Search Results (11,075)

Dravet syndrome (DS) is a severe, catastrophic childhood epilepsy predominantly caused by loss-of-function mutations in the SCN1A gene, which encodes the voltage-gated sodium channel Na_v1.1. In this study, we evaluated the therapeutic potential of 5-(Benzofuran-2-yl)-3-(2-chloro-4-fluorobenzyl)-1,3,4-oxadiazol-2(3H)-one (GM-90663), a novel small molecule designed to address the complex pathophysiology of DS. Using scn1lab knockout (KO) zebrafish larvae—a robust vertebrate model for DS—we demonstrated that GM-90663 significantly alleviates seizure-like behavioral movements and rescues deficit in cognitive-like functions. Whole-cell patch-clamp recordings in hippocampal slices revealed that GM-90663 modulates voltage-gated Na⁺ channel kinetics; specifically, it suppresses slow ramp-induced currents, thereby effectively attenuating neuronal hyperexcitability. Furthermore, neurochemical profiling indicated that GM-90663 treatment leads to a marked increase in endogenous serotonin (5-HT) levels in both wild-type and KO larvae. Molecular docking simulations and subsequent in vitro enzymatic assays confirmed that this elevation in serotonin is mediated through the potent inhibition of monoamine oxidase (MAO) activity. Collectively, our findings suggest that GM-90663 exerts its anti-seizure effects through a synergistic dual mechanism—stabilizing sodium channel conductance and elevating serotonergic activity—positioning it as a promising multi-target candidate for the treatment of DS. Full article

Liver cancer remains a significant global health burden, requiring the development of precise nucleic acid delivery systems. Lipid nanoparticles (LNPs) are leading candidates; however, their efficiency is governed by the pK_a of ionizable lipids, which dictates nanoparticle stability and endosomal escape. In this study, we employed a machine learning–driven quantitative structure–activity relationship framework to predict the pK_a of ionizable lipids derived from the DLin–KC2–DMA scaffold. Utilizing a dataset of 56 compounds, we compared Random Forest, Artificial Neural Network, and Extreme Gradient Boosting (XGB) models integrated with Permutation Importance (PI) for feature selection. The optimized PI–XGB model exhibited exceptional predictive accuracy (R² = 0.970, R²_CV = 0.901, RMSE_test = 0.115) and robust generalization confirmed via external validation (RMSE_ext. = 0.313). Mechanistic insights derived from SHapley Additive exPlanation analysis identified charge distribution, molecular topology, and polarity as critical determinants of lipid ionization. These results demonstrate the power of interpretable machine learning in elucidating molecular structure–property relationships, offering a robust computational strategy for the rational design of next–generation ionizable lipids to optimize LNP–mediated gene therapy for liver cancer. Full article

Colorectal cancer (CRC) is the third most prevalent cancer globally. TASK-1, encoded by the KCNK3 gene, is emerging as a putative target in cancer; it regulates resting membrane potential, cell proliferation, and apoptosis. A series of 27 novel xanthene derivatives, modified at position 9, were synthesized via azide coupling of 2-(9H-xanthen-9-yl)acetohydrazide with selected amines and amino acids, followed by hydrazine-mediated conversion to the corresponding hydrazides. The cytotoxic activity of selected compounds (5a–5g, 6a–6h, 7b, 7f–7h) was evaluated against the HCT-116 cell line in vitro. In addition, molecular docking and molecular dynamics simulations were performed to investigate binding interactions and assess the stability of the protein–ligand complexes. Several compounds (5f, 5g, 6c, 6d, 6f, 6g, 7b, 7f, and 7h) exhibited moderate cytotoxic activity against HCT-116 cells (IC₅₀: 66.97–99.62 µM), compared to cisplatin (IC₅₀: 18.25 µM). Compound 7h demonstrated pronounced antiproliferative effects, evidenced by DAPI staining showing chromatin condensation and apoptotic body formation, along with a marked reduction in cell count and coverage. Molecular docking indicated favorable binding within the TASK-1 potassium channel, and molecular dynamics simulations confirmed the stability of the protein–ligand complex, with consistent interactions, including a key hydrogen bond with Asn240. These findings support 7h as a promising lead candidate. These findings identify xanthene-based derivatives as promising lead compounds for further optimization as TASK-1-targeted therapeutic candidates in colorectal cancer Full article

