that the skewness and kurtosis of the light-curve magnitude distribution within the primary eclipse can distinguish EBs with a complex-shaped eclipse from those without. Two systems with previously identified eclipsing discs (OGLE-LMC-ECL-11893 and OGLE-LMC-ECL-17782) are identified with near zero skewness (| S | 〈 0.5) and positive kurtosis. No additional eclipsing disc systems were found in the OGLE-III LMC, Small Magellanic Cloud or Galactic Disc EB light curves. We estimate that the fraction of detached early-type LMC EBs (which have a primary with an I -band magnitude brighter than ~=19 mag) that exhibit atypical eclipses and so could host a disc is approximately 1/1000. As circumstellar disc lifetimes are short, we expected to primarily find eclipsing discs around young stars. In addition, as there is more room for a disc in a widely separated binary and because a disc close to a luminous star would be above the dust sublimation temperature, we expected to primarily find eclipsing discs in long-period binaries. However, OGLE-LMC-ECL-17782 is a 13.3 d period B star system with a transient and hot (~6000 K, ~0.1 au radius) disc and Scott et al. estimate an age of 150 Myr for OGLE-LMC-ECL-11893. Both discs are unexpected in the EB sample and impel explanation.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 2
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    MERAV: a tool for comparing gene expression across human tissues and cell types (2016)
    Oxford University Press
    Details
    Publication Date: 2016-01-07
    Description: The oncogenic transformation of normal cells into malignant, rapidly proliferating cells requires major alterations in cell physiology. For example, the transformed cells remodel their metabolic processes to supply the additional demand for cellular building blocks. We have recently demonstrated essential metabolic processes in tumor progression through the development of a methodological analysis of gene expression. Here, we present the Metabolic gEne RApid Visualizer (MERAV, http://merav.wi.mit.edu ), a web-based tool that can query a database comprising ~4300 microarrays, representing human gene expression in normal tissues, cancer cell lines and primary tumors. MERAV has been designed as a powerful tool for whole genome analysis which offers multiple advantages: one can search many genes in parallel; compare gene expression among different tissue types as well as between normal and cancer cells; download raw data; and generate heatmaps; and finally, use its internal statistical tool. Most importantly, MERAV has been designed as a unique tool for analyzing metabolic processes as it includes matrixes specifically focused on metabolic genes and is linked to the Kyoto Encyclopedia of Genes and Genomes pathway search.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    Translational control of the innate immune response through IRF-7 (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-02-15
    Description: Transcriptional activation of cytokines, such as type-I interferons (interferon (IFN)-alpha and IFN-beta), constitutes the first line of antiviral defence. Here we show that translational control is critical for induction of type-I IFN production. In mouse embryonic fibroblasts lacking the translational repressors 4E-BP1 and 4E-BP2, the threshold for eliciting type-I IFN production is lowered. Consequently, replication of encephalomyocarditis virus, vesicular stomatitis virus, influenza virus and Sindbis virus is markedly suppressed. Furthermore, mice with both 4E- and 4E-BP2 genes (also known as Eif4ebp1 and Eif4ebp2, respectively) knocked out are resistant to vesicular stomatitis virus infection, and this correlates with an enhanced type-I IFN production in plasmacytoid dendritic cells and the expression of IFN-regulated genes in the lungs. The enhanced type-I IFN response in 4E-BP1-/- 4E-BP2-/- double knockout mouse embryonic fibroblasts is caused by upregulation of interferon regulatory factor 7 (Irf7) messenger RNA translation. These findings highlight the role of 4E-BPs as negative regulators of type-I IFN production, via translational repression of Irf7 mRNA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Colina, Rodney -- Costa-Mattioli, Mauro -- Dowling, Ryan J O -- Jaramillo, Maritza -- Tai, Lee-Hwa -- Breitbach, Caroline J -- Martineau, Yvan -- Larsson, Ola -- Rong, Liwei -- Svitkin, Yuri V -- Makrigiannis, Andrew P -- Bell, John C -- Sonenberg, Nahum -- Howard Hughes Medical Institute/ -- England -- Nature. 