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246 results for “aged 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>
Age estimation of captive Asian elephants (Elephas maximus) based on DNA methylation: An exploratory analysis using methylation-sensitive high-resolution melting (MS-HRM)
<p>Age is an important parameter for bettering the understanding of biodemographic trends-development, survival, reproduction and environmental effects-critical for conservation. However, current age estimation methods are challenging to apply to many species, and no standardised technique has been adopted yet. This study examined the potential use of methylation-sensitive high-resolution melting (MS-HRM), a labour, time, and cost-effective method to estimate chronological age from DNA methylation in Asian elephants (<em>Elephas maximus</em>). The objective of this study was to investigate the accuracy and validation of MS-HRM use for age determination in long-lived species, such as Asian elephants. The average lifespan of Asian elephants is between 50-70 years but some have been known to survive for more than 80 years. DNA was extracted from 53 blood samples of captive Asian elephants across 11 zoos in Japan, with known ages ranging from a few months to 65 years. Methylation rates of two candidate age-related epigenetic genes, <em>RALYL</em> and <em>TET2,</em> were significantly correlated with chronological age. Finally, we established a linear, unisex age estimation model with a mean absolute error (MAE) of 7.36 years. This exploratory study suggests an avenue to further explore MS-HRM as an alternative method to estimate the chronological age of Asian elephants.</p>
Data from: A cost-effective blood DNA methylation-based age estimation method in domestic cats, Tsushima leopard cats (Prionailurus bengalensis euptilurus), and Panthera species, using targeted bisulfite sequencing and machine learning models
<p><span>Knowledge of individual age can help both in-situ and ex-situ conservation programs to design more efficient and suitable management plans for targeted wildlife species. DNA methylation is one of the epigenetic aging markers that has emerged as a promising tool that can estimate age with high accuracy using only a tiny amount of biological material, which can be collected in a minimally invasive way. Here, we sequenced five targeted genetic regions and used </span><span>8–23</span><span> selected CpG sites to build age estimation models with machine learning methods </span><span>with about only $3–7 per sample</span><span>, using blood samples of seven Felidae species—ranging from small to big, and domestic to endangered species: domestic cats (<em>Felis catus</em>, 139 samples), Tsushima leopard cats (<em>Prionailurus bengalensis euptilurus</em>, 84 samples), and five<em> Panthera </em>species (96 samples). </span><span>The models built achieved satisfactory accuracy—the mean absolute error of the best models was 1.966, 1.348, and 1.552 years in domestic cats, Tsushima leopard cats, and <em>Panthera</em> spp., respectively.</span><span> Our models in domestic cats and Tsushima leopard cats were applicable to individuals regardless of health conditions, indicating the high applicability of our models to samples collected from diverse situations, e.g., rescued individuals in the context of conservation. We also showed the possibility of developing universal age estimation models for the five<em> Panthera</em> spp. using two of the five genetic regions, suggesting an even lower cost to use our models for future applications.</span></p>
Title: Health-Related Quality of Life and DNA Methylation-Based Aging Biomarkers among Survivors of Childhood Cancer
<p><strong><span>Abstract</span></strong></p> <p><strong><span>Background: </span></strong><span>Childhood cancer survivors are at high risk for morbidity and mortality and poor patient-reported outcomes, typically health-related-quality-of-life (HRQOL). However, </span><span>associations between DNA methylation (DNAm)-based aging biomarkers and HRQOL have not been evaluated.</span></p> <p><strong><span>Methods: </span></strong><span>DNAm was generated with Infinium EPIC BeadChip on blood-derived DNA (median[range] for age at blood draw=34.5[18.5-66.6] years) and HRQOL was assessed with age at survey (32.3[18.4-64.5] years) from 2,206 survivors in the St. Jude Lifetime Cohort. DNAm-based aging biomarkers, including epigenetic age using multiple clocks (e.g., <span>GrimAge</span>) and others (e.g., DNAmB2M: beta-2-microglobulin; DNAmADM: adrenomedullin), were derived from the DNAm Age Calculator (https://dnamage.genetics.ucla.edu). HRQOL was assessed using the Medical Outcomes Study 36-Item Short-Form Health Survey to capture eight domains, and physical and mental component summaries (PCS and MCS). General linear models evaluated associations between HRQOL and epigenetic age acceleration (EAA, e.g., EAA_GrimAge) or other age-adjusted DNAm-based biomarkers (e.g., ageadj_DNAmB2M) after adjusting for age at blood draw, sex, cancer treatments, and DNAm-based surrogate for smoking pack-years. All P values were 2-sided.</span></p> <p><strong><span>Results: </span></strong><span>Worse HRQOL was associated with greater EAA_GrimAge (</span><span>PCS: β[95%CI]=-0.18[-0.251,-0.11] years, P=1.85×10<sup>-5</sup>; and four individual HRQOL domains), followed by ageadj_DNAmB2M (PCS: -0.08[-0.124,-0.037], P=0.003; and three individual HRQOL domains), and ageadj_DNAmADM (PCS: -0.082[-0.125,-0.039], P=0.002; and two HRQOL domains). EAA_Hannum (Hannum clock) was not associated with any HRQOL.</span></p> <p><strong>Conclustion: </strong>Overall and domain-specific measures of HRQOL are associated with DNAm measures of biological aging. Future longitudinal studies should test biological aging as a potential mechanism.</p>
