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176 results for “cell density”
The role of cell-envelope synthesis for envelope growth and cytoplasmic density in Bacillus subtilis
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From hidden hearing loss to supranormal auditory processing by neurotrophin 3-mediated modulation of inner hair cell synapse density
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The temporal response of a glioma cell population to irradiation: modeling the effect of dose and cell density
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Robust surface-to-mass coupling and turgor-dependent cell width determine bacterial dry-mass density
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Epidermal club cell densities in fathead minnows: assessment of method and application to a case study
<p><strong>Abstract</strong></p> <p>Many fishes possess epidermal club cells that are the presumptive source of chemical alarm cues and also play a role in innate immune defense. Club cell density has been estimated in some studies but a standardized method for quantifying these cells is lacking.</p> <p>Here, we assess the repeatability of estimating club cell density in fathead minnows (<em>Pimephales promelas</em>). Thin-sectioned histological samples of fathead minnows were stained and mounted on slides and then digitally scanned for scoring. We estimated epidermal area using the segment tool in ImageJ to simulate the traditional method of scoring microscope slides using an ocular micrometer, where epidermal area was estimated by the lengths of straight-line segments of epidermal thickness and length of the tissue sample. The second approach measured epidermal area using the freehand tool in ImageJ.</p> <p>The R<sup>2</sup> value for repeated estimates of club cell density (club cells/mm<sup>2</sup>) ranged from 0.959 and 0.969, depending on the method used to estimate epidermal area. Measurement error in estimates of epidermal area was greater than measurement error in cell counts and the freehand tool was more repeatable than the segment tool as a method to measure epidermal area.</p> <p>We applied these methods to test differences in club cell densities between two sources of fathead minnows; wild-caught fish versus lab-reared fish provided by the Environmental Protection Agency. Lab-reared fish had higher densities of club cells than wild-caught fish did, likely reflecting differences in body condition.epidermal club cells</p>
Confocal images from: Cell density, alignment, and orientation correlate with C-signal-dependent gene expression during Myxococcus xanthus development
<p>Starving <em>Myxococcus xanthus</em> bacteria use short-range C-signaling to coordinate their movements and construct multicellular mounds, which mature into fruiting bodies as rods differentiate into spherical spores. Differentiation requires efficient C-signaling to drive the expression of developmental genes, but how the arrangement of cells within nascent fruiting bodies (NFBs) affects C-signaling is not fully understood. Here, we used confocal microscopy and cell segmentation to visualize and quantify the arrangement, morphology, and gene expression of cells near the bottom of NFBs at much higher resolution than previously achieved. We discovered that "transitioning cells" (TCs), intermediate in morphology between rods and spores, comprised 10 to 15% of the total population. Spores appeared midway between the center and the edge of NFBs early in their development and near the center as maturation progressed. The developmental pattern as well as C-signal-dependent gene expression in TCs and spores were correlated with cell density, the alignment of neighboring rods, and the tangential orientation of rods early in the development of NFBs. These dynamic radial patterns support a model in which the arrangement of cells within the NFBs affects C-signaling efficiency to regulate precisely the expression of developmental genes and cellular differentiation in space and time. Developmental patterns in other bacterial biofilms may likewise rely on short-range signaling to communicate multiple aspects of cellular arrangement, analogous to juxtacrine and paracrine signaling during animal development.</p>
Secondary_data_Temporal evolution of cell density
<p>Dataset containing secondary data regarding the temporal evolution of cell density. This data was used for the generation the temporal evolution plot related to the article: <strong>The distinctive chemotactic responses of three marine herbivore protists to DMSP and related compounds.</strong> Therefore, provides information about the cell accumulation (cell density) along the incubation of three cultured dinoflagellates (<em>Karlodinium armiger, Gyrodinium dominans</em> and<em> Oxyrrhis marina</em>) responding to gradients of DMSP, DMS and and acrylate diffusing from a microcapillary. </p> <p>Nomenclature:</p> <p>time_frames: cell density on each frame of the video recorded / time_s: time in seconds corresponding to the frame analyzed.</p> <p>concentration: uM</p> <p>Total_substrate: cell density in both zones analyzed (Inside and outside) in the capillary with the substrate (DMSP, DMS or ACRYLATE)</p> <p>Total_control: cell density in both zones analyzed (inside and outside) in the control capillary.</p>
Hexanematic crossover in epithelial monolayers depends on cell adhesion and cell density.
