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42 results for “Non-invasive DNA”
Data from: Non-invasive age estimation based on fecal DNA using methylation-sensitive high-resolution melting for Indo-Pacific bottlenose dolphins
<p class="MsoNormal"><span>Age is necessary information for the study of life history of wild animals. A general method to estimate the age of odontocetes is counting dental growth layer groups (GLGs). However, this method is highly invasive as it requires the capture and handling of individuals to collect their teeth.</span><span> Recently, the development of DNA-based age </span><span>estimation methods has been actively studied as an alternative to such invasive methods, of which many have used biopsy samples. However, if DNA-based age estimation can be developed from fecal samples, age estimation can be performed without touching or disrupting individuals, thus establishing an entirely non-invasive method. </span><span>We developed an age estimation model using the methylation rate of two gene regions, <em>GRIA2</em> and <em>CDKN2A,</em> measured through methylation-sensitive high-resolution melting (MS-HRM) from fecal samples of wild Indo-Pacific bottlenose dolphins (<em>Tursiops aduncus</em>). The age of individuals was known through conducting longitudinal individual identification surveys underwater. Methylation rates were quantified from 36 samples. Both gene regions showed a significant correlation between age and methylation rate. The age estimation model was constructed based on the methylation rates of both genes which achieved sufficient accuracy (after LOOCV: MAE = 5.08, <em>R<sup>2</sup></em> = 0.34) for the ecological studies of the Indo-Pacific bottlenose dolphins, with a lifespan of 40-50 years. This is the first study to report the use of non-invasive fecal samples to estimate the age of marine mammals.</span></p>
Data from: Non-invasive age estimation based on fecal DNA using methylation-sensitive high-resolution melting for Indo-Pacific bottlenose dolphins
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DNA sequence data generated using non-invasive feather and eggshell samples from the Grenada Dove for two gene regions: Cyt b and ND2
<p>As an island endemic with a decreasing population, the Critically Endangered Grenada Dove <em>Leptotila wellsi</em> is threatened by accelerated loss of genetic diversity resulting from ongoing habitat fragmentation. Small, threatened populations are difficult to sample directly but advances in molecular methods mean that non-invasive samples can be used. We performed the first assessment of genetic diversity of populations of Grenada Dove by a) assessing mtDNA genetic diversity in the only two areas of occupancy on Grenada, b) defining the number of haplotypes present at each site and c) evaluating evidence of isolation between sites. We used non-invasively collected samples from two locations: Mt Hartman (n=18) and Perseverance (n=12). DNA extraction and PCR were used to amplify 1,751 bps of mtDNA from two mitochondrial markers: NADH dehydrogenase 2 (<em>ND2</em>) and Cytochrome b (<em>Cyt b</em>). Haplotype diversity (<em>h</em>) of 0.4, a nucleotide diversity (π) of 0.00023 and two unique haplotypes were identified within the <em>ND2</em> sequences; a single haplotype was identified within the <em>Cyt b </em>sequences. Of the two haplotypes identified; the most common haplotype (haplotype A = 73.9%) was observed at both sites and the other (haplotype B = 26.1%) was unique to Perseverance. Our results show low mitochondrial genetic diversity and clear evidence for genetically isolated populations. The Grenada Dove needs urgent conservation action, including habitat protection and potential augmentation of gene flow by translocation in order to increase genetic resilience and diversity with the ultimate aim of securing the long-term survival of this Critically Endangered species. </p>
Multimodal Epigenetic Sequencing Analysis (MESA) of Cell-free DNA for Non-invasive Colorectal Cancer Detection
<p>Processed data (feature-by-sample matrices) of non-disruptive bisulfite-free methylation sequencing for cfDNA samples from 4 clinical cohorts (Cohort 1, Cohort 2, Cohort 3, and cfTAPS dataset). Codes used to repeat the results in our paper can be found https://rpubs.com/LiYumei/926228 and https://github.com/ChaorongC/MESA. </p>
Predictive modelling of brain metastasis risk and non-invasive biomarker detection using DNA methylation signatures
<p>Methylated cell-free DNA was sequenced for 123 BM plasma and compared to plasma methylomes from 107 gliomas, central nervous system (CNS) lymphomas (CNSL), and non-CNS tumor controls. Plasma methylome-based classifiers of BM from other entities were built in fifty 80% discovery set iterations of 92/123 BM samples. External publicly-available tissue methylation data on 442 LUAD, 85 BM, and 146 glioma/CNSL/control samples were acquired for validation and the remaining 31/123 BM plasma samples were used for additional validation.</p>
DNA sequence data generated using non-invasive feather and eggshell samples from the Grenada Dove for two gene regions: Cyt b and ND2
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Data from: Environmental DNA analysis as a non-invasive quantitative tool for reproductive migration of a threatened endemic fish in rivers
Quantitative information regarding reproduction is essential for conserving endangered animals; however, some conventional quantitative methods can be damaging to the target population and their habitats. In the present study, the reproductive migration of a threatened endemic fish, three-lips (Opsariichthys uncirostris uncirostris), was non-invasively monitored by quantitative PCR of species-specific environmental DNA (eDNA), the usefulness of which has been under-studied. Water sampling and from-shore visual inspection were performed weekly along a tributary of Lake Biwa (Japan), where adult fish seasonally migrate upstream to reproduce as well as at lake sites near the river mouth. Species-specific eDNA was collected at all locations at times when the fish were visually observed and at certain sites where the fish were not observed. Log-transformed individual counts from visual inspection were positively correlated with log-transformed eDNA concentration in the river sites, indicating that eDNA analysis can be a reliable quantitative tool for fish abundance in rivers. Furthermore, distance from the lake did not influence eDNA concentration, suggesting that eDNA transport by river flow had a negligible effect on eDNA quantification. eDNA concentration and individual counts both gradually increased from May–July, then both decreased in August. Importantly, eDNA analysis showed that the fish occupied more habitats in the peak reproductive season and stayed for longer time at any given site. An additional underwater survey confirmed unexpected eDNA detections as true positives. eDNA analysis has great potential to quantitatively monitor reproductive fish migrations under certain conditions.
