Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
366
datasets available to search
ShareScore release 0.9.0
Dataset results
366 results for “Cytoplasm”
The role of cell-envelope synthesis for envelope growth and cytoplasmic density in Bacillus subtilis
<p>All cells must increase their volumes in response to biomass growth to maintain intracellular mass density within physiologically permissive bounds. Here, we investigate the regulation of volume growth in the Gram-positive bacterium <em>Bacillus subtilis</em>. To increase volume, bacteria enzymatically expand their cell envelopes and insert new envelope material. First, we demonstrate that cell-volume growth is determined indirectly, by expanding their envelopes in proportion to mass growth, similarly to the Gram-negative <em>Escherichia coli</em>, despite their fundamentally different envelope structures. Next, we studied, which pathways might be responsible for robust surface-to-mass coupling: We found that both peptidoglycan synthesis and membrane synthesis are required for proper surface-to-mass coupling. However, surprisingly, neither pathway is solely rate-limiting, contrary to wide-spread belief, since envelope growth continues at a reduced rate upon complete inhibition of either process. To arrest cell-envelope growth completely, the simultaneous inhibition of both envelope-synthesis processes is required. Thus, we suggest that multiple envelope-synthesis pathways collectively confer an important aspect of volume regulation, the coordination between surface growth and biomass growth.</p>
Structural Basis for Redox Regulation of Cytoplasmic and Chloroplastic Triosephosphate Isomerases from Arabidopsis thaliana
<p>Mass spectrometry raw data files for the determination of the molecular weight of the intact proteins.</p> <p>López-Castillo LM, Jiménez-Sandoval P, Baruch-Torres N, Trasviña-Arenas CH, Díaz-Quezada C, Lara-González S, Winkler R and Brieba LG (2016) Structural Basis for Redox Regulation of Cytoplasmic and Chloroplastic Triosephosphate Isomerases from <em>Arabidopsis thaliana</em>. <em>Front. Plant Sci</em>. 7:1817. doi: 10.3389/fpls.2016.01817</p>
Treponema pallidum Cytoplasmic filament protein gene partial sequence
<p>A partial sequence of the Cytoplasmic filament protein gene (cfpA) of treponema pallidum from non human primates</p>
Supplementary material for Proctor et al., "Warm temperature inhibits cytoplasmic incompatibility induced by endosymbiotic Rickettsiella in a spider host"
<p>Included are two supplemental files: SupplementaryDocument1 includes primers and cycling conditions for qPCR quanitification of the symbiont Rickettsiella. SupplementaryDocument2 includes all raw data for the experiments included in this manuscript.</p>
Cytoplasmic male sterility and abortive seed traits generated through mitochondrial genome editing coupled with allotopic expression of atp1 in tobacco
<p>Genome editing tools have recently been developed that are capable of generating deletions and/or rearrangements in plant mitochondrial genomes. We utilized custom-designed meganuclease constructs targeting the essential mitochondrial gene <em>atp1</em> in tobacco plants carrying a version of atp1 that had been repurposed to function as a nuclear gene. Leaf extracts enriched in mitochondria from three independent genome editing events were evaluated by PacBio sequencing and analysis. Contigs that display sequence homology to the reference mitochondrial genome BA000042 are deposited here. Some of the contigs correspond to the tobacco mitochondrial genome as expected, while others corresponded to sequences from the nucleus where the ancient transfer of portions of the mitochondrial genome became incorporated into the nuclear genome. Still other contigs correspond to the chloroplast genome, or pieces of the chloroplast genome anciently transferred to the nucleus, as small fragments of the chloroplast genome are interspersed in plant mitochondrial genomes. Analysis of contigs of genuine mitochondrial origin demonstrated that the double-strand breaks imposed by the genome editing enzymes resulted in the deletion of <em>atp1</em> and neighboring sequences, along with rearrangements in overall genome structure.</p>
Anti-neutrophil Cytoplasmic Antibody in Interstitial Lung Disease.
ClinicalTrials.gov study NCT04413149. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Plasma Exchange and Glucocorticoids for Treatment of Anti-Neutrophil Cytoplasm Antibody (ANCA) - Associated Vasculitis
ClinicalTrials.gov study NCT00987389. IPD Sharing: Not stated. Countries: 15. Publications: 4.
Data from: Loss of cytoplasmic incompatibility and minimal fecundity effects explain relatively low Wolbachia frequencies in Drosophila mauritiana
Open the record for dataset details and reuse information.
Suppression of cytoplasmic incompatibility in the leaf-mining fly Liriomyza sativae with a nuclear Wolbachia insert
Open the record for dataset details and reuse information.
The genetic basis of cytoplasmic male sterility and fertility restoration in wheat
Open the record for dataset details and reuse information.
The role of cell-envelope synthesis for envelope growth and cytoplasmic density in Bacillus subtilis
Open the record for dataset details and reuse information.
