Search Results (3,303)

Soil fungal communities play a central role in nutrient cycling and ecosystem functioning in tropical montane forests, yet the relative influence of topographic heterogeneity and soil depth on their assembly remains poorly understood. This study evaluated the composition, diversity, and functional structure of soil fungal communities associated with an experimental Podocarpus oleifolius plantation in the Colombian Andes. Using ITS2 rDNA sequencing, fungal assemblages were characterized from soil samples collected around ten trees distributed along a topographic gradient. For each tree, samples were collected at two soil depths (0–10 cm and 10–20 cm), yielding a total of 17 samples after quality control. Topographic variables derived from a digital elevation model were used to evaluate their influence on community structure. A total of 1875 Operational Taxonomic Units (OTUs) were detected, dominated by Ascomycota. No significant differences in alpha or beta diversity were observed between soil depths. In contrast, slope emerged as the strongest environmental driver of community composition. A high proportion of unassigned OTUs highlighted the presence of poorly characterized fungal diversity. These findings highlight the importance of incorporating fine-scale terrain heterogeneity into restoration strategies with native species and into future studies of soil microbial dynamics in tropical montane ecosystems. Full article

Skin aging is a complex, multifactorial process driven by intrinsic biological mechanisms and environmental exposures, resulting in progressive functional and structural decline. Chronological age does not adequately capture this variability, highlighting the need for molecular biomarkers that reflect biological aging. In this context, transcriptomic aging clocks have emerged as a promising approach, as gene-expression profiles provide a dynamic representation of cellular and tissue states. This narrative review is based on a targeted literature search in PubMed and IEEE Xplore and focuses on transcriptomic aging clocks in human skin, with emphasis on gene-expression signatures, key biological pathways, and computational modeling strategies. These models consistently capture coordinated alterations in processes such as cellular senescence, DNA damage response, inflammation, and extracellular matrix remodeling. Representative transcriptomic frameworks, including models such as SkinAGE, illustrate the ability of gene-expression-based approaches to quantify biologically meaningful and dynamic aging states in the skin. Advances in machine-learning approaches, including deep learning and pathway-guided models, are critically evaluated, alongside the role of explainable artificial intelligence in enhancing model transparency and biological interpretability. Future developments are expected to integrate multi-omics data and digital twin frameworks, enabling the transition from static biomarkers toward dynamic, predictive, and personalized models of skin aging Full article

Brucellosis remains one of the most widespread zoonotic infections worldwide, causing serious veterinary, medical, and socio-economic consequences. The disease, caused by bacteria of the genus Brucella, affects a wide range of domestic and wild animals as well as humans, with global incidence potentially reaching 1.6–2.1 million new cases annually. The most effective approach to combating brucellosis is specific prevention through vaccination. Therefore, we conducted this review to summarize data from existing studies on modern strategies for brucellosis vaccination, types of vaccine platforms, their efficacy, safety, and applicability in veterinary and human medicine. We searched databases including PubMed, Scopus, and Web of Science to identify relevant scientific articles in English published from 1990 to 2025. The aim of this work is to conduct a systematic analysis of modern brucellosis vaccination strategies in livestock and humans, as well as to evaluate the prospects of new vaccine platforms. The review examines live attenuated, inactivated, subunit, vector, and DNA vaccines, as well as their immunological mechanisms of action, advantages, and limitations of application. This information allows for a better understanding of the mechanisms of protective immunity formation and challenges related to DIVA diagnostics (Differentiating Infected from Vaccinated Animals). The “One Health” concept demonstrated the interconnection between human, animal, and environmental factors, emphasizing the need for an interdisciplinary approach to brucellosis monitoring, prevention, and control. Vector vaccines based on influenza virus (Flu-BA), developed in Kazakhstan, have shown high promise, combining immunogenicity, protective efficacy, and a favorable safety profile. Promising directions remain mRNA vaccines, nanoparticles, CRISPR/Cas9 technologies, and mucosal vaccines. Full article

