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425 results for “motility”
RMSD and Trp assays for "Structural analysis of a motor with increased mechanical output reveals new transitions in kinesin microtubule motility"
<p>This entry is for our manuscript, "Structural analysis of a motor with increased mechanical output reveals new transitions in kinesin microtubule motility" by Satoki Shibata*, Matthew Y. Wang*, Tsuyoshi Imasaki*, Hideki Shigematsu, Diego Ugarte La Torre, Yuanyuan Wei, Chacko Jobichen, Hajime Hagio, J. Sivaraman, Yuji Sugita, Sharyn A. Endow & Ryo Nitta.</p> <p>*Equal contribution</p> <p>Corresponding Authors: Tsuyoshi Imasaki*, Sharyn A. Endow, Ryo Nitta</p> <p>The deposited datasets are 1) beta-strand residue all-atom RMSD between kinesin-14 NcdY485K ADP and ADP + free Pi nucleotide states and 2) fluorimeter assays of NcdY485K intrinsic Trp fluorescence changes upon addition of free Pi . The data are presented in Fig. 6e, Fig. 7b,c and Supplementary Fig 10. Files are named for the figures in which the data are shown. A computer script for the RMSD analysis and methods for the fluorimeter assays and data analysis are included in the deposited files.</p>
Cilia density and flow velocity affect alignment of motile cilia from brain cells
<p>Here we store the supplementary Materials and Methods for the publication Cilia density and flow velocity affect alignment of motile cilia from brain cells.</p> <p>In the Supplementary methods we included additional information on the hydrodynamic simulations. </p> <p>Video1 and Video2 are videos referenced in the main text of the paper</p> <p>In the archive 'raw data and code.tar' , we provide raw images and codes to support the article.The complete dataset of raw images is more than 1 Tb. Here we are limited to 50Gb. The full dataset is available upon request.<br> <br> We choose to provide a full dataset of two culture at DIV 16, one treated with shear flow and a control without flow.</p> <p>For each of the two cultures, the videos with propelled particles are in the directory FL,<br> The bright field images without particles are stored in BF. Unfortunately we uploaded only few videos because of their large size. The results of the analysis of this dataset is reported in the directory analysis (available for each culture).</p> <p>Moreover we provide the code to analyse these data.<br> The analysis routine:</p> <p>Step 1: for each field of view (fov) getting the cilia beating direction from the FL images. This is done with PIV. The code is Step1_PIVanalysis.mat</p> <p>Step 2: for each fov getting ciliated cell position and CBF from the BF movies. Gather the cilia beating direction and cilia posion and frequency in a unique figure and matlab class (Res.mat). This is done in Step2_gatherResults.mat</p> <p>The results of these analysis are stored in the analysis folder for each culture.</p> <p>These routines are repeated for each experiment and results are then plotted to get trends. In the folder code4figures we report the code that we used to make the figures in the papers starting from a matlab file "all_results*.mat", where are gathered all the analysis.</p> <p>The code may improve in the future with more comments. please check Nicola's github page for the latest update. Please contact us for any problem. https://github.com/NicolaPellicciotta/Code4-Cilia-density-and-flow-velocity-affect-alignment-of-motile-cilia-from-brain-cells</p> <p>All the raw videos and code are in the archive.</p> <p> </p>
Data from Evidence for elevated diversification rate associated with the evolution of active motility in diatoms
<p>These are data files for Evidence for elevated diversification rate associated with the evolution of active motility in diatoms</p>
Dataset for: Phenotyping single-cell motility in microfluidic confinement
<p>Associated dataset and simulation codes for the publication "Phenotyping single-cell motility in microfluidic confinement" (2022), by Samuel A. Bentley, Hannah Laeverenz-Schlogelhofer, Vasileios Anagnostidis, Jan Cammann, Marco G. Mazza, Fabrice Gielen, Kirsty Y. Wan. </p>
Figure 3 in Effect of Vicia sativa L. on Motility, Mortality and Expression Levels of hsp Genes in J2 Stage of Meloidogyne hapla
Figure 3: Influence of Vicia sativa cv. Ina diffusate treatment on Hsp gene expression in Meloidogyne Hapla J2 stage. Each value represents the mean ± s.d. of three biological replicates. The expression levels are indicated as the fold-change normalized to the control (untreated diffusate), normalized to the value of 1 (dashed line). Values were expressed as the mean fold difference, and statistically significant differences between treated and control samples are shown; *p≤0.01 based on t-Student test.
Figure 2 in Effect of Vicia sativa L. on Motility, Mortality and Expression Levels of hsp Genes in J2 Stage of Meloidogyne hapla
Figure 2: Distribution of 36 combinations of temperatures, cultivars, and variants in the space of the first two canonical variables.
Figure 1 in Effect of Vicia sativa L. on Motility, Mortality and Expression Levels of hsp Genes in J2 Stage of Meloidogyne hapla
Figure 1: Dendrogram of the nearest neighbour cluster grouping of combinations of temperature, cultivars, and variants on the basis of four traits.
