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Frontiers in Plant Science 2022Pore structure is a key determinant of soil functioning, and both root growth and activity of soil fauna are modified by and interact with pore structure in multiple...
Pore structure is a key determinant of soil functioning, and both root growth and activity of soil fauna are modified by and interact with pore structure in multiple ways. Cover cropping is a rapidly growing popular strategy for improving agricultural sustainability, including improvements in pore structure. However, since cover crop species encompass a variety of contrasting root architectures, they can have disparate effects on formation of soil pores and their characteristics, thus on the pore structure formation. Moreover, utilization of the existing pore systems and its modification by new root growth, in conjunction with soil fauna activity, can also vary by cover crop species, affecting the dynamics of biopores (creation and demolition). The objectives of this study were (i) to quantify the influence of 5 cover crop species on formation and size distribution of soil macropores (>36 μm Ø); (ii) to explore the changes in the originally developed pore architecture after an additional season of cover crop growth; and (iii) to assess the relative contributions of plant roots and soil fauna to fate and modifications of biopores. Intact soil cores were taken from 5 to 10 cm depth after one season of cover crop growth, followed by X-ray computed micro-tomography (CT) characterization, and then, the cores were reburied for a second root growing period of cover crops to explore subsequent changes in pore characteristics with the second CT scanning. Our data suggest that interactions of soil fauna and roots with pore structure changed over time. While in the first season, large biopores were created at the expense of small pores, in the second year these biopores were reused or destroyed by the creation of new ones through earthworm activities and large root growth. In addition, the creation of large biopores (>0.5 mm) increased total macroporosity. During the second root growing period, these large sized macropores, however, are reduced in size again through the action of soil fauna smaller than earthworms, suggesting a highly dynamic equilibrium. Different effects of cover crops on pore structure mainly arise from their differences in root volume, mean diameter as well as their reuse of existing macropores.
PubMed: 36160999
DOI: 10.3389/fpls.2022.928569 -
Molecules (Basel, Switzerland) Oct 2018A group of stable, water-soluble and membrane-bound proteins constitute the pore forming toxins (PFTs) in cnidarians. They interact with membranes to physically alter... (Review)
Review
A group of stable, water-soluble and membrane-bound proteins constitute the pore forming toxins (PFTs) in cnidarians. They interact with membranes to physically alter the membrane structure and permeability, resulting in the formation of pores. These lesions on the plasma membrane causes an imbalance of cellular ionic gradients, resulting in swelling of the cell and eventually its rupture. Of all cnidarian PFTs, actinoporins are by far the best studied subgroup with established knowledge of their molecular structure and their mode of pore-forming action. However, the current view of necrotic action by actinoporins may not be the only mechanism that induces cell death since there is increasing evidence showing that pore-forming toxins can induce either necrosis or apoptosis in a cell-type, receptor and dose-dependent manner. In this review, we focus on the response of the cellular immune system to the cnidarian pore-forming toxins and the signaling pathways that might be involved in these cellular responses. Since PFTs represent potential candidates for targeted toxin therapy for the treatment of numerous cancers, we also address the challenge to overcoming the immunogenicity of these toxins when used as therapeutics.
Topics: Animals; Apoptosis; Cell Membrane; Cnidaria; Humans; Immunity, Innate; Necrosis; Pore Forming Cytotoxic Proteins; Signal Transduction; Toxins, Biological
PubMed: 30287801
DOI: 10.3390/molecules23102537 -
Materials (Basel, Switzerland) Mar 2021This paper aims to develop frost-resistant concretes, and investigate their pore structures and freeze-thaw damage mechanism. The frost-resistant concrete mixtures are...
This paper aims to develop frost-resistant concretes, and investigate their pore structures and freeze-thaw damage mechanism. The frost-resistant concrete mixtures are designed by using rubber particles and nano-SiO to partially replace sands. The chord lengths, specific surface areas, contents and spacing coefficients of the pores in the designed concretes are measured and analyzed. The results show that concrete mixture incorporated with 5% silanized rubber and 3% nanosilica shows good synergetic effect by considering both mass loss and relative dynamic modulus of elasticity (RDME). The freeze-thaw damage degree of the concrete could be reduced by adding high elastic rubber particles, due to filling and constraining pores, and resulting in better uniform pore distribution and smaller pore spacing coefficient. Furthermore, the correlations between frost resistance and pore are analyzed and proposed.
PubMed: 33801516
DOI: 10.3390/ma14051170 -
Autophagy Oct 2020Selective autophagy is critical for the regulation of cellular homeostasis in organisms from yeast to humans. This process is a specific degradation pathway for a wide...
UNLABELLED
Selective autophagy is critical for the regulation of cellular homeostasis in organisms from yeast to humans. This process is a specific degradation pathway for a wide variety of substrates including unwanted cytosolic components, such as protein aggregates, damaged and/or superfluous organelles, and pathogens. However, it has been less clear as to whether a protein complex or substructure of an organelle can be targeted for removal by selective autophagy. One example of such a substrate is the nuclear pore complex (NPC), a large macromolecular assembly that is present throughout the nuclear envelope. Here, we highlight two recent studies that demonstrate for the first time that NPCs are targeted for vacuolar degradation through selective autophagy.
