1366 research outputs found
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The 2011 edition of “The Freshwater Algal Flora of the British Isles”: additions, corrections, nomenclatural and taxonomic changes
Full text linkTaxonomic, nomenclatural and distributional changes since the publication of the 2011 edition (reprinted 2021) of The Freshwater Algal Flora of the British Isles (“Flora”) are reviewed together with some changes overlooked earlier. Many of the more recent changes are a result of studies combining an analysis of morphological and DNA sequence data. Of the 473 changes reported most concern the Chlorophyta (131) and the Charophyta (156) followed by the Cyanobacteria (101), with most of the alterations to the Charophyta involving the desmids (136). Also included are 83 new additions to the British and Irish freshwater algal floras, including 20 overlooked in the Flora. Most of these additions are new records: four are newly described desmids and Synura hibernica (Ochrophyta, Chrysophyceae, Synurales) and Chlorococcum turfosum (Chlorophyta, Chlorophyceae, Chlamydomonadales) are also new. The new additions to Flora include information on locality, collector and publication source. Reference is made to discussions in the Flora giving reasons why some genera and species combinations were not accepted, particularly concerning the Cyanobacteria for which a relatively conservative approach had been adopted in
the previous edition of the Flora.Copyright © 2022 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The attached file is the published version of the article.NHM Repositor
The genome sequence of the Dark Crimson Underwing moth, Catocala sponsa Linnaeus, 1767
Full text linkWe present a genome assembly from an individual female Catocala sponsa (the Dark Crimson Underwing; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence spans 803.70 megabases. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.57 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,493 protein-coding genes.Copyright: © 2024 Broad GR et al. This is an open access article distributed under the terms of the Creative Commons Attribution
License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The attached file is the published version of the article.NHM Repositor
The genome sequence of the chalcid wasp, Chalcis sispes Linnaeus, 1761
Full text linkWe present a genome assembly from an individual female Chalcis sispes (chalcid wasp; Arthropoda; Insecta; Hymenoptera; Chalcididae). The genome sequence is 412.4 megabases in span. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 15.9 kilobases in length.Copyright: © 2024 Sivell O et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The attached file is the published version of the article.NHM Repositor
Diversity of myxozoans (Cnidaria) infecting Neotropical fishes in southern Mexico
Full text linkAbstractMyxozoans are a unique group of microscopic parasites that infect mainly fishes. These extremely reduced cnidarians are highly diverse and globally distributed in freshwater and marine habitats. Myxozoan diversity dimension is unknown in Mexico, a territory of an extraordinary biological diversity. This study aimed to explore, for the first time, myxozoan parasite diversity from fishes of the Neotropical region of Mexico. We performed a large morphological and molecular screening using host tissues of 22 ornamental and food fish species captured from different localities of Veracruz, Oaxaca and Chiapas. Myxozoan infections were detected in 90% of the fish species, 65% of them had 1 or 2 and 35% had 3 and up to 8 myxozoan species. Forty-one putative new species were identified using SSU rDNA phylogenetic analyses, belonging to two main lineages: polychaete-infecting (5 species) and oligochaete-infecting (36 species) myxozoans; from those we describe 4 new species:Myxidium zapotecussp. n.,Zschokkella guelaguetzasp. n.,Ellipsomyxa papantlasp. n. andMyxobolus zoqueussp. n. Myxozoan detection increased up to 6 × using molecular screening, which represents 3.7 × more species detected than by microscopy. This study demonstrated that Neotropical fishes from Mexico are hosts of a multitude of myxozoans, representing a source of emerging diseases with large implications for economic and conservation reasons.</jats:p
Comparison of multi-parallel quantitative real-time PCRs targeting different DNA regions and detecting soil-transmitted helminths in stool
Full text linkAbstract
Background
Soil-transmitted helminths infect an estimated 18% of the world’s population, causing a significant health burden. Microscopy has been the primary tool for diagnosing eggs from fecal samples, but its sensitivity drops in low-prevalence settings. Quantitative real-time polymerase chain reaction (qPCR) is slowly increasing in research and clinical settings. However, there is still no consensus on preferred qPCR targets.
