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CTLA4 Alteration and Neurologic Manifestations: A New Family with Large Phenotypic Variability and Literature Review.
IF 2.8 3区 生物学
Genes Pub Date : 2025-03-03 DOI: 10.3390/genes16030306
Edoardo Genio, Mauro Lecca, Rachele Ciccocioppo, Edoardo Errichiello
{"title":"<i>CTLA4</i> Alteration and Neurologic Manifestations: A New Family with Large Phenotypic Variability and Literature Review.","authors":"Edoardo Genio, Mauro Lecca, Rachele Ciccocioppo, Edoardo Errichiello","doi":"10.3390/genes16030306","DOIUrl":"10.3390/genes16030306","url":null,"abstract":"<p><p>Cytotoxic-T-lymphocyte-antigen-4 (CTLA-4), a member of the immunoglobulin superfamily, is an essential negative regulator of immune responses that is constitutively expressed on both regulatory (Treg) and activated T cells. To date, heterozygous germline variants in <i>CTLA4</i>, leading to haploinsufficiency, have been associated with several immunological disorders, including hypogammaglobulinemia, multi-organ autoimmunity, lymphoproliferative disorders, and enlarged lymphoid organs. Indeed, <i>CTLA4</i> carriers display highly heterogeneous clinical manifestations with a phenotypic spectrum ranging from asymptomatic carrier status to fatal autoimmunity. Here, we describe a family with autoimmune phenotypes (Hashimoto thyroiditis, psoriasiform dermatitis, celiac disease/inflammatory bowel disease, and rheumatoid arthritis), segregating across three different generations due to a recurrent missense variant [c.436G>A, p.(Gly146Arg)] in the <i>CTLA4</i> gene. Interestingly, the proband showed prominent neurological manifestations, including seizures, hydrocephalus, and demyelination, which are less frequently reported in individuals with pathogenic variants in <i>CTLA4</i>. A detailed literature review of neurologic features that have been reported so far in <i>CTLA4</i> carriers is also provided.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11942126/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729433","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Identification of Metabolism-Related Hub Genes in Heart Failure via Comprehensive Transcriptome Analysis.
IF 2.8 3区 生物学
Genes Pub Date : 2025-03-03 DOI: 10.3390/genes16030305
Hanlin Peng, Boyang Lv, Junbao Du, Yaqian Huang, Qinghua Cui, Chunmei Cui, Hongfang Jin
{"title":"Identification of Metabolism-Related Hub Genes in Heart Failure via Comprehensive Transcriptome Analysis.","authors":"Hanlin Peng, Boyang Lv, Junbao Du, Yaqian Huang, Qinghua Cui, Chunmei Cui, Hongfang Jin","doi":"10.3390/genes16030305","DOIUrl":"10.3390/genes16030305","url":null,"abstract":"<p><strong>Background: </strong>Metabolic dysfunction is a key driver of heart failure (HF) progression. Identifying metabolic hub genes in HF may reveal novel therapeutic targets.</p><p><strong>Methods: </strong>Transcriptomic datasets from HF patients (GEO database) and metabolism-related genes (PathCards) were analyzed. Differentially expressed genes (DEGs) were intersected with metabolism-related genes, followed by the application of the LASSO, Random Forest, and XGBoost algorithms to prioritize hub genes. Candidate genes were validated via WGCNA, an HF mouse model, and plasma metabolomics. Diagnostic performance and metabolic associations were assessed using ROC analysis and ssGSEA.</p><p><strong>Results: </strong>We identified 1115 HF-associated DEGs (701 upregulated, 414 downregulated), with 119 linked to metabolism. The machine learning algorithms prioritized five genes, including <i>SDC2</i>, which was also validated using WGCNA and the mouse HF model. <i>SDC2</i> mRNA and protein expression levels were markedly elevated in HF and demonstrated strong diagnostic accuracy. ssGSEA revealed the expression of <i>SDC2</i> was correlated with dysregulated metabolic pathways, including fatty acid biosynthesis and glycerolipid metabolism, which are potentially associated with metabolic alterations in HF.</p><p><strong>Conclusions: </strong>SDC2 emerges as a central regulator bridging metabolic dysfunction and HF pathogenesis, showing potential as a diagnostic biomarker and therapeutic target.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11941980/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729676","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Complete Mitochondrial Genome of Platygyra daedalea and Characteristics Analysis of the Mitochondrial Genome in Merulinidae.
