Search Results (215)

Intermittent fasting confers protection in diverse diseases through various mechanisms, including the clearance of senescent and pathogenic cells, modulation of tissue inflammation and enhancement of stem/progenitor cell niche and functionality. Our previous study demonstrated the beneficial impact of alternate-day fasting (ADF) on xerostomia and sialadenitis, along with an improvement in salivary gland ductal compartments, where salivary gland progenitor cells reside, in non-obese diabetic mice, a spontaneous model of Sjögren’s syndrome (SS). In the present study, we induced SS-associated hyposalivation in KRT5^CreERT2; R26^tdTomato lineage tracing mice by immunizing them with submandibular gland proteins from wild-type C57BL/6 mice. ADF alleviated salivary gland hypofunction, which was accompanied by decreased expression of the senescent cell marker p16^INK4a, reduced protein levels of anti-apoptotic proteins BCL-2, BCL-XL, and MCL-1, and attenuated NLRP3 inflammasome activity in the submandibular glands, particularly within the ductal compartments, of this inducible model. Furthermore, immunofluorescence staining of submandibular gland sections revealed the expression of the acinar cell marker aquaporin 5 in a small subset of Keratin 5⁺ cells in 2 of 9 mice that were subjected to ADF, whereas no such cells were detected in the control mice. Taken together, these findings indicate that ADF favorably modulates the salivary gland progenitor cell niche, potentially by promoting apoptosis-mediated senescent cell clearance, suppressing NLRP3 inflammasome signaling, and promoting Keratin 5⁺ progenitor cell-derived acinar cell replenishment, thereby contributing to the structural and functional restoration of damaged salivary glands in autoimmune exocrinopathy. Full article

Ulcerative colitis (UC) is a chronic inflammatory bowel disease characterized by dysbiosis of the gut microbiota. Helminth infections are known to modulate host immunity and intestinal microbial composition; however, the therapeutic use of live parasites poses safety challenges. The recombinant Fasciola hepatica fatty acid-binding protein Fh15 is a helminth-derived molecule with anti-inflammatory effects in models of septic shock and dextran sulfate sodium (DSS)-induced colitis. Whether Fh15 also influences gut microbial composition during colitis remains unknown. Male C57BL/6 mice received 4% DSS in drinking water for 7 days to induce colitis and were treated intraperitoneally with Fh15 (2 mg/kg) on days 1, 3, and 5. Fecal samples were collected on days 2, 4, and 7 for 16S rRNA gene sequencing. Standard microbiota pipelines were used to evaluate community diversity. Acute DSS treatment disrupted gut microbial diversity and community structure compared with non-colitic controls. Fh15 treatment partially restored early microbial balance by shifting microbial composition toward that of healthy mice and reducing microbial dispersion, indicating enhanced community stability despite severe dysbiosis. Although alpha diversity did not return to control levels, Fh15 mitigated the expansion of pro-inflammatory genera (Enterococcus and Turicibacter) and preserved beneficial taxa, including Adlercreutzia. Full article

Background: Emergency department evaluation of suspected urolithiasis increasingly relies on non-contrast CT, yet not all patients require imaging. Existing clinical prediction rules help stratify stone probability, but by converting continuous measurements into fixed binary indicators, they offer little insight into why a particular patient is at risk or how much uncertainty remains after each testing stage—questions that bear directly on individualized diagnostic decisions. Methods: We retrospectively analyzed 1000 ED patients with suspected urolithiasis who underwent non-contrast CT (stone prevalence 85.0%). A gradient boosting classifier was trained on 17 continuous clinical and laboratory features and compared against binary-thresholded counterparts and an established scoring system; the 17-feature model achieved AUC 0.771 (95% CI 0.726–0.813) versus 0.723 (95% CI 0.675–0.771) for the reference score on this cohort (DeLong p = 0.001). Individual predictions were explained using an interventional Shapley value approach, and a Shannon entropy-based framework was applied to quantify the marginal diagnostic contribution of each sequential testing stage. Results: Held-out permutation importance identified red blood cell count on microscopy, age, pain duration, and prior stone history as the most influential predictors. Several features showed non-linear contributions that diverged from conventional binary thresholds: creatinine effect crossed zero near 0.90 mg/dL and pain duration peaked between 2 and 5 h. C-reactive protein, absent from existing scoring systems, emerged as a meaningful negative predictor. Sequential entropy analysis showed that dipstick urinalysis provided the largest marginal information gain among non-history stages (6.1% of prior entropy), while physical examination contributed 2.3%. A prevalence sensitivity analysis projected that the framework’s threshold behavior would differ substantially in lower-prevalence populations, underscoring that the cohort-specific cut-points are not portable decision rules. We therefore position the framework as a reasoning aid that complements clinical judgment and imaging, not as a stand-alone triage tool. Conclusions: Explainable machine learning can address questions that aggregate discrimination metrics cannot: which features drive risk for a given patient, how those effects behave across the continuous measurement range, and how much diagnostic uncertainty each testing stage resolves. The Shapley-based explanations and entropy framework developed here offer a structured approach to individualized diagnostic reasoning in the ED evaluation of suspected urolithiasis, functioning as an interpretive adjunct to, rather than a replacement for, existing clinical tools and CT imaging. Full article

