Structure Mechanism Research Articles

Structural basis of chorismate isomerization by Arabidopsis ISOCHORISMATE SYNTHASE1.

Salicylic acid (SA) plays a crucial role in plant defense against biotrophic and semi-biotrophic pathogens. In Arabidopsis (Arabidopsis thaliana), isochorismate synthase 1 (AtICS1) is a key enzyme for the pathogen-induced biosynthesis of SA via catalytic conversion of chorismate into isochorismate, an essential precursor for SA synthesis. Despite the extensive knowledge of ICS1-related menaquinone, siderophore, tryptophan (MST) enzymes in bacteria, the structural mechanisms for substrate binding and catalysis in plant isochorismate synthase (ICS) enzymes are unknown. This study reveals that plant ICS enzymes catalyze the isomerization of chorismate through a magnesium-dependent mechanism, with AtICS1 exhibiting the most substantial catalytic activity. Additionally, we present high-resolution crystal structures of apo AtICS1 and its complex with chorismate, offering detailed insights into the mechanisms of substrate recognition and catalysis. Importantly, our investigation indicates the existence of a potential substrate entrance channel and a gating mechanism regulating substrate into the catalytic site. Structural comparisons of AtICS1 with MST enzymes suggest a shared structural framework with conserved gating and catalytic mechanisms. This work provides valuable insights into the structural and regulatory mechanisms governing substrate delivery and catalysis in AtICS1, as well as other plant ICS enzymes.

Black TiO2 and Oxygen Vacancies: Unraveling the Role in the Thermal Anatase-to-Rutile Transformation

Understanding the role of oxygen vacancies in the phase transformation of metal oxide nanomaterials is fundamental to design more efficient opto-electronic devices for a variety of applications, including sensing, spintronics, photocatalysis, and photo-electrochemistry. However, the structural mechanisms behind the phase transformation in reducible oxides remain poorly described. Here, we compare P25 and black TiO2 during the thermal anatase-to-rutile transformation using in situ synchrotron powder diffraction. The precise measurement of the phase fractions, unit cell parameters, and Ti-O bond sheds light on the phase transformation dynamics. Notably, we observe distinct temperature-dependent shifts in the relative phase fractions of anatase and rutile in both materials highlighting the role of the oxygen vacancy in promoting the phase transformation. We employ bond valence concepts for structural modeling, revealing unique trends in temperature evolution of Ti-O distances of black rutile, confirming that this TiO2 phase is preferentially reduced over anatase. These findings not only enhance our understanding of phase transitions in TiO2 but also open new ways for the design of advanced photocatalytic materials through targeted phase control.

Sound absorber based on a sonic black hole and multi-layer micro-perforated panels

Abstract In order to achieve low-frequency and broadband sound absorption simultaneously, we propose a structure that combines a sonic black hole with multilayer micro-perforated panels. Firstly, we present finite element models for composite structures based on sonic black holes and micro-perforated panels and describe the sound absorption mechanism of the composite structure by comparing the sound absorption phenomena of micro-perforated panels with sonic black holes and micro-perforated panels with ordinary circular tubes. Secondly, the effects of the end coordinates of the sonic black hole, the number of panels and the parameters of the micro-perforated panels are discussed. Thirdly, the theoretical model of the proposed structure is developed using the transfer matrix method. Finally, the sound absorption test is carried out on the proposed structure using impedance tubes. The test results show that the sound absorption coefficient of the sample with a geometric length of 203mm reaches 0.8 at 223 Hz and stabilizes above 0.9 at 398-1600 Hz. The multilayer micro-perforated panel with sonic black hole has excellent sound absorption performance and has great research potential and application value.

