Search Results (439)

Silver nanoparticles (AgNPs) possess distinct physicochemical characteristics and demonstrate high antibacterial potential that highlights them as promising alternatives against a wide range of pathogens. The immense antibacterial potential of AgNPs is primarily attributed to the release of silver ions that lead to the disruption of bacterial cell membrane, generation of reactive oxygen species (ROS), inhibition of protein synthesis and interference with DNA replication. Variations in AgNPs’ shape, size, and surface characteristics are also considered key factors determining their effectivity as well as specificity. AgNPs are considered potent antibacterial agents, including against antibiotic- and drug-resistant strains. However, inappropriate dosages or unoptimized application of may result in potential toxicity, consisting one of the main drawbacks of the AgNPs’ safer administration. This article reviews the recent literature on the antibacterial potential of AgNPs, focusing on their broad mechanisms of action, applicability, especially in agriculture, biomedical and environmental fields, toxicity and future perspectives. Full article

The Water Framework Directive 2000/60/EC requires the assessment of the ecological quality in all surface waters using biological indices, yet the effective application of these indices often demands extensive and long-term monitoring data. Oxidative stress biomarkers offer a promising complementary approach, as they can detect early biochemical responses of organisms to environmental degradation. In this study, we evaluated the suitability of two oxidative stress biomarkers—malondialdehyde (MDA) levels and DNA damage—in the gonads of a freshwater fish species, the Prussian carp Carassius gibelio (Bloch, 1782) as indicators of ecological condition in lakes of differing environmental quality. Fish were sampled from four lakes (Doirani, Vegoritida, Volvi, Petron; Northern Greece) representing a gradient of physicochemical and ecological quality. Both MDA concentrations and DNA damage showed significant (p < 0.05) differences among lakes. However, only DNA damage in the gonads was significantly (p < 0.05) associated with lake ecological quality as determined by the Greek Lake Fish Index (GLFI), with higher biomarker responses observed in lakes of poorer status. These findings demonstrate that oxidative stress biomarkers in C. gibelio reflect variations in lake ecological quality and may serve as sensitive, early-warning tools for biomonitoring and pollution assessment in freshwater ecosystems. Full article

Alzheimer’s disease (AD) and related dementias (ADRD) are neurodegenerative conditions that cause gradual deterioration of cognition, memory and language in the elderly. AD has been declared as a health priority by the World Health Organization (WHO) considering its severity and unavailability of a permanent cure. Although the global AD/ADRD population is made up of many ethno-racial groups, the majority of AD studies have focused on the Caucasian population. The few AD studies conducted on minority populations in the US have found that significant AD health disparities exist, demonstrating that African Americans and Hispanics have a significantly higher prevalence of AD and related dementias, with their risk often approaching twice that of White individuals. For the past few years, epigenomic research has played an important role in understanding health disparities among diverse racial and ethnic groups. Unlike genetic studies, which focus on the DNA sequence that one is born with, epigenomics investigates how changes in gene expression due to extrinsic environmental exposures may impact disease pathophysiology. Recent epigenomic studies appear to be promising in not only understanding disease pathology but also in developing diagnostic and therapeutic tools for AD with population specificity. However, there is only a handful of studies and review articles available addressing the epigenomic applications in irradicating racial disparities in AD/ADRD. Therefore, the aim of this review is to discuss the recent findings of epigenomic studies in AD and related dementias, their contribution in irradicating racioethnic disparities and insights into the future direction of their application in precision medicine. Full article

