Search Results (27,766)

Cryopreservation is vital for conserving the elite germplasm of the hybrid poplar Populus davidiana × P. tremuloides, which is difficult to propagate conventionally. This study established optimized vitrification and encapsulation–vitrification protocols, achieving high regeneration rates of 85.91% and 79.70%, respectively, with confirmed genetic stability. The process induced oxidative stress, altering markers (MDA, H₂O₂) and antioxidant enzyme activities (SOD, POD, CAT). Integrated transcriptomic and metabolomic analysis of key steps—preculture/loading (DLA) and osmotic dehydration (DLB)—revealed extensive stress-responsive reprogramming. A central finding was the robust activation of the flavonoid biosynthesis pathway during DLB, marked by upregulation of key genes (PAL, CHS) and accumulation of flavonols (e.g., quercetin). This response was linked to hormone signaling and antioxidant systems, forming a coordinated defense network. Our multi-omics findings demonstrate that successful cryopreservation relies on an adaptive response where flavonoid biosynthesis plays a critical role in conferring oxidative stress tolerance, providing a theoretical basis for improving woody plant cryopreservation. Full article

Nodal marginal zone lymphoma (NMZL) is an indolent B-cell lymphoma that may pose diagnostic challenges due to the absence of distinct markers. In rare atypical cases, an overabundance of PD1+ T follicular helper (TFH) cells in tumor tissue may mimic peripheral T-cell lymphoma (PTCL) of TFH origin, further complicating the diagnosis. A 72-year-old woman with progressive lymphadenopathy had a cervical lymph node biopsy showing a disrupted architecture with monomorphic nodules of CD20+/MNDA+ B-cells and a prominent central population of proliferating CD4+/PD1+ T-cells, initially suggestive of a PTCL-TFH. The bone marrow contained aggregates of CD20+ B-cells intermixed with CD3+/CD4+/PD1+ T-cells. Next-generation sequencing (NGS) revealed clonal immunoglobulin heavy-chain rearrangements in the lymph node and bone marrow, with T-cell receptor genes displaying a polyclonal pattern. Targeted NGS showed no PTCL-related alterations but identified NMZL-associated mutations with different distributions across lymph node and bone marrow compartments. NOTCH2 mutations (c.6418C>T; p.Gln2140*) were found in both tissues, while the (c.69+2T>A; p.?) TNFRSF14 gene mutation was only detected in the lymph node. The KMT2D gene displayed a frameshift variant in the lymph node (c.4801_4802delinsT; p.Arg1601Leufs*3) and an in-frame deletion (c.11756_11758del; p.Gln3919del) in the bone marrow. Notably, NGS and digital droplet PCR confirmed a TP53 frameshift mutation (c.902del; p.Pro301Glnfs*44) with a fractional abundance of 0.31% in the lymph node and a (c.742C>T; p.Arg248Trp) mutation (0.309%) in the bone marrow. Results underscore the importance of NGS-based clonality to diagnose NMZL with prominent PD1+ T-cell hyperplasia, and prompt further investigation into tissue-specific mutational signatures in these unusual cases. Full article

This study aimed to evaluate the response mechanisms of zebrafish larvae to Norfloxacin nicotinate (NOR-N) exposure. Embryos were exposed to NOR-N from 4 h post-fertilization (hpf) until 96 hpf. The exposure concentrations included 0.002, 0.2, 1, and 5 mg/L (simulating both normal and exceptionally high environmentally relevant levels of NOR), as well as a high dose of 25 mg/L. Subsequent analyses focused on apoptosis, neurodevelopment, and DNA methylation in the resulting zebrafish larvae. The results showed that high-dose NOR-N (≥5 mg/L) induced obvious apoptotic cell death in zebrafish larvae, accompanied by increased activities of Cas3 and Cas9, up-regulated P53, Bax, Puma, Apaf1, Cas3 and Cas9 genes expression, and reduced Mdm2 levels and Bcl2/Bax ratio. Moreover, exposure to 5 and/or 25 mg/L NOR-N resulted in a significant up-regulation of neurodevelopment-related genes (Sox2, Sox3 and Sox19a), concomitantly with a marked decline in the transcription of DNA methylation genes, including Dnmt1, Dnmt3a1, Dnmt3b1, Dnmt3b2 and Dnmt3b4. Overall, our findings demonstrated that NOR-N exposure could induce apoptosis, developmental neurotoxicity and aberrant DNA methylation in zebrafish larvae. These findings provide insights to guide the safe application of NOR-N in aquaculture and support the assessment of its potential ecological risks to aquatic ecosystems. Full article

