Search Results (39,794)

Sprouty-related proteins with enabled/vasodilator-stimulated phosphoprotein homology 1 (EVH1) domain (SPREDs) are negative regulators of the Ras/MAPK signaling pathway and are known to modulate developmental and endocrine processes. While the roles of SPRED1 and SPRED2 are increasingly understood, the physiological relevance of SPRED3 remains elusive. To elucidate its function, we generated SPRED3 knockout (KO) mice and performed phenotypic, molecular, and hormonal analyses. SPRED3-deficient mice exhibited growth retardation and a non-Mendelian genotype distribution. X-Gal staining revealed Spred3 promoter activity in the thyroid, adrenal gland, pituitary, cerebral cortex, and kidney. Hormonal profiling identified elevated thyroid-stimulating hormone (TSH) and reduced thyroxine (T₄) levels, indicating primary hypothyroidism. Thyroidal extracellular signal-regulated kinase (ERK) signaling was mildly reduced in SPRED3 KO mice, and immunoblotting revealed altered expression of autophagy regulators, including reduced sequestosome 1 (p62), increased autophagy-related gene 5 (ATG5), as well as an elevated microtubule-associated protein 1 light chain 3 (LC3) II/I ratio and a decreased pBeclin/Beclin ratio in SPRED3 KO mice. Our findings indicate that SPRED3 is involved in thyroidal homeostasis and plays a regulatory role in autophagy processes within the thyroid gland. Full article

The Mycoplasmataceae are a family of bacteria that typically cause respiratory, arthritic, and genitourinary disease in humans. Mycoplasma spp. of animal origin are also the causative agents of porcine wheezing disease, chronic respiratory disease and arthritis in chickens and other conditions. These diseases have a significant impact on public health and the economic development of livestock breeding. Clinical prevention and treatment of mycoplasma infections is primarily dependent on the use of antibiotics. However, inappropriate and excessive use of antimicrobials has enabled resistance development that has become a significant clinical concern. Mycoplasma are also robust biofilm producers, and this process is a major factor for the persistence of these infections, especially in conjunction with common antibiotic resistance mechanisms, including target gene mutations and the action of efflux pumps. A mycoplasma biofilm refers to a structured and stable microbial community formed by Mycoplasma spp. adhering to biological or non-biological surfaces under suitable conditions and secreting extracellular polymers (EPS) such as polysaccharides. This process allows the microorganisms to adapt to their surrounding environment and survive during the growth process. These biofilms render bacteria more resistant to antimicrobials than planktonic bacteria, resulting in biofilm-associated infections that are more challenging to eradicate and more likely to recur. The current study reviews progress from the fields of biofilm formation, structure and identification, correlations between biofilms and drug resistance and virulence as well as methods of biofilm prevention and control. Our aim was to provide a reference basis for the subsequent in-depth understanding of the research of mycoplasma biofilms. Full article

Obstructive sleep apnea (OSA), characterized by intermittent hypoxia (IH), is strongly associated with metabolic syndrome and metabolic dysfunction-associated steatotic liver disease (MASLD). IH exacerbates MASLD progression through oxidative stress, inflammation, and lipid accumulation. This study aims to investigate the impact of oxygen normalization on metabolic dysfunction in OSA patients using continuous positive airway pressure (CPAP) therapy, and in mice exposed to IH followed by a reoxygenation period. In the clinical study, 76 participants (44 OSA patients and 32 controls) were analyzed. OSA patients had higher insulin resistance, triglycerides, very low density lipoprotein (VLDL) content, and liver enzyme levels, along with a higher prevalence of liver steatosis. After 18 months of CPAP therapy, OSA patients showed significant improvements in insulin resistance, lipid profiles (total cholesterol and VLDL), liver function markers (AST and albumin), and steatosis risk scores (Fatty Liver Index and OWLiver test). In the experimental study, IH induced hepatic lipid accumulation, oxidative stress, and inflammation, and reoxygenation reversed these deleterious effects in mice. At the molecular level, IH downregulated fatty acid oxidation (FAO)-related genes, thus impairing the FAO process. Reoxygenation maintained elevated levels of lipogenic genes but restored FAO gene expression and activity, suggesting enhanced lipid clearance despite ongoing lipogenesis. Indeed, serum β hydroxybutyrate, a key marker of hepatic FAO in patients, was impaired in OSA patients but normalized after CPAP therapy, supporting improved FAO function. CPAP therapy improves lipid profiles, liver function, and MASLD progression in OSA patients. Experimental findings highlight the therapeutic potential of oxygen normalization in reversing IH-induced liver damage by FAO pathway restoration, indicating a metabolic reprogramming in the liver. Full article

