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.
289
datasets available to search
ShareScore release 0.9.0
Dataset results
289 results for “Cell Wall”
Supplementary tables S5, S7, S9, S10, original protein models fasta files used for alignments, aligned and manually curated protein modes files used for phylogenies (PHYLIP format), and phylogenetic trees of plant cell wall decomposition gene families from 44 basidiomycete genomes (.tre files)
<p><span><span><span><span><span><span><span><span><span><span><span>Litter-decomposing Agaricales play key role in terrestrial carbon cycling, but little is known about their decomposition mechanisms. We assembled datasets of 42 gene families involved in plant-cell-wall decomposition from seven newly sequenced litter decomposers and 35 other Agaricomycotina members, mostly white-rot and brown-rot species. Using sequence similarity and phylogenetics, we split the families into phylogroups and compared their gene composition across nutritional strategies. Subsequently, we used Raman spectroscopy to examine the ability of litter decomposers, white-rot fungi, and brown-rot fungi to decompose crystalline cellulose. Both litter decomposers and white-rot fungi share the enzymatic cellulose decomposition, whereas brown-rot fungi possess a distinct mechanism that disrupts cellulose crystallinity. However, litter decomposers and white-rot fungi differ with respect to hemicellulose and lignin degradation phylogroups, suggesting adaptation of the former group to the litter environment. Litter decomposers show high phylogroup diversity, which is indicative of high functional versatility within the group, whereas a set of white-rot species shows adaptation to bulk-wood decomposition. In both groups, we detected species that have unique characteristics associated with hitherto unknown adaptations to diverse wood and litter substrates. Our results suggest that the terms white-rot fungi and litter decomposers mask a much larger functional diversity.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Cell wall composition and bioenergy potential of rice straw tissues are influenced by environment, tissue type, and genotype
Breeding has transformed wild plant species into modern crops, increasing the allocation of their photosynthetic assimilate into grain, fiber, and other products for human use. Despite progress in increasing the harvest index, much of the biomass of crop plants is not utilized. Potential uses for the large amounts of agricultural residues that accumulate are animal fodder or bioenergy, though these may not be economically viable without additional efforts such as targeted breeding or improved processing. We characterized leaf and stem tissue from a diverse set of rice genotypes (varieties) grown in two environments (greenhouse and field) and report bioenergy-related traits across these variables. Among the 16 traits measured, cellulose, hemicelluloses, lignin, ash, total glucose, and glucose yield changed across environments, irrespective of the genotypes. Stem and leaf tissue composition differed for most traits, consistent with their unique functional contributions and suggesting that they are under separate genetic control. Plant variety had the least influence on the measured traits. High glucose yield was associated with high total glucose and hemicelluloses, but low lignin and ash content. Bioenergy yield of greenhouse-grown biomass was higher than field-grown biomass, suggesting that greenhouse studies overestimate bioenergy potential. Nevertheless, glucose yield in the greenhouse predicts glucose yield in the field (ρ = 0.85, p < 0.01) and could be used to optimize greenhouse (GH) and field breeding trials. Overall, efforts to improve cell wall composition for bioenergy require consideration of production environment, tissue type, and variety.
Class-A penicillin binding proteins do not contribute to cell shape but repair cell-wall defects
Cell shape and cell-envelope integrity of bacteria are determined by the peptidoglycan cell wall. In rod-shaped Escherichia coli, two conserved sets of machinery are essential for cell-wall insertion in the cylindrical part of the cell: the Rod complex and the class-A penicillin-binding proteins (aPBPs). While the Rod complex governs rod-like cell shape, aPBP function is less well understood. aPBPs were previously hypothesized to either work in concert with the Rod complex or to independently repair cell-wall defects. First, we demonstrate through modulation of enzyme levels that aPBPs do not contribute to rod-like cell shape but are required for mechanical stability, supporting their independent activity. By combining measurements of cell-wall stiffness, cell-wall insertion, and PBP1b motion at the single-molecule level, we then present evidence that PBP1b, the major aPBP, contributes to cell-wall integrity by repairing cell wall defects.
