Search Results (8,032)

Lonicera japonica is a widely utilized medicinal and ornamental plant. Its secondary metabolism is highly sensitive to cold stress. Previous studies have demonstrated how L. japonica accumulates anthocyanin in response to cold stress, with calcium ions playing a potential role in the regulation. To further clarify the regulatory function of calcium ions regarding pigment formation under cold stress, transcriptomic analysis was conducted on exogenous calcium ions and calcium chelator EGTA-treated L. japonica under cold stress. The CaCl₂ treatment markedly delayed changes in the pigmentation, and the plant maintained a higher chlorophyll content, whereas EGTA treatment enhanced anthocyanin accumulation and induced earlier and more intense leaf coloration. A total of 17,296 differentially expressed genes were co-expressed during cold stress, and calcium-responsive genes were predominantly enriched in phenylpropanoid biosynthesis, hormone signaling, and stress response pathways. Notably, key transcription factors such as MYBS3 and BRH1 were identified with expression patterns that closely correlated with pigment changes and stress adaptation. These results indicate the deep involvement of molecular mechanisms of calcium signaling in modulating pigment accumulation in response to cold stress, providing a theoretical foundation for improving both the ornamental and medicinal value of L. japonica under adverse environmental conditions. Full article

The heat shock protein 70 (Hsp70) family mediates responses to environmental stress in insects. The wheat midge Sitodiplosis mosellana, a worldwide pest, avoids summer and winter temperature extremes by diapause of the third-instar larvae in the soil. To explore the functions of Hsp70s in this process, we characterized two cytoplasmic Hsp70 genes (SmHsp70A1-1 and SmHsp70A1-2) from this insect. Both SmHsp70s contained three signature motifs of the family and lacked introns. Developmental expression profiling revealed maximal SmHsp70A1-1 expression during early larval stages, while the expression of SmHsp70A1-2 was highest in the pupal stages. The expression of SmHsp70A1-1 was significantly upregulated during diapause, particularly during summer and winter, whereas SmHsp70A1-2 showed marked downregulation and dose-dependent induction by 20-hydroxyecdysone (20E). Furthermore, both genes exhibited similar expression patterns in over-summering and over-wintering larvae under thermal stress, with maximal expression at 40 °C and −10 °C, respectively, but were not significantly induced at prolonged extreme temperatures (50 °C or −15 °C). Knockdown of the two SmHsp70 genes ‌by RNA interference (RNAi) significantly increased‌ the susceptibility of the larvae to cold stress. These results suggest the important role of both SmHsp70 genes in diapause-associated stress tolerance and provide crucial insights into the mechanisms underlying thermal adaptation in S. mosellana. Full article

Adolescent idiopathic scoliosis (AIS) is a multifactorial disease with environmental and genetic components. AIS clinical management is complicated by the lack of reliable predictive markers of progression. Recent studies have highlighted a potential role for epigenetic mechanisms in disease progression. However, most findings derive from peripheral blood analyses, with little data available on musculoskeletal tissues directly affected by AIS. Given the tissue-specific nature of epigenetic regulation, validating blood-based biomarkers in disease-relevant tissues is essential. We performed a comparative multi-gene RT-qPCR analysis, arranged in a custom array format, to assess the local expression of candidate epigenetically regulated genes associated with AIS progression across bone, paravertebral muscle, spinal ligament, and peripheral blood, all collected from the same patients. Tissue- and gene-specific expression patterns were observed, supporting the presence of local regulatory mechanisms. Peripheral blood expression of HAS2, PCDH10, H19, ADIPOQ, ESR1, GREM1, SOX9, FRZB, LRP6, and FBN1 resembled bone expression, while PITX1, CRTC1, APC, CTNNB1, FZD1, and AXIN1 reflected muscle and ligament; WNT1 reflected only muscle. In contrast, GREM1 and SOX9 were expressed only in muscle and ligament and FGF4 and NPY only in muscle, suggesting limited systemic biomarker potential. Compared to non-AIS tissues, AIS samples showed downregulation of PCDH10 and FBN2 in bone and CRTC1, FRZB, LRP6, and MSTN in muscle. WNT1 and WNT10 were upregulated in muscle and FBN1 in ligament. In conclusion, the results highlight differential gene expression across AIS tissues, supporting tissue-specific regulation in some of the genes analyzed. Only a subset of markers exhibited blood expression patterns that reflected those in specific tissues, suggesting that certain blood biomarkers may act as surrogates for distinct tissue compartments. These results lay the groundwork for future DNA-based studies to confirm the epigenetic nature of this regulation and to identify reliable biomarkers for AIS progression. Full article