Methods
We aimed to compare soil-transmitted helminth (STH) DNA detection methods by testing naïve stool samples spiked with known quantities of STH eggs and larvae. DNA extracts from spiked samples were tested using independent quantitative realtime PCR (qPCR) assays targeting ribosomal or putative non-protein coding satellite sequences.
Results
For Trichuris trichiura, there was a strong correlation between egg/larvae counts and qPCR results using either qPCR method (0.86 and 0.87, respectively). Strong correlations also existed for A. lumbricoides (0.60 and 0.63, respectively), but weaker correlations were found for Ancylostoma duodenale (0.41 for both assays) and Strongyloides stercoralis (0.48 and 0.65, respectively). No correlation for Necator americanus was observed when testing with either qPCR assay. Both assays had fair-to-moderate agreement across targets when using field-collected stool samples (0.28–0.45, for all STHs), except for S. stercoralis (0.12) with slight agreement.
Conclusions
There is a strong correlation between qPCR results and egg/larvae counts. Our study confirms that qPCR is an effective diagnostic tool, even with low-intensity infections, regardless of the DNA-based diagnostic marker used. However, the moderate agreement between the two different qPCR assays when testing field samples highlights the need to understand the role of these targets in the genome so that the parasite burden can be quantified more accurately and consistently by qPCR.
Graphical abstract
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Integrated Approach Reveals Role of Mitochondrial Germ-Line Mutation F18L in Respiratory Chain, Oxidative Alterations, Drug Sensitivity, and Patient Prognosis in Glioblastoma
Full text linkGlioblastoma is the most common and malignant primary brain tumour in adults, with a dismal prognosis. This is partly due to considerable inter- and intra-tumour heterogeneity. Changes in the cellular energy-producing mitochondrial respiratory chain complex (MRC) activities are a hallmark of glioblastoma relative to the normal brain, and associate with differential survival outcomes. Targeting MRC complexes with drugs can also facilitate anti-glioblastoma activity. Whether mutations in the mitochondrial DNA (mtDNA) that encode several components of the MRC contribute to these phenomena remains underexplored. We identified a germ-line mtDNA mutation (m. 14798T > C), enriched in glioblastoma relative to healthy controls, that causes an amino acid substitution F18L within the core mtDNA-encoded cytochrome b subunit of MRC complex III. F18L is predicted to alter corresponding complex III activity, and sensitivity to complex III-targeting drugs. This could in turn alter reactive oxygen species (ROS) production, cell behaviour and, consequently, patient outcomes. Here we show that, despite a heterogeneous mitochondrial background in adult glioblastoma patient biopsy-derived cell cultures, the F18L substitution associates with alterations in individual MRC complex activities, in particular a 75% increase in MRC complex II_III activity, and a 34% reduction in CoQ10, the natural substrate for MRC complex III, levels. Downstream characterisation of an F18L-carrier revealed an 87% increase in intra-cellular ROS, an altered cellular distribution of mitochondrial-specific ROS, and a 64% increased sensitivity to clomipramine, a repurposed MRC complex III-targeting drug. In patients, F18L-carriers that received the current standard of care treatment had a poorer prognosis than non-carriers (373 days vs. 415 days, respectively). Single germ-line mitochondrial mutations could predispose individuals to differential prognoses, and sensitivity to mitochondrial targeted drugs. Thus, F18L, which is present in blood could serve as a useful non-invasive biomarker for the stratification of patients into prognostically relevant groups, one of which requires a lower dose of clomipramine to achieve clinical effect, thus minimising side-effects.</jats:p
A revision of Lycianthes (Solanaceae) in tropical Asia
No full textThe genus Lycianthes (Dunal) Hassl. (Solanaceae) has in the past been treated as a section of the large genus Solanum L. but is more closely related to Capsicum L. Outside of the Americas, where the highest species diversity occurs, the genus is found in tropical and subtropical habitats from India to Japan and the Philippines, including the islands of Indonesia, New Guinea and the Solomons. The 19 species from Australia, New Guinea and the Pacific were treated in ‘PhytoKeys 209’. Here I treat the remaining 10 species occurring across Asia; including two native species, L. biflora (Lour.) Bitter and L. oliveriana (Lauterb. & K.Schum) Bitter, and one cultivated species, L. rantonnetii (Carrière) Bitter that were also included in the earlier work. The Asian species treated here occupy a wide range of forested and