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45 results for “biomineralization”
Data for "Microstructural mapping of A. islandica shells reveals environmental and physiological controls on biomineral size"
<p>This data contains the image segmentation workflow, data processing procedure and all data generated for the publication "Microstructural mapping of A. islandica shells reveals environmental and physiological controls on biomineral size" currently under review.</p>
Supplementary data for calcium-vesicles perform active diffusion in the sea urchin embryo during larval biomineralization
<p><strong>Supplementary datasets for the paper Calcium-vesicles perform active diffusion in the sea urchin embryo during larval biomineralization.</strong></p> <p>Two deskewed and deconvolved lattice light-sheet datasets (100 frames each) from the live-cell experiments are available, a control embryo dataset (01-07-2016_TimeLapse4_DMSO_21hrs_Calcein_FM464) and a VEGFR inhibited dataset (24-06-2016_Timelapse1_Axtinib_150_19hrs_Calcein_FM464). These datasets were used for collecting size and motion statistics. The control embryo dataset is available in raw microscope output without deskew or deconvolution applied (Raw_01-07-2016_TimeLapse4_DMSO_21hrs_Calcein_FM464).</p> <p>Four confocal datasets from the cytoskeletal remodeling experiments are also included, phalloidin stained images, control (Phalloidin PMC DMSO 5 zoom4s) and VEGFR inhibited (Phalloidin PMC Axt 18 zoom4); and myosinIIP stained images, control (Myosin PMC 30h DMSO new slid 4a zoom4) and VEGFR inhibited (Phalloidin PMC Axt 18 zoom4).</p> <p>Source code and instructions for the analysis tools used for both the lattice light-sheet and confocal data is available at: <a href="https://git-bioimage.coe.drexel.edu/opensource/llsm-calcium-vesicles-lever">https://git-bioimage.coe.drexel.edu/opensource/llsm-calcium-vesicles-lever</a></p> <p>Code for the deconvolution and deskew algorithms is available from the Janelia research center at: <a href="https://www.janelia.org/open-science/lattice-light-deconvolution-software-cudadeconv">https://www.janelia.org/open-science/lattice-light-deconvolution-software-cudadeconv</a></p> <p> </p> <p> </p>
Fig. 11 in A new polyphysacean alga from the Miocene of Romania and its biomineralization
Fig. 11. Scheme of intracellular mineralization in polyphysaceans (gametophores are sketched in cross section). A. Gametangia and intergametangial space not mineralized. B. Gametangia unmineralized, intergametangial space mineralized. C. Gametangia mineralized, intergametangial space not mineralized. D. Gametangia and intergametangial space mineralized.
Fig. 5 in A new polyphysacean alga from the Miocene of Romania and its biomineralization
Fig. 5. Polyphysacean alga Acetabularia moldavica sp. nov. early Sarmatian, Pătrăuți (Suceava County, Romania). A. Paratype, MP-UAIC 8228/PD.1/10, → fertile cap in lower view (A1) and detail (lower side) of fertile rays (A2). B. Paratype, MP-UAIC 8228/PD.3/8, fertile cap in upper view with an extracellular mineralized thin layer preserved (lower side). C. Paratype, MP-UAIC 8228/PD.1/3, detail of the fertile cap showing the upper coronae (see also Fig. 4G). D. Holotype, MP-UAIC 8228/PD.1/6, detail of the fertile cap showing lower coronae, notice the extracellular mineralization preserved between spicules (see also Fig. 4F). E. Paratype, MP-UAIC 8228/PD.1/12, detail of a fertile cap in upper view showing the upper coronae and aggregates of compacted mineralized cysts. F. Paratype, MP-UAIC 8228/PD.2/14, detail of two spicules with broken cysts.
