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Utrecht University Repository: Recent submissions

  • Changes to virus taxonomy and the ICTV Statutes ratified by the International Committee on Taxonomy of Viruses (2023) 
    Zerbini, Francisco Murilo; Siddell, Stuart G; Lefkowitz, Elliot J; Mushegian, Arcady R; Adriaenssens, Evelien M; Alfenas-Zerbini, Poliane; Dempsey, Donald M; Dutilh, Bas E; García, María Laura; Hendrickson, R Curtis; Junglen, Sandra; Krupovic, Mart; Kuhn, Jens H; Lambert, Amy J; Łobocka, Małgorzata; Oksanen, Hanna M; Robertson, David L; Rubino, Luisa; Sabanadzovic, Sead; Simmonds, Peter; Smith, Donald B; Suzuki, Nobuhiro; Van Doorslaer, Koenraad; Vandamme, Anne-Mieke; Varsani, Arvind (Springer, 2023-07)
    This article reports changes to virus taxonomy and taxon nomenclature that were approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in April 2023. The entire ICTV membership was invited to ...
  • iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria 
    Roux, Simon; Camargo, Antonio Pedro; Coutinho, Felipe H; Dabdoub, Shareef M; Dutilh, Bas E; Nayfach, Stephen; Tritt, Andrew (Public Library of Science, 2023-04)
    The extraordinary diversity of viruses infecting bacteria and archaea is now primarily studied through metagenomics. While metagenomes enable high-throughput exploration of the viral sequence space, metagenome-derived ...
  • Guidelines for public database submission of uncultivated virus genome sequences for taxonomic classification 
    Adriaenssens, Evelien M; Roux, Simon; Brister, J Rodney; Karsch-Mizrachi, Ilene; Kuhn, Jens H; Varsani, Arvind; Yigang, Tong; Reyes, Alejandro; Lood, Cédric; Lefkowitz, Elliot J; Sullivan, Matthew B; Edwards, Robert A; Simmonds, Peter; Rubino, Luisa; Sabanadzovic, Sead; Krupovic, Mart; Dutilh, Bas E (Nature Publishing Group, 2023-07)
  • Author Correction: Guidelines for public database submission of uncultivated virus genome sequences for taxonomic classification (Nature Biotechnology, (2023), 41, 7, (898-902), 10.1038/s41587-023-01844-2) 
    Adriaenssens, Evelien M; Roux, Simon; Brister, J Rodney; Karsch-Mizrachi, Ilene; Kuhn, Jens H; Varsani, Arvind; Yigang, Tong; Reyes, Alejandro; Lood, Cédric; Lefkowitz, Elliot J; Sullivan, Matthew B; Edwards, Robert A; Simmonds, Peter; Rubino, Luisa; Sabanadzovic, Sead; Krupovic, Mart; Dutilh, Bas E (Nature Publishing Group, 2023-09)
    In the version of this article initially published, there were mistakes in Fig. 1 (ICTV-ratified species growth): in the 2022 column for the 15-rank structure, the value for “Family” was 260 instead of 264; the value for ...
  • A social niche breadth score reveals niche range strategies of generalists and specialists 
    von Meijenfeldt, F A Bastiaan; Hogeweg, Paulien; Dutilh, Bas E (Nature Publishing Group, 2023-05)
    Generalists can survive in many environments, whereas specialists are restricted to a single environment. Although a classical concept in ecology, niche breadth has remained challenging to quantify for microorganisms because ...
  • Virus taxonomy and the role of the International Committee on Taxonomy of Viruses (ICTV) 
    Siddell, Stuart G; Smith, Donald B; Adriaenssens, Evelien; Alfenas-Zerbini, Poliane; Dutilh, Bas E; Garcia, Maria Laura; Junglen, Sandra; Krupovic, Mart; Kuhn, Jens H; Lambert, Amy J; Lefkowitz, Elliot J; Łobocka, Małgorzata; Mushegian, Arcady R; Oksanen, Hanna M; Robertson, David L; Rubino, Luisa; Sabanadzovic, Sead; Simmonds, Peter; Suzuki, Nobuhiro; Van Doorslaer, Koenraad; Vandamme, Anne-Mieke; Varsani, Arvind; Zerbini, F Murilo (Society for General Microbiology, 2023-05)
    The taxonomy of viruses is developed and overseen by the International Committee on Taxonomy of Viruses (ICTV), which scrutinizes, approves and ratifies taxonomic proposals, and maintains a list of virus taxa with approved ...
