Search Results (806)

Tripterygium wilfordii has extremely important pharmaceutical value in both traditional and modern medicine. The mitogenome of T. wilfordii was subjected to assembly and annotation with Nanopore long reads and Illumina short reads in this study. The mitogenome is 720,306 bp in length and is responsible for encoding 55 specific genes, including 35 protein-coding genes (PCGs), 17 transfer RNA (tRNA) genes, and 3 ribosomal RNA (rRNA) genes. Upon repetitive sequence analysis, 223 simple sequence repeats (SSRs), 24 long tandem repeats (LTRs), and 47 dispersed repetitive sequences (DRSs) were identified. The 24 common PCGs were used for phylogenetic analysis, which revealed that T. wilfordii is more closely related to Euonymus alatus. Moreover, mitochondrial plastid DNA (MTPT) analysis revealed eight MTPTs in the mitochondrial genome. Furthermore, 600 RNA-editing sites were detected in the protein-coding genes according to RNA-seq results. Among these genes, the ccmB gene contained the greatest number of sites, followed by the nad4 gene. This is the first study to report the T. wilfordii mitogenome and illustrate its linear structure. The findings of this study will help elucidate the evolution of the T. wilfordii mitogenome and facilitate its potential application in genetic breeding. Full article

Rare genetic diseases are often caused by structural variants (SVs), such as insertions, deletions, duplications, inversions, and complex rearrangements. However, due to the technical limitations of short-read sequencing, these variants remain underdiagnosed. Long-read sequencing technologies, including Oxford Nanopore and Pacific Biosciences high-fidelity (HiFi), have recently advanced to the point that they can accurately find SVs throughout the genome, including in previously unreachable areas like repetitive sequences and segmental duplications. This study underscores the transformative role of long-read sequencing in diagnosing rare diseases, emphasizing the bioinformatics tools designed for detecting and interpreting structural variants (SVs). Comprehensive methods are reviewed, including methylation profiling, RNA-seq, phasing analysis, and long-read sequencing. The effectiveness and applications of well-known tools like Sniffles2, SVIM, and cuteSV are also assessed. Case studies illustrate how this technique has revealed new pathogenic pathways and solved cases that were previously undetected. Along with outlining potential future paths like telomere-to-telomere assemblies and pan-genome integration, we also address existing issues, including cost, clinical validation, and computational complexity. For uncommon genetic illnesses, long-read sequencing has the potential to completely change the molecular diagnostic picture as it approaches clinical adoption. Full article

Hippophae rhamnoides subsp. sinensis is extensively found in China, where the annual precipitation ranges from 400 to 800 mm. It is the most dominant species in natural sea buckthorn forests and the primary cultivar for artificial ecological plantations. Additionally, it exhibits significant nutritional and medicinal value, making it a renowned eco-economic tree species. Despite extensive research into its ecological functions and health benefits, the mitochondrial genome of this widespread species has not yet been published, and knowledge of the mitochondrial genome is crucial for understanding plant environmental adaptation, evolution, and maternal inheritance. Therefore, the complete mitochondrial genome was successfully assembled by aligning third-generation sequencing data to the reference genome sequence using the Illumina NovaSeq 6000 platform and Nanopore Prometh ION technologies. Additionally, the gene structure, composition, repeat sequences, codon usage bias, homologous fragments, and phylogeny-related indicators were also analyzed. The results showed that the length of the mitochondrial genome is 454,489 bp, containing 30 tRNA genes, three rRNA genes, 40 PCGs, and two pseudogenes. A total of 411 C-to-U RNA editing sites were identified in 33 protein-coding genes (PCGs), with higher frequencies observed in ccmFn, ccmB, nad5, ccmC, nad2, and nad7 genes. Moreover, 31 chloroplast-derived fragments were detected, accounting for 11.86% of the mitochondrial genome length. The ccmB, nad4L, and nad7 genes related to energy metabolism exhibited positive selection pressure. The mitochondrial genome sequence similarity between H. rhamnoides subsp. sinensis and H. tibetana or H. salicifolia was 99.34% and 99.40%, respectively. Fifteen shared gene clusters were identified between H. rhamnoides subsp. sinensis and H. tibetana. Phylogenetically, the Rosales order showed close relationships with Fagales, Fabales, Malpighiales, and Celastrales. These findings provide fundamental data for exploring the widespread distribution of H. rhamnoides subsp. sinensis and offer theoretical support for understanding the evolutionary mechanisms within the Hippophae genus and the selection of molecular breeding targets. Full article