DNA methylation in sperm of rats at two ages exposed or not to 2,2',4,4'-tetrabromodiphenyl ether
<p><strong>Introduction</strong></p> <p>This study was designed to determine the potential of environmentally relevant levels of 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) to induce age-dependent changes in a rat’s sperm epigenome. The methods used to generate the files are described below.</p> <p> </p> <p><strong>Experimental design</strong></p> <p>Twelve seven-week-old pregnant Wistar rats were divided into two groups (6 per group) – control and BDE-47 exposed group. Between pregnancy day 8 and postnatal day 21 (PND21), dams in each group were fed from the tip of pipette 0.2 µL/g body weight of the vehicle (tocopherol-stripped corn oil) or the same volume of a 1 mg/mL solution of BDE-47 daily. The BDE-47 group resulted in an exposure level of 0.2 mg/kg body weight of BDE-47 per day. On PND65 and PND120, one male pup randomly selected from each litter was euthanized, and epididymal motile spermatozoa were collected via the swim-up procedure as described in detail elsewhere (Suvorov et al., 2018). Sperm DNA was extracted using the rapid method (Wu et al., 2015). Extracted sperm DNA was subjected to reduced representation bisulfite sequencing (RRBS).</p> <p> </p> <p><strong>Reduced representation bisulfite sequencing</strong></p> <p>For RRBS, bisulfite-converted libraries were prepared from 100 ng of the sperm DNA using Ovation RRBS Methyl-Seq System and EpiTect Fast DNA Bisulfite Kit (Cat. #59824, Qiagen) following manufacturers’ protocols. Sequencing of libraries was done using the HiSeq 2500 sequencing system (Illumina) in Deep Sequencing Core Facility of the University of Massachusetts Medical School (Schrewsbury, MA) with an average of 18.0 million unique reads per sample.</p> <p> </p> <p><strong>Bioinformatic analysis</strong></p> <p>Raw reads from the sequence were processed following the recommended protocol for libraries prepared with Ovation RRBS Methyl-Seq System (NuGEN) and then mapped to the rn6 Rattus norvegicus reference genome using Bismark (version 0.16.1) and bowtie-2 (version 2.2.9). PCR duplicates were removed using nudup.py (version 2.2). The resulting SAM files for the control and BDE-47 group for the two ages, PND65 and 120 are uploaded. </p> <p> </p>
Distinct chromatin signatures of DNA hypomethylation in aging and cancer (Datasets and additional files)
<p>Cancer is an aging-associated disease but the underlying molecular links between these processes are still largely unknown. Gene promoters that become hypermethylated in aging and cancer share a common chromatin signature in ES cells. In addition, there is also global DNA hypomethylation in both processes. However, any similarities of the regions where this loss of DNA methylation occurs is currently not well characterized, nor is it known whether such regions also share a common chromatin signature in aging and cancer.<strong> </strong>To address this issue we analysed TCGA DNA methylation data from a total of 2,311 samples, including control and cancer cases from patients with breast, kidney, thyroid, skin, brain and lung tumors and healthy blood, and integrated the results with histone, chromatin state and transcription factor binding site data from the NIH Roadmap Epigenomics and ENCODE projects. We identified 98,857 CpG sites differentially methylated in aging, and 286,746 in cancer. Hyper- and hypomethylated changes in both processes each had a similar genomic distribution across tissues and displayed tissue-independent alterations. The identified hypermethylated regions in aging and cancer shared a similar bivalent chromatin signature. In contrast, hypomethylated DNA sequences occurred in very different chromatin contexts. DNA hypomethylated sequences were enriched at genomic regions marked with the activating histone posttranslational modification H3K4me1 in aging, whilst in cancer, loss of DNA methylation was primarily associated with the repressive H3K9me3 mark.<strong> </strong></p>
Suppl. figures of otoliths of pelagic shorefish larvae captured over the Galapagos Rift for Victor, B.C. (2023) Rapid long-distance multispecies transport of shorefish larvae to the oceanic tropical eastern Pacific, revealed by DNA-barcodes and otolith aging of larvae captured over the Galapagos Rift
<p>Supplementary figures of otoliths of pelagic shorefish larvae captured over the Galapagos Rift</p> <p>Victor, B.C. (2023)</p> <p><strong>Rapid long-distance multispecies transport of shorefish larvae to the oceanic tropical eastern Pacific, revealed by DNA-barcodes and otolith aging of larvae captured over the Galapagos Rift</strong></p> <p>in volume: Early Life History and Biology of Marine Fishes: Research inspired by the work of H Geoffrey Moser</p> <p>Figure Sup A1 Sagittal otolith of 5.9 mm SL Stegastes sp. fish larva (Pomacentridae) captured over the Galapagos Rift, age since hatching is 23 days.</p>
Suppl. figures of pelagic shorefish larvae captured over the Galapagos Rift for Victor, B.C. (2023) Rapid long-distance multispecies transport of shorefish larvae to the oceanic tropical eastern Pacific, revealed by DNA-barcodes and otolith aging of larvae captured over the Galapagos Rift
