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SNP data: Comparison of molecular surveillance methods to assess changes in the population genetics of Plasmodium falciparum in high-transmission
<p>Genetic diversity and population structure of <em>Plasmodium falciparum</em> are assessed here using three established methods (i) SNP barcoding (panel of 24-biallelic loci), (ii) microsatellite genotyping (panel of 12-multiallelic loci), and (iii) varcoding (fingerprinting var gene diversity, akin to microhaplotyping) to identify changes in parasite population genetics in response to a short-term indoor residual spraying (IRS) intervention. Typical of high seasonal transmission in Africa, multiclonal infections were found in <span>82.3% (median 3; range 1–18) and 57.8% (median 2; range 1–12) of asymptomatic individuals pre- and post-IRS, respectively, in Bongo District, Ghana. </span>Since directly phasing multilocus haplotypes for population genetic analysis is not possible for biallelic SNPs and microsatellites, we chose 200 low-complexity infections for analysis. Each genotyping method presented a different pattern of change in population diversity and structure as a consequence of variability in usable data and the relative polymorphism of the molecular markers (<a>SNPs < microsatellites < var</a>). In terms of neutral variation, the 24-SNP barcode was the least informative, largely due to the bi-allelic nature of SNPs leading to a high proportion of double-allele calls (<a>DACs</a>), whereas multiallelic microsatellites showed high haplotype diversity with ten markers but no measurable change in population structure after IRS. Varcoding provided the most informative and nuanced description of changes in population structure, showing high diversity with a subtle but measurable change to less related var repertoires as a result of the IRS intervention. Relative performance, suitability, and cost-effectiveness of the methods relevant to local malaria elimination in high-transmission endemic areas are discussed. </p>
Supporting data and code for: Investigation on the sensitivity of Plasmopara viticola to amisulbrom and ametoctradin in French vineyards using bioassays and molecular tools
<p>This is a small modification of the first release of the final data and code for the article entitled "Investigation on the sensitivity of Plasmopara viticola to amisulbrom and ametoctradin in French vineyards using bioassays and molecular tools" accepted for publication in Pest Management Science.</p>
FIGURE 7 in A review of species recognition in the Phenacoccus aceris species-group (Hemiptera: Coccomorpha: Pseudococcidae) using molecular and morphological data
FIGURE 7. Habitus photographs of PACE2 (upper) and PACE4B (lower) from different populations.
Supplementary material 1 from: Radek R, Wurzbacher C, Gisder S, Nilsson RH, Owerfeldt A, Genersch E, Kirk PM, Voigt K (2017) Morphologic and molecular data help adopting the insect-pathogenic nephridiophagids (Nephridiophagidae) among the early diverging fungal lineages, close to the Chytridiomycota. MycoKeys 25: 31-50. https://doi.org/10.3897/mycokeys.25.12446
Figure S1 : Data type: molecular data
Supplementary material 2 from: Balakirev A, Abramov A, Rozhnov V (2014) Phylogenetic relationships in the Niviventer-Chiromyscus complex (Rodentia, Muridae) inferred from molecular data, with description of a new species. ZooKeys 451: 109-136. https://doi.org/10.3897/zookeys.451.7210
The list of samples used for combined Cyt b+COI+IRBP+GHR analysis:
Supplementary material 1 from: Balakirev A, Abramov A, Rozhnov V (2014) Phylogenetic relationships in the Niviventer-Chiromyscus complex (Rodentia, Muridae) inferred from molecular data, with description of a new species. ZooKeys 451: 109-136. https://doi.org/10.3897/zookeys.451.7210
Complete list of samples used for phylogenetic reconstructions:
Figures 1-9 from: Radek R, Wurzbacher C, Gisder S, Nilsson RH, Owerfeldt A, Genersch E, Kirk PM, Voigt K (2017) Morphologic and molecular data help adopting the insect-pathogenic nephridiophagids (Nephridiophagidae) among the early diverging fungal lineages, close to the Chytridiomycota. MycoKeys 25: 31-50. https://doi.org/10.3897/mycokeys.25.12446
Figures 1-9 Nephridiophaga maderae, 1, 2, 5–9 bright field 3 phase contrast 4 scanning electron microscopy. 1 Three sporogonial plasmodia with different numbers of included spores. Arrows point to plasma membrane. 2 Merogonial plasmodium with numerous nuclei. 3 Mature spores. 4 The upper surface of the spore possesses a central spore opening (arrow, left spore) while the lower surface of the spore lacks an opening (right spore). 5, 6 Paraffin sections stained with hematoxylin-eosin. Generally, the plasmodia (pl) are found in the lumen of the Malpighian tubule but are often attached to the microvilli (mv) (5). Rarely, aggregates of vegetative plasmodia (arrow) occur in the epithelial cells of the Malpighian tubules (6). n = nuclei of epithelial cells. 7–9 Smears of macerated tubules stained with Giemsa depicting vegetative plasmodia (7), stained young spores (8), and unstained mature spores with residual nuclei (arrows) of the mother sporoplasm. Scale bars: 5 µm (1–4), 50 µm (5), 10 µm (6–9).
