Genes最新文献

Autophagy, an evolutionarily conserved intracellular recycling pathway, is essential for maintaining cellular homeostasis and enhancing plant resilience to a variety of abiotic stresses, including drought, salinity, extreme temperatures, and heavy metal toxicity. Be-yond its canonical role in nutrient recycling, autophagy is now recognized as a central regulator of stress signaling, hormonal crosstalk, and metabolic reprogramming. Here we synthesize the functions of autophagy under diverse abiotic stresses, highlighting its role in organellar quality control, metabolic adaptation, and stress-specific responses. We further discuss innovative strategies for enhancing crop resilience, including genome editing, integrative multi-omics analyses, and synthetic biology applications. Elucidating the autophagy regulatory network provides the foundation for designing next-generation crops that maintain high yield and resilience under climate-driven stress.

Background: Parkinson's disease (PD) is a complex neurodegenerative disorder in aged people with multifaceted molecular underpinnings. It poses a severe threat to millions of older adults worldwide. The understanding of the molecular mechanisms of PD development and the performance of its therapeutic strategies has not yet reached a satisfactory level. Methods: This study integrated six transcriptomic datasets to uncover key genes (KGs) and their underlying pathogenic mechanisms, providing insights into potential therapeutic strategies for PD. We designed a comprehensive computational pipeline using various bioinformatics tools and databases to investigate PD-causing KGs, focusing on their functions, pathways, regulatory mechanisms, and potential therapeutic drug molecules. Results: In order to explore PD-causing KGs, we initially identified 303 differentially expressed genes (DEGs) between PD and control samples with 204 upregulated and 99 downregulated DEGs using the LIMMA approach with threshold values at Adj. p-value < 0.05 and abs (log₂FC) ≥ 1.0. Then, protein-protein interaction (PPI) network analysis pinpointed seven top-ranked DEGs (GAPDH, PTEN, CCND1, APOE, ESR1, MAPK3/ERK1, and SNCA) as KGs or central modulators of PD pathogenesis. Regulatory network analysis of KGs identified 3 top-ranked transcription factors (FOXC1, NFKB1, and TFAP2A) and 6 microRNAs (hsa-let-7b-5p, hsa-mir-16-5p, and others) as the pivotal regulators of KGs. Gene Ontology (GO) terms and KEGG pathway enrichment analyses with KGs revealed several crucial biological processes, molecular functions, cellular components, and neurodegenerative pathways associated with the development of PD. Finally, the top five molecules guided by KGs (Nilotinib, Bromocriptine, Withaferin-A, Celastrol, and Donepezil) were identified as promising drug candidates against PD and validated computationally through ADME/T analysis and molecular dynamics simulation studies. Conclusions: The findings of this study may serve as valuable resources for developing effective treatment strategies for PD patients.

Background: Curcuma bakerii is a species of the family Zingiberaceae, endemic to Bangladesh. This genus of rhizomatous plants is widely distributed in tropical regions worldwide and is valued for its medicinal, aromatic, and culinary properties. Methods: The complete chloroplast (cp) genome of C. bakerii was reconstructed using high-throughput sequencing data. Subsequently, the genome was functionally annotated, assembled, and analyzed to clarify its evolutionary dynamics and structural organization. Results: The study's findings indicate that the genome size is 162,189 base pairs (bp) and that it has a normal quadripartite structure with a large single-copy (LSC) region also comprises a small single-copy (SSC) region and two inverted repeats (IRa and IRb). The GC content of the genome was 36.18%, consisting of 135 genes: 88 protein-coding, 39 tRNA, and 8 rRNA. The codon usage analysis revealed 22 high-frequency and five optimal codons indicative of codon bias. Analysis of repetitive sequences revealed 213 Simple Sequence Repeats (SSRs), most of which were A/T. Additionally, seven mutation hotspots were reported, with 68.08% of single-nucleotide polymorphisms (SNPs) detected in the coding region and 31.91% in the noncoding region. Nonsynonymous substitutions accounted for 63.78%, while synonymous substitutions accounted for 36.11%. Conclusions: Based on this study, cp genome sequencing is a useful tool for understanding the intrageneric relationships among Curcuma species. The research presents a complete cp genome of C. bakerii from Bangladesh and provides a useful genomic resource for the molecular evolution, phylogeny, and genetic diversity study of the genus Curcuma.

