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202. The induction of manganese superoxide dismutase in response to stress in Nicotiana plumbaginifolia.

Author

Bowler, C., Alliotte, T., De Loose, M., Van Montagu, M., and Inzé, D.

Abstract

Superoxide dismutases (SODs) are metalloproteins that catalyse the dismutation of superoxide radicals to oxygen and hydrogen peroxide. The enzyme has been found in all aerobic organisms examined, where it plays a major role in the defence against toxic reduced oxygen species which are generated in many biological oxidations. Here we report the complete primary structure of a plant manganese superoxide dismutase (MnSOD), deduced from a cDNA clone of Nicotiana plumbaginifolia. The plant protein is highly homologous to MnSODs from other organisms and also contains an N‐terminal leader sequence resembling a transit peptide for mitochondrial targeting. The location of the mature protein within the mitochondria has been demonstrated by subcellular fractionation experiments. We have analysed the expression profile of this MnSOD and found that it is dramatically induced during stress conditions, most notably in tissue culture as a result of sugar metabolism and also as part of the pathogenesis response of the plant, being induced by ethylene, salicylic acid, and Pseudomonas syringae infection. This induction is always accompanied by an increase in cytochrome oxidase activity, which suggests a specific protective role for MnSOD during conditions of increased mitochondrial respiration.

Published
1989
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203. A New Plant for Management of Radioactive Waste

Author

Schumann, F., Pfefferkorn, G., and Loose, M.

Abstract

By 1991 a new plant for management of radioactive waste will be erected in the CINR. Thus increased atomic safety and radiation protection will be attained, the economy of waste management and the quality of the conditioned waste will simultaneously be improved. Facilities for volume reduction (evaporation, press compaction, solidification) and conditioning (solidification, packing) will be available for the treatment of radioactive waste. A novel handling technique will ensure safe handling of radioactive waste conditioned for repository. The facilities mentioned above will be installed in a building of about 25000 m3.

Published
1990
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204. Primary structure of a hormonally regulated β-glucanase of Nicotiana plumbaginifolia

Author

De Loose, M., Alliotte, T., Gheysen, G., Genetello, C., Gielen, J., Soetaert, P., Van Montagu, M., and Inzé, D.

Abstract

A cDNA clone for a hormonally regulated β-glucanase from Nicotiana plumbaginifoliahas been isolated by using an oligodeoxynucleotide probe, synthesized to match the previously determined N-tenninal amino acid sequence. The cDNA has the complete sequence of the mature protein and contains at least part of a hydrophobic signal peptide. At the amino acid level, the β-glucanase of N. plumbaginifoliais 73% homologous to a β(l,3)-glucanase from tobacco and 52% homologous to a β(1,3;1,4)-glucanase from barley. Southern-blot analysis clearly demonstrated that N. plumbaginifoliacontains at least two related genes encoding β-glucanase. The extent of the complete signal peptide of the cloned β-glucanase was determined by sequencing part of the corresponding gene. Northern analysis showed that the expression of the β-glucanase gene is influenced by auxins and cytokinins.

Published
1988
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205. Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020

Author

Alm E., Broberg E.K., Connor T., Hodcroft E.B., Komissarov A.B., Maurer-Stroh S., Melidou A., Neher R.A., O'Toole A., Pereyaslov D., Beerenwinkel N., Posada-Cespedes S., Jablonski K.P., Ferreira P.F., Topolsky I., Avsic-Zupanc T., Korva M., Poljak M., Zakotnik S., Zorec T.M., Bragstad K., Hungnes O., Stene-Johansen K., Reusken C., Meijer A., Vennema H., Ruiz-Roldan L., Bracho M.A., Garcia-Gonzalez N., Chiner-Oms A., Cancino-Munoz I., Comas I., Goig G.A., Torres-Puente M., Lopez M.G., Martinez-Priego L., D'Auria G., Ruiz-Hueso P., Ferrus-Abad L., de Marco G., Galan-Vendrell I., Carbo-Ramirez S., Ruiz-Rodriguez P., Coscolla M., Polackova K., Kramna L., Cinek O., Richter J., Krashias G., Tryfonos C., Bashiardes S., Koptides D., Christodoulou C., Bartolini B., Gruber C.E., Di Caro A., Castilletti C., Stefani F., Rimoldi S.G., Romeri F., Salerno F., Polesello S., Nagy A., Jirincova H., Vecerova J., Novakova L., Cordey S., Murtskhvaladze M., Kotaria N., Schar T., Beisel C., Vugrek O., Rokic F., Trgovec-Greif L., Jurak I., Rukavina T., Sucic N., Schonning K., Karst S.M., Kirkegaard R.H., Michaelsen T.Y., Sorensen E.A., Knutson S., Brandt J., Le-Quy V., Sorensen T., Petersen C., Pedersen M.S., Larsen S.L., Skov M.N., Rasmussen M., Fonager J., Fomsgaard A., Maksyutov R.A., Gavrilova E.V., Pyankov O.V., Bodnev S.A., Tregubchak T.V., Shvalov A.N., Antonets D.V., Resende P.C., Goya S., Perrin A., Lee R.T., Yadahalli S., Han A.X., Russell C.A., Schmutz S., Zaheri M., Kufner V., Huber M., Trkola A., Antwerpen M., Walter M.C., van der Werf S., Gambaro F., Behillil S., Enouf V., Donati F., Ustinova M., Rovite V., Klovins J., Savicka O., Wienecke-Baldacchino A.K., Ragimbeau C., Fournier G., Mossong J., Aberle S.W., Haukland M., Enkirch T., Advani A., Karlberg M.L., Lindsjo O.K., Broddesson S., Slavikova M., Lickova M., Klempa B., Staronova E., Ticha E., Szemes T., Rusnakova D., Stadler T., Quer J., Anton A., Andres C., Pinana M., Garcia-Cehic D., Pumarola T., Izopet J., Gioula G., Exindari M., Papa A., Chatzidimitriou D., Metallidis S., Pappa S., Macek M., Geryk J., Broz P., Briksi A., Hubacek P., Drevinek P., Zajac M., Kvapil P., Holub M., Kvapilova K., Novotny A., Kasny M., Klempt P., Vapalahti O., Smura T., Sironen T., Selhorst P., Anthony C., Arien K., Simon-Loriere E., Rabalski L., Bienkowska-Szewczyk K., Borges V., Isidro J., Gomes J.P., Guiomar R., Pechirra P., Costa I., Duarte S., Vieira L., Pyrc K., Zuckerman N.S., Turdikulova S., Abdullaev A., Dalimova D., Abdurakhimov A., Tagliabracci A., Alessandrini F., Melchionda F., Onofri V., Turchi C., Bagnarelli P., Menzo S., Caucci S., Di Sante L., Popa A., Genger J.-W., Agerer B., Lercher A., Endler L., Smyth M., Penz T., Schuster M., Senekowitsch M., Laine J., Bock C., Bergthaler A., Shevtsov A., Kalendar R., Ramanculov Y., Graf A., Muenchhoff M., Keppler O.T., Krebs S., Blum H., Marcello A., Licastro D., D'Agaro P., Laubscher F., Vidanovic D., Tesovic B., Volkening J., Clementi N., Mancini N., Rupnik M., Mahnic A., Walker A., Houwaart T., Wienemann T., Vasconcelos M.K., Strelow D., Jensen B.-E.O., Senff T., Hulse L., Adams O., Andree M., Hauka S., Feldt T., Keitel V., Kindgen-Milles D., Timm J., Pfeffer K., Dilthey A.T., Moore C., Ozdarendeli A., Pavel S.T.I., Yetiskin H., Aydin G., Holyavkin C., Uygut M.A., Cevik C., Shchetinin A., Gushchin V., Dinler-Doganay G., Doganay L., Kizilboga-Akgun T., Karacan I., Pancer K., Maes P., Marti-Carreras J., Wawina-Bokalanga T., Vanmechelen B., Thurmer A., Wedde M., Durrwald R., von Kleist M., Drechsel O., Wolff T., Fuchs S., Kmiecinski R., Michel J., Nitsche A., Casas I., Caballero M.I., Zaballos A., Jimenez P., Jimenez M., Fernandez S.M., Fernandez S.V., de la Plaza I.C., Fadeev A., Ivanova A., Sergeeva M., Stefanelli P., Estee Torok M., Hall G., da Silva Filipe A., Turtle L., Afifi S., McCluggage K., Beer R., Ledesma J., Maksimovic J., Spellman K., Hamilton W.L., Marchbank A., Southgate J.A., Underwood A., Taylor B., Yeats C., Abudahab K., Gemmell M.R., Eccles R., Lucaci A., Nelson C.A., Rainbow L., Whitehead M., Gregory R., Haldenby S., Paterson S., Hughes M.A., Curran M.D., Baker D., Tucker R., Green L.R., Feltwell T., Halstead F.D., Wyles M., Jahun A.S., Ahmad S.S.Y., Georgana I., Goodfellow I., Yakovleva A., Meredith L.W., Gavriil A., Awan A.R., Fisher C., Edgeworth J., Lynch J., Moore N., Williams R., Kidd S.P., Cortes N., Brunker K., McCrone J.T., Quick J., Duckworth N., Walsh S., Sloan T., Ludden C., George R.P., Eltringham G., Brown J.R., Aranday-Cortes E., Shepherd J.G., Hughes J., Li K.K., Williams T.C., Johnson N., Jesudason N., Mair D., Thomson E., Shah R., Parr Y.A., Carmichael S., Robertson D.L., Nomikou K., Broos A., Niebel M., Smollett K., Tong L., Miah S., Wittner A., Phillips N., Payne B., Dewar R., Holmes A., Bolt F., Price J.R., Mookerjee S., Sethi D.K., Potter W., Stanley R., Prakash R., Dervisevic S., Graham J.C., Nelson A., Smith D., Young G.R., Yew W.C., Todd J.A., Trebes A., Andersson M., Bull M., Watkins J., Birchley A., Gatica-Wilcox B., Gilbert L., Kumziene-Summerhayes S., Rey S., Chauhan A., Butcher E., Bicknell K., Elliott S., Glaysher S., Lackenby A., Bibby D., Platt S., Mohamed H., Machin N.W., Mbisa J.L., Evans J., Perry M., Pacchiarini N., Corden S., Adams A.G., Gaskin A., Coombs J., Graham L.J., Cottrell S., Morgan M., Gifford L., Kolyva A., Rudder S.J., Trotter A.J., Mather A.E., Aydin A., Page A.J., Kay G.L., de Oliveira Martins L., Yasir M., Alikhan N.-F., Thomson N.M., Gilroy R., Kingsley R.A., O'Grady J., Gutierrez A.V., Diaz M., Viet T.L., Tedim A.P., Adriaenssens E.M., Patrick Mcclure C., Sang F., Clark G., Howson-Wells H.C., Debebe J., Ball J., Chappell J., Khakh M., Carlile M., Loose M., Lister M.M., Holmes N., Tsoleridis T., Fleming V.M., Wright V., Smith W., Gallagher M.D., Parker M., Partridge D.G., Evans C., Baker P., Essex S., Liggett S., Keeley A.J., Bashton M., Rooke S., Dervisavic S., Meader E.J., Lopez C.E.B., Angyal A., Kristiansen M., Tutill H.J., Findlay J., Mestek-Boukhibar L., Forrest L., Dyal P., Williams R.J., Panchbhaya Y., Williams C.A., Roy S., Pandey S., Stockton J., Loman N.J., Poplawski R., Nicholls S., Rowe W.P.M., Khokhar F., Pinckert M.L., Hosmillo M., Chaudhry Y., Caller L.G., Davidson R.K., Griffith L., Rambaut A., Jackson B., Colquhoun R., Hill V., Nichols J., Asamaphan P., Darby A., Jackson K.A., Iturriza-Gomara M., Vamos E.E., Green A., Aanensen D., Bonsall D., Buck D., Macintyre-Cockett G., de Cesare M., Pybus O., Golubchik T., Scarlett G., Loveson K.F., Robson S.C., Beckett A., Lindsey B., Groves D.C., Parsons P.J., McHugh M.P., Barnes J.D., Manso C.F., Grammatopoulos D., Menger K.E., Harrison E., Gunson R., Peacock S.J., Gonzalez G., Carr M., Mihaela L., Popovici O., Brytting M., Bresner C., Fuller W., Workman T., Mentis A.F., Kossyvakis A., Karamitros T., Pogka V., Kalliaropoulos A., Horefti E., Kontou A., Martinez-Gonzalez B., Labropoulou V., Voulgari-Kokota A., Evangelidou M., Bizta P., Belimezi M., Lambrechts L., Doymaz M.Z., Yazici M.K., Cetin N.S., Karaaslan E., Kallio-Kokko H., Virtanen J., Suvanto M., Nguyen P.T., Ellonen P., Hannula S., Kangas H., Sreenu V.B., Burian K., Terhes G., Gombos K., Gyenesei A., Urban P., Herczeg R., Jakab F., Kemenesi G., Toth G.E., Somogyi B., Zana B., Zeghbib S., Kuczmog A., Foldes F., Lanszki Z., Madai M., Papp H., Pereszlenyi C.I., Babinszky G.C., Dudas G., Csoma E., Abou Tayoun A.N., Alsheikh-Ali A.A., Loney T., Nowotny N., Abdul-Wahab O., Gonzalez-Candelas F., Andersen M.H., Taylor S., MARTI CARRERAS, Joan, Vanmechelen, Bert, Wawina, Tony, Medical Microbiology and Infection Prevention, AII - Infectious diseases, WHO European Region Sequencing Lab, GISAID EpiCoV Grp, Erik, Alm, Eeva K, Broberg, Thomas, Connor, Emma B, Hodcroft, Andrey B, Komissarov, Sebastian, Maurer-Stroh, Angeliki, Melidou, Richard A, Neher, Áine, O’Toole, Dmitriy, Pereyaslov, WHO European Region sequencing laboratories and GISAID EpiCoV group (Niko Beerenwinkel, The, Posada-Céspedes, Susana, Philipp, Kim, Jablonski, Falé Ferreira, Pedro, Topolsky, Ivan, Avšičžupanc, Tatjana, Korva, Miša, Poljak, Mario, Zakotnik, Samo, Tomaž, Zorec, Mark, Bragstad, Karoline, Hungnes, Olav, Stene-Johansen, Kathrine, Reusken, Chantal, Meijer, Adam, Vennema, Harry, Ruiz-Roldán, Lidia, Alma Bracho, María, García-González, Neri, Chiner-Oms, Álvaro, Cancino-Muñoz, Irving, Comas, Iñaki, A Goig, Galo, Torres-Puente, Manuela, G López, Mariana, Martínez-Priego, Llúcia, D’Auria, Giuseppe, LoretoFerrús-Abad, de Marco, Griselda, Galan-Vendrell, Inmaculada, Carbó-Ramirez, Sandra, Ruíz-Hueso, Paula, Coscollá, Mireia, Polackova, Katerina, Kramna, Lenka, Cinek, Ondrej, Richter, Jan, Krashias, George, Tryfonos, Christina, Bashiardes, Stavro, Koptides, Dana, Christodoulou, Christina, Bartolini, Barbara, Em Gruber, Cesare, Di Caro, Antonino, Castilletti, Concetta, Stefani, Fabrizio, Giordana Rimoldi, Sara, Romeri, Francesca, Salerno, Franco, Polesello, Stefano, Nagy, Alexander, Jirincova, Helena, Vecerova, Jaromira, Novakova, Ludmila, Cordey, Samuel, Murtskhvaladze, Marine, Kotaria, Nato, Schär, Tobia, Beisel, Christian, Vugrek, Oliver, Rokić, Filip, Trgovecgreif, Lovro, Jurak, Igor, Rukavina, Tomislav, Sučić, Neven, Schønning, Kristian, M Karst, Søren, H Kirkegaard, Rasmu, Y Michaelsen, Thoma, Aa Sørensen, Emil, Knutson, Simon, Brandt, Jakob, Le-Quy, Vang, Sørensen, Trine, Petersen, Celine, Schou Pedersen, Martin, Løkkegaard Larsen, Sanne, Nielsine Skov, Marianne, Rasmussen, Morten, Fonager, Jannik, Fomsgaard, Ander, Amirovich Maksyutov, Rinat, Vasil’Evna Gavrilova, Elena, Victorovich Pyankov, Oleg, Alexandrovich Bodnev, Sergey, Vladimirovna Tregubchak, Tatyana, Nikolayevich Shvalov, Alexander, Victorovich Antonets, Deni, Cristina Resende, Paola, Goya, Stephanie, Perrin, Amandine, Tc Lee, Raphael, Yadahalli, Shilpa, X Han, Alvin, A Russell, Colin, Schmutz, Stefan, Zaheri, Maryam, Kufner, Verena, Huber, Michael, Trkola, Alexandra, Antwerpen, Marku, C Walter, Mathia, van der Werf, Sylvie, Gambaro, Fabiana, Behillil, Sylvie, Enouf, Vincent, Donati, Flora, Ustinova, Monta, Rovite, Vita, Klovins, Jani, Savicka, Oksana, K Wienecke-Baldacchino, Anke, Ragimbeau, Catherine, Fournier, Guillaume, Mossong, Joël, W Aberle, Stephan, Haukland, Mattia, Enkirch, Theresa, Advani, Abdolreza, Lind Karlberg, Maria, Karlsson Lindsjö, Oskar, Broddesson, Sandra, Sláviková, Monika, Ličková, Martina, Klempa, Bori, Staroňová, Edita, Tichá, Elena, Szemes, Tomáš, Rusňáková, Diana, Stadler, Tanja, Quer, Josep, Anton, Andre, Andres, Cristina, Piñana, Maria, Garcia-Cehic, Damir, Pumarola, Toma, Izopet, Jacque, Gioula, Georgia, Exindari, Maria, Papa, Anna, Chatzidimitriou, Dimitrio, Metallidis, Symeon, Pappa, Stella, Macek Jr, Milan, Geryk, Jan, Brož, Petr, Briksí, Aleš, Hubáček, Petr, Dřevínek, Pavel, Zajac, Miroslav, Kvapil, Petr, Holub, Michal, Kvapilová, Kateřina, Novotný, Adam, Kašný, Martin, Klempt, Petr, Vapalahti, Olli, Smura, Teemu, Sironen, Tarja, Selhorst, Philippe, Anthony, Colin, Ariën, Kevin, Simon-Loriere, Etienne, Rabalski, Lukasz, Bienkowska-Szewczyk, Krystyna, Borges, Vítor, Isidro, Joana, Paulo Gomes, João, Guiomar, Raquel, Pechirra, Pedro, Costa, Inê, Duarte, Sílvia, Vieira, Luí, Pyrc, Krzysztof, S Zuckerman, Neta, Turdikulova, Shahlo, Abdullaev, Alisher, Dalimova, Dilbar, Abdurakhimov, Abror, Tagliabracci, Adriano, Alessandrini, Federica, Melchionda, Filomena, Onofri, Valerio, Turchi, Chiara, Bagnarelli, Patrizia, Menzo, Stefano, Caucci, Sara, Di Sante, Laura, Popa, Alexandra, Genger, Jakob-Wendelin, Agerer, Benedikt, Lercher, Alexander, Endler, Luka, Smyth, Mark, Penz, Thoma, Schuster, Michael, Senekowitsch, Martin, Laine, Jan, Bock, Christoph, Bergthaler, Andrea, Shevtsov, Alexandr, Kalendar, Ruslan, Ramanculov, Yerlan, Graf, Alexander, Muenchhoff, Maximilian, T Keppler, Oliver, Krebs, Stefan, Blum, Helmut, Marcello, Alessandro, Licastro, Danilo, D’Agaro, Pierlanfranco, Laubscher, Florian, Vidanovic, Dejan, Tesovic, Bojana, Volkening, Jeremy, Clementi, Nicola, Mancini, Nicasio, Rupnik, Maja, Mahnic, Aleksander, Walker, Andrea, Houwaart, Torsten, Wienemann, Tobia, Kohns Vasconcelos, Malte, Strelow, Daniel, Ole Jensen, Björn-Erik, Senff, Tina, Hülse, Lisanna, Adams, Ortwin, Andree, Marcel, Hauka, Sandra, Feldt, Torsten, Keitel, Verena, Kindgen-Milles, Detlef, Timm, Jörg, Pfeffer, Klau, T Dilthey, Alexander, Moore, Catherine, Ozdarendeli, Aykut, Terkis Islam Pavel, Shaikh, Yetiskin, Hazel, Aydin, Gunsu, Holyavkin, Can, Ali Uygut, Muhammet, Cevik, Ceren, Shchetinin, Alexey, Gushchin, Vladimir, Dinler-Doganay, Gizem, Doganay, Levent, Kizilboga-Akgun, Tugba, Karacan, Ilker, Pancer, Katarzyna, Maes, Piet, Martí-Carreras, Joan, Wawina-Bokalanga, Tony, Thürmer, Andrea, Wedde, Marianne, Dürrwald, Ralf, Von Kleist, Max, Drechsel, Oliver, Wolff, Thorsten, Fuchs, Stephan, Kmiecinski, Rene, Michel, Janine, Nitsche, Andrea, Casas, Inmaculada, Iglesias Caballero, María, Zaballos, Ángel, Jiménez, Pilar, Jiménez, Mercede, Monzón Fernández, Sara, Varona Fernández, Sarai, Cuesta De La Plaza, Isabel, Fadeev, Artem, Ivanova, Anna, Sergeeva, Mariia, Stefanelli, Paola, Estee Torok, M, Hall, Grant, da Silva Filipe, Ana, Turtle, Lance, Afifi, Safiah, Mccluggage, Kathryn, Beer, Robert, Ledesma, Juan, Maksimovic, Joshua, Spellman, Karla, L Hamilton, William, Marchbank, Angela, Alexander Southgate, Joel, Underwood, Anthony, Taylor, Ben, Yeats, Corin, Abudahab, Khalil, R Gemmell, Matthew, Eccles, Richard, Lucaci, Anita, Abigail Nelson, Charlotte, Rainbow, Lucille, Whitehead, Mark, Gregory, Richard, Haldenby, Sam, Paterson, Steve, A Hughes, Margaret, D Curran, Martin, Baker, David, Tucker, Rachel, R Green, Luke, Feltwell, Theresa, D Halstead, Fenella, Wyles, Matthew, S Jahun, Aminu, Y Ahmad, Shazaad S, Georgana, Iliana, Goodfellow, Ian, Yakovleva, Anna, W Meredith, Luke, Gavriil, Artemi, Raza Awan, Ali, Fisher, Chloe, Jonathan, European Centre for Disease Prevention and Control [Stockholm, Sweden] (ECDC), Cardiff University, Public Health Wales [Cardiff, Royaume uni], University of Basel (Unibas), Research Institute of Influenza, St. Petersburg, Russia, Agency for science, technology and research [Singapore] (A*STAR), National University of Singapore (NUS), University of Edinburgh, WHO Regional Office for Europe [Copenhagen], We gratefully acknowledge the authors, originating and submitting laboratories of the sequences from GISAID’s EpiCoV Database used in the phylogenetic analysis. We gratefully acknowledge all the staff working with sample collection, sample preparation, sequencing, data analysis and data sharing in all laboratories in the WHO European Region for making this work possible, The WHO European Region sequencing laboratories and GISAID EpiCoV group*: Niko Beerenwinkel, Susana Posada-Céspedes, Kim Philipp Jablonski, Pedro Falé Ferreira, Ivan Topolsky, Tatjana Avšič-Županc, Miša Korva, Mario Poljak, Samo Zakotnik, Tomaž Mark Zorec, Karoline Bragstad, Olav Hungnes, Kathrine Stene-Johansen, Chantal Reusken, Adam Meijer, Harry Vennema, Lidia Ruiz-Roldán, María Alma Bracho, Neris García-González, Álvaro Chiner-Oms, Irving Cancino-Muñoz, Iñaki Comas, Galo A Goig, Manuela Torres-Puente, Mariana G López, Llúcia Martínez-Priego, Giuseppe D'Auria, Paula Ruíz-Hueso, Loreto Ferrús-Abad, Griselda de Marco, Inmaculada Galan-Vendrell, Sandra Carbó-Ramirez, Paula Ruiz-Rodriguez, Mireia Coscollá, Katerina Polackova, Lenka Kramna, Ondrej Cinek, Jan Richter, George Krashias, Christina Tryfonos, Stavros Bashiardes, Dana Koptides, Christina Christodoulou, Barbara Bartolini, Cesare Em Gruber, Antonino Di Caro, Concetta Castilletti, Fabrizio Stefani, Sara Giordana Rimoldi, Francesca Romeri, Franco Salerno, Stefano Polesello, Alexander Nagy, Helena Jirincova, Jaromira Vecerova, Ludmila Novakova, Samuel Cordey, Marine Murtskhvaladze, Nato Kotaria, Tobias Schär, Christian Beisel, Oliver Vugrek, Filip Rokić, Lovro Trgovec-Greif, Igor Jurak, Tomislav Rukavina, Neven Sučić, Kristian Schønning, Søren M Karst, Rasmus H Kirkegaard, Thomas Y Michaelsen, Emil Aa Sørensen, Simon Knutson, Jakob Brandt, Vang Le-Quy, Trine Sørensen, Celine Petersen, Martin Schou Pedersen, Sanne Løkkegaard Larsen, Marianne Nielsine Skov, Morten Rasmussen, Jannik Fonager, Anders Fomsgaard, Rinat Amirovich Maksyutov, Elena Vasil'Evna Gavrilova, Oleg Victorovich Pyankov, Sergey Alexandrovich Bodnev, Tatyana Vladimirovna Tregubchak, Alexander Nikolayevich Shvalov, Denis Victorovich Antonets, Paola Cristina Resende, Stephanie Goya, Amandine Perrin, Raphael Tc Lee, Shilpa Yadahalli, Alvin X Han, Colin A Russell, Stefan Schmutz, Maryam Zaheri, Verena Kufner, Michael Huber, Alexandra Trkola, Markus Antwerpen, Mathias C Walter, Sylvie van der Werf, Fabiana Gambaro, Sylvie Behillil, Vincent Enouf, Flora Donati, Monta Ustinova, Vita Rovite, Janis Klovins, Oksana Savicka, Anke K Wienecke-Baldacchino, Catherine Ragimbeau, Guillaume Fournier, Joël Mossong, Stephan W Aberle, Mattias Haukland, Theresa Enkirch, Abdolreza Advani, Maria Lind Karlberg, Oskar Karlsson Lindsjö, Sandra Broddesson, Monika Sláviková, Martina Ličková, Boris Klempa, Edita Staroňová, Elena Tichá, Tomáš Szemes, Diana Rusňáková, Tanja Stadler, Josep Quer, Andres Anton, Cristina Andres, Maria Piñana, Damir Garcia-Cehic, Tomas Pumarola, Jacques Izopet, Georgia Gioula, Maria Exindari, Anna Papa, Dimitrios Chatzidimitriou, Symeon Metallidis, Stella Pappa, Milan Macek Jr, Jan Geryk, Petr Brož, Aleš Briksí, Petr Hubáček, Pavel Dřevínek, Miroslav Zajac, Petr Kvapil, Michal Holub, Kateřina Kvapilová, Adam Novotný, Martin Kašný, Petr Klempt, Olli Vapalahti, Teemu Smura, Tarja Sironen, Philippe Selhorst, Colin Anthony, Kevin Ariën, Etienne Simon-Loriere, Lukasz Rabalski, Krystyna Bienkowska-Szewczyk, Vítor Borges, Joana Isidro, João Paulo Gomes, Raquel Guiomar, Pedro Pechirra, Inês Costa, Sílvia Duarte, Luís Vieira, Krzysztof Pyrc, Neta S Zuckerman, Shahlo Turdikulova, Alisher Abdullaev, Dilbar Dalimova, Abror Abdurakhimov, Adriano Tagliabracci, Federica Alessandrini, Filomena Melchionda, Valerio Onofri, Chiara Turchi, Patrizia Bagnarelli, Stefano Menzo, Sara Caucci, Laura Di Sante, Alexandra Popa, Jakob-Wendelin Genger, Benedikt Agerer, Alexander Lercher, Lukas Endler, Mark Smyth, Thomas Penz, Michael Schuster, Martin Senekowitsch, Jan Laine, Christoph Bock, Andreas Bergthaler, Alexandr Shevtsov, Ruslan Kalendar, Yerlan Ramanculov, Alexander Graf, Maximilian Muenchhoff, Oliver T Keppler, 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H., Taylor, S., European Centre for Disease Prevention and Control (ECDC), Public Health Wales Microbiology Cardiff, Faculty of Agriculture and Forestry, Department of Agricultural Sciences, and Institute of Biotechnology