Excessive alcohol consumption is associated with systemic health risks due to the production of acetaldehyde, a primary carcinogen that not only pollutes the environment but also endangers human health. In this study, a promising bacterial strain for biodegrading both ethanol and acetaldehyde was successfully isolated from the traditional fermented food Jiaosu and identified as Acetobacter ghanensis JN01 based on average nucleotide identity (ANI) analysis. Initial ethanol of 1 g/L was completely biodegraded within 4 h, while initial acetaldehyde of 1 g/L was also rapidly removed at 2 or 1 h by whole cells or cell-free extracts (CEs) of JN01, respectively, which indicated that JN01 indeed has a strong ability in the biodegradation of both ethanol and acetaldehyde. Whole-genome sequencing revealed a 2.85 Mb draft genome of JN01 with 57.0% guanine–cytosine (GC) content and the key metabolic genes (adh1, adh2, and aldh) encoding involving alcohol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH), co-located with NADH dehydrogenase genes and ethanol-responsive regulatory motifs, supporting the metabolic pathway of transforming ethanol to acetaldehyde, and, subsequently, converting acetaldehyde to acetic acid. Furthermore, selected in vitro safety-related traits of JN01 were also assessed, which is very important in the development of microbial catalysts against both ethanol and acetaldehyde. Full article

Tooth development (odontogenesis) is regulated by interactions between epithelial and mesenchymal tissues through signaling pathways such as Bone Morphogenetic Protein (BMP), Wingless-related integration site (Wnt), Sonic Hedgehog (SHH), and Fibroblast Growth Factor (FGF). Mesenchymal stem cells (MSCs) derived from dental tissues—including dental pulp stem cells (DPSCs), periodontal ligament stem cells (PDLSCs), and dental follicle progenitor cells (DFPCs)—show promise for regenerative dentistry due to their multilineage differentiation potential. Epigenetic regulation, particularly DNA methylation, is hypothesized to underpin their distinct regenerative capacities. This study reanalyzed publicly available DNA methylation data generated with Illumina Infinium HumanMethylation450 BeadChip arrays (450K arrays) from DPSCs, PDLSCs, and DFPCs. High-confidence CpG sites were selected based on detection p-values, probe variance, and genomic annotation. Principal Component Analysis (PCA) and hierarchical clustering identified distinct methylation profiles. Functional enrichment analyses highlighted biological processes and pathways associated with specific methylation clusters. Noncoding RNA analysis was integrated to construct regulatory networks linking DNA methylation patterns with key developmental genes. Distinct epigenetic signatures were identified for DPSCs, PDLSCs, and DFPCs, characterized by differential methylation across specific genomic contexts. Functional enrichment revealed pathways involved in odontogenesis, osteogenesis, and neurodevelopment. Network analysis identified central regulatory nodes—including genes, such as PAX6, FOXC2, NR2F2, SALL1, BMP7, and JAG1—highlighting their roles in tooth development. Several noncoding RNAs were also identified, sharing promoter methylation patterns with developmental genes and being implicated in regulatory networks associated with stem cell differentiation and tissue-specific function. Altogether, DNA methylation profiling revealed that distinct epigenetic landscapes underlie the developmental identity and differentiation potential of dental-derived mesenchymal stem cells. This integrative analysis highlights the relevance of noncoding RNAs and regulatory networks, suggesting novel biomarkers and potential therapeutic targets in regenerative dentistry and orthodontics. Full article

Background: Merkel cell polyomavirus (MCPyV) has been established as an etiological agent in Merkel cell carcinoma (MCC), yet its role in other cutaneous neoplasms remains under investigation. The impact of the host’s immunogenetic characteristics on the persistence of Merkel cell polyomavirus (MCPyV) in non-melanoma skin cancer (NMSC) is not yet well understood. Objective: Our aim was to investigate the presence of MCPyV in various skin lesions, particularly NMSC, and its association with cytokine gene polymorphisms related to immune regulation. Methods: We analyzed 274 skin biopsies (lesional, perilesional, and healthy skin) from 84 patients undergoing dermatological evaluation. MCPyV DNA and polymorphisms in IL-6, IL-10, IFN-γ, and TNF-α genes were detected using PCR-based assays. Results: MCPyV was significantly more prevalent in NMSC and non-cancerous lesions than in surgical margins or healthy skin (p = 0.050 and 0.048, respectively). Concordance between lesion and margin samples was low (κ = 0.305), suggesting microenvironment-specific viral persistence. Notably, high-expression IL-10 genotypes (-1082 GG) and low-expression IL-6 genotypes (-174 AA) were significantly associated with MCPyV detection (p = 0.048 and p = 0.015, respectively). Conclusions: MCPyV preferentially localizes to NMSC lesions, particularly in individuals with immunogenetic profiles favoring viral persistence. Since the role of MCPyV in the pathogenesis of NMSC remains uncertain, our results highlight the need for further studies to clarify whether the lesion’s microenvironment supports viral persistence or indicates a more intricate interaction between the virus and the host, which could be significant for the development of skin cancer. Full article