This study aimed to elucidate the molecular mechanisms underlying phenotypic divergence between two Lentinula edodes strains, Le_L and Le_S, which exhibit distinct fruiting body morphologies. While phenotypic variation among mushroom strains has been widely observed, the relative contributions of transcriptional regulation and structural genomic variation to these differences remain poorly understood. Comparative transcriptome analysis identified 8541 differentially expressed genes (DEGs), revealing clear functional divergence between the two strains. Genes upregulated in Le_S were predominantly enriched in ribosomal components and translation-related processes, indicating enhanced protein synthesis activity. In contrast, Le_L-upregulated genes were associated with transporters, transcription factors, and diverse metabolic pathways, suggesting broader regulatory and physiological functions. Protein–protein interaction network analysis further highlighted distinct regulatory architectures, with ribosomal proteins forming highly interconnected hub gene modules in Le_S, whereas Le_L hub genes were functionally diverse and included multiple members of the Major Facilitator Superfamily (MFS). Ortholog analysis across 33 L. edodes strains demonstrated that most hub genes were conserved, indicating their roles as core genetic components. Despite widespread genome-wide variation, including 7931 SNPs and 1149 INDELs, sequence variation within hub genes was limited, and allele-specific expression analysis revealed no significant allelic imbalance. In contrast, presence–absence variation (PAV) analysis identified structural differences affecting MFS transporter genes, which were absent in Le_S but present and upregulated in Le_L. Collectively, these findings suggest that structural genomic variation, particularly involving transporter genes, may play a more prominent role than sequence-level variation in driving phenotypic divergence. This study provides new insights into the genetic basis of strain-specific traits in L. edodes and highlights the importance of integrating multi-level genomic analyses. Full article

Escherichia coli, a facultative anaerobic Gram-negative member of the Enterobacteriaceae, is an increasingly important opportunistic pathogen driven in part by rising resistance to clinically important antibiotics. Regulation of multidrug efflux systems by two-component signal transduction pathways, particularly the BaeSR system, plays a central role in this process. However, the functional residues governing signal transduction through the sensor kinase BaeS remain incompletely defined. In this study, we integrated domain prediction, homology-guided site-directed mutagenesis, in vitro protein purification, autophosphorylation assays, and reverse-transcription quantitative polymerase chain reaction (RT-qPCR)-based transcriptional analysis of selected BaeSR-regulated genes to delineate key residues required for BaeS function. Sequence analysis identified His250 as a candidate autophosphorylation site and Asn364 as a conserved residue within the catalytic domain. Biochemical characterization of purified wild-type BaeS and an H250A mutant demonstrated that His250 is indispensable for autophosphorylation. Consistently, RT-qPCR analysis showed that BaeS activation markedly induced the transcription of BaeSR-regulated efflux-associated genes, whereas genetic deletion of baeS or selective disruption of kinase activity by the N364A mutation abolished this response. Together, these findings establish His250 as a key residue for BaeS autophosphorylation and identify Asn364 as essential for inducible BaeSR signaling and activation of resistance-associated target genes, thereby establishing an experimental framework for elucidating BaeSR-mediated efflux regulation and informing future studies of resistance regulatory networks and potential intervention strategies centered on key signaling nodes. Full article