Design of SBS molecular structure and contribution mechanism from its soft and hard segments to modify asphalt

ABSTRACT The excellent performance of SBS-modified asphalt is attributed to the release of the SBS soft segment (PB segment) and hard segment (PS segment) in the asphalt. The release mechanism of the SBS soft and hard segments was studied using MD simulation and laboratory experiments, and the optimal molecular structure of SBS for asphalt modification was determined. MD simulation results revealed that SBS with a higher PS content exhibited better compatibility with asphalt. The larger and stronger molecular aggregates of the PS segment improved the high-temperature shear resistance of the asphalt but reduced the molecular mobility of the system. Additionally, radial distribution function analysis showed varying degrees of aggregation behaviour of asphaltenes with different segment ratios of polymer modifiers. Laboratory experiments were conducted using synthetically prepared SBS modifiers with specific segment ratios, as well as PB and PS monomer modifiers. Conventional tests and rheological experiments indicated that the PB segment improved the low-temperature performance of the asphalt, while the PS segment enhanced its high-temperature performance. The experimental results of the Cole–Cole plots are consistent with the solubility parameter results. Morphological studies revealed a two-phase continuous structure formed between SBS and asphalt when the SBS segment ratio was approximately 30/70.

Subject-verb agreement in Arabic

Agreement in grammar refers to formal relationship between elements, whereby a form of one word conforms to   the form of another. The preservation of agreement between a controlling phrase and a controlled phrase under various conditions provides a clear indication that agreement relations are sensitive to linear or directional properties, otherwise, we would expect agreement to be affected by word order changes.      In this paper I shall work on subject-verb agreement in Modern Standard Arabic (MSA) whose rich inflectional agreement system is fascinating. I intend to examine its rich agreement patterns in the minimalist framework and find out the structural mechanism of the assignment system followed by a detailed study of the three phi- features in Arabic, i.e. person, number, and gender.      This paper will address the following issues of subject-verb agreement in Arabic: a) why the verb in VSO order does not show the person and number agreement and only shows gender agreement with the post-verbal subject and b) the ambiguity of the first person in Arabic that is unspecified. 

Effect of Phenol and Alkylamide Interaction on α-Glucosidase Inhibition and Cellular Antioxidant Activity during In Vitro Digestion: Using Szechuan Pepper (Zanthoxylum genus) as a Model.

Although recent evidence indicated significant phenol and alkylamide interaction in aqueous solutions, the gastrointestinal digestion influence of the combination remains unclear. This study aims to investigate phenol and alkylamide interaction during in vitro digestion, focusing on bioaccessibility and bioactivity, including α-glucosidase inhibition and cellular antioxidant activity. Additionally, the structural mechanism of phenol and alkylamide interaction during in vitro digestion was explored. The results indicated that the presence of phenols and alkylamides significantly increased or decreased their respective bioaccessibility, depending on the Zanthoxylum varieties. Furthermore, although antagonistic phenol/alkylamide interaction was evident during α-glucosidase inhibition, cellular oxidative stress alleviation, and antioxidant gene transcription upregulation, this effect weakened gradually as digestion progressed. Glycoside bond cleavage and the methylation of phenols as well as alkylamide isomerization and addition were observed during digestion, modifying the hydrogen bonding sites and interaction behavior. This study provided insights into the phenol/alkylamide interaction in the gastrointestinal tract.

Structural mechanisms of Tad pilus assembly and its interaction with an RNA virus.

Caulobacter crescentus Tad (tight adherence) pili, part of the type IV pili family, are crucial for mechanosensing, surface adherence, bacteriophage (phage) adsorption, and cell-cycle regulation. Unlike other type IV pilins, Tad pilins lack the typical globular β sheet domain responsible for pilus assembly and phage binding. The mechanisms of Tad pilus assembly and its interaction with phage ΦCb5 have been elusive. Using cryo-electron microscopy, we unveiled the Tad pilus assembly mechanism, featuring a unique network of hydrogen bonds at its core. We then identified the Tad pilus binding to the ΦCb5 maturation protein (Mat) through its β region. Notably, the amino terminus of ΦCb5 Mat is exposed outside the capsid and phage/pilus interface, enabling the attachment of fluorescent and affinity tags. These engineered ΦCb5 virions can be efficiently assembled and purified in Escherichia coli, maintaining infectivity against C. crescentus, which presents promising applications, including RNA delivery and phage display.

