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63 results for “DNA isolation”
Data from: Sorting states of environmental DNA: Effects of isolation method and water matrix on recovery of membrane-bound, dissolved, and adsorbed states of eDNA
<p>Environmental DNA (eDNA) once shed can exist in numerous states with varying behaviors including degradation rates and transport potential. In this study we consider three states of eDNA: 1) a membrane-bound state referring to DNA enveloped in a cellular or organellar membrane, 2) a dissolved state defined as the extracellular DNA molecule in the environment without any interaction with other particles, and 3) an adsorbed state defined as extracellular DNA adsorbed to a particle surface in the environment. Capturing, isolating, and analyzing a target state of eDNA provides utility for better interpretation of eDNA degradation rates and transport potential. While methods for separating different states of DNA have been developed, they remain poorly evaluated due to the lack of state-controlled experimentation. We evaluated the methods for separating states of eDNA from a single sample by spiking DNA from three different species to represent the three states of eDNA as state-specific controls. We used chicken DNA to represent the dissolved state, cultured mouse cells for the membrane-bound state, and salmon DNA adsorbed to clay particles as the adsorbed state. We performed the separation in three water matrices, two environmental and one synthetic, spiked with the three eDNA states. The membrane-bound state was the only state that was isolated with minimal contamination from non-target states. The membrane-bound state also had the highest recovery (54.11 ± 19.24 %), followed by the adsorbed state (5.08 ± 2.28 %), and the dissolved state had the lowest total recovery (2.21 ± 2.36 %). This study highlights the potential to sort the states of eDNA from a single sample and independently analyze them for more informed biodiversity assessments. However, further method development is needed to improve recovery and reduce cross-contamination.</p>
Fig. 3. Agarose gel image Fig. 4 in Optimization Of Dna Extraction Protocol For Dna Isolation From Air-Dried Collection Material For Further Phylogenetic Analysis (Coleoptera: Carabidae)
Fig. 3. Agarose gel image Fig. 4. Agarose gel image (successful PCR amplification) (failed PCR amplification) M: marker (bp) M: marker (bp) A1: Agonum fuliginosum Panzer, 1809 A: Agonum fuliginosum Panzer, 1809 A2: Agonum thoreyi Dejean, 1828 O: Omophron aequale aequale Morawitz, 1863 O: Omophron aequale aequale Morawitz, 1863 N: Notiophilus semistriatus Say, 1823 N: Notiophilus semistriatus Say, 1823 Nk: negative control. Nk: negative control.
Fig. 1 in Optimization Of Dna Extraction Protocol For Dna Isolation From Air-Dried Collection Material For Further Phylogenetic Analysis (Coleoptera: Carabidae)
Fig. 1. Photo of Omophron aequale jacobsoni Fig. 2. Photo of Omophron aequale jacobsoni Semenov, 1922 before incubation. Semenov, 1922 after 16 h (56°C) incubation time in tissue lysis buffer with proteinase K.
Optimization of nuclei isolation for high-molecular weight DNA extraction of wild plants
<p><strong>Optimization of nuclei isolation for high-molecular weight DNA extraction from wild plants</strong></p> <p><strong>Authors</strong></p> <p>Irene Martínez-García<sup>1</sup>; Martina Degli Alberti<sup>2</sup>; Aureliano, Bombarely<sup>2</sup>; Mario Xavier Ruiz-González<sup>1</sup>; Santiago Vilanova<sup>1</sup>; Silvia Manrique<sup>1</sup></p> <p> </p> <p><strong>Affiliations</strong></p> <p>1 Instituto Universitario para la Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universidad Politécnica de Valencia (UPV), Camino de Vera s/n 46022, Valencia, Spain) 2 Instituto de Biología Molecular y Celular de Plantas (IBMCP) Primo-Yufera, Consejo Superior de Investigaciones Científicas (CSIC)- Universidad Politécnica de Valencia (UPV), Camino de Vera s/n 46022, Valencia, Spain)</p> <p> </p> <p><strong>Abstract</strong></p> <p>Obtaining high-quality, high-molecular-weight (HMW) DNA is mandatory for constructing reference genomes, yet it remains a significant challenge, particularly for non-model plant species. Many plants contain polysaccharides and secondary metabolites such as polyphenols and tannins, which hinder DNA extraction. Exposure to multiple environmental stresses along their lives exacerbate this issue in wild plants collected from nature, as they may synthesize additional compounds that impair DNA extraction.</p> <p>This study investigates the efficacy of various DNA extraction protocols on four recalcitrant plant species—<em>Pistacia lentiscus</em>, <em>Phyllirea angustifolia</em>, <em>Sarcocornia fruticosa</em>, and <em>Limbarda crithmoides</em>—each possessing unique traits complicating DNA extraction (e.g., succulence, lignification, coloration). Samples were collected from El Saler (Valencia), and multiple protocols for nuclei isolation and DNA extraction were tested. The results were systematically evaluated to compile a comprehensive best practices guide, aiding researchers in selecting optimal methods tailored to their species of interest. This guide serves as a valuable resource for future endeavours in genome research, facilitating advancements in understanding and conservation efforts for diverse plant species.</p> <p>Funding: </p> <p>This work was supported by Erasmus+ Program (to MD), Programa María Zambrano 2021 (to SM and MXRG, UPV Ministerio de Universidades, Plan de Recuperación, Transformación y Resiliencia - Financiado por la Unión Europea – NextGenerationEU) and Catalan Initiative For the Earth Biogenome Project (Call1A-2023 to SM and call 2-2023 to AB and SM) and Primeros Proyectos UPV (PAID-06-22 to MXRG).</p>
Data from: Sorting states of environmental DNA: Effects of isolation method and water matrix on recovery of membrane-bound, dissolved, and adsorbed states of eDNA
Open the record for dataset details and reuse information.
