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160 results for “Molecular detection”
Data from: A new multiplex SNP genotyping assay for detecting hybridization and introgression between the M and S molecular forms of Anopheles gambiae
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Data from: A Bayesian approach for detecting the impact of mass-extinction events on molecular phylogenies when rates of lineage diversification may vary
The paleontological record chronicles numerous episodes of mass extinction that severely culled the Tree of Life. Biologists have long sought to assess the extent to which these events may have impacted particular groups. We present a novel method for detecting the impact of mass-extinction events on molecular phylogenies, even in the presence of tree-wide diversification-rate variation and in the absence of additional information from the fossil record. Our approach is based on an episodic stochastic-branching process model in which rates of speciation and extinction are constant between events. We model three types of events: (i) instantaneous tree-wide shifts in speciation rate; (ii) instantaneous tree-wide shifts in extinction rate and (iii) instantaneous tree-wide mass-extinction events. Each type of event is modelled as an independent compound Poisson process (CPP), where the waiting times between events are exponentially distributed with event-specific rate parameters. The magnitude of each event is drawn from an event-specific prior distribution. Parameters of the model are then estimated in a Bayesian statistical framework using a reversible-jump Markov chain Monte Carlo algorithm. This Bayesian approach enables us to distinguish between tree-wide diversification-rate variation and mass-extinction events by specifying a biologically informed prior on the magnitude of mass-extinction events and empirical hyperpriors on the diversification-rate parameters. We demonstrate via simulation that this method has substantial power to detect the number of mass-extinction events and provides unbiased estimates of the timing of mass-extinction events, while exhibiting an appropriate (i.e. <5%) false-discovery rate, even when background diversification rates vary. Finally, we provide an empirical demonstration of this approach, which reveals that conifers experienced a major episode of mass extinction ≈23 Ma. This new approach – the CPP on Mass-Extinction Times (CoMET) model – provides an effective tool for detecting the impact of mass-extinction events on molecular phylogenies, even when the history of those groups includes temporal variation in diversification rates and when the fossil history of those groups is poorly known.
Data from: Transgenes in Mexican maize: molecular evidence and methodological considerations for GMO detection in landrace populations
A possible consequence of planting GMOs in centers of crop origin is unintended gene flow into traditional landraces. In 2001, a study reported the presence of the transgenic 35S promoter in maize landraces sampled in 2000 from the Sierra Juarez of Oaxaca, Mexico. Analysis of a large sample taken from the same region in 2003 and 2004 could not confirm the existence of transgenes, thereby casting doubt on the earlier results. These two studies were based on different sampling and analytical procedures and are thus hard to compare. Here we present new molecular data for this region that confirm the presence of transgenes in three of 23 localities sampled in 2001. Transgene sequences were not detected in samples taken in 2002 from nine localities, while directed samples taken in 2004 from two of the positive 2001 localities were again found to contain transgenic sequences. These findings suggest the persistence or re-introduction of transgenes up until 2004 in this area. We address variability in recombinant sequence detection by analyzing the consistency of current molecular assays. We also present theoretical results on the limitations of estimating the probability of transgene detection in samples taken from landraces. The inclusion of a limited number of female gametes, but more importantly, aggregated transgene distributions may significantly lower detection probabilities. Our analytical and sampling considerations help explain discrepancies among different detection efforts, including the one presented here, and provide considerations for the establishment of monitoring protocols to detect the presence of transgenes among structured populations of landraces.
Supplementary material 1 from: Leite BR, Vieira PE, Troncoso JS, Costa FO (2021) Comparing species detection success between molecular markers in DNA metabarcoding of coastal macroinvertebrates. Metabarcoding and Metagenomics 5: e70063. https://doi.org/10.3897/mbmg.5.70063
Table S1, Figures S1–S5
Supplementary material 2 from: Leite BR, Vieira PE, Troncoso JS, Costa FO (2021) Comparing species detection success between molecular markers in DNA metabarcoding of coastal macroinvertebrates. Metabarcoding and Metagenomics 5: e70063. https://doi.org/10.3897/mbmg.5.70063
Tables S2, S3
Figure 1 in Ecological aspects and molecular detection of Leishmania DNA (Kinetoplastida: Trypanosomatidae) in phlebotomine sand flies (Diptera: Psychodidae) from a rural settlement in the Eastern Amazon, Brazil
Figure 1 Map of the study area and sand flies collection points, Perimetral Norte Rural Seattlement, Pedra Branca Municipality, Amapá State, Brazil.
Fig. 2 in Molecular characterization and phylogenetic analysis of Trypanosoma spp. detected from striped leaf-nosed bats (Hipposideros vittatus) in Zambia
Fig. 2. Phylogeny of Trypanosoma cruzi clade. Phylogenetic trees of Trypanosoma cruzi clade inferred using combined gGAPDH and 18S rRNA gene sequences (1,363 bp). The phylogenetic trees with outgroup (Trypanosoma lewisi) were generated using a maximum likelihood method (A), neighbor joining method (B), and minimum evolution method (C). All bootstrap values from 1,000 replications are shown on the interior branch nodes. Our isolated Trypanosoma spp. are highlighted in bold and under line. GenBank accession numbers used in this phylogeny are listed in Table S1.
Fig. 1 in Cryptosporidium spp. in wild rats (Rattus spp.) from the Hainan Province, China: Molecular detection, species/genotype identification and implications for public health
Fig. 1. Geographical locations of rat sources involved in the present study in Hainan Province, China.
