Search Results (92)

The fungal kingdom, with an estimated five million species, has undergone extensive diversification over the past billion years and now occupies a wide array of ecological niches from terrestrial to aquatic ecosystems. To thrive in such diverse environments, fungi must exhibit finely tuned physiological and morphological responses orchestrated by conserved molecular pathways. Increasing evidence suggests that aquaporins (AQPs) play a key role in mediating these adaptive responses, particularly under varying abiotic and biotic stress conditions. However, despite notable advances in recent decades, the precise functional roles of AQPs within the fungal kingdom remains largely unresolved in the field of cell biology. AQPs are transmembrane proteins belonging to the major intrinsic proteins (MIPs) superfamily, which is characterized by remarkable sequence and structural diversity. Beyond their established function in facilitating water transport, MIPs mediated the bidirectional diffusion of a range of small inorganic and organic solutes, ions, and gases across cellular membranes. In fungi, MIPs are classified into three main subfamilies: orthodox (i.e., classical) AQPs, aquaglyceroporins (AQGP), and X-intrinsic proteins (XIPs). This review provides a concise summary of the fundamental structural and functional characteristics of fungal aquaporins, including their structure, classification, and known physiological roles. While the majority of the current literature has focused on the aquaporin and aquaglyceroporin subfamilies, this review also aims to offer a comprehensive and original overview of the relatively understudied X-intrinsic protein subfamily, highlighting its potential implication in fungal biology. Full article

Anion exchange membranes (AEMs) are vital for electrochemical energy devices such as alkaline fuel cells and water electrolyzers, enabling the use of non-precious metal catalysts despite challenges from alkaline degradation. Hyperbranched polymers (hbPs) with their globular structure, high functional group density, and simple synthesis, offer a promising platform for enhancing transport and stability. In this study, multifunctional hbPs were synthesized from 4-vinylbenzyl chloride (VBC) and 2-hydroxyethyl methacrylate (HEMA) via atom transfer radical self-condensing vinyl polymerization (ATR-SCVP) and crosslinked into polyurethane-based AEMs. Characterization confirmed successful copolymerization and crosslinking, with excellent alkaline stability. Membranes crosslinked with higher molecular weight (MW) and VBC-richer hbPs (e.g., OH-hbP1-PU) exhibited high water uptake (75%) but low ion-exchange capacity (1.54 mmol/g) and conductivity (186 µS/cm), attributed to steric hindrance and insufficient ionic network connectivity. In contrast, OH-hbP2-PU exhibited optimal properties, with the highest OH⁻ conductivity (338 µS/cm) and IEC (2.64 mmol/g), highlighting a balanced structure for efficient ion transport. This work offers a tunable strategy for high-performance AEM development through tailored hbP architecture. Full article

Aquaporins in rice (Oryza sativa L.) represent a pivotal class of transmembrane channel proteins that mediate the bidirectional transport of water and small solutes, which have critical functions in cellular osmoregulation and ion homeostasis maintenance. Their evolutionary diversity and functional plasticity constitute fundamental mechanisms underlying the adaptive responses to diversified environmental challenges. This review systematically summarizes rice AQPs’ evolutionary origins, structural characteristics, and spatiotemporal expression patterns under both physiological and stress conditions, highlighting the high conservation of their key functional domains across evolution and their environment-driven functional diversification. The molecular mechanisms governing AQPs in water utilization, nutrient uptake, and stress responses are unraveled. Furthermore, the potential of precision gene editing and multi-omics integration is discussed to decipher the intricate relationships between AQP evolutionary history, environmental adaptability, and functional specialization, thereby providing a theoretical basis for advancing crop stress resistance and high-quality breeding. Full article

Declining freshwater resources have spurred interest in saline–alkali (SA) water aquaculture, with species like tilapia and rainbow trout demonstrating ecological plasticity in such environments. However, the molecular mechanisms underlying fish adaptation and quality impacts remain unclear. This study investigated the hybrid fish “Xianfeng No. 1” (Erythroculter ilishaeformis × Ancherythroculter nigrocauda), a key aquaculture species in China, under 60-day SA exposure. The results showed increased levels of oxidative stress markers (MDA) and antioxidant enzymes (SOD, CAT, GSH-Px), alongside improved quality traits. Transcriptomics revealed differentially expressed genes (DEGs) in muscle tissue associated with oxidative stress (UQCRFS1, UQCR10, CYC1), ion transport (COX5A, COX7C, COX7B), and the immune response (ATG9A, ATG2B, ATG2A, ULK1, ULK2, CFI, CFH). Metabolomics identified increased non-volatile flavors (e.g., glycine, proline) and collagen-related compounds. Integrated analysis highlighted the upregulation of GSR and GGT, and the downregulation of CHDH and GBSA, potentially driving glycine accumulation. These findings suggest that SA stress enhances antioxidant capacity, activates immune pathways, and modulates ion transport, enabling adaptation while improving meat quality. This study elucidates molecular mechanisms of fish acclimation to SA environments, providing insights for sustainable aquaculture development and breeding of stress-tolerant species in SA regions. Full article

