Search Results (949)

Human astroviruses are small, non-enveloped RNA viruses belonging to the family Astroviridae. Among the four species known to infect humans, the species Mamastrovirus hominis (the classical human astroviruses, formerly MAstV1) is associated with gastrointestinal illness worldwide, while three more recently identified species have been linked to lethal central nervous system infections. High substitution rates and recombination drive their rapid evolution, yet recombination patterns in classical human astroviruses remain poorly characterized. This study systematically analyzes patterns and temporal dynamics of natural recombination in classical human astroviruses. Publicly available genomes of classical human astroviruses were analyzed to identify recombination hotspots. Recombinant forms were defined as stable phylogenetic lineages unaffected by recombination, and their half-lives were estimated based on time-scaled phylogenies (BEAST2v2.7.7). Recombination in classical human astroviruses occurred most frequently at the ORF1b/ORF2 junction, but also within ORF1a, at the ORF1a/ORF1b junction, and within ORF2. Only the 3′-part of ORF1a and a fragment of ORF1b exhibited robust temporal signal, yielding substitution rates of 2.35 × 10⁻³ and 2.14 × 10⁻³ s/s/y, respectively. The half-lives of recombinant forms varied considerably by genomic region: longest for exchanges between the parts of ORF1a (21 years), intermediate for ORF1a/ORF1b recombinants (7–9 years), and shortest for ORF1ab/ORF2 recombinants (2.5–3.6 years). The estimated half-lives for recombinants align with those reported for human enteroviruses and noroviruses. These findings highlight the dynamics of the generation of astrovirus diversity and may inform advanced surveillance of emerging strains. Full article

Elm (Ulmus pumila), an ecologically and economically valuable tree, exhibits significant tolerance to abiotic stress. However, the physiological and molecular mechanisms underlying its stress adaptabilities are largely unknown. Here, two elm salt-tolerant cultivars (ST-Y and ST-Q) and two salt-sensitive cultivars (SS-J and SS-JX) were identified in the 13 elm accessions collected from Shandong province, China via phenotypic salt tolerance screening. The key salt tolerance mechanisms were explored in ST-Y and SS-J via transcriptomic (RNA-Seq) assays, and subsequently validated in ST-Q and SS-JX via quantitative real-time polymerase chain reaction (RT-qPCR) analyses. Under salt treatment, ST-Y maintained leaf intactness and enhanced activation of antioxidant enzymes with a reduction in reactive oxygen species (ROS) accumulation, while SS-J suffered leaf defoliation and showed compromised antioxidant capacity with higher ROS levels. KEGG pathway analysis revealed that ST-Y leaves exhibited a unique enrichment of differentially expressed genes (DEGs) in the “oxidative phosphorylation (OXPHOS)” pathway after salt stress treatment. Both ST-Y and SS-J exhibited significant enrichment in the “metabolic pathway”, but the number of DEGs in the “arachidonic acid (AA) metabolism” pathway was much higher in ST-Y than in SS-J. Further RT-qPCR analysis verified the accuracy of the RNA-Seq data and revealed that genes related to the “OXPHOS” pathway were significantly up-regulated in ST-Y and ST-Q, but down-regulated in SS-J and SS-JX. Our results suggested that OXPHOS efficiency is critical to antioxidant capacity in elm salt tolerance, suggesting new avenues for forest tree improvement for climate change. Full article

The C-terminus of the Y14 protein, which is also known as RBM8A and is encoded by the gene responsible for human thrombocytopenia absent radius syndrome, contains two serines that undergo phosphorylation inside an intrinsically disordered region (IDR). Although both serines are frequently phosphorylated in cells, their biological role remains unclear; therefore, we estimated the peptide structure using PEPstrMOD, which predicts peptide conformations through molecular dynamics. For this analysis, amino acid residues 151–174 of Y14, identified as an IDR in UniProt, were targeted. Structural prediction via PEPstrMOD revealed that the target peptide adopts an elongated structure in its unphosphorylated state, while simulating its phosphorylated state revealed an increase in hydrogen bonds and a more compact conformation. The compact structure of Y14 induced by phosphorylation may aid in the formation of the exon–exon junction complex at the exon–exon junction, which facilitates mRNA transport and translation. The prevalence of phosphorylated Y14 in cells may indicate that this higher-order structure is also essential for mRNA metabolism. Full article