Host receptors can detect traces of non-self-pathogenic RNAs within a sea of cellular mRNA molecules. In host cells, mRNA cap methylation occurs in the nucleus, generating Cap1 and Cap2 structures (m⁷GpppNm and m⁷GpppNmNm, respectively). By contrast, alphavirus genomes carry a Cap0 structure (m⁷GpppN), which lacks 2′-O-methylation. This difference in the structure of the host and viral caps serves as a molecular signature that enables discrimination between self and non-self RNAs. Several host immune sensors, such as RIG-I and IFIT1, recognize the alphavirus Cap0 structure and trigger an antiviral response to restrict viral replication. It has been proposed that IFIT1 sequesters aberrant RNAs, preventing their translation by host ribosomes and blocking viral protein synthesis. However, alphaviruses have evolved molecular strategies to circumvent IFIT1-mediated restriction and facilitate infection in mammalian cells. One such strategy involves the folding of a 5′ RNA structure that hides the cap from host immune sensors. This highlights the dynamic interplay between viral evasion tactics and host immune defenses. This review will discuss how specific modifications at the 5′ end of alphavirus RNA modulate host defenses and how a deeper understanding of the virus–host interaction may inform the development of novel vaccine strategies. Full article

Polygonatum cyrtonema Hua (PCH) is traditionally recognized as both an edible and medicinal food source. Its rhizomes contain numerous bioactive compounds, notably polysaccharides and flavonoids, which serve as key constituents in functional food development. However, the cultivation of PCH is often hindered by allelopathic effects, which diminish its quality and restrict its industrial application. To mitigate these allelopathic influences, three types of biochars derived from maize straw (MB), rice husk (RB), and tea stem (TB) were applied at concentrations of 0%, 2%, and 4%. Initially, the physicochemical properties of these biochars were characterized, followed by an evaluation of their impact on (1) the synthesis of quality-related components, secondary metabolites, and allelochemicals within PCH rhizomes and (2) the fundamental physicochemical properties and bacterial community structure of the PCH rhizosphere soil. The findings indicated that the application of 4% RB significantly enhanced the content of total polysaccharides by 48.5%, total flavonoids by 30.2%, total saponins by 28.6%, and total polyphenols by 18.3%, while concurrently reducing protein (PRO) and free amino acid (FAA) concentrations in the rhizomes. Non-targeted metabolomic analyses revealed that biochar amendments (1) upregulated metabolites involved in the citrate cycle and galactose metabolism pathways, thereby facilitating energy supply and precursors for polysaccharide biosynthesis; (2) downregulated metabolites involved in the arginine biosynthesis pathway, which is unfavorable for protein and amino acid synthesis; (3) decreased the abundance of six identified allelochemicals, including 5-hydroxy-L-tryptophan and andrographolide, with the most pronounced effect observed in the 4% TB treatment (T2); (4) improved soil physicochemical parameters such as pH, soil organic matter (SOM), total nitrogen (TN), and available potassium (AK); and (5) altered the rhizosphere bacterial community by enriching beneficial phyla, notably Myxococcota and Gemmatimonadota. These modifications in soil properties and bacterial community composition were closely associated with enhanced rhizome quality and a reduction in allelochemical accumulation. Collectively, the results of this study elucidate the potential mechanisms linking biochar application to allelopathy mitigation, optimization of soil microbial communities, and improvement of PCH rhizome quality. This research provides a theoretical basis for the production of high-quality PCH while concurrently minimizing allelochemical accumulation in its rhizomes. Full article

