Search Results (828)

Nanoporous gold nanoparticles (np-AuNPs) combine inertness, a nanoscale structure, and a porous framework with high surface area, conductivity, and biocompatibility, making them ideal for biosensing, catalysis, fuel cells, and drug delivery. Their open pore structure and low-coordinated atoms enhance biomolecule capture and mass transfer, while their tunable size, pore volume, and ease of surface modification make them promising biosensor transducers. However, synthesizing colloidal np-AuNPs in a simple way with controllable size and scalability remains challenging. The existing approaches mostly rely on specialized equipment, complex setups, and expert knowledge, while still facing challenges in terms of scalability. In this study, we present a simple, seedless, wet-chemical synthesis of colloidal np-AuNPs via the co-reduction of Au/Ag alloys followed by dealloying. By adjusting the Au:Ag ratio, we produced np-AuNPs sized ~120–530 nm, which were immobilized on electrodes for detecting lipopolysaccharide (LPS), a toxic component of Gram-negative bacterial membranes. The LPS biosensor exhibited excellent sensitivity towards detecting wild-type LPS, with a low limit of detection (LOD) of 0.1244 ng/L. This work demonstrates the effective synthesis and application of np-AuNPs in LPS biosensing. Full article

Tight sandstone gas is currently one of the largest unconventional oil and gas resources being developed. In actual reservoir development, the complex pore structure affects the distribution of residual gas and water during the displacement process. However, there is still a lack of experimental research on the multi-scale visualization of pore structures in high-water-content tight gas reservoirs. Therefore, based on the porosity and permeability properties of reservoir cores and the micropore throat structural characteristics, this study designs and prepares three micro-physical models with different permeability ranges. Through micro-experiments and visualization techniques, the microscopic flow phenomena and gas–water distribution in the pore medium are observed. When the water–gas ratio exceeds 5, the produced water type is free water; when the water–gas ratio is between 2 and 5, the produced water type is weak capillary water; and when the water–gas ratio is less than 2, the produced water type is strong capillary water. The latter two types are collectively referred to as capillary water. In the Jin 30 well area, the main types of produced water are first free water, followed by capillary water, accounting for 58.5%. The experimental results of the micro-physical models with different permeability levels show that the production pattern of formation water varies due to differences in pore connectivity. In the low-permeability model, the high proportion of nano-pores and small pore throats requires a large pressure difference to mobilize capillary water, resulting in a higher proportion of residual water. Although the pores in the medium-permeability model are larger, the poor connectivity of nano-pores leads to local water phase retention. In the high-permeability model, micro-fractures and micropores are highly developed with good connectivity, allowing for rapid mobilization of multi-scale water phases under low pressure. The connectivity of nano-pores directly impacts the mobilization of formation water in micron-scale fractures, and poor pore connectivity significantly increases the difficulty of capillary water mobilization, thus changing the production mechanism of formation water at different scales. Full article

A comprehensive analysis of the molecular epidemiology of SARS-CoV-2 in the Kandy District of Sri Lanka from November 2020 to March 2022 was conducted to address the limited genomic surveillance data available across the country. The study investigated the circulating SARS-CoV-2 lineages, their temporal dynamics, and the associated mutational profiles in the study area. A total of 280 SARS-CoV-2-positive samples were selected, and 252 complete genomes were successfully sequenced using Oxford Nanopore Technology. Lineage classification was performed using the EPI2ME tool, while phylogenetic relationships were inferred through maximum likelihood and time-scaled phylogenetic trees using IQ-TREE2 and BEAST, respectively. Amino acid substitutions were analyzed to understand lineage-specific mutation patterns. Fifteen SARS-CoV-2 lineages were identified, and of those B.1.411 (36%) was the most prevalent, followed by Q.8 (21%), AY.28 (9.5%), and the Delta and Omicron variants. The lineage distribution showed a temporal shift from B.1.411 to Alpha, Delta, and finally the Omicron, mirroring the global trends. Time to the most recent common ancestor analyses provided estimates for the introduction of major variants, while mutation analysis revealed the widespread occurrence of D614G in the spike protein and lineage-specific mutations across structural, non-structural, and accessory proteins.Detection of the Epsilon variant (absent in other national-level studies) in November 2020, highlighted the regional heterogeneity viral spread. This study emphasizes the importance of localized genomic surveillance to capture the true diversity and evolution of SARS-CoV-2, to facilitate containment strategies in resource-limited settings. Full article