Epigenetic mechanisms profoundly regulate gene expression, developmental trajectories, and phenotypic variation, extending biological influence beyond DNA sequence alone. A growing body of evidence suggests that environmental exposures, including pollutants, drugs, stress, and diet, can induce germline and early embryonic epimutations that alter developmental programs with lasting consequences for neurodevelopmental and cognitive outcomes. However, the fields most relevant to these processes have largely developed independently. These include germline epigenetics, early embryonic patterning, neurodevelopment and cognitive regulation, and intergenerational or transgenerational inheritance. Each field has its own conceptual frameworks and mechanistic models. This fragmentation obscures the biological reality that these systems are tightly interconnected: environmentally induced epigenetic perturbations in gametes can reshape the epigenetic landscape of the early embryo, influence lineage allocation during gastrulation, and ultimately modify the molecular architecture of the developing central nervous system. A systems–biology perspective capable of linking germline epimutations and early embryonic epigenetic instability to later neurodevelopmental and cognitive phenotypes and their potential inheritance is therefore required. This review synthesizes current evidence across these traditionally isolated domains and proposes a coherent mechanistic framework linking germ cell epimutations and early embryonic epigenetic instability to the emergence of neurodevelopmental and cognitive phenotypes. By bridging these conceptual gaps, we aim to establish a cohesive foundation for understanding how early epigenetic disruptions generate long-lasting and in some cases heritable effects on brain development and cognitive function. Full article

Cadmium (Cd) is a pervasive environmental contaminant with potent cytotoxic effects in a wide range of organisms. Although autophagy and apoptosis are recognized as major cellular responses to heavy metal stress, the molecular basis of Cd-induced cell death in insects remains insufficiently understood. In this study, we used fifth-instar day-4 (5L4D) larvae of Bombyx mori and the silkworm-derived Bm-12 cell line to investigate the involvement of three core autophagy-related proteins, Bombyx mori Autophagy-related protein 5(BmATG5), Bombyx mori Autophagy-related protein 6(BmATG6), and Autophagy-related protein 8(BmATG8), in Cd-induced autophagy and apoptosis. Exposure to CdCl₂ markedly induced autophagic and apoptotic responses in both larval midgut tissue and Bm-12 cells, as demonstrated by monodansylcadaverine(MDC) staining, Lyso-Tracker Red staining, DAPI and Hoechst 33258 staining, and DNA fragmentation assays. qPCR and Western blot analyses showed significant upregulation of BmATG5, BmATG6, and BmATG8 following Cd exposure. Notably, the cleaved forms tBmATG5-N (24 kDa) and tBmATG6-C (35 and 37 kDa), as well as the lipidated form BmATG8-PE (12 kDa), accumulated substantially under Cd stress. In parallel, intracellular Ca²⁺ levels and calpain activity were significantly increased, suggesting activation of a calcium-dependent regulatory pathway. Pharmacological inhibition experiments further indicated that autophagy and apoptosis are functionally interconnected during the Cd response. Collectively, these findings demonstrate that BmATG5, BmATG6, and BmATG8, together with their processed forms, play central roles in coordinating autophagy–apoptosis crosstalk during Cd-induced cytotoxicity in Bombyx mori. This study provides new mechanistic insight into heavy metal toxicity in insects and expands our understanding of stress-induced programmed cell death during silkworm metamorphosis. Full article

Endophytic bacteria from plants adapted to arid and semi-arid environments represent an underexplored reservoir of microbial diversity with potential agricultural applications. Here, we report a polyphasic taxonomic and genome-based characterization of Achromobacter sp. isolates recovered from root and foliar tissues of Citrullus colocynthis and Peganum harmala, two medicinal plants thriving under harsh environmental conditions. Whole-genome sequencing, phylogenomic analyses, average nucleotide identity (ANI), digital DNA–DNA hybridization (dDDH), multilocus sequence typing, and detailed phenotypic profiling revealed three previously undescribed species, for which we propose the names Achromobacter colocynthi sp. nov., Achromobacter maghribensis sp. nov., and Achromobacter semiaridum sp. nov. Genome assemblies were highly complete (98.7–99.2%) with minimal contamination (<1%), supporting robust taxonomic inference. All three species displayed ANI and dDDH values below accepted thresholds relative to their closest phylogenetic neighbors, despite partial inconsistencies in 16S rRNA similarity for one isolate, highlighting the value of genome-wide metrics for species delineation. Phylogenomic analyses placed the novel taxa within Achromobacter sp. as distinct evolutionary lineages. Phenotypic characterization indicated broad metabolic versatility, including utilization of carbohydrates, organic acids, and amino acids, tolerance to moderate salinity and acidic pH, and resistance to multiple antimicrobial compounds, traits likely linked to adaptation to endophytic lifestyles under semi-arid conditions. Beyond their taxonomic novelty, the isolates exhibited in vitro traits associated with plant adaptation and stress tolerance, including IAA production, ACC deaminase activity, and tolerance to Zn, Cu, and Cd. Genomic analyses further indicated functions related to phosphate acquisition and stress response. These findings expand the taxonomic framework of Achromobacter sp., establish C. colocynthis and P. harmala as reservoirs of novel endophytic bacteria, and highlight their potential relevance for agricultural biotechnology in stress-prone environments. Full article