Figures 10-14 from: Radek R, Wurzbacher C, Gisder S, Nilsson RH, Owerfeldt A, Genersch E, Kirk PM, Voigt K (2017) Morphologic and molecular data help adopting the insect-pathogenic nephridiophagids (Nephridiophagidae) among the early diverging fungal lineages, close to the Chytridiomycota. MycoKeys 25: 31-50. https://doi.org/10.3897/mycokeys.25.12446
Figures 10-14 Nephridiophaga blattellae, 10–13 transmission electron microscopy, 14 Calcofluor white staining. 10 Meront with several nuclei (n) and mitochondria (mi) in the lumen of Malpighian tubule. Inset: Mitochondrium with tubular to sac-like cristae. 11 Sporogenic plasmodium containing mature spores (sp), mitochondria (mi), and vegetative nuclei (n) in the cytoplasm. The plasmodium is anchored to the microvilli (mv) of epithelial cells (ep) of the tubule. 12 Young spore within the cytoplasm of a sporogenic plasmodium, surrounded by a layer of vesicles. The spore cytoplasm contains one nucleus (n), mitochondria (mi), and endoplasmic reticulum (er). 13 An infectious sporoplasm hatches through the central spore opening, leaving behind the spore wall of the emptying spore (sp). The nucleus (n) is squeezed through the tiny spore opening. 14 Calcofluor white stains the spore wall indicating the presence of chitin (bluish color). Scale bars: 1 µm (10–13), inset 0.1 µm (10), 5 µm (14).
Figure 15 from: Radek R, Wurzbacher C, Gisder S, Nilsson RH, Owerfeldt A, Genersch E, Kirk PM, Voigt K (2017) Morphologic and molecular data help adopting the insect-pathogenic nephridiophagids (Nephridiophagidae) among the early diverging fungal lineages, close to the Chytridiomycota. MycoKeys 25: 31-50. https://doi.org/10.3897/mycokeys.25.12446
Figure 15 - Bayesian phylogenetic tree including major lineages of the Holomycota (Liu et al. 2009; syn.: Nucletmycea, Brown et al. 2009), i.e. Fungi, Cryptomycota, and the basal Nucleariida, together with Holomycota sister clades Choanomonada, Ichthyosporea, and Filasterea (Holozoa; Lang et al. 2002). Nephridiophaga species (star) form a clade together with the flagellate fungi, here indicated as Chytridiomycota s.l. The scale indicates expected changes per site. Branch support is given as Bayesian posterior probabilities above 0.95 (black circles) and maximum likelihood resampling values above 90% (white circles). Filled black circles mark support from both methods.
Figure 5 from: Esmaeili-Rineh S, Mirghaffari SA, Sharifi M (2017) The description of a new species of Niphargus from Iran based on morphological and molecular data. Subterranean Biology 22: 43-58. https://doi.org/10.3897/subtbiol.22.11286
Figure 5 - Niphargus hakani sp. n., male 9 mm (holotype, ZCRU Amph.1010). A Pleopod I B Pleopod II C Pleopod III D Uropod I E Uropod II F Uropod III. G Epimeral plates H Telson. Scale bars: 1=0.5 mm (G–H). 2=1 mm (A–E). 3=2mm F.
Figure 4 from: Esmaeili-Rineh S, Mirghaffari SA, Sharifi M (2017) The description of a new species of Niphargus from Iran based on morphological and molecular data. Subterranean Biology 22: 43-58. https://doi.org/10.3897/subtbiol.22.11286
Figure 4 - Niphargus hakani sp. n., male 9 mm (holotype, ZCRU Amph.1010). A Pereopod III B Pereopod IV C Pereopod V D Pereopod VI E Pereopod VII. Scale bars: 1mm (A–E).
Figure 3 from: Esmaeili-Rineh S, Mirghaffari SA, Sharifi M (2017) The description of a new species of Niphargus from Iran based on morphological and molecular data. Subterranean Biology 22: 43-58. https://doi.org/10.3897/subtbiol.22.11286
Figure 3 - Niphargus hakani sp. n., male 9 mm (holotype, ZCRU Amph.1010). A Gnathopod I B Gnathopod II C Maxilliped D Labium E Maxilla II. Scale bars: 1=0.5 mm (C–E). 2=1 mm (A–B).