Five-year Performance Contracts and Service Delivery in Local Authorities in Zimbabwe: The Case of Ruwa

Globally, public sector institutions are struggling to offer public services effectively and efficiently. Zimbabwe has introduced five-year performance contracts in the public sector in order to address challenges bedeviling the public sector institutions. This study sought to analyse the impact of five-year performance contracts on local authorities’ service delivery. The literature reviewed showed that Zimbabwe’s public sector organization have a long-standing history of under performance. Performance contracts were therefore, introduced to rectify performance challenges in the public sector. A qualitative inquiry of a case study indicated that political interference, financial challenges, lack of skills of the employees and lack of commitment of the leaders are among the factors leading to poor implementation of performance contracts. As a way forward research recommends the transformation of the structural mechanisms underlying the implementation of performance contracts, training of employees, reimbursement of local authorities by the central government and inclusion of the lower-level employees in setting of targets. Widespread awareness-raising campaigns of both the need for performance contracts and the benefits of such measures are needed.

Structural basis of TRPV1 modulation by endogenous bioactive lipids.

TRP ion channels are modulated by phosphoinositide lipids, but the underlying structural mechanisms remain unclear. The capsaicin- and heat-activated receptor, TRPV1, has served as a model for deciphering lipid modulation, which is relevant to understanding how pro-algesic agents enhance channel activity in the setting of inflammatory pain. Identification of a pocket within the TRPV1 transmembrane core has provided initial clues as to how phosphoinositide lipids bind to and regulate the channel. Here we show that this regulatory pocket in rat TRPV1 can accommodate diverse lipid species, including the inflammatory lipid lysophosphatidic acid, whose actions are determined by their specific modes of binding. Furthermore, we show that an empty-pocket channel lacking an endogenous phosphoinositide lipid assumes an agonist-like state, even at low temperature, substantiating the concept that phosphoinositide lipids serve as negative TRPV1 modulators whose ejection from the binding pocket is a critical step toward activation by thermal or chemical stimuli.

Remodeling mechanism of gel network structure of soy protein isolate amyloid fibrils mediated by cellulose nanocrystals

The differences in the gelling properties of soy protein isolate (SPI) and soy protein isolate amyloid fibrils (SAFs) as well as the role of cellulose nanocrystals (CNC) in regulating their gel behaviors were investigated in this study. The binding of CNC to β-conglycinin (7S), glycinin (11S), and SAFs was predominantly driven by non-covalent interactions. CNC addition reduced the particle size, turbidity, subunit segments, and crystallinity of SPI and SAFs, promoted the conversion of α-helix to β-sheet, improved the thermal stability, exposed more tyrosine and tryptophan residues, and enhanced the intermolecular interactions. A more regular and ordered lamellar network structure was formed in the SAFs-CNC composite gel, which could be conducive to the improvement of gel quality. This study would provide theoretical reference for the understanding of the regulatory mechanism of protein amyloid fibrils gelation as well as the high-value utilization of SAFs-CNC complex as a functional protein-based material or food ingredient in food field.

Enhancing ferroelectricity in HfAlOx-based ferroelectric tunnel junctions: A comparative study of MFS and MFIS structures with ultrathin interfacial layers

