Author: "Ministry of Innovation and Technology (Hungary)" - Searchworks@Jio Institute Digital Library Search Results

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36 results on '"Ministry of Innovation and Technology (Hungary)"'

1. Global fine-resolution data on springtail abundance and community structure

Author: Russian Science Foundation, Leipzig University, German Research Foundation, Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brasil), Federal Ministry of Education and Research (Germany), Carl Tryggers Foundation, Royal Marsden NHS Foundation Trust, Centre National de la Recherche Scientifique (France), Australian Research Council, National Science Foundation (US), American Association of University Women, German Centre for Integrative Biodiversity Research, Ministry of Innovation and Technology (Hungary), National Natural Science Foundation of China, South African National Antarctic Programme, Ministerio de Ciencia e Innovación (España), Agencia Estatal de Investigación (España), European Commission, Estonian Science Foundation, Government of Canada, St. John's University, Ministére de l'Education Nationale de la Recherche et de la Technologie (France), Latvian Council of Science, Massey University, Austrian Academy of Sciences, Royal Society Te Apārangi, Slovak Research and Development Agency, Higher Education Commission (Pakistan), Natural Resources Canada, Ontario Ministry of Natural Resources and Forestry, Nanyang Technological University, Potapov, Anton [0000-0002-4456-1710], Striuchkova, Anastasia V. [0000-0002-6666-5844], Alatalo, Juha M. [0000-0001-5084-850X], Arbea, Javier I. [0000-0001-6122-1331], Babenko, Anatoly [0000-0002-6077-0619], Barnes, Andrew D. [0000-0002-6499-381X], Bellini, Bruno C. [0000-0001-7881-9436], Bernava, Verónica [0000-0002-7654-7913], Bokhorst, Stef [0000-0003-0184-1162], Castaño-Meneses, Gabriela [0000-0002-5405-5221], Chauvat, Matthieu [0000-0002-4831-5904], Chomel, Mathilde [0000-0001-5110-2355], Chown, Steven L. [0000-0001-6069-5105], Classen, Aimme T. [0000-0002-6741-3470], de Lima, Estevam C. A. [0000-0002-1680-4818], Doblas-Miranda, E. [0000-0003-3366-2759], Drescher. Jochen [0000-0002-5162-9779], Eisenhauer, Nico [0000-0002-0371-6720], Ferlian, Olga [0000-0002-2536-7592], Filser, Juliane [0000-0003-1535-6168], Franken, Oscar [0000-0001-8361-3117], Greve, Michelle [0000-0002-6229-8506], Holmstrup, Martin [0000-0001-8395-6582], Homet, Pablo [0000-0002-4285-6953], Høye, Toke T. [0000-0001-5387-3284], Janion-Scheepers, C. [0000-0001-5942-7912], Jochum, Malte [0000-0002-8728-1145], Jucevica, Edite [0000-0002-0710-9450], Kapinga, Esther M. [0000-0002-2454-6820], Kovac, L'ubomír [0000-0001-8194-2128], Krab, Eveline J. [0000-0001-8262-0198], Henning Krogh, Paul [0000-0003-2033-553X], Lindo, Zoë [0000-0001-9942-7204], Lu, Jing-Zhong [0000-0002-4051-8993], Luciánez Sánchez, Mª J. [0000-0001-5679-0951], Mawan, Amanda [0000-0003-1820-7432], Moreno Mateos, D. [0000-0002-1539-5848], Negri, Ilaria [0000-0001-5188-1408], Nielsen, Uffe N. [0000-0003-2400-7453], Ochoa-Hueso, Raúl [0000-0002-1839-6926], Oliveira Filho, Luís Carlos I. [0000-0002-9010-481X], Palacios-Vargas, José [0000-0001-9097-6813], Pollierer, Melani M. [0000-0002-1498-2362], Potapov, Mikhail B. [0000-0002-6111-3354], Rashid, Muhammad Imtiaz [0000-0002-5178-4445], Raymond-Léonard, Laura J. [0000-0002-7324-7843], Saifutdinov, Ruslan [0000-0002-8878-3630], Sayer, Emma J. [0000-0002-3322-4487], Seeber, Julia [0000-0003-0189-7377], Shveenkova, Yulia B. [0000-0003-1887-8551], Slade, Eleanor M. [0000-0002-6108-1196], Sterzynska, Maria [0000-0001-9712-4285], Sun, Xin [0000-0002-3988-7847], Taskaeva, Anastasia A. [0000-0002-4519-8458], Thakur, Madhav P. [0000-0001-9426-1313], Tsiafouli, Maria A. [0000-0003-0203-8347], Twala, Mthokozisi N. [0000-0001-6499-1892], Winck, Bruna [0000-0002-7996-9855], Winkler, Daniel E.[0000-0002-6008-0562], Yin, Rui [0000-0002-4580-1317], Zeppelini, Douglas [0000-0002-9026-1129], Scheu, Stefan [0000-0003-4350-9520], Potapov, Anton, Chen, Ting-Wen, Striuchkova, Anastasia V., Alatalo, Juha M., Alexandre, Douglas, Arbea, Javier I., Ashton, Thomas, Ashwood, Frank, Babenko, Anatoly, Bandyopadhyaya, Ipsa, Duarte Maluche Baretta, Carolina R., Joimel, Sophie, Jorge, Bruna Claudia S., Jucevica, Edite, Kapinga, Esther M., Kovac, L'ubomír, Krab, Eveline J., Henning Krogh, Paul, Kuu, Annely, Kuznetsova, Natalia A., Lam Weng, Ngai, Russell, David J., Lin, Dunmei, Lindo, Zoë, Liu, Amy, Lu, Jing-Zhong, Luciánez Sánchez, Mª J., Marx, Michael T., Mawan, Amanda, McCary, Matthew A., Minor, María A., Mitchell, Grace I., Saifutdinov, Ruslan, Moreno Mateos, D., Nakamori, Taizo, Negri, Ilaria, Nielsen, Uffe N., Ochoa-Hueso, Raúl, Oliveira Filho, Luís Carlos I., Palacios-Vargas, José, Pollierer, Melani M., Ponge, Jean-François, Potapov, Mikhail B., Salmon, Sandrine, Querner, Pascal, Rai, Bibishan, Raschmanová, Natália, Rashid, Muhammad Imtiaz, Raymond-Léonard, Laura J., Reis, Aline S., Ross, Giles M., Rousseau, Laurent, Santoja, Mathieu, Saraeva, Anna K., Sayer, Emma J., Scheunemann, Nicole, Scholz, Cornelia, Seeber, Julia, Shaw, Peter, Baretta, Dilmar, Shveenkova, Yulia B., Slade, Eleanor M., Stebaeva, Sophya K., Sterzynska, Maria, Sun, Xin, Susanti, Winda I., Taskaeva, Anastasia A., Tay, Li Si, Thakur, Madhav P., Treasure, Anne M., Barnes, Andrew D., Tsiafouli, Maria A., Twala, Mthokozisi N., Uvarov, Alexei V., Vernier, Lisa A., Widenfalk, Lina A., Widyastuti, Rahayu, Winck, Bruna, Winkler, Daniel E., Wu, Donghui, Xie, Zhijing, Bellini, Bruno C., Yin, Rui, Zampaulo, Robson A., Zeppelini, Douglas, Zhang, Bing, Zoughailech, Abdelmalek, Ashford, Oliver, Klauberg-Filho, Osmar, Scheu, Stefan, Bendjaballah, Mohamed, Berg, Matty P., Bernava, Verónica, Bokhorst, Stef, Bokova, Anna I., Bolger, Thomas, Bouchard, Mathieu, Brito, Roniere A., Buchori, Damayanti, Castaño-Meneses, Gabriela, Chauvat, Matthieu, Chomel, Mathilde, Chow, Yasuko, Chown, Steven L., Classen, Aimme T., Cortet, Jérôme, Čuchta, Peter, Pedrosa, Ana M. de la, de Lima, Estevam C. A., Deharveng, Louis, Doblas-Miranda, E., Drescher. Jochen, Eisenhauer, Nico, Ellers, J., Ferlian, Olga, Ferreira, Susana S. D., Ferreira, Alisa S., Fiera, Cristina, Filser, Juliane, Franken, Oscar, Fujii, S., Gagnon Koudji, Essivi, Gao, Meixiang, Gendreau-Berthiaume, Benoit, Gers. Charles, Greve, Michelle, Hamra-Kroua, Salah, Tanya Handa, Ira, Hasegawa, Motohiro, Heiniger, Charlène, Hishi, Takuo, Holmstrup, Martin, Homet, Pablo, Høye, Toke T., Ivask, Mari, Jacques, Bob, Janion-Scheepers, C., Jochum, Malte, Russian Science Foundation, Leipzig University, German Research Foundation, Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brasil), Federal Ministry of Education and Research (Germany), Carl Tryggers Foundation, Royal Marsden NHS Foundation Trust, Centre National de la Recherche Scientifique (France), Australian Research Council, National Science Foundation (US), American Association of University Women, German Centre for Integrative Biodiversity Research, Ministry of Innovation and Technology (Hungary), National Natural Science Foundation of China, South African National Antarctic Programme, Ministerio de Ciencia e Innovación (España), Agencia Estatal de Investigación (España), European Commission, Estonian Science Foundation, Government of Canada, St. John's University, Ministére de l'Education Nationale de la Recherche et de la Technologie (France), Latvian Council of Science, Massey University, Austrian Academy of Sciences, Royal Society Te Apārangi, Slovak Research and Development Agency, Higher Education Commission (Pakistan), Natural Resources Canada, Ontario Ministry of Natural Resources and Forestry, Nanyang Technological University, Potapov, Anton [0000-0002-4456-1710], Striuchkova, Anastasia V. [0000-0002-6666-5844], Alatalo, Juha M. [0000-0001-5084-850X], Arbea, Javier I. [0000-0001-6122-1331], Babenko, Anatoly [0000-0002-6077-0619], Barnes, Andrew D. [0000-0002-6499-381X], Bellini, Bruno C. [0000-0001-7881-9436], Bernava, Verónica [0000-0002-7654-7913], Bokhorst, Stef [0000-0003-0184-1162], Castaño-Meneses, Gabriela [0000-0002-5405-5221], Chauvat, Matthieu [0000-0002-4831-5904], Chomel, Mathilde [0000-0001-5110-2355], Chown, Steven L. [0000-0001-6069-5105], Classen, Aimme T. [0000-0002-6741-3470], de Lima, Estevam C. A. [0000-0002-1680-4818], Doblas-Miranda, E. [0000-0003-3366-2759], Drescher. Jochen [0000-0002-5162-9779], Eisenhauer, Nico [0000-0002-0371-6720], Ferlian, Olga [0000-0002-2536-7592], Filser, Juliane [0000-0003-1535-6168], Franken, Oscar [0000-0001-8361-3117], Greve, Michelle [0000-0002-6229-8506], Holmstrup, Martin [0000-0001-8395-6582], Homet, Pablo [0000-0002-4285-6953], Høye, Toke T. [0000-0001-5387-3284], Janion-Scheepers, C. [0000-0001-5942-7912], Jochum, Malte [0000-0002-8728-1145], Jucevica, Edite [0000-0002-0710-9450], Kapinga, Esther M. [0000-0002-2454-6820], Kovac, L'ubomír [0000-0001-8194-2128], Krab, Eveline J. [0000-0001-8262-0198], Henning Krogh, Paul [0000-0003-2033-553X], Lindo, Zoë [0000-0001-9942-7204], Lu, Jing-Zhong [0000-0002-4051-8993], Luciánez Sánchez, Mª J. [0000-0001-5679-0951], Mawan, Amanda [0000-0003-1820-7432], Moreno Mateos, D. [0000-0002-1539-5848], Negri, Ilaria [0000-0001-5188-1408], Nielsen, Uffe N. [0000-0003-2400-7453], Ochoa-Hueso, Raúl [0000-0002-1839-6926], Oliveira Filho, Luís Carlos I. [0000-0002-9010-481X], Palacios-Vargas, José [0000-0001-9097-6813], Pollierer, Melani M. [0000-0002-1498-2362], Potapov, Mikhail B. [0000-0002-6111-3354], Rashid, Muhammad Imtiaz [0000-0002-5178-4445], Raymond-Léonard, Laura J. [0000-0002-7324-7843], Saifutdinov, Ruslan [0000-0002-8878-3630], Sayer, Emma J. [0000-0002-3322-4487], Seeber, Julia [0000-0003-0189-7377], Shveenkova, Yulia B. [0000-0003-1887-8551], Slade, Eleanor M. [0000-0002-6108-1196], Sterzynska, Maria [0000-0001-9712-4285], Sun, Xin [0000-0002-3988-7847], Taskaeva, Anastasia A. [0000-0002-4519-8458], Thakur, Madhav P. [0000-0001-9426-1313], Tsiafouli, Maria A. [0000-0003-0203-8347], Twala, Mthokozisi N. [0000-0001-6499-1892], Winck, Bruna [0000-0002-7996-9855], Winkler, Daniel E.[0000-0002-6008-0562], Yin, Rui [0000-0002-4580-1317], Zeppelini, Douglas [0000-0002-9026-1129], Scheu, Stefan [0000-0003-4350-9520], Potapov, Anton, Chen, Ting-Wen, Striuchkova, Anastasia V., Alatalo, Juha M., Alexandre, Douglas, Arbea, Javier I., Ashton, Thomas, Ashwood, Frank, Babenko, Anatoly, Bandyopadhyaya, Ipsa, Duarte Maluche Baretta, Carolina R., Joimel, Sophie, Jorge, Bruna Claudia S., Jucevica, Edite, Kapinga, Esther M., Kovac, L'ubomír, Krab, Eveline J., Henning Krogh, Paul, Kuu, Annely, Kuznetsova, Natalia A., Lam Weng, Ngai, Russell, David J., Lin, Dunmei, Lindo, Zoë, Liu, Amy, Lu, Jing-Zhong, Luciánez Sánchez, Mª J., Marx, Michael T., Mawan, Amanda, McCary, Matthew A., Minor, María A., Mitchell, Grace I., Saifutdinov, Ruslan, Moreno Mateos, D., Nakamori, Taizo, Negri, Ilaria, Nielsen, Uffe N., Ochoa-Hueso, Raúl, Oliveira Filho, Luís Carlos I., Palacios-Vargas, José, Pollierer, Melani M., Ponge, Jean-François, Potapov, Mikhail B., Salmon, Sandrine, Querner, Pascal, Rai, Bibishan, Raschmanová, Natália, Rashid, Muhammad Imtiaz, Raymond-Léonard, Laura J., Reis, Aline S., Ross, Giles M., Rousseau, Laurent, Santoja, Mathieu, Saraeva, Anna K., Sayer, Emma J., Scheunemann, Nicole, Scholz, Cornelia, Seeber, Julia, Shaw, Peter, Baretta, Dilmar, Shveenkova, Yulia B., Slade, Eleanor M., Stebaeva, Sophya K., Sterzynska, Maria, Sun, Xin, Susanti, Winda I., Taskaeva, Anastasia A., Tay, Li Si, Thakur, Madhav P., Treasure, Anne M., Barnes, Andrew D., Tsiafouli, Maria A., Twala, Mthokozisi N., Uvarov, Alexei V., Vernier, Lisa A., Widenfalk, Lina A., Widyastuti, Rahayu, Winck, Bruna, Winkler, Daniel E., Wu, Donghui, Xie, Zhijing, Bellini, Bruno C., Yin, Rui, Zampaulo, Robson A., Zeppelini, Douglas, Zhang, Bing, Zoughailech, Abdelmalek, Ashford, Oliver, Klauberg-Filho, Osmar, Scheu, Stefan, Bendjaballah, Mohamed, Berg, Matty P., Bernava, Verónica, Bokhorst, Stef, Bokova, Anna I., Bolger, Thomas, Bouchard, Mathieu, Brito, Roniere A., Buchori, Damayanti, Castaño-Meneses, Gabriela, Chauvat, Matthieu, Chomel, Mathilde, Chow, Yasuko, Chown, Steven L., Classen, Aimme T., Cortet, Jérôme, Čuchta, Peter, Pedrosa, Ana M. de la, de Lima, Estevam C. A., Deharveng, Louis, Doblas-Miranda, E., Drescher. Jochen, Eisenhauer, Nico, Ellers, J., Ferlian, Olga, Ferreira, Susana S. D., Ferreira, Alisa S., Fiera, Cristina, Filser, Juliane, Franken, Oscar, Fujii, S., Gagnon Koudji, Essivi, Gao, Meixiang, Gendreau-Berthiaume, Benoit, Gers. Charles, Greve, Michelle, Hamra-Kroua, Salah, Tanya Handa, Ira, Hasegawa, Motohiro, Heiniger, Charlène, Hishi, Takuo, Holmstrup, Martin, Homet, Pablo, Høye, Toke T., Ivask, Mari, Jacques, Bob, Janion-Scheepers, C., and Jochum, Malte
Abstract: Springtails (Collembola) inhabit soils from the Arctic to the Antarctic and comprise an estimated ~32% of all terrestrial arthropods on Earth. Here, we present a global, spatially-explicit database on springtail communities that includes 249,912 occurrences from 44,999 samples and 2,990 sites. These data are mainly raw sample-level records at the species level collected predominantly from private archives of the authors that were quality-controlled and taxonomically-standardised. Despite covering all continents, most of the sample-level data come from the European continent (82.5% of all samples) and represent four habitats: woodlands (57.4%), grasslands (14.0%), agrosystems (13.7%) and scrublands (9.0%). We included sampling by soil layers, and across seasons and years, representing temporal and spatial within-site variation in springtail communities. We also provided data use and sharing guidelines and R code to facilitate the use of the database by other researchers. This data paper describes a static version of the database at the publication date, but the database will be further expanded to include underrepresented regions and linked with trait data.
Published: 2024

2. A kinetic finite volume discretization of the multidimensional PIDE model for gene regulatory networks

Author: Xunta de Galicia, European Commission, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Ministerio de Ciencia e Innovación (España), National Research, Development and Innovation Office (Hungary), Ministry of Innovation and Technology (Hungary), Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72], Vághy, Mihály A., Otero-Muras, Irene, Pájaro, Manuel, Szederkényi, Gábor, Xunta de Galicia, European Commission, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Ministerio de Ciencia e Innovación (España), National Research, Development and Innovation Office (Hungary), Ministry of Innovation and Technology (Hungary), Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72], Vághy, Mihály A., Otero-Muras, Irene, Pájaro, Manuel, and Szederkényi, Gábor
Abstract: In this paper, a finite volume discretization scheme for partial integro-differential equations (PIDEs) describing the temporal evolution of protein distribution in gene regulatory networks is proposed. It is shown that the obtained set of ODEs can be formally represented as a compartmental kinetic system with a strongly connected reaction graph. This allows the application of the theory of nonnegative and compartmental systems for the qualitative analysis of the approximating dynamics. In this framework, it is straightforward to show the existence, uniqueness and stability of equilibria. Moreover, the computation of the stationary probability distribution can be traced back to the solution of linear equations. The discretization scheme is presented for one and multiple dimensional models separately. Illustrative computational examples show the precision of the approach, and good agreement with previous results in the literature.
Published: 2024