Background: Four genotypes of human bocaviruses (HBoVs) have been identified, with only HBoV1 being detected in respiratory specimens, and with HBoV2 being the predominant human bocavirus in fecal specimens, which implies different tissue tropisms for HBoV1 and HBoV2. It is vital to determine the factors that influence the tissue tropisms. Methods: The major capsid proteins VP3 of HBoV1 and HBoV2 were expressed in eukaryotic cells. Then co-immunoprecipitation (Co-IP) and liquid chromatography–tandem mass spectrometry (LC-MS/MS) (IP-MS) was employed, along with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, to screen host proteins interacting with VP3 of different genotypes. Subsequently, in vitro pull-down assays were conducted to verify the direct virus–host interaction proteins with VP3. Furthermore, molecular docking was performed to predict the interaction interfaces between viral and host proteins. Results: Through IP-MS and enrichment analyses, 50 host proteins that displayed ≥10-fold differential binding affinities between HBoV1 VP3 and HBoV2 VP3 were identified. Among these, seven were considered as high-confidence candidate interactors. Notably, SPLUNC1 and VAMP8 showed predominant expression in respiratory and intestinal tissues, respectively. Subsequent in vitro pull-down assays confirmed that SPLUNC1 specifically bound to HBoV1 VP3, whereas VAMP8 specifically interacted with HBoV2 VP3. Molecular docking analysis further revealed that the binding between SPLUNC1 with HBoV1 VP3, as well as VAMP8 with HBoV2 VP3, was stabilized by extensive hydrophobic interfaces along with specific hydrogen bonds. Conclusions: The specific interactions of host proteins SPLUNC1 with HBoV1 VP3 and VAMP8 with HBoV2 VP3, respectively, provided fundamental evidence that the distinct tissue tropisms of HBoVs may be governed by specific host factors. Full article

Ponatinib, a third-generation BCR::ABL1 inhibitor, has antileukemic activity but is associated with cardiovascular toxicity, for which transcriptome-level responses remain incompletely characterized. Here, we defined a ponatinib-associated transcriptomic signature and examined its mechanistic implications using two public RNA sequencing (RNA-Seq) datasets: GSE186341 (11 cancer cell lines treated with kinase inhibitors) and GSE217421 (induced pluripotent stem cell (iPSC)-derived cardiomyocytes treated with approved drugs). Principal component analysis (PCA) and k-means clustering were used to define expression-based subgroups of vehicle-treated (DMSO) controls. DESeq2, followed by fixed-effect meta-analysis, estimated subgroup-specific treatment effects and pooled effect estimates across subgroups. In GSE186341, we identified 2,639 meta-analytic differentially expressed genes (meta-DEGs). Among these, 81 genes were also differentially expressed in GSE217421 after ponatinib treatment, identifying an overlapping gene set across datasets. In contrast, imatinib showed no overlap with these 81 genes under the same cross-dataset analysis framework. Cardiotoxicity-relevant functions were represented by directionally consistent genes linked to cardiac repolarization-associated ion handling (KCNN3), insulin-responsive metabolic regulation (FOXO1, HK2), cyclic adenosine monophosphate (cAMP)-responsive stress signaling (RAPGEF3), and mitochondrial homeostasis and redox regulation (MCL1, GCH1). Collectively, these results define a ponatinib-associated transcriptomic signature and nominate cross-dataset transcript-level candidates for subsequent mechanistic and experimental validation in ponatinib-associated cardiotoxicity. Full article

Nuclear factor kappa B (NF-κB) signaling plays a central role in inflammation, immunity, cell survival, and cancer progression. Its constitutive activation is frequently observed in breast cancer, contributing to tumor growth, treatment resistance, and metastasis. MicroRNAs (miRNAs) are key post-transcriptional regulators of gene expression and may modulate NF-κB signaling in a subtype-specific or -independent manner. The aim of the study was to identify miRNAs that may potentially regulate the activity of genes associated with NF-κB signaling across five molecular subtypes of breast cancer in Polish women. Tumor and matched normal tissue samples were collected from 405 patients with five breast cancer subtypes: luminal A (n = 130), HER2-negative luminal B (n = 100), HER2-positive luminal B (n = 96), non-luminal HER2-positive (n = 36), and triple-negative breast cancer (TNBC, n = 43). Expression profile of selected NF-κB-related genes were evaluated using mRNA microarrays and RT-qPCR. Protein levels were assessed by ELISA. Candidate regulatory miRNAs were identified via miRNA microarrays and validated using the miRDB database. A consistent upregulation of MAP3K7, TAB2, TNFAIP3, CSNK2A1, BCL2L1, XIAP, CXCL2, and PLAU was observed across all subtypes, suggesting activation of canonical NF-κB signaling. Downregulation of specific miRNAs, miR-1297 and miR-30a (targeting MAP3K7), miR-134 (TAB2), miR-125b (TNFAIP3), and miR-4329 (XIAP), may contribute to this deregulation. For CSNK2A1, BCL2L1, CXCL2, and PLAU, no regulatory miRNAs meeting our criteria were identified. Our study reveals a subtype-independent activation of the canonical NF-κB signaling pathway in breast cancer, underpinned by consistent upregulation of key components (at both the transcript and protein levels. Dysregulation of specific miRNAs likely contributes to this altered gene expression. These findings suggest the presence of a common NF-κB-driven oncogenic program across molecular subtypes, with potential implications for developing miRNA-based therapeutic strategies targeting inflammation, survival signaling, and treatment resistance in breast cancer. Full article