2008 Mar 20;452(7185):323-8. doi: 10.1038/nature06730. Epub 2008 Feb 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and McGill Cancer Center, McGill University, Montreal, Quebec H3G 1Y6, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18272964" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Carrier Proteins/genetics/metabolism ; Cells, Cultured ; Dendritic Cells/immunology ; Embryo, Mammalian/cytology ; Eukaryotic Initiation Factors/deficiency/genetics/metabolism ; Fibroblasts/virology ; Gene Deletion ; Immunity, Innate/genetics/*immunology ; Interferon Regulatory Factor-7/*biosynthesis/genetics/metabolism ; Interferon Type I/biosynthesis/immunology ; Mice ; Mice, Knockout ; Phosphoproteins/deficiency/genetics/metabolism ; *Protein Biosynthesis ; RNA, Messenger/genetics/metabolism ; Vesicular stomatitis Indiana virus/physiology ; Virus Physiological Phenomena ; Virus Replication
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 4
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    Two-dimensional normal-state quantum oscillations in a superconducting heterostructure (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-11-27
    Description: Semiconductor heterostructures provide an ideal platform for studying high-mobility, low-density electrons in reduced dimensions. The realization of superconductivity in heavily doped diamond, silicon, silicon carbide and germanium suggests that Cooper pairs eventually may be directly incorporated in semiconductor heterostructures, but these newly discovered superconductors are currently limited by their extremely large electronic disorder. Similarly, the electron mean free path in low-dimensional superconducting thin films is usually limited by interface scattering, in single-crystal or polycrystalline samples, or atomic-scale disorder, in amorphous materials, confining these examples to the extreme 'dirty limit'. Here we report the fabrication of a high-quality superconducting layer within a thin-film heterostructure based on SrTiO(3) (the first known superconducting semiconductor). By selectively doping a narrow region of SrTiO(3) with the electron-donor niobium, we form a superconductor that is two-dimensional, as probed by the anisotropy of the upper critical magnetic field. Unlike in previous examples, however, the electron mobility is high enough that the normal-state resistance exhibits Shubnikov-de Haas oscillations that scale with the perpendicular field, indicating two-dimensional states. These results suggest that delta-doped SrTiO(3) provides a model system in which to explore the quantum transport and interplay of both superconducting and normal electrons. They also demonstrate that high-quality complex oxide heterostructures can maintain electron coherence on the macroscopic scales probed by transport, as well as on the microscopic scales demonstrated previously.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kozuka, Y -- Kim, M -- Bell, C -- Kim, B G -- Hikita, Y -- Hwang, H Y -- England -- Nature. 2009 Nov 26;462(7272):487-90. doi: 10.1038/nature08566.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Advanced Materials Science, University of Tokyo, Kashiwa, Chiba 277-8561, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19940921" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 5
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    International network of cancer genome projects (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-04-16