  • Four principles to establish a universal virus taxonomy 
    Simmonds, Peter; Adriaenssens, Evelien M; Zerbini, F Murilo; Abrescia, Nicola G A; Aiewsakun, Pakorn; Alfenas-Zerbini, Poliane; Bao, Yiming; Barylski, Jakub; Drosten, Christian; Duffy, Siobain; Duprex, W Paul; Dutilh, Bas E; Elena, Santiago F; García, Maria Laura; Junglen, Sandra; Katzourakis, Aris; Koonin, Eugene V; Krupovic, Mart; Kuhn, Jens H; Lambert, Amy J; Lefkowitz, Elliot J; Łobocka, Małgorzata; Lood, Cédric; Mahony, Jennifer; Meier-Kolthoff, Jan P; Mushegian, Arcady R; Oksanen, Hanna M; Poranen, Minna M; Reyes-Muñoz, Alejandro; Robertson, David L; Roux, Simon; Rubino, Luisa; Sabanadzovic, Sead; Siddell, Stuart; Skern, Tim; Smith, Donald B; Sullivan, Matthew B; Suzuki, Nobuhiro; Turner, Dann; Van Doorslaer, Koenraad; Vandamme, Anne-Mieke; Varsani, Arvind; Vasilakis, Nikos (Public Library of Science, 2023-02)
    A universal taxonomy of viruses is essential for a comprehensive view of the virus world and for communicating the complicated evolutionary relationships among viruses. However, there are major differences in the ...
  • 28 minutes later: investigating the role of aflatrem-like compounds in Ophiocordyceps parasite manipulation of zombie ants 
    Beckerson, William C.; Krider, Courtney; Mohammad, Umar A.; de Bekker, Charissa (Academic Press Inc., 2023-09)
    Coevolutionary relationships between parasites and their hosts can lead to the emergence of diverse phenotypes over time, as seen in Ophiocordyceps fungi that manipulate insect and arachnid behaviour to aid fungal spore ...
  • Using machine learning to predict protein-protein interactions between a zombie ant fungus and its carpenter ant host 
    Will, Ian; Beckerson, William C; de Bekker, Charissa (NLM (Medline), 2023-12)
    Parasitic fungi produce proteins that modulate virulence, alter host physiology, and trigger host responses. These proteins, classified as a type of "effector," often act via protein-protein interactions (PPIs). The fungal ...
  • Dinoflagellate cyst and pollen assemblages as tracers for marine productivity and river input in the northern Gulf of Mexico 
    Yedema, Yord W.; Donders, Timme; Peterse, Francien; Sangiorgi, Francesca (Geological Society of London, 2023-11-27)
    Both marine dinoflagellate cysts and terrestrially derived pollen and spores are abundant in coastal sediments close to river mouths, making sediment records from such settings ideal to simultaneously study land– ocean ...
  • Multiomic interpretation of fungus-infected ant metabolomes during manipulated summit disease 
    Will, I; Attardo, G M; de Bekker, C (NLM (Medline), 2023-12)
    Camponotus floridanus ants show altered behaviors followed by a fatal summiting phenotype when infected with manipulating Ophiocordyceps camponoti-floridani fungi. Host summiting as a strategy to increase transmission is ...
  • Plant commensal type VII secretion system causes iron leakage from roots to promote colonization 
    Liu, Yunpeng; Shu, Xia; Chen, Lin; Zhang, Huihui; Feng, Haichao; Sun, Xiting; Xiong, Qin; Li, Guangqi; Xun, Weibing; Xu, Zhihui; Zhang, Nan; Pieterse, Corné M.J.; Shen, Qirong; Zhang, Ruifu (Nature Publishing Group, 2023-08)
    Competition for iron is an important factor for microbial niche establishment in the rhizosphere. Pathogenic and beneficial symbiotic bacteria use various secretion systems to interact with their hosts and acquire limited ...
