Search Results (2,661)

Linezolid represents a critical last-resort treatment for severe multidrug-resistant (MDR) Gram-positive bacterial infections. Rising linezolid resistance in Enterococcus isolates threatens its efficacy; this study characterized the molecular features and transfer potential of plasmid-encoded linezolid resistance genes optrA and poxtA in a linezolid-resistant Enterococcus asini isolate from chickens. An E. asini strain was isolated during a surveillance program focusing on drug-resistant Gram-positive bacteria in poultry. PCR screened linezolid resistance genes, conjugation and plasmid stability assays evaluated gene transferability and stability, and whole-genome sequencing (WGS) was performed using both the Illumina and Nanopore platforms. We present the first detection of optrA and poxtA genes in E. asini recovered from chicken feces in China. Sequence analysis of the complete genome showed that poxtA and optrA were situated on two distinct plasmids. The poxtA positive plasmid, pHNGXN23C145Ea-1, also carried multiple resistance genes, including tet(S), fexB, erm(B), ant(6)-Ia, aph(3′)-III. Furthermore, the poxtA gene was flanked by IS1216E mobile elements. The optrA bearing plasmid, pHNGXN23C145Ea-2, harbours a common genetic array of ‘IS1216E fexA-optrA-erm(A)-IS1216E’. Conjugation experiments indicated that neither the poxtA- nor the optrA-bearing plasmid was transferred to recipient strains, which was consistent with sequence analysis showing that both plasmids lacked intact conjugative transfer regions. Stability assays confirmed that poxtA and optrA remained highly stable in the absence of selective pressure. Notably, this discovery was made in a livestock sample, despite the non-use of linezolid in food animals, suggesting that such niches may act as silent reservoirs for resistance genes, which could persist and potentially transfer to clinically relevant MDR pathogens. Full article

High-quality genomic DNA extraction remains a major bottleneck for fungal genomics, particularly for worldwide aerobic and non-photosynthetic mushroom species that rely on their rigid cell walls, interference between metabolites, polysaccharides, etc., and complex genomes. This study systematically compares five DNA extraction protocols involving four distinct sample preparation procedures (fresh (A), filtered (B), frozen (C) and cryogenic mycelium (D)) across mycelial cultures of eight Tunisian fungal strains representing Ascomycota and Basidiomycota to identify the optimal combination for genomic DNA extraction from mycelium. The eight phylogenetically diverse fungal species were analyzed using short-read (MiSeq and NextSeq550) and/or long-read (MinION Mk1C) sequencing technologies, giving a depth coverage between 3.7× and 83×. The generation and quality of the assemblies were assessed within the Galaxy platform, which revealed a gap percentage of 0–0.509%. Taxonomic characterization and phylogenetic inference were performed with SANGER technology using the Internal Transcribed Spacer (ITS) and D1/D2 region of the 26S rRNA gene, assigning the species to our eight different strains: Clitopilus baronii (BS6), Porostereum spadiceum (BS200), Trametes versicolor (BS22-9), Schizophyllum commune (BS23-13), Gloeophyllum abietinum (BS23-14), Irpex laceratus (BS100), Trichoderma asperellum (GC9) and Trichoderma harzianum (S3). The optimized DNeasy Plant Pro Kit protocol with cryogenic biomass treatment presents a safe and cost-effective method for fungal genome sequencing and taxonomic resolution. This integrated comparative evaluation of extraction for sequencing identifies an optimal Qiagen-based extraction strategy combined with cryogenic treatment for eight diverse Tunisian fungal species, guiding method selection based on specific cell wall characteristics rather than proposing a universal protocol limited by unequal replication and strain numbers. Full article

