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59 results for “DNA preservation”
Sutra to DNA : An interdisciplinary approach to cultural heritage preservation
<p>Materials pertaining to the project Sutra2DNA. We have chosen the Diamond Sūtra as the first Buddhist text to be encoded in DNA. The DNA is encased in metal capsule, which in turn are housed in specially designed, 3D printed miniature stūpas.</p> <p>A QR code with the DOI of this archive will be printed on the miniature stūpas. Interested finders who have arrived here because of the QR code should first read the final report of the project.</p> <p>The upload contains the following files:</p> <p>* Sutra2DNA_finalReport.odt<br> Explains the project and outcome.</p> <p>* diamondSutraT235_textOnly.txt<br> The Chinese text of the Diamond Sūtra as provided to the encoder.</p> <p>* Twist-Decoding Instructions-DS14.pdf<br> Contains some of the decoding options available in 2022.</p> <p>* twist_bioscience_codec_v2_external.tar.gz<br> Docker file with the decoder for the DNA sequence as provided by TwistBioscience. </p> <p>* miniatureStupa_STLfiles/*.stl<br> Three files to 3D print the three parts of the miniature stūpa that houses the capsule with the DNA.</p> <p>* dna-fountain-master.zip<br> Justin Brody's porting of Erlich's fountain code algorithm (2017) to Python 3. (2022-06 code from https://github.com/jdbrody/dna-fountain)</p>
Effects of soil preservation for biodiversity monitoring using environmental DNA
Environmental DNA metabarcoding is becoming a key tool for biodiversity monitoring over large geographical or taxonomic scales and for elusive taxa like soil organisms. Increasing sample sizes and interest in remote or extreme areas often require the preservation of soil samples and thus deviations from optimal standardized protocols. However, we still ignore the impact of different methods of soil sample preservation on the results of metabarcoding studies and there is no guidelines for best practices so far. Here, we assessed the impact of four methods of soil sample preservation commonly used in metabarcoding studies (preservation at room temperature for 6h, preservation at 4°C for three days, desiccation immediately after sampling and preservation for 21 days, and desiccation after 6h at room temperature and preservation for 21 days). For each preservation method, we benchmarked resulting estimates of taxon diversity and community composition of three different taxonomic groups (bacteria, fungi and eukaryotes) in three different habitats (forest, river bank and grassland) against results obtained under optimal conditions (i.e. extraction of eDNA right after sampling). Overall, the different preservation methods only marginally impaired results and only under certain conditions. When rare taxa were considered, we detected small but significant changes in MOTU richness of bacteria, fungi and eukaryotes across treatments, while the exclusion of rare taxa led to robust results across preservation methods. The differences in community structure among habitats were evident for all treatments, and the communities retrieved using the different preservation conditions were extremely similar. We propose guidelines on the selection of the optimal soil sample preservation conditions for metabarcoding studies, depending on the practical constraints, costs and ultimate research goals.
Data from: Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing
<p>Studies in vertebrate genomics require sampling from a broad range of tissue types, taxa, and localities. Recent advancements in long-read and long-range genome sequencing have made it possible to produce high-quality chromosome-level genome assemblies for almost any organism. However, adequate tissue preservation for the requisite ultra-high molecular weight DNA (uHMW DNA) remains a major challenge. Here we present a comparative study of preservation methods for field and laboratory tissue sampling, across vertebrate classes and different tissue types. We find that no single method is best for all cases. Instead, the optimal storage and extraction methods vary by taxa, by tissue, and by down-stream application. Therefore, we provide sample preservation guidelines that ensure sufficient DNA integrity and amount required for use with long-read and long-range sequencing technologies across vertebrates. Our best practices generate the uHMW DNA needed for the high-quality reference genomes for Phase 1 of the Vertebrate Genomes Project (VGP), whose ultimate mission is to generate chromosome-level reference genome assemblies of all ~70,000 extant vertebrate species.</p>
First large-scale quantification study of DNA preservation in insects from natural history collections using genome-wide sequencing
<p>Insect declines are a global issue with significant ecological and economic ramifications. Yet we have a poor understanding of the genomic impact these losses can have. Genome-wide data from historical specimens has the potential to provide baselines of population genetic measures to study population change, with natural history collections representing large repositories of such specimens. However, an initial challenge in conducting historical DNA data analyses, is to understand how molecular preservation varies between specimens. Here, we highlight how Next Generation Sequencing methods developed for studying archaeological samples can be applied to determine DNA preservation from only a single leg taken from entomological museum specimens, some of which are more than a century old. An analysis of genome-wide data from a set of 113 red-tailed bumblebee (Bombus lapidarius) specimens, from five British museum collections, was used to quantify DNA preservation over time. Additionally, to improve our analysis and further enable future research we generated a novel assembly of the red-tailed bumblebee genome. Our approach shows that museum entomological specimens are comprised of short DNA fragments with mean lengths below 100 base pairs (BP), suggesting a rapid and large-scale post-mortem reduction in DNA fragment size. After this initial decline, however, we find a relatively consistent rate of DNA decay in our dataset, and estimate a mean reduction in fragment length of 1.9bp per decade. The proportion of quality filtered reads mapping our assembled reference genome was around 50 %, and decreased by 1.1 % per decade. We demonstrate that historical insects have significant potential to act as sources of DNA to create valuable genetic baselines. The relatively consistent rate of DNA degradation, both across collections and through time, mean that population level analyses - for example for conservation or evolutionary studies - are entirely feasible, as long as the degraded nature of DNA is accounted for. </p>
