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1. Borgs are giant extrachromosomal elements with the potential to augment methane oxidation

Author

West-Roberts J, Michael J. Wilkins, Jennifer A. Doudna, Kenneth H. Williams, Basem Al-Shayeb, Mullen S, Alexander Crits-Christoph, Marie Charlotte Schoelmerich, Luis E. Valentin-Alvarado, Rohan Sachdeva, and Jillian F. Banfield

Subjects
biology, Phylogenetics, Evolutionary biology, Chemistry, Extrachromosomal DNA, Anaerobic oxidation of methane, Direct repeat, biology.organism_classification, Gene, Genome, Genomic organization, Archaea
Abstract

SummaryAnaerobic methane oxidation exerts a key control on greenhouse gas emissions 1, yet factors that modulate the activity of microorganisms performing this function remain little explored. In studying groundwater, sediments, and wetland soil where methane production and oxidation occur, we discovered extraordinarily large, diverse DNA sequences that primarily encode hypothetical proteins. Four curated, complete genomes are linear, up to ~1 Mbp in length and share genome organization, including replicore structure, long inverted terminal repeats, and genome-wide unique perfect tandem direct repeats that are intergenic or generate amino acid repeats. We infer that these are a new type of archaeal extrachromosomal element with a distinct evolutionary origin. Gene sequence similarity, phylogeny, and local divergence of sequence composition indicate that many of their genes were assimilated from methane-oxidizing Methanoperedens archaea. We refer to these elements as “Borgs”. We identified at least 19 different Borg types coexisting with Methanoperedens in four distinct ecosystems. Borg genes expand redox and respiratory capacity (e.g., clusters of multiheme cytochromes), ability to respond to changing environmental conditions, and likely augment Methanoperedens capacity for methane oxidation (e.g., methyl coenzyme M reductase). By this process, Borgs could play a previously unrecognized role in controlling greenhouse gas emissions.