AI enhances aquatic resource management by automating species detection, optimizing feed, forecasting water quality, protecting species interactions, and strengthening the detection of illegal, unreported, and unregulated fishing activities. However, these advancements are inconsistently employed, subject to domain shifts, limited by the availability of labeled data, and poorly benchmarked across operational contexts. Recent developments in technology and applications in fisheries genetics and monitoring, precision aquaculture, management, and sensing infrastructure are summarized in this paper. We studied automated species recognition, genomic trait inference, environmental DNA metabarcoding, acoustic analysis, and trait-based population modeling in fisheries genetics and monitoring. We used digital-twin frameworks for supervised learning in feed optimization, reinforcement learning for water quality control, vision-based welfare monitoring, and harvest forecasting in aquaculture. We explored automatic identification system trajectory analysis for illicit fishing detection, global effort mapping, electronic bycatch monitoring, protected species tracking, and multi-sensor vessel surveillance in fisheries management. Acoustic echogram automation, convolutional neural network-based fish detection, edge-computing architectures, and marine-domain foundation models are foundational developments in sensing infrastructure. Implementation challenges include performance degradation across habitat and seasonal transitions, insufficient standardized multi-region datasets for rare and protected taxa, inadequate incorporation of model uncertainty into management decisions, and structural inequalities in data access and technology adoption among smallholder producers. Standardized multi-region benchmarks with rare-taxa coverage, calibrated uncertainty quantification in assessment and control systems, domain-robust energy-efficient algorithms, and privacy-preserving data partnerships are our priorities. These integrated priorities enable transition from experimental prototypes to a reliable, collaborative infrastructure for sustainable wild capture and farmed aquatic systems. Full article

Extracellular polymeric substances (EPSs) produced by actinomycetes of the genus Rhodococcus play crucial roles in their ecological success, metabolic versatility, and biotechnological value. This review summarizes existing studies of Rhodococcus EPSs, emphasizing the biochemical composition, functional attributes, and practical significance of EPSs, as well as their importance in biomedicine, bioremediation, and other applications (food industry, biomineralization) with respect to the EPS chemical composition and biological roles. Rhodococcus species synthesize complex EPSs composed primarily of polysaccharides, proteins and lipids that, like in other bacteria, support cell adhesion, aggregation, biofilm formation, and horizontal gene transfer (and can prevent exogenous DNA binding) and are highly important for resistance against toxicants and dissolution/assimilation of hydrophobic compounds. EPSs produced by different species of Rhodococcus exhibit diverse structures (soluble EPSs, loosely bound and tightly bound fractions, capsules, linear and branched chains, amorphous coils, rigid helices, mushroom-like structures, extracellular matrix, and a fibrillar structure with a sheet-like texture), leading to variations in their properties (rheological features, viscosity, flocculation, sorption abilities, compression, DNA binding, and interaction with hydrophobic substrates). Notably, the EPSs exhibit marked emulsifying and flocculating properties, contributing to their recognized role in bioremediation. Furthermore, EPSs possess antiviral, antibiofilm, anti-inflammatory, and anti-proliferating activities and high viscosity, which are valuable in terms of biomedical and food applications. Despite extensive industrial and environmental interest, the molecular regulation, biosynthetic pathways, and structural diversity of Rhodococcus EPSs remain insufficiently characterized. Advancing our understanding of these biopolymers could expand new applications in biomedicine, bioremediation, and biotechnology. Full article

L. monocytogenes is the causative agent of human listeriosis, a deadly disease with fatality rates up to 20%. L. monocytogenes has the ability to grow under harsh environmental conditions. It can form biofilms in food industries, making it capable of persisting in facilities. Given this scenario, it is of utmost importance to rapidly detect this bacterium not only in foods but also on food-contact surfaces. For the successful outcome of any given detection technology, it is imperative to properly process the samples. In the present work, PBS, LPT, and LPT-Pronase were compared to determine which one could provide better results in DNA-based detection. Additionally, the effect of a short TSB pre-enrichment was assessed. To better mimic a real scenario, L. monocytogenes monospecies and multispecies biofilms were analyzed. It was observed that supplementing LPT with pronase, a protein-degrading enzyme, could better detach the biofilm, which achieved a 0.5 cycle reduction compared to the other broths, and the pre-enrichment reduced the real-time PCR by ~2 cycles. The samples were analyzed by real-time PCR and colorimetric LAMP, and the same results were obtained with both techniques regardless of the concentration of L. monocytogenes present in the biofilm; the initial concentration was 1.8 log CFU/cm² 15 min after the pre-enrichment. The results were confirmed by real-time PCR, which demonstrated the applicability of the methodology to be applied in decentralized setups, such as food-processing facilities, with minimal laboratory infrastructure. Full article