IF 2.8 3区 生物学
Genes Pub Date : 2025-03-02 DOI: 10.3390/genes16030304
Shuwen Jia, Tongtong Shen, Wenqi Cai, Jian Zhang, Shiquan Chen
{"title":"Complete Mitochondrial Genome of <i>Platygyra daedalea</i> and Characteristics Analysis of the Mitochondrial Genome in Merulinidae.","authors":"Shuwen Jia, Tongtong Shen, Wenqi Cai, Jian Zhang, Shiquan Chen","doi":"10.3390/genes16030304","DOIUrl":"10.3390/genes16030304","url":null,"abstract":"<p><strong>Background: </strong>The Merulinidae family belonging to the order Scleractinia is mainly distributed in the Indo-Pacific and Caribbean regions and often constitute the most dominant species of coral reefs. Mitochondrial genome is a key tool for studying the phylogeny and adaptation. Only a few studies have conducted the characteristics analyses of mitochondrial genome in the Merulinidae family.</p><p><strong>Methods: </strong>Therefore, we used high-throughput sequencing technology to describe the mitochondrial genome of <i>Platygyra daedalea</i>, a member of this family. Bioinformatics was used to analyze the composition characteristics of the mitochondrial genome of 10 Merulinidae species.</p><p><strong>Results: </strong>The mitochondrial genome of <i>P. daedalea</i> had a total length of 16,462 bp and a GC content of 33.0%. Thirteen unique protein-coding genes (PCGs), two transfer RNA (tRNA) genes, and two ribosomal RNA (rRNA) genes were annotated. Each species of Merulinidae had 13 unique PCGs in the mitochondrial genome. In contrast, the number of tRNAs and rRNAs significantly varied in Merulinidae species. Collinearity and gene rearrangement analyses indicated that the mitochondrial evolution of species in the Merulinidae family was relatively conserved. Divergence time analysis indicated that Merulinidae originated in the Oligocene, whereas the <i>Platygyra</i> genus originated in the Miocene. The formation and intraspecific divergence of coral species were consistent with geological changes in the ocean.</p><p><strong>Conclusions: </strong>The results of this study help better understand the characteristics of the mitochondrial genome in the Merulinidae family and provide insights into the utility of mitochondrial genes as molecular markers of phylogeny.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11942114/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729621","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Integrating Artificial Intelligence and Bioinformatics Methods to Identify Disruptive STAT1 Variants Impacting Protein Stability and Function.
IF 2.8 3区 生物学
Genes Pub Date : 2025-03-01 DOI: 10.3390/genes16030303
Ebtihal Kamal, Lamis A Kaddam, Mehad Ahmed, Abdulaziz Alabdulkarim
{"title":"Integrating Artificial Intelligence and Bioinformatics Methods to Identify Disruptive STAT1 Variants Impacting Protein Stability and Function.","authors":"Ebtihal Kamal, Lamis A Kaddam, Mehad Ahmed, Abdulaziz Alabdulkarim","doi":"10.3390/genes16030303","DOIUrl":"10.3390/genes16030303","url":null,"abstract":"<p><p><b>Background:</b> The Signal Transducer and Activator of Transcription 1 (<i>STAT1</i>) gene is an essential component of the JAK-STAT signaling pathway. This pathway plays a pivotal role in the regulation of different cellular processes, including immune responses, cell growth, and apoptosis. Mutations in the <i>STAT1</i> gene contribute to a variety of immune system dysfunctions. <b>Objectives:</b> We aim to identify disease-susceptible single-nucleotide polymorphisms (SNPs) in <i>STAT1</i> gene and predict structural changes associated with the mutations that disrupt normal protein-protein interactions using different computational algorithms. <b>Methods:</b> Several in silico tools, such as SIFT, Polyphen v2, PROVEAN, SNAP2, PhD-SNP, SNPs&GO, Pmut, and PANTHER, were used to determine the deleterious nsSNPs of the <i>STAT1</i>. Further, we evaluated the potentially deleterious SNPs for their effect on protein stability using I-Mutant, MUpro, and DDMUT. Additionally, we predicted the functional and structural effects of the nsSNPs using MutPred. We used Alpha-Missense to predict missense variant pathogenicity. Moreover, we predicted the 3D structure of STAT1 using an artificial intelligence system, alphafold, and the