Data from: Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing
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Data from: Characterizing DNA preservation in degraded specimens of Amara alpina (Carabidae: Coleoptera)
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First large-scale quantification study of DNA preservation in insects from natural history collections using genome-wide sequencing
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Liquid crystal-guided DNA information storage: Non-destructive recovery and long-term preservation
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Effects of soil preservation for biodiversity monitoring using environmental DNA
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Data from: An assessment of ancient DNA preservation in Holocene-Pleistocene fossil bone excavated from the world heritage Naracoorte Caves, South Australia
Although there is a long history of research into the fossil deposits of the Naracoorte Caves (South Australia), ancient DNA (aDNA) has not been integrated into any palaeontological study from this World Heritage site. Here, we provide the first evidence of aDNA preservation in Holocene- and Pleistocene-aged fossil bone from a deposit inside Robertson Cave. Using a combination of metabarcoding and shotgun next-generation sequencing approaches, we demonstrate that aDNA from diverse taxa can be retrieved from bulk bone as old as 18 600 cal a BP. However, the DNA is highly degraded and contains a lower relative proportion of endogenous sequences in bone older than 8400 cal a BP. Furthermore, modelling of DNA degradation suggests that the decay rate is rapid, and predicts a very low probability of obtaining informative aDNA sequences from extinct megafaunal bones from Naracoorte (ca. 50 000 cal a BP). We also provide new information regarding the past faunal biodiversity of Robertson Cave, including families that have not been formerly described in the fossil record from here before. Collectively, these data demonstrate the potential for future aDNA studies to be conducted on material from Naracoorte, which will aid in the understanding of faunal turnover in southern Australia.
Fig. 1 in Effect of Propylene Glycol Concentration on Mid-Term DNA Preservation of Coleoptera
Fig. 1. Gel electrophoresis results showing amplification of mitochondrial COI, ∼800 bp, at two weeks, three months, and six months for A) Athetini sp. and B) Cylindera lemniscata. The lane marked L denotes the molecular weight standard, quantities represent percentage of preservative agent (20 = 20% propylene glycol, etc.), and C denotes the negative control.
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>
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.
Network Medicine Approaches to Classify Heart Failure With PReserved Ejection Fraction by Signatures of DNA Methylation and Point-of-carE Risk calculaTors (PRESMET)
ClinicalTrials.gov study NCT05475028. IPD Sharing: NO. Countries: 1. Publications: 1.
Data from: High-throughput sequencing of ancient plant and mammal DNA preserved in herbivore middens
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Data from: An assessment of ancient DNA preservation in Holocene-Pleistocene fossil bone excavated from the world heritage Naracoorte Caves, South Australia
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Data from: Preservation-induced morphological change in salamanders and failed DNA extraction from a decades-old museum specimen: implications for Plethodon ainsworthi
<p>Natural history collections are important data repositories, but different chemical treatments of specimens can influence morphological measurements and DNA extraction, complicating taxonomic and conservation decisions dependent upon these data. One such example is the Bay Springs Salamander (<i>Plethodon ainsworthi</i>), the only United States amphibian categorized as Extinct by the IUCN.<i> </i>Recent research has proposed that <i>P. ainsworthi </i>is an invalid taxon, arguing that the 55-year-old type specimens' morphological distinctiveness from syntopic <i>P. mississippi</i> is a preservation artifact. To address this controversy, we tested for morphological changes across five experimental treatments in proxy <i>P. shermani</i> specimens, and we re-examined the datasets used to support the invalidity of <i>P. ainsworthi</i>. We also tested recently developed DNA extraction techniques on the putatively formalin-fixed <i>P. ainsworthi</i> holotype. We used Bayesian models to demonstrate that preservation method can differentially bias morphological measurements, with most methods causing lower estimates of mass and modestly higher estimates of snout-vent-length:head width ratio. These results are broadly consistent with previous studies of other vertebrates, but inconsistent with the hypothesis that <i>P. ainsworthi </i>type specimens are actually poorly preserved <i>P. mississippi</i>. Attempts to extract DNA from the <i>P. ainsworthi</i> holotype unfortunately proved unsuccessful, preventing conclusive resolution of its status and emphasizing the limitations of promising new methods. Nonetheless, we tentatively recommend continued recognition of <i>P. ainsworthi</i> as a valid but possibly extinct taxon. More generally, we invite all authors who study preserved specimens to recognize and report how certain chemical treatments might impact their results.</p>
Figure 1 from: Szinwelski N, Fialho V, Yotoko K, Seleme L, Sperber C (2012) Ethanol fuel improves arthropod capture in pitfall traps and preserves DNA. ZooKeys 196: 11-22. https://doi.org/10.3897/zookeys.196.3130
Figure 1 - Boxplot showing sampling efficiency of different kinds of pitfall traps' killing solution. Traps with Solution 1 (100% ethanol fuel) captured more species and individuals than Solution 2 (80% commercial alcohol (80°GL) + 10% glycerin (P.A) + 10% formaldehyde (P.A)) and Solution 3 (90% commercial alcohol (80°GL) + 10% glycerin (P.A)). A Total number of species per pitfalls' set. B Total number of individuals per pitfalls' set. Different lower case letters correspond to significant differences between killing solution levels, evaluated through contrast analyses.
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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.