Author
Laszlo Irinyi
Other affiliations: United States Department of Agriculture, University of Debrecen, Westmead Hospital ...read more
Bio: Laszlo Irinyi is an academic researcher from University of Sydney. The author has contributed to research in topics: Phoma & Biology. The author has an hindex of 16, co-authored 55 publications receiving 1561 citations. Previous affiliations of Laszlo Irinyi include United States Department of Agriculture & University of Debrecen.
Papers published on a yearly basis
Papers
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Agriculture and Agri-Food Canada1, University of Sydney2, Institut national de la recherche agronomique3, Aix-Marseille University4, university of lille5, University of Amsterdam6, American Museum of Natural History7, Leibniz Association8, Ruhr University Bochum9, Universidade Nova de Lisboa10, Federal University of Paraná11, Agro ParisTech12, University of Perugia13, Tuscia University14, Pasteur Institute15, Spanish National Research Council16, Second Military Medical University17, University of Pretoria18, King Abdulaziz University19, Staatliches Museum für Naturkunde Stuttgart20
TL;DR: A novel high fidelity primer pair for TEF1α has potential as a supplementary DNA barcode with superior resolution to ITS, while TOPI and LNS2 are attractive for the Pucciniomycotina, for which universal primers for ribosomal subunits often fail.
Abstract: Primer development and testing by partners in the
European Consortium of Microbial Resource Centres (EMbaRC) was supported
through funding of the European Community’s Seventh Framework
Programme (FP7, 2007–2013), Research Infrastructures action, under grant
agreement no. FP7-228310. Part of sequencing work in CBS was supported
by Fonds Economische Structuurversterking (FES), Dutch Ministry of Education,
Culture and Science grant BEK/BPR-2009/137964-U). WM and VR
were supported by research grant NH&MRC #APP1031952. Genome mining
at CBS and AAFC, and primer development and testing at AAFC, were supported
by grants from the A.P. Sloan Foundation Programme on the Microbiology
of the Built Environment. We acknowledge the Deanship of Scientific
Research (DSR), King Abdulaziz University, under grant No. 1-965/1434 HiCi
for technical and financial support. AY was supported by Fundacao para a
Ciencia e a Tecnologia (Portugal), project PTDC/BIA-BIC/4585/2012. MPM
was supported by grant CGL2012-359 (Spain).
385 citations
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National Institutes of Health1, Centraalbureau voor Schimmelcultures2, University of Perugia3, University of Sydney4, University of Gothenburg5, University of Tennessee6, University of Illinois at Urbana–Champaign7, Royal Botanic Gardens8, University of Tartu9, Purdue University10, Mae Fah Luang University11, Kunming Institute of Botany12, Complutense University of Madrid13, American Museum of Natural History14, University of Pretoria15, Spanish National Research Council16, University of British Columbia17, Academy of Sciences of the Czech Republic18, University of Toronto19, Aberystwyth University20, University of Graz21, University of the Free State22, Commonwealth Scientific and Industrial Research Organisation23, Swedish Museum of Natural History24, Rural Development Administration25, University of California, Davis26, Landcare Research27, Eötvös Loránd University28, Hungarian Academy of Sciences29, Field Museum of Natural History30, University of Szeged31, United States Department of Agriculture32, University of Alabama33, University of Helsinki34, Thailand National Science and Technology Development Agency35, University of Wisconsin-Madison36, National Research Council37, University of North Carolina at Greensboro38, Sungkyunkwan University39, Hirosaki University40, Brandon University41, University of Jena42, University of Findlay43, University of Tübingen44, McMaster University45, Rutgers University46
TL;DR: A set of standards and protocols are proposed to improve the data quality of new sequences, and it is suggested how type and other reference sequences can be used to improve identification of Fungi.
Abstract: DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.