Background/objectives: The article presents data on Duchenne muscular dystrophy (DMD) in the Republic of North Ossetia-Alania (RNOA), describing the population characteristics of the disease among children in RNOA (2006-2023).

Methods: The number of newborns was 172,115, with 86,057 boys from 2006 to 2023. During the reporting period, 19 families (23 patients, including 22 boys) were identified. The molecular and genetic characteristics of the patients were analyzed throughout the entire observation period, which began in 1998.

Results: The prevalence of the disease was 1:3912 among newborn boys (95%CI: 1:2584-1:6242), which is slightly higher than in other regions of the Russian Federation (RF) and most countries around the world. The spectrum of DMD genetic variants in RNOA aligns with worldwide patterns but reveals differences in frequencies compared to RF data. The frequency of exon deletions in the DMD gene range from 65.0 to 70.0% (60% in RNOA vs. <50% in RF) worldwide, for duplications-9.0-11.0% globally (16% in RNOA), and for nonsense variants-9.7-26.5% worldwide (20% in RNOA). Twelve patients (41.0%) in RNOA qualified for therapy, and Translarna was prescribed in most cases. In the cohort of children, one girl was identified with classic DMD, confirmed by genetic studies. Different limitations of the study were hindered by the small cohort size, patients' remote residences, and poor therapy compliance of our patients.

Conclusions: The heterogeneity of mutation spectrum across different populations underscores the influence of ethnic background. Consequently, this study highlights the importance of population-specific studies for improving DMD care.

Background: Antimicrobial resistance (AMR) is a growing public health concern affecting both medicine and food safety. While Listeria monocytogenes is the primary pathogen of concern, Listeria innocua-commonly found in food and food-processing environments-may serve as a reservoir for resistance genes and a useful indicator of species for surveillance. This study aimed to assess the phenotypic antibiotic susceptibility and detect resistance-associated genes in L. innocua isolates from meat products and processing environments in Poland. Methods: A total of 51 L. innocua isolates were analyzed, originating from raw and processed meat products as well as meat-processing environments. Antimicrobial susceptibility was determined using the disc diffusion method against 18 antibiotics representing multiple classes. Phenotypic resistance was interpreted following CLSI guidelines (CLSI, 2020). Isolates exhibiting resistance or intermediate resistance were further screened for resistance-associated genes using PCR. Results: All isolates were fully susceptible to ampicillin, benzylpenicillin, chloramphenicol, gentamicin, rifampin, trimethoprim-sulfamethoxazole, and vancomycin. High susceptibility was observed for ciprofloxacin, erythromycin, meropenem, trimethoprim, and nitrofurantoin, with only sporadic intermediate responses. Moderate resistance levels were noted for streptomycin (10%) and tetracycline (12%). The lowest susceptibility was recorded for clindamycin and linezolid, with most isolates exhibiting intermediate or resistant phenotypes. Universal resistance to cefotaxime and oxacillin was found. Eighteen distinct resistance patterns were identified. PCR confirmed the presence of several resistance-associated genes, including mecA, lnuA, lnuB, cfr, optrA, and poxtA, consistent with observed phenotypes. Conclusions: This study provides the first detailed characterization of AMR in L. innocua from Polish meat and processing environments. The findings highlight its heterogeneous resistance profiles and potential role as a reservoir of clinically relevant resistance genes. Incorporating L. innocua into surveillance programs may strengthen early detection of emerging resistance and enhance food safety monitoring.

