156 research outputs found

    Integrative taxonomy of platygastrine wasps of Germany

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    In the context of the sixth mass extinction, our understanding of insect decline is severely limited by a lack of information on biodiversity. Many highly abundant and diverse insect groups remain unidentifiable to species or even to genus. The parasitoid wasp superfamily Platygastroidea is one such dark taxon. The taxonomic impediment is especially severe in the Palearctic Platygastrinae due to the proliferation of names with vague concepts. Platygastrine wasps parasitize the hyper-diverse Cecidomyiidae (Diptera), suggesting that their species richness may be correspondingly high. Revisionary work is needed to identify named species and to discover new ones. This work applies integrative taxonomic methods to address the most pressing problems within the subfamily. The research presented in this dissertation focuses on Europe, particularly Germany, which is the current center of insect decline research as well as a historical center of platygastrine taxonomy. As part of this work, historical descriptions and their associated type material were examined and clarified so that further revisionary work can occur. The dissertation is structured in five chapters, of which two are published and three are unpublished. The first chapter reviews 18 genera of Platygastridae described by Arnold F√∂rster (1856), most of which represent distinct and recognizable lineages. The study provides their taxonomic history, diagnostic remarks, English translations, and illustrations of important specimens from the F√∂rster collection in the Natural History Museum Vienna. The collection also includes original exemplar specimens of European species whose types have been lost. Potential neotypes and lectotypes from this material are noted, with the aim of improving nomenclatural stability in the group. Potential neotypes were found for Amblyaspis forticornis (Nees, 1834), Isocybus grandis (Nees, 1834), Platygaster striolata Nees, 1834, and Trichacis tristis (Nees, 1834). Lectotypes will be designated for Platygaster spinigera Nees, 1834, which will be transferred to Leptacis, and for Platygaster corvina F√∂rster, 1861, with Platygaster henkvlugi Buhl, 1996 treated as a junior synonym. Synopeas mutica (Nees, 1834) should be transferred back to Platygaster. The second chapter addresses generic concepts within Platygastrinae sensu Ashmead. Part of Platygastrinae (former Inostemmatinae sensu Ashmead) was reviewed and keyed by Masner & Huggert (1989). However, more than half of the genera in the subfamily, including the vast majority of species, have not been revised. A working key to 14 major world genera, the first of its kind, is provided. An additional six genera and three subgenera of uncertain placement are discussed. The third chapter focuses on nomenclatural problems in the genus Platygaster Latreille, which is the type genus for its subfamily, family, and superfamily. It is also the largest genus in Platygastroidea with nearly 700 species, and recent evidence indicates that it is not monophyletic. It is necessary to establish the identity of the type specimen, as well as the identities of the 13 generic junior synonyms and four subgenera, in order to proceed with taxonomic divisions. The type specimen Scelio ruficornis Latreille, 1805, lost to science for 192 years, was rediscovered. However, it does not belong to the prevailing concept of Platygaster, but to Isocybus F√∂rster, which has extreme taxonomic ramifications. The proposed solution would replace the type species of each genus in order to retain prevailing usage and prevent widespread confusion. A petition is presented to designate Epimeces ensifer Westwood as the type of Platygaster