Central Pore Research Articles

High Thermopower of Agarose‐Based Ionic Thermoelectric Gel Through Micellization Effect Decoupling the Cation/Anion Thermodiffusion

AbstractIonic thermoelectric (i‐TE) gels can have a high thermopower, if the thermodiffusion of mobile cation/anion is decoupled, attracting increasing attentions. Herein, it is shown a high p‐type i‐TE thermopower of 41.8 mV K−1 in agarose‐based ionic thermoelectric gels of AG‐x Na:DBS (AG: agarose, Na:DBS: sodium dodecyl benzene sulfonate). The exclusively high thermopower is relative to the successfully decoupling the thermodiffusion of cation Na+ and anion DBS−. A unique porous structure is formed due to the micellization of the amphiphilic DBS− with the hydrophilic benzenesulfonic group attached to the hydrous agarose gel chains, while the hydrophobic alkyl chain point to the pore centers. As a result, the DBS− micelles are almost immobile as compared with Na+, which can be reconsidered as a part of the gel matrix. The work shines a light on decoupling of cation/anion thermodiffusion through tailoring the microstructure of the quasi‐solid i‐TE materials.

Taxonomic significance of pollen morphology of selected taxa of Bassia, Sedobassia, Spirobassia and Neokochia (Chenopodiaceae/Amaranthaceae sensu APG IV)

ABSTRACT Based on molecular phylogenetic and morphological studies, new genera Sedobassia Freitag & G. Kadereit and Spirobassia Freitag & G. Kadereit were described in the tribe Camphorosmeae (Chenopodiaceae/Amaranthaceae sensu APG IV). Palynomorphological peculiarities are often used in taxonomy as additional diagnostic features. Pollen grains from 26 herbarium specimens belonging to 13 taxa of Bassia, Sedobassia, Spirobassia and Neokochia genera in Eurasia and North America were acetolyzed and studied using both light microscopy and scanning electron microscopy. Dry pollen grains were also studied. The structure of columellae of pollen grains was analyzed for the first time in the current study. The aim of this research was to provide data on their pollen characteristics and to evaluate the taxonomic value of these data for generic and species-specific identification. Pollen grains are pantoporate, spheroidal in shape, circular in outline, slightly undulate, undulate or straight on the edges; medium or small-sized. Pores are circular, with distinct or indistinct margins. Exine sculpture is nanoechinate; tectum psilate or psilate-perforate. Pore membranes with nanoechini. Taxonomic relevance of the most important characters of pollen grains is discussed (pollen diameter, pore number, pore diameter, distance between pores and between pore centers, C/D value, nanoechini density, presenсe/absence of perforations, structure of columellae, number of nanoechini on pore membranes). Pollen morphology proved to be an important additional source of information for species-specific identification. This study provides new data and analyzes the morphological features of pollen grains of Bassia (in the currently accepted circumscription), palynomorphological similarities, and differences between the taxa of Bassia, Sedobassia, Spirobassia, and Neokochia genera.

Bioceramic scaffolds with triply periodic minimal surface architectures guide early-stage bone regeneration.

The pore architecture of porous scaffolds is a critical factor in osteogenesis, but it is a challenge to precisely configure strut-based scaffolds because of the inevitable filament corner and pore geometry deformation. This study provides a pore architecture tailoring strategy in which a series of Mg-doped wollastonite scaffolds with fully interconnected pore networks and curved pore architectures called triply periodic minimal surfaces (TPMS), which are similar to cancellous bone, are fabricated by a digital light processing technique. The sheet-TPMS pore geometries (s-Diamond, s-Gyroid) contribute to a 3‒4-fold higher initial compressive strength and 20%-40% faster Mg-ion-release rate compared to the other-TPMS scaffolds, including Diamond, Gyroid, and the Schoen's I-graph-Wrapped Package (IWP) in vitro. However, we found that Gyroid and Diamond pore scaffolds can significantly induce osteogenic differentiation of bone marrow mesenchymal stem cells (BMSCs). Analyses of rabbit experiments in vivo show that the regeneration of bone tissue in the sheet-TPMS pore geometry is delayed; on the other hand, Diamond and Gyroid pore scaffolds show notable neo-bone tissue in the center pore regions during the early stages (3-5 weeks) and the bone tissue uniformly fills the whole porous network after 7 weeks. Collectively, the design methods in this study provide an important perspective for optimizing the pore architecture design of bioceramic scaffolds to accelerate the rate of osteogenesis and promote the clinical translation of bioceramic scaffolds in the repair of bone defects.