Background: Pathogenic variants in the TRIP12 gene are associated with Clark-Baraitser syndrome, a condition characterized by neurodevelopmental disorders, including intellectual disability, autism spectrum disorder (ASD), and speech delay. Phenotypic expression is variable, and facial features are not consistently present. Familial inheritance is rare.

Methods: Whole-exome sequencing (WES) was performed on a proband with speech disorder and ASD, as well as on her parents. Clinical assessment included developmental, cognitive, and physical evaluations.

Results: A heterozygous missense variant c.3404A>T (p. Asp1135Val) in the TRIP12 gene was identified in both the proband and her father. Both presented with speech disorder and ASD without facial features or severe intellectual disability.

Conclusions: In line with recent genotype-phenotype studies, missense TRIP12 variants tend to be associated with milder neurodevelopmental presentations, typically characterized by mild to moderate intellectual impairment, variable autistic traits, limited or absent facial features, and a low incidence of epilepsy. This familial case further presents the phenotypic spectrum of TRIP12 missense variants and highlights that ASD and speech disorder may occur as isolated neurodevelopmental findings without syndromic features. The report reinforces the relevance of TRIP12 analysis in the differential diagnosis of ASD and language disorders, even in individuals lacking physical traits, supporting more accurate genetic counseling and broader awareness of inherited TRIP12-related conditions.

Background: Heterosis (hybrid vigor) is a fundamental phenomenon in plant breeding, but its molecular basis remains poorly understood in perennial crops such as tea (Camellia sinensis). This study aimed to elucidate the molecular mechanisms underlying heterosis in tea and its hybrids by performing integrated transcriptomic and metabolomic analyses of F₁ hybrids derived from two elite cultivars, Fuding Dabaicha (FD) and Baojing Huangjincha 1 (HJC).

Methods: Comprehensive RNA sequencing and widely targeted metabolomic profiling were conducted on the parental lines and F₁ hybrids at the one-bud-one-leaf stage. Primary metabolites (including amino acids, nucleotides, saccharides, and fatty acids) were quantified, and gene expression profiles were obtained. Transcriptomic and metabolomic datasets were integrated using KEGG pathway enrichment and co-expression network analysis to identify coordinated molecular changes underlying heterosis.

Results: Metabolomic profiling detected 977 primary metabolites, many of which displayed non-additive accumulation patterns. Notably, linoleic acid derivatives (9(S)-HODE, 13(S)-HODE) and nucleotides (guanosine, uridine) exhibited significant positive mid-parent heterosis. Transcriptomic analysis revealed extensive non-additive gene expression in F₁ hybrids, and upregulated genes were enriched in fatty acid metabolism, nucleotide biosynthesis, and stress signaling pathways. Integrated analysis demonstrated strong coordination between differential gene expression and metabolite accumulation, especially in linoleic acid metabolism, cutin/suberine biosynthesis, and pyrimidine metabolism. Positive correlations between elevated fatty acid levels and transcript abundance of lipid metabolism genes suggest that the transcriptional remodeling of lipid pathways contributes to heterosis.

Conclusions: These findings provide novel insights into tea plant heterosis and identify potential molecular targets for breeding high-quality cultivars.

Background: As key members of the plant receptor-like kinase family, rice CrRLK1Ls play diverse roles in plant growth, development, and stress responses. Although rice CrRLK1Ls have been initially characterized, our understanding of their functions remains limited. Methods: We identified OsCrRLK1L genes via Hidden Markov Model (HMM) searches against the rice genome. Subsequent analyses encompassed their physicochemical properties, chromosomal distribution, gene structure, phylogenetic relationships, conserved domains, and cis-acting elements.Salt-responsive candidates were screened using a GEO dataset, and their expression profiles were validated under salt stress using quantitative real-time PCR. Result: A total of 36 OsCrRLK1L genes, all containing both Malectin and tyrosine kinase domains, were identified in the rice genome and showed an uneven chromosomal distribution. Phylogenetic analysis classified them into three subclades, with Group II and Group III being specific to rice and Arabidopsis thaliana, respectively. Promoter analysis revealed that the promoter regions of these genes contained an abundance of cis-acting elements related to hormone and stress responses. RNA-Seq and enrichment analysis indicated that OsCrRLK1L genes exhibit tissue specificity and participate in salt stress responses. Furthermore, CrRLK1L2 and CrRLK1L10 showed tissue-specific differential expression under salt stress. Conclusions: In summary, our study lays the groundwork for future research into the biological roles of OsCrRLK1L genes during salt stress.