Fig. 4 in A new polyphysacean alga from the Miocene of Romania and its biomineralization
Fig. 4. Polyphysacean alga Acetabularia moldavica sp. nov. (A–H) and Patruliuspora sp. (I), early Sarmatian, Pătrăuți (Suceava County, Romania). → A. Paratype, MP-UAIC 8228/PD.1/15, fertile cap in upper view. B. Paratype, MP-UAIC 8228/PD.2/17, fertile cap in lower view. C. Paratype, MPUAIC 8228/PD.1/1, fertile cap in lower view. D. Paratype, MP-UAIC 8228/PD.2/25, fertile cap in upper view. E. Paratype, MP-UAIC 8228/PD.1/16, fertile cap in lower view. F. Holotype, MP-UAIC 8228/PD.1/6, fertile cap in lower view. G. Paratype, MP-UAIC 8228/PD.1/3, fertile cap in upper view. H. Paratype, MP-UAIC 8228/PD.2/21, an isolated spicule in the matrix. I. Group of five cysts in the matrix, MP-UAIC 8228/PD.3/22.
Dataset for Additive Manufacturing of Porous Biominerals
<p>This dataset contains results of rheology, SEM, polarized microscopic and X-ray tomography pictures,XRD results and mechanical testing. There are also results of EDX mapping and 2D scanning synchrotron XRD maps.</p>
Geology constrains biomineralization expression and functional trait distribution in the Mountainsnails (Oreohelix)
<p><strong>Aim</strong>: Geographic variation in metabolic resources necessary for functional trait expression can set limits on species distributions. For species that need to produce and maintain biomineralized traits for survival, spatial variation in mineral macronutrients may constrain species' distributions by limiting the expression of biomineralized traits. Here, we examine whether threatened, heavily biomineralized <em>Oreohelix</em> land snails are restricted to CaCO<sub>3</sub> rock regions, if they incorporate greater amounts of CaCO<sub>3</sub> rock carbon in their shell than less biomineralized smooth forms, and if ornamentation increases shell strength.</p> <p><strong>Location</strong>: Western United States</p> <p><strong>Methods</strong>: We used random forest (RF) classification models at multiple spatial resolutions to evaluate the contribution of topographic, vegetation, climate, and geologic variables in predicting the presence of heavily biomineralized shell ornaments. We then measured and compared shell biometric variables, <sup>14</sup>C/<sup>12</sup>C ratios, and peak force for fracture for ornamented and smooth forms from calcareous and non-calcareous substrates.</p> <p><strong>Results</strong>: Distance to CaCO<sub>3</sub> rock was the most important variable in all trait distribution models and was highly associated with local ornamentation classification and forecasted distribution. Pairwise comparisons of <sup>14</sup>C/<sup>12</sup>C ratios in closely occurring ornamented vs. smooth population pairs revealed ornamented forms incorporate greater CaCO<sub>3</sub> rock carbon than smooth forms. Ornamented types measured in this study were generally heavier and required greater peak force for fracture than smooth snails, except when compared to smooth forms sampled from CaCO<sub>3</sub> rock.</p> <p><strong>Main</strong> <strong>conclusions</strong>: Biomineralization expression, species distribution, and trait function appear to be constrained by mineral supply in a highly diverse group of land snails. This trait-environment relationship suggests similar CaCO<sub>3</sub> macronutrient constraints may modulate biomineralization expression and restrict species distribution in other terrestrial molluscs and has a direct impact on the management of <em>Oreohelix</em> species.</p>
Geology constrains biomineralization expression and functional trait distribution in the Mountainsnails (Oreohelix)
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Data, Figures and Codes for "Experimental analyses of pore-size dependent biomineralization in porous media under various flow rate and bacterial density scenarios"
<pre>This repository contains the data, codes and figures for the manuscript <br>"Experimental analyses of pore-size-dependent biomineralization in porous media under various flow rate and bacterial density scenarios". <br><br>Comments welcome. </pre>
Viruses participate in biomineralization of travertines
<p>Fasta files with contigs based on raw sequences. </p> <p>Sample codes:<br> E12 - Egerszalók<br> PAM-TR1 - Pamukkale<br> KAR-TR3 - Karahayit<br> SA-01 - Terme di Saturnia<br> Met3B - Bath<br> B221 - Bešeňová<br> Bul-IT6 - Bullicame<br> As-IT5 - Asitello</p>
