Search Results (598)

Contaminated poultry is one of the major sources of food-borne non-typhoidal Salmonella (NTS). The aim of this study was to evaluate the presence of Salmonella along the slaughter process in low- and high-throughput poultry abattoirs in South Africa and to determine their characteristics. Samples were collected from 500 chicken carcass rinsates at various processing stages in three abattoirs. Salmonella detection and identification was conducted in accordance with the ISO 6579 methodology. NTS serotyping was performed with serotype-specific PCRs. The Kirby–Bauer disk diffusion method was used to determine antimicrobial resistance in Salmonella. PCR was used to analyze thirteen antimicrobial genes and four virulence genes. Salmonella spp. was detected in 11.8% (59/500; CI: 9.5–15) of the samples tested. The predominant serovars were Salmonella Enteritidis (n = 21/59; 35.59%) and Salmonella Typhimurium (n = 35; 59.32%). Almost all Salmonella isolates were susceptible to all tested antimicrobials except three. Despite the low resistance to tetracyclines at the phenotypic level, approximately half of the strains carried tetA genes, which may be due to “silent” antimicrobial resistance genes. Diverse virulence genes were detected among the confirmed NTS serotypes. We found a predominance of S. Enteritidis and S. Typhimurium from chicken carcasses with diverse virulence and resistance genes. As we detected differences between the slaughterhouses, an in-depth study should be performed on the risk of Salmonella in low- and high-throughput abattoirs. The integrated monitoring and surveillance of NTS in poultry is warranted in South Africa to aid in the design of mitigation strategies. Full article

Pleurotus ostreatus is a widely cultivated edible fungus in China, renowned for its rich nutritional composition and diverse medicinal compounds. However, the quality of the currently published P. ostreatus genomes remained suboptimal, which limited in-depth research on its evolution, growth, and development. In this study, we conducted a chromosome-level genome assembly of the monokaryotic basidiospore strain PC80. The assembled genome spanned 40.6 Mb and consisted of 15 scaffolds. Ten of these scaffolds contained complete telomere-to-telomere structures. The scaffold N50 value was 3.6 Mb. Genome annotation revealed 634 carbohydrate-active enzyme (CAZyme) family genes. Through collinearity analysis, we further confirmed that the PC80 genome exhibited higher completeness and greater accuracy compared to the currently published genomes of P. ostreatus. At the matA locus of PC80, three hd1 genes and one hd2 gene were identified. At the matB locus, seven pheromone receptor genes and two pheromone precursor genes were detected. Further phylogenetic analysis indicated that three of these pheromone receptor genes are likely to have mating-specific functions. This complete genome assembly could provide a foundation for future genomic and genetic studies, facilitate the identification of key genes related to growth and developmental regulation, and promote technological innovations in P. ostreatus breeding and efficient utilization. Full article

Machine learning (ML)-based techniques have received significant attention in various fields of industry and science. In civil and bridge engineering, they can facilitate the identification of specific patterns through the analysis of data acquired from structural health monitoring (SHM) systems. To evaluate the prediction capabilities of ML, this study examines the performance of several ML algorithms in estimating the total weight and location of vehicles on a bridge using strain sensing. A novel framework based on a combined model and data-driven approach is described, consisting of the establishment of the finite element (FE) model, its updating according to load testing results, and data augmentation to facilitate the training of selected physics-informed regression models. The article discusses the design of the Fiber Bragg Grating (FBG) sensor-based Bridge Weigh-in-Motion (BWIM) system, specifically focusing on several supervised regression models of different architectures. The current work proposes the use of the updated FE model to generate training data and evaluate the accuracy of regression models with the possible exclusion of selected input features enabled by the structural specificity of a bridge. The data were sourced from the SHM system installed on a network arch bridge in Wolin, Poland. It confirmed the possibility of establishing the BWIM system based on strain measurements, characterized by a reduced number of sensors and a satisfactory level of accuracy in the estimation of loads, achieved by exploiting the network arch bridge structural specificity. Full article