    Description: The International Cancer Genome Consortium (ICGC) was launched to coordinate large-scale cancer genome studies in tumours from 50 different cancer types and/or subtypes that are of clinical and societal importance across the globe. Systematic studies of more than 25,000 cancer genomes at the genomic, epigenomic and transcriptomic levels will reveal the repertoire of oncogenic mutations, uncover traces of the mutagenic influences, define clinically relevant subtypes for prognosis and therapeutic management, and enable the development of new cancer therapies.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2902243/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2902243/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉International Cancer Genome Consortium -- Hudson, Thomas J -- Anderson, Warwick -- Artez, Axel -- Barker, Anna D -- Bell, Cindy -- Bernabe, Rosa R -- Bhan, M K -- Calvo, Fabien -- Eerola, Iiro -- Gerhard, Daniela S -- Guttmacher, Alan -- Guyer, Mark -- Hemsley, Fiona M -- Jennings, Jennifer L -- Kerr, David -- Klatt, Peter -- Kolar, Patrik -- Kusada, Jun -- Lane, David P -- Laplace, Frank -- Youyong, Lu -- Nettekoven, Gerd -- Ozenberger, Brad -- Peterson, Jane -- Rao, T S -- Remacle, Jacques -- Schafer, Alan J -- Shibata, Tatsuhiro -- Stratton, Michael R -- Vockley, Joseph G -- Watanabe, Koichi -- Yang, Huanming -- Yuen, Matthew M F -- Knoppers, Bartha M -- Bobrow, Martin -- Cambon-Thomsen, Anne -- Dressler, Lynn G -- Dyke, Stephanie O M -- Joly, Yann -- Kato, Kazuto -- Kennedy, Karen L -- Nicolas, Pilar -- Parker, Michael J -- Rial-Sebbag, Emmanuelle -- Romeo-Casabona, Carlos M -- Shaw, Kenna M -- Wallace, Susan -- Wiesner, Georgia L -- Zeps, Nikolajs -- Lichter, Peter -- Biankin, Andrew V -- Chabannon, Christian -- Chin, Lynda -- Clement, Bruno -- de Alava, Enrique -- Degos, Francoise -- Ferguson, Martin L -- Geary, Peter -- Hayes, D Neil -- Johns, Amber L -- Kasprzyk, Arek -- Nakagawa, Hidewaki -- Penny, Robert -- Piris, Miguel A -- Sarin, Rajiv -- Scarpa, Aldo -- van de Vijver, Marc -- Futreal, P Andrew -- Aburatani, Hiroyuki -- Bayes, Monica -- Botwell, David D L -- Campbell, Peter J -- Estivill, Xavier -- Grimmond, Sean M -- Gut, Ivo -- Hirst, Martin -- Lopez-Otin, Carlos -- Majumder, Partha -- Marra, Marco -- McPherson, John D -- Ning, Zemin -- Puente, Xose S -- Ruan, Yijun -- Stunnenberg, Hendrik G -- Swerdlow, Harold -- Velculescu, Victor E -- Wilson, Richard K -- Xue, Hong H -- Yang, Liu -- Spellman, Paul T -- Bader, Gary D -- Boutros, Paul C -- Flicek, Paul -- Getz, Gad -- Guigo, Roderic -- Guo, Guangwu -- Haussler, David -- Heath, Simon -- Hubbard, Tim J -- Jiang, Tao -- Jones, Steven M -- Li, Qibin -- Lopez-Bigas, Nuria -- Luo, Ruibang -- Muthuswamy, Lakshmi -- Ouellette, B F Francis -- Pearson, John V -- Quesada, Victor -- Raphael, Benjamin J -- Sander, Chris -- Speed, Terence P -- Stein, Lincoln D -- Stuart, Joshua M -- Teague, Jon W -- Totoki, Yasushi -- Tsunoda, Tatsuhiko -- Valencia, Alfonso -- Wheeler, David A -- Wu, Honglong -- Zhao, Shancen -- Zhou, Guangyu -- Lathrop, Mark -- Thomas, Gilles -- Yoshida, Teruhiko -- Axton, Myles -- Gunter, Chris -- Miller, Linda J -- Zhang, Junjun -- Haider, Syed A -- Wang, Jianxin -- Yung, Christina K -- Cros, Anthony -- Liang, Yong -- Gnaneshan, Saravanamuttu -- Guberman, Jonathan -- Hsu, Jack -- Chalmers, Don R C -- Hasel, Karl W -- Kaan, Terry S H -- Lowrance, William W -- Masui, Tohru -- Rodriguez, Laura Lyman -- Vergely, Catherine -- Bowtell, David D L -- Cloonan, Nicole -- deFazio, Anna -- Eshleman, James R -- Etemadmoghadam, Dariush -- Gardiner, Brooke B -- Kench, James G -- Sutherland, Robert L -- Tempero, Margaret A -- Waddell, Nicola J -- Wilson, Peter J -- Gallinger, Steve -- Tsao, Ming-Sound -- Shaw, Patricia A -- Petersen, Gloria M -- Mukhopadhyay, Debabrata -- DePinho, Ronald A -- Thayer, Sarah -- Shazand, Kamran -- Beck, Timothy -- Sam, Michelle -- Timms, Lee -- Ballin, Vanessa -- Lu, Youyong -- Ji, Jiafu -- Zhang, Xiuqing -- Chen, Feng -- Hu, Xueda -- Yang, Qi -- Tian, Geng -- Zhang, Lianhai -- Xing, Xiaofang -- Li, Xianghong -- Zhu, Zhenggang -- Yu, Yingyan -- Yu, Jun -- Tost, Jorg -- Brennan, Paul -- Holcatova, Ivana -- Zaridze, David -- Brazma, Alvis -- Egevard, Lars -- Prokhortchouk, Egor -- Banks, Rosamonde Elizabeth -- Uhlen, Mathias -- Viksna, Juris -- Ponten, Fredrik -- Skryabin, Konstantin -- Birney, Ewan -- Borg, Ake -- Borresen-Dale, Anne-Lise -- Caldas, Carlos -- Foekens, John A -- Martin, Sancha -- Reis-Filho, Jorge S -- Richardson, Andrea L -- Sotiriou, Christos -- Thoms, Giles -- van't Veer, Laura -- Birnbaum, Daniel -- Blanche, Helene -- Boucher, Pascal -- Boyault, Sandrine -- Masson-Jacquemier, Jocelyne D -- Pauporte, Iris -- Pivot, Xavier -- Vincent-Salomon, Anne -- Tabone, Eric -- Theillet, Charles -- Treilleux, Isabelle -- Bioulac-Sage, Paulette -- Decaens, Thomas -- Franco, Dominique -- Gut, Marta -- Samuel, Didier -- Zucman-Rossi, Jessica -- Eils, Roland -- Brors, Benedikt -- Korbel, Jan O -- Korshunov, Andrey -- Landgraf, Pablo -- Lehrach, Hans -- Pfister, Stefan -- Radlwimmer, Bernhard -- Reifenberger, Guido -- Taylor, Michael D -- von Kalle, Christof -- Majumder, Partha P -- Pederzoli, Paolo -- Lawlor, Rita A -- Delledonne, Massimo -- Bardelli, Alberto -- Gress, Thomas -- Klimstra, David -- Zamboni, Giuseppe -- Nakamura, Yusuke -- Miyano, Satoru -- Fujimoto, Akihiro -- Campo, Elias -- de Sanjose, Silvia -- Montserrat, Emili -- Gonzalez-Diaz, Marcos -- Jares, Pedro -- Himmelbauer, Heinz -- Bea, Silvia -- Aparicio, Samuel -- Easton, Douglas F -- Collins, Francis S -- Compton, Carolyn C -- Lander, Eric S -- Burke, Wylie -- Green, Anthony R -- Hamilton, Stanley R -- Kallioniemi, Olli P -- Ley, Timothy J -- Liu, Edison T -- Wainwright, Brandon J -- 077198/Wellcome Trust/United Kingdom -- 088340/Wellcome Trust/United Kingdom -- 093867/Wellcome Trust/United Kingdom -- 6613/Cancer Research UK/United Kingdom -- K08 DK071329/DK/NIDDK NIH HHS/ -- K08 DK071329-04/DK/NIDDK NIH HHS/ -- K08 DK071329-05/DK/NIDDK NIH HHS/ -- P01 CA117969/CA/NCI NIH HHS/ -- P01 CA117969-04S1/CA/NCI NIH HHS/ -- P01 CA117969-05/CA/NCI NIH HHS/ -- P50 CA102701/CA/NCI NIH HHS/ -- P50 CA102701-08/CA/NCI NIH HHS/ -- P50 CA127003/CA/NCI NIH HHS/ -- P50 CA127003-04/CA/NCI NIH HHS/ -- P50 CA127003-05/CA/NCI NIH HHS/ -- R01 HG001806-02/HG/NHGRI NIH HHS/ -- England -- Nature. 2010 Apr 15;464(7291):993-8. doi: 10.1038/nature08987.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20393554" target="_blank"〉PubMed〈/a〉
    Keywords: DNA Methylation ; DNA Mutational Analysis/trends ; Databases, Genetic ; Genes, Neoplasm/genetics ; Genetics, Medical/*organization & administration/trends ; Genome, Human/*genetics ; Genomics/*organization & administration/trends ; Humans ; Intellectual Property ; *International Cooperation ; Mutation ; Neoplasms/classification/*genetics/pathology/therapy
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 6
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    Intravenous delivery of a multi-mechanistic cancer-targeted oncolytic poxvirus in humans (2011)
    Nature Publishing Group (NPG)
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    Publication Date: 2011-09-03
    Description: The efficacy and safety of biological molecules in cancer therapy, such as peptides and small interfering RNAs (siRNAs), could be markedly increased if high concentrations could be achieved and amplified selectively in tumour tissues versus normal tissues after intravenous administration. This has not been achievable so far in humans. We hypothesized that a poxvirus, which evolved for blood-borne systemic spread in mammals, could be engineered for cancer-selective replication and used as a vehicle for the intravenous delivery and expression of transgenes in tumours. JX-594 is an oncolytic poxvirus engineered for replication, transgene expression and amplification in cancer cells harbouring activation of the epidermal growth factor receptor (EGFR)/Ras pathway, followed by cell lysis and anticancer immunity. Here we show in a clinical trial that JX-594 selectively infects, replicates and expresses transgene products in cancer tissue after intravenous infusion, in a dose-related fashion. Normal tissues were not affected clinically. This platform technology opens up the possibility of multifunctional products that selectively express high concentrations of several complementary therapeutic and imaging molecules in metastatic solid tumours in humans.