disturbed habitats and are diverse in habit, ranging from epiphytic vines to small or medium sized trees, shrubs or creeping herbs. Many of the species are weedy plants of highly disturbed habitats and are best characterised as “ochlospecies”, with complex polymorphic variation. Lycianthes rantonnetii, a species native to southern South America, is recorded as cultivated in India and Pakistan, but may be more widespread than collections indicate. The history of taxonomic treatments of Lycianthes in Asia is discussed, along with details of morphology found in all species. All species are treated in full, with complete morphological descriptions, including synonymy, lecto- or neotypifications, discussions of ecology and vernacular names, distribution maps and preliminary conservation assessments (for all except the cultivated L. rantonnetii). Searchable lists of all specimens examined are presented as Suppl. materials 1, 2.</jats:p
Secrets of a Silent Miniaturist: Findings from a Technical Study of Miniatures Attributed to Isaac Oliver
No full textAn evidently accomplished draughtsman, Isaac Oliver (circa 1565–1617) remains an enigmatic artist in many respects. While Nicholas Hilliard’s treatise on the art of limning provides considerable insight into his material use, techniques, and self-perception, no equivalent documentary evidence survives from Oliver’s hand, and many questions regarding his training, approach, and oeuvre have yet to be answered. This article presents key findings from the collaborative and technically focused research project “Secrets of a Silent Miniaturist: Technical Analysis of Isaac Oliver’s Miniatures”, undertaken by the Fitzwilliam Museum and the Hamilton Kerr Institute in Cambridge (UK). The project aims to shed light on Oliver’s artistic practice through the detailed, technical study of a representative selection of his surviving miniatures, investigated through an up-to-date, non-invasive analytical and technical lens. The article discusses the discovery of near-invisible changes to compositions implemented during the initial execution, differences in execution and later history between two versions of a portrait of Henry Frederick Prince of Wales, the first identification in a miniature of a rare mercury-based white pigment whose deterioration led to later campaigns of repainting, and the use of a hitherto unacknowledged range of pigments and media in Oliver’s landscape miniatures that raises further questions about Oliver’s connection with artistic traditions on the Continent.This is an open access article issued under the Creative Commons Licence (CC-BY-NC). The linked file is the published version of the article.NHM Repositor
Facilitating high throughput collections-based genomics: a comparison of DNA extraction and library building methods
Full text linkWhile DNA barcoding methods are an increasingly important tool in biological conservation, the resource requirements of constructing reference libraries frequently reduce their efficacy. One efficient way of sourcing taxonomically validated DNA for reference libraries is to use museum collections. However, DNA degradation intrinsic to historical museum specimens can, if not addressed in the wet lab, lead to low quality data generation and severely limit scientific output. Several DNA extraction and library build methods that are designed to work with degraded DNA have been developed, although the ability to implement these methods at scale and at low cost has yet to be formally addressed. Here, the performance of widely used DNA extraction and library build methods are compared using museum specimens. We find that while our selected DNA extraction methods do not significantly differ in DNA yield, the Santa Cruz Reaction (SCR) library build method is not only the most effective at retrieving degraded DNA from museum specimens but also easily implemented at high throughput for low cost. Results highlight the importance of lab protocol on data yield. An optimised “sample to sequencing” high-throughput protocol which incorporates SCR is included to allow for easy uptake by the wider scientific community.Copyright © The Author(s) 2025, corrected publication 2025 . This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.NHM Repositor
The Seaweeds of the Emirates
No full textCopyright © The Author(s) 2024. Open Access This chapter is licensed under the terms of the Creative Commons Attribution 4.0 International License http://creativecommons.org/licenses/by/4.0/), which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license and indicate if changes were made. The images or other third party material in this chapter are included in the chapter's Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the chapter's Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. The attached file is the published version of the book chapter.NHM Repositor