360 citations
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University of Tartu1, American Museum of Natural History2, University of Gothenburg3, Swedish University of Agricultural Sciences4, University of Oslo5, University of Hawaii at Manoa6, University of Copenhagen7, Purdue University8, Academy of Sciences of the Czech Republic9, University of Turin10, Harvard University11, Synlab Group12, Universidad Santo Tomás13, Universidad Mayor14, University of Electronic Science and Technology of China15, University of Warsaw16, Swedish Museum of Natural History17, Mae Fah Luang University18, University of Florida19, Laos Ministry of Agriculture and Forestry20, São Paulo Federal Institute of Education, Science and Technology21, Estonian University of Life Sciences22, Federal University of Pernambuco23, United States Department of Energy24, Del Rosario University25, National Autonomous University of Mexico26, Ghent University27, West Bengal State University28, Beijing Forestry University29, Pontifical Catholic University of Chile30, Chinese Academy of Sciences31, Field Museum of Natural History32, Leibniz Association33, University of Potsdam34, University of Gilan35, University of Alaska Fairbanks36, University of Tokyo37, University of Costa Rica38, Forest Research Institute39, University of Sydney40, Westmead Hospital41, Uppsala University42, Landcare Research43, University of Chittagong44, University of Memphis45, United Arab Emirates University46, Ministry of Land and Resources of the People's Republic of China47, University of Pretoria48, Royal Botanic Gardens49, Ocean University of China50, Guizhou University51, Mie University52, Hokkaido University53
TL;DR: Fungal traits and character database FungalTraits operating at genus and species hypothesis levels is presented in this article, which includes 17 lifestyle related traits of fungal and Stramenopila genera.
Abstract: The cryptic lifestyle of most fungi necessitates molecular identification of the guild in environmental studies. Over the past decades, rapid development and affordability of molecular tools have tremendously improved insights of the fungal diversity in all ecosystems and habitats. Yet, in spite of the progress of molecular methods, knowledge about functional properties of the fungal taxa is vague and interpretation of environmental studies in an ecologically meaningful manner remains challenging. In order to facilitate functional assignments and ecological interpretation of environmental studies we introduce a user friendly traits and character database FungalTraits operating at genus and species hypothesis levels. Combining the information from previous efforts such as FUNGuild and Fun(Fun) together with involvement of expert knowledge, we reannotated 10,210 and 151 fungal and Stramenopila genera, respectively. This resulted in a stand-alone spreadsheet dataset covering 17 lifestyle related traits of fungal and Stramenopila genera, designed for rapid functional assignments of environmental studies. In order to assign the trait states to fungal species hypotheses, the scientific community of experts manually categorised and assigned available trait information to 697,413 fungal ITS sequences. On the basis of those sequences we were able to summarise trait and host information into 92,623 fungal species hypotheses at 1% dissimilarity threshold.
245 citations
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University of Sydney1, Pasteur Institute2, National and Kapodistrian University of Athens3, University of Perugia4, Aix-Marseille University5, Federal University of São Paulo6, Universidade Federal de Goiás7, University of Minho8, Oswaldo Cruz Foundation9, National Autonomous University of Mexico10, Westmead Hospital11, University of Adelaide12, Lille University of Science and Technology13, National Institutes of Health14
TL;DR: An international consortium of medical mycology laboratories was formed aiming to establish a quality controlled ITS database, containing 2800 ITS sequences representing 421 fungal species, providing the medical community with a freely accessible tool to rapidly and reliably identify most agents of mycoses.
Abstract: This study was supported by an National Health and Medical Research Council of Australia (NHM CNPq [350338/2000-0] and FAPERJ [E-26/103.157/2011] grants to RM Zancope-Oliveira; CNPq [308011/2010-4] and FAPESP [2007/08575-1] Fundacao de Amparo Pesquisa do Estado de So Paulo (FAPESP) grants to AL Colombo; PEst-OE/BIA/UI4050/2014 from Fundacao para a Ciencia e Tecnologia (FCT) to C Pais; the Belgian Science Policy Office (Belspo) to BCCM/IHEM; the MEXBOL program of CONACyT-Mexico, [ref. number: 1228961 to ML Taylor and [122481] to C Toriello; the Institut Pasteur and Institut de Veil le Sanitaire to F Dromer and D Garcia-Hermoso; and the grants from the Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq) and the Fundacao de Amparo a Pesquisa do Estado de Goias (FAPEG) to CM de Almeida Soares and JA Parente Rocha. I Arthur would like to thank G Cherian, A Higgins and the staff of the Molecular Diagnostics Laboratory, Division of Microbiology and Infectious Diseases, Path West, QEII Medial Centre. Dromer would like to thank for the technical help of the sequencing facility and specifically that of I, Diancourt, A-S Delannoy-Vieillard, J-M Thiberge (Genotyping of Pathogens and Public Health, Institut Pasteur). RM Zancope-Oliveira would like to thank the Genomic/DNA Sequencing Platform at Fundacao Oswaldo Cruz-PDTIS/FIOCRUZ [RPT01A], Brazil for the sequencing. B Robbertse and CL Schoch acknowledge support from the Intramural Research Program of the NIH, National Library of Medicine. T Sorrell's work is funded by the NHM she is a Sydney Medical School Foundation Fellow.
