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189 results for “DNA specimens”
FIGURES NJ7–NJ12. Neighbor-joining trees. Scale bar = 1%. Blue circles indicate Nearctic specimens, red circles Palearctic specimens, and mixed circles indicate a combination of the two; diamonds indicate outgroups. In parentheses are numbers of specimens per node. NJ7, Parornix betulae; NJ8, Phyllonorycter maestingella; NJ9, Paraswammerdamia albicapitella; NJ10, Paraswammerdamia conspersella; NJ11, Plutella hyperboreella; NJ12, Lyonetia pulverulentella. in Shared but overlooked: 30 species of Holarctic Microlepidoptera revealed by DNA barcodes and morphology
FIGURES NJ7–NJ12. Neighbor-joining trees. Scale bar = 1%. Blue circles indicate Nearctic specimens, red circles Palearctic specimens, and mixed circles indicate a combination of the two; diamonds indicate outgroups. In parentheses are numbers of specimens per node. NJ7, Parornix betulae; NJ8, Phyllonorycter maestingella; NJ9, Paraswammerdamia albicapitella; NJ10, Paraswammerdamia conspersella; NJ11, Plutella hyperboreella; NJ12, Lyonetia pulverulentella.
FIGURES NJ1–NJ6. Neighbor-joining trees. Scale bar = 1%. Blue circles indicate Nearctic specimens, red circles Palearctic specimens, and mixed circles indicate a combination of the two; diamonds indicate outgroups. In parentheses are numbers of specimens per node. NJ1, Scardia amurensis; NJ2, Triaxomera parasitella; NJ3, Nemapogon cloacella; NJ4, Elabotia montelliella; NJ5, Tinea svenssoni; NJ6, Caloptilia suberinella. in Shared but overlooked: 30 species of Holarctic Microlepidoptera revealed by DNA barcodes and morphology
FIGURES NJ1–NJ6. Neighbor-joining trees. Scale bar = 1%. Blue circles indicate Nearctic specimens, red circles Palearctic specimens, and mixed circles indicate a combination of the two; diamonds indicate outgroups. In parentheses are numbers of specimens per node. NJ1, Scardia amurensis; NJ2, Triaxomera parasitella; NJ3, Nemapogon cloacella; NJ4, Elabotia montelliella; NJ5, Tinea svenssoni; NJ6, Caloptilia suberinella.
FIGURES 11–15 in Recovery of mitochondrial DNA for systematic studies of Pentatomoidea (Hemiptera: Heteroptera): successful PCR on early 20 century dry museum specimens
FIGURES 11–15. Trace files (electropherograms) showing the fragment (between 230/240bp and 340/350bp) of the subunit 16S. 11, Parastrachiidae: Dismegistus binotatus; 12–13, Thyreocoridae: Strombosoma impictum (12), Galgupha difficilis (13); 14–15. Dinidoridae: Coridius nepalensis (14), Megymenum brevicorne (15).
FIGURES 16–17 in Recovery of mitochondrial DNA for systematic studies of Pentatomoidea (Hemiptera: Heteroptera): successful PCR on early 20 century dry museum specimens
FIGURES 16–17. Trace files (electropherograms) showing the fragment (between 240bp and 350bp) of the subunit 16S. 16, Dinidoridae: Megymenum parallelum; 17, Tessaratomidae: Tessaratoma quadrata.
FIGURES 1–5 in Recovery of mitochondrial DNA for systematic studies of Pentatomoidea (Hemiptera: Heteroptera): successful PCR on early 20 century dry museum specimens
FIGURES 1–5. Trace files (electropherograms) showing the same fragment (between 120bp and 230bp) of the subunit 12S. 1– 2, Cydnidae: Chilocoris assmuthi (1), Linospa orbicularis (2); 3, Parastrachiidae: Dismegistus binotatus; 4–5, Thyreocoridae: Strombosoma impictum (4), Galgupha difficilis (5).
Supplementary material 4 from: Colgan DJ, Ahyong ST, Mardon K, Brereton IM (2021) Rare specimen identification in an un-integrated taxonomy: implications of DNA sequences from a Taiwanese Philine (Mollusca, Philinidae). ZooKeys 1060: 93-110. https://doi.org/10.3897/zookeys.1060.28809
Figure S3. Phylogenetic relationships of C.559479 based on Maximum Likelihood analysis of the histone H3 dataset.
