Search Results (513)

Background/Objectives: The retromer protein complex is involved in various physiological processes, especially endosomal trafficking, and its dysregulation has been linked to Alzheimer’s disease and Parkinson’s disease, as well as VPS35 knockout (KO), causing early embryonic lethality. We aimed to investigate the cellular consequences of VPS35 deficiency. Methods: To investigate the effects of VPS35 loss, we used CRISPR/Cas9 to generate VPS35 KO human embryonic kidney 293 (HEK293) cells. We analyzed changes in retromer component expression, cell proliferation, apoptosis, and mitochondrial dynamics using Western blotting, terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) assay, and confocal microscopy. Results: VPS35 KO led to a significant reduction in cell proliferation and decreased expression of VPS29 and VPS26, both essential for retromer complex assembly. Consequently, retromer formation was impaired. Compared to control cells, KO cells exhibited elevated levels of cleaved caspase-3, poly(ADP-ribose) polymerase, cytochrome C, and p21, while the expression of Ki-67, CDK4, and cyclin D was reduced. Additionally, VPS35 deletion also promoted mitochondrial fragmentation, associated with increased expression of mitochondrial fission-related proteins. Finally, the rescue experiment using the human VPS35 gene confirmed that the recovery of VPS35 not only led to the recovery of the essential elements constituting the retromer but also the recovery of molecules related to the cell cycle, restoring cell death to a normal level. Conclusions: These findings suggest that VPS35 plays a critical role in cell growth and survival by modulating apoptosis, mitochondrial dynamics, and cell cycle progression. Full article

An accurate prediction of aircraft wheel and brake (W&B) temperatures is increasingly important for ensuring landing gear safety, supporting turnaround decision-making, and allowing for more effective condition monitoring. Although the thermal behavior of brake assemblies has been studied through component-level testing, analytical formulations, and numerical simulation, current understandings remain fragmented and limited in operational relevance. This paper discusses research across landing gear sensing, thermal modeling, and data-driven prediction to evaluate the state of knowledge supporting a non-intrusive, temperature-centric monitoring framework. Methods surveyed include optical, electromagnetic, acoustic, and infrared sensing techniques as well as traditional machine-learning methods, sequence-based models, and emerging hybrid physics–data approaches. The review synthesizes findings on conduction, convection, and radiation pathways; phase-dependent cooling behavior during landing roll, taxi, and wheel-well retraction; and the capabilities and limitations of existing numerical and empirical models. This study highlights four core gaps: the scarcity of real-flight thermal datasets, insufficient multi-physics integration, limited use of infrared thermography for spatial temperature mapping, and the absence of advanced predictive models for transient brake temperature evolution. Opportunities arise from emissivity-aware infrared thermography, multi-modal dataset development, and machine learning models capable of capturing transient thermal dynamics, while notable challenges relate to measurement uncertainty, environmental sensitivity, model generalization, and deployment constraints. Overall, this review establishes a coherent foundation for thermography-enabled temperature prediction framework for aircraft wheels and brakes. Full article

Industrialised construction (IC) represents a foundational strategy for overcoming entrenched productivity constraints and supply shortfalls in the housing sector. By enabling the mass production and mass customisation of advanced kit-of-parts systems, IC supports more efficient, predictable, scalable, and sustainable building delivery through integrated, standardised, and digitally enabled processes. However, adoption remains uneven due to fragmentation across regulatory, organisational, and technological systems. This paper presents a systematic literature review and thematic synthesis of the literature published between 2000 and 2025 to examine performance outcomes, adoption trends, digital integration maturity, and emerging platform-based design for manufacture and assembly (P-DfMA) approaches, and the main drivers. The review shows that significant performance gains are achievable, including notable reductions in construction time and cost variability, along with substantial reductions in material waste, together with measurable improvements in quality, safety, and delivery predictability. However, widespread uptake of IC remains constrained. This is largely driven by regulatory misalignment, rigid and bespoke procurement and delivery models, inconsistent and unstable supply chain capacity, and the lack of standardised components and integrated digital workflows. Building on these insights, this paper examines the key enablers required for sector-wide transformation toward an ecosystem that supports standardised kit-of-parts solutions, digitally driven design-to-production workflows, and aligned policy and procurement frameworks that are capable of delivering scalable and repeatable industrialised housing. The findings provide a consolidated evidence base and identify the key enablers for policymakers, industry stakeholders, and researchers working to move from project-centred delivery models to platform-based, digitally integrated, and industrialised construction systems. We searched Scopus, Web of Science, ScienceDirect, and Google Scholar, complemented by targeted industry and policy repositories; the searches were last updated on 1 December 2025. After screening, 117 sources were included. The review was not registered, and no review protocol was prepared. Full article