Polyamide membranes, such as nanofiltration (NF) membranes, are widely used for water purification. However, the mechanisms of solute transport and solute rejection due to solute charge interactions with the membrane remain unclear at the molecular level. Here, we use molecular dynamics simulations to examine the transport of single-solute feeds through charged nanofiltration membranes with different membrane charge concentrations of ${\mathrm{COO}}^{-}$ and NH${}_2^{+}$ resulting from the deprotonation or protonation of polymeric end groups according to the pH level that the membrane experiences. The results show that ${\mathrm{Na}}^{+}$ and ${\mathrm{Cl}}^{-}$ solute ions are better rejected when the membrane has a higher concentration of negatively charged groups, corresponding to a higher pH, whereas ${\mathrm{CaCl}}_2$ is well rejected at all pH levels studied. These results are consistent with those of experiments performed at the same pH conditions as the simulation setup. Moreover, solute transport behavior depends on the membrane functional group distribution. When ${\mathrm{COO}}^{-}$ functional groups are concentrated at membrane feed surface, ion permeation into the membrane is reduced. Counter-ions tend to associate with charged functional groups while co-ions seem to pass by the charged groups more easily. In addition, steric effects play a role when ions of opposite charge cluster in pores of the membrane. This study reveals solute transport and rejection mechanisms related to membrane charge and provides insights into how membranes might be designed to achieve specific desired solute rejection. Full article

Steel fiber-reinforced concrete structures designed for marine environments can become compromised by the ingress of water and ions. Water and ion transport through the pores between steel fibers and concrete gels significantly affects the durability of such structures, but the mechanisms of this transport are not sufficiently understood. Reported here is a molecular dynamics-based investigation of the transport of water, NaCl, Na₂SO₄, and mixed solutions of NaCl and Na₂SO₄ through γ–FeOOH/CSH pores. The effect of pore width on the capillary transport of NaCl + Na₂SO₄ solutions was also investigated and reported. It is shown that the depth of water penetration in NaCl solution increases parabolically with time. It is further shown that the CSH surface forms bonds with different ions to form Na–O_CSH, Cl–Ca_CSH, and S–Ca_CSH compounds, which results in reduced rates of solution transport. The mixed NaCl + Na₂SO₄ solution was found to have the lowest transport rate. A reduction in pore width was found to reduce the transport rate of water molecules and diminish the transport of ions. In pores smaller than 2.5 nm in width, the immobilized ions aggregate into clusters, occupying pore inlets and blocking more ions from entering the channels. Compared with the matrix on both sides, solutions are transported significantly faster along the CSH side than along the γ–FeOOH side, indicating that the addition of steel fibers can effectively slow down the transport of water molecules and ions in concrete. These data on the difference in the transport of solutions along the two sides of the matrix may provide molecular-level insights to support studies on the durability of concrete materials. Full article

Metamorphosis is a common developmental process in invertebrate development. It is essential for the degeneration of larval organs, formation of adult organs, and adaptation transformation of the living environment. However, the underlying molecular regulatory mechanism remains to be elucidated. In this study, we used tail regression of ascidian Styela clava as a model to understand the gene regulation pathway and molecular mechanism in organ metamorphosis. The TGFβ signaling pathway was screened and demonstrated to be involved in tail regression based on RNA sequencing on the different larval stages and verification with inhibitor treatment experiments. We further investigated the downstream gene network of the TGFβ signaling pathway through comparative transcriptome data analysis on the TGFβ pathway inhibition samples. Together with qRT-PCR verification, we identified four critical gene functional categories, including ion transporters/water channel, extracellular matrix structural constituent, extracellular matrix organization, and cell polarity establishment. Furthermore, a cross-species comparative analysis between Ciona robusta and S. clava was performed to understand the conservation and divergence of gene regulation in ascidians. Overall, our work identifies a crucial gene regulation pathway in ascidian tail regression and provides several potential downstream targets for understanding the molecular mechanism of larval metamorphosis. Full article