Published
2021

2. Craters, boulders and regolith of (101955) Bennu indicative of an old and dynamic surface

Author

Walsh, KJ, Jawin, ER, Ballouz, R-L, Barnouin, OS, Bierhaus, EB, Jr, CHC, Molaro, JL, McCoy, TJ, Delbo', M, Hartzell, CM, Pajola, M, Schwartz, SR, Trang, D, Asphaug, E, Becker, KJ, Beddingfield, CB, Bennett, CA, Bottke, WF, Burke, KN, Clark, BC, Daly, MG, Dellagiustina, DN, Dworkin, JP, Elder, CM, Golish, DR, Hildebrand, AR, Malhotra, R, Marshall, J, Michel, P, Nolan, MC, Perry, ME, Rizk, B, Ryan, A, Sandford, SA, Scheeres, DJ, Susorney, HCM, Thuillet, F, Lauretta, DS, Highsmith, DE, Small, J, Vokrouhlicky, D, Bowles, NE, Brown, E, Hanna, KLD, Warren, T, Brunet, C, Chicoine, RA, Desjardins, S, Gaudreau, D, Haltigin, T, Millington-Veloza, S, Rubi, A, Aponte, J, Gorius, N, Lunsford, A, Allen, B, Grindlay, J, Guevel, D, Hoak, D, Hong, J, Schrader, DL, Bayron, J, Golubov, O, Sanchez, P, Stromberg, J, Hirabayashi, M, Oliver, S, Rascon, M, Harch, A, Joseph, J, Squyres, S, Richardson, D, Emery, JP, McGraw, L, Ghent, R, Binzel, RP, Asad, MM, Johnson, CL, Philpott, L, Cloutis, EA, Hanna, RD, Ciceri, F, Ibrahim, E-M, Breitenfeld, L, Glotch, T, Rogers, AD, Clark, BE, Ferrone, S, Thomas, CA, Campins, H, Fernandez, Y, Chang, W, Cheuvront, A, Tachibana, S, Yurimoto, H, Brucato, JR, Poggiali, G, Dotto, E, Epifani, EM, Crombie, MK, Lantz, C, Izawa, MRM, De Leon, J, Licandro, J, Garcia, JLR, Clemett, S, Thomas-Keprta, K, Van Wal, S, Yoshikawa, M, Bellerose, J, Bhaskaran, S, Boyles, C, Chesley, SR, Farnocchia, D, Harbison, A, Kennedy, B, Knight, A, Martinez-Vlasoff, N, Mastrodemos, N, McElrath, T, Owen, W, Park, R, Rush, B, Swanson, L, Takahashi, Y, Velez, D, Yetter, K, Thayer, C, Adam, C, Antreasian, P, Bauman, J, Bryan, C, Carcich, B, Corvin, M, Geeraert, J, Hoffman, J, Leonard, JM, Lessac-Chenen, E, Levine, A, McAdams, J, McCarthy, L, Nelson, D, Page, B, Pelgrift, J, Sahr, E, Stakkestad, K, Stanbridge, D, Wibben, D, Williams, B, Williams, K, Wolff, P, Hayne, P, Kubitschek, D, Barucci, MA, Deshapriya, JDP, Fornasier, S, Fulchignoni, M, Hasselmann, P, Merlin, F, Praet, A, Billett, O, Boggs, A, Buck, B, Carlson-Kelly, S, Cerna, J, Chaffin, K, Church, E, Coltrin, M, Daly, J, Deguzman, A, Dubisher, R, Eckart, D, Ellis, D, Falkenstern, P, Fisher, A, Fisher, ME, Fleming, P, Fortney, K, Francis, S, Freund, S, Gonzales, S, Haas, P, Hasten, A, Hauf, D, Hilbert, A, Howell, D, Jaen, F, Jayakody, N, Jenkins, M, Johnson, K, Lefevre, M, Ma, H, Mario, C, Martin, K, May, C, McGee, M, Miller, B, Miller, C, Miller, G, Mirfakhrai, A, Muhle, E, Norman, C, Olds, R, Parish, C, Ryle, M, Schmitzer, M, Sherman, P, Skeen, M, Susak, M, Sutter, B, Tran, Q, Welch, C, Witherspoon, R, Wood, J, Zareski, J, Arvizu-Jakubicki, M, Audi, E, Bandrowski, R, Becker, TL, Bendall, S, Bloomenthal, H, Blum, D, Boynton, WV, Brodbeck, J, Chojnacki, M, Colpo, A, Contreras, J, Cutts, J, D'Aubigny, CYD, Dean, D, Diallo, B, Drinnon, D, Drozd, K, Enos, HL, Enos, R, Fellows, C, Ferro, T, Fisher, MR, Fitzgibbon, G, Fitzgibbon, M, Forelli, J, Forrester, T, Galinsky, I, Garcia, R, Gardner, A, Habib, N, Hamara, D, Hammond, D, Hanley, K, Harshman, K, Hergenrother, CW, Herzog, K, Hill, D, Hoekenga, C, Hooven, S, Howell, ES, Huettner, E, Janakus, A, Jones, J, Kareta, TR, Kidd, J, Kingsbury, K, Balram-Knutson, SS, Koelbel, L, Kreiner, J, Lambert, D, Lewin, C, Lovelace, B, Loveridge, M, Lujan, M, Maleszewski, CK, Marchese, K, McDonough, E, Mogk, N, Morrison, V, Morton, E, Munoz, R, Nelson, J, Padilla, J, Pennington, R, Polit, A, Ramos, N, Reddy, V, Riehl, M, Roper, HL, Salazar, S, Selznick, S, Shultz, N, Smith, PH, Stewart, S, Sutton, S, Swindle, T, Tang, YH, Westermann, M, Wolner, CWV, Worden, D, Zega, T, Zeszut, Z, Bjurstrom, A, Bloomquist, L, Dickinson, C, Keates