and Scelio ruficornis as the type of Isocybus. In the fourth chapter, the genus Trichacis F√∂rster is revised for Europe. Examination of historical and modern collections combined with DNA barcoding revealed the presence of only a single species in Europe, Trichacis tristis (Nees, 1834), redescribed here. The results suggest that T. tristis has 14 junior synonyms: T. abdominalis (Thomson, 1859); T. bidentiscutum Szab√≥, 1981; T. didas (Walker, 1835); T. fusciala Szab√≥, 1981; T. hajduica Szab√≥, 1981; T. illusor Kieffer, 1916; T. nosferatus Buhl, 1997; T. pisis (Walker, 1835); T. persicus Asadi & Buhl, 2021; T. pulchricornis Szel√©nyi, 1953; T. quadriclava Szab√≥, 1981; T. remulus (Walker, 1835); T. vitreus Buhl, 1997; and T. weiperti Buhl, 2019. Four species should be transferred to Amblyaspis F√∂rster: T. afurcata Szab√≥, 1977, T. hungarica Szab√≥, 1977, T. pannonica Szab√≥, 1977, and T. tatika Szab√≥, 1977. Intraspecific variation, biological associations, and taxonomic history are discussed. DNA barcodes are provided and analyzed in the context of worldwide Trichacis and its sister genus Isocybus F√∂rster. The fifth chapter examines platygastrid diversity in Germany in the context of insect decline. DNA barcodes indicate the presence of 178 observed species, with an estimated total of 290. GBOL sampling captured an estimated 93.7% of total species richness, but only 45.8% of rare species. A case study from Isocybus compares historical specimens, DNA barcode vouchers, and ecological data to illustrate the possible decline of a wetland parasitoid species. Altogether, the research demonstrates the importance of historical material, especially type specimens, in understanding biodiversity through time, and provides an essential taxonomic foundation for much-needed modern identification resources for Platygastrinae in the western Palearctic and beyond.Mitten im sechsten Massensterben ist unser Verst√§ndnis des Insektenr√ľckgangs durch mangelhafte Informationen √ľber die biologische Vielfalt noch immer stark eingeschr√§nkt. Viele der h√§ufigen und artenreichen Insektengruppen lassen sich nicht bis zur Art oder Gattung bestimmen, verweilen daher im Dunkeln. Platygastroidea, eine √úberfamilie parasitoider Wespen, stellt ein solches "dark Taxon" dar. Bei pal√§arktischen Platygastrinae ist die taxonomische Bearbeitung besonders schwer, da es in einer Vielzahl von Taxa Unklarheiten gibt. Platygastrinae parasitieren die sehr artenreichen Cecidomyiidae (Diptera), was darauf schlie√üen l√§sst, dass ihr Artenreichtum ebenfalls entsprechend gro√ü sein k√∂nnte. Taxonomische Revisionen sind erforderlich, um beschriebene Arten zu identifizieren und neue zu entdecken. Die vorliegende Arbeit nutzt integrative Taxonomie, um die dringendsten Probleme dieser Unterfamilie anzugehen. Der Forschungsschwerpunkt liegt auf Europa, insbesondere Deutschland, das aktuelle Zentrum der Erforschung des Insektensterben, sowie ein historisches Zentrum der Platygastrinen-Taxonomie. Die Dissertation ist in f√ľnf Kapitel unterteilt, von denen zwei ver√∂ffentlich und drei unver√∂ffentlicht sind. Das erste Kapitel liefert einen √úberblick √ľber die 18 von Arnold F√∂rster (1856) beschriebenen Gattungen der Platygastridae. Informationen √ľber ihre Taxonomie, Anmerkungen zur Diagnose, √úbersetzungen sowie Abbildungen wichtiger Exemplare aus der F√∂rster-Sammlung im Naturhistorischen Museum Wien werden bereitgestellt. Die Sammlung F√∂rster enth√§lt zudem wichtige Original-Exemplare europ√§ischer Arten, deren Typen unauffindbar sind. Potenzielle Neotypen und Lectotypen aus diesem Material sind vermerkt, um die nomenklatorische Stabilit√§t der Gruppe zu verbessern. Potenzielle Neotypen wurden f√ľr Amblyaspis forticornis (Nees, 1834), Isocybus grandis (Nees, 1834), Platygaster striolata Nees, 1834, und Trichacis