The valorization of agri-food by-products aligns with circular economy principles and offers sustainable sources of bioactive compounds. This study investigated the peels of the purple-fleshed Solanum tuberosum L. cv. Vitelotte Noire (VN), cultivated in Sardinia, as a potential resource for nutraceutical antioxidants. Extracts were obtained using solvents of different polarities (water, 80% and 96% ethanol) and characterized. Phytochemical screening revealed high concentrations of total phenolics, flavonoids, and anthocyanins, with the 96% ethanolic extract showing superior anthocyanin content. Antioxidant capacity, assessed via ORAC-PYR, TEAC-ABTS, and DPPH assays, was highest in the alcoholic extracts. Furthermore, all extracts showed protective effects in an in vitro model of AAPH-induced oxidative DNA damage, as indicated by the preservation of plasmid supercoiling. Untargeted LC-QTOF-MS analysis detailed a rich metabolomic profile, including organic acids, amino acids, and vitamins. The findings confirm VN peel as a potent, sustainable source of antioxidants, supporting its valorization for developing high-added-value nutraceutical and functional food ingredients, while reducing waste disposal costs and environmental impact. Full article

The increasing demand for sustainable agriculture has intensified interest in beneficial microbes as eco-friendly alternatives to chemical pesticides for plant disease control. Among these, plant growth-promoting rhizobacteria (PGPR) have attracted great interest because they can suppress plant pathogens and strengthen plant health through molecular mechanisms. Recent studies suggest that PGPR protect plants from disease not only by directly attacking pathogens but also by changing how plant immune genes are expressed through epigenetic processes. This review brings together current knowledge on epigenetic regulation in plant–PGPR interactions, focusing on DNA methylation, histone modifications, and non-coding RNA pathways. PGPR colonization activates plant immune signaling through pattern recognition receptors, MAPK cascades, reactive oxygen species, and plant hormones. The review also covers the range of bacterial signals—including lipopolysaccharides, flagellin, cyclic lipopeptides, and volatile organic compounds—that prepare plant defenses, and explains how the recognition of these signals reshapes chromatin structure at defense genes. In addition, the review discusses how these changes may influence induced systemic resistance and examines emerging, though still limited, evidence on whether they could potentially be transmitted to subsequent generations. A better understanding of how microbial signals regulate host epigenetics may reveal new ways to improve plant immunity and balance growth with defense. Overall, available evidence indicates that PGPR-induced epigenetic changes represent a promising and environmentally friendly approach to crop protection; however, field-level validation and mechanistic confirmation in non-model crop species remain necessary before this strategy can be considered practically applicable. Full article

Environmental DNA (eDNA) metabarcoding has emerged as a powerful tool for biodiversity monitoring, yet its accuracy is fundamentally constrained by the completeness and taxonomic reliability of reference sequence databases. For the Three Gorges Reservoir (TGR), no integrated multi-marker eDNA reference library exists, hampering standardized fish conservation monitoring under the Yangtze River Ten-Year Fishing Ban. Here, we constructed a comprehensive, multi-marker eDNA reference database for the fish fauna of the TGR, encompassing mitochondrial 12S rRNA, 16S rRNA, and cytochrome c oxidase subunit I (COI) gene sequences from 173 specimens (120 species) collected between 2021 and 2024. After integrating publicly available sequences, the final database comprised 161 species. Then, we quantitatively compared species annotation performance between this local database and public repositories. Results showed that while public databases achieved higher nominal species coverage (94.67%), they exhibited critical deficiencies in annotation accuracy, correctly annotating only 77.97% (12S rRNA), 75.00% (16S rRNA), and 38.14% (COI) of sequences from shared species under controlled conditions. In contrast, the local database exhibited 92.37%, 93.10% and 100% annotation accuracy for the respective markers. Optimal interspecific Kimura 2-parameter (K2P) thresholds for species delimitation were 0.00448 (12S rRNA), 0.00531 (16S rRNA), and 0.00734 (COI). In addition, 15, 0, and 4 species pairs exhibited zero interspecific distance for 12S rRNA, 16S rRNA, and COI, respectively. These limitations reinforce the need for cautious interpretation of eDNA metabarcoding results and the integration of multiple markers or complementary nuclear loci. This study provides preliminary evidence that regionally curated, multi-marker reference libraries could improve taxonomic assignment reliability in eDNA metabarcoding compared to uncurated public repositories, providing a foundational resource for biodiversity conservation. Full article