Subjects
Infecções Respiratórias, 0301 basic medicine, MESH: Coronavirus Infections, Epidemiology, [SDV]Life Sciences [q-bio], Distribution (economics), Wastewater, MESH: Base Sequence, Severe Acute Respiratory Syndrome, MESH: World Health Organization, Pandemic, MESH: Coronavirus, MESH: COVID-19, Sequencing, Viral, Clade, Nomenclature, Genome, biology, COVID-19, Europe, NGS, SARS-CoV-2, WGS, nomenclature, sequencing, Base Sequence, Betacoronavirus, Coronavirus, Coronavirus Infections, Genome, Viral, Humans, Phylogeography, Pneumonia, Viral, RNA, Viral, RNA-Dependent RNA Polymerase, Spatio-Temporal Analysis, World Health Organization, Pandemics, C500, European region, 3. Good health, Geography, MESH: Phylogeography, MESH: RNA-Dependent RNA Polymerase, MESH: RNA, Viral, MESH: Betacoronavirus, Spatio-Temporal Analysi, MESH: Genome, Viral, Cartography, Human, Bioquímica, MESH: Pandemics, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Coronaviru, 030106 microbiology, 03 medical and health sciences, MESH: Spatio-Temporal Analysis, MESH: Severe Acute Respiratory Syndrome, Virology, MESH: SARS-CoV-2, Whole genome sequencing, MESH: Humans, Whole Genome Sequencing, Betacoronaviru, Coronavirus Infection, business.industry, Public Health, Environmental and Occupational Health, Pneumonia, biology.organism_classification, B900, 030104 developmental biology, MESH: Pneumonia, Viral, RNA, SARS_CoV-2, 3111 Biomedicine, MESH: Europe, Human medicine, business
Abstract

8 páginas, 3 figuras, We show the distribution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic clades over time and between countries and outline potential genomic surveillance objectives. We applied three genomic nomenclature systems to all sequence data from the World Health Organization European Region available until 10 July 2020. We highlight the importance of real-time sequencing and data dissemination in a pandemic situation, compare the nomenclatures and lay a foundation for future European genomic surveillance of SARS-CoV-2., We gratefully acknowledge the authors, originating and submitting laboratories of the sequences from GISAID’s EpiCoV Database used in the phylogenetic analysis. We gratefully acknowledge all the staff working with sample collection, sample preparation, sequencing, data analysis and data sharing in all laboratories in the WHO European Region for making this work possible.

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207. ACS after SM4: On-orbit Verification of the HST Advanced Camera for Surveys Repair

Author

Golimowski, David A., Cheng, E. S., Loose, M., Sirianni, M., Lupie, O. L., Linda Smith, Arslanian, S., Boyce, K. R., Chapman, G., Chiaberge, M., Desjardins, T., Dye, D., Ellis, T., Grogin, N. A., Lim, P., Lucas, R. A., Maybhate, A., Mil, K. J., Mutchler, M., Ricardo, R., Scott, B., Serrano, B., Suchkov, A., Waczynski, A., Welty, A. D., Wheeler, T., and Wilson, E.

209. Nanopore sequencing and assembly of a human genome with ultra-long reads

Author

Jain, M., Koren, S., Miga, K.H., Quick, J., Rand, A.C., Sasani, T.A., Tyson, J.R., Beggs, A.D., Dilthey, A.T., Fiddes, I.T., Malla, S., Marriott, H., Nieto, T., O'Grady, J., Olsen, H.E., Pedersen, B.S., Rhie, A., Richardson, H., Quinlan, A.R., Snutch, T.P., Tee, L., Paten, B., Phillippy, A.M., Simpson, J.T., Loman, N.J., Loose, M., Jain, M., Koren, S., Miga, K.H., Quick, J., Rand, A.C., Sasani, T.A., Tyson, J.R., Beggs, A.D., Dilthey, A.T., Fiddes, I.T., Malla, S., Marriott, H., Nieto, T., O'Grady, J., Olsen, H.E., Pedersen, B.S., Rhie, A., Richardson, H., Quinlan, A.R., Snutch, T.P., Tee, L., Paten, B., Phillippy, A.M., Simpson, J.T., Loman, N.J., and Loose, M.

Abstract

We report the sequencing and assembly of a reference genome for the human GM12878 Utah/Ceph cell line using the MinION (Oxford Nanopore Technologies) nanopore sequencer. 91.2 Gb of sequence data, representing ~30× theoretical coverage, were produced. Reference-based alignment enabled detection of large structural variants and epigenetic modifications. De novo assembly of nanopore reads alone yielded a contiguous assembly (NG50 ~3 Mb). Next, we developed a protocol to generate ultra-long reads (N50 > 100kb, up to 882 kb). Incorporating an additional 5×-coverage of these data more than doubled the assembly contiguity (NG50 ~6.4 Mb). The final assembled genome was 2,867 million bases in size, covering 85.8% of the reference. Assembly accuracy, after incorporating complementary short-read sequencing data, exceeded 99.8%. Ultra-long reads enabled assembly and phasing of the 4 Mb major histocompatibility complex (MHC) locus in its entirety, measurement of telomere repeat length and closure of gaps in the reference human genome assembly GRCh38.

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210. Recurrent SARS-CoV-2 mutations in immunodeficient patients

