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231 results for “Oncorhynchus”
Underlying data - Digital Twin for Rainbow Trout (Oncorhynchus mykiss) land-based aquaculture
<p>Datasets for replicating Figures 5, 6, 7 and 8 of the article "Digital twins for land-based aquaculture: a case study for rainbow trout (<em>Oncorhynchus mykiss</em>)", by Adriano C. Lima, Edouard Royer, Matteo Bolzonella, and Roberto Pastres.</p>
Data from: Development of Single Nucleotide Polymorphism (SNP) Panel for determination of environmental influence on genome for wild Columbia River redband trout (Oncorhynchus mykiss gairdnerii) in Southwest Idaho streams
<p>DNA were derived from fin tissue samples taken from individual trout captured from Little Jacks Creek, Big Jacks Creek , and Duncan Creek of the Owyhee mountains and Keithly Creek and Upper Mann Creek in the Hitt mountains of Western Idaho, United States. Fin tissues were collected from individual trout from each stream during monthly sampling events in June through October 2020. </p> <p><em>DNA Extraction:</em> Extraction of DNA from caudal fin tissues were performed using Quick-DNA Miniprep Plus purification kits (Zymo Research Inc.©). Small sections of fin tissue (≤ 25 mg) were collected from each sample. This was mixed with a digesting solution comprised of ultra-pure water, solid tissue buffer (Zymo Research Inc.©) and proteinase K. All tissues were digested in sealed microcentrifuge tubes for at minimum 3 h at 55°C in a water bath. We then aliquoted 100 µL of digestion supernatant and combined with 200 µL of genomic binding buffer (Zymo Research Inc.©). DNA was eluted in 50, 75, and 100 µL of elution buffer to determine which volume provided sufficient DNA concentration for genotyping. After it was determined all quantities produced suitable concentrations, going forward, 50 µL of elution buffer used.</p> <p><em>Genotyping:</em> Following extraction, genotyping-in-thousands sequencing took place at the Hagerman National Fish Hatchery’s genetics research facility with the assistance of the Columbia River Intertribal Fish Commission (CRTFC). Genotyping protocols were as described in Campbell et al. (2015) and summarized below. First, samples were prepared for amplification via PCR by combining DNA extracts with a Qiagen Plus multiplex master mix and a species-specific pooled primer mix. This step added the Illumina sequencing primer sites to amplicons. Following the creation of the PCR cocktail, thermocycling was conducted for amplification. Amplified samples were then diluted 20-fold. Diluted samples were transferred to new 96-well PCR plates where two genetic indexes and barcodes provides a unique set of tagging primers to each well and plate. Tagged plates then underwent a second PCR step. After the second PCR, all DNA were transferred to Charm Biotech normalization plates where DNA was bound to wells, washed, and finally eluted. After normalization, all DNA was pooled together and a purification step using magnetized beads in two steps to selectively remove fragments of DNA that are both too large and too small for sequencing. Following purification, each plate was quantified via qPCR using Life Technologies QuantStudio 6 Flex Instrument (Life Technologies). Finally, sequencing was performed using an Illumina HiSeq 1500 instrument.</p> <p><strong>Ancillary peer-reviewed manuscripts:</strong><br> <em>Genotyping protocols</em><br> Campbell NR, Harmon SA, Narum SR. 2015. Genotyping-in-Thousands by sequencing (GT-seq): A cost effective SNP genotyping method based on custom amplicon sequencing. Mol Ecol Resour, 15: 855-867. https://doi.org/10.1111/1755-0998.12357<br> <em>SNP loci reference</em><br> Collins EE, Hargrove JS, Delomas TA, Narum SR. 2020. Distribution of genetic variation underlying adult migration timing in steelhead of the Columbia River basin. Ecology and Evolution, 10(17): 9486-9502. https://doi.org/10.1002/ece3.6641 </p> <p><strong>Data Use</strong>:<br> <em>License</em>: <a href="https://creativecommons.org/licenses/by/4.0/">CC-BY 4.0</a> <br> <em>Recommended Citation</em>: Wooding AP, Narum SR, Pradhan DS. 2022. Data from: Development of Single Nucleotide Polymorphism (SNP) Panel for determination of environmental influence on genome for wild Columbia River redband trout (Oncorhynchus mykiss gairdnerii) in Southwest Idaho streams (0.1) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.7055582</p> <p>Funding for this project is provided by US National Science Foundation and Idaho EPSCoR through award: OIA-1757324 </p>