3. Globally invariant metabolism but density-diversity mismatch in springtails

Author: Russian Science Foundation, University of Göttingen, Securing Antarctica's Environmental Future (Australia), National Natural Science Foundation of China, South African National Antarctic Programme, Natural Resources Canada, Natural Sciences and Engineering Research Council of Canada, Independent Research Fund Denmark, Estonian Science Foundation, European Research Council, European Commission, German Research Foundation, Agence Nationale de la Recherche (France), Ministère de l'Agriculture et de la Souveraineté alimentaire (France), Ministére de l'Education Nationale de la Recherche et de la Technologie (France), Ministère de la Transition écologique et de la Cohésion des territoires (France), Agence de l'Environnement et de la Maîtrise de l'Energie (France), Fundamental Research Funds for the Central Universities (China), Massey University, Austrian Academy of Sciences, Higher Education Commission (Pakistan), Government of Austria, Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brasil), Fundação de Apoio à Pesquisa Científica e Tecnológica do Estado de Santa Catarina, Latvian Council of Science, Ministerio de Ciencia e Innovación (España), Ministry of Innovation and Technology (Hungary), Potapov, Anton [0000-0002-4456-1710], Guerra, Carlos A. [0000-0003-4917-2105], Babenko, Anatoly [0000-0002-6077-0619], Bellini, Bruno C. [0000-0001-7881-9436], Chown, Steven L. [0000-0001-6069-5105], Kovac, L'ubomír [0000-0001-8194-2128], Alatalo, Juha M. [0000-0001-5084-850X], Arbea, Javier I. [0000-0001-6122-1331], Bokhorst, Stef [0000-0003-0184-1162], Castaño-Meneses, Gabriela [0000-0002-5405-5221], Chauvat, Matthieu [0000-0002-4831-5904], Chomel, Mathilde [0000-0001-5110-2355], Classen, Aimme T. [0000-0002-6741-3470], Filser, Juliane [0000-0003-1535-6168], Franken, Oscar [0000-0001-8361-3117], Greve, Michelle [0000-0002-6229-8506], Holmstrup, Martin [0000-0001-8395-6582], Homet, Pablo [0000-0002-4285-6953], Janion-Scheepers, C. [0000-0001-5942-7912], Jochum, Malte [0000-0002-8728-1145], Jucevica, Edite [0000-0002-0710-9450], Ferlian, Olga [0000-0002-2536-7592], Oliveira Filho, Luís Carlos I. [0000-0002-9010-481X], Krab, Eveline J. [0000-0001-8262-0198], de Lima, Estevam C. A. [0000-0002-1680-4818], Lindo, Zoë [0000-0001-9942-7204], Lu, Jing-Zhong [0000-0002-4051-8993], Negri, Ilaria [0000-0001-5188-1408], Ochoa-Hueso, Raúl [0000-0002-1839-6926], Palacios-Vargas, José [0000-0001-9097-6813], Pollierer, Melani M. [0000-0002-1498-2362], Rashid, Muhammad Imtiaz [0000-0002-5178-4445], Raymond-Léonard, Laura J. [0000-0002-7324-7843], Saifutdinov, Ruslan [0000-0002-8878-3630], Sayer, Emma J. [0000-0002-3322-4487], Seeber, Julia [0000-0003-0189-7377], Shveenkova, Yulia B. [0000-0003-1887-8551], Sterzynska, Maria [0000-0001-9712-4285], Sun, Xin [0000-0002-3988-7847], Taskaeva, Anastasia A. [0000-0002-4519-8458], Thakur, Madhav P. [0000-0001-9426-1313], Tsiafouli, Maria A. [0000-0003-0203-8347], Twala, Mthokozisi N. [0000-0001-6499-1892], Winck, Bruna [0000-0002-7996-9855], Winkler, Daniel E.[0000-0002-6008-0562], Yin, Rui [0000-0002-4580-1317], Zeppelini, Douglas [0000-0002-9026-1129], Crowther, Thomas W. [0000-0001-5674-8913], Eisenhauer, Nico [0000-0002-0371-6720], Scheu, Stefan [0000-0003-4350-9520], Luciánez Sánchez, Mª J. [0000-0001-5679-0951], Potapov, Mikhail B. [0000-0002-6111-3354], Potapov, Anton, Guerra, Carlos A., van den Hoogen, Johan, Babenko, Anatoly, Bellini, Bruno C., Berg, Matty P., Chown, Steven L., Deharveng, Louis, Kovac, L'ubomír, Kuznetsova, Natalia A., Ponge, Jean-François, Yin, Rui, Zeppelini, Douglas, Crowther, Thomas W., Eisenhauer, Nico, Scheu, Stefan, Potapov, Mikhail B., Russell, David J., Alexandre, Douglas, Alatalo, Juha M., Arbea, Javier I., Bandyopadhyaya, Ipsa, Bernava, Verónica, Bokhorst, Stef, Bolger, Thomas, Castaño-Meneses, Gabriela, Chauvat, Matthieu, Chen, Ting-Wen, Chomel, Mathilde, Classen, Aimme T., Cortet, Jérôme, Čuchta, Peter, Pedrosa, Ana M. de la, Ferreira, Susana S. D., Fiera, Cristina, Filser, Juliane, Franken, Oscar, Fujii, S., Gagnon Koudji, Essivi, Gao, Meixiang, Gendreau-Berthiaume, Benoit, Gómez-Pamies, Diego F., Greve, Michelle, Handa, I. Tanya, Heiniger, Charlène, Holmstrup, Martin, Homet, Pablo, Ivask, Mari, Janion-Scheepers, C., Jochum, Malte, Joimel, Sophie, Jorge, Bruna Claudia S., Jucevica, Edite, Ferlian, Olga, Oliveira Filho, Luís Carlos I., Klauberg-Filho, Osmar, Baretta, Dilmar, Krab, Eveline J., Kuu, Annely, de Lima, Estevam C. A., Lin, Dunmei, Lindo, Zoë, Liu, Amy, Lu, Jing-Zhong, Luciánez Sánchez, Mª J., Marx, Michael T., McCary, Matthew A., Minor, María A., Nakamori, Taizo, Negri, Ilaria, Ochoa-Hueso, Raúl, Palacios-Vargas, José, Pollierer, Melani M., Querner, Pascal, Raschmanová, Natália, Rashid, Muhammad Imtiaz, Raymond-Léonard, Laura J., Rousseau, Laurent, Saifutdinov, Ruslan, Salmon, Sandrine, Sayer, Emma J., Scheunemann, Nicole, Scholz, Cornelia, Seeber, Julia, Shveenkova, Yulia B., Stebaeva, Sophya K., Sterzynska, Maria, Sun, Xin, Susanti, Winda I., Taskaeva, Anastasia A., Thakur, Madhav P., Tsiafouli, Maria A., Turnbull, Matthew S., Twala, Mthokozisi N., Uvarov, Alexei V., Vernier, Lisa A., Widenfalk, Lina A., Winck, Bruna, Winkler, Daniel E., Wu, Donghui, Xie, Zhijing, Russian Science Foundation, University of Göttingen, Securing Antarctica's Environmental Future (Australia), National Natural Science Foundation of China, South African National Antarctic Programme, Natural Resources Canada, Natural Sciences and Engineering Research Council of Canada, Independent Research Fund Denmark, Estonian Science Foundation, European Research Council, European Commission, German Research Foundation, Agence Nationale de la Recherche (France), Ministère de l'Agriculture et de la Souveraineté alimentaire (France), Ministére de l'Education Nationale de la Recherche et de la Technologie (France), Ministère de la Transition écologique et de la Cohésion des territoires (France), Agence de l'Environnement et de la Maîtrise de l'Energie (France), Fundamental Research Funds for the Central Universities (China), Massey University, Austrian Academy of Sciences, Higher Education Commission (Pakistan), Government of Austria, Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brasil), Fundação de Apoio à Pesquisa Científica e Tecnológica do Estado de Santa Catarina, Latvian Council of Science, Ministerio de Ciencia e Innovación (España), Ministry of Innovation and Technology (Hungary), Potapov, Anton [0000-0002-4456-1710], Guerra, Carlos A. [0000-0003-4917-2105], Babenko, Anatoly [0000-0002-6077-0619], Bellini, Bruno C. [0000-0001-7881-9436], Chown, Steven L. [0000-0001-6069-5105], Kovac, L'ubomír [0000-0001-8194-2128], Alatalo, Juha M. [0000-0001-5084-850X], Arbea, Javier I. [0000-0001-6122-1331], Bokhorst, Stef [0000-0003-0184-1162], Castaño-Meneses, Gabriela [0000-0002-5405-5221], Chauvat, Matthieu [0000-0002-4831-5904], Chomel, Mathilde [0000-0001-5110-2355], Classen, Aimme T. [0000-0002-6741-3470], Filser, Juliane [0000-0003-1535-6168], Franken, Oscar [0000-0001-8361-3117], Greve, Michelle [0000-0002-6229-8506], Holmstrup, Martin [0000-0001-8395-6582], Homet, Pablo [0000-0002-4285-6953], Janion-Scheepers, C. [0000-0001-5942-7912], Jochum, Malte [0000-0002-8728-1145], Jucevica, Edite [0000-0002-0710-9450], Ferlian, Olga [0000-0002-2536-7592], Oliveira Filho, Luís Carlos I. [0000-0002-9010-481X], Krab, Eveline J. [0000-0001-8262-0198], de Lima, Estevam C. A. [0000-0002-1680-4818], Lindo, Zoë [0000-0001-9942-7204], Lu, Jing-Zhong [0000-0002-4051-8993], Negri, Ilaria [0000-0001-5188-1408], Ochoa-Hueso, Raúl [0000-0002-1839-6926], Palacios-Vargas, José [0000-0001-9097-6813], Pollierer, Melani M. [0000-0002-1498-2362], Rashid, Muhammad Imtiaz [0000-0002-5178-4445], Raymond-Léonard, Laura J. [0000-0002-7324-7843], Saifutdinov, Ruslan [0000-0002-8878-3630], Sayer, Emma J. [0000-0002-3322-4487], Seeber, Julia [0000-0003-0189-7377], Shveenkova, Yulia B. [0000-0003-1887-8551], Sterzynska, Maria [0000-0001-9712-4285], Sun, Xin [0000-0002-3988-7847], Taskaeva, Anastasia A. [0000-0002-4519-8458], Thakur, Madhav P. [0000-0001-9426-1313], Tsiafouli, Maria A. [0000-0003-0203-8347], Twala, Mthokozisi N. [0000-0001-6499-1892], Winck, Bruna [0000-0002-7996-9855], Winkler, Daniel E.[0000-0002-6008-0562], Yin, Rui [0000-0002-4580-1317], Zeppelini, Douglas [0000-0002-9026-1129], Crowther, Thomas W. [0000-0001-5674-8913], Eisenhauer, Nico [0000-0002-0371-6720], Scheu, Stefan [0000-0003-4350-9520], Luciánez Sánchez, Mª J. [0000-0001-5679-0951], Potapov, Mikhail B. [0000-0002-6111-3354], Potapov, Anton, Guerra, Carlos A., van den Hoogen, Johan, Babenko, Anatoly, Bellini, Bruno C., Berg, Matty P., Chown, Steven L., Deharveng, Louis, Kovac, L'ubomír, Kuznetsova, Natalia A., Ponge, Jean-François, Yin, Rui, Zeppelini, Douglas, Crowther, Thomas W., Eisenhauer, Nico, Scheu, Stefan, Potapov, Mikhail B., Russell, David J., Alexandre, Douglas, Alatalo, Juha M., Arbea, Javier I., Bandyopadhyaya, Ipsa, Bernava, Verónica, Bokhorst, Stef, Bolger, Thomas, Castaño-Meneses, Gabriela, Chauvat, Matthieu, Chen, Ting-Wen, Chomel, Mathilde, Classen, Aimme T., Cortet, Jérôme, Čuchta, Peter, Pedrosa, Ana M. de la, Ferreira, Susana S. D., Fiera, Cristina, Filser, Juliane, Franken, Oscar, Fujii, S., Gagnon Koudji, Essivi, Gao, Meixiang, Gendreau-Berthiaume, Benoit, Gómez-Pamies, Diego F., Greve, Michelle, Handa, I. Tanya, Heiniger, Charlène, Holmstrup, Martin, Homet, Pablo, Ivask, Mari, Janion-Scheepers, C., Jochum, Malte, Joimel, Sophie, Jorge, Bruna Claudia S., Jucevica, Edite, Ferlian, Olga, Oliveira Filho, Luís Carlos I., Klauberg-Filho, Osmar, Baretta, Dilmar, Krab, Eveline J., Kuu, Annely, de Lima, Estevam C. A., Lin, Dunmei, Lindo, Zoë, Liu, Amy, Lu, Jing-Zhong, Luciánez Sánchez, Mª J., Marx, Michael T., McCary, Matthew A., Minor, María A., Nakamori, Taizo, Negri, Ilaria, Ochoa-Hueso, Raúl, Palacios-Vargas, José, Pollierer, Melani M., Querner, Pascal, Raschmanová, Natália, Rashid, Muhammad Imtiaz, Raymond-Léonard, Laura J., Rousseau, Laurent, Saifutdinov, Ruslan, Salmon, Sandrine, Sayer, Emma J., Scheunemann, Nicole, Scholz, Cornelia, Seeber, Julia, Shveenkova, Yulia B., Stebaeva, Sophya K., Sterzynska, Maria, Sun, Xin, Susanti, Winda I., Taskaeva, Anastasia A., Thakur, Madhav P., Tsiafouli, Maria A., Turnbull, Matthew S., Twala, Mthokozisi N., Uvarov, Alexei V., Vernier, Lisa A., Widenfalk, Lina A., Winck, Bruna, Winkler, Daniel E., Wu, Donghui, and Xie, Zhijing
Abstract: Soil life supports the functioning and biodiversity of terrestrial ecosystems. Springtails (Collembola) are among the most abundant soil arthropods regulating soil fertility and flow of energy through above- and belowground food webs. However, the global distribution of springtail diversity and density, and how these relate to energy fluxes remains unknown. Here, using a global dataset representing 2470 sites, we estimate the total soil springtail biomass at 27.5 megatons carbon, which is threefold higher than wild terrestrial vertebrates, and record peak densities up to 2 million individuals per square meter in the tundra. Despite a 20-fold biomass difference between the tundra and the tropics, springtail energy use (community metabolism) remains similar across the latitudinal gradient, owing to the changes in temperature with latitude. Neither springtail density nor community metabolism is predicted by local species richness, which is high in the tropics, but comparably high in some temperate forests and even tundra. Changes in springtail activity may emerge from latitudinal gradients in temperature, predation and resource limitation in soil communities. Contrasting relationships of biomass, diversity and activity of springtail communities with temperature suggest that climate warming will alter fundamental soil biodiversity metrics in different directions, potentially restructuring terrestrial food webs and affecting soil functioning.
Published: 2023

4. Electrically driven singlet-triplet transition in triangulene spin-1 chains

Author: Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), European Commission, Principado de Asturias, Ministry of Innovation and Technology (Hungary), National Research, Development and Innovation Office (Hungary), Hungarian Academy of Sciences, Martínez-Carracedo, Gabriel, Oroszlány, László, García-Fuente, Amador, Szunyogh, László, Ferrer, Jaime, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), European Commission, Principado de Asturias, Ministry of Innovation and Technology (Hungary), National Research, Development and Innovation Office (Hungary), Hungarian Academy of Sciences, Martínez-Carracedo, Gabriel, Oroszlány, László, García-Fuente, Amador, Szunyogh, László, and Ferrer, Jaime
Abstract: Recently, graphene triangulene chains have been synthesized, and their magnetic response has been analyzed by scanning tunneling microscopy methods by Mishra et al. [Nature (London) 598, 287 (2021)]. Motivated by this study, we determine the exchange bilinear and biquadratic constants of the triangulene chains by calculating two-spin rotations in the spirit of the magnetic force theorem. We then analyze open-ended, odd-numbered chains, whose edge states pair up forming a triplet ground state. We propose three experimental approaches that enable us to trigger and control a singlet-triplet spin transition. Two of these methods are based on applying a mechanical distortion to the chain. We finally show that the transition can be controlled efficiently by the application of an electric field.
Published: 2023

5. Responsiveness of the Scale for the Assessment and Rating of Ataxia and Natural History in 884 Recessive and Early Onset Ataxia Patients

Author: Federal Ministry of Education and Research (Germany), German Research Foundation, University of Tübingen, Research Foundation - Flanders, European Commission, Ministero della Salute, Ministry of Innovation and Technology (Hungary), University of Szeged, Traschütz, Andreas, Adarmes Gómez, A. D., Anheim, Mathieu, Baets, Jonathan, Brais, Bernard, Gagnon, Cynthia, Gburek-Augustat, Janina, Doss, Sarah, Hanagasi, Hasmet, Kamm, Christoph, Klivenyi, Peter, Klockgether, Thomas, Klopstock, Thomas, Minnerop, Martina, Münchau, Alexander, Renaud, Mathilde, Santorelli, Filippo M., Schöls, Ludger, Thieme, Andreas, Vielhaber, Stefan, Warrenburg, Bart van de, Zanni, Ginevra, Hilgers, Ralf-Dieter, PREPARE Consortium, Synofzik, Matthis, Federal Ministry of Education and Research (Germany), German Research Foundation, University of Tübingen, Research Foundation - Flanders, European Commission, Ministero della Salute, Ministry of Innovation and Technology (Hungary), University of Szeged, Traschütz, Andreas, Adarmes Gómez, A. D., Anheim, Mathieu, Baets, Jonathan, Brais, Bernard, Gagnon, Cynthia, Gburek-Augustat, Janina, Doss, Sarah, Hanagasi, Hasmet, Kamm, Christoph, Klivenyi, Peter, Klockgether, Thomas, Klopstock, Thomas, Minnerop, Martina, Münchau, Alexander, Renaud, Mathilde, Santorelli, Filippo M., Schöls, Ludger, Thieme, Andreas, Vielhaber, Stefan, Warrenburg, Bart van de, Zanni, Ginevra, Hilgers, Ralf-Dieter, PREPARE Consortium, and Synofzik, Matthis
Abstract: [Objective] The Scale for the Assessment and Rating of Ataxia (SARA) is the most widely applied clinical outcome assessment (COA) for genetic ataxias, but presents metrological and regulatory challenges. To facilitate trial planning, we characterize its responsiveness (including subitem-level relations to ataxia severity and patient-focused outcomes) across a large number of ataxias, and provide first natural history data for several of them., [Methods] Subitem-level correlation and distribution-based analysis of 1,637 SARA assessments in 884 patients with autosomal recessive/early onset ataxia (370 with 2–8 longitudinal assessments) were complemented by linear mixed effects modeling to estimate progression and sample sizes., [Results] Although SARA subitem responsiveness varied between ataxia severities, gait/stance showed a robust granular linear scaling across the broadest range (SARA < 25). Responsiveness was diminished by incomplete subscale use at intermediate or upper levels, nontransitions (“static periods”), and fluctuating decreases/increases. All subitems except nose-finger showed moderate-to-strong correlations to activities of daily living, indicating that metric properties—not content validity—limit SARA responsiveness. SARA captured mild-to-moderate progression in many genotypes (eg, SYNE1-ataxia: 0.55 points/yr, ataxia with oculomotor apraxia type 2: 1.14 points/yr, POLG-ataxia: 1.56 points/yr), but no change in others (autosomal recessive spastic ataxia of Charlevoix-Saguenay, COQ8A-ataxia). Whereas sensitivity to change was optimal in mild ataxia (SARA < 10), it substantially deteriorated in advanced ataxia (SARA > 25; 2.7-fold sample size). Use of a novel rank-optimized SARA without subitems finger-chase and nose-finger reduces sample sizes by 20 to 25%., [Interpretation] This study comprehensively characterizes COA properties and annualized changes of the SARA across and within a large number of ataxias. It suggests specific approaches for optimizing its responsiveness that might facilitate regulatory qualification and trial design. ANN NEUROL 2023;94:470–485
Published: 2023

6. Autosomal Recessive Cerebellar Ataxias in Europe: Frequency, Onset, and Severity in 677 Patients

Author: European Commission, Federal Ministry of Education and Research (Germany), ZonMw, Dutch Research Council, Brain Foundation (The Netherlands), Jacques and Gloria Gossweiler Foundation, Radboud University, University of Tübingen, University of Szeged, Ministry of Innovation and Technology (Hungary), Research Foundation - Flanders, Ministero della Salute, Projekt DEAL, Traschütz, Andreas, Adarmes Gómez, A. D., Anheim, Mathieu, Baets, Jonathan, Falkenburger, Björn H., Gburek-Augustat, Janina, Doss, Sarah, Kamm, Christoph, Klivenyi, Peter, Grobe-Einsler, Marcus, Klopstock, Thomas, Minnerop, Martina, Münchau, Alexander, Pane, Chiara, Renaud, Mathilde, Santorelli, Filippo M., Schöls, Ludger, Timmann, Dagmar, Vielhaber, Stefan, Haack, Tobias B., Warrenburg, Bart van de, Zanni, Ginevra, Synofzik, Matthis, European Commission, Federal Ministry of Education and Research (Germany), ZonMw, Dutch Research Council, Brain Foundation (The Netherlands), Jacques and Gloria Gossweiler Foundation, Radboud University, University of Tübingen, University of Szeged, Ministry of Innovation and Technology (Hungary), Research Foundation - Flanders, Ministero della Salute, Projekt DEAL, Traschütz, Andreas, Adarmes Gómez, A. D., Anheim, Mathieu, Baets, Jonathan, Falkenburger, Björn H., Gburek-Augustat, Janina, Doss, Sarah, Kamm, Christoph, Klivenyi, Peter, Grobe-Einsler, Marcus, Klopstock, Thomas, Minnerop, Martina, Münchau, Alexander, Pane, Chiara, Renaud, Mathilde, Santorelli, Filippo M., Schöls, Ludger, Timmann, Dagmar, Vielhaber, Stefan, Haack, Tobias B., Warrenburg, Bart van de, Zanni, Ginevra, and Synofzik, Matthis
Published: 2023

7. Different prognostic impact of recurrent gene mutations in chronic lymphocytic leukemia depending on IGHV gene somatic hypermutation status: a study by ERIC in HARMONY

Author: Associazione Italiana per la Ricerca sul Cancro, Ministero della Salute, Fundación la Caixa, American Association for Cancer Research, European Hematology Association, Lady Tata Memorial Trust, European Association for Cancer Research, Instituto de Salud Carlos III, Ministry of Innovation and Technology (Hungary), Università degli Studi di Ferrara, Associazione Italiana Contro le Leucemie - Linfomi e Mieloma, Danish Cancer Society Research Center, Cancer Research UK, Swedish Cancer Society, Swedish Research Council, Knut and Alice Wallenberg Foundation, Lions Cancerforskningsfond, Mansouri, Larry, Thorvaldsdottir, Birna, Sutton, Lesley-Ann, Karakatsoulis, Georgios, Meggendorfer, Manja, Parker, Helen, Nadeu, Ferran, Brieghel, Christian, Laidou, Stamatia, Moia, Riccardo, Rossi, Davide, Catherwood, Mark, Kotaskova, Jana, Delgado, Julio, Rodríguez-Vicente, Ana Eugenia, Benito, Rocío, Rigolin, Gian Matteo, Bonfiglio, Silvia, Scarfo, Lydia, Mattsson, Mattias, Davis, Zadie, Gogia, Ajay, Rani, Lata, Baliakas, Panagiotis, Foroughi-Asl, Hassan, Jylhä, Cecilia, Skaftason, Aron, Rapado, Inmaculada, Mirás, Fátima, Martínez-López, Joaquín, Serna, Javier de la, De Las Rivas, Javier, Thornton, Patrick, Larráyoz, María José, Calasanz, Mª Jose, Fésüs, Viktória, Mátrai, Zoltán, Bödör, Csaba, Smedby, Karin E, Espinet, Blanca, Puiggros, Anna, Gupta, Ritu, Bullinger, Lars, Bosch, Francesc, Tazón‐Vega, Bárbara, Baran-Marszak, Fanny, Oscier, David, Nguyen-Khac, Florence, Zenz, Thorsten, Terol, María José, Cuneo, Antonio, Hernández-Sánchez, María, Pospisilova, Sarka, Mills, Ken, Gaidano, Gianluca, Niemann, Carsten U, Campo, Elías, Strefford, Jonathan C, Ghia, Paolo, Stamatopoulos, Kostas, Rosenquist, Richard, Associazione Italiana per la Ricerca sul Cancro, Ministero della Salute, Fundación la Caixa, American Association for Cancer Research, European Hematology Association, Lady Tata Memorial Trust, European Association for Cancer Research, Instituto de Salud Carlos III, Ministry of Innovation and Technology (Hungary), Università degli Studi di Ferrara, Associazione Italiana Contro le Leucemie - Linfomi e Mieloma, Danish Cancer Society Research Center, Cancer Research UK, Swedish Cancer Society, Swedish Research Council, Knut and Alice Wallenberg Foundation, Lions Cancerforskningsfond, Mansouri, Larry, Thorvaldsdottir, Birna, Sutton, Lesley-Ann, Karakatsoulis, Georgios, Meggendorfer, Manja, Parker, Helen, Nadeu, Ferran, Brieghel, Christian, Laidou, Stamatia, Moia, Riccardo, Rossi, Davide, Catherwood, Mark, Kotaskova, Jana, Delgado, Julio, Rodríguez-Vicente, Ana Eugenia, Benito, Rocío, Rigolin, Gian Matteo, Bonfiglio, Silvia, Scarfo, Lydia, Mattsson, Mattias, Davis, Zadie, Gogia, Ajay, Rani, Lata, Baliakas, Panagiotis, Foroughi-Asl, Hassan, Jylhä, Cecilia, Skaftason, Aron, Rapado, Inmaculada, Mirás, Fátima, Martínez-López, Joaquín, Serna, Javier de la, De Las Rivas, Javier, Thornton, Patrick, Larráyoz, María José, Calasanz, Mª Jose, Fésüs, Viktória, Mátrai, Zoltán, Bödör, Csaba, Smedby, Karin E, Espinet, Blanca, Puiggros, Anna, Gupta, Ritu, Bullinger, Lars, Bosch, Francesc, Tazón‐Vega, Bárbara, Baran-Marszak, Fanny, Oscier, David, Nguyen-Khac, Florence, Zenz, Thorsten, Terol, María José, Cuneo, Antonio, Hernández-Sánchez, María, Pospisilova, Sarka, Mills, Ken, Gaidano, Gianluca, Niemann, Carsten U, Campo, Elías, Strefford, Jonathan C, Ghia, Paolo, Stamatopoulos, Kostas, and Rosenquist, Richard
Abstract: Recent evidence suggests that the prognostic impact of gene mutations in patients with chronic lymphocytic leukemia (CLL) may differ depending on the immunoglobulin heavy variable (IGHV) gene somatic hypermutation (SHM) status. In this study, we assessed the impact of nine recurrently mutated genes (BIRC3, EGR2, MYD88, NFKBIE, NOTCH1, POT1, SF3B1, TP53, and XPO1) in pre-treatment samples from 4580 patients with CLL, using time-to-first-treatment (TTFT) as the primary end-point in relation to IGHV gene SHM status. Mutations were detected in 1588 (34.7%) patients at frequencies ranging from 2.3–9.8% with mutations in NOTCH1 being the most frequent. In both univariate and multivariate analyses, mutations in all genes except MYD88 were associated with a significantly shorter TTFT. In multivariate analysis of Binet stage A patients, performed separately for IGHV-mutated (M-CLL) and unmutated CLL (U-CLL), a different spectrum of gene alterations independently predicted short TTFT within the two subgroups. While SF3B1 and XPO1 mutations were independent prognostic variables in both U-CLL and M-CLL, TP53, BIRC3 and EGR2 aberrations were significant predictors only in U-CLL, and NOTCH1 and NFKBIE only in M-CLL. Our findings underscore the need for a compartmentalized approach to identify high-risk patients, particularly among M-CLL patients, with potential implications for stratified management.
Published: 2023