The development of China’s manganese (Mn) industries has caused severe water and soil pollution, threatening ecological and human health. Microbes are usually regarded as an important indicator of environmental pollution assessment. However, the current understanding of microbial community characteristics and their formation mechanisms in Mn production areas remains limited. In order to address this, soil properties and microbial structural characteristics across different functional zones in a typical Mn electrolysis plant in China’s “Manganese Triangle” were investigated via metagenomic sequencing. Results showed soil Mn levels significantly exceeded background values, indicating high environmental risk. Acidobacteria and Proteobacteria were dominant phyla. Microbial abundance was lowest in the adjacent natural reservoir, whereas diversity was highest in the sewage treatment plant. Correlation analyses identified Mn, nitrate nitrogen, ammonium nitrogen, pH, and moisture as key environmental drivers, with Mn being the primary one. Metagenomic analysis revealed abundant Mn resistance genes, enabling microbial survival under high Mn stress. This study demonstrated that excessive Mn exposure enriched Mn-resistant genes, thereby shaping unique microbial communities dominated by Mn-resistant bacteria. These findings clarified the structural characteristics and adaptive mechanisms of soil microbial communities in Mn-contaminated areas, providing a theoretical basis for ecological risk management and bioremediation. Full article

In this study, we focused on the screening and identification of reference genes for Paracarophenax alternatus Xu and Zhang. The laboratory population was used as the laboratory population, and samples were collected from mites at four different stages, including physogastry, viviparous, 5 d viviparous and phoresy. Then, the expression levels of seven candidate reference genes (α-tubulin, β-tubulin, RPS18, RPL13, GAPDH, EF1A, SDHA) were detected through qRT-PCR. Melting curves showed good gene specificity, and the amplification efficiency ranged from 90% to 102%. ΔCt analysis indicated that GAPDH was the most stable reference gene. The GeNorm software determined that the optimal number of reference genes was two, with GAPDH and RPS18 forming the most stable combination, and NormFinder identified RPS18 as the most stable reference gene. Although the BestKeeper software suggested that EF1A was the most stable, its p-value exceeded 0.05, rendering it unsuitable for use as a reference gene. Finally, through the RefFinder network tool, the most stable reference genes were identified as GAPDH and RPS18. Full article

The growth process of poplar faces severe environmental challenges. Notably, poplar canker, caused by Botryosphaeria dothidea, has significantly impaired poplar productivity and ecological functions. However, research on the molecular mechanisms underlying poplar resistance to this disease remains incomplete. This study systematically elucidated the molecular mechanisms of Populus davidiana × P. alba var. pyramidalis (Pdpap) in response to B. dothidea stress by integrating phenotypic, physiological, biochemical, and transcriptomic analyses. The results demonstrated that 5 d post-inoculation with B. dothidea, the stem wound sites darkened and developed lesions. Following pathogen infection, H₂O₂ content and SOD and POD activity initially increased then decreased, while MDA content overall showed a declining trend with prolonged infection time. KEGG enrichment analysis revealed that DEGs were significantly enriched in the MAPK signaling pathway, plant hormone signal transduction, and phenylpropanoid biosynthesis pathways. Gene modules significantly associated with physiological indices were screened using WGCNA. Within these modules, hub genes in the regulatory network were further identified, leading to the selection of P2C76. The genome-wide identification of PtrPP2Cs classified 124 members into 13 subgroups. Collectively, this study dissects the gene expression regulation and molecular defense mechanisms of poplar under B. dothidea infection, providing novel molecular insights for its molecular breeding. Full article