Monolayer fullerene network: A promising material for VOCs sensor

Carbon materials hold a great promise for gas sensors due to their diversified dimensionality, tunable structures and easy doping functionalization. Two dimensional polymeric fullerene (2DC60), which was experimentally synthesized recently (Hou et al. Nature 2022, 606, 507), offers a new candidate for gas sensors due to its moderate bandgap and high carrier mobility. Remarkably, the challenging aggregation and restacking issue of conventional 2D materials can be avoided for 2DC60 because of its unique topological structure. In this work, we deliver the first attempt to study the volatile organic compounds (VOCs) sensing capability of 2DC60 by density functional theory (DFT) calculations. Compared with pure C60 nanoclusters, 2DC60 exhibits stronger gas sensing due to formed pore center between C60 nanocages. The quasi-hexagonal 2DC60 (qHP 2DC60) possesses relatively high acetone selectivity while quasi-tetragonal 2DC60 (qTP 2DC60) possesses relatively high ethanol selectivity. B-doping for qHP 2DC60 can significantly facilitate electron transfer and sharply enhance its acetone selectivity. Our theoretical results suggest that 2DC60 is a promising candidate for VOCs sensors, which offers a fresh perspective and opportunity on the application of novel 2DC6.

Chromogranin B (CHGB) is dimorphic and responsible for dominant anion channels delivered to cell surface via regulated secretion.

Regulated secretion is conserved in all eukaryotes. In vertebrates granin family proteins function in all key steps of regulated secretion. Phase separation and amyloid-based storage of proteins and small molecules in secretory granules require ion homeostasis to maintain their steady states, and thus need ion conductances in granule membranes. But granular ion channels are still elusive. Here we show that granule exocytosis in neuroendocrine cells delivers to cell surface dominant anion channels, to which chromogranin B (CHGB) is critical. Biochemical fractionation shows that native CHGB distributes nearly equally in soluble and membrane-bound forms, and both reconstitute highly selective anion channels in membrane. Confocal imaging resolves granular membrane components including proton pumps and CHGB in puncta on the cell surface after stimulated exocytosis. High pressure freezing immuno-EM reveals a major fraction of CHGB at granule membranes in rat pancreatic β-cells. A cryo-EM structure of bCHGB dimer of a nominal 3.5 Å resolution delineates a central pore with end openings, physically sufficient for membrane-spanning and large single channel conductance. Together our data support that CHGB-containing (CHGB+) channels are characteristic of regulated secretion, and function in granule ion homeostasis near the plasma membrane or possibly in other intracellular processes.

WeiTsing, a pericycle-expressed ion channel, safeguards the stele to confer clubroot resistance

Plant roots encounter numerous pathogenic microbes that often cause devastating diseases. One such pathogen, Plasmodiophora brassicae (Pb), causes clubroot disease and severe yield losses on cruciferous crops worldwide. Here, we report the isolation and characterization of WeiTsing (WTS), a broad-spectrum clubroot resistance gene from Arabidopsis. WTS is transcriptionally activated in the pericycle upon Pb infection to prevent pathogen colonization in the stele. Brassica napus carrying the WTS transgene displayed strong resistance to Pb. WTS encodes a small protein localized in the endoplasmic reticulum (ER), and its expression in plants induces immune responses. The cryoelectron microscopy (cryo-EM) structure of WTS revealed a previously unknown pentameric architecture with a central pore. Electrophysiology analyses demonstrated that WTS is a calcium-permeable cation-selective channel. Structure-guided mutagenesis indicated that channel activity is strictly required for triggering defenses. The findings uncover an ion channel analogous to resistosomes that triggers immune signaling in the pericycle.

Nuclear export of pre-60S particles through the nuclear pore complex.