visualization of the 3D structures of the wild-type amino acids and the mutant residues was performed using ChimeraX 1.9 software. Furthermore, we analyzed the structural and conformational variations that have resulted from SNPs using Project Hope, while changes in the biological interactions between wild type, mutant amino acids, and neighborhood residues was studied using DDMUT. Conservational analysis and surface accessibility prediction of STAT1 was performed using ConSurf. We predicted the protein-protein interaction using STRING database. <b>Results:</b> In the current study, we identified six deleterious nsSNPs (R602W, I648T, V642D, L600P, I578N, and W504C) and their effect on protein structure, function, and stability. <b>Conclusions:</b> These findings highlight the potential of approaches to pinpoint pathogenic SNPs, providing a time- and cost-effective alternative to experimental approaches. To the best of our knowledge, this is the first comprehensive study in which we analyze <i>STAT1</i> gene variants using both bioinformatics and artificial-intelligence-based model tools.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11942549/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143728489","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Clinical Significance of Fragile X Syndrome 2 (FXR2) in Breast Cancer.
IF 2.8 3区 生物学
Genes Pub Date : 2025-03-01 DOI: 10.3390/genes16030302
Ohud A Alsalmi, Abrar I Aljohani, Shahad M Almutairi, Rana O Alsufyani, Abdulrahman R Alrubayee, Khalid J Alzahrani, Ghaida E Alkhammash, Hessa M Aljuaid, Hanan S Alghamdi, Fouzeyyah A Alsaeedi
{"title":"Clinical Significance of Fragile X Syndrome 2 (FXR2) in Breast Cancer.","authors":"Ohud A Alsalmi, Abrar I Aljohani, Shahad M Almutairi, Rana O Alsufyani, Abdulrahman R Alrubayee, Khalid J Alzahrani, Ghaida E Alkhammash, Hessa M Aljuaid, Hanan S Alghamdi, Fouzeyyah A Alsaeedi","doi":"10.3390/genes16030302","DOIUrl":"10.3390/genes16030302","url":null,"abstract":"<p><p><b>Background</b>: The fragile X protein family comprises three members: the fragile X syndrome protein (FMRP) and its structural homologs, fragile X syndrome 1 and 2 (FXR1 and FXR2). FMRP has a significant role in controlling the genesis and progression of various forms of human cancer. However, studies on the prognostic significance of FXR2 in cancer are scarce. Thus, this study aimed to investigate the clinicopathological significance of FXR2, a member of the FMRP family, in primary breast cancer (BC). <b>Methods</b>: A total of 100 formalin-fixed paraffin-embedded (FFPE) tissue blocks from invasive BC cases were collected from King Abdulaziz Hospital in Saudi Arabia. Immunohistochemistry (IHC) was used to assess FXR2 protein expression in the BC tissues, and the results were correlated with clinicopathological parameters, such as tumor grade, tumor size and hormone receptor status. Additionally, the association between clinicopathological features and <i>FXR2</i> mRNA expression was assessed using the BC Gene-Expression Miner v5.0 tool on all publicly available DNA microarray (<i>n</i> = 10,872) and RNA sequence (<i>n</i> = 4421) data to validate the results. <b>Results</b>: FXR2 protein expression was significantly associated with human epidermal growth factor 2 (HER2) negativity (<i>p</i> = 0.010) and low Ki67 (<i>p</i> < 0.001). Both DNA microarray and RNA sequence data showed that HER2 negativity was strongly linked to high levels of <i>FXR2</i> mRNA. High <i>FXR2</i> mRNA levels were also correlated with hormone receptor negativity and mutated p53. <b>Conclusions</b>: This study suggests that FXR2 may have indirect clinical significance in BC. However, further studies are warranted to deepen our understanding of the association between FXR2 and other clinicopathological parameters, which could lead to improved diagnostic, treatment, and prognostic strategies for BC patients.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11942179/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729615","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Genetic Diversity in Candidate Single-Nucleotide Polymorphisms Associated with Resistance in Honeybees in the Czech Republic Using the Novel SNaPshot Genotyping Panel.
