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366 results for “Cytoplasm”
Dataset for the Intensity Ratio Nuclei Cytoplasm Tool
<p>Pairs of fluorescently stained images of nuclei and cytoplasm. Example input data for the Intensity Ratio Nuclei Cytoplasm Tool.</p>
In vitro cell cycle oscillations exhibit a robust and hysteretic response to changes in cytoplasmic density
<p>Cells control the properties of the cytoplasm to ensure proper functioning of biochemical processes. Recent studies showed that cytoplasmic density varies in both physiological and pathological states of cells undergoing growth, division, differentiation, apoptosis, senescence, and metabolic starvation. Little is known about how cellular processes cope with these cytoplasmic variations. Here, we study how a cell cycle oscillator comprising cyclin-dependent kinase (Cdk1) responds to changes in cytoplasmic density by systematically diluting or concentrating cycling <em>Xenopus</em> egg extracts in cell-like microfluidic droplets. We found that the cell cycle maintains robust oscillations over a wide range of deviations from the endogenous density: as low as 0.2× to more than 1.22× relative cytoplasmic density (RCD). A further dilution or concentration from these values arrested the system in a low or high steady state of Cdk1 activity, respectively. Interestingly, diluting an arrested cytoplasm of 1.22× RCD recovers oscillations at lower than 1× RCD. Thus, the cell cycle switches reversibly between oscillatory and stable steady states at distinct thresholds depending on the direction of tuning, forming a hysteresis loop. We propose a mathematical model which recapitulates these observations and predicts that the Cdk1/Wee1/Cdc25 positive feedback loops do not contribute to the observed robustness, supported by experiments. Our system can be applied to study how cytoplasmic density affects other cellular processes.</p>
Cytoplasmic components of the machinery mediating telomere-led rapid chromosome movements in mouse meiosis
<p>Telomere-led rapid chromosome movements (RPMs) are a prominent characteristic of chromosome dynamics during meiosis. Although of crucial importance in maintaining germ cell integrity, the extranuclear portion of the machinery supporting RPMs in mammals is poorly understood. Using an unbiased proteomic approach to identify motor proteins associated to microtubules in mouse meiotic cells, complemented with co-immunoprecipitation confirmation, we uncovered kinesins as candidate of the machinery mediating RPMs in mouse spermatocytes. Further biochemical, microscopy, and functional analysis shows that KIF5B and KIF2B interact with KASH5 and act as motor proteins mediating the LINC complex-microtubule interactions. Our results show that member of the kinesin family of molecular motors act as novel critical modules of the machinery promoting complex dynamic chromosomes in mammals.</p>
Rickettsia induces strong cytoplasmic incompatibility in a predatory insect
<p><em>Rickettsia</em>, a group of intracellular bacteria found in eukaryotes, exhibits diverse lifestyles, with some acting as vertebrate pathogens transmitted by arthropod vectors and others serving as maternally transmitted arthropod endosymbionts, some of which manipulate host reproduction for their own benefit. Two phenotypes, namely male killing and parthenogenesis induction are known as <em>Rickettsia</em>-induced host reproductive manipulations, but it remains unknown whether <em>Rickettsia</em> can induce other types of host manipulation. In this study, we discovered that <em>Rickettsia</em> induced strong cytoplasmic incompatibility (CI), in which uninfected females produce no offspring when mated with infected males, in the predatory insect <em>Nesidiocoris tenuis </em>(Hemiptera: Miridae). Molecular phylogenetic analysis revealed that the <em>Rickettsia</em> strain was related to <em>Rickettsia bellii</em>, a common insect endosymbiont. Notably, this strain carried plasmid-encoded homologues of the CI-inducing factors (namely <em>cifA</em>-like and <em>cifB</em>-like genes), typically found in <em>Wolbachia</em>, which are well-known CI-inducing endosymbionts. Protein domain prediction revealed that the <em>cifB</em>-like gene encodes PD-(D/E)XK nuclease and deubiquitinase domains, which are responsible for <em>Wolbachia</em>-induced CI, as well as OTU-like cysteine protease and ankyrin repeat domains. These findings suggest that <em>Rickettsia</em> and <em>Wolbachia</em> endosymbionts share underlying mechanisms of CI and that CI-inducing ability was acquired by microbes through horizontal plasmid transfer.</p>