  • Chemical symphony of coumarins and phenazines in rhizosphere iron solubilization 
    Pieterse, Corné M.J.; Stringlis, Ioannis A. (National Academy of Sciences, 2023-04-24)
  • Dynamic Currency Conversion Payment Options Specifically Harm Less Financially Literate Customers 
    Gerritsen, Dirk F.; Lancee, Bora S.; Rigtering, J. P.Coen (American Marketing Association, 2023-07)
    International customers are increasingly exposed to dynamic currency conversion, that is, the option during checkout to proceed with a transaction in the home currency instead of a foreign currency. As conversion markups ...
  • The Use of Synthetic Microbial Communities to Improve Plant Health 
    Martins, Samuel J.; Pasche, Josephine; Silva, Hiago Antonio O.; Selten, Gijs; Savastano, Noah; Abreu, Lucas Magalhães; Bais, Harsh P.; Garrett, Karen A.; Kraisitudomsook, Nattapol; Pieterse, Corné M.J.; Cernava, Tomislav (American Phytopathological Society, 2023-08)
    Despite the numerous benefits plants receive from probiotics, maintaining consistent results across applications is still a challenge. Cultivationindependent methods associated with reduced sequencing costs have considerably ...
  • Training law students like athletes: experimenting with the constraints-led approach in law clinics 
    Sluijs, Jasper P.; Gilissen, Herman Kasper; Look, Karin (C.J.) van (Taylor and Francis Ltd., 2023-11-24)
    We studied to what extent insights from the “constraints-led approach” (CLA) in physical education can be applied to skills teaching for law students in preparation for law clinics. In the CLA, athletes are challenged to ...
  • Obligate biotroph downy mildew consistently induces near-identical protective microbiomes in Arabidopsis thaliana 
    Goossens, Pim; Spooren, Jelle; Baremans, Kim C.M.; Andel, Annemiek; Lapin, Dmitry; Echobardo, Nakisa; Pieterse, Corné M.J.; Van den Ackerveken, Guido; Berendsen, Roeland L. (Nature Publishing Group, 2023-12)
    Hyaloperonospora arabidopsidis (Hpa) is an obligately biotrophic downy mildew that is routinely cultured on Arabidopsis thaliana hosts that harbour complex microbiomes. We hypothesized that the culturing procedure proliferates ...
  • Developers talking about code quality 
    Börstler, Jürgen; Bennin, Kwabena E; Hooshangi, Sara; Jeuring, Johan; Keuning, Hieke; Kleiner, Carsten; MacKellar, Bonnie; Duran, Rodrigo; Störrle, Harald; Toll, Daniel; van Assema, Jelle (Springer Netherlands, 2023-11)
    There are many aspects of code quality, some of which are difficult to capture or to measure. Despite the importance of software quality, there is a lack of commonly accepted measures or indicators for code quality that ...
  • Teleportation of quantum coherence 
    Sohail Pati, Arun K.; Aradhya, Vijeth; Chakrabarty, Indranil; Patro, Subhasree (American Physical Society, 2023-10-26)
    We investigate whether it is possible to teleport the coherence of an unknown quantum state from Alice to Bob by communicating a smaller number of classical bits in comparison to what is required for teleporting an unknown ...
  • Amphipathic Cell-Penetrating Peptide-Aided Delivery of Cas9 RNP for In Vitro Gene Editing and Correction 
    Öktem, Mert; Mastrobattista, Enrico; de Jong, Olivier G (American Chemical Society, 2023-10-20)
    The therapeutic potential of the CRISPR-Cas9 gene editing system in treating numerous genetic disorders is immense. To fully realize this potential, it is crucial to achieve safe and efficient delivery of CRISPR-Cas9 ...