Background: Dihydroflavonol 4-reductase (DFR) is pivotal for anthocyanin biosynthesis and plays a crucial role in plant development and stress adaptation. However, a systematic characterization of the DFR gene family is lacking in Lonicera japonica Thunb. Methods: In the present study, based on genome and transcriptome data of L. japonica, the research identified six LjDFR gene family members throughout the entire genome. Results: The LjDFR genes were located on Chr.04 and Chr.09 and the full-length coding sequences of LjDFR1-LjDFR6 were cloned. Subcellular localization analysis showed that LjDFRs are primarily found at the cell membrane and in the nucleus. Phylogenetic analysis showed closer clustering of LjDFR genes with Capsicum annuum and Camellia sinensis. Promoter analysis linked LjDFR genes to light response, hormone signaling, and stress-responses. qRT-PCR analysis demonstrated tissue-specific and stage-specific expression patterns among LjDFR members. Notably, LjDFR2 expression was significantly higher in the intensely pigmented tissues of Lonicera japonica Thunb. var. chinensis (Wats.) Bak. compared to L. japonica. Coupled with its phylogenetic proximity to the anthocyanin-related CsDFRa and CaDFR5 genes, this suggests that LjDFR2 may be positively correlated with anthocyanin accumulation. Additionally, the expression of LjDFR2 and LjDFR4 was markedly induced by both drought and salt stress, indicating their roles in abiotic stress responses. Conclusions: This research provides a foundation for further functional studies of LjDFR genes in anthocyanin biosynthesis and stress resistance and offers candidate genes for molecular breeding of L. japonica.

Background/Objectives: Hepcidin is a cysteine-rich antimicrobial peptide that links iron homeostasis and innate immunity in vertebrates, but its functions in amphibians remain poorly understood. The Chinese spiny frog (Quasipaa spinosa) is an economically important species that suffers serious losses from bacterial diseases. This study aimed to identify and functionally characterize a hepcidin homolog (QsHep) from Q. spinosa, focusing on its antibacterial activity, immunomodulatory effects on primary macrophages, and protective efficacy against Elizabethkingia miricola infection. Methods: The QsHep gene was cloned and analyzed, its tissue distribution and inducible expression were examined by qRT-PCR, and the synthetic peptide was tested for antimicrobial, membrane-disruptive, and immunomodulatory activities in vitro, as well as for in vivo protection in an E. miricola infection model. Results: QsHep encodes a typical preprohepcidin with a signal peptide, prodomain, and a conserved mature peptide containing eight cysteine residues. QsHep was widely expressed, with the highest levels in liver, and was significantly upregulated in liver and spleen following bacterial challenge. Synthetic QsHep displayed broad-spectrum antibacterial activity, including strong inhibition of E. miricola, and induced dose-dependent membrane damage in E. miricola. QsHep showed no obvious cytotoxicity but significantly enhanced chemotaxis, phagocytic activity, and respiratory burst in primary macrophages. In vivo, QsHep treatment markedly improved the survival of E. miricola-infected frogs in a dose-dependent manner. Conclusions: QsHep is an amphibian hepcidin that combines membrane-disruptive antibacterial activity with the activation of macrophage effector functions and confers significant protection against bacterial infection in vivo. These findings expand our understanding of hepcidin-mediated innate immunity in amphibians and highlight QsHep as a promising peptide candidate for controlling bacterial diseases in frog aquaculture.