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3,878 results for “Molecular Data”
Data from: Learning to count: determining the stoichiometry of bio-molecular complexes using fluorescence microscopy and statistical modelling
<p>As stated in the Read Me file:</p> <p>These data and resources are associated with the manuscript:</p> <p><em>Learning to count: determining the stoichiometry of bio-molecular complexes using fluorescence microscopy and statistical modelling</em>, Mersmann et. al., as submitted to biorXiv in July 2020.</p> <p>The raw imaging data relates to Figure 5, S1, S2 and Table S1. The images are fluorescent micrographs displaying immobilised adenovirus particles bound to a monoclonal antibody 9C12.</p> <p>Each experiment folder is numbered, as in Table S1, and appended with the mixing proportion (Fl), as defined in the manuscript. Within each folder there are 6 subfolders, representing samples incubated with different concentrations of 9C12 antibody.</p> <p>Each image is a 3 channel 1024x1024 tif. Channel 1 = 9C12 Alexa Fluor 647. Channel 2 = 9C12 Biotin + QDot655. Channel 3 = Adenovirus Alexa Fluor 488. Samples were illuminated in TIRF mode using a 100X objective, images were captured on a Hamamatsu OCRA Flash 4 sCMOS camera. Further details are available in the header of each file.</p> <p>The control samples are labelled with 100% 9C12 Alexa Fluor 647 or 100% 9C12 Biotin, as described in the manuscript.</p> <p>The data analysis script is an imageJ macro. It runs on the FIJI version of ImageJ with the NanoJ package installed (https://github.com/HenriquesLab). It outputs fluorescent measurements for each identified AdV particle. Note that the script rearranges the channel order such that Channel 1 = Adenovirus Alexa Fluor 488, Channel 2 = 9C12 Alexa Fluor 647, Channel 3 = 9C12 Biotin + QDot655. </p> <p>The channels require registration due to chromatic aberration, this is achieved using the Realign Channels function in NanoJ, appropriate translation masks are provided along with the script.</p> <p>Any question about the data or script should be addressed in Joe Grove (j.grove@ucl.ac.uk)</p>
Complementary data to "Molecular dynamics trajectories for 630 drug-membrane potentials of mean force"
<p>Missing data from "Molecular dynamics trajectories for 630 drug-membrane potentials of mean force"</p> <p>Hoffmann, Christian; Centi, Alessia; Menichetti, Roberto; Bereau, Tristan (2020): Molecular dynamics trajectories for 630 drug-membrane potentials of mean force. figshare. Collection.</p> <p>https://doi.org/10.6084/m9.figshare.c.4641551.v1</p> <p>Includes:</p> <ul> <li>'bsResult.xvg' of DIM_P2-P3 in DLPC</li> </ul>
Data from: Phylogeny of Tetillidae (Porifera, Demospongiae, Spirophorida) based on three molecular markers
Tetillidae are spherical to elliptical cosmopolitan demosponges. The family comprises eight genera: namely, Acanthotetilla Burton, 1959, Amphitethya Lendenfeld, 1907, Cinachyra Sollas, 1886, Cinachyrella Wilson, 1925, Craniella Schmidt, 1870, Fangophilina Schmidt, 1880, Paratetilla Dendy, 1905, and Tetilla Schmidt, 1868. These genera are characterized by few conflicting morphological characters, resulting in an ambiguity of phylogenetic relationships. The phylogeny of tetillid genera was investigated using the cox1, 18S rRNA and 28S rRNA (C1-D2 domains) genes in 88 specimens (8 genera, 28 species). Five clades were identified: (i) Cinachyrella, Paratetilla and Amphitethya species, (ii) Cinachyrella levantinensis, (iii) Tetilla, (iv) Craniella, Cinachyra and Fangophilina and (v) Acanthotetilla. Consequently, the phylogenetic analysis supports the monophyly of Tetilla, a genus lacking any known morphological synapomorphy. Acanthotetilla is also recovered. In contrast, within the first clade, species of the genera Paratetilla and Amphitethya were nested within Cinachyrella. Similarly, within the fourth clade, species of the genera Cinachyra and Fangophilina were nested within Craniella. As previously postulated by taxonomists, the loss of ectodermal specialization (i.e., a cortex) has occurred several times independently. Nevertheless, the presence or absence of a cortex and its features carry a phylogenetic signal. Surprisingly, the common view that assumes close relationships among sponges with porocalices (i.e., surface depressions) is refuted.