<p>Raw data files concerning the publication,</p> <p><strong>Hexanematic crossover in epithelial monolayers depends on cell adhesion and cell density</strong><br>Julia Eckert, Benoit Ladoux, Rene-Marc Mege, Luca Giomi and Thomas Schmidt<br>Nature Communications (2023) <strong>14</strong>:5762.<br>doi: <span>https://doi.org/10.1038/s41467-023-41449-6</span><br><br><strong>Abstract:</strong></p> <p>Changes in tissue geometry during developmental processes are associated with collective migration of cells. Recent experimental and numerical results suggest that these changes could leverage on the coexistence of nematic and hexatic orientational order at different length scales. How this multiscale organization is affected by the material properties of the cells and their substrate is presently unknown. In this study, we address these questions in monolayers of Madin-Darby canine kidney cells having various cell densities and molecular repertoires. At small length scales, confluent monolayers are characterized by a prominent hexatic order, independent of the presence of E-cadherin, monolayer density, and underlying substrate stiffness. However, all three properties affect the meso-scale tissue organization. The length scale at which hexatic order transits to nematic order, the ”hexanematic” crossover scale, strongly depends on cell-cell adhesions and correlates with monolayer density. Our study demonstrates how epithelial organization is affected by mechanical properties, and provides a robust description of tissue organization during developmental processes.</p> <p> </p> <p><strong>Data description:</strong></p> <p>WT.zip - zipped raw image data and extracted vertices of experiments on wild-type cells<br>KO.zip - zipped raw image data and extracted vertices of experiments on eCad KO-cells<br>FigureData.zip - zipped data referring to each of the figures in the paper</p> <p> </p> <p><strong>Software:</strong></p> <p>The software to analyze the data presented here is found on GitHub, [https://github.com/hexanematic/orientation tracker]</p>
Effect of Two Different Preoperative Training Densities in Patients With Non-small-cell Lung Cancer Before Lung Resection Surgery
ClinicalTrials.gov study NCT03936764. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Interest of Nutritional Care of Children With Sickle Cell Disease on Bone Mineral Density and Body Composition
ClinicalTrials.gov study NCT04754711. IPD Sharing: YES. Countries: 1. Publications: 8.
Effect of Exercise Training on the Function of the High Density Lipoprotein (HDL)-Cholesterol, Endothelial Function and Endothelial Progenitor Cells in Patients With Metabolic Syndrome(HERMET-Study)
ClinicalTrials.gov study NCT00515476. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Symbiodiniaceae cell densities in feces of coral reef fish, sediments and seawater in Mo'orea, French Polynesia, July-August 2019
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Epidermal club cell densities in fathead minnows: assessment of method and application to a case study
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Confocal images from: Cell density, alignment, and orientation correlate with C-signal-dependent gene expression during Myxococcus xanthus development
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Thermal pressure in the laser heated diamond anvil cell: a quantitative study and implications for the density vs. mineralogy correlation of the mantle
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Data from: Collective cell migration without proliferation: density determines cell velocity and wave velocity
Collective cell migration contributes to embryogenesis, wound healing and tumor metastasis. Cell monolayer migration experiments help understanding what determines the movement of cells far from the leading edge. Inhibiting cell proliferation limits cell density increase and prevents jamming; we observe long-duration migration and quantify space-time characteristics of the velocity profile over large length- and time-scales. Velocity waves propagate backwards and their frequency depends only on cell density at the moving front. Both cell average velocity and wave velocity increase linearly with the cell effective radius regardless of the distance to the front. Inhibiting lamellipodia decreases cell velocity while waves either disappear or have a lower frequency. Our model combines conservation laws, monolayer mechanical properties and a phenomenological coupling between strain and polarity: advancing cells pull on their followers which then become polarized. With reasonable values of parameters, this model agrees with several of our experimental observations. Together, our experiments and model disantangle the respective contributions of active velocity and of proliferation in monolayer migration, explain how cells maintain their polarity far from the moving front, and highlight the importance of strain-polarity coupling and density in long-range information propagation.
