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57 results for “DNA content”
FIG. 3 in Intraindividual variation in nuclear DNA content in Durvillaea antarctica (Chamisso) Hariot, Macrocystis pyrifera (Linnaeus) C. Agardh and Lessonia spicata (Suhr) Santelices (Phaeophyceae)
FIG. 3. — Developmental stages of sporangia in Macrocystis pyrifera (Linnaeus) C. Agardh stained with DAPI: A-C, four-nucleate sporangium (4-ns) and sporangial mother cells (smc); D, mature sporangia. Scale bars: A-D, 5 μm.
FIG. 1 in Intraindividual variation in nuclear DNA content in Durvillaea antarctica (Chamisso) Hariot, Macrocystis pyrifera (Linnaeus) C. Agardh and Lessonia spicata (Suhr) Santelices (Phaeophyceae)
FIG. 1. — Cells of Durvillaea antarctica (Chamisso) Hariot stained with DAPI: A, mitotic figure (mf) of dividing cortical cells (cc); B, uninucleate cortical cells; C, D, mature antheridia (ma), antheridia germinative cells (agc), antheridium (a) and four-nucleate antheridium (4-na); E, five-nucleate antheridium (5-na); F, antheridia germinative cells. Scale bars: A-D, 5 μm.
Processed data from "Chromatin information content landscapes inform transcription factor and DNA interactions"
<p><strong>Chromatin information content landscapes inform transcription factor and DNA interactions</strong></p> <p>Authors: Ricardo D’Oliveira Albanus, Yasuhiro Kyono, John Hensley, Arushi Varshney, Peter Orchard, Jacob O. Kitzman, Stephen C. J. Parker</p> <p><a href="https://doi.org/10.1101/777532">https://doi.org/10.1101/777532</a></p> <p> </p> <p>This record contains the processed data used in our manuscript. For instructions on how to use or regenerate this data, please refer to <a href="https://github.com/ParkerLab/chromatin_information">https://github.com/ParkerLab/chromatin_information</a>.</p>
Stomach content DNA from Loligo vulgaris paralarvae in W Iberian Peninsula waters
<p>This dataset contains the DNA sequences obtained from 31 Loligo vulgaris paralarvae ranging from 1.61 to 6.01 mm that were between two and 28 days old. Digestive system of each paralarvae was dissected and DNA was extracted amplifying 300 bp fragment of the mitochondrial cytochrome c oxidase subunit I gene.</p> <p>The generated DNA fragments (DNA libraries) were sequenced with MiSeq Reagent Kit v3 in the lllumina MiSeq platform, using 300bp paired-end sequencing reads.</p> <p> </p>
Gut content metabarcoding of specialized feeders is not a replacement for environmental DNA assays of their reef environment
<p>In tropical marine ecosystems, the coral-based diet of benthic-feeding reef fishes provides a window into the composition and health of coral reefs. In this study, for the first time, we compare multi-assay metabarcoding sequences of environmental DNA (eDNA) isolated from seawater and partially digested gut items from an obligate corallivore butterflyfish (<em>Chaetodon</em> <em>lunulatus</em>) resident at coral reef sites in the South China Sea. We specifically tested the proportional and statistical overlap of the different approaches (seawater versus gut content metabarcoding) in characterizing eukaryotic community composition on coral reefs. Based on 18S rRNA and ITS2 rRNA sequence data, which differed in their taxonomic sensitivity, we found that gut content detections were only partially representative of the eukaryotic communities detected in the seawater. Overall, our results indicate that dietary metabarcoding of specialized feeders can be complimentary to, but is no replacement for, more comprehensive environmental DNA assays of reef environments that can include the processing of different substrates (seawater, sediment, plankton) or traditional observational surveys. These molecular assays, in tandem, might be best suited to highly productive but cryptic oceanic environments (coral reefs, kelp forests, seagrass meadows) that contain an abundance of organisms that are often small, epiphytic, symbiotic, or cryptic.</p>
Gut content metabarcoding of specialized feeders is not a replacement for environmental DNA assays of their reef environment
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Data from: DNA metabarcoding reveals changes in the contents of carnivorous plants along an elevation gradient
Resource variation along abiotic gradients influences subsequent trophic interactions and these effects can be transmitted through entire food webs. Interactions along abiotic gradients can provide clues as to how organisms will face changing environmental conditions, such as future range shifts. However, it is challenging to find replicated systems to study these effects. Phytotelmata, such as those found in carnivorous plants, are isolated aquatic communities and thus form a good model for the study of replicated food webs. Due to the degraded nature of the prey, molecular techniques provide a useful tool to study these communities. We studied the pitcher plant Sarracenia purpurea L. in allochthonous populations along an elevational gradient in the Alps and Jura. We predicted that invertebrate richness in the contents of the pitcher plants would decrease with increasing elevation, reflecting harsher environmental conditions. Using metabarcoding of the COI gene, we sequenced the invertebrate contents of these pitcher plants. We assigned Molecular Operational Taxonomic Units at ordinal level as well as recovering species-level data. We found small but significant changes in community composition with elevation. These recovered sequences could belong to invertebrate prey, rotifer inquilines, pollinators and other animals possibly living inside the pitchers. However, we found no directional trend or site-based differences in MOTU richness with elevational gradient. Use of molecular techniques for dietary or contents analysis is a powerful way to examine numerous degraded samples, although factors such as DNA persistence and the relationship to species presence still have to be completely determined.
