Search Results (2,857)

Foodborne diseases represent a major public health concern, particularly those associated with dairy products contaminated with Staphylococcus aureus, a pathogen capable of producing heat-stable enterotoxins. This study evaluated the potential of native lactic acid bacteria (LAB) isolated from artisanal kefir grains as natural biocontrol agents in fermented dairy foods. Kefir grains obtained from three artisanal producers were microbiologically characterized, revealing LAB as the dominant group and the absence of Enterobacteriaceae. Strains belonging mainly to the genera Lactobacillus sensu lato, Leuconostoc, and Pediococcus were isolated and exhibited differentiated metabolic profiles. Safety assessment showed no hemolytic activity and an overall susceptibility to clinically relevant antibiotics, although genus-dependent intrinsic resistance patterns were observed. Several strains displayed enzymatic activities related to carbohydrate digestion and high tolerance to simulated gastrointestinal conditions, with survival rates exceeding 90% during both gastric and intestinal phases. Neutralized cell-free supernatant (CFS) demonstrated differential inhibitory activity, with significant antagonism of S. aureus and E. coli, comparable to those of commercial reference strains. In a yogurt model system stored at 4 °C, selected Lactobacillus and Pediococcus strains induced a progressive and significant reduction in S. aureus populations, achieving complete elimination to undetectable levels in shorter times than commercial probiotic strains. Overall, these results demonstrate that native LAB from artisanal kefir grains exhibit an adequate safety and functional profile, together with strong antagonistic activity, supporting their potential application as natural protective cultures to improve the food hygiene of fermented dairy products. Full article

We reported the first isolation and characterization of Neopestalotiopsis spp. from symptomatic strawberry plants in Nova Scotia, Canada. Morphological and multilocus sequence analyses confirmed that these isolates were closely related to previously identified aggressive Neopestalotiopsis spp. strains from strawberry and blueberry in the southeastern United States and other countries. Five representative isolates were evaluated for pathogenicity on detached leaves, whole plants, and fruits of multiple strawberry cultivars. The results revealed significant variation in virulence, with isolate NS-1 causing the most severe necrosis across all tissue types. Statistical analysis revealed significant effects of isolate, cultivar, and their interaction on disease severity, indicating differential cultivar responses to the tested isolates. Notably, tissue-specific differences were observed, with some isolates being aggressive on leaves but less virulent on fruit or whole plants, reinforcing the importance of multi-organ phenotyping in resistance screening. Phylogenetic analysis clustered the Nova Scotia isolates within the same clade as Neopestalotiopsis isolate 17–43 L from strawberry and isolates from blueberry, suggesting a potential epidemiological link. The shared nursery propagation system of strawberries and blueberries raises the risk of cross-infection, posing a substantial challenge to disease management strategies in both crops. Collectively, these findings underscore the urgent need for continued surveillance, population-level pathogen analysis, and the development of resistant cultivars to mitigate the spread of this emerging and rapidly evolving pathogen. Full article

Differential operators often admit multiple algebraically equivalent symbolic formulations, yet those formulations can differ in the organization of their internal structure prior to solution analysis. A reproducible symbolic framework is introduced to compare such formulations at the level of operator expressions. Within a declared symbolic specification consisting of a fixed grammar, an admissible weight class, canonical compression rules, and an admissible family of reformulations, we define four encoding-relative structural descriptors: structural strain τ, structural curvature κ, compressibility σ, and the balance ratio Γ = κ/τ. Structural strain compares an encoding to a designated reference representation, while compressibility measures reduction under canonical symbolic compression. These quantities are deterministic descriptors within the declared encoding class rather than coordinate-free invariants of the underlying operator. The structural length functional underlying these descriptors is developed, canonical compression is formalized, and finite symbolic comparison is distinguished from pathwise symbolic deformation. A robustness theorem shows that, away from the threshold surface Γ = σ, sufficiently small admissible perturbations preserve the induced diagnostic label. A supporting weight-robustness result further shows that qualitative labels persist across a local admissible family of weight choices under corresponding nondegeneracy conditions. The framework serves as a reproducible diagnostic for operator representations alongside Lyapunov, spectral, pseudospectral, and energy-based stability theories. Examples of representative ordinary and partial differential operators illustrate how the descriptors are computed and how they behave under admissible re-expression, while the appendices provide the technical backbone of the paper: formal definitions, reproducibility protocol, extended perturbation arguments, and explicit failure-mode analysis. Additional sensitivity checks regarding encoding, weights, and threshold variation clarify the method’s scope, and explicit failure modes delineate the boundary cases in which the descriptors cease to apply. The main contribution of this study is a formally delimited and reproducible symbolic framework for comparing differential operators under a fixed, declared specification, together with robustness results and worked examples that clarify the method’s scope. Full article

