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118 results for “qPCR”
Data from: Functional antibodies against Plasmodium falciparum sporozoites are associated with a longer time to qPCR-detected infection among schoolchildren in Burkina Faso
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Data from: Seasonal dynamics and co-occurrence patterns of honey bee pathogens revealed by high-throughput RT-qPCR analysis
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Metabolite, qPCR, and metadata for relationships between Sphaerulina musiva infection and the Populus microbiome and metabolome
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Data from: Primers to highly conserved elements optimized for qPCR-based telomere length measurements in vertebrates
<p>Telomere length dynamics are an established biomarker of health and aging in animals. The study of telomeres in numerous species has been facilitated by methods to measure telomere length by real-time quantitative PCR (qPCR). In this method, telomere length is determined by quantifying the amount of telomeric DNA repeats in a sample and normalizing this to the total amount of genomic DNA. This normalization requires the development of genomic reference primers suitable for qPCR, which remains challenging in non-model organism with genomes that have not been sequenced. Here we report reference primers that can be used in qPCR to measure telomere lengths in any vertebrate species. We designed primer pairs to amplify genetic elements that are highly conserved between evolutionarily distant taxa and tested them in species that span the vertebrate tree of life. We report five primer pairs that meet the specificity and reproducibility standards of qPCR. In addition, we demonstrate an approach to choose the best primers for a given species by testing the primers on multiple individuals within a species and then applying an established computational tool. These reference primers can facilitate qPCR-based telomere length measurements in any vertebrate species of ecological or economic interest.</p>
Data from: DNA extraction method affects the detection of a fungal pathogen in formalin-fixed specimens using qPCR
Museum collections provide indispensable repositories for obtaining information about the historical presence of disease in wildlife populations. The pathogenic amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) has played a significant role in global amphibian declines, and examining preserved specimens for Bd can improve our understanding of its emergence and spread. Quantitative PCR (qPCR) enables Bd detection with minimal disturbance to amphibian skin and is significantly more sensitive to detecting Bd than histology; therefore, developing effective qPCR methodologies for detecting Bd DNA in formalin-fixed specimens can provide an efficient and effective approach to examining historical Bd emergence and prevalence. Techniques for detecting Bd in museum specimens have not been evaluated for their effectiveness in control specimens that mimic the conditions of animals most likely to be encountered in museums, including those with low pathogen loads. We used American bullfrogs (Lithobates catesbeianus) of known infection status to evaluate the success of qPCR to detect Bd in formalin-fixed specimens after three years of ethanol storage. Our objectives were to compare the most commonly used DNA extraction method for Bd (PrepMan, PM) to Macherey-Nagel DNA FFPE (MN), test optimizations for Bd detection with PM, and provide recommendations for maximizing Bd detection. We found that successful detection is relatively high (80–90%) when Bd loads before formalin fixation are high, regardless of the extraction method used; however, at lower infection levels, detection probabilities were significantly reduced. The MN DNA extraction method increased Bd detection by as much as 50% at moderate infection levels. Our results indicate that, for animals characterized by lower pathogen loads (i.e., those most commonly encountered in museum collections), current methods may underestimate the proportion of Bd-infected amphibians. Those extracting DNA from archived museum specimens should ensure that the techniques they are using are known to provide high-quality throughput DNA for later analysis.
R code and data for "Multiple imputation and direct estimation for qPCR data with non-detects"
<p>R code and data to reproduce figures and tables in the manuscript: Multiple imputation and direct estimation for qPCR data with non-detects.</p>
Fig. 2. A-B in Species-level identification of trypanosomes infecting Australian wildlife by High-Resolution Melting - Real Time Quantitative Polymerase Chain Reaction (HRM-qPCR)
Fig. 2. A-B: (A) Derivative melt curves of T. copemani, T. noyesi G8, T. vegrandis G7; (B) Derivative melt curves of T. microti, T. cruzi and T. rangeli.
Fig. 6. A-D in Species-level identification of trypanosomes infecting Australian wildlife by High-Resolution Melting - Real Time Quantitative Polymerase Chain Reaction (HRM-qPCR)
Fig. 6. A-D: (A) Derivative melt curves of wildlife samples containing T. copemani and T. vegrandis G7 infections from woylie tissue and the (B) the respective normalised melt domains; (C) Derivative melt curves of wildlife samples containing mixed infections with T. copemani and T. noyesi G8 in woylie blood; (D) Derivative melt curves showing wildlife samples containing mixed infections of T. copemani, T. noyesi G8 and T. vegrandis G7 in woylie tissue.
PMA-qPCR
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Supplementary Table S1. Primer sequence information for RT-qPCR used in this study.
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qPCR
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P1-P15_unict_utm_glucosinolate_qPCR
<p>P1-P15_unict_utm genes in glucosinolate pathway qPCR data</p>
Bacterial 16s rRNA gene amplicon data (V3-V4) and qPCR data
<p><span>Within a given species, considerable inter-individual, spatial, and temporal variation in the composition of the host microbiome exists. In group-living animals, social interactions homogenize microbiome composition among group members, nevertheless, divergence in microbiome composition among related groups arises. Such variation can result from deterministic and stochastic processes. Stochastic changes, or ecological drift, can occur among symbionts with potential for colonizing a host and within individual hosts, and drive divergence in microbiome composition among hosts or host groups. We tested whether ecological drift associated with dispersal and foundation of new groups cause divergence in microbiome composition between natal and newly formed groups in the social spider <em>Stegodyphus</em> <em>dumicola</em>. We simulated initiation of new groups and compared variation in microbiome composition among and within groups. Theory predicts a decrease in beta diversity with increasing group size, and we found that single founders harboured the highest diversity. Divergence in microbiome composition from the natal nest was mainly driven by a higher number of non-core symbionts. This suggests that stochastic divergence in host microbiomes can arise during the process of group formation by individual founders, which could explain the existence of among-group variation in microbiome composition in the wild. Consistent host-symbiont relationships in the species must then be maintained by other processes. Individual founders harboured higher relative abundances of non-core symbionts some of which are possible pathogens, compared with founders in small groups. These symbionts vary in occurrence with group size, indicating that group dynamics influence various core and non-core symbionts differently.</span></p>
Data from: DNA extraction method affects the detection of a fungal pathogen in formalin-fixed specimens using qPCR
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Data from: 60 specific eDNA qPCR assays to detect invasive, threatened and exploited freshwater vertebrates and invertebrates in Eastern Canada
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Bacterial 16s rRNA gene amplicon data (V3-V4) and qPCR data
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Data from: Increasing the accuracy and precision of relative telomere length estimates by RT qPCR
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Data from: Primers to highly conserved elements optimized for qPCR-based telomere length measurements in vertebrates
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qPCR array study for cell cycle related genes in Caco-2 cells treated with human lectin ZG16p
GEO Series GSE84321. Homo sapiens. 6 samples. Type: Expression profiling by RT-PCR.
Identification of extremely GC-rich micro RNAs for RT-qPCR data normalization in human plasma
GEO Series GSE209568. Homo sapiens. 2 samples. Type: Non-coding RNA profiling by high throughput sequencing.
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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.