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504 results for “pores”
Data from: Cell migration through three-dimensional confining pores: speed accelerations by deformation and recoil of the nucleus
Directional cell migration in dense three-dimensional (3D) environments critically depends upon shape adaptation and is impeded depending on the size and rigidity of the nucleus. Accordingly, the nucleus is primarily understood as a physical obstacle, however, its pro-migratory functions by step-wise deformation and reshaping remain unclear. Using atomic force spectroscopy, time-lapse fluorescence microscopy and shape change analysis tools, we determined nuclear size, deformability, morphology and shape change of HT1080 fibrosarcoma cells expressing the Fucci cell cycle indicator or being pre-treated with chromatin-decondensating agent TSA. We show oscillating peak accelerations during migration through 3D collagen matrices and microdevices that occur during shape reversion of deformed nuclei (recoil), and increase with confinement. During G1 cell cycle phase, nucleus stiffness was increased and yielded further increased speed fluctuations together with sustained cell migration rates in confinement as compared to interphase populations, or to periods of intrinsic nuclear softening in the S/G2 cell cycle phase. Likewise, nuclear softening by pharmacological chromatin decondensation or after lamin A/C depletion reduced peak oscillations in confinement. In conclusion, deformation and recoil of the stiff nucleus contributes to saltatory locomotion in dense tissues.
Data from: Mouthpart conduit sizes of fluid-feeding insects determine the ability to feed from pores
Fluid-feeding insects, such as butterflies, moths and flies (20% of all animal species), are faced with the common selection pressure of having to remove and feed on trace amounts of fluids from porous surfaces. Insects able to acquire fluids that are confined to pores during drought conditions would have an adaptive advantage and increased fitness over other individuals. Here, we performed feeding trials using solutions with magnetic nanoparticles to show that butterflies and flies have mouthparts adapted to pull liquids from porous surfaces using capillary action as the governing principle. In addition, the ability to feed on the liquids collected from pores depends on a relationship between the diameter of the mouthpart conduits and substrate pore size diameter; insects with mouthpart conduit diameters larger than the pores cannot successfully feed, thus there is a limiting substrate pore size from which each species can acquire liquids for fluid uptake. Given that natural selection independently favoured mouthpart architectures that support these methods of fluid uptake (Diptera and Lepidoptera share a common ancestor 280 Ma that had chewing mouthparts), we suggest that the convergence of this mechanism advocates this as an optimal strategy for pulling trace amounts of fluids from porous surfaces.
Data from: Agonist-specific voltage-dependent gating of lysosomal Two-Pore Na + Channels
Mammalian Two-Pore-Channels (TPC1, 2; TPCN1, TPCN2) are ubiquitously-expressed cation channels in the endosomes and lysosomes that regulate luminal pH homeostasis, membrane trafficking, and Ebola viral infection. Lysosomal patch-clamp studies and high-resolution structural determinations have demonstrated that TPCs are Na+-selective channels activated by lysosome-localized PI(3,5)P2. Whereas the channel activity of TPC1 is strongly dependent on membrane voltage, TPC2 lacks such voltage dependence despite the presence of several positively-charged amino acid (AA) residues in the presumed "S4 voltage-sensing" domains. By performing a Ca2+-imaging-based high-throughput screening followed by lysosomal electrophysiology, here we identified a class of tri-cyclic anti-depressants (TCAs) as small-molecule agonists of TPC channels. TCAs activate both TPC1 and TPC2 in a voltage-dependent manner, so we refer to them as Lysosomal Na+ channel Voltage-dependent Activators (LyNa-VAs). We also identified another compound which, like PI(3,5)P2, activates TPC2 independent of voltage, suggesting the existence of agonist-specific gating mechanisms. Our identification of small-molecule TPC agonists should facilitate the studies of the cell biological roles of TPCs, and can also readily explain the reported effects of TCAs in the modulation of autophagy and lysosomal function.
Data from: Extensive reduction of the nuclear pore complex in nucleomorphs
The nuclear pore complex (NPC) is a large macromolecular assembly situated within the pores of the nuclear envelope. Through interactions between its subcomplexes and import proteins, the NPC mediates the transport of molecules into and out of the nucleus and facilitates dynamic chromatin regulation and gene expression. Accordingly, the NPC constitutes a highly integrated nuclear component that is ubiquitous and conserved amongst eukaryotes. Potential exceptions to this are nucleomorphs: highly reduced, relict nuclei that were derived from green and red algae following their endosymbiotic integration into two lineages, the chlorarachniophytes and the cryptophyceans. A previous investigation failed to identify NPC genes in nucleomorph genomes suggesting that these genes have either been relocated to the host nucleus or lost. Here we sought to investigate the composition of the NPC in nucleomorphs by using genomic and transcriptomic data to identify and phylogenetically classify NPC proteins in nucleomorph-containing algae. Although we found NPC proteins in all examined lineages, most of those found in chlorarachniophytes and cryptophyceans were single copy, host-related proteins that lacked signal peptides. Two exceptions were Nup98 and Rae1, which had clear nucleomorph-derived homologues. However, these proteins alone are likely insufficient to structure a canonical NPC and previous reports revealed that Nup98 and Rae1 have other nuclear functions. Ultimately, these data indicate that nucleomorphs represent eukaryotic nuclei without a canonical NPC, raising fundamental questions about their structure and function.