8. Topological superconductivity from first principles. II. Effects from manipulation of spin spirals: Topological fragmentation, braiding, and quasi-Majorana bound states

Author: National Research, Development and Innovation Office (Hungary), Ministry of Education and Culture (Hungary), Ministry of Innovation and Technology (Hungary), Lászlóffy, András, Nyári, Bendegúz, Csire, Gábor, Szunyogh, László, Újfalussy, Balázs, National Research, Development and Innovation Office (Hungary), Ministry of Education and Culture (Hungary), Ministry of Innovation and Technology (Hungary), Lászlóffy, András, Nyári, Bendegúz, Csire, Gábor, Szunyogh, László, and Újfalussy, Balázs
Abstract: Recent advances in electron spin resonance techniques have allowed the manipulation of the spin of individual atoms, making magnetic atomic chains on superconducting hosts one of the most promising platform where topological superconductivity can be engineered. Motivated by this progress, we provide a detailed, quantitative description of the effects of manipulating spins in realistic nanowires by applying a first-principles-based computational approach to a recent experiment: an iron chain deposited on top of an Au/Nb heterostructure. As a continuation of the preceding paper, experimentally relevant computational experiments are performed in spin spiral chains that shed light on several concerns about practical applications and add new aspects to the interpretation of recent experiments. We explore the stability of topological zero-energy states, the formation and distinction of topologically trivial and nontrivial zero energy edge states, the effect of local changes in the exchange fields, the emergence of topological fragmentation, and the shift of Majorana zero modes along the superconducting nanowires, opening avenues toward the implementation of a braiding operation.
Published: 2023

9. Topological superconductivity from first principles. I. Shiba band structure and topological edge states of artificial spin chains

Author: National Research, Development and Innovation Office (Hungary), Ministry of Education and Culture (Hungary), Ministry of Innovation and Technology (Hungary), Nyári, Bendegúz, Lászlóffy, András, Csire, Gábor, Szunyogh, László, Újfalussy, Balázs, National Research, Development and Innovation Office (Hungary), Ministry of Education and Culture (Hungary), Ministry of Innovation and Technology (Hungary), Nyári, Bendegúz, Lászlóffy, András, Csire, Gábor, Szunyogh, László, and Újfalussy, Balázs
Abstract: Magnetic chains on superconductors hosting Majorana zero modes (MZMs) have attracted a great deal of interest due to their possible applications in fault-tolerant quantum computing. However, this is hindered by the lack of a detailed, quantitative understanding of these systems. As a significant step forward, we present a first-principles computational approach based on a microscopic relativistic theory of inhomogeneous superconductors applied to an iron chain on the top of Au-covered Nb(110) to study the Shiba band structure and the topological nature of the edge states. Contrary to contemporary considerations, our method enables the introduction of quantities indicating band inversion without fitting parameters in realistic experimental settings, holding thus the power to determine the topological nature of zero-energy edge states in an accurate ab initio based description of the experimental systems. We confirm that ferromagnetic Fe chains on an Au/Nb(110) surface do not support any separated MZM; however, a broad range of spin-spirals can be identified with robust zero-energy edge states displaying signatures of MZMs. For these spirals, we explore the structure of the superconducting order parameter, shedding light on the internally antisymmetric triplet pairing hosted by MZMs. We also reveal a twofold effect of spin-orbit coupling: although it tends to enlarge the topological phase regarding spin spiraling angles, it also extends the localization of MZMs. Due to the presented predictive power, our work fills a big gap between experimental efforts and theoretical models while paving the way for engineering platforms for topological quantum computation.
Published: 2023

10. Dispersal of aquatic invertebrates by lesser black-backed gulls and white storks within and between inland habitats

Author: Conferencia de Rectores de las Universidades Españolas, Consejo Superior de Investigaciones Científicas (España), Fundación la Caixa, Ministerio de Economía, Industria y Competitividad (España), Agencia Estatal de Investigación (España), European Commission, Hungarian Academy of Sciences, Ministry of Innovation and Technology (Hungary), Martín-Vélez, Víctor, Sánchez, Marta I., Lovas-Kiss, Ádám, Hortas, Francisco, Green, Andy J., Conferencia de Rectores de las Universidades Españolas, Consejo Superior de Investigaciones Científicas (España), Fundación la Caixa, Ministerio de Economía, Industria y Competitividad (España), Agencia Estatal de Investigación (España), European Commission, Hungarian Academy of Sciences, Ministry of Innovation and Technology (Hungary), Martín-Vélez, Víctor, Sánchez, Marta I., Lovas-Kiss, Ádám, Hortas, Francisco, and Green, Andy J.
Abstract: Waterbirds can transport aquatic invertebrates internally, contributing to metapopulation dynamics between aquatic habitats in a terrestrial matrix. However, research into this dispersal process to date has focused on individual field sites or laboratory studies. We investigated the invertebrates dispersed by endozoochory by the lesser black-backed gull Larus fuscus wintering in Andalusia, south-west Spain in 2016–2017, comparing seven sites interconnected by their movements, with different degrees of anthropogenization [three landfills, two saltpan complexes, a natural lake, and a large (370 km2) ricefield area]. In the ricefields, we also compared invertebrates dispersed by gulls with those dispersed by the larger white stork Ciconia ciconia. A total of 642 intact invertebrates and their propagules (mainly plumatellid bryozoans, cladocerans, and other branchiopods) were recorded in excreta (faeces and pellets) from gulls and storks. A greater diversity and abundance of invertebrates were recorded in ricefields, notably 43 individuals of the alien snail Physella acuta. One snail was still alive in a gull pellet 3 weeks after being stored in a fridge. This represents the first record of snail dispersal within waterbird pellets. Viability was also confirmed for the cladoceran Macrothrix rosea recorded in ricefields, and the alien brine shrimp Artemia franciscana recorded mainly in saltpans. In ricefields, gulls and pellets had significantly fewer propagules and fewer taxa per gram of excreta than storks and faeces, respectively. Through their high mobility, gulls and storks can disperse invertebrates between different natural and artificial habitats, and even to landfills. They can promote metapopulation dynamics for native bryozoans and branchiopods, but also the spread of invasive snails and brine shrimp.
Published: 2022

11. Functional Traits Drive Dispersal Interactions Between European Waterfowl and Seeds

Author: Consejo Superior de Investigaciones Científicas (España), Agencia Estatal de Investigación (España), Hungarian Academy of Sciences, National Research, Development and Innovation Office (Hungary), Ministry of Innovation and Technology (Hungary), Almeida, Bia A., Lukács, Balázs A., Lovas-Kiss, Ádám, Reynolds, Chevonne, Green, Andy J., Consejo Superior de Investigaciones Científicas (España), Agencia Estatal de Investigación (España), Hungarian Academy of Sciences, National Research, Development and Innovation Office (Hungary), Ministry of Innovation and Technology (Hungary), Almeida, Bia A., Lukács, Balázs A., Lovas-Kiss, Ádám, Reynolds, Chevonne, and Green, Andy J.
Abstract: Endozoochory by waterfowl is important for a broad range of angiosperms, most of which lack a fleshy fruit. This dispersal function contributes to the formation and maintenance of plant communities and may allow range shifts for plant species under global change. However, our current understanding of what seed or plant traits are important for this dispersal mechanism, and how they relate to variation in waterbird traits, is extremely limited. We addressed this question using a unique dataset identifying the plant species whose seeds are ingested by 31 different waterfowl species in Europe. We used RLQ and fourth-corner analyses to explore relationships between (1) bird morphological and foraging strategy traits, and (2) plant traits related to seed morphology, environmental preferences, and growth form. We then used Generalized Additive Models to identify relationships between plant/seed traits and the number of waterfowl species that disperse them. Although many waterfowl feed intentionally on seeds, available seed trait data provided little explanation for patterns compared to plant traits such as Ellenberg indicators of habitat preference and life form. Geese were associated with terrestrial plants, ingesting seeds as they graze on land. Diving ducks were associated with strictly aquatic plants, ingesting seeds as they feed at greater depths. Dabbling ducks ingest seeds from plants with high light and temperature requirements, especially shoreline and ruderal species growing in or around the dynamic and shallow microhabitats favored by these birds. Overall, the number of waterfowl vector species (up to 13 per plant species) increases for plants with greater soil moisture requirements and salinity tolerance, reflecting the inclination of most waterfowl species to feed in coastal wetlands. Our findings underline the importance of waterfowl dispersal for plants that are not strictly aquatic, as well as for plants associated with high salinities. Furthermore, our re
Published: 2022

12. Deciphering metasomatic events beneath Mindszentkálla (Bakony-Balaton Highland Volcanic Field, western Pannonian Basin) revealed by single-lithology and composite upper mantle xenoliths

Author: Ministry of Innovation and Technology (Hungary), Patkó, Levente, Kovács, Z., Liptai, Norá, Aradi, László Elöd, Berkesi, Márta, Ciazela, Jakub, Hidas, Károly, Garrido, Carlos J., Kovács, István J., Szabó, C., Ministry of Innovation and Technology (Hungary), Patkó, Levente, Kovács, Z., Liptai, Norá, Aradi, László Elöd, Berkesi, Márta, Ciazela, Jakub, Hidas, Károly, Garrido, Carlos J., Kovács, István J., and Szabó, C.
Abstract: Single-lithology and composite xenoliths from Mindszentkálla (Bakony-Balaton Highland Volcanic Field) in the Carpathian-Pannonian region record geochemical evolution of the subcontinental lithospheric mantle. The dominant single-lithology xenoliths are orthopyroxene-rich (22 vol% on average) harzburgites. Three composite xenoliths contain either two or more domains including dunite, olivine-orthopyroxenite, orthopyroxenite, apatite-bearing websterite and amphibole-phlogopite-bearing vein. The presence of different lithologies is a result of at least two metasomatic events that affected the lithospheric mantle. The first event resulted in orthopyroxene enrichment thus formed harzburgitic mantle volumes (Group I xenoliths). Major- and trace element distributions of the bulk harzburgites differ from the geochemical trends expected in residues of mantle melting. In contrast, petrographic and geochemical attributes suggest that the harzburgite was formed by silica-rich melt - peridotitic wall rock interactions in a supra-subduction zone. Within the Group I xenoliths, two subgroups were identified based on the presence or lack of enrichment in U, Pb and Sr. Since these elements are fluid mobile, their enrichment in certain Group I xenoliths indicate reaction with a subduction-related fluid, subsequent to the harzburgite formation. The effect of a second event overprints the features of the Group I xenoliths and is evidenced in all domains of two composite xenoliths (Group II xenoliths). The general geochemical character involves enrichment of basaltic major and minor elements (Fe, Mn, Ti, Ca) in the rock-forming minerals and convex-upward rare earth element (REE) patterns in clinopyroxenes. We suggest that the different domains represent reaction products with variably evolved basaltic melts of a single magmatic event. The tectonic background to the formation of Group I xenoliths is likely linked to the subduction of oceanic crust during the Mesozoic–Paleogene. This happe
Published: 2022

13. Relativistic first-principles theory of Yu-Shiba-Rusinov states applied to Mn adatoms and Mn dimers on Nb(110)

Author: Ministry of Innovation and Technology (Hungary), Ministerio de Economía y Competitividad (España), European Commission, Ministerio de Ciencia, Innovación y Universidades (España), Generalitat de Catalunya, Nyári, Bendegúz, Lászlóffy, András, Szunyogh, László, Csire, Gábor, Park, Kyungwha, Újfalussy, Balázs, Ministry of Innovation and Technology (Hungary), Ministerio de Economía y Competitividad (España), European Commission, Ministerio de Ciencia, Innovación y Universidades (España), Generalitat de Catalunya, Nyári, Bendegúz, Lászlóffy, András, Szunyogh, László, Csire, Gábor, Park, Kyungwha, and Újfalussy, Balázs
Abstract: We present a fully relativistic first-principles-based theoretical approach for the calculation of the spectral properties of magnetic impurities on the surface of a superconducting substrate, providing a material specific framework for the investigation of the Yu-Shiba-Rusinov (YSR) states. By using a suitable orbital decomposition of the local densities of states we discuss in great detail the formation of the YSR states for an Mn adatom and for two kinds of Mn dimers placed on the Nb(110) surface and compare our results to recent experimental findings. In the case of the adatom we find that the spin-orbit coupling slightly shifts some of the YSR peaks and also the local spin polarization on the Nb atoms has marginal effects on their positions. Moreover, by scaling the exchange field on the Mn site we could explain the lack of the dx2−y2-like YSR state in the spectrum. While our results for a close packed ferromagnetic dimer are in satisfactory agreement with the experimentally observed splitting of the YSR states, in the case of an antiferromagnetic dimer we find that the spin-orbit coupling is not sufficiently large to explain the splitting of the YSR states seen in the experiment. Changing the relative orientation of the magnetic moments in this dimer induces splitting of the YSR states and also shifts their energy, leading even to the formation of a zero bias peak in the case of the deepest YSR state.
Published: 2021

14. Fungal Planet description sheets: 1284-1382

Author: Ministry of Business, Innovation, and Employment (New Zealand), Ministry of Health of the Czech Republic, Japan Society for the Promotion of Science, Charles University (Czech Republic), European Commission, Fundação para a Ciência e a Tecnologia (Portugal), Ministério da Ciência, Tecnologia e Ensino Superior (Portugal), Research Foundation - Flanders, Russian Science Foundation, Lomonosov Moscow State University, Kerala State Council for Science, Technology and Environment, Universidad de Alcalá, Ministry of Innovation and Technology (Hungary), National Research, Development and Innovation Office (Hungary), Hungarian Academy of Sciences, Agencia Nacional de Investigación y Desarrollo (Chile), Ministerio de Ciencia, Tecnología, Conocimiento e Innovación (Chile), Fondo Nacional de Desarrollo Científico y Tecnológico (Chile), Estonian Research Council, Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brasil), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (Brasil), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Swedish Taxonomy Initiative, Australian Biological Resources Study, Croatian Science Foundation, Fundación Séneca, National Science Foundation (US), New York Botanical Garden, National Science Centre (Poland), Russian Academy of Sciences, Crous, P. W., Osieck, E. R., Jurjević, Željko, Boers, J., Iperen, A. L. van, Starink-Willemse, M., Dima, B., Balashov, S., Bulgakov, T. S., Johnston, P. R., Morozova, O. V., Barreto, R. W., Baseia, I. G., Miller, A. N., Bellanger, J.-M., Berraf-Tebbal, Akila, Biketova, A. Yu., Malysheva, V. F, Bukharova, N. V., Burgess, T. I., Cabero, J., Navarro-Ródenas, A., Câmara, M. P. S., Cano-Lira, J. F., Ceryngier, P., Mironova, P., Chávez, R., Cowan, D. A., Lima, A. F. de, Oliveira, R. L., Martín, B., Denman, S., Nel, W. J., Dang, Q. N., Dovana, F., Duarte, I. G., Eichmeier, Ales, Pinruan, U., Erhard, A., Esteve-Raventós, F., Fellin, A., Ferisin, G., Ferreira, Renato Juciano, Zhao, L., Martín, María P., Ferrer, A., Finy, P., Gaya, E., Geering, A. D. W., Moreau, Pierre-Arthur, Gil-Durán, C., Glässnerová, K., Glushakova, A. M., Gramaje, David, Nguyen, T. H., Guard, F. E., Guarnizo, A.L., Matočec, N., Haelewaters, D., Halling, R. E., Hill, R., Morte, A., Hirooka, Y., Hubka, V., Iliushin, V. A., Nóbrega, T. F., Ivanova, D. D., Ivanushkina, N. E., Jangsantear, P., Justo, A., McTaggart, Alistair R., Kachalkin, A.V., Kato, S., Müller, K., Khamsuntorn, P., Kirtsideli, I. Y., Noordeloos, M. E., Knapp, D. G., Kochkina, G. A., Koukol, O., Kovács, G. M., Kruse, J., Kumar, T. K. A., Mehrabi-Koushki, M., Kušan, I., Nagy, L. G., Læssøe, T., Sommai, S., Larsson, E., Lebeuf, R., Levicán, G., Loizides, M., Marinho, P., Luangsa-Ard, J. J., Lukina, E. G., Magaña-Dueñas, V., Mešić, A., Nanu, S., Olariaga, I., Maggs-Kölling, G., Overton, B. E., Ozerskaya, S. M., Angelini, C., Palani, P., Pancorbo, F., Papp, V., Abdollahzadeh, J., Pawłowska, J., Pham, T. Q., Phosri, C., Popov, E. S., Alvarado, P., Portugal, A., Antonín, V., Pošta, A., Reschke, K., Reul, M., Ricci, G. M., Abrinbana, M., Rodríguez, A., Romanowski, J., Ruchikachorn, N., Saar, I., Safi, A., Malysheva, E. F., Decock, Cony A., Sakolrak, B., Salzmann, F., Sandoval-Denis, M., Sangwichein, E., Ageev, D. V., Sanhueza, L., Sato, T., Sastoque, A., Senn-Irlet, B., Arenas, F., Shibata, A., Siepe, K., Lebel, T., Somrithipol, S., Spetik, M., Sridhar, P., Akhmetova, G., Stchigel, A. M., Stuskova, Katerina, Suwannasai, N., Asselman, P., Tan, Y. P., Thangavel, R., Tiago, I., Tiwari, S., McMullan-Fisher, S., Tkalčec, Z., Tomashevskaya, M. A., Alexandrova, A. V., Tonegawa, C., Tran, H. X., Badali, F., Tran, N. T., Trovão, J., Trubitsyn, V. E., Wyk, J. van, Vieira, Willie A. S., Vila, J., Moreno, G., Visagie, C. M., Altés, A., Vizzini, Alfredo, Baghela, A., Volobuev, S. W., Vu, D. T., Wangsawat, N., Yaguchi, T., Ercole, E., Ferreira, B. W., Souza, A. P. de, Vieira, B. S., Shivas, R. G., Amaral, A. G. G., Bañares, Ángel, Groenewald, J. Z., Ministry of Business, Innovation, and Employment (New Zealand), Ministry of Health of the Czech Republic, Japan Society for the Promotion of Science, Charles University (Czech Republic), European Commission, Fundação para a Ciência e a Tecnologia (Portugal), Ministério da Ciência, Tecnologia e Ensino Superior (Portugal), Research Foundation - Flanders, Russian Science Foundation, Lomonosov Moscow State University, Kerala State Council for Science, Technology and Environment, Universidad de Alcalá, Ministry of Innovation and Technology (Hungary), National Research, Development and Innovation Office (Hungary), Hungarian Academy of Sciences, Agencia Nacional de Investigación y Desarrollo (Chile), Ministerio de Ciencia, Tecnología, Conocimiento e Innovación (Chile), Fondo Nacional de Desarrollo Científico y Tecnológico (Chile), Estonian Research Council, Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brasil), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (Brasil), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Swedish Taxonomy Initiative, Australian Biological Resources Study, Croatian Science Foundation, Fundación Séneca, National Science Foundation (US), New York Botanical Garden, National Science Centre (Poland), Russian Academy of Sciences, Crous, P. W., Osieck, E. R., Jurjević, Željko, Boers, J., Iperen, A. L. van, Starink-Willemse, M., Dima, B., Balashov, S., Bulgakov, T. S., Johnston, P. R., Morozova, O. V., Barreto, R. W., Baseia, I. G., Miller, A. N., Bellanger, J.-M., Berraf-Tebbal, Akila, Biketova, A. Yu., Malysheva, V. F, Bukharova, N. V., Burgess, T. I., Cabero, J., Navarro-Ródenas, A., Câmara, M. P. S., Cano-Lira, J. F., Ceryngier, P., Mironova, P., Chávez, R., Cowan, D. A., Lima, A. F. de, Oliveira, R. L., Martín, B., Denman, S., Nel, W. J., Dang, Q. N., Dovana, F., Duarte, I. G., Eichmeier, Ales, Pinruan, U., Erhard, A., Esteve-Raventós, F., Fellin, A., Ferisin, G., Ferreira, Renato Juciano, Zhao, L., Martín, María P., Ferrer, A., Finy, P., Gaya, E., Geering, A. D. W., Moreau, Pierre-Arthur, Gil-Durán, C., Glässnerová, K., Glushakova, A. M., Gramaje, David, Nguyen, T. H., Guard, F. E., Guarnizo, A.L., Matočec, N., Haelewaters, D., Halling, R. E., Hill, R., Morte, A., Hirooka, Y., Hubka, V., Iliushin, V. A., Nóbrega, T. F., Ivanova, D. D., Ivanushkina, N. E., Jangsantear, P., Justo, A., McTaggart, Alistair R., Kachalkin, A.V., Kato, S., Müller, K., Khamsuntorn, P., Kirtsideli, I. Y., Noordeloos, M. E., Knapp, D. G., Kochkina, G. A., Koukol, O., Kovács, G. M., Kruse, J., Kumar, T. K. A., Mehrabi-Koushki, M., Kušan, I., Nagy, L. G., Læssøe, T., Sommai, S., Larsson, E., Lebeuf, R., Levicán, G., Loizides, M., Marinho, P., Luangsa-Ard, J. J., Lukina, E. G., Magaña-Dueñas, V., Mešić, A., Nanu, S., Olariaga, I., Maggs-Kölling, G., Overton, B. E., Ozerskaya, S. M., Angelini, C., Palani, P., Pancorbo, F., Papp, V., Abdollahzadeh, J., Pawłowska, J., Pham, T. Q., Phosri, C., Popov, E. S., Alvarado, P., Portugal, A., Antonín, V., Pošta, A., Reschke, K., Reul, M., Ricci, G. M., Abrinbana, M., Rodríguez, A., Romanowski, J., Ruchikachorn, N., Saar, I., Safi, A., Malysheva, E. F., Decock, Cony A., Sakolrak, B., Salzmann, F., Sandoval-Denis, M., Sangwichein, E., Ageev, D. V., Sanhueza, L., Sato, T., Sastoque, A., Senn-Irlet, B., Arenas, F., Shibata, A., Siepe, K., Lebel, T., Somrithipol, S., Spetik, M., Sridhar, P., Akhmetova, G., Stchigel, A. M., Stuskova, Katerina, Suwannasai, N., Asselman, P., Tan, Y. P., Thangavel, R., Tiago, I., Tiwari, S., McMullan-Fisher, S., Tkalčec, Z., Tomashevskaya, M. A., Alexandrova, A. V., Tonegawa, C., Tran, H. X., Badali, F., Tran, N. T., Trovão, J., Trubitsyn, V. E., Wyk, J. van, Vieira, Willie A. S., Vila, J., Moreno, G., Visagie, C. M., Altés, A., Vizzini, Alfredo, Baghela, A., Volobuev, S. W., Vu, D. T., Wangsawat, N., Yaguchi, T., Ercole, E., Ferreira, B. W., Souza, A. P. de, Vieira, B. S., Shivas, R. G., Amaral, A. G. G., Bañares, Ángel, and Groenewald, J. Z.
Abstract: Novel species of fungi described in this study include those from various countries as follows: Antartica, Cladosporium austrolitorale from coastal sea sand. Australia, Austroboletus yourkae on soil, Crepidotus innuopurpureus on dead wood, Curvularia stenotaphri from roots and leaves of Stenotaphrum secundatum and Thecaphora stajsicii from capsules of Oxalis radicosa. Belgium, Paraxerochrysium coryli (incl. Paraxerochrysium gen. nov.) from Corylus avellana. Brazil, Calvatia nordestina on soil, Didymella tabebuiicola from leaf spots on Tabebuia aurea, Fusarium subflagellisporum from hypertrophied floral and vegetative branches of Mangifera indica and Microdochium maculosum from living leaves of Digitaria insularis. Canada, Cuphophyllus bondii fromagrassland. Croatia, Mollisia inferiseptata from a rotten Laurus nobilis trunk. Cyprus, Amanita exilis oncalcareoussoil. Czech Republic, Cytospora hippophaicola from wood of symptomatic Vaccinium corymbosum. Denmark, Lasiosphaeria deviata on pieces of wood and herbaceousdebris. Dominican Republic, Calocybella goethei among grass on a lawn. France (Corsica) , Inocybe corsica onwetground. France (French Guiana) , Trechispora patawaensis on decayed branch of unknown angiosperm tree and Trechispora subregularis on decayed log of unknown angiosperm tree. [...]
Published: 2021