Silver(I) ions and organometallic complexes thereof are well-established antimicrobial agents. They have been employed in medical applications for centuries. It is also known that some bacteria can resist silver(I) treatments through an efflux mechanism. However, the exact mechanism of action remains unclear. All-atom force-field simulations can provide valuable structural and thermodynamic insights into the molecular processes of the underlying mechanism. Lennard-Jones parameters of silver(I) have been available for quite some time; their applicability to properly describing the binding properties (affinity, binding distance) between silver(I) and peptide-based binding motifs is, however, still an open question. Here, we demonstrate that the standard 12-6 Lennard-Jones parameters (previously developed to describe the hydration free energy with the TIP3P water model) significantly underestimate the interaction strength between silver(I) and both methionine and histidine. These are two key amino-acid residues in silver(I)-binding motifs of proteins involved in the efflux process. Using free-energy calculations, we calibrated non-bonded fix (NBFIX) parameters for the CHARMM36m force field to reproduce the experimental binding constant between amino acid sidechain fragments and silver(I) ions. We then successfully validated the new parameters on a set of small silver-binding peptides with experimentally known binding constants. In addition, we monitored how silver(I) ions increased the α-helical content of the LP1 oligopeptide, in agreement with previously reported Circular Dichroism (CD) experiments. Future improvements are outlined. The implementation of these new parameters is straightforward in all simulation packages that can use the CHARMM36m force field. It sets the stage for the modeling community to study more complex silver(I)-binding processes such as the interaction with silver(I)-binding-transporter proteins. Full article

Thermal gradients induce thermodiffusion in aqueous solutions, a non-equilibrium effect arising from the coupling of thermal and mass fluxes. While thermal transport processes have garnered significant attention under standard conditions, thermal transport at high pressures and temperatures, typical of the Earth’s crust, has escaped scrutiny. Non-equilibrium thermodynamics theory and non-equilibrium molecular dynamics simulations provide an excellent means to quantify thermal transport under extreme conditions and establish a connection between the behaviour of the solutions and their microscopic structure. Here, we investigate the thermal conductivity and thermal diffusion of NaCl and LiCl solutions in the GPa pressure regime, targeting temperatures between 300 K and 1000 K at 1 molal concentration. We employ non-equilibrium molecular dynamics simulations along with the Madrid-2019 and TIP4P/2005 force fields. The thermal conductivity of the solutions increases significantly with pressure, and following the behaviour observed at standard pressure, the thermal conductivity is lower than that of pure water. The reduction in thermal conductivity is significant in the GPa pressure regime, ∼3% for 1 molal NaCl and LiCl solutions. We demonstrate that under GPa pressure conditions, the solutions feature thermophobic behaviour, with ions migrating towards colder regions. The pronounced impact of pressure is more evident in LiCl solutions, which display a thermophilic to thermophobic “transition” at pressures above 0.25 GPa. We discuss a correlation between the solution’s thermophobicity and the disruption of the water hydrogen bond structure at high pressure, where the water structure resembles that observed in simple liquids. Full article

Graphene-based materials, including graphene oxide (GO) and functionalized derivatives, have demonstrated exceptional potential in addressing environmental challenges related to heavy metal detection and wastewater treatment. This review presents the latest advancements in graphene-based electrochemical and fluorescence sensors, emphasizing their superior sensitivity and selectivity in detecting metal ions, such as Pb²⁺, Cd²⁺, and Hg²⁺, even in complex matrices. The key focus of this review is on the use of molecular dynamics (MD) simulations to understand and predict ion transport through graphene membranes, offering insights into their mechanisms and efficiency in removing contaminants. Particularly, this article reviews the effects of external conditions, pore radius, functionalization, and multilayers on water purification to provide comprehensive insights into filtration membrane design. Functionalized graphene membranes exhibit enhanced ion rejection through tailored electrostatic interactions and size exclusion effects, achieving up to 100% rejection rates for selected heavy metals. Multilayered and hybrid graphene composites further improve filtration performance and structural stability, enabling sustainable, large-scale water purification. However, challenges related to fabrication scalability, environmental impact, and cost remain. This review also highlights the importance of computational approaches and innovative material designs in overcoming these barriers, paving the way for future breakthroughs in graphene-based filtration technologies. Full article

Plasma membrane intrinsic proteins (PIPs), as members of the aquaporin (AQPs) family, can transport not only water but also urea, CO₂, H₂O₂, metal ions, and trace elements. They are crucial for maintaining water balance, substance transport, and responding to various stresses. This article delves into the structure, function, response mechanism, molecular mechanism, and regulatory mechanism of PIPs as a result of biological and abiotic stresses. It also summarizes current research trends surrounding PIPs and highlights potential research directions for further exploration. The aim is to assist researchers in related fields in gaining a more comprehensive understanding and precise insight into the advancements in PIP research. Full article