Environmental pH plays a critical role in microbial fermentation processes. Weizmannia coagulans attracts particular attention for exceptional acid tolerance and lactic acid productivity. Yet acidic stress impacts on its cell division regulation remain unclear. Here, a critical pH value (pH 4.20) for growth inhibition of the Gram-positive bacterium Weizmannia coagulans strain BC99 was first established. Transcriptomic analysis of metabolic pathways was then performed. The multi-layered regulatory network underlying acid stress-induced cell division was elucidated. Integrated transcriptomic and physiological analyses reveal that acid stress triggers multigene expression reprogramming. This drives core metabolic network reorganization, coordinately regulating division processes. RNA-seq analysis demonstrated acid stress triggered differential expression of division genes (FtsZ/Q downregulation), ATP synthase suppression, and peptidoglycan transport reduction, while enhancing membrane rigidification (Cfa) and magnesium homeostasis (CorA). The PhoPR dual-component system emerged as a central regulator, inhibiting septal assembly via RipA hydrolase and RpsU ribosomal suppression while rerouting carbon flux to glycolysis, elucidating bacterial acid adaptation mechanisms. Collectively, these adaptive changes prioritize cell survival over active proliferation under acidic conditions. This study provides molecular insights into how W. coagulans preserves viability under acid stress, offering a theoretical basis for optimizing its performance in probiotic applications. Full article

Background/Objectives: Since 2023, a significant increase in measles cases has been reported worldwide, and Italy has been among the most affected European countries. In this context, the integration of laboratory and epidemiological data enables timely case classification and helps distinguish between imported and indigenous cases, supporting disease control. However, most studies address only selected aspects of surveillance. Therefore, this study aimed to provide an integrated analysis of virological and epidemiological surveillance activities conducted between November 2023 and December 2025 by the Regional Reference Laboratory in the Emilia-Romagna Region (ERR). Methods: A total of 806 clinical samples (269 urine, 267 oral fluids—saliva or oropharyngeal swabs—and 270 sera) from 291 suspected measles cases were tested by molecular and/or serological methods, and MV genotyping was performed. Samples from discarded cases were also analysed for parvovirus B19 (B19V), human herpesvirus 6 (HHV-6), enterovirus (EV), and varicella zoster virus (VZV), chikungunya virus (CHIKV) and dengue virus (DENV). Results: Of 291 suspected cases, 176 (60.5%) were confirmed. Median age was 33 years, with 46% in the 15–39 year group. Vaccination status was available for 165: 90.3% were unvaccinated, 5.4% had one dose, and 4.2% had two doses. Notably, over half of confirmed cases occurred in areas with vaccine-hesitant communities. MV strain characterisation was performed in 99.4% of MV-RNA positive cases, with 84.3% genotype D8 and 15.6% genotype B3; 83% of strains were of indigenous origin, suggesting an ongoing endemic circulation. Clinical data showed complications in 19.3%, mainly pneumonia and diarrhoea. Additionally, differential diagnosis enabled the identification of the etiological agent in 37.5% of measles/rubella discarded cases, and 37.6% (29/77) tested positive for B19V. Conclusions: The study results highlight that effective measles surveillance must be supported by integrating timely virological diagnosis, molecular and epidemiological investigations, and differential diagnosis, to achieve the WHO goals of eliminating measles transmission. Full article

