Surface diffusion limitation at the interfaces of nanoporous crystals has emerged as a critical factor limiting mass transport, thereby impeding the catalytic and separation efficiencies. The crux in further optimization of nanoporous solids lies in visualizing nanoscale mass transport under confinement and correlating the observed phenomena with specific surface nanostructures. Here, we revealed that the bottom-up synthesized surface nanoconcavities markedly mitigate benzene traffic control (molecular accumulation) at the ZSM-5 nanocrystal periphery, a phenomenon indicative of surface diffusion limitation, by integrating atomic in situ low-dose scanning transmission electron microscopy with multiscale molecular dynamic simulations. Unexpectedly, the sinusoidal open pores terminated by a half Si10-ring at sidewalls of the nanoconcavity become additional accessible pathways, compared to the smooth surface, for molecular ingress and egress. Besides, the confinement inherent to nanoconcavities increases the residence time of benzene molecules on the concave surface, promoting their capture by pore mouths. This study establishes a nanoscale methodology for correlating local structure with mass transport in nanoporous materials and highlights a termination structure-engineering viewpoint for controlling surface diffusion limitation.

Introduction: Metatranscriptomic analyses provide critical insights into differentially expressed genes (DEGs) and their clinical implications. By leveraging wastewater-based epidemiology (WBE) and high-throughput sequencing, we can monitor viral pathogens cost-effectively, offering a robust approach to public health surveillance. Materials and methods: Our study utilized short-read Illumina whole transcriptome shotgun sequencing (WTSS) and long-read Oxford Nanopore Technologies (ONT) to identify DEGs associated with SARS-CoV-2 pathogenesis and viral–host interactions. We processed 10 samples via an Illumina metatranscriptomic approach and 48 samples using the ONT midnight protocol, followed by downstream statistical and pathway analyses. Results: The merged assembly between Illumina and ONT yielded 381,524 transcripts mapped to 340,439 unigenes, with a total transcript length of 287,252,541 and an average unigene length of 752.9 bases. Our research reveals distinct transcriptional and microbial diversity patterns across sample types, likely reflecting both environmental and host-specific factors. We identified distinct alpha diversity clades between WBE and clinical microbiomes, suggesting concurrent infections. Conclusions: Host transcriptional signatures, such as methyl-accepting chemotaxis proteins (MCP) signals and ATP-binding cassette (ABC) transporters, clarify the role of DEGs in the infectious cycle. This analysis advances our understanding of the molecular basis of SARS-CoV-2 and underscores the importance of WBE in combating infectious diseases.

The properties of nanoporous metal oxides depend on their pore structure and the internal structure of the pore walls, and precise control of such factors is crucial. In particular, single-crystalline nanoporous metal oxides, in which the pore walls consist of a single crystal, exhibit characteristics of both single crystals and nanoporous materials that are distinct from conventional polycrystalline materials. Herein, we report the synthesis of single-crystalline mesoporous indium tin oxide (ITO) with a pore diameter of ∼30 nm and a controlled Sn/In ratio. The synthesis was achieved using regularly arranged silica nanospheres (silica colloidal crystals) as a template, followed by crystal growth of ITO within the template by oxidation of metal chloride precursors. By increasing the oxygen-to-metal chloride ratio, crystal growth outside the template was suppressed and the volatilization of Sn species was reduced, thereby enabling an increase in the Sn/In molar ratio to 0.10, which is critical for electrical conductivity.

Stemona tuberosa is a medicinally important species, however, a complete telomere-to-telomere (T2T) genome assembly has remained unavailable. Here, we present the first T2T genome assembly for S. tuberosa, generated by integrating PacBio HiFi, ultra-long Oxford Nanopore, Illumina, and Hi-C sequencing technologies. The assembly produced two highly contiguous haplotype-resolved genomes, with total sizes of 803.04 Mb and 795.04 Mb, and contig N50 values of 113.29 Mb and 111.11 Mb, respectively. The proportion of fully assembled chromosomes reached 100% in both haplotypes. In addition, 14 putative centromeric regions were successfully identified across 7 pseudochromosomes, along with the annotation of 25,561 and 25,854 genes in the two haplotypes, respectively. This T2T genome assembly of S. tuberosa provides a valuable reference for elucidating the genetic architecture of the species. It significantly advances our capacity to investigate structural variations, gene function, and evolutionary processes within Stemona and related medicinal plant lineages.

