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251 results for “Swabs”
The Prevent Anal Cancer Self-Swab Study
ClinicalTrials.gov study NCT03489707. IPD Sharing: YES. Countries: 1. Publications: 2.
Data from: Targeted genome-wide SNP genotyping in feral horses using non-invasive fecal swabs
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Recovered microbiome of an oviparous lizard differs across gut and reproductive tissues, cloacal swabs, and feces
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Data from: A comparison of non-destructive visceral swab and tissue biopsy sampling methods for genotyping-by-sequencing in the freshwater mussel Fusconaia askewi
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Data from: Imperfect pathogen detection from non-invasive skin swabs biases disease inference
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Data from: Unlocking the story in the swab: A new genotyping assay for the amphibian chytrid fungus Batrachochytrium dendrobatidis
One of the most devastating emerging pathogens of wildlife is the chytrid fungus, Batrachochytrium dendrobatidis (Bd), which affects hundreds of amphibian species around the world. Genomic data from pure Bd cultures has advanced our understanding of Bd phylogenetics, genomic architecture, and mechanisms of virulence. However pure cultures are laborious to obtain and whole genome sequencing is comparatively expensive, so relatively few isolates have been genetically characterized. Thus we still know little about the genetic diversity of Bd in natural systems. The most common non-invasive method of sampling Bd from natural populations is to swab amphibian skin. Hundreds of thousands of swabs have been collected from amphibians around the world, but Bd DNA collected via swabs is often low in quality and/or quantity. In this study, we developed a custom Bd genotyping assay using the Fluidigm Access Array platform to amplify 192 carefully-selected regions of the Bd genome. We obtained robust sequence data for pure Bd cultures and field-collected skin swabs. This new assay has the power to accurately discriminate among the major Bd clades, recovering the basic tree topology previously revealed using whole genome data. Additionally, we established a critical value for initial Bd load for swab samples (150 Bd genomic equivalents) above which our assay performs well. By leveraging advances in microfluidic multiplex PCR technology and the globally distributed resource of amphibian swab samples, non-invasive skin swabs can now be used to address critical spatial and temporal questions about Bd and its effects on declining amphibian populations.
Data from: Pros and cons of external swabbing of amphibians for genetic analyses
Non-invasive DNA sampling is an important tool in amphibian conservation. Buccal swabs are nowadays replacing the wounding toe-clipping method. Skin and cloaca swabbing are even less invasive and easier to handle than buccal swabbing, but could result in contaminations of genetic material. Therefore, we test if external skin and cloaca swabs are as reliable as buccal swabs for genetic analysis of amphibians. We analysed eight microsatellite loci for the common frog (Rana temporaria, Linnaeus 1758) and compared genotyping results for buccal, skin and cloaca swabs regarding allelic dropouts and false alleles. Furthermore, we compared two DNA extraction methods regarding efficiency and cost. DNA quality and quantity (amplification success, genotyping error rate, in nanogram per microlitre) were comparable among DNA sources and extraction methods. However, skin and cloaca samples exhibited high degrees of contamination with foreign individuals, which was due to sample collection during mating season. Here, we established a simple low budget procedure to receive DNA of amphibians avoiding stressful buccal swabbing or harmful toe clipping. However, the possibility of contaminations of external swabs has to be considered.