Isolation and characterization of cell wall and extracellular polysaccharides from cultures of the mycoparasitic strain Tirochoderma koningiopsis
<p>The results obtained are part of the Miniatura 6 (2022/06/X/NZ9/00569) project</p>
Phenotypic differences between interfertile Chlamydomonas species - Cell Wall Analysis
<p>This repository contains raw .TIF image data of Chlamydomonas reinhardtii (cc-124) and Chlamydomonas smithii (cc-1373) stained with Calcofluor White with Evan's blue, fixed in 4% PFA, and imaged on a spinning disk confocal microscope. The protocol to generate this data is described in the associated publication, <a href="https://doi.org/10.57844/arcadia-35f0-3e16">"Phenotypic differences between interfertile <i>Chlamydomonas</i> species". </a><br><br>Cells grown in TAP media were collected through centrifugation at 2,000 RPM for 1 minute. Cells were suspended in TAP media with the noted concentration of Calcofluor White (CFW) stain (Sigma-Aldrich, SKU 18909) for 10 minutes while rotating at ambient temperature. Afterward, cells were washed twice in fresh TAP media. For initial protocol development, cells were immediately imaged after washes. For the datasets quantified in this pub, cells were fixed in freshly made 4% paraformaldehyde in PBS for 15 minutes at ambient temperature while protected from light. Fixed cells were washed twice in PBS and stored at 4 C until imaged. <br><br>We acquired micrographs with a Yokogawa CSU W1-SoRa scanner unit attached to a Nikon Ti2-E confocal microscope. We used a Plan Apo λ 40× air objective to collect images using standard DAPI channel settings. We acquired images at the medial focal plane of the cells in the field of view.<br><br>File Name Description: <br>[well position]_[strain number]_[Treatment]_[prep]_[microscope]_[secondary magnification]_[image number]<br><br>The code to analyze these images is available on GitHub</p>
Fig. 1 in Reactive oxygen species in cell wall metabolism and development in plants
Fig. 1. Schematic representation of the enzymes at the plasma membrane and in the cell wall that are able to form reactive oxygen species (ROS: superoxide anion radical · — hydrogen peroxide hydroxyl radical. into the apoplast. · — is dismutated either enzymatically catalyzed by superoxide dismutase, (O 2 ), (H2O2), ( OH)) O 2 to H2O2 or nonenzymatically in the acidic pH that is typical in the cell wall. ROS play important roles both in cell wall loosening during cell elongation and cross-link formation involved in cell growth restriction..OH is considered as a cell wall-loosening agent formed from H O either non-enzymatically by Fenton reaction involving a transition metal such as 2 2 Fe2+ or Cu +, or enzymatically by peroxidases (not depicted). Di- and oligoferulate bridges, bonds between tyrosine residues abundant in cell wall structural proteins, lignin formation, or cross-linkages between ferulates and lignin are possible cross-links involved in cell growth restriction. For the cross-link formation, oxidative enzymes (peroxidase in a peroxidative cycle using H2O2 as an oxidant, or laccase using O2 as an oxidant) catalyze the oxidation of the phenolic residues after which they make a crosslink. In addition to cell wall modifications, ROS are important signalling components in various biological processes. The left cell shows the enzymes producing ROS, and the right cell shows the enzymes consuming ROS during cell wall cross-linking. Note that all enzymes and the cross-link types mentioned may not be present in the same cell, or in all species. In case of quinone reductases, further studies are needed to find out whether enough quinones are present in the plasma membranes to be able to mediate electron transport from the cytoplasmic reductant to apoplastic molecular oxygen.
Simulation Input Data for "Quantifying acetylation-induced changes in the plant secondary cell wall structure and dynamics"
<p>This is the reduced data behind an upcoming manuscript investigating impact of acetylation on plant secondary cell wall. The data is taken directly from the directory structure that contains both the simulation and analysis, with excluded trajectory files and intermediate products to fit within the zenodo upload limit. The tar command used to generate this tarball was: </p> <p> </p> <pre><code>tar -zcvf Acetylatedcellwall.tar.gz --exclude="*BAK" --exclude="*dcd" --exclude="*poster*" --exclude="*old" --exclude="*out" --exclude="*vel" --exclude="*ppm" --exclude="*mp4" --exclude="*txt" --exclude="*tga" --exclude="*vmd" --exclude="*log" --exclude="fixed*png" --exclude="frame*png" --exclude="nonacetylation*png" . </code></pre>
FIGURE. Morphology of the studied Coelastrella strains. (4) IRK–A 2. (5) IRK–A 173. (А–D) vegetative cells and autosporangia. (E–G) cell wall ribs. (H) morphology of the old cells. Scale bar: 10μm. in Morphological and phylogenetic relations of members of the genus Coelastrella (Scenedesmaceae, Chlorophyta) from the Ural and Khentii Mountains (Russia, Mongolia)
FIGURE. Morphology of the studied Coelastrella strains. (4) IRK–A 2. (5) IRK–A 173. (А–D) vegetative cells and autosporangia. (E–G) cell wall ribs. (H) morphology of the old cells. Scale bar: 10μm.