◂Fig. 1 Morphology of thecate and coccoid cells, with labelled thecal plates. a–c, i, m Light microscopy, d–h, k–l scanning electron microscopy. a Ventral view of strain GeoM*788; b dorsal view of strain GeoM*793; c apical view of strain GeoK*044; d ventral view of strain GeoK*037; e dorsal view of strain GeoM*788; f apical view of strain GeoK*024, with the dehiscence of epithecal opening indicated by a blue line; g antapical view of strain GeoK*044; h leftlateral view of strain GeoM*866; i motile cell of strain GeoK*037; k–m coccoid cells showing variability in shape and size of strains k GeoM*866, l GeoM*793 and m GeoK*024. Abbreviations: n′: apical plate, n′′: precingular plate, n′′′: postcingular plate, n′′′′: antapical plate, na: anterior intercalary plate, nC: cingular plate, Sa: anterior sulcal plate, Sd: right sulcal plate, Sp: posterior sulcal plate. Ss: left sulcal plate. Scale bar: 10 µm. UA: 15 kV in Morphological and molecular variability of Peridinium volzii Lemmerm. (Peridiniaceae, Dinophyceae) and its relevance for infraspecific taxonomy
◂Fig. 1 Morphology of thecate and coccoid cells, with labelled thecal plates. a–c, i, m Light microscopy, d–h, k–l scanning electron microscopy. a Ventral view of strain GeoM*788; b dorsal view of strain GeoM*793; c apical view of strain GeoK*044; d ventral view of strain GeoK*037; e dorsal view of strain GeoM*788; f apical view of strain GeoK*024, with the dehiscence of epithecal opening indicated by a blue line; g antapical view of strain GeoK*044; h leftlateral view of strain GeoM*866; i motile cell of strain GeoK*037; k–m coccoid cells showing variability in shape and size of strains k GeoM*866, l GeoM*793 and m GeoK*024. Abbreviations: n′: apical plate, n′′: precingular plate, n′′′: postcingular plate, n′′′′: antapical plate, na: anterior intercalary plate, nC: cingular plate, Sa: anterior sulcal plate, Sd: right sulcal plate, Sp: posterior sulcal plate. Ss: left sulcal plate. Scale bar: 10 µm. UA: 15 kV
Figure 1 in DNA damage, oxidative stress, decreased viability and motility in common carp (Cyprinuscarpio L.) spermatozoa induced by tryptophan, phenylalanine and cysteine amino acids during short-term storage
Figure 1. Effect of tryptophan (T), phenylalanine (P), cysteine (C) at concentrations of 1, 5, 25, and 50 mM on DNA fragmentation of common carp (Cyprinuscarpio L.) spermatozoa at 6 (a), 24 (b), and 48 (c) h.
Gliding motility of the diatom Craspedostauros australis correlates with the intracellular movement of raphid-specific myosins
<p>Abstract:</p> <p>Raphid diatoms are one of the few eukaryotes capable of gliding motility, which is remarkably fast and allows for quasi-instantaneous directional reversals. Besides other mechanistic models, it has been suggested that an actomyosin system provides the force for diatom gliding. However, <em>in vivo</em> data on the dynamics of actin and myosin in diatoms are lacking. In this study we demonstrate that the raphe-associated actin bundles required for diatom movement do not exhibit a directional turnover of subunits and thus their dynamics do not contribute directly to force generation. By phylogenomic analysis we identified four raphid diatom-specific myosins in <em>Craspedostauros australis</em> (CaMyoA-D) and investigated their <em>in vivo</em> localization and dynamics through GFP-tagging. Only CaMyoB-D but not CaMyoA exhibited coordinated movement during gliding, consistent with a role in force generation. The characterization of raphid diatom-specific myosins lays the foundation for unraveling the molecular mechanisms that underlie the gliding motility of diatoms.</p> <p><br>This dataset contains all microscopy data used for confocal and TIRFM imaging, with all additional elements required to reproduce figures in the manuscript "Gliding motility of the diatom Craspedostauros australis correlates with the intracellular movement of raphid-specific myosins". The dataset also contains code used to generate plots and analyze microscopy data, as well as protein sequences and code used to generate the phylogenomic tree in the paper. </p>
Data for: Characterization of a sperm motility signaling pathway in a gonochoric coral suggests conservation across sexual systems
<p>Most stony corals liberate their gametes into the water column via broadcast spawning, where fertilization hinges upon the activation of directional sperm motility. Sperm from gonochoric and hermaphroditic corals display distinct morphological and molecular phenotypes, yet it is unknown whether the signaling pathways controlling sperm motility are also distinct between these sexual systems. Here, we addressed this knowledge gap using the gonochoric broadcast spawning coral <em>Astrangia</em> <em>poculata</em>. We found that cytosolic alkalinization of sperm activates the pH-sensing enzyme soluble adenylyl cyclase (sAC), which is required for motility. Additionally, we demonstrate for the first time in any cnidarian that sAC activity is necessary for PKA activation, and PKA activity is also required for motility. Ultrastructures of <em>A. poculata</em> sperm displayed morphological homology with other gonochoric cnidarians, and investigation of cnidarian proteomes revealed that sAC exhibits broad structural and functional conservation across this phylum. These results indicate a conserved role for pH-dependent sAC-PKA signaling in sperm motility across coral sexual systems and suggest that the role of this pathway in sperm motility is likely ancestral in metazoans. Finally, the dynamics of this pH-sensitive pathway may play a critical role in determining the sensitivity of marine invertebrate reproduction to anthropogenic ocean acidification.</p>
Does motility-restricting fibrosis influence dispersal? An experiment in nature with threespine stickleback
Open the record for dataset details and reuse information.