Precision glycerine jelly swab for removing pollen from small and fragile insect specimens
<p><span>Historical datasets can establish a critical baseline of plant-animal interactions for understanding contemporary interactions in the context of global change. Pollen is often incidentally preserved on animals in natural history collections. Techniques for removing pollen from insects have largely been developed for fresh insect specimens or historical specimens with large amounts of pollen on specialised structures. However, many key pollinating insects do not have these specialised structures and thus, there is a need for a method to extract pollen from these small, and fragile insects.</span></p> <p><span>Here, we propose a precision glycerine jelly swab tool to allow for the precise removal of pollen from old, small, and fragile insect specimens. We use this tool to remove pollen from five families of insects collected in the late 1970s. Additionally, we compare our method with four previously published techniques for removing pollen from pinned contemporary specimens.</span></p> <p><span>We show the functionality of the precision glycerine jelly swab for removing small quantities of pollen across insect families. We found that across the five methods, all removed pollen; yet, it was clear that some are better suited for fragile specimens<em>.</em> In particular, the traditional glycerine jelly swab and the precision glycerine jelly swabs both performed well for removing pollen from bee faces. The shaking wash resulted in specimen fracture and residue left behind, the ethanol rinses left setae matted, and the glycerol swabbing left residue on the specimen. Additionally, we present photographs documenting the effects of these methods on pinned honey bee specimens.</span></p> <p><span>The precision glycerine jelly swab opens up opportunities to sample pollen from a variety of insects in natural history collections. These pollen samples can be incorporated into downstream analyses for pollen identification either via microscopy or DNA sequencing, and the resulting plant-insect interaction data can establish historical baselines for contemporary comparison. Beyond our application of this method to pollen on insects, this precision glycerine jelly swab tool could be used to explore pollen placement specialisation or to sample bryophyte, fungal, and tree fern spores dispersing on animals.</span></p>
Nasopharyngeal swabs vs. saliva sampling for SARS-CoV-2 detection: A cross-sectional survey of acceptability for caregivers and children after experiencing both methods
<p><span>Background: </span><span>Saliva sampling is a promising alternative to nasopharyngeal swabs for SARS-CoV-2 testing, but acceptability data is lacking. We characterize the acceptability of saliva sampling and nasopharyngeal swabs for primary decision makers and their children after experiencing both testing modalities.</span></p> <p><span>Results: </span><span>48 participants and 48 primary decision makers completed the survey. Nasopharyngeal swab acceptability differed between scenarios, ranging 79% [95%CI: 66, 88] to 100% [95%CI: 95, 100]); saliva sampling acceptability was similar across scenarios, ranging 92% [95%CI: 82, 97]) to </span><span> </span><span>98% [95%CI: 89, 99]. 58% of youth described significant pain with nasopharyngeal swabbing, versus none with saliva sampling. 90% of children prefer saliva sampling. 66% of primary decision makers would prefer nasopharyngeal swabbing if it were 10% more sensitive.</span></p> <p><span>Conclusion: </span><span>Though youth prefer saliva sampling over nasopharyngeal swabs, primary decision makers present for testing remain highly accepting of both. Acceptance of nasopharyngeal swabs, however, varies with the testing indication and is influenced by perceived test accuracy. Understanding factors that influence sampling acceptance will inform more successful testing strategies.</span></p>
Optimising recovery of DNA from minimally-invasive sampling methods: efficacy of buccal swabs, preservation strategy and DNA extraction approaches for amphibian studies_Dataset_Rscript
<p>Datasets and Rscript associated with paper draft titled: "<span>Optimising recovery of DNA from minimally-invasive sampling methods: efficacy of buccal swabs, preservation strategy and DNA extraction approaches for amphibian studies".</span></p> <p> </p> <p>Abstract: <span>Studies in evolution, ecology and conservation are increasingly based on genetic and genomic inferences. With increased focus on molecular approaches, ethical concerns about destructive or more invasive techniques need to be considered, with a push for minimally invasive sampling to be optimised. Buccal swabs have been increasingly used to collect DNA in a number of taxa, including amphibians.<span> </span>However, DNA yield and purity from swabs is often low, limiting its use. In this study we compare different types of swabs, preservation method and storage, and DNA extraction technique in three case studies to assess the optimal approach for recovering DNA in anurans. Out of the five different types of swab that we tested, Isohelix MS-02 and Rapidry swabs generated higher DNA yields than other swabs. When comparing storage buffers, ethanol is a better preservative than a non-alcoholic alternative. Dried samples resulted in similar or better final DNA yields than ethanol-fixed samples if kept cool. DNA extraction via a Qiagen</span><span>™</span><span> DNeasy Blood and Tissue Kit and McHale’s salting out extraction method resulted in similar DNA yields but the Qiagen</span><span>™</span><span> kit extracts contained less contamination. We also found that samples produce better DNA recovery if frozen as soon as possible after collection. We provide recommendations for sample collection and extraction under different conditions, including budgetary considerations, size of individual sampled, access to cold storage facilities, and DNA extraction methodology. Maximising efficacy of all of these factors for better DNA recovery will allow buccal swabs to be used for genetic and genomic studies in a range of vertebrates.</span></p>
Data from: Skin swabbing of amphibian larvae yields sufficient DNA for efficient sequencing and reliable microsatellite genotyping
Skin swabbing, a minimally invasive DNA sampling method recently developed on adult amphibians, was tested on larvae of fire salamanders (Salamandra salamandra). The quality and quantity of the sampled DNA was evaluated by (i) measuring DNA concentration in DNA extracts, (ii) sequencing part of the mtDNA cytochrome b gene (692 bp) and (iii) genotyping eight polymorphic nuclear microsatellite loci. The multiple-tubes approach was used for calculating allelic dropout (ADO) and false allele (FA) rates to evaluate the reliability of the genotypes. DNA extracts from tissue samples of road-killed individuals were included in the study as positive controls. Our results showed that skin swabs of fire salamander larvae can provide DNA in sufficient quantity and quality, as sequencing was successful and no allelic dropouts or false alleles were detected. This method, tested for the first time on amphibian larvae, has proven to be an efficient and reliable alternative to the controversial tail fin clipping procedure.