Cyprinid herpesvirus 3 (CyHV-3) is a pathogen that causes high mortality in common carp (Cyprinus carpio) and koi. Common carp breeding lines with different genetic backgrounds exhibit different resistance levels to viral pathogens. This study aimed to determine the differences in CyHV-3 disease resistance performance between the hybrid offspring (Y × M and M × Y) of the mirror carp ‘Longke 11’ (resistant to CyHV-3) and Yellow River carp, as well as the self-crossed offspring (M and Y). The M, Y × M, M × Y and Y groups were infected with CyHV-3 by immersion. The order of mortality and the duration of death for the four groups of carp were as follows: Y group > Y × M group > M × Y group > M group. Throughout the entire infection stage, the mRNA expression levels of the viral factors thymidine kinase (TK) and open reading frame 72 (ORF72) in the four groups of carp tended to first increase but then decrease. The viral factor expression evaluated on days 30 and 31 post-infection (p.i.), which was the peak of infection mortality, was the highest in the Y group and the lowest in the M group, and compared with the Y × M group, the M × Y group had considerably lower viral gene expression (p < 0.05). The immune-related enzyme activity and content levels of the four carp groups matched the patterns of viral gene expression. On day 29 p.i., a time point with high mortality, the levels of alkaline phosphatase (AKP), glutathione peroxidase (GSH-Px) and total antioxidant capacity (T-AOC) were significantly the lowest in the Y group and significantly the highest in the M group, while the Y × M group showed a significant decrease compared to the M × Y group (p < 0.05). Quantitative real-time (q-PCR) analysis revealed that interleukin-21 receptor (IL21R), interferon regulatory factor 9 (IRF9), interferon type I (IFN-I), interleukin-6 (IL-6) and microtubule-associated protein light chain 3 (LC3), exhibited an initial increase followed by a decrease among the four experimental groups of common carp. In the peak mortality period of carp in the four groups (30 days post-infection), the expression levels of IL21R, IRF9, LC3, and IFN-I were significantly the highest in the M group and significantly the lowest in the Y group, with the mRNA expression of these genes in the M × Y group being significantly higher than that in the Y × M group (p < 0.05). In contrast, IL-6 expression levels exhibited the opposite trend. In this study, the M group exhibited the greatest resistance to CyHV-3, followed by the M × Y group, whose resistance was greater than that of the Y × M group, with the Y group showing the lowest disease resistance. Our findings demonstrate that hybridization modulates resistance to CyHV-3. Furthermore, we identified conserved immune signatures common to both susceptible and resistant carp, including the activation of nonspecific immunity and the upregulation of immune-associated genes. Full article

Salt stress severely restricts grape (Vitis vinifera L.) production. Serine/arginine-rich (SR) proteins, as a class of RNA-binding proteins, play important roles in plant growth, development and stress responses. However, the function and regulatory mechanism of VvSR34a in grape salt tolerance remain unclear. In this study, grape callus and cutting seedlings were used as materials to explore the role and molecular mechanism of VvSR34a in grape salt stress response. The results showed that, under 100 mM NaCl treatment, the relative level of VvSR34a in grape callus exhibited a ‘first increase and then decrease’ pattern, reaching a peak at 2 h, and the gene was localized in the nucleus. Transgenic experiments confirmed that the overexpression of VvSR34a significantly enhanced salt tolerance in grape callus and cuttings, as evidenced by better growth status, higher chlorophyll content and root activity, as well as lower electrolyte leakage and malondialdehyde (MDA) content under salt stress. In contrast, the silencing of VvSR34a significantly increased salt sensitivity in grapes. Y2H and LCI assays verified that VvSR34a physically interacts with VvCOP9. VvCOP9 may play a negative regulatory role in the salt stress response of the grapevine, and through the loss of the high salt-tolerant phenotype in the VvSR34a/VvCOP9-RNAi lines, it demonstrated that VvCOP9 is genetically upstream of VvSR34a. Furthermore, the ubiquitination and degradation assay demonstrated that VvCOP9 can significantly promote the degradation of VvSR34a. RNA-seq analysis showed that a total of 2834 differentially expressed genes and 202 alternative splicing events were detected in VvSR34a overexpression lines. These differentially expressed genes were significantly enriched in ATPase activity, redox and hormone signaling pathways. This study demonstrates that VvSR34a positively regulates salt tolerance in grapes, providing an important theoretical basis for molecular breeding of salt-tolerant grapevines. Full article