Background: Borderline Personality Disorder (BPD) is a complex psychiatric condition with multifactorial origins, with a high proportion of patients reporting early trauma. Stressors such as adverse childhood experiences (ACEs) can shape the epigenetic landscape including DNA methylation (DNAm) and act on gene expression. DNAm is increasingly being investigated as a molecular link between environmental exposures such as ACE and psychiatric outcomes. Differential DNAm of the gene PR domain zinc finger protein 8 (PRDM8), a histone methyltransferase, has recently been reported to be sensitive to early life trauma. Its role in BPD, especially in the context of ACE, remains to be elucidated. Methods: This study investigated DNAm patterns of PRDM8 in peripheral blood and saliva obtained from BPD patients undergoing Dialectic Behavioral Therapy (DBT) compared to healthy control (HC) participants. Associations with ACE and BPD symptom severity were assessed, and therapy-related changes in DNAm were examined. Results: At baseline, BPD patients demonstrated significant hypomethylation of PRDM8 in blood relative to the HC group. Following DBT, a nominally significant increase in DNAm was observed, aligning with inversely correlated symptom severity. No significant differences in saliva were detected. ACE was not associated with PRDM8 DNAm. Conclusions: Our findings suggest that PRDM8 DNAm might be associated with BPD and therapeutic intervention but not with ACE. Together with prior research, the results underscore the importance of future investigation of gene–environment interactions and the functional significance of PRDM8 regulation in the pathophysiology of BPD. Full article

Microplastics (MPs) are a growing environmental concern due to their ability to adsorb hazardous chemicals, such as estrogens, and be ingested by marine organisms. This study focuses on low-density polyethylene (LDPE), a polymer widely used in Kuwait, to assess its role as a carrier of endocrine-disrupting chemicals (EDCs), specifically estrogens. Biological effects were evaluated using biomarkers such as cytochrome P450 1A (CYP1A) and vitellogenin (Vtg) gene expression. Virgin LDPE MPs were exposed to influent and effluent from a wastewater treatment plant (WWTP) for four weeks to facilitate estrogen absorption. The MPs were then incorporated into fish feed pellets for dietary exposure experiments. Fish were divided into three treatment groups—exposed to either virgin MPs, WWTP-influent MPs, or WWTP-effluent MPs—and monitored over four weeks. The results showed that WWTP-exposed MPs carried detectable levels of estrogen, leading to physiological effects on yellowfin bream. Fish in the control group, which received MP-enriched diets without estrogen, experienced significant weight loss due to nutrient deprivation. In contrast, weight patterns in the treatment groups were influenced by estrogen exposure. The condition factor (CF) decreased across groups during the experiment but remained within acceptable health ranges. A significant reduction in the hepatosomatic index (HSI) was observed in the effluent-exposed group, likely due to lower estrogen levels reducing physiological stress. The findings confirm that LDPE MPs can act as carriers for estrogens, impairing fish growth and metabolism while disrupting biological processes such as cytochrome oxidase function. These results highlight the potential risks of MPs in marine ecosystems and underscore the need for further research to understand their long-term effects. Full article

Tachypleus tridentatus is a rare and endangered marine organism with considerable scientific and economic value. It has existed on Earth for about 450 million years and its continuation to the present day may be related to its unique immune system. Owing to its drastic population decline, diverse technical approaches are required for its recovery, and the development and growth of its larvae are crucial in this context. Vibrio parahaemolyticus is a common marine pathogen that impairs the healthy growth of marine organisms. The peak period of V. parahaemolyticus occurrence is from May to November, which significantly overlaps with the T. tridentatus spawning period from April to September. However, the response mechanisms of juvenile T. tridentatus to V. parahaemolyticus stress remain unknown. Hence, in this study, we aimed to investigate these response mechanisms through acute toxicity assays, histological observations, and transcriptome analysis. The results showed that the 48 h LD₅₀ of V. parahaemolyticus-infected T. tridentatus larvae was determined to be 1.81 × 10⁸ CFU/g. Histological analysis showed that V. parahaemolyticus damaged the larval tissue. In addition, RNA sequencing (RNA-Seq) identified 2347 differentially expressed genes (DEGs; 1440 upregulated and 907 downregulated genes) and 243 enriched signaling pathways. Functional enrichment analysis revealed the enrichment of immunoregulatory pathways, including the Wnt signaling pathway, ECM-receptor interaction, aminoacyl-tRNA biosynthesis, and Toll and Imd signaling pathways. Seventeen DEGs were randomly selected for real-time RT-PCR (RT-qPCR) validation, and their expression patterns were consistent with those obtained via RNA-Seq. The study of the response mechanism of T. tridentatus larvae to V. parahaemolyticus stress provides scientific references for the protection of T. tridentatus habitats and the recovery of its population size. Full article