Background: Antibiotic tolerance in Staphylococcus aureus biofilms poses a major clinical challenge in prosthetic joint infections (PJIs). This study aimed to characterize the antibiotic tolerance of clinical S. aureus isolates recovered from cases of PJI under different stress conditions, including biofilm formation and antibiotic exposure. The correlation between tolerance level, the presence of specific tolerance-related genes, and clinical outcome was also evaluated. Methods: Twelve clinical S. aureus isolates were analyzed. To assess tolerance, the TDtest was used on exponentially growing bacteria, 48 h biofilms, and biofilms treated with levofloxacin and/or rifampin. Whole-genome sequencing was performed to identify tolerance-associated genes. Results: All isolates were phenotypically susceptible to rifampin and levofloxacin. Although all strains exhibited basal tolerance levels, biofilm formation led to heightened antibiotic tolerance, particularly those treated with rifampin as compared to levofloxacin: 29.5 vs. 17 (p = 0.01). Rifampin tolerance in biofilm-embedded bacteria was significantly higher in isolates from patients with treatment failure (p < 0.0001). Levofloxacin tolerance showed no significant association with clinical outcomes. There was no correlation between reduction in biofilm bacterial burden after treatment and tolerance levels. Genomic analysis identified associations between higher levofloxacin tolerance and the presence of sspA and leuS in biofilm isolates, and between rifampin tolerance and prs and pgm. Conclusions: In this study, clinical S. aureus strains isolated from prosthetic joint infections exhibited considerable inter-strain variability in antibiotic tolerance, particularly under biofilm conditions. Elevated rifampin tolerance in biofilm-embedded bacteria was associated with poor clinical outcomes, underscoring the need for tolerance assessment beyond standard susceptibility testing. Full article

Background/Objectives: The environmental dissemination of antimicrobial-resistant Enterobacteriaceae poses a remarkable threat to public health. This study investigates the environmental presence and dissemination of carbapenemase-producing Enterobacteriaceae (CPE) in 30 important water bodies selected according to their interconnection with and utilization by livestock and community people in central Thailand. Methods: Water samples were collected from 30 selected water bodies. Enterobacteriaceae were isolated and screened for CPE and multidrug resistance. Carbapenemase genes (bla_NDM-5, bla_NDM-1 and bla_IMI-1) were detected and their locations (plasmid and chromosome) determined. Plasmid types were further characterized, and conjugation experiments were performed to assess transferability among bacterial species. Results: From all selected samples, six isolates (20%) were identified as multidrug-resistant CPE including one Escherichia coli, one Klebsiella pneumoniae and four Enterobacter roggenkampii carrying bla_NDM-5, bla_NDM-1 and bla_IMI-1 genes, respectively. The bla_NDM-5 and bla_NDM-1 genes were located on phage-like pO111 type plasmid and IncC plasmid, while bla_IMI-1 was located on chromosomes. The plasmids also consisted of components that closely resembled those found in resistance plasmids obtained from clinical and environmental isolates worldwide. Additionally, through plasmid conjugation experiment, carbapenemase genes were transferable with a high rate among bacterial species. Conclusions: These findings indicated that water bodies are polluted and there is an urgent need for integrated strategies to monitor and mitigate the spread of antibiotic resistance across human, animal and environmental health domains in aquatic environments. Full article

DES encodes the muscle-specific intermediate filament protein desmin, which is highly relevant to the structural integrity of cardiomyocytes. Mutations in this gene cause different cardiomyopathies including dilated cardiomyopathy. Here, we functionally validate DES-p.L112Q using SW-13, H9c2 cells, and cardiomyocytes derived from induced pluripotent stem cells by confocal microscopy in combination with deconvolution analysis. These experiments reveal an aberrant cytoplasmic aggregation of mutant desmin. In conclusion, these functional analyses support the re-classification of DES-p.L112Q as a likely pathogenic variant leading to dilated cardiomyopathy. Full article

Background/Objectives: Immune checkpoint inhibitors (ICIs) show durable efficacy in tumors with deficient mismatch repair (dMMR) or high microsatellite instability (MSI-H), yet clinical responses remain heterogeneous. This study aimed to define immune subgroups within dMMR/MSI-H tumors and develop a reproducible transcriptomic signature predictive of ICI response. Methods: Four MSI-H-enriched cancer types (UCEC, COAD, READ, STAD) from The Cancer Genome Atlas were analyzed. Tumors were stratified by immune cell infiltration (MCP-counter immune composite score) and T-cell-inflamed gene expression profiles (GEP score). Integrating these two axes defined four immune subgroups. Differential expression, random forest feature selection, and pathway enrichment were performed to identify immune programs. A 20-gene immune signature representing the most immune-active subgroup was developed and validated across TCGA, GEO (GSE39582), and IMvigor210 cohorts. Results: Among the four subgroups, the most immune-active group showed strong activation of interferon signaling, antigen presentation, and T-cell-mediated pathways. The 20-gene signature—including CD74, STAT1, TAP1, and HLA-class genes—achieved high reproducibility (mean AUC = 0.95 ± 0.02; accuracy ≈ 89%). In the IMvigor210 cohort, this signature identified tumors with higher PD-L1 blockade response (55.6% vs. 32.8%, p = 0.034) and improved survival trends in the TMB-high subset. Conclusions: The proposed 20-gene signature quantitatively captures immune heterogeneity in dMMR/MSI-H tumors and serves as a practical, interpretable biomarker to identify true ICI responders and guide precision immunotherapy. Full article