Telomere-to-telomere phased assemblies are emerging as a benchmark for reference-quality genomes1,2, although they remain technically and financially demanding, particularly at scale. Generating such assemblies for diploid and polyploid genomes typically involves combining high-accuracy long reads, such as PacBio HiFi3 or the now-deprecated Oxford Nanopore Technologies (ONT) Duplex4 reads, with ultra-long ONT Simplex reads. Using multiple platforms or methods increases the cost and the required amount of genomic DNA. Here we show that comparable results are possible using error correction of ultra-long Simplex reads and then assembling them using state-of-the-art de novo assembly methods. To achieve this, we developed the deep learning-based HERRO (haplotype-aware error correction) framework, which corrects Simplex reads while carefully preserving differences in related genomic sequences. Taking into account informative positions that differentiate the haplotypes or genomic repeat copies, HERRO achieves an increase of read accuracy of up to 100-fold for diploid human genomes. By combining HERRO with the Verkko2 assembler, we reconstruct up to 32 chromosomes telomere-to-telomere, including chromosomes X and Y, and consistently achieve NGA50 (normalized genome assembly 50) values of 100 Mb or higher across several human genomes. HERRO supports both R9.4.1 and R10.4.1 Simplex reads and generalizes well to other species. These results show that error-corrected ONT reads can lower sequencing costs and improve the quality of genomic analyses.

Manganese-based cathodes offer high capacity, low cost, and safety for aqueous zinc-ion batteries (AZIBs), yet suffer from Mn dissolution, Jahn–Teller distortion, and sluggish Zn2+ kinetics. Herein, a Zn/Co co-doped MnO nanoporous carbon composite (denoted as ZnCo-MnO@NPC) derived from a bimetallic ZnCoMn metal–organic framework (ZnCoMn-MOF-74) is successfully synthesized and proposed as a high-performance cathode to address these challenges. The introduction of Zn2+ increases the initial specific capacity of MnO, while Co doping effectively suppresses the Jahn–Teller distortion and improves the integrity of the structure. Furthermore, the nanoporous carbon matrix facilitates electrolyte infiltration and accelerates ionic transport. To further suppress dendrite growth and enhance cycling stability, a zeolitic imidazolate framework (ZIF-8) protective layer is engineered on the zinc anode (denoted as ZIF-8@Zn), effectively mitigating dendrite formation. The ZnCo-MnO@NPC//ZIF-8@Zn full cell demonstrates superior electrochemical performance, delivering 281.3 mAh g−1 at 0.1 A g−1 and retaining 98.7% of this value after 3500 long-term cycles at 2.0 A g−1, a remarkable finding that underscores its potential for high-performance energy storage. Collectively, this work highlights that transition metal ion doping represents an effective way to design efficient high-performance MOF-derived cathodes of AZIBs.

Aeromonas dhakensis and Aeromonas hydrophila cause significant economic losses within the global aquaculture sector, affecting numerous farmed fish species and posing a zoonotic threat to human health. In this study, we sequenced, assembled and analysed the genomes of seven and five A. dhakensis and A. hydrophila isolates, respectively, recovered from disease outbreaks in various fish hosts across Southeast Asia using a hybrid sequencing approach with Illumina and Oxford Nanopore technologies. To assess the relatedness of our isolates with those from the global aquatic environment, with particular reference to aquaculture-relevant systems, and compare their resistome and virulome profiles, we also conducted comparative genomic analysis with an additional 57 publicly available genomes of A. dhakensis and A. hydrophila, recovered from different aquatic sources. Findings from this study revealed large genomic variability across global Aeromonas populations, with a clear distinction in the pan-genome between Aeromonas species. In silico multi-locus sequence type analysis revealed a wide distribution of sequence types (STs) 656 and 251 in Asia in A. dhakensis and A. hydrophila, respectively, although the novel STs detected in Indonesia and the Philippines suggest local adaptation of populations circulating in these countries. Analysis of mobile genetic elements revealed plasmids, insertion sequences and genomic islands to be country- or host-specific. Exploration of resistome data revealed a high prevalence of multidrug resistance across Southeast Asia, with genomes frequently carrying resistance genes against antibiotic classes commonly used across the aquaculture sector, including potentiated sulphonamides and tetracyclines. However, several antimicrobial resistance genes were found to be country- or host-specific, suggesting local adaptation to anthropogenic or environmental conditions within specific regions. A diverse repertoire of virulence genes was also detected in this study, with A. hydrophila demonstrating greater diversity in virulence genes compared with A. dhakensis. Country-specific virulence pathways were also noted for several toxins and secretion systems, including aerA/act, rtx and type III and IV secretion systems. This work provides new insights into the genomic features and relatedness of Aeromonas spp. circulating within aquaculture systems in Southeast Asia. Further, findings from comparative genomic analysis highlight the influence of geographical or host pressures on the molecular drivers of antimicrobial resistance and pathogenicity, directly impacting animal health and aquaculture production.