The core perturbome is defined as a central response to multiple disturbances, functioning as a complex molecular network to overcome the disruption of homeostasis under stress conditions, thereby promoting tolerance and survival under stress conditions. Based on the biological and clinical relevance of Escherichia coli and Staphylococcus aureus, we characterized their molecular responses to multiple perturbations. Gene expression data from E. coli (8815 target genes—based on a pangenome—across 132 samples) and S. aureus (3312 target genes across 156 samples) were used. Accordingly, this study aimed to identify and describe the functionality of the core perturbome of these two prokaryotic models using a machine learning approach. For this purpose, feature selection and classification algorithms (KNN, RF and SVM) were implemented to identify a subset of genes as core molecular signatures, distinguishing control and perturbation conditions. After verifying effective dimensional reduction (with median accuracies of 82.6% and 85.1% for E. coli and S. aureus, respectively), a model of molecular interactions and functional enrichment analyses was performed to characterize the selected genes. The core perturbome was composed of 55 genes (including nine hubs) for E. coli and 46 (eight hubs) for S. aureus. Well-defined interactomes were predicted for each model, which are jointly associated with enriched pathways, including energy and macromolecule metabolism, DNA/RNA and protein synthesis and degradation, transcription regulation, virulence factors, and other signaling processes. Taken together, these results may support the identification of potential therapeutic targets and biomarkers of stress responses in future studies. Full article

Motor Neuron Diseases (MNDs) such as Amyotrophic Lateral Sclerosis (ALS), Primary Lateral Sclerosis (PLS), Hereditary Spastic Paraplegia (HSP), Spinal Muscular Atrophy with Respiratory Distress Type 1 (SMARD1), Multisystem Proteinopathy (MSP), Spinal and Bulbar Muscular Atrophy (SBMA), and ALS associated to Frontotemporal Dementia (ALS-FTD), have traditionally been studied as distinct entities, each one with unique genetic and clinical characteristics. However, emerging research reveals that these seemingly disparate conditions converge on shared molecular mechanisms that drive progressive neuroaxonal degeneration. This narrative review addresses a critical gap in the field by synthesizing the most recent findings into a comprehensive, cross-disease mechanisms framework. By integrating insights into RNA dysregulation, protein misfolding, mitochondrial dysfunction, DNA damage, kinase signaling, axonal transport failure, and immune activation, we highlight how these converging pathways create a common pathogenic landscape across MNDs. Importantly, this perspective not only reframes MNDs as interconnected neurodegenerative models but also identifies shared therapeutic targets and emerging strategies, including antisense oligonucleotides, autophagy modulators, kinase inhibitors, and immunotherapies that transcend individual disease boundaries. The diagnostic and prognostic potential of Neurofilament Light Chain (NfL) biomarkers is also emphasized. By shifting focus from gene-specific to mechanism-based approaches, this paper offers a much-needed roadmap for advancing both research and clinical management in MNDs, paving the way for cross-disease therapeutic innovations. Full article

The rugose surface trait in pepper (Capsicum annuum L.), marked by ridges and depressions on the fruit epidermis, is linked to improved fruit texture. To investigate its regulatory basis, histological, textural, and transcriptomic differences, contrasting genotypes were analyzed. Histological analysis revealed that disorganized epidermal cell layers contribute to rugosity, with morphological differences emerging around 10 days post-anthesis (DPA). A computer-aided design (CAD)-based rugosity index (RI) was developed and showed strong correlation with sensory rugosity scores (R² = 0.659, p < 0.001). Texture analysis demonstrated that increasing surface rugosity was associated with reduced rupture force and hardness, as well as elevated pectinase activity. Comparative transcriptome profiling identified 10 differentially expressed genes (DEGs) related to microtubule dynamics (e.g., CA03g18310 and CA09g13510) and phytohormone signaling (e.g., CA03g35180 and CA08g12070), which exhibited distinct spatial and temporal expression patterns. These findings suggest that coordinated cytoskeletal remodeling and hormonal regulation drive epidermal disorganization, leading to surface rugosity and altered fruit texture. The study provides novel insights into the molecular basis of fruit surface morphology and identifies promising targets for breeding high-quality pepper cultivars. Full article