This research reveals the coupling mechanism between structural deformation and hydrocarbon accumulation. The Dibei area in the Kuqa Depression represents a key hydrocarbon exploration domain within the northern Tarim foreland basin. Although extensive studies on stratigraphy, sedimentology, and accumulation mechanisms have been conducted, the control of segmented deformation on traps remains poorly understood. Furthermore, the synergistic regulation mechanism involving paleo-uplifts, salt thickness, synsedimentation, and erosion is still ambiguous. Based on high-quality 2D and 3D seismic data, this study integrates tectonic evolution balanced restoration with physical modeling. We conducted two sets of 3D sandbox experiments: “differential paleo-uplift and salt thickness” and “synsedimentation-erosion.” This approach systematically investigates the control of tectonic evolution on trap formation. Results show a strong correspondence between the “subsalt–salt–supra-salt” structural deformation and trap types. The supra-salt layer is dominated by detachment fold traps, whereas the subsalt layer features thrust-fold anticline traps. The basement paleo-uplift governs structural segmentation and trap distribution. Salt thickness modulates strain partitioning and trap stability. Synsedimentation optimizes trap conditions via tectono-sedimentary coupling. Erosional unconformities serve dual functions as both migration pathways and seal beds. These four factors work synergistically throughout the entire petroleum system, from “trap formation–migration–accumulation–preservation.” It enriches the genetic theory of salt-related structures in foreland basins. The findings provide a reference for predicting favorable exploration zones, evaluating trap characteristics, and assessing resource potential in the Kuqa Depression. Full article

The excessive use of chemical fertilizers in rice cultivation has contributed to soil degradation, creating a need for sustainable biological alternatives. This study examined the functional diversity of three indigenous nostocalean cyanobacterial strains (UP1, UP2, and UP3) isolated from forest and paddy field ecosystems by comparing the effects of their cellular biomass and extracellular polymeric substances (EPS) on rice seedling growth and soil properties. Morphological observations and partial 16S rRNA sequence analysis indicated that strains UP1 and UP2 were affiliated with the genus Ahomia, whereas UP3 was placed within the genus Nostoc. Together, these results placed all three isolates within the heterocystous cyanobacterial order Nostocales. The strains were further characterized based on EPS production and its degree of polymerization. Seed germination and seedling vigor assays were conducted to select the most effective biomass and EPS treatments, which were subsequently evaluated in 21-day pot experiments. Fresh biomass from strain UP2 most effectively enhanced rice growth, whereas EPS from strain UP3 promoted root development. EPS application from strain UP3 significantly increased root elongation to 13.44 cm, while high biomass levels of UP2 increased total sugar and free amino acid contents, indicating distinct plant response patterns. Soil analyses revealed differential responses between biomass- and EPS-based applications, with biomass generally producing stronger effects. Biomass from all strains was associated with higher physical soil function index (PSFI) values (up to 1.35). In contrast, improvements in chemical soil function index (CSFI) were observed across treatments, with variable responses and relatively higher values recorded in biomass from strain UP3 (up to 1.24). These findings suggest strain- and form-dependent response patterns of nostocalean cyanobacteria with potential for enhancing rice growth and improving soil functionality under the controlled conditions. Full article