The nuclear pore complex (NPC) is the bidirectional gate that mediates the exchange of macromolecules or their assemblies between nucleus and cytoplasm1-3. The assembly intermediates of the ribosomal subunits, pre-60S and pre-40S particles, are among the largest cargoes of the NPC and the export of these gigantic ribonucleoproteins requires numerous export factors4,5. Here we report the cryo-electron microscopy structure of native pre-60S particles trapped in the channel of yeast NPCs. In addition to known assembly factors, multiple factors with export functions are also included in the structure. These factors in general bind to either the flexible regions or subunit interface of the pre-60S particle, and virtually form many anchor sites for NPC binding. Through interactions with phenylalanine-glycine (FG)repeats from various nucleoporins of NPC, these factors collectively facilitate the passage of the pre-60S particle through the central FG repeat network of the NPC. Moreover, in silico analysis of the axial and radial distribution of pre-60S particles within the NPC shows that a single NPC can take up to four pre-60S particles simultaneously, and pre-60S particles are enriched in theinner ring regions close to the wall of the NPC with the solvent-exposed surface facing the centre of the nuclear pore. Our data suggest a translocation model for the export of pre-60S particles through the NPC.

Void growth in ductile materials with realistic porous microstructures

In this paper, we have investigated void growth in von Mises materials which contain realistic porous microstructures. For that purpose, we have performed finite element calculations of cubic unit-cells which are subjected to periodic boundary conditions and include porosity distributions representative of three additively manufactured metals. The initial void volume fraction in the calculations varies between 0.00564% and 1.75%, the number of actual voids between 14 and 5715, and the pores size from 2.3μm to 110μm. Several tests with different void sizes and positions have been generated for each of the three porous microstructures considered, and for each test we have performed several realizations with different spatial arrangement of the voids. The simulations have been carried out with random spatial distributions of pores and with clusters of the same size and different void densities. The macroscopic stress state in the unit-cell is controlled by prescribing constant triaxiality and Lode parameter throughout the loading. Calculations performed exchanging the loading directions for a given distribution of void sizes and positions have shown that the porous microstructure makes the macroscopic strain softening of the unit-cell (slightly) anisotropic. Moreover, the results obtained with the realistic porous microstructures have been compared with unit-cell calculations having an equivalent single central pore, and with calculations in which the material behavior is modeled with Gurson plasticity. It has been shown that both initial void volume fraction and spatial and size distribution of voids affect the macroscopic response of the porous aggregate and the void volume fraction evolution. Moreover, the calculations with random spatial distribution of voids have brought out that different tests of the same microstructure carry significant variations to the effective behavior of the porous aggregate, and that the interaction between neighboring pores dictates the volume evolution of individual voids, especially at higher macroscopic triaxiality. The calculations with clusters have shown that pores clustering promotes localization/coalescence due to increased interaction between the voids, which results in an increased growth rate of voids in clusters with large number of pores. Moreover, the results for the evolution of the distribution of plastic strains in the unit-cell have provided quantitative indications of the role of porous microstructure on the development of heterogeneous plastic strain fields which promote macroscopic strain softening. Namely, the accelerated growth rate of the plastic strains near the voids which indicates the onset of localization/coalescence has been shown to occur earlier as the number of voids in the microstructure increases.

Low-Temperature Dynamics of Water Confined in Unidirectional Hydrophilic Zeolite Nanopores.

The dynamical properties of water molecules confined in the unidirectional hydrophilic nanopores of AlPO4-54 are investigated with quasi-elastic neutron scattering as a function of temperature down to 118 K. AlPO4-54 has among the largest pores known for aluminophosphates and zeolites (about 1.3 nm), though they are small enough to prevent water crystallization due to the high degree of confinement. Water molecular diffusion into the pore is here measured down to 258 K. Diffusion is slower than in bulk water and has an activation energy of Ea = (20.8 ± 2.8) kJ/mol, in agreement with previous studies on similar confining media. Surprisingly, local hydrogen dynamics associated with water reorientation is measured down to temperatures (118 K), i.e., well below the expected glass transition temperature of bulk water. The reorientational time scale shows the well-known non-Arrhenius behavior down to the freezing of water mass diffusion, while it shows a feeble temperature dependence below. This fast local dynamics, of the order of fractions of nanoseconds, is believed to take place in the dense, highly disordered amorphous water occupying the pore center, indicating its possible plastic nature.