Data from: Two new species of Limbodessus diving beetles from New Guinea - short verbal descriptions flanked by online content (digital photography, μCT scans, drawings and DNA sequence data)
Background: To date only one species of Limbodessus diving beetles has been reported from the Island of New Guinea, L. compactus (Clark, 1862), which is widerspread in the Australian region. New information: We describe two new species of microendemic New Guinea Limbodessus and use a compact descriptive format flanked by enriched online content in wiki powered species pages. Limbodessus baliem sp.n. is described from ca. 1,600 m altitude in the Baliem Valley of Papua and Limbodessus alexanderi sp.n. from >3,000 m altitude north of Sugapa, Papua. Based on our analysis, we also transfer three species from other genera to Limbodessus Guignot, 1939, with the following changes: Limbodessus deflectus (Ordish, 1966), new combination; Limbodessus leveri (J. Balfour-Browne, 1944), new combination; and Limbodessus plicatus (Sharp, 1882), new combination.
Figure 3. Example relative fluorescence histograms for samples stained with propidium iodide. The 2C in Peaceful revolution in genome size: polyploidy in the Nabidae (Heteroptera); autosomes and nuclear DNA content doubling
Figure 3. Example relative fluorescence histograms for samples stained with propidium iodide. The 2C peaks represent diploid cells, and 4C peaks represent cells in the G2 phase of the cell cycle, with replicated DNA. Standard used: Solanum pseudocapsicum 2C = 2.61 pg. A, Himacerus apterus female with 2n = 36 + XX and 2C = 9.71 pg. B, Nabis maoricus female with 2n = 16 + XX and 2C = 4.21 pg.
Figure 2 in Peaceful revolution in genome size: polyploidy in the Nabidae (Heteroptera); autosomes and nuclear DNA content doubling
Figure 2. Nuclear DNA content stained with propidium iodide (PI) compared with relative nuclear DNA content stained with 4′,6-diamidino-2-phenylindole (DAPI). The line represents the trend in GC content, with a minimum of 33.34% and a maximum of 37.83%. Each pair of black and white symbols represents one specimen, as follows: circles, females; squares, males; white symbols, DAPI; black symbols, PI.
Figure 1 in Peaceful revolution in genome size: polyploidy in the Nabidae (Heteroptera); autosomes and nuclear DNA content doubling
Figure 1. Chromosomes of Nabidae species studied, stained with Giemsa (A, D, F, G, M) or with an 18S ribosomal DNA (rDNA) probe (red) applied via fluorescence in situ hybrization (FISH) (B, C, E, H–L, N–P). A, B, Nabis punctatus ♀ 2n = 16 + XX, mitotic metaphase. C, Himacerus apterus ♀ 2n = 36 + XX, mitotic metaphase. D, Nabis rugosus ♂ 2n = 16 + XY + 1 metaphase I, specimen with an additional chromosome (arrow). E, Nabis maoricus ♀ 2n = 18 + XX, mitotic metaphase. F, N. maoricus ♂ 2n = 16 + XY, postpachytene, with sex chromosomes superspiralized. G, H, Nabis biformis ♀ 2n = 16 + XX, mitotic metaphase, with two 18S rDNA signals on each X chromosome. I, Nabis limbatus ♀ 2n = 16 + XX, mitotic metaphase, species with the most distal 18S rDNA signal. J, N. rugosus ♂ 2n = 16 + XY, mitotic metaphase, species with the two 18S rDNA signals on Y chromosome. K, Prostemma guttula ♂ 2n = 26 + XY, metaphase II. L, N. maoricus ♂ 2n = 16 + XY, metaphase II, with Y chromosome showing no 18S rDNA signal. M, N, Prostemma aeneicolle ♀ 2n = 26 + XX, mitotic metaphase. O, H. apterus ♀ 2n = 36 + XXXX, mitotic metaphase, with terminal 18S rDNA signals on four X chromosomes originated by fragmentation. P, N. maoricus ♀ 2n = 18 + XXX, mitotic metaphase, with one X chromosome fragmented outside of the 18S rDNA position. Arrowheads indicate 18S rDNA signal; X and Y are the sex chromosomes. Scale bars: 10 μm.