FIGURE 3 in Habitat associations of rainbow trout Oncorhynchus mykiss and brown trout Salmo trutta fry
FIGURE 3 Salmo trutta fry abundances from the four sites in which three pass removals were conducted in July through October 2018 and associations with D50 and presence of wood. The trendline shows the relationship between S. trutta fry abundance and D50 in the three sites in which wood was absent () Wood () No Wood
FIGURE 5 in Habitat associations of rainbow trout Oncorhynchus mykiss and brown trout Salmo trutta fry
FIGURE 5 Oncorhynchus mykiss fry abundances from the four sites in which three pass removals were conducted in July through October 2018 and associations with (a) velocity and (b) depth. A trendline shows the relationship between each habitat variable and the fry abundance data for both the sites that were stocked (dotted line) and not stocked (solid line) () Not Stocked () Stocked
FIGURE 1 in Habitat associations of rainbow trout Oncorhynchus mykiss and brown trout Salmo trutta fry
FIGURE 1 Fry site locations used to obtain abundance estimates or single-pass counts for Salmo trutta and Oncorhynchus mykiss in the upper Colorado River study section in Grand County, Colorado, downstream of Windy Gap Reservoir. The 20 15.2 m sites, sampled five times from July through October 2018, included one abundance estimation and four single-pass sites at the Sheriff Ranch, four single-pass sites at Kinney Creek, two abundance estimation and five single-pass sites in the Red Barn area and one abundance estimation and three single-pass sites at Hitching Post
FIGURE 2 in Habitat associations of rainbow trout Oncorhynchus mykiss and brown trout Salmo trutta fry
FIGURE 2 Salmo trutta fry single-pass counts and associations with (a) D50, (b) depth and (c) velocity
FIGURE 4 in Habitat associations of rainbow trout Oncorhynchus mykiss and brown trout Salmo trutta fry
FIGURE 4 Oncorhynchus mykiss fry counts from sites in which O. mykiss were or were not (i.e., natural reproduction) stocked and associations with (a) D50 and (b) velocity. A trendline shows the relationship between each habitat variable and the fry count data for both the sites that were stocked (dotted line) and not stocked (solid line) () Not Stocked () Stocked
F I G U R E 1 in Evidence of successful recruitment of non-native pink salmon Oncorhynchus gorbuscha in Iceland
F I G U R E 1 Distribution of pink salmon Oncorhynchus gorbuscha in Iceland. (a) Location of rivers in Iceland with reported catches of adult O. gorbuscha in 2000, 2005, and annually from 2015 according to Bárðarson et al. (2022), and (b) locations of fishing surveys in 2022 to catch smolts of O. gorbuscha in three rivers of southwest Iceland
FIGURE 2 in The thermal dependence of the protein-sparing effect in rainbow trout (Oncorhynchus mykiss, Walbaum 1792)
FIGURE 2 Ammonia quotient (AQ) of rainbow trout (Oncorhynchus mykiss) fed three isonitrogenous diets with different energy contents [high energy (HE) = 20.50 MJ kg 1, medium energy (ME) = 18.76 MJ kg 1, low energy (LE) = 17.35 MJ kg 1) at five temperatures (12 C, 14 C, 16 C, 18 C, 20 C). A quadratic dependency model was used to analyse the data. Parabolas describe the quadratic dependency of AQ values on temperature. Calculated lowest AQ values for each parabola are marked with a cross (). Each data point represents the measurement of one tank with rainbow trout at each respective diet and temperature. (n = 3)
FIGURE 1 in The thermal dependence of the protein-sparing effect in rainbow trout (Oncorhynchus mykiss, Walbaum 1792)
FIGURE 1 Percentage of retainable energy (RE) relative to gross energy intake (GEI) of rainbow trout (Oncorhynchus mykiss) fed three isonitrogenous diets with different energy contents [high energy (HE) = 20.50 MJ kg 1, medium energy (ME) = 18.76 MJ kg 1, low energy (LE) = 17.35 MJ kg 1) at five temperatures (12 C, 14 C, 16 C, 18 C, 20 C). Each data point represents measurement of one tank with rainbow trout at each respective diet and temperature (n = 3)
Fig. 1 in Survival Of Embryos And Larvae Of The Rainbow Trout (Oncorhynchus Mykiss, Walbaum, 1792) Under Influence Of Optical Radiation At Various Temperature Regimes
Fig. 1. Linear dependencies of the probit (logit) effect of the death of rainbow trout larvae in vitro from the logarithm of days of fasting for various types of optical radiation at a temperature of 12 (a), 11 (b), 10 (c), 9 (d), 8(e) ° C.