Chloroidium saccharophilum is a resilient green microalga with a broad ecological distribution and an increasing biotechnological interest due to its tolerance of extreme environmental conditions. In this study, a sample of C. saccharophilum from the Laguna Blanca aquifer (Magallanes, southern Chile) was physiologically and phylogenetically characterized. This is the first confirmed evidence of this strain in the Southern Cone. Molecular identification based on ITS rDNA sequencing and ITS2 secondary structure analysis confirmed its taxonomic location, showing high similarity with reference strains and no compensatory base changes. Growth performance was analyzed under controlled laboratory conditions and under outdoor desert cultivation in the Atacama Desert, focusing on temperature, salinity, nutrients limitation, and high solar irradiance operational conditions. The strain exhibited optimal growth at 22 °C under laboratory conditions and demonstrated a strong tolerance to high salinity (150 g L⁻¹ NaCl). Outdoor raceways cultivation revealed a negative relationship between temperatures above 25 °C and biomass accumulation, while nutrients depletion and strong irradiance caused moderate carotenoid accumulation. However, the low amount of carotenoid yields remained constant, even under combined stress conditions. In general, the results highlight the ecological adaptability and the stress tolerance of C. saccharophilum, supporting its potential application in saline bioprocesses and bioremediation. Nevertheless, the limited production of carotenoid synthesis suggests that additional or combined stress strategies will be required to enhance the production of high-value metabolites. This study expands the biogeographical knowledge of C. saccharophilum and provides a physiological baseline for future optimization studies in extreme and Mars-analog environments. Full article

Conventional Escherichia coli (E. coli) detection methods are often time-consuming, while molecular diagnostics typically rely on expensive thermocycling equipment. To address these limitations, this study developed a rapid nucleic acid detection method for E. coli by integrating multienzyme isothermal rapid amplification (MIRA) with Pyrococcus furiosus Argonaute (PfAgo)-mediated targeted cleavage. The conserved housekeeping gene phoA was selected as the target, and specific MIRA primers and 5′-phosphorylated guide DNAs (gDNAs) were designed accordingly. After exponential amplification at 39 °C, the amplicons were specifically recognized by PfAgo at 95 °C, leading to molecular beacon cleavage and generation of a detectable FAM fluorescence signal. Among the tested guides, gDNA6 showed the highest cleavage efficiency. Optimal performance was achieved with 1 μM PfAgo, 0.5 μM gDNA, and 5 mM MnCl₂. The optimized MIRA-PfAgo assay demonstrated a limit of detection of 10⁰ copies/μL, comparable to qPCR, and exhibited high specificity with no cross-reactivity against common enteric pathogens. In 28 clinical and environmental samples, the assay results were fully consistent with those of qPCR. Overall, the MIRA-PfAgo platform provides a rapid, sensitive, and specific approach for E. coli detection, demonstrating strong potential to reduce reliance on precision thermal cyclers for resource-limited applications. Full article

Background: Gaucher disease (GD) arises from pathogenic variants in the GBA1 gene and is known for its wide range of clinical presentations—a variability that genotype alone cannot adequately account for. Objective: This study aimed to explore transcriptomic factors that might help explain why two genetically identical twins with type 1 GD developed noticeably different clinical outcomes. Methods: We isolated peripheral blood mononuclear cells from both twins and two age-matched controls, then differentiated them into macrophages in vitro before conducting RNA sequencing. Gene expression differences were analyzed using established bioinformatics pipelines, and a subset of genes were subsequently assessed by quantitative real-time PCR (qRT-PCR) to confirm the sequencing findings. Results: Both twins shared a GD-associated transcriptional signature broadly reflecting immune activation and lysosomal stress. Interestingly, the twin who experienced systemic complications had a relative enrichment of interferon-responsive transcripts, while the less severely affected twin showed more pronounced suppression of small nucleolar RNA clusters. That said, neither difference held up after correcting for multiple comparisons, so these patterns are best viewed as exploratory trends rather than definitive findings. The qRT-PCR results lend partial support to this picture: stress- and immune-related genes (DDIT4, RPH3A, SAMSN1) trended toward higher expression in patients versus controls, and interferon-stimulated genes (ISG15, RSAD2, IFI44L) were more elevated in M2 than in M1. Conclusions: Taken together, these findings suggest that factors beyond genetics—whether epigenetic, environmental, or otherwise—may play a meaningful role in shaping how GD manifests differently even between individuals with identical DNA. Although the data are preliminary, they point to transcriptomic profiling, paired with targeted validation, as a useful starting point for building hypotheses about why this disease looks so different from one patient to the next, even when the underlying mutation is the same. Full article