ABBREVIATIONS
AIM: Atg8-interacting motif; NE: nuclear envelope; NPC: nuclear pore complex; Nup: nucleoporin; PMN/micronucleophagy: piecemeal microautophagy of the nucleus.
Topics: Autophagy; Cell Nucleus; Cytosol; Macroautophagy; Nuclear Envelope; Nuclear Pore; Nuclear Pore Complex Proteins; Organelles; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins; Vacuoles
PubMed: 32713250
DOI: 10.1080/15548627.2020.1798199 -
ACS Omega Nov 2021When hydraulic fracturing is utilized to eliminate coal and gas outbursts and rockburst in dynamic disaster coal-rock formations, the stress disturbance of hydraulic...
When hydraulic fracturing is utilized to eliminate coal and gas outbursts and rockburst in dynamic disaster coal-rock formations, the stress disturbance of hydraulic fracturing may have negative effects such as causing local stress concentration. The method of combining physical model experiments and numerical simulations is adopted to study the distribution relationship of pore pressure and matrix stress during hydraulic fracturing. The research results show that the pore pressure and matrix stress gradually attenuate farther away from the hydraulic fracture in the process of hydraulic fracturing. The attenuation rate of matrix stress is less than that of pore pressure. The range of the matrix stress disturbance zone is larger than the range of the pore pressure disturbance zone. With the increase of pumping time, the increasing speed of the matrix stress disturbance zone is greater than that of the pore pressure disturbance zone. This indicates that the squeezing force on both sides of the hydraulic fracture increases correspondingly with the increase in crack opening, which causes the range and magnitude of the matrix stress disturbance zone to increase gradually. The stress disturbance zone around the hydraulic fracture includes the pore pressure disturbance zone and the matrix stress disturbance zone. In the pore pressure disturbance zone, the pore pressure and the matrix stress increase and interact at the same time, which together lead to the deformation and failure of coal and rock mass. The relationship between the pore pressure and the matrix stress in this region conforms to the natural logarithmic attenuation relationship. Outside the pore pressure disturbance zone, the deformation and failure of coal and rock mass are mainly caused by the matrix stress effect.
PubMed: 34805686
DOI: 10.1021/acsomega.1c04268 -
Bioactive Materials Jul 2022The scaffold pore size influences many critical physical aspects of tissue engineering, including tissue infiltration, biodegradation rate, and mechanical properties....
The scaffold pore size influences many critical physical aspects of tissue engineering, including tissue infiltration, biodegradation rate, and mechanical properties. Manual measurements of pore sizes from scanning electron micrographs using ImageJ/FIJI are commonly used to characterize scaffolds, but these methods are both time-consuming and subject to user bias. Current semi-automated analysis tools are limited by a lack of accessibility or limited sample size in their verification process. The work here describes the development of a new MATLAB algorithm, PoreScript, to address these limitations. The algorithm was verified using three common scaffold fabrication methods (e.g., salt leaching, gas foaming, emulsion templating) with varying pore sizes and shapes to demonstrate the versatility of this new tool. Our results demonstrate that the pore size characterization using PoreScript is comparable to manual pore size measurements. The PoreScript algorithm was further evaluated to determine the effect of user-input and image parameters (relative image magnification, pixel intensity threshold, and pore structure). Overall, this work validates the accuracy of the PoreScript algorithm across several fabrication methods and provides user-guidance for semi-automated image analysis and increased throughput of scaffold characterization.
PubMed: 35224287
DOI: 10.1016/j.bioactmat.2021.11.006 -
Journal of Colloid and Interface Science Mar 2022Imbibition of a fluid into a porous material involves the invasion of a wetting fluid in the pore space through piston-like displacement, film and corner flow, snap-off...
HYPOTHESIS
Imbibition of a fluid into a porous material involves the invasion of a wetting fluid in the pore space through piston-like displacement, film and corner flow, snap-off and pore bypassing. These processes have been studied extensively in two-dimensional (2D) porous systems; however, their relevance to three-dimensional (3D) natural porous media is poorly understood. Here, we investigate these pore-scale processes in a natural rock sample using time-resolved 3D (i.e., four-dimensional or 4D) X-ray imaging.
EXPERIMENTS
We performed a capillary-controlled drainage-imbibition experiment on an initially brine-saturated carbonate rock sample. The sample was imaged continuously during imbibition using 4D X-ray imaging to visualize and analyze fluid displacement and snap-off processes at the pore-scale.
FINDINGS
We discover a new type of snap-off that occurs in pores, resulting in the entrapment of a small portion of the non-wetting phase in pore corners. This contrasts with previously-observed snap-off in throats which traps the non-wetting phase in pore centers. We relate the new type of pore-snap-off to the pinning of fluid-fluid interfaces at rough surfaces, creating contact angles close to 90°. Subsequently, we provide correlations for displacement events as a function of pore-throat geometry. Our findings indicate that having a small throat does not necessarily favor snap-off: the key criterion is the throat radius in relation to the pore radius involved in a displacement event, captured by the aspect ratio.