15. Fungal Planet description sheets: 1182-1283

Author: Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brasil), Fundação de Amparo à Ciência e Tecnologia do Estado de Pernambuco, Russian Foundation for Basic Research, Russian Academy of Sciences, Swedish Taxonomy Initiative, German Research Foundation, LOEWE Center for Insect Biotechnology & Bioresources, Russian Government, Lomonosov Moscow State University, Ministry of Science and Higher Education of the Russian Federation, University of Warsaw, European Commission, Hemvati Nandan Bahuguna Garhwal University, Russian Science Foundation, Rural Industries Research and Development Corporation (Australia), Department of Agriculture and Water Resources (Australia), Croatian Science Foundation, Department of Science and Technology (India), International Centre for Genetic Engineering and Biotechnology, Bulgarian National Science Fund, Universidad de Alcalá, Charles University (Czech Republic), Ministry of Agriculture of the Czech Republic, Ministry of Innovation and Technology (Hungary), National Research, Development and Innovation Office (Hungary), Norwegian Biodiversity Information Centre, University of Oslo, Ministerio de Economía y Competitividad (España), Fundación Séneca, Ministry of Health of the Czech Republic, Crous, P. W., Cowan, D. A., Maggs-Kölling, G., Yilmaz, N., Thangavel, R., Wingfield, M. J., Noordeloos, M. E., Dima, B., Brandrud, T. E., Jansen, G. M., Morozova, O. V., Cunnington, J. H., Biketova, A. Yu., Blomquist, C. L., Boekhout, T., Boertmann, D., Bulyonkova, T. M., Burgess, T. I., Cruz, M. O. da, Damm, U., Davoodian, N., Matočec, N., Santiago, A. L. C. M. de A., Dearnaley, J., Freitas, L. W. S., Mahamedi, A. E., Dhileepan, K., Dimitrov, R., Di Piazza, S., Fatima, S., Fuljer, F., Galera, H., Kušan, I., Ghosh, A., Giraldo, A., Glushakova, A. M., Gorczak, M., Malysheva, V. F, Gouliamova, D. E., Gramaje, David, Groenewald, M., Gunsch, C. K., Gutierrez-Aguirregabiria, A., Lad, S., Holdom, D., Houbraken, J., Ismailov, A. B., Istel, Ł., Iturriaga, T., Mateos, A., Jeppson, M., Jurjević, Željko, Kalinina, L. B., Kapitonov, V. I., Læssøe, T., Kautmanová, I., Khalid, Abdul Nasir, Kiran, M., Kiss, L., Kovács, A., Kurose, D., Lee, H. B., Luangsa-Ard, J. J., Lynch, M., Mešić, A., Miller, A. N., Mongkolsamrit, S., Bishop-Hurley, S., Moreno, G., Morte, A., Mostowfizadeh-Ghalamfarsa, R., Vila, J., Naseer, Arooj, Navarro-Ródenas, A., Nguyen, T. T. T., Noisripoom, W., Ntandu, J. E., Nuytinck, J., Volobuev, S. V., Ostrý, V., Pankratov, T. A., Pawłowska, J., Pečenka, Jakub, Shivas, R. G., Pham, T. H. G., Polhorský, A., Pošta, A., Raudabaugh, D. B., Reschke, K., Weill, A., Rodríguez, A., Romero, M., Rooney-Latham, S., Roux, J., Sandoval-Denis, M., Tan, Y. P., Smith, M. Th., Steinrucken, T. V., Svetasheva, T. Y., Tkalčec, Z., Wrzosek, M., Linde, E. J. van der, Vegte, M., Vauras, J., Verbeken, A., Visagie, C. M., Vitelli, J. S., Zmitrovich, I. V., Zvyagina, E. A., Groenewald, J. Z., Lacey, E., Marney, T. S., Larsson, K.-H., Carnegie, A. J., Le Floch, G, Lombard, L., Nodet, P., Hubka, V., Alvarado, P., Berraf-Tebbal, Akila, Reyes, J. D., Delgado, Gregorio, Eichmeier, Ales, Jordal, J. B., Cobo-Díaz, José F., Kachalkin, A.V., Kubátová, A., Maciá-Vicente, José G., Malysheva, E. F., Papp, V., Rajeshkumar, Kunhiraman C., Sharma, A., Spetik, M., Szabóová, D., Tomashevskaya, M. A., Corriol, G., Abad, J. A., Abad, Z. G., Alexandrova, A. V., Anand, G., Arenas, F., Ashtekar, N., Balashov, S., Bañares, Ángel, Baroncelli, R., Bera, I., Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brasil), Fundação de Amparo à Ciência e Tecnologia do Estado de Pernambuco, Russian Foundation for Basic Research, Russian Academy of Sciences, Swedish Taxonomy Initiative, German Research Foundation, LOEWE Center for Insect Biotechnology & Bioresources, Russian Government, Lomonosov Moscow State University, Ministry of Science and Higher Education of the Russian Federation, University of Warsaw, European Commission, Hemvati Nandan Bahuguna Garhwal University, Russian Science Foundation, Rural Industries Research and Development Corporation (Australia), Department of Agriculture and Water Resources (Australia), Croatian Science Foundation, Department of Science and Technology (India), International Centre for Genetic Engineering and Biotechnology, Bulgarian National Science Fund, Universidad de Alcalá, Charles University (Czech Republic), Ministry of Agriculture of the Czech Republic, Ministry of Innovation and Technology (Hungary), National Research, Development and Innovation Office (Hungary), Norwegian Biodiversity Information Centre, University of Oslo, Ministerio de Economía y Competitividad (España), Fundación Séneca, Ministry of Health of the Czech Republic, Crous, P. W., Cowan, D. A., Maggs-Kölling, G., Yilmaz, N., Thangavel, R., Wingfield, M. J., Noordeloos, M. E., Dima, B., Brandrud, T. E., Jansen, G. M., Morozova, O. V., Cunnington, J. H., Biketova, A. Yu., Blomquist, C. L., Boekhout, T., Boertmann, D., Bulyonkova, T. M., Burgess, T. I., Cruz, M. O. da, Damm, U., Davoodian, N., Matočec, N., Santiago, A. L. C. M. de A., Dearnaley, J., Freitas, L. W. S., Mahamedi, A. E., Dhileepan, K., Dimitrov, R., Di Piazza, S., Fatima, S., Fuljer, F., Galera, H., Kušan, I., Ghosh, A., Giraldo, A., Glushakova, A. M., Gorczak, M., Malysheva, V. F, Gouliamova, D. E., Gramaje, David, Groenewald, M., Gunsch, C. K., Gutierrez-Aguirregabiria, A., Lad, S., Holdom, D., Houbraken, J., Ismailov, A. B., Istel, Ł., Iturriaga, T., Mateos, A., Jeppson, M., Jurjević, Željko, Kalinina, L. B., Kapitonov, V. I., Læssøe, T., Kautmanová, I., Khalid, Abdul Nasir, Kiran, M., Kiss, L., Kovács, A., Kurose, D., Lee, H. B., Luangsa-Ard, J. J., Lynch, M., Mešić, A., Miller, A. N., Mongkolsamrit, S., Bishop-Hurley, S., Moreno, G., Morte, A., Mostowfizadeh-Ghalamfarsa, R., Vila, J., Naseer, Arooj, Navarro-Ródenas, A., Nguyen, T. T. T., Noisripoom, W., Ntandu, J. E., Nuytinck, J., Volobuev, S. V., Ostrý, V., Pankratov, T. A., Pawłowska, J., Pečenka, Jakub, Shivas, R. G., Pham, T. H. G., Polhorský, A., Pošta, A., Raudabaugh, D. B., Reschke, K., Weill, A., Rodríguez, A., Romero, M., Rooney-Latham, S., Roux, J., Sandoval-Denis, M., Tan, Y. P., Smith, M. Th., Steinrucken, T. V., Svetasheva, T. Y., Tkalčec, Z., Wrzosek, M., Linde, E. J. van der, Vegte, M., Vauras, J., Verbeken, A., Visagie, C. M., Vitelli, J. S., Zmitrovich, I. V., Zvyagina, E. A., Groenewald, J. Z., Lacey, E., Marney, T. S., Larsson, K.-H., Carnegie, A. J., Le Floch, G, Lombard, L., Nodet, P., Hubka, V., Alvarado, P., Berraf-Tebbal, Akila, Reyes, J. D., Delgado, Gregorio, Eichmeier, Ales, Jordal, J. B., Cobo-Díaz, José F., Kachalkin, A.V., Kubátová, A., Maciá-Vicente, José G., Malysheva, E. F., Papp, V., Rajeshkumar, Kunhiraman C., Sharma, A., Spetik, M., Szabóová, D., Tomashevskaya, M. A., Corriol, G., Abad, J. A., Abad, Z. G., Alexandrova, A. V., Anand, G., Arenas, F., Ashtekar, N., Balashov, S., Bañares, Ángel, Baroncelli, R., and Bera, I.
Abstract: Novel species of fungi described in this study include those from various countries as follows: Algeria, Phaeoacremonium adelophialidum from Vitis vinifera. Antarctica, Comoclathris antarctica from soil. Australia, Coniochaeta salicifolia as endophyte from healthy leaves of Geijera salicifolia, Eremothecium peggii in fruit of Citrus australis, Microdochium ratticaudae from stem of Sporobolus natalensis, Neocelosporium corymbiae on stems of Corymbia variegata, Phytophthora kelmanii from rhizosphere soil of Ptilotus pyramidatus, Pseudosydowia backhousiae on living leaves of Backhousia citriodora, Pseudosydowia indoor oopillyensis, Pseudosydowia louisecottisiae and Pseudosydowia queenslandica on living leaves of Eucalyptus sp. Brazil, Absidia montepascoalis from soil. Chile, Ilyonectria zarorii from soil under Maytenus boaria. Costa Rica, Colletotrichum filicis from an unidentified fern. Croatia, Mollisia endogranulata on deteriorated hardwood. Czech Republic, Arcopilus navicularis from tea bag with fruit tea, Neosetophoma buxi as endophyte from Buxus sempervirens, Xerochrysium bohemicum on surface of biscuits with chocolate glaze and filled with jam. France, Entoloma cyaneobasale on basic to calcareous soil, Fusarium aconidiale from Triticum aestivum, Fusarium juglandicola from buds of Juglans regia. Germany, Tetraploa endophytica as endophyte from Microthlaspi perfoliatum roots. India, Castanediella ambae on leaves of Mangifera indica, Lactifluus kanadii on soil under Castanopsis sp., Penicillium uttarakhandense from soil. Italy, Penicillium ferraniaense from compost. Namibia, Bezerromyces gobabebensis on leaves of unidentified succulent, Cladosporium stipagrostidicola on leaves of Stipagrostis sp., Cymostachys euphorbiae on leaves of Euphorbia sp., Deniquelata hypolithi from hypolith under a rock, Hysterobrevium walvisbayicola on leaves of unidentified tree, Knufia hypolithi and Knufia walvisbayicola from hypolith under a rock, Lapidomyces stipagrostidicola on leave
Published: 2021

16. Mapping of Genomic Vulnerabilities in the Post-Translational Ubiquitination, SUMOylation and Neddylation Machinery in Breast Cancer

Author: Instituto de Salud Carlos III, Acepain Albacete, Diputación de Albacete, Fundación CRIS contra el Cáncer, Ministerio de Economía y Competitividad (España), Junta de Castilla y León, Ministry of Innovation and Technology (Hungary), Semmelweis University, Fuentes-Antrás, Jesús, Alcaraz-Sanabria, Ana, Cabañas Morafraile, Esther, Noblejas-López, María del Mar, Galán-Moya, Eva María, Baliu-Piqué, Mariona, López-Cade, Igor, García-Barberán, Vanesa, Pérez-Segura, Pedro, Manzano, Aranzazu, Pandiella, Atanasio, Győrffy, Balázs, Ocaña, Alberto, Instituto de Salud Carlos III, Acepain Albacete, Diputación de Albacete, Fundación CRIS contra el Cáncer, Ministerio de Economía y Competitividad (España), Junta de Castilla y León, Ministry of Innovation and Technology (Hungary), Semmelweis University, Fuentes-Antrás, Jesús, Alcaraz-Sanabria, Ana, Cabañas Morafraile, Esther, Noblejas-López, María del Mar, Galán-Moya, Eva María, Baliu-Piqué, Mariona, López-Cade, Igor, García-Barberán, Vanesa, Pérez-Segura, Pedro, Manzano, Aranzazu, Pandiella, Atanasio, Győrffy, Balázs, and Ocaña, Alberto
Abstract: The dysregulation of post-translational modifications (PTM) transversally impacts cancer hallmarks and constitutes an appealing vulnerability for drug development. In breast cancer there is growing preclinical evidence of the role of ubiquitin and ubiquitin-like SUMO and Nedd8 peptide conjugation to the proteome in tumorigenesis and drug resistance, particularly through their interplay with estrogen receptor signaling and DNA repair. Herein we explored genomic alterations in these processes using RNA-seq and mutation data from TCGA and METABRIC datasets, and analyzed them using a bioinformatic pipeline in search of those with prognostic and predictive capability which could qualify as subjects of drug research. Amplification of UBE2T, UBE2C, and BIRC5 conferred a worse prognosis in luminal A/B and basal-like tumors, luminal A/B tumors, and luminal A tumors, respectively. Higher UBE2T expression levels were predictive of a lower rate of pathological complete response in triple negative breast cancer patients following neoadjuvant chemotherapy, whereas UBE2C and BIRC5 expression was higher in luminal A patients with tumor relapse within 5 years of endocrine therapy or chemotherapy. The transcriptomic signatures of USP9X and USP7 gene mutations also conferred worse prognosis in luminal A, HER2-enriched, and basal-like tumors, and in luminal A tumors, respectively. In conclusion, we identified and characterized the clinical value of a group of genomic alterations in ubiquitination, SUMOylation, and neddylation enzymes, with potential for drug development in breast cancer.
Published: 2021

17. Genomic mapping of splicing-related genes identify amplifications in lsm1, clns1a, and ilf2 in luminal breast cancer

Author: Instituto de Salud Carlos III, Acepain Albacete, Fundación CRIS contra el Cáncer, Diputación de Albacete, European Commission, Ministerio de Educación (España), Ministry of Innovation and Technology (Hungary), Noblejas-López, María del Mar, López-Cade, Igor, Fuentes-Antrás, Jesús, Fernández-Hinojal, Gonzalo, Esteban-Sánchez, Ada, Manzano, Aranzazu, García-Saenz, José Ángel, Pérez-Segura, Pedro, Hoya, Miguel de la, Pandiella, Atanasio, Győrffy, Balázs, García-Barberán, Vanesa, Ocaña, Alberto, Instituto de Salud Carlos III, Acepain Albacete, Fundación CRIS contra el Cáncer, Diputación de Albacete, European Commission, Ministerio de Educación (España), Ministry of Innovation and Technology (Hungary), Noblejas-López, María del Mar, López-Cade, Igor, Fuentes-Antrás, Jesús, Fernández-Hinojal, Gonzalo, Esteban-Sánchez, Ada, Manzano, Aranzazu, García-Saenz, José Ángel, Pérez-Segura, Pedro, Hoya, Miguel de la, Pandiella, Atanasio, Győrffy, Balázs, García-Barberán, Vanesa, and Ocaña, Alberto
Abstract: Alternative splicing is an essential biological process, which increases the diversity and complexity of the human transcriptome. In our study, 304 splicing pathway-related genes were evaluated in tumors from breast cancer patients (TCGA dataset). A high number of alterations were detected, including mutations and copy number alterations (CNAs), although mutations were less frequently present compared with CNAs. In the four molecular subtypes, 14 common splice genes showed high level amplification in >5% of patients. Certain genes were only amplified in specific breast cancer subtypes. Most altered genes in each molecular subtype clustered to a few chromosomal regions. In the Luminal subtype, amplifications of LSM1, CLNS1A, and ILF2 showed a strong significant association with prognosis. An even more robust association with OS and RFS was observed when expression of these three genes was combined. Inhibition of LSM1, CLNS1A, and ILF2, using siRNA in MCF7 and T47D cells, showed a decrease in cell proliferation. The mRNA expression of these genes was reduced by treatment with BET inhibitors, a family of epigenetic modulators. We map the presence of splicing-related genes in breast cancer, describing three novel genes, LSM1, CLNS1A, and ILF2, that have an oncogenic role and can be modulated with BET inhibitors.
Published: 2021