Data from: An ignored anatomical variable: pore shape shows a nonrandom variation pattern in xylem cross section
Anatomical characteristics of vessels have a profound impact on the hydraulic conductivity of the xylem. However, pore shape, the cross-section shape of a vessel, has been ignored in previous hydraulic architecture studies. In this study, we examined whether pore shape tended to be circular, and whether this variation tendency might be affected by water flow path-length and cambial age. The circularity pores in <i>Betula platyphylla</i> Roth and Quercus mongolica (only earlywood) were analyzed from the pith to the bark along the water flow path. It was found that although there were very few pores with absolutely circular shape, solitary pores did tend to be regularly circular. The pore shape of sequentially formed vessels in the xylem was influenced by cambial age and flow path-length. Pore shape tended to be more circular as flow path-length increased or cambial age decreased. Moreover, circular pore shape is an important morphogenetic mechanism for hydraulic architecture development, which can also expand the understanding of structure-function relationships for the xylem.
Data from: Ribosomal RNA gene repeats associate with the nuclear pore complex for maintenance after DNA damage
The ribosomal RNA genes (rDNA) comprise a highly repetitive gene cluster. The copy number of genes at this locus can readily change and is therefore one of the most unstable regions of the genome. DNA damage in rDNA occurs after binding of the replication fork blocking protein Fob1 in S phase, which triggers unequal sister chromatid recombination. However, the precise mechanisms by which such DNA double-strand breaks (DSBs) are repaired is not well understood. Here, we demonstrate that the conserved protein kinase Tel1 maintains rDNA stability after replication fork arrest. We show that rDNA associates with nuclear pores, which is dependent on DNA damage checkpoint kinases Mec1/Tel1 and replisome component Tof1. These findings suggest that rDNA-nuclear pore association is due to a replication fork block and subsequent DSB. Indeed, quantitative microscopy revealed that rDNA is relocated to the nuclear periphery upon induction of a DSB. Finally, rDNA stability was reduced in strains where this association with the nuclear envelope was prevented, which suggests its importance for avoiding improper recombination repair that could induce repeat instability.
Data from: Pore pressure evolution and mass loss of broken gangue during the seepage
Broken gangue consists of different particles, and it has more complicated seepage characteristics than intact rock sample. Using the self-designed instrument, the permeability, mass loss and pore pressure of crushed gangue during the seepage are tested. The result shows that: permeability parameter k of crushed rock has polynomial relationship with effective stress ' in inverse proportion, and permeability parameter β of crushed gangue has power exponent relationship with effective stress ' increasing in direct proportion. 8.0 – 10.0 mm particle size has a good support effect. Inner pressure of crushed rock is mostly linear distribution along the tube wall. After seepage,mass loss of broken gangue mainly increases with large particle size out of proportion.
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.
FIGURES 2 in Liolaemus carlosgarini and Liolaemus riodamas (Squamata: Liolaemidae), two new species of lizards lacking precloacal pores, from Andean areas of central Chile
FIGURES 2 to 4.—Different morphotypes of Liolaemus carlosgarini. Pictures: Carlos Garín.
FIGURE 6 in Liolaemus carlosgarini and Liolaemus riodamas (Squamata: Liolaemidae), two new species of lizards lacking precloacal pores, from Andean areas of central Chile
FIGURE 6.—Holotype of Liolaemus riodamas. MNHNCL-4684
FIGURES 7 in Liolaemus carlosgarini and Liolaemus riodamas (Squamata: Liolaemidae), two new species of lizards lacking precloacal pores, from Andean areas of central Chile
FIGURES 7 to 9.—Different morphotypes of Liolaemus riodamas. Pictures: Damien Esquerré
FIGURES 1–3. 1—Head lateral view. 2— Ostiolar pore lateral view. 3 in (Heteroptera: Tingidae) from Argentina
FIGURES 1–3. 1—Head lateral view. 2— Ostiolar pore lateral view. 3— General dorsal view.
Clogging and Unclogging of Fine Particles in Porous Media: Micromechanical Insights from an Analog Pore System
<p>Contain data for supporting and replicating the article results</p>
Supplementary Information for "Deciphering controls of pore-pressure evolution on sediment bed erosion by debris flows"
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Gas permeability through swelling porous media: Insights from coarse-grained pore-scale simulations
<p>CGMD data for gas transport in swelling porous media</p>
Data and SI movies of pore-scale CO2-brine interfacial mass transfer during imbibition
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Predicting pore structure and oil-bearing characteristics in saline-alkaline lacustrine shale strata via transfer learning
<p>玛湖凹陷凤城组样品的原始数据和吉木萨凹陷芦草沟组样品的原始数据</p>
Predicting pore structure and oil-bearing characteristics in saline-alkaline lacustrine shale strata via transfer learning
<p>玛湖凹陷凤城组和吉木萨尔凹陷芦草沟组样本的原始数据,以及核心 Python 代码。</p>
Dataset for "An approach for the pore-centred description of adsorption in hierarchical porous materials"
<p>Supporting dataset for: “An approach for the pore-centred description of adsorption in hierarchical porous materials”, J. D. Evans, <strong>2022</strong></p> <p><strong>Contains:</strong></p> <ul> <li>structures: Structural models used in YAFF .chk format.</li> <li>code: All the code used to generate the pore distributions, adsorption simulations and analysis.</li> <li>geometricporosity: Output from zeo++ used in this analysis.</li> <li>porestructure: Pore size distribution probes labeled by Pr, Nd, Pm.</li> <li>clustering: Metadata produced from the clustering analysis.</li> <li>porecenters: Locations of the pore centres combined with the </li> <li>structure in CIF format, where each pore is labeled by Pr, Nd, Pm.</li> <li>adsorption: Results of Ar simulation at 87K.</li> </ul>
Computational dataset, scripts and models for 'Lipid unsaturation promotes BAX and BAK pore activity during apoptosis'
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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