Supplementary material 3 from: Colgan DJ, Ahyong ST, Mardon K, Brereton IM (2021) Rare specimen identification in an un-integrated taxonomy: implications of DNA sequences from a Taiwanese Philine (Mollusca, Philinidae). ZooKeys 1060: 93-110. https://doi.org/10.3897/zookeys.1060.28809
Figure S2. Phylogenetic relationships of C.559479 based on maximum likelihood analysis of the D1 28S rRNA dataset
, phillipsi holotype. the M of of Measurements Measurements. . n purposes size sample comparative and , range for , SD shown ± 0 are as presented Lanka Sri and Measurements India in authors . occurring Lanka different Sri, Idulgashinna Miniopterus of of assortment from species an . by nov other. sp and specimens phillipsi species other . M new the of ) the while mm of (, TK measurements individuals by taken other were Cranial and types . 4. ABLE paratypes nov. T sp in DNA barcoding and morphological analyses reveal a cryptic species of Miniopterus from India and Sri Lanka
, phillipsi holotype. the M of of Measurements Measurements. . n purposes size sample comparative and , range for , SD shown ± 0 are as presented Lanka Sri and Measurements India in authors . occurring Lanka different Sri, Idulgashinna Miniopterus of of assortment from species an . by nov other. sp and specimens phillipsi species other . M new the of ) the while mm of (, TK measurements individuals by taken other were Cranial and types . 4. ABLE paratypes nov. T sp
Unlocking the genomes of formalin-fixed freshwater fish specimens: An assessment of factors influencing DNA extraction quantity and quality
<p>DNA quality and quantity metrics (Microsoft Excel worksheet with 3 sheets, one per species).</p> <p>We compared two protocols developed to extract DNA from formalin-fixed tissues using specimens of three freshwater fishes: Southern Brook Lamprey <em>Ichthyomyzon gagei</em>, Slimy Sculpin <em>Cottus cognatus</em>, and Brown Trout <em>Salmo trutta</em>. Extractions were attempted using hot alkali digestion with and without buffer wash pretreatments to compare the DNA concentration, purity, and fragment length of DNA recovered between extraction protocols, tissue types (muscle and caudal fin tissue for Brown Trout and Slimy Sculpin), and preservation periods (5 or 7 years for Southern Brook Lamprey).</p> <p>Four metrics were collected: DNA quantity (measured using Qubit 3.0 instrument with dsDNA high sensitivity kit); DNA purity measured by A260/A280 ratio (measured using NanoDrop 2000 spectrophotometer); DNA purity measured by A260/A230 ratio (measured using NanoDrop 2000 spectrophotometer); and percent fragments >= 300 base pairs (measured using ImageJ). For spectrophotometric absorbance ratios, an A260/A280 ratio of 1.8 and an A260/ A230 ratio of 2.0 were considered to represent “pure” DNA (i.e., free of contaminants). For analyses of DNA purity, deviations from 1.8 for the A260/A280 ratio and from 2.0 for the A260/A230 ratio were used as the response variables, such that larger deviation values corresponded to less-pure DNA.</p> <p>Please see attached README.md file for additional information.</p>
Data from: Sequencing historical specimens: successful preparation of small specimens with low amounts of degraded DNA
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Data from: Which specimens from a museum collection will yield DNA barcodes? A time series study of spiders in alcohol
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Data from: Specimens at the center: an informatics workflow and toolkit for specimen-level analysis of public DNA database data
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Data from: Collecting in collections: a PCR strategy and primer set for DNA barcoding of decades-old dried museum specimens
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Data from: Cost-efficient high throughput capture of museum arthropod specimen DNA using PCR-generated baits
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Data from: Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform
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Integrative biodiversity inventories: characterizing lichen-forming fungal diversity in Glen Canyon National Recreation Area using DNA barcoding and vouchered specimens
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Data from: Disentangling the Pelomedusa complex using type specimens and historical DNA (Testudines: Pelomedusidae)
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Figure 1 from: Bravničar J, Palandačić A, Bajec SS, Snoj A (2020) Neotype designation for Thymallus aeliani Valenciennes, 1848 from a museum topotype specimen and its affiliation with Adriatic grayling on the basis of mitochondrial DNA. ZooKeys 999: 165-178. https://doi.org/10.3897/zookeys.999.56636
Figure 1 Photo (a) and radiograph (b) of the neotype Thymallus aeliani (NMW 68027:2) with fork length of 267.7 mm.
Figure 2 from: Bravničar J, Palandačić A, Bajec SS, Snoj A (2020) Neotype designation for Thymallus aeliani Valenciennes, 1848 from a museum topotype specimen and its affiliation with Adriatic grayling on the basis of mitochondrial DNA. ZooKeys 999: 165-178. https://doi.org/10.3897/zookeys.999.56636
Figure 2 Phylogenetic tree with different evolutionary lineages of grayling found in Europe. Museum specimen haplotypes are shown in red, and the proposed neotype specimen is underlined. Posterior probabilities are shown above branches.
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.
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Allen Brain Atlas
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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.