Coyote prey DNA from coyote saliva to test efficacy of obtaining diet information from oral swabs
<p>Human-carnivore conflicts often involve the depredation of domestic livestock. These depredation events are rarely observed, yet mitigation typically involves identifying the species or individual involved for removal or relocation. We tested a molecular method to identify individuals involved in depredation events using mouth swabs to determine if prey DNA could be detected, and for how long. We fed mule deer (<em>Odocoileus hemionus</em>) meat to captive coyotes (<em>Canis latrans</em>) and swabbed their mouths at five predetermined intervals between 2-72 hours after consumption of the deer meat. We assessed two different molecular forensic methods to analyze the saliva swabs: qPCR for species identification and microsatellites for individual prey identification. We found that qPCR analysis was highly effective, detecting the deer DNA in the coyote saliva for up to 72 hours post-deer consumption. Our results suggest that if an individual carnivore suspected of livestock depredation is captured within 72 hours of a depredation incident, it is possible to confirm their potential involvement with a buccal swab and qPCR analysis. Utilizing this method could aid in more targeted and effective removal of individual problem carnivores as opposed to widespread removal of involved species.</p>
Gastric Swab for Helicobacter Pylori Detection
ClinicalTrials.gov study NCT05349578. IPD Sharing: UNDECIDED. Countries: 1. Publications: 1.
Self-Obtained Vaginal Swabs for Chlamydia and Gonorrhea Testing
ClinicalTrials.gov study NCT01849653. IPD Sharing: Not stated. Countries: 1. Publications: 19.
Carbapenem-resistant Organisms (CRO) Screening From Rectal Swabs in Patients With Hematological Diseases in China
ClinicalTrials.gov study NCT05002582. IPD Sharing: NO. Countries: 1. Publications: 2.
HPVPro Study: Comparison of HPV Detection in Clinician-collected Cervical Swabs and Self-sampled Cervicovaginal Swabs
ClinicalTrials.gov study NCT04133610. IPD Sharing: NO. Countries: 1. Publications: 1.
Evaluation of in Vitro Devices on Self-collected Vaginal Swab and Urine Sample for Testing of Human Papilloma Virus
ClinicalTrials.gov study NCT04312737. IPD Sharing: Not stated. Countries: 3. Publications: 1.
Assessing Acceptability and Feasibiity of STI Self-swab Testing, to be Offered at the Time of Telemed Medication Abortion Provision
ClinicalTrials.gov study NCT06951438. IPD Sharing: NO. Countries: 1. Publications: 12.
Comparing Two Types of Swabs in Collecting Cell Samples for Anal Pap Tests and Human Papillomavirus Tests in Men Who Have Sex With Men
ClinicalTrials.gov study NCT00955591. IPD Sharing: Not stated. Countries: 1. Publications: 1.
PCR and Rapid Diagnostic Test on Saliva and Nasopharyngeal Swabs for the Detection of SARS-CoV-2 (COVID-19)
ClinicalTrials.gov study NCT04613310. IPD Sharing: Not stated. Countries: 1. Publications: 1.
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OpenNeuro
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