To investigate the micro-mechanism of the erosion of hydrated calcium silicate (C-S-H gel) in a sulfate environment, a solid–liquid molecular dynamics model of C-S-H gel/sodium sulfate was developed. This model employs molecular dynamics methods to simulate the transport processes between C-S-H gel and corrosive ions at concentrations of 5%, 8%, and 10% sodium sulfate (Na₂SO₄), aiming to elucidate the interaction mechanism between sulfate and C-S-H gel. The micro-morphology of the eroded samples was also investigated using scanning electron microscopy (SEM). The findings indicate that the adsorption capacity of C-S-H for ions significantly increases with higher concentrations of Na₂SO₄ solution. Notably, the presence of sulfate ions facilitates the decalcification reaction of C-S-H, leading to the formation of swollen gypsum and AFt (ettringite). This process results not only in the hydrolysis of the C-S-H gel but also in an increase in the diffusion coefficients of Na⁺ and Ca²⁺, thereby exacerbating the erosion. Additionally, the pore surfaces of the C-S-H structure exhibited strong adsorption of Na⁺, and as the concentration of Na₂SO₄ solution increased, Na+ was more stably adsorbed onto the C-S-H pore surfaces via Na-O_s bonds. The root-mean-square displacement curves of water molecules were significantly higher than those of ${\mathrm{SO}}_4^{2-}$, Na⁺ and Ca²⁺, which indicated that ${\mathrm{SO}}_4^{2-}$ could co-penetrate and migrate with water molecules faster compared with other ions in the solution containing ${\mathrm{SO}}_4^{2-}$, resulting in stronger corrosion and hydrolysis effects on the C-S-H structure. Full article

Cementitious material durability is affected by the transport and adsorption of water molecules and ions in the nanopore channels of cement hydration products. Hydrated calcium silicate (C-S-H) accounts for about 70% of the hydration product. It determines the mechanical properties of cementitious materials and their internal transport properties. The molecular dynamics method provides a complementary understanding of experimental and theoretical results. It can further reveal water molecules and ions’ adsorption and transport mechanisms in C-S-H gel pores. This review article provides an overview of the current state of research on the structure of C-S-H gels and the adsorption and transport properties of water molecules and ions within C-S-H gels, as studied through molecular dynamics simulations. This paper summarizes the results of the molecular dynamics-based adsorption transport properties of water molecules and ions in C-S-H gels. The deficiencies in the current study were analyzed, and the fundamental problems to be solved and further research directions were clarified to provide scientific references for revealing the structural properties of C-S-H gels using molecular dynamics. Full article

Oxidative stress plays a major role in the formation of the cataract that is the result of advancing age, diabetes or which follows vitrectomy surgery. Glutathione (GSH) is the principal antioxidant in the lens, and so supplementation with GSH would seem like an intuitive strategy to counteract oxidative stress there. However, the delivery of glutathione to the lens is fraught with difficulties, including the limited bioavailability of GSH caused by its rapid degradation, anatomical barriers of the anterior eye that result in insufficient delivery of GSH to the lens, and intracellular barriers within the lens that limit delivery of GSH to its different regions. Hence, more attention should be focused on alternative methods by which to enhance GSH levels in the lens. In this review, we focus on the following three strategies, which utilize the natural molecular machinery of the lens to enhance GSH and/or antioxidant potential in its different regions: the NRF2 pathway, which regulates the transcription of genes involved in GSH homeostasis; the use of lipid permeable cysteine-based analogues to increase the availability of cysteine for GSH synthesis; and the upregulation of the lens’s internal microcirculation system, which is a circulating current of Na⁺ ions that drives water transport in the lens and with it the potential delivery of cysteine or GSH. The first two strategies have the potential to restore GSH levels in the epithelium and cortex, while the ability to harness the lens’s internal microcirculation system offers the exciting potential to deliver and elevate antioxidant levels in its nucleus. This is an important distinction, as the damage phenotypes for age-related (nuclear) and diabetic (cortical) cataract indicate that antioxidant delivery must be targeted to different regions of the lens in order to alleviate oxidative stress. Given our increasing aging and diabetic populations it has become increasingly important to consider how the natural machinery of the lens can be utilized to restore GSH levels in its different regions and to afford protection from cataract. Full article

In order to investigate the interphase mass transfer and component distribution characteristics of the CO₂–water system under micro-scale and nano-scale transport conditions, a micro-scale kinetic model representing interphase mass transfer in the CO₂–water/saline system is developed in this paper. The molecular dynamics method is employed to delineate the diffusion and mass transfer processes of the system’s components, revealing the extent of the effects of variations in temperature, pressure, and salt ion concentration on interphase mass transfer and component distribution characteristics. The interphase mass transfer process in the CO₂–water system under transport conditions can be categorized into three stages: approach, adsorption, and entrance. As the system temperature rises and pressure decreases, the peak density of CO₂ molecules at the gas–liquid interface markedly drops, with their aggregation reducing and their diffusion capability enhancing. The specific hydration structures between salt ions and water molecules hinder the entry of CO₂ into the aqueous phase. Additionally, as the salt concentration in water increases, the density peak of CO₂ molecules at the gas–liquid interface slightly increases, while the density value in the water phase region significantly decreases. Full article