This study investigates the potential for the microbial transformation of camelliagenin B, a saponin derived from Camellia oleifera seed cake meal, to develop novel metabolites. We employed three microbial strains, specifically Bacillus subtilis ATCC 6633, Bacillus megaterium CGMCC 1.1741, and Streptomyces griseus ATCC 13273, to biotransform camelliagenin B into its derivatives. The compounds were purified and separated using chromatographic techniques, such as high-performance liquid chromatography (HPLC). Structural identification was carried out using spectroscopic methods, including nuclear magnetic resonance (NMR) and mass spectrometry (MS). Ten bioactive compounds were obtained (1a-1j), of which nine were novel with multiple tailoring reactions, such as allyl oxidation, C-C double-bond rearrangement, hydroxylation, dehydrogenation, and glycosylation, observed in camelliagenin B analogs. The structures of these compounds were determined by 1D/2D NMR and HR-ESI-MS analysis. Therefore, this study showcases the capacity of microbial transformation as a sustainable and environmentally friendly method for generating bioactive compounds from C. oleifera seed cake meals. The individual chemicals can potentially facilitate the design of novel medicinal agents, functional foods, and natural preservatives. Full article

Malaria continues to pose a significant global health burden, driving the search for novel antimalarial agents to address emerging drug resistance. This study evaluated the antiplasmodial potential of Ziziphus mauritiana Lam. (Rhamnaceae) roots through an integrated phytochemical and pharmacological approach. The ethanol extract, along with its derived fractions, demonstrated potent in vitro activity against the chloroquine-sensitive Plasmodium falciparum strain 3D7 (Pf3D7), with the ethyl acetate-soluble (IC₅₀ = 11.35 µg/mL) and alkaloid-rich (IC₅₀ = 4.75 µg/mL) fractions showing particularly strong inhibition. UHPLC-DAD-ESI-QTOF-MS/MS-based molecular networking enabled the identification of thirty-two secondary metabolites (1–32), comprising twenty-five cyclopeptide alkaloids (CPAs), five of which had not yet been described (11, 20, 22, 23, 25), and seven known triterpenoids. Bioactivity-guided isolation yielded thirteen purified compounds (5, 6, 14, 26–30, 32–36), with betulinic acid (30; IC₅₀ = 19.0 µM) and zizyberenalic acid (32; IC₅₀ = 20.45 µM) exhibiting the most potent antiplasmodial effects. Computational ADMET analysis identified mauritine F (4), hemisine A (10), and nummularine R (21) as particularly promising lead compounds, demonstrating favourable pharmacokinetic properties, low toxicity profiles, and predicted activity against both family A G protein-coupled receptors and evolutionarily distinct Plasmodium protein kinases. Quantitative analysis revealed exceptionally high concentrations of key bioactive constituents, notably zizyberenalic acid (24.3 mg/g) in the root extracts. These findings provide robust scientific validation for the traditional use of Z. mauritiana in malaria treatment while identifying specific cyclopeptide alkaloids and triterpenoids as valuable scaffolds for antimalarial drug development. The study highlights the effectiveness of combining advanced metabolomics, bioassay-guided fractionation, and computational pharmacology in natural product-based drug discovery against resistant malaria strains. Full article

Peste des petits ruminants virus (PPRV) has been classified into four lineages based on the nucleocapsid and fusion genes, with lineage IV strains being the most widely distributed. In Africa, recent epidemiological data revealed that PPRV lineage IV is increasingly displacing other lineages in prevalence, suggesting a competitive advantage in viral transmission and adaptability. Moreover, a lineage IV strain was the only confirmed strain in Europe and Asia. In this study, a one-step Taqman quantitative real-time reverse transcription polymerase chain reaction (RT-qPCR) assay for lineage IV PPRV was established by targeting the hemagglutinin (H) gene. The results indicated that this method could detect approximately six copies of PPRV RNA, indicating high sensitivity. No cross-reactions with related viruses or other lineages of PPRV were observed. The results of a repeatability test indicated that the coefficient of variation values were low in both the inter-assay and intra-assay experimental groups. Detection of field samples indicated that all positive samples could be detected successfully using the developed method. This RT-qPCR assay provides a valuable tool to facilitate targeted surveillance and rapid differential diagnosis in regions with active circulation of PPRV lineage IV, enabling timely epidemiological investigations and strain-specific identification. Full article