An integrated model based on transient flow and the nanoconfinement effect of water transport through nanopores

The property of water confined in nanopores is significantly different from that of bulk water, resulting in a great influence on the rate of water development during the unsteady state. In this study, we focused on the unsteady behavior of water transport in nanopores. We established a transient equation and applied the Laplace transform and Bessel function of the imaginary argument according to the time-dependent momentum conservation equation of Poiseuille-flow. The apparent density, apparent viscosity, and slip of the confined water were modeled by considering the water-wall interactions and the pore size. Moreover, the transient transport equation was modified by these three models to obtain a transient analytical model, which considered the effect of the nanoconfinement effect. We verified the credibility of the proposed model compared with other models as well as through experiments and molecular dynamics simulations. The results indicated that the development rate of water confinement in the superhydrophobic nanopores was much greater than that in intermediate wettability and hydrophilic pores, and its velocity profile behaved as an approximately straight line throughout the unsteady state. Slip in the intermediate wettability pores was more likely to transmit its effects to the pore center than in hydrophilic pores. We found that small hydrophilic pores were dominated by the apparent density and apparent viscosity in the unsteady state, whereas large hydrophilic pores were dominated by slip in the initial state, which gradually changed to apparent density and apparent viscosity with time. For the superhydrophobic pores, regardless of pore size, slip was the main controlling factor in the unsteady state. Additionally, the sensitivity of confined water stabilization time to pore size was much greater in the superhydrophobic pores than in the hydrophilic pores.

An Insight into the Potassium Currents of hERG and Their Simulation.

By assuming that a stepwise outward movement of the four S4 segments of the hERG potassium channel determines a concomitant progressive increase in the flow of the permeant potassium ions, the inward and outward potassium currents can be simulated by using only one or two adjustable (i.e., free) parameters. This deterministic kinetic model differs from the stochastic models of hERG available in the literature, which usually require more than 10 free parameters. The K+ outward current of hERG contributes to the repolarization of the cardiac action potential. On the other hand, the K+ inward current increases with a positive shift in the transmembrane potential, in apparent contrast to both the electric and osmotic forces, which would concur in moving K+ ions outwards. This peculiar behavior can be explained by the appreciable constriction of the central pore midway along its length, with a radius < 1 Å and hydrophobic sacks surrounding it, as reported in an open conformation of the hERG potassium channel. This narrowing raises a barrier to the outward movement of K+ ions, inducing them to move increasingly inwards under a gradually more positive transmembrane potential.

Woronin body hitchhiking on early endosomes is dispensable for septal localization in Aspergillus nidulans.

The proper functioning of organelles depends on their intracellular localization, mediated by motor protein-dependent transport on cytoskeletal tracks. Rather than directly associating with a motor protein, peroxisomes move by hitchhiking on motile early endosomes in the filamentous fungus Aspergillus nidulans. However, the physiological role of peroxisome hitchhiking is unclear. Peroxisome hitchhiking requires the protein PxdA, which is conserved within the fungal subphylum Pezizomycotina but absent from other fungal clades. Woronin bodies are specialized peroxisomes that are also unique to the Pezizomycotina. In these fungi, multinucleate hyphal segments are separated by incomplete cell walls called septa that possess a central pore enabling cytoplasmic exchange. Upon damage to a hyphal segment, Woronin bodies plug septal pores to prevent widespread leakage. Here, we tested whether peroxisome hitchhiking is important for Woronin body motility, distribution, and function in A. nidulans. We show that Woronin body proteins are present within all motile peroxisomes and hitchhike on PxdA-labeled early endosomes during bidirectional, long-distance movements. Loss of peroxisome hitchhiking significantly affected Woronin body distribution and motility in the cytoplasm, but Woronin body hitchhiking is ultimately dispensable for septal localization and plugging.

