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FIGURE 1 in Description of a new Fridericia species (Oligochaeta: Enchytraeidae) and its molecular comparison with two morphologically similar species by PCRRFLP
FIGURE 1. Fridericia crassiductata sp.n. A = setal bundles of a praeclitellar segment (lateroventral view), B = Photograph of the cutaneous glands of a praeclitellar segment (dorsal view), C = Photograph of the head (head pore marked with arrows), D = Photograph of the head (brain marked with arrows), E = Photograph of the coelomocytes. Each photograph is sized with a black line representing 50 μm length.
FIGURE 6 in Description of a new Fridericia species (Oligochaeta: Enchytraeidae) and its molecular comparison with two morphologically similar species by PCRRFLP
FIGURE 6. The gel image BsuRI of restriction digestion. The numbering of samples corresponds with the number in Table 1. The character M nominates the molecular marker, the length of fragments are represented on the left side of the photo (also by Fig. 7–10).
FIGURE 5 in Description of a new Fridericia species (Oligochaeta: Enchytraeidae) and its molecular comparison with two morphologically similar species by PCRRFLP
FIGURE 5. Fridericia crassiductata sp.n. A = Photograph of the spermatheca. (the diverticle fill with sperm around the ampulla marked with black arrows, the ectal duct with white arrows, ectal gland with asterisk, B = Photograph of the opening of spermathecal ectal duct (glands marked with black arrows, duct with white arrow), C = Photograph of the opening of spermathecal ectal duct three glands marked with black arrows, duct with white arrow).
Aj_H18N11_Exp_PCR_data
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Supplementary data for "Validation of a quantitative PCR assay for detection of sugar kelp (Saccharina latissima) in coastal marine sediments"
<p>Raw data for a paper in preparation: "Validation of a quantitative PCR assay for detection of sugar kelp (Saccharina latissima) in coastal marine sediments".</p><p>Contains:</p><ol><li>Spreadsheet of curated raw data used to calculated <i>S. latissima</i> COI gene copy number per gram of dry sediment for a biomass spiking experiment to determine how gene copy number correlates with known amounts of added kelp biomass.</li><li>Spreadsheet of curated raw data from a field study looking at <i>S. latissima</i> gene copy numbers in field samples from the Damariscotta River estuary in Maine, from three sites, one under a small kelp farm, one under a site with a single kelp line, and another in a control site with no known influence of kelp farming activity.</li></ol>
Fig. 10 in Identifying PCR primers to facilitate molecular phylogenetics in Caddisflies (Trichoptera)
Fig. 10. Results of maximum likelihood analysis in PAUP* (Swofford, 2002) using sequences from all 8 species. Bootstrap values are labeled for each node.
Figs 1–9 in Identifying PCR primers to facilitate molecular phylogenetics in Caddisflies (Trichoptera)
Figs 1–9. Results of maximum likelihood analysis in PAUP* (Swofford, 2002). 1. 16s rRNA. 2. 18s rRNA. 3. CAD. 4. COI. 5. COII. 6. EF-1. 7. IDH. 8. POL-II. 9. RPS2. All trees were rooted with A. deflata except for RPS2 for which no A. deflata sequence was
Data on the Weather and Habitat and Representative results of qPCR and PCR
<p>We used weather and habitat characteristics, which collected from studied 49 sampling sites, to know how those affect ranavirus infection rate in amphibian larvae of Dryophytes japonicus (Japanese tree frog), Pelophylax nigromaculatus (Black-spotted pond frog), and Lithobates catesbeianus (American bullfrog) in South Korea.