229 citations
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Free University of Berlin1, Purdue University2, National Institutes of Health3, University of Illinois at Urbana–Champaign4, National Taiwan University5, National Agriculture and Food Research Organization6, University of Perugia7, Wageningen University and Research Centre8, Utrecht University9, Nanjing Agricultural University10, Vienna University of Technology11, Pennsylvania State University12, University of Sydney13, University of Mauritius14, Landcare Research15, Royal Botanic Gardens16, Federal University of Pernambuco17, University of Tartu18, Goethe University Frankfurt19, Leibniz Association20, Rutgers University21
TL;DR: A conceptual framework for the identification of fungi is provided, encouraging the approach of integrative (polyphasic) taxonomy for species delimitation, i.e. the combination of genealogy, phenotype, and phenotype-based approaches to catalog the global diversity of fungi and establish initial species hypotheses.
Abstract: True fungi (Fungi) and fungus-like organisms (e.g. Mycetozoa, Oomycota) constitute the second largest group of organisms based on global richness estimates, with around 3 million predicted species. Compared to plants and animals, fungi have simple body plans with often morphologically and ecologically obscure structures. This poses challenges for accurate and precise identifications. Here we provide a conceptual framework for the identification of fungi, encouraging the approach of integrative (polyphasic) taxonomy for species delimitation, i.e. the combination of genealogy (phylogeny), phenotype (including autecology), and reproductive biology (when feasible). This allows objective evaluation of diagnostic characters, either phenotypic or molecular or both. Verification of identifications is crucial but often neglected. Because of clade-specific evolutionary histories, there is currently no single tool for the identification of fungi, although DNA barcoding using the internal transcribed spacer (ITS) remains a first diagnosis, particularly in metabarcoding studies. Secondary DNA barcodes are increasingly implemented for groups where ITS does not provide sufficient precision. Issues of pairwise sequence similarity-based identifications and OTU clustering are discussed, and multiple sequence alignment-based phylogenetic approaches with subsequent verification are recommended as more accurate alternatives. In metabarcoding approaches, the trade-off between speed and accuracy and precision of molecular identifications must be carefully considered. Intragenomic variation of the ITS and other barcoding markers should be properly documented, as phylotype diversity is not necessarily a proxy of species richness. Important strategies to improve molecular identification of fungi are: (1) broadly document intraspecific and intragenomic variation of barcoding markers; (2) substantially expand sequence repositories, focusing on undersampled clades and missing taxa; (3) improve curation of sequence labels in primary repositories and substantially increase the number of sequences based on verified material; (4) link sequence data to digital information of voucher specimens including imagery. In parallel, technological improvements to genome sequencing offer promising alternatives to DNA barcoding in the future. Despite the prevalence of DNA-based fungal taxonomy, phenotype-based approaches remain an important strategy to catalog the global diversity of fungi and establish initial species hypotheses.
191 citations
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TL;DR: The approach to utilizing available RNA-Seq and other data types in the authors' manual curation process for vertebrate, plant, and other species is summarized, and a new direction for prokaryotic genomes and protein name management is described.
Abstract: The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, and protein sequence records (http://www.ncbi.nlm.nih.gov/refseq/). The RefSeq project leverages the data submitted to the International Nucleotide Sequence Database Collaboration (INSDC) against a combination of computation, manual curation, and collaboration to produce a standard set of stable, non-redundant reference sequences. The RefSeq project augments these reference sequences with current knowledge including publications, functional features and informative nomenclature. The database currently represents sequences from more than 55,000 organisms (>4800 viruses, >40,000 prokaryotes and >10,000 eukaryotes; RefSeq release 71), ranging from a single record to complete genomes. This paper summarizes the current status of the viral, prokaryotic, and eukaryotic branches of the RefSeq project, reports on improvements to data access and details efforts to further expand the taxonomic representation of the collection. We also highlight diverse functional curation initiatives that support multiple uses of RefSeq data including taxonomic validation, genome annotation, comparative genomics, and clinical testing. We summarize our approach to utilizing available RNA-Seq and other data types in our manual curation process for vertebrate, plant, and other species, and describe a new direction for prokaryotic genomes and protein name management.
4,104 citations
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TL;DR: UNITE is a web-based database and sequence management environment for the molecular identification of fungi that targets the formal fungal barcode—the nuclear ribosomal internal transcribed spacer region—and offers all public fungal ITS sequences for reference.