In biological systems, DNA serves as the primary carrier of genetic information, and the stability of its structure is fundamental to cellular function. Metal ions and temperature are critical environmental factors that modulate DNA conformation and activity. However, the differential morphological effects of alkali, alkaline earth, and transition metal ions, especially when combined with thermal treatment, have not been systematically visualized and quantified. In this work, atomic force microscopy (AFM) was employed to investigate the effects of different metal ions (Na⁺, K⁺, Mg²⁺, Ca²⁺, Cu²⁺) and temperature on DNA structure. The results demonstrated that monovalent ions (Na⁺ and K⁺) neutralized the negative charges on the DNA backbone, thereby reducing intermolecular electrostatic repulsion and promoting DNA aggregation into dendritic structures. Divalent ions (Mg²⁺ and Ca²⁺) not only provided more effective charge screening but also formed ion bridges between DNA strands, leading to more compact and cross-linked networks. In contrast, Cu²⁺ ions directly coordinated with DNA bases, causing local structural distortion and strand scission. Elevated temperatures induced DNA melting, with distinct morphological transitions from extended double strands to condensed single-stranded globules observed at temperatures exceeding the melting point (T_m). These findings elucidate the mechanisms by which environmental factors govern DNA morphology, providing in-sights relevant to nanotechnology and molecular biology applications. Full article

Mitochondria are increasingly recognized as multifunctional organelles that integrate metabolic, redox, immune, and cell fate signaling, thereby maintaining cellular and tissue homeostasis under physiological conditions. Beyond their classical role in ATP production, mitochondria act as central regulatory hubs coordinating adaptive responses to metabolic demands and environmental stress. These functions are sustained through tightly regulated quality control mechanisms, including mitochondrial biogenesis, dynamic fusion–fission remodeling, redox signaling, and selective removal of damaged organelles via mitophagy. Disruption of these processes compromises cellular resilience and contributes to disease initiation and progression. This review summarizes and critically evaluates current evidence on mitochondrial function in health and its dysregulation in pathological conditions, with a particular focus on rheumatoid arthritis (RA), ischemic stroke (IS), and autism spectrum disorder (ASD). Despite their distinct clinical manifestations, these disorders share convergent mitochondrial abnormalities, including metabolic reprogramming toward glycolysis, excessive or persistent reactive oxygen species production, impaired mitophagy, mitochondrial DNA-driven innate immune activation, and hypoxia-related stress. In RA, mitochondrial dysfunction sustains chronic inflammation and joint destruction; in IS, acute mitochondrial failure and reperfusion-associated oxidative stress drive neuronal injury; and in ASD, mitochondrial metabolic inflexibility and defective quality control contribute to chronic low-grade inflammation and neurodevelopmental vulnerability. A variety of methods for the assessment of mitochondrial function are available to study these pathological conditions. Collectively, these findings position mitochondrial dysfunction as a unifying pathogenic mechanism linking inflammatory, neurodegenerative, and neurodevelopmental processes. Targeting mitochondrial metabolism, redox balance, and quality control pathways therefore represents a promising cross-disease therapeutic strategy. Full article

The development of self-powered environmental sensors is of great practical significance for addressing the power supply dilemma of traditional sensors in remote areas and avoiding environmental pollution from waste batteries. Given that the majority of the self-powered environmental sensors are based on the TENG principle, especially the active self-powered sensors, this paper reviews recent advances in triboelectric nanogenerator (TENG)-based self-powered environmental sensors. What distinguishes this review from the previous ones published on TENG is that it systematically discusses the application of TENG-based self-powered sensors for environmental monitoring. TENG-based self-powered sensors are classified into two types: TENG as a power supply for professional biochemical sensors and active self-powered sensors where TENG acts as both power source and sensing unit. This paper illustrates the applications of these devices in detecting targets in the environment, such as heavy metal ions, toxic gases, bacterial DNA, and bacteria, and summarizes the relevant performance parameters. It also analyzes key challenges including efficient mechanical energy harvesting, material durability and sensing specificity. Finally, the outlook notes that TENG-based sensors will expand detection ranges and integrate with other technologies, providing valuable guidance for their environmental monitoring applications. Full article