Lupus nephritis (LN) can affect up to 60% of patients with systemic lupus erythematosus (SLE). The NLRP3 inflammasome has been implicated in the pathogenesis of LN. This study aimed to evaluate the role of the NLRP3 inflammasome as a predictor of response to immunosuppressive treatment in patients with active LN. A prospective cohort study was conducted with 20 adult patients with active LN, classes III, IV, and V, from January 2021 to September 2023. Patients were followed up at biopsy (T0) and 6 months (T6) and 12 months (T12) after treatment and classified according to the primary efficacy renal response (PERR) at 12 months. Gene expression of NLRP3, CARD8, CASP1, IL1B, and IL18 was evaluated by RT-qPCR in PBMCs. Immunohistochemistry (IHC) for NLRP3 was performed on kidney tissue. The concentration of cytokine IL-1β was measured using the BD™ Cytometric Bead Array (CBA). The mean age was 31.9 ± 8.3 years, with 19 females and 1 male. After 12 months, 65% of patients achieved PERR. The IHC intensity in inflammatory cells was higher in patients with no PERR (p = 0.0426). In the no-PERR group, the gene expression of IL1B showed a significant increase at T6 (FC = 2.22: p = 0.0037) and T12 (FC = 2.91; p = 0.0001) compared with T0. Relative expression of IL1B was higher in no-PERR patients at T12 compared to the PERR group (p = 0.0477). The no-PERR group also had higher serum IL-1β levels compared to the PERR group at 12 months (2.9 ± 0.5 vs. 2.5 ± 0.7, p = 0.0164). In conclusion, our study evidenced an increase in IL1B expression and IL-1β levels over the 12 months of treatment in no-PERR patients, suggesting a potential biomarker of disease activity. Furthermore, a strong NLRP3 IHC staining score was associated with a higher likelihood of no PERR, highlighting the potential of the NLRP3 inflammasome as a predictor of worse clinical outcomes. Full article

Common ragweed, Ambrosia artemisiifolia L., a noxious invasive plant, produces novel secondary metabolites. However, it attracts soybean aphid, Aphis glycines, a significant pest of soybean, to feed on it. Elucidating the molecular mechanisms of A. glycines adaptation to A. artemisiifolia may help identify target genes useful for pest management. High-throughput transcriptome sequencing identified 4250 differentially expressed genes (DEGs), with 2399 upregulated and 1851 downregulated. KEGG pathway enrichment analysis suggested that these DEGs were significantly involved in core detoxification-related pathways, including metabolism of xenobiotics by cytochrome P450, drug metabolism, ascorbate and aldarate metabolism, and pentose and glucuronate interconversions. Further analysis revealed significant upregulation of 17 UDP-glycosyltransferase (UGT) genes, with AgUGT342B2, AgUGT343B2, AgUGT344J2, AgUGT344L2, and AgUGT344N2 showing 6.34-, 6.22-, 2.14-, 3.98-, and 7.49-fold higher expression, respectively, than in A. glycines fed on soybean. Bioassays demonstrated that A. glycines reared on A. artemisiifolia exhibited significantly reduced sensitivity to three common insecticides, imidacloprid, thiamethoxam, and lambda-cyhalothrin, with LC₅₀ values increasing by 5.8-fold, 2.8-fold, and 3.6-foldhigher, respectively, than those reared on soybean. These findings indicate that feeding on A. artemisiifolia induces UGT gene family upregulation in A. glycines, conferring cross-resistance to multiple insecticide classes. This study reveals a molecular mechanism linking host adaptation to insecticide resistance, highlighting the ecological and evolutionary consequences of invasive plant-herbivore interactions. Full article