Figure 4 in Peaceful revolution in genome size: polyploidy in the Nabidae (Heteroptera); autosomes and nuclear DNA content doubling
Figure 4. Comparison of three alternative hypotheses on the ancestral 2n number of chromosomes of Nabidae: fusions, proposed by Nokkala et al. (2007); autosomal polyploidy, suggested by Kuznetsova & Maryańska-Nadachowska (2000) and supported by nuclear DNA content data from the present study; and the hypothetical fission theory. Abbreviations: 2C, nuclear DNA content; F, autosomal fusions; Fis, fissions; P, polyploidy.
Deciphering the diet of a wandering spider (Phoneutria boliviensis; Araneae: Ctenidae) by DNA metabarcoding of gut contents
<p>Arachnids are the most abundant land predators. Despite the importance of their functional roles as predators and the necessity to understand their diet for conservation, the trophic ecology of many arachnid species has not been sufficiently studied. In the case of the wandering spider, <i>Phoneutria boliviensis</i> F. O. Pickard-Cambridge, 1897, only field and laboratory observational studies on their diet exist. By using a DNA metabarcoding approach, we compared the prey found in the gut content of males and females from three distant Colombian populations of <i>P. boliviensis</i>. By DNA metabarcoding of the cytochrome <i>c</i> oxidase subunit I (COI), we detected and identified 234 prey items (individual captured by the spider) belonging to 96 operational taxonomic units (OTUs), as prey for this wandering predator. Our results broaden the known diet of <i>P. boliviensis</i> with at least 75 prey taxa not previously registered in fieldwork or laboratory experimental trials. These results suggest that <i>P. boliviensis</i> feeds predominantly on invertebrates (Diptera, Lepidoptera, Coleoptera and Orthoptera) and opportunistically on small squamates. Intersex and interpopulation differences were also observed. Assuming that prey preference does not vary between populations, these differences are likely associated with a higher local prey availability. Finally, we suggest that DNA metabarcoding can be used for evaluating subtle differences in the diet of distinct populations of <i>P. boliviensis, </i>particularly when predation records in the field cannot be established or quantified using direct observation.</p>
FIGURE 4 in Taxonomic remarks on the genus Sternbergia L. (Amaryllidaceae) in Turkey based on leaf anatomy, karyosystematic analysis and nuclear DNA content
FIGURE 4. Leaf cross sections: 1) Sternbergia candida, 2) S. clusiana, 3) S. colchiciflora, 4) S. lutea, 5) S. sicula, 6) S. vernalis.
FIGURE 1 in Taxonomic remarks on the genus Sternbergia L. (Amaryllidaceae) in Turkey based on leaf anatomy, karyosystematic analysis and nuclear DNA content
FIGURE 1. Distribution of the genus Sternbergia in Turkey: S.candida, S.clusianȧ, S. colchiciflora, S.lutea, S. sicula, S. vernalis, S.schubertii?.
FIGURE 3 in Taxonomic remarks on the genus Sternbergia L. (Amaryllidaceae) in Turkey based on leaf anatomy, karyosystematic analysis and nuclear DNA content
FIGURE 3. Mitotic chromosomes and idiograms of Sternbergia; 4) S. lutea, 5) S. sicula, 6) S. vernalis, (Scale bar = 10μm).
FIGURE 6 in Taxonomic remarks on the genus Sternbergia L. (Amaryllidaceae) in Turkey based on leaf anatomy, karyosystematic analysis and nuclear DNA content
FIGURE 6. UPGMA cluster of the considered taxa, based on the morpho-anatomical data matrix presented in Table 3.
FIGURE 2 in Taxonomic remarks on the genus Sternbergia L. (Amaryllidaceae) in Turkey based on leaf anatomy, karyosystematic analysis and nuclear DNA content
FIGURE 2. Mitotic chromosomes and idiograms of Sternbergia; 1) S. candida, 2) S. clusiana, 3) S. colchiciflora (Scale bar = 10μm).
FIGURE 5 in Taxonomic remarks on the genus Sternbergia L. (Amaryllidaceae) in Turkey based on leaf anatomy, karyosystematic analysis and nuclear DNA content
FIGURE 5. Leaf cross sections: 1) Sternbergia candida, 2) S. clusiana, 3) S. colchiciflora, 4) S. lutea, 5) S. sicula, 6) S. vernalis. (e: epidermis, s: stomata, pp: palisade parenchyma, sp: spongy parenchyma, ls: laticifer systems) (scale bar 0.1 mm).
Figure 4 in Peaceful revolution in genome size: polyploidy in the Nabidae (Heteroptera); autosomes and nuclear DNA content doubling
Figure 4. Comparison of three alternative hypotheses on the ancestral 2n number of chromosomes of Nabidae: fusions, proposed by Nokkala et al. (2007); autosomal polyploidy, suggested by Kuznetsova & Maryańska-Nadachowska (2000) and supported by nuclear DNA content data from the present study; and the hypothetical fission theory. Abbreviations: 2C, nuclear DNA content; F, autosomal fusions; Fis, fissions; P, polyploidy.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.