Abstract 4834: Mitochondrial ClpXP degrades serine phosphorylated protein aggregates

Abstract ClpXP is a serine protease localized to the mitochondrial matrix and maintains mitochondrial proteostasis by degrading damaged/aggregated respiratory chain complex proteins. Both inhibition and hyperactivation of ClpP lead to impaired OXPHOS function and kill leukemic cells in vitro and in vivo. Yet, the marks that tag proteins for degradation by ClpXP remain unknown. The bacterial homologue of ClpXP degrades damaged proteins with arginine phosphorylation. Therefore, we assessed how phosphorylation affects ClpXP protease activity. Recombinant ClpXP was incubated with its unnatural substrate, FITC-tagged casein, in the presence of increasing concentrations of phospho-serine (pSer), phospho-threonine (pThr), phospho-arginine (pArg), or phospho-tyrosine (pTyr). In a dose-dependent manner, pSer and pThr free amino acids and short peptides inhibited casein degradation by ClpXP. In contrast, free Ser, Thr, phosphate, pArg and pTyr did not inhibit ClpXP protease activity. In addition, we characterized ClpP peptidase activity and ClpX ATPase activity using the Ac-Trp-Leu-Ala-AMC (Ac-WLA-AMC) peptidase activity assay and the Malachite Green ATPase assay. Neither pSer nor pThr inhibited ClpX ATPase activity or ClpP peptidase activity. Thus, pSer and pThr only blocked ClpXP from degrading full-length protein without altering the enzymatic activity of the complex. Next, we characterized pSer and pThr binding to ClpXP by thermal shift binding assay. pSer and pThr free amino acids and short peptides bound to ClpX but not ClpP. All the dephosphorylated counterparts did not bind to ClpX. Therefore, pSer and pThr interact with ClpX outside the ATPase site. cyroEM studies of ClpX and pSer peptides indicated a putative pSer docking site in the central pore of ClpX. Previously, we identified OXPHOS complex II subunit SDHA as a potential ClpXP endogenous substrate. Therefore, we used SDHA as a model to assess whether serine phosphorylation influenced ClpXP protein degradation in intact cells. Using pSer immunoprecipitation, we observed increased serine phosphorylated SDHA in AML cells after ClpP and ClpX knockdown. The increased serine phosphorylated SDHA was specifically found in the insoluble fraction of the mitochondrial proteins. Supporting that serine phosphorylated SDHA represents aggregated protein, treatment of cells with ROS-inducing antimycin or 42°C heat shock also increased levels of serine phosphorylated SDHA in the fraction of insoluble mitochondrial proteins. Finally, adding recombinant ClpXP to mitochondrial lysates specifically degraded SDHA with serine phosphorylation. In summary, mitochondrial ClpXP degrades aggregated mitochondrial proteins marked by serine phosphorylated. Thus, this work identifies new degradation machinery for mitochondrial protease, advances the function of mitochondrial ClpXP, and highlights a new therapeutic strategy to target this protease. Citation Format: Yue Feng, Yulia Jitkova, Alexander Keszei, Jonathan St-Germain, Yongran Yan, Brian Raught, Mohammad Mazhab-Jafari, Aaron Schimmer. Mitochondrial ClpXP degrades serine phosphorylated protein aggregates. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4834.

Vitamin A deficiency in peafowl with secondary visceral urate deposition

Clinical History: In a flock of approximately 180 peafowl, several were showing signs of a possible upper respiratory infection and had mouth gaping per the owner. They were also reported to be lethargic, to have excessive phlegm or mucus in the mouths, had trouble swallowing, and were losing weight. They were being treated with Baytril and Metronidazole with no improvement. Approximately eight had died. Five peafowl were submitted for necropsy and diagnostic work-up, including three peahens and two peacocks. Gross Findings: In all five peafowl, the oral cavity contained excess mucus. The oral, crop, and esophageal mucosa had disseminated, smooth, raised, round nodules with a central pore. The proximal esophagus was the most severely affected site. The nodules measured on average ~2 mm in diameter. Upon squeezing some of these nodules, pale tan, caseous material could be expressed. In all five peafowl, the heart was diffusely coated by abundant white, chalky, urate material. Similar though lesser amounts of urates partially coated the surface of the liver and other coelomic membranes. In one peahen, the ureters were multifocally distended and contained consolidated accumulations of tan to pale yellow, caseous material. The kidneys in this bird were pale.

