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337 results for “cell shape”
CellMet: Extracting 3D shape metrics from cells and tissues
<p>This dataset supports the manuscript title "CellMet: Extracting 3D shape metrics from cells and tissues". It contains segmented images (mask.tif) of severals tissues. </p>
Dataset from: Changes in cell size and shape during 50,000 generations of experimental evolution with Escherichia coli
<p>Bacteria adopt a wide variety of sizes and shapes, with many species exhibiting stereotypical morphologies. How morphology changes, and over what timescales, is less clear. Previous work examining cell morphology in an experiment with Escherichia coli showed that populations evolved larger cells and, in some cases, cells that were less rod-like. That experiment has now run for over two more decades. Meanwhile, genome sequence data are available for these populations, and new computational methods enable high-throughput microscopic analyses. In this study, we measured stationary-phase cell volumes for the ancestor and 12 populations at 2,000, 10,000, and 50,000 generations, including measurements during exponential growth at the last time point. We measured the distribution of cell volumes for each sample using a Coulter counter and microscopy, the latter of which also provided data on cell shape. Our data confirm the trend toward larger cells while also revealing substantial variation in size and shape across replicate populations. Most populations first evolved wider cells but later reverted to the ancestral length-to-width ratio. All but one population evolved mutations in rod shape maintenance genes. We also observed many ghost-like cells in the only population that evolved the novel ability to grow on citrate, supporting the hypothesis that this lineage struggles with maintaining balanced growth. Lastly, we show that cell size and fitness remain correlated across 50,000 generations. Our results suggest that larger cells are beneficial in the experimental environment, while the reversion toward ancestral length-to-width ratios suggests partial compensation for the less favorable surface area-to-volume ratios of the evolved cells.</p>
Data from: T cell morphodynamics reveal periodic shape oscillations in 3D migration
<p>Surface segmentation data of cytotoxic T cells migrating in 3D collagen matrices, imaged by lattice light-sheet microscopy and used for quantitative morphodynamic analysis in the manuscript: T Cell Morphodynamics Reveal Periodic Shape Oscillations in 3D Migration.</p>
FIGURE 1 in Boletus recapitulatus (Boletaceae), a new species from India with peculiar mushroom-shaped cells
FIGURE 1. Best maximum likelihood phylogram of ITS sequences from DC 14-001 (Boletus recapitulatus, in red font) and 35 best matching sequences in GenBank and UNITE databases. Numbers above/below/next to branches are nonparametric bootstrap percentages after 450 bootstrap replicates. The tree was rooted at the node leading to Butyriboletus.
FIGURE 3 in Boletus recapitulatus (Boletaceae), a new species from India with peculiar mushroom-shaped cells
FIGURE 3. Boletus recapitulatus sp. nov. (DC 14-001): a. Section through plugged pores showing tube edge b. Pleurocystidia c. Gelatinous hyphae in hymenophoral trama d. Cross-section through pileipellis e–g. Mushroom like terminal cells in the hyphae of pileipellis & stipitipellis i. Basidiospores j. Scanning Electron Micrograph of a basidiospore h. Granular spore surface under SEM. Bars: a = 100 μm, b–c & e–I = 10 μm, d = 50 μm, j = 5 μm, h = 500 nm.
FIGURE 2 in Boletus recapitulatus (Boletaceae), a new species from India with peculiar mushroom-shaped cells
FIGURE 2. Boletus recapitulatus sp. nov. (DC 14-001): a & b. Fresh basidioma in field c. Macrochemical reaction on exposed context d. Pore- & stipe surface e. Pore surface showing red mouth.
FIGURE 4 in Boletus recapitulatus (Boletaceae), a new species from India with peculiar mushroom-shaped cells
FIGURE 4. Boletus recapitulatus sp. nov. (DC 14-001) a. Basidiospores b. Pleurocystidia c. Cheilocystidia d. Basidia and basidiole e. Caulocystidia f & g. Hyphal elements on pileipellis. Bars: a–g = 10 μm.