Steel fiber reinforced concrete in marine environments often suffers from stress corrosion coupling. Under mechanical loading, the formation of penetrating cracks in the matrix increases susceptibility to seawater penetration and interfacial degradation. Using molecular dynamics simulations, this study investigated the effects of calcium-to-silicon (Ca/Si) ratios on the interfacial bonding and transport properties of a γ-FeOOH/CSH system. The results show that higher Ca/Si ratios strengthen ionic bonding between CSH and γ-FeOOH, thereby improving interfacial adhesion. Additionally, increased Ca/Si ratios significantly slow the transport of water molecules and ions (Na⁺, Cl⁻, SO₄²⁻) within γ-FeOOH/CSH nanopores. It was observed that Cl⁻ and SO₄²⁻ exhibited pronounced filtration effects at Ca/Si = 2.0. These findings suggest that optimizing the Ca/Si ratio in concrete can simultaneously enhance interfacial strength and reduce permeability. This provides an effective strategy for improving the marine erosion resistance of steel fiber reinforced concrete structures. Full article

Pyrola decorata Andres (P. decorata) is a traditional medicinal plant in China. However, its chloroplast genome and the deep evolutionary relationships among its genus remain unexplored. This study identified the samples as P. decorata using morphological observations from Flora of China (FOC) and ITS sequences. It is the first to analyze the complete chloroplast genome of P. decorata using Illumina and Nanopore sequencing technologies, confirming a typical chloroplast dumbbell structure. The chloroplast DNA (cpDNA) of P. decorata is 179,999 bp in length, consisting of a large single copy (LSC) (62.3% of total length (112,150 bp)), a small single copy (SSC) (6.5% of total length (11,701 bp)), and two inverted repeat regions (IRA and IRB) (31.2% combined (28,074 bp × 2)). Functional annotation revealed 128 genes: 77 conserved coding sequences (CDS) genes, 43 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. Phylogenetic analysis placed P. decorata, Pyrola atropurpurea (P. atropurpurea), Pyrola rotundifolia (P. rotundifolia), and Chimaphila japonica within Group I, with P. decorata exhibiting the closest chloroplast genomic affinity to P. atropurpurea. These findings integrate morphological and molecular evidence to facilitate further identification, classification, and evolutionary analysis of this genus. Full article

More and more chemosensors and biosensors are turning to electronic transistors, as they are ideal transducers, precise in current response, miniaturized in size and capable of providing sub-picomolar detection limits. Among these devices, ISFET transistors—Ion-Sensitive Field-Effect Transistors—have the capacity of integrating ion-sensitive layers together with field effect transistors of ultimate generations. Recent studies have indicated that nanoporous materials deposited or grown within the transistor gate space offer a dual advantage—a favorable environment for an optimal capture of liquid state receptors through capillary effects, but also of direct anchoring of these nanoporous structures on a Si wafer. This article aims to review the constructive evolutions of ISFET transistors, along with some newer nanowire devices, as well as their co-integration techniques with nanoporous materials, which are beneficial in the optimization of many chemosensors but of enzymatic biosensors in particular. Full article