English

Myiasis is the infestation of living tissues of human and animals with larvae of flies in the Order Diptera. This study determined the gross and histopathological lesions due to Cordylobia anthropophaga infestations of Dogs in Kitui County, Kenya. Four dogs identified and confirmed to have canine cutaneous myiasis (CCM) infestation were purchased for the study. All the study animals were clinically examined for skin lesions characteristic of CCM and euthanized for complete necropsy examination and histopathological sample collection. Tissue sections were collected from areas with lesions of CCM namely; skin, skeletal muscles and regional draining lymph nodes. They were preserved in 10% buffered formalin and were processed and analyzed using standard methods. Grossly, all dogs had poor body condition, patches of alopecia, emaciated and had the pathognomonic lesions for canine cutaneous myiasis (CCM) characterized by multifocal coalescent nodular lesions (harboring Cordylobia anthropophaga larvae) with 3 mm diameter central pore (furuncles) and erythematous base. Some had serous, hemorrhagic or purulent discharges from the furuncles that matted surrounding hairs. Lesions were distributed mainly on the ventral abdomen, axilla, flanks, legs, perineum and external reproductive organs. Examination of the skin revealed that the furuncular lesions extended throughout the skin thickness from epidermis to the sub-cutis and underlying pale skeletal muscles. There was regional lymphadenopathy in affected body regions. Histopathology confirmed the main lesions in all the dogs were parasitic granulomas, congested blood vessels in the surrounding tissues and eosinophilic lymphadenitis. The granulomas were located in the skin and the underlying skeletal muscles. The lesions were characterized by centrally located parasite, surrounded by connective tissue and heavy infiltration with inflammatory cells predominantly eosinophils. Draining lymph nodes had eosinophilic lymphadenitis. The reported pathological lesions resulted in unthriftiness, alopecia, lethargy and anorexia due to pain and stress resulting to emaciation and possible death. There is need to eradicate the etiological agent as it affects the wellbeing of dogs in the study area. Key words: Canine, Cordylobia anthropophaga, Myiasis, gross pathology, histopathology, Kitui County.

Thermodynamic‐kinetic synergistic separation of CH4/N2 on a robust aluminum‐based metal‐organic framework

AbstractA robust aluminum‐based metal–organic framework (Al‐MOF) MIL‐120Al with 1D rhombic ultra‐microporous was reported. The nonpolar porous walls composed of para‐benzene rings with a comparable pore size to the kinetic diameter of methane allow it to exhibit a novel thermodynamic‐kinetic synergistic separation of CH4/N2 mixtures. The CH4 adsorption capacity was as high as 33.7 cm3/g (298 K, 1 bar), which is the highest uptake value among the Al‐MOFs reported to date. The diffusion rates of CH4 were faster than N2 in this structure as confirmed by time‐dependent kinetic adsorption profiles. Breakthrough experiments confirm that this MOF can completely separate the CH4/N2 mixture and the separation performance is not affected in the presence of H2O. Theoretical calculations reveal that pore centers with more energetically‐favorable binding sites for CH4 than N2. The results of pressure swing adsorption (PSA) simulations indicate that MIL‐120Al is a potential candidate for selective capture coal‐mine methane.

Optical control of PIEZO1 channels

PIEZO proteins are unusually large, mechanically-activated trimeric ion channels. The central pore features structural similarities with the pore of other trimeric ion channels, including purinergic P2X receptors, for which optical control of channel gating has been previously achieved with photoswitchable azobenzenes. Extension of these chemical optogenetics methods to mechanically-activated ion channels would provide tools for specific manipulation of pore activity alternative to non-specific mechanical stimulations. Here we report a light-gated mouse PIEZO1 channel, in which an azobenzene-based photoswitch covalently tethered to an engineered cysteine, Y2464C, localized at the extracellular apex of the transmembrane helix 38, rapidly triggers channel gating upon 365-nm-light irradiation. We provide evidence that this light-gated channel recapitulates mechanically-activated PIEZO1 functional properties, and show that light-induced molecular motions are similar to those evoked mechanically. These results push the limits of azobenzene-based methods to unusually large ion channels and provide a simple stimulation means to specifically interrogate PIEZO1 function.