</p> <p>Description on the method section: To investigate the relationship between the ranavirus infection rate and habitat characteristics, we analyzed 16 habitat characteristics at each sampling location. The land cover rate (urban area, agricultural area, forest area, grass area, wetland area, bare area, hydrosphere area) within a radius of 3 km2 from the mid-sampling point was calculated on the 2020 South Korean land cover map(http://egis.me.go.kr ). From the land cover data, greenhouse cultivation areas within agricultural areas, salt fields and tidal flat areas within wetland areas, and sea areas within hydrosphere areas were excluded during data handling because these areas are inhabitable for amphibians. Additionally, the shortest distance from the mid-sampling point to agricultural land, mountains, water bodies, and urban areas was calculated in units of 1 m. When a sampling point was located within a specific coverage area, the distance was set to 2 m. All land cover rates, distance data, and altitude values of each sampling point were calculated using QGIS (ver. 3.4.7, QGIS.org 2021). Furthermore, the average air temperature, lowest air temperature, highest air temperature, and average precipitation for the immediately preceding quarter, based on the sampling date of the tadpoles used in the qPCR experiment, were obtained from the local meteorological station closest to the sampling point.</p> <p>We also provided the igures of representative positive qPCR results of D. japonicus (A, B) collected at Haenam, P. nigromaculatus (C, D) collected at Pohang, and L. catesbeianus (E, F) collected at Gmchoen, which showing positive ranavirus detection from the samples, and the Photographs of representative gel electrophoresis of the MCP fragment (~500bp), which confirmed the qPCR result again by sequencing the fragment (G, H) in the further study.</p>
Supplementary FIle S4. PCR conditions
<p>Supplementary FIle S4.</p> <p>PCR conditions applied in the study: Open access in a taxonomic sense: a morphological and molecular guide to Western Palaearctic Dusona (Hymenoptera, Ichneumonidae).</p>
SARS-CoV-2 nucleocapsid and RT-PCR results
<p><span>We collected blood samples from patients admitted to the hospital during a period with RT-PCR based-screening of patients for Severe Acute Respiratory Syndrome Cornavirus-2 (SARS-CoV-2). Retrospectively the SARS-CoV-2 nucleocapsid protein (NP) plasma concentrations were measured with an ELISA method and used for an initial time course study to find the optimal time-point for sampling blood. Next, we estimated the diagnostic accuracy i.e. the clinical sensitivity and specificity at different plasma NP cut-off concentrations.</span></p> <p><span>The time course study revealed profiles with rapid or more slow declines in NP titers after the RT-PCR result. Nevertheless, in the time interval 0 – 7 days after the RT-PCR result, the NP concentration was always above the level of detection at 1.66 pg/ml suggesting that the diagnosis could be established in the time interval of 0 - 7 days.</span></p> <p><span>The median time gap between the plasma NP and RT-PCR results was 0.0 days (n = 1957, interval: -26 to + 21 days). Reducing the time gap to seven days, the clinical sensitivity was 90.0% (n= 60, 95% CI, 82.4% to 97.6%) at a specificity of 95.9% (n=1876, 95% CI, 95.0% to 96.8%). Curve analysis by receiver operation characteristics identified a cut-off concentration of 1.87 pg/mL NP as optimal resulting in a positive predictive value of 41.2%, a negative predictive value of 99.7% and a prevalence of 3.1%.</span></p> <p><span>In conclusion, the NP method is acceptable for making the laboratory diagnosis of SARS-CoV-2, and an intended use of plasma NP as a prospective nosocomial screening method is considered feasible.</span></p>
Supplementary material 2 from: Wahlberg N, Peña C, Ahola M, Wheat CW, Rota J (2016) PCR primers for 30 novel gene regions in the nuclear genomes of Lepidoptera. ZooKeys 596: 129-141. https://doi.org/10.3897/zookeys.596.8399
Sequences used for designing primers : Explanation note: A zip-file containing reference sequences for all 48 gene regions used for designing primers.
Supplementary material 1 from: Wahlberg N, Peña C, Ahola M, Wheat CW, Rota J (2016) PCR primers for 30 novel gene regions in the nuclear genomes of Lepidoptera. ZooKeys 596: 129-141. https://doi.org/10.3897/zookeys.596.8399
Table S1 : Explanation note: Details of the success of sequencing of the new gene regions. GenBank accession number indicates successful sequencing, dash indicates unsuccessful amplification.