Microbial contamination in aquatic environments poses severe threats to aquaculture sustainability, ecological balance and public health. Traditional culture-based detection methods, while standardized, are time-consuming and labor-intensive, often failing to meet the urgent need for rapid on-site monitoring required to prevent disease outbreaks and manage water quality effectively. By integrating latest research advances (2020–2025), this study reviews advances in rapid detection technologies for aquatic microorganisms, including the evolution of nucleic acid amplification strategies, with a focused comparison of the analytical sensitivity and field deployability of quantitative polymerase chain reaction (qPCR) and mainstream isothermal amplification techniques (loop-mediated isothermal amplification, LAMP; recombinase polymerase amplification, RPA). Furthermore, this study reports on the emergence of Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-associated protein (Cas) systems as next-generation diagnostic tools, highlighting their integration with microfluidic Lab-on-a-Chip (LOC) platforms to achieve attomolar sensitivity. We also consider the application of portable nanopore sequencing for real-time pathogen identification and the growing role of Artificial Intelligence (AI) in analyzing complex diagnostic datasets. Advanced molecular methods have achieved significant reductions in time consumption—from days to less than one hour—while challenges regarding sample preparation and environmental matrix inhibition remain. The future of aquatic monitoring lies in integrated, automated systems that combine the specificity of CRISPR-Cas diagnostics with the connectivity of IoT-enabled biosensors. Comparative analysis indicates that isothermal amplification methods (LAMP, RPA) coupled with CRISPR-Cas systems offer the optimal balance of sensitivity, speed, and field deployability for point-of-care aquaculture diagnostics, while qPCR/dPCR remain indispensable for quantitative regulatory applications. We propose a structured technology selection framework to guide researchers and practitioners in choosing appropriate detection modalities based on specific sensitivity, cost, throughput, and deployment requirements. Full article

The marine shale of the Longmaxi Formation is the main layer for shale gas exploration and development in the Sichuan Basin. That said, the pore structure in the Longmaxi shale is strongly heterogeneous, and how these pores form and are preserved remains unclear—which limits our understanding of what makes a good reservoir and holds back efficient shale gas development. To investigate the coupling relationship between hydrocarbon generation and pore evolution in marine shale, medium-maturity shale from the Longmaxi Formation in NE Sichuan was collected for thermal maturation experiments. Shale samples and pyrolysis products from different evolutionary stages were obtained for a series of analyses, including gas composition and pore structure. The influence of organic hydrocarbon generation and inorganic diagenesis on the development of shale nanopores was revealed, and a pore evolution model for marine shale was established. The results show the following: (1) The hydrocarbon generation process of medium-maturity marine shale consists of three stages. The maximum methane yield is 362.58 mL/g. (2) As the thermal maturity increases, the quartz content shows a gradual increase, while the content of clay minerals, feldspar, and carbonate minerals decreases. (3) As the thermal maturity increases, pore evolution is observed in four stages: “slow decrease,” “rapid increase,” “relatively stable,” and “slow decrease.” The first stage is characterized by pore reduction dominated by intense compaction. The second stage is dominated by pore expansion driven by mineral transformation and dissolution. The third stage is the pore preservation stage, during which continuous natural gas generation occurs. The fourth stage is characterized by pore reduction, mainly driven by weak compaction. This study has enriched the theoretical understanding of the dynamic evolution of shale pores, providing a theoretical basis for the research on the formation and enrichment mechanism of shale gas and the exploration practice of shale gas reservoirs. Full article

The red cusk-eel (Genypterus chilensis) is an endemic Chilean teleost fish of significant importance to fisheries and aquaculture; however, no reference genome is available for this species. In this study, we present the first hybrid genome assembly of G. chilensis using Nanopore long-reads and Illumina short-reads, integrated with structural and functional annotations from RNA-seq data of the intestine and head kidney. The resulting genome assembly was 439.89 Mb in size, with an N50 of 7.96 Mb, containing 35,029 coding genes. Comparative genomics with G. blacodes revealed high similarity in genome size and completeness. Additionally, 14,681 lncRNAs were annotated, with 641 lncRNAs and 7323 coding genes differentially expressed in a tissue-specific expression pattern. These findings provide a high-quality genomic resource that enhances the understanding of lncRNA regulation and genome structure in the Genypterus genus. This study establishes a foundation for future research on commercial traits, conservation, and the evolution of the Ophidiiformes order. Full article

Sol–gel processing provides an unusually controllable route to nanoporous solids, making silica aerogels the leading reference systems for extremely low thermal conductivity due to their high porosity, nanoscale pore sizes, and tunable solid frameworks. Under near-ambient conditions, thermal transport is multi-scale and multiphase, arising primarily from coupled solid conduction through the skeletal network and gas conduction within the pore space. Accordingly, aerogel design has emphasized suppressing solid-phase transport by reducing network connectivity, increasing tortuosity, and enhancing boundary scattering, while also limiting gaseous conduction through the control of pore size and gas pressure. This critical review provides an integrated overview of these mechanisms and the theory-to-experiment toolbox used to quantify the separate and combined contributions of the solid and gas phases to the effective thermal conductivity. We link key structural and environmental parameters (porosity, pore size distribution, density, backbone morphology, and pressure) to dominant transport regimes and the assumptions embedded in common models. Classical approaches, including effective-medium and percolation-based models, are assessed alongside phonon-scaling descriptions that incorporate characteristic length scales. Particular attention is given to the Knudsen effect and pressure-sensitive gas-conduction models, which are central to interpreting performance at atmospheric conditions and under vacuum or low-pressure operation. This review highlights inconsistencies across datasets and modeling practices, identifies persistent knowledge gaps, and outlines practical directions toward processable structure–property guidelines for manufacturing aerogels with targeted thermal performance, with regard to conduction-dominated heat transport mechanisms. Full article