, E, Liang, J, Nifo, V, Taylor, A, Teti, F, Caplinger, M, Bowles, H, Carter, S, Dickenshied, S, Doerres, D, Fisher, T, Hagee, W, Hill, J, Miner, M, Noss, D, Piacentine, N, Smith, M, Toland, A, Wren, P, Bernacki, M, Munoz, DP, Watanabe, S-I, Aqueche, A, Ashman, B, Barker, M, Bartels, A, Berry, K, Bos, B, Burns, R, Calloway, A, Carpenter, R, Castro, N, Cosentino, R, Donaldson, J, Cook, JE, Emr, C, Everett, D, Fennell, D, Fleshman, K, Folta, D, Gallagher, D, Garvin, J, Getzandanner, K, Glavin, D, Hull, S, Hyde, K, Ido, H, Ingegneri, A, Jones, N, Kaotira, P, Lim, LF, Liounis, A, Lorentson, C, Lorenz, D, Lyzhoft, J, Mazarico, EM, Mink, R, Moore, W, Moreau, M, Mullen, S, Nagy, J, Neumann, G, Nuth, J, Poland, D, Reuter, DC, Rhoads, L, Rieger, S, Rowlands, D, Sallitt, D, Scroggins, A, Shaw, G, Simon, AA, Swenson, J, Vasudeva, P, Wasser, M, Zellar, R, Grossman, J, Johnston, G, Morris, M, Wendel, J, Burton, A, Keller, LP, McNamara, L, Messenger, S, Nakamura-Messenger, K, Nguyen, A, Righter, K, Queen, E, Bellamy, K, Dill, K, Gardner, S, Giuntini, M, Key, B, Kissell, J, Patterson, D, Vaughan, D, Wright, B, Gaskell, RW, Le Corre, L, Li, J-Y, Palmer, EE, Siegler, MA, Tricarico, P, Weirich, JR, Zou, X-D, Ireland, T, Tait, K, Bland, P, Anwar, S, Bojorquez-Murphy, N, Christensen, PR, Haberle, CW, Mehall, G, Rios, K, Franchi, I, Rozitis, B, Brack, DN, French, AS, McMahon, JW, Russell, S, Killgore, M, Hamilton, VE, Kaplan, HH, Bandfield, JL, Chodas, M, Lambert, M, Masterson, RA, Freemantle, J, Seabrook, JA, Craft, K, Daly, RT, Ernst, C, Espiritu, RC, Holdridge, M, Jones, M, Nair, AH, Nguyen, L, Peachey, J, Plescia, J, Roberts, JH, Steele, R, Turner, R, Backer, J, Edmundson, K, Mapel, J, Milazzo, M, Sides, S, Manzoni, C, May, B, Delbo, M, Libourel, G, Marty, B, Team, O-R, Centro di Ateneo di Studi e Attività Spaziali 'Giuseppe Colombo' (CISAS), Universita degli Studi di Padova, Laboratoire de Géophysique Interne et Tectonophysique (LGIT), Observatoire des Sciences de l'Univers de Grenoble (OSUG), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Laboratoire Central des Ponts et Chaussées (LCPC)-Institut des Sciences de la Terre (ISTerre), Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-PRES Université de Grenoble-Institut de recherche pour le développement [IRD] : UR219-Institut national des sciences de l'Univers (INSU - CNRS)-Institut Français des Sciences et Technologies des Transports, de l'Aménagement et des Réseaux (IFSTTAR)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-PRES Université de Grenoble-Institut de recherche pour le développement [IRD] : UR219-Institut Français des Sciences et Technologies des Transports, de l'Aménagement et des Réseaux (IFSTTAR), ASU School of Earth and Space Exploration (SESE), Arizona State University [Tempe] (ASU), IHU-LIRYC, Université Bordeaux Segalen - Bordeaux 2-CHU Bordeaux [Bordeaux], NASA Goddard Space Flight Center (GSFC), National Dairy Research Institute, SETI Institute, Institute of Northern Engineering, 455 Duckering Bldg, Lunar and Planetary Laboratory [Tucson] (LPL), University of Arizona, Centre de Mise en Forme des Matériaux (CEMEF), Centre National de la Recherche Scientifique (CNRS)-PSL Research University (PSL)-MINES ParisTech - École nationale supérieure des mines de Paris, Institut des Sciences de la Terre (ISTerre), Institut Français des Sciences et Technologies des Transports, de l'Aménagement et des Réseaux (IFSTTAR)-Institut national des sciences de l'Univers (INSU - CNRS)-Institut de recherche pour le développement [IRD] : UR219-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), MINES ParisTech - École nationale supérieure des mines de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), and ANR-15-IDEX-0001,UCA JEDI,Idex UCA JEDI(2015)