Dataset of prokaryotic and eukaryotic community structures from sediment and surface water eDNA of a sustainable mangrove fisheries (SMF) aquaculture pond

Next-generation sequencing (NGS) can generate gigabytes of genome data. Unlike Sanger sequencing, NGS generates a ‘read’ from a single DNA molecule, reflecting directly the starting DNA, including non-target organisms such as symbionts and pathogens. Non-target organism sequences are usually discarded during genome assembly as contaminants; these are potentially a great source of information for understanding the microbiome surrounding the plant. The present study explores bioinformatically the identification of the non-target organisms from genome NGS datasets of two cultivated Gesneriaceae species. The datasets were generated using different NGS technologies: one is from Streptocarpus rexii (Bowie ex Hook.) Lindl., sequenced using Oxford Nanopore Technologies long-read sequencing, and the second from Aeschynanthus angustifolius (Blume) Steud., sequenced using Illumina short-read sequencing. The reads were first assembled and then analysed using BlobTools to identify the contaminants. For S. rexii, Actinomycetota and Basidiomycota occupied the highest ratio among genome contaminants, followed by Arthropoda, Ascomycota and Acidobacteriota. In A. angustifolius, the highest contaminant class was Pseudomonadota and the second Actinomycetota, followed by Basidiomycota and Chordata. Arthropoda included mealybugs which were also observed in the glasshouse. The differences in contaminant composition between S. rexii and A. angustifolius may be linked to the relatively short-lived leaves of the former and the long-lived ones of the latter. This pilot study demonstrates that, in principle, this method is suitable to detect and identify associated organisms, and the pipelines designed here greatly facilitated this process. This approach might be useful in a horticultural setting for the assessment of plant material in quarantine or biosecure conditions and may be able to detect pathogens prior to plants showing symptoms. It also has potentially more widespread applications for studying plant–microbiome interactions.

Hydropotes inermis (Chinese water deer, 2n = 70) is a relatively primitive small Cervidae species naturally distributed along the eastern coast of China and the Korean Peninsula. High-quality genomic resources are essential for investigating its unique adaptive and biological traits. In this study, we assembled the telomere-to-telomere (T2T) gap-free genome of a female H. inermis using PacBio HiFi, Oxford Nanopore Technologies (ONT), and Hi-C sequencing technologies. The assemblies were 3.45 Gb with a contig N50 of 101.09 Mb in size, which were anchored on 35 chromosomes, carrying 60 telomeres and 35 centromeres. Genome annotation annotated 33.36% repetitive sequences and 24,398 protein-coding genes. Comparative analyses with genomes of closely related species confirmed high genome integrity, continuity, and accuracy, supported by a quality value (QV) of 52.56 and a BUSCO completeness of 99.40%. This study provides a valuable genetic resource for H. inermis and serves as an important reference for investigating the evolutionary history of Cervidae.