Individuals may be prone or resistant to the development of type 2 diabetes. The basis for susceptibility is in part genetic, but environmental factors are likely to come into play. The gut microbiome stands at the interface of genetics and the host microenvironment. Its role in mediating susceptibility to diabetes, however, has not been resolved. Here we investigated whether the gut microbial composition contributes to susceptibility to diabetes, as distinct from disease development. We hypothesized that distinct microbial signatures modulate sensitivity or resistance to a diabetogenic diet (DD) and that separate signatures are linked to disease development. To test this hypothesis, we studied the Cohen diabetic rat model, comprising a diabetes-sensitive strain (CDs/y) and a diabetes-resistant strain (CDr/y). When exposed to DD, diabetes develops in CDs/y but not in CDr/y rats; on a regular diet (RD), both strains remain metabolically normal. To establish the contribution of the gut microbiome to susceptibility, we studied the fecal microbial composition in young, metabolically healthy CDs/y and CDr/y rats, using 16S rRNA gene sequencing, measures of α- and β-diversity, and differential taxonomic abundance. We found distinct, strain-specific gut microbiota profiles that differentiated diabetes-sensitive from -resistant animals, indicating an association between microbial composition and susceptibility. To test causality, we co-housed sensitive and resistant animals to allow passive microbial cross-transfer and fed the animals with DD. Co-housing led to partial convergence of microbial communities and significantly attenuated the diabetic phenotype in CDs/y rats, supporting a contributory and causal role for the gut microbiome in modulating sensitivity to diabetes. The resistance phenotype, on the other hand, remained unchanged. To distinguish between the contribution of the gut microbiome to susceptibility to diabetes as opposed to the development of the disease, we studied the gut microbial profiles across strains after feeding with DD or RD and the development of diabetes in CDs/y but not in CDr/y. We found distinct taxonomic signatures that differentiated diabetic from non-diabetic animals. These findings demonstrate that the gut microbiome contributes to susceptibility to diabetes with separate pathways from those linked to the development of diabetes and may represent an important modifiable determinant of diabetes risk and a target for early intervention. Full article

Members of the genus Streptomyces possess large genomes, a vast and largely unexplored metabolic potential, and a distinctive life cycle characterized by pronounced morphological differentiation. However, despite extensive molecular, genomic, and microbiological research, the functions of many genes in this genus remain poorly characterized. In this study, 929 complete Streptomyces genomes were analyzed. From the predicted proteomes of these genomes, proteins conserved in at least 75% of strains and lacking annotation in the KEGG GENES database were identified and clustered. To expand the annotation, synteny and co-occurrence analyses were performed between these unannotated proteins and annotated genes. A total of 330 conserved clusters were identified; 284 out of 330 clusters contain proteins encoded by genes that are syntenic with those associated with transcriptional regulation, fatty acid metabolism, two-component signaling systems, and morphological development. Additional clusters included metalloproteins and enzymes such as dehydrogenases, suggesting a wide functional spectrum. The conserved yet uncharacterized proteins identified in this analysis represent promising targets for future research, both for elucidating the molecular biology of Streptomyces and for expanding the range of secondary metabolites produced by these ecologically and industrially significant microorganisms Full article

Accurate prediction of surface rupture induced by seismogenic fault displacement is essential for the seismic safety assessment of major engineering projects. Most existing numerical simulations adopt quasi-static approaches, in which the effect of fault displacement is simplified as static loading. As a result, these methods cannot represent the dynamic characteristics of the fault rupture process, such as stress-wave propagation, soil inertial effects, and the influence of dynamic loading paths on rupture extension in soil layers. To address this issue, a full-process simulation method is established for simulating rupture of overlying soil subjected to dynamic fault displacement: Firstly, a non-uniform dynamic fault displacement loading is formulated for the two sides of the fault based on viscoelastic artificial boundaries, allowing the differential motion of the bedrock on both sides of the fault to be represented. Secondly, an improved dynamic skeleton curve constitutive model of soil is developed by introducing a minimum modulus constraint, providing an improved description of soil nonlinear dynamic behavior from small-strain hysteresis to large-strain shear failure. The reliability of the proposed method is verified through element-level tests and horizontal-site response simulation. As a benchmark, its ability to reproduce key rupture characteristics under quasi-static conditions is also assessed by comparison with classical quasi-static rupture studies. The method is then applied to simulate rupture extension and deformation response of overlying soil under strike-slip fault displacement. The results show that, compared to quasi-static analysis, dynamic fault displacement produces similar cumulative slip for surface rupture initiation and full connection, but induces transient amplification of peak surface displacement and a wider deformation zone with gentler displacement gradients. These findings demonstrate the necessity of considering dynamic fault dislocation of bedrock–overlying soil interaction in seismic assessments of engineering projects crossing active faults. Full article