Author

Wilkinson, S. A. J., Sparks, N., Kele, B., Peacock, T. P., Robson, S. C., Connor, T. R., Loman, N. J., Golubchik, T., Martinez Nunez, R. T., Bonsall, D., Rambaut, A., Snell, L. B., Livett, R., Ludden, C., Corden, S., Nastouli, E., Nebbia, G., Johnston, I., Lythgoe, K., Estee Torok, M., Goodfellow, I. G., Prieto, J. A., Saeed, K., Jackson, D. K., Houlihan, C., Frampton, D., Hamilton, W. L., Witney, A. A., Bucca, G., Pope, C. F., Moore, C., Thomson, E. C., Harrison, E. M., Smith, C. P., Rogan, F., Beckwith, S. M., Murray, A., Singleton, D., Eastick, K., Sheridan, L. A., Randell, P., Jackson, L. M., Ariani, C. V., Gonçalves, S., Fairley, D. J., Loose, M. W., Watkins, J., Moses, S., Nicholls, S., Bull, M., Amato, R., Smith, D. L., Aanensen, D. M., Barrett, J. C., Aggarwal, D., Shepherd, J. G., Curran, M. D., Parmar, S., Parker, M. D., Williams, C., Glaysher, S., Underwood, A. P., Bashton, M., Pacchiarini, N., Loveson, K. F., Byott, M., Carabelli, A. M., Templeton, K. E., de Silva, T. I., Wang, D., Langford, C. F., Sillitoe, J., Gunson, R. N., Cottrell, S., O’Grady, J., Kwiatkowski, D., Lillie, P. J., Cortes, N., Moore, N., Thomas, C., Burns, P. J., Mahungu, T. W., Liggett, S., Beckett, A. H., Holden, M. T. G., Levett, L. J., Osman, H., Hassan-Ibrahim, M. O., Simpson, D. A., Chand, M., Gupta, R. K., Darby, A. C., Paterson, S., Pybus, O. G., Volz, E. M., de Angelis, D., Robertson, D. L., Page, A. J., Martincorena, I., Aigrain, L., Bassett, A. R., Wong, N., Taha, Y., Erkiert, M. J., Spencer Chapman, M. H., Dewar, R., McHugh, M. P., Mookerjee, S., Aplin, S., Harvey, M., Sass, T., Umpleby, H., Wheeler, H., McKenna, J. P., Warne, B., Taylor, J. F., Chaudhry, Y., Izuagbe, R., Jahun, A. S., Young, G. R., McMurray, C., McCann, C. M., Nelson, A., Elliott, S., Price, A., Crown, M. R., Rey, S, Roy, S., Temperton, B., Shaaban, S., Hesketh, A. R., Laing, K. G., Monahan, I. M., Heaney, J., Pelosi, E., Silviera, S., Wilson-Davies, E., Fryer, H., Adams, H., du Plessis, L., Johnson, R., Harvey, W. T., Hughes, J., Orton, R. J., Spurgin, L. G., Bourgeois, Y., Ruis, C., O’Toole, Á., Gourtovaia, M., Sanderson, T., Fraser, C., Edgeworth, J., Breuer, J., Michell, S. L., Todd, J. A., John, M., Buck, D., Gajee, K., Kay, G. L., Peacock, S. J., Heyburn, D., Kitchman, K., McNally, A., Pritchard, D. T., Dervisevic, S., Muir, P., Robinson, E., Vipond, B. B., Ramadan, N. A., Jeanes, C., Weldon, D., Catalan, J., Jones, N., da Silva Filipe, A., Fuchs, M., Miskelly, J., Jeffries, A. R., Oliver, K., Park, N. R., Ash, A., Koshy, C., Barrow, M., Buchan, S. L., Mantzouratou, A., Clark, G., Holmes, C. W., Campbell, S., Davis, T., Tan, N. K., Brown, J. R., Harris, K. A., Kidd, S. P., Grant, P. R., Xu-McCrae, L., Cox, A., Madona, P., Pond, M., Randell, P. A., Withell, K. T., Graham, C., Denton-Smith, R., Swindells, E., Turnbull, R., Sloan, T. J., Bosworth, A., Hutchings, S., Pymont, H. M., Casey, A., Ratcliffe, L., Jones, C. R., Knight, B. A., Haque, T., Hart, J., Irish-Tavares, D., Witele, E., Mower, C., Watson, L. K., Collins, J., Eltringham, G., Crudgington, D., Macklin, B., Iturriza-Gomara, M., Lucaci, A. O., McClure, P. C., Carlile, M., Holmes, N., Storey, N., Rooke, S., Yebra, G., Craine, N., Perry, M., Alikhan, N. F., Bridgett, S., Cook, K. F., Fearn, C., Goudarzi, S., Lyons, R. A., Williams, T., Haldenby, S. T., Durham, J., Leonard, S., Davies, R. M., Batra, R., Blane, B., Spyer, M. J., Smith, P., Yavus, M., Williams, R. J., Mahanama, A. I. K., Samaraweera, B., Girgis, S. T., Hansford, S. E., Green, A., Beaver, C., Bellis, K. L., Dorman, M. J., Kay, S., Prestwood, L., Rajatileka, S., Quick, J., Poplawski, R., Reynolds, N., Mack, A., Morriss, A., Whalley, T., Patel, B., Georgana, I., Hosmillo, M., Pinckert, M. L., Stockton, J., Henderson, J. H., Hollis, A., Stanley, W., Yew, W. C., Myers, R., Thornton, A., Adams, A., Annett, T., Asad, H., Birchley, A., Coombes, J., Evans, J. M., Fina, L., Gatica-Wilcox, B., Gilbert, L., Graham, L., Hey, J., Hilvers, E., Jones, S., Jones, H., Kumziene-Summerhayes, S., McKerr, C., Powell, J., Pugh, G., Taylor, S., Trotter, A. J., Williams, C. A., Kermack, L. M., Foulkes, B. H., Gallis, M., Hornsby, H. R., Louka, S. F., Pohare, M., Wolverson, P., Zhang, P., MacIntyre-Cockett, G., Trebes, A., Moll, R. J., Ferguson, L., Goldstein, E. J., Maclean, A., Tomb, R., Starinskij, I., Thomson, L., Southgate, J., Kraemer, M. U. G., Raghwani, J., Zarebski, A. E., Boyd, O., Geidelberg, L., Illingworth, C. J., Jackson, C., Pascall, D., Vattipally, S., Freeman, T. M., Hsu, S. N., Lindsey, B. B., James, K., Lewis, K., Tonkin-Hill, G., Tovar-Corona, J. M., Cox, M., Abudahab, K., Menegazzo, M., Taylor, B. E. W., Yeats, C. A., Mukaddas, A., Wright, D. W., de Oliveira Martins, L., Colquhoun, R., Hill, V., Jackson, B., McCrone, J. T., Medd, N., Scher, E., Keatley, J. P., Curran, T., Morgan, S., Maxwell, P., Smith, K., Eldirdiri, S., Kenyon, A., Holmes, A. H., Price, J. R., Wyatt, T., Mather, A. E., Skvortsov, T., Hartley, J. A., Guest, M., Kitchen, C., Merrick, I., Munn, R., Bertolusso, B., Lynch, J., Vernet, G., Kirk, S., Wastnedge, E., Stanley, R., Idle, G., Bradley, D. T., Poyner, J., Mori, M., Jones, O., Wright, V., Brooks, E., Churcher, C. M., Fragakis, M., Galai, K., Jermy, A., Judges, S., McManus, G. M., Smith, K. S., Westwick, E., Attwood, S. W., Bolt, F., Davies, A., De Lacy, E., Downing, F., Edwards, S., Meadows, L., Jeremiah, S., Smith, N., Foulser, L., Charalampous, T., Patel, A., Berry, L., Boswell, T., Fleming, V. M., Howson-Wells, H. C., Joseph, A., Khakh, M., Lister, M. M., Bird, P. W., Fallon, K., Helmer, T., McMurray, C. L., Odedra, M., Shaw, J., Tang, J. W., Willford, N. J., Blakey, V., Raviprakash, V., Sheriff, N., Williams, L. A., Feltwell, T., Bedford, L., Cargill, J. S., Hughes, W., Moore, J., Stonehouse, S., Atkinson, L., Lee, J. C. D., Shah, D., Alcolea-Medina, A., Ohemeng-Kumi, N., Ramble, J., Sehmi, J., Williams, R., Chatterton, W., Pusok, M., Everson, W., Castigador, A., Macnaughton, E., El Bouzidi, K., Lampejo, T., Sudhanva, M., Breen, C., Sluga, G., Ahmad, S. S. Y., George, R. P., Machin, N. W., Binns, D., James, V., Blacow, R., Coupland, L., Smith, L., Barton, E., Padgett, D., Scott, G., Cross, A., Mirfenderesky, M., Greenaway, J., Cole, K., Clarke, P., Duckworth, N., Walsh, S., Bicknell, K., Impey, R., Wyllie, S., Hopes, R., Bishop, C., Chalker, V., Harrison, I., Gifford, L., Molnar, Z., Auckland, C., Evans, C., Johnson, K., Partridge, D. G., Raza, M., Baker, P., Bonner, S., Essex, S., Murray, L. J., Lawton, A. I., Burton-Fanning, S., Payne, B. A. I., Waugh, S., Gomes, A. N., Kimuli, M., Murray, D. R., Ashfield, P., Dobie, D., Ashford, F., Best, A., Crawford, L., Cumley, N., Mayhew, M., Megram, O., Mirza, J., Moles-Garcia, E., Percival, B., Driscoll, M., Ensell, L., Lowe, H. L., Maftei, L., Mondani, M., Chaloner, N. J., Cogger, B. J., Easton, L. J., Huckson, H., Lewis, J., Lowdon, S., Malone, C. S., Munemo, F., Mutingwende, M., Nicodemi, R., Podplomyk, O., Somassa, T., Beggs, A., Richter, A., Cormie, C., Dias, J., Forrest, S., Higginson, E. E., Maes, M., Young, J., Davidson, R. K., Jackson, K. A., Turtle, L., Keeley, A. J., Ball, J., Byaruhanga, T., Chappell, J. G., Dey, J., Hill, J. D., Park, E. J., Fanaie, A., Hilson, R. A., Yaze, G., Lo, S., Afifi, S., Beer, R., Maksimovic, J., McCluggage, K., Spellman, K., Bresner, C., Fuller, W., Marchbank, A., Workman, T., Shelest, E., Debebe, J., Sang, F., Zamudio, M. E., Francois, S., Gutierrez, B., Vasylyeva, T. I., Flaviani, F., Ragonnet-Cronin, M, Smollett, K. L., Broos, A., Mair, D., Nichols, J., Nomikou, K., Tong, L., Tsatsani, I., O’Brien, S., Rushton, S., Sanderson, R., Perkins, J., Cotton, S., Gallagher, A., Allara, E., Pearson, C., Bibby, D., Dabrera, G., Ellaby, N., Gallagher, E., Hubb, J., Lackenby, A., Lee, D., Manesis, N., Mbisa, T., Platt, S., Twohig, K. A., Morgan, M., Aydin, A., Baker, D. J., Foster-Nyarko, E., Prosolek, S. J., Rudder, S., Baxter, C., Carvalho, S. F., Lavin, D., Mariappan, A., Radulescu, C., Singh, A., Tang, M., Morcrette, H., Bayzid, N., Cotic, M., Balcazar, C. E, Gallagher, M. D., Maloney, D., Stanton, T. D., Williamson, K. A., Manley, R., Michelsen, M. L., Sambles, C. M., Studholme, D. J., Warwick-Dugdale, J., Eccles, R., Gemmell, M., Gregory, R., Hughes, M., Nelson, C., Rainbow, L., Vamos, E. E., Webster, H. J., Whitehead, M., Wierzbicki, C., Angyal, A., Green, L. R., Whiteley, M., Betteridge, E., Bronner, I. F., Farr, B. W., Goodwin, S., Lensing, S. V., McCarthy, S. A., Quail, M. A., Rajan, D., Redshaw, N. M., Scott, C., Shirley, L., Thurston, S. A. J., Rowe, W., Gaskin, A., Le-Viet, T., Bonfield, J., Liddle, J., Whitwham, A., Wilkinson, S. A. J., Sparks, N., Kele, B., Peacock, T. P., Robson, S. C., Connor, T. R., Loman, N. J., Golubchik, T., Martinez Nunez, R. T., Bonsall, D., Rambaut, A., Snell, L. B., Livett, R., Ludden, C., Corden, S., Nastouli, E., Nebbia, G., Johnston, I., Lythgoe, K., Estee Torok, M., Goodfellow, I. G., Prieto, J. A., Saeed, K., Jackson, D. K., Houlihan, C., Frampton, D., Hamilton, W. L., Witney, A. A., Bucca, G., Pope, C. F., Moore, C., Thomson, E. C., Harrison, E. M., Smith, C. P., Rogan, F., Beckwith, S. M., Murray, A., Singleton, D., Eastick, K., Sheridan, L. A., Randell, P., Jackson, L. M., Ariani, C. V., Gonçalves, S., Fairley, D. J., Loose, M. W., Watkins, J., Moses, S., Nicholls, S., Bull, M., Amato, R., Smith, D. L., Aanensen, D. M., Barrett, J. C., Aggarwal, D., Shepherd, J. G., Curran, M. D., Parmar, S., Parker, M. D., Williams, C., Glaysher, S., Underwood, A. P., Bashton, M., Pacchiarini, N., Loveson, K. F., Byott, M., Carabelli, A. M., Templeton, K. E., de Silva, T. I., Wang, D., Langford, C. F., Sillitoe, J., Gunson, R. N., Cottrell, S., O’Grady, J., Kwiatkowski, D., Lillie, P. J., Cortes, N., Moore, N., Thomas, C., Burns, P. J., Mahungu, T. W., Liggett, S., Beckett, A. H., Holden, M. T. G., Levett, L. J., Osman, H., Hassan-Ibrahim, M. O., Simpson, D. A., Chand, M., Gupta, R. K., Darby, A. C., Paterson, S., Pybus, O. G., Volz, E. M., de Angelis, D., Robertson, D. L., Page, A. J., Martincorena, I., Aigrain, L., Bassett, A. R., Wong, N., Taha, Y., Erkiert, M. J., Spencer Chapman, M. H., Dewar, R., McHugh, M. P., Mookerjee, S., Aplin, S., Harvey, M., Sass, T., Umpleby, H., Wheeler, H., McKenna, J. P., Warne, B., Taylor, J. F., Chaudhry, Y., Izuagbe, R., Jahun, A. S., Young, G. R., McMurray, C., McCann, C. M., Nelson, A., Elliott, S., Price, A., Crown, M. R., Rey, S, Roy, S., Temperton, B., Shaaban, S., Hesketh, A. R., Laing, K. G., Monahan, I. M., Heaney, J., Pelosi, E., Silviera, S., Wilson-Davies, E., Fryer, H., Adams, H., du Plessis, L., Johnson, R., Harvey, W. T., Hughes, J., Orton, R. J., Spurgin, L. G., Bourgeois, Y., Ruis, C., O’Toole, Á., Gourtovaia, M., Sanderson, T., Fraser, C., Edgeworth, J., Breuer, J., Michell, S. L., Todd, J. A., John, M., Buck, D., Gajee, K., Kay, G. L., Peacock, S. J., Heyburn, D., Kitchman, K., McNally, A., Pritchard, D. T., Dervisevic, S., Muir, P., Robinson, E., Vipond, B. B., Ramadan, N. A., Jeanes, C., Weldon, D., Catalan, J., Jones, N., da Silva Filipe, A., Fuchs, M., Miskelly, J., Jeffries, A. R., Oliver, K., Park, N. R., Ash, A., Koshy, C., Barrow, M., Buchan, S. L., Mantzouratou, A., Clark, G., Holmes, C. W., Campbell, S., Davis, T., Tan, N. K., Brown, J. R., Harris, K. A., Kidd, S. P., Grant, P. R., Xu-McCrae, L., Cox, A., Madona, P., Pond, M., Randell, P. A., Withell, K. T., Graham, C., Denton-Smith, R., Swindells, E., Turnbull, R., Sloan, T. J., Bosworth, A., Hutchings, S., Pymont, H. M., Casey, A., Ratcliffe, L., Jones, C. R., Knight, B. A., Haque, T., Hart, J., Irish-Tavares, D., Witele, E., Mower, C., Watson, L. K., Collins, J., Eltringham, G., Crudgington, D., Macklin, B., Iturriza-Gomara, M., Lucaci, A. O., McClure, P. C., Carlile, M., Holmes, N., Storey, N., Rooke, S., Yebra, G., Craine, N., Perry, M., Alikhan, N. F., Bridgett, S., Cook, K. F., Fearn, C., Goudarzi, S., Lyons, R. A., Williams, T., Haldenby, S. T., Durham, J., Leonard, S., Davies, R. M., Batra, R., Blane, B., Spyer, M. J., Smith, P., Yavus, M., Williams, R. J., Mahanama, A. I. K., Samaraweera, B., Girgis, S. T., Hansford, S. E., Green, A., Beaver, C., Bellis, K. L., Dorman, M. J., Kay, S., Prestwood, L., Rajatileka, S., Quick, J., Poplawski, R., Reynolds, N., Mack, A., Morriss, A., Whalley, T., Patel, B., Georgana, I., Hosmillo, M., Pinckert, M. L., Stockton, J., Henderson, J. H., Hollis, A., Stanley, W., Yew, W. C., Myers, R., Thornton, A., Adams, A., Annett, T., Asad, H., Birchley, A., Coombes, J., Evans, J. M., Fina, L., Gatica-Wilcox, B., Gilbert, L., Graham, L., Hey, J., Hilvers, E., Jones, S., Jones, H., Kumziene-Summerhayes, S., McKerr, C., Powell, J., Pugh, G., Taylor, S., Trotter, A. J., Williams, C. A., Kermack, L. M., Foulkes, B. H., Gallis, M., Hornsby, H. R., Louka, S. F., Pohare, M., Wolverson, P., Zhang, P., MacIntyre-Cockett, G., Trebes, A., Moll, R. J., Ferguson, L., Goldstein, E. J., Maclean, A., Tomb, R., Starinskij, I., Thomson, L., Southgate, J., Kraemer, M. U. G., Raghwani, J., Zarebski, A. E., Boyd, O., Geidelberg, L., Illingworth, C. J., Jackson, C., Pascall, D., Vattipally, S., Freeman, T. M., Hsu, S. N., Lindsey, B. B., James, K., Lewis, K., Tonkin-Hill, G., Tovar-Corona, J. M., Cox, M., Abudahab, K., Menegazzo, M., Taylor, B. E. W., Yeats, C. A., Mukaddas, A., Wright, D. W., de Oliveira Martins, L., Colquhoun, R., Hill, V., Jackson, B., McCrone, J. T., Medd, N., Scher, E., Keatley, J. P., Curran, T., Morgan, S., Maxwell, P., Smith, K., Eldirdiri, S., Kenyon, A., Holmes, A. H., Price, J. R., Wyatt, T., Mather, A. E., Skvortsov, T., Hartley, J. A., Guest, M., Kitchen, C., Merrick, I., Munn, R., Bertolusso, B., Lynch, J., Vernet, G., Kirk, S., Wastnedge, E., Stanley, R., Idle, G., Bradley, D. T., Poyner, J., Mori, M., Jones, O., Wright, V., Brooks, E., Churcher, C. M., Fragakis, M., Galai, K., Jermy, A., Judges, S., McManus, G. M., Smith, K. S., Westwick, E., Attwood, S. W., Bolt, F., Davies, A., De Lacy, E., Downing, F., Edwards, S., Meadows, L., Jeremiah, S., Smith, N., Foulser, L., Charalampous, T., Patel, A., Berry, L., Boswell, T., Fleming, V. M., Howson-Wells, H. C., Joseph, A., Khakh, M., Lister, M. M., Bird, P. W., Fallon, K., Helmer, T., McMurray, C. L., Odedra, M., Shaw, J., Tang, J. W., Willford, N. J., Blakey, V., Raviprakash, V., Sheriff, N., Williams, L. A., Feltwell, T., Bedford, L., Cargill, J. S., Hughes, W., Moore, J., Stonehouse, S., Atkinson, L., Lee, J. C. D., Shah, D., Alcolea-Medina, A., Ohemeng-Kumi, N., Ramble, J., Sehmi, J., Williams, R., Chatterton, W., Pusok, M., Everson, W., Castigador, A., Macnaughton, E., El Bouzidi, K., Lampejo, T., Sudhanva, M., Breen, C., Sluga, G., Ahmad, S. S. Y., George, R. P., Machin, N. W., Binns, D., James, V., Blacow, R., Coupland, L., Smith, L., Barton, E., Padgett, D., Scott, G., Cross, A., Mirfenderesky, M., Greenaway, J., Cole, K., Clarke, P., Duckworth, N., Walsh, S., Bicknell, K., Impey, R., Wyllie, S., Hopes, R., Bishop, C., Chalker, V., Harrison, I., Gifford, L., Molnar, Z., Auckland, C., Evans, C., Johnson, K., Partridge, D. G., Raza, M., Baker, P., Bonner, S., Essex, S., Murray, L. J., Lawton, A. I., Burton-Fanning, S., Payne, B. A. I., Waugh, S., Gomes, A. N., Kimuli, M., Murray, D. R., Ashfield, P., Dobie, D., Ashford, F., Best, A., Crawford, L., Cumley, N., Mayhew, M., Megram, O., Mirza, J., Moles-Garcia, E., Percival, B., Driscoll, M., Ensell, L., Lowe, H. L., Maftei, L., Mondani, M., Chaloner, N. J., Cogger, B. J., Easton, L. J., Huckson, H., Lewis, J., Lowdon, S., Malone, C. S., Munemo, F., Mutingwende, M., Nicodemi, R., Podplomyk, O., Somassa, T., Beggs, A., Richter, A., Cormie, C., Dias, J., Forrest, S., Higginson, E. E., Maes, M., Young, J., Davidson, R. K., Jackson, K. A., Turtle, L., Keeley, A. J., Ball, J., Byaruhanga, T., Chappell, J. G., Dey, J., Hill, J. D., Park, E. J., Fanaie, A., Hilson, R. A., Yaze, G., Lo, S., Afifi, S., Beer, R., Maksimovic, J., McCluggage, K., Spellman, K., Bresner, C., Fuller, W., Marchbank, A., Workman, T., Shelest, E., Debebe, J., Sang, F., Zamudio, M. E., Francois, S., Gutierrez, B., Vasylyeva, T. I., Flaviani, F., Ragonnet-Cronin, M, Smollett, K. L., Broos, A., Mair, D., Nichols, J., Nomikou, K., Tong, L., Tsatsani, I., O’Brien, S., Rushton, S., Sanderson, R., Perkins, J., Cotton, S., Gallagher, A., Allara, E., Pearson, C., Bibby, D., Dabrera, G., Ellaby, N., Gallagher, E., Hubb, J., Lackenby, A., Lee, D., Manesis, N., Mbisa, T., Platt, S., Twohig, K. A., Morgan, M., Aydin, A., Baker, D. J., Foster-Nyarko, E., Prosolek, S. J., Rudder, S., Baxter, C., Carvalho, S. F., Lavin, D., Mariappan, A., Radulescu, C., Singh, A., Tang, M., Morcrette, H., Bayzid, N., Cotic, M., Balcazar, C. E, Gallagher, M. D., Maloney, D., Stanton, T. D., Williamson, K. A., Manley, R., Michelsen, M. L., Sambles, C. M., Studholme, D. J., Warwick-Dugdale, J., Eccles, R., Gemmell, M., Gregory, R., Hughes, M., Nelson, C., Rainbow, L., Vamos, E. E., Webster, H. J., Whitehead, M., Wierzbicki, C., Angyal, A., Green, L. R., Whiteley, M., Betteridge, E., Bronner, I. F., Farr, B. W., Goodwin, S., Lensing, S. V., McCarthy, S. A., Quail, M. A., Rajan, D., Redshaw, N. M., Scott, C., Shirley, L., Thurston, S. A. J., Rowe, W., Gaskin, A., Le-Viet, T., Bonfield, J., Liddle, J., and Whitwham, A.

Abstract

Long-term severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in immunodeficient patients are an important source of variation for the virus but are understudied. Many case studies have been published which describe one or a small number of long-term infected individuals but no study has combined these sequences into a cohesive dataset. This work aims to rectify this and study the genomics of this patient group through a combination of literature searches as well as identifying new case series directly from the COVID-19 Genomics UK (COG-UK) dataset. The spike gene receptor-binding domain and N-terminal domain (NTD) were identified as mutation hotspots. Numerous mutations associated with variants of concern were observed to emerge recurrently. Additionally a mutation in the envelope gene, T30I was determined to be the second most frequent recurrently occurring mutation arising in persistent infections. A high proportion of recurrent mutations in immunodeficient individuals are associated with ACE2 affinity, immune escape, or viral packaging optimisation.There is an apparent selective pressure for mutations that aid cell–cell transmission within the host or persistence which are often different from mutations that aid inter-host transmission, although the fact that multiple recurrent de novo mutations are considered defining for variants of concern strongly indicates that this potential source of novel variants should not be discounted. © The Author(s) 2022. Published by Oxford University Press.

211. Nanopore sequencing and assembly of a human genome with ultra-long reads

Author

Jain, M., Koren, S., Miga, K.H., Quick, J., Rand, A.C., Sasani, T.A., Tyson, J.R., Beggs, A.D., Dilthey, A.T., Fiddes, I.T., Malla, S., Marriott, H., Nieto, T., O'Grady, J., Olsen, H.E., Pedersen, B.S., Rhie, A., Richardson, H., Quinlan, A.R., Snutch, T.P., Tee, L., Paten, B., Phillippy, A.M., Simpson, J.T., Loman, N.J., Loose, M., Jain, M., Koren, S., Miga, K.H., Quick, J., Rand, A.C., Sasani, T.A., Tyson, J.R., Beggs, A.D., Dilthey, A.T., Fiddes, I.T., Malla, S., Marriott, H., Nieto, T., O'Grady, J., Olsen, H.E., Pedersen, B.S., Rhie, A., Richardson, H., Quinlan, A.R., Snutch, T.P., Tee, L., Paten, B., Phillippy, A.M., Simpson, J.T., Loman, N.J., and Loose, M.

Abstract

We report the sequencing and assembly of a reference genome for the human GM12878 Utah/Ceph cell line using the MinION (Oxford Nanopore Technologies) nanopore sequencer. 91.2 Gb of sequence data, representing ~30× theoretical coverage, were produced. Reference-based alignment enabled detection of large structural variants and epigenetic modifications. De novo assembly of nanopore reads alone yielded a contiguous assembly (NG50 ~3 Mb). Next, we developed a protocol to generate ultra-long reads (N50 > 100kb, up to 882 kb). Incorporating an additional 5×-coverage of these data more than doubled the assembly contiguity (NG50 ~6.4 Mb). The final assembled genome was 2,867 million bases in size, covering 85.8% of the reference. Assembly accuracy, after incorporating complementary short-read sequencing data, exceeded 99.8%. Ultra-long reads enabled assembly and phasing of the 4 Mb major histocompatibility complex (MHC) locus in its entirety, measurement of telomere repeat length and closure of gaps in the reference human genome assembly GRCh38.

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212. Nanopore sequencing and assembly of a human genome with ultra-long reads

Author

Jain, M., Koren, S., Miga, K.H., Quick, J., Rand, A.C., Sasani, T.A., Tyson, J.R., Beggs, A.D., Dilthey, A.T., Fiddes, I.T., Malla, S., Marriott, H., Nieto, T., O'Grady, J., Olsen, H.E., Pedersen, B.S., Rhie, A., Richardson, H., Quinlan, A.R., Snutch, T.P., Tee, L., Paten, B., Phillippy, A.M., Simpson, J.T., Loman, N.J., Loose, M., Jain, M., Koren, S., Miga, K.H., Quick, J., Rand, A.C., Sasani, T.A., Tyson, J.R., Beggs, A.D., Dilthey, A.T., Fiddes, I.T., Malla, S., Marriott, H., Nieto, T., O'Grady, J., Olsen, H.E., Pedersen, B.S., Rhie, A., Richardson, H., Quinlan, A.R., Snutch, T.P., Tee, L., Paten, B., Phillippy, A.M., Simpson, J.T., Loman, N.J., and Loose, M.

Abstract

We report the sequencing and assembly of a reference genome for the human GM12878 Utah/Ceph cell line using the MinION (Oxford Nanopore Technologies) nanopore sequencer. 91.2 Gb of sequence data, representing ~30× theoretical coverage, were produced. Reference-based alignment enabled detection of large structural variants and epigenetic modifications. De novo assembly of nanopore reads alone yielded a contiguous assembly (NG50 ~3 Mb). Next, we developed a protocol to generate ultra-long reads (N50 > 100kb, up to 882 kb). Incorporating an additional 5×-coverage of these data more than doubled the assembly contiguity (NG50 ~6.4 Mb). The final assembled genome was 2,867 million bases in size, covering 85.8% of the reference. Assembly accuracy, after incorporating complementary short-read sequencing data, exceeded 99.8%. Ultra-long reads enabled assembly and phasing of the 4 Mb major histocompatibility complex (MHC) locus in its entirety, measurement of telomere repeat length and closure of gaps in the reference human genome assembly GRCh38.

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213. Nanopore sequencing and assembly of a human genome with ultra-long reads

Author

Jain, M., Koren, S., Miga, K.H., Quick, J., Rand, A.C., Sasani, T.A., Tyson, J.R., Beggs, A.D., Dilthey, A.T., Fiddes, I.T., Malla, S., Marriott, H., Nieto, T., O'Grady, J., Olsen, H.E., Pedersen, B.S., Rhie, A., Richardson, H., Quinlan, A.R., Snutch, T.P., Tee, L., Paten, B., Phillippy, A.M., Simpson, J.T., Loman, N.J., Loose, M., Jain, M., Koren, S., Miga, K.H., Quick, J., Rand, A.C., Sasani, T.A., Tyson, J.R., Beggs, A.D., Dilthey, A.T., Fiddes, I.T., Malla, S., Marriott, H., Nieto, T., O'Grady, J., Olsen, H.E., Pedersen, B.S., Rhie, A., Richardson, H., Quinlan, A.R., Snutch, T.P., Tee, L., Paten, B., Phillippy, A.M., Simpson, J.T., Loman, N.J., and Loose, M.