MALDI-TOF spectra of archaeological (Oncorhynchus) and modern (Salmo salar) bone collagen
<p>SPECIES INFORMATION<br> csv containing information about the samples that links the information about the species and files</p> <p><br> MALDI TOF-MS</p> <p>MALDI Spectra from a Bruker Ultraflex II range m/z 800-3500<br> Three technical replicates were averaged in mMass<br> Each of these spectra a tab delimited .txt file are uploaded</p> <p><br> SEQUENCE DATA<br> An aligned FASTA file containing the bovine reference collagen sequence and both versions of S. salar and O. mykiss sequences. The sequences are concatenated with COL1A1, COL1A2, and COL1A3 for the two fish and COL1A1, COL1A2, COL1A1 for bovine.</p> <p>Three annotated gff files containing the sequence from version 1 of S. salar annotated with the locations of the published mammal markers and the biomarkers presented in this paper. Each gff file corresponds to one of the three collagen proteins COL1A1, COL1A2, and COL1A3.</p>
Figure 14. A, B in giant, spike-toothed salmon, Oncorhynchus rastrosus and the "Proto-Tuolumne River" (early Pliocene) of Central California
Figure 14. A, B. Measurements of O. rastrosus premaxillary teeth (31 specimens total), freshwater (pink/red) vs. coastal marine (grey/black). A. Average lengths of osseous bases. B. Average lengths of tooth cusps. Freshwater specimens are from the Mehrten Formation (pink) and Pinole Formation (red). Coastal marine specimens are from the Monterey, Santa Margarita, and Capistrano formations. How measurements were taken is shown in Fig. 10).
Figure 13 in giant, spike-toothed salmon, Oncorhynchus rastrosus and the "Proto-Tuolumne River" (early Pliocene) of Central California
Figure 13. Coastal marine specimens of O. rastrosus premaxillary teeth from the Santa Margarita Formation, Monterey Formation, and Capistrano Formation. A. LACM 135697. B. LACM 58915. C. LACM 158730. D. LACM 147601. E. LACM 147597. Freshwater specimens from O. rastrosus from the Pinole Tuff Formation. F. UCMP 61550. G. UCMP 61554. H. UCMP 65630. All are lateral views.
Figure 10. A in giant, spike-toothed salmon, Oncorhynchus rastrosus and the "Proto-Tuolumne River" (early Pliocene) of Central California
Figure 10. A. Photograph of fossil salmon locality, T-6, showing beach and overlying cliff. Specimens were collected from the surface of the beach area from ~1957–1964. B. Photograph taken at salmon locality, T-6, showing exposed water-lain tuff within the sands. C. Photograph of sharp unconformity underlying salmon locality. Below the unconformity is pink/tan tuffaceous silt. D. Photograph of T-5, a nearby site to T-6, with the sharp unconformity and large, rounded cobbles.
Figure 8 in giant, spike-toothed salmon, Oncorhynchus rastrosus and the "Proto-Tuolumne River" (early Pliocene) of Central California
Figure 8. Map showing locations of all California specimens examined/measured in this study. Blue circles indicate marine deposits while orange indicates freshwater.
Figure 12 in giant, spike-toothed salmon, Oncorhynchus rastrosus and the "Proto-Tuolumne River" (early Pliocene) of Central California
Figure 12. Freshwater specimens of O. rastrosus premaxillary teeth from the Mehrten Formation (Turlock Lake, CA; UCMP V5405). All are lateral views. A. Left tooth (UCMP 93181). B. Left tooth (UCMP 93183). C. Right tooth (UCMP 136029). D. Right tooth (UCMP 93179). E. Right tooth (UCMP 93184). F. Left tooth (UCMP 61951).
Figure 9. A–F in giant, spike-toothed salmon, Oncorhynchus rastrosus and the "Proto-Tuolumne River" (early Pliocene) of Central California
Figure 9. A–F. Measurements taken of O. rastrosus premaxillary teeth. A. Greatest length of the osseous base. B. Greatest length of the tooth cusp. C. Greatest height of the tooth cusp and osseous base. D. Greatest height of the osseous base. E. Greatest width of the osseous base. F. Greatest width of the tooth cusp.
Figure 5 in giant, spike-toothed salmon, Oncorhynchus rastrosus and the "Proto-Tuolumne River" (early Pliocene) of Central California
Figure 5. Generalized stratigraphy of the Mehrten Formation highlighted in grey. Modified from Wagner 1981.
Figure 3 in giant, spike-toothed salmon, Oncorhynchus rastrosus and the "Proto-Tuolumne River" (early Pliocene) of Central California
Figure 3. Map of California showing the location of Turlock Lake in relation to nearby cities, towns, and landmarks.
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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.