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143 results for “DNA extraction”
FIGURE 4 in DNA extracted from museum specimens of the 19 century provides a taxonomic resolution on the identity of the characid fish Psalidodon jequitinhonhae (Ostariophysi: Characiformes)
FIGURE 4 | Psalidodon jequitinhonhae. Specimens from Jequitinhonha River, Itaobim Municipality, Minas Gerais State, Brazil, 16°30'36"S 41°20'02"W. LBP 8311, male, 57.7 mm SL, female, 57.4 mm SL.
FIGURE 1 in DNA extracted from museum specimens of the 19 century provides a taxonomic resolution on the identity of the characid fish Psalidodon jequitinhonhae (Ostariophysi: Characiformes)
FIGURE 1 | A. Tetragonopterus rutilus var. Jequitinhonhae [sic] as illustrated by Steindachner (1877: plate II, fig. 3). B. Astyanax fasciatus jequitinhonhae as illustrated by Eigenmann (1921: plate 50, fig. 3; MCZ 20901; 83 mm; Jequitinhonha Rive, Brazil.
FIGURE 3 in DNA extracted from museum specimens of the 19 century provides a taxonomic resolution on the identity of the characid fish Psalidodon jequitinhonhae (Ostariophysi: Characiformes)
FIGURE 3 | Neighbor-joining tree based on p-distance model generated with a sequence fragment of the gene COI with 197 base pairs. The tree includes the lectotype of Tetragonopterus rutilus jequitinhonhae (NWM 57760:2) (dark blue) and species of the stethaprionine genera Psalidodon, Astyanax, Andromakhe, and Deuterodon. Sequences obtained from modern specimens of P. jequitinhonhae in light blue. Rooted in Serrapinnus heterodon.
FIGURE 7 in DNA extracted from museum specimens of the 19 century provides a taxonomic resolution on the identity of the characid fish Psalidodon jequitinhonhae (Ostariophysi: Characiformes)
FIGURE 7 | Distribution map of Psalidodon jequitinhonhae, encompassing its occurrence in the Jequitinhonha and Pardo river basins, Minas Gerais and Bahia States, Brazil.
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>
Linked collectors and determiners for: NEON Biorepository Tick Collection (DNA Extracts [Pathogen Extracts]).
Natural history specimen data linked to collectors and determiners held within, "NEON Biorepository Tick Collection (DNA Extracts [Pathogen Extracts])". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/922feca7-a681-4f61-89a7-9ac8fe968d82">https://bionomia.net/dataset/922feca7-a681-4f61-89a7-9ac8fe968d82</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/922feca7-a681-4f61-89a7-9ac8fe968d82">https://gbif.org/dataset/922feca7-a681-4f61-89a7-9ac8fe968d82</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: NEON Biorepository Mosquito Collection (DNA Extracts [Pathogen Extracts]).
Natural history specimen data linked to collectors and determiners held within, "NEON Biorepository Mosquito Collection (DNA Extracts [Pathogen Extracts])". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/53c520c9-f945-45df-8d0f-4a590b462c98">https://bionomia.net/dataset/53c520c9-f945-45df-8d0f-4a590b462c98</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/53c520c9-f945-45df-8d0f-4a590b462c98">https://gbif.org/dataset/53c520c9-f945-45df-8d0f-4a590b462c98</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: NEON Biorepository Mosquito Collection (DNA Extracts).
Natural history specimen data linked to collectors and determiners held within, "NEON Biorepository Mosquito Collection (DNA Extracts)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/e8185de6-f375-4e6c-8bd0-788656b79609">https://bionomia.net/dataset/e8185de6-f375-4e6c-8bd0-788656b79609</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/e8185de6-f375-4e6c-8bd0-788656b79609">https://gbif.org/dataset/e8185de6-f375-4e6c-8bd0-788656b79609</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: NEON Biorepository Benthic Macroinvertebrate Collection (DNA Extracts).
Natural history specimen data linked to collectors and determiners held within, "NEON Biorepository Benthic Macroinvertebrate Collection (DNA Extracts)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/39af39be-ccd5-4a36-800a-c6ca4a4bb3b5">https://bionomia.net/dataset/39af39be-ccd5-4a36-800a-c6ca4a4bb3b5</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/39af39be-ccd5-4a36-800a-c6ca4a4bb3b5">https://gbif.org/dataset/39af39be-ccd5-4a36-800a-c6ca4a4bb3b5</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: NEON Biorepository Fish Collection (DNA Extracts).
Natural history specimen data linked to collectors and determiners held within, "NEON Biorepository Fish Collection (DNA Extracts)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/97255e25-4983-4e2b-bf18-2127d29e12a9">https://bionomia.net/dataset/97255e25-4983-4e2b-bf18-2127d29e12a9</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/97255e25-4983-4e2b-bf18-2127d29e12a9">https://gbif.org/dataset/97255e25-4983-4e2b-bf18-2127d29e12a9</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: NEON Biorepository Mammal Collection (DNA Extracts).