Abstract

We report the sequencing and assembly of a reference genome for the human GM12878 Utah/Ceph cell line using the MinION (Oxford Nanopore Technologies) nanopore sequencer. 91.2 Gb of sequence data, representing ~30× theoretical coverage, were produced. Reference-based alignment enabled detection of large structural variants and epigenetic modifications. De novo assembly of nanopore reads alone yielded a contiguous assembly (NG50 ~3 Mb). Next, we developed a protocol to generate ultra-long reads (N50 > 100kb, up to 882 kb). Incorporating an additional 5×-coverage of these data more than doubled the assembly contiguity (NG50 ~6.4 Mb). The final assembled genome was 2,867 million bases in size, covering 85.8% of the reference. Assembly accuracy, after incorporating complementary short-read sequencing data, exceeded 99.8%. Ultra-long reads enabled assembly and phasing of the 4 Mb major histocompatibility complex (MHC) locus in its entirety, measurement of telomere repeat length and closure of gaps in the reference human genome assembly GRCh38.

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219. The new navy: Global transformation

Author

Loose, Mike K., RADM

Subjects
NAVAL FACILITIES ENGINEERING COMMAND, ROLES AND MISSIONS - Navy - United States, OPERATIONAL READINESS
Abstract

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Published
2005

221. Performance overview of the Euclid infrared focal plane detector subsystems

Author

Holland, Andrew D., Beletic, James, Waczynski, A., Barbier, R., Cagiano, S., Chen, J., Cheung, S., Cho, H., Cillis, A., Clémens, J-C., Dawson, O., Delo, G., Farris, M., Feizi, A., Foltz, R., Hickey, M., Holmes, W., Hwang, T., Israelsson, U., Jhabvala, M., Kahle, D., Kan, Em., Kan, Er., Loose, M., Lotkin, G., Miko, L., Nguyen, L., Piquette, E., Powers, T., Pravdo, S., Runkle, A., Seiffert, M., Strada, P., Tucker, C., Turck, K., Wang, F., Weber, C., and Williams, J.

Published
2016
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222. Two different network topologies yield bistability in models of mesoderm and anterior mesendoderm specification in amphibians.

Author

Brown, L.E., King, J.R., and Loose, M.

Subjects
*MESODERM, *AMPHIBIANS, *GENE regulatory networks, *SYSTEMS biology, *XENOPUS laevis, *EMBRYOLOGY
Abstract

Abstract: Understanding the Gene Regulatory Networks (GRNs) that underlie development is a major question for systems biology. The establishment of the germ layers is amongst the earliest events of development and has been characterised in numerous model systems. The establishment of the mesoderm is best characterised in the frog Xenopus laevis and has been well studied both experimentally and mathematically. However, the Xenopus network has significant differences from that in mouse and humans, including the presence of multiple copies of two key genes in the network, Mix and Nodal. The axolotl, a urodele amphibian, provides a model with all the benefits of amphibian embryology but crucially only a single Mix and Nodal gene required for the specification of the mesoderm. Remarkably, the number of genes within the network is not the only difference. The interaction between Mix and Brachyury, two transcription factors involved in the establishment of the endoderm and mesoderm respectively, is not conserved. While Mix represses Brachyury in Xenopus, it activates Brachyury in axolotl. Thus, whilst the topology of the networks in the two species differs, both are able to form mesoderm and endoderm in vivo. Based on current knowledge of the structure of the mesendoderm GRN we develop deterministic models that describe the time evolution of transcription factors in a single axolotl cell and compare numerical simulations with previous results from Xenopus. The models are shown to have stable steady states corresponding to mesoderm and anterior mesendoderm, with the in vitro model showing how the concentration of Activin can determine cell fate, while the in vivo model shows that β-catenin concentration can determine cell fate. Moreover, our analysis suggests that additional components must be important in the axolotl network in the specification of the full range of tissues. [Copyright &y& Elsevier]

Published
2014
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223. Wave pinning and spatial patterning in a mathematical model of Antivin/Lefty–Nodal signalling.

Author

Middleton, A. M., King, J. R., and Loose, M.

Subjects
*MESODERM, *ENDODERM, *GENE regulatory networks, *XENOPUS, *MATHEMATICAL models, *GENETICS
Abstract

Nodal signals are key regulators of mesoderm and endoderm development in vertebrate embryos. It has been observed experimentally that in Xenopus embryos the spatial range of Nodal signals is restricted by the signal Antivin (also known as Lefty). Nodal signals can activate both Nodal and Antivin, whereas Antivin is thought to antagonise Nodal by binding either directly to it or to its receptor. In this paper we develop a mathematical model of this signalling network in a line of cells. We consider the heterodimer and receptor-mediated inhibition mechanisms separately and find that, in both cases, the restriction by Antivin to the range of Nodal signals corresponds to wave pinning in the model. Our analysis indicates that, provided Antivin diffuses faster than Nodal, either mechanism can robustly account for the experimental data. We argue that, in the case of Xenopus development, it is wave pinning, rather than Turing-type patterning, that is underlying Nodal–Antivin dynamics. This leads to several experimentally testable predictions, which are discussed. Furthermore, for heterodimer-mediated inhibition to prevent waves of Nodal expression from propagating, the Nodal–Antivin complex must be turned over, and diffusivity of the complex must be negligible. In the absence of molecular mechanisms regulating these, we suggest that Antivin restricts Nodal signals via receptor-mediated, and not heterodimer-mediated, inhibition. [ABSTRACT FROM AUTHOR]

Published
2013
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224. Ecological, morphological and allozymic differentiation between diploid and tetraploid knapweeds (Centaurea jacea) from a contact zone in the Belgian Ardennes.

Author

Hardy, O. J., Vanderhoeven, S., De Loose, M., and Meerts, P.

Subjects
*GENETICS, *ALTITUDES, *CELL nuclei, *CHROMOSOMES, *ASTERACEAE, *POPULATION
Abstract

In the northeastern part of Belgium, the Centaurea jacea complex shows extensive morphological variation and is represented by a diploid (2n = 22) and a tetraploid (2n = 44) cytotype. Polysomic inheritance of allozyme markers in the tetraploids, suggesting autopolyploidy, is here demonstrated for the first time. In order to test whether the two cytotypes occupy distinct habitats and possess different gene pools, patterns of allozymic and morhpological variation were investigated in relation to ploidy level and site characteristics in 26 populations from the Belgian Ardennes. The two cytotypes showed a parapatric distribution, the diploids occurring at higher elevations (mostly above 500 m) than the tetraploids (mostly below 500 m). Three mixed populations were found near the contact zone of the two cytotypes. Within the mixed populations no triploid plant and no evidence for gene flow between cytotuypes were found, despite widely overlapping flowering periods. The two cytotypes can be distinguished on the basis of morphological traits and enzymatic gene pools. The congruence of morphological and allozymic variation with chromosome numbers suggests a secondary contact between the two cytotypes with limited gene flow between them. The origin and persistence of the parapatric distribution are discussed. [ABSTRACT FROM AUTHOR]

Published
2000
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225. Selection of egg peptide biomarkers in processed food products by high resolution mass spectrometry.

Author

Gavage, M., Van Vlierberghe, K., Van Poucke, C., De Loose, M., Gevaert, K., Dieu, M., Renard, P., Arnould, T., and Gillard, N.

Subjects
*EGG processing, *BIOMARKERS, *HIGH resolution imaging, *MASS spectrometry, *PROCESSED foods
Abstract

Highlights • Empirical identification of 16 potential peptide biomarkers for egg with HRMS. • Analysis of processed egg matrices produced in semi-industrial conditions. • Strategy for peptide biomarker selection for allergen detection and quantification. • Tandem Lys-C/trypsin enzymatic digestion. • Identification of amino acid modifications in proteins from processed food products. Abstract Food allergy is a growing health problem worldwide; thus, there is an urgent need for robust, specific, and sensitive analytical methods for detecting allergens. Mass spectrometry is an alternative to the existing methods, and it can overcome their limitations. One of the first steps in the development of any analytical method is the identification of the analytes to be further studied. In the case of allergen detection by mass spectrometry, the analytes are peptides. In this study, a strategy was developed for identifying potential peptide biomarkers in processed food products. This strategy was applied to processed egg matrices, and 16 potential peptide biomarkers were identified for the further detection and quantification of egg by means of mass spectrometry. With an empirical approach based on dedicated sample preparation, including tandem Lys-C/trypsin enzymatic digestion and high-resolution mass spectrometry analysis, hundreds of peptides from egg proteins were identified. This list of peptides was further refined with a series of criteria, obtained from empirical evidence, to identify the ideal biomarkers for the development of a quantitative method. These criteria include the resistance to food processing and the specificity of the peptides for eggs but also the effects of amino acid modifications and enzymatic digestion efficiency. [ABSTRACT FROM AUTHOR]

Published
2019
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226. Development of incurred chocolate bars and broth powder with six fully characterised food allergens as test materials for food allergen analysis

Author

Huet, Anne-Catherine, Paulus, Melody, Henrottin, Jean, Brossard, Chantal, Tranquet, Olivier, Bernard, Hervé, Pilolli, Rosa, Nitride, Chiara, Larré, Colette, Adel-Patient, Karine, Monaci, Linda, Mills, E., de Loose, Marc, Gillard, Nathalie, van Poucke, Christof, CER Groupe, Unité de recherche sur les Biopolymères, Interactions Assemblages (BIA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biodiversité et Biotechnologie Fongiques (BBF), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Service de Chimie Bio-Organique et de Marquage (SCBM), Médicaments et Technologies pour la Santé (MTS), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institute of Sciences of Food Production (ISPA), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), University of Manchester [Manchester], Research Institute for Agricultural, Fisheries and Food (ILVO), European Food Safety Authority (EFSA) : GP/EFSA/AFSCO/2017/03, UK Food Standards Agency : FS101209, UK FSA : FS101206., Huet, A. -C., Paulus, M., Henrottin, J., Brossard, C., Tranquet, O., Bernard, H., Pilolli, R., Nitride, C., Larre, C., Adel-Patient, K., Monaci, L., Mills, E. N. C., De Loose, M., Gillard, N., and Van Poucke, C.

Subjects
Detection method, Arachis, Allergen, Incurred matrice, food and beverages, Enzyme-Linked Immunosorbent Assay, Allergens, Incurred matrices, Biochemistry, Analytical Chemistry, Humans, Homogeneity, Chocolate, Powders, [SDV.IMM.ALL]Life Sciences [q-bio]/Immunology/Allergology, Stability, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Food Analysis, Food Hypersensitivity
Abstract

The design and production of incurred test materials are critical for the development and validation of methods for food allergen analysis. This is because production and processing conditions, together with the food matrix, can modify allergens affecting their structure, extractability and detectability. For the ThRAll project, which aims to develop a mass spectrometry–based reference method for the simultaneous accurate quantification of six allergenic ingredients in two hard to analyse matrices. Two highly processed matrices, chocolate bars and broth powder, were selected to incur with six allergenic ingredients (egg, milk, peanut, soy, hazelnut and almond) at 2, 4, 10 and 40 mg total allergenic protein/kg food matrix using a pilot-scale food manufacturing plant. The allergenic activity of the ingredients incurred was verified using food-allergic patient serum/plasma IgE, the homogeneity of the incurred matrices verified and their stability at 4 °C assessed over at least 30-month storage using appropriate enzyme-linked immunosorbent assays (ELISA). Allergens were found at all levels from the chocolate bar and were homogenously distributed, apart from peanut and soy which could only be determined above 4 mg total allergenic ingredient protein/kg. The homogeneity assessment was restricted to analysis of soy, milk and peanut for the broth powder but nevertheless demonstrated that the allergens were homogeneously distributed. All the allergens tested were found to be stable in the incurred matrices for at least 30 months demonstrating they are suitable for method development. Graphical abstract: [Figure not available: see fulltext.]

Published
2022

227. Multicellular Mathematical Modelling of Mesendoderm Formation in Amphibians.

Author

Brown, L., Middleton, A., King, J., and Loose, M.

Subjects
*AMPHIBIAN embryology, *MESODERM, *CELL determination, *GENE regulatory networks, *ENDODERM
Abstract

The earliest cell fate decisions in a developing embryo are those associated with establishing the germ layers. The specification of the mesoderm and endoderm is of particular interest as the mesoderm is induced from the endoderm, potentially from an underlying bipotential group of cells, the mesendoderm. Mesendoderm formation has been well studied in an amphibian model frog, Xenopus laevis, and its formation is driven by a gene regulatory network (GRN) induced by maternal factors deposited in the egg. We have recently demonstrated that the axolotl, a urodele amphibian, utilises a different topology in its GRN to specify the mesendoderm. In this paper, we develop spatially structured mathematical models of the GRNs governing mesendoderm formation in a line of cells. We explore several versions of the model of mesendoderm formation in both Xenopus and the axolotl, incorporating the key differences between these two systems. Model simulations are able to reproduce known experimental data, such as Nodal expression domains in Xenopus, and also make predictions about how the positional information derived from maternal factors may be interpreted to drive cell fate decisions. We find that whilst cell-cell signalling plays a minor role in Xenopus, it is crucial for correct patterning domains in axolotl. [ABSTRACT FROM AUTHOR]

Published
2016
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228. Thermal degradation of cloudy apple juice phenolic constituents.

Author

De Paepe, D., Valkenborg, D., Coudijzer, K., Noten, B., Servaes, K., De Loose, M., Voorspoels, S., Diels, L., and Van Droogenbroeck, B.

Subjects
*THERMAL analysis, *BIODEGRADATION, *APPLE juice, *PHENOLS, *FOOD pasteurization, *PROCYANIDINS
Abstract

Highlights: [•] Degradation susceptibility of cloudy apple juice phenolic constituents. [•] Untargeted metabolomics approach conducted for process optimisation. [•] Procyanidin were the most heat labile phenolic compounds. [•] Low impact of the high-temperature short-time pasteurisation. [Copyright &y& Elsevier]

Published
2014
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229. An improved mass spectrometric method for identification and quantification of phenolic compounds in apple fruits

Author

De Paepe, D., Servaes, K., Noten, B., Diels, L., De Loose, M., Van Droogenbroeck, B., and Voorspoels, S.

Subjects
*MASS spectrometry, *PHENOLS, *COMPOSITION of apples, *HIGH performance liquid chromatography, *PLANT extracts, *ELECTROSPRAY ionization mass spectrometry
Abstract

Abstract: Thirty-nine phenolic compounds were analysed using ultra high performance liquid chromatography (UHPLC) coupled with diode array and accurate mass spectrometry detection using electrospray ionisation (DAD/ESI-am-MS). Instrumental parameters such as scan speed, resolution, and mass accuracy were optimised to establish accurate mass measurements. The method was fully validated in terms of model deviation (r 2 >0.9990), range (typically 10–3500ngg−1), intra/inter-day precision (<6% and <8%, respectively) and accuracy (typically 100±10%). The mass accuracy of each selected phenolic compound was below 1.5ppm. The results confirmed that the UHPLC-DAD/ESI-am-MS method developed here was convenient and reliable for the determination of phenolic compounds in apple extracts. [Copyright &y& Elsevier]

Published
2013
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230. Detection and Quantification of Allergens in Foods and Minimum Eliciting Doses in Food-Allergic Individuals (ThRAll)

Author

Karine Adel-Patient, Anne-Catherine Huet, Rosa Pilolli, Nathalie Gillard, Chiara Nitride, Collette Larré, Olivier Tranquet, Hervé Bernard, Marc De Loose, Linda Monaci, Christof Van Pouke, E. N. Clare Mills, Adel-Patient, Karine, University of Manchester [Manchester], Service de Pharmacologie et d'Immunoanalyse (SPI), Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Research Institute for Agricultural, Fisheries and Food (ILVO), CER Groupe, Unité de recherche sur les Biopolymères, Interactions Assemblages (BIA), Institut National de la Recherche Agronomique (INRA), Institute of Sciences of Food Production (ISPA), Consiglio Nazionale delle Ricerche (CNR), Clare Mills, E. N., Adel-Patient, K., Bernard, H., De Loose, M., Gillard, N., Huet, A. -C., Larre, C., Nitride, C., Pilolli, R., Tranquet, O., Pouke, C. V., Monaci, L., Service de Pharmacologie et Immunoanalyse (SPI), Médicaments et Technologies pour la Santé (MTS), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR)

Subjects
food industry, ThRAll, Food industry, [SDV]Life Sciences [q-bio], Dose-Response Relationship, Immunologic, Food Contamination, 01 natural sciences, Analytical Chemistry, food allergens, 0404 agricultural biotechnology, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Environmental Chemistry, Animals, Humans, Nuts, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, Food allergens, Chocolate, ThRAll project, mass spectrometry, 2. Zero hunger, Pharmacology, Food protein, business.industry, 010401 analytical chemistry, digestive, oral, and skin physiology, peptide markers, analytical method, 04 agricultural and veterinary sciences, Allergens, Plants, 040401 food science, 3. Good health, 0104 chemical sciences, Biotechnology, Milk, reference method, Data quality, Food processing, Fast Foods, allergens, food-allergic consumers, business, Agronomy and Crop Science, Food Hypersensitivity, food allergen, Food Science
Abstract

International audience; Risk-based approaches to managing allergens in foods are being developed by the food industry and regulatory authorities to support food-allergic consumers to avoid ingestion of their problem food, especially in relation to the traces of unintended allergens. The application of such approaches requires access to good quality data from clinical studies to support identification of levels of allergens in foods that are generally safe for most food-allergic consumers as well as analytical tools that are able to quantify allergenic food protein. The ThRAll project aims to support the application of risk-based approaches to food-allergen management in two ways. First, a harmonized quantitative MS-based prototype reference method will be developed for the detection of multiple food allergens in standardized incurred food matrices. This will be undertaken for cow’s milk, hen’s egg, peanut, soybean, hazelnut, and almond incurred into two highly processed food matrices, chocolate and broth powder. This activity is complemented by a second objective to support the development and curation of data on oral food challenges, which are used to define thresholds and minimum eliciting doses. This will be achieved through the development of common protocols for collection and curation of data that will be applied to allergenic foods for which there are currently data gaps.