Insights into the structure-function relationship of the NorQ/NorD chaperones from Paracoccus denitrificans reveal shared principles of interacting MoxR AAA+/VWA domain proteins

BackgroundNorQ, a member of the MoxR-class of AAA+ ATPases, and NorD, a protein containing a Von Willebrand Factor Type A (VWA) domain, are essential for non-heme iron (FeB) cofactor insertion into cytochrome c-dependent nitric oxide reductase (cNOR). cNOR catalyzes NO reduction, a key step of bacterial denitrification. This work aimed at elucidating the specific mechanism of NorQD-catalyzed FeB insertion, and the general mechanism of the MoxR/VWA interacting protein families.ResultsWe show that NorQ-catalyzed ATP hydrolysis, an intact VWA domain in NorD, and specific surface carboxylates on cNOR are all features required for cNOR activation. Supported by BN-PAGE, low-resolution cryo-EM structures of NorQ and the NorQD complex show that NorQ forms a circular hexamer with a monomer of NorD binding both to the side and to the central pore of the NorQ ring. Guided by AlphaFold predictions, we assign the density that “plugs” the NorQ ring pore to the VWA domain of NorD with a protruding “finger” inserting through the pore and suggest this binding mode to be general for MoxR/VWA couples.ConclusionsBased on our results, we present a tentative model for the mechanism of NorQD-catalyzed cNOR remodeling and suggest many of its features to be applicable to the whole MoxR/VWA family.

Structure, substrate binding and activity of a unique AAA+protein: the BrxL phage restriction factor.

Bacteriophage exclusion ('BREX') systems are multi-protein complexes encoded by a variety of bacteria and archaea that restrict phage by an unknown mechanism. One BREX factor, termed BrxL, has been noted to display sequence similarity to various AAA+protein factors including Lon protease. In this study we describe multiple CryoEM structures of BrxL that demonstrate it to be a chambered, ATP-dependent DNA binding protein. The largest BrxL assemblage corresponds to a dimer of heptamers in the absence of bound DNA, versus a dimer of hexamers when DNA is bound in its central pore. The protein displays DNA-dependent ATPase activity, and ATP binding promotes assembly of the complex on DNA. Point mutations within several regions of the protein-DNA complex alter one or more in vitro behaviors and activities, including ATPase activity and ATP-dependent association with DNA. However, only the disruption of the ATPase active site fully eliminates phage restriction, indicating that other mutations can still complement BrxL function within the context of an otherwise intact BREX system. BrxL displays significant structural homology to MCM subunits (the replicative helicase in archaea and eukaryotes), implying that it and other BREX factors may collaborate to disrupt initiation of phage DNA replication.

Effect of wettability on oil and water distribution and production performance in a tight sandstone reservoir

Wettability is an important factor that dominates the micro-distribution of initial oil and water, residual oil, and subsequent oil recovery in a tight oil reservoir. In this paper, integrated experimental techniques have been developed to examine the effect of wettability on oil and water micro-distribution together with production performance in a tight reservoir. Wettability alteration indicated by contact angles during the aging process was firstly monitored and measured continuously. Then, nuclear magnetic resonance (NMR) measurements were integrated with rate-controlled mercury injection (RMI) tests to determine pore and throat size distribution. Subsequently, NMR measurements were performed to not only characterize the oil and water distribution in the process of wettability change, but also evaluate the production performance and recovery potential. Furthermore, displacement experiments were carried out to visually observe the microscopic distribution of residual oil under different wettability conditions. For a strong water-wetting rock, oil is separated from the surface of a pore/throat on which a thin water film is adsorbed, and then fills the center of the pore in the form of oil droplets. The displacement experiments show that water saturation of a two-phase flow zone on relative permeability curves ranges from 22.5% to 55.1% and that water saturation at the isotonic point is 43.6% with its waterflooding oil recovery of 42.1%. For a weak oil-wetting rock, oil is mainly distributed in porous media in the form of an oil film. The water saturation of a two-phase flow zone ranges from 22.3% to 48.1%, while that of the isotonic point is 38.1% with waterflooding oil recovery of 33.2%. With wettability altering from strong water-wetting to weak oil-wetting, oil either is adsorbed on the pore and throat surface or migrates from the center of a larger pore to a smaller pore and/or throat. It is more unfavorable to the seepage of oil due to the fact that the two-phase flow zone is narrowed and a decrease in water saturation at the isotonic point, leading to a lower waterflooding oil recovery. After waterflooding, oil droplets caused by the Jamin effect, oil clusters resulted from heterogeneity, and small oil droplets dispersed at the corner of a pore are visually observed in cores with strong water-wetting. Within weak oil-wetting cores, residual oil is mainly distributed in a membrane-like form due to adsorption and oil clusters resulted from heterogeneity.