FIGURE 3. Asteridiella elaeocarpicola var. gadgilii. a. Appressorium. b. Phialide. c. Perithecial wall cells. d in A new species and a new variety of Meliolaceae fungi from India
FIGURE 3. Asteridiella elaeocarpicola var. gadgilii. a. Appressorium. b. Phialide. c. Perithecial wall cells. d. Ascospores. Illustrator: Aliyarukunju Sabeena.
FIGURE. Aneura pinguis (L.) Dumort. I (A) Dorsal surface of thallus with archegonia (female receptacles). (B & C) Sporophytes. D) Cells of the capsule wall. (E) Elater (F) Light microscope view of spore. A–F Ruklani & Rubasinghe 47-14SR (PDA). in Thalloid Liverworts (Marchantiopsida) of Sri Lanka
FIGURE. Aneura pinguis (L.) Dumort. I (A) Dorsal surface of thallus with archegonia (female receptacles). (B & C) Sporophytes. D) Cells of the capsule wall. (E) Elater (F) Light microscope view of spore. A–F Ruklani & Rubasinghe 47-14SR (PDA).
FIGURES –. Euastrum subalpinum (114–117), apical view (115), lateral view (116), morphological variability (117); Euastrum subalpinum var. crassum (118–121), apical view (119), lateral view (120), semicell face with wart (arrow) (121); Micrasterias laticeps var. aequilobata (122–123), morphological variability (123); Micrasterias truncata var. pusilla (124–125), median sinus, lobes and lobules – detail (125); Spondylosium pulchellum var. constrictum (126–128), apical view (127), lateral view (128); Staurastrum capitulum (129–132), apical view (130), lateral view (131), cell wall (132); Staurastrum circulare var. americanum (133–135), apical view (134), lateral view (135); Staurastrum cosmarioides (136–138), triangular apical view (137), quadrangular apical view (138); Staurastrum margaritaceum var.alpinum (139–142), apical view (140), cell wall (141), apical view and cell wall (142); Staurastrum orbiculare (143–145), apical view (144), closed basal angles (145); Staurastrum punctulatum (146–147), apical view (147); Staurodesmus controversus (148–149), apical view (149); Staurodesmus convergens (150–151), apical view (151); Staurodesmus croasdaleae (152–153), morphological variability (153). Scale bar 10 µm (114–121, 125–135, 137–151)), 50 µm (122–124, 136, 152–153). in The forgotten world of subaerial desmids (Zygnematophyceae) in the Atlantic Forest, southeast Brazil
FIGURES –. Euastrum subalpinum (114–117), apical view (115), lateral view (116), morphological variability (117); Euastrum subalpinum var. crassum (118–121), apical view (119), lateral view (120), semicell face with wart (arrow) (121); Micrasterias laticeps var. aequilobata (122–123), morphological variability (123); Micrasterias truncata var. pusilla (124–125), median sinus, lobes and lobules – detail (125); Spondylosium pulchellum var. constrictum (126–128), apical view (127), lateral view (128); Staurastrum capitulum (129–132), apical view (130), lateral view (131), cell wall (132); Staurastrum circulare var. americanum (133–135), apical view (134), lateral view (135); Staurastrum cosmarioides (136–138), triangular apical view (137), quadrangular apical view (138); Staurastrum margaritaceum var.alpinum (139–142), apical view (140), cell wall (141), apical view and cell wall (142); Staurastrum orbiculare (143–145), apical view (144), closed basal angles (145); Staurastrum punctulatum (146–147), apical view (147); Staurodesmus controversus (148–149), apical view (149); Staurodesmus convergens (150–151), apical view (151); Staurodesmus croasdaleae (152–153), morphological variability (153). Scale bar 10 µm (114–121, 125–135, 137–151)), 50 µm (122–124, 136, 152–153).