Published
2019

231. LOFAR MSSS: detection of a low-frequency radio transient in 400 h of monitoring of the North Celestial Pole

Author

Rebecca McFadden, Martin Bell, Sera Markoff, G. Kokotanekov, R. J. van Weeren, D. McKay-Bukowski, James M. Anderson, Jason W. T. Hessels, Peter G. Jonker, Ralph A. M. J. Wijers, H. Munk, Casey J. Law, Frank Breitling, B. Scheers, Marcus Brüggen, M. C. Toribio, A. Horneffer, George Heald, M. A. Garrett, Aris Karastergiou, Luke Pratley, Rudy Wijnands, Y. Cendes, F. de Gasperin, A. Alexov, Michael W. Wise, Gianni Bernardi, Jörg R. Hörandel, B. Ciardi, M. Kuniyoshi, James Miller-Jones, J. van Leeuwen, T. Munoz-Darias, Aleksandar Shulevski, John McKean, J.-M. Grießmeier, John D. Swinbank, Jochen Eislöffel, P. Maat, Cyril Tasse, Wilfred Frieswijk, M. J. Norden, J. W. Broderick, A. G. Polatidis, Arthur Corstanje, T E Hassall, Heino Falcke, Harvey Butcher, E. de Geus, V. I. Kondratiev, E. Juette, Anna M. M. Scaife, M. Pandey-Pommier, Benjamin Stappers, H. Paas, A. W. Gunst, I. M. Avruch, Volker Heesen, D. Carbone, Mark J. Bentum, Antonia Rowlinson, Annalisa Bonafede, Rob Fender, J. Sluman, E. Rol, Matthias Steinmetz, Chiara Ferrari, Gijs Molenaar, S. Duscha, G. Kuper, D. D. Mulcahy, Sarod Yatawatta, Philip Best, M. Pietka, H. J. A. Röttgering, Satyendra Thoudam, A. O. Clarke, Adam Stewart, M. P. van Haarlem, Charlotte Sobey, M. Iacobelli, Olaf Wucknitz, Matthias Hoeft, Emanuela Orrú, M. Loose, Ph. Zarka, Adam Deller, Martin J. Hardcastle, Tim D. Staley, Ashish Asgekar, J. Moldon, Dominik J. Schwarz, A. J. van der Horst, Christian Vocks, Rene P. Breton, John Conway, Stephane Corbel, R. C. Vermeulen, Stefan J. Wijnholds, S. van Velzen, T. L. Grobler, Oleg Smirnov, Astronomy, Laboratory for Atmospheric and Space Physics [Boulder] (LASP), University of Colorado [Boulder], University of Southampton, Jodrell Bank Centre for Astrophysics, University of Manchester [Manchester], School of Physics and Astronomy [Southampton], Netherlands Institute for Radio Astronomy (ASTRON), Astronomical Institute Anton Pannekoek (AI PANNEKOEK), University of Amsterdam [Amsterdam] (UvA), Oxford Astrophysics, University of Oxford [Oxford], Rhodes University, Grahamstown, CSIRO Astronomy and Space Science, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Jacobs University [Bremen], Astrophysique Interprétation Modélisation (AIM (UMR_7158 / UMR_E_9005 / UM_112)), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7), Unité Scientifique de la Station de Nançay (USN), Université d'Orléans (UO)-Observatoire des Sciences de l'Univers en région Centre (OSUC), Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, PSL Research University (PSL)-PSL Research University (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, PSL Research University (PSL)-Centre National de la Recherche Scientifique (CNRS), Universität Hamburg (UHH), Thüringer Landessternwarte Tautenburg (TLS), Radboud university [Nijmegen], Département de Géologie, Université de Montréal [Montréal], Laboratoire de Physique et Chimie de l'Environnement et de l'Espace (LPC2E), Observatoire des Sciences de l'Univers en région Centre (OSUC), PSL Research University (PSL)-PSL Research University (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Centre National d’Études Spatiales [Paris] (CNES), University of Hertfordshire [Hatfield] (UH), Max-Planck-Institut für Radioastronomie (MPIFR), Leiden Observatory [Leiden], Universiteit Leiden [Leiden], Institute for Mathematics, Astrophysics and Particle Physics (IMAPP), Curtin University [Perth], Planning and Transport Research Centre (PATREC), Centre de Recherche Astrophysique de Lyon (CRAL), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Victoria University of Wellington, Kapteyn Astronomical Institute [Groningen], University of Groningen [Groningen], SKA South Africa, Ska South Africa, Galaxies, Etoiles, Physique, Instrumentation (GEPI), PSL Research University (PSL)-PSL Research University (PSL)-Centre National de la Recherche Scientifique (CNRS), Department of Mathematics, The George Washington University, Washington State University (WSU), Harvard-Smithsonian Center for Astrophysics (CfA), Harvard University [Cambridge]-Smithsonian Institution, Anton Pannekoek Institute for Astronomy, Observatoire de Paris - Site de Paris (OP), Centre National de la Recherche Scientifique (CNRS)-Observatoire de Paris, PSL Research University (PSL)-PSL Research University (PSL)-Institut national des sciences de l'Univers (INSU - CNRS), Laboratoire d'études spatiales et d'instrumentation en astrophysique (LESIA), Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Observatoire de Paris, PSL Research University (PSL)-PSL Research University (PSL)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC), Institute for Mathematics Applied to Geoscience, National Center for Atmospheric Research [Boulder] (NCAR), SRON Netherlands Institute for Space Research (SRON), Laboratoire de Physique Nucléaire et de Hautes Énergies (LPNHE), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), University of Edinburgh, Leibniz-Institut für Astrophysik Potsdam (AIP), Max Planck Institute for Astrophysics, Max-Planck-Gesellschaft, Onsala Space Observatory, Dept. of Radio and Space Science, Chalmers University of Technology, Chalmers University of Technology [Göteborg], Ruhr-Universität Bochum [Bochum], University of Oulu, The Netherlands Institute for Radio Astronomy (ASTRON), 7990-AA Dwingeloo, Netherlands, Departament d'Astronomia i Meteorologia [Barcelona], Institut de Ciènces del Cosmos (ICC), Universitat de Barcelona (UB)-Universitat de Barcelona (UB), Center for Information Technology CIT, Université de Groningen, Interactions Son Musique Mouvement, Sciences et Technologies de la Musique et du Son (STMS), Université Pierre et Marie Curie - Paris 6 (UPMC)-IRCAM-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-IRCAM-Centre National de la Recherche Scientifique (CNRS), Rhodes University, Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH / Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures (DSMZ), Finca El Encin, Instituto Madrileño de Investigación y Desarrollo Rural, Agrario y Alimentario (IMIDRA), Argelander-Institut für Astronomie (AlfA), Rheinische Friedrich-Wilhelms-Universität Bonn, High Energy Astrophys. & Astropart. Phys (API, FNWI), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire des Sciences de l'Univers en région Centre (OSUC), Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université d'Orléans (UO)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université d'Orléans (UO)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université d'Orléans (UO), Université de Montréal (UdeM), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National d’Études Spatiales [Paris] (CNES), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Department of Mathematics [George Washington University] (GW), The George Washington University (GW), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université Pierre et Marie Curie - Paris 6 (UPMC), Universitat de Barcelona (UB), Institut de Recherche et Coordination Acoustique/Musique (IRCAM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche et Coordination Acoustique/Musique (IRCAM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), University of Oxford, Astrophysique Interprétation Modélisation (AIM (UMR7158 / UMR_E_9005 / UM_112)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS), Radboud University [Nijmegen], Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Centre National d’Études Spatiales [Paris] (CNES), Universiteit Leiden, École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Harvard University-Smithsonian Institution, Stewart, A.J., Fender, R.P., Broderick, J.W., Hassall, T.E., Muñoz-Darias, T., Rowlinson, A., Swinbank, J.D., Staley, T.D., Molenaar, G.J., Scheers, B., Grobler, T.L., Pietka, M., Heald, G., McKean, J.P., Bell, M.E., Bonafede, A., Breton, R.P., Carbone, D., Cendes, Y., Clarke, A.O., Corbel, S., De Gasperin, F., Eislöffel, J., Falcke, H., Ferrari, C., Grießmeier, J.-M., Hardcastle, M.J., Heesen, V., Hessels, J.W.T., Horneffer, A., Iacobelli, M., Jonker, P., Karastergiou, A., Kokotanekov, G., Kondratiev, V.I., Kuniyoshi, M., Law, C.J., van Leeuwen, J., Markoff, S., Miller-Jones, J.C.A., Mulcahy, D., Orru, E., Pandey-Pommier, M., Pratley, L., Rol, E., Röttgering, H.J.A., Scaife, A.M.M., Shulevski, A., Sobey, C.A., Stappers, B.W., Tasse, C., van der Horst, A.J., van Velzen, S., van Weeren, R.J., Wijers, R.A.M.J., Wijnands, R., Wise, M., Zarka, P., Alexov, A., Anderson, J., Asgekar, A., Avruch, I.M., Bentum, M.J., Bernardi, G., Best, P., Breitling, F., Brüggen, M., Butcher, H.R., Ciardi, B., Conway, J.E., Corstanje, A., de Geus, E., Deller, A., Duscha, S., Frieswijk, W., Garrett, M.A., Gunst, A.W., Van Haarlem, M.P., Hoeft, M., Hörandel, J., Juette, E., Kuper, G., Loose, M., Maat, P., McFadden, R., McKay-Bukowski, D., Moldon, J., Munk, H., Norden, M.J., Paas, H., Polatidis, A.G., Schwarz, D., Sluman, J., Smirnov, O., Steinmetz, M., Thoudam, S., Toribio, M.C., Vermeulen, R., Vocks, C., Wijnholds, S.J., Wucknitz, O., Yatawatta, S., ITA, GBR, FRA, DEU, and NLD

Subjects
Astronomy, media_common.quotation_subject, interferometers [instrumentation], radio continuum: general, FOS: Physical sciences, techniques: image processing, 02 engineering and technology, Astrophysics, Low frequency, 01 natural sciences, Instrumentation: interferometer, Celestial pole, 0103 physical sciences, IR-102656, 0202 electrical engineering, electronic engineering, information engineering, instrumentation: interferometers, Instrumentation and Methods for Astrophysics (astro-ph.IM), 010303 astronomy & astrophysics, media_common, EWI-27481, High Energy Astrophysical Phenomena (astro-ph.HE), Physics, image processing [techniques], METIS-320906, 020206 networking & telecommunications, Astronomy and Astrophysics, LOFAR, Limiting, Astronomy and Astrophysic, instrumentation: interferometers – techniques: image processing – radio continuum: general, radio, continuum: general, Observation duration, Space and Planetary Science, Sky, [SDU]Sciences of the Universe [physics], ComputingMethodologies_DOCUMENTANDTEXTPROCESSING, general [radio continuum], Astrophysics - High Energy Astrophysical Phenomena, Astrophysics - Instrumentation and Methods for Astrophysics
Abstract

We present the results of a four-month campaign searching for low-frequency radio transients near the North Celestial Pole with the Low-Frequency Array (LOFAR), as part of the Multifrequency Snapshot Sky Survey (MSSS). The data were recorded between 2011 December and 2012 April and comprised 2149 11-minute snapshots, each covering 175 deg^2. We have found one convincing candidate astrophysical transient, with a duration of a few minutes and a flux density at 60 MHz of 15-25 Jy. The transient does not repeat and has no obvious optical or high-energy counterpart, as a result of which its nature is unclear. The detection of this event implies a transient rate at 60 MHz of 3.9 (+14.7, -3.7) x 10^-4 day^-1 deg^-2, and a transient surface density of 1.5 x 10^-5 deg^-2, at a 7.9-Jy limiting flux density and ~10-minute time-scale. The campaign data were also searched for transients at a range of other time-scales, from 0.5 to 297 min, which allowed us to place a range of limits on transient rates at 60 MHz as a function of observation duration., 23 pages, 16 figures, 5 tables, accepted for publication in MNRAS

Published
2016

232. Imaging Jupiter's radiation belts down to 127 MHz with LOFAR

Author

Gianni Bernardi, Jörg R. Hörandel, A. G. Polatidis, Ashish Asgekar, A. Nelles, Angélica Sicard, H. Munk, R. J. van Weeren, Jason W. T. Hessels, D. McKay-Bukowski, I. de Pater, Matthias Hoeft, Oleg Smirnov, A. W. Gunst, Frank Breitling, Arthur Corstanje, Sebastien Hess, Quentin Nénon, Mark J. Bentum, J. van Leeuwen, R. C. Vermeulen, M. Loose, P. Zarka, H. J. A. Röttgering, P. Maat, M. J. Norden, M. Tagger, J. Moldón, F. de Gasperin, S. Bourdarie, Rene P. Breton, Annalisa Bonafede, John D. Swinbank, I. van Bemmel, Stephane Corbel, Martin Bell, V. I. Kondratiev, M. Pandey-Pommier, M. Iacobelli, James M. Anderson, Roberto Pizzo, Marcus Brüggen, Satyendra Thoudam, M. C. Toribio, Gerard H. Kuper, Antonia Rowlinson, Jochen Eislöffel, S. Duscha, Rebecca McFadden, M. A. Garrett, Daniel Santos-Costa, Julien N. Girard, Matthias Steinmetz, B. Ciardi, O. Wucknitz, J.-M. Grießmeier, M. Kuniyoshi, Ralph A. M. J. Wijers, Wilfred Frieswijk, Heino Falcke, C. Tasse, W. N. Brouw, S. Markov, Emanuela Orrú, H. Paas, Adam Deller, W. Reich, Dominik J. Schwarz, J. W. Broderick, E. Juette, G. Mann, Philip Best, C. Vocks, E. de Geus, Girard, J.N., Zarka, P., Tasse, C., Hess, S., De Pater, I., Santos-Costa, D., Nenon, Q., Sicard, A., Bourdarie, S., Anderson, J., Asgekar, A., Bell, M.E., Van Bemmel, I., Bentum, M.J., Bernardi, G., Best, P., Bonafede, A., Breitling, F., Breton, R.P., Broderick, J.W., Brouw, W.N., Brüggen, M., Ciardi, B., Corbel, S., Corstanje, A., De Gasperin, F., De Geus, E., Deller, A., Duscha, S., Eislöffel, J., Falcke, H., Frieswijk, W., Garrett, M.A., Grießmeier, J., Gunst, A.W., Hessels, J.W.T., Hoeft, M., Hörandel, J., Iacobelli, M., Juette, E., Kondratiev, V.I., Kuniyoshi, M., Kuper, G., Van Leeuwen, J., Loose, M., Maat, P., Mann, G., Markoff, S., McFadden, R., McKay-Bukowski, D., Moldon, J., Munk, H., Nelles, A., Norden, M.J., Orru, E., Paas, H., Pandey-Pommier, M., Pizzo, R., Polatidis, A.G., Reich, W., Röttgering, H., Rowlinson, A., Schwarz, D., Smirnov, O., Steinmetz, M., Swinbank, J., Tagger, M., Thoudam, S., Toribio, M.C., Vermeulen, R., Vocks, C., Van Weeren, R.J., Wijers, R.A.M.J., Wucknitz, O., Astrophysique Interprétation Modélisation (AIM (UMR7158 / UMR_E_9005 / UM_112)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'études spatiales et d'instrumentation en astrophysique (LESIA), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Galaxies, Etoiles, Physique, Instrumentation (GEPI), Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, ONERA - The French Aerospace Lab [Toulouse], ONERA, Netherlands Institute for Radio Astronomy (ASTRON), University of Southampton, Laboratoire de Physique Nucléaire et de Hautes Énergies (LPNHE (UMR_7585)), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université Paris Diderot - Paris 7 (UPD7)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Royal Observatory Edinburgh (ROE), University of Edinburgh, Jacobs University [Bremen], Leibniz-Institut für Astrophysik Potsdam (AIP), Jodrell Bank Centre for Astrophysics (JBCA), University of Manchester [Manchester], Max Planck Institute for Astrophysics, Max-Planck-Gesellschaft, Radboud University [Nijmegen], Hamburger Sternwarte/Hamburg Observatory, Universität Hamburg (UHH), Thüringer Landessternwarte Tautenburg (TLS), Leiden Observatory [Leiden], Universiteit Leiden, Unité Scientifique de la Station de Nançay (USN), Observatoire des Sciences de l'Univers en région Centre (OSUC), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique et Chimie de l'Environnement et de l'Espace (LPC2E), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Centre National d’Études Spatiales [Paris] (CNES), Astronomical Institute Anton Pannekoek (AI PANNEKOEK), University of Amsterdam [Amsterdam] (UvA), Department of Pure Mathematics and Mathematical Statistics (DPMMS), Faculty of mathematics Centre for Mathematical Sciences [Cambridge] (CMS), University of Cambridge [UK] (CAM)-University of Cambridge [UK] (CAM), Ruhr-Universität Bochum [Bochum], Max-Planck-Institut für Radioastronomie (MPIFR), University of Oulu, University of Groningen [Groningen], Centre de Recherche Astrophysique de Lyon (CRAL), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), CSIRO Astronomy and Space Science, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Universität Bielefeld, Rhodes University, Grahamstown, Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH / Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures (DSMZ), Harvard-Smithsonian Center for Astrophysics (CfA), Harvard University-Smithsonian Institution, ANR-11-IDEX-0005,USPC,Université Sorbonne Paris Cité(2011), European Project: 228261,EC:FP7:ERC,ERC-2008-AdG,SPARSEASTRO(2009), ITA, GBR, FRA, DEU, NLD, Astrophysique Interprétation Modélisation (AIM (UMR_7158 / UMR_E_9005 / UM_112)), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7), Radboud university [Nijmegen], Universiteit Leiden [Leiden], Centre National de la Recherche Scientifique (CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire des Sciences de l'Univers en région Centre (OSUC), Université Paris sciences et lettres (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Université d'Orléans (UO), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS), Harvard University [Cambridge]-Smithsonian Institution, Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Observatoire de Paris, PSL Research University (PSL)-PSL Research University (PSL)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC), PSL Research University (PSL)-PSL Research University (PSL)-Centre National de la Recherche Scientifique (CNRS), Jodrell Bank Centre for Astrophysics, Université d'Orléans (UO)-Observatoire des Sciences de l'Univers en région Centre (OSUC), PSL Research University (PSL)-PSL Research University (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, PSL Research University (PSL)-Centre National de la Recherche Scientifique (CNRS), PSL Research University (PSL)-PSL Research University (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Centre National d’Études Spatiales [Paris] (CNES), DPMMS/CMS, University of Cambridge [UK] (CAM), ANR-11-IDEX-0005-02/10-LABX-0023,UnivEarthS,Earth - Planets - Universe: observation, modeling, transfer(2011), Astronomy, High Energy Astrophys. & Astropart. Phys (API, FNWI), and Faculty of Science

Subjects
radio continuum: planetary systems, Brightness, 010504 meteorology & atmospheric sciences, radio continuum: planetary, EWI-27447, Astronomy, Astrophysics::High Energy Astrophysical Phenomena, Magnetosphere, FOS: Physical sciences, Astrophysics, Electron, METIS-321662, 7. Clean energy, 01 natural sciences, Jupiter, symbols.namesake, 0103 physical sciences, Emission spectrum, IR-103183, 010303 astronomy & astrophysics, Instrumentation and Methods for Astrophysics (astro-ph.IM), 0105 earth and related environmental sciences, Physics, Earth and Planetary Astrophysics (astro-ph.EP), [SDU.ASTR]Sciences of the Universe [physics]/Astrophysics [astro-ph], Radio continuum: planetary system, Planets and satellites: magnetic field, Astronomy and Astrophysics, LOFAR, Astronomy and Astrophysic, planets and satellites: magnetic fields, Spectral flux density, 13. Climate action, Space and Planetary Science, Van Allen radiation belt, Techniques: interferometric, symbols, ComputingMethodologies_DOCUMENTANDTEXTPROCESSING, systems, Astrophysics::Earth and Planetary Astrophysics, Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Earth and Planetary Astrophysics
Abstract

Context. Observing Jupiter's synchrotron emission from the Earth remains today the sole method to scrutinize the distribution and dynamical behavior of the ultra energetic electrons magnetically trapped around the planet (because in-situ particle data are limited in the inner magnetosphere). Aims. We perform the first resolved and low-frequency imaging of the synchrotron emission with LOFAR at 127 MHz. The radiation comes from low energy electrons (~1-30 MeV) which map a broad region of Jupiter's inner magnetosphere. Methods (see article for complete abstract) Results. The first resolved images of Jupiter's radiation belts at 127-172 MHz are obtained along with total integrated flux densities. They are compared with previous observations at higher frequencies and show a larger extent of the synchrotron emission source (>=4 $R_J$). The asymmetry and the dynamic of east-west emission peaks are measured and the presence of a hot spot at lambda_III=230 {\deg} $\pm$ 25 {\deg}. Spectral flux density measurements are on the low side of previous (unresolved) ones, suggesting a low-frequency turnover and/or time variations of the emission spectrum. Conclusions. LOFAR is a powerful and flexible planetary imager. The observations at 127 MHz depict an extended emission up to ~4-5 planetary radii. The similarities with high frequency results reinforce the conclusion that: i) the magnetic field morphology primarily shapes the brightness distribution of the emission and ii) the radiating electrons are likely radially and latitudinally distributed inside about 2 $R_J$. Nonetheless, the larger extent of the brightness combined with the overall lower flux density, yields new information on Jupiter's electron distribution, that may shed light on the origin and mode of transport of these particles., Comment: 10 pages, 12 figures, accepted for publication in A&A (27/11/2015) - abstract edited because of limited characters