Heatwave tolerance of a marine polychaete (Hediste diversicolor): physiological and molecular data archive
<p>The aim of this work was to test the effect of long-lasting heatwaves on the intertidal polychaete <em>Hediste diversicolor</em> (24 ºC <em>vs</em> 30 ºC for a month). We analysed the whole-body proteome and carried out fatty acid analysis after 28 days of exposure and then estimated cumulative survival and upper thermal tolerance limits (after 30 days of exposure). Worms' wet weight was also compared between temperatures (after 30 days) to understand if elevated temperature has effects on growth. </p> <p>NOTE: The associated mass spectrometry proteomics dataset has been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD020635</p> <p>Dataset associated to the paper DOI:<a href="https://doi.org/10.1016/j.envres.2021.110885">10.1016/j.envres.2021.110885</a></p>
Data from: Molecular underpinnings and biogeochemical consequences of enhanced diatom growth in a warming Southern Ocean
<p>The Southern Ocean (SO) harbours some of the most intense phytoplankton blooms on Earth. Changes in temperature and iron availability are expected to alter the intensity of SO phytoplankton blooms, but little is known about how environmental change will influence community composition and downstream biogeochemical processes. We performed experimental manipulations on surface ocean microbial communities from McMurdo Sound in the Ross Sea, with and without iron addition, at -0.5 °C, 3 °C, and 6 °C. We then examined nutrient uptake patterns as well as the growth and molecular responses of two dominant diatoms, Fragilariopsis and Pseudo-nitzschia, to these conditions. We found that nitrate uptake and primary productivity were elevated at increased temperature in the absence of iron addition, and were even greater at high temperature with added iron. Pseudo-nitzschia became more abundant under increased temperature without added iron, while Fragilariopsis required additional iron to benefit from warming. We attribute the apparent advantage Pseudo-nitzschia shows under warming to upregulation of iron-conserving photosynthetic processes, utilization of iron-economic nitrogen assimilation mechanisms, and increased iron uptake and storage. These data identify important molecular and physiological differences between dominant diatom groups and add to the growing evidence for the increasingly important role of Pseudo-nitzschia in warming SO ecosystems. This study also suggests that temperature-driven shifts in SO phytoplankton assemblages may increase utilization of the vast pool of excess nutrients in iron-limited SO surface waters, and thereby influence global nutrient distributions and carbon cycle.</p>
Data from: Integrating palaeontological and molecular data uncovers multiple ancient and recent dispersals in the pantropical Hamamelidaceae
Aim: The integration of palaeontological and phylogenetic data can improve our understanding in the spatio-temporal evolutionary processes of living organisms. However, how best to use fossil data in divergence time estimation and ancestral range reconstruction remains challenging. Here, we integrated palaeontological and molecular data to investigate the historical biogeography of Hamamelidaceae, a pantropical angiosperm family with abundant fossils outside its present distribution. Location: Global tropical/subtropical areas. Methods: Using seven DNA regions (> 7,500 bp) from plastid and nuclear genomes, we reconstructed a robust phylogenetic framework for Hamamelidaceae with the first complete genus-level sampling. We used the tip-dating method with the 22 fossils to estimate divergence times for the family, and inferred the ancestral range of lineages under the dispersal-extinction-cladogenesis model by incorporating the fossils. Results: Our biogeographic analysis indicates that extant Hamamelidaceae most likely originated in tropical Asia during the mid-Cretaceous, and in the family 20 dispersals occurred during three major time intervals: the Upper Cretaceous (c. 93–69 Ma), Paleocene–Eocene (c. 63–39 Ma) and late Oligocene (c. 27–23 Ma). Main conclusions: Overland migrations through available land bridges and island chains may have been mainly responsible for hamamelidaceous range expansions during these three episodes. This study contributes to our knowledge on the assembly and evolution of angiosperm-dominated tropical and subtropical forests.
Figures 8-10 from: Zhang D, Chen K, Xiang L (2020) Revision of the genus Epiparbattia Caradja, 1925 (Lepidoptera, Crambidae, Pyraustinae), based on morphology and molecular data. ZooKeys 960: 143-155. https://doi.org/10.3897/zookeys.960.54986
Figures 8-10 Female genitalia of Epiparbattia spp. 8E. gloriosalis, Guangdong (genitalia slide no. SYSU1036) 9E. oligotricha, Sichuan (genitalia slide no. SYSU1035) 10E. multispinalis sp. nov., Hubei (genitalia slide no. ZDD12074). Scale bars: 1.0 mm.
Figures 5-7 from: Zhang D, Chen K, Xiang L (2020) Revision of the genus Epiparbattia Caradja, 1925 (Lepidoptera, Crambidae, Pyraustinae), based on morphology and molecular data. ZooKeys 960: 143-155. https://doi.org/10.3897/zookeys.960.54986
Figures 5-7 Male genitalia of Epiparbattia spp. 5E. gloriosalis, Guangdong (genitalia slide no. CXH12039) 6E. oligotricha, Yunnan (genitalia slide no. ZDD12109) 7E. multispinalis sp. nov., Hubei (genitalia slide no. ZDD12101). Scale bars: 1.0 mm.