Background and Objectives: Parkinson’s disease (PD) entails the progressive degeneration of dopaminergic neurons in the substantia nigra (SN), accompanied by α-synuclein (α-syn)-enriched Lewy bodies. ITGA7 mediates cell–extracellular matrix adhesion and modulates apoptosis, though its involvement in PD pathogenesis warrants further investigation. Although acupuncture demonstrates neuroprotective effects in PD models, its precise molecular mechanisms remain incompletely understood; therefore, in this study, we explored the relationship between ITGA7 and α-synuclein expression in an MPTP-induced PD mouse model to determine the association between LR3/GB34 acupuncture-induced changes in α-synuclein levels and ITGA7 modulation. Materials and Methods: In the in vivo model, MPTP-induced PD mice underwent immunohistochemistry, immunofluorescence, and Western blotting to assess ITGA7, α-synuclein, and TH levels in the SN and striatal tissues following LR3/GB34 acupuncture. In parallel, for the in vitro mechanistic study, SH-SY5Y neuroblastoma cells treated with MPP⁺ and transfected with ITGA7-siRNA were utilized to examine the involvement of apoptosis-related signaling pathways. Results: In the in vivo model, MPTP administration downregulated ITGA7 and upregulated α-synuclein in SN tissues. Similarly, in vitro exposure of SH-SY5Y cells to MPP⁺ yielded comparable results, revealing an inverse correlation between ITGA7 and α-synuclein. LR3/GB34 acupuncture treatment in the mouse model significantly increased ITGA7 and TH expression while reducing α-synuclein accumulation. To further understand the specific role of ITGA7 observed in these animal findings, we silenced ITGA7 in the MPP⁺-treated cellular model. ITGA7 silencing exacerbated the neurotoxic effects, leading to further TH downregulation, α-synuclein upregulation, Bcl-2 reduction, and Bax/Bcl-2 ratio elevation. Conclusions: Collectively, the histological preservation of dopaminergic neurons following LR3/GB34 acupuncture in the PD mouse model appears to be linked to ITGA7 upregulation. Furthermore, our in vitro findings implicate ITGA7 in the regulation of apoptosis-related signaling cascades, supporting its potential role in mitigating α-synuclein pathology. 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

Potato purple top is a complex phytoplasma disease that poses a serious threat to potato cultivation worldwide. To verify the presence of different phytoplasma strains in potato disease outbreaks in Iran, six major potato-growing provinces in the central and western regions of the country were surveyed, and a total of 270 potato plants, 230 symptomatic and 40 asymptomatic, was sampled. Nested PCR analysis revealed the phytoplasma presence in 45% of symptomatic and 7% of asymptomatic plants. Molecular analysis was performed, analyzing the sequences of the 16S rRNA gene and the ribosomal protein rp, secY, and tufB genes. Four ‘Candidatus Phytoplasma’ species were identified in the tested potato samples: ‘Ca. P. asteris’ (16SrI-B), ‘Ca. P. tritici’ (16SrI-R), ‘Ca. P. trifolii’ (16SrVI-A), and ‘Ca. P. solani’ (16SrXII-A). The ‘Ca. P. solani’ strains were prevalent, occurring in all the surveyed provinces, whereas the ‘Ca. P. tritici’ strains were restricted to the Chaharmahal and Bakhtiari province. Phylogenetic and multilocus sequence analyses provided a finer resolution, distinguishing among some of the closely related phytoplasma strains. This study represents the first comprehensive molecular survey of potato-infecting phytoplasmas across a wide geographical region of Iran. The findings will aid studies regarding insect vector(s), pathogen biology, host range and disease management strategies. Full article

Age estimation is an important component of forensic investigation, with applications in criminal casework, immigration assessments, and disaster victim identification. Determining whether an individual is a minor or an adult, or estimating the age at death of unidentified remains, can have significant legal and humanitarian implications. Traditional forensic age estimation methods rely primarily on anthropological and radiological assessment of skeletal development and degeneration; however, these approaches may be limited by subjectivity, population-specific reference standards, and reduced precision in adult age estimation. In recent years, molecular biomarkers have emerged as promising complementary tools for age prediction. Molecular approaches, including DNA methylation profiling, Y-chromosome-associated markers, RNA-based biomarkers, mitochondrial DNA alterations, proteomic signatures, and telomere length analysis, reflect biological processes associated with aging and may provide objective indicators that can be measured from biological samples. Among these methods, DNA methylation-based models currently demonstrate the strongest predictive performance and represent the most extensively studied molecular strategy for forensic age estimation. Nevertheless, several challenges remain before widespread forensic implementation can be achieved, including tissue specificity, environmental influences on biomarker stability, population variability, and the need for robust validation across laboratories and forensic sample types. This review summarises the current molecular approaches investigated for forensic age estimation, evaluates their biological basis and methodological limitations, and discusses their potential integration into forensic workflows. While molecular techniques offer promising avenues for improving age estimation, further standardisation, validation, and careful interpretation are required before they can be routinely applied in forensic practice. Full article