Published
2015

233. The LOFAR Multifrequency Snapshot Sky Survey (MSSS): I. Survey description and first results

Author

G. H. Heald, R. F. Pizzo, E. Orrú, R. P. Breton, D. Carbone, C. Ferrari, M. J. Hardcastle, W. Jurusik, G. Macario, D. Mulcahy, D. Rafferty, A. Asgekar, M. Brentjens, R. A. Fallows, W. Frieswijk, M. C. Toribio, B. Adebahr, M. Arts, M. R. Bell, A. Bonafede, J. Bray, J. Broderick, T. Cantwell, P. Carroll, Y. Cendes, A. O. Clarke, J. Croston, S. Daiboo, F. de Gasperin, J. Gregson, J. Harwood, T. Hassall, V. Heesen, A. Horneffer, A. J. van der Horst, M. Iacobelli, V. Jelić, D. Jones, D. Kant, G. Kokotanekov, P. Martin, J. P. McKean, L. K. Morabito, B. Nikiel-Wroczyński, A. Offringa, V. N. Pandey, M. Pandey-Pommier, M. Pietka, L. Pratley, C. Riseley, A. Rowlinson, J. Sabater, A. M. M. Scaife, L. H. A. Scheers, K. Sendlinger, A. Shulevski, M. Sipior, C. Sobey, A. J. Stewart, A. Stroe, J. Swinbank, C. Tasse, J. Trüstedt, E. Varenius, S. van Velzen, N. Vilchez, R. J. van Weeren, S. Wijnholds, W. L. Williams, A. G. de Bruyn, R. Nijboer, M. Wise, A. Alexov, J. Anderson, I. M. Avruch, R. Beck, M. E. Bell, I. van Bemmel, M. J. Bentum, G. Bernardi, P. Best, F. Breitling, W. N. Brouw, M. Brüggen, H. R. Butcher, B. Ciardi, J. E. Conway, E. de Geus, A. de Jong, M. de Vos, A. Deller, R.-J. Dettmar, S. Duscha, J. Eislöffel, D. Engels, H. Falcke, R. Fender, M. A. Garrett, J. Grießmeier, A. W. Gunst, J. P. Hamaker, J. W. T. Hessels, M. Hoeft, J. Hörandel, H. A. Holties, H. Intema, N. J. Jackson, E. Jütte, A. Karastergiou, W. F. A. Klijn, V. I. Kondratiev, L. V. E. Koopmans, M. Kuniyoshi, G. Kuper, C. Law, J. van Leeuwen, M. Loose, P. Maat, S. Markoff, R. McFadden, D. McKay-Bukowski, M. Mevius, J. C. A. Miller-Jones, R. Morganti, H. Munk, A. Nelles, J. E. Noordam, M. J. Norden, H. Paas, A. G. Polatidis, W. Reich, A. Renting, H. Röttgering, A. Schoenmakers, D. Schwarz, J. Sluman, O. Smirnov, B. W. Stappers, M. Steinmetz, M. Tagger, Y. Tang, S. ter Veen, S. Thoudam, R. Vermeulen, C. Vocks, C. Vogt, R. A. M. J. Wijers, O. Wucknitz, S. Yatawatta, P. Zarka, Heald, G.H., Pizzo, R.F., Orrú, E., Breton, R.P., Carbone, D., Ferrari, C., Hardcastle, M.J., Jurusik, W., Macario, G., Mulcahy, D., Rafferty, D., Asgekar, A., Brentjens, M., Fallows, R.A., Frieswijk, W., Toribio, M.C., Adebahr, B., Arts, M., Bell, M.R., Bonafede, A., Bray, J., Broderick, J., Cantwell, T., Carroll, P., Cendes, Y., Clarke, A.O., Croston, J., Daiboo, S., De Gasperin, F., Gregson, J., Harwood, J., Hassall, T., Heesen, V., Horneffer, A., Van Der Horst, A.J., Iacobelli, M., Jelić, V., Jones, D., Kant, D., Kokotanekov, G., Martin, P., McKean, J.P., Morabito, L.K., Nikiel-Wroczyński, B., Offringa, A., Pandey, V.N., Pandey-Pommier, M., Pietka, M., Pratley, L., Riseley, C., Rowlinson, A., Sabater, J., Scaife, A.M.M., Scheers, L.H.A., Sendlinger, K., Shulevski, A., Sipior, M., Sobey, C., Stewart, A.J., Stroe, A., Swinbank, J., Tasse, C., Trüstedt, J., Varenius, E., Van Velzen, S., Vilchez, N., Van Weeren, R.J., Wijnholds, S., Williams, W.L., De Bruyn, A.G., Nijboer, R., Wise, M., Alexov, A., Anderson, J., Avruch, I.M., Beck, R., Bell, M.E., Van Bemmel, I., Bentum, M.J., Bernardi, G., Best, P., Breitling, F., Brouw, W.N., Brüggen, M., Butcher, H.R., Ciardi, B., Conway, J.E., De Geus, E., De Jong, A., De Vos, M., Deller, A., Dettmar, R.-J., Duscha, S., Eislöffel, J., Engels, D., Falcke, H., Fender, R., Garrett, M.A., Grießmeier, J., Gunst, A.W., Hamaker, J.P., Hessels, J.W.T., Hoeft, M., Hörandel, J., Holties, H.A., Intema, H., Jackson, N.J., Jütte, E., Karastergiou, A., Klijn, W.F.A., Kondratiev, V.I., Koopmans, L.V.E., Kuniyoshi, M., Kuper, G., Law, C., Van Leeuwen, J., Loose, M., Maat, P., Markoff, S., McFadden, R., McKay-Bukowski, D., Mevius, M., Miller-Jones, J.C.A., Morganti, R., Munk, H., Nelles, A., Noordam, J.E., Norden, M.J., Paas, H., Polatidis, A.G., Reich, W., Renting, A., Röttgering, H., Schoenmakers, A., Schwarz, D., Sluman, J., Smirnov, O., Stappers, B.W., Steinmetz, M., Tagger, M., Tang, Y., Ter Veen, S., Thoudam, S., Vermeulen, R., Vocks, C., Vogt, C., Wijers, R.A.M.J., Wucknitz, O., Yatawatta, S., Zarka, P., High Energy Astrophys. & Astropart. Phys (API, FNWI), Netherlands Institute for Radio Astronomy (ASTRON), Jodrell Bank Centre for Astrophysics (JBCA), University of Manchester [Manchester], University of Hertfordshire [Hatfield] (UH), Uniwersytet Jagielloński w Krakowie = Jagiellonian University (UJ), Joseph Louis LAGRANGE (LAGRANGE), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de la Côte d'Azur, COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), University of Southampton, Jacobs University [Bremen], Astronomical Institute Anton Pannekoek (AI PANNEKOEK), University of Amsterdam [Amsterdam] (UvA), Laboratoire d'études spatiales et d'instrumentation en astrophysique (LESIA), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Hamburger Sternwarte/Hamburg Observatory, Universität Hamburg (UHH), School of Physics and Astronomy [Southampton], Leiden Observatory, Leiden University (Leiden Observatory), Centre de Recherche Astrophysique de Lyon (CRAL), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), CSIRO Astronomy and Space Science, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Max-Planck-Institut für Radioastronomie (MPIFR), Laboratory for Atmospheric and Space Physics [Boulder] (LASP), University of Colorado [Boulder], Laboratoire d'études spatiales et d'instrumentation en astrophysique (LESIA (UMR_8109)), Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut de recherche en astrophysique et planétologie (IRAP), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Harvard-Smithsonian Center for Astrophysics (CfA), Harvard University-Smithsonian Institution, Leiden Observatory [Leiden], Universiteit Leiden, SRON Netherlands Institute for Space Research (SRON), Leibniz-Institut für Astrophysik Potsdam (AIP), Research School of Astronomy and Astrophysics [Canberra] (RSAA), Australian National University (ANU), Max Planck Institute for Astrophysics, Max-Planck-Gesellschaft, Los Alamos National Laboratory (LANL), Astronomisches Institut der Ruhr-Universität Bochum, Ruhr-Universität Bochum [Bochum], Thüringer Landessternwarte Tautenburg (TLS), Radboud University [Nijmegen], Unité Scientifique de la Station de Nançay (USN), Observatoire des Sciences de l'Univers en région Centre (OSUC), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique et Chimie de l'Environnement et de l'Espace (LPC2E), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Centre National d’Études Spatiales [Paris] (CNES), Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH / Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures (DSMZ), Institute for Mathematics, Astrophysics and Particle Physics (IMAPP), ANR-09-JCJC-0001,OPALES(2009), European Project: 247295,EC:FP7:ERC,ERC-2009-AdG,AARTFAAC(2010), European Project: 267697,EC:FP7:ERC,ERC-2010-AdG_20100224,4PI-SKY(2011), ITA, GBR, FRA, DEU, NLD, Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Observatoire de la Côte d'Azur, Université Côte d'Azur (UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre d'études européennes et de politique comparée (CEE), Sciences Po (Sciences Po)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS), Institut national des sciences de l'Univers (INSU - CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), Harvard University [Cambridge]-Smithsonian Institution, Universiteit Leiden [Leiden], Laboratoire de Physique Nucléaire et de Hautes Énergies (LPNHE (UMR_7585)), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université Paris Diderot - Paris 7 (UPD7)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Radboud university [Nijmegen], Centre National de la Recherche Scientifique (CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire des Sciences de l'Univers en région Centre (OSUC), Université Paris sciences et lettres (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Université d'Orléans (UO), Astronomy, Kapteyn Astronomical Institute, Jodrell Bank Centre for Astrophysics, Jagiellonian University [Krakow] (UJ), Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Observatoire de la Côte d'Azur, Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Observatoire de Paris, PSL Research University (PSL)-PSL Research University (PSL)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC), PSL Research University (PSL)-PSL Research University (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Smithsonian Institution-Harvard University [Cambridge], Université d'Orléans (UO)-Observatoire des Sciences de l'Univers en région Centre (OSUC), Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université d'Orléans (UO)-Observatoire de Paris, PSL Research University (PSL)-PSL Research University (PSL)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université d'Orléans (UO)-Observatoire de Paris, PSL Research University (PSL)-PSL Research University (PSL)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, PSL Research University (PSL)-Centre National de la Recherche Scientifique (CNRS), PSL Research University (PSL)-PSL Research University (PSL)-Centre National d’Études Spatiales [Paris] (CNES), ANR-09-JCJC-0001,OPALES,nOn-thermal Processes in gALaxy cluStErs(2009), and Database Architectures

Subjects
010504 meteorology & atmospheric sciences, Computer science, Astronomy, media_common.quotation_subject, FOS: Physical sciences, METIS-315082, 01 natural sciences, Radio spectrum, Radio continuum: general, surveys, 0103 physical sciences, radio continuum: general, Survey, GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries), 010303 astronomy & astrophysics, Instrumentation and Methods for Astrophysics (astro-ph.IM), 0105 earth and related environmental sciences, Remote sensing, media_common, Giant Metrewave Radio Telescope, [SDU.ASTR]Sciences of the Universe [physics]/Astrophysics [astro-ph], Astronomy and Astrophysics, LOFAR, Astronomy and Astrophysic, Square kilometre array, IR-98663, Sky, [SDU]Sciences of the Universe [physics], Space and Planetary Science, Experimental High Energy Physics, EWI-26540, Snapshot (computer storage), general [radio continuum], Astrophysics - Instrumentation and Methods for Astrophysics
Abstract

We present the Multifrequency Snapshot Sky Survey (MSSS), the first northern-sky LOFAR imaging survey. In this introductory paper, we first describe in detail the motivation and design of the survey. Compared to previous radio surveys, MSSS is exceptional due to its intrinsic multifrequency nature providing information about the spectral properties of the detected sources over more than two octaves (from 30 to 160 MHz). The broadband frequency coverage, together with the fast survey speed generated by LOFAR's multibeaming capabilities, make MSSS the first survey of the sort anticipated to be carried out with the forthcoming Square Kilometre Array (SKA). Two of the sixteen frequency bands included in the survey were chosen to exactly overlap the frequency coverage of large-area Very Large Array (VLA) and Giant Metrewave Radio Telescope (GMRT) surveys at 74 MHz and 151 MHz respectively. The survey performance is illustrated within the "MSSS Verification Field" (MVF), a region of 100 square degrees centered at J2000 (RA,Dec)=(15h,69deg). The MSSS results from the MVF are compared with previous radio survey catalogs. We assess the flux and astrometric uncertainties in the catalog, as well as the completeness and reliability considering our source finding strategy. We determine the 90% completeness levels within the MVF to be 100 mJy at 135 MHz with 108" resolution, and 550 mJy at 50 MHz with 166" resolution. Images and catalogs for the full survey, expected to contain 150,000-200,000 sources, will be released to a public web server. We outline the plans for the ongoing production of the final survey products, and the ultimate public release of images and source catalogs., Comment: 23 pages, 19 figures. Accepted for publication in Astronomy & Astrophysics. MSSS Verification Field images and catalog data may be downloaded from http://vo.astron.nl

Published
2015

234. LOFAR: The LOw-Frequency ARray

Author

M. P. van Haarlem, M. W. Wise, A. W. Gunst, G. Heald, J. P. McKean, J. W. T. Hessels, A. G. de Bruyn, R. Nijboer, J. Swinbank, R. Fallows, M. Brentjens, A. Nelles, R. Beck, H. Falcke, R. Fender, J. Hörandel, L. V. E. Koopmans, G. Mann, G. Miley, H. Röttgering, B. W. Stappers, R. A. M. J. Wijers, S. Zaroubi, M. van den Akker, A. Alexov, J. Anderson, K. Anderson, A. van Ardenne, M. Arts, A. Asgekar, I. M. Avruch, F. Batejat, L. Bähren, M. E. Bell, M. R. Bell, I. van Bemmel, P. Bennema, M. J. Bentum, G. Bernardi, P. Best, L. Bîrzan, A. Bonafede, A.-J. Boonstra, R. Braun, J. Bregman, F. Breitling, R. H. van de Brink, J. Broderick, P. C. Broekema, W. N. Brouw, M. Brüggen, H. R. Butcher, W. van Cappellen, B. Ciardi, T. Coenen, J. Conway, A. Coolen, A. Corstanje, S. Damstra, O. Davies, A. T. Deller, R.-J. Dettmar, G. van Diepen, K. Dijkstra, P. Donker, A. Doorduin, J. Dromer, M. Drost, A. van Duin, J. Eislöffel, J. van Enst, C. Ferrari, W. Frieswijk, H. Gankema, M. A. Garrett, F. de Gasperin, M. Gerbers, E. de Geus, J.-M. Grießmeier, T. Grit, P. Gruppen, J. P. Hamaker, T. Hassall, M. Hoeft, H. A. Holties, A. Horneffer, A. van der Horst, A. van Houwelingen, A. Huijgen, M. Iacobelli, H. Intema, N. Jackson, V. Jelic, A. de Jong, E. Juette, D. Kant, A. Karastergiou, A. Koers, H. Kollen, V. I. Kondratiev, E. Kooistra, Y. Koopman, A. Koster, M. Kuniyoshi, M. Kramer, G. Kuper, P. Lambropoulos, C. Law, J. van Leeuwen, J. Lemaitre, M. Loose, P. Maat, G. Macario, S. Markoff, J. Masters, R. A. McFadden, D. McKay-Bukowski, H. Meijering, H. Meulman, M. Mevius, E. Middelberg, R. Millenaar, J. C. A. Miller-Jones, R. N. Mohan, J. D. Mol, J. Morawietz, R. Morganti, D. D. Mulcahy, E. Mulder, H. Munk, L. Nieuwenhuis, R. van Nieuwpoort, J. E. Noordam, M. Norden, A. Noutsos, A. R. Offringa, H. Olofsson, A. Omar, E. Orrú, R. Overeem, H. Paas, M. Pandey-Pommier, V. N. Pandey, R. Pizzo, A. Polatidis, D. Rafferty, S. Rawlings, W. Reich, J.-P. de Reijer, J. Reitsma, G. A. Renting, P. Riemers, E. Rol, J. W. Romein, J. Roosjen, M. Ruiter, A. Scaife, K. van der Schaaf, B. Scheers, P. Schellart, A. Schoenmakers, G. Schoonderbeek, M. Serylak, A. Shulevski, J. Sluman, O. Smirnov, C. Sobey, H. Spreeuw, M. Steinmetz, C. G. M. Sterks, H.-J. Stiepel, K. Stuurwold, M. Tagger, Y. Tang, C. Tasse, I. Thomas, S. Thoudam, M. C. Toribio, B. van der Tol, O. Usov, M. van Veelen, A.-J. van der Veen, S. ter Veen, J. P. W. Verbiest, R. Vermeulen, N. Vermaas, C. Vocks, C. Vogt, M. de Vos, E. van der Wal, R. van Weeren, H. Weggemans, P. Weltevrede, S. White, S. J. Wijnholds, T. Wilhelmsson, O. Wucknitz, S. Yatawatta, P. Zarka, A. Zensus, J. van Zwieten, Netherlands Institute for Radio Astronomy (ASTRON), Astronomical Institute Anton Pannekoek (AI PANNEKOEK), University of Amsterdam [Amsterdam] (UvA), Institute of Mathematical and Physical Sciences, Radboud university [Nijmegen], Laboratoire de Chimie Physique Moléculaire (LCPM), Ecole Polytechnique Fédérale de Lausanne (EPFL), Max-Planck-Institut für Radioastronomie (MPIFR), University of Southampton, Leibniz-Institut für Astrophysik Potsdam (AIP), Leiden Observatory [Leiden], Universiteit Leiden [Leiden], Jodrell Bank Centre for Astrophysics, University of Manchester [Manchester], Max Planck Institute for Astrophysics, Max-Planck-Gesellschaft, Medical Center Haaglanden, SRON Netherlands Institute for Space Research (SRON), University of Edinburgh, Jacobs University [Bremen], Technische Universität Dresden = Dresden University of Technology (TU Dresden), Kapteyn Astronomical Institute [Groningen], University of Groningen [Groningen], Department of Reproduction and Development, Erasmus University Rotterdam, London Institute for Mathematical Sciences, Netherlands Centre for Biodiversity, Leiden, The Netherlands, Thüringer Landessternwarte Tautenburg (TLS), Laboratoire Réactions et Génie des Procédés (LRGP), Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Medstar Research Institute, Laboratoire de Physique et Chimie de l'Environnement et de l'Espace (LPC2E), Observatoire des Sciences de l'Univers en région Centre (OSUC), Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Centre National d’Études Spatiales [Paris] (CNES), Plant Research International, Business Unit Bioscience, Wageningen University and Research [Wageningen] (WUR), Dipartimento di Matematica 'Guido Castelnuovo' [Roma I] (Sapienza University of Rome), Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome], Centre de Mathématiques Laurent Schwartz (CMLS), Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université de La Réunion (UR), Ruhr-Universität Bochum [Bochum], Oxford Astrophysics, University of Oxford [Oxford], Amsterdam Center for Multiscale Modeling, Vrije Universiteit Amsterdam [Amsterdam] (VU), Vrije Universiteit Medical Centre (VUMC), Queen's Medical Centre, National Radio Astronomy Observatory (NRAO), University of Oulu, Department of Economics, Bryant University, Center for Agricultural Research in Suriname CELOS and Department of Biology, Anton de Kom Universiteit van Suriname - Anton de Kom University of Suriname [Paramaribo] (UVS), DLR Institute of Aerospace Medicine, Deutsches Zentrum für Luft- und Raumfahrt [Köln] (DLR), Onsala Space Observatory (OSO), Chalmers University of Technology [Göteborg], Geophysical Institute [Bergen] (GFI / BiU), University of Bergen (UiB), Centre de Recherche Astrophysique de Lyon (CRAL), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS), Department of Astronomy and Astrophysics [PennState], Pennsylvania State University (Penn State), Penn State System-Penn State System, Academic Medical Center - Academisch Medisch Centrum [Amsterdam] (AMC), School of Physics and Astronomy [Southampton], Unité Scientifique de la Station de Nançay (USN), Centre National de la Recherche Scientifique (CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire des Sciences de l'Univers en région Centre (OSUC), Université Paris sciences et lettres (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Université d'Orléans (UO), Rhodes University, Grahamstown, Center for Information Technology CIT, Université de Groningen, Processus d'Activation Sélective par Transfert d'Energie Uni-électronique ou Radiatif (UMR 8640) (PASTEUR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'études spatiales et d'instrumentation en astrophysique (LESIA), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Center for Operations and Econometrics, Center of Operation Research and Econometrics [Louvain] (CORE), Université Catholique de Louvain = Catholic University of Louvain (UCL)-Université Catholique de Louvain = Catholic University of Louvain (UCL), Finca El Encin, Instituto Madrileño de Investigación y Desarrollo Rural, Agrario y Alimentario (IMIDRA), Department of Surgery (EINDHOVEN - Surgery), Catharina Hospital, Institute for Mathematics, Astrophysics and Particle Physics (IMAPP), Harvard-Smithsonian Center for Astrophysics (CfA), Smithsonian Institution-Harvard University [Cambridge], Argelander-Institut für Astronomie (AlfA), Rheinische Friedrich-Wilhelms-Universität Bonn, ANR-09-JCJC-0001,OPALES(2009), Astronomy, KVI - Center for Advanced Radiation Technology, Radboud University [Nijmegen], Universiteit Leiden, Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome] (UNIROMA), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), University of Oxford, École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Université Paris sciences et lettres (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Harvard University-Smithsonian Institution, UMR Peuplement Végétaux et Bioagresseurs en Milieu Tropical (UMR PVBMT - INRA), Institut National de la Recherche Agronomique (INRA), Laboratoire de Physique Nucléaire et de Hautes Énergies (LPNHE), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Technische Universität Dresden (TUD), university Rotterdam, PSL Research University (PSL)-PSL Research University (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, PSL Research University (PSL)-PSL Research University (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Centre National d’Études Spatiales [Paris] (CNES), Wageningen University and Research Centre [Wageningen] (WUR), Università degli Studi di Roma 'La Sapienza' [Rome], Department of Physics, University of Crete [Heraklion] (UOC), Institute of Electronic Structure and Laser, Foundation for Research and Technology - Hellas (FORTH), Anton de Kom University of Suriname, Geophysical Institute [Bergen], University of Bergen (UIB), Université d'Orléans (UO)-Observatoire des Sciences de l'Univers en région Centre (OSUC), PSL Research University (PSL)-Centre National de la Recherche Scientifique (CNRS), Rhodes University, École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Centre National de la Recherche Scientifique (CNRS), SKA South Africa, Ska South Africa, Center for Operations and Econometrics, Universit´e catholique de Louvain and Fonds National de la Recherche Scientifique, Harvard University [Cambridge]-Smithsonian Institution, Observatoire de Paris - Site de Paris (OP), PSL Research University (PSL)-PSL Research University (PSL)-Institut national des sciences de l'Univers (INSU - CNRS), ANR-09-JCJC-0001,OPALES,nOn-thermal Processes in gALaxy cluStErs(2009), High Energy Astrophys. & Astropart. Phys (API, FNWI), Van Haarlem, M.P., Wise, M.W., Gunst, A.W., Heald, G., McKean, J.P., Hessels, J.W.T., De Bruyn, A.G., Nijboer, R., Swinbank, J., Fallows, R., Brentjens, M., Nelles, A., Beck, R., Falcke, H., Fender, R., Hörandel, J., Koopmans, L.V.E., Mann, G., Miley, G., Röttgering, H., Stappers, B.W., Wijers, R.A.M.J., Zaroubi, S., Van Den Akker, M., Alexov, A., Anderson, J., Anderson, K., Van Ardenne, A., Arts, M., Asgekar, A., Avruch, I.M., Batejat, F., Bähren, L., Bell, M.E., Bell, M.R., Van Bemmel, I., Bennema, P., Bentum, M.J., Bernardi, G., Best, P., Bîrzan, L., Bonafede, A., Boonstra, A.-J., Braun, R., Bregman, J., Breitling, F., Van De Brink, R.H., Broderick, J., Broekema, P.C., Brouw, W.N., Brüggen, M., Butcher, H.R., Van Cappellen, W., Ciardi, B., Coenen, T., Conway, J., Coolen, A., Corstanje, A., Damstra, S., Davies, O., Deller, A.T., Dettmar, R.-J., Van Diepen, G., Dijkstra, K., Donker, P., Doorduin, A., Dromer, J., Drost, M., Van Duin, A., Eislöffel, J., Van Enst, J., Ferrari, C., Frieswijk, W., Gankema, H., Garrett, M.A., De Gasperin, F., Gerbers, M., De Geus, E., Grießmeier, J.-M., Grit, T., Gruppen, P., Hamaker, J.P., Hassall, T., Hoeft, M., Holties, H.A., Horneffer, A., Van Der Horst, A., Van Houwelingen, A., Huijgen, A., Iacobelli, M., Intema, H., Jackson, N., Jelic, V., De Jong, A., Juette, E., Kant, D., Karastergiou, A., Koers, A., Kollen, H., Kondratiev, V.I., Kooistra, E., Koopman, Y., Koster, A., Kuniyoshi, M., Kramer, M., Kuper, G., Lambropoulos, P., Law, C., Van Leeuwen, J., Lemaitre, J., Loose, M., Maat, P., Macario, G., Markoff, S., Masters, J., McFadden, R.A., McKay-Bukowski, D., Meijering, H., Meulman, H., Mevius, M., Middelberg, E., Millenaar, R., Miller-Jones, J.C.A., Mohan, R.N., Mol, J.D., Morawietz, J., Morganti, R., Mulcahy, D.D., Mulder, E., Munk, H., Nieuwenhuis, L., Van Nieuwpoort, R., Noordam, J.E., Norden, M., Noutsos, A., Offringa, A.R., Olofsson, H., Omar, A., Orrú, E., Overeem, R., Paas, H., Pandey-Pommier, M., Pandey, V.N., Pizzo, R., Polatidis, A., Rafferty, D., Rawlings, S., Reich, W., De Reijer, J.-P., Reitsma, J., Renting, G.A., Riemers, P., Rol, E., Romein, J.W., Roosjen, J., Ruiter, M., Scaife, A., Van Der Schaaf, K., Scheers, B., Schellart, P., Schoenmakers, A., Schoonderbeek, G., Serylak, M., Shulevski, A., Sluman, J., Smirnov, O., Sobey, C., Spreeuw, H., Steinmetz, M., Sterks, C.G.M., Stiepel, H.-J., Stuurwold, K., Tagger, M., Tang, Y., Tasse, C., Thomas, I., Thoudam, S., Toribio, M.C., Van Der Tol, B., Usov, O., Van Veelen, M., Van Der Veen, A.-J., Ter Veen, S., Verbiest, J.P.W., Vermeulen, R., Vermaas, N., Vocks, C., Vogt, C., De Vos, M., Van Der Wal, E., Van Weeren, R., Weggemans, H., Weltevrede, P., White, S., Wijnholds, S.J., Wilhelmsson, T., Wucknitz, O., Yatawatta, S., Zarka, P., Zensus, A., and Van Zwieten, J.