FIGURE 5. The COI PCR amplicons generated via LepF1-LepR1 in First record of the genus Haritalodes Warren, 1890 and H. derogata (Fabricius, 1775) (Lepidoptera: Crambidae: Spilomelinae) from Türkiye and its morphological and molecular identification
FIGURE 5. The COI PCR amplicons generated via LepF1-LepR1 (Lanes 1-2), LCO1490-HCO2198 (Lanes 3-4), and Jerry-Pat (Lanes 5-6) primer pairs using DNA from the larvae (L) or adult (A) at 1% agarose gel. L refers to ladder (100 bp ladder marker, Invitrogen, USA).
RT PCR data for publication Transplantation of neural stem cells improves recovery of stroke affected mice and induces cell-specific changes in GSDMD and MLKL expression
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FIGURE 2 in A multiplex PCR method for identification of two common true cutworm species (Lepidoptera: Noctuidae) tested in the central plain of Guilan province, Iran
FIGURE 2. Multiplex PCR by combination of three equimolar primers for COI (IpsiloF1/ XestiaF1/LepR1). 1: 100 bp DNA ladder; 2,3: Agrotis ipsilon; 4,5: Xestia c-nigrum, 6–9, Agrotis ipsilon. 6,7: larvae specimens collected from Chaf (Langroud), 8,9: larvae specimens collected from Rasht.
Supplementary Figure S1 Identification the integrity of isolated endometrium and decidual tissues using quantitative PCR.
<p>Supplementary Figure S1 Identification the integrity of isolated endometrium and decidual tissues using quantitative PCR. The typical decidualization marker genes of <em>Dtprp</em> (A) and <em>Alpl</em> (B) were determined by qRT-PCR. (C) <em>ACTA2</em> mRNA levels of the smooth muscle maker gene was examined by qRT-PCR. Results were normalized to the housekeeping gene GAPDH and presented as the mean ± SD of three separate experiments, with different letters (a, b, c) indicating statistical difference (p < 0.05; one-way ANOVA and Tukey’s test).</p>
Assessment of a multiplex PCR and Nanopore-based method for portable dengue virus sequencing in Indonesia
<p>Multiplex primer sets for amplification of the complete coding region of Indonesian dengue virus.</p>
Correlation between the introduction of gastrointestinal PCR panels and the antibiotic prescription in outpatients with gastroentiritis
<p>Excel table summarising the data of 2 cohorts having symptoms of gastroenteritis:</p> <p>- cohort from 2016 investigated by traditional methods</p> <p>- cohort from 2017 investigated by gastrointestinal PCR panels</p>
Fig. 2 ELAVI8 PCR yield and stringency across using a 1.1 in ELAV Intron 8: a single-copy sequence marker for shallow to deep phylogeny in Eupulmonata Hasprunar & Huber, 1990 and Hygrophila Férussac, 1822 (Gastropoda: Mollusca)
Fig. 2 ELAVI8 PCR yield and stringency across using a 1.1% Agarose gel in 1 × TBE buffer with GoldView Dye and 3 µl of PCR product from each reaction. Panel A represents 50° C annealing temperature for 40 cycles while B represents the modified touchdown procedure of 54° C anneal for 10 cycles followed by 50° C for 30 cycles. The
Quantitative real-time PCR assays Q2 for species-specific detection and quantification of Baltic Sea spring bloom dinoflagellates
<p>These are the data behind figures 2 to 7 in the paper: Brink AM, Kremp A and Gorokhova E (2024) Quantitative real-time PCR assays for species-specific detection and quantification of Baltic Sea spring bloom dinoflagellates. Front. Microbiol. 15:1421101. doi: 10.3389/fmicb.2024.1421101</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)
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.