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135 results for “Metazoans”
Detecting local variations across metazoan communities in backreef depressions of Reunion Island (Mascarene Archipelago) through environmental DNA survey
<p>The back-reef depressions, or lagoons, of Reunion Island (western Indian Ocean) host a high abundance of organisms living amongst the coral reefs and are critical sites for artisanal fishing, tourism, and shoreline stability for the island. Over time, increasing degradation of Reunionese reefs has been observed due to overexploitation, beach erosion and eutrophication. Efforts to mitigate the impact of these pressures on aquatic organisms include biodiversity surveys primarily performed through visual censuses that can be logistically complex and may unintentionally overlook organisms. Surveys integrating environmental DNA (eDNA) collections have provided rapid biodiversity assessments, while helping to circumvent some limitations of visual surveys. The present study describes the results of an exploratory eDNA survey, which aims to characterize metazoan communities of four Reunionese lagoons located along the west coast of the island. As eDNA surveys first require deliberate study design and optimization for each new context, we sought to establish a modernized workflow implementing specialized equipment to collect and preserve samples to facilitate future studies in these lagoons. During the austral summer of 2023, samples were pumped directly from surface and bottom depths at each site through self-preserving filters which were then processed for DNA metabarcoding using regions of the 12S ribosomal RNA (12S), small ribosomal subunit 18S (18S) and Cytochrome Oxidase I (COI) genes. The survey detected high species richness that varied by site, and in a single collection period, recovered the presence of 60 teleost families and numerous invertebrate taxa, including members of the coral faunal community that are less studied in Reunion. Distinct biological communities were observed at each site, and within a single lagoon, suggesting that these differences are due to site-specific factors (e.g., environmental variables, geographic distance, etc.). Although continued protocol optimization is needed, the present findings demonstrate the successful application of an eDNA-based survey for biodiversity assessment within Reunionese lagoons.</p>
MATEdb2, a Collection of High-Quality Metazoan Proteomes across the Animal Tree of Life to Speed Up Phylogenomic Studies
<p>Recent advances in high-throughput sequencing have exponentially increased the number of genomic data available for animals (Metazoa) in the last decades, with high-quality chromosome-level genomes being published almost daily. Nevertheless, generating a new genome is not an easy task due to the high cost of genome sequencing, the high complexity of assembly, and the lack of standardized protocols for genome annotation. The lack of consensus in the annotation and publication of genome files hinders research by making researchers lose time in reformatting the files for their purposes but can also reduce the quality of the genetic repertoire for an evolutionary study. Thus, the use of transcriptomes obtained using the same pipeline as a proxy for the genetic content of species remains a valuable resource that is easier to obtain, cheaper, and more comparable than genomes. In a previous study, we presented the Metazoan Assemblies from Transcriptomic Ensembles database (MATEdb), a repository of high-quality transcriptomic and genomic data for the two most diverse animal phyla, Arthropoda and Mollusca. Here, we present the newest version of MATEdb (MATEdb2) that overcomes some of the previous limitations of our database: (i) we include data from all animal phyla where public data are available, and (ii) we provide gene annotations extracted from the original GFF genome files using the same pipeline. In total, we provide proteomes inferred from high-quality transcriptomic or genomic data for almost 1,000 animal species, including the longest isoforms, all isoforms, and functional annotation based on sequence homology and protein language models, as well as the embedding representations of the sequences. We believe this new version of MATEdb will accelerate research on animal phylogenomics while saving thousands of hours of computational work in a plea for open, greener, and collaborative science.</p>
Mitochondrial COXI sequences and associated metazoan abundances in soils collected from the McMurdo Dry Valleys, Antarctica from 1995 to 2022
As part of an ongoing long-term sampling effort conducted by the McMurdo Dry Valleys Long Term Ecological Research (LTER) project, the top 10 cm of soil was collected from sampling sites across the McMurdo Dry Valleys region of Antarctica. A subset of these samples representing each valley and a differing disturbance legacy from the last glacial maximum were analyzed for this data package. Samples were collected between 1995 and 2022. In each sample, the abundances of three genera of nematodes (Scottnema, Eudorylaimus, and Plectus), tardigrades, and rotifers were calculated. Following metazoan extractions, individual Scottnema lindsayae were selected for mitochondrial Cytochrome c oxidase I (COX1) Sanger dideoxy sequencing. Sequencing resulted in 249 assembled sequences of 285 base pairs after alignment and trimming.