Broccoli (Brassica oleracea var. italica) is a widely cultivated cruciferous vegetable valued for its abundant bioactive compounds and nutraceutical properties. Among these, anthocyanins are not only important secondary metabolites contributing to nutritional and medicinal benefits, but also influence stress tolerance and the commercial quality of broccoli through purple pigmentation. However, the molecular mechanisms regulating anthocyanin biosynthesis in broccoli remain poorly understood, partly due to the incomplete genomic resources currently available. In this study, we constructed a telomere-to-telomere gap-free assembly of the broccoli genome using a combination of Oxford Nanopore Technology ultralong reads, PacBio high-fidelity reads, and Hi-C datasets. The resulting genome is 633.61Mb in length, with an N50 of 60.36Mb, and comprises gap-free assemblies of all 18 chromosomes, including complete telomere-to-telomere assemblies for nine chromosomes. Using this high-quality reference, we identified BoF3'H, a key gene regulating anthocyanin accumulation, which controlling the purple coloration of broccoli buds. To validate the function of the BoF3'H gene in anthocyanin biosynthesis, we used CRISPR-Cas9 gene editing to target and knock out the BoF3'H gene. The bof3'h mutant exhibited an 81.4% reduction in cyanidin and delphinidin derivative levels compared with those in the control. Metabolomic and transcriptomic profiling showed that the expression of 12 anthocyanin-related genes, including PAL, C4H, CL3, CHS, F3'H, and ANS, was downregulated. These findings elucidate the molecular basis of anthocyanin regulation in broccoli and provide a foundational genomic resource for evolutionary studies, gene discovery, and future breeding.

Nanoporous materials including zeolites, metal-organic frameworks, and covalent organic frameworks offer high tunability and surface area, making them ideally suited to address global challenges such as CO2 capture and conversion, utilization of renewable feedstocks, and air purification. Molecular modeling is essential to enable atomic-scale design for optimal performance. Chemical transformations in these materials include not only catalytic reactions, but also local or global structural rearrangements and are strongly dependent on extreme operating conditions typical for industrial processes. The performance of industrial catalysts is governed by complex reaction networks and multiscale phenomena like diffusion and reactions, spanning a broad range of timescales and length scales. Recent advances at the intersection of quantum mechanics, statistical physics, and machine learning have significantly improved our ability to model complex chemical transformations in industrial catalysts and nanoporous materials. Herein, we review current modeling strategies and highlight future directions for predictive, multiscale simulations of nanoporous catalysts under realistic conditions.

Neuronal intranuclear inclusion disease (NIID) is a rare, progressive neurodegenerative disorder caused by abnormal GGC repeat expansions in the NOTCH2NLC gene, leading to multisystem involvement. Electrophysiological abnormalities in NIID have gained increasing attention in recent years. However, subclinical peripheral neuropathy preceding the onset of typical NIID manifestations has not been reported. In this study, we systematically evaluated the clinical characteristics of a family carrying pathogenic NOTCH2NLC expansions. Electrophysiological assessments revealed demyelinating changes in some family members, with or without the classic clinical features of NIID. Notably, one individual with biallelic NOTCH2NLC GGC repeat expansions exhibited subclinical peripheral neuropathy in the absence of overt NIID symptoms. As NIID is typically inherited in an autosomal dominant manner, cases with biallelic GGC repeat expansions are exceedingly rare. To explore the genotype–phenotype relationship, we employed long-read whole-genome sequencing using Oxford Nanopore and Pacific Biosciences (PacBio) technologies. Our results suggest that biallelic repeat expansions do not necessarily exacerbate the severity or progression of NIID. Although larger studies are warranted to confirm these findings, this investigation broadens the clinical and genetic spectrum of NIID and provides new insights into its underlying pathogenesis.

Long non-coding RNAs (lncRNAs) are critical regulators of gene expression in eukaryotes. Short reads from Illumina sequencing, reverse transcriptase artefacts, and incomplete second-strand degradation in strand-specific cDNA libraries hamper genome-wide identification of lncRNAs, especially in gene-dense genomes such as Plasmodium. Here, we integrated long-read Oxford Nanopore Technology direct RNA sequencing, ribosome profiling, and single-cell transcriptomics to generate a robust and stage-specific characterization of P. falciparum lncRNAs. We generated comprehensive annotations of lncRNAs expressed in both asexual and sexual blood stages and confirmed their non-coding nature using ribosome profiling. Most lncRNAs showed pronounced stage-specific expression and appeared to be particularly abundant in mature gametocytes. Single-cell RNA sequencing revealed differential expression of many lncRNAs in female and male gametocytes, suggesting important roles in gametocytogenesis and transmission. Many lncRNAs are located antisense to protein-coding genes and are co-expressed with their sense mRNA, possibly from putative bidirectional promoters, while others overlap mRNA coding sequences or 3' untranslated regions and showed negatively correlated expression patterns. Overall, our study shows the prevalence of P. falciparum lncRNAs and highlights their possible roles in controlling the regulation of gene expression, particularly during gametocytogenesis.