This study explores the potential advantages of metal–ferroelectric–insulator–semiconductor (MFIS) structures compared with established metal–ferroelectric–semiconductor (MFS) and metal–ferroelectric–metal structures in the context of nonvolatile memory devices. Despite the superior performance of MFS structures in terms of electric field maintenance, switching speed, and power consumption, the presence of interface-related issues between the ferroelectric material and the semiconductor may degrade device performance. We propose an MFIS structure incorporating ultrathin interfacial layers (ILs) of SiO2, HfO2, and ZrO2 to address these issues. These insulator layers enhance device endurance by reducing physical stress and trap density at the interface, thereby improving electrical performance and long-term stability. Moreover, the presence of an IL reduces charge leakage between the ferroelectric layer and semiconductor, contributing to the resolution of the sneak path current problem. An additional feature of MFIS devices is their self-rectifying behavior, simplifying circuit design and manufacturing processes by eliminating the need for an external rectification circuit, consequently reducing costs. Through a series of experiments, this study evaluates the performance of the MFIS structure, investigates the ferroelectric properties of HfAlOx-based FTJs, and examines the conduction mechanism of the MFIS structure. By comparing the o-phase of MFS, SiO2, HfO2, and ZrO2 devices via grazing incidence X-ray diffraction (GIXRD) and using the positive-up-negative-down method to extract polarization and coercive voltage, we provide a comprehensive investigation of the impact of ultrathin ILs on ferroelectric properties. This research aims to offer valuable insights into the advancement of memory device technologies, presenting the MFIS structure as a promising platform for next-generation memory technologies. Further sections will elaborate on the experimental setup, methodology, and detailed study findings.

Structural characterization and anti-inflammatory activities of a purified polysaccharide from fruits remnants of Alpinia zerumbet (Pers.) Burtt. et Smith.

We reported here an interesting source of Alpinia zerumbet Polysaccharides (named AZPs) from the residues after extracting essential oil by steam distillation from Alpinia zerumbet fructus. After a series of purifications, a homogeneous polysaccharide (AZP-2) of molecular weight 1.25×105Da was obtained. Structure, anti-inflammatory activity, and anti-inflammatory mechanism were investigated. AZP-2 was mainly composed of galactose, arabinose, xylopyranose, glucose, and galacturonic acid. The main linkage structure of AZP-2 was determined after integrating the nuclear magnetic resonance (NMR) and methylation analysis, and the structure was comparatively complex. The results indicated that AZP-2 significantly decreased the production of NO and ROS in the inflammatory model established by lipopolysaccharide (LPS) stimulated RAW264.7, particularly at the concentration of 200μg/mL. Furthermore, AZP-2 significantly modulated the secretion of both pro-inflammatory and anti-inflammatory cytokines. Notably, the mechanism of AZP-2 exhibiting inhibitory effects was related to regulating the NF-κB signaling pathway. Overall, AZP-2 could be used as a potential anti-inflammatory agent for further in-depth studies.

Transglutaminase-crosslinked cold-set pea protein isolate gels modified by pH shifting: Properties, structure and formation mechanisms

Transglutaminase-crosslinked cold-set pea protein isolate gels modified by pH shifting: Properties, structure and formation mechanisms

Effect of cobalt on CeO2 nanorod supported Pt catalyst: Structure, performance, kinetics and reaction mechanism in CO oxidation

Catalytic oxidation represents a highly efficient and extensively employed approach for the elimination of CO in exhaust gas. Rationally designing and preparing catalysts with exceptional activity and stability in the presence of H2O and SO2 at low temperatures represent crucial avenues for future advancements. In this work, a series of Pt catalysts supported on CeO2 nanorods incorporated with varying amounts of Cobalt (Co/CeO2 ratio ranging from 0 to10) were prepared and evaluated for their catalytic activity in CO oxidation under both dry and wet conditions. The ultrahigh dispersion of Pt, outstanding redox properties, and abundant oxygen vacancies on the surface of Co-doped CeO2 nanorod supported Pt catalysts were revealed by XRD, HAADF-STEM, Raman spectroscopy and H2-TPR techniques. The catalytic activity for CO oxidation strongly depends on the Co content and reaction conditions. Among them, Pt/Co-CeO2-5 % exhibits the highest CO oxidation performance with a T90 (the temperature to achieve 90 % conversion of CO) of 170 °C under dry conditions, which is significantly lower by 140 °C compared to T90 of Pt/CeO2. Pt/Co-CeO2-1 % demonstrates superior CO oxidation performance with a T90 of 195 °C under wet conditions, exhibiting a reduction in temperature by 65 °C compared to the T90 of Pt/CeO2. Moreover, Pt/Co-CeO2 exhibits excellent resistance to SO2 compared to Pt/CeO2. Kinetic studies, in situ DRIFT analysis and isotopic experiments demonstrated direct participation of H2O in the reaction. On the catalysts with a low Co/Ce ratio (Co/Ce < 0.03), CO readily reacts with hydroxyl groups dissociated from H2O to form carboxyl intermediates, which subsequently undergo rapid decomposition into CO2, resulting in an enhanced reaction rate of CO oxidation at low temperature.