Рис. 7. Варианты преΑсказанной Αоменной структуры моΛекуΛ аΑгезии гемоцитов моΛΛюсков Planorbarius corneus. УсΛовные обозначения и сокращения: 1–3 — β-интегрины, 4–5 — α-интегрины, 6–7 — сеΛектины, 8–11 — моΛекуΛы семейства САМ (сell adhesiom molecues), INB — субъеΑиницы β-интегрина, IntegrinBcyt — цитопΛазматический Αомен β-интегрина, CY — цистатинопоΑобный Αомен, Int alpha — Αомен α-интегрина, FN3 — Αомен фибронектина типа 3, CCP — Αомен контроΛя компΛемента Fig. 7. Variants of the predicted domain structure of adhesion molecules from hemocytes of Planorbarius corneus molluscs. Symbols and abbreviations: 1–3 — β-integrins, 4–5 — α–integrins, 6–7 — selectins, 8–11 — molecules of the СAM family (cell adhesion molecules), INB — β-integrin subunits, IntegrinBcyt — cytoplasmic domain of β-integrin, CY — cystatin-like domain, Int alpha — α-integrin domain, FN3 — fibronectin type 3 domain, CCP — complement control protein domain in Pathogen recognition molecules from hemocytes of Planorbarius corneus molluscs (Planorbidae, Pulmonata)
Рис. 7. Варианты преΑсказанной Αоменной структуры моΛекуΛ аΑгезии гемоцитов моΛΛюсков Planorbarius corneus. УсΛовные обозначения и сокращения: 1–3 — β-интегрины, 4–5 — α-интегрины, 6–7 — сеΛектины, 8–11 — моΛекуΛы семейства САМ (сell adhesiom molecues), INB — субъеΑиницы β-интегрина, IntegrinBcyt — цитопΛазматический Αомен β-интегрина, CY — цистатинопоΑобный Αомен, Int alpha — Αомен α-интегрина, FN3 — Αомен фибронектина типа 3, CCP — Αомен контроΛя компΛемента Fig. 7. Variants of the predicted domain structure of adhesion molecules from hemocytes of Planorbarius corneus molluscs. Symbols and abbreviations: 1–3 — β-integrins, 4–5 — α–integrins, 6–7 — selectins, 8–11 — molecules of the СAM family (cell adhesion molecules), INB — β-integrin subunits, IntegrinBcyt — cytoplasmic domain of β-integrin, CY — cystatin-like domain, Int alpha — α-integrin domain, FN3 — fibronectin type 3 domain, CCP — complement control protein domain
Structure and Function of the Nuclear Pore Complex Cytoplasmic mRNA Export Platform
<p>These scripts demonstrate the use of <a href="https://integrativemodeling.org/">IMP</a>, <a href="https://salilab.org/modeller">MODELLER</a>, and <a href="https://github.com/salilab/pmi">PMI</a> in the modeling of the Nup82 complex using DSS/EDC chemical cross-links and electron microscopy (EM) 2D class averages.</p> <p>First, <a href="https://salilab.org/modeller">MODELLER</a> is used to generate initial structures for the individual components in the Nup82 complex. Then, IMP is used to model these components using DSS/EDC crosslinks and the electron microscopy 2D class averages for the entire Nup82 complex.</p> <p>The modeling protocol will work with a default build of IMP, but for most effective sampling, IMP should be built with <a href="https://integrativemodeling.org/2.5.0/doc/ref/namespaceIMP_1_1mpi.html">MPI</a> so that replica exchange can be used.</p> <p><strong>For more information</strong> about how to reproduce this modeling, see the <a href="https://salilab.org/nup82/">Sali lab website</a> or the README file.</p>
Growth and fitness measures of cytoplasmic male sterility (CMS) of Physa acuta
Open the record for dataset details and reuse information.
In vitro cell cycle oscillations exhibit a robust and hysteretic response to changes in cytoplasmic density
Open the record for dataset details and reuse information.
Rickettsia induces strong cytoplasmic incompatibility in a predatory insect
Open the record for dataset details and reuse information.