A fungal endophyte induces local cell-wall mediated resistance in wheat roots against take-all disease
<p>Datasets to accompany 'A fungal endophyte induces local cell-wall mediated resistance in wheat roots against take-all disease', <span>DOI: 10.3389/fpls.2024.1444271.</span></p> <p><span>These are datasheet 1 and table S2.</span></p> <p> </p>
Effect of the overexpression of the GGP1 gene on cell wall remodelling and redox state in the tomato fruit
<p> </p> <p>The deposited data were collected as a part of the studies entitled ‘Effect of the overexpression of the GGP1 gene on cell wall remodelling and redox state in the tomato fruit’.</p> <p>The research is the result of cooperation between institutions: </p> <ul> <li>Group for Plant Molecular Biology, Institute of Molecular Genetics and Genetic Engineering (IMGGE) at the University of Belgrade (Serbia),</li> <li>Institute of Agrophysics, Polish Academy of Sciences (Poland),</li> <li>Department of Pharmaceutical Sciences, at the Aristotle University of Thessaloniki (Greece).</li> </ul> <p>The use of advanced microscopic techniques (immunolabeling method), methods of molecular biology (Western blotting), and biochemistry (HPLC, measurement of enzyme activities) allows for expanding knowledge in the field of plant cell physiology and horticulture. </p> <p> The attached files have been compressed to *.zip format. The dataset consists of the following files:</p> <p>A_1_Antioxidant enzymes activities</p> <p>A_2_CLSM imaging</p> <p>A_3_Native polyacrylamide electrophoresis of antioxidant enzymes</p> <p>A_4_Phenolic components in the fruit tissue</p> <p>A_5_Western Blotting with quantitative analysis</p>
The cell wall changes as a result of the disturbed presence of AGPs by Yariv reagent addition.
<p>The deposited data were collected as a part of the studies entitled ‘How does the structure of the cell wall change as a result of the disturbed presence of AGPs by Yariv reagent addition?’</p> <p>The research is the result of cooperation between institutions: Institute of Agrophysics, Polish Academy of Sciences (Poland), and Department of Chemistry, Brown University (USA). The use of advanced microscopic techniques (immunolabeling method), methods of molecular biology (Western blotting, ELISA) allows for expanding knowledge in the field of plant cell physiology and biochemistry. </p> <p> </p> <p>The attached files have been compressed to *.zip format. The dataset consists of the following files:</p> <p>A_1_CLSM imaging</p> <p>A_2_ELISA</p> <p>A_3_Western blotting.</p>
Cell wall thickness and composition are involved in photosynthetic limitation
<p><span><span><span><span><span><span><span><span><span><span><span>The key role of cell walls in setting mesophyll conductance to CO<sub>2</sub> (<i>g</i><sub>m</sub>) and, consequently, photosynthesis, is reviewed. First, the theoretical properties of cell walls that can affect <i>g</i><sub>m</sub> are presented. Then, we focus on cell wall thickness (<i>T</i><sub>cw</sub>) reviewing empirical evidence showing that <i>T</i><sub>cw</sub> varies strongly among species and phylogenetic groups in a way that correlates with <i>g</i><sub>m</sub> and photosynthesis i.e. the thicker the mesophyll cell walls, the lower <i>g</i><sub>m</sub> and photosynthesis. Potential interplays of <i>g</i><sub>m</sub>, <i>T</i><sub>cw</sub>, dehydration tolerance and hydraulic properties of leaves are also discussed. Dynamic variations of <i>T</i><sub>cw</sub> in response to the environment and their implications in the regulation of photosynthesis are discussed, and recent evidence suggesting an influence of cell wall composition on <i>g</i><sub>m</sub> are presented. We then propose a hypothetical mechanism for the influence of cell walls on photosynthesis, combining the effects of thickness and composition, particularly pectins. Finally, we discuss the prospects for using biotechnology for enhancing photosynthesis by means of altering cell wall-related genes.</span></span></span></span></span></span></span></span></span></span></span></p>
Binding From both sides: TolR and full-length OmpA bind and maintain the local structure of the E. coli cell wall.