Data from: Reliable genotyping of the koala (Phascolarctos cinereus) using DNA isolated from a single faecal pellet
The koala, an Australian icon, has been added to the threatened species list. Rationale for the listing includes proposed declines in population size, threats to populations (e.g. disease) and loss and fragmentation of habitat. There is now an urgent need to obtain accurate data to assess the status of koala populations in Australia, to ensure the long-term viability of this species. Advances in genetic techniques have enabled DNA analysis to study and inform the management of wild populations; however, sampling of individual koalas is difficult in tall, often remote, eucalypt forest. The collection of faecal pellets (scats) from the forest floor presents an opportunistic sampling strategy, where DNA can be collected without capturing or even sighting an individual. Obtaining DNA via noninvasive sampling can be used to rapidly sample a large proportion of a population; however, DNA from noninvasively collected samples is often degraded. Factors influencing DNA quality and quantity include environmental exposure, diet and methods of sample collection, storage and DNA isolation. Reduced DNA quality and quantity can introduce genotyping errors and provide inaccurate DNA profiles, reducing confidence in the ability of such data to inform management/conservation strategies. Here, we present a protocol that produces a reliable individual koala genotype from a single faecal pellet and highlight the importance of optimizing DNA isolation and analysis for the species of interest. This method could readily be adapted for genetic studies of mammals other than koalas, particularly those whose diet contains high proportions of volatile materials that are likely to induce DNA damage.
Supplementary material 1 from: Ang Y, Rajaratnam G, Su KFY, Meier R (2017) Hidden in the urban parks of New York City: Themira lohmanus, a new species of Sepsidae described based on morphology, DNA sequences, mating behavior, and reproductive isolation (Sepsidae, Diptera). ZooKeys 698: 95-111. https://doi.org/10.3897/zookeys.698.13411
Aligned COI sequences for Themira putris, T. biloba, and Themira 'biloba-like' (i.e., T. lohmanus n. sp.) specimens : Data type: Fasta file
FIGURE 2 in Plastid DNA fingerprinting of the rare Fritillaria moggridgei (Liliaceae) reveals population differentiation and genetic isolation within the Fritillaria tubiformis complex
FIGURE 2. Strict consensus tree of more than 2600 most parsimonious trees from analysis of the combined plastid matK and rpl16 intron sequences. Tree length = 451 steps, CI = 0.89 and RI = 0.85. Bootstrap percentages (> 50%) are indicated above branches. Cardiocrinum giganteum and Notholirion thomsonianum are the outgroups. See also Table 2.
FIGURE 4 in Plastid DNA fingerprinting of the rare Fritillaria moggridgei (Liliaceae) reveals population differentiation and genetic isolation within the Fritillaria tubiformis complex
FIGURE 4. Principal coordinate analysis (PCO) of eleven populations of Fritillaria tubiformis s.l. analyzed for ten microsatellite loci. The first (PCO1) and the second (PCO2) axes explain 50.4% and 20.9% of total variation, respectively. Acronyms correspond to populations (see Table 1). The two genetic groups corresponding to the two subspecific taxa are circled.
FIGURE 1 in Plastid DNA fingerprinting of the rare Fritillaria moggridgei (Liliaceae) reveals population differentiation and genetic isolation within the Fritillaria tubiformis complex
FIGURE 1. Map of the Italian populations of F. tubiformis s.l. Populations belonging to var. burnatii are labelled with a star and those belonging to subsp. moggridgei with a solid circle. Most sampled populations are located at the boundary between Piedmont (P) and Liguria (L) (Italy). Insets show, top left, sampling sites numbered as for populations (see Table 1) and, top right, the position of the sampled area within the Alps.
DNA Analysis From Isolated Cardiomyocytes in the Molecular Diagnosis of Arrhythmogenic Right Ventricular Cardiomyopathy/Dysplasia
ClinicalTrials.gov study NCT03177018. IPD Sharing: NO. Countries: 1. Publications: 1.
Isolation of Cell Free Fetal DNA From Spent Culture Medium and Its Potential Role for Preimplantation Genetic Diagnosis (PGD).
ClinicalTrials.gov study NCT06084377. IPD Sharing: UNDECIDED. Countries: 1. Publications: 6.