Diffusion of nanoparticles in the cell cytoplasm
<p>In Etoc 2018, we presented the diffusive behavior inside the cytosol of living cells for different kind of nanometric sized nanoparticles. We showed that the passivation of the particles is the main parameter that regulate the diffusion properties of particles smaller than 70nm not only in Hela cells but also in RPE1 and MSC cells.</p> <p>Here we open the data for the MSC cells.</p> <p>Experiments consists in the recording of small subregions of the cytoplasm located at the periphery of the cell.</p> <p>A README file is included in the archive with the recording parameters.</p> <p>DATA were recorded by Elie BALLOUL</p> <p>Scripts were written by Mathieu COPPEY, Fred ETOC and modified by Elie BALLOUL.(to use polyfit instead of ezyfit)</p> <p>We also make available the scripts that we used to generate the maps.</p> <p>Some functions were found in Matlab Central and their corresponding license is in their respective folders.</p>
Supplementary data for Ün et. al. 2020 "Cytoplasmic incompatibility between New and Old World populations of a tramp ant"
<p>Supplementary annotation and phylogenetic data. See included README file for details.</p>
The genetic basis of cytoplasmic male sterility and fertility restoration in wheat
<p><span><span><span><span><span><span><span><span><span><span><span>Hybrid wheat varieties give higher yields than conventional lines but are difficult to produce due to a lack of effective control of male fertility in breeding lines. One promising system involves the <i>Rf1</i> and <i>Rf3</i> genes that restore fertility of wheat plants carrying <i>Triticum timopheevii</i>-type cytoplasmic male sterility (T-CMS). By genetic mapping and comparative sequence analyses we identified <i>Rf1</i> and <i>Rf3</i> candidates that could restore normal pollen production in transgenic wheat plants carrying T-CMS. We show that Rf1 and Rf3 bind to the mitochondrial <i>orf279</i> transcript and induce cleavage, preventing expression of the CMS trait. The identification of restorer genes in wheat is an important step towards the development of hybrid wheat varieties based on a CMS-<i>Rf</i> system. The characterisation of their mode of action brings new insights into the molecular basis of CMS and fertility restoration in plants.</span></span></span></span></span></span></span></span></span></span></span><br> <br> This dataset includes transcript count and coverage data from 2 RNA-seq experiments looking at gene expression in various male-sterile or male-fertile wheat lines examined in the course of this research.</p>
Data from: Loss of cytoplasmic incompatibility and minimal fecundity effects explain relatively low Wolbachia frequencies in Drosophila mauritiana
Maternally transmitted Wolbachia bacteria infect about half of all insect species. Many Wolbachia cause cytoplasmic incompatibility (CI), reduced egg hatch when uninfected females mate with infected males. Although CI produces a frequency-dependent fitness advantage that leads to high equilibrium Wolbachia frequencies, it does not aid Wolbachia spread from low frequencies. Indeed, the fitness advantages that produce initial Wolbachia spread and maintain non-CI Wolbachia remain elusive. wMau Wolbachia infecting Drosophila mauritiana do not cause CI, despite being very similar to CI-causing wNo from D. simulans (0.068% sequence divergence over 682,494 bp), suggesting recent CI loss. Using draft wMau genomes, we identify a deletion in a CI-associated gene, consistent with theory predicting that selection within host lineages does not act to increase or maintain CI. In the laboratory, wMau shows near-perfect maternal transmission; but we find no significant effect on host fecundity, in contrast to published data. Intermediate wMau frequencies on the island Mauritius are consistent with a balance between unidentified small, positive fitness effects and imperfect maternal transmission. Our phylogenomic analyses suggest that group-B Wolbachia, including wMau and wPip, diverged from group-A Wolbachia, such as wMel and wRi, 6–46 million years ago, more recently than previously estimated.
Fluorescence Microscopy Images of Hela Cell infected with Plasmodium Berghei parasite expressing mCherry in cytoplasm
<p>The purpose of our experiments was to delve into the liver stage development of the P. berghei parasite and examine the host-parasite interactions using HeLa cells. This research is primarily focused on in vitro analysis and does not extend to in vivo applications. Our study investigated the integration of fluorescent microscopy with artificial intelligence to <br>track and predict the developmental milestones of Plasmodium liver stage development. </p> <p>This is the dataset used in our study.</p>
3D localization AFM (3D-LAFM) density map of glutamate transporter GltPh outward facing state (OFS) conformation at apo condition, imaged from the cytoplasmic side
<p>3D localization AFM (3D-LAFM) density map of glutamate transporter GltPh outward facing state (OFS) conformation at apo condition, imaged from the cytoplasmic side, in <code>.afm</code> format and in <code>.mrc</code> format.</p> <p>Note: The <code>.afm</code> file encodes details for constructing 3D-LAFM density maps and includes experimental conditions in its header. Using <code>.afm</code> files requires the additional installation of the AFM file encoder (available from <a href="https://github.com/rafaeljiang23/3D-LAFM/tree/main/ChimeraX-AfmFormat_v2">GitHub</a>). Once the relevant installation is complete, <code>.afm</code> files can be opened in ChimeraX via drag-and-drop. In contrast, <code>.mrc</code> files, which encode only the density values equivalent to <code>.afm</code> files, can be directly opened in ChimeraX without requiring additional software installation.</p> <p>The deposited <code>.afm</code> file follows the 'AFM1' (metacode) format standard.</p>