Accurate quantification of Bifidobacterium animalis subsp. lactis HN019, a clinically validated probiotic strain conferring immune modulation, gastrointestinal health, and gut barrier integrity benefits, is essential for diverse applications. To address the critical need for strain-specific detection, we developed a quantitative PCR (qPCR) assay targeting a unique single-nucleotide polymorphism (SNP) within the galK gene, identified through comparative whole-genome sequencing (WGS) analysis of 31 B. animalis subsp. lactis strains. The assay exhibited exceptional specificity, distinguishing HN019 from 19 other Bifidobacterium strains. Sensitivity tests indicated a detection limit of 0.5 pg of DNA and 10³ CFU/mL of bacterial cells, making it suitable for industrial-scale applications. Additionally, the method exhibited strong repeatability, reproducibility across different qPCR platforms, and resistance to interference from high cell density of B. animalis subsp. lactis DSMZ 10140. Successful quantification of HN019 in complex multi-strain probiotic powders confirmed its practical reliability. This work establishes a rapid, robust, and scalable tool for precise probiotic strain tracking, addressing critical quality control and regulatory compliance needs within the rapidly expanding probiotic industry. Full article

Saccharomyces cerevisiae plays a fundamental role in winemaking, not only driving alcoholic fermentation but also producing secondary metabolites that contribute to the organoleptic properties of wine. To ensure consistent quality and process efficiency, wineries commonly employ selected starter strains. Accordingly, the ability to control strain purity and traceability is of critical importance. Currently, the inter-delta PCR method is widely used for the strain-specific genotyping of S. cerevisiae. However, its resolution diminishes when analyzing genetically similar strains, such as those isolated from related grape types or during genotyping of large yeast collections. To address this limitation, we developed a novel strategy that integrates computational and experimental approaches to identify highly specific allelic variants (single nucleotide polymorphisms, SNPs) within the S. cerevisiae genome. Comparative genomic analysis of twenty-eight different strains led to the identification of multiple strain-specific SNPs. From these, nine SNPs spanning five strains were selected and validated through targeted PCR assays. These assays confirmed the feasibility of using SNPs as reliable genetic markers for strain discrimination and traceability. Overall, our findings demonstrate that this SNP-based approach, implemented via multiplex allele-specific (AS) PCR assays, offers a rapid, cost-effective, and highly discriminatory alternative to current genotyping methods, particularly for differentiating closely related strains. Full article

Background: Diabetic kidney disease (DKD) affects 20–50% of individuals with diabetes. The aim of this review was to identify interventions that positively influence the gut microbiota in DKD. Methods: Identification of relevant studies was conducted via a systematic search of databases and registers using the PRISMA guidelines. This review examined the relevant literature published up to 5 January 2025, using a systematic search in PubMed and Scopus. The search was conducted with combinations of keywords including DKD and therapy, supplementation and gut microbiota, and supplementation or probiotics or fecal microbiota transplant. The initial search fielded 132 results from PubMed and 72 from Scopus, which was narrowed to 135 relevant studies. The exclusion criteria included non-English language studies, letters to the editor, and conference abstracts. Eligible studies were independently assessed by a minimum of three authors, with discrepancies resolved through consensus. Results: Gut microbiota-targeted interventions, including probiotics, synbiotics, and dietary modifications, show promise in modulating the gut microbiota, but evidence specific to DKD remains limited. Some natural food components such as polyphenols and anthocyanins modulate the composition of the gut microbiota translocation of uremic toxins, which slows down the progression of diabetic kidney disease. In animal models, fecal microbiota transplantation (FMT) has shown positive effects in regulating dysbiosis and beneficial effects in chronic kidney disease, but studies involving humans with DKD are insufficient. Conclusions: Lactobacillus and Bifidobacterium strains, administered at doses ranging from 0.6 to 90 billion CFU, may help lower urea and creatinine levels, but outcomes vary by disease stage, duration of therapy, and amount used. High-fiber diets (>10.1 g/1000 kcal/day) and supplements such as resistant starch and curcumin (400–1500 mg/day) may reduce uremic toxins through gut microbiota modulation and reduction in oxidative stress. The effect of sodium butyrate requires further human studies. Full article