Background/Objectives: The emergence of antimicrobial-resistant (AMR) pathogens in aquaculture ecosystems poses a significant risk to both food security and human health. Shewanella species are recognized as significant AMR reservoirs, yet their prevalence and resistance mechanisms within a shrimp-related ecosystem remain poorly characterized. This study aimed to perform a genotypic and phenotypic characterization of S. algae VK101, isolated from wild-caught black tiger shrimp (Penaeus monodon) broodstock. Methods: A complete 5.21 Mb genome was generated using a hybrid Illumina and Oxford Nanopore sequencing approach. Antimicrobial susceptibility was evaluated for 21 antibiotics via Minimum Inhibitory Concentration (MIC) testing. Comparative pangenomics and genome-wide association studies (GWAS) across 125 S. algae genomes were conducted to identify novel resistance determinants. Results: MIC analysis revealed that VK101 was resistant to ampicillin (>16 µg/mL) and colistin (8 µg/mL), while showing intermediate susceptibility to imipenem and ciprofloxacin. In silico analysis identified 205 antimicrobial resistance genes (ARGs), including a perfect hit for the fluoroquinolone resistance gene qnrA3. Notably, no mcr genes were detected. Although VK101 exhibited moderate resistance (8 µg/mL), GWAS across the broader S. algae population linked a specific lptA mutation (K140N) to high-level resistance (64 µg/mL). Other GWAS-identified genes (e.g., czcA, ampC, and oprM) likely represent indirect associations driven by genetic linkage or clade-specific markers rather than direct causal factors. Conclusions: These findings highlighted the presence of multidrug-resistant S. algae in wild-caught P. monodon broodstock, reflecting the occurrence of antimicrobial resistance in aquatic environments. Colistin resistance in these isolates was primarily mediated by chromosomal variants rather than mobile mcr elements, indicating the need for integrated genomic surveillance within the aquaculture value chain. Full article

Saffron (Crocus sativus L.) is a high-value crop vulnerable to potyvirus infections threatening its yield and quality. In this study, we combined Oxford Nanopore long-read sequencing with exploratory transcriptomic profiling to characterize the saffron virome and to describe expression profiles associated with two distinct infection histories: (i) saffron plants experimentally inoculated with cucumber mosaic virus (CMV; Cucumovirus CMV) and turnip mosaic virus (TuMV; Potyvirus rapae) under controlled greenhouse conditions, and (ii) saffron plants naturally infected by diverse viruses. We identified six plant-infecting viral families in both conditions, including Potyviridae, Geminiviridae, Caulimoviridae, Tymoviridae, Aspiviridae, and Partitiviridae. Transcriptomic profiling revealed distinct expression profiles associated with each infection background. Given the limitations of the experimental design, gene expression differences are interpreted descriptively. We describe pathway enrichments associated with antiviral responses. Naturally infected plants exhibited a broad-spectrum, tolerance-based response characterized by the upregulation of photosynthesis-related genes, calcium-mediated signaling components, and stress-responsive transcription factors. In contrast, virus-inoculated plants activated a targeted antiviral program involving RNA silencing, autophagy, ubiquitin-mediated proteolysis, and hormonal regulation. Both GO and KEGG enrichment analyses supported these findings, highlighting photosynthesis and metabolic flexibility in naturally infected plants versus hypersensitive response, RNA surveillance, and lignin biosynthesis in virus-inoculated plants. This work provides a comprehensive view of the saffron virome and offers a hypothesis-generating overview of transcriptional responses associated with natural versus experimental virus infections. These findings advance the understanding of the saffron virome and provide a valuable resource for breeding virus-resistant cultivars. Full article