18. Top ten birds indicators of high environmental quality in European cities

Author: Czech Science Foundation, Ministerio de Ciencia e Innovación (España), Ministry of Innovation and Technology (Hungary), Agencia Estatal de Investigación (España), Charles University (Czech Republic), Morelli, Federico, Reif, Jiri, Díaz Esteban, Mario, Tryjanowski, Piotr, Ibáñez-Álamo, Juan Diego, Suhonen, Jukka, Jokimäki, Jukka, Kaisanlahti-Jokimäki, Marja-Liisa, Moller, Anders Pape, Bussière, Raphaël, Mägi, Marko, Kominos, Theodoros, Glanaki, Antonia, Bukas, Nikos, Markó, Gábor, Pruscini, Fabio, Jerzak, Leszek, Ciebiera, Olaf, Benedetti, Yanina, Czech Science Foundation, Ministerio de Ciencia e Innovación (España), Ministry of Innovation and Technology (Hungary), Agencia Estatal de Investigación (España), Charles University (Czech Republic), Morelli, Federico, Reif, Jiri, Díaz Esteban, Mario, Tryjanowski, Piotr, Ibáñez-Álamo, Juan Diego, Suhonen, Jukka, Jokimäki, Jukka, Kaisanlahti-Jokimäki, Marja-Liisa, Moller, Anders Pape, Bussière, Raphaël, Mägi, Marko, Kominos, Theodoros, Glanaki, Antonia, Bukas, Nikos, Markó, Gábor, Pruscini, Fabio, Jerzak, Leszek, Ciebiera, Olaf, and Benedetti, Yanina
Abstract: Urban and suburban areas are among the fastest-growing land-use types globally, reducing and fragmenting natural habitats for many animal species and making human-wildlife interactions more common. However, cities also create habitat for several species considered urban tolerant or urban exploiter species. Additionally, the environmental characteristics of urban areas can strongly affect the life quality of citizens. This study aimed to assess the effectiveness of common bird species as indicators of urban areas with high environmental quality within cities. Our study recorded 128 bird species in 1441 point counts distributed in fifteen different European cities. We classified urban areas as “high environmental quality” – HEQ when they were simultaneously characterized by a high vegetation cover and heterogeneity, low level of light pollution, and avian communities with high potential resilience to face ecological stress. Species indicators of HEQ urban areas were identified using the species-level indicator value (IndVal) analysis. Such species can be used as ecological indicators of HEQ in different European cities. The list of top ten birds indicators of HEQ in European cities is led by the Eurasian blackcap, selected as an indicator in more than half of the survey cities. Other birds indicators of HEQ in multiple cities are Blackbird (47%), Great tit (40%), Blue tit, Tree sparrow and Magpie (all 33%). The mean specificity of the top-ranked bird indicator of HEQ urban areas (Eurasian blackcap) was 0.778. Most of the HEQ-indicators are resident or resident/short migratory species characterized by territorial behaviour. Our findings support using multiple species as bioindicators of urban changes by using specific groups with few common species as sur-rogates of HEQ urban areas. The approach proposed in this study can be applied in different European cities to monitor biodiversity status periodically, even involving citizen science initiatives.
Published: 2021

19. Coevolution between MHC Class I and Antigen-Processing Genes in Salamanders

Author: National Science Centre (Poland), University of Connecticut, Japan Society for the Promotion of Science, Ministry of Innovation and Technology (Hungary), National Research Foundation of Korea, Ministerio de Ciencia e Innovación (España), Palomar, Gemma, Dudek, Katarzyna, Migalska, Magdalena, Arntzen, J.W., Ficetola, Gentile Francesco, Jelic, Dusan, Jockusch, Elizabeth, Martínez-Solano, Íñigo, Matsunami, Masatoshi, Shaffer, H. Bradley, Vörös, Judith, Waldman, Bruce, Wielstra, Ben, Babik, Wieslaw, National Science Centre (Poland), University of Connecticut, Japan Society for the Promotion of Science, Ministry of Innovation and Technology (Hungary), National Research Foundation of Korea, Ministerio de Ciencia e Innovación (España), Palomar, Gemma, Dudek, Katarzyna, Migalska, Magdalena, Arntzen, J.W., Ficetola, Gentile Francesco, Jelic, Dusan, Jockusch, Elizabeth, Martínez-Solano, Íñigo, Matsunami, Masatoshi, Shaffer, H. Bradley, Vörös, Judith, Waldman, Bruce, Wielstra, Ben, and Babik, Wieslaw
Abstract: Proteins encoded by antigen-processing genes (APGs) provide major histocompatibility complex (MHC) class I (MHC-I) with antigenic peptides. In mammals, polymorphic multigenic MHC-I family is served by monomorphic APGs, whereas in certain nonmammalian species both MHC-I and APGs are polymorphic and coevolve within stable haplotypes. Coevolution was suggested as an ancestral gnathostome feature, presumably enabling only a single highly expressed classical MHC-I gene. In this view coevolution, while optimizing some aspects of adaptive immunity, would also limit its flexibility by preventing the expansion of classical MHC-I into a multigene family. However, some nonmammalian taxa, such as salamanders, have multiple highly expressed MHC-I genes, suggesting either that coevolution is relaxed or that it does not prevent the establishment of multigene MHC-I. To distinguish between these two alternatives, we use salamanders (30 species from 16 genera representing six families) to test, within a comparative framework, a major prediction of the coevolution hypothesis: the positive correlation between MHC-I and APG diversity. We found that MHC-I diversity explained both within-individual and species-wide diversity of two APGs, TAP1 and TAP2, supporting their coevolution with MHC-I, whereas no consistent effect was detected for the other three APGs (PSMB8, PSMB9, and TAPBP). Our results imply that although coevolution occurs in salamanders, it does not preclude the expansion of the MHC-I gene family. Contrary to the previous suggestions, nonmammalian vertebrates thus may be able to accommodate diverse selection pressures with flexibility granted by rapid expansion or contraction of the MHC-I family, while retaining the benefits of coevolution between MHC-I and TAPs.
Published: 2021

20. Argonaute 2 controls antiviral activity against sweet potato mild mottle virus in Nicotiana benthamiana

Author: Ministry of Innovation and Technology (Hungary), Generalitat de Catalunya, Ministerio de Economía y Competitividad (España), Agencia Estatal de Investigación (España), Ministerio de Ciencia e Innovación (España), European Commission, Ministerio de Ciencia, Innovación y Universidades (España), Kenesi, Erzsébet, López-Moya Gómez, Juan José, Orosz, László, Burgyán, József, Lakatos, Lóránt, Ministry of Innovation and Technology (Hungary), Generalitat de Catalunya, Ministerio de Economía y Competitividad (España), Agencia Estatal de Investigación (España), Ministerio de Ciencia e Innovación (España), European Commission, Ministerio de Ciencia, Innovación y Universidades (España), Kenesi, Erzsébet, López-Moya Gómez, Juan José, Orosz, László, Burgyán, József, and Lakatos, Lóránt
Abstract: RNA silencing is a sequence specific post-transcriptional mechanism regulating important biological processes including antiviral defense in plants. Argonaute (AGO) proteins, the catalytic subunits of the silencing complexes, are loaded with small RNAs to execute the sequence specific RNA cleavage or translational inhibition. Plants encode several AGO proteins and a few of them, especially AGO1 and AGO2, have been shown to be required for antiviral silencing. Previously, we have shown that the P1 protein of the sweet potato mild mottle virus (SPMMV) suppresses the primary RNA silencing response by inhibiting AGO1. To analyze the role of AGO2 in antiviral defense against the SPMMV, we performed a comparative study using a wild type and ago2−/− mutant Nicotiana benthamiana. Here we show that the AGO2 of N. benthamiana attenuates the symptoms of SPMMV infection. Upon SPMMV infection the levels of AGO2 mRNA and protein are greatly increased. Moreover, we found that AGO2 proteins are loaded with SPMMV derived viral small RNAs as well as with miRNAs. Our results indicate that AGO2 protein takes over the place of AGO1 to confer antiviral silencing. Finally, we provide a plausible explanation for the AGO2 mediated recovery of an SPMMV-infected sweet potato.
Published: 2021

21. Effects of climate variation on bird escape distances modulate community responses to global change

Author: Ministry of Innovation and Technology (Hungary), Ministry of Education and Research (Estonia), Agencia Estatal de Investigación (España), Ministerio de Ciencia e Innovación (España), Díaz Esteban, Mario, Grim, T., Markó, Gábor, Morelli, Federico, Ibáñez-Álamo, Juan Diego, Jokimäki, Jukka, Kaisanlahti-Jokimäki, Marja-Liisa, Tätte, K., Tryjanowski, Piotr, Moller, A.P., Ministry of Innovation and Technology (Hungary), Ministry of Education and Research (Estonia), Agencia Estatal de Investigación (España), Ministerio de Ciencia e Innovación (España), Díaz Esteban, Mario, Grim, T., Markó, Gábor, Morelli, Federico, Ibáñez-Álamo, Juan Diego, Jokimäki, Jukka, Kaisanlahti-Jokimäki, Marja-Liisa, Tätte, K., Tryjanowski, Piotr, and Moller, A.P.
Abstract: Climate and land use are rapidly changing environmental conditions. Behavioral responses to such global perturbations can be used to incorporate interspecific interactions into predictive models of population responses to global change. Flight initiation distance (FID) reflects antipredator behaviour defined as the distance at which an individual takes flight when approached by a human, under standardized conditions. This behavioural trait results from a balance between disturbance, predation risk, food availability and physiological needs, and it is related to geographical range and population trends in European birds. Using 32,145 records of flight initiation distances for 229 bird species during 2006–2019 in 24 European localities, we show that FIDs decreased with increasing temperature and precipitation, as expected if foraging success decreased under warm and humid conditions. Trends were further altered by latitude, urbanisation and body mass, as expected if climate effects on FIDs were mediated by food abundance and need, differing according to position in food webs, supporting foraging models. This provides evidence for a role of behavioural responses within food webs on how bird populations and communities are affected by global change.
Published: 2021

22. Autism, problematic internet use and gaming disorder: a systematic review

Author: Mark D. Griffiths, Alayna Murray, Arlene Mannion, Geraldine Leader, Beatrix Koronczai, Orsolya Király, Zsolt Demetrovics, Eötvös Loránd University, Hungarian National Research, Development and Innovation Office, Hungarian Academy of Sciences, and Ministry for Innovation and Technology, Hungary
Subjects: Internet addiction, Autism Spectrum Disorder, Gaming disorder, Autism, Cognitive Neuroscience, medicine.medical_treatment, Comorbidity, Autistic traits, 03 medical and health sciences, Behavioral Neuroscience, 0302 clinical medicine, Developmental Neuroscience, mental disorders, medicine, 0501 psychology and cognitive sciences, Subclinical infection, Internet use, Rehabilitation, 05 social sciences, medicine.disease, Psychiatry and Mental health, Autism spectrum disorder, Psychology, Inclusion (education), 030217 neurology & neurosurgery, 050104 developmental & child psychology, Systematic search, Clinical psychology
Abstract: The present study investigated the association between autism and problematic internet use (PIU) and gaming disorder (GD). A systematic literature search was conducted in accordance with PRISMA guidelines. A total of 2286 publications were screened, and 21 were deemed eligible for inclusion in the review. The majority of the studies found positive associations between PIU and subclinical autistic-like traits with weak and moderate effect sizes and between PIU and Autism Spectrum Disorder (ASD) with varying effect sizes. Additionally, individuals with ASD were more likely to exhibit symptoms of GD with moderate and strong effect sizes. Future research would benefit from high-quality studies examining GD and PIU at a clinical level and their relationship with both clinical and subclinical autism. Open access funding provided by Eötvös Loránd University. This study was supported by the Hungarian National Research, Development and Innovation Office (KKP126835; ELTE Thematic Excellence Programme 2020, KP2020-IKA-05). Orsolya Király and Beatrix Koronczai was supported by the János Bolyai Research Scholarship of the Hungarian Academy of Sciences and by the ÚNKP-20-5 New National Excellence Program of the Ministry for Innovation and Technology from the source of the National Research, Development and Innovation Fund. peer-reviewed
Published: 2022

23. Investigation of the molecular details of the interactions of selenoglycosides and human galectin-3

Author: Raics, Mária, Kálmán Balogh, Álex, Kishor, Chandan, Timári, István, Medrano, Francisco Javier, Romero, Antonio, Go, Rob Marc, Blanchard, Helen, Szilágyi, László, Kövér, Katalin E., Fehér, K., National Research, Development and Innovation Office (Hungary), European Commission, Hungarian Academy of Sciences, Ministry of Innovation and Technology (Hungary), Debrecen University, Kálmán Balogh, Álex, Kishor, Chandan, Timári, István, Medrano, Francisco Javier, Romero, Antonio, Go, Rob Marc, Blanchard, Helen, Szilágyi, László, and Kövér, Katalin E.
Subjects: NMR spectroscopy, Galectin-3, Molecular dynamics, Lectin, Selenoglycosides, Fluorescence anisotropy, X-ray crystallography
Abstract: 17 p.-5 fig.-2 tab., Human galectin-3 (hGal-3) is involved in a variety of biological processes and is implicated in wide range of diseases. As a result, targeting hGal-3 for clinical applications has become an intense area of research. As a step towards the development of novel hGal-3 inhibitors, we describe a study of the binding of two Se-containing hGal-3 inhibitors, specifically that of di(β-D-galactopyranosyl)selenide (SeDG), in which two galactose rings are linked by one Se atom and a di(β-D-galactopyranosyl)diselenide (DSeDG) analogue with a diseleno bond between the two sugar units. The binding affinities of these derivatives to hGal-3 were determined by 15N-1H HSQC NMR spectroscopy and fluorescence anisotropy titrations in solution, indicating a slight decrease in the strength of interaction for SeDG compared to thiodigalactoside (TDG), a well-known inhibitor of hGal-3, while DSeDG displayed a much weaker interaction strength. NMR and FA measurements showed that both seleno derivatives bind to the canonical S face site of hGal-3 and stack against the conserved W181 residue also confirmed by X-ray crystallography, revealing canonical properties of the interaction. The interaction with DSeDG revealed two distinct binding modes in the crystal structure which are in fast exchange on the NMR time scale in solution, explaining a weaker interaction with hGal-3 than SeDG. Using molecular dynamics simulations, we have found that energetic contributions to the binding enthalpies mainly differ in the electrostatic interactions and in polar solvation terms and are responsible for weaker binding of DSeDG compared to SeDG. Selenium-containing carbohydrate inhibitors of hGal-3 showing canonical binding modes offer the potential of becoming novel hydrolytically stable scaffolds for a new class of hGal-3 inhibitors., Our studies were supported by the National Research, Development and Innovation Office of Hungary (grant numbers: NN 128368 (to L.S.Z. and K.E.K.) and PD 135034 (to I.T.) and co-financed by the European Regional Development Fund (projects GINOP-2.3.3-15-2016-00004 and GINOP-2.3.2-15-2016-00008). The research of I.T. was supported by the János Bolyai Research Scholarship of the Hungarian Academy of Sciences (BO/00372/20/7) and the ÚNKP-21-5-DE-471 New National Excellence Program of the Ministry for Innovation and Technology from the source of the National Research, Development and Innovation Fund. K.F. acknowledges the support of the János Bolyai Research Scholarship of the Hungarian Academy of Sciences (BO/004333/18/7) and the New National Excellence Program of Debrecen University (ÚNKP-21-4-DE-165 Bolyai+). We acknowledge the Governmental Information Technology Development Agency for awarding us access to supercomputing resources based in Debrecen, Hungary.
Published: 2022

24. Functional Traits Drive Dispersal Interactions Between European Waterfowl and Seeds

Author: Bia A. Almeida, Balázs A. Lukács, Ádám Lovas-Kiss, Chevonne Reynolds, Andy J. Green, Consejo Superior de Investigaciones Científicas (España), Agencia Estatal de Investigación (España), Hungarian Academy of Sciences, National Research, Development and Innovation Office (Hungary), and Ministry of Innovation and Technology (Hungary)
Subjects: migratory birds, waterbirds, fungi, Plant culture, food and beverages, feeding behavior, Plant Science, Anatidae, endozoochory, SB1-1110, seed dispersal, long distance dispersal, functional trait
Abstract: Endozoochory by waterfowl is important for a broad range of angiosperms, most of which lack a fleshy fruit. This dispersal function contributes to the formation and maintenance of plant communities and may allow range shifts for plant species under global change. However, our current understanding of what seed or plant traits are important for this dispersal mechanism, and how they relate to variation in waterbird traits, is extremely limited. We addressed this question using a unique dataset identifying the plant species whose seeds are ingested by 31 different waterfowl species in Europe. We used RLQ and fourth-corner analyses to explore relationships between (1) bird morphological and foraging strategy traits, and (2) plant traits related to seed morphology, environmental preferences, and growth form. We then used Generalized Additive Models to identify relationships between plant/seed traits and the number of waterfowl species that disperse them. Although many waterfowl feed intentionally on seeds, available seed trait data provided little explanation for patterns compared to plant traits such as Ellenberg indicators of habitat preference and life form. Geese were associated with terrestrial plants, ingesting seeds as they graze on land. Diving ducks were associated with strictly aquatic plants, ingesting seeds as they feed at greater depths. Dabbling ducks ingest seeds from plants with high light and temperature requirements, especially shoreline and ruderal species growing in or around the dynamic and shallow microhabitats favored by these birds. Overall, the number of waterfowl vector species (up to 13 per plant species) increases for plants with greater soil moisture requirements and salinity tolerance, reflecting the inclination of most waterfowl species to feed in coastal wetlands. Our findings underline the importance of waterfowl dispersal for plants that are not strictly aquatic, as well as for plants associated with high salinities. Furthermore, our results reveal a soil moisture gradient that drives seedbird interactions, in line with differences between waterfowl groups in their microhabitat preferences along the land-water continuum. This study provides an important advance in our understanding of the interactions that define plant dispersal in wetlands and their surroundings, and of what plants might be affected by ongoing changes in the distributions of waterfowl species., This study was partly funded by CSIC (PIE 202030E247) and AEI (PID2020-112774GB-I00) projects. ÁL-K and BL received grants OTKAFK-127939 and FK-138698 from the NKFIH and János Bolyai Research Scholarship of the Hungarian Academy of Sciences and the New National Excellence Programme of the Ministry of Innovation and Technology ÚNKP-21-5, NKFIH OTKA.
Published: 2022

25. Dispersal of aquatic invertebrates by lesser black-backed gulls and white storks within and between inland habitats

Author: Víctor Martín-Vélez, Marta I. Sánchez, Ádam Lovas-Kiss, Francisco Hortas, Andy J. Green, Conferencia de Rectores de las Universidades Españolas, Consejo Superior de Investigaciones Científicas (España), Fundación 'la Caixa', Ministerio de Economía, Industria y Competitividad (España), Agencia Estatal de Investigación (España), European Commission, Hungarian Academy of Sciences, and Ministry of Innovation and Technology (Hungary)
Subjects: Endozoochory, Ecology, Gastropoda, Waterbirds, Aquatic Science, Artemia, Cladocera, Ecology, Evolution, Behavior and Systematics, Water Science and Technology
Abstract: Waterbirds can transport aquatic invertebrates internally, contributing to metapopulation dynamics between aquatic habitats in a terrestrial matrix. However, research into this dispersal process to date has focused on individual field sites or laboratory studies. We investigated the invertebrates dispersed by endozoochory by the lesser black-backed gull Larus fuscus wintering in Andalusia, south-west Spain in 2016–2017, comparing seven sites interconnected by their movements, with different degrees of anthropogenization [three landfills, two saltpan complexes, a natural lake, and a large (370 km2) ricefield area]. In the ricefields, we also compared invertebrates dispersed by gulls with those dispersed by the larger white stork Ciconia ciconia. A total of 642 intact invertebrates and their propagules (mainly plumatellid bryozoans, cladocerans, and other branchiopods) were recorded in excreta (faeces and pellets) from gulls and storks. A greater diversity and abundance of invertebrates were recorded in ricefields, notably 43 individuals of the alien snail Physella acuta. One snail was still alive in a gull pellet 3 weeks after being stored in a fridge. This represents the first record of snail dispersal within waterbird pellets. Viability was also confirmed for the cladoceran Macrothrix rosea recorded in ricefields, and the alien brine shrimp Artemia franciscana recorded mainly in saltpans. In ricefields, gulls and pellets had significantly fewer propagules and fewer taxa per gram of excreta than storks and faeces, respectively. Through their high mobility, gulls and storks can disperse invertebrates between different natural and artificial habitats, and even to landfills. They can promote metapopulation dynamics for native bryozoans and branchiopods, but also the spread of invasive snails and brine shrimp., Open Access funding provided thanks to the CRUE-CSIC agreement with Springer Nature. “La Caixa-Severo Ochoa 2016” (VMV). Ministerio de Economía, Industria y Competitividad project CGL2016-76067-P (AEI/FEDER, EU) (AJG, MIS). János Bolyai Research Scholarship of the Hungarian Academy of Sciences, New National Excellence Programme of the Ministry of Innovation and Technology ÚNKP-21-5-DE-457 and NKFIH OTKA FK-127939 and FK138698 grants (ÁLK).
Published: 2022