<p>We present a molecular modelling and simulation study of the <em>E. coli </em>cell envelope, with a particular focus on the role of TolR, a native protein of the <em>E. coli </em>inner membrane in interactions with the cell wall. TolR has been proposed to bind to peptidoglycan, but the only structure of this protein thus far is in a conformation in which the putative peptidoglycan binding domain is not accessible. We show that a model of the extended conformation of the protein in which this domain is exposed, binds peptidoglycan largely through electrostatic interactions. Non-covalent interactions of TolR and OmpA with the cell wall, from the inner membrane and outer membrane sides respectively, maintain the position of the cell wall even in the absence of Braun’s lipoprotein. The charged residues that mediate the cell-wall interactions of TolR in our simulations, are conserved across a number of species of Gram-negative bacteria.</p>
Data for "Coordination of bacterial cell wall and outer membrane biosynthesis"
<p>Raw data used in the paper "Coordination of bacterial cell wall and outer membrane biosynthesis" by Katherine R. Hummels, Samuel P. Berry, Zhaoqi Li, Atsushi Taguchi, Joseph K. Min, Suzanne Walker, Debora S. Marks, and Thomas G. Bernhardt. These data were collected with the aim of understanding how the lipopolysaccharide biosynthetic enzyme LpxC is regulated in diverse gram-negative bacteria, particularly Pseudomonas aeruginosa. The dataset contains the following tarred directories:</p> <p><em><strong>Experimental data</strong></em></p> <ul> <li>Microscopy (microscopy.tar.gz)</li> <li>LC-MS/MS (lc-ms_ms.tar.gz)</li> </ul> <p><strong><em>Covariation analysis</em></strong></p> <ul> <li>Multiple sequence alignments (alignments.tar.gz)</li> <li>AlphaFold structures (alphafold.tar.gz)</li> <li>EVcomplex models and couplings (evcomplex.tar.gz)</li> <li>Phylogenetic trees (trees.tar.gz)</li> </ul> <p>For more detailed methods and file descriptions, please see README.md. Associated code for analysis can be found at https://github.com/samberry19/evcomplex-interaction-scoring.</p>
Fig. 3 in The role of cell wall phenolics during the early remodelling of cellulosedeficient maize cells
Fig. 3. Representative HPLC-PAD elution profile of phenolic compounds after alkali hydrolysis of protoplasmic fraction from non-habituated (NH, A, C) and DCBhabituated (H, B, D) suspension-cultured cells corresponding at their early logarithmic (A, B) and late logarithmic (C, D) growth phase. Peaks were detected at 300 nm. 50 μl of sample was injected without dilution. Key to peak identity as Fig. 2.
Fig. 4 in The role of cell wall phenolics during the early remodelling of cellulosedeficient maize cells
Fig. 4. Structural models of the primary cell wall of non-habituated (A, B) and DCB-habituated (C, D) maize suspension-cultured cells at their early-logarithmic (A, C) and late-logarithmic (B, D) growth phases. The model shows the molecular interactions between cellulose, arabinoxylans and hydroxycinnamic acids (phenolic compounds). Based on Gómez and McQueen-Mason (2018). Dehydrodiferulates can also be ether-linked to lignin.
Fig. 2 in The role of cell wall phenolics during the early remodelling of cellulosedeficient maize cells
Fig. 2. Representative HPLC-PAD elution profile of phenolic compounds after alkali hydrolysis of cell walls from non-habituated (NH, A, C) and DCB-habituated (H, B, D) suspension-cultured cells corresponding at their early logarithmic (A, B) and late logarithmic (C, D) growth phase. Peaks were detected at 300 nm. 50 μl of sample was injected in a 1:10 dilution. Key to peak identity: 1, vanillin; 2, trans-p-coumaric acid; 3, trans-ferulic acid; 4, cis-p-coumaric acid; 5, cis-ferulic acid; 6, 5-5′- DFA; 7, 8-O-4′-DFA; 8, 8-5′-DFA.
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.