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The genome sequence of the chalcid wasp, Chalcis sispes Linnaeus, 1761
Get PDFWe 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
Get PDFAbstractMyxozoans 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
Get PDFAbstract
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
Get PDFGlioblastoma 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
Get PDFWhile 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
Bone retouchers and technological continuity in the Middle Stone Age of North Africa
Get PDFEvidence for specialised bone tools has recently been reported for the Middle Stone Age of North Africa [one], which complements similar finds of slightly younger age in South Africa [two, three]. However, until now scant reference has been made to lesser known tools also made of bone ('bone retouchers') that were employed specifically as intermediaries for working or refining stone artefacts, that are sometimes present in these assemblages. In this paper we describe 20 bone retouchers from the cave of Grotte des Pigeons at Taforalt in north-east Morocco. This is the largest stratified assemblage of bone retouchers from a North African MSA site, and the biggest single collection so far from the African Continent. A total of 18 bone retouchers was recovered in securely dated archaeological levels spanning a period from ~ 84.5 ka to 24 ka cal BP. A further two bone retouchers were found in a layer at the base of the deposits in association with Aterian artefacts dating to around 85,000 BP and so far represent the earliest evidence of this type of tool at Taforalt. In this paper we present a first, detailed description of the finds and trace the stages of their production, use and discard (chaîne opératoire). At the same time, we assess if there were diachronic changes in their form and function and, finally, explore their presence in relation to stone tools from the same occupation layers of the cave.Copyright: © 2020 Turner 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 author and source are credited. The attached file is the published version of the article.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
An expanded diversity of oomycetes in Carboniferous forests: Reinterpretation of Oochytrium lepidodendri (Renault 1894) from the Esnost chert, Massif Central, France
Get PDF335–330 million-year-old cherts from the Massif Central, France, contain exceptionally well-preserved remains of an early forest ecosystem, including plants, fungi and other microorganisms. Here we reinvestigate the original material prepared by Renault and Roche from collections of the Muséum National d’Histoire Naturelle, Paris, and present a re-evaluation of Oochytrium lepidodendri (Renault 1894), originally described as a zoosporic fungus. Confocal laser scanning microscopy (CLSM) was used to study the microfossils, enabling us in software to digitally reconstruct them in three-dimensional detail. We reinterpret O. lepidodendri as a pseudofungus and favour placement within the oomycetes, a diverse clade of saprotrophs and both animal and plant parasites. Phylogenetically, O. lepidodendri appears to belong to a group of oomycetes distinct from those previously described from Paleozoic rocks and most likely related to the Peronosporales s.l. This study adds to our knowledge of Paleozoic eukaryotic diversity and reinforces the view that oomycetes were early and diverse constituents of terrestrial biotas, playing similar ecological roles to those they perform in modern ecosystems.Copyright: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication. The attached file is the published version of the article.NHM Repositor