Leaf senescence is the final stage of plant leaf development, closely related to the yield and quality of cereal crops. However, the molecular regulatory mechanism of rice (Oryza sativa L.) leaf senescence is not yet very clear. This study conducted weighted gene co-expression network analysis (WGCNA) using two independent senescence-related transcriptome datasets of rice. Modules positively/negatively correlated with leaf senescence were obtained for each dataset. The additional intersection analysis screened out 180 and 248 common genes highly and positively/negatively correlated with leaf senescence. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses showed that these identified common genes were mainly enriched in senescence-related biological processes and pathways, such as reactive oxygen metabolism, hormone pathway, cell death regulation, stimulus–response, amino acid metabolism, photosynthetic metabolism, etc. Transcription factors and studied genes were identified from these common genes, finding that transcription regulation, hormone regulation, reactive oxygen species metabolism, and photosynthesis pathways play an essential role in rice leaf senescence. Protein–protein interaction (PPI) network analysis identified 28 key genes probably involved in leaf senescence. Hub network analysis identified 68 hub genes probably participating in leaf senescence. Twelve genes from the PPI network and the hub gene network were selected for RT-qPCR validation of their expression patterns during leaf senescence. The functions of the senescence-correlated genes identified in this study are discussed in detail. These results provide valuable insights into the regulatory mechanisms of leaf senescence in rice and lay a foundation for functional research on candidate senescence genes. Full article

Background: Fatty acyl–ACP thioesterase (FAT) genes regulate fatty acid composition and content, yet the FAT family in maize has not been systematically characterized. Methods: Ten ZmFAT genes were identified from the maize genome and analyzed for gene structure, protein properties, phylogeny, collinearity, cis-acting elements, and predicted interactions. Transcriptome and qRT–PCR data were used to assess expression patterns during seed development. Results: The ten ZmFAT genes were grouped into two subfamilies (three ZmFATA and seven ZmFATB genes). Two pairs of collinear genes were detected within maize and one pair between maize and rice. Promoter analysis revealed light- and development-responsive elements. Two genes were functionally annotated in fatty acid biosynthesis, while five proteins exhibited interactions and 14 miRNAs were predicted to regulate ZmFAT genes. Expression analysis showed that ZmFATA1/2 and ZmFATB4/6/7 maintained high expression in both upper and lower seed parts, and qRT–PCR confirmed their gradual upregulation during seed development. Conclusion: This study provides the first comprehensive characterization of the maize ZmFAT family, offering insights into fatty acid metabolism and valuable genetic resources for improving maize oil composition. Full article

Cattle marketed through auction market systems and/or that remain unvaccinated are considered higher risk for BRD, but impacts on host response remain unclear. We sought to identify specific genomic patterns of beef calves vaccinated against BRD viruses or not and commercially marketed or directly transported in a split-plot randomized controlled trial. Forty-one calves who remained clinically healthy from birth through backgrounding were selected (randomly stratified) from a larger cohort of cattle (n = 81). Treatment groups included VAX/DIRECT (n = 12), VAX/AUCTION (n = 11), NOVAX/DIRECT (n = 7), and NOVAX/AUCTION (n = 11). Blood RNA was acquired across five time points, sequenced, and bioinformatically processed via HISAT2 and StringTie2. Significant transcriptional changes (FDR < 0.05) were observed at backgrounding entry (T5) in NOVAX/AUCTION cattle exhibiting 2809 uniquely differentially expressed genes and relative activation of immune, inflammatory, and metabolic pathways with upregulation of interferon-stimulated genes (e.g., IFIT3, MX2, and TRIM25) and downregulation of specialized proresolving mediator (SPM) enzymes (ALOX5 and ALOX15). VAX/AUCTION cattle exhibited modulated immune activation and preserved expression of SPM-associated genes when compared to NOVAX/AUCTION cattle. Both marketing route and vaccination shape the molecular immune landscape during high-stress transitions, with preweaning vaccination potentially modulating this response. This study provides mechanistic insight into how management practices influence immunological resilience and highlights the value of integrating transcriptomics into BRD risk mitigation. Full article