An increasing number of studies have focused on the redundant roles of genes in various cellular processes. For instance, 37,000 and 127,300 publications are associated with P53 and Tumor Protein 53 (TP53) respectively, and numerous other genes are also repeatedly interpreted like them. Thus, it is crucial to reduce such non-essential duplicated studies. In this study, RNA sequencing (RNA-seq) data of 6 commonly used tool cell lines and 43 tissue types from pigs were analyzed. The results indicated that genes relatively highly or specifically expressed in each cell type most likely perform that cell’s primary function. Specifically, such genes in skeletal muscle cells mainly regulate skeletal muscle structure, differentiation and development, with similar phenomena seen in the other 5 cell types. In addition, RNA expression levels of genes show high similarity and commonality between cells and tissues, with a total of 4117 ubiquitously expressed genes screened out overall. Meanwhile, embryonic samples display the largest number of RNA-specific expressed genes and the strongest tissue specificity. In conclusion, investigating highly and specifically expressed genes across cells, tissues and organs enables more efficient identification of core functional genes, whereas cataloging ubiquitously expressed genes in a species helps reduce redundant and unnecessary gene functional characterization. Full article

Background/Objectives: Dietary fibers play key roles in shaping gut microbiome and intestinal homeostasis. While purified diets offer experimental precision and reproducibility in rodent models, they omit the complex mixture of fermentable and non-fermentable fibers found in grain-based chow diets. We hypothesized that excluding fermentable fiber impairs intestinal homeostasis by reducing microbial metabolites and altering the colonic epithelial transcriptome, thereby increasing susceptibility to inflammation. Methods: Wildtype male C57BL/6 mice were maintained on either a standard grain-based chow diet or a purified low-fat diet (LFD) containing 5% non-fermentable cellulose for ten weeks. Fecal microbiomes, short-chain fatty acid (SCFA) profiles, and colonic epithelial transcriptomes were analyzed. A separate group was challenged with dextran sodium sulfate (DSS) following a five-week dietary intervention to compare colitis severity between the two diet groups. Results: Relative to mice fed the grain-based chow, those consuming the purified LFD (containing only non-fermentable cellulose) showed decreased gut microbial diversity and significantly lower SCFA levels. These changes were accompanied by marked differences in colonic epithelial cell transcriptomes. In LFD-fed mice, the top upregulated gene networks included ribosomal pathways and MHC complex protein binding, suggesting increased growth and gut inflammation. The most downregulated pathways included mineral absorption, actin and tubulin binding, and membrane organelle assembly, indicating major alterations in cellular structure and transport. LFD-fed mice also exhibited increased colonic expression of S100a9, a gut inflammation biomarker, and more severe disease symptoms when challenged with DSS compared to chow-fed mice. Conclusions: Fermentable fibers are one of the factors contributing to intestinal homeostasis and mitigating the severity of ulcerative colitis. Full article

Foot-and-mouth disease virus (FMDV) is a highly contagious pathogen of cloven-hoofed livestock. Recombination is one of the mechanisms that contribute to genetic diversity of FMDV and facilitate the generation of new viral lineages, or recombinant forms. While the general patterns of recombination in FMDV are well-known, the temporal dynamics of this process remain unexplored. This study systematically analyzed recombination across 1485 publicly available complete genome sequences of FMDV, collected from 1934 to 2024. In addition to the well-known general recombination pattern with hotspots on the borders of the genome region that encodes capsid proteins VP2-VP3-VP1, we identified serotype-specific recombination patterns. A significant temporal signal required to analyze temporal dynamics was found in serotypes A, Asia1, O, and SAT1 in the VP2-VP3-VP1 genome region. To assess the lifetimes of FMDV recombinant forms, we compared these time-scaled phylogenetic trees with phylogenies for other genomic regions exchanged by recombination events. The median lifetimes of FMDV recombinant forms ranged from 2 to 18 years, depending on the serotype and the nonstructural genomic region involved in recombination. These timescales are comparable to human (+)RNA viruses, such as enteroviruses and caliciviruses. In distinct serotypes, recombination could be more frequent on the 5′ or 3′ border of the capsid-encoding genome region, without a uniform pattern. Full article

Triplexes (TRX) are a class of flipons that can form due to the interaction of RNA with B-DNA. While many proteins have been proposed to bind triplexes, structural models of these interactions do not exist. Here, I present AlphaFold V3 (AF3) models that reveal interactions between the high-mobility group protein B1 (HMGB1), HNRNPU (SAF-A), TP53, ARGONAUTE (AGO), and REL domain proteins. The TRXs result from the sequence-specific docking of RNAs to DNA via Hoogsteen base pairing. The RNA and DNA strands in apolar TRX are oriented in the opposite 5′ to 3′ direction, while copolar TRX have RNA and DNA strands pointing in the same 5′ to 3′ direction. TRXs can incorporate different RNA classes, including long noncoding RNAs (lncRNAs), short RNAs, such as miRNAs, piRNAs, and tRNAs, nascent RNA fragments, and non-canonical base triplets. Many pathways regulated by TRX formation have evolved to constrain retroelements (EREs), which are both an existential threat to the host and a source of genotypic variation. TRXs help set the boundaries of active chromatin, repressing the expression of most EREs, while depending on other flipons to modulate cellular programs. The TRXs help nucleate folding of intrinsically disordered proteins. Full article