Carbonaceous zinc-ion capacitors (ZICs) offer inherent advantages for energy storage, yet the role of pore structures in enabling high zinc-ion capacitance remains underexplored. Herein, a dual-molten-salt regulation strategy is employed to derive N/O/S-doped porous carbon nanomaterials, achieving a high specific surface area (SSA) of 2523 m2g-1 with ultramicropores (< 0.86nm) contributing 30.6% of the total SSA. Structural analyses reveal that increasing molten FeCl3 content yields materials with comparable heteroatom contents and defect structures, but a progressive shift from ultramicropores to mesopores. Crucially, the individual contributions of the pore structure are decoupled by both in situ characterizations and theoretical simulations: The ultramicropores facilitate the desolvation of [Zn(H2O)6]2+ (ultramicropore effect), while the hierarchical pores ensure rapid ion transport (hierarchical pore effect). The optimized HHPC-2 delivers a high specific capacitance of 222.6Fg-1 at 1Ag-1 and an energy density of 120.0Whkg-1 in ZICs. Intriguingly, its outstanding oxygen reduction reaction catalytic activity enables self-charging upon air exposure after a full discharge, achieving a self-charging rate of 15mAhg-1h-1 and recovering 80% of the externally charged capacity in subsequent discharge cycles. This positions the device as highly promising for practical deployment in regions with intermittent grid power supplies.

The development and validation of long-read ITS-1/5.8S/ITS-2 nemabiome metabarcoding for ovine gastrointestinal nematodes using Oxford Nanopore Technologies (ONT) sequencing.

Providencia stuartii (Ps) is a clinically significant opportunistic pathogen often associated with “difficult-to-treat resistance” (DTR) infections due to pan-resistance to first-line antimicrobials. We report the clinical diagnosis and rapid genomic characterization of strain Ps-CMC-4104, recovered from a human splenic abscess in a patient with infected necrotizing pancreatitis. To resolve the complex genetic architecture of this strain, we utilized hybrid sequencing combining Oxford Nanopore (long-read) and Illumina (short-read) technologies. Analysis revealed a 4,504,925 bp circular chromosome featuring a unique genomic resistance island (GRI) closely related to Salmonella SGI1. Notably, the PsGRI contains multiple copies of NDM-1 and PER-1 carbapenem-resistance and -inhibitor genes, a repetitive structure typically unresolvable by standard short-read methods. Additionally, a large 278,489 bp low-copy circular plasmid harbored single copies of these carbapenemase and extended-spectrum β-lactamase genes alongside other antimicrobial resistance determinants and ISCR1 insertion sequences. Nanopore technology allowed us to precisely identify the duplications, providing critical insights into the strain’s pan-resistant phenotype. This study serves as proof-of-concept for the importance of integrating long-read sequencing into clinical workflows to identify complex resistance mechanisms in DTR pathogens, facilitating targeted antimicrobial stewardship and infection control.