Breast cancer (BC) remains a leading cause of cancer-related mortality in women. Extracellular matrix (ECM) remodeling is a critical modulator of tumor invasion and metastasis. Three-dimensional (3D) cell culture models have been proposed as advanced systems better mimicking the tumor microenvironment (TME), potentially offering enhanced insights into underlying mechanisms compared to conventional two-dimensional (2D) cultures. This study highlights how BC cells develop metastatic potential and tumor progression independently from ECM contact using advanced 3D spheroid culture models compared to traditional 2D cultures in triple-negative breast cancer (TNBC) cell lines. Spheroids were formed using ultra-low adhesion plates, and their morphological and functional properties were assessed via phase-contrast and scanning electron microscopy (SEM), along with functional assays. Both cell lines formed compact spheroids exhibiting mesenchymal-to-epithelial transition (MET) characteristics. Functional assays showed enhanced cell migration and dissemination of spheroid-derived cancer cells. Gene expression profiling revealed increased expression of ECM remodeling enzymes, cell surface receptors, and adhesion molecules in 3D cultures compared to 2D. MicroRNA analysis highlighted distinct regulatory patterns specifically associated with metastasis and epithelial-to-mesenchymal transition (EMT). These findings demonstrate that 3D spheroid models effectively recapitulate the complexity of TNBC, providing valuable insights into ECM dynamics, epigenetic regulation, and metastatic behavior and potentially guiding improved therapeutic strategies. Full article

(1) Background: This study highlights the diversity and distribution of non-reducing polyketide synthases (NR-PKSs) in Ascomycota and their role in producing bioactive aromatic polyketides. (2) Methods: A reference dataset of non-NR-PKSs was compiled from published literature and cross-examined using NaPDoS2 and Kyoto Encyclopedia of Genes and Genomes Ortholog (KEGG KO) databases. Signature domains were validated through Pfam and CDD, while phylogenetic classification was conducted by comparing the dataset with the NaPDoS2 reference tree. Cluster support was derived from KEGG KO and homology-based modeling. Additionally, NR-PKS clade distribution across KEGG genomes was analyzed, and co-expression patterns were examined using STRING. (3) Results: This study identified nine distinct clades of NR-PKSs, six of which are supported by unique KEGG Orthology (KO) numbers. These clades are as follows: clade 1: polyketide synthase A (PksA, K15316); clade 2: fusarubinsynthase 1 (Fsr1); clade 3: white A (WA, K15321); clade 4: polyketide synthase citrinin (PksCT); clade 5: zearalenone synthase 1 (Zea1, K15417); clade 6: orsellinic acid synthase A (OrsA, K15416); clade 7: aurofusarin polyketide synthase A (AptA, K15317); clade 8: monodictyphenone polyketide synthase G (MdpG, K15415); and clade 9: bikaverin polyketide synthase (Bik1). The present investigation also reports incongruency in the distribution of different NR-PKSs and fungi phylogeny within the phylum Ascomycota. (4) Conclusions: The distribution of NR-PKSs in Ascomycota defies phylogenetic boundaries, reflecting the impact of horizontal gene transfer, gene loss, and ecological adaptation. Full article

NIN-like proteins (NLPs) are conserved, plant-specific transcription factors that play crucial roles in the nitrate signaling response, plant growth and development, and abiotic stress responses. However, their functions have not been explored in sweet potato. In this study, we identified 7 NLPs in cultivated hexaploid sweet potato (Ipomoea batatas, 2n = 6x = 90), 9 NLPs in the diploid relative Ipomoea trifida (2n = 2x = 30), and 12 NLPs in Ipomoea triloba (2n = 2x = 30) via genome structure analysis and phylogenetic characterization, respectively. The protein physiological properties, chromosome localization, phylogenetic relationships, syntenic analysis maps, gene structure, promoter cis-acting regulatory elements, and protein interaction networks were systematically investigated to explore the possible roles of homologous NLPs in the nitrate signaling response, growth and development, and abiotic stress responses in sweet potato. The expression profiles of the identified NLPs in different tissues and treatments revealed tissue specificity and various expression patterns in sweet potato and its two diploid relatives, supporting differences in the evolutionary trajectories of the hexaploid sweet potato. These results are a critical first step in understanding the functions of sweet potato NLPs and offer more candidate genes for improving nitrogen use efficiency and increasing yield in cultivated sweet potato. Full article