Abstract: Alfred P. Sloan Foundation [G-2015-14062]; Swedish Research Council of Environment, Agricultural Sciences, and Spatial Planning [FORMAS, 215-2011-498]; European Regional Development Fund (Centre of Excellence EcolChange) [TK131]; Estonian Research Council [IUT20-30]. Funding for open access charge: Swedish Research Council of Environment, Agricultural Sciences and Spatial Planning.
1,674 citations
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University of Sydney1, University of Michigan2, Duke University3, University of Alabama at Birmingham4, University of Pittsburgh5, University of Florida6, Centers for Disease Control and Prevention7, University of Münster8, University of Udine9, Ankara University10, University of Wisconsin-Madison11, Paris Diderot University12, University of Arkansas for Medical Sciences13, University of Paris14, University of Lausanne15, Brown University16, Istituto Giannina Gaslini17, Carlos III Health Institute18, Uniformed Services University of the Health Sciences19, National Institutes of Health20, University of Pennsylvania21, St George's, University of London22, Heidelberg University23, University of Copenhagen24, University College London25, University of Texas MD Anderson Cancer Center26, Katholieke Universiteit Leuven27, Goethe University Frankfurt28, University of Würzburg29, Johns Hopkins University30, Monash University31, Federal University of Rio de Janeiro32, Catholic University of the Sacred Heart33, University of Texas Health Science Center at San Antonio34, Masaryk University35, RMIT University36, Radboud University Nijmegen37, University of Melbourne38, Stanford University39, University of California, Davis40, Georgia Regents University41, Cornell University42, University of Aberdeen43, University Hospital of Wales44
TL;DR: These updated definitions of IFDs should prove applicable in clinical, diagnostic, and epidemiologic research of a broader range of patients at high-risk.
Abstract: BACKGROUND: Invasive fungal diseases (IFDs) remain important causes of morbidity and mortality. The consensus definitions of the Infectious Diseases Group of the European Organization for Research and Treatment of Cancer and the Mycoses Study Group have been of immense value to researchers who conduct clinical trials of antifungals, assess diagnostic tests, and undertake epidemiologic studies. However, their utility has not extended beyond patients with cancer or recipients of stem cell or solid organ transplants. With newer diagnostic techniques available, it was clear that an update of these definitions was essential. METHODS: To achieve this, 10 working groups looked closely at imaging, laboratory diagnosis, and special populations at risk of IFD. A final version of the manuscript was agreed upon after the groups' findings were presented at a scientific symposium and after a 3-month period for public comment. There were several rounds of discussion before a final version of the manuscript was approved. RESULTS: There is no change in the classifications of "proven," "probable," and "possible" IFD, although the definition of "probable" has been expanded and the scope of the category "possible" has been diminished. The category of proven IFD can apply to any patient, regardless of whether the patient is immunocompromised. The probable and possible categories are proposed for immunocompromised patients only, except for endemic mycoses. CONCLUSIONS: These updated definitions of IFDs should prove applicable in clinical, diagnostic, and epidemiologic research of a broader range of patients at high-risk.
1,211 citations
01 Oct 2004
TL;DR: The nature and function of the immune response to fungi is an exciting challenge that might set the stage for new approaches to the treatment of fungal diseases, from immunotherapy to vaccines.
Abstract: Fungal diseases represent an important paradigm in immunology, as they can result from either a lack of recognition by the immune system or overactivation of the inflammatory response. Research in this field is entering an exciting period of transition from studying the molecular and cellular bases of fungal virulence to determining the cellular and molecular mechanisms that maintain immune homeostasis with fungi. The fine line between these two research areas is central to our understanding of tissue homeostasis and its possible breakdown in fungal infections and diseases. Recent insights into immune responses to fungi suggest that functionally distinct mechanisms have evolved to achieve optimal host-fungus interactions in mammals.
992 citations
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TL;DR: The atlas compiled by these editors is a commendable effort and welcome addition to the mycology textbook sector.
Abstract: The atlas compiled by these editors is a commendable effort and welcome addition to the mycology textbook sector. Up until now, the publication of medical mycology textbooks has been sparse and those that have been published are either too detailed for a resident in training or practicing physician or do not provide sufficient photographs or illustrations of the main features of the mycotic organisms. As a lecturer in mycology for the dermatology residents at my local teaching hospital and program, there are 3 key objectives of my mycology lectures: (1) to provide some type of organizational approach to mycotic organisms, (2) to provide a concise clinical history, and (3) to provide as many photographs and illustrations of mycotic organisms as possible. This atlas provides an exemplary addition to my book collection on medical mycology textbooks and sources for illustrations of mycotic organisms. The electron photomicrographs, photoplates, and line drawings of
965 citations