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100 results for “Environmental Development”
Modeling the metabolic profile of Mytilus edulis reveals molecular signatures linked to gonadal development, sex and environmental site
<p>Metabolomics dataset used in the publication "Modeling the metabolic profile of Mytilus edulis reveals molecular signatures linked to gonadal development, sex and environmental site"</p> <p>Jaanika Kronberg, Jonathan J. Byrne, Jeroen Jansen, Philipp Antczak, Adam Hines, John Bignell, Ioanna Katsiadaki, Mark R. Viant and Francesco Falciani </p> <p>Metabolomics dataset for metabolic bins 1 to 1045 for 376 mussels as used in the publication.</p> <p>Mussel metadata are described in a separate file (spectrum number, sample label, sex, site, species, month, temperature of water, salinity of water, ADG rate, gonadal stage, parasite load)</p> <p>Species 1: Mytilus edulis, species 2: hybrid, species 3: Mytilus galloprovincialis</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 20 in Environmental control versus phylogenic fingerprint in ontogeny: The example of the development of the stalk in the genus Guillecrinus (stalked crinoids, Echinodermata)
Figure 20. Modifications in the profile of the levels of organization of the columnals along the stalk during ontogeny. (a) Guillecrinus neocaledonicus; (b) comparison of adult stages of the two species of Guillecrinus. A, Adult stage (A1 and A2: see Figure 17); J, juvenile stage; Prox. 1, new columnals appearing proximally (proximal vertical axis on Figure 17).
Figure 18 in Environmental control versus phylogenic fingerprint in ontogeny: The example of the development of the stalk in the genus Guillecrinus (stalked crinoids, Echinodermata)
Figure 18. Reconstruction of the growth curves in Guillecrinus, from specimens retaining the proximal part of the stalk. (a) Ontogenic index (kH) provided by the most proximal segment of the simplified biometric profiles of the heights of the columnals (see Figure 16); (b) ontogenic growth curves using the proximal diameter of the stalk as an index of the size and kH as an index of relative age. AC, aboral cup. See text for explanations.
Figure 17 in Environmental control versus phylogenic fingerprint in ontogeny: The example of the development of the stalk in the genus Guillecrinus (stalked crinoids, Echinodermata)
Figure 17. Ontogeny of the columnals in relation to their place within the stalk in Guillecrinus. Horizontal row of columnals represents a succession of columnals along individual stalks; lines connecting columnals of adjacent rows represent a succession of ontogenetic stages with a growth in size. For the axial sections below and to the right each columnal cross-section, the black areas schematize the place and the amplitude of the ligamentary depressions. J, juvenile stage; A, adult stage; J2 and A2, observed stages; J1 and A1, earlier stages deduced from observations on J2 and A2; solid lines, ontogenetic trends of G. neocaledonicus; dotted lines, hypothetical relationships with G. reunionensis; r, rigid; f, flexible; a, ankylosis. See text for explanations.
Figure 16 in Environmental control versus phylogenic fingerprint in ontogeny: The example of the development of the stalk in the genus Guillecrinus (stalked crinoids, Echinodermata)
Figure 16. Simplified schemes of the principal modifications in the biometric profiles of Guillecrinus stalks during ontogeny. Hm, minimal proximal height; Dc, diameter of the base of the aboral cup; DM, maximum proximal diameter; Dm, minimal proximal diameter; dotted area, proxistele; open area, mesistele; short scattered lines, dististele.
Figure 15 in Environmental control versus phylogenic fingerprint in ontogeny: The example of the development of the stalk in the genus Guillecrinus (stalked crinoids, Echinodermata)
Figure 15. Distribution of the types of articular facets along the adult stalk of Guillecrinus. (A) Ontogenetic distal process (subsidiary crests); (B) proximal ontogenetic process (only interareolar ridges).
Figure 13 in Environmental control versus phylogenic fingerprint in ontogeny: The example of the development of the stalk in the genus Guillecrinus (stalked crinoids, Echinodermata)
Figure 13. Biometric profiles of the stalk of three specimens of Guillecrinus reunionensis. (m) Fixation disk.
Figure 12 in Environmental control versus phylogenic fingerprint in ontogeny: The example of the development of the stalk in the genus Guillecrinus (stalked crinoids, Echinodermata)
Figure 12. Proximal and median columnals of Guillecrinus reunionensis. (a) Proximal facet of holotype. (b–f) paratype: (b) columnal under the basal circlet, not visible externally; (c) first visible columnal, proximal facet; (d) the same, distal facet; (e) 62nd columnal, proximal facet; (f) 63rd columnal, proximal facet. ra, radials; ba, basals; col, first columnal; s, suture visible externally. Scale bars: 1 mm.
Figure 9 in Environmental control versus phylogenic fingerprint in ontogeny: The example of the development of the stalk in the genus Guillecrinus (stalked crinoids, Echinodermata)
Figure 9. Proximal and median columnals of the adult specimens of Guillecrinus neocaledonicus. (a–d) Proximal columnals of the N6 specimen: (a) most proximal columnal, distal facet; (b) same columnal, proximal facet; (c) second columnal, proximal facet; (d) third columnal; (e) one of the proximal columnals of the N7 specimen; (f) most frequent type of columnal in the N7 specimen. Scale bars: 1 mm.
