Whose Ear?: Proposal to conserve the name Auricularia auricula (L.) Underw. for Auricularia auricula-judae (Bull.) Quél. [version 1; peer review: 2 approved]

Auricularia auricula-judae is a saprobic European jelly fungus with traditional culinary and medicinal significance, often said to resemble a human ear. It was originally named Tremella auricula by Linnaeus and has been moved to different genera since, but its specific epithet was also changed from auricula to auricula-judae by Bulliard in 1789, which is not normally a valid nomenclatural alteration. However, due to the practice of "name sanctioning" in the mycological nomenclatural code, this change has been accepted. This article outlines the nomenclatural and cultural history of the controversial name Auricularia auricula-judae and suggests its return to the original specific epithet auricula, as well as the designation of an epitype specimen

Comparing COI and ITS as DNA Barcode Markers for Mushrooms and Allies (Agaricomycotina)

DNA barcoding is an approach to rapidly identify species using short, standard genetic markers. The mitochondrial cytochrome oxidase I gene (COI) has been proposed as the universal barcode locus, but its utility for barcoding in mushrooms (ca. 20,000 species) has not been established. We succeeded in generating 167 partial COI sequences (∼450 bp) representing ∼100 morphospecies from ∼650 collections of Agaricomycotina using several sets of new primers. Large introns (∼1500 bp) at variable locations were detected in ∼5% of the sequences we obtained. We suspect that widespread presence of large introns is responsible for our low PCR success (∼30%) with this locus. We also sequenced the nuclear internal transcribed spacer rDNA regions (ITS) to compare with COI. Among the small proportion of taxa for which COI could be sequenced, COI and ITS perform similarly as a barcode. However, in a densely sampled set of closely related taxa, COI was less divergent than ITS and failed to distinguish all terminal clades. Given our results and the wealth of ITS data already available in public databases, we recommend that COI be abandoned in favor of ITS as the primary DNA barcode locus in mushrooms

Introduction to "Working Across Species"

Comparison between different animal species is omnipresent in the history of science and medicine but rarely subject to focussed historical analysis. The articles in the ‘‘Working Across Species’’ topical collection address this deficit by looking directly at the practical and epistemic work of cross-species comparison. Drawn from papers presented at a Wellcome-Trust-funded workshop in 2016, these papers investigate various ways that comparison has been made persuasive and successful, in multiple locations, by diverse disciplines, over the course of two centuries. They explore the many different animal features that have been considered to be (or else made) comparable, and the ways that animals have shaped science and medicine through the use of comparison. Authors demonstrate that comparison between species often transcended the range of practices typically employed with experimental animal models, where standardised practises and apparatus were applied to standardised bodies to produce generalizable, objective data; instead, comparison across species has often engaged diverse groups of nonstandard species, made use of subjective inferences about phenomena that cannot be directly observed, and inspired analogies that linked physiological and behavioural characteristics with the apparent affective state of non-human animals. Moreover, such comparative practices have also provided unusually fruitful opportunities for collaborative connections between different research traditions and disciplines

Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi

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

Introduction: microbes, networks, knowledge—disease ecology and emerging infectious diseases in time of COVID-19

This is an introduction to the topical collection Microbes, Networks, Knowledge: Disease Ecology in the twentieth Century, based on a workshop held at Queen Mary, University London on July 6–7 2016. More than twenty years ago, historian of science and medicine Andrew Mendelsohn asked, “Where did the modern, ecological understanding of epidemic disease come from?” Moving beyond Mendelsohn’s answer, this collection of new essays considers the global history of disease ecology in the past century and shows how epidemics and pandemics have made “microbes complex”

Finding needles in haystacks: Linking scientific names, reference specimens and molecular data for Fungi

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. Reannotated 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.B.R. and C.L.S. acknowledge support from the Intramural Research Program of the National Institutes of Health, National Library of MedicinePeer Reviewe

Spatial and Temporal Dynamics of Hepatitis B Virus D Genotype in Europe and the Mediterranean Basin

Hepatitis B virus genotype D can be found in many parts of the world and is the most prevalent strain in south-eastern Europe, the Mediterranean Basin, the Middle East, and the Indian sub-continent. The epidemiological history of the D genotype and its subgenotypes is still obscure because of the scarcity of appropriate studies. We retrieved from public databases a total of 312 gene P sequences of HBV genotype D isolated in various countries throughout the world, and reconstructed the spatio-temporal evolutionary dynamics of the HBV-D epidemic using a Bayesian framework

Work and Well-Being of Informal Caregivers in Europe

Informal caregivers provide valuable services to elderly persons with long-term care needs, but the consequences of caregiving on caregivers are not yet fully understood. This paper illustrates the interrelation between caregiving and caregivers' labour force participation, cognitive ability, and health in a simple theoretical model, and estimates the effects of caregiving using panel data from 13 European countries, which allows to analyze the effect of institutions on caregivers' outcomes. The results show that caregiving severely and signicantly reduces caregivers' probability of being employed, but only in countries with few formal care alternatives. Furthermore, caregivers in all countries suffer from worse mental health when caregiving is prompted by poor parental health. The results for the effects of caregiving on physical health and cognitive ability are mixed.Informelle Pflegerinnen und Pfleger leisten einen wertvollen Beitrag zu der Pflege älterer Menschen. Welche Folgen die Erbringung von Pflege auf die pflegende Person hat, ist jedoch noch nicht vollständig bekannt. Diese Studie verdeutlicht den Zusammenhang zwischen Pflegeerbringung, Arbeit, kognitiven Fähigkeiten und Gesundheit in einem theoretischen Modell und schätzt die Auswirkung von Pflegeerbringung anhand von Längsschnittdaten aus 13 europäischen Ländern. Dabei wird insbesondere der Einfluss institutioneller Faktoren auf die Auswirkungen von Pflegeerbringung analysiert. Die Ergebnisse zeigen, dass Pflegeerbringung die Erwerbstätigkeit in Ländern mit einem geringeren professionellen Pflegeangebot stark reduziert. Dagegen leiden in allen Ländern pflegende Personen häufiger an depressiven Symptomen. Die Ergebnisse für kognitive Fähigkeiten und Gesundheit sind gemischt