The Kazakh horse represents a significant genetic resource within China’s equine population, characterized by notable resilience and an ability to thrive on coarse forage. Nevertheless, a decline in its numbers has been observed recently, making the improvement of its reproductive performance crucial for the preservation of this breed and the advancement of the related industry. In this study, testicular tissues from 1-year-old (pre-pubertal) and 2-year-old (post-pubertal) Kazakh horses were analyzed. miRNA sequencing was conducted on tissues from these age groups, followed by bioinformatics analyses to elucidate the functions of differentially expressed miRNAs (DEmiRNAs). The reliability of the sequencing data was subsequently verified using RT-qPCR. Analysis revealed 165 differentially expressed miRNAs (DEmiRNAs) in the testicular tissues between the two age groups. Of these, 118 DEmiRNAs (e.g., eca-miR-206 and eca-miR-2483) were significantly up-regulated (p < 0.05), and 47 DEmiRNAs (e.g., eca-miR-196a and eca-miR-211) were significantly down-regulated (p < 0.05). These DEmiRNAs were mainly implicated in biological processes including lipid metabolism and signal transduction. Their predicted target genes are potentially involved in key reproductive processes, notably testicular development and spermatogenesis. This study identifies candidate miRNAs and potential regulatory pathways associated with sexual maturation in Kazakh horses, providing a preliminary molecular basis for future functional validation and improvement of equine reproductive performance. Full article

Background/Objectives: Tuberculosis (TB), caused by Mycobacterium tuberculosis (MTB), remains a major global health problem. Drug resistance and the limitations of sputum-based diagnostic methods highlight the need for additional host-response biomarkers. Protein tyrosine phosphatase receptor type O (PTPRO) has been implicated in inflammatory signaling and macrophage immune regulation, but its relationship with TB-related host transcriptional responses remains unclear. This study aimed to identify and preliminarily evaluate a PTPRO-related blood transcriptional signature with potential relevance to TB discrimination and treatment-response assessment. Methods: Genes correlated with PTPRO expression were first screened using TCGA-LUSC as a large human transcriptomic discovery resource. The resulting candidate genes were then filtered in TB-related whole-blood datasets by intersecting genes upregulated in TB compared with healthy controls, pneumonia, and lung cancer. This strategy yielded a five-gene PTPRO-related signature, termed PO5. The signature was evaluated in independent GEO cohorts and further explored by RT-qPCR in H37Ra-infected THP-1-derived macrophages and in a small clinical blood cohort. A PO5-derived TB risk score was calculated for each sample, and receiver operating characteristic analysis was used to assess discriminatory performance. Changes in TB risk scores during anti-TB treatment were also examined. Results: PTPRO expression was increased in TB whole-blood transcriptomic data and in H37Ra-infected macrophages. In public datasets, PO5 showed potential for distinguishing TB from healthy controls, latent TB, pneumonia, and lung cancer. PO5-derived TB risk scores also decreased after anti-TB treatment. In the exploratory clinical cohort, several PO5 genes showed expression changes in the same general direction as those observed in the public datasets, although the small sample size limited the strength of this evidence. Conclusions: PO5 represents a preliminary PTPRO-related blood transcriptional signature with potential relevance to TB discrimination and treatment-response assessment. These findings remain exploratory and require validation in larger prospective multicenter cohorts, together with further mechanistic studies. Full article