Figures 1-4 from: Zhang D, Chen K, Xiang L (2020) Revision of the genus Epiparbattia Caradja, 1925 (Lepidoptera, Crambidae, Pyraustinae), based on morphology and molecular data. ZooKeys 960: 143-155. https://doi.org/10.3897/zookeys.960.54986
Figures 1-4 Adults of Epiparbattia spp. 1E. gloriosalis, male (Renhua, Guangdong) 2E. oligotricha, female (Tianquan, Sichuan) 3E. multispinalis sp. nov., holotype, male (Shuangping, Zhuxi, Hubei) 4E. multispinalis sp. nov., paratype, female (Shuangping, Zhuxi, Hubei). Scale bars: 5.0 mm.
Figure 11 from: Zhang D, Chen K, Xiang L (2020) Revision of the genus Epiparbattia Caradja, 1925 (Lepidoptera, Crambidae, Pyraustinae), based on morphology and molecular data. ZooKeys 960: 143-155. https://doi.org/10.3897/zookeys.960.54986
Figure 11 Phylogenetic hypothesis inferred from Bayesian inference. Numbers on branches indicate Bayesian posterior probabilities and ML bootstrap values respectively.
Figure 5 in The contribution of molecular data to our understanding of cephalopod evolution and systematics: a review
Figure 5. Maximum likelihood phylogenies of Octopodidae sensu Strugnell et al. 2013 (= Octopodinae sensu Sweeney and Roper 1998) based on (A) amino acid sequences of two mitochondrial genes: cytochrome oxidase subunit III and cytochrome b apoenzyme, and the nuclear gene Elongation Factor-1α (Guzik et al. 2005); (B) 12S ribosomal RNA, 16S ribosomal RNA and cytochrome oxidase subunit I (Takumiya et al. 2005); (C) a multigene approach (four to ten genes depending on sequence availability) (Lindgren et al. 2012); (D) three nuclear and three mitochondrial genes tested and treated for saturation (Strugnell et al. 2013). All trees redrawn from original sources using updated nomenclature for clarity.
Figure 4 in The contribution of molecular data to our understanding of cephalopod evolution and systematics: a review
Figure 4. Consensus tree depicting phylogenetic relationships supported by all analyses conducted by Strugnell et al. (2013).
Fig. 19 in The Indo-Pacific Amalda (Neogastropoda, Olivoidea, Ancillariidae) revisited with molecular data, with special emphasis on New Caledonia
Fig. 19. Sequenced species of Amalda H. Adams & A. Adams, 1853. A–B. Amalda sp., MNHN IM-2013-63891, SL 20 mm. C–D. A. contusa (Reeve, 1864), MNHN IM-2009-22263, SL 24.9 mm. E. A. optima (G.B. Sowerby III, 1897), MNHN IM-2007-38287. F–G. A. monilifera (Reeve, 1864), MNHN IM-2013-63898, SL 11.7 mm. H–I. A. hinomotoensis (Yokoyama, 1922), MNHN IM-2019-618, SL 41.4 mm. J–K. A. hayashii Ninomiya, 1988, MNHN IM-2013-44413, SL 38.4 mm. L–M. A. bellonarum Kilburn & Bouchet, 1988, MNHN IM-2007-33273. Shells not to scale.
Fig. 15 in The Indo-Pacific Amalda (Neogastropoda, Olivoidea, Ancillariidae) revisited with molecular data, with special emphasis on New Caledonia
Fig. 15. Amalda alabaster sp. nov. A–B. Holotype, MNHN IM-2007-43627, SL 26.7 mm. C-D. MNHN IM-2007-43583, SL 24.8 mm. E. MNHN IM-2007-43621, SL 27.1 mm. F. MNHN IM-2007-43626, SL 22.2 mm, specimen not sequenced. G. MNHN IM-2007-43633, SL 22 mm, specimen not sequenced. H–I. A. cf. alabaster, MNHN IM-2013-63897, SL 18.1 mm. Shells at the same scale, all specimens except F–G sequenced.
Fig. 16. A–F. Amalda allaryi Bozzetti, 2007. A–B in The Indo-Pacific Amalda (Neogastropoda, Olivoidea, Ancillariidae) revisited with molecular data, with special emphasis on New Caledonia
Fig. 16. A–F. Amalda allaryi Bozzetti, 2007. A–B. Holotype, MNHN IM-2000-20532, SL 29.4 mm. C–D. MNHN IM-2007-43630, SL 27.2 mm. E. MNHN IM-2007-43628, SL 24.4 mm. F. KANACONO, stn CP4656, 22°40′ S, 167°12′ E, 219–244 m, W of Île des Pins, SL 64.5 mm. G–H. A. maritzae Bozzetti, 2007, holotype, MNHN IM-2000-24475, SL 54.4 mm. A–E = at the same scale; F–H = at the same scale; C–E = sequenced specimens.