MetaCOXI: An integrated collection of metazoan cytochrome oxidase subunit-I DNA sequences
<p><strong>MetaCOXI Sequences Taxonomy and Metadata</strong></p> <p>This collection is based on the integration of the European Nucleotide Archive (ENA, release 142) and the Barcode of Life Data Systems (BOLD: <a href="http://www.boldsystems.org/">http://www.boldsystems.org/</a>) data.</p> <p><strong>CONTENT: </strong>Currently it contains 5,608,848 entries of metazoan COXI sequences and their corresponding taxonomic classification and metadata. <em>MetaCOXI_Seqs.tar.gz</em> contains the full sequence collection in 'fasta' format. <em>MetaCOXI_Taxonomy_Metadata.tar.gz</em> contains the entries-associated taxonomy path and additional metadata</p> <p>Taxonomic path are provided for the following seven levels with their NCBI-TaxIDs: Kingdom, Phylum, Class, Order, Family, Genus, Species.</p> <p>For additional information visit: https://github.com/bachob5/MetaCOXI</p>
MetaCOXI: An integrated collection of metazoan cytochrome oxidase subunit-I DNA sequences
<p><strong>MetaCOXI Sequences in fasta format</strong></p> <p>This collection is based on the integration of the European Nucleotide Archive (ENA, release 142) and the Barcode of Life Data Systems (BOLD: http://www.boldsystems.org/) data.</p> <p><strong>CONTENT: </strong>Currently it contains 5,608,848 entries of metazoan COXI sequences and their corresponding taxonomic classification and metadata. MetaCOXI_Seqs_1.tar.gz contains the full sequence collection in 'fasta' format. MetaCOXI_Taxonomy_Metadata.tar.gz contains the entries-associated taxonomy path and additional metadata</p> <p>Taxonomic path are provided for the following seven levels with their NCBI-TaxIDs: Kingdom, Phylum, Class, Order, Family, Genus, Species.</p> <p>For additional information visit: https://github.com/bachob5/MetaCOXI</p>
Fig. 3. A in Metazoan Parasites Infecting Xiphias Gladius From The Eastern Coast Of Algeria (Sw Mediterranean Sea)
Fig. 3. A — Pennella instructa (Wilson, 1917) attached to the host's body with Conchoderma virgatum (red star); B — section of P. instructa surrounded by connective tissue; C — general morphology of parasite P. instructa (female); D — cystic forms found into the musculature: n — neck; lh — lateral horns; t — trunk; p — plumes; (ct) — connective tissue and (pi) — P. instructa. Scale bars:, C, D = 2 cm; B— x4 = 300 Μm.
Fig. 4 in Metazoan Parasites Infecting Xiphias Gladius From The Eastern Coast Of Algeria (Sw Mediterranean Sea)
Fig. 4. General morphology of the species Hysterothylacium aduncum (Rudolphi, 1802) observed under an optical microscope. A — anterior part showing lips (l); nerve ring (nr); oesophagus (e); intestinal caecum (ic); ventriculus (v); ventricular appendix (va) and intestine (i), lateral view. B — middle part showing oesophagus (e); intestinal caecum (ic); ventriculus (v); ventricular appendix (va) and intestine (i), lateral view. C — dorsal labium showing labia (lb) lateral view. D — posterior end showing spinous tail (sp); lateral view. Scale bars: A — x10 = 100 µm; B, C, D — x40 = 50 µm.
Fig. 2. A, B in Metazoan Parasites Infecting Xiphias Gladius From The Eastern Coast Of Algeria (Sw Mediterranean Sea)
Fig. 2. A, B — Tristoma coccineum Cuvier, 1817 and Tristoma integrum Diesing, 1850 (see red circles) attached to gills of X. gladius: C — ventral view and D — dorsal view, of General morphology of the species Tristoma coccineum Cuvier, 1817; E — ventral view and F — dorsal view of General morphology of the species Tristoma integrum Diesing, 1850 observed under binocular magnifying glass: P — parasite, hap — haptor, alv — alveoli, pp — papillae. Scale bars: A, B — 2 cm; C, D, E, F — 2 m.
