Genes最新文献

Background/objectives: Carvacrol, a major active component of oregano oil and common feed additive, has been widely studied for its effects on fish growth, immunity, and intestinal health. But its transcriptional/metabolic impacts on fish liver remain unclear. This study investigated these effects in Pengze crucian carp (Carassius auratus var. Pengze).

Methods: Fish were fed a basal diet (control) or basal diet supplemented with 10% microencapsulated carvacrol (600 mg/kg) for 56 days; liver samples were analyzed via transcriptomics and metabolomics.

Results: Transcriptomic analysis revealed 482 differentially expressed genes (DEGs) in the liver of Pengze crucian carp following carvacrol supplementation, with 158 upregulated and 324 downregulated genes. Functional annotation highlighted enrichment in translation, signal transduction, amino acid metabolism, and posttranslational modification pathways. GO analysis further identified key processes, including carboxylic acid transport, tRNA aminoacylation, and mitochondrial nucleoid function, while KEGG pathways were implicated in amino acid biosynthesis, lipid metabolism (e.g., alpha-linolenic acid), and insulin signaling. Metabolomic profiling identified 679 significantly altered metabolites, including 113 upregulated and 566 downregulated ones. Among these, upregulated compounds like L-asparaginyl-L-lysine (Log₂FC = 4.36) and 2'-Deoxyadenosine-5'-diphosphate (Log₂FC = 4.31) are linked to nucleotide metabolism, and downregulated peptides (e.g., Ala-Phe-Tyr-Arg) suggesting modulated protein turnover. Joint omics analysis revealed convergent pathways in glycerophospholipid metabolism, aminoacyl-tRNA biosynthesis, and autophagy. Notably, the chaperone gene dnaja3b was correlated strongly with neuroactive metabolites (e.g., normetanephrine), potentially implicating carvacrol in stress response regulation.

Conclusions: Our findings demonstrate that carvacrol modulates liver gene expression and metabolic profiles, primarily influencing amino acid and lipid metabolism pathways, autophagy, and stress responses. The observed correlations between dnaja3b and specific metabolites offer mechanistic insights into the action of carvacrol in fish liver.

Background: Chili pepper (Capsicum annuum L.), a globally cultivated and ancient domesticated crop, carries considerable significance in agriculture. While radiation-induced mutagenesis has found application in this crop, the mutagenic efficacy and molecular-level impacts of 7Li ion beam radiation remain poorly elucidated.

Methods: We irradiated pepper with a beam of 7Li ions to create a mutant, which showed good economic traits, and phenotypic and physio-biochemical characterization were combined with proteomic and metabolomic profiling to delineate the mutagenic mechanisms. Quantitative real-time PCR (qRT-PCR) was further utilized to assess the biological impact and underlying response pathways. We used this to evaluate the biological impact and the reaction mechanisms behind it.

Results: 7Li beam radiation positively influenced morphology and physiological traits, notably chlorophyll and anthocyanin content. Leveraging proteomic profiling detected 6082 proteins, including 355 differential proteins (139 upregulated, 216 downregulated), enriched in 4 KEGG pathways. Based on GO and KEGG network analysis, 250 metabolites were quantified, with 120 being differentially abundant (112 upregulated, 8 downregulated), enriched in 9 metabolic pathways. Furthermore, qRT-PCR results revealed that differentially expressed genes were consistent with the corresponding metabolomic data. Joint analysis revealed the coordinated enrichment of differential metabolites and proteins in pathways related to amino acid and carbohydrate metabolism. These findings suggest that these active pathways in pepper are related to its response to ion beam radiation. Overall, this study is a valuable resource for subsequent genomic research on peppers and 7Li ion beam radiation research.