A superhydrophobic surface with hierarchical micro/nano-array structures was successfully fabricated on 6061 aluminum alloy through a combination of femtosecond laser etching and anodic oxidation. Femtosecond laser etching formed a regularly arranged microscale “pit-protrusion” array on the aluminum alloy surface. After modification with a fluorosilane ethanol solution, the surface exhibited superhydrophobicity with a contact angle of 154°. Subsequently, the anodic oxidation process formed an anodic oxide film dominated by an array of aluminum oxide (Al₂O₃) nanopores at the submicron scale. Scanning electron microscopy (SEM) and X-ray diffraction (XRD) analyses revealed that the nanopore structures uniformly and continuously covered the laser-ablated layer. This hierarchical structure significantly increased the surface water contact angle to 162°. Wettability analysis showed that the prepared composite coating formed an air layer accounting for 91% of the surface area. Compared with the sample only treated by femtosecond laser etching, the presence of the Al₂O₃ nanopore structure significantly enhanced the mechanical durability, superhydrophobic durability, and corrosion resistance of the superhydrophobic surface. The proposed multi-step fabrication strategy offers an innovative method for creating multifunctional, durable superhydrophobic coatings and has important implications for their large-scale industrial use. Full article

The pore-throat structure of the extremely low-permeability sandstone reservoir in the Huachi area of the Ordos Basin is complex and highly heterogeneous. Currently, there are issues such as unclear understanding of the micro-pore-throat structural characteristics, primary controlling factors of reservoir quality, and classification boundaries of the reservoir in the study area, which seriously restricts the exploration and development effectiveness of the reservoir in this region. It is necessary to use a combination of various analytical techniques to comprehensively characterize the pore-throat structure and establish reservoir classification evaluation standards in order to better understand the reservoir. This study employs a suite of analytical and testing techniques, including cast thin sections (CTS), scanning electron microscopy (SEM), cathodoluminescence (CL), X-ray diffraction (XRD), as well as high-pressure mercury injection (HPMI) and constant-rate mercury injection (CRMI), and applies fractal theory for analysis. The research findings indicate that the extremely low-permeability sandstone reservoir of the Chang 3 section primarily consists of arkose and a minor amount of lithic arkose. The types of pore-throat are diverse, with intergranular pores, feldspar dissolution pores, and clay interstitial pores and microcracks being the most prevalent. The throat types are predominantly sheet-type, followed by pore shrinkage-type and tubular throats. The pore-throat network of low-permeability sandstone is primarily composed of nanopores (pore-throat radius r < 0.01 μm), micropores (0.01 < r < 0.1 μm), mesopores (0.1 < r < 1.0 μm), and macropores (r > 1.0 μm). The complexity of the reservoir pore-throat structure was quantitatively characterized by fractal theory. Nanopores do not exhibit ideal fractal characteristics. By splicing high-pressure mercury injection and constant-rate mercury injection at a pore-throat radius of 0.12 μm, a more detailed characterization of the full pore-throat size distribution can be achieved. The average fractal dimensions for micropores (Dh2), mesopores (Dc3), and macropores (Dc4) are 2.43, 2.75, and 2.95, respectively. This indicates that the larger the pore-throat size, the rougher the surface, and the more complex the structure. The degree of development and surface roughness of large pores significantly influence the heterogeneity and permeability of the reservoir in the study area. Dh2, Dc3, and Dc4 are primarily controlled by a combination of pore-throat structural parameters, sedimentary processes, and diagenetic processes. Underwater diversion channels and dissolution are key factors in the formation of effective storage space. Based on sedimentary processes, reservoir space types, pore-throat structural parameters, and the characteristics of mercury injection curves, the study area is divided into three categories. This classification provides a theoretical basis for predicting sweet spots in oil and gas exploration within the study area. Full article

As a crucial energy source and chemical raw material, coal’s micro-pore structure holds a pivotal influence on the occurrence and development of coalbed methane (CBM). This study systematically analyzed the nano-pore structure, surface roughness, and fractal characteristics of six coal samples with varying volatile matter content (V_daf) using Atomic Force Microscopy (AFM) combined with Scanning Electron Microscopy (SEM), revealing the correlation between volatile matter and the micro-physical properties of coal. Through AFM three-dimensional topographical observations, it was found that coal samples with higher volatile matter exhibited significant gorge-like undulations on their surfaces, with pores predominantly being irregular macropores, whereas low volatile matter coal samples had smoother surfaces with dense and regular pores. Additionally, the surface roughness parameters (R_a, R_q) of coal positively correlated with volatile matter content. Meanwhile, quantitative analysis of nano-pore parameters using Gwyddion software showed that an increase in volatile matter led to a decline in pore count, shape factor, and area porosity, while the average pore diameter increased. The fractal dimension of samples with different volatile matter contents was calculated, revealing a decrease in fractal dimension with rising volatile matter. Nano-ring analysis indicated that the total number of nano-rings was significantly higher in low volatile matter coal samples compared to high volatile matter ones, but the nano-ring roughness (R_r) increased with volatile matter content. SEM images further validated the AFM results. Through multi-scale characterization and quantitative analysis, this study clarified the extent to which volatile matter affects the nano-pore structure and surface properties of coal, providing critical data support for efficient CBM development and reservoir evaluation. Full article