Data supporting the analysis of lymphatic endothelial cell junctions and shape
<p><strong>Data in support of: </strong></p> <p><span><strong>Dynamic cytoskeletal regulation of cell shape supports<span> </span>resilience of lymphatic endothelium</strong></span></p> <p>Hans Schoofs<sup>1#</sup>, Nina Daubel<sup>1#</sup>, Sarah Schnabellehner<sup>1</sup>, Max Grönloh<sup>2</sup>, Sebastián Palacios Martínez<sup>3</sup>, Aleksi Halme<sup>4</sup>, Amanda M. Marks<sup>1</sup>, Marie Jeansson<sup>1</sup>, Sara Barcos<sup>5</sup>, Cord Brakebusch<sup>6</sup>, Rui Benedito<sup>7</sup>, Britta Engelhardt<sup>5</sup>, Dietmar Vestweber<sup>8</sup>, Konstantin Gängel<sup>1</sup>, Fabian Linsenmeier<sup>9</sup>, Sebastian Schürmann<sup>9</sup>, Pipsa Saharinen<sup>4,10</sup>, Jaap D. van Buul<sup>2,3,11</sup>, Oliver Friedrich<sup>9</sup>, Richard S. Smith<sup>12</sup>, Mateusz Majda<sup>13</sup>, and Taija Mäkinen<sup>1,4,10</sup>*</p> <p> </p> <p><sup>1</sup>Uppsala University, Department of Immunology, Genetics and Pathology, Dag Hammarskjölds väg 20, 751 85 Uppsala, Sweden.</p> <p><sup>2</sup>Department of Medical Biochemistry at the Amsterdam UMC, location AMC, The Netherlands.</p> <p><sup>3</sup>Department of Molecular Cytology, Leeuwenhoek Centre for Advanced Microscopy at Swammerdam Institute for Life Sciences at the University of Amsterdam, The Netherlands.</p> <p><sup>4</sup>Translational Cancer Medicine Program and Department of Biochemistry and Developmental Biology, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland.</p> <p><sup>5</sup>Theodor Kocher Institute, University of Bern, Bern, Switzerland.</p> <p><sup>6</sup>Biotech Research and Innovation Center, University of Copenhagen, Ole Maaløes Vej 5, 2200 Denmark.</p> <p><sup>7</sup>Centro Nacional de Investigaciones Cardiovasculares, Melchor Fernández Almagro 3, E-28029 Madrid, Spain.</p> <p><sup>8</sup>Max Planck Institute for Molecular Biomedicine, Münster, Germany.</p> <p><sup>9</sup>Institute of Medical Biotechnology, Department of Chemical and Biological Engineering, Friedrich-Alexander-University, Erlangen-Nürnberg, Paul-Gordan-Str.3, 91052 Erlangen, Germany.</p> <p><sup>10</sup>Wihuri Research Institute, Haartmaninkatu 8, 00290 Helsinki, Finland.</p> <p><sup>11</sup>Amsterdam UMC, Sanquin Research and Landsteiner Laboratory, The Netherlands.</p> <p><sup>12</sup>John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.</p> <p><sup>13</sup>Department of Plant Molecular Biology, University of Lausanne, CH-1015 Lausanne, Switzerland.</p> <p><sup>#</sup>These authors contributed equally.</p> <p>*Corresponding author: Taija Mäkinen, E-mail: <a href="mailto:taija.makinen@igp.uu.se">taija.makinen@igp.uu.se</a>, <a href="mailto:taija.makinen@helsinki.fi">taija.makinen@helsinki.fi</a></p> <p> </p> <p><strong>DATASET A: Annotated cell-cell junction types in lymphatic capillaries of wild type mouse ear skin at different ages <br></strong>__________________________________________________________________________________________________________</p> <p><strong>Contents</strong></p> <ul> <li>SOURCE DATA Fig1 FINAL. xlsx</li> <li>3w <ul> <li>animal 1</li> <li>animal 2</li> <li>animal 3</li> <li>animal 4</li> <li>animal 5</li> <li>sprouts</li> </ul> </li> <li>5w <ul> <li>animal 1</li> <li>animal 2</li> <li>animal 3</li> <li>animal 4</li> <li>animal 5</li> <li>diaphragm <ul> <li>Overview of diaphragm and high mag. of different capillary ends</li> </ul> </li> <li>trachea</li> </ul> </li> <li>25w <ul> <li>animal 1</li> <li>animal 2</li> <li>animal 3</li> <li>animal 4</li> <li>animal 5</li> <li>diaphragm</li> <li>trachea</li> </ul> </li> </ul> <p><strong>File legends<br></strong></p> <p>C1 images: inverted LYVE1 signal (.tif)<br>C2 images: inverted VE-cadherin signal (.tif)<br>MAX images: RGB merge of LYVE1 (cyan) and VE-cadherin (red) (.tif)<br>"NAME".roi: Regions of interest (ROI) of annotated junctions can be imported in ImageJ</p> <p><strong>Methods</strong></p> <p><em>Junctional classification:</em> <br>Analysis of junction morphology was done on blunt-ended initial lymphatic capillaries in the segment between the intial tip and the first valve. Junction types were quantified in Z-stack projection by numbering of individual lobes of LYVE1 and VE-cadherin-stained LECs and subsequent categorizing of lobe-associated junctions based on VE-cadherin signal.