Personalizing therapy using medical marijuana (MM) is based on understanding the pharmacogenomics (PGx) and drug-drug interactions (DDIs) involved, as well as identifying potential epigenetic risk markers. In this work, the evidence regarding the role of variants in phase I (CYP2C9, CYP2C19, CYP3A4/5) and II (UGT1A9/UGT2B7) genes, transporters (ABCB1), and selected neurobiological factors (AKT1/COMT) in differentiating responses to Δ⁹-tetrahydrocannabinol (THC) and cannabidiol (CBD) has been reviewed. Data indicating enzyme inhibition by CBD and the possibility of phenoconversion were also considered, which highlights the importance of a dynamic interpretation of PGx in the context of current pharmacotherapy. Simultaneously, the results of epigenetic studies (DNA methylation, histone modifications, and ncRNA) in various tissues and developmental windows were summarized, including the reversibility of some signatures in sperm after a period of abstinence and the persistence of imprints in blood. Based on this, practical frameworks for personalization are proposed: the integration of PGx testing, DDI monitoring, and phenotype correction into clinical decision support systems (CDS), supplemented by cautious dose titration and safety monitoring. The culmination is a proposal of tables and diagrams that organize the most important PGx-DDI-epigenetics relationships and facilitate the elimination of content repetition in the text. The paper identifies areas of implementation maturity (e.g., CYP2C9/THC, CBD-CYP2C19/clobazam, AKT1, and acute psychotomimetic effects) and those requiring replication (e.g., multigenic analgesic signals), indicating directions for future research.

Background: Semisulcospiridae is a family of freshwater gastropods with over 100 species, primarily distributed in East Asia and North America. They play crucial ecological roles and are of medical importance as intermediate hosts for parasites. However, their phylogenetic relationship remains unclear. Most previous studies, which focused on fewer molecular markers (e.g., COI, 16S, 28S), have shown limitations in resolving relationships with low resolution. Mitochondrial genomes, with their richer phylogenetic information, offer a promising tool to infer the evolutionary relationships within this family. Methods: This study sequenced, assembled, and annotated the complete mitochondrial genomes of three Semisulcospiridae species from China: Koreoleptoxis friniana, Hua textrix, and Hua yangi. Phylogenetic analyses were conducted using Maximum Likelihood (ML) and Bayesian Inference (BI) methods on five distinct datasets derived from the mitochondrial genomes, including nucleotide sequences of protein-coding genes (with and without third codon positions), amino acid sequences, and combinations with two ribosomal RNA genes. Results: The complete (or near-complete) mitochondrial genomes of K. friniana, H. textrix, and H. yangi were 15,474 bp, 15,660 bp, and 15,744 bp in length, respectively, showing typical gene content and an A+T bias. The gene order was highly conserved. Phylogenetic analyses consistently recovered the family Semisulcospiridae as monophyletic and revealed three well-supported, distinct clades corresponding to the genera Semisulcospira, Koreoleptoxis, and Hua. While the overall tree topologies were robust for Semisulcospiridae, some incongruences were observed in the placements of other cerithioidean families depending on the dataset used. Evolutionary rate analysis (Ka/Ks) indicated strong purifying selection across all protein-coding genes, with COX1 being the most conserved. Conclusions: This study provided three new mitochondrial genomes for Semisulcospiridae: K. friniana, H. textrix, and H. yangi. Phylogenetic analysis based on mitochondrial genome datasets offers new evidence that supports the monophyly of the three Asian genera of Semisulcospiridae. Future research should include broader taxonomic sampling, particularly of the North American genus Juga and the atypical Japanese Semisulcospira lineages, to achieve a comprehensive phylogenetic framework.

Background: Acute coronary syndrome (ACS) is a major cardiovascular emergency influenced by environmental and genetic factors. Thrombophilic variants such as prothrombin G20210A (rs1799963) and factor V Leiden G1691A (rs6025) may influence thrombin generation and has been reported to show associations with coronary events.

Methods: This case-control study included 100 ACS patients and 131 age and sex-matched healthy controls. Genotyping of rs1799963 and rs6025 was performed using polymerase chain reaction followed by restriction fragment length polymorphism (PCR-RFLP) analysis.