Subjects
Near-Earth object, 010504 meteorology & atmospheric sciences, Mass movement, [SDU.ASTR.EP]Sciences of the Universe [physics]/Astrophysics [astro-ph]/Earth and Planetary Astrophysics [astro-ph.EP], Geomorphology, 010502 geochemistry & geophysics, 01 natural sciences, Billion years, Regolith, Astrobiology, [SPI]Engineering Sciences [physics], Asteroids comets and Kuiper belt, Impact crater, Asteroid, General Earth and Planetary Sciences, Asteroid belt, Early solar system, Geology, 0105 earth and related environmental sciences
Abstract

著者人数: 38名ほか (The OSIRIS-REx Team: 所属. 宇宙航空研究開発機構宇宙科学研究所(JAXA)(ISAS): Van wal, S; 吉川, 真; 渡邊, 誠一郎), Number of authors: 38 and The OSIRIS-REx Team (Affiliation. Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency(JAXA)(ISAS): Van wal, S; Yoshikawa, Makoto; Watanabe, Sei-icihro), Accepted: 2019-02-11, 資料番号: SA1190038000

Published
2019

3. Genome-wide linkage meta-analysis identifies susceptibility loci at 2q34 and 13q31.3 for genetic generalized epilepsies

Author

EPICURE Consortium, Leu C., de Kovel C. G., Zara F., Striano P., Pezzella M., Robbiano A., Bianchi A., Coppola A., Giallonardo A. T., Beccaria F., Trenité D. K., Lindhout D., Gaus V., Schmitz B., Janz D., Weber Y. G., Becker F., Lerche H., Kleefuss Lie A. A., Hallman K., Kunz W. S., Elger C. E., Muhle H., Stephani U., Møller R. S., Hjalgrim H., Mullen S., Scheffer I. E., Berkovic S. F., Everett K. V., Gardiner M. R., Marini C., Guerrini R., Lehesjoki A. E., Siren A., Nabbout R., Baulac S., Leguern E., Serratosa J. M., Rosenow F., Feucht M., Unterberger I., Covanis A., Suls A., Weckhuysen S., Kaneva R., Caglayan H., Turkdogan D., Baykan B., Bebek N., Ozbek U., Hempelmann A., Schulz H., Rüschendorf F., Trucks H., Nürnberg P., Avanzini G., Koeleman B. P., Sander T., BISULLI, FRANCESCA, TINUPER, PAOLO, YÜCESAN, EMRAH, EPICURE Consortium, Leu C., de Kovel C.G., Zara F., Striano P., Pezzella M., Robbiano A., Bianchi A., Bisulli F., Coppola A., Giallonardo A.T., Beccaria F., Trenité D.K., Lindhout D., Gaus V., Schmitz B., Janz D., Weber Y.G., Becker F., Lerche H., Kleefuss-Lie A.A., Hallman K., Kunz W.S., Elger C.E., Muhle H., Stephani U., Møller R.S., Hjalgrim H., Mullen S., Scheffer I.E., Berkovic S.F., Everett K.V., Gardiner M.R., Marini C., Guerrini R., Lehesjoki A.E., Siren A., Nabbout R., Baulac S., Leguern E., Serratosa J.M., Rosenow F., Feucht M., Unterberger I., Covanis A., Suls A., Weckhuysen S., Kaneva R., Caglayan H., Turkdogan D., Baykan B., Bebek N., Ozbek U., Hempelmann A., Schulz H., Rüschendorf F., Trucks H., Nürnberg P., Avanzini G., Koeleman B.P., Sander T., and Tinuper P.

Subjects
Male, Chromosomes, Human, Pair 13, Genotype, Genetic Linkage, Chromosome Mapping, complex inheritance, Pedigree, genetic generalized epilepsy, myoclonic seizure, Phenotype, Genetic Loci, Chromosomes, Human, Pair 2, Humans, Epilepsy, Generalized, Family, Female, Genetic Predisposition to Disease, linkage analysis, absence seizure, Genome-Wide Association Study
Abstract

PURPOSE: Genetic generalized epilepsies (GGEs) have a lifetime prevalence of 0.3% with heritability estimates of 80%. A considerable proportion of families with siblings affected by GGEs presumably display an oligogenic inheritance. The present genome-wide linkage meta-analysis aimed to map: (1) susceptibility loci shared by a broad spectrum of GGEs, and (2) seizure type-related genetic factors preferentially predisposing to either typical absence or myoclonic seizures, respectively. METHODS: Meta-analysis of three genome-wide linkage datasets was carried out in 379 GGE-multiplex families of European ancestry including 982 relatives with GGEs. To dissect out seizure type-related susceptibility genes, two family subgroups were stratified comprising 235 families with predominantly genetic absence epilepsies (GAEs) and 118 families with an aggregation of juvenile myoclonic epilepsy (JME). To map shared and seizure type-related susceptibility loci, both nonparametric loci (NPL) and parametric linkage analyses were performed for a broad trait model (GGEs) in the entire set of GGE-multiplex families and a narrow trait model (typical absence or myoclonic seizures) in the subgroups of JME and GAE families. KEY FINDINGS: For the entire set of 379 GGE-multiplex families, linkage analysis revealed six loci achieving suggestive evidence for linkage at 1p36.22, 3p14.2, 5q34, 13q12.12, 13q31.3, and 19q13.42. The linkage finding at 5q34 was consistently supported by both NPL and parametric linkage results across all three family groups. A genome-wide significant nonparametric logarithm of odds score of 3.43 was obtained at 2q34 in 118 JME families. Significant parametric linkage to 13q31.3 was found in 235 GAE families assuming recessive inheritance (heterogeneity logarithm of odds = 5.02). SIGNIFICANCE: Our linkage results support an oligogenic predisposition of familial GGE syndromes. The genetic risk factor at 5q34 confers risk to a broad spectrum of familial GGE syndromes, whereas susceptibility loci at 2q34 and 13q31.3 preferentially predispose to myoclonic seizures or absence seizures, respectively. Phenotype- genotype strategies applying narrow trait definitions in phenotypic homogeneous subgroups of families improve the prospects of disentangling the genetic basis of common familial GGE syndromes.

Published
2012

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