Subjects
instrumentation: interferometers -radio continuum: general -radio lines: general -dark ages, Computer science, Astronomy, INTERPLANETARY SCINTILLATION, radio continuum: general, 7. Clean energy, 01 natural sciences, Precision Array for Probing the Epoch of Reionization, law.invention, Observatory, law, first stars - telescopes, dark ages, instrumentation: interferometers, 010303 astronomy & astrophysics, Telescope, UNDERSTANDING RADIO POLARIMETRY, Instrumentation: Interferometer, SELF-CALIBRATION, Interferometry, ComputingMethodologies_DOCUMENTANDTEXTPROCESSING, reionization, Astrophysics - Instrumentation and Methods for Astrophysics, radio lines: general, first stars, Z-GREATER-THAN-5.7 QUASARS, FOS: Physical sciences, Murchison Widefield Array, 0103 physical sciences, RAY AIR-SHOWERS, Angular resolution, dark ages, reionization, first stars, Instrumentation and Methods for Astrophysics (astro-ph.IM), Remote sensing, 010308 nuclear & particles physics, telescopes, Astronomy and Astrophysics, LOFAR, Astronomy and Astrophysic, Sextant (astronomical), Dark ages, reionization, first star, Space and Planetary Science, [SDU]Sciences of the Universe [physics], PROBE WMAP OBSERVATIONS, DIGITAL SKY SURVEY, HIGH-REDSHIFT, MONTE-CARLO SIMULATIONS, INTERGALACTIC MEDIUM
Abstract

LOFAR, the LOw-Frequency ARray, is a new-generation radio interferometer constructed in the north of the Netherlands and across europe. Utilizing a novel phased-array design, LOFAR covers the largely unexplored low-frequency range from 10-240 MHz and provides a number of unique observing capabilities. Spreading out from a core located near the village of Exloo in the northeast of the Netherlands, a total of 40 LOFAR stations are nearing completion. A further five stations have been deployed throughout Germany, and one station has been built in each of France, Sweden, and the UK. Digital beam-forming techniques make the LOFAR system agile and allow for rapid repointing of the telescope as well as the potential for multiple simultaneous observations. With its dense core array and long interferometric baselines, LOFAR achieves unparalleled sensitivity and angular resolution in the low-frequency radio regime. The LOFAR facilities are jointly operated by the International LOFAR Telescope (ILT) foundation, as an observatory open to the global astronomical community. LOFAR is one of the first radio observatories to feature automated processing pipelines to deliver fully calibrated science products to its user community. LOFAR's new capabilities, techniques and modus operandi make it an important pathfinder for the Square Kilometre Array (SKA). We give an overview of the LOFAR instrument, its major hardware and software components, and the core science objectives that have driven its design. In addition, we present a selection of new results from the commissioning phase of this new radio observatory., Comment: 56 pages, 34 figures, accepted for publication by A&A

Published
2013
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235. Wide-field LOFAR imaging of the field around the double-double radio galaxy B1834+620

Author

E. Orrù, S. van Velzen, R. F. Pizzo, S. Yatawatta, R. Paladino, M. Iacobelli, M. Murgia, H. Falcke, R. Morganti, A. G. de Bruyn, C. Ferrari, J. Anderson, A. Bonafede, D. Mulcahy, A. Asgekar, I. M. Avruch, R. Beck, M. E. Bell, I. van Bemmel, M. J. Bentum, G. Bernardi, P. Best, F. Breitling, J. W. Broderick, M. Brüggen, H. R. Butcher, B. Ciardi, J. E. Conway, A. Corstanje, E. de Geus, A. Deller, S. Duscha, J. Eislöffel, D. Engels, W. Frieswijk, M. A. Garrett, J. Grießmeier, A. W. Gunst, J. P. Hamaker, G. Heald, M. Hoeft, A. J. van der Horst, H. Intema, E. Juette, J. Kohler, V. I. Kondratiev, M. Kuniyoshi, G. Kuper, M. Loose, P. Maat, G. Mann, S. Markoff, R. McFadden, D. McKay-Bukowski, G. Miley, J. Moldon, G. Molenaar, H. Munk, A. Nelles, H. Paas, M. Pandey-Pommier, V. N. Pandey, G. Pietka, A. G. Polatidis, W. Reich, H. Röttgering, A. Rowlinson, A. Scaife, A. Schoenmakers, D. Schwarz, M. Serylak, A. Shulevski, O. Smirnov, M. Steinmetz, A. Stewart, J. Swinbank, M. Tagger, C. Tasse, S. Thoudam, M. C. Toribio, R. Vermeulen, C. Vocks, R. J. van Weeren, R. A. M. J. Wijers, M. W. Wise, O. Wucknitz, High Energy Astrophys. & Astropart. Phys (API, FNWI), Kapteyn Astronomical Institute, Astronomy, Orru, E., Van Velzen, S., Pizzo, R.F., Yatawatta, S., Paladino, R., Iacobelli, M., Murgia, M., Falcke, H., Morganti, R., De Bruyn, A.G., Ferrari, C., Anderson, J., Bonafede, A., Mulcahy, D., Asgekar, A., Avruch, I.M., Beck, R., Bell, M.E., Van Bemmel, I., Bentum, M.J., Bernardi, G., Best, P., Breitling, F., Broderick, J.W., Bruggen, M., Butcher, H.R., Ciardi, B., Conway, J.E., Corstanje, A., De Geus, E., Deller, A., Duscha, S., Eisloffel, J., Engels, D., Frieswijk, W., Garrett, M.A., Grießmeier, J., Gunst, A.W., Hamaker, J.P., Heald, G., Hoeft, M., Van Der Horst, A.J., Intema, H., Juette, E., Kohler, J., Kondratiev, V.I., Kuniyoshi, M., Kuper, G., Loose, M., Maat, P., Mann, G., Markoff, S., McFadden, R., McKay-BGBRowski, D., Miley, G., Moldon, J., Molenaar, G., Munk, H., Nelles, A., Paas, H., Pandey-Pommier, M., Pandey, V.N., Pietka, G., Polatidis, A.G., Reich, W., Rottgering, H., Rowlinson, A., Scaife, A., Schoenmakers, A., Schwarz, D., Serylak, M., Shulevski, A., Smirnov, O., Steinmetz, M., Stewart, A., Swinbank, J., Tagger, M., Tasse, C., Thoudam, S., Toribio, M.C., Vermeulen, R., Vocks, C., Van Weeren, R.J., Wijers, R.A.M.J., Wise, M.W., and Wucknitz, O.

Subjects
Cosmology and Nongalactic Astrophysics (astro-ph.CO), Radio galaxy, Astrophysics::High Energy Astrophysical Phenomena, interferometers [instrumentation], galaxies: active, Population, FOS: Physical sciences, Field of view, Astrophysics::Cosmology and Extragalactic Astrophysics, Astrophysics, Astroparticle physic, Radio continuum: galaxie, 01 natural sciences, Instrumentation: interferometer, law.invention, Telescope, law, 0103 physical sciences, Bow shock (aerodynamics), instrumentation: interferometers, education, 010303 astronomy & astrophysics, Astrophysics::Galaxy Astrophysics, radio continuum: galaxies, Physics, education.field_of_study, Accretion (meteorology), 010308 nuclear & particles physics, Astronomy and Astrophysics, LOFAR, Astronomy and Astrophysic, radiation mechanisms: non-thermal, non-thermal [radiation mechanisms], Astrophysics - Astrophysics of Galaxies, galaxies [radio continuum], Redshift, interferometric [techniques], techniques: interferometric, astroparticle physics, Space and Planetary Science, Astrophysics of Galaxies (astro-ph.GA), active [galaxies], Astrophysics - Cosmology and Nongalactic Astrophysics
Abstract

The existence of double-double radio galaxies (DDRGs) is evidence for recurrent jet activity in AGN, as expected from standard accretion models. A detailed study of these rare sources provides new perspectives for investigating the AGN duty cycle, AGN-galaxy feedback, and accretion mechanisms. Large catalogues of radio sources provide statistical information about the evolution of the radio-loud AGN population out to high redshifts. Using wide-field imaging with the LOFAR telescope, we study both a well-known DDRG as well as a large number of radio sources in the field of view. We present a high resolution image of the DDRG B1834+620 obtained at 144 MHz using LOFAR commissioning data. Our image covers about 100 square degrees and contains over 1000 sources. The four components of the DDRG B1834+620 have been resolved for the first time at 144 MHz. Inner lobes were found to point towards the direction of the outer lobes, unlike standard FR~II sources. Polarized emission was detected in the northern outer lobe. The high spatial resolution allows the identification of a large number of small double-lobed radio sources; roughly 10% of all sources in the field are doubles with a separation smaller than 1 arcmin. The spectral fit of the four components is consistent with a scenario in which the outer lobes are still active or the jets recently switched off, while emission of the inner lobes is the result of a mix-up of new and old jet activity. From the presence of the newly extended features in the inner lobes of the DDRG, we can infer that the mechanism responsible for their formation is the bow shock that is driven by the newly launched jet. We find that the density of the small doubles exceeds the density of FR-II sources with similar properties at 1.4 GHz, but this difference becomes smaller for low flux densities., Comment: 13 pages, 8 figures, Accepted for publication in Astronomy & Astrophysics

Published
2015

236. Disordered regions in the IRE1α ER lumenal domain mediate its stress-induced clustering.

Author

Kettel P, Marosits L, Spinetti E, Rechberger M, Giannini C, Radler P, Niedermoser I, Fischer I, Versteeg GA, Loose M, Covino R, and Karagöz GE

Abstract

Conserved signaling cascades monitor protein-folding homeostasis to ensure proper cellular function. One of the evolutionary conserved key players is IRE1, which maintains endoplasmic reticulum (ER) homeostasis through the unfolded protein response (UPR). Upon accumulation of misfolded proteins in the ER, IRE1 forms clusters on the ER membrane to initiate UPR signaling. What regulates IRE1 cluster formation is not fully understood. Here, we show that the ER lumenal domain (LD) of human IRE1α forms biomolecular condensates in vitro. IRE1α LD condensates were stabilized both by binding to unfolded polypeptides as well as by tethering to model membranes, suggesting their role in assembling IRE1α into signaling-competent stable clusters. Molecular dynamics simulations indicated that weak multivalent interactions drive IRE1α LD clustering. Mutagenesis experiments identified disordered regions in IRE1α LD to control its clustering in vitro and in cells. Importantly, dysregulated clustering of IRE1α mutants led to defects in IRE1α signaling. Our results revealed that disordered regions in IRE1α LD control its clustering and suggest their role as a common strategy in regulating protein assembly on membranes., (© 2024. The Author(s).)

Published
2024
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237. A hot-Jupiter progenitor on a super-eccentric retrograde orbit.

Author

Gupta AF, Millholland SC, Im H, Dong J, Jackson JM, Carleo I, Libby-Roberts J, Delamer M, Giovinazzi MR, Lin ASJ, Kanodia S, Wang XY, Stassun K, Masseron T, Dragomir D, Mahadevan S, Wright J, Alvarado-Montes JA, Bender C, Blake CH, Caldwell D, Cañas CI, Cochran WD, Dalba P, Everett ME, Fernandez P, Golub E, Guillet B, Halverson S, Hebb L, Higuera J, Huang CX, Klusmeyer J, Knight R, Leroux L, Logsdon SE, Loose M, McElwain MW, Monson A, Ninan JP, Nowak G, Palle E, Patel Y, Pepper J, Primm M, Rajagopal J, Robertson P, Roy A, Schneider DP, Schwab C, Schweiker H, Sgro L, Shimizu M, Simard G, Stefánsson G, Stevens DJ, Villanueva S, Wisniewski J, Will S, and Ziegler C

Abstract

Giant exoplanets orbiting close to their host stars are unlikely to have formed in their present configurations 1 . These 'hot Jupiter' planets are instead thought to have migrated inward from beyond the ice line and several viable migration channels have been proposed, including eccentricity excitation through angular-momentum exchange with a third body followed by tidally driven orbital circularization 2,3 . The discovery of the extremely eccentric (e = 0.93) giant exoplanet HD 80606 b (ref.  4 ) provided observational evidence that hot Jupiters may have formed through this high-eccentricity tidal-migration pathway 5 . However, no similar hot-Jupiter progenitors have been found and simulations predict that one factor affecting the efficacy of this mechanism is exoplanet mass, as low-mass planets are more likely to be tidally disrupted during periastron passage 6-8 . Here we present spectroscopic and photometric observations of TIC 241249530 b, a high-mass, transiting warm Jupiter with an extreme orbital eccentricity of e = 0.94. The orbit of TIC 241249530 b is consistent with a history of eccentricity oscillations and a future tidal circularization trajectory. Our analysis of the mass and eccentricity distributions of the transiting-warm-Jupiter population further reveals a correlation between high mass and high eccentricity., (© 2024. The Author(s).)

Published
2024
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238. Multiple novel caliciviruses identified from stoats (Mustela erminea) in the United Kingdom.

Author

Hinds J, Apaa T, Parry RH, Withers AJ, MacKenzie L, Staley C, Morrison J, Bennett M, Bremner-Harrison S, Chadwick EA, Hailer F, Harrison SWR, Lambin X, Loose M, Mathews F, Tarlinton R, and Blanchard A

Abstract

The Caliciviridae family , comprising positive-sense RNA viruses, is characterised by its non-enveloped, small virions, broad host range, and notable tendency for host switching. These viruses are primarily associated with gastroenteric disease, though they can lead to haemorrhagic or respiratory infections. Our study employed a metagenomics analysis of faecal samples from stoats ( Mustela erminea ), identifying two novel calicivirus species, named stoat vesivirus and stoat valovirus. Stoat vesivirus was identified in three samples (ST008, ST006, ST004), exhibiting a genome wide nucleotide identity of approximately 92 %. The complete coding sequences of these samples were 8471 (ST004) and 8322 (ST006) nucleotides in length, respectively. Each comprised three open reading frames (ORF), closely resembling the Vesivirus mink calicivirus (China/2/2016), with 70-72 % similarity in ORF1, 61-62 % in ORF2 and 71 % in ORF3. Phylogenetic analysis robustly supported stoat vesivirus as belonging within the Vesivirus genus. The second calivicirus (stoat valovirus), detected solely in sample ST008, was 6527 nucleotides in length and with complete coding sequences present. It shared highest similarity with St-Valérien swine virus and marmot norovirus HT16, showing 39.5 and 38.8 % protein identity with ORF1 and 43.3 and 42.9 % for VP1. Stoat valovirus is borderline for meeting the ICTV criteria for a new genus, demonstrating 60 % divergence in ORF1 compared to the other valovirus', however it clusters basally within the Valovirus genus, supporting leaving it included in this genus., Competing Interests: The authors declare that there are no conflicts of interest., (Copyright © 2024 The Authors.)

Published
2024
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239. Impact of whole-genome duplications on structural variant evolution in Cochlearia.

Author

Hämälä T, Moore C, Cowan L, Carlile M, Gopaulchan D, Brandrud MK, Birkeland S, Loose M, Kolář F, Koch MA, and Yant L

Subjects
Genomic Structural Variation genetics, Mutation, Polyploidy, Genome, Plant genetics, Evolution, Molecular, Gene Duplication
Abstract

Polyploidy, the result of whole-genome duplication (WGD), is a major driver of eukaryote evolution. Yet WGDs are hugely disruptive mutations, and we still lack a clear understanding of their fitness consequences. Here, we study whether WGDs result in greater diversity of genomic structural variants (SVs) and how they influence evolutionary dynamics in a plant genus, Cochlearia (Brassicaceae). By using long-read sequencing and a graph-based pangenome, we find both negative and positive interactions between WGDs and SVs. Masking of recessive mutations due to WGDs leads to a progressive accumulation of deleterious SVs across four ploidal levels (from diploids to octoploids), likely reducing the adaptive potential of polyploid populations. However, we also discover putative benefits arising from SV accumulation, as more ploidy-specific SVs harbor signals of local adaptation in polyploids than in diploids. Together, our results suggest that SVs play diverse and contrasting roles in the evolutionary trajectories of young polyploids., (© 2024. The Author(s).)

Published
2024
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240. A single-cell atlas of pig gastrulation as a resource for comparative embryology.

Author

Simpson L, Strange A, Klisch D, Kraunsoe S, Azami T, Goszczynski D, Le Minh T, Planells B, Holmes N, Sang F, Henson S, Loose M, Nichols J, and Alberio R

Subjects
Animals, Swine, Mice, Cell Differentiation, Mesoderm cytology, Mesoderm embryology, Mesoderm metabolism, Transcriptome, Hepatocyte Nuclear Factor 3-beta metabolism, Hepatocyte Nuclear Factor 3-beta genetics, Cell Lineage, T-Box Domain Proteins metabolism, T-Box Domain Proteins genetics, Epithelial-Mesenchymal Transition genetics, Gastrulation, Endoderm cytology, Endoderm metabolism, Endoderm embryology, Single-Cell Analysis, Gene Expression Regulation, Developmental, Embryo, Mammalian cytology, Embryo, Mammalian metabolism
Abstract

Cell-fate decisions during mammalian gastrulation are poorly understood outside of rodent embryos. The embryonic disc of pig embryos mirrors humans, making them a useful proxy for studying gastrulation. Here we present a single-cell transcriptomic atlas of pig gastrulation, revealing cell-fate emergence dynamics, as well as conserved and divergent gene programs governing early porcine, primate, and murine development. We highlight heterochronicity in extraembryonic cell-types, despite the broad conservation of cell-type-specific transcriptional programs. We apply these findings in combination with functional investigations, to outline conserved spatial, molecular, and temporal events during definitive endoderm specification. We find early FOXA2 + /TBXT- embryonic disc cells directly form definitive endoderm, contrasting later-emerging FOXA2/TBXT+ node/notochord progenitors. Unlike mesoderm, none of these progenitors undergo epithelial-to-mesenchymal transition. Endoderm/Node fate hinges on balanced WNT and hypoblast-derived NODAL, which is extinguished upon endodermal differentiation. These findings emphasise the interplay between temporal and topological signalling in fate determination during gastrulation., (© 2024. Crown.)

Published
2024
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241. Efficacy of ramucirumab combination chemotherapy as second-line treatment in patients with advanced adenocarcinoma of the stomach or gastroesophageal junction after exposure to checkpoint inhibitors and chemotherapy as first-line therapy.