</p> <p>Four categories were defined:</p> <p>1) Button junction – a punctate VE-cadherin<sup>+</sup> deposit at the neck of LYVE1<sup>+</sup> lobe/overlap, with no detectable VE-cadherin at the borders of the overlap,</p> <p>2) Curvilinear junction – unsegmented(continous) or segmented (discontinuous) distribution of VE-cadherin within one border of LYVE1<sup>+</sup> lobe/cellular overlap,</p> <p>3) Double junction – unsegmented(continous) or segmented (discontinuous) distribution of VE-cadherin within both borders of LYVE1<sup>+</sup> lobe/cellular overlap, and</p> <p>4) LYVE1- curvilineair junction – unsegmented(continous) linear VE-cadherin distribution at cell-cell contacts in the absence of LYVE1.</p> <p>Wild-type C57BL/6J mice were used for analysis of junction types, and 4-5 blunt ended vessels per mouse from five mice per age group and condition were analysed; in total 1785 junctions were annoted</p> <p><em>Imaging:<br></em>Confocal images were obtained using a Leica Stellaris 5 confocal microscope equipped with 405 nm and white light lasers, 63x/1.3 HC PL APO CORR CS2 Glycerol immersion objective, and Leica LAS X software. Images were aquired at 1.51 digital zoom using a 2048x2048 resolution</p> <p><em>Tissue processing and staining: </em><strong> <br></strong>Tissues were fixed in 4% paraformaldehyde for 2 h at RT and permeabilized in 0.3% Triton X-100 in PBS (PBST) for 10 min. After blocking in PBST with 2% bovine serum albumin, 1% FBS for 2 h, tissues were incubated with primary antibodies in blocking buffer overnight, followed by PBST washing and incubation with fluorescent dye-conjugated secondary antibodies for 2 h. All incubation steps were carried out at RT. Prior to mounting in Mowiol, samples were repeatedly washed in PBST and water. Antibodies used: Goat anti-mouse VE-cadherin (R&D Systems, AF1002; 1:200), Rat anti-mouse LYVE1 (R&D Systems, MAB2125; 1:200)</p> <p> </p> <p><strong>DATASET B: Finite element method (FEM) simulations of cellular stresses<br>_______________________________________________________________</strong></p> <p>The FEM simulations were performed with MorphoMechanX using available models adapted from Sapala et al, <em>eLife</em> <strong>7</strong>, e32794 (2018). A regular cylindrical grid 45 µm wide and 200 µm long was created and outlines from the cells of a lymphatic vessel were projected onto it and smoothed. These cells were then extruded inward to make 3D volumetric cells with a depth of 2 µm and triangulated using a threshold area of 4 µm. The template was then used as the reference configuration for triangular 3 node membrane elements which were given a thickness of 0.1um. An isotropic St. Venant material model (linear, large deformation) was used with the Young's modulus set to 100 kPa to match a 10 kPa cell level Young's modulus estimated from the literature (ignoring the cell ends, the 2 x 0.1 µm membrane thickness occupied roughly 1/10<sup>th</sup> the cross-sectional area of the cell that were 2 µm deep). A uniform internal pressure was applied normal to the inside faces of the elements, which cancels out on the shared walls between cells. For simulations with a lower pressure inside the vessel, the inside faces were assigned a higher pressure. Stresses were visualized as the trace of the stress tensor.</p> <p><strong> </strong></p>
Code and data for "Coupling cell shape and velocity leads to oscillation and circling in keratocyte galvanotaxis"
<p>Code and data to reproduce "Coupling cell shape and velocity leads to oscillation and circling in keratocyte galvanotaxis" Biophys. J. doi: <a href="https://doi.org/10.1016/j.bpj.2022.11.021">https://doi.org/10.1016/j.bpj.2022.11.021</a></p>
CAD files of the spirally shaped chemiluminescence flow cells with distinct cross-sectional geometries and confluence types