Seasonal estrus limits sheep farming efficiency, making enhanced reproductive capacity and year-round estrus crucial for efficient breeding. GRM1 could modulates neuronal signals and stimulates neuron excitability. Our preliminary transcriptomic analysis of hypothalamic tissues from Kazakh ewes during nonbreeding season anestrus and nonbreeding season nutritionally induced estrus strongly suggested that GRM1 is a candidate gene that regulates estrus. The role of GRM1 in sheep estrus remains to be investigated. GRM1 expression was measured in hypothalamic tissues of Kazakh sheep during nonbreeding anestrus and nutritionally induced estrus via qPCR and immunohistochemistry. GRM1’s regulatory role in GnRH secretion and gene expression was studied in hypothalamic neurons via overexpression and RNAi. GnRH secretion changes were quantified by ELISA. GRM1 mRNA expression was significantly increased in the hypothalamus of estrous Kazakh sheep, as confirmed by immunohistochemical staining. The results of hypothalamic neuron experiments revealed that the expression of GRM1 was significantly upregulated after overexpression, which affected the expression of GnAQ, ITPR1, PLCB1 and PRKCB and ultimately promoted the secretion of GnRH. The expression of GnRH decreased after the interference in GRM1 expression. GRM1 modulates the secretion of GnRH in the hypothalamic nerve cells of Kazakh sheep through the glutamatergic synapse–calcium signaling pathway. Full article

Background/Objectives: Necrotic enteritis (NE), induced by Clostridium perfringens, is responsible for significant economic losses in the poultry industry worldwide. The growing restrictions on antibiotic use have driven the search for alternative strategies for disease control. The purpose of this study is to isolate and characterize lytic phages targeting multidrug-resistant C. perfringens type G recovered from chickens with NE. Methods: C. perfringens was isolated from chickens with NE using a culture method with selective TSC agar. Bacterial identification was carried out using biochemical tests and PCR. C. perfringens isolates were toxinotyped by PCR. Antibiotic susceptibility test was performed using the agar dilution method. Bacteriophages were isolated from chicken intestine samples collected from wet markets using the double-layer agar technique. Phage isolates were characterized by host range, one-step growth, stability, and whole genome sequencing. The efficacy of phage CPP8 in controlling multidrug-resistant C. perfringens type G was evaluated in GAM broth. Results: In this study, 16 C. perfringens strains were isolated from 100 chickens suspected of NE. Among these isolates, 10 (62.5%) belonged to type G, while the remaining 6 (37.5%) were type A. A total of 11 phages capable of lysing C. perfringens type G were isolated from the chicken intestine. Among them, phage CPP8 has the widest host range, short latent period, large burst size, and high stability. Moreover, the genome of CPP8 lacked genes related to antibiotic resistance, toxins, virulence factors, or lysogeny. Treatment with CPP8 resulted in a significant reduction in viable counts of C. perfringens at 37 °C. Conclusions: Our findings highlight phage CPP8 as a promising candidate for bio-control of multidrug-resistant C. perfringens type G. Full article