Glucosamine (GlcN) is an essential amino monosaccharide widely used in pharmaceuticals, nutraceuticals, and cosmetics. Microbial fermentation presents a sustainable alternative to its traditional chemical production. However, in Saccharomyces cerevisiae, competitive carbon flux towards ethanol significantly limits GlcN yields. In this study, an S. cerevisiae strain for GlcN biosynthesis was engineered by integrating heterologous GlmD (glucosamine-6-phosphate deaminase) and GlmP (glucosamine-6-phosphate phosphatase) genes. To redirect carbon flux, the pyruvate decarboxylase genes pdc1, pdc5, and pdc6 were sequentially knocked out using the Clustered Regularly Interspaced Short Palindromic Repeats Cas9 (CRISPR-Cas9) approach, generating strains S. cerevisiaeGlmDP/pdc1Δ, GlmDP/pdc1Δpdc5Δ, and GlmDP/pdc1Δpdc5Δpdc6Δ. S. cerevisiae GlmDP/pdc1Δpdc5Δpdc6Δ achieved a GlcN titer of 2.20 ± 0.11 g/L, a 1.54-fold increase over the parental S. cerevisia GlmDP strain, while its ethanol yield decreased by 26%. This enhancement was achieved without significantly affecting cell growth or glucose consumption. Comparative transcriptomics between the triple-knockout and parental yeasts revealed 892 differentially expressed genes. Pathways related to glycolysis and ethanol formation were predominantly downregulated, whereas pathways potentially supporting GlcN synthesis were upregulated. The engineered strain demonstrated high genetic stability over 50 generations. Our findings demonstrate that disrupting ethanol formation is an effective strategy to enhance GlcN production in S. cerevisiae, providing valuable insights for carbon flux redistribution. Full article

Transcriptome atlases can be used to examine the spatiotemporal dynamics of gene expression, thereby enabling the generation of genome-wide resources for understanding complex biological processes. In the silkworm Bombyx mori, transcriptomes serve as crucial datasets for elucidating the mechanisms underlying economically important traits. In this study, we integrated 832 transcriptome datasets across all developmental stages and tissues and performed whole-genome-scale transcriptome sequencing (RNAseq) on five critical tissues from silkworm strains Xian8 and 9211. We identified 5773 and 3323 housekeeping genes expressed across all developmental stages and tissues, respectively, and these genes were primarily enriched in cellular signaling, transport, structural organization, DNA repair, and RNA processing pathways. We also identified 27 stage-specific genes and 58 tissue-specific genes, providing candidate markers for future single-cell and spatial transcriptomics. A large number of alternative splicing events were detected from 832 NGS samples, indicating the critical roles of alternative splicing in silkworm development. Interestingly, only 10 long-read full-length transcriptome samples from Xian8 and 9211 yielded results comparable to the NGS in terms of novel genes and alternative splicing events, and these multi-tissue comparative analyses also revealed significant differences in alternative splicing patterns, underlining the necessity of long-read sequencing for such research. These datasets not only advance functional genomics research in Lepidoptera but also provide molecular signatures for silkworm strain-specific comparisons and association analyses with differential phenotypes. Silkworm pan-transcriptomics, by analyzing multidimensional transcriptional regulatory networks and gene-expression dynamics, can facilitate multidisciplinary integration and accelerate the breeding of high-yield and high-quality silkworm varieties. Full article

Soybean mosaic virus (SMV) is a major constraint on global soybean (Glycine max (L.) Merr.) production, causing substantial economic losses worldwide. Despite these losses, the potential of resistance genes as a solution remains largely unexplored. In this study, the COPPER CHAPERONE FOR SUPEROXIDE DISMUTASE (GmCCS) was initially employed as a bait to screen the soybean cDNA library, leading to the identification of a protein homologous to Arabidopsis thaliana COP9 signalosome complex subunit 5B (AtCSN5B), designated as GmCSN5B. Quantitative real-time PCR (qRT-PCR) analysis revealed differential expression of GmCSN5B in the SMV-resistant (Qihuang No.1, QH) and susceptible (Nannong 1138-2, NN) variety following SMV-SC3 strain inoculation. Knockdown of GmCSN5B via Bean pod mottle virus (BPMV)-induced gene silencing (VIGS) significantly enhanced SMV resistance compared to control plants. This work further demonstrated that GmCSN5B can interact with the downstream GmVTC1 protein, which was potentially associated with ascorbic acid (AsA; Vitamin C) synthesis. Moreover, GmVTC1 also responded to SMV infection, and its knockdown led to a reduction in endogenous AsA levels within the host, thereby compromising the plant’s resistance to SMV. Together, these findings suggest that the GmCCS-GmCSN5B-GmVTC1 pathway in soybean modulates host resistance to SMV through the regulation of AsA synthesis. Full article

