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76 results for “molecular tool”
Molecular Docking - AutoDock tool
<p>Docking studies will help in appropriate consideration of the protein’s active site and its interaction with the ligand. The interaction between a small molecule and a protein may result in inhibition of the protein. Molecular docking program Autodock 4.2 was used in this study.</p>
FIGURE 5 in Anacroneuria flintorum Froehlich 2002 (Plecoptera: Perlidae): Notes, distribution, and life stages association using molecular tools
FIGURE 5. Fully developed specimen: head and pronotum (A), pronotum and mesonotum in lateral view (B) and mesonotum and forewings (C). Teneral specimen: head and pronotum (D), pronotum and mesonotum in lateral view (E), mesonotum and forewings (F). Lateral folds pointed in B and remnants of gills in thoracic segments in E. Scale: 1 mm.
FIGURE 4 in Anacroneuria flintorum Froehlich 2002 (Plecoptera: Perlidae): Notes, distribution, and life stages association using molecular tools
FIGURE 4. Males from ES (A), SC (B), PECJ (C) and Paranapiacaba mountains (D and E). Male collected in 2014 (D) and male collected in 1999 (E) not preserved in alcohol.
FIGURE 3 in Anacroneuria flintorum Froehlich 2002 (Plecoptera: Perlidae): Notes, distribution, and life stages association using molecular tools
FIGURE 3. Nymph of Anacroneuria flintorum: labium (A), right mandible (B), right maxilla (C), pronotum left leg, dorsal view (D); cerci in proximal, medial and distal view (E). Scales: 0.5 mm for A, B and C; 0.5 mm for D; 0.5 mm and 0.25 mm for E, respectively.
FIGURE 2 in Anacroneuria flintorum Froehlich 2002 (Plecoptera: Perlidae): Notes, distribution, and life stages association using molecular tools
FIGURE 2. Nymph of Anacroneuria flintorum: head and pronotum (A), abdominal segments and cercus (B), mesonotum and metanotum in dorsal view (C) and ventral view (D). Scale: 1 mm.
FIGURE 1. Neighbor-joining tree for cytochrome c oxidase subunit I in Anacroneuria flintorum Froehlich 2002 (Plecoptera: Perlidae): Notes, distribution, and life stages association using molecular tools
FIGURE 1. Neighbor-joining tree for cytochrome c oxidase subunit I (COI) sequences (433 bp) from Anacroneuria flintorum Froehlich and related stoneflies from Espírito Santo and São Paulo States, Brazil, modeled by Kimura-2-parameter (K2P).
Fig. 6 in Molecular tools for resolving Merodon ruficornis group (Diptera, Syrphidae) taxonomy
Fig. 6 Taxa tree chronogram of Merodon ruficornis species group obtained by BEAST. Mean node ages were estimated using a Lognormal relaxed clock model and Birth–Death tree model. The numbers represent the divergence time in million years ago (Mya)
Fig. 4 in Molecular tools for resolving Merodon ruficornis group (Diptera, Syrphidae) taxonomy
Fig. 4 Bayesian trees of the Merodon ruficornis species group based on ITS2 sequences. Bayesian posterior probabilities are indicated near nodes. a Sequences without gaps. b Sequences with binary coded gaps
Fig. 1 in Molecular tools for resolving Merodon ruficornis group (Diptera, Syrphidae) taxonomy
Fig. 1 Utility of analysed molecular tools for resolving taxonomy in Merodon ruficornis species group. Each species and/or population is represented by a different colour. Solid colour boxes indicate successful species/population delimitation by a particular tool. Multicolour boxes depict clusters formed by multiple taxa. The amplification of ITS2 sequences from M. fulvitarsis samples was not successful (NA)
Data from: Defining conservation units with enhanced molecular tools to reveal fine scale structuring among Mediterranean green turtle rookeries
Understanding the connectivity among populations is a key research priority for species of conservation concern. Genetic tools are widely used for this purpose, but the results can be limited by the resolution of the genetic markers in relation to the species and geographic scale. Here, we investigate natal philopatry in green turtles (Chelonia mydas) from four rookeries within close geographic proximity (~ 200km) on the Mediterranean island of Cyprus. We genotyped hypervariable mtSTRs, a mtDNA control region sequence (CR) and 13 microsatellite loci to genetically characterise 479 green turtles using markers with different modes of inheritance. We demonstrated matrilineal stock structure for the first time among Mediterranean green turtle rookeries. This result contradicts previous regional assessments and supports a growing body of evidence that green turtles exhibit a more precise level of natal site fidelity than has commonly been recognised. The microsatellites detected weak male philopatry with significant stock structure among three of the six pairwise comparisons. The absence of Atlantic CR haplotypes and mtSTRs among these robust sample sizes reaffirm the reproductive isolation of Mediterranean green turtles and supports their status as a subpopulation. A power analysis effectively demonstrated that the mtDNA genetic markers previously employed to evaluate regional stock identity were confounded by an insufficient resolution considering the recent colonisation of this region. These findings improve the regional understanding of stock connectivity and illustrate the importance of using suitable genetic markers to define appropriate units for management and conservation.