Porcine epidemic diarrhea virus (PEDV) has emerged as a major pathogen responsible for porcine diarrheal diseases, causing outbreaks of severe diarrhea and high mortality in neonatal piglets, thereby inflicting severe economic losses on the global swine industry. Current commercial PED vaccines, comprising conventional inactivated and live attenuated formulations, have exhibited progressively diminished efficacy in the face of emerging PEDV variants. The development of high-efficiency vaccine platforms is therefore critical for PED control. This study engineered a cellular membrane nanovesicle (CMN)-based vaccine, which differs from existing inactivated or subunit vaccines by presenting the PEDV spike (S) protein on the cell membranes to mimic the bilayer phospholipid structure of the viral envelope. The full-length S protein (FS, aa 19-1309) or a truncated S protein fragment (TS, aa 19-726) was expressed in Expi293F cells, followed by extraction of cell membranes to assemble antigen-displaying CMN vaccines. Compared with commercial live attenuated vaccine, administration of the CMN vaccine elicited high-titer neutralizing antibodies and elevated IFN-γ-producing CD8⁺ T cells in murine studies. Safety assessments revealed no adverse effects on body weight, hepatic/renal function indices, or histopathological parameters in vaccinated mice. Furthermore, immunization of piglets elicited notable humoral and CD8⁺ T cell immune responses. Collectively, the strategy of CMN-based vaccine described herein delivers a potential PEDV vaccine platform, thereby offering a novel avenue for next-generation veterinary vaccine development. Full article

Infectious Bronchitis Virus is one of several major viral infections in poultry, affecting the respiratory, reproductive, and renal systems and causing significant economic losses worldwide. Current vaccines, including the H120 strain, provide limited cross-protection against emerging variants, underscoring the need for improved vaccine strategies. In this study, the complete genome of IBV H120 was divided into 12 fragments, synthesized, and assembled using the Golden Gate Assembly (GGA) method. The recombinant virus (rH120) was successfully rescued in chicken fibroblast cells and propagated in embryonated specific-pathogen-free (SPF) chicken eggs. Growth kinetics in embryonated SPF chicken eggs revealed similar replication patterns between rH120 and the original H120 strain. In broiler chickens, rH120 replicated efficiently, as confirmed by viral RNA detection in throat and cloacal swabs, and induced a stronger antibody response by 14 days post-infection. The rH120 virus proved to be genetically stable, infectious, and immunogenic, indicating that GGA-based reverse genetics is an effective system for IBV vaccine development. Full article

Background: Stenotrophomonas maltophilia is an increasingly important multidrug-resistant opportunistic pathogen frequently isolated from clinical, environmental, and plant-associated niches. Despite its medical relevance, the global population structure, species-complex boundaries, and genomic determinants of antimicrobial resistance (AMR) and ecological adaptation remain poorly resolved, partly due to inconsistent annotations and fragmented genomic datasets. Methods: Approximately 2400 genome assemblies annotated as Stenotrophomonas maltophilia were available in the NCBI Assembly database at the time of query. After pre-download filtering to exclude metagenome-assembled genomes and atypical lineages, 1750 isolate genomes were retrieved and subjected to stringent quality control (completeness ≥ 90%, contamination ≤ 5%, ≤500 contigs, N50 ≥ 10 kb, and ≤1% ambiguous bases), yielding a final curated dataset of 1518 high-quality genomes used for downstream analyses. Genomes were assessed using CheckM, annotated with Prokka, and compared using average nucleotide identity (ANI), pan-genome analysis, core-genome phylogenomics, and functional annotation. AMR genes, mobile genetic elements (MGEs), and metadata (source, host, and geographic origin) were integrated to assess lineage-specific genomic features and ecological distributions. Results: ANI-based clustering resolved the S. maltophilia complex into multiple distinct genomospecies and revealed extensive misidentification of publicly deposited genomes. The pan-genome was highly open, reflecting strong genomic plasticity driven by accessory gene acquisition. Core-genome phylogeny resolved well-supported clades associated with clinical, environmental, and plant-related niches. Resistome profiling showed widespread intrinsic MDR determinants, with certain lineages enriched for efflux pumps, β-lactamases, and trimethoprim–sulfamethoxazole resistance markers. MGE analysis identified lineage-specific integrative conjugative elements, prophages, and transposases that correlated with source and geographic distribution. Conclusions: This large-scale analysis provides the most comprehensive genomic overview of the S. maltophilia complex to date. Our findings clarify species boundaries, highlight substantial taxonomic misannotation in public databases, and reveal lineage-specific AMR and mobilome patterns linked to ecological and clinical origins. The curated dataset and evolutionary insights generated here establish a foundation for global genomic surveillance, epidemiological tracking, and future studies on the evolution of antimicrobial resistance in S. maltophilia. Full article