 Porcine epidemic diarrhea virus (PEDV) continues to circulate globally, causing substantial economic losses to the swine industry. Historically, PEDV strains are classified into the classical G1, epidemic G2, and S-INDEL genotypes. Among these genotypes, the highly virulent and prevalent G2 genotype has been extensively studied. However, recent clinical outbreaks in China necessitate a reevaluation of the epidemiological and evolutionary dynamics of circulating strains. This study analyzed 37 newly sequenced S genes and public sequences to characterize the genetic variations of S-INDEL strains. Our analysis revealed that S-INDEL strains are endemic throughout China, with a phylogenetic analysis identifying two distinct clades: clade 1, comprising early endemic strains, and clade 2, representing a recently dominant, geographically restricted lineage in China. While inter-genotypic recombination has been documented, our findings also demonstrate that intra-genotypic and intra-clade recombination events contributed significantly to the emergence of clade 2, distinguishing its evolutionary pattern from clade 1. A comparative analysis identified 22 clade-specific amino acid changes, 11 of which occurred in the D0 domain. Notably, mutations at positively selected sites—113 and 114 within the D0 domain, a domain associated with pathogenicity—were specific to clade 2. A phylodynamic analysis indicated Germany as the epicenter of S-INDEL dispersal, with China acting as a sink population characterized by localized transmission networks and frequent recombination events. These results demonstrate that contemporary S-INDEL strains, specifically clade 2, exhibit unique recombination patterns and mutations potentially impacting virulence. Continuous surveillance is essential to assess the pathogenic potential of these evolving recombinant variants and the efficacy of vaccines against them.  Full article

Gut microbiota plays a vital role in host resilience but may be disrupted under environmental antibiotic pressure. The goitered gazelle (Gazella subgutturosa), a keystone ungulate in the Qaidam Basin, is crucial for ecosystem stability. We aimed to investigate how this species responds to antibiotic pressure through gut microbial adaptation. Using 16S rRNA sequencing and weighted gene co-expression network analysis (WGCNA) on fecal and soil samples from six regions, we identified 18 microbial modules, of which three were strongly associated with antibiotics (|r| ≥ 0.75, p < 0.05). Gut microbial α-diversity was lowest in the antibiotic-rich, vegetation-poor TGL region and highest in XRH, where diverse vegetation appeared to buffer antibiotic impact. Antibiotic pressure can reshape gut microbial communities, exerting both adaptive benefits and adverse effects. High-quality habitats may alleviate the negative impacts of antibiotic pressure. Full article

Mycoplasmal pneumonia of sheep (MPS), caused by Mesomycoplasma (Mycoplasma) ovipneumoniae, profoundly impacts ovine productivity and survival. Although gut–lung microbiota interactions are increasingly recognized in respiratory diseases, whether similar crosstalk occurs between the lung and rumen microbiota in MPS-affected sheep remains unknown. To investigate alterations in the lung and rumen microbiota of sheep with MPS, the crosstalk between these microbial communities, and their impacts on growth phenotypes. From a cohort of 414 naturally infected six-month-old male Hu sheep, we selected 10 individuals with severe pulmonary pathology and 10 healthy controls for detailed phenotypic and microbiome analyses. Assessment of 359 phenotypic traits revealed that MPS significantly impairs feed efficiency and growth rate (p < 0.05). Through 16S rRNA gene sequencing, we found that MPS significantly altered the pulmonary microbiota community structure (p < 0.01), with a noticeable impact on the rumen microbiota composition (p = 0.059). Succinivibrionaceae_UCG-001 was significantly depleted in both the rumen and lungs of diseased sheep (p < 0.05) and strongly associated with reduced average daily feed intake (p < 0.05). In addition, pulmonary Pasteurella and ruminal Succinivibrionaceae_UCG-002 were significantly enriched in MPS-affected sheep, showed a strong positive correlation (p < 0.05), and were both negatively associated with feed efficiency (p < 0.05). Notably, Pasteurella multocida subsp. gallicida may act as a keystone species influencing feed efficiency. These findings point to a previously unrecognized rumen-lung microbial axis that may modulate host productivity in sheep affected by MPS. This work provides new insights into the pathogenesis of MPS and offers potential targets for therapeutic intervention and management. Full article