Data for: Periplasmic biomineralization for semi-artificial photosynthesis
<p><span>Semiconductor-based biointerfaces are typically established either on the surface of the plasma membrane or within the cytoplasm. In gram-negative bacteria, the periplasmic space, characterized by its confinement and the presence of numerous enzymes and peptidoglycans, offers additional opportunities for biomineralization, allowing for non-genetic modulation interfaces. Here, we demonstrate semiconductor nanocluster precipitation containing single- and multiple-metal elements within the periplasm, as observed through various electron- and X-ray-based imaging techniques. The periplasmic semiconductors are metastable and display defect-dominant fluorescent properties. Surprisingly, the defect-rich (i.e., the low-grade) semiconductor nanoclusters produced in situ can still increase adenosine triphosphate levels and malate production when coupled with photosensitization. We expand the sustainability levels of the biohybrid system to include reducing heavy metals at the primary level, building living bioreactors at the secondary level, and creating semi-artificial photosynthesis at the tertiary level. The biomineralization-enabled periplasmic biohybrids have the potential to serve as defect-tolerant platforms for diverse sustainable applications.</span></p>
Data for: Periplasmic biomineralization for semi-artificial photosynthesis
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Data from: Biogenic origin of secondary eggshell units in dinosaur eggshells elucidates lost biomineralization process in maniraptoran dinosaurs
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Data from: The relationship between microbial community succession, decay, and anatomical character loss in non-biomineralized animals
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Data from: The earliest known fungal-induced biomineralization in fossil bones, and its role in the marine ecosystem
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Ptychographic X-ray spackle tracking (PXST) scan of the biomineralized shell of a marine planktonic diatom
<p>The PXST scan of the biomineralized shell of a marine planktonic diatom sample measured at P11 beamtime of the PETRA III synchrotron radiation facility. The beam was focused with a pair of MLLs with focal lengths of 1.25 mm and 1.15 mm and numerical apertures of 0.014 and 0.015, in the vertical and horizontal directions, respectively. The X-ray beam photon energy was 17.5 keV.</p>
Data from: Differences in the regulation of growth and biomineralization genes revealed through long-term common garden acclimation and experimental genomics in the purple sea urchin
Across heterogeneous landscapes, populations may have adaptive differences in gene regulation that adjust their physiologies to match local environments. Such differences could have origins in acclimation or in genetically fixed variation between habitats. Here we use common garden experiments to evaluate differences in gene expression between populations of the purple sea urchin, Strongylocentrotus purpuratus, spanning 1700 km and average temperature differences of 5 °C to 8 °C. Across expression profiles from 18,883 genes after three years of common conditions, we find highly correlated expression patterns (Pearson's r = 0.992) among most genes. However, sixty-six genes were differentially expressed, including many ribosomal protein and biomineralization genes, all of which had higher expression in urchins originally from the southern population. Gene function analyses revealed slight but pervasive expression differences in genes related to ribosomal function, metabolism, transport, "bone" development, and response to stimuli. In accord with gene expression patterns, a post-hoc spine re-growth experiment revealed that urchins of southern origin re-grew spines at a faster rate than northern urchins. These results suggest that there may be genetically controlled, potentially adaptive differences in gene regulation across habitats and that gene expression differences may be under strong enough selection to overcome high dispersal-mediated gene flow in this marine species.