26. The β-decay of 70Kr into 70Br: Restoration of the pseudo-SU(4) symmetry

Author: Vitéz-Sveiczer, A., Algora, A., Morales, A.I., Rubio, B., Kiss, G.G., Sarriguren, P., van Isacker, P., de Angelis, G., Recchia, F., Nishimura, S., Agramunt, J., Guadilla, V., Montaner-Pizá, A., Orrigo, S.E.A., Horváth, A., Napoli, D., Lenzi, S., Boso, A., Phong, V.H., Wu, J., Söderström, P.-A., Sumikama, T., Suzuki, H., Takeda, H., Ahn, D.S., Baba, H., Doornebal, P., Fukuda, N., Inabe, N., Isobe, T., Kubo, T., Kubono, S., Sakurai, H., Shimizu, Y., Sidong, C., Blank, B., Ascher, P., Gerbaux, M., Goigoux, T., Giovinazzo, J., Grévy, S., Kurtukián Nieto, T., Magron, C., Gelletly, W., Dombrádi, Zs., Fujita, Y., Tanaka, M., Aguilera, P., Molina, F., Eberth, J., Diel, F., Lubos, D., Borcea, C., Ganioglu, E., Nishimura, D., Oikawa, H., Takei, Y., Yagi, S., Korten, W., de France, G., Davies, P., Liu, J., Lee, J., Lokotko, T., Kojouharov, I., Kurz, N., Shaffner, H., Petrovici, A., Ministry of Innovation and Technology (Hungary), Agencia Nacional de Investigación y Desarrollo (Chile), RIKEN Nishina Center for Accelerator-Based Science, University of Tokyo, Ministerio de Ciencia e Innovación (España), Ministerio de Ciencia, Innovación y Universidades (España), Consejo Superior de Investigaciones Científicas (España), Science and Technology Facilities Council (UK), Ministry of Human Capacities (Hungary), Japan Society for the Promotion of Science, Hungarian Academy of Sciences, Grand Accélérateur National d'Ions Lourds (GANIL), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Centre d'Etudes Nucléaires de Bordeaux Gradignan (CENBG), Université Sciences et Technologies - Bordeaux 1 (UB)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherches sur les lois Fondamentales de l'Univers (IRFU), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay
Subjects: Nuclear and High Energy Physics, QRPA calculations, Kr, Pseudo-SU(4) symmetry, pn pairing, [PHYS.NEXP]Physics [physics]/Nuclear Experiment [nucl-ex], Beta decay of, 70, GT strength distribution, Beta decay of Kr 70 | GT strength distribution | pn pairing | Pseudo-SU(4) symmetry | QRPA calculations
Abstract: 8 pags., 4 figs., 1 tab., The β-decay of the even-even nucleus 70Kr with Z=N+2, has been investigated at the Radioactive Ion Beam Factory (RIBF) of the RIKEN Nishina Center using the BigRIPS fragment separator, the ZeroDegree Spectrometer, the WAS3ABI implantation station and the EURICA HPGe cluster array. Fifteen γ-rays associated with the β-decay of 70Kr into 70Br have been identified for the first time, defining ten populated states below Eexc=3300 keV. The half-life of 70Kr was derived with increased precision and found to be t1/2=45.19±0.14 ms. The β-delayed proton emission probability has also been determined as εp=0.545(23)%. An increase in the β-strength to the yrast 1+ state in comparison with the heaviest Z=N+2 system studied so far (62Ge decay) is observed that may indicate increased np correlations in the T=0 channel. The β-decay strength deduced from the results is interpreted in terms of the proton-neutron quasiparticle random-phase approximation (pnQRPA) and also with a schematic model that includes isoscalar and isovector pairing in addition to quadrupole deformation. The application of this last model indicates an approximate realization of pseudo-SU(4) symmetry in this system., This work was supported by the National Research, Development and Innovation Fund of the Ministry for Innovation and Technology, Hungary with project no. TKP2021-NKTA-42 under the TKP2021 funding scheme. FM acknowledges the support of ANID/FONDECYT Regular 1171467 and ANID/FONDECYT Regular 1221364 national projects. This work was carried out at the RIBF operated by RIKEN Nishina Center and CNS, University of Tokyo. We acknowledge the EUROBALL Owners Committee for the loan of germanium detectors and the PreSpec Collaboration for the readout electronics of the cluster detectors. This work was supported by the Spanish MICINN grants FPA2014-52823-C2-1-P, FPA2017- 83946-C2-1-P (MCIU/AEI/FEDER); Ministerio de Ciencia e Innovación grant PID2019-104714GB-C21; Centro de Excelencia Severo Ochoa del IFIC SEV-2014-0398; Junta para la Ampliación de Estudios Programme (CSIC JAE-Doc contract) co-financed by FSE, by NKFIH (NN128072), the National Research, Development and Innovation Fund of Hungary Project No. K 128729 the STFC (UK) through Grant No. ST/P005314/, the PROMETEO/2019/007 project and by the ÚNKP-20-5-DE-02 New National Excellence Program of the Ministry of Human Capacities of Hungary and by the JSPS KAKENHI of Japan (Grant No. 25247045). G.G. Kiss acknowledges support from the János Bolyai research fellowship of the Hungarian Academy of Sciences. A. A. acknowledges partial support of the JSPS Invitational Fellowships for Research in Japan (ID: L1955) P. S. acknowledges support from MCI/AEI/FEDER,UE (Spain) under grant PGC2018-093636-B-I00.
Published: 2022

27. Genomic Mapping of Splicing-Related Genes Identify Amplifications in LSM1, CLNS1A, and ILF2 in Luminal Breast Cancer

Author: Balázs Győrffy, Vanesa García-Barberán, Alberto Ocaña, María Del Mar Noblejas-López, Miguel de la Hoya, José A. García-Sáenz, Igor López-Cade, Atanasio Pandiella, Pedro Pérez-Segura, Jesús Fuentes-Antrás, Ada Esteban-Sánchez, Gonzalo Fernández-Hinojal, Aránzazu Manzano, Instituto de Salud Carlos III, Acepain Albacete, Fundación CRIS contra el Cáncer, Diputación de Albacete, European Commission, Ministerio de Educación (España), and Ministry of Innovation and Technology (Hungary)
Subjects: Cancer Research, Alternative splicing, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, Biology, medicine.disease, Article, Novel gene, Transcriptome, Breast cancer, luminal breast cancer, Splicing pathway, Luminal breast cancer, Oncology, RNA splicing, splicing pathway, medicine, Cancer research, splice, Epigenetics, BET inhibitors, Gene, RC254-282
Abstract: © 2021 by the authors., Alternative splicing is an essential biological process, which increases the diversity and complexity of the human transcriptome. In our study, 304 splicing pathway-related genes were evaluated in tumors from breast cancer patients (TCGA dataset). A high number of alterations were detected, including mutations and copy number alterations (CNAs), although mutations were less frequently present compared with CNAs. In the four molecular subtypes, 14 common splice genes showed high level amplification in >5% of patients. Certain genes were only amplified in specific breast cancer subtypes. Most altered genes in each molecular subtype clustered to a few chromosomal regions. In the Luminal subtype, amplifications of LSM1, CLNS1A, and ILF2 showed a strong significant association with prognosis. An even more robust association with OS and RFS was observed when expression of these three genes was combined. Inhibition of LSM1, CLNS1A, and ILF2, using siRNA in MCF7 and T47D cells, showed a decrease in cell proliferation. The mRNA expression of these genes was reduced by treatment with BET inhibitors, a family of epigenetic modulators. We map the presence of splicing-related genes in breast cancer, describing three novel genes, LSM1, CLNS1A, and ILF2, that have an oncogenic role and can be modulated with BET inhibitors., A.O.’s lab is supported by the Instituto de Salud Carlos III (ISCIII, PI19/00808); ACEPAIN; CRIS Cancer Foundation and Diputación de Albacete. This research is also supported by PI18/01020 from the Instituto de Salud Carlos III and co-financed by the European Development Regional Fund (FEDER) “A way to achieve Europe” (ERDF); N.L. MDM was supported by the Spanish Ministry of Education (FPU grant; Ref.: FPU18/01319). B.G. was financed by the 2018-2.1.17-TETKR-00001, 2020-1.1.6-JÖVO-2021-00013, and 2018-1.3.1-VKE-2018-00032 grants and by the Higher ˝ Education Institutional Excellence Programme (2020-4.1.1.-TKP2020) of the Ministry for Innovation and Technology in Hungary.
Published: 2021
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28. Effects of climate variation on bird escape distances modulate community responses to global change

Author: Kunter Tätte, Federico Morelli, Anders Pape Møller, Piotr Tryjanowski, Tomáš Grim, Juan Diego Ibáñez-Álamo, Gábor Markó, Manuel A. Diaz, Marja-Liisa Kaisanlahti-Jokimäki, Jukka Jokimäki, Ministry of Innovation and Technology (Hungary), Ministry of Education and Research (Estonia), Agencia Estatal de Investigación (España), and Ministerio de Ciencia e Innovación (España)
Subjects: 0106 biological sciences, 0301 basic medicine, Climate, Climate Change, Ecology (disciplines), media_common.quotation_subject, Science, Population Dynamics, Public administration, 010603 evolutionary biology, 01 natural sciences, Article, Birds, 03 medical and health sciences, Excellence, Agency (sociology), Animals, Humans, Climate variation, Author Correction, media_common, Multidisciplinary, Geography, Ecology, Global change, Estonian, Readability, language.human_language, Environmental sciences, 030104 developmental biology, Institutional research, language, Medicine, Animal Migration, Zoology, Climate sciences
Abstract: Warm thanks to Jacqui Sykoff for substantially improving the readability of former versions of the manuscript. GM was supported by the Hungarian Ministry for Innovation and Technology within the framework of the Thematic Excellence Programme 2020 (TKP2020-IKA-12, TKP2020-NKA-16).. KT was supported by institutional research funding IUT (34-8) of the Estonian Ministry of Education and Research. This paper is a contribution to the project URBILAND (PID2019-107423GA-I00/SRA 1013039/501100011033), funded by the Spanish Research Agency., Climate and land use are rapidly changing environmental conditions. Behavioral responses to such global perturbations can be used to incorporate interspecific interactions into predictive models of population responses to global change. Flight initiation distance (FID) reflects antipredator behaviour defined as the distance at which an individual takes flight when approached by a human, under standardized conditions. This behavioural trait results from a balance between disturbance, predation risk, food availability and physiological needs, and it is related to geographical range and population trends in European birds. Using 32,145 records of flight initiation distances for 229 bird species during 2006-2019 in 24 European localities, we show that FIDs decreased with increasing temperature and precipitation, as expected if foraging success decreased under warm and humid conditions. Trends were further altered by latitude, urbanisation and body mass, as expected if climate effects on FIDs were mediated by food abundance and need, differing according to position in food webs, supporting foraging models. This provides evidence for a role of behavioural responses within food webs on how bird populations and communities are affected by global change., Hungarian Ministry for Innovation and Technology TKP2020-IKA-12 TKP2020-NKA-16, Ministry of Education and Research, Estonia 34-8, Spanish Research Agency PID2019-107423GA-I00/SRA 1013039/501100011033
Published: 2021

29. Mapping of Genomic Vulnerabilities in the Post-Translational Ubiquitination, SUMOylation and Neddylation Machinery in Breast Cancer

Author: Mariona Baliu-Piqué, María Del Mar Noblejas-López, Alberto Ocaña, Balázs Győrffy, Esther Cabañas Morafraile, Vanesa García-Barberán, Eva María Galán-Moya, Pedro Pérez-Segura, Ana Alcaraz-Sanabria, Atanasio Pandiella, Igor López-Cade, Jesús Fuentes-Antrás, Aránzazu Manzano, Instituto de Salud Carlos III, Acepain Albacete, Diputación de Albacete, Fundación CRIS contra el Cáncer, Ministerio de Economía y Competitividad (España), Junta de Castilla y León, Ministry of Innovation and Technology (Hungary), and Semmelweis University
Subjects: 0301 basic medicine, Cancer Research, Estrogen receptor, Gene mutation, medicine.disease_cause, ubiquitination, NEDD8, lcsh:RC254-282, Article, 03 medical and health sciences, 0302 clinical medicine, Breast cancer, neddylation, breast cancer, medicine, Neddylation, Triple-negative breast cancer, business.industry, Ubiquitination, Cancer, biomarkers, medicine.disease, Prognosis, lcsh:Neoplasms. Tumors. Oncology. Including cancer and carcinogens, SUMOylation, 030104 developmental biology, Oncology, post-translational modification, 030220 oncology & carcinogenesis, Cancer research, prognosis, Post-translational modification, Carcinogenesis, business, Biomarkers
Abstract: © 2021 by the authors., The dysregulation of post-translational modifications (PTM) transversally impacts cancer hallmarks and constitutes an appealing vulnerability for drug development. In breast cancer there is growing preclinical evidence of the role of ubiquitin and ubiquitin-like SUMO and Nedd8 peptide conjugation to the proteome in tumorigenesis and drug resistance, particularly through their interplay with estrogen receptor signaling and DNA repair. Herein we explored genomic alterations in these processes using RNA-seq and mutation data from TCGA and METABRIC datasets, and analyzed them using a bioinformatic pipeline in search of those with prognostic and predictive capability which could qualify as subjects of drug research. Amplification of UBE2T, UBE2C, and BIRC5 conferred a worse prognosis in luminal A/B and basal-like tumors, luminal A/B tumors, and luminal A tumors, respectively. Higher UBE2T expression levels were predictive of a lower rate of pathological complete response in triple negative breast cancer patients following neoadjuvant chemotherapy, whereas UBE2C and BIRC5 expression was higher in luminal A patients with tumor relapse within 5 years of endocrine therapy or chemotherapy. The transcriptomic signatures of USP9X and USP7 gene mutations also conferred worse prognosis in luminal A, HER2-enriched, and basal-like tumors, and in luminal A tumors, respectively. In conclusion, we identified and characterized the clinical value of a group of genomic alterations in ubiquitination, SUMOylation, and neddylation enzymes, with potential for drug development in breast cancer., Work in Alberto Ocaña’s lab is supported by the Instituto de Salud Carlos III (ISCIII, PI19/00808); ACEPAIN; Diputación de Albacete; and the CRIS Cancer Foundation. Work in Atanasio Pandiella’s lab is supported by the Ministry of Economy and Competitiveness of Spain (BFU2015- 71371-R, the Junta de Castilla y León (CSI146P20), and the CRIS Foundation. Balázs Györffy is financed by the 2018-2.1.17-TET-KR-00001 grant and by the Higher Education Institutional Excellence Programme of the Ministry for Innovation and Technology (MIT) in Hungary, within the framework of the Bionic thematic programme of the Semmelweis University.
Published: 2021

30. Relativistic first-principles theory of Yu-Shiba-Rusinov states applied to Mn adatoms and Mn dimers on Nb(110)

Author: Bendegúz Nyári, András Lászlóffy, László Szunyogh, Gábor Csire, Kyungwha Park, Balázs Ujfalussy, Ministry of Innovation and Technology (Hungary), Ministerio de Economía y Competitividad (España), European Commission, Ministerio de Ciencia, Innovación y Universidades (España), and Generalitat de Catalunya
Subjects: Korringa-Kohn-Rostoker method, Superconductivity, Magnetic order, Condensed Matter - Superconductivity, FOS: Physical sciences, Bogoliubov-de Gennes equations, 02 engineering and technology, Local density of states, 021001 nanoscience & nanotechnology, 01 natural sciences, Superconducting gap, Superconductivity (cond-mat.supr-con), Surfaces, First-principles calculations, 0103 physical sciences, Impurities in superconductors, Adsorption, Spin-orbit coupling, 010306 general physics, 0210 nano-technology
Abstract: We present a fully relativistic first-principles-based theoretical approach for the calculation of the spectral properties of magnetic impurities on the surface of a superconducting substrate, providing a material specific framework for the investigation of the Yu-Shiba-Rusinov (YSR) states. By using a suitable orbital decomposition of the local densities of states we discuss in great detail the formation of the YSR states for an Mn adatom and for two kinds of Mn dimers placed on the Nb(110) surface and compare our results to recent experimental findings. In the case of the adatom we find that the spin-orbit coupling slightly shifts some of the YSR peaks and also the local spin polarization on the Nb atoms has marginal effects on their positions. Moreover, by scaling the exchange field on the Mn site we could explain the lack of the dx2−y2-like YSR state in the spectrum. While our results for a close packed ferromagnetic dimer are in satisfactory agreement with the experimentally observed splitting of the YSR states, in the case of an antiferromagnetic dimer we find that the spin-orbit coupling is not sufficiently large to explain the splitting of the YSR states seen in the experiment. Changing the relative orientation of the magnetic moments in this dimer induces splitting of the YSR states and also shifts their energy, leading even to the formation of a zero bias peak in the case of the deepest YSR state., Among the authors B.N., A.L., L.S., and B.U. are grateful for the financial support by the Ministry for Innovation and Technology and the National Research, Development and Innovation Office under Project No. K131938 and within the Quantum Information National Laboratory of Hungary. B.N. is also grateful for the support of ÚNKP-20-3-II-BME-249 New National Excellence Program of the Ministry for Innovation and Technology of Hungary. G.C. gratefully acknowledges support from the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 754510. This work was supported by Spanish MINECO (the Severo Ochoa Centers of Excellence Program under Grant No. SEV- 2017-0706), Spanish MICIU, AEI and EU FEDER (Grant No. PGC2018-096955-B-C43), and Generalitat de Catalunya (Grant No. 2017SGR1506 and the CERCA Program). The work was also supported by the European Union MaX Center of Excellence (EU-H2020 Grant No. 824143).
Published: 2021
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31. Fungal Planet description sheets:1284-1382