Background/Objectives: Salidroside, a bioactive phenylethanol glycoside primarily derived from Rhodiola rosea, and its major in vivo metabolite tyrosol exhibit diverse pharmacological activities. However, their direct molecular targets remain poorly defined. Methods: In the present study, an integrated strategy combining transcriptomic profiling, Connectivity Map (CMap) analysis, and multi-level experimental validation was employed. Transcriptomic signatures derived from A549 cells treated with salidroside or tyrosol were queried against the CMap database. Molecular docking, surface plasmon resonance (SPR), and cellular thermal shift assays (CETSA) were performed to predict and validate binding interactions. Functional validation was performed in SH-SY5Y cells. The phosphorylation level of extracellular signal-regulated kinase (ERK), a downstream signaling event of dopamine D2 receptor (DRD2), was detected after salidroside and tyrosol treatment. DRD2 antagonist sulpiride pre-intervention and small interfering RNA (siRNA)-mediated DRD2 knockdown were conducted to verify the receptor dependence of the compounds’ effects. Results: CMap analysis revealed that the transcriptomic signatures of salidroside and tyrosol showed significant similarity to known DRD2 modulators. Molecular docking predicted potential binding interactions between the two compounds and DRD2, which was confirmed by SPR and CETSA to be direct physical binding. Functional studies showed that both compounds rapidly induced DRD2 downstream ERK phosphorylation in SH-SY5Y cells; this effect was abrogated by sulpiride or DRD2 knockdown, indicating DRD2-dependent signaling activation. Conclusions: These findings identify DRD2 as a direct molecular target of salidroside and tyrosol and provide mechanistic insight into their dopaminergic regulatory effects. This study highlights the utility of CMap-guided target discovery combined with rigorous experimental validation for elucidating the molecular mechanisms of natural products. Full article

Background/Objectives: Non-coding RNAs provide new chances of targeting multiple oncogenic pathways. Many long non-coding RNAs (lncRNAs) are being characterized as relevant in cancer initiation, progression, and recurrence. Mitochondrial D-loop 1 antisense lncRNA (MDL1AS) is a novel lncRNA that might be important in cancer development, so the aim of this project was to understand its function in differently differentiated cancer cells. Methods: The effects of MDL1AS downregulation on the cellular behavior of NTERA2 and SH-SY5Y cell lines were studied. Results: MDL1AS reduction inhibited oxidative phosphorylation in NTERA2 cells and induced neuritic differentiation in SH-SY5Y cells. This downregulation also produced a strong DNA damage response (DDR) and an increased apoptotic signature by RNAseq analysis, and decreased proliferation in both cell lines. It also decreased radiosensitivity in NTERA2 cells but not in SH-SY5Y. Conclusions: These results suggest that MDL1AS reduction can modulate radiosensitivity, metabolism, and differentiation in a cell type-specific manner. Furthermore, MDL1AS may constitute a predictive biomarker and a molecular target for new therapies. Full article

Drought stress severely restricts the growth of pear trees. As a widely used drought-tolerant rootstock, Pyrus betulifolia exhibits stable growth performance; however, the molecular mechanisms underlying its drought tolerance remain to be elucidated. In this study, we investigated the molecular responses of P. betulifolia leaves to osmotic stress induced by 20% PEG-4000 using time-series RNA-seq technology. A total of 3745 differentially expressed genes were identified, with transcriptional changes peaking at 6 h, indicating a critical phase of transcriptional reprogramming during drought response. Genes associated with osmotic adjustment (e.g., P5CS) and oxidative stress responses (e.g., SOD and POD) were significantly upregulated between 6 and 12 h. Weighted gene co-expression network analysis (WGCNA) identified three distinct temporal modules and screened out NF-Y, RVE1, COL9, COL6, C2C2 zinc finger proteins, and Pseudo ARR-B as putative key regulators, whose expression patterns were validated using qRT-PCR. Collectively, these results provide a comprehensive view of the temporal transcriptional dynamics of drought response in P. betulifolia and offer valuable candidate gene resources for further functional studies and drought tolerance breeding. Full article