To date, the problem of mastitis in cattle remains relevant for both the industrial sector and scientific research. Despite numerous active investigations, the causes of this disease have not been fully established. It is postulated that several factors may be involved, such as bacterial pathogens, animal husbandry practices, and weather and climatic conditions. In this study, we selected cows from farms in Yakutia to investigate microbial isolates present in the milk of cows affected by mastitis and treated with antibiotics. Five identified Staphylococcus aureus isolates were investigated using whole-genome sequencing (Illumina sequencing and nanopore sequencing), followed by analysis of virulence factors in the genomes and cultural properties of the isolates. The profile of S. aureus virulence genes (exotoxins, cytotoxins, superantigen-like proteins, adhesins) was identified via WGS. Hemolysin gene (hla) was detected in all isolates. An investigation of the cultural properties of the isolates, specifically through hemolysis of rabbit erythrocytes and Western blot analysis of the culture liquid of S. aureus, revealed different expression levels of alpha-hemolysin among the strains. One isolate (17-21) exhibited the highest secretion level of about 320 ± 37 ng, both in the hemolysis test and immunoblotting assay. An investigation of the isolates’ antibiotic resistance showed that all isolates exhibited multidrug resistance, as confirmed by the presence of antibiotic resistance genes in these isolates. One isolate (7-7) exhibited the broadest range of phenotypic resistance and was resistant to all tested antibiotics (except clindamycin). Phylogenetic analysis suggested that the evolution of these isolates occurred independently in their respective ecological niches, although their transfer from cattle to humans, and vice versa, is possible. Isolates 7-7, 18-22, 33-40, and 35-42 are most typical to Yakutian cattle, while isolate 17-21 might have been introduced from a different region. To the best of our knowledge, this is the first in-depth study into a range of S. aureus isolates associated with mastitis infection in Yakutian cattle. Full article

Microfluidics enables spatially controlled nanostructure synthesis by coupling confined flows with surface reactions. In this work, we study how geometry-induced laminar microenvironments govern the in situ formation of Au and Ag nanostructures inside 3D-printed microfluidic reactors. Proof-of-concept fish-scale valves were fabricated by masked stereolithography in three architectures designed to define three recurring zones in the microreactor, inside the fish-scales (zone 1), between the fish-scales (zone 2), and along the rows of fish-scales (zone 3). A Cu thin film was deposited on the inner walls of the channel to serve as the sacrificial surface for galvanic replacement using AgNO₃ or HAuCl₄. Distinct 0D, 1D, and 2D nanostructures were simultaneously obtained in a zone-dependent manner across the valves, including nanoparticle and nanopore-rich regions, nanowires, nanoflakes and clustered 2D features. COMSOL simulations were used to solve the Navier–Stokes equation and extract specific-zone flow descriptors, including Reynolds number, velocity, and wall shear stress, and relate them to the nanostructure morphologies observed by SEM. The flow throughout the devices is strongly laminar, with local Reynolds numbers up to 0.04, exhibiting systematic spatial gradients imposed by the valve geometry. These results provide a design-guided route to tune nanostructure morphology through microchannel architecture under constant global operating conditions. Full article

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. Full article

This research investigates the effects of electrochemical oxidation on surface properties and corrosion performance of the Ti-6Al-4V ELI alloy intended for biomedical applications. Electrochemical anodization is performed in 1 M H₂SO₄ and 1 M H₃PO₄ electrolytes at applied potentials of 200, 250, and 275 V for 1 min. Morphological characteristics and chemical constitution of the oxide films are investigated by SEM-EDS analysis, while surface roughness, wettability, and microhardness are evaluated using profilometry, contact angle measurements, and Vickers microhardness testing. Electrochemical behavior is assessed by monitoring free potential (OCP) and electrochemical impedance spectroscopy in Ringer solution and Ringer solution containing 40 g/L hydrogen peroxide. Among the investigated conditions, anodization at 200 V for 1 min provides the most favorable surface morphology, producing well-defined and uniformly distributed nanopores while maintaining the structural stability of the oxide layer. Oxidation in 1 M H₂SO₄ leads to a more homogeneous nanoporous structure, higher surface roughness, improved hydrophilicity, and increased microhardness compared to 1 M H₃PO₄ treatment. Electrochemical impedance spectroscopy analysis reveals superior corrosion resistance for all oxidized samples in comparison with the untreated alloy. The oxide layers obtained in sulfuric acid exhibit the highest polarization resistance and electrochemical stability in simulated physiological environments. Full article