Fig. 1 in First Japanese Record of Epistylis wuhanensis (Ciliophora: Epistylididae) Attached to Lernaea cyprinacea (Copepoda), with a List of Epistylis Species Attached to Metazoans in Japan
Fig. 1. Scanning electron micrographs of Epistylis wuhanensis Wang, Zhou, Guo, and Gu, 2017 from Japan. A, E. wuhanensis attached to exposed cephalothorax of Lernaea cyprinacea; B, extended zooid, lateral view; C, contracted zooid, lateral view; D, extended zooid, apical view; E, scopula of extended zooid. Abbreviations: AMZ, adoral zone of membranelles; ATB, aboral trochal band; PD, peristomial disc; PL, peristomial lip; SC, scopula; ST, stalk; ZO, zooid.
Fig. 2 in First Japanese Record of Epistylis wuhanensis (Ciliophora: Epistylididae) Attached to Lernaea cyprinacea (Copepoda), with a List of Epistylis Species Attached to Metazoans in Japan
Fig. 2. In vivo and protargol stained specimens of Epistylis wuhanensis Wang, Zhou, Guo, and Gu, 2017 from Japan (MPM 21760). A, Colony of zooids; B–D, extended zooid, lateral view; E, abstomal region of infraciliature polykineties; F, extended zooid, apical view. Abbreviations: ATB, aboral trochal band; AZM, adoral zone of membranelles; CV: contractile vacuole; CY, cytopharynx; G, germinal kinety; H, haplokinety; MN, macronucleus; P1–3, infundibular polykineties 1–3; PD, peristomial disc; PL, peristomial lip; Po, polykinety; SC, scopula; ST, stalk; ZO, zooid.
miRNAture v.1.1: updated dataset with curated metazoan miRBase v.22.1 and Rfam-14.4 miRNA families.
<p>This folder contains the updated data to annotate miRNAs using miRNAture v.1.1. As usual, it includes CMs, HMMs and required pre-calculated data to validate mature miRNAs (corrected hairpins, mature files and miRBase genomes). It contains a 1034 and 1124 metazoan miRNA families curated from miRBase v.22.1 and Rfam 14.4, respectively. To use this dataset, refer the path of this uncompressed folder with the -dataF/-datadir flag in miRNature v.1.1.</p>
Fig. 5 in First report of molecular taxonomic analyses of European beaver metazoan parasites from Hungary
Fig. 5 Phylogenetic tree of Schizocarpus beaver fur mites and related astigmated mites based on the cytochrome c oxidase subunit I (COI) gene. The tree was generated with the maximum likelihood method and GTR model in MEGA 7.0. Nucleotide sequences obtained in this study are indicated in red. Branch lengths represent the number of substitutions per site inferred according to the scale shown
Fig. 4 in First report of molecular taxonomic analyses of European beaver metazoan parasites from Hungary
Fig. 4 Phylogenetic tree of Stichorchis subtriquetrus beaver fluke and related flukes based on the 18S rRNA gene. The tree was generated with the maximum likelihood method and Kimura model in MEGA 7.0. Nucleotide sequences obtained in this study are indicated in red. Branch lengths represent the number of substitutions per site inferred according to the scale shown
Fig. 3 in First report of molecular taxonomic analyses of European beaver metazoan parasites from Hungary
Fig. 3 Characteristics of Schizocarpus sp. adult male mite from Castor fiber in Hungary, a habitus in ventral view, b ventral opisthosoma with the suckers and the setae, c opisthosoma and the opisthonotal shield, d anterioventral part of the mite with the mouthparts and legs in higher magnification
Fig. 2 in First report of molecular taxonomic analyses of European beaver metazoan parasites from Hungary
Fig. 2 Dorsal and abdominal view of Platypsyllus castoris adult removed from Castor fiber in Hungary
Fig. 1 in First report of molecular taxonomic analyses of European beaver metazoan parasites from Hungary
Fig. 1 Castor fiber trapping sites in Hungary 2017–2021. a Győr-Moson-Sopron county 13 individuals; b Jász-Nagykun-Szolnok county 26 individuals; c Zala county 6 individuals; location; d Veszprém county 2 individuals
Fig. 1 in Metazoan parasites of California sea lions (Zalophus californianus): A new data and review