Author

Masetti M, Al-Batran SE, Goetze TO, Thuss-Patience P, Knorrenschild JR, Goekkurt E, Folprecht G, Ettrich TJ, Lindig U, Luley KB, Pink D, Dechow T, Sookthai D, Junge S, Loose M, Pauligk C, and Lorenzen S

Subjects
Humans, Ramucirumab, B7-H1 Antigen, Nivolumab therapeutic use, Retrospective Studies, Antibodies, Monoclonal, Humanized therapeutic use, Antineoplastic Combined Chemotherapy Protocols adverse effects, Esophagogastric Junction pathology, Stomach Neoplasms pathology, Adenocarcinoma drug therapy, Adenocarcinoma pathology
Abstract

FOLFOX plus nivolumab represents a standard of care for first-line therapy of advanced gastroesophageal cancer (aGEC) with positive PD-L1 expression. The efficacy of second-line VEGFR-2 inhibition with ramucirumab (RAM) plus chemotherapy after progression to immunochemotherapy remains unclear. Medical records of patients with aGEC enrolled in the randomized phase II AIO-STO-0417 trial after treatment failure to first-line FOLFOX plus nivolumab and ipilimumab were retrospectively analyzed. Patients were divided into two groups based on second-line therapy: RAM plus chemotherapy (RAM group) or treatment without RAM (control group). Eighty three patients were included. In the overall population, progression-free survival (PFS) in the RAM group was superior to the control (4.5 vs 2.9 months). Responders (CR/PR) to first-line immunochemotherapy receiving RAM containing second-line therapy had prolonged OS from start of first-line therapy (28.9 vs 16.5 months), as well as second-line OS (9.6 vs 7.5 months), PFS (5.6 vs 2.9 months) and DCR (53% vs 29%) compared to the control. PD-L1 CPS ≥1 was 42% and 44% for the RAM and the control, respectively. Patients with CPS ≥1 in the RAM group showed better tumor control (ORR 25% vs 10%) and improved survival (total OS 11.5 vs 8.0 months; second-line OS 6.5 vs 3.9 months; PFS 4.5 vs 1.6 months) compared to the control. Prior exposure to first-line FOLFOX plus dual checkpoint inhibition followed by RAM plus chemotherapy shows favorable response and survival rates especially in patients with initial response and positive PD-L1 expression and has the potential to advance the treatment paradigm in aGEC., (© 2024 The Authors. International Journal of Cancer published by John Wiley & Sons Ltd on behalf of UICC.)

Published
2024
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242. Adjuvant Gemcitabine Versus Neoadjuvant/Adjuvant FOLFIRINOX in Resectable Pancreatic Cancer: The Randomized Multicenter Phase II NEPAFOX Trial.

Author

Goetze TO, Reichart A, Bankstahl US, Pauligk C, Loose M, Kraus TW, Elshafei M, Bechstein WO, Trojan J, Behrend M, Homann N, Venerito M, Bohle W, Varvenne M, Bolling C, Behringer DM, Kratz-Albers K, Siegler GM, Hozaeel W, and Al-Batran SE

Subjects
Humans, Male, Female, Middle Aged, Aged, Chemotherapy, Adjuvant, Survival Rate, Follow-Up Studies, Prognosis, Pancreatectomy, Adult, Adenocarcinoma drug therapy, Adenocarcinoma pathology, Adenocarcinoma surgery, Adenocarcinoma mortality, Pancreatic Neoplasms drug therapy, Pancreatic Neoplasms pathology, Pancreatic Neoplasms surgery, Antineoplastic Combined Chemotherapy Protocols therapeutic use, Deoxycytidine analogs & derivatives, Deoxycytidine administration & dosage, Neoadjuvant Therapy, Leucovorin administration & dosage, Leucovorin therapeutic use, Gemcitabine, Irinotecan administration & dosage, Irinotecan therapeutic use, Fluorouracil administration & dosage, Oxaliplatin administration & dosage, Oxaliplatin therapeutic use
Abstract

Background: Although addition of adjuvant chemotherapy is the current standard, the prognosis of pancreatic cancers still remains poor. The NEPAFOX trial evaluated perioperative treatment with FOLFIRINOX in resectable pancreatic cancer., Patients and Methods: This multicenter phase II trial randomized patients with resectable or borderline resectable pancreatic cancer without metastases into arm (A,) upfront surgery plus adjuvant gemcitabine, or arm (B,) perioperative FOLFIRINOX. The primary endpoint was overall survival (OS)., Results: Owing to poor accrual, recruitment was prematurely stopped after randomization of 40 of the planned 126 patients (A: 21, B: 19). Overall, approximately three-quarters were classified as primarily resectable (A: 16, B: 15), and the remaining patients were classified as borderline resectable (A: 5, B: 4). Of the 12 evaluable patients, 3 achieved partial response under neoadjuvant FOLFIRINOX. Of the 21 patients in arm A and 19 patients in arm B, 17 and 7 underwent curative surgery, and R0-resection was achieved in 77% and 71%, respectively. Perioperative morbidity occurred in 72% in arm A and 46% in arm B, whereas non-surgical toxicity was comparable in both arms. Median RFS/PFS was almost doubled in arm B (14.1 months) compared with arm A (8.4 months) in the population with surgical resection, whereas median OS was comparable between both arms., Conclusions: Although the analysis was only descriptive owing to small patient numbers, no safety issues regarding surgical complications were observed in the perioperative FOLFIRINOX arm. Thus, considering the small number of patients, perioperative treatment approach appears feasible and potentially effective in well-selected cohorts of patients. In pancreatic cancer, patient selection before initiation of neoadjuvant therapy appears to be critical., (© 2024. The Author(s).)

Published
2024
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243. Role of the dynamin-related protein 2 family and SH3P2 in clathrin-mediated endocytosis in Arabidopsis thaliana.

Author

Gnyliukh N, Johnson A, Nagel MK, Monzer A, Babić D, Hlavata A, Alotaibi SS, Isono E, Loose M, and Friml J

Subjects
Clathrin metabolism, Clathrin genetics, GTP-Binding Proteins, Mutation genetics, Arabidopsis metabolism, Arabidopsis genetics, Arabidopsis Proteins metabolism, Arabidopsis Proteins genetics, Dynamins metabolism, Dynamins genetics, Endocytosis genetics
Abstract

Clathrin-mediated endocytosis (CME) is vital for the regulation of plant growth and development through controlling plasma membrane protein composition and cargo uptake. CME relies on the precise recruitment of regulators for vesicle maturation and release. Homologues of components of mammalian vesicle scission are strong candidates to be part of the scission machinery in plants, but the precise roles of these proteins in this process are not fully understood. Here, we characterised the roles of the plant dynamin-related protein 2 (DRP2) family (hereafter DRP2s) and SH3-domain containing protein 2 (SH3P2), the plant homologue to recruiters of dynamins, such as endophilin and amphiphysin, in CME by combining high-resolution imaging of endocytic events in vivo and characterisation of the purified proteins in vitro. Although DRP2s and SH3P2 arrive similarly late during CME and physically interact, genetic analysis of the sh3p123 triple mutant and complementation assays with non-SH3P2-interacting DRP2 variants suggest that SH3P2 does not directly recruit DRP2s to the site of endocytosis. These observations imply that, despite the presence of many well-conserved endocytic components, plants have acquired a distinct mechanism for CME., Competing Interests: Competing interests The authors declare no competing or financial interests., (© 2024. Published by The Company of Biologists Ltd.)

Published
2024
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244. Icarust, a real-time simulator for Oxford Nanopore adaptive sampling.

Author

Munro R, Wibowo S, Payne A, and Loose M

Subjects
Sequence Analysis, DNA, Software, High-Throughput Nucleotide Sequencing, Nanopores, Nanopore Sequencing
Abstract

Motivation: Oxford Nanopore Technologies (ONT) sequencers enable real-time generation of sequence data, which allows for concurrent analysis during a run. Adaptive sampling leverages this real-time capability in extremis, rejecting or accepting reads for sequencing based on assessment of the sequence from the start of each read. This functionality is provided by ONT's software, MinKNOW (Oxford Nanopore Technologies). Designing and developing software to take advantage of adaptive sampling can be costly in terms of sequencing consumables, using precious samples and preparing sequencing libraries. MinKNOW addresses this in part by allowing the replay of previously sequenced runs for testing. However, as we show, the sequencing output only partially changes in response to adaptive sampling instructions. Here we present Icarust, a tool enabling more accurate approximations of sequencing runs. Icarust recreates all the required endpoints of MinKNOW to perform adaptive sampling and writes output compatible with current base-callers and analysis pipelines. Icarust serves nanopore signal simulating a MinION or PromethION flow cell experiment from any reference genome using either R9 or R10 pore models. We show that simulating sequencing runs with Icarust provides a realistic testing and development environment for software exploiting the real-time nature of Nanopore sequencing., Availability and Implementation: All code is open source and freely available here-https://github.com/LooseLab/Icarust. Icarust is implemented in Rust, with a docker container also available. The data underlying this article will be shared on reasonable request to the corresponding author., (© The Author(s) 2024. Published by Oxford University Press.)

Published
2024
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245. Nanopore sequencing of 1000 Genomes Project samples to build a comprehensive catalog of human genetic variation.

Author

Gustafson JA, Gibson SB, Damaraju N, Zalusky MP, Hoekzema K, Twesigomwe D, Yang L, Snead AA, Richmond PA, De Coster W, Olson ND, Guarracino A, Li Q, Miller AL, Goffena J, Anderson Z, Storz SH, Ward SA, Sinha M, Gonzaga-Jauregui C, Clarke WE, Basile AO, Corvelo A, Reeves C, Helland A, Musunuri RL, Revsine M, Patterson KE, Paschal CR, Zakarian C, Goodwin S, Jensen TD, Robb E, McCombie WR, Sedlazeck FJ, Zook JM, Montgomery SB, Garrison E, Kolmogorov M, Schatz MC, McLaughlin RN Jr, Dashnow H, Zody MC, Loose M, Jain M, Eichler EE, and Miller DE

Abstract

Less than half of individuals with a suspected Mendelian condition receive a precise molecular diagnosis after comprehensive clinical genetic testing. Improvements in data quality and costs have heightened interest in using long-read sequencing (LRS) to streamline clinical genomic testing, but the absence of control datasets for variant filtering and prioritization has made tertiary analysis of LRS data challenging. To address this, the 1000 Genomes Project ONT Sequencing Consortium aims to generate LRS data from at least 800 of the 1000 Genomes Project samples. Our goal is to use LRS to identify a broader spectrum of variation so we may improve our understanding of normal patterns of human variation. Here, we present data from analysis of the first 100 samples, representing all 5 superpopulations and 19 subpopulations. These samples, sequenced to an average depth of coverage of 37x and sequence read N50 of 54 kbp, have high concordance with previous studies for identifying single nucleotide and indel variants outside of homopolymer regions. Using multiple structural variant (SV) callers, we identify an average of 24,543 high-confidence SVs per genome, including shared and private SVs likely to disrupt gene function as well as pathogenic expansions within disease-associated repeats that were not detected using short reads. Evaluation of methylation signatures revealed expected patterns at known imprinted loci, samples with skewed X-inactivation patterns, and novel differentially methylated regions. All raw sequencing data, processed data, and summary statistics are publicly available, providing a valuable resource for the clinical genetics community to discover pathogenic SVs., Competing Interests: COMPETING INTEREST STATEMENT WDC, ML, FS, and DEM have received research support and/or consumables from ONT. WDC, JG, FS, and DEM have received travel funding to speak on behalf of ONT. DEM is on a scientific advisory board at ONT. FS has received research support from Illumina, Genetech, and PacBio. SBM is an advisor to BioMarin, MyOme, and Tenaya Therapeutics. EEE is a scientific advisory board (SAB) member of Variant Bio, Inc. DEM holds stock options in MyOme.

Published
2024
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246. A dynamic duo: Understanding the roles of FtsZ and FtsA for Escherichia coli cell division through in vitro approaches.

Author

Radler P and Loose M

Subjects
Cell Cycle Proteins metabolism, Cell Division, Carrier Proteins metabolism, Escherichia coli metabolism, Escherichia coli Proteins genetics, Escherichia coli Proteins metabolism
Abstract

Bacteria divide by binary fission. The protein machine responsible for this process is the divisome, a transient assembly of more than 30 proteins in and on the surface of the cytoplasmic membrane. Together, they constrict the cell envelope and remodel the peptidoglycan layer to eventually split the cell into two. For Escherichia coli, most molecular players involved in this process have probably been identified, but obtaining the quantitative information needed for a mechanistic understanding can often not be achieved from experiments in vivo alone. Since the discovery of the Z-ring more than 30 years ago, in vitro reconstitution experiments have been crucial to shed light on molecular processes normally hidden in the complex environment of the living cell. In this review, we summarize how rebuilding the divisome from purified components - or at least parts of it - have been instrumental to obtain the detailed mechanistic understanding of the bacterial cell division machinery that we have today., Competing Interests: Declaration of Competing Interest We wish to confirm that there are no known conflicts of interest associated with this publication and there has been no significant financial support for this work that could have influenced its outcome., (Copyright © 2024 The Authors. Published by Elsevier GmbH.. All rights reserved.)

Published
2024
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247. Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division.

Author

Nußbaum P, Kureisaite-Ciziene D, Bellini D, van der Does C, Kojic M, Taib N, Yeates A, Tourte M, Gribaldo S, Loose M, Löwe J, and Albers SV

Subjects
Cell Division, Cytoskeleton, Microscopy, Fluorescence, Haloferax volcanii genetics, Photosynthetic Reaction Center Complex Proteins
Abstract

Cell division in all domains of life requires the orchestration of many proteins, but in Archaea most of the machinery remains poorly characterized. Here we investigate the FtsZ-based cell division mechanism in Haloferax volcanii and find proteins containing photosynthetic reaction centre (PRC) barrel domains that play an essential role in archaeal cell division. We rename these proteins cell division protein B 1 (CdpB1) and CdpB2. Depletions and deletions in their respective genes cause severe cell division defects, generating drastically enlarged cells. Fluorescence microscopy of tagged FtsZ1, FtsZ2 and SepF in CdpB1 and CdpB2 mutant strains revealed an unusually disordered divisome that is not organized into a distinct ring-like structure. Biochemical analysis shows that SepF forms a tripartite complex with CdpB1/2 and crystal structures suggest that these two proteins might form filaments, possibly aligning SepF and the FtsZ2 ring during cell division. Overall our results indicate that PRC-domain proteins play essential roles in FtsZ-based cell division in Archaea., (© 2024. The Author(s), under exclusive licence to Springer Nature Limited.)

Published
2024
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248. Perioperative Atezolizumab Plus Fluorouracil, Leucovorin, Oxaliplatin, and Docetaxel for Resectable Esophagogastric Cancer: Interim Results From the Randomized, Multicenter, Phase II/III DANTE/IKF-s633 Trial.

Author

Lorenzen S, Götze TO, Thuss-Patience P, Biebl M, Homann N, Schenk M, Lindig U, Heuer V, Kretzschmar A, Goekkurt E, Haag GM, Riera-Knorrenschild J, Bolling C, Hofheinz RD, Zhan T, Angermeier S, Ettrich TJ, Siebenhuener AR, Elshafei M, Bechstein WO, Gaiser T, Loose M, Sookthai D, Kopp C, Pauligk C, and Al-Batran SE

Subjects
Humans, Antineoplastic Combined Chemotherapy Protocols adverse effects, B7-H1 Antigen therapeutic use, Docetaxel therapeutic use, Esophagogastric Junction pathology, Fluorouracil adverse effects, Leucovorin adverse effects, Neoadjuvant Therapy methods, Oxaliplatin therapeutic use, Adenocarcinoma drug therapy, Adenocarcinoma surgery, Adenocarcinoma pathology, Antibodies, Monoclonal, Humanized, Esophageal Neoplasms drug therapy, Esophageal Neoplasms surgery, Stomach Neoplasms drug therapy, Stomach Neoplasms surgery, Stomach Neoplasms pathology
Abstract

Purpose: This trial evaluates the addition of the PD-L1 antibody atezolizumab (ATZ) to standard-of-care fluorouracil, leucovorin, oxaliplatin, and docetaxel (FLOT) as a perioperative treatment for patients with resectable esophagogastric adenocarcinoma (EGA)., Methods: DANTE started as multicenter, randomized phase II trial, which was subsequently converted to a phase III trial. Here, we present the results of the phase II proportion, focusing on surgical pathology and safety outcomes on an exploratory basis. Patients with resectable EGA (≥cT2 or cN+) were assigned to either four preoperative and postoperative cycles of FLOT combined with ATZ, followed by eight cycles of ATZ maintenance (arm A) or FLOT alone (arm B)., Results: Two hundred ninety-five patients were randomly assigned (A, 146; B, 149) with balanced baseline characteristics between arms. Twenty-three patients (8%) had tumors with microsatellite instability (MSI), and 58% patients had tumors with a PD-L1 combined positive score (CPS) of ≥1. Surgical morbidity (A, 45%; B, 42%) and 60-day mortality (A, 3%; B, 2%) were comparable between arms. Downstaging favored arm A versus arm B (ypT0, 23% v 15% [one-sided P = .044]; ypT0-T2, 61% v 48% [one-sided P = .015]; ypN0, 68% v 54% [one-sided P = .012]). Histopathologic complete regression rates (pathologic complete response or TRG1a) were higher after FLOT plus ATZ (A, 24%; B, 15%; one-sided P = .032), and the difference was more pronounced in the PD-L1 CPS ≥10 (A, 33%; B, 12%) and MSI (A, 63%; B, 27%) subpopulations. Complete margin-free (R0) resection rates were relatively high in both arms (A, 96%; B, 95%). The incidence and severity of adverse events were similar in both groups., Conclusion: Within the limitations of the exploratory nature of the data, the addition of ATZ to perioperative FLOT is safe and improved postoperative stage and histopathologic regression.

Published
2024
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249. Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts.

Author

Arslan FN, Hannezo É, Merrin J, Loose M, and Heisenberg CP

Subjects
Animals, Cell Adhesion physiology, Cadherins genetics, Cadherins metabolism, Cytoskeletal Proteins, Myosins, Actins metabolism, Actomyosin metabolism
Abstract

Metazoan development relies on the formation and remodeling of cell-cell contacts. Dynamic reorganization of adhesion receptors and the actomyosin cell cortex in space and time plays a central role in cell-cell contact formation and maturation. Nevertheless, how this process is mechanistically achieved when new contacts are formed remains unclear. Here, by building a biomimetic assay composed of progenitor cells adhering to supported lipid bilayers functionalized with E-cadherin ectodomains, we show that cortical F-actin flows, driven by the depletion of myosin-2 at the cell contact center, mediate the dynamic reorganization of adhesion receptors and cell cortex at the contact. E-cadherin-dependent downregulation of the small GTPase RhoA at the forming contact leads to both a depletion of myosin-2 and a decrease of F-actin at the contact center. At the contact rim, in contrast, myosin-2 becomes enriched by the retraction of bleb-like protrusions, resulting in a cortical tension gradient from the contact rim to its center. This tension gradient, in turn, triggers centrifugal F-actin flows, leading to further accumulation of F-actin at the contact rim and the progressive redistribution of E-cadherin from the contact center to the rim. Eventually, this combination of actomyosin downregulation and flows at the contact determines the characteristic molecular organization, with E-cadherin and F-actin accumulating at the contact rim, where they are needed to mechanically link the contractile cortices of the adhering cells., Competing Interests: Declaration of interests C.-P.H. is a member of the Current Biology advisory board., (Copyright © 2023 The Author(s). Published by Elsevier Inc. All rights reserved.)

Published
2024
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250. In-house validation of an LC-MS method for the multiplexed quantitative determination of total allergenic food in chocolate.

Author

Pilolli R, Lamonaca A, Nitride C, De Angelis E, van Poucke C, Gillard N, Huet AC, De Loose M, Henrottin J, Mills ECN, and Monaci L

Subjects
Cattle, Animals, Female, Liquid Chromatography-Mass Spectrometry, Chromatography, Liquid methods, Chickens, Tandem Mass Spectrometry methods, Eggs analysis, Allergens analysis, Food Analysis methods, Chocolate analysis, Food Hypersensitivity, Cacao
Abstract

Mass spectrometry has been widely accepted as a confirmatory tool for the sensitive detection of undeclared presence of allergenic ingredients. Multiple methods have been developed so far, achieving different levels of sensitivity and robustness, still lacking harmonization of the analytical validation and impairing comparability of results. In this investigation, a quantitative method has been validated in-house for the determination of six allergenic ingredients (cow's milk, hen's egg, peanut, soybean, hazelnut, and almond) in a chocolate-based matrix. The latter has been produced in a food pilot plant to provide a real and well-characterized matrix for proper assessment of method performance characteristics according to official guidelines. In particular, recent considerations issued by the European Committee for Standardization have been followed to guide a rigorous single-laboratory validation and to feature the main method performance, such as selectivity, linearity, and sensitivity. Synthetic surrogates of the peptide markers have been used both in native and labelled forms in matrix-matched calibration curves as external calibrants and internal standards, respectively. A two-order of magnitude range was investigated, focusing on the low concentration range for proper assessment of the detection and quantification limits (LOD and LOQ) by rigorous calibration approach. Conversion factors for all six allergenic ingredients have been determined for the first time to report the final quantitative information as fraction of total allergenic food protein (TAFP) per mass of food (µg TAFP /g food ), since such a reporting unit is exploitable in allergenic risk assessment plans. The method achieved good sensitivity with LOD values ranging between 0.08 and 0.2 µg TAFP /g food , for all ingredients besides egg and soybean, whose quantitative markers reported a slightly higher limit (1.1 and 1.2 µg TAFP /g food , respectively). Different samples of chocolate bar incurred at four defined concentration levels close to the currently available threshold doses have been analyzed to test the quantitative performance of the analytical method, with a proper estimate of the measurement uncertainty from different sources of variability. The sensitivity achieved resulted in compliance with the various threshold doses issued or recommended worldwide., (© 2023. The Author(s).)

Published
2024
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