Background: Malaria remains a significant global health burden, particularly in sub-Saharan Africa, accounting for high rates of illness and death. The growing resistance to frontline antimalarial therapies underscores the urgent need for novel drug targets and therapeutics. Bromodomain-containing proteins, which regulate gene expression through chromatin remodeling, have gained attention as potential targets. Plasmodium falciparum bromodomain protein 1 (PfBDP1), a 55 kDa nuclear protein, plays a key role in recognizing acetylated lysine residues and facilitating transcription during parasite development. Methods: This study investigated ex vivo PfBDP1 gene mutations and identified potential small molecule inhibitors using computational approaches. Malaria-positive blood samples were collected. Genomic DNA was extracted, assessed for quality, and amplified using PfBDP1-specific primers. DNA sequencing and alignment were performed to determine single-nucleotide polymorphism (SNP). Structural modeling used the PfBDP1 crystal structure (PDB ID: 7M97), and active site identification was conducted using CASTp 3.0. Virtual screening and pharmacophore modeling were performed using Pharmit and AutoDock Vina, followed by ADME/toxicity evaluations with SwissADME, OSIRIS, and Discovery Studio. GROMACS was used for 100 ns molecular dynamics simulations. Results: The malaria prevalence rate stood at 12.24%, and the sample size was 165. Sequencing results revealed conserved PfBDP1 gene sequences compared to the 3D7 reference strain. Virtual screening identified nine lead compounds with binding affinities ranging from −9.8 to −10.7 kcal/mol. Of these, CHEMBL2216838 had a binding affinity of −9.9 kcal/mol, with post-screening predictions of favorable drug-likeness (8.60), a high drug score (0.78), superior pharmacokinetics, and a low toxicity profile compared to chloroquine. Molecular dynamics simulations confirmed its stable interaction within the PfBDP1 active site. Conclusions: Overall, this study makes a significant contribution to the ongoing search for novel antimalarial drug targets by providing both molecular and computational evidence for PfBDP1 as a promising therapeutic target. The prediction of CHEMBL2216838 as a lead compound with favorable binding affinity, drug-likeness, and safety profile, surpassing those of existing drugs like chloroquine, sets the stage for preclinical validation and further structure-based drug design efforts. These findings are supported by prior experimental evidence showing significant parasite inhibition and gene suppression capability of predicted hits. Full article

Although nitric oxide (NO) production in bacteria has traditionally been associated with denitrification or stress responses in model or symbiotic organisms, functionally validated L-arginine-dependent nitric oxide synthase (bNOS) activity has not been documented in free-living, non-denitrifying soil bacteria. This paper reports Paenibacillus nitricinens sp. nov., a bacterium isolated from rainforest soil capable of synthesizing NO via a bNOS under aerobic conditions. A bnos-specific PCR confirmed gene presence, while whole-genome sequencing (6.7 Mb, 43.79% GC) revealed two nitrogen metabolism pathways, including a bnos-like gene. dDDH (<70%) and ANI (<95%) values with related Paenibacillus strains support the delineation of this isolate as a distinct species. Extracellular and intracellular NO measurements under aerobic conditions showed a dose-dependent response, with detectable production at 0.1 µM L-arginine and saturation at 100 µM. The addition of L-NAME reduced NO formation, confirming enzymatic mediation. The genomic identification of a bnos-like gene strongly supports the presence of a functional pathway. The absence of canonical nitric oxide reductase (Nor) genes or other typical denitrification-related enzymes reinforces that NO production arises from an alternative, intracellular enzymatic mechanism rather than classical denitrification. Consequently, P. nitricinens expands the known repertoire of microbial NO synthesis and suggests a previously overlooked source of NO flux in well-aerated soils. Full article

Neisseria meningitidis is a pathogenic bacterial agent that causes meningococcal meningitis in humans. Developing a rapid and low-cost N. meningitidis detection method is crucial, especially for developing countries. This study focuses on the development of an efficient loop-mediated isothermal amplification (LAMP) method for accurate N. meningitidis identification. A new LAMP primer set was designed, and a LAMP reaction was optimized. The colorimetric detection method was also applied, and the assay characteristics were evaluated using clinical samples. The results demonstrated a specific LAMP reaction for N. meningitidis detection of genotypes A, B, and C, with a limit of detection of 10² cfu/mL, 100% specificity and sensitivity, and a rapid detection time of only 40 min by colorimetric visual inspection. No cross-reactivity with reference strains of Streptococcus pneumoniae, Staphylococcus aureus, Neisseria lactamica, Mycobacterium tuberculosis, and Haemophilus influenzae type b was observed in the LAMP reaction with the new primer set. This result suggests that the LAMP reaction could be a promising tool for developing a rapid N. meningitidis detection method suitable for use in Vietnam and other developing countries. Full article