Human non-polio enteroviruses (NPEVs) cause a plethora of infections in humans, ranging from mild to severe neurological diseases including aseptic meningitis. NPEVs are the leading cause of aseptic meningitis in both children and adults worldwide. In Russia, reports of NPEV infections have surged, especially in the post-COVID era starting in 2022, with elevated infection rates into 2023. A comprehensive examination of the whole genome is crucial for understanding the evolution of NPEV genes and for predicting potential outbreaks. This study focused on identifying the circulating NPEV strains in the Ural Federal District and Western Siberia, using Sanger sequencing and next-generation sequencing (NGS) methodologies. Biological samples were collected from (n = 225) patients diagnosed with aseptic meningitis. Bioinformatics analysis targeted the nucleotide sequences of the major capsid protein (partial VP1) gene fragment, and the assembly of whole NPEV genomes. A total of 159 NPEVs were characterized, representing 70.7% of the collected samples. The main capsid variants forming the predominant genotypic profile included E30 (n = 39, 24.3%), E6 (n = 31, 19.3%), and CVA9 (n = 25, 15.6%). Using NGS, we successfully assembled 13 whole genomes for E6, E30, EV-B80, CVA9, CVB5, E11, and EV-A71 and 3 partial genomes for E6 and EV-B87. This molecular-genetic analysis provides contemporary insights into the genotypic composition, circulation patterns, and evolutionary dynamics of the dominant NPEV associated with aseptic meningitis in the Ural Federal District and Western Siberia. The laboratory-based monitoring and epidemiological surveillance for genetic changes and evolutionary studies are important for improving prevention and healthcare. Full article

Choy sum (Brassica rapa var. parachinensis) is an important vegetable crop in Brassicaceae. However, its mitochondrial genome has not been well studied. In this study, Illumina and Nanopore sequencing technologies were combined to assemble the complete mitochondrial genome of choy sum. The mitochondrial genome is a circular molecule of 219,775 bp, with a GC content of 45.23%. A total of 60 genes were annotated, including 33 protein-coding genes (PCGs), 23 transfer RNA (tRNA) genes, 3 ribosomal RNA (rRNA) genes, and one pseudogene. A total of 466 RNA editing sites were identified in the PCGs. Codon usage analysis revealed that leucine (leu) was the most frequently used amino acid. Twenty-nine codons showed a relative synonymous codon usage (RSCU) value greater than 1. Most of these preferred codons ended with A or U. A total of 308 repetitive sequences were detected, including 136 dispersed repeats, 17 tandem repeats, and 55 simple sequence repeats (SSRs). Evolutionary analysis indicated that most mitochondrial genes are under negative selection. The highest nucleotide diversity detected in the cox2 gene suggests that this gene could serve as a valuable molecular marker for mitochondrial research in the species. Homology analysis found 22 homologous fragments between the mitochondrial and chloroplast genomes of choy sum. These fragments total 13,325 bp, representing 6.06% of the mitochondrial genome. Phylogenetic analysis showed that choy sum is most closely related to B. rapa var. purpuraria. This study offers a genomic resource for genetic improvement and breeding of choy sum. It also provides molecular insights into the evolution of Brassica species. Full article

This study presents an in silico proof of concept exploring whether deep learning models can perform conditional mitochondrial DNA (mtDNA) sequence prediction across species boundaries. A CNN–BiLSTM model was trained under a leave-one-species-out (LOSO) scheme on complete mitochondrial genomes from 21 vertebrate species, primarily archosaurs. Model behavior was evaluated through multiple complementary tests. Under context-conditioned settings, the model performed next-nucleotide prediction using overlapping 200 bp windows to assemble contiguous 2000 bp fragments for held-out species; the resulting high token-level accuracy (>99%) under teacher forcing is reported as a diagnostic of conditional modeling capacity. To assess leakage-free performance, a two-flank masked-span imputation task was conducted as the primary evaluation, requiring free-running reconstruction of 500 bp interior spans using only distal flanking context; in this setting, the model consistently outperformed nearest-neighbor and demonstrated competitive performance relative to flank-copy baselines. Additional robustness analyses examined sensitivity to window placement, genomic region (coding versus D-loop), and random initialization. Biological plausibility was further assessed by comparing predicted fragments to reconstructed ancestral sequences and against composition-matched null models, where observed identities significantly exceeded null expectations. Using the National Center for Biotechnology Information (NCBI) BLAST web interface, BLASTn species identification was performed solely as a biological plausibility check, recovering the correct species as the top hit in all cases. Although limited by dataset size and the absence of ancient DNA damage modeling, these results demonstrate the feasibility of conditional mtDNA sequence prediction as an initial step toward more advanced generative and evolutionary modeling frameworks. Full article