Donkeys (Equus asinus) are economically and ecologically important livestock species whose genetic potential remains underexplored. This review synthesizes recent advances in donkey genomics, tracing their evolutionary history while evaluating current applications in selective breeding, conservation genetics, and agricultural management. By integrating evidence from population genomics, functional genomics, and comparative evolutionary studies, we summarize major genomic discoveries and identify persistent knowledge gaps, with a focus on translating genomic information into practical breeding outcomes. High-quality reference genomes, population resequencing, and ancient DNA analyses have clarified the African origin, global dispersal history, and environmental adaptation of donkeys. Genome-wide approaches, including GWAS, QTL mapping, and multi-omics analyses, have further identified genes and regulatory pathways associated with thermotolerance, metabolism, reproduction, and milk production. Nevertheless, progress is still limited by small sample sizes, variable sequencing depth, and inconsistencies in phenotyping and bioinformatic pipelines, which constrain cross-population comparisons and practical applications. Addressing these challenges through standardized phenotyping, improved data integration, and collaborative research frameworks will lay the groundwork for effective conservation strategies and sustainable genomic breeding of global donkey populations. Full article

Early-onset colorectal cancer (EOCRC) in people < 50 years of age has been rising globally, yet its causes remain unknown. Emerging evidence suggests that environmental factors, including exposure to micro-and nanoplastics (MNPs), may contribute to colorectal carcinogenesis. MNPs can enter the gastrointestinal tract through ingestion, translocate across the epithelial barrier via endocytosis or paracellular pathways, and interact directly with epithelial and immune cells. Once internalized, they may generate events associated with tumor initiation including oxidative stress, disruption of membrane integrity, pro-inflammatory signaling, and disruption of genomic and epigenomic stability. Patient-derived colorectal organoids offer a physiologically relevant and scalable 3D model that closely mimics the cellular architecture and genetic landscape of primary tumors. We highlight how organoid models can be leveraged to study the impact of MNPs on the key processes of inflammation, DNA damage, senescence, and epigenetic modifications. Furthermore, we discuss the application of organoid-based systems to model EOCRC driven by environmental exposures, including the integration of organoid platforms with high-throughput assays, omics profiling, and microfluidics to better capture MNP-induced pathogenic mechanisms. Altogether, colorectal organoids provide a powerful bridge between environmental plastic exposure and EOCRC etiology, offering a tractable platform to identify mechanistic pathways and potential biomarkers of early disease. Full article

This study aimed to evaluate the response mechanisms of zebrafish larvae to Norfloxacin nicotinate (NOR-N) exposure. Embryos were exposed to NOR-N from 4 h post-fertilization (hpf) until 96 hpf. The exposure concentrations included 0.002, 0.2, 1, and 5 mg/L (simulating both normal and exceptionally high environmentally relevant levels of NOR), as well as a high dose of 25 mg/L. Subsequent analyses focused on apoptosis, neurodevelopment, and DNA methylation in the resulting zebrafish larvae. The results showed that high-dose NOR-N (≥5 mg/L) induced obvious apoptotic cell death in zebrafish larvae, accompanied by increased activities of Cas3 and Cas9, up-regulated P53, Bax, Puma, Apaf1, Cas3 and Cas9 genes expression, and reduced Mdm2 levels and Bcl2/Bax ratio. Moreover, exposure to 5 and/or 25 mg/L NOR-N resulted in a significant up-regulation of neurodevelopment-related genes (Sox2, Sox3 and Sox19a), concomitantly with a marked decline in the transcription of DNA methylation genes, including Dnmt1, Dnmt3a1, Dnmt3b1, Dnmt3b2 and Dnmt3b4. Overall, our findings demonstrated that NOR-N exposure could induce apoptosis, developmental neurotoxicity and aberrant DNA methylation in zebrafish larvae. These findings provide insights to guide the safe application of NOR-N in aquaculture and support the assessment of its potential ecological risks to aquatic ecosystems. Full article