Data from: Reliable genotyping of the koala (Phascolarctos cinereus) using DNA isolated from a single faecal pellet
Open the record for dataset details and reuse information.
Supplementary material 2 from: Buzan E, Potušek S, Urzi F, Pokorny B, Šprem N (2020) Genetic characterisation of wild ungulates: successful isolation and analysis of DNA from widely available bones can be cheap, fast and easy. ZooKeys 965: 141-156. https://doi.org/10.3897/zookeys.965.54862
Microsatellite loci for muscle tissue samples and recent bone samples
Figure 1 from: Buzan E, Potušek S, Urzi F, Pokorny B, Šprem N (2020) Genetic characterisation of wild ungulates: successful isolation and analysis of DNA from widely available bones can be cheap, fast and easy. ZooKeys 965: 141-156. https://doi.org/10.3897/zookeys.965.54862
Figure 1 Micro-locations of sampling bone material for DNA isolation (see arrows) A roe deer mandibles B ethmoid bone of chamois C wild boar mandible D chamois skull.
Supplementary material 1 from: Buzan E, Potušek S, Urzi F, Pokorny B, Šprem N (2020) Genetic characterisation of wild ungulates: successful isolation and analysis of DNA from widely available bones can be cheap, fast and easy. ZooKeys 965: 141-156. https://doi.org/10.3897/zookeys.965.54862
Tables S1–S4
Data from: Robust DNA isolation and high-throughput sequencing library construction for herbarium specimens
Herbaria are an invaluable source of plant material that can be used in a variety of biological studies. The use of herbarium specimens is associated with a number of challenges including sample preservation quality, degraded DNA, and destructive sampling of rare specimens. In order to more effectively use herbarium material in large sequencing projects, a dependable and scalable method of DNA isolation and library preparation is needed. This paper demonstrates a robust, beginning-to-end protocol for DNA isolation and high-throughput library construction from herbarium specimens that does not require modification for individual samples. This protocol is tailored for low quality dried plant material and takes advantage of existing methods by optimizing tissue grinding, modifying library size selection, and introducing an optional reamplification step for low yield libraries. Reamplification of low yield DNA libraries can rescue samples derived from irreplaceable and potentially valuable herbarium specimens, negating the need for additional destructive sampling and without introducing discernible sequencing bias for common phylogenetic applications. The protocol has been tested on hundreds of grass species, but is expected to be adaptable for use in other plant lineages after verification. This protocol can be limited by extremely degraded DNA, where fragments do not exist in the desired size range, and by secondary metabolites present in some plant material that inhibit clean DNA isolation. Overall, this protocol introduces a fast and comprehensive method that allows for DNA isolation and library preparation of 24 samples in less than 13 hours, with only 8 hours of active hands-on time with minimal modifications.
Data from: Soil sampling and isolation of extracellular DNA from large amount of starting material suitable for metabarcoding studies
DNA metabarcoding corresponds to the DNA-based identification of multiple species from a single complex and degraded environmental sample. We developed new sampling and extraction protocols suitable for DNA metabarcoding analyses, targeting soil extracellular DNA. The proposed sampling protocol has been designed to reduce as much as possible the influence of the local heterogeneity by processing large amount of soil, resulting from the mixing of many different cores. The DNA extraction is based on the use of saturated phosphate buffer. The sampling and extraction protocols were validated first by analyzing plant DNA from a set of 12 plots corresponding to four plant communities in alpine meadows, and second by conducting pilot experiments on fungi and earthworms. The results of the validation experiments clearly demonstrated that sound biological information can be retrieved when following these sampling and extraction procedures. Such a protocol can be implemented at any time of the year without any preliminary knowledge of specific types of organisms during the sampling. It offers the opportunity to analyze all groups of organisms using a single sampling/extraction procedure and opens the possibility to fully standardize biodiversity surveys.
Figure 1 from: Ang Y, Rajaratnam G, Su KFY, Meier R (2017) Hidden in the urban parks of New York City: Themira lohmanus, a new species of Sepsidae described based on morphology, DNA sequences, mating behavior, and reproductive isolation (Sepsidae, Diptera). ZooKeys 698: 95-111. https://doi.org/10.3897/zookeys.698.13411
Figure 1 - Surstyli (dorsal view) for male Themira biloba (A) and Themira "biloba-like" (B). Red arrows indicate basal process on left surstylus; green arrow for basal process on right surstylus.
Figure 3 from: Ang Y, Rajaratnam G, Su KFY, Meier R (2017) Hidden in the urban parks of New York City: Themira lohmanus, a new species of Sepsidae described based on morphology, DNA sequences, mating behavior, and reproductive isolation (Sepsidae, Diptera). ZooKeys 698: 95-111. https://doi.org/10.3897/zookeys.698.13411
Figure 3 - Adult female (A–H), showing lateral (A) and dorsal (B) views of habitus (sans abdomen), anterior (C) and ventral (D) views of head capsule, anterior and posterior views of fore leg (E), mid leg (F) and rear leg (G), and ventral view of abdomen (H).
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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)
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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
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