IF 2.8 3区 生物学
Genes Pub Date : 2025-03-01 DOI: 10.3390/genes16030301
Martin Šotek, Antonín Přidal, Tomáš Urban, Aleš Knoll
{"title":"Genetic Diversity in Candidate Single-Nucleotide Polymorphisms Associated with Resistance in Honeybees in the Czech Republic Using the Novel SNaPshot Genotyping Panel.","authors":"Martin Šotek, Antonín Přidal, Tomáš Urban, Aleš Knoll","doi":"10.3390/genes16030301","DOIUrl":"10.3390/genes16030301","url":null,"abstract":"<p><p><b>Background/Objectives</b>: The increasing pressure from pathogens and parasites on <i>Apis mellifera</i> populations is resulting in significant colony losses. It is desirable to identify resistance-associated single-nucleotide polymorphisms (SNPs) and their variability for the purpose of breeding resilient honeybee lines. This study examined the genetic diversity of 13 SNPs previously studied for associations with various resistance-providing traits, including six linked to Varroa-specific hygiene, five linked to suppressed mite reproduction, one linked to immune response, and one linked to chalkbrood resistance. <b>Methods</b>: Genotyping was performed using a novel SNaPshot genotyping panel designed for this study. The sample pool consisted of 308 honeybee samples in total, covering all 77 administrative districts of the Czech Republic. <b>Results</b>: All examined loci were polymorphic. The frequency of positive alleles in our population is medium to low, depending on the specific SNP. An analysis of genotype frequencies revealed that most loci exhibited the Hardy-Weinberg equilibrium. A comparison of the allele and genotype frequencies of the same locus between samples from hives and samples from flowers revealed no significant differences. The genetic diversity, as indicated by the heterozygosity values, ranged from 0.05 to 0.50. The fixation index (<i>F</i>) was, on average, close to zero, indicating minimal influence of inbreeding or non-random mating on the genetic structure of the analyzed samples. <b>Conclusions</b>: The obtained results provide further insights into the genetic variation of SNPs associated with the immune response and resistance to pathogens in honeybee populations in the Czech Republic. This research provides a valuable foundation for future studies of honeybee diversity and breeding.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11942514/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729684","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Optimizing Model Performance and Interpretability: Application to Biological Data Classification.
IF 2.8 3区 生物学
Genes Pub Date : 2025-02-28 DOI: 10.3390/genes16030297
Zhenyu Huang, Xuechen Mu, Yangkun Cao, Qiufen Chen, Siyu Qiao, Bocheng Shi, Gangyi Xiao, Yan Wang, Ying Xu
{"title":"Optimizing Model Performance and Interpretability: Application to Biological Data Classification.","authors":"Zhenyu Huang, Xuechen Mu, Yangkun Cao, Qiufen Chen, Siyu Qiao, Bocheng Shi, Gangyi Xiao, Yan Wang, Ying Xu","doi":"10.3390/genes16030297","DOIUrl":"10.3390/genes16030297","url":null,"abstract":"<p><p>This study introduces a novel framework that simultaneously addresses the challenges of performance accuracy and result interpretability in transcriptomic-data-based classification. <b>Background/objectives</b>: In biological data classification, it is challenging to achieve both high performance accuracy and interpretability at the same time. This study presents a framework to address both challenges in transcriptomic-data-based classification. The goal is to select features, models, and a meta-voting classifier that optimizes both classification performance and interpretability. <b>Methods</b>: The framework consists of a four-step feature selection process: (1) the identification of metabolic pathways whose enzyme-gene expressions discriminate samples with different labels, aiding interpretability; (2) the selection of pathways whose expression variance is largely captured by the first principal component of the gene expression matrix; (3) the selection of minimal sets of genes, whose collective discerning power covers 95% of the pathway-based discerning power; and (4) the introduction of adversarial samples to identify and filter genes sensitive to such samples. Additionally, adversarial samples are used to select the optimal classification model, and a meta-voting classifier is constructed based on the optimized model results. <b>Results</b>: The framework applied to two cancer classification problems showed that in the binary classification, the prediction performance was comparable to the full-gene model, with F1-score differences of between -5% and 5%. In the ternary classification, the performance was significantly better, with F1-score differences ranging from -2% to 12%, while also maintaining excellent interpretability of the selected feature genes. <b>Conclusions</b>: This framework effectively integrates feature selection, adversarial sample handling, and model optimization, offering a valuable tool for a wide range of biological data classification problems. Its ability to balance performance accuracy and high interpretability makes it highly applicable in the field of computational biology.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11942234/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729706","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The Emerging Role of MicroRNAs in Nasal Inflammatory Diseases and Tumors: From Bench to Bedside.