Figure 8 in Environmental control versus phylogenic fingerprint in ontogeny: The example of the development of the stalk in the genus Guillecrinus (stalked crinoids, Echinodermata)
Figure 8. Biometric profiles of the stalk of the specimens of Guillecrinus neocaledonicus which do not belong to the type series. (m) Fixation disk.
Figure 6 in Environmental control versus phylogenic fingerprint in ontogeny: The example of the development of the stalk in the genus Guillecrinus (stalked crinoids, Echinodermata)
Figure 6. Columnals of the mesistele and dististele of juvenile specimen N3. (a) Columnal 5b; (b, c) columnal 5c; (d) columnal 4; (e) columnal 39; (f) columnal 2 (see their place on the biometric profile on Figure 3). Scale bars: 0.2 mm.
Figure 5 in Environmental control versus phylogenic fingerprint in ontogeny: The example of the development of the stalk in the genus Guillecrinus (stalked crinoids, Echinodermata)
Figure 5. Columnals of the stalk from the juvenile specimen N5, from the most proximal (a) to the distal extremity of the stalk (f). Scale bars: 0.5 mm.
Figure 7 in Environmental control versus phylogenic fingerprint in ontogeny: The example of the development of the stalk in the genus Guillecrinus (stalked crinoids, Echinodermata)
Figure 7. Modifications in the biometric profile of columnal height during stalk ontogeny in Guillecrinus neocaledonicus. Specimens of the type series.
Figure 10 in Environmental control versus phylogenic fingerprint in ontogeny: The example of the development of the stalk in the genus Guillecrinus (stalked crinoids, Echinodermata)
Figure 10. Distal columnals of the adult specimens of Guillecrinus neocaledonicus. (a–f) Increasingly distal columnals with an increasingly early development of subsidiary crests: (a–d) facets with a pentaradiate symmetry; (e) facet with a four-part symmetry inherited from a juvenile stage similar to that of Figure 5d; (f) facet with bilateral symmetry and with two generations of subsidiary crests, inherited from a juvenile stage similar to that of Figure 5f, note the growth in diameter of the axial canal resulting from resorption of the perilumen stereom of the initial fulcral ridge. Scale bars: 1 mm.
Figure 4 in Environmental control versus phylogenic fingerprint in ontogeny: The example of the development of the stalk in the genus Guillecrinus (stalked crinoids, Echinodermata)
Figure 4. Biometric profiles of the stalk of the juvenile specimens of Guillecrinus neocaledonicus. The numbers in circles refer to the symmetry of the articulations (for 5b, 5c, 39 see Figure 6). Dotted area with the single line defines transitional zone of mesistele; double vertical lines define the entire mesistele.
Figure 19 in Environmental control versus phylogenic fingerprint in ontogeny: The example of the development of the stalk in the genus Guillecrinus (stalked crinoids, Echinodermata)
Figure 19. Variations in the level of organization of the columnals during their ontogeny in relation to their position on the stalk at the juvenile stage in Guillecrinus neocaledonicus. Ontogenetic stages of Figure 16 (J1 and J2, juvenile stage; A1 and A2, adult stage). Position on the stalk at the juvenile stage (P, proxistele; M, mesistele; D, dististele). See text for explanations.
Figure 2 in Environmental control versus phylogenic fingerprint in ontogeny: The example of the development of the stalk in the genus Guillecrinus (stalked crinoids, Echinodermata)
Figure 2. Developmental stages of the stalk in the genus Guillecrinus. The shaded portion represents columnals that appear earliest during development.
Figure 3 in Environmental control versus phylogenic fingerprint in ontogeny: The example of the development of the stalk in the genus Guillecrinus (stalked crinoids, Echinodermata)
Figure 3. Morphological units versus functional units, and symmetries at two levels of integration (ossicle and stalk). (a) A columnal viewed along its proximal/distal axis; (b) symmetry produced by superimposing the proximal and distal fulcral ridges of the columnal in (a); (c) superposition of articular fulcra of all columnals along the stalk; (d) schematic diagram of morphological and functional stalk units and their interactions.
Figure 1 in Environmental control versus phylogenic fingerprint in ontogeny: The example of the development of the stalk in the genus Guillecrinus (stalked crinoids, Echinodermata)
Figure 1. External morphology of the proximal part of the arms of the stalk. (a–d) Guillecrinus neocaledonicus: (a) specimen N1, holotype; (b) specimen N2; (c, d) specimen N3, juvenile. (e–h) G. reunionensis: (e, f) specimen R2; (g, h) specimen R1, holotype. ba, basals; ib?, pseudo-infrabasals. Scale bars: 1 mm (a, b, e, g, h); 0.5 mm (c, f); 0.2 mm (d).
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