One of the aggressive and lethal cancers, pancreatic ductal adenocarcinoma (PDAC) is characterized by poor prognosis and resistance to conventional treatments. Moreover, the tumor immune microenvironment (TIME) plays a crucial role in the progression and therapeutic resistance of PDAC. It is associated with T-cell exhaustion, leading to the progressive loss of T-cell functions with an impaired ability to kill tumor cells. Therefore, this study employed single-cell RNA sequencing (scRNA-seq) analysis of a publicly available human PDAC dataset, with cells isolated from the primary tumor and adjacent normal tissues, identifying upregulated genes of T-cells and cancer cells in two groups (“cancer cells_vs_all-PDAC” and “cancer-PDAC_vs_all-normal”). Common and unique markers of cancer cells from both groups were identified. The Reactome pathways of cancer and T-cells were selected, while the genes implicated in those pathways were used to perform PPI analysis, revealing the hub genes of cancer and T-cells. The gene expression validation of cancer and T-cells hub-genes was performed using GEPIA2 and TISCH2, while the overall survival analysis of cancer cells hub-genes was performed using GEPIA2. Conclusively, this study unraveled 16 novel markers of cancer and T-cells, providing the groundwork for future research into the immune landscape of PDAC, particularly T-cell exhaustion. However, further clinical studies are needed to validate these novel markers as potential therapeutic targets in PDAC patients. Full article

Objective: Retinal capillary dropout, characterized by acellular capillaries or “ghost vessels,” is an early pathological sign of diabetic retinopathy (DR) that remains undetectable through standard clinical imaging techniques until visible morphological changes, such as microaneurysms or hemorrhages, occur. This study aims to develop a non-destructive artificial intelligence (AI)-based method using fluorescein angiography (FA) images to detect early-stage, silent retinal capillary dropout. Methods: We utilized 94 FA images and corresponding destructive retinal capillary density measurements obtained through retinal trypsin digestion from 51 Nile rats. Early capillary dropout was defined as having an acellular capillary density of ≥18 counts per mm². A DenseNet based deep learning model was trained to classify images into early capillary dropout or normal. A Bayesian framework incorporating diabetes duration was used to enhance model predictions. RNA sequencing was conducted on retinal vasculature to identify molecular markers associated with capillary early dropout. Results: The AI-based FA imaging model demonstrated an accuracy of 80.85%, sensitivity of 84.21%, specificity of 75.68%, and an AUC of 0.86. Integration of diabetes duration into a Bayesian predictive framework further improved the model’s performance (AUC = 0.90). Transcriptomic analysis identified 43 genes significantly upregulated in retinal tissues preceding capillary dropout. Notably, inflammatory markers such as Bcl2a1, Birc5, and Il20rb were among these genes, indicating that inflammation might play a critical role in early DR pathogenesis. Conclusions: This study demonstrates that AI-enhanced FA imaging can predict silent retinal capillary dropout before conventional clinical signs of DR emerge. Combining AI predictions with diabetes duration data significantly improves diagnostic performance. The identified gene markers further highlight inflammation as a potential driver in early DR, offering novel insights and potential therapeutic targets for preventing DR progression. Full article

Background. Studies of comorbid (syntropic) and inversely comorbid (rarely occurring together, i.e., dystropic) diseases have focused on the search for molecular causes of this phenomenon. Materials. We investigated DNA methylation levels in regulatory regions of 23 apoptosis-associated genes as candidate loci associated with the “cancer–neurodegeneration” dystropy in patients with Huntington’s disease (HD) and patients with non–small cell lung cancer (LC). Results. Statistically significant differences in methylation levels between the HD and LC groups were found for 41 CpG sites in 16 genes. The results show that five genes (SETDB1, TWIST1, HDAC1, SP1, and GRIA2) are probably involved in the phenomenon of inverse comorbidity of these diseases. For these genes, the methylation levels of the studied CpG sites were altered in opposite directions in the two groups of patients, compared to the control group. Conclusions. For the SP1 gene, the above hypothesis is supported by our analysis of open-access data on gene expression in patients with the aforementioned diagnoses and fits a probable mechanism of the “HD–LC” dystropy. Full article