The increasing demand for sustainable and cost-effective energy storage solutions has driven interest in biomass-derived carbon materials for supercapacitor electrodes. This study explores the valorization of coconut residue (CR), an abundant agricultural waste, as a carbon precursor for nanoporous carbon (NPC) production. NPC was synthesized via hydrothermal carbonization (HTC) of CR, followed by chemical activation using potassium hydroxide (KOH) at varying temperatures (700, 800, and 900 °C). The effects of activation temperature on the structure and electrochemical performance of the NPC were systematically investigated. The activated materials exhibited amorphous, highly porous structures, with surface areas increasing alongside activation temperature—reaching a maximum of 1969 m² g⁻¹ at 900 °C. Electrochemical characterization was conducted using a three-electrode setup through cyclic voltammetry (CV) and galvanostatic charge–discharge (GCD) in a 1 M Na₂SO₄ electrolyte. The sample activated at 900 °C with a CR:KOH weight ratio of 1:2.5 achieved the highest specific capacitance of 52 F g⁻¹ at a specific current of 1 A g⁻¹. These findings underscore the potential of CR as a low-cost and sustainable raw material for fabricating efficient electrode materials in energy storage applications. Full article

Cu-based nanomaterials have received considerable attention as promising and cost-effective substrates for surface-enhanced Raman spectroscopy (SERS) applications despite their relatively low enhancement factor (EF) compared to noble metals like gold and silver. In this study, a fast and affordable synthesis route is proposed to obtain a three-dimensional porous copper film (NPC) via an electrodeposition technique based on the dynamic hydrogen bubbling template (DHBT). Two sets of NPC film were synthesized, one without additives and the other with cetyltrimethylammonium bromide (CTAB). The impacts of deposition time on the NPCs’ porous morphology, thickness, and SERS performance were systematically investigated. With the optimal deposition time, the nanopore sizes could be tailored from 26.8 to 73 μm without additives and from 12.8 to 24 µm in the presence of CTAB. The optimal additive-free NPC film demonstrated excellent SERS performance at 180 s of deposition, while the CTAB-modified film showed strong enhancement at 120 s towards methylene blue (MB), a highly toxic dye, achieving a detection limit of 10⁻⁶ M. Additionally, the samples with CTAB showed better efficiency than those without CTAB. The calculated EF of NPC was found to be 5.9 × 10³ without CTAB and 2.5 × 10³ with the CTAB, indicating the potential of NPC as a cost-effective candidate for high-performance SERS substrates. This comprehensive study provides insights into optimizing the structural morphology of the NPCs to maximize their SERS enhancement factor and improve their detection sensitivity toward MB, thus overcoming the limitations associated with conventional copper-based SERS substrates. Full article

Single-phase ternary Mn-Cu-Al alloy ribbons were fabricated by melt-spinning a Mn₄₈Cu₂₈Al₂₄ ingot on a rotating copper roller. They were used as dealloying precursor for forming the nanoporous structure in HCl solution. The basic dealloying behavior was examined by controlling the dealloying time from 5 min to 180 min at 50 °C. Due to the active chemical property, Mn and Al elements are easily etched in acid solutions. Meanwhile, Cu elements retained and rearranged. A three-dimensional bicontinous nanoporous structure was fabricated, with a ligament size of 55 nm~100 nm and pore size of 35 nm~85 nm. The porosity evolution of dealloyed MnCuAl alloy was divided into three stages. First, the dissolution of Mn and Al is so significant that formation of pores is dominant. Stage two, the rapid growth of both ligament size and pore size. The ligament/pore ratio is nearly unchanged. The last stage is ligament coarsening. Moreover, the electrocatalytic activity for glucose oxidation of dealloyed samples is examined. The 40 min dealloyed MnCuAl ribbon exhibited the highest sensitivity and relatively maximum current density. Full article