The increasing demand for high-throughput, real-time, and single-molecule protein analysis in precision medicine has propelled the development of novel sensing technologies. Among these, nanopore-based methods have garnered significant attention for their unique capabilities, including label-free detection, ultra-sensitivity, and the potential for miniaturization and portability. Originally designed for nucleic acid sequencing, nanopore technology is now being adapted for peptide and protein analysis, offering promising applications in biomarker discovery and disease diagnostics. This review examines the latest advances in biological, solid-state, and hybrid nanopores for protein sensing, focusing on their ability to detect amino acid sequences, structural variants, post-translational modifications, and dynamic protein–protein or protein–drug interactions. We critically compare these systems to conventional proteomic techniques, such as mass spectrometry and immunoassays, discussing advantages and persistent technical challenges, including translocation control and signal deconvolution. Particular emphasis is placed on recent advances in protein sequencing using biological and solid-state nanopores and the integration of machine learning and signal-processing algorithms that enhance the resolution and accuracy of protein identification. Nanopore protein sensing represents a disruptive innovation in biosensing, with the potential to revolutionize clinical diagnostics, therapeutic monitoring, and personalized healthcare. Full article

The nanoporous structure of coal is crucial for the occurrence and development of coalbed methane (CBM). This study, leveraging the combined characterization of atomic force microscopy (AFM) and Gwyddion software (v2.62), investigated six anthracite samples with varying degrees of metamorphism (R_o = 2.11–3.36%). It revealed the intrinsic relationships between their nanoporous structures, surface morphologies, fractal characteristics, and coalification processes. The research found that as R_o increases, the surface relief of coal decreases significantly, with pore structures evolving from being macropore-dominated to micropore-enriched, and the surface tending towards smoothness. Surface roughness parameters (R_a, R_q) exhibit a negative correlation with R_o. Quantitative data indicate that area porosity, pore count, and shape factor positively correlate with metamorphic grade, while mean pore diameter negatively correlates with it. The fractal dimensions calculated using the variance partition method, cube-counting method, triangular prism measurement method, and power spectrum method all show nonlinear correlations with R_o, moisture (M_ad), ash content (A_ad), and volatile matter (V_daf). Among these, the fractal dimension obtained by the triangular prism measurement method has the highest correlation with R_o, A_ad, and V_daf, while the variance partition method shows the highest correlation with M_ad. This study clarifies the regulatory mechanisms of coalification on the evolution of nanoporous structures and surface properties, providing a crucial theoretical foundation for the precise evaluation and efficient exploitation strategies of CBM reservoirs. Full article

Anodised metal matrices represent a versatile and multifunctional platform for the development of advanced materials with tunable physicochemical properties. Through electrochemical oxidation processes—commonly referred to as anodisation—metals such as aluminium, titanium, niobium, zinc and tantalum can be transformed into structured oxide layers with defined porosity, thickness and surface morphology. These methods enable the fabrication of ordered nanoporous arrays, nanotubes and nanowires, depending on the process parameters and the type of metal. The review introduces and outlines the various anodisation techniques and parameters. This is crucial, since each individual metal requires specified optimal conditions to obtain a stable anodised oxide layer. This review provides an overview of recent advances in the design and application of anodised metal substrates, with the focus on their role as functional platforms in catalysis, sensing, energy storage and biomedical engineering. Special attention is given to post-anodisation surface modification strategies, such as chemical functionalisation, thin-film deposition and molecular-level integration, which significantly expand the utility of these materials. The review also highlights the challenges, limitations and future perspectives of anodising technologies, aiming to guide the rational design of next-generation devices based on engineered oxide architectures. Full article

The anodization of aluminium/aluminium alloys is widely used to produce anodic nanoporous networks for metal layered structures, with applications in energy harvesting technologies and sensor systems. Anodic aluminium oxide (AAO) with thickness of ~10 μm and average pore diameter of 13, 33, and 95 nm is prepared by tuning acids and voltages, being further used for electroless nickel deposition, performed for 10 min using conventional electrolyte with sodium hypophosphite reductor and pH 4.5. The formation of Ni nanotubes or nanorods is found to be strongly dependent on AAO pore size. Ni is detected in the whole pore depth and found to form 5–7 μm long continuous tube-like structures only in AAO with pore diameter of 95 nm, being kept just on the AAO top for smaller pore diameters. Nickel distribution in pores along cross-section of AAO is studied as well revealing continuously decreasing ratio to phosphorus amount. The magnetic properties of the resulting Ni 3D structure of a flat conductive layer and nanotubes perpendicular to it do not show significant differences in parallelly and perpendicularly oriented magnetic fields. These observations are discussed considering possible formation mechanisms for an electroless deposited Ni layer on AAO with different structures. Full article