Data from: High cell density upregulates calcium oscillation by increasing calcium store content via basal mitogen-activated protein kinase activity
Calcium releases of non-excitable cells are generally a combination of oscillatory and non-oscillatory patterns, and factors affecting the calcium dynamics are still to be determined. Here we report the influence of cell density on calcium increase patterns of clonal cell lines. The majority of HeLa cells seeded at 1.5 x 104/cm2 showed calcium oscillations in response to histamine and ATP, whereas cells seeded at 0.5 x 104/cm2 largely showed transient and sustained calcium increases. Cell density also affected the response of HEK293 cells to ATP in a similar manner. High cell density increased the basal activity of the mitogen-activated protein (MAP) kinase and calcium store content, and both calcium oscillation and calcium store content were down-regulated by a MAP kinase inhibitor, U0126. Thus, MAP kinase-mediated regulation of calcium store likely underlie the effect of cell density on calcium oscillation. Calcium increase patterns of HeLa cells were conserved at any histamine concentrations tested, whereas the overexpression of histamine H1 receptor, which robustly increased histamine-induced inositol phospholipid hydrolysis, converted calcium oscillations to sustained calcium increases only at high histamine concentrations. Thus, the consequence of modulating inositol phospholipid metabolism was distinct from that of changing cell density, suggesting the effect of cell density is not attributed to inositol phospholipid metabolism. Collectively, our results propose that calcium increase patterns of non-excitable cells reflect calcium store, which is regulated by the basal MAP kinase activity under the influence of cell density.
Data from: Cell wall microstructure, pore size distribution and absolute density of hemp shiv
This paper, for the first time, fully characterises the intrinsic physical parameters of hemp shiv including cell wall microstructure, pore size distribution and absolute density. Scanning Electron Microscopy revealed microstructural features similar to hardwoods. Confocal Microscopy revealed three major layers in the cell wall: middle lamella, primary cell wall and secondary cell wall. Computed tomography improved the visualisation of pore shape and pore connectivity in three dimensions. Mercury intrusion porosimetry showed the average accessible porosity was 76.67 ± 2.03 % and pore size classes could be distinguished into micropores (3-10 nm) and macropores (0.1-1 µm and 20-80 µm). The absolute density was evaluated by helium pycnometry, mercury intrusion porosimetry (MIP) and Archimedes' methods. The results show that these methods can lead to misinterpretation of absolute density. The MIP method showed a realistic absolute density (1.45 g/cm3) consistent with the density of the known constituents: including lignin, cellulose and hemi-cellulose. However, helium pycnometry and Archimedes' methods gave falsely low values due to 10% of the volume being inaccessible pores, which require sample pretreatment in order to be filled by liquid or gas. This indicates that the determination of the cell wall density is strongly dependent on sample geometry and preparation.
Continuous Protein-Density gradients: A new approach to correlate physical cues with cell response
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Quantifying Cell-State Densities in Single-Cell Phenotypic Landscapes using Mellon
<p>Processed data use in the the Mellon manuscript</p> <p>The following scanpy anndata objects are also available</p> <ol> <li>preprocessed_t-cell-depleted-bm-rna.h5ad: Anndata object for the RNA modality of the T-cell depleted bone marrow multiome dataset with normalized data, cell type annotations, clusters, pseudo time, fate propensities, MAGIC imputed expression data, cell-state densities, B-cell primed and lineage accessibility scores.</li> <li>preprocessed_t-cell-depleted-bm-atac.h5ad: Anndata object for the RNA modality of the T-cell depleted bone marrow multiome dataset with normalized data, cell type annotations, clusters, cell-state densities, B-cell primed and lineage peaks.</li> <li>preprocessed_t-cell-depleted-bm-rna-metacells.h5ad: Anndata object with metacells for the RNA modality of the T-cell depleted bone marrow multiome dataset .</li> <li>preprocessed_mouse-gastrulation-atlas.h5ad: Anndata object of the preprocessed mouse gastrulation data with normalized data, cell type annotations, clusters, pseudo time, fate propensities, MAGIC imputed expression data,</li> </ol>
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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.