<p>CAD files of (i) 3D-printed chemiluminescence flow-through cells with triangular, circular, semicircular, square and irregular pentagonal cross-section geometries, (ii) serpentine mixing coil, and (iii) T, Y and Y'-junction formats (in STL format, ready to print) associated to Figures 1, 2 and S1 of the paper "3D-printed chemiluminescence flow cells with customized cross-section geometry for enhances analytical performance" published in Talanta 2023 (DOI:10.1016/j.talanta.2022.124211)</p>
Supplementary data to "Small-scale variation prevails in the cell shape patterning of green microalgae belonging to the genus Micrasterias (Zygnematophyceae, Viridiplantae)"
<p>The supplementary data consist of 24 TPS files including the landmark coordinates of 12 Micrasterias datasets (two separate digitisations for each dataset). In addition, the R script used for the analyses described in the paper submitted to "Evolutionary Biology" and the utility file with factors for Procrustes ANOVA are also included.</p> <p> </p>
Efficacy, Safety and Tolerability Study of SHAPE in IA, IB or IIA Cutaneous T-cell Lymphoma
ClinicalTrials.gov study NCT02213861. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Dataset from: Changes in cell size and shape during 50,000 generations of experimental evolution with Escherichia coli
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Class-A penicillin binding proteins do not contribute to cell shape but repair cell-wall defects
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Data from: T cell morphodynamics reveal periodic shape oscillations in 3D migration
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METHODS. Bovine ilia were used in the simulations because their histological structure (a fibrolamellar cortex overlying cancellous bone26) was found to match that of the Triceratops ilium. Bone sections 10 x 50 x 縠 3.0 cm with cortices ranging from 0.5 to 5.5 mm in depth (the range of initial cortical-thickness estimates based on gross morphology) were mounted on a servohydraulic mechanical loading frame (MTS Bionix, Minneapolis) and penetrated with an aluminium-bronze T. rex tooth replica. The replica was cast from an actual adult T. rex maxillary tooth, after casts made from some ofthe deeper bite marks revealed the size and shape of the teeth that had impacted the pelvis8 • The replica was penetrated into the ilia sections at 1 mm s-1 to a depth of 11.5 mm, equivalent to the maximum depth of the deepest ilium bite mark8 • Forces were measured with an MTS 25 N strain-gauge-based axial load cell accurate to 0.2%. The forces increased with increasing penetration depth even after the cortical layer had been perforated and the underlying cancellous bone was being crushed. The increase in force with penetration depth is attributed to a greater cortical surface area coming into contact with the semi-conical penetrator tooth as it descended through the ilia. in Bite-force estimation for Tyrannosaurus rex from tooth-marked bones
METHODS. Bovine ilia were used in the simulations because their histological structure (a fibrolamellar cortex overlying cancellous bone26) was found to match that of the Triceratops ilium. Bone sections 10 x 50 x 縠 3.0 cm with cortices ranging from 0.5 to 5.5 mm in depth (the range of initial cortical-thickness estimates based on gross morphology) were mounted on a servohydraulic mechanical loading frame (MTS Bionix, Minneapolis) and penetrated with an aluminium-bronze T. rex tooth replica. The replica was cast from an actual adult T. rex maxillary tooth, after casts made from some ofthe deeper bite marks revealed the size and shape of the teeth that had impacted the pelvis8 • The replica was penetrated into the ilia sections at 1 mm s-1 to a depth of 11.5 mm, equivalent to the maximum depth of the deepest ilium bite mark8 • Forces were measured with an MTS 25 N strain-gauge-based axial load cell accurate to 0.2%. The forces increased with increasing penetration depth even after the cortical layer had been perforated and the underlying cancellous bone was being crushed. The increase in force with penetration depth is attributed to a greater cortical surface area coming into contact with the semi-conical penetrator tooth as it descended through the ilia.