Results: The GG genotype was markedly more common among ACS patients for both variants. For rs1799963, carriers of the A allele (GA + AA) were less common in ACS (2.0%) than controls (9.2%; p = 0.039), corresponding to an 8.6-fold higher odds of ACS in GG carriers (OR = 8.624; 95% CI: 1.757-42.345; p = 0.008). For rs6025, A allele carriers (9.0%) were also reduced in ACS versus controls (18.3%; p = 0.049), and GG homozygotes exhibited a 2.6-fold higher risk (OR = 2.635; 95% CI: 1.104-6.290; p = 0.029). Age was independently associated with higher ACS risk (OR = 1.047; 95% CI: 1.029-1.066; p < 0.001).

Conclusions: Our findings indicate that the rs1799963 and rs6025 variants were independently associated with ACS, together with advancing age. Both the GG genotype and older age were associated with higher odds of ACS, whereas A-allele carriers appeared less common among ACS cases.

Background/objectives: Psoriasis and age-related macular degeneration (AMD) may share immune-related pathophysiologic characteristics. However, few studies have investigated the relationship between psoriasis and AMD. We assessed the possible causal link between psoriasis and AMD in European populations.

Methods: Single-nucleotide polymorphisms associated with psoriasis exposure were employed as instrumental variables (IVs) based on genome-wide significance (p < 5.0 × 10-8) in the FinnGen genome-wide association study (GWAS). The GWAS data for AMD were obtained from 11 studies performed by the International AMD Genomics Consortium. We performed a two-sample Mendelian randomisation (MR) study to estimate causal effects using the inverse-variance weighted, weighted median, and MR-Egger methods, as well as the MR-Pleiotropy Residual Sum and Outlier (MR-PRESSO) test.

Results: We observed significant causal associations of psoriasis with AMD. Using the weighted median method, the odds ratio (OR) was 1.09 (95% CI = [1.03-1.16] and p = 0.005), and using the MR-PRESSO test, the OR was 1.04 (95% CI = [1.00-1.09] and p = 0.043).

Conclusions: A potential causal association between psoriasis and AMD underscores the need to investigate inflammation as a risk factor for AMD.

Background: The developmental differences between female and male early embryos regarding sex development remain a topic of controversy.

Objectives: This study aims to investigate whether there are significant developmental differences between female and male bovine embryos during in vivo development.

Methods: The CIDR + FSH + PGF2α + GnRH method was employed to induce superovulation in 20 donor cows. Subsequently, artificial insemination was performed on the donor cows using high-purity X and Y frozen semen, with 10 cows receiving each type of semen. Seven days later, the embryos were flushed from the donor cows. The flushed embryos underwent embryonic sex determination, followed by immunofluorescence analysis to observe proliferation and apoptosis, and finally, RT-PCR was conducted to detect genes associated with proliferation and apoptosis.

Results: The results indicated that the sex ratio of embryos obtained through artificial insemination using X/Y semen did not significantly differ based on semen purity (p ≥ 0.05). However, the fluorescence intensity of apoptotic cells in the X-BL group was significantly higher than that in the Y-BL group (p < 0.05). Conversely, the fluorescence intensity of proliferating cells in the X-BL group was significantly lower than that in the Y-BL group (p < 0.05). Furthermore, the expression levels of apoptosis-related genes in the X-BL group were significantly higher compared to the Y-BL group (p < 0.05), while the expression levels of proliferation-related genes in the X-BL group were significantly lower than those in the Y-BL group (p < 0.01).

Conclusions: The above results indicate that during in vivo development of bovine early embryos, male embryos develop at a faster rate than female embryos.