3D localization AFM (3D-LAFM) density map of glutamate transporter GltPh inward facing state closed (IFSclosed) conformation at apo condition, imaged from the cytoplasmic side
<p>3D localization AFM (3D-LAFM) density map of glutamate transporter GltPh inward facing state closed (IFSclosed) conformation at apo condition, imaged from the cytoplasmic side, in <code>.afm</code> format and in <code>.mrc</code> format.</p> <p>Note: The <code>.afm</code> file encodes details for constructing 3D-LAFM density maps and includes experimental conditions in its header. Using <code>.afm</code> files requires the additional installation of the AFM file encoder (available from <a href="https://github.com/rafaeljiang23/3D-LAFM/tree/main/ChimeraX-AfmFormat_v2">GitHub</a>). Once the relevant installation is complete, <code>.afm</code> files can be opened in ChimeraX via drag-and-drop. In contrast, <code>.mrc</code> files, which encode only the density values equivalent to <code>.afm</code> files, can be directly opened in ChimeraX without requiring additional software installation.</p> <p>The deposited <code>.afm</code> file follows the 'AFM1' (metacode) format standard.</p>
3D localization AFM (3D-LAFM) density map of glutamate transporter GltPh inward facing state open (IFSopen) conformation at apo condition, imaged from the cytoplasmic side
<p>3D localization AFM (3D-LAFM) density map of glutamate transporter GltPh inward facing state open (IFSopen) conformation at apo condition, imaged from the cytoplasmic side , in <code>.afm</code> format and in <code>.mrc</code> format.</p> <p>Note: The <code>.afm</code> file encodes details for constructing 3D-LAFM density maps and includes experimental conditions in its header. Using <code>.afm</code> files requires the additional installation of the AFM file encoder (available from <a href="https://github.com/rafaeljiang23/3D-LAFM/tree/main/ChimeraX-AfmFormat_v2">GitHub</a>). Once the relevant installation is complete, <code>.afm</code> files can be opened in ChimeraX via drag-and-drop. In contrast, <code>.mrc</code> files, which encode only the density values equivalent to <code>.afm</code> files, can be directly opened in ChimeraX without requiring additional software installation.</p> <p>The deposited <code>.afm</code> file follows the 'AFM1' (metacode) format standard.</p>
3D localization AFM (3D-LAFM) density map of glutamate transporter GltPh inward facing state open, kinetically locked, (IFSopen-1) conformation at apo condition, imaged from the cytoplasmic side
<p>3D localization AFM (3D-LAFM) density map of glutamate transporter GltPh inward facing state open, kinetically locked, (IFSopen-1) conformation at apo condition, imaged from the cytoplasmic side , in <code>.afm</code> format and in <code>.mrc</code> format.</p> <p>Note: The <code>.afm</code> file encodes details for constructing 3D-LAFM density maps and includes experimental conditions in its header. Using <code>.afm</code> files requires the additional installation of the AFM file encoder (available from <a href="https://github.com/rafaeljiang23/3D-LAFM/tree/main/ChimeraX-AfmFormat_v2">GitHub</a>). Once the relevant installation is complete, <code>.afm</code> files can be opened in ChimeraX via drag-and-drop. In contrast, <code>.mrc</code> files, which encode only the density values equivalent to <code>.afm</code> files, can be directly opened in ChimeraX without requiring additional software installation.</p> <p>The deposited <code>.afm</code> file follows the 'AFM1' (metacode) format standard.</p>
White Blood Cells with cytoplasm and surrounding red blood cells
<p>This dataset is taken from doi:10.17632/w7cvnmn4c5.1 and is used for segmentation of irregular shaped white blood cells in 2D. We also provide dataset for cytoplasm and we trained StarDist and UNET models to be applied in the VollSeg setting on this dataset.</p>
Transcription feedback dynamics in the wake of cytoplasmic mRNA degradation shutdown
<p>In the last decade, multiple studies demonstrated that cells maintain a balance of mRNA production and degradation, but the mechanisms by which cells implement this balance remain unknown. Here, we monitored cells’ total and recently-transcribed mRNA profiles immediately following an acute depletion of Xrn1—the main 5′-3′ mRNA exonuclease—which was previously implicated in balancing mRNA levels. We captured the detailed dynamics of the adaptation to rapid degradation of Xrn1 and observed a significant accumulation of mRNA, followed by a delayed global reduction in transcription and a gradual return to baseline mRNA levels. We found that this transcriptional response is not unique to Xrn1 depletion; rather, it is induced earlier when upstream factors in the 5′-3′ degradation pathway are perturbed. Our data suggest that the mRNA feedback mechanism monitors the accumulation of inputs to the 5′-3′ exonucleolytic pathway rather than its outputs.</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.
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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.
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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.