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Breitbach, Caroline J -- Burke, James -- Jonker, Derek -- Stephenson, Joe -- Haas, Andrew R -- Chow, Laura Q M -- Nieva, Jorge -- Hwang, Tae-Ho -- Moon, Anne -- Patt, Richard -- Pelusio, Adina -- Le Boeuf, Fabrice -- Burns, Joe -- Evgin, Laura -- De Silva, Naomi -- Cvancic, Sara -- Robertson, Terri -- Je, Ji-Eun -- Lee, Yeon-Sook -- Parato, Kelley -- Diallo, Jean-Simon -- Fenster, Aaron -- Daneshmand, Manijeh -- Bell, John C -- Kirn, David H -- Canadian Institutes of Health Research/Canada -- England -- Nature. 2011 Aug 31;477(7362):99-102. doi: 10.1038/nature10358.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Jennerex Inc., 450 Sansome Street, 16th floor, San Francisco, California 94111, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21886163" target="_blank"〉PubMed〈/a〉
    Keywords: Adult ; Aged ; Aged, 80 and over ; DNA, Viral/blood ; Female ; Gene Expression Regulation, Enzymologic ; Humans ; Infusions, Intravenous ; Male ; Middle Aged ; Neoplasms/pathology/surgery/*therapy/virology ; *Oncolytic Virotherapy ; Oncolytic Viruses/*physiology ; Organisms, Genetically Modified/physiology ; Poxviridae/*physiology ; Transgenes/genetics ; beta-Galactosidase/genetics/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 7
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    Direct imaging of RecA nucleation and growth on single molecules of SSB-coated ssDNA (2012)
    Nature Publishing Group (NPG)
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    Publication Date: 2012-10-30
    Description: Escherichia coli RecA is the defining member of a ubiquitous class of DNA strand-exchange proteins that are essential for homologous recombination, a pathway that maintains genomic integrity by repairing broken DNA. To function, filaments of RecA must nucleate and grow on single-stranded DNA (ssDNA) in direct competition with ssDNA-binding protein (SSB), which rapidly binds and continuously sequesters ssDNA, kinetically blocking RecA assembly. This dynamic self-assembly on a DNA lattice, in competition with another protein, is unique for the RecA family compared to other filament-forming proteins such as actin and tubulin. The complexity of this process has hindered our understanding of RecA filament assembly because ensemble measurements cannot reliably distinguish between the nucleation and growth phases, despite extensive and diverse attempts. Previous single-molecule assays have measured the nucleation and growth of RecA--and its eukaryotic homologue RAD51--on naked double-stranded DNA and ssDNA; however, the template for RecA self-assembly in vivo is SSB-coated ssDNA. Using single-molecule microscopy, here we directly visualize RecA filament assembly on single molecules of SSB-coated ssDNA, simultaneously measuring nucleation and growth. We establish that a dimer of RecA is required for nucleation, followed by growth of the filament through monomer addition, consistent with the finding that nucleation, but not growth, is modulated by nucleotide and magnesium ion cofactors. Filament growth is bidirectional, albeit faster in the 5'--〉3' direction. Both nucleation and growth are repressed at physiological conditions, highlighting the essential role of recombination mediators in potentiating assembly in vivo. We define a two-step kinetic mechanism in which RecA nucleates on transiently exposed ssDNA during SSB sliding and/or partial dissociation (DNA unwrapping) and then the RecA filament grows. We further demonstrate that the recombination mediator protein pair, RecOR (RecO and RecR), accelerates both RecA nucleation and filament growth, and that the introduction of RecF further stimulates RecA nucleation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4112059/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4112059/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bell, Jason C -- Plank, Jody L -- Dombrowski, Christopher C -- Kowalczykowski, Stephen C -- CA136103/CA/NCI NIH HHS/ -- F32 CA136103/CA/NCI NIH HHS/ -- GM62653/GM/NIGMS NIH HHS/ -- GM64745/GM/NIGMS NIH HHS/ -- R01 GM062653/GM/NIGMS NIH HHS/ -- R01 GM064745/GM/NIGMS NIH HHS/ -- T32 CA10052159/CA/NCI NIH HHS/ -- T32 CA108459/CA/NCI NIH HHS/ -- T32 GM007377/GM/NIGMS NIH HHS/ -- England -- Nature. 2012 Nov 8;491(7423):274-8. doi: 10.1038/nature11598. Epub 2012 Oct 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology, University of California, Davis, California 95616, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23103864" target="_blank"〉PubMed〈/a〉