PubMed: 34902675
DOI: 10.1016/j.jcis.2021.11.109 -
Materials Today. Bio Jun 2023The pore morphology design of bioceramic scaffolds plays a substantial role in the induction of bone regeneration. Specifically, the effects of different scaffold pore...
The pore morphology design of bioceramic scaffolds plays a substantial role in the induction of bone regeneration. Specifically, the effects of different scaffold pore geometry designs on angiogenesis and new bone regeneration remain unclear. Therefore, we fabricated Mg/Sr co-doped wollastonite bioceramic (MS-CSi) scaffolds with three different pore geometries (gyroid, cylindrical, and cubic) and compared their effects on osteogenesis and angiogenesis and . The MS-CSi scaffolds were fabricated by digital light processing (DLP) printing technology. The pore structure, mechanical properties, and degradation rate of the scaffolds were investigated. Cell proliferation on the scaffolds was evaluated using CCK-8 assays while angiogenesis was assessed using Transwell migration assays, tube formation assays, and immunofluorescence staining. The underlying mechanism was explored by western blotting. Osteogenic ability of scaffolds was evaluated by alkaline phosphatase (ALP) staining, western blotting, and qRT-PCR. Subsequently, a rabbit femoral defect model was prepared to compare differences in the scaffolds in osteogenesis and angiogenesis . Cell culture experiments showed that the gyroid pore scaffold downregulated YAP/TAZ phosphorylation and enhanced YAP/TAZ nuclear translocation, thereby promoting proliferation, migration, tube formation, and high expression of CD31 in human umbilical vein endothelial cells (HUVECs) while strut-based (cubic and cylindrical pore) scaffolds promoted osteogenic differentiation in bone marrow mesenchymal stem cells and upregulation of osteogenesis-related genes. The gyroid pore scaffolds were observed to facilitate early angiogenesis in the femoral-defect model rabbits while the strut-based scaffolds promoted the formation of new bone tissue. Our study indicated that the pore geometries and pore curvature characteristics of bioceramic scaffolds can be precisely tuned for enhancing both osteogenesis and angiogenesis. These results may provide new ideas for the design of bioceramic scaffolds for bone regeneration.
PubMed: 37273795
DOI: 10.1016/j.mtbio.2023.100667 -
Current Protocols Sep 2022There is a significant current question regarding the viable copy numbers of nucleoporins required for the function of the nuclear pore complex (NPC) in eukaryotic...
There is a significant current question regarding the viable copy numbers of nucleoporins required for the function of the nuclear pore complex (NPC) in eukaryotic cells. The NPC consists of approximately 30 different nucleoporins in an eight-fold symmetry, meaning that there are multiple duplicates of each nucleoporin present within the nuclear pore. We recently developed a method that combines auxin-inducible degrons and single-molecule super-resolution microscopy to evaluate the copy number of nuclear basket nucleoporins required for the successful function of the NPC. Here, we describe the theory behind this auxin-inducible degron and single-molecule super-resolution microscopy method, and we detail a step-by-step process to selectively degrade nucleoporins either completely or in a stepwise manner. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Degradation of target nucleoporins Basic Protocol 2: Quantification of nucleoporin copy number via narrow-field fluorescence microscopy.
Topics: Cell Nucleus; Indoleacetic Acids; Nuclear Pore; Nuclear Pore Complex Proteins; Single Molecule Imaging
PubMed: 36063146
DOI: 10.1002/cpz1.520 -
Nucleus (Austin, Tex.) 2013Previous experience alters the rate of transcriptional induction of many genes in yeast and this phenomenon persists through several cell division cycles. This... (Review)
Review
Previous experience alters the rate of transcriptional induction of many genes in yeast and this phenomenon persists through several cell division cycles. This phenomenon is called epigenetic transcriptional memory. For the yeast gene INO1, transcriptional memory requires a physical interaction with the nuclear pore complex (NPC) and changes in the chromatin structure of the promoter. These changes lead to binding of a preinitiation form of RNA Polymerase II (RNAPII) to the INO1 promoter, bypassing the need to recruit RNAPII to the promoter during reactivation. In our recent study, we found that in human cells, hundreds of interferon-γ responsive genes exhibit a mechanistically similar form of transcriptional memory. Transcriptional memory requires a homologous nuclear pore protein in yeast and humans, which interacts with the promoters of genes that exhibit transcriptional memory and promotes both alteration of chromatin structure and binding of RNAPII. Whereas the interaction of yeast genes with nuclear pore proteins occurs at the NPC, the interaction of human genes with nuclear pore proteins occurs in the nucleoplasm. Thus, the interaction of nuclear pore proteins with genes plays an important and conserved role in affecting long-term epigenetic changes in transcriptional regulation.
Topics: Chromatin; Humans; Nuclear Pore; Nuclear Pore Complex Proteins; RNA Polymerase II; Transcription, Genetic
PubMed: 23962805
DOI: 10.4161/nucl.26209