Search Results (76)

Tocosh, a traditional Peruvian fermented potato product, is known for its health-promoting properties, including its antioxidant, anti-inflammatory, probiotic, and antibiotic effects, which have popularized its consumption, particularly in rural areas. To gain a better understanding of its antimicrobial properties, this study aimed to perform a comprehensive whole-genome analysis and functional assessment of the Bacillus velezensis TCSH0001 strain isolated from tocosh. The isolate was identified through whole-genome sequencing using the MinION nanopore platform. AntiSMASH analysis revealed nine biosynthetic gene clusters (BGCs) potentially responsible for producing secondary metabolites with antibiotic potential. Notably, seven BGCs showed a 100% similarity to known clusters involved in the biosynthesis of polyketide synthases (PKSs) and non-ribosomal peptides (NRPSs), including difficidin, bacillibactin, bacilysin, macrolactin H, bacillaene, fengycin, and bacillomycin D. In vitro analysis revealed antimicrobial activity against S. aureus strains. In addition, RT-qPCR indicated that the expression of the baeJ (bacillaene), bmyA (bacillomycin D), and pks2A (macrolactin H) occurs predominantly during the exponential growth phase. Our results suggest that this B. velezensis strain has the capacity to produce a diverse array of bioactive compounds, supporting the traditional use of tocosh as a natural antimicrobial agent, and revealing the potential of the strain as a high NRPS producer. Full article

Background: The search for reliable aging biomarkers using proteomic databases and large-scale proteomic studies presents a significant challenge in biogerontology. Existing proteomic databases and studies contain valuable information; however, there is inconsistency in approaches to biomarker selection and data integration. This creates barriers to translating existing knowledge into clinical practice and use in biomedical research. This work analyzed experimental proteomic studies, the content of proteomic databases, and proposed recommendations for optimization and improvement of proteomic database formation and enrichment. Methods: The study utilized publications devoted to proteomic data acquisition methods, proteomic databases, and experimental studies. Results: Methods for obtaining proteomic data were analyzed (Protein Pathway Array (PPA), Tissue Microarray (TMA), Luminex (Bead Array), MSD (Meso Scale Discovery), Simoa (Quanterix), SOMAscan (SomaLogic), Olink (PEA), Alamar NULISA (PEA+), and Oxford Nanopore. A total of 16 proteomic databases were investigated (HAGR, KEGG, STRING, Aging Atlas, HALL, Human Protein Atlas, UniProt, AgeAnnoMO, AgeFactDB, AgingBank, iProX, jMorp, jPOSTrepo, MassIVE, MetaboAge DB, PRIDE Archive). Additionally, 22 proteomic studies devoted to aging and age-associated diseases were analyzed. Conclusions: Proteomic databases and experimental studies individually contain valuable information about aging biomarkers. Using data from different sources within biomedical research poses challenges for improving and optimizing methodological solutions for publication selection, database formation, and marker development. Full article

Cinnamomum burmanni (Nees & T. Nees) Blume, a member of the Lauraceae family, exhibits adaptability to diverse environmental conditions by synthesizing a diverse array of specialized secondary metabolites, including terpenoids and cinnamaldehyde. Nevertheless, the molecular mechanisms underlying the chemical diversity in the leaves of C. burmanni and their remarkable adaptation to subtropical and tropical forests in South China have not been thoroughly investigated. This research integrates transcriptomic and proteomic analyses across five chemotypes of C. burmanni, namely, the borneol-type (BORCB), cinnamaldehyde-type (PROCB), eucalyptol-type (EUCCB), phytol-type (PHYCB), and chlorophyllinol-type (CARCB), by means of the Nanopore and Nano UPLC-MS/MS sequencing data. The findings indicate that PROCB demonstrates an up-regulation of the phenylpropanoid pathway (such as PAL, C4H, PR proteins), which is associated with biotic stress defense. In contrast, the terpenoid-dominated chemotypes (BORCB, EUCCB, PHYCB) prioritize the biosynthesis of monoterpenes and diterpenes as well as redox homeostasis. Protein–protein interaction networks highlight functional specialization; BORCB up-regulates the expression of enzymes GGPPS and TPS2, which are involved in monoterpene production; PHYCB enhances the activity of diterpene synthases (CPS, KSL) and chloroplast retrograde signaling; EUCCB activates SOD/GST to mitigate oxidative stress. PROCB induced defense hubs (NPR1, WRKY33) mediated by salicylic acid and pathogenesis-related proteins. The study establishes a comprehensive multi-omics resource for a gene–protein–metabolite framework, elucidating the mechanisms of stress resilience of C. burmanni in South China. Full article