Egg quality is a critical economic trait in poultry production, influencing consumer preference and production efficiency. The genetic and epigenetic regulation of egg quality involves complex biological pathways across various traits such as shell quality, albumen composition, and yolk biochemistry. This review synthesizes recent advances in the genetic, molecular, and epigenetic mechanisms that determine poultry egg quality. Specifically, it focuses on external traits such as eggshell strength, color, and thickness, and internal traits including albumen height, yolk composition, and the Haugh unit. Through genome-wide association studies (GWAS), quantitative trait loci (QTL) mapping, whole-genome sequencing (WGS), and multi-omics approaches, key candidate genes such as OC-116, CALB1, CA2 (shell formation), OVAL, SPINK5, SERPINB14 (albumen quality), and FGF9, PIAS1, NOX5 (lipid metabolism) have been identified. These genes play a pivotal role in shell biomineralization, albumen protein regulation, and yolk lipid transport. This review also explores the heritability of these traits, emphasizing the challenges posed by polygenic architecture and the influence of environmental factors. Furthermore, it addresses the dynamic spatiotemporal regulation of egg quality traits, including epigenetic layers such as DNA methylation, histone modifications, RNA methylation, and post-translational protein modifications. This paper highlights the application of these findings to breeding programs via genomic selection, marker-assisted breeding, and epigenetic engineering approaches. Future directions for precision breeding and the development of functional eggs with enhanced quality are also discussed. Full article

Nitrogen (N) is an essential nutrient for the growth and development of rice. However, excessive N fertiliser application and low N Use Efficiency (NUE) have led to serious environmental problems and threatened agricultural sustainability. In this study, we compared the physiological and transcriptomic profiles of roots of two cultivars exposed to normal nitrogen (NN) and low nitrogen (LN). The results showed that the LN treatment suppressed root growth and severely affected enzymatic activities in the roots of both rice cultivars compared to the NN treatment. Moreover, HJ753 exhibited significantly higher activities of NITRATE REDUCTASE (NR) and GLUTAMINE SYNTHETASE (GS) in its roots than DJ8 under both LN and NN conditions. Transcriptomic analysis identified 23,205 genes across all samples, with more than 5000 differentially expressed genes (DEGs) detected in response to LN stress in both cultivars. The KEGG analysis revealed that the DEGs were primarily involved in DNA replication, tryptophan metabolism, phenylpropanoid biosynthesis, plant hormone signal transduction, and N metabolism. Under LN stress, most genes associated with tryptophan metabolism and phenylpropanoid biosynthesis pathways remained stable or were upregulated in both cultivars. In contrast, genes related to auxin signalling transduction, N metabolism, and N utilisation exhibited significant genotype-specific expression patterns between HJ753 and DJ8. In conclusion, this study elucidated the genotypic differences in root development and N response mechanisms under LN stress at the molecular level, providing new insights into the regulatory mechanisms of N efficiency that may be used to develop and support the breeding of N-efficient rice cultivars. Full article

Shiga toxin-producing Escherichia coli (STEC) is a major foodborne pathogen, responsible for severe gastrointestinal disease and hemolytic uremic syndrome (HUS). Here, we report Click Detect, a novel diagnostic platform that leverages click display to efficiently produce sensing probes for sandwich-style antigen detection. Click display is an in vitro protein display technology that generates uniform and covalently linked protein–cDNA conjugates in a simple one-pot reaction format within 2 h. The captured sensing probe can be quantified by standard nucleic acid amplification assays. Using click displayed DARPin (D_#20) as the sensing probe and a high-affinity nanobody (N_G1) as the capture reagent, Click Detect reliably detected Shiga toxin 2 (Stx2) at 600 fM by quantitative PCR (qPCR) and 6 pM by loop-mediated isothermal amplification (LAMP). The assay maintained comparable sensitivity in matrices containing up to 40% public swimming pool water or lettuce extract, highlighting robustness for real-world surveillance applications. Key advantages of Click Detect include simple, rapid, and cost-effective (~USD 0.04 per assay) sensing probe preparation, as well as a versatile plug-and-play probe format for detecting other targets. We believe that Click Detect has great potential as a novel sensing platform for food/environmental monitoring and point-of-care diagnostics, with potentially broad applicability to other toxins and protein targets. Full article