BASIC PENTACYSTEINE (BPC) is a small family of plant-specific transcription factors that play crucial roles in plant growth, development processes, and response to abiotic stresses. However, the specific roles of Nicotiana tabacum BPCs (NtBPCs) remain ambiguous. Here, we identified 12 NtBPC genes, 5 of which were mapped to four chromosomes. Phylogenetic analysis classified these genes into three subfamilies. Collinearity was observed among BPC genes of N. tabacum, Capsicum annuum, and Solanum lycopersicum. Moreover, polypeptides encoded by NtBPC genes within the same subfamily shared similar conserved motifs and protein domains. Subcellular localization showed that 10 NtBPC proteins are localized in the nucleus. Promoter analysis revealed the presence of abiotic stress response elements in the promoters of NtBPCs. Further tissue-specific expression analysis using RT-qPCR revealed that NtBPCs are highly expressed in stems and leaves. After drought, NaCl, and cold treatments, NtBPCs exhibited varied expression patterns. These findings provide valuable insights into the evolutionary dynamics of the NtBPC gene family and lay the groundwork for subsequent investigations into the functions of NtBPC genes. Full article

Q-type C2H2 zinc finger protein (ZFP) transcription factors, a plant-specific subfamily of C2H2 ZFP, have been implicated in regulating abiotic stress responses, growth, and developmental processes in plants. Rapeseed (Brassica napus L.) is a crucial oil crop widely used for the production of high-quality vegetable oil, animal feed, and biodiesel. Compared with studies on Q-type C2H2-ZFP genes in other plant species, systematic research has not been performed in B. napus. In this study, a comprehensive genome-wide analysis of Q-type C2H2-ZFPs in B. napus was conducted. A total of 216 Q-type C2H2-ZFP genes were identified, exhibiting extensive and uneven distribution across the 19 chromosomes. Phylogenetic analysis, based on homologs from Arabidopsis, classified these genes into eight distinct subfamilies, with each containing one to three conserved “QALGGH” motifs. Each subfamily exhibited similar motif compositions and gene structures. Evolutionary studies revealed that segmental duplication events played a crucial role in the expansion of the BnaQ-type C2H2-ZFP gene family. Expression pattern analysis in different tissues and under abiotic stress identified BnaA03g09250D, BnaC09g35160D, BnaC03g11570D, and BnaA10g25850D as candidate genes involved in the response to freezing stress. Overexpression of BnaC09g35160D provided preliminary evidence that it enhances freezing tolerance in plants. This comprehensive study of Q-type C2H2-ZFPs in B. napus will enhance our understanding of the BnaQ-type C2H2-ZFP gene family and provide valuable insights for further functional investigations of BnaC09g35160D. Full article

Background: Cardiomyocyte death is a key factor in myocardial ischemia–reperfusion injury (MI/RI), and the expression patterns and molecular mechanisms of pyroptosis-related genes (PRGs) in ischemia–reperfusion injury are poorly understood. Methods: The mouse MI/RI injury-related datasets GSE61592 and GSE160516 were obtained from the Gene Expression Omnibus database, and differential expression analysis was performed on each to identify differentially expressed genes (DEGs). The DEGs were intersected with the PRGs obtained from GeneCards to identify differentially expressed PRGs in MI/RI. Enrichment analysis identified key pathways, while PPI network analysis revealed hub genes. The expression patterns and immune cell infiltration of hub genes were also investigated. The molecular docking prediction of key genes was performed using MOE software in conjunction with the ZINC small molecular compounds database. Key gene expression was validated in an external dataset (GSE4105), a mouse MI/RI model, and an HL-1 cell hypoxia/reoxygenation model via RT-qPCR. Results: A total of 29 differentially expressed PRGs were identified, which are primarily associated with pathways such as “immune system process”, “response to stress”, “identical protein binding”, and “extracellular region”. Seven key genes (Fkbp10, Apoe, Col1a2, Ppic, Tlr2, Fstl1, Serpinh1) were screened, all strongly correlated with immune infiltration. Seven FDA-approved small molecule compounds exhibiting the highest docking potential with each key gene were selected based on a comprehensive evaluation of S-scores and hydrogen bond binding energies. Apoe, Tlr2, and Serpinh1 were successfully validated across external datasets, the mouse MI/RI model, and the cardiomyocyte H/R model. Conclusions: Apoe, Tlr2, and Serpinh1 may be key genes involved in MI/RI-related pyroptosis. Targeting these genes may provide new insights into the treatment of MI/RI. Full article