Gaming expertise induces meso-scale brain plasticity and efficiency mechanisms as revealed by whole-brain modeling

Video games are a valuable tool for studying the effects of training and neural plasticity on the brain. However, the underlying mechanisms related to plasticity-associated brain structural changes and their impact on brain dynamics are unknown. Here, we used a semi-empirical whole-brain model to study structural neural plasticity mechanisms linked to video game expertise. We hypothesized that video game expertise is associated with neural plasticity-mediated changes in structural connectivity that manifest at the meso-scale level, resulting in a more segregated functional network topology. To test this hypothesis, we combined structural connectivity data of StarCraft II video game players (VGPs, n = 31) and non-players (NVGPs, n = 31), with generic fMRI data from the Human Connectome Project and computational models, to generate simulated fMRI recordings. Graph theory analysis on simulated data was performed during both resting-state conditions and external stimulation. VGPs’ simulated functional connectivity was characterized by a meso-scale integration, with increased local connectivity in frontal, parietal, and occipital brain regions. The same analyses at the level of structural connectivity showed no differences between VGPs and NVGPs. Regions that increased their connectivity strength in VGPs are known to be involved in cognitive processes crucial for task performance such as attention, reasoning, and inference. In-silico stimulation suggested that differences in FC between VGPs and NVGPs emerge in noisy contexts, specifically when the noisy level of stimulation is increased. This indicates that the connectomes of VGPs may facilitate the filtering of noise from stimuli. These structural alterations drive the meso-scale functional changes observed in individuals with gaming expertise. Overall, our work sheds light on the mechanisms underlying structural neural plasticity triggered by video game experiences.

Madrid immigrants' perceptions of urban food environments and their dietary behaviours.

Large cities are home to several groups of immigrants who undergo important changes in their environmental conditions and lifestyles that significantly modify their risk of chronic diseases. Quantitative evidence indicates that both their health and diet worsen over time; much less is known about the qualitative mechanisms that cause these changes. The aim of this article is to understand how immigrants in the city of Madrid perceive the relation between the urban food environment and dietary behaviour. Based on a Social Ecological Framework, we conducted a secondary qualitative analysis derived from data from 41 immigrant residents, collected in eight focus groups (FGs), conducted in two neighbourhoods in the city of Madrid. We identified the following main categories: 1) Transnational identity and dietary behaviour in the neighbourhood; 2) Transitions in dietary behaviour; and 3) Societal/structural factors determining dietary behaviour in the neighbourhood. The participants in the FGs mentioned that they try to maintain traditional dietary customs and perceive that the taste of their typical dishes is better than those of Spanish dishes. Contradictorily, some participants considered their traditional dietary patterns to be less healthy than Mediterranean ones (consuming olive oil, vegetables, fish). Some participants acknowledged having adapted to the latter voluntarily or through dietary negotiations with their children. Immigrant families with two working parents have difficulties cooking homemade food and resort to less healthy options, such as eating fast food or ready-made meals. Due to their low purchasing power, they buy both ethnic products and other products, as well as considering the prices and offers in supermarkets. Our study highlights several structural mechanisms connecting the physical and social urban food environment with dietary behaviours among immigrant residents of a large city.