Soil-transmitted helminths (STHs) are parasitic nematodes that infect humans, particularly in tropical and subtropical regions, where they contribute substantially to neglected tropical diseases (NTDs). Among them, hookworms (Ancylostoma duodenale, Necator americanus and Ancylostoma ceylanicum) cause substantial morbidity, leading to anaemia, malnutrition, and developmental impairment. Despite the global impact of hookworm disease, genomic research on A. duodenale has lagged behind that of other hookworms, limiting comparative and molecular biological investigations. Here, we report the first chromosome-level reference genome of A. duodenale, assembled from a single adult specimen archived in ethanol at −20 °C for more than 27 years. Using third-generation sequencing (PacBio Revio, Menlo Park, CA, USA, Oxford Nanopore, Oxford, UK), Hi-C scaffolding, and advanced computational tools, we produced a high-quality 319 Mb genome, filling a critical gap in hookworm genomics. Comparative analyses with N. americanus and the related, free-living nematode Caenorhabditis elegans provided new insights into genome organisation, synteny, and specific adaptations. While A. duodenale exhibited strong chromosomal synteny with N. americanus, its limited synteny with C. elegans highlights its distinct parasitic adaptations. We identified 20,015 protein-coding genes, including conserved single-copy orthologues (SCOs) linked to host–pathogen interactions, immune evasion and essential biological processes. The first comprehensive secretome analysis of A. duodenale revealed a diverse repertoire of excretory/secretory (ES) proteins, including immunomodulatory candidates predicted to interact with host structural and immune-related proteins. This study advances hookworm genomics, establishes a basis for the sequencing of archival specimens, and provides fundamental insights into the molecular biology of A. duodenale. The genomic resource for this hookworm species creates new opportunities for diagnostic, therapeutic, and vaccine development within a One Health framework. It complements recent epidemiological work and aligns with the WHO NTD roadmap (2021–2030) and Sustainable Development Goal 3.3. Full article

Dewatering and gas production are applied on a large scale in shale gas development. The fundamental mechanisms of water flow in shale nanoporous media are essential for the development of shale oil and gas resources. In this work, we use molecular dynamic simulations to investigate water flow in two different quartz surface ($(10\overline{1}0)\text{-}\alpha$ and $(10\overline{1}0)\text{-}\beta$) nanopores. Results show that the $(10\overline{1}0)\text{-}\beta$ surface exhibits stronger water molecule structuring with a structure arranged in two layers and higher first-layer adsorption density (2.44 g/cm³) compared to the ($(10\overline{1}0)\text{-}\alpha$ surface (1.68 g/cm³). The flow flux under the $(10\overline{1}0)\text{-}\alpha$ surface is approximately 1.2 times higher than that under the $(10\overline{1}0)\text{-}\beta$ surface across various pressure gradients. We developed a theoretical model dividing the pore space into non-flowing, adsorbed, and bulk water regions, with critical thicknesses of 0.14 nm and 0.27 nm for the non-flowing region, and 0.15 nm for the adsorbed region in both surfaces. This model effectively predicts velocity distributions and volumetric flow rates with errors generally below 5%. Our findings provide insights into water transport mechanisms in shale inorganic nanopores and offer practical guidance for numerical simulation of shale gas production through dewatering operations. Full article

Traditional β-eucryptite (LiAlSiO₄) is renowned for its unique characteristics of low thermal expansion and high temperature thermal stability, making it an ideal material for precision instruments and aerospace applications. In this study, β-eucryptite was fabricated into an aerogel structure through the sol–gel process and supercritical drying method and using alumina sol as a cost-effective precursor. The synthesized β-eucryptite aerogel demonstrated unique properties including a negative thermal expansion coefficient (−7.85 × 10⁻⁶ K⁻¹), low density (0.60 g/cm³), and high specific surface area (18.1 m²/g). X-ray diffraction (XRD) and transmission electron microscopy (TEM) mutually corroborated the crystalline structure of β-eucryptite, with XRD confirming the phase purity and TEM imaging revealing well-defined crystal lattice characteristics. Combined nitrogen adsorption–desorption analysis and scanning electron microscopy observations supported the hierarchical porous microstructure, with SEM visualizing interconnected nanoporous networks and nitrogen sorption data verifying the porosity. The negative thermal expansion behavior was directly linked to the β-eucryptite crystal structure, as collectively validated by thermal expansion measurements. Additionally, Fourier transform infrared spectroscopy (FTIR) independently confirmed the aluminosilicate framework structure through characteristic vibrational modes. This research shows the innovation in the synthesis of β-eucryptite aerogel, especially its application potential in precision instruments and building materials that need low thermal expansion and high stability, and the use of aluminum sol as an aluminum source has simplified the preparation steps and reduced production costs. Full article