Non-invasive surveys of mammalian viruses using environmental DNA
<p class="BodyA">This dataset provides supplemental information to interpret the data published in Alfano & Dayaram et al. 2021. The study investigates how environmental DNA (eDNA) and invertebrate-derived DNA (iDNA) can be used to characterize the yet largely unknown virome present in mammalian wildlife. <span>Environmental DNA and iDNA are used to survey biodiversity non-invasively to mitigate difficulties in obtaining wildlife samples, particularly in remote areas or for rare species. Recently, eDNA/iDNA were used to monitor known wildlife pathogens, however, most wildlife pathogens are unknown and often evolutionarily divergent. To detect and identify known and novel mammalian viruses from eDNA/iDNA, we used a curated set of RNA oligonucleotides as viral baits in a hybridization capture system coupled with high throughput sequencing. We detected multiple known and novel mammalian RNA and DNA viruses from multiple viral families from both waterhole eDNA and leech derived iDNA. Congruence was found between detected hosts and viruses identified in leeches and waterholes. Our results demonstrate that eDNA/iDNA samples represent an effective non-invasive resource for studying wildlife viral diversity and for detecting novel potentially zoonotic viruses prior to their emergence.</span></p>
FIGURE 5 in Non-invasive ancient DNA protocol for fluid-preserved specimens and phylogenetic systematics of the genus Orestias (Teleostei: Cyprinodontidae)
FIGURE 5. Molecular phylogeny of Orestias complexes including 'fresh' species and morphotype ("morpho") representatives, and type specimens. Maximum clade credibility tree for rhodopsin sequences. Values at branch nodes refer to highest posterior probability of occurrence for clades (> 0.95); within parenthesis are shown posterior values when removing type specimens from the analysis. Scale bar below tree indicates sequence divergence. Type specimens are highlighted with an asterisk. See Table 2 for specimen acronyms.
FIGURE 2 in Non-invasive ancient DNA protocol for fluid-preserved specimens and phylogenetic systematics of the genus Orestias (Teleostei: Cyprinodontidae)
FIGURE 2. Gel electrophoresis displaying extracted DNA (a) and amplified PCR fragments (b) in two historical samples of O. mulleri (MNHN 1981-1428#4 and #13). In a, columns 1–2: extracted DNA for specimen #4 (aliquots a and b); columns 3–4: extracted DNA for specimen #13 (aliquot a and b); column 5: negative DNA extraction control; M: molecular weight marker (100 bp ladder). In b, PCR amplification products for control region and rhodopsin are left and right to the molecular weight marker, respectively. Columns 1–2: specimen #4 (aliquots a and b); columns 3–4: specimen #13 (aliquots a and b); column 5: negative PCR control; column 6: positive PCR control. M: molecular weight marker (100 bp ladder).
FIGURE 3 in Non-invasive ancient DNA protocol for fluid-preserved specimens and phylogenetic systematics of the genus Orestias (Teleostei: Cyprinodontidae)
FIGURE 3. Example of type specimens treated by incubation in GuSCN bath. Left/right sides: specimens before/after DNA extraction procedure. Damage scale (see Material and Methods): A and B = 1, C = 2 and D = 3. Scale bar represents 2 cm.
Cell-free DNA Analysis of Spent Embryo Culture Media as a Non-invasive Approach for Preimplantation Genetic Diagnosis
ClinicalTrials.gov study NCT07076719. IPD Sharing: UNDECIDED. Countries: 1. Publications: 24.
Non-invasive Biomarker Discovery for Pre-cervical or/and Cervical Cancer-HPV DNA and Other Biomarkers in Urine
ClinicalTrials.gov study NCT06261892. IPD Sharing: NO. Countries: 1. Publications: 4.
Development of Non-invasive Prenatal Test for Microdeletion and Other Genetic Syndromes Based on Cell Free DNA
ClinicalTrials.gov study NCT02109770. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Cell-free DNA: a Non-invasive Test for Assessing Embryo Quality
ClinicalTrials.gov study NCT01397136. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Development of Non-invasive Cell-free DNA to Supplant Invasive Biopsy in Heart Transplantation
ClinicalTrials.gov study NCT05309382. IPD Sharing: NO. Countries: 1. Publications: 0.
Non-invasive surveys of mammalian viruses using environmental DNA
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Data from: Environmental DNA analysis as a non-invasive quantitative tool for reproductive migration of a threatened endemic fish in rivers
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Environmental DNA as a non-invasive alternative for surveying aquatic communities in tank bromeliads
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Non-invasive Preimplantation Genetic Testing for Aneuploidies Using Cell-free DNA in Spent Culture Media
ClinicalTrials.gov study NCT04711239. IPD Sharing: UNDECIDED. Countries: 0. Publications: 10.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.