Author: Crous, Pedro Willem, Osieck, Eduard R., Jurjević, Ž., Boers, J., Iperen, A.L., Starink-Willemse, M., Dima, B., Balashov, S., Bulgakov, T.S., Johnston, P.R., Morozova, O.V., Pinruan, U., Sommai, S., Alvarado, P., Decock, C.A., Lebel, T., McMullan-Fisher, S., Moreno, G., Shivas, R.G., Zhao, L., Abdollahzadeh, J., Abrinbana, M., Ageev, D.V., Akhmetova, G., Alexandrova, A.V., Altés, A., Amaral, A.G.G., Angelini, C., Antonín, Vladimír, Arenas, F., Asselman, P., Badali, F., Baghela, A., Banares, Á., Barreto, R.W., Baseia, I.G., Bellanger, J.-M., Berraf-Tebbal, A., Biketova, A. Yu., Bukharova, N.V., Burgess, T.I., Cabero, J., Câmara, M.P.S., Cano-Lira, J.F., Ceryngier, P., Chávez, R., Cowan, D.A., de Lima, A.F., Oliveira, R.L., Denman, S., Dang, Q.N., Dovana, F., Duarte, I.G., Eichmeier, A., Erhard, A., Esteve-Raventós, F., Fellin, A., Ferisin, G., Ferreira, R.J., Ferrer, A., Finy, P., Gaya, E., Geering, A.D.W., Gil-Durán, C., Glässnerová, K., Glushakova, A.M., Gramaje, D., Guard, F.E., Guarnizo, A.L., Haelewaters, D., Halling, R.E., Hill, R., Hirooka, Y., Hubka, V., Iliushin, V.A., Ivanova, D.D., Ivanushkina, N.E., Jangsantear, P., Justo, A., Kachalkin, A.V., Kato, S., Khamsuntorn, P., Kirtsideli, I.Y., Knapp, D.G., Kochkina, G.A., Koukol, O., Kovács, G.M., Kruse, J., Kumar, T.K.A., Kušan, I., Læssøe, T., Larsson, E., Lebeuf, R., Levicán, G., Loizides, M., Marinho, P., Luangsa-ard, J.J., Lukina, E.G., Magaña-Dueñas, V., Maggs-Kölling, G., Malysheva, E.F., Malysheva, V.F., Martín, B., Martín, M.P., Matočec, N., McTaggart, A.R., Mehrabi-Koushki, M., Mešić, A., Miller, A.N., Mironova, P., Moreau, Pierre-Arthur, Morte, A., Müller, K., Nagy, L.G., Nanu, S., Navarro-Ródenas, A., Nel, W.J., Nguyen, T.H., Nóbrega, T.F., Noordeloos, Machiel E., Olariaga, I., Overton, B.E., Ozerskaya, S.M., Palani, P., Pancorbo, F., Papp, V., Pawłowska, J., Pham, T.Q., Phosri, C., Popov, E.S., Portugal, A., Pošta, A., Reschke, K., Reul, M., Ricci, G.M., Rodríguez, A., Romanowski, J., Ruchikachorn, N., Saar, I., Safi, A., Sakolrak, B., Salzmann, F., Sandoval-Denis, M., Sangwichein, E., Sanhueza, L., Sato, T., Sastoque, A., Senn-Irlet, Beatrice, Shibata, A., Siepe, K., Somrithipol, S., Spetik, M., Sridhar, P., Stchigel, A.M., Stuskova, K., Suwannasai, N., Tan, Y.P., Thangavel, R., Tiago, I., Tiwari, S., Tkalčec, Z., Tomashevskaya, M.A., Tonegawa, C., Tran, H.X., Tran, N.T., Trovão, J., Trubitsyn, V.E., Van Wyk, J., Vieira, W.A.S., Vila, J., Visagie, C.M., Vizzini, A., Volobuev, S.V., Vu, D., Wangsawat, N., Yaguchi, T., Ercole, E., Ferreira, B.W., de Souza, A.P., Vieira, B.S., Groenewald, J.Z., Westerdijk Fungal Biodiversity Institute, Westerdijk Fungal Biodiversity Institute - Evolutionary Phytopathology, Westerdijk Fungal Biodiversity Institute - Collection, Ministry of Business, Innovation, and Employment (New Zealand), Ministry of Health of the Czech Republic, Japan Society for the Promotion of Science, Charles University (Czech Republic), European Commission, Fundação para a Ciência e a Tecnologia (Portugal), Ministério da Ciência, Tecnologia e Ensino Superior (Portugal), Research Foundation - Flanders, Russian Science Foundation, Lomonosov Moscow State University, Kerala State Council for Science, Technology and Environment, Universidad de Alcalá, Ministry of Innovation and Technology (Hungary), National Research, Development and Innovation Office (Hungary), Hungarian Academy of Sciences, Agencia Nacional de Investigación y Desarrollo (Chile), Ministerio de Ciencia, Tecnología, Conocimiento e Innovación (Chile), Fondo Nacional de Desarrollo Científico y Tecnológico (Chile), Estonian Research Council, Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brasil), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (Brasil), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Swedish Taxonomy Initiative, Australian Biological Resources Study, Croatian Science Foundation, Fundación Séneca, National Science Foundation (US), New York Botanical Garden, National Science Centre (Poland), Russian Academy of Sciences, and Naturalis journals & series
Subjects: new species, ITS nrDNA barcodes, LSU, Ecology, Evolution, TAXA, Biology and Life Sciences, SMALL CONIDIA, IQ-TREE, BAYESIAN PHYLOGENETIC INFERENCE, new taxa, ASPERGILLUS SECTION FUMIGATI, taxonomy, MULTIPLE SEQUENCE ALIGNMENT, GENUS, Behavior and Systematics, systematics, SP-NOV, NATURAL CLASSIFICATION, GENERA, Ecology, Evolution, Behavior and Systematics
Abstract: Novel species of fungi described in this study include those from various countries as follows: Antartica, Cladosporium austrolitorale from coastal sea sand. Australia, Austroboletus yourkae on soil, Crepidotus innuopurpureus on dead wood, Curvularia stenotaphri from roots and leaves of Stenotaphrum secundatum and Thecaphora stajsicii from capsules of Oxalis radicosa. Belgium, Paraxerochrysium coryli (incl. Paraxerochrysium gen. nov.) from Corylus avellana. Brazil, Calvatia nordestina on soil, Didymella tabebuiicola from leaf spots on Tabebuia aurea, Fusarium subflagellisporum from hypertrophied floral and vegetative branches of Mangifera indica and Microdochium maculosum from living leaves of Digitaria insularis. Canada, Cuphophyllus bondii fromagrassland. Croatia, Mollisia inferiseptata from a rotten Laurus nobilis trunk. Cyprus, Amanita exilis oncalcareoussoil. Czech Republic, Cytospora hippophaicola from wood of symptomatic Vaccinium corymbosum. Denmark, Lasiosphaeria deviata on pieces of wood and herbaceousdebris. Dominican Republic, Calocybella goethei among grass on a lawn. France (Corsica) , Inocybe corsica onwetground. France (French Guiana) , Trechispora patawaensis on decayed branch of unknown angiosperm tree and Trechispora subregularis on decayed log of unknown angiosperm tree. [...], P.R. Johnston thanks J. Sullivan (Lincoln University) for the habitat image of Kowai Bush, Duckchul Park (Manaaki Whenua – Landcare Research) for the DNA sequencing, and the New Zealand Department of Conservation for permission to collect the specimens; this research was supported through the Manaaki Whenua – Landcare Research Biota Portfolio with funding from the Science and Innovation Group of the New Zealand Ministry of Business, Innovation and Employment. V. Hubka was supported by the Czech Ministry of Health (grant number NU21-05-00681), and is grateful for the support from the Japan Society for the Promotion of Science – grant-in-aid for JSPS research fellow (grant no. 20F20772). K. Glässnerová was supported by the Charles University Grant Agency (grant No. GAUK 140520). J. Trovão and colleagues were financed by FEDERFundo Europeu de Desenvolvimento Regional funds through the COMPETE 2020 – Operational Programme for Competitiveness and Internationalisation (POCI), and by Portuguese funds through FCT – Fundação para a Ciência e a Tecnologia in the framework of the project POCI-01-0145-FEDER-PTDC/ EPH-PAT/3345/2014. This work was carried out at the R&D Unit Centre for Functional Ecology – Science for People and the Planet (CFE), with reference UIDB/04004/2020, financed by FCT/MCTES through national funds (PIDDAC). J. Trovão was also supported by POCH – Programa Operacional Capital Humano (co-funding by the European Social Fund and national funding by MCTES), through a ‘FCT – Fundação para a Ciência e Tecnologia’ PhD research grant (SFRH/BD/132523/2017). D. Haelewaters acknowledges support from the Research Foundation – Flanders (Junior Postdoctoral Fellowship 1206620N). M. Loizides and colleagues are grateful to Y. Cherniavsky for contributing collections AB A12-058-1 and AB A12- 058-2, and Á. Kovács and B. Kiss for their help with molecular studies of these specimens. C. Zmuda is thanked for assisting with the collection of ladybird specimens infected with Hesperomyces parexochomi. A.V. Kachalkin and colleagues were supported by the Russian Science Foundation (grant No. 19-74-10002). The study of A.M. Glushakova was carried out as part of the Scientific Project of the State Order of the Government of Russian Federation to Lomonosov Moscow State University No. 121040800174-6. S. Nanu acknowledges the Kerala State Council for Science, Technology and Environment (KSCSTE) for granting a research fellowship and is grateful to the Chief Conservator of Forests and Wildlife for giving permission to collect fungal samples. A. Bañares and colleagues thank L. Monje and A. Pueblas of the Department of Drawing and Scientific Photography at the University of Alcalá for their help in the digital preparation of the photographs, and J. Rejos, curator of the AH herbarium for his assistance with the specimens examined in the present study. The research of V. Antonín received institutional support for long-term conceptual development of research institutions provided by the Ministry of Culture (Moravian Museum, ref. MK000094862). The studies of E.F. Malysheva, V.F. Malysheva, O.V. Morozova, and S.V. Volobuev were carried out within the framework of a research project of the Komarov Botanical Institute RAS, St Petersburg, Russia (АААА-А18-118022090078-2) using equipment of its Core Facility Centre ‘Cell and Molecular Technologies in Plant Science’.The study of A.V. Alexandrova was carried out as part of the Scientific Project of the State Order of the Government of Russian Federation to Lomonosov Moscow State University No. 121032300081-7. The Kits van Waveren Foundation (Rijksherbariumfonds Dr E. Kits van Waveren, Leiden, Netherlands) contributed substantially to the costs of sequencing and travelling expenses for M.E. Noordeloos. The work of B. Dima was partly supported by the ÚNKP- 20-4 New National Excellence Program of the Ministry for Innovation and Technology from the source of the National Research, Development and Innovation Fund. The work of L. Nagy was supported by the ‘Momentum’ program of the Hungarian Academy of Sciences (contract No. LP2019- 13/2019 to L.G.N.). G.A. Kochkina and colleagues acknowledge N. Demidov for the background photograph, and N. Suzina for the SEM photomicrograph. The research of C.M. Visagie and W.J. Nel was supported by the National Research Foundation grant no 118924 and SFH170610239162. C. Gil-Durán acknowledges Agencia Nacional de Investigación y Desarrollo, Ministerio de Ciencia, Tecnología, Conocimiento e Innovación, Gobierno de Chile, for grant ANID – Fondecyt de Postdoctorado 2021 – N° 3210135. R. Chávez and G. Levicán thank DICYT-USACH and acknowledges the grants INACH RG_03-14 and INACH RT_31-16 from the Chilean Antarctic Institute, respectively. S. Tiwari and A. Baghela would like to acknowledge R. Avchar and K. Balasubramanian from the Agharkar Research Institute, Pune, Maharashtra for helping with the termite collection. S. Tiwari is also thankful to the University Grants Commission, Delhi (India) for a junior research fellowship (827/(CSIR-UGC NET DEC.2017)). R. Lebeuf and I. Saar thank D. and H. Spencer for collecting and photographing the holotype of C. bondii, and R. Smith for photographing the habitat. A. Voitk is thanked for helping with the colour plate and review of the manuscript, and the Foray Newfoundland and Labrador for providing the paratype material. I. Saar was supported by the Estonian Research Council (grant PRG1170) and the European Regional Development Fund (Centre of Excellence EcolChange). M.P.S. Câmara acknowledges the ‘Conselho Nacional de Desenvolvimento Científico e Tecnológico – CNPq’ for the research productivity fellowship, and financial support (Universal number 408724/2018-8). W.A.S. Vieira acknowledges the ‘Coordenação de Aperfeiçoamento Pessoal de Ensino Superior – CAPES’ and the ‘Programa Nacional de Pós-Doutorado/CAPES – PNPD/CAPES’ for the postdoctoral fellowship. A.G.G. Amaral acknowledges CNPq, and A.F. Lima and I.G. Duarte acknowledge CAPES for the doctorate fellowships. F. Esteve-Raventós and colleagues were financially supported by FEDER/ Ministerio de Ciencia, Innovación y Universidades – Agencia Estatal de Investigación (Spain)/ Project CGL2017-86540-P. The authors would like to thank L. Hugot and N. Suberbielle (Conservatoire Botanique National de Corse, Office de l’Environnement de la Corse, Corti) for their help. The research of E. Larsson is supported by The Swedish Taxonomy Initiative, SLU Artdatabanken, Uppsala. Financial support was provided to R.J. Ferreira by the National Council for Scientific and Technological Development (CNPq), and to I.G. Baseia, P.S.M. Lúcio and M.P. Martín by the National Council for Scientific and Technological Development (CNPq) under CNPq-Universal 2016 (409960/2016-0) and CNPq-visiting researcher (407474/2013-7). J. Cabero and colleagues wish to acknowledge A. Rodríguez for his help to describe Genea zamorana, as well as H. Hernández for sharing information about the vegetation of the type locality. S. McMullan-Fisher and colleagues acknowledge K. Syme (assistance with illustrations), J. Kellermann (translations), M. Barrett (collection, images and sequences), T. Lohmeyer (collection and images) and N. Karunajeewa (for prompt accessioning). This research was supported through funding from Australian Biological Resources Study grant (TTC217-06) to the Royal Botanic Gardens Victoria. The research of M. Spetik and co-authors was supported by project No. CZ.02.1.01/0.0/0.0 /16_017/0002334. N. Wangsawat and colleagues were partially supported by NRCT and the Royal Golden Jubilee Ph.D. programme, grant number PHD/0218/2559. They are thankful to M. Kamsook for the photograph of the Phu Khiao Wildlife Sanctuary and P. Thamvithayakorn for phylogenetic illustrations. The study by N.T. Tran and colleagues was funded by Hort Innovation (Grant TU19000). They also thank the turf growers who supported their surveys and specimen collection. N. Matočec, I. Kušan, A. Pošta, Z. Tkalčec and A. Mešić thank the Croatian Science Foundation for their financial support under the project grant HRZZ-IP-2018-01-1736 (ForFungiDNA). A. Pošta thanks the Croatian Science Foundation for their support under the grant HRZZ-2018-09-7081. A. Morte is grateful to Fundación Séneca – Agencia de Ciencia y Tecnología de la Región de Murcia (20866/ PI/18) for financial support. The research of G. Akhmetova, G.M. Kovács, B. Dima and D.G. Knapp was supported by the National Research, Development and Innovation Office, Hungary (NKFIH KH-130401 and K-139026), the ELTE Thematic Excellence Program 2020 supported by the National Research, Development and Innovation Office (TKP2020-IKA-05) and the Stipendium Hungaricum Programme. The support of the János Bolyai Research Scholarship of the Hungarian Academy of Sciences and the Bolyai+ New National Excellence Program of the Ministry for Innovation and Technology to D.G. Knapp is highly appreciated. F.E. Guard and colleagues are grateful to the traditional owners, the Jirrbal and Warungu people, as well as L. and P. Hales, Reserve Managers, of the Yourka Bush Heritage Reserve. Their generosity, guidance, and the opportunity to explore the Bush Heritage Reserve on the Einasleigh Uplands in far north Queensland is greatly appreciated. The National Science Foundation (USA) provided funds (DBI#1828479) to the New York Botanical Garden for a scanning electron microscope used for imaging the spores. V. Papp was supported by the ÚNKP-21-5 New National Excellence Program of the Ministry for Innovation and Technology from the National Research, Development and Innovation Fund of Hungary. A.N. Miller thanks the WM Keck Center at the University of Illinois Urbana – Champaign for sequencing Lasiosphaeria deviata. J. Pawłowska acknowledges support form National Science Centre, Poland (grant Opus 13 no 2017/25/B/NZ8/00473). The research of T.S. Bulgakov was carried out as part of the State Research Task of the Subtropical Scientific Centre of the Russian Academy of Sciences (Theme No. 0492-2021- 0007). K. Bensch (Westerdijk Fungal Biodiversity Institute, Utrecht) is thanked for correcting the spelling of various Latin epithets.
Published: 2021

32. Top ten birds indicators of high environmental quality in European cities

Author: Piotr Tryjanowski, Jukka Jokimäki, Raphaël Bussière, Nikos Bukas, Leszek Jerzak, Antonia Galanaki, Juan Diego Ibáñez-Álamo, Federico Morelli, Marja-Liisa Kaisanlahti-Jokimäki, Anders Pape Møller, Theodoros Kominos, Mario Díaz, Jukka Suhonen, Gábor Markó, Jiri Reif, Fabio Pruscini, Olaf Ciebiera, Marko Mägi, Yanina Benedetti, Czech Science Foundation, Ministerio de Ciencia e Innovación (España), Ministry of Innovation and Technology (Hungary), Agencia Estatal de Investigación (España), and Charles University (Czech Republic)
Subjects: Environmental quality, Urban trees, Sparrow, biology, Ecology, Bird species richness, Biodiversity, Light pollution, General Decision Sciences, Conservation, Ecological indicator, Urban bird diversity, Geography, Habitat, Common species, biology.animal, Greenery, Indicator value, Ecology, Evolution, Behavior and Systematics, QH540-549.5
Abstract: We are grateful to Vojt.ech Brlik and all people who helped observers during the fieldwork in the 15 European cities. F.M., Y.B. and J.R. were financially supported by the Czech Science Foundation GA.CR (project number 18-16738S). J.D.I.A. and M.D. were funded by the Spanish Ministry of Science and Innovation (PID2019-107423GA-I00/SRA State Research Agency/10.13039/501100011033). G.M. was supported by the Hungarian Ministry for Innovation and Technology within the framework of the Thematic Excellence Programme 2020 (TKP2020-IKA12, TKP2020-NKA-16). J.R. was supported by Charles University (PRIMUS/17/SCI/16)., Urban and suburban areas are among the fastest-growing land-use types globally, reducing and fragmenting natural habitats for many animal species and making human-wildlife interactions more common. However, cities also create habitat for several species considered urban tolerant or urban exploiter species. Additionally, the environmental characteristics of urban areas can strongly affect the life quality of citizens. This study aimed to assess the effectiveness of common bird species as indicators of urban areas with high environmental quality within cities. Our study recorded 128 bird species in 1441 point counts distributed in fifteen different European cities. We classified urban areas as “high environmental quality” – HEQ when they were simultaneously characterized by a high vegetation cover and heterogeneity, low level of light pollution, and avian communities with high potential resilience to face ecological stress. Species indicators of HEQ urban areas were identified using the species-level indicator value (IndVal) analysis. Such species can be used as ecological indicators of HEQ in different European cities. The list of top ten birds indicators of HEQ in European cities is led by the Eurasian blackcap, selected as an indicator in more than half of the survey cities. Other birds indicators of HEQ in multiple cities are Blackbird (47%), Great tit (40%), Blue tit, Tree sparrow and Magpie (all 33%). The mean specificity of the top-ranked bird indicator of HEQ urban areas (Eurasian blackcap) was 0.778. Most of the HEQ-indicators are resident or resident/short migratory species characterized by territorial behaviour. Our findings support using multiple species as bioindicators of urban changes by using specific groups with few common species as surrogates of HEQ urban areas. The approach proposed in this study can be applied in different European cities to monitor biodiversity status periodically, even involving citizen science initiatives., Grant Agency of the Czech Republic 18-16738S, Spanish Government PID2019-107423GA-I00/SRA, Hungarian Ministry for Innovation and Technology TKP2020-IKA12 TKP2020-NKA-16, Charles University PRIMUS/17/SCI/16
Published: 2021

33. Argonaute 2 Controls Antiviral Activity against Sweet Potato Mild Mottle Virus in Nicotiana benthamiana

Author: László Orosz, Lóránt Lakatos, József Burgyán, Juan José López-Moya, Erzsébet Kenesi, Ministry of Innovation and Technology (Hungary), Generalitat de Catalunya, Ministerio de Economía y Competitividad (España), Agencia Estatal de Investigación (España), Ministerio de Ciencia e Innovación (España), European Commission, and Ministerio de Ciencia, Innovación y Universidades (España)
Subjects: 0106 biological sciences, 0301 basic medicine, AGO1, AGO2, viruses, Mutant, Nicotiana benthamiana, Plant Science, 01 natural sciences, 03 medical and health sciences, microRNA, Gene silencing, Ecology, Evolution, Behavior and Systematics, Messenger RNA, Ecology, biology, Sweet potato mild mottle virus, fungi, Botany, food and beverages, Argonaute, sweet potato mild mottle virus, biology.organism_classification, Virology, RNA silencing, 030104 developmental biology, QK1-989, 010606 plant biology & botany
Abstract: This article belongs to the Special Issue Plant Defense Responses against Viruses., RNA silencing is a sequence specific post-transcriptional mechanism regulating important biological processes including antiviral defense in plants. Argonaute (AGO) proteins, the catalytic subunits of the silencing complexes, are loaded with small RNAs to execute the sequence specific RNA cleavage or translational inhibition. Plants encode several AGO proteins and a few of them, especially AGO1 and AGO2, have been shown to be required for antiviral silencing. Previously, we have shown that the P1 protein of the sweet potato mild mottle virus (SPMMV) suppresses the primary RNA silencing response by inhibiting AGO1. To analyze the role of AGO2 in antiviral defense against the SPMMV, we performed a comparative study using a wild type and ago2−/− mutant Nicotiana benthamiana. Here we show that the AGO2 of N. benthamiana attenuates the symptoms of SPMMV infection. Upon SPMMV infection the levels of AGO2 mRNA and protein are greatly increased. Moreover, we found that AGO2 proteins are loaded with SPMMV derived viral small RNAs as well as with miRNAs. Our results indicate that AGO2 protein takes over the place of AGO1 to confer antiviral silencing. Finally, we provide a plausible explanation for the AGO2 mediated recovery of an SPMMV-infected sweet potato., This study was supported by grants of the Hungarian Ministry of Technology and Innovation by grant numbers GINOP-2.3.2-15-2016-00015 and GINOP-2.3.2-15-2016-00032). Additional financial support at CRAG was provided by Generalitat de Catalunya CERCA institution and by the Ministry of Science and Innovation-State Research Agency (AEI, Spain) through the “Severo Ochoa Programme for Centres of Excellence in R&D” SEV-2015-0533 and CEX2019-000902-S and the grant PID2019-105692RB-100 to JLM.
Published: 2021

34. Coevolution between MHC Class I and Antigen-Processing Genes in Salamanders

Author: Elizabeth L. Jockusch, Iñigo Martínez-Solano, Judit Vörös, Katarzyna Dudek, Magdalena Migalska, G. Francesco Ficetola, Jan W. Arntzen, Wiesław Babik, H. Bradley Shaffer, Gemma Palomar, Masatoshi Matsunami, Dušan Jelić, Ben Wielstra, Bruce Waldman, National Science Centre (Poland), University of Connecticut, Japan Society for the Promotion of Science, Ministry of Innovation and Technology (Hungary), National Research Foundation of Korea, Ministerio de Ciencia e Innovación (España), and Kim Yuseob
Subjects: antigen-processing genes, Major histocompatibility complex, Urodela, chemical and pharmacologic phenomena, Biology, AcademicSubjects/SCI01180, MHC class I, Genetics, Animals, Gene family, comparative methods, Molecular Biology, Gene, Discoveries, Ecology, Evolution, Behavior and Systematics, Coevolution, Antigen-processing genes, Mammals, Antigen Presentation, Antigen processing, Histocompatibility Antigens Class I, Haplotype, AcademicSubjects/SCI01130, Comparative methods, major histocompatibility complex, Evolutionary biology, Multigene Family, Vertebrates, coevolution, biology.protein, TAP1
Abstract: Proteins encoded by antigen-processing genes (APGs) provide major histocompatibility complex (MHC) class I (MHC-I) with antigenic peptides. In mammals, polymorphic multigenic MHC-I family is served by monomorphic APGs, whereas in certain nonmammalian species both MHC-I and APGs are polymorphic and coevolve within stable haplotypes. Coevolution was suggested as an ancestral gnathostome feature, presumably enabling only a single highly expressed classical MHC-I gene. In this view coevolution, while optimizing some aspects of adaptive immunity, would also limit its flexibility by preventing the expansion of classical MHC-I into a multigene family. However, some nonmammalian taxa, such as salamanders, have multiple highly expressed MHC-I genes, suggesting either that coevolution is relaxed or that it does not prevent the establishment of multigene MHC-I. To distinguish between these two alternatives, we use salamanders (30 species from 16 genera representing six families) to test, within a comparative framework, a major prediction of the coevolution hypothesis: the positive correlation between MHC-I and APG diversity. We found that MHC-I diversity explained both within-individual and species-wide diversity of two APGs, TAP1 and TAP2, supporting their coevolution with MHC-I, whereas no consistent effect was detected for the other three APGs (PSMB8, PSMB9, and TAPBP). Our results imply that although coevolution occurs in salamanders, it does not preclude the expansion of the MHC-I gene family. Contrary to the previous suggestions, nonmammalian vertebrates thus may be able to accommodate diverse selection pressures with flexibility granted by rapid expansion or contraction of the MHC-I family, while retaining the benefits of coevolution between MHC-I and TAPs., The work was supported by the Polish National Science Centre (Grant No. 2016/23/B/NZ8/00738) to W.B. D.J. was supported by PROTEUS project in Croatia; E.J. was supported by the University of Connecticut Research Foundation; M.Ma. was supported by a KAKENHI Grant-in-Aid for Young Scientists (B) (No. JP16K18613) from the Japan Society for the Promotion of Science; M.Mi. was supported by the Foundation for Polish Science (FNP) START stipend and the Polish National Science Centre Sonatina 3 (Grant No. 2019/32/C/NZ8/00440); J.V. was supported by Project No. KH130360 implemented with the support provided from the National Research, Development and Innovation Fund of Hungary, financed under the KH_18 funding scheme; B.Wa. was funded by the National Research Foundation of Korea (Ministry of Education, 2015R1D1A01057282); Ministry of Science, ICT, and Future Planning (2018R1A2B6006833).
Published: 2021