Understanding the formability limits of thin-walled tubes with square cross-sections and L-section profiles is crucial for improving manufacturing efficiency and ensuring structural reliability in industries such as automotive and aerospace. Unlike the usually studied circular tubes, square tubes and L-section profiles geometries present unique deformation and fracture behaviours that require specific analysis. To address this gap, this research establishes a novel methodology combining digital image correlation (DIC) with a time-dependent approach and precise thickness measurements, enabling accurate strain measurements essential to the onset of necking and fracture strain identification. Two experimental tests under different forming conditions allowed capturing a distinct range of strain paths leading to failure. This approach allowed the determination of the forming limit points associated with necking and the fracture forming lines associated with crack opening by tension (mode I) and by in-plane shear (mode II). The findings highlight the strong influence of geometry on the fracture mechanisms and provide valuable data for optimizing tube-forming processes for square tubes and L-section profiles, ultimately enhancing the design and performance of lightweight structural components. Full article

The genome of Geobacillus sp. G4, a thermophilic bacterium isolated from a geothermal field in Peru, was sequenced and analyzed to evaluate its taxonomic and biotechnological potential. This strain exhibits optimal growth at temperatures between 50 and 70 °C and at a pH range of 6.0–7.5. Phenotypic assays demonstrated extracellular enzymatic activities, including amylases, cellulases, pectinases, and xylanases, highlighting its potential for efficient polysaccharide degradation. The assembled genome comprises approximately 3.4 Mb with a G+C content of 52.59%, containing 3,490 genes, including coding sequences, rRNAs, and tRNAs. Functional annotation revealed genes associated with key metabolic pathways such as glycogen and trehalose biosynthesis, indicating adaptation to carbohydrate-rich environments. Phylogenetic analyses based on ANI and dDDH values identified Geobacillus thermoleovorans KCTC3570 as its closest relative, suggesting a strong evolutionary relationship. Additionally, the genome harbors gene clusters for secondary metabolites such as betalactone and fengycin, suggesting potential industrial and pharmaceutical applications, including bioremediation. The identification of antibiotic resistance genes, specifically those conferring glycopeptide resistance, underscores their relevance for antimicrobial resistance studies. The presence of enzymes like amylases and pullulanase further emphasizes its biotechnological potential, particularly in starch hydrolysis and biofuel production. Overall, this research highlights the significant potential of Geobacillus species as valuable sources of thermostable enzymes and biosynthetic pathways for industrial applications. Full article

Cyanobacteria are gram-negative prokaryotic microorganisms composed of both broad morphological and phylogenetic diversity inherited from diverse ecosystems like aquatic, terrestrial, or extremophilic environments. In this study, three cyanobacteria strains from the Blue Biotechnology and Ecotoxicology Culture Collection (LEGE-CC) were obtained from different environments in Portugal. Polyphasic analysis was applied for taxonomic identification. The proximate composition analysis indicated the lipid content (6.2% to 9.1% dry weight (DW)), protein content (28.2% to 62.9% DW), and carbohydrate content (19.5% to 46.1% DW). The fatty acid (FA) profiles of the strains revealed the presence of 19 different FAs, with FA 16:0 found in the highest abundance. The lipidomic analysis revealed 230 lipid species, with Laspinema sp. LEGE 06078 displaying the highest diversity (125 lipid species). These included species-specific and common lipids species that denote biochemical uniqueness that are also carriers of omega-3 FA (n−3). Biological assays exhibited strong antioxidant activity against ABTS^•+ and DPPH^• in Laspinema sp. LEGE 06078, while Sphaerospermopsis sp. LEGE 00249 was renowned for reducing lipids in zebrafish larvae. The findings are of immense significance on the lipidomics diversity of cyanobacteria in terms of nutrition, health, and biotechnology, such as addressing obesity and sustainable resource production. Full article