Local nuclear to cytoplasmic ratio regulates H3.3 incorporation via cell cycle state during zygotic genome activation
Open the record for dataset details and reuse information.
Colistin kills bacteria by targeting lipopolysaccharide in the cytoplasmic membrane - primary data for all experiments described in the manuscript
Open the record for dataset details and reuse information.
The facultative intracellular symbiont Lariskella is neutral for lifetime fitness and spreads through cytoplasmic incompatibility in the leaffooted bug, Leptoglossus zonatus
Open the record for dataset details and reuse information.
An alternative cytoplasmic SFPQ isoform with reduced phase separation potential is upregulated in ALS
Open the record for dataset details and reuse information.
Cytoplasmic male sterility and abortive seed traits generated through mitochondrial genome editing coupled with allotopic expression of atp1 in tobacco
Open the record for dataset details and reuse information.
Cardinium localization during its parasitoid wasp host's development provides insights into cytoplasmic incompatibility
<p>Arthropods harbor heritable intracellular symbionts that may manipulate host reproduction to favor symbiont transmission. In cytoplasmic incompatibility (CI), the symbiont sabotages the reproduction of infected males such that high levels of offspring mortality result when they mate with uninfected females. In crosses with infected males and infected females, however, (the "rescue" cross), normal numbers of offspring are produced. A common CI-inducing symbiont, <i>Cardinium hertigii</i>, causes variable levels of CI mortality in the parasitoid wasp, <i>Encarsia</i> <i>suzannae. </i>Previous work correlated CI-induced mortality with male development time in this system, although the timing of <i>Cardinium</i> CI-induction and the relationship between development time and CI mortality was not well understood. Here, using a combination of crosses, manipulation of development time, and fluorescence microscopy, we identify the localization and the timing of the CI-induction step in the <i>Cardinium-E. suzannae </i>system. Antibiotic treatment of adult <i>Cardinium-</i>infected males did not reduce the mortality associated with the CI phenotype, suggesting that CI-alteration occurs prior to adulthood. Our results suggest that the alteration step occurs during the pupal period, and is limited by the duration of pupal development: 1) <i>Encarsia </i>produces most sperm prior to adulthood, 2), FISH localization of <i>Cardinium </i>in testes showed an association with sperm nuclei throughout spermatogenesis but not with mature sperm and 3) two methods of prolonging the pupal period (cool temperatures and the juvenile hormone analog methoprene) both caused greater CI mortality, suggesting the degree of alteration is limited by the duration of the pupal stage. Based on these results, we compare two models for potential mechanisms of <i>Cardinium</i> sperm modification in the context of what is known about analogous mechanisms of <i>Wolbachia, </i>a more extensively studied CI-inducing symbiont.</p>
Data from: "Darwin's corollary" and cytoplasmic incompatibility induced by Cardinium may contribute to speciation in Encarsia wasps (Hymenoptera: Aphelinidae)
The potential importance of cytoplasmic incompatibility (CI) – inducing bacterial symbionts in speciation of their arthropod hosts has been debated. Theoretical advances have led to a consensus that a role is plausible when CI is combined with other isolating barriers. However, the insect model systems Nasonia and Drosophila are the only two experimental examples documented. Here we analyzed the components of reproductive isolation between the parasitoid wasp Encarsia suzannae, which is infected by the CI-inducing symbiont Cardinium, and its uninfected sibling species Encarsia gennaro. Laboratory crosses demonstrated that: 1) sexual isolation is incomplete; 2) hybrid offspring production is greatly reduced in the interspecific CI cross; 3) viable hybrids may be produced by curing E. suzannae males of Cardinium with antibiotics; 4) hybrid offspring production in the reciprocal cross is greatly reduced by hybrid inviability due to genetic incompatibilities; 5) hybrid sterility is nearly complete in both directions at the F1 stage. Thus, asymmetrical hybrid incompatibilities and CI act as complementary isolating mechanisms. We propose a new model for contributions of CI symbionts to speciation, with CI reducing gene flow between species in one direction, and in the other, a symbiont sweep resulting in accelerated mtDNA evolution, negative cytonuclear interactions and hybrid incompatibilities.