Background: Ionic liquids like 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]) possess unusual physicochemical properties that make them appealing for catalytic use. Nevertheless, they have bulkphase disadvantages, e.g., low surface area and mass transfer problems, which can be counteracted by restricting them between nanoporous materials. The nano-confinement influences the movement of the ionic, the interaction potential, and the dynamics of the reaction so that a better catalytic behaviour can be achieved. Objective: This paper seeks to explore the structural as well as the catalytic properties of [BMIM][PF6] upon its confinement within nanoporous materials and the consequent effect of confinement upon the catalytic efficiency through statistical analysis of survey perceptual data. Methods: A questionnaire was composed of a structured Likert scale, in which 310 responses were attained by sending the aged group of 20 experts and researchers working in the field of catalysis and material science. Analyses were performed as statistical tests, such as the Shapiro-Wilk test of normality, Cronbach's Alpha test of reliability, KMO and Bartlett's test of construct validity, Pearson correlation coefficient, and multiple regression equation by utilizing SPSS and Python. All the tests were done in the light of the big sample parameter applicability. Results: The data set approximated normality, had perfect internal consistency (Cronbach Alpha = 0.911), as well as strong construct validity (KMO = 0.812; Bartlett p &lt; 0.001). These results indicated strong positive correlations of the ionic structure, confinement effects, and catalytic activity. Regression analysis also proved that all independent variables exerted a positive impact on the dependent variable, which was expected, as the key hypothesis is that nano-confinement enhances the efficiency of the catalyst. Conclusions: This study concludes that nano-confinement is an efficient approach to the improvement of the catalytic performance of [BMIM][PF6], but by restoring molecular orientation, optimization of energy barriers, and facilitation of accessibility to substrates. These results affirm the extended use of confined ionic liquids in the development of efficient, selective, and sustainable catalytic systems.

Advances in sequencing technologies continue to improve the resolution and completeness with which human genetic variation can be characterized. Short-read sequencing remains widely used due to its high base accuracy, throughput, and cost efficiency; however, its limited ability to resolve repetitive and structurally complex regions has accelerated adoption of long-read sequencing platforms, including those from Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT). We systematically compared sequencing technologies and variant calling pipelines for small variants and structural variants across diverse genomic contexts and sequencing depths. Short-read sequencing combined with DRAGEN achieved high accuracy for single-nucleotide variants (SNVs) and indels in well-mapped and moderately complex regions but showed reduced sensitivity and completeness for structural variant detection. In contrast, long-read sequencing platforms demonstrated clear advantages in detecting structural variants and resolving small variants in difficult genomic regions, although challenges remain in specific indel-prone sequence contexts. Among long-read pipelines, PacBio Revio with DeepVariant achieved the highest SNV and indel accuracy genome-wide, while ONT R10 with DeepVariant performed particularly well in clinically relevant loci. Structural variant detection was dominated by long-read optimized callers, with SVIM and Sawfish performing best for PacBio, and Sniffles2 and CuteSV2 for ONT, consistently outperforming short-read-based methods across variant classes and sizes. Coverage analyses indicated that long-read sequencing reached accuracy saturation between 20 × and 45 × , whereas short-read sequencing required more than 60 × coverage to approach maximal genome completeness. These results provide practical guidance for platform and pipeline selection. Long-read sequencing enables more comprehensive detection and resolution of structural variants and variation in complex genomic regions, while short-read sequencing remains a cost-effective and scalable solution for high-throughput genotyping and clinically focused applications.

Ectoparasites that penetrate host skin can act as biological or mechanical vectors for pathogens and, in some cases, serve as reservoirs. Crustacean ectoparasites of fish are potential vectors of pathogens, which is especially relevant for obligate pathogens (e.g., Aeromonas salmonicida) with limited seawater survival. Sea lice (Lepeophtheirus salmonis), affecting Atlantic salmon, cause dermal damage and can facilitate secondary infections, resulting in economic losses. While the physical impact of sea lice is well known, their role in pathogen transmission is less clear. The gut bacterial microbiome of lice collected over four months from a salmon farm in Ireland was analysed using Illumina MiSeq and Oxford Nanopore Technologies (ONT) PromethION sequencing for comparison. Illumina and Nanopore sequencing identified 15 and 24 genera of known fish pathogens, respectively. Moreover, Nanopore data revealed up to 15 putative pathogenic species, including Tenacibaculum maritimum, T. dicentrarchi and Vibrio anguillarum, causative agents of tenacibaculosis and vibriosis. The results of this study provide a gut bacterial microbiome characterisation of L. salmonis in a commercial aquaculture setting and demonstrate the potential of sea lice to act as pathogen vectors or reservoirs. These findings have important implications for pathogen surveillance, management, and prevention strategies in salmon aquaculture.