    Keywords: DNA, Single-Stranded/chemistry/*metabolism ; DNA-Binding Proteins/*metabolism ; Escherichia coli/*chemistry/enzymology ; Escherichia coli Proteins/*metabolism ; Hydrogen-Ion Concentration ; Ligands ; Microscopy, Fluorescence/*methods ; Models, Biological ; Models, Molecular ; Molecular Conformation ; Protein Multimerization ; Rec A Recombinases/*chemistry/*metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 8
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    Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs (2012)
    Nature Publishing Group (NPG)
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    Publication Date: 2012-12-04
    Description: Cryptophyte and chlorarachniophyte algae are transitional forms in the widespread secondary endosymbiotic acquisition of photosynthesis by engulfment of eukaryotic algae. Unlike most secondary plastid-bearing algae, miniaturized versions of the endosymbiont nuclei (nucleomorphs) persist in cryptophytes and chlorarachniophytes. To determine why, and to address other fundamental questions about eukaryote-eukaryote endosymbiosis, we sequenced the nuclear genomes of the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans. Both genomes have 〉21,000 protein genes and are intron rich, and B. natans exhibits unprecedented alternative splicing for a single-celled organism. Phylogenomic analyses and subcellular targeting predictions reveal extensive genetic and biochemical mosaicism, with both host- and endosymbiont-derived genes servicing the mitochondrion, the host cell cytosol, the plastid and the remnant endosymbiont cytosol of both algae. Mitochondrion-to-nucleus gene transfer still occurs in both organisms but plastid-to-nucleus and nucleomorph-to-nucleus transfers do not, which explains why a small residue of essential genes remains locked in each nucleomorph.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Curtis, Bruce A -- Tanifuji, Goro -- Burki, Fabien -- Gruber, Ansgar -- Irimia, Manuel -- Maruyama, Shinichiro -- Arias, Maria C -- Ball, Steven G -- Gile, Gillian H -- Hirakawa, Yoshihisa -- Hopkins, Julia F -- Kuo, Alan -- Rensing, Stefan A -- Schmutz, Jeremy -- Symeonidi, Aikaterini -- Elias, Marek -- Eveleigh, Robert J M -- Herman, Emily K -- Klute, Mary J -- Nakayama, Takuro -- Obornik, Miroslav -- Reyes-Prieto, Adrian -- Armbrust, E Virginia -- Aves, Stephen J -- Beiko, Robert G -- Coutinho, Pedro -- Dacks, Joel B -- Durnford, Dion G -- Fast, Naomi M -- Green, Beverley R -- Grisdale, Cameron J -- Hempel, Franziska -- Henrissat, Bernard -- Hoppner, Marc P -- Ishida, Ken-Ichiro -- Kim, Eunsoo -- Koreny, Ludek -- Kroth, Peter G -- Liu, Yuan -- Malik, Shehre-Banoo -- Maier, Uwe G -- McRose, Darcy -- Mock, Thomas -- Neilson, Jonathan A D -- Onodera, Naoko T -- Poole, Anthony M -- Pritham, Ellen J -- Richards, Thomas A -- Rocap, Gabrielle -- Roy, Scott W -- Sarai, Chihiro -- Schaack, Sarah -- Shirato, Shu -- Slamovits, Claudio H -- Spencer, David F -- Suzuki, Shigekatsu -- Worden, Alexandra Z -- Zauner, Stefan -- Barry, Kerrie -- Bell, Callum -- Bharti, Arvind K -- Crow, John A -- Grimwood, Jane -- Kramer, Robin -- Lindquist, Erika -- Lucas, Susan -- Salamov, Asaf -- McFadden, Geoffrey I -- Lane, Christopher E -- Keeling, Patrick J -- Gray, Michael W -- Grigoriev, Igor V -- Archibald, John M -- BB/G00885X/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- Howard Hughes Medical Institute/ -- England -- Nature. 2012 Dec 6;492(7427):59-65. doi: 10.1038/nature11681. Epub 2012 Nov 28.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23201678" target="_blank"〉PubMed〈/a〉