Structural mechanism of voltage-gated sodium channel slow inactivation

Voltage-gated sodium (NaV) channels mediate a plethora of electrical activities. NaV channels govern cellular excitability in response to depolarizing stimuli. Inactivation is an intrinsic property of NaV channels that regulates cellular excitability by controlling the channel availability. The fast inactivation, mediated by the Ile-Phe-Met (IFM) motif and the N-terminal helix (N-helix), has been well-characterized. However, the molecular mechanism underlying NaV channel slow inactivation remains elusive. Here, we demonstrate that the removal of the N-helix of NaVEh (NaVEhΔN) results in a slow-inactivated channel, and present cryo-EM structure of NaVEhΔN in a potential slow-inactivated state. The structure features a closed activation gate and a dilated selectivity filter (SF), indicating that the upper SF and the inner gate could serve as a gate for slow inactivation. In comparison to the NaVEh structure, NaVEhΔN undergoes marked conformational shifts on the intracellular side. Together, our results provide important mechanistic insights into NaV channel slow inactivation.

Segmentation of liver CT images based on weighted medical transformer model.

Deep convolutional neural networks have made significant strides in the field of medical image segmentation. Although existing convolutional structures enhance performance by leveraging local image information, they often lose the interdependence information between contexts. Therefore, the article utilizes the multi-attention mechanism of the Transformer structure to more comprehensively express relationships between contexts and introduced the Transformer network architecture into the field of medical image segmentation. Most models based on this Transformer structure typically require large datasets for training. However, in the medical field, the limited size of datasets makes training models with the Transformer structure challenging. To address this, the article propose a Weighted Medical Transformer (WMT) model that imposes low requirements on dataset quantity. The weighting mechanism in the WMT model aims to improve the issue of inaccurate relative positional coding when dealing with small medical datasets. Additionally, a coarse-grained and fine-grained segmentation mechanism is introduced, focusing on both the detailed aspects within image blocks and the boundary information connecting blocks. Experimental results on a liver dataset demonstrate that the model achieves F1 and IoU scores of 88.48% and 79.41%, respectively. Results on the MoNuSeg dataset show comparable high F1 and IoU scores of 79.58% and 66.19%, respectively. The model's accuracy surpasses that of U-Net++ and U-Net models. Compared to other models, this approach is applicable to scenarios with limited datasets, exhibiting high execution efficiency and accuracy.

Preparation of Superhydrophobic Coating on X80 Steel and Its Corrosion Resistance in Oilfield Produced Water.

Corrosion is an unavoidable issue that steel encounters during service; however, the generic methods employed for corrosion prevention often need high cost or preparation conditions. In this study, a facile chemical replacement deposition method was proposed to realize an anticorrosion superhydrophobic coating on a X80 steel surface. The growth mechanism of the rough structure and its impact on the wettability of the superhydrophobic coating were analyzed. The superhydrophobic coating, deposited for 50 s and modified for 30 min, achieved optimal electrochemical properties and a maximum water contact angle. The immersion test, in the saturated CO2 oilfield produced water, demonstrated the better corrosion resistance of superhydrophobic coating than X80 steel. Correspondingly, a kinetic corrosion model was established to analyze the anticorrosion mechanism. In summary, this method significantly improves the corrosion resistance of X80 steel and is attractive for other industrial fields.

Structural and Cognitive Mechanisms of Group Cohesion in Primates.

Group-living creates stresses that, all else equal, naturally lead to group fragmentation, and hence loss of the benefits that group-living provides. How species that live in large stable groups counteract these forces is not well understood. I use comparative data on grooming networks and cognitive abilities in primates to show that living in large, stable groups has involved a series of structural solutions designed to create chains of 'friendship' (friends-of-friends effects), increased investment in bonding behaviours (made possible by dietary adjustments) to ensure that coalitions work effectively, and neuronally expensive cognitive skills of the kind known to underpin social relationships in humans. The first ensures that individuals synchronise their activity cycles; the second allows the stresses created by group-living to be defused; and the third allows a large number of weak ties to be managed. Between them, these create a form of multilevel sociality based on strong versus weak ties similar to that found in human social networks. In primates, these strategies appear successively at quite specific group sizes, suggesting that they are solutions to 'glass ceilings' that would otherwise limit the range of group sizes that animals can live in (and hence the habitats they can occupy). This sequence maps closely onto the grades now known to underpin the Social Brain Hypothesis and the fractal pattern that is known to optimise information flow round networks.