Challenges of copro-parasitological surveys in wild Iberian ibex (Capra pyrenaica) populations addressed through a combination of molecular and statistical tools
<p><span>Copro-parasitological surveys in wildlife face challenges due to the secretive nature of many species and the unknown performance of the diagnostic tests employed. To overcome these issues, we used a combination of hierarchical models (site-occupancy and N-mixture models) applied to copro-parasitological data obtained from faecal samples assigned to the host species by molecular methods in the Iberian ibex in north-western Iberian Peninsula. The aims were to compare the performance of four diagnostic tests (Mini-FLOTAC, McMaster, Willis flotation, and natural sedimentation) and to use this methodological approach (molecular analysis with hierarchical models) to better estimate positivity proportion and shedding intensity in a wild ibex population. Pooled faecal samples were collected, and those confirmed by molecular analyses to be the host species in question were included in the study. Hierarchical models confirmed different performances of each diagnostic test, with Mini-FLOTAC showing higher sensitivity for eimeriid coccidia, Willis flotation (for proportion positive) and McMaster (for shedding intensity) in gastrointestinal Strongylida, and equal performance of MiniFlotac/Willis flotation (for proportion positive) and MiniFlotac/McMaster (for shedding intensity) in <em>Moniezia</em> spp. This study employed a combination of molecular and statistical methods that improved the estimates of prevalence and shedding intensity and allowed us to compare the performance of four diagnostic tests while assessing the effect of covariates. Such improvements are critical to enhancing inference in non-invasive wildlife copro-parasitological studies.</span></p>
Combined sequence matrix for: Molecular phylogenetic tools reveal the phytogeographic history of the genus Capparis L. and suggest its reclassification
<p><em><span>Capparis</span></em><span> L. is the largest genus of the family Capparaceae, represented by 142 species in the tropics and subtropics of the Old World. Despite being one of the medicinally and economically important genera with its unique distribution pattern, the evolutionary history of <em>Capparis</em> remained unexplored. Moreover, the phylogenetic relationships, origin, dispersal, and character evolution of the genus were poorly understood. With the objectives to (i) test the congruence between the molecular and morphological datasets, (ii) validate Jacobs' hypothesis on the origin, dispersal, and speciation pattern of <em>Capparis</em> using new fossil data, and (iii) understand the possible evolutionary role of some key morphological characters, we sampled across the five speciation centres of <em>Capparis</em>. The results derived from three plastidial markers (<em>matK</em>, <em>trnL</em>-<em>F</em> and <em>rbcL</em>) revealed incongruence with the morphological datasets and suggested a new sectional classification in <em>Capparis</em>. Divergence dating analysis revealed that Capparaceae originated in Africa at 47.25 MYA and <em>Capparis</em> in Peninsular India at about 29.32 MYA. <em>Capparis</em> followed multiple forward and backward dispersal, supporting the "into and out of India" hypothesis. These dispersal events were consistent with the various land bridges present during the Eocene to Miocene in different parts of the old world. The only long-distance dispersal event was observed in the case of the new world Capparaceae, corroborating the earlier findings. Our results suggest West Asia to the North African region as another centre of speciation for <em>Capparis</em> and present a robust age estimate for the genus. The character state reconstruction of <em>Capparis</em> revealed a unique evolutionary adaptation due to exposure to various climatic conditions and the acquisition of suitable pollination strategies. We hypothesize that the gynophore length, calyx shape, and blotches on petals contribute substantially to the pollination success. </span></p>
Novel Molecular Spectrometric Biomarkers in Blood Plasma as an Early Diagnostic Tool in HCC
ClinicalTrials.gov study NCT04221347. IPD Sharing: NO. Countries: 1. Publications: 1.