Post-transcriptional regulation of gene expression is influenced by RNA-binding proteins (RBPs) and small non-coding RNAs that bind to conserved mRNA sequences to modulate mRNA processing. These regulatory molecules affect the structural conformation of mRNAs, creating formations like G-quadruplexes (G4s), which alter translation initiation and regulatory-factor site accessibility. Recent studies have highlighted Nuclear factor erythroid 2–related factor 2 (NRF2) as a key regulator of cellular redox homeostasis and cellular response to oxidative stress. An intriguing feature of NRF2 is the structural formation of its 5′ untranslated region (UTR), which may promote or inhibit translation initiation depending on the cellular context. In this study with minigenes, we provide in vitro evidence of RNA G4s in the NRF2 mRNA’s 5′ UTR under basal (no stress) conditions. Achieved via electrophoretic mobility shift assay and fluorescence spectra in the presence of Pyridostatin. Understanding how structural motifs within NRF2 5′ UTRs influence mRNA function provides insights into a common molecular mechanism underlying diseases where NRF2 is dysregulated, like cancers, cardiovascular disease, and neurodegeneration, and highlights potential therapeutic avenues through regulation of NRF2. Full article

The functional properties of high-pressure processing (HPP)-assisted protein hydrolysate from tamarind kernel powder (TKP-HD) and the physicochemical characteristics of its foam-mat powder were studied. TKP-HD consisted of more non-polar than polar amino acids, with higher solubility at pH 5 and 7 than soy protein isolate (SPI) but lower than egg white (EW). The water-binding capacity of TKP-HD increased at pH 5 while TKP-HD had a higher foaming capacity than SPI at pH 5, and the highest oil-binding capacity. The physicochemical properties of TKP-HD after foam-mat drying were investigated using 1 and 1.5% (w/w) hydroxypropyl methylcellulose (HPMC), with drying at 60, 70, and 80 °C. Samples with 1.5% HPMC had lower water activity than those with 1% HPMC at all drying temperatures. The sample with 1% HPMC had higher antioxidant capacity at 60 °C than at 70 °C, but this decreased at 1.5% HPMC. Samples with 1.5% HPMC and dried at 60 °C recorded the highest solubility and viscosity, with increased porosity of the powder structure. The most suitable foam-mat drying conditions for TKP-HD were the addition of 1.5% HPMC and drying at 60 °C. Full article

Background/Objectives: Self-collection devices are more widely used than ever for detecting sexually transmitted infections and cervical cancer. Despite this, we still lack a clear understanding of how well these tools actually collect and release the necessary molecular samples. This study compared the in vitro uptake and release performance of commonly used self-sampling devices for total proteins, nucleic acids, and episomal human papillomavirus type 16 (HPV-16) DNA. Methods: An artificial cervicovaginal fluid composed of phosphate-buffered saline supplemented with serum and nucleic acid extracts was serially diluted 2-fold. Each dilution was applied for 5 min to the external surfaces of a vaginal veil (Vaginal Veil Collector V-Veil UP2^TM device), a flocked swab (FLOQSwabs^®), and a commercial vaginal tampon. Non-woven surgical tissue and plastic film served as controls. Total proteins and nucleic acids were quantified by spectrophotometry, and HPV-16 DNA by real-time quantitative PCR. Results: Recovery rates for proteins and nucleic acids were highest for the vaginal veil (81% and 91%), followed by the swab (66% and 70%) and non-woven tissue (44% and 47%). In contrast, the tampon and plastic film performed poorly, releasing less than 30% of proteins and negligible amounts of nucleic acids. Episomal HPV-16 DNA release was highest for the veil (89%), compared with the swab (57%), non-woven tissue (37%), tampon (4%), and plastic film (2%). Conclusions: The vaginal veil demonstrated superior uptake and release of proteins, nucleic acids, and HPV-16 DNA at physiological concentrations. Its non-absorbent structure allows high saturation with efficient release of genital components, including microbial genomes, whereas vaginal tampons retained these components, limiting analytical recovery. Full article