Fig. 14. A–B in The Indo-Pacific Amalda (Neogastropoda, Olivoidea, Ancillariidae) revisited with molecular data, with special emphasis on New Caledonia
Fig. 14. A–B. Live specimens of Amalda montrouzieri (Souverbie, 1860), Nouméa, 8 m. C–E. Shell and live specimen of A. herberti Cossignani, 2013, Nouméa, South Lagoon, about 250 m. Photos courtesy of David Massemin.
Fig. 13 in The Indo-Pacific Amalda (Neogastropoda, Olivoidea, Ancillariidae) revisited with molecular data, with special emphasis on New Caledonia
Fig. 13. Radulae of species of Amalda H. Adams & A. Adams, 1853. A–C. A. montrouzieri (Souverbie, 1860). A–B. Île Ouen – Baie du Prony, LAGON, stn DW239, 22°24.3′ S, 166°57.8′ E, 42–43 m, SL 20.2 mm. C. Grand Récif Sud, LAGON, stn DW544, 22°50.8′ S, 166°48.5′ E, 25 m, SL 25.4 mm (shell on Fig. 12I). D–E. A. alabaster sp. nov. D. Holotype, MNHN IM-2007-43627, SL 26.7 mm (shell on Fig. 15A–B). E. MNHN IM-2007-43636, SL 17.6 mm. F. A. cf. alabaster, MNHN IM-2013-63897, SL 18.1 mm (shell on Fig. 15H–I). G. A. allaryi Bozzetti, 2007, MNHN IM-2013- 68272 (shell on Fig. 17A). H. A. coriolis Kilburn & Bouchet, 1988, MNHN IM-2013-63899 (shell on Fig. 18H–I).
Fig. 10 in The Indo-Pacific Amalda (Neogastropoda, Olivoidea, Ancillariidae) revisited with molecular data, with special emphasis on New Caledonia
Fig. 10. Amalda miriky sp. nov., Madagascar. A–E. Holotype, MNHN IM-2007-36868, SL 39.6 mm (D–E = enlarged lateral and apical views of the protoconch). F. MNHN IM-2007-38073, SL 35.8 mm (specimen not sequenced). G. MNHN IM-2007-36842, SL 35.7 mm. H. MNHN IM-2007-36866, SL 37.9 mm. I. MNHN IM-2007-38064, SL 30 mm. J. Miriky, stn DW3215, between Nosy-Be and Banc du Leven, 12°32′ S, 47°54′ E, 316–433 m, SL 38.9 mm (specimen not sequenced, radula on Fig. 7J). Scale bars: A–C, F–J= 2 cm; D–E = 1 mm.
Fig. 8. A–H in The Indo-Pacific Amalda (Neogastropoda, Olivoidea, Ancillariidae) revisited with molecular data, with special emphasis on New Caledonia
Fig. 8. A–H. Amalda aureomarginata Kilburn & Bouchet, 1988, southern New Caledonia. A–C. Holotype, MNHN IM-2000-1345, SL 34.1 mm. D. MNHN IM-2007-43644, SL 26.6 mm. E. MNHN IM-2007- 43655, SL 31.5 mm. F. MNHN IM-2007-43551, SL 30.5 mm. G–H. MNHN IM-2007-43654, SL 28.2 mm. I–J. A. hilgendorfi (von Martens, 1897), MNHN IM-2009-11968, northern New Caledonia, SL 31.6 mm. Shells at the same scale; H, J = enlarged upper part of the shell. Arrow on H points at dark brown line, bordering secondary spire callus.
Fig. 7 in The Indo-Pacific Amalda (Neogastropoda, Olivoidea, Ancillariidae) revisited with molecular data, with special emphasis on New Caledonia
Fig. 7. Radulae of species of Amalda H. Adams & A. Adams, 1853. A–G. A. hilgendorfi (von Martens, 1897). A–B. MNHN IM-2019-621 (shell on Fig. 4D). C. MNHN IM-2009-11961 (shell on Fig. 4J). D. MNHN IM-2013-58045, Papua New Guinea. E. MNHN IM-2013-19909, Papua New Guinea. F. MNHN IM-2013-63430, southern New Caledonia. G. MNHN IM-2007-33312 (shell on Fig. 5F). H. A. aureomarginata Kilburn & Bouchet, 1988, MNHN IM-2013-63421, specimen not sequenced, southern New Caledonia. I–J. A. miriky sp. nov. I. Miriky, stn CP3210, specimen not sequenced, Madagascar. J. Miriky, stn DW3215 (shell on Fig. 10J). K–L. A. cacao sp. nov., holotype, MNHN IM-2000-35296 (shell on Fig. 11A–E).
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
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