Background: Centella asiatica, a medicinally important species that is rich in bioactive compounds, lacks a characterized mitochondrial genome, despite nuclear and chloroplast assemblies. We sequenced and annotated its mitochondrial genome to elucidate its genetic foundations and evolutionary mechanisms. Methods: Assembly using Illumina short-reads and Nanopore long-reads was used to characterize the mitochondrial genome. Analyses included structural characterization, codon usage bias, repetitive sequences, horizontal gene transfer (HGT), collinearity, and phylogeny. The resulting tissue-specific (root, stem, and leaf) long non-coding RNA (lncRNA) profiles identified RNA editing sites. Results: The complete mitochondrial genome (249,777 bp, 45.5% GC) comprises three circular contigs encoding 51 genes (33 protein-coding, 15 tRNA, and 3 rRNA). Comparative genomics revealed synteny with the Apiaceae family of plants and evidence of HGT. Phylogenetic analysis resolved taxonomic relationships within Apiales. We predicted that 547 RNA editing sites would be identified in its protein-coding genes. Tissue profiling identified 725 (root), 711 (stem), and 668 (leaf) editing sites, with >71% concordance to predictions. RNA editing-generated cryptic promoters/terminators occur in mitochondrial core function genes (e.g., ATP synthase, cytochrome c reductase/oxidase, ribosome large subunit, and cytochrome c biogenesis), exhibiting a lower frequency in the leaves compared to the roots and stems. Conclusions: We provide the first complete mitochondrial genome assembly for C. asiatica, delineating its complex structure, tissue-modulated RNA editing, and evolutionary trajectory. This high-quality genomic resource establishes a foundation for molecular evolutionary studies and enhances the genomic toolkit for this pharmacologically significant species. Full article

Background/Objectives: Messenger RNA (mRNA) modifications regulate key steps in gene expression, including splicing, translation, and stability. Despite over 300 known RNA modifications, the relatively small subset occurring in mRNA remains understudied compared with tRNA and rRNA. This review aims to systematically evaluate 15 known naturally occurring mRNA-specific modifications, rank them by publication frequency, and highlight emerging frontiers in epitranscriptomics, including discovering new naturally occurring mRNA modifications and environmental RNA (eRNA) epitranscriptomics. Methods: We conducted a structured literature review of PubMed-indexed publications to rank mRNA modifications by citation prevalence. Key modifications such as m⁶A, m⁵C, Ψ, and m¹A were analyzed in terms of enzymatic machinery (“writers,” “erasers,” and “readers”), molecular functions, and physiological relevance. We also reviewed technological advances, with a focus on nanopore sequencing for detection of RNA modifications in native and environmental contexts. Results: The modification m⁶A was identified as the most studied mRNA modification, followed by Ψ, m⁵C, and A-to-I editing (inosine). These modifications influence diverse mRNA processes, including translation efficiency, localization, and immune evasion. Cap-specific modifications such as Cap0, Cap1, and Cap2 were also described, highlighting their role in transcript stability and innate immune regulation. Advances in nanopore sequencing have enabled direct detection of RNA modifications and offer promise for eRNA (environmental RNA) surveys. The potential for nanopore sequencing of many other of the 335 known RNA modifications in the MODOMICS database using existing nanopore technologies is also discussed. Conclusions: mRNA modifications represent a critical, yet incompletely mapped, layer of gene regulation. Continued research—especially using nanopore and machine learning technologies—will help uncover their full biological significance. Exploration of eRNA and identifying new mRNA modifications will redefine our understanding of RNA biology. Full article