Background/Objective: Genetic factors contribute significantly to Parkinson's disease (PD), especially in cases with early onset or positive family history. However, previous investigations of the genetic landscape in PD populations were mainly based on targeted genotyping. The aim of this study was to investigate the prevalence of pathogenic variants in known PD-associated genes in a series of Swedish PD patients. Methods: We performed whole-exome sequencing on 285 PD probands from southern Sweden. Our series was enriched for patients with early disease onset or positive family history. We focused on 44 genes previously linked to PD. Results: We identified a CHCHD2 p.(Phe84LeufsTer6) frameshift variant in two unrelated patients and report the first PD case of Swedish ancestry carrying the VPS35 p.(Asp620Asn) variant. Additionally, in one patient each, we found an SNCA duplication, an SNCA p.(Ala53Thr) variant, and a LRRK2 p.(Gly2019Ser) variant. Thus, only 2.1% (n = 6) of patients in this series had Mendelian monogenic PD forms. In addition, forty-three patients carried variants in GBA1, including T369M, which may lack disease-association in our population (n = 12); E326K (n = 22), which is classified as a PD risk variant; as well as N370S (n = 3), R329H (n = 3), S107L (n = 1), and L444P (n = 1), with one patient harboring both T369M and E326K. Pathogenic variants in ARSA, ATP7B, and PRKN genes were also detected in heterozygote form, but their role in PD remains uncertain. Conclusions: Monogenic forms of PD are rare in southern Sweden, even among the familial and early-onset PD patients that were overrepresented in our study. Our findings highlight the genetic diversity in Swedish PD patients and identify key variants for further functional and clinical studies.

(1) Background: Backcross (BC) breeding is a key technology of crop improvement, yet its efficiency largely depends on the precise assessment of the genetic background recovery. Conventional molecular marker-assisted techniques suffer from inadequate genomic coverage or an inability to resolve true chromosomal structure. (2) Methods: To address major issues in maize BC breeding, we devised a G2H block-scanning strategy. This approach converts high-density point markers into haplotype blocks, enabling precise evaluation of the genetic background in backcross progenies. A key innovation is the CFDI, which quantifies the distribution of unrecovered fragments, allowing for visual tracking of chromosomal recombination and identification of ideal individuals with both a high genetic background recovery rate and few small fragments retention. (3) Results: We validated the accuracy and effectiveness of the G2H strategy across multiple backcross generations. Through enabling a precise "point-to-line-to-area" panoramic assessment of genetic background, G2H provides a powerful tool for developing ideal breeding materials with pure genetic background and minimized linkage drag. (4) Conclusions: Notably, this strategy significantly shortens the breeding cycle by 2-3 generations compared to conventional background assessment methods, thereby accelerating precision molecular design breeding in crops.

Background/objectives: X-linked hypohidrotic ectodermal dysplasia (XLHED) is a rare monogenic disorder characterized by hypohidrosis, hypotrichosis, and hypodontia, caused primarily by pathogenic variants in the EDA gene. XLHED predominantly affects males due to its X-linked recessive inheritance, while female carriers may exhibit variable phenotypes due to random X-inactivation. Early diagnosis is critical for timely counseling and emerging therapeutic interventions. We report a rare prenatal diagnosis of XLHED in dizygotic dichorionic male twins during a dichorionic diamniotic pregnancy. At 24 weeks' gestation, ultrasonographic anomalies-facial dysmorphisms, oligodontia, and hypoechogenic skin-raised suspicion for ectodermal dysplasia.

Methods: Non-invasive prenatal test and targeted next-generation sequencing (NGS) of Cell-free DNA identified an hemizygous EDA deletion (c.612_629del; p.Ile205_Gly210del) with 52% variant allele frequency.

Results: This in-frame deletion affects a highly conserved region in the TNF homology domain of ectodysplasin-A1, likely compromising protein function. The variant was confirmed in both fetuses via genetic analysis on amniotic fluid and in the heterozygous state in the mother, consistent with X-linked recessive inheritance. Family history revealed a maternal uncle with XLHED. Additional heterozygous variants were also identified in CPT2, GBA1, GJB2, and SMN1 genes. Following comprehensive genetic counseling, the mother opted for abortion.

Conclusions: This case underscores the value of applying advanced genomic technologies-cfDNA-based NGS-for prenatal diagnosis of rare genetic disorders. The identification of apathogenic EDA variant expands the mutational spectrum of XLHED and supports early diagnosis for informed reproductive decisions and potential access to emerging prenatal therapies. Broader application of such technologies may improve outcomes in future pregnancies at risk for monogenic disorders.