Pneumocystis is a respiratory fungal pathogen that causes life-threatening pneumonia in immunocompromised patients. While Pneumocystis can colonize healthy hosts by resisting and transiently evading innate immunity, a functional adaptive immune response is essential to prevent progressive infection. Impairments in adaptive immunity, particularly defects in CD4⁺ T cell function, are strongly associated with the development of severe Pneumocystis pneumonia (PCP) in humans and a wide range of mammalian species. Immune activation by Pneumocystis has strong genetic determinants, and a major gap in our understanding of PCP pathogenesis lies in uncovering the mechanisms by which Pneumocystis escapes alveolar macrophages and evades pulmonary innate immunity. Prior research determined that FVB/NJ mice display an unusual resistance to Pneumocystis infection. Further susceptibility testing across several inbred mouse strains revealed that the AKR/J strain, which is phylogenetically distant from the FVB/NJ strain, also exhibits a rarely described form of protective innate immunity against PCP. Notably, the mechanism of AKR/J resistance does not require CD4⁺ or CD8⁺ T lymphocytes. However, depleting alveolar macrophages prior to infection rendered AKR/J mice susceptible to PCP, highlighting the critical role of macrophages for this protective innate immune response. These novel findings establish the AKR/J inbred strain as a valuable model for investigating the interaction between Pneumocystis and macrophages, offering a unique opportunity to explore how these interactions lead to differential outcomes between resistant and susceptible mouse strains. Additionally, it may offer key insights into the mechanisms by which Pneumocystis evades macrophage-mediated innate immunity in the majority of mammalian hosts, including humans. Full article

Lactiplantibacillus plantarum EL2, isolated from traditional fermented yak milk in the high-altitude Gannan Tibetan Autonomous Prefecture, produces the class IIb bacteriocin PlnJK. This study established three distinct cultivation models that critically influenced bacteriocin yield. Microbial co-culture was found to enhance the stress tolerance of EL2, significantly boosting PlnJK production. The optimal inducing strain, Enterococcus faecalis MH2, increased the bacteriocin inhibition zone diameter from 15.38 mm to 25.58 mm. Following optimization of key parameters—initial inoculum concentration (10⁷ CFU/mL), inoculation ratio (3:1, EL2:MH2), and initial pH (6.0)—the inhibition zone diameter reached 30.32 mm, representing a 1.97-fold increase over pure culture. Co-culture not only advanced the onset but also extended the duration of bacteriocin synthesis. Throughout the 24 h incubation, cell density, AI-2 autoinducer concentration, and the expression of key regulatory genes were significantly elevated in co-culture compared to monoculture, aligning with a cell-density-dependent, quorum-sensing (QS) regulatory paradigm. Bacteriocin production was co-regulated by two QS pathways: the AI-2/luxS system and the plnA-mediated autoinducing peptide (AIP). Gene expression analysis revealed differential temporal regulation: luxS expression was higher during the exponential phase (2.29 vs. 1.42 in stationary phase), while plnA exhibited the opposite pattern (1.42 in exponential vs. 2.21 in stationary phase). This indicates that the AI-2/luxS pathway drives strong induction during active growth, whereas plnA/AIP-mediated promotion becomes predominant later. The stationary-phase effect is likely triggered by the accumulation of specific MH2 metabolites, which impose an environmental stress on EL2, stimulating the pln-encoded regulatory system and further enhancing bacteriocin yield. This work provides an economically viable strategy and a novel theoretical framework for optimizing microbial cultivation, enhancing bacteriocin production, and elucidating the complex QS-mediated regulatory mechanisms involved. Full article