tristis (Nees, 1834) gefunden. Lectotypen werden f√ľr P. spinigera Nees, 1834, die zu Leptacis gestellt wird, und f√ľr P. corvina F√∂rster, 1861, bestimmt, wobei Platygaster henkvlugi Buhl, 1996 als j√ľngeres Synonym zur letztgenannten Art behandelt wird. Synopeas mutica (Nees, 1834) sollte zur√ľck zu Platygaster gestellt werden. Das zweite Kapitel befasst sich mit Gattungskonzepten innerhalb der Platygastrinae sensu Ashmead. Ein Teil der Platygastrinae (fr√ľher Inostemmatinae sensu Ashmead) wurde von Masner & Huggert (1989) √ľberarbeitet und ein Bestimmungsschl√ľssel bereitgestellt. Viele Gattungen dieser Unterfamilie, einschlie√ülich der meisten Arten, wurden jedoch nicht √ľberarbeitet. Ein Bestimmungsschl√ľssel f√ľr 14 wichtige Gattungen der Welt wird vorgelegt. Weitere sechs Gattungen und drei Untergattungen mit unsicherer Stellung werden diskutiert. Das dritte Kapitel stellt die nomenklatorischen Probleme in der Gattung Platygaster Latreille dar, die Typusgattung der √úberfamilie. Mit fast 700 Arten ist sie die gr√∂√üte Gattung der Platygastroidea, die nach neueren Erkenntnissen nicht monophyletisch ist. Das Aufkl√§ren der Identit√§ten des Typusexemplars, 13 j√ľngerer Synonyme und vier Untergattungen ist wichtig, um mit der taxonomischen Aufarbeitung fortzufahren. Das Typusexemplar von Scelio ruficornis, das 192 Jahre lang f√ľr die Wissenschaft als verschollen galt, wurde wiederentdeckt. Der Typus passt jedoch nicht zum vorherrschenden Konzept von Platygaster, sondern von Isocybus. Dies hat bedeutende taxonomische Auswirkungen. Als L√∂sung wird empfohlen, die Typusarten der einzelnen Gattungen zu ersetzen, um die aktuelle Namensnutzung beizubehalten und Verwirrung zu verhindern. Die Designation von Epimeces ensifer Westwood als Typusart von Platygaster und Scelio ruficornis als Typusart von Isocybus wird vorgeschlagen. In Kapitel vier wird die Gattung Trichacis F√∂rster f√ľr Europa √ľberarbeitet. Eine Untersuchung von historischem und neuem Sammlungsmaterial in Kombination mit DNA-Barcoding offenbarte das Vorhandensein einer einzigen Art in Europa, Trichacis tristis (Nees, 1834), die hier neu beschrieben wird. Die Ergebnisse zeigen, dass T. tristis 14 j√ľngere Synonyme hat: T. abdominalis (Thomson, 1859); T. bidentiscutum Szab√≥, 1981; T. didas (Walker, 1835); T. fusciala Szab√≥, 1981; T. hajduica Szab√≥, 1981; T. illusor Kieffer, 1916; T. nosferatus Buhl, 1997; T. pisis (Walker, 1835); T. persicus Asadi & Buhl, 2021; T. pulchricornis Szel√©nyi, 1953; T. quadriclava Szab√≥, 1981; T. remulus (Walker, 1835); T. vitreus Buhl, 1997; und T. weiperti Buhl, 2019. Vier Arten sollten zu Amblyaspis F√∂rster gestellt werden: T. afurcata Szab√≥, 1977, T. hungarica Szab√≥, 1977, T. pannonica Szab√≥, 1977 und T. tatika Szab√≥, 1977. Intraspezifische Variationen, biologische Assoziationen und die taxonomische Geschichte werden diskutiert. DNA-Barcodes werden bereitgestellt und im Kontext der weltweiten Arten von Trichacis und ihrer Schwestergattung Isocybus F√∂rster analysiert. Im f√ľnften Kapitel wird die Diversit√§t der Platygastriden in Deutschland im Hinblick auf das Insektensterben untersucht. DNA-Barcodes weisen auf das Vorhandensein von 178 Arten hin, bei einer gesch√§tzten Gesamtzahl von 290 Arten. Die Studie erfasste gesch√§tzt 93,7 % des gesamten Artenreichtums, aber nur 45,8 % der seltenen Arten. Eine Untersuchung der Gattung Isocybus mittels historischer Belege, DNA-Barcodes und √∂kologischer Daten zeigt den potentiellen R√ľckgang einer Parasitoidenart. Diese Arbeit demonstriert, wie wichtig Sammlungen, insbesondere Typusexemplare, f√ľr das Verst√§ndnis der Artenvielfalt im Laufe der Zeit sind und liefert die taxonomische Grundlage f√ľr die dringend ben√∂tigten modernen Bestimmungshilfen der Platygastrinae in der westlichen Pal√§arktis und dar√ľber hinaus

    Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus

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    The marine cyanobacterium Prochlorococcus is the numerically dominant photosynthetic organism in the oligotrophic oceans, and a model system in marine microbial ecology. Here we report 27 new whole genome sequences (2 complete and closed; 25 of draft quality) of cultured isolates, representing five major phylogenetic clades of Prochlorococcus. The sequenced strains were isolated from diverse regions of the oceans, facilitating studies of the drivers of microbial diversity‚ÄĒboth in the lab and in the field. To improve the utility of these genomes for comparative genomics, we also define pre-computed clusters of orthologous groups of proteins (COGs), indicating how genes are distributed among these and other publicly available Prochlorococcus genomes. These data represent a significant expansion of Prochlorococcus reference genomes that are useful for numerous applications in microbial ecology, evolution and oceanography.Gordon and Betty Moore Foundation (Grant GBMR #495.01)National Science Foundation (U.S.) (Grant OCE-1153588)National Science Foundation (U.S.) (Grant OCE-0425602)National Science Foundation (U.S.) (Grant DBI-0424599)Center for Microbial Oceanography: Research and Educatio

    Antimicrobial resistance among migrants in Europe: a systematic review and meta-analysis

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    BACKGROUND: Rates of antimicrobial resistance (AMR) are rising globally and there is concern that increased migration is contributing to the burden of antibiotic resistance in Europe. However, the effect of migration on the burden of AMR in Europe has not yet been comprehensively examined. Therefore, we did a systematic review and meta-analysis to identify and synthesise data for AMR carriage or infection in migrants to Europe to examine differences in patterns of AMR across migrant groups and in different settings. METHODS: For this systematic review and meta-analysis, we searched MEDLINE, Embase, PubMed, and Scopus with no language restrictions from Jan 1, 2000, to Jan 18, 2017, for primary data from observational studies reporting antibacterial resistance in common bacterial pathogens among migrants to 21 European Union-15 and European Economic Area countries. To be eligible for inclusion, studies had to report data on carriage or infection with laboratory-confirmed antibiotic-resistant organisms in migrant populations. We extracted data from eligible studies and assessed quality using piloted, standardised forms. We did not examine drug resistance in tuberculosis and excluded articles solely reporting on this parameter. We also excluded articles in which migrant status was determined by ethnicity, country of birth of participants' parents, or was not defined, and articles in which data were not disaggregated by migrant status. Outcomes were carriage of or infection with antibiotic-resistant organisms. We used random-effects models to calculate the pooled prevalence of each outcome. The study protocol is registered with PROSPERO, number CRD42016043681. FINDINGS: We identified 2274 articles, of which 23 observational studies reporting on antibiotic resistance in 2319 migrants were included. The pooled prevalence of any AMR carriage or AMR infection in migrants was 25·4% (95% CI 19·1-31·8; I2 =98%), including meticillin-resistant Staphylococcus aureus (7·8%, 4·8-10·7; I2 =92%) and antibiotic-resistant Gram-negative bacteria (27·2%, 17·6-36·8; I2 =94%). The pooled prevalence of any AMR carriage or infection was higher in refugees and asylum seekers (33·0%, 18·3-47·6; I2 =98%) than in other migrant groups (6·6%, 1·8-11·3; I2 =92%). The pooled prevalence of antibiotic-resistant organisms was slightly higher in high-migrant community settings (33·1%, 11·1-55·1; I2 =96%) than in migrants in hospitals (24·3%, 16·1-32·6; I2 =98%). We did not find evidence of high rates of transmission of AMR from migrant to host populations. INTERPRETATION: Migrants are exposed to conditions favouring the emergence of drug resistance during transit and in host countries in Europe. Increased antibiotic resistance among refugees and asylum seekers and in high-migrant community settings (such as refugee camps and detention facilities) highlights the need for improved living conditions, access to health care, and initiatives to facilitate detection of and appropriate high-quality treatment for antibiotic-resistant infections during transit and in host countries. Protocols for the prevention and control of infection and for antibiotic surveillance need to be integrated in all aspects of health care, which should be accessible for all migrant groups, and should target determinants of AMR before, during, and after migration. FUNDING: UK National Institute for Health Research Imperial Biomedical Research Centre, Imperial College Healthcare Charity, the Wellcome Trust, and UK National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infections and Antimictobial Resistance at Imperial College London