A biofilm is a self-protective material formed by microorganisms to resist adverse environments. As an important group of microorganisms in the food industry and the human intestine, lactic acid bacteria (LAB) demonstrate enhanced probiotic activity in their biofilm state. In this study, a total of 90 LAB isolates from various traditional fermented foods across China were evaluated for their biofilm-forming capacity using the crystal violet staining method. Of these, eight isolates showed strong biofilm-forming capacity. These eight isolates were further evaluated for environmental stress responses, including tolerance to high acid and high bile salt concentrations, resistance to simulated gastrointestinal conditions, and adherence to Caco-2 cells. Four isolates with strong resistance to these stresses and adhesion to Caco-2 cells were selected for comparison between their planktonic and biofilm forms. Among these, the two isolates demonstrating the highest biofilm production capacity were AQ-4 and SY1-3, which were isolated from fermented pear juice and apple juice, respectively. Isolate AQ-4 was then identified as Lactiplantibacillus plantarum based on 16S rDNA sequencing. By integrating biofilm-forming capacity with key biological properties, including stress tolerance and epithelial adhesion, this study focuses on L. plantarum AQ-4, which exhibits distinct microstructural differences between planktonic and biofilm states, as revealed by scanning electron microscopy. The findings suggest that L. plantarum AQ-4 could be used to investigate the differential mechanisms in the planktonic and biofilm states and to act as the theoretical basis for the application of LAB biofilms in the food industry. Full article

Agrobacterium tumefaciens (A. tumefaciens), the causal agent of crown gall disease, is a major threat to crop production worldwide. In this study, a novel lytic bacteriophage, designated P284, was identified and characterized for its antibacterial potential against A. tumefaciens. High-throughput sequencing revealed a 44,922 bp double-stranded DNA genome (G+C content 54.3%), with 66 predicted coding sequences, none associated with virulence, lysogeny, or antibiotic resistance. Genomic and phylogenetic analyses allocated P284 within the genus Atuphduovirus (subfamily Dunnvirinae), showing 94% nucleotide sequence identity and 100% query coverage with phage PAT1, representing a distinct species. Turbidity assays revealed that P284 (MOI = 1) strongly inhibits A. tumefaciens growth up to 48 h, achieving a 92% reduction in bacterial density. Transmission electron microscopy confirmed rapid adsorption and host cell lysis within 30 min. In silico predictions identified three putative depolymerases with properties suitable for recombinant applications. The phage exhibited stability across a wide pH range (3–9) and temperatures from −20 to 60 °C. These findings highlight the lytic activity and environmental resilience of P284, and whether it can control crown gall disease in planta remains to be evaluated. Full article

Chemical fungicides play a key role in protecting crops, but their use can result in environmental problems. We tested a novel fungicide, composed of endophytic microorganisms, for its effect on wheat yield, grain quality, plant development, and the rhizosphere microbiome, assessed by 16S and ITS metabarcoding. The fungicide increased the grain yield, the effect being similar to a well-known commercial bacterial fungicide, without affecting its quality. Ascomycota, Zygomycota and Mucoromycota together comprised 80% of the mycobiome. Mucoromycota/Mucoromycetes/Rhizopodaceae/Rhizopus arrhizus were significantly decreased. The dominant (≥10%) bacterial phyla were Pseudomonadota, Acidobacteriota, Bacteroidota and Actinomycetota, but their fungicide-related differences were small or random. Different modes of fungicide application (seeds only, seeds plus one or two foliar applications) had no effect on wheat characteristics. Neither of the fungicide’s agents (Raoultella ornithinolytica and Pantoea allii) were found in the rhizosphere. The changes in the mycobiome seemed more pronounced than in the bacteriobiome. The proposed preparation is concluded to have good prospects as a fungicide. However, the low species/strain resolution of the DNA metabarcoding did not allow us to fully interpret shifts in the microbiome diversity, both agronomically and environmentally. These aspects need more comprehensive investigation, using methodology with higher species resolution. Full article