    Keywords: Algal Proteins/genetics/metabolism ; Alternative Splicing/genetics ; Cell Nucleus/*genetics ; Cercozoa/cytology/*genetics/metabolism ; Cryptophyta/cytology/*genetics/metabolism ; Cytosol/metabolism ; *Evolution, Molecular ; Gene Duplication/genetics ; Gene Transfer, Horizontal/genetics ; Genes, Essential/genetics ; Genome/*genetics ; Genome, Mitochondrial/genetics ; Genome, Plant/genetics ; Genome, Plastid/genetics ; Molecular Sequence Data ; *Mosaicism ; Phylogeny ; Protein Transport ; Proteome/genetics/metabolism ; Symbiosis/*genetics ; Transcriptome/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 9
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    A self-consistent, absolute isochronal age scale for young moving groups in the solar neighbourhood (2015)
    Oxford University Press
    Details
    Publication Date: 2015-09-26
    Description: We present a self-consistent, absolute isochronal age scale for young ( 200 Myr), nearby ( 100 pc) moving groups in the solar neighbourhood based on homogeneous fitting of semi-empirical pre-main-sequence model isochrones using the 2 maximum-likelihood fitting statistic of Naylor & Jeffries in the M V , V – J colour–magnitude diagram. The final adopted ages for the groups are as follows: $149^{+51}_{-19}\,\rm {Myr}$ for the AB Dor moving group, 24 ± 3 Myr for the β Pic moving group (BPMG), $45^{+11}_{-7}\,\rm {Myr}$ for the Carina association, $42^{+6}_{-4}\,\rm {Myr}$ for the Columba association, 11 ± 3 Myr for the Cha cluster, 45 ± 4 Myr for the Tucana–Horologium moving group (Tuc–Hor), 10 ± 3 Myr for the TW Hya association and $22^{+4}_{-3}\,\rm {Myr}$ for the 32 Ori group. At this stage we are uncomfortable assigning a final, unambiguous age to the Argus association as our membership list for the association appears to suffer from a high level of contamination, and therefore it remains unclear whether these stars represent a single population of coeval stars. Our isochronal ages for both the BPMG and Tuc–Hor are consistent with recent lithium depletion boundary (LDB) ages, which unlike isochronal ages, are relatively insensitive to the choice of low-mass evolutionary models. This consistency between the isochronal and LDB ages instils confidence that our self-consistent, absolute age scale for young, nearby moving groups is robust, and hence we suggest that these ages be adopted for future studies of these groups. Software implementing the methods described in this study is available from http://www.astro.ex.ac.uk/people/timn/tau-squared/ .
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 10
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    Crystal structures of Escherichia coli exonuclease I in complex with single-stranded DNA provide insights into the mechanism of processive digestion (2013)
    Oxford University Press
    Details
    Publication Date: 2013-06-08
    Description: Escherichia coli Exonuclease I (ExoI) digests single-stranded DNA (ssDNA) in the 3'-5' direction in a highly processive manner. The crystal structure of ExoI, determined previously in the absence of DNA, revealed a C-shaped molecule with three domains that form a central positively charged groove. The active site is at the bottom of the groove, while an extended loop, proposed to encircle the DNA, crosses over the groove. Here, we present crystal structures of ExoI in complex with four different ssDNA substrates. The structures all have the ssDNA bound in essentially the predicted manner, with the 3'-end in the active site and the downstream end under the crossover loop. The central nucleotides of the DNA form a prominent bulge that contacts the SH3-like domain, while the nucleotides at the downstream end of the DNA form extensive interactions with an ‘anchor’ site. Seven of the complexes are similar to one another, but one has the ssDNA bound in a distinct conformation. The highest-resolution structure, determined at 1.95 Å, reveals an Mg 2+ ion bound to the scissile phosphate in a position corresponding to Mg B in related two-metal nucleases. The structures provide new insights into the mechanism of processive digestion that will be discussed.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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