Background/Objectives: Castanopsis tibetana Hance (C. tibetana) is a valuable timber species in southern China. Its chloroplast and nuclear genomes have been characterized, but its mitochondrial genome (mitogenome) remains unknown. This study assembles and characterizes the first complete mitogenome of C. tibetana, elucidating its structural and evolutionary features. Methods: A hybrid approach combining Oxford Nanopore long reads and Illumina short reads was used. The mitogenome was assembled via iterative seed-based mapping and annotated via GeSeq and tRNAscan-SE. Repeats were identified via MISA, TRF, and REPuter. The RNA editing sites were predicted with the PREP suite. Phylogenetic analysis was performed on 14 conserved protein-coding genes from 13 species via maximum likelihood and Bayesian inference. Results: The mitogenome is a 554,078 bp circular molecule (GC 45.27%) encoding 51 genes (32 PCGs, 16 tRNAs, 3 rRNAs). It contains 202 simple sequence repeats (37.1% tetrameric). We predicted 53 C-to-U RNA editing sites, most frequently in nad7 and nad5. Codon usage showed bias, with 28 codons having RSCU > 1. Twenty fragments (6001 bp, 1.08% of the mitogenome) were transferred from the chloroplast. Phylogenomic analysis placed C. tibetana within Fagaceae, close to other Castanopsis species. Conclusions: This study provides the first comprehensive characterization of the C. tibetana mitogenome, revealing its structural architecture, repetitive landscape, RNA editing profile, and phylogenetic placement. These findings offer valuable genomic resources for understanding mitogenome evolution in Fagaceae and support future research on the conservation genetics and molecular breeding of this important tree species. Full article

Both the Lower Silurian Longmaxi Formation and the Upper Permian Dalong Formation shales in southern China are organic-rich with well-developed nanoscale reservoir pores, demonstrating significant shale gas exploration potential. However, the current lack of in-depth research on the differential depositional and reservoir evolution characteristics of these two shale sequences has left the main controlling factors of the reservoirs unclear, thereby constraining breakthroughs in shale gas development. Focusing on the Longmaxi and Dalong formation shales in the Sichuan Basin, this study employed various analytical methods, including major and trace element analyses, X-ray diffraction (XRD), high-pressure mercury intrusion (HPMI), nitrogen adsorption, CO₂ adsorption, and scanning electron microscopy (SEM). Investigations into the depositional paleoenvironment, paleoproductivity, organic matter enrichment, and microscopic difference mechanisms of nanoscale reservoirs reveal that the Longmaxi Formation shale represents a passive continental margin shelf facies. It is characterized by strong terrigenous input, a predominance of quartz and clay minerals, and consists mainly of siliceous and argillaceous shale facies with high organic matter abundance. In contrast, the Dalong Formation shale was deposited in an intra-platform basin under the influence of intra-platform rifting. It features weak terrigenous input, highly reducing conditions, and strong paleoproductivity. Dominated by quartz and carbonate minerals, its lithofacies are primarily siliceous and calcareous shales. Within the Dalong Formation, the diagenetic dissolution of carbonate minerals promotes the development of micrometer-scale pores larger than 100 μm, while the extensive thermal evolution of organic matter fosters the formation of honeycomb- and embayment-like nanoscale micropores and mesopores, rendering it a relatively superior shale reservoir. Ultimately, the high-TOC shales in the lower part of the Longmaxi Formation and the upper part of the Dalong Formation are identified as the primary sweet spot intervals for future shale gas development. Full article

Tick-borne encephalitis virus (TBEV) is primarily transmitted by Ixodes spp. and poses significant health risks, leading to morbidity and mortality in humans. Two of the five subtypes, Siberian and Far Eastern are known to circulate in Mongolia. In 2021, Ixodes persulcatus ticks were collected from Bulgan aimag (province) using flagging and dragging methods and subsequently screened for TBEV using PCR. Positive samples underwent sequencing using an Oxford Nanopore Technologies-based hybrid capture approach, resulting in two coding-complete TBEV genomes from separate tick pools. Phylogenetic analysis classified both genomes within the Siberian subtype, grouping them with other Mongolian sequences from I. persulcatus collected in 2014, 2020, 2021, and 2023. The study sequences, PX654173 and PX654174, showed high genetic similarity (99.9% and 99.8%, respectively) to the sequence PQ479142, obtained from I. persulcatus ticks in Selenge, Mongolia, in 2021. The estimated time to most recent common ancestor (TMRCA) of the Siberian genotype was approximately 981 CE (95% HPD: 646–1347) with the emergence of a distinct Mongolian clade of TBEV around 1888 CE (95% HPD: 1834–1934). These findings highlight the value of expanded whole-genome sequencing to improve our understanding of TBEV’s genetic diversity and evolutionary history in Central Asia. Full article