Development of a Molecular Diagnostic Tool for Endometrial Cancer.
ClinicalTrials.gov study NCT06192017. IPD Sharing: NO. Countries: 1. Publications: 15.
Challenges of copro-parasitological surveys in wild Iberian ibex (Capra pyrenaica) populations addressed through a combination of molecular and statistical tools
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Data from: New molecular tools for the identification of two endangered smooth-hound sharks, Mustelus mustelus and Mustelus punctulatus
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Combined sequence matrix for: Molecular phylogenetic tools reveal the phytogeographic history of the genus Capparis L. and suggest its reclassification
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Data from: Defining conservation units with enhanced molecular tools to reveal fine scale structuring among Mediterranean green turtle rookeries
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Molecular ecological network analyses: An effective conservation tool for the assessment of biodiversity, trophic interactions, and community structure
<p>Global biodiversity is threatened by the anthropogenic restructuring of animal communities, which rewires species interaction networks in real-time as individuals are extirpated or introduced. Conservation science and adaptive ecosystem management demands more rapid, quantitative, and non-invasive technologies for robustly capturing changing biodiversity and quantifying species interactions. Here we develop molecular ecological network analyses (MENA) as an ecosystem assessment tool to address these needs. To construct the ecological network, we used environmental DNA from feces to identify the plant and mammal diet of two carnivores: puma (<i>Puma concolor</i>) and bobcat (<i>Lynx rufus</i>); two omnivores: coyote (<i>Canis latrans</i>) and gray fox (<i>Urocyon cinereoargenteus</i>); and two herbivores: black-tailed deer (<i>Odocoileus hemionus</i>) and black-tailed jackrabbit (<i>Lepus californicus)</i> in a well-studied Californian reserve<i>. </i>To evaluate MENA as a comprehensive biodiversity tool, we applied our framework to identify the structure of the network, patterns of trophic interactions, key species, and to assess its utility in capturing the biodiversity of the area. The high dietary taxonomic resolution enabled the assessment of species diversity, niche breadth and overlap. The network analysis revealed a dense ecological network with a high diversity of weakly connected species and a community that is highly modular and non-nested. The significant prevalence of tri-trophic chain and exploitative competition patterns indicates (i) the removal or reintroduction of a top predator would trigger a trophic cascade within this community, directly affecting their prey and indirectly the plant communities, and (ii) the potential impact of indirect effects between two predators that consume the same prey. These results suggest that the recent resurgence of puma in the study area may impact the herbaceous and woody vegetation and the population size of other predators. This effect of fluctuating predator populations and plant communities could be predicted through MENA's fine-scale assessment of the diet selection and the identified keystone species. Although just using a subset of species, MENA more rapidly, accurately, and effectively captured the broader biodiversity of the area in comparison to other methodologies. MENA reconstructed and unveiled the hidden complexity in trophic structure and interaction networks within the community, providing a promising toolkit for biodiversity and ecosystem management.</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>
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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.