Agricultural materials frequently undergo fragmentation due to high-stress conditions during processing, storage, and transportation. Throughout these processes, the spatial arrangement and morphology of particles continuously evolve, rendering the breakage behaviour of particle groups particularly complex. Thus, an in-depth understanding of the fracture processes and breakage mechanisms within particle beds holds significant research value. This study systematically investigates the breakage behaviour of rice particle groups under confined compression through an integrated methodology combining experimental testing, X-ray CT imaging, and finite element modelling (FEM) based on the cohesive zone model (CZM). Results demonstrate that, at the granular assembly scale, external loads are transmitted through force chains and progressively attenuate. As compression proceeds, stress disseminates toward peripheral particle regions. At the individual particle level, particle breakage results from the intricate interaction between coordination number (CN) and localized contact stress, with tensile stress playing a predominant role in the fracture process. An increase in coordination number promotes a more uniform stress distribution and inhibits breakage, thereby exhibiting a “protective effect”. These findings provide valuable insights for the design and optimization of grain processing equipment, contributing to a deeper comprehension of particle breakage characteristics. Full article

Providing effective post-disaster housing remains a globally complex challenge shaped by interrelated constraints, including environmental sustainability, socio-cultural compatibility, logistical capacity, and economic feasibility. Contemporary responses therefore require housing solutions that extend beyond rapid deployment to incorporate flexibility, adaptability, and long-term spatial transformation. In this context, this study advances a design-oriented, computational framework that positions parametric design at the core of post-disaster housing production within the broader digital transformation of the construction sector. The research proposes an adaptive parametric–modular housing system in which standardized architectural units are governed by a rule-based aggregation logic capable of generating context-responsive spatial configurations across multiple scales and typologies. The methodology integrates a qualitative synthesis of global post-disaster housing literature with a quantitative computational workflow developed in Grasshopper for Rhinoceros 3D (version 8). Algorithmic scripting defines a standardized spatial grid and parametrically regulates key building components structural systems, façade assemblies, and site-specific environmental parameters, enabling real-time configuration, customization, and optimization of housing units in response to diverse user needs and varying climatic, social, and economic conditions while maintaining constructability. The applicability of the framework is examined through a case study of the Düzce Permanent Housing context, where limitations of existing post-disaster stock, such as spatial rigidity, restricted growth capacity, and fragmented public-space integration, are contrasted with alternative settlement scenarios generated by the proposed system. The findings demonstrate that the framework supports multi-scalar and multi-typological reconstruction, extending beyond individual dwellings to include public, service, and open-space components. Overall, the study contributes a transferable computational methodology that integrates modular standardization with configurational diversity and user-driven adaptability, offering a sustainable pathway for transforming temporary post-disaster shelters into permanent, resilient, and socially integrated community assets. Full article

The assembly of telomere-to-telomere (T2T) genomes is essential for understanding genomic architecture, especially in fungal pathogens with complex karyotypes, such as Colletotrichum lini, causing flax anthracnose disease. This study provides optimized guidelines for the T2T genome assembly using Oxford Nanopore Technologies (ONT) R9.4.1 and R10.4.1 sequencing data processed with the Hifiasm 0.25.0 assembler (with --ont module). We analyzed ONT sequencing data for four C. lini strains and compared basecalling tools (Guppy and Dorado), read filtration strategies (quality thresholds Q10/Q15 and length cut-offs 5 kb/10 kb), and genome coverage levels from 5× to 160×. Our results demonstrated that Dorado-basecalled reads consistently had higher average quality, especially the R10.4.1 data, leading to improved telomere resolution and complete mitochondrial genome assembly. Moderate genome coverage (40–65×) combined with Q15 quality and 5 kb length filtration for R10.4.1 data, or Q10 and 5 kb for R9.4.1 data, produced the most contiguous and complete assemblies. Overfiltration of reads by length and quality or conversely excessive coverage (>90×) reduced assembly quality, causing fragmentation or erroneous chromosome merging. With optimized parameters of ONT R9.4.1 and R10.4.1 sequencing data preprocessing, Hifiasm efficiently generated T2T and near-T2T assemblies of C. lini genomes: 53.7–56.1 Mb length, 13–30 contigs, 12–13 chromosomes (including 3–12 T2T chromosomes), complete mitochondrial genome, and >98.5% BUSCO completeness. These findings provide a solid framework for ONT-based fungal genome assembly, facilitating future research on genomic variation and pathogenicity in Colletotrichum and related genera. Full article