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

Synthetic nanopores were recently demonstrated with memristive and nonlinear voltage-current behaviors, akin to ion channels in a cell membrane. Such ionic devices are considered a promising candidate for the development of brain-inspired neuromorphic computing techniques. In this work, we show the composite behavior of nanopore-array large memristors, formed with different membrane materials, pore sizes, electrolytes, and device arrangements. Anodic aluminum oxide (AAO) membranes with 5 nm and 20 nm diameter pores and track-etched polycarbonate (PCTE) membranes with 10 nm diameter pores are tested and shown to demonstrate memristive and nonlinear behaviors with approximately 10⁷–10¹⁰ pores in parallel when electrolyte concentration across the membranes is asymmetric. Ion diffusion through the large number of channels induces time-dependent electrolyte asymmetry that drives the system through different memristive states. The behaviors of series composite memristors with different configurations are also presented. In addition to helping understand fluidic devices and circuits for neuromorphic computing, the results also shed light on the development of field-assisted ion-selection-membrane filtration techniques as well as the investigations of large neurons and giant synapses. Further work is needed to de-embed parasitic components of the measurement setup to obtain intrinsic large memristor properties. Full article

Background/Objectives: Advances in nanopore sequencing have opened new avenues for studying DNA methylation at single-base resolution, yet their application in epigenetic ageing research remains underdeveloped. Methods: We present a novel framework that leverages the unique capabilities of nanopore sequencing to profile and interpret age-associated methylation patterns in native DNA. Results: Unlike conventional array-based approaches, long reads sequencing captures full CpG context, accommodates diverse and repetitive genomic regions, removes bisulfite conversion steps, and is compatible to the latest reference genome. Conclusions: This work establishes nanopore sequencing as a powerful tool for next-generation epigenetic ageing studies, offering a scalable and biologically rich platform for anti-ageing interventions monitoring and longitudinal ageing studies. 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

In this research work, two distinct types of three-dimensional (3D) capacitors were successfully fabricated, each with its own unique features and advantages. The first type of capacitor is centered around a 3D nanoporous structure. This structure is formed on a nickel substrate through anodic oxidation. After undergoing high-temperature thermal oxidation, a monolithic Ni-NiO-Pt metal–insulator–metal (MIM) capacitor with a nanoporous dielectric architecture is achieved. Structurally, this innovative design brings about several remarkable benefits. Due to the nanoporous structure, it has a significantly increased surface area, which can effectively store more charges. As a result, it exhibits an equivalent capacitance density of 69.95 nF/cm², which is approximately 18 times higher than that of its planar, non-porous counterpart. This high capacitance density enables it to store more electrical energy in a given volume, making it highly suitable for applications where miniaturization and high energy storage in a small space is crucial. The second type of capacitor makes use of Through-Glass Via (TGV) technology. This technology is employed to create an interdigitated blind-via array within a glass substrate, attaining an impressively high aspect ratio of 22.5:1 (with a via diameter of 20 μm and a depth of 450 μm). By integrating atomic layer deposition (ALD), a conformal interdigital electrode structure is realized. Glass, as a key material in this capacitor, has outstanding insulating properties. This characteristic endows the capacitor with a high breakdown field strength exceeding 8.2 MV/cm, corresponding to a withstand voltage of 5000 V. High breakdown field strength and withstand voltage mean that the capacitor can handle high-voltage applications without breaking down easily, which is essential for power-intensive systems like high-voltage power supplies and some high-power pulse-generating equipment. Moreover, due to the low-loss property of glass, the capacitor can achieve an energy conversion efficiency of up to 95%. Such a high energy conversion efficiency ensures that less energy is wasted during the charge–discharge process, which is highly beneficial for energy-saving applications and systems that require high-efficiency energy utilization. Full article