Tumour-intrinsic features shape T-cell differentiation through myeloma disease evolution - raw data
<p><strong><em>sample_id</em>.h5</strong></p> <ul> <li>Feature-barcode matrix (<em>filtered_feature_bc_matrix.h5</em>, 10x-Genomics-formatted hdf5 file) for indicated sample.</li> </ul> <p><strong><em>sample_id</em>-VDJ.csv</strong></p> <ul> <li><em>filtered_contig_annotations.csv</em> file for indicated sample.</li> </ul> <p><strong>sample-metadata.csv</strong></p> <ul> <li>Metadata for each sample: donor_id (donor of origin), sort (sorting strategy), batch (sequencing batch).</li> </ul> <p> </p>
Text-fig. 12. Silutanispermum kvacekiorum gen. et sp. nov. seeds from the Early Cretaceous Famalicão locality (sample 025), Portugal; Synchrotron radiation X-ray tomographic microscopy (SRXTM, orthoslices). a) Longitudinal orthoslice (yz1170) through the median plane of the seed (S170238) in the micropylar region showing exotestal cells lining the micropylar slit (mi) and hilum (hi); note the well-preserved mesotestal cells (me). b) Longitudinal orthoslice (xz0805) of seed perpendicular to the median plane through the micropylar region showing the transverse micropylar slit (mi) lined by radiating exotestal cells; note abundant mesotestal cells (me). c) Transverse orthoslice (xy0768) through seed below hilum and micropyle showing exotesta (ex) and mesotesta (me) that is strongly developed along the raphe (ra) (S174352). d) Transverse orthoslice (xy2113) through middle of the seed showing well-preserved cellular nutritive tissue with empty cells; note that the raphe (ra) is enclosed in mesotestal tissue (S174352). e) Longitudinal orthoslice (yz0970) through seed coat showing exotesta (ex) of tall palisade-shaped cells and thick mesotesta (me) of low cells (S174352). Scale bars = 500 µm (a, c, d); 250 µm (b); 125 µm (e). in Extinct Taxa Of Exotestal Seeds Close To Austrobaileyales And Nymphaeales From The Early Cretaceous Of Portugal
Text-fig. 12. Silutanispermum kvacekiorum gen. et sp. nov. seeds from the Early Cretaceous Famalicão locality (sample 025), Portugal; Synchrotron radiation X-ray tomographic microscopy (SRXTM, orthoslices). a) Longitudinal orthoslice (yz1170) through the median plane of the seed (S170238) in the micropylar region showing exotestal cells lining the micropylar slit (mi) and hilum (hi); note the well-preserved mesotestal cells (me). b) Longitudinal orthoslice (xz0805) of seed perpendicular to the median plane through the micropylar region showing the transverse micropylar slit (mi) lined by radiating exotestal cells; note abundant mesotestal cells (me). c) Transverse orthoslice (xy0768) through seed below hilum and micropyle showing exotesta (ex) and mesotesta (me) that is strongly developed along the raphe (ra) (S174352). d) Transverse orthoslice (xy2113) through middle of the seed showing well-preserved cellular nutritive tissue with empty cells; note that the raphe (ra) is enclosed in mesotestal tissue (S174352). e) Longitudinal orthoslice (yz0970) through seed coat showing exotesta (ex) of tall palisade-shaped cells and thick mesotesta (me) of low cells (S174352). Scale bars = 500 µm (a, c, d); 250 µm (b); 125 µm (e).
Data from: Cell shape and the microenvironment regulate nuclear translocation of NF-kappaB in breast epithelial and tumor cells
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Crosstalk between Regnase-1 and -3 shapes mast cell survival and cytokine expression
GEO Series GSE240210. Mus musculus. 20 samples. Type: Expression profiling by high throughput sequencing; Expression profiling by array.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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