    Acquired Resistance to KRAS (G12C) Inhibition in Cancer

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    BACKGROUND: Clinical trials of the KRAS inhibitors adagrasib and sotorasib have shown promising activity in cancers harboring KRAS glycine-to-cysteine amino acid substitutions at codon 12 (KRAS(G12C)). The mechanisms of acquired resistance to these therapies are currently unknown. METHODS: Among patients with KRAS(G12C) -mutant cancers treated with adagrasib monotherapy, we performed genomic and histologic analyses that compared pretreatment samples with those obtained after the development of resistance. Cell-based experiments were conducted to study mutations that confer resistance to KRAS(G12C) inhibitors. RESULTS: A total of 38 patients were included in this study: 27 with non-small-cell lung cancer, 10 with colorectal cancer, and 1 with appendiceal cancer. Putative mechanisms of resistance to adagrasib were detected in 17 patients (45% of the cohort), of whom 7 (18% of the cohort) had multiple coincident mechanisms. Acquired KRAS alterations included G12D/R/V/W, G13D, Q61H, R68S, H95D/Q/R, Y96C, and high-level amplification of the KRAS(G12C) allele. Acquired bypass mechanisms of resistance included MET amplification; activating mutations in NRAS, BRAF, MAP2K1, and RET; oncogenic fusions involving ALK, RET, BRAF, RAF1, and FGFR3; and loss-of-function mutations in NF1 and PTEN. In two of nine patients with lung adenocarcinoma for whom paired tissue-biopsy samples were available, histologic transformation to squamous-cell carcinoma was observed without identification of any other resistance mechanisms. Using an in vitro deep mutational scanning screen, we systematically defined the landscape of KRAS mutations that confer resistance to KRAS(G12C) inhibitors. CONCLUSIONS: Diverse genomic and histologic mechanisms impart resistance to covalent KRAS(G12C) inhibitors, and new therapeutic strategies are required to delay and overcome this drug resistance in patients with cancer. (Funded by Mirati Therapeutics and others; ClinicalTrials.gov number, NCT03785249.)

    The khmer software package: enabling efficient nucleotide sequence analysis [version 1; referees: 2 approved, 1 approved with reservations]

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    The khmer package is a freely available software library for working efficiently with fixed length DNA words, or k-mers. khmer provides implementations of a probabilistic k-mer counting data structure, a compressible De Bruijn graph representation, De Bruijn graph partitioning, and digital normalization. khmer is implemented in C++ and Python, and is freely available under the BSD license at https://github.com/dib-lab/khmer/

    The khmer software package: enabling efficient nucleotide sequence analysis

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    The khmer package is a freely available software library for working efficiently with fixed length DNA words, or k-mers. khmer provides implementations of a probabilistic k-mer counting data structure, a compressible De Bruijn graph representation, De Bruijn graph partitioning, and digital normalization. khmer is implemented in C++ and Python, and is freely available under the BSD license at https://github.com/dib-lab/khmer/

    Surgical site infection after gastrointestinal surgery in high-income, middle-income, and low-income countries: a prospective, international, multicentre cohort study