Electrochemical nitrogen reduction reaction (NRR) has emerged as a promising approach for sustainable ammonia synthesis under ambient conditions, offering a low-energy alternative to the traditional Haber–Bosch process. However, the development of efficient and sustainable electrocatalysts for NRR remains a significant challenge. Noble metals, known for their exceptional chemical stability under electrocatalytic conditions, have garnered considerable attention in this field. In this study, we report the successful synthesis of nanoporous CuAuPtPd quasi-high-entropy alloy (quasi-HEA) prism arrays through “melt quenching” and “dealloying” techniques. The as-obtained alloy demonstrates remarkable performance as an NRR electrocatalyst, achieving an impressive ammonia synthesis rate of 17.5 μg h⁻¹ mg⁻¹ at a potential of −0.2 V vs. RHE, surpassing many previously reported NRR catalysts. This work not only highlights the potential of quasi-HEAs as advanced NRR electrocatalysts but also provides valuable insights into the design of nanoporous multicomponent materials for sustainable energy and catalytic applications. Full article

The 2024 Nobel Prize in Physiology or Medicine was awarded to the pioneers who reported that microRNAs (miRNAs) regulate and direct the switch between physiological and pathological pathways via their over- or underexpression. The discovery changed the medical landscape and there are many completed and on-going clinical studies based on miRNAs. MiRNAs occur at the femtomolar level in biological fluids and are typically quantified using amplification-based techniques. Experimental nanopores have illustrated potential for trace analysis including amplification-free miRNA quantification. We repurposed the MinION, the only commercially available nanopore array device, and developed unique probes and protocols to detect and measure miRNA copies in blood and urine. Here, we report that miRNA copies are proportional to the total RNA isolated from the biospecimen, and that three known miRNA cancer biomarkers, i.e., miR-21, miR-375, and miR-141, were more than 1.5-fold overexpressed in blood samples from breast, ovarian, prostate, pancreatic, lung, and colorectal cancer patients compared to healthy patients. In these cancer samples, miR-15b was not overexpressed, in agreement with earlier studies. In contrast to literature reports, sample variability was undetectable in this study. The potential and limitations of this ready-to-use MinION/Yenos platform for multiple-cancer early detection (MCED) using blood or urine are discussed. Full article

Saccharides, being one of the fundamental molecules of life, play essential roles in the physiological and pathological functions of cells. However, their intricate structures pose challenges for detection. Nanopore technology, with its high sensitivity and capability for single-molecule-level analysis, has revolutionized the identification and structural analysis of saccharide molecules. This review focuses on recent advancements in nanopore technology for carbohydrate detection, presenting an array of methods that leverage the molecular complexity of saccharides. Biological nanopore techniques utilize specific protein binding or pore modifications to trigger typical resistive pulses, enabling the high-sensitivity detection of monosaccharides and oligosaccharides. In solid-state nanopore sensing, boronic acid modification and pH gating mechanisms are employed for the specific recognition and quantitative analysis of polysaccharides. The integration of artificial intelligence algorithms can further enhance the accuracy and reliability of analyses. Serving as a crucial tool in carbohydrate detection, we foresee significant potential in the application of nanopore technology for the detection of carbohydrate molecules in disease diagnosis, drug screening, and biosensing, fostering innovative progress in related research domains. Full article

Anodized aluminum oxide (AAO) molds were used for the production of large-area and inexpensive superhydrophobic polymer films. A controlled anodization methodology was developed for the fabrication of hierarchical micro–nanoporous (HMN) AAO imprint molds (HMN-AAO), where phosphoric acid was used as both an electrolyte and a widening agent. Heat generated upon repetitive high-voltage (195 V) anodization steps is effectively dissipated by establishing a cooling channel. On the HMN-AAO, within the hemispherical micropores, arrays of hexagonal nanopores are formed. The diameter and depth of the micro- and nanopores are 18/8 and 0.3/1.25 µm, respectively. The gradual removal of micropatterns during etching in both the vertical and horizontal directions is crucial for fabricating HMN-AAO with a high aspect ratio. HMN-AAO rendered polycarbonate (PC) and polymethyl methacrylate (PMMA) films with respective water contact angles (WCAs) of 153° and 151°, respectively. The increase in the WCA is 80% for PC (85°) and 89% for PMMA (80°). On the PC and PMMA films, mechanically robust arrays of nanopillars are observed within the hemispherical micropillars. The micro–nanopillars on these polymer films are mechanically robust and durable. Regular nanoporous AAO molds resulted in only a hydrophobic polymer film (WCA = 113–118°). Collectively, the phosphoric acid-based controlled anodization strategy can be effectively utilized for the manufacturing of HMN-AAO molds and roll-to-roll production of durable superhydrophobic surfaces. Full article