Fig. 1. Microphotographs of the metazoan parasites of California sea lions Zalophus califronianus. A, B – Apophallus zalophi, intestine (Digenea), C – Zalophotrema hepaticum, liver (Digenea), D, G – Contracaecum ogmorhini s. l., stomach (Nematoda), E, H – Pseudoterranova decipiens s. l., stomach (Nematoda), F – Anisakis simplex s. l., stomach (Nematoda), I, S – Diphyllobothrium sp., intestine (Cestoda), J, K – Orthohalarchne attenuata, nasal cavity (Acarina), L – Orthohalarchne diminuata (Acarina), M, R – Anophryocephalus sp., intestine (Cestoda), N, O – Corynosoma obtuscens, intestine (Acanthocephala), P, Q – Profilicollis altmani, intestine (Acanthocephala). A, C, F–I, K, M, N, P – under dissecting scope. B, Q – at light microscope. D, E, O, R, S, – at scanning electron microscope. J – in situ.
Fig. 2 in Metazoan parasites of California sea lions (Zalophus californianus): A new data and review
Fig. 2. Prevalence and proportion of separate species in the gastrointestinal helminth community of California sea lions (Zalophus californianus). Abbreviations of the genera: A – Anisakis, An – Andracantha, Ap – Apophallus, C – Contracaecum, Co – Corynosoma, P – Pseudoterranova, Pa – Parafilaroides, Pr – Profilicollis, Z – Zalophotrema.
Fig. 3 in Raccoons contraband - The metazoan parasite fauna of free-ranging raccoons in central Europe
Fig. 3. Several factors influence the spread of Baylisascaris procyonis, infestation rates are higher in urban and agricultural environments than in semi-natural sites. Thus, a denser population of raccoons in urban areas has a beneficial effect on infestation numbers. However, other factors such as vegetation density as well as available food resources, microclimate, soil characteristics, and land use also influence the rate of B. procyonis infestation and zoonotic potential. An Unembryonated eggs are shed by the raccoon. Eggs undergo 2–4 weeks of development outside the body until the embryonated and infective stage is reached. Embryonated eggs can remain in the environment for several months and remain infectious. B In urban and agricultural areas, new intermediate hosts are frequently infected. These are either eaten by the raccoon or can become infected like the raccoon (e.g., dogs) and then also excrete eggs. C In urban and agricultural areas, there are usually other off-target hosts than in semi-natural areas. Here, for example, cattle or chickens have been confirmed as false hosts. In these hosts, visceral or ocular larva migrans is induced without the larvae being ingested by the raccoon. D Children can become infected with infectious stages and contract Larva migrans through constructed latrines as well as simple defecation in or near play facilities (e.g., sandboxes, climbing houses). E Due to the steady spread of raccoons, new false hosts are increasingly infected with eggs of B. procyonis, such as chicken birds (pheasants), even in semi-natural areas. F The normal life cycle of B. procyonis includes the prey of P. lotor such as various small mammals or birds. In Europe, these species also play the main role in semi-natural habitats. G Raccoons, as the primary host, become infected with B. procyonis by direct ingestion of embryonated eggs through contact with latrines and via excreted feces of infected raccoons. Numerous small mammals or birds serve as paratenic or intermediate hosts, passing larvae directly to the raccoon. The worms grow in the raccoon and can reach high densities in the raccoon's intestine.
Fig. 2 in Raccoons contraband - The metazoan parasite fauna of free-ranging raccoons in central Europe
Fig. 2. Light micrographs of different endo- and ectoparasite species showing the general morphology of the identified parasites in the investigated raccoons; A: Euryhelmis squamula, B: Plagiorchis muris, C: Porrocaecum ensicaudatum, D: Polymorphus minutus, E: Neotrombicula autumnalis, F: Sarcoptes scabiei.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.