Figure 2 from: Degawa Y, Hosoya T, Hosaka K, Hirayama Y, Saito Y, Zhao Y-J (2015) Rediscovery of Roesleria subterranea from Japan with a discussion of its infraspecific relationships detected using molecular analysis. MycoKeys 9: 1-9. https://doi.org/10.3897/mycokeys.9.6564
Figure 2 - A single most parsimonious tree of Roesleria subterranea (ITS-5.8S sequences). Tree length = 31, CI = 0.8065, HI = 0.1935, RI = 0.8723, RC = 0.7035. The tree was constructed from a dataset of all available ITS-5.8S sequences of Roesleria subterranea from various hosts and localities. The numbers on the branches indicate the bootstrap values (BP) of 1000 replications in maximum parsimony analysis when the BP exceeds 50%. The scale bar indicates the number of substitutions. Abbreviations indicate the localities of the isolates: AU, Austria; GE, German; IT, Italy; NE, Netherlands; US, USA; JP, Japan.
Figure 1 from: Degawa Y, Hosoya T, Hosaka K, Hirayama Y, Saito Y, Zhao Y-J (2015) Rediscovery of Roesleria subterranea from Japan with a discussion of its infraspecific relationships detected using molecular analysis. MycoKeys 9: 1-9. https://doi.org/10.3897/mycokeys.9.6564
Figure 1 - Roesleria subterranea (TNS-F-38701). 1 Growing habits of two mature mazaedia on the root tip of an unidentified tree 2 Hymenium of mazaedium, showing protruding paraphyses 3 Enlarged hymenium showing developmental stages of asci and paraphyses 4 Mature ascus containing eight ascospores 5 Paraphysis 6 Discharged matured ascospores; on the right, a transversely one-septate spore is shown in side view 7 Germination of ascospores on MEYE, showing that germination tubes from one of the two-celled spores 2–6 Mounted in Meltzer's solution 7 Mounted in lacto-aniline blue. Bars: 1 = 2 mm; 2 = 50 ?m; 3–7 = 10 ?m.
Figure 3 from: Bidondo LF, Colombo RP, Recchi M, Silvani VA, Pérgola M, Martínez A, Godeas AM (2018) Detection of arbuscular mycorrhizal fungi associated with pecan (Carya illinoinensis) trees by molecular and morphological approaches. MycoKeys 42: 73-88. https://doi.org/10.3897/mycokeys.42.26118
Figure 3 Arbuscular mycorrhizal intraradical colonisation in pecan roots (a–b). A: arbuscules, AP: appressoria, ILH: intraradical longitudinal hyphae. Spore of Claroideoglomuslamellosum (c), Entrophosporainfrequens (d), Cetrasporapellucida (e), Rhizoglomusmicroaggregatum (f) inside another, dead AMF spore, resembling E.infrequens.
Figure 2 from: Bidondo LF, Colombo RP, Recchi M, Silvani VA, Pérgola M, Martínez A, Godeas AM (2018) Detection of arbuscular mycorrhizal fungi associated with pecan (Carya illinoinensis) trees by molecular and morphological approaches. MycoKeys 42: 73-88. https://doi.org/10.3897/mycokeys.42.26118
Figure 2 Rank-abundance diagrams of morphological AM fungal species (a–b) and rank-abundance diagrams of AM MOTUs (c–d) detected on C.illinoinensis rhizosphere in T0 (field) and T1 (containers) samples. RA: Relative abundance. Cl: Claroideoglomuslamellosum, Rm: Rhizoglomusmicroaggregatum, Fc: Funneliformiscoronatum, Ei: Entrophosporainfrequens, Fm: Funneliformismosseae, Gi Gigasporamargarita, Ce: Claroideoglomusetunicatum, Cp: Cetrasporapellucida, De: Diversisporaeburnea, Fr: Fuscutatarubra, Sc: Septoglomusconstrictum, Re: Rhizoglomusirregulare, Ri: Rhizoglomusintraradices, Di: Dominikiairanica, Da: Dominikiaindica, Gsp: Glomus sp.
Figure 1 from: Bidondo LF, Colombo RP, Recchi M, Silvani VA, Pérgola M, Martínez A, Godeas AM (2018) Detection of arbuscular mycorrhizal fungi associated with pecan (Carya illinoinensis) trees by molecular and morphological approaches. MycoKeys 42: 73-88. https://doi.org/10.3897/mycokeys.42.26118
Figure 1 Morphological AM fungal species accumulation curves (a) and rarefaction curves (± errors, ten replicates for each subset) of observed AM MOTUs (b) detected on C.illinoinensis rhizosphere in T0 (field) and T1 (containers) samples.
Clinical Study of a Single-Use, Point-of-Care Molecular Diagnostic Device for the Detection of Neisseria Gonorrhoeae (NG), Trichomonas Vaginalis (TV), and Chlamydia Trachomatis (CT) Utilizing Vaginal
ClinicalTrials.gov study NCT03596151. IPD Sharing: Not stated. Countries: 1. Publications: 0.
EXActDNA-003 / NSABP B-64: Study of Molecular Residual Disease Detection in Breast Cancer (MRD)
ClinicalTrials.gov study NCT06401421. IPD Sharing: YES. Countries: 2. Publications: 0.
Data from: Transgenes in Mexican maize: molecular evidence and methodological considerations for GMO detection in landrace populations
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Environmental DNA detection of Arctic char (Salvelinus alpinus) in Irish lakes: development and application of a species-specific molecular assay
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Data from: Species and hybrid identification of sturgeon caviar: a new molecular approach to detect illegal trade
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Data from: A Bayesian approach for detecting the impact of mass-extinction events on molecular phylogenies when rates of lineage diversification may vary
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Non-invasive detection of molecular biomarkers in subjects with a history of insulin resistance and colorectal adenomas
GEO Series GSE14797. Homo sapiens. 86 samples. Type: Expression profiling by array.
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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.