Figure 2 from: Esmaeili-Rineh S, Mirghaffari SA, Sharifi M (2017) The description of a new species of Niphargus from Iran based on morphological and molecular data. Subterranean Biology 22: 43-58. https://doi.org/10.3897/subtbiol.22.11286
Figure 2 - Niphargus hakani sp. n., male 9 mm (holotype, ZCRU Amph.1010). A Antenna I B Antenna II C Head D–E Maxilla I F Left mandible. G Right mandible. H Mandibular palp. Scale bars: 1=0.25 mm (F–G). 2=0.5 mm (C–E, H). 3=1mm (A–B).
Figure 6 from: Esmaeili-Rineh S, Mirghaffari SA, Sharifi M (2017) The description of a new species of Niphargus from Iran based on morphological and molecular data. Subterranean Biology 22: 43-58. https://doi.org/10.3897/subtbiol.22.11286
Figure 6 - Bayesian consensus tree of 49 Niphargus species (48 taxa from Esmaeili-Rineh et al. 2015a, 2016), based on the 28S ribosomal DNA sequences. Species are identified and named according to the valid taxonomic description. Posterior probabilities are indicated on main branches.
Data From: Investigating the Effect of GLU283 Protonation State on the Conformational Heterogeneity of CCR5 by Molecular Dynamics Simulations
<p>This dataset contains MD simulation results for CCR5 receptor in different states. There are three states this GPCR could be in: 1.apo state, i.e. not bound to any other protein or ligand 2.holo state, i.e. bound by maraviroc (MRV) 3.GP120 bound state, i.e. bounded to HIV envelope protein GP120 and human receptor CD4. </p> <p>For apo state simulations, three different starting structure were used and the simulation results for them are given in three different folders named after the PDB ID of initial structures. </p> <p>One critical residue of CCR5 receptor, GLU283, was considered in two different protonation state, hence there are two folders for each studied system, GLU283 and GLH283 for differently protonated systems. </p> <p>The MD trajectories of studied systems are in dcd format and due to size issues waters, ions and membrane atoms were removed. </p> <p>For each system, three replica MD simulations were performed, hence, there are three folders with names REPLICA1, REPLICA2, REPLICA3.</p> <p> </p>
Supplementary material 1 from: Xu K-W, Han Y-T, Dong Y-R, Guo J-Q, Mao L-F, Liao W-B (2024) Asplenium guodanum (Aspleniaceae), a distinct new fern species from northern Guangdong, China, based on morphological data and molecular phylogeny. PhytoKeys 241: 191-200. https://doi.org/10.3897/phytokeys.241.122789
List of voucher specimens and Genbank accession numbers used in phylogenetic analyses
Figure 3 from: Xu K-W, Han Y-T, Dong Y-R, Guo J-Q, Mao L-F, Liao W-B (2024) Asplenium guodanum (Aspleniaceae), a distinct new fern species from northern Guangdong, China, based on morphological data and molecular phylogeny. PhytoKeys 241: 191-200. https://doi.org/10.3897/phytokeys.241.122789
Figure 3 Maximum Likelihood phylogeny of the Asplenium bullatum clade, based on six plastid markers (atpB, rbcL, rps4 & rps4-trnS and trnL & trnL-F). The numbers associated with branches are Maximum Likelihood bootstrap support (MLBS) and Bayesian Posterior Probability (BIPP). The asterisk indicates MLBS = 100 or BIPP = 1.00.
Figure 1 from: Xu K-W, Han Y-T, Dong Y-R, Guo J-Q, Mao L-F, Liao W-B (2024) Asplenium guodanum (Aspleniaceae), a distinct new fern species from northern Guangdong, China, based on morphological data and molecular phylogeny. PhytoKeys 241: 191-200. https://doi.org/10.3897/phytokeys.241.122789
Figure 1 Macromorphology of Asplenium guodanum sp. nov. A habitat B habit C abaxial lamina D frond E adaxial lamina F rachis G abaxial view of pinna H adaxial view of pinna I reduced pinna base J scales at base stipe K rhizome L fiddlehead.
Data For Hybrid Monte-Carlo Molecular Dynamics Methods For Estimation of Solidus and Liquidus Compositions, a Case Study in Cu-Ni and Au-Si
Open the record for dataset details and reuse information.
Figure 49. Pachyula crassilabris, AMS B 9961 in A new classification of the family Ariidae (Osteichthyes: Ostariophysi: Siluriformes) based on combined analyses of morphological and molecular data
Figure 49. Pachyula crassilabris, AMS B 9961, New Guinea, type species of the genus.
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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.