Understanding concrete creep aging is essential for ensuring structural safety and long-term durability, while the lack of robust numerical models limits the ability to thoroughly investigate and accurately predict time-dependent deformation and cracking behaviors. This study proposes a numerical framework integrating a discrete model and the microprestress solidification (MPS) theory to describe the aging creep and quasi-static performance of concrete at early-age and beyond. Hydration kinetics were formulated into constitutive equations to consider the time-dependent evolution of elastic modulus, strength, and fracture properties. Derived from the MPS theory, a unified creep model is developed within the equivalent rheological framework based on strain additivity. This formulation accounts for both visco-elastic and purely viscous creep phases while coupling environmental humidity effects with aging through the hydration degree. The proposed model is validated against experimental datasets encompassing diverse curing conditions, loading histories, and environmental exposures. The simulation results demonstrate that extended curing age enhances concrete strength (compression and fracture), while increased curing temperature has minimal impact due to the competing effects of microstructural refinement and thermal microcracking; both drying-induced transient creep and thermally induced microcracking contribute to increased creep deformation, driven by changes in microprestress resulting from variations in the chemical potential of nanopore water. The proposed numerical model can provide an effective tool to design and predict the long-term performance of concrete under various environmental conditions. Full article

Background: Structural variants (SVs) play a significant role in gene function and are implicated in numerous human diseases. With advances in sequencing technologies, identifying SVs through whole-genome sequencing (WGS) has become a key area of research. However, variability in SV detection persists due to the wide range of available tools and the absence of standardized methodologies. Methods: We assessed the accuracy of SV detection across various short-read (srWGS) and long-read (lrWGS) sequencing technologies—including Illumina short reads, PacBio long reads, and Oxford Nanopore Technologies (ONT) long reads—using deletion calls from the HG002 benchmark dataset. We examined how variables such as variant calling algorithms, reference genome choice, alignment strategies, and sequencing coverage influence SV detection performance. Results: DRAGEN v4.2 delivered the highest accuracy among ten srWGS callers tested. Notably, leveraging a graph-based multigenome reference improved SV calling in complex genomic regions. Moreover, we proved that combining minimap2 with Manta achieved performance comparable to DRAGEN for srWGS. For PacBio lrWGS data, Sniffles2 outperformed the other two tested tools. For ONT lrWGS, alignment with minimap2—among four aligners tested—consistently led to the best results. At up to 10× coverage, Duet achieved the highest accuracy, while at higher coverages, Dysgu yielded the best results. Conclusions: These results show for the first time that alignment software choice significantly impacts SV calling from srWGS, with results comparable to commercial solutions. For lrWGS, the performance depends on the technology and coverage. Full article

Bionic synthesis technology has made significant breakthroughs in porous functional materials by replicating and optimizing biological structures. For instance, biomimetic titanium dioxide-coated carbon multilayer materials, prepared via biological templating, exhibit a hierarchical structure, abundant nanopores, and synergistic effects. Bionic mineralization further enhances microcapsules by forming a secondary inorganic wall, granting them superior impermeability, high elastic modulus, and hardness. Through techniques like molecular self-assembly, electrospinning, and pressure-driven fusion, researchers have successfully fabricated centimeter-scale artificial lamellar bones without synthetic polymers. In environmental applications, electrospun membranes inspired by lotus leaves and bird bones achieve 99.94% separation efficiency for n-hexane–water mixtures, retaining nearly 99% efficiency after 20 cycles. For energy applications, an all-ceramic silica nanofiber aerogel with a bionic blind bristle structure demonstrates ultralow thermal conductivity (0.0232–0.0643 W·m⁻¹·K⁻¹) across a broad temperature range (−50 to 800 °C). This review highlights the preparation methods and recent advances in biomimetic porous materials for practical applications. Full article