The shellome of the crocus clam Tridacna crocea emphasizes essential components of mollusc shell biomineralization
<p class="FirstParagraph">Molluscan shells are among the most fascinating research objects because of their diverse morphologies and textures. The formation of these delicate biomineralized structures is a matrix-mediated process. A question that arises is what are the essential components required to build these exoskeletons. In order to understand the molecular mechanisms of molluscan shell formation, it is crucial to identify organic macromolecules in different shells from diverse taxa. In the case of bivalves, however, taxon sampling in previous shell proteomics studies are biased and focus exclusively on representatives of the class Pteriomorphia such as pearl oysters, edible oysters and mussels. In this study, we have characterized the shell organic matrix from the crocus clam, <i>Tridacna crocea</i>, (Heterodonta) using various biochemical techniques, including SDS-PAGE, FT-IR, monosaccharide analysis, and enzyme-linked lectin assay (ELLA). Furthermore, we have identified a number of shell matrix proteins (SMPs) using a comprehensive proteomics approach combined to RNA-seq. The biochemical studies confirmed the presence of proteins, polysaccharides, and sulphates in the <i>T. crocea</i> shell organic matrix. Proteomics analysis revealed that the majority of the <i>T. crocea</i> SMPs are novel and dissimilar to known SMPs identified from the other bivalve species. Meanwhile, the SMP repertoire of the crocus clam also includes proteins with conserved functional domains such as chitin-binding domain, VWA domain, and protease inhibitor domain. We also identified BMSP (Blue Mussel Shell Protein, originally reported from <i>Mytilus</i>), which is widely distributed among molluscan shell matrix proteins. <i>Tridacna</i> SMPs also include low-complexity regions or LCRs that are absent in the other molluscan genomes, indicating that these genes may have evolved in specific lineage. These results highlight the diversity of the organic molecules - in particular proteins - that are essential for molluscan shell formation.</p>
Data in support of: Biomineralization of plastic waste to improve the strength of plastic-reinforced cement mortar
<p></p><p>The development of methods to reuse large volumes of plastic waste is essential to curb the environmental impact of plastic pollution. Plastic-reinforced cementitious materials (PRCs), such as plastic-reinforced mortar (PRM), may be potential avenues to productively use large quantities of low-value plastic waste. However, poor bonding between the plastic and cement matrix reduces the strength of PRCs, limiting its viable applications. In this study, calcium carbonate biomineralization techniques were applied to coat plastic waste and improved the compressive strength of PRM. Two biomineralization treatments were examined: enzymatically induced calcium carbonate precipitation (EICP) and microbially induced calcium carbonate precipitation (MICP). MICP treatment of polyethylene terephthalate (PET) resulted in PRMs with compressive strengths similar to that of plastic-free mortar and higher than the compressive strengths of PRMs with untreated or EICP-treated PET. Based on the results of this study, MICP was used to treat hard-to-recycle types 3–7 plastic waste. No plastics investigated in this study inhibited the MICP process. PRM samples with 5% MICP-treated polyvinyl chloride (PVC) and mixed type 3–7 plastic had compressive strengths similar to plastic-free mortar. These results indicate that MICP treatment can improve PRM strength and that MICP-treated PRM shows promise as a method to reuse plastic waste.</p><p></p>
Dataset for Disordered dolomite as an unusual biomineralization product found in the center of a natural Cassis pearl
<p>Natural pearls are produced without human intervention, mainly due to various irritations from the surrounding environment to their mantle tissues. Pearls usually possess similar mineral compositions to the host shells, which means they are also dominated by aragonite and calcite. In this study, we report a natural pearl from a <em>Cassis</em> species mollusk containing granular central structures. Raman spectroscopy, laser ablation inductively coupled plasma mass spectrometry (LA-ICPMS), energy dispersive X-ray spectroscopy (EDS) coupled with scanning electron microscope (SEM), and X-ray diffraction (XRD) analyses were carried out in order to characterize the mineral composition in the center region of this pearl. Our results showed that this pearl's center was made of mostly disordered dolomite (Ca<sub>0.53</sub>Mg<sub>0.47</sub>CO<sub>3</sub>) mixing with small amount of aragonite and high magnesium-calcite. To the best of our knowledge, this is the first time disordered dolomite was conclusively identified inside of a natural pearl and such information expanded our knowledge on internal growth structures and formation of natural pearls.</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)
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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.