Data for: Characterization of a sperm motility signaling pathway in a gonochoric coral suggests conservation across sexual systems
Open the record for dataset details and reuse information.
Evaluation of the impact of imprinted polymer particles on morphology and motility of breast cancer cells by using digital holographic cytometry
<p>Supplemented Videos used in "Evaluation of the impact of imprinted polymer particles on morphology and motility of breast cancer cells by using digital holographic cytometry"</p>
Image recognition based on deep learning in Haemonchus contortus motility assays
<p>The repository contains the data associated with the paper `Image recognition based on deep learning in Haemonchus contortus motility assays`. The following folders form part of the repository:</p> <p>- Annotation Data - annotated microscope images used for the training of the Mask R-CNN model. The data are divided into `train` and `val`<br> - Mask R-CNN - contains the trained weights for the Mask R-CNN model<br> - Motility Output - output of the 3 compared algorithms (Wiggle Index, WF-NTP and Mask R-CNN).<br> - Motility Videos - input videos used for the motility detection. The naming convetno is `XXXzYYY.avi`, where `XXX` denotes the motility group and `YYY` the sequence number for the video within a given group</p>
A test for plasticity in sperm motility activation
<p>Evolutionary theory predicts that selection will favour phenotypic plasticity in sperm traits that maximise fertilisation success in dynamic fertilisation environments. In species with external fertilisation, osmolality of the fertilisation medium is known to play a critical role in activating sperm motility, but evidence for osmotic-induced sperm plasticity is limited to euryhaline fish and marine invertebrates. Whether this capacity extends to freshwater taxa remains unknown. Here, we provide the first test for plasticity in sperm-motility activation in response to osmotic environment in an anuran amphibian. Unexpectedly, there was no detectable shift in the optimal osmolality for sperm-motility activation after approximately 13 weeks of acclimation (a period reflecting the duration of the winter breeding season). However, in both the low and high acclimation treatments, the optimal osmolality for sperm-motility activation mirrored the osmolality at the natural breeding site, indicating a phenotypic match to the local environment. Previously it has been shown that <em>C. signifera</em> display among-population covariation between environmental osmolality and sperm performance. Coupled with this finding, the results of the present study suggest that inter-population differences reflect genetic divergence and local adaptation. We discuss the need for experimental tests of osmotic-induced sperm plasticity in more freshwater taxa to better understand the environmental and evolutionary contexts favouring adaptive plasticity in sperm-motility activation.</p>
Data for "Sperm motility in modulated microchannels"
<p>Data for "Sperm motility in modulated microchannels" as published in NJP.</p> <p> </p> <p>Plots are generated by the jupyter notebook sperm_microchannels.ipynb</p> <p>All necessary python packages are specified in requirements.txt</p> <p> </p> <p>SETUP:</p> <p>- use python 2</p> <p> - pip install -r requirements.txt</p> <p> - jupyter notebook sperm_microchannels.ipynb</p> <p> </p>
Supplementary files for "Tristetraprolin Affects Invasion-Associated Genes Expression and Cell Motility in Triple-Negative Breast Cancer Model"
<p>Track1 and Track3 - raw numerical data on cell tracking; Morphology-DXR treated - raw images of the cells, treated with DXR; Morphology ecTTP+WT - morphology of wild-type and TTP-overexpressing cells; RAW data qPCR - rew data of gene expression experiments</p>
Single molecule motility data of DYNEIN-DYNACTIN-HOOK3-KIF1C (DDHK) complexes plus various controls
<p>Single molecule motility data of DYNEIN-DYNACTIN-HOOK3-KIF1C (DDHK) complexes plus various controls leaving out components or using truncated motors without motor domains (KS - KIF1C stalk; Dt - Dynein tail).</p>
FIGURE 1 in A New Species Of Tegoprionus Keifer (Prostigmata: Eriophyidae) From Brazil, Described From All Motile Stages, With An Overview Of The Genus Tegoprionus
FIGURE 1: Tegoprionus mesogibbosus n.sp. female: D dorsal habitus; V ventral habitus; IG internal genital structures.
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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.