Pine wilt disease (PWD), caused by the pine wood nematode (PWN) Bursaphelenchus xylophilus, is a devastating pine disease that is characterized by rapid transmission, high lethality, and limited control options. In our previous study, the fucosyltransferase gene (fut) which encoded fucosyltransferase (FUT) was found to be a putative virulence determinant in PWN, which regulates pathogenicity of nematodes. To investigate the functional role of the fut gene in PWN, a comprehensive analysis was conducted to understand its molecular structure and biological activity. The full-length open reading frame (ORF) of fut was amplified using reverse transcription PCR (RT-PCR) and successfully ligated into the pET-28a expression vector. Heterologous expression of the recombinant FUT was achieved in Escherichia coli Rosetta (DE3) through induction with 1.0 mM isopropyl-β-D-thiogalactoside (IPTG), followed by purification via nickel-nitrilotriacetic acid (Ni-NTA) affinity chromatography. Biochemical characterization revealed that the recombinant FUT exhibited optimal enzymatic activity at ‌30 °C‌ and ‌pH 8.0‌, respectively. Furthermore, RNA interference (RNAi) validated by RT-qPCR was used to explore the biological functions of fut in PWN, and results indicated that downregulation of the fut gene could significantly reduce the vitality, reproduction, pathogenicity, development, and lifespan of PWN. Furthermore, gallic acid as an inhibitor of FUT displayed a strong inhibitory effect on recombinant FUT activity and nematicidal activity against PWNs in vitro and could alleviate the wilt symptom of pine seedlings inoculated with PWNs at a concentration of 100 μg/mL, indicating that it has the potential to be a novel nematicide. Collectively, these results establish fut as a critical virulence determinant in PWN and highlight its potential as a molecular target for controlling pine wilt disease. Full article

Background: Systemic lupus erythematosus is a multi-faceted auto-immune disease. Growing evidence points to gut permeability and microbiota as key players in the development of the disease. Cinnamomum cassia is gaining attention as a potential modifier of the gut and liver health. We aim in this study to explore the effect of cinnamon on key elements of the gut–liver axis in imiquimod-induced lupus. Methods: Female C57BL/6J mice were stratified into five experimental groups: sham, sham plus cinnamon, lupus, lupus with cinnamon treatment, and lupus with pre- and post-induction cinnamon treatment. Lupus was induced through application of 1.25 mg of 5% imiquimod cream to the right ear, three times per week over six weeks. Cinnamomum cassia was given orally at 200 mg/kg, five days weekly. High-Throughput Sequencing of Bacterial 16S rRNA Gene was used on fecal samples with subsequent bioinformatic analysis of microbiota. Western blot and antibody array were used to measure E. coli translocation, and hepatic inflammatory, oxidative, and apoptotic markers. Results: Cinnamon treatment mitigated the trend toward a lower Firmicutes/Bacteroidota ratio in the lupus mice. While not statistically significant, cinnamon also led to a decrease in Lachnospiraceae abundance. Interestingly, sham mice given cinnamon had more Lactobacillus and Limosilactobacillus. Furthermore, cinnamon effectively reversed the increase in E. coli protein in the liver and normalized the enhanced expression of TLR-7, p-NFκB/NFκB, SOD1 and SOD2 induced by lupus. Conclusions: Cinnamomum cassia modulates oxidative, inflammatory, and microbial elements of the gut–liver axis in lupus, offering a new perspective on lupus pathogenesis and potential nutritional interventions. Full article

Neuroinflammation is a common pathophysiological feature of many disorders affecting the central nervous system, including migraine—one of the most prevalent neurological conditions, which significantly impairs quality of life, particularly when it progresses to the chronic form. The aim of the present study was to analyze oxidative changes following a single administration of nitroglycerin (NTG), as well as to investigate alterations in the glial microenvironment and inflammatory processes induced by chronic NTG administration. Registration of biosensor signals (HyPer7 and SypHer3s) in vivo did not reveal changes in hydrogen peroxide levels or pH following single NTG administration in striatum and cortex. In contrast, analysis of chronic NTG administration indicates neuroinflammatory processes occurring in the thalamus and the dentate gyrus of the hippocampus, but not in the somatosensory cortex without disruption of the BBB and decreased degranulation of meningeal mast cells. We observed a decrease in the mRNA expression in the thalamic tissue of the neuroprotective transforming growth factor beta 1 gene and an increase in the expression of the pro-inflammatory interferon gamma. The regional specificity of neuroinflammation supports the suggestion that maladaptive changes in these structures could play a critical role in the transition from episodic to chronic migraine. Full article