Up-regulation of sarcoplasmic reticulum function protects skeletal muscle against cytoplasmic calcium overload during hibernation in ground squirrels
<p>We investigated the potential mechanism of the SR in maintenance of calcium (Ca<sup>2+</sup>) homeostasis of slow-twitch muscle (soleus, SOL), fast-twitch muscle (extensor digitorum longus, EDL) and mixed muscle (gastrocnemius, GAS) in hibernating ground squirrels (<i>Spermophilus dauricus</i>). Results showed that cytosolic and SR Ca<sup>2+</sup> concentrations in distinct skeletal muscle fibers increased and decreased during late torpor, respectively, but both returned to summer-active levels during early torpor. Ryanodine receptor1 (RyR1) and sarco/endoplasmic reticulum Ca<sup>2+</sup> ATPase isoform 1 (SERCA1) protein expression increased during hibernation. Up-regulation factors of SERCA activity: Phospholamban phosphorylation increased in the SOL and GAS, β-adrenergic receptor-2 protein expression increased in the GAS, and calmodulin kinase-2 phosphorylation increased in the SOL during hibernation. Down-regulation factors of SERCA activity: Sarcolipin and SERCA1 co-localization decreased in the EDL and GAS. These data suggest that SERCA activity in skeletal muscle fibers increases likely during hibernation. FKBP12/calsequestrin1 (negative regulatory factors of RyR1) and RyR1 co-localization decreased in the GAS, indicating that the RyR1 channel opening probability increased during hibernation. Dihydropyridine receptors protein expression and its co-localization with RYR1 decreased during hibernation prompts that the contractility of skeletal muscle was weakened. Protein expression of Ca<sup>2+</sup>-binding proteins calsequestrin1 and calmodulin increased indicating that the ability of intracellular free calcium binding increased during whole hibernation period. These findings confirm that the release, uptake, and binding of free Ca<sup>2+</sup> in the SR were enhanced in different skeletal muscles during hibernation. Up-regulation of muscular sarcoplasmic reticulum function protects skeletal muscle fibers against cytoplasmic calcium overload during hibernation in ground squirrels.We investigated the potential mechanism of the SR in maintenance of calcium (Ca<sup>2+</sup>) homeostasis of slow-twitch muscle (soleus, SOL), fast-twitch muscle (extensor digitorum longus, EDL) and mixed muscle (gastrocnemius, GAS) in hibernating ground squirrels (<i>Spermophilus dauricus</i>). Results showed that cytosolic and SR Ca<sup>2+</sup> concentrations in distinct skeletal muscle fibers increased and decreased during late torpor, respectively, but both returned to summer-active levels during early torpor. Ryanodine receptor1 (RyR1) and sarco/endoplasmic reticulum Ca<sup>2+</sup> ATPase isoform 1 (SERCA1) protein expression increased during hibernation. Up-regulation factors of SERCA activity: Phospholamban phosphorylation increased in the SOL and GAS, β-adrenergic receptor-2 protein expression increased in the GAS, and calmodulin kinase-2 phosphorylation increased in the SOL during hibernation. Down-regulation factors of SERCA activity: Sarcolipin and SERCA1 co-localization decreased in the EDL and GAS. These data suggest that SERCA activity in skeletal muscle fibers increases likely during hibernation. FKBP12/calsequestrin1 (negative regulatory factors of RyR1) and RyR1 co-localization decreased in the GAS, indicating that the RyR1 channel opening probability increased during hibernation. Dihydropyridine receptors protein expression and its co-localization with RYR1 decreased during hibernation prompts that the contractility of skeletal muscle was weakened. Protein expression of Ca<sup>2+</sup>-binding proteins calsequestrin1 and calmodulin increased indicating that the ability of intracellular free calcium binding increased during whole hibernation period. These findings confirm that the release, uptake, and binding of free Ca<sup>2+</sup> in the SR were enhanced in different skeletal muscles during hibernation. Up-regulation of muscular sarcoplasmic reticulum function protects skeletal muscle fibers against cytoplasmic calcium overload during hibernation in ground squirrels.</p>
Data from: Wolbachia in the Drosophila yakuba complex: pervasive frequency variation and weak cytoplasmic incompatibility, but no apparent effect on reproductive isolation
Three hybridizing species-the clade ((Drosophila yakuba, D. santomea), D. teissieri) -comprise the yakuba complex in the D. melanogaster subgroup. Their ranges overlap on Bioko and São Tomé, islands off west Africa. All three species are infected with Wolbachia, maternally inherited, endosymbiotic bacteria, best known for manipulating host reproduction to favor infected females. Previous analyses reported no cytoplasmic incompatibility (CI) in these species. However, we discovered that Wolbachia from each species cause intra- and interspecific CI. In D. teissieri, analyses of F1 and backcross genotypes show that both host genotype and Wolbachia variation modulate CI intensity. Wolbachia-infected females seem largely protected from intra- and interspecific CI, irrespective of Wolbachia and host genotypes. Wolbachia do not affect host mating behavior or female fecundity, within or between species. The latter suggests little apparent effect of Wolbachia on premating or gametic RI between host species. In nature, Wolbachia frequencies varied spatially for D. yakuba in 2009, with 76% (N = 155) infected on São Tomé, and only 3% (N = 36) infected on Bioko; frequencies also varied temporally in D. yakuba and D. santomea on São Tomé between 2009 and 2015. These temporal frequency fluctuations could generate asymmetries in interspecific mating success, and contribute to postzygotic RI. However, the fluctuations in Wolbachia frequencies that we observe also suggest that asymmetries are unlikely to persist. Finally, we address theoretical questions that our empirical findings raise about Wolbachia persistence when conditions fluctuate and about the stable coexistence of Wolbachia and host variants that modulate Wolbachia effects.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.