The SARS-CoV-2 nucleocapsid protein (Np) is essential for viral RNA replication and genomic RNA packaging. Phosphorylation of Np within its central Ser-Arg-rich (SRR) linker is proposed to modulate these functions. To gain mechanistic insights into these distinct roles, we performed in vitro biophysical and biochemical studies using recombinantly expressed ancestral Np and phosphomimetic SRR variants. Limited-proteolysis showed minor cleavage differences between wild-type (WT) and phosphomimetic Np, but no major structure or stability changes in the N- and C-terminal domains were observed by circular dichroism spectroscopy and differential scanning fluorimetry, respectively. Mass photometry (MP) revealed that WT Np dimerized more readily than phosphomimetic variants. Crosslinking-MP showed that WT Np formed discrete complexes on viral 5′ UTR stem-loop (SL) 5 RNA, whereas phosphomimetic Np assembled preferentially on SL1–4. WT Np bound non-specifically to all RNAs tested primarily via hydrophobic interactions, whereas phosphomimetic Np showed selectivity for SARS-CoV-2-derived RNAs despite binding more electrostatically. A major difference was observed in the binding kinetics; WT Np compacted and irreversibly bound single-stranded DNA, whereas phosphomimetic Np displayed reduced compaction and fast on/off binding kinetics. These mechanistic insights support a model where phosphorylated Np functions in RNA replication and chaperoning, while non-phosphorylated Np facilitates genomic RNA packaging. The findings also help to explain infectivity differences and clinical outcomes associated with SRR linker variants. Full article

Respiratory viruses such as SARS-CoV-2, influenzas A and B, respiratory syncytial virus (RSV), human metapneumovirus (hMPV), human parainfluenza virus type 3 (HPIV-3), and rhinoviruses remain major causes of global morbidity. Their rapid evolution, high transmissibility, and limited therapeutic options, together with the absence of approved vaccines for several pathogens, highlight the need for broad-acting and pathogen-independent antiviral strategies. Nitric oxide exhibits antiviral activity through redox-dependent mechanisms, including S-nitrosylation of cysteine-containing viral proteins and disruption of redox-sensitive structural domains. Clinical studies conducted during the SARS-CoV-2 pandemic demonstrated that a nitric oxide nasal spray (NONS) rapidly reduced nasal viral load and transmission. In this study, we evaluated the in vitro virucidal activity of the NONS against a panel of clinically relevant respiratory viruses representing four major virus families. Virus suspensions of approximately 10⁴ CCID₅₀ were exposed to a full-strength NONS for contact times ranging from 5 s to 2 min at room temperature, followed by neutralization and quantification of residual infectivity using endpoint dilution assays. The NONS rapidly reduced viral infectivity across all viruses tested, achieving >3 log₁₀ reductions within 2 min. SARS-CoV-2 variants including Alpha, Beta, Gamma, Delta, Omicron BA.1, and XBB 2.0 were reduced to levels at or below the assay detection limit within 30 s to 2 min. Influenza A and B viruses showed the fastest loss of infectivity, reaching detection limits within 10–15 s. RSV, hMPV, HPIV-3, and human rhinovirus 14 were similarly inactivated within 1–2 min. These findings demonstrate that the NONS exhibits rapid and broad-spectrum virucidal activity against diverse respiratory viruses and supports its potential role in pandemic preparedness but also seasonal use. Full article

Resveratrol (RES) suffers from low bioavailability and poor gastrointestinal stability, limiting its health benefits. To overcome these challenges, we developed biomimetic mineralized nanoparticles based on walnut protein peptides (WPP-RES@CaP) for intestinal-targeted RES delivery. WPP with a 31.83% degree of hydrolysis was optimal for RES encapsulation. Subsequent mineralization with 5 mM Ca²⁺ significantly enhanced the encapsulation efficiency (EE) to 95.86%, compared to 73.69% for non-mineralized WPP-RES nanoparticles. The particle size and zeta potential of WPP-RES@CaP were 795 ± 16 nm and −27 ± 1 mV, respectively. Beyond the initial hydrophobic and π-π interactions, mineralization introduced additional stabilizing forces, including metal–ligand coordination, salt bridges, and electrostatic interactions, which collectively enhanced the structural integrity and RES retention of WPP-RES@CaP. During in vitro gastrointestinal digestion, the formation of a CaP shell protected RES and WPP from excessive degradation in the gastric phase. The 77.57% RES in WPP-RES@CaP was continuously released in the intestinal phase, which was higher than that of WPP-RES (49.73%). Meanwhile, the introduction of Ca²⁺ promoted the antioxidant activity of WPP-RES@CaP, which demonstrated higher DPPH and ABTS radical-scavenging activity assays than WPP-RES both before and after digestion. It was probably due to the synergistic effect of more released RES, antioxidant-free amino acids, and peptides. This mineralized peptide-based system provided a strategy for improving the delivery of hydrophobic bioactive compounds in functional foods. Full article