Natural history specimen data linked to collectors and determiners held within, "NEON Biorepository Mammal Collection (DNA Extracts)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/66da3373-5cca-4d00-a477-af751b5ed052">https://bionomia.net/dataset/66da3373-5cca-4d00-a477-af751b5ed052</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/66da3373-5cca-4d00-a477-af751b5ed052">https://gbif.org/dataset/66da3373-5cca-4d00-a477-af751b5ed052</a>. Formatted as a Frictionless Data package.
Extracting abundance information from DNA-based data
Open the record for dataset details and reuse information.
Evaluation of DNA extracted from timber rattlesnake (Cotalus horridus) cloacal and blood swabs for microsatellite genotyping
Open the record for dataset details and reuse information.
Monitoring the compaction of single DNA molecules in Xenopus egg extract in real time
Open the record for dataset details and reuse information.
Application of high-throughput sequencing (HTS) metabarcoding to diatom biomonitoring: Do DNA extraction methods matter?
<p>The 8 benthic samples from Mainland France (stream Edian, stream Aire, lake Geneva), Sweden (stream Dåmman, Agricultural stream, lake Båtkåjaure) and Mayotte (stream Dapani, stream Majimbini) were collected by scraping material from the surface of stones, following the French standard (AFNOR 2007) used in routine biomonitoring programs.DNA was extracted from each sample (2 replicates) using five DNA extraction methods, followed by the amplification of a short rbcL DNA barcode (312bp) specific to diatoms. PCR products were then sequenced in one random direction using the Ion Torrent™ Personal Genome Machine® (PGM) System according to the manufacturer’s instructions. The data file contains one fastq file per library sequenced with the raw DNA reads, as provided by the sequencing platform (demultiplexing performed by the sequencing platform). An excel file is also provided to make the link between the fastq file number and the sample information (sample origin, DNA extraction method used, number of raw reads).</p>
Supplementary Table S1 (raw data) of "Filtration extraction method using microfluidic channel for measuring environmental DNA "
<p>Supplementary Table S1 (all raw data) of "Filtration extraction method using microfluidic channel for measuring environmental DNA ". Each data of the validation experiment; Experiment 1-4 was located in different sheets..</p>
Nanopore MinION Run Metrics and genomic DNA fragment size analysis data from automated phenol-chloroform extractions (RBI LabDroid Maholo)
<p>Nanopore MinION run MinKNOW statistical metrics output, Agilent Femto Pulse and Tape Station gDNA fragment size analysis reports of genomic DNA isolated from automated RBI LabDroid Maholo organic extractions.</p>
Protocol for Extraction of High-Molecular-Weight Genomic DNA from Gram-Negative Bacteria
<p>Video demonstrating the protocol for extraction of High-Molecular-Weight Genomic DNA from Gram-negative bacteria based on MagAttract HMW DNA kit QIAGEN. Training video elaborated within the ArtiSaneFood project.</p>
Protocol for DNA Extraction from Cheese
<p>Video demonstrating the protocol for DNA extraction from cheese based on PowerFood Microbial DNA isolation kit MO BIO, according to Yang et al. (2016) procedure. Training video elaborated within the ArtiSaneFood project.</p>
Data for: Environmental DNA storage and extraction method affects detectability for multiple aquatic invasive species
<p>Environmental DNA (eDNA) refers to genetic material released by organisms into their surrounding environment. Collecting and identifying eDNA has gained popularity for monitoring and surveillance of aquatic invasive species. Invasive species management is most successful when an invasion is identified early while population size is likely to be low, highlighting the importance of eDNA detection sensitivity. Various factors influence DNA yield recovered from environmental samples. Environmental DNA storage and extraction methods, for example, can be adjusted to maximize DNA yield, thereby improving detectability. In this study, we compared the performance of two eDNA storage and extraction methods in detecting three common aquatic invasive species (<em>Bythotrephes longimanus</em>, <em>Dreissena polymorpha</em>, and <em>Faxonius rusticus</em>) across five natural ecosystems of Minnesota, United States. One method involved storing filters in 95% ethanol (EtOH) and extracting DNA using a DNeasy PowerSoil Pro Kit (Qiagen, Hilden, Germany), whereas the other method used cetyl trimethylammonium bromide (CTAB) for storage and a phenol–chloroform–isoamyl (PCI) procedure for DNA extraction. We also investigated the effect of DNA extract volume (1 μL relative to 3 μL) in qPCR reactions on eDNA detections for the commercial kit method. The CTAB‐PCI method yielded significantly more positive detections, across all three species, compared to the EtOH‐Qiagen method. Moreover, we found that using 1 μL of DNA extract in qPCR reactions was equally effective as using 3 μL. To improve detections of aquatic invasive species, we recommend that researchers store eDNA sample filters in CTAB or a similar lysis buffer such as Longmire's solution and extract with PCI when feasible, but note that lower extract volumes might be used without negative effect when either increasing technical replicates or repurposing samples for the detection of multiple species.</p>
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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
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.