Hepatitis E virus, a single-stranded positive-sense RNA virus, is the causative agent of acute viral hepatitis in humans and can lead to chronic infection in immunocompromised individuals. In this setting, strains containing host genome insertions within the polyproline region (PPR) of the pORF1 polyprotein were characterized and shown to display an increased replication rate across all systems. Using in silico modeling of pORF1 across 25 strains, combined with molecular dynamics (MD) simulations, we explored the structural variations caused by these insertions to investigate potential mechanisms underlying the increased replication rate compared to wild-type (WT) strains. Our results showed that the insertions neither induced structural organization within the PPR nor altered its intrinsically disordered nature. MD simulations further demonstrated that the overall stability of pORF1 remained unchanged in strains with insertions compared to WT strains. On the other hand, MD analyses revealed that strains with insertions exhibited an increased number of hydrogen bonds between the PPR and two other domains of pORF1: the MetY domain and the RNA-dependent RNA polymerase (RdRp). The stability of the MetY domain of the strains in the presence of host insertion events was higher than in the WT strains. These additional hydrogen bonds could position the MetY domain and the RdRp closer together, potentially promoting more efficient viral RNA synthesis. Validation of this hypothesis will require experimental structural studies, as well as computational modeling of the proposed dodecameric pORF1 structure. Full article

Background: Oral Submucous Fibrosis (OSMF) is a significant global oral health problem, particularly prevalent in India, with a high risk of progression to Oral Squamous Cell Carcinoma (OSCC). This study investigates the molecular mechanisms involved in the transformation of OSMF to OSCC using transcriptomic profiling. Methods: High-throughput RNA sequencing was performed on fresh de novo OSCC samples (n = 8) and OSMF derived OSCC using Illumina-compatible NEXTflex Rapid Directional RNA Sequencing. Normalization and differential gene expression analysis were conducted, and genes exhibiting an absolute log2 fold change of ≥2 with a co-variate-adjusted p-value ≤ 0.05 were identified as significant. Results: Upregulated genes were associated with cytokine and immune responses (ABRA, TTTY14, EIF1AY), cellular proliferation and apoptosis (LINC00314, RPS4Y1, SERPINA5, TRIM63, FABP7), and energy metabolism, indicating metabolic adaptations during malignant progression. Pathway analysis showed increased expression of TNNT1, TNNI1, MYL4, and ACTN3, implicating muscle development and embryonic pathways in OSMF transformation. Conversely, genes related to epithelial differentiation and keratinization (FLG, FLG2, HRNR, TCHH, KRT73), immune regulation and tumor suppression (HLA-G, UNC5D), and metabolic signaling were downregulated, reflecting loss of tissue integrity and immune control. Conclusions: OSMF-derived OSCC exhibits a distinct transcriptomic landscape compared with de novo OSCC, characterized by altered epithelial differentiation, immune modulation, and activation of developmental pathways. The observed gene dysregulation findings establish that OSCC developing in the background of OSMF is molecularly distinct from de novo OSCC, underscoring the biological impact of the pre-existing fibrotic milieu on tumor transcriptional architecture. Full article

Gamma-aminobutyric acid (GABA) has been implicated in gut–brain interactions and neuronal activation. We hypothesized that GABA could ameliorate memory decline. We investigated whether oral GABA administration ameliorated age-related cognitive decline in aged mice (C57BL/6J, male) and explored the role of circulating exosomes in mediating these effects. Aged mice that drank water containing 0.5% GABA exhibited significantly improved discrimination index scores compared with that of controls, indicating enhanced memory function. Their plasma-derived exosomes induced neurite outgrowth and mitochondrial activation and restored neuronal activity in SH-SY5Y cells. GABA enhanced the exosomal expression of several miRNAs linked to neuronal activation, longevity, and anti-senescence pathways. Plasma-derived exosomes also restored object recognition memory, reduced hippocampal neuroinflammation, and decreased senescent cell markers (p21 and γH2AX) in aged mice. Additionally, mitochondria- and neurite-related genes were upregulated, and pathways associated with oxidative phosphorylation and Alzheimer’s disease were enriched. Collectively, long-term GABA administration was found to improve cognitive function of aged mice through the secretion of functional exosomes. Full article