Obstetrical diseases are complications associated with pregnancy or childbirth that can cause maternal sequelae and fetal complications. Among them, preeclampsia (PE) and preterm labor (PTL) are major causes of premature birth and are associated with an increased risk of cerebral palsy, developmental delay, and hearing impairment in infants. However, reliable diagnostic markers and therapeutic strategies for obstetrical diseases remain limited. The aim of this study was to investigate genes associated with obstetrical diseases and to evaluate the correlation between phosphocholine cytidylyltransferase 1 beta (PCYT1B) and miRNAs targeting PCYT1B for diagnostic analysis in PE and PTL. Using miRNA array analysis and luciferase assays, we identified PCYT1B, a key enzyme involved in phosphocholine metabolism in reproductive tissues, together with several candidate miRNAs targeting PCYT1B, including miR-3065-3p, miR-4660, miR-6752-5p, miR-6842-5p and miR-7110-5p. qRT-PCR analysis revealed a significant correlation between PCYT1B and these miRNAs in placental tissues from patients with PE and PTL (p < 0.05). Immunofluorescence staining further demonstrated that PCYT1B was localized in the syncytiotrophoblast layer of placental tissues, and its protein expression was consistent with mRNA expression levels. To investigate the functional role of these miRNAs, trophoblast cells were treated with miRNA mimics and inhibitors. These treatments significantly altered trophoblast invasion capacity and regulated the expression of migration-related genes, including RhoA, Rac1 and ROCK. Collectively, our findings suggest that miRNAs targeting PCYT1B may regulate trophoblast function and may play a key role in placental development and obstetrical diseases. These results indicate that PCYT1B and its regulatory miRNAs could serve as potential biomarkers for PE and PTL and may provide insights into the development of miRNA-based diagnostic strategies. Full article

Soil contamination by complex pesticide mixtures poses a systemic threat to ecosystem health, yet the mechanisms of microbial community assembly under the coexistence of legacy and modern pollutants remain insufficiently understood. This study evaluated the influence of legacy organochlorine pesticides (OCPs) versus current-use agrochemicals on the structure and inferred functional potential of soil bacterial communities in the Almaty Region, Kazakhstan, using high-throughput 16S rRNA gene sequencing and GC–MS/MS analysis of 217 compounds. Results revealed a clear contrast between contamination regimes: modern organophosphate insecticides and herbicides, such as simazine (up to 32.3 mg kg⁻¹ at the Amangeldy site), were associated with lower alpha diversity (Shannon ≈ 3.03) and enrichment of copiotrophic taxa such as Pseudomonas and Sphingobium. In contrast, persistent OCP residues, such as p,p′-DDE (up to 1.43 mg kg⁻¹ at the Kyzylkairat site), were associated with higher diversity (Shannon ≈ 5.46) and enrichment of more stress-tolerant oligotrophic lineages, including Acidobacteria and Vicinamibacteraceae. Procrustes analysis supported significant concordance between pesticide profiles and taxonomic structure (M² = 0.286, p < 0.001), indicating that pesticide residue composition was strongly associated with bacterial community structure across the studied soils. The observed shift in community balance, particularly the relative increase in Pseudomonas versus Acidobacteria, is proposed as a candidate compositional indicator of ecosystem instability in semi-arid agricultural soils and may inform future remediation-oriented studies. Full article

Soybean rust caused by the fungus Phakopsora pachyrhizi threatens global soybean production, causing yield losses of up to 80%. Race-specific Rpp genes provide short-term resistance due to pathogen variability, whereas partial resistance (PR) offers durable, broad-spectrum protection, though its genetic basis remains unclear. This study aimed to identify genomic regions and candidate genes underlying PR using the Fixed and Random Model Circulating Probability Unification (FarmCPU) genome-wide association study (GWAS) and machine learning (ML) methods, Random Forest (RF) and Support Vector Regression (SVR). A panel of 312 soybean accessions was evaluated under natural infection across six Ugandan environments. Rust index (RI), derived from rust severity and sporulation level, was used to estimate heritability (H²) and rank genotypes through Best Linear Unbiased Predictions (BLUPs), while Best Linear Unbiased Estimators (BLUEs) supported GWAS input. After quality control, 8272 SNPs were analyzed within a ±60 kb linkage disequilibrium (LD) window. Multi-environmental Analysis (MEA) of RI showed significant genetic effects (p < 0.01); H² = 0.57–0.68. Sixty-one loci were detected: six by FarmCPU, 15 by RF, and 41 by SVR. Key genes included Glyma.01G128100 (a WRKY transcription factor) and Glyma. 13G228000, receptor-like kinase) and Glyma.20G173100 (WD40-domain regulator). Integrating ML with GWAS improved locus detection, confirming the polygenic nature of PR and supporting the use of genomic selection and locus pyramiding for durable rust resistance. Full article