Reversible addition-fragmentation chain transfer mediated polymerization-induced self-assembly (RAFT-PISA) offers an efficient approach for the preparation of polymeric nanomaterials, giving access not only to common structures such as spheres, worm-like micelles and vesicles, but also to much more complex meso-objects. However, when the core forming block polymer possesses a high glass transition temperature (Tg), like poly(methyl methacrylate) or polystyrene (PS), high-order morphologies are particularly difficult to achieve since the glassy core can prevent polymer chain reorganization during PISA. To overcome this issue, we chose to perform visible light-initiated RAFT-PISA of poly(tert-butyl acrylate)-block-polystyrene (PtBA-b-PS) in solvent systems with varying degrees of polarity. More specifically, we prepared different mixtures of diisopropyl ether and ethanol and chose PtBA as macro-CTA due to its broad range of solubility. By varying the ratio between ethanol and diisopropyl ether, we could observe a transition from spherical micelles to vesicles via intermediate structures (e.g., necklace-like micelles, network-like micellar aggregates and wedding rings). This result was particularly remarkable since the experiments were performed near room temperature. We believe that these multiple morphologies were induced by the interactions between the solvent and the corona and the change in swelling of the polystyrene core with styrene monomer that facilitated its rearrangement. We anticipate that this approach could be applied to other polymeric systems with high Tgs. Full article

Ormosia henryi, a rare and endemic timber tree in China, possesses exceptional economic and ecological value, but it has experienced a critical decline in wild populations. We integrated PacBio HiFi and Hi-C technologies to generate a superior, chromosome-level genome assembly, establishing a more robust genetic foundation than existing draft sequences. The resulting assembly (2.64 Gb; Contig N50 = 39.17 Mb; and Scaffold N50 = 338.40 Mb) exhibits high continuity and completeness, effectively overcoming the assembly challenges associated with high heterozygosity (1.37%) and repetitive sequence content (83.89%). Comparative genomic analysis revealed that O. henryi diverged from Lupinus albus approximately 53.82 million years ago and underwent two independent whole-genome duplication events. The historical accumulation of evolutionary resilience is reflected in the significant expansion of 276 gene families enriched in photosynthesis and phenylpropanoid biosynthesis, alongside 122 genes under positive selection involved in DNA repair and proteostasis. These genomic signatures elucidate a stable genetic foundation. While wild populations have sharply declined in recent decades, this suggests that this status underscores the overwhelming impact of intense external anthropogenic pressures, such as overexploitation and habitat fragmentation, which may have overridden the species’ inherent adaptive capacity and slow life-history strategy. This high-quality genomic resource identifies key candidate loci, such as the PIF1 helicase for growth regulation, and provides a critical framework for screening elite germplasm for population restoration. Consequently, this study establishes a theoretical and molecular basis for transitioning from fundamental research to the precision conservation and sustainable industrial application of this high-value woody species. Full article

Herein, we report the synthesis via controlled reversible addition-fragmentation chain transfer (RAFT) polymerization of amphiphilic 2-vinylpyridine-b-styrene (2VPy-b-Sty) diblock copolymers of high molar masses (range: 52,100–304,000 g mol⁻¹) and various compositions (range: 2VP content 11.6–59.2 mol%) and their use for the fabrication of nanoporous membranes. The successful synthesis of the amphiphilic diblock copolymers was confirmed through the characterization of their molar masses, molar mass distribution, and composition using GPC and ¹H-NMR spectroscopy, respectively. Subsequently, membranes of the diblock copolymers were fabricated following the “phase inversion” technique. The resulting membranes were characterized via scanning electron microscopy which revealed the presence of sphere percolation networks morphology for all diblock copolymers with M_n ranging from 120 to 300 kDa and 2VPy content between 10 and 15 mol% at the optimal conditions. Afterward, the developed membranes were evaluated in terms of their permeability towards water and in terms of their ability to retain two different microorganisms, namely, Enterococcus faecalis and Escherichia coli, that are known to be harmful to human health. The experimental water flux for a membrane with pore size around 60 nm was equal to 31,400 L h⁻¹ m² and expectedly decreased with the decrease in membrane pore diameter. The retention ability of membranes for Enterococcus faecalis and Escherichia coli was higher than 90%. In particular, the retention ability for Enterococcus faecalis was equal to 98.9% and for Escherichia coli was 91.4%. The toxicity of the produced membrane was also determined, and the measured value was relatively low, at 17%. Full article