<p>Supplementary figures of pelagic shorefish larvae captured over the Galapagos Rift</p> <p>Victor, B.C. (2023)</p> <p><strong>Rapid long-distance multispecies transport of shorefish larvae to the oceanic tropical eastern Pacific, revealed by DNA-barcodes and otolith aging of larvae captured over the Galapagos Rift</strong></p> <p>in volume: Early Life History and Biology of Marine Fishes: Research inspired by the work of H Geoffrey Moser</p> <p>Figure S1 Gobioid fish larvae captured over the Galapagos Rift.</p> <p>Figure S2 Labrid fish larvae captured over the Galapagos Rift.</p> <p>Figure S2. Pomacentrid fish larvae captured over the Galapagos Rift.</p> <p>Figure S4 Lythrypnus sp 5.4 mm SL fish larva captured over the Galapagos Rift.</p> <p>Figure S4a Lythrypnus sp 5.4 mm SL fish larva (head) captured over the Galapagos Rift.</p> <p>Figure S5 Abudefduf troschelii 7.3 mm SL fish larva captured over the Galapagos Rift.</p> <p>Figure S6 Chaetodon humeralis 8.9 mm SL fish larva captured over the Galapagos Rift.</p> <p>Figure S7 Gerreidae 10.6 mm SL fish larva captured over the Galapagos Rift.</p> <p>Figure S8 Neoniphon suborbitalis 6.8 mm SL fish larva captured over the Galapagos Rift.</p> <p>Figure S9 Ophioblennius steindachneri 10.6 mm SL fish larva captured over the Galapagos Rift.</p> <p>Figure S9a Ophioblennius steindachneri 10.6 mm SL fish larva (head) captured over the Galapagos Rift.</p> <p>Figure S9b Ophioblennius steindachneri 10.6 mm SL fish larva (ventral) captured over the Galapagos Rift.</p> <p>Figure Sup10 Sphoeroides lobatus 12.0 mm SL fish larva captured over the Galapagos Rift.</p>
An Evaluation of a Multi-target Stool DNA (Mt-sDNA) Test, Cologuard, for CRC Screening in Individuals Aged 45-49 and at Average Risk for Development of Colorectal Cancer: Act Now
ClinicalTrials.gov study NCT03728348. IPD Sharing: YES. Countries: 1. Publications: 1.
DNA methylation-based age prediction and sex-specific epigenetic aging in a lizard with female-biased longevity
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Data from: A cost-effective blood DNA methylation-based age estimation method in domestic cats, Tsushima leopard cats (Prionailurus bengalensis euptilurus), and Panthera species, using targeted bisulfite sequencing and machine learning models
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Spatio-temporal variation in diet among age and sex cohorts of a model generalist bird species, the Great Tit Parus major: new insights revealed by DNA metabarcoding
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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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Age estimation of captive Asian elephants (Elephas maximus) based on DNA methylation: An exploratory analysis using methylation-sensitive high-resolution melting (MS-HRM)
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Quantitative translation of dog-to-human aging by conserved remodeling of the DNA methylome
<p>This repository contains processed data files, custom python scripts and jupyter notebooks containing analyses accompanying the manuscript, <em>Quantitative translation of dog-to-human aging by conserved remodeling of the DNA methylome.</em></p>
Age estimation based on blood DNA methylation levels in brown bears
<p><span>Age is an essential trait for understanding the ecology and management of wildlife. A conventional method of estimating age in wild animals is counting annuli formed in the cementum of teeth. This method has been used in bears despite some disadvantages, such as high invasiveness and the requirement for experienced observers. In this study, we established a novel age estimation method based on DNA methylation levels using blood collected from 49 brown bears</span><span> </span><span>of known ages living in both captivity and the wild. We performed bisulfite pyrosequencing and obtained methylation levels at 39 cytosine-phosphate-guanine (CpG) sites adjacent to 12 genes. The methylation levels of CpGs adjacent to four genes showed a significant correlation with age. The best model was based on DNA methylation levels at just four CpG sites adjacent to a single gene, SLC12A5, and it had high accuracy with a mean absolute error of 1.3 years and median absolute error of 1.0 year after leave-one-out cross-validation. This model represents the first epigenetic method of age estimation in brown bears, which provides benefits over tooth-based methods, including high accuracy, less invasiveness, and a simple procedure. Our model has the potential for application to other bear species, which will greatly improve ecological research, conservation, and management.</span></p>
DNA methylation manipulation of memory genes is involved in sevoflurane induced cognitive impairments in aged rats
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Age estimation based on blood DNA methylation levels in brown bears
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Data from: A clockwork fish. Age-prediction using DNA methylation-based biomarkers in the European seabass
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Data for: Mouse sperm DNA-methylation changes induced by age and mechanistic target of rapamycin (mTOR) manipulation in Sertoli cells
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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.