Staphylococcus pseudintermedius, a commensal opportunistic bacterium predominantly residing in the skin of companion animals, particularly dogs, has the potential to induce skin and soft tissue infections in pets, and zoonotic infections, including catheter-related complications. This study documents four cases of S. pseudintermedius infection or colonization in patients who had close contact with dogs or cats. Identification of the bacterial species was performed using MALDI-TOF mass spectrometry, and antibiotic susceptibility was determined using microdilution assay. DNA was sequenced using Nanopore technology followed by in silico analysis. Three isolates were multidrug resistant, including resistance to methicillin, with one belonging to the prevalent European lineage ST551, and the other two were attributed to a novel multilocus sequence type, ST2672. The remaining isolate was attributed to the novel multilocus sequence type ST2673 and was methicillin susceptible. All four isolates exhibited an array of virulence factors that contributed to colonization, damage to host immune cells, and biofilm formation. All the ST551 isolates included in the comparative analysis displayed clonality within the European continent. The importance of describing zoonotic infections associated with S. pseudintermedius resides in the scarcity of available scientific literature, further accentuated by its heightened resistance profile and potential complications, particularly in the context of catheter-related infections. Full article

We developed a technology for detecting and quantifying trace nucleic acids using a bracketing protocol designed to yield a copy number with approximately ± 20% accuracy across all concentrations. The microRNAs (miRNAs) let-7b, miR-15b, miR-21, miR-375 and miR-141 were measured in serum and urine samples from healthy subjects and patients with breast, prostate or pancreatic cancer. Detection and quantification were amplification-free and enabled using osmium-tagged probes and MinION, a nanopore array detection device. Combined serum from healthy men (Sigma-Aldrich, St. Louis, MO, USA #H6914) was used as a reference. Total RNA isolated from biospecimens using commercial kits was used as the miRNA source. The unprecedented ± 20% accuracy led to the conclusion that miRNA copy numbers must be normalized to the same RNA content, which in turn illustrates (i) independence from age, sex and ethnicity, as well as (ii) equivalence between serum and urine. miR-21, miR-375 and miR-141 copies in cancers were 1.8-fold overexpressed, exhibited zero overlap with healthy samples and had a p-value of 1.6 × 10⁻²², tentatively validating each miRNA as a multi-cancer biomarker. miR-15b was confirmed to be cancer-independent, whereas let-7b appeared to be a cancer biomarker for prostate and breast cancer, but not for pancreatic cancer. Full article

5S ribosomal DNAs (rDNAs) are arranged in tandem and are often under-represented in genome assemblies. In the present study, we performed a global and in-depth analysis of the 5S rDNAs in the model insect Tribolium castaneum and its closely related species Tribolium freemani. To accomplish this goal, we used our recently published genome assemblies based on Nanopore and PacBio long-read sequencing. Although these closely related species share the 5S rRNA gene sequence with high homology, they show a different organization of the 5S rDNA locus. Analysis of 5S rDNA arrays in T. castaneum revealed a typical tandemly repeated organization characterized by repeat units consisting of the 121 bp long 5S rRNA gene and the 71 bp long nontranscribed spacer (NTS). In contrast, T. freemani showed a much more complex organization of 5S rDNA arrays characterized by two patterns. The first is based on the association of 5S rRNA gene with arrays of a satellite DNA, representing the NTS sequence of the 5S rDNA genes in T. freemani. The second, more complex type is characterized by a somewhat less frequent occurrence of the 5S rRNA gene and its association with longer satellite DNA arrays that are regularly interrupted by Jockey-like retrotransposons. This organization, in which the ribosomal gene is associated with two completely different repetitive elements such as satellite DNAs and retrotransposons, suggests that the 5S rRNA gene, regardless of its crucial function in the genome, could be a subject of extremely dynamic genomic rearrangements. Full article