With the evolution of micro/nanotechnology, anodic aluminum oxide (AAO) has received attention for sensor applications due to its regular and high-aspect-ratio nanopore structure with an excellent sensing performance, especially for electrical and optical sensors. Here, we propose the application of these capacitance and porous properties in a facile nanoporous AAO liquid sensor and study an efficient and economical method for preparing AAO substrates for liquid-phase substance sensing. By applying hybrid pulse anodization (HPA), a growth rate of approximately 5.9 μm/h was achieved in AAO fabrication. Compared to traditional low-temperature (0–10 °C) and two-step anodization with a growth rate of 1–3 μm/h, this process is significantly improved. The effect of pore widening on the performance of electrical sensors is also investigated and discussed. After pore widening, the capacitance values of AAO for air as a reference and various liquids, namely deionized water, alcohol, and acetone, are measured as 3.8 nF, 295.3 nF, 243.5 nF, and 210.1 nF, respectively. These results align with the trend in the dielectric constants and demonstrate the ability to clearly distinguish between different substances. The mechanism of AAO capacitive liquid-phase sensors can mainly be explained from two perspectives. First, since an AAO capacitive sensor is a parallel capacitor structure, the dielectric constant of the substance directly influences the capacitance value. In addition, pore widening increases the proportion of liquid filling the structure, enabling the sensor to clearly differentiate between substances. The other is the affinity between the substance and the AAO sensor, which can be determined using a contact angle test. The contact angles are measured as values of 93.2° and 67.7° before and after pore widening, respectively. The better the substance can fully fill the pores, the higher the capacitance value it yields. Full article

Kimchi is a fermented Korean food typically made with napa cabbage, garlic, radish, ginger, and chili pepper. It is becoming increasingly popular due to its flavor, high fiber content, and purported probiotic benefits. The microbial ecology of the fermentation community has been extensively studied, though what’s less understood is how its microbial community changes when nutrients or pathogens are introduced. To study this, we used gnotobiotic cabbage media inoculated with a kimchi starter culture as a model system. These inoculated samples were exposed to E. coli or Bacillus cereus, with or without added nutrients in the form of tryptic soy broth (TSB). We tracked pH, colony-forming units (CFUs), and community composition over time. We also used Oxford Nanopore sequencing to analyze the 16S rRNA gene (V4–V9), followed by use of the Emu algorithm for taxonomic assignments. As expected, LABs suppressed pathogens, but this effect was weaker early on in the nutrient-rich condition. Pathogen exposure changed the overall community—Lactobacillus species became more common, and Leuconostoc mesenteroides less so. Interestingly, adding nutrients alone caused similar microbial shifts to those seen with pathogen exposure. This could suggest that nutrient levels have a larger impact on the final microbiome structure than direct microbial competition. Together, these findings suggest that monitoring total microbial composition, and not just the presence of pathogens, may be important for ensuring kimchi fermentation reproducibility. Full article

In order to better understand the micropore structure of shale reservoir in Jiyang Depression, permeability damage test, low temperature nitrogen adsorption and scanning electron microscopy (SEM) were carried out on six cores in the target block. The adsorption isotherms were analyzed by Frenkel–Halsey–Hill (FHH) model, and the fractal dimensions of different layers were calculated. The results show that the shale pore system is mainly composed of organic nanopores, inorganic nanopores and micro-fractures. The inorganic pores are mainly distributed around or inside the mineral particles, while microcracks are commonly found between mineral particles or at the organic–mineral interface. Organic pores are located within or between organic particles. The results of nitrogen adsorption show that the shale pores are mainly H2/H3 hysteresis loops with wedge, plate or ink bottle shapes. The pore structure is highly complex, and the fractal dimension is high. The mean D1 fractal dimension, which represents pore surface roughness, is 2.3788, and the mean D2 fractal dimension, which represents pore structure complexity, is 2.7189. The fractal dimension is positively correlated with specific surface area and total pore volume and negatively correlated with average pore radius. The permeability damage rates of the N layer, B layer, and F layer are 17.39%, 20.2%, and 21.6%, respectively. The contact Angle of the core decreases with the increase in water skiing time. In this study, the micropore structure of different formations in Jiyang Depression is compared and analyzed, which provides valuable insights for the optimization and differentiated development of shale oil and gas resources. Full article