35. Fungal Planet description sheets: 1182–1283

Author: Akila Berraf-Tebbal, Johannes Z. Groenewald, Neriman Yilmaz, J. Vauras, J. Vila, P. Nodet, S. Balashov, S. Di Piazza, Teun Boekhout, J. D. Reyes, D. Kurose, Jose G. Maciá-Vicente, Thomas S. Marney, A. E. Mahamedi, Milan Špetík, Suzanne Rooney-Latham, J. Jennifer Luangsa-ard, Francisco Arenas, G. Le Floch, Yu Pei Tan, T. T. T. Nguyen, W. Noisripoom, Ivan V. Zmitrovich, Ellen Larsson, Teresa Iturriaga, Jorinde Nuytinck, A. Rodríguez, C. L. Blomquist, A. Yu. Biketova, Z. G. Abad, Gabriel Moreno, M.Th. Smith, S. Lad, Abdul Nasir Khalid, G. Delgado, Halina Galera, A. Naseer, N. Ashtekar, Asunción Morte, Thomas Læssøe, James H. Cunnington, A. Polhorský, Mikael Jeppson, I. Bera, Cobus M. Visagie, A. Mateos, Lorenzo Lombard, Michael J. Wingfield, V. Ostrý, D. A. Cowan, A. V. Alexandrova, J. Pecenka, A. Ghosh, T. H. G. Pham, M. V. D. Vegte, Á Bañares, Armin Mešić, John Dearnaley, M. A. Tomashevskaya, Łukasz Istel, D. Szabóová, Ivona Kautmanová, A. Desantiago, Annemieke Verbeken, Jos Houbraken, Bálint Dima, J. A. Abad, J. S. Vitelli, L. W. S. De Freitas, Claudia K. Gunsch, N. Davoodian, Ulrike Damm, H. B. Lee, D.E. Gouliamova, Alena Kubátová, Treena I. Burgess, Andrew N. Miller, D. G. Holdom, E. F. Malysheva, J. B. Jordal, David Gramaje, Angus J. Carnegie, Aleš Eichmeier, Alfonso Navarro-Ródenas, A. Giraldo, F. Fuljer, T. V. Steinrucken, K. Reschke, S. Bishop-Hurley, G. Anand, A. M. Glushakova, Levente Kiss, J. E. Ntandu, M. Lynch, Kunjithapatham Dhileepan, Suchada Mongkolsamrit, E. J. Van Der Linde, V. I. Kapitonov, Machiel E. Noordeloos, L. B. Kalinina, A. Pošta, G. Corriol, Reza Mostowfizadeh-Ghalamfarsa, Roger G. Shivas, T. M. Bulyonkova, Ernest Lacey, A. Sharma, Tor Erik Brandrud, Marta Wrzosek, Julia Pawłowska, Zdenko Tkalčec, Marcelo Sandoval-Denis, E. A. Zvyagina, J. F. Cobo-Diaz, Aleksey V. Kachalkin, T. A. Pankratov, Raja Thangavel, M. O. Da Cruz, S. V. Volobuev, I. Kusan, Jolanda Roux, Kunhiraman C. Rajeshkumar, O.V. Morozova, A. Weill, Viktor Papp, Marizeth Groenewald, Roumen Dimitrov, Željko Jurjević, G. M. Jansen, S. Fatima, Munazza Kiran, M. Romero, Michał Gorczak, D. Boertmann, Pedro W. Crous, Tatyana Yu. Svetasheva, Vit Hubka, Neven Matočec, A. Gutiérrez, D. B. Raudabaugh, A. B. Ismailov, Riccardo Baroncelli, Pablo Alvarado, V. F. Malysheva, Á Kovács, G. Maggs-Kölling, Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brasil), Fundação de Amparo à Ciência e Tecnologia do Estado de Pernambuco, Russian Foundation for Basic Research, Russian Academy of Sciences, Swedish Taxonomy Initiative, German Research Foundation, LOEWE Center for Insect Biotechnology & Bioresources, Russian Government, Lomonosov Moscow State University, Ministry of Science and Higher Education of the Russian Federation, University of Warsaw, European Commission, Hemvati Nandan Bahuguna Garhwal University, Russian Science Foundation, Rural Industries Research and Development Corporation (Australia), Department of Agriculture and Water Resources (Australia), Croatian Science Foundation, Department of Science and Technology (India), International Centre for Genetic Engineering and Biotechnology, Bulgarian National Science Fund, Universidad de Alcalá, Charles University (Czech Republic), Ministry of Agriculture of the Czech Republic, Ministry of Innovation and Technology (Hungary), National Research, Development and Innovation Office (Hungary), Norwegian Biodiversity Information Centre, University of Oslo, Ministerio de Economía y Competitividad (España), Fundación Séneca, Ministry of Health of the Czech Republic, Evolutionary and Population Biology (IBED, FNWI), Laboratoire Universitaire de Biodiversité et Ecologie Microbienne (LUBEM), Université de Brest (UBO), Westerdijk Fungal Biodiversity Institute - Evolutionary Phytopathology, Westerdijk Fungal Biodiversity Institute, Westerdijk Fungal Biodiversity Institute - Yeast Research, Westerdijk Fungal Biodiversity Institute - Collection, Westerdijk Fungal Biodiversity Institute - Food and Indoor Mycology, Crous P.W., Cowan D.A., Maggs-Kolling G., Yilmaz N., Thangavel R., Wingfield M.J., Noordeloos M.E., Dima B., Brandrud T.E., Jansen G.M., Morozova O.V., Vila J., Shivas R.G., Tan Y.P., Bishop-Hurley S., Lacey E., Marney T.S., Larsson E., Le Floch G., Lombard L., Nodet P., Hubka V., Alvarado P., Berraf-Tebbal A., Reyes J.D., Delgado G., Eichmeier A., Jordal J.B., Kachalkin A.V., Kubatova A., Macia-Vicente J.G., Malysheva E.F., Papp V., Rajeshkumar K.C., Sharma A., Spetik M., Szaboova D., Tomashevskaya M.A., Abad J.A., Abad Z.G., Alexandrova A.V., Anand G., Arenas F., Ashtekar N., Balashov S., Banares A., Baroncelli R., Bera I., Yu. Biketova A., Blomquist C.L., Boekhout T., Boertmann D., Bulyonkova T.M., Burgess T.I., Carnegie A.J., Cobo-Diaz J.F., Corriol G., Cunnington J.H., Da Cruz M.O., Damm U., Davoodian N., Desantiago A., Dearnaley J., De Freitas L.W.S., Dhileepan K., Dimitrov R., Di Piazza S., Fatima S., Fuljer F., Galera H., Ghosh A., Giraldo A., Glushakova A.M., Gorczak M., Gouliamova D.E., Gramaje D., Groenewald M., Gunsch C.K., Gutierrez A., Holdom D., Houbraken J., Ismailov A.B., Istel L., Iturriaga T., Jeppson M., Jurjevic Z., Kalinina L.B., Kapitonov V.I., Kautmanova I., Khalid A.N., Kiran M., Kiss L., Kovacs A., Kurose D., Kusan I., Lad S., Laessoe T., Lee H.B., Luangsa-Ard J.J., Lynch M., Mahamedi A.E., Malysheva V.F., Mateos A., Matocec N., Mesic A., Miller A.N., Mongkolsamrit S., Moreno G., Morte A., Mostowfizadeh-Ghalamfarsa R., Naseer A., Navarro-Rodenas A., Nguyen T.T.T., Noisripoom W., Ntandu J.E., Nuytinck J., Ostry V., Pankratov T.A., Pawlowska J., Pecenka J., Pham T.H.G., Polhorsky A., Posta A., Raudabaugh D.B., Reschke K., Rodriguez A., Romero M., Rooney-Latham S., Roux J., Sandoval-Denis M., Smith M.Th., Steinrucken T.V., Svetasheva T.Y., Tkalcec Z., Van Der Linde E.J., Vegte M.V.D., Vauras J., Verbeken A., Visagie C.M., Vitelli J.S., Volobuev S.V., Weill A., Wrzosek M., Zmitrovich I.V., Zvyagina E.A., and Groenewald J.Z.
Subjects: 0106 biological sciences, Zoology and botany: 480 [VDP], 01 natural sciences, BLACK FUNGI, 030308 mycology & parasitology, MULTIPLE SEQUENCE ALIGNMENT, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, 2. Zero hunger, 0303 health sciences, Rhizosphere, LSU, biology, Ecology, SPECIES-DIVERSITY, Ziziphus, Plant litter, Syzygium, visual_art, visual_art.visual_art_medium, Bark, GENERA, INHABITING, Systematic, ITS nrDNA barcodes, Evolution, Entoloma, Umbellularia, SYSTEMATICS, 03 medical and health sciences, Behavior and Systematics, New taxa, Systematics, Botany, ITS nrDNA barcode, LEATHERLEAF FERN, Zoologiske og botaniske fag: 480 [VDP], Biology, Ecology, Evolution, Behavior and Systematics, COLLETOTRICHUM-ACUTATUM, Biology and Life Sciences, IQ-TREE, INHABITING BLACK FUNGI, 15. Life on land, BAYESIAN PHYLOGENETIC INFERENCE, biology.organism_classification, Leucadendron, new taxa, systematics, GEN. NOV, SP. NOV, 010606 plant biology & botany
Abstract: Novel species of fungi described in this study include those from various countries as follows: Algeria, Phaeoacremonium adelophialidum from Vitis vinifera. Antarctica, Comoclathris antarctica from soil. Australia, Coniochaeta salicifolia as endophyte from healthy leaves of Geijera salicifolia, Eremothecium peggii in fruit of Citrus australis, Microdochium ratticaudae from stem of Sporobolus natalensis, Neocelosporium corymbiae on stems of Corymbia variegata, Phytophthora kelmanii from rhizosphere soil of Ptilotus pyramidatus, Pseudosydowia backhousiae on living leaves of Backhousia citriodora, Pseudosydowia indoor oopillyensis, Pseudosydowia louisecottisiae and Pseudosydowia queenslandica on living leaves of Eucalyptus sp. Brazil, Absidia montepascoalis from soil. Chile, Ilyonectria zarorii from soil under Maytenus boaria. Costa Rica, Colletotrichum filicis from an unidentified fern. Croatia, Mollisia endogranulata on deteriorated hardwood. Czech Republic, Arcopilus navicularis from tea bag with fruit tea, Neosetophoma buxi as endophyte from Buxus sempervirens, Xerochrysium bohemicum on surface of biscuits with chocolate glaze and filled with jam. France, Entoloma cyaneobasale on basic to calcareous soil, Fusarium aconidiale from Triticum aestivum, Fusarium juglandicola from buds of Juglans regia. Germany, Tetraploa endophytica as endophyte from Microthlaspi perfoliatum roots. India, Castanediella ambae on leaves of Mangifera indica, Lactifluus kanadii on soil under Castanopsis sp., Penicillium uttarakhandense from soil. Italy, Penicillium ferraniaense from compost. Namibia, Bezerromyces gobabebensis on leaves of unidentified succulent, Cladosporium stipagrostidicola on leaves of Stipagrostis sp., Cymostachys euphorbiae on leaves of Euphorbia sp., Deniquelata hypolithi from hypolith under a rock, Hysterobrevium walvisbayicola on leaves of unidentified tree, Knufia hypolithi and Knufia walvisbayicola from hypolith under a rock, Lapidomyces stipagrostidicola on leaves of Stipagrostis sp., Nothophaeotheca mirabibensis (incl. Nothophaeotheca gen. nov.) on persistent inflorescence remains of Blepharis obmitrata, Paramyrothecium salvadorae on twigs of Salvadora persica, Preussia procaviicola on dung of Procavia sp., Sordaria equicola on zebra dung, Volutella salvadorae on stems of Salvadora persica. Netherlands, Entoloma ammophilum on sandy soil, Entoloma pseudocruentatum on nutrient poor(acid)soil, Entoloma pudens on plant debris, amongst grasses. [...], Leslie W.S. de Freitas and colleagues express their gratitude to Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) for scholarships provided to Leslie Freitas and for the research grant provided to André Luiz Santiago; their contribution was financed by the projects ‘Diversity of Mucoromycotina in the different ecosystems of the Atlantic Rainforest of Pernambuco’ (FACEPE–First Projects Program PPP/ FACEPE/CNPq–APQ–0842-2.12/14) and ‘Biology of conservation of fungi s.l. in areas of Atlantic Forest of Northeast Brazil’ (CNPq/ICMBio 421241/ 2017-9) H.B. Lee was supported by the Graduate Program for the Undiscovered Taxa of Korea (NIBR202130202). The study of O.V. Morozova, E.F. Malysheva, V.F. Malysheva, I.V. Zmitrovich, and L.B. Kalinina was carried out within the framework of a research project of the Komarov Botanical Institute RAS (АААА-А19-119020890079-6) using equipment of its Core Facility Centre ‘Cell and Molecular Technologies in Plant Science’. The work of O. V. Morozova, L.B. Kalinina, T. Yu. Svetasheva, and E.A. Zvyagina was financially supported by Russian Foundation for Basic Research project no. 20-04-00349. E.A. Zvyagina and T.Yu. Svetasheva are grateful to A.V. Alexandrova, A.E. Kovalenko, A.S. Baykalova for the loan of specimens, T.Y. James, E.F. Malysheva and V.F. Malysheva for sequencing. J.D. Reyes acknowledges B. Dima for comparing the holotype sequence of Cortinarius bonachei with the sequences in his database. A. Mateos and J.D. Reyes acknowledge L. Quijada for reviewing the phylogeny and S. de la Peña- Lastra and P. Alvarado for their support and help. Vladimir I. Kapitonov and colleagues are grateful to Brigitta Kiss for help with their molecular studies. This study was conducted under research projects of the Tobolsk Complex Scientific Station of the Ural Branch of the Russian Academy of Sciences (N АААА-А19-119011190112-5). E. Larsson acknowledges the Swedish Taxonomy Initiative, SLU Artdatabanken, Uppsala (dha.2019.4.3-13). The study of D.B. Raudabaugh and colleagues was supported by the Schmidt Science Fellows, in partnership with the Rhodes Trust. Gregorio Delgado is grateful to Michael Manning and Kamash Pillai (Eurofins EMLab P&K) for provision of laboratory facilities. Jose G. Maciá-Vicente acknowledges support from the German Research Foundation under grant MA7171/1-1, and from the Landes-Offensive zur Entwicklung Wissenschaftlich-ökonomischer Exzellenz (LOEWE) of the state of Hesse within the framework of the Cluster for Integrative Fungal Research (IPF). Thanks are also due to the authorities of the Cabañeros National Park and Los Alcornocales Natural Park for granting the collection permit and for support during field work. The study of Alina V. Alexandrova was carried out as part of the Scientific Project of the State Order of the Government of Russian Federation to Lomonosov Moscow State University No. 121032300081-7. Michał Gorczak was financially supported by the Ministry of Science and Higher Education through the Faculty of Biology, University of Warsaw intramural grant DSM 0117600- 13. M. Gorczak acknowledges M. Klemens for sharing a photo of the Białowieża Forest logging site and M. Senderowicz for help with preparing the illustration. Ivona Kautmanová and D. Szabóová were funded by the Operational Program of Research and Development and co-financed with the European Fund for Regional Development (EFRD). ITMS 26230120004: ‘Building of research and development infrastructure for investigation of genetic biodiversity of organisms and joining IBOL initiative’. Ishika Bera, Aniket Ghosh, Jorinde Nuytinck and Annemieke Verbeken are grateful to the Director, Botanical Survey of India (Kolkata), Head of the Department of Botany & Microbiology & USIC Dept. HNB Garhwal University, Srinagar, Garhwal for providing research facilities. Ishika Bera and Aniket Ghosh acknowledge the staff of the forest department of Arunachal Pradesh for facilitating the macrofungal surveys to the restricted areas. Sergey Volobuev was supported by the Russian Science Foundation (RSF project N 19-77- 00085). Aleksey V. Kachalkin and colleagues were supported by the Russian Science Foundation (grant No. 19-74-10002). The study of Anna M. Glushakova was carried out as part of the Scientific Project of the State Order of the Government of Russian Federation to Lomonosov Moscow State University No. 121040800174-6. Tracey V. Steinrucken and colleagues were supported by AgriFutures Australia (Rural Industries Research and Development Corporation), through funding from the Australian Government Department of Agriculture, Water and the Environment, as part of its Rural Research and Development for Profit program (PRJ-010527). Neven Matočec and colleagues thank the Croatian Science Foundation for their financial support under the project grant HRZZ-IP-2018-01-1736 (ForFungiDNA). Ana Pošta thanks the Croatian Science Foundation for their support under the grant HRZZ-2018-09-7081. The research of Milan Spetik and co-authors was supported by Internal Grant of Mendel University in Brno No. IGAZF/ 2021-SI1003. K.C. Rajeshkumar thanks SERB, the Department of Science and Technology, Government of India for providing financial support under the project CRG/2020/000668 and the Director, Agharkar Research Institute for providing research facilities. Nikhil Ashtekar thanks CSIR-HRDG, INDIA, for financial support under the SRF fellowship (09/670(0090)/2020-EMRI), and acknowledges the support of the DIC Microscopy Facility, established by Dr Karthick Balasubramanian, B&P (Plants) Group, ARI, Pune. The research of Alla Eddine Mahamedi and co-authors was supported by project No. CZ.02.1.01/0.0/0.0/16_017/0002334, Czech Republic. Tereza Tejklová is thanked for providing useful literature. A. Polhorský and colleagues were supported by the Operational Program of Research and Development and co-financed with the European fund for Regional Development (EFRD), ITMS 26230120004: Building of research and development infrastructure for investigation of genetic biodiversity of organisms and joining IBOL initiative. Yu Pei Tan and colleagues thank R. Chen for her technical support. Ernest Lacey thanks the Cooperative Research Centres Projects scheme (CRCPFIVE000119) for its support. Suchada Mongkolsamrit and colleagues were financially supported by the Platform Technology Management Section, National Center for Genetic Engineering and Biotechnology (BIOTEC), Project Grant No. P19-50231. Dilnora Gouliamova and colleagues were supported by a grant from the Bulgarian Science Fund (KP-06-H31/19). The research of Timofey A. Pankratov was supported by the Russian Foundation for Basic Research (grant No. 19-04-00297a). Gabriel Moreno and colleagues wish to express their gratitude to L. Monje and A. Pueblas of the Department of Drawing and Scientific Photography at the University of Alcalá for their help in the digital preparation of the photographs, and to J. Rejos, curator of the AH herbarium, for his assistance with the specimens examined in the present study. Vit Hubka was supported by the Charles University Research Centre program No. 204069. Alena Kubátová was supported by The National Programme on Conservation and Utilization of Microbial Genetic Resources Important for Agriculture (Ministry of Agriculture of the Czech Republic). The Kits van Waveren Foundation (Rijksherbariumfonds Dr E. Kits van Waveren, Leiden, Netherlands) contributed substantially to the costs of sequencing and travelling expenses for M. Noordeloos. The work of B. Dima was supported by the ÚNKP-20-4 New National Excellence Program of the Ministry for Innovation and Technology from the source of the National Research, Development and Innovation Fund, and by the ELTE Thematic Excellence Programme 2020 supported by the National Research, Development and Innovation Office of Hungary (TKP2020-IKA-05). The Norwegian Entoloma studies received funding from the Norwegian Biodiversity Information Centre (NBIC), and the material was partly sequenced through NorBOL. Gunnhild Marthinsen and Katriina Bendiksen (Natural History Museum, University of Oslo, Norway) are acknowledged for performing the main parts of the Entoloma barcoding work. Asunción Morte is grateful to AEI/FEDER, UE (CGL2016-78946-R) and Fundación Séneca - Agencia de Ciencia y Tecnología de la Región de Murcia (20866/PI/18) for financial support. Vladimír Ostrý was supported by the Ministry of Health, Czech Republic - conceptual development of research organization (National Institute of Public Health – NIPH, IN 75010330). Konstanze Bensch (Westerdijk Fungal Biodiversity Institute, Utrecht) is thanked for correcting the spelling of various Latin epithets.
Published: 2021

36. In silico transcriptomic mapping of integrins and immune activation in Basal-like and HER2+ breast cancer

Author: Katerin Rojas, Vanesa García-Barberán, Atanasio Pandiella, Aránzazu Manzano, Pedro Pérez-Segura, Balázs Győrffy, Francisco J. Cimas, Cristina Saiz-Ladera, Alberto Ocaña, Mariona Baliu-Piqué, Instituto de Salud Carlos III, Acepain Albacete, Diputación de Albacete, Fundación CRIS contra el Cáncer, Ministerio de Economía y Competitividad (España), Asociación Española Contra el Cáncer, European Commission, Ministry of Innovation and Technology (Hungary), and Semmelweis University
Subjects: 0301 basic medicine, HER2+, Cancer Research, Integrins, Receptor, ErbB-2, Antigen presentation, Integrin, Breast Neoplasms, Biology, Tumor-infiltrating lymphocytes, 03 medical and health sciences, 0302 clinical medicine, Immune system, Breast cancer, medicine, Tumor Microenvironment, Humans, ITGAV, ITGB7, Tumor microenvironment, Gene Expression Profiling, Cancer, Tumor biomarkers, General Medicine, medicine.disease, Chemotaxis, Leukocyte, 030104 developmental biology, Oncology, 030220 oncology & carcinogenesis, Cancer research, biology.protein, Molecular Medicine, Female, Basal-like, Transcriptome
Abstract: [Purpose]: Integrins, transmembrane receptors that mediate cell-extracellular matrix and cell-cell interactions, have been linked to several cancer-associated features. A less explored function of integrins in cancer is their role in leukocyte homing and activation. Understanding their relationship with immune cell infiltrates and immune checkpoints is an area of interest in cancer research. [Methods]: The expression of 33 different integrins was evaluated in relation with breast cancer patient outcome using transcriptomic data (Affymetrix dataset, exploratory cohort) and the METABRIC study (validation cohort). The TIMER online tool was used to assess the association of the identified integrin genes with immune cell infiltration, and the TCGA and METABRIC studies to assess correlations between integrin gene expression and genomic signatures of immune activation. [Results]: We identified 7 genes coding for integrin α and β subunits, i.e., ITGA4, ITGB2, ITGAX, ITGB7, ITGAM, ITGAL and ITGA8, which predict a favorable prognosis in Basal-like and HER2+ breast cancers. Their expression positively correlated with the presence of immune cell infiltrates within the tumor (dendritic cells, CD4+ T-cells, neutrophils, CD8+ T-cells and B-cells), with markers of T-cell activation and antigen presentation, and with gene signatures of immune surveillance (cytotoxic T lymphocyte activation and IFN gamma signature). By contrast, we found that genes coding for integrins that predicted a detrimental outcome (IBSP, ITGB3BP, ITGB6, ITGB1 and ITGAV) were not associated with any of these parameters. [Conclusions]: We identified an integrin signature composed of 7 genes with potential to recognize immune infiltrated and activated Basal-like and HER2+ breast cancers with a favorable prognosis., This work was supported by the Instituto de Salud Carlos III (PI19/00808), ACEPAIN, Diputación de Albacete, CIBERONC and CRIS Cancer Foundation (to A. Ocaña) and the Ministry of Economy and Competitiveness of Spain (BFU2015-71371-R), the Instituto de Salud Carlos III through the Spanish Cancer Centers Network Program (RD12/0036/0003) and CIBERONC, the scientific foundation of the AECC and the CRIS Foundation (to A. Pandiella). Our laboratories receive support from the European Community through the regional development funding program (FEDER). BG was supported by a 2018 − 2.1.17-TET-KR-00001 grant and by the Higher Education Institutional Excellence Programme (2020 − 4.1.1.-TKP2020) of the Ministry for Innovation and Technology of Hungary, within the framework of the Bionic thematic programme of the Semmelweis University.
Published: 2020

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