IF 2.8 3区 生物学
Genes Pub Date : 2025-02-28 DOI: 10.3390/genes16030295
Antonella Loperfido, Carlo Cavaliere, Bruno Fionda, Simonetta Masieri, Gianluca Bellocchi, Massimo Re, Marco Tomasetti
{"title":"The Emerging Role of MicroRNAs in Nasal Inflammatory Diseases and Tumors: From Bench to Bedside.","authors":"Antonella Loperfido, Carlo Cavaliere, Bruno Fionda, Simonetta Masieri, Gianluca Bellocchi, Massimo Re, Marco Tomasetti","doi":"10.3390/genes16030295","DOIUrl":"10.3390/genes16030295","url":null,"abstract":"<p><strong>Background/objectives: </strong>MicroRNAs (miRNAs) play a crucial role in regulating immune responses and have been implicated in the pathogenesis of various nasal diseases, including chronic rhinosinusitis (CRS), allergic rhinitis (AR), and sinonasal tumors. This review comprehensively explores the emerging role of miRNAs in inflammatory and oncological nasal diseases, highlighting their diagnostic, prognostic, and therapeutic potential.</p><p><strong>Methods: </strong>A comprehensive review of the literature was conducted to summarize current findings on miRNA expression in nasal inflammatory conditions and tumors. Key studies evaluating miRNA-mediated regulatory mechanisms, potential biomarker applications, and therapeutic approaches were analyzed.</p><p><strong>Results: </strong>Altered miRNA expression profiles contribute to the pathogenesis of CRS, AR, and sinonasal tumors. Specific miRNAs, such as miR-125b and miR-155 are upregulated in CRS and AR, promoting inflammation and tissue remodeling. In sinonasal tumors, dysregulated miRNAs, including miR-126 and miR-34/miR-449 clusters, influence tumor progression and therapeutic response. Exosome-mediated miRNA delivery emerges as a promising avenue for precision medicine, offering novel strategies for miRNA-based diagnostics and therapies.</p><p><strong>Conclusions: </strong>miRNAs are key regulators of nasal diseases, with potential applications in non-invasive diagnostics and targeted therapies. Further research into miRNA-based interventions may improve treatment outcomes and contribute to the development of personalized medicine approaches for nasal inflammatory disorders and malignancies.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11942466/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729743","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Integrated RNA-Seq and Metabolomics Analyses of Biological Processes and Metabolic Pathways Involved in Seed Development in Arachis hypogaea L.
IF 2.8 3区 生物学
Genes Pub Date : 2025-02-28 DOI: 10.3390/genes16030300
Long Li, Yutong Wang, Xiaorui Jin, Qinglin Meng, Zhihui Zhao, Lifeng Liu
{"title":"Integrated RNA-Seq and Metabolomics Analyses of Biological Processes and Metabolic Pathways Involved in Seed Development in <i>Arachis hypogaea</i> L.","authors":"Long Li, Yutong Wang, Xiaorui Jin, Qinglin Meng, Zhihui Zhao, Lifeng Liu","doi":"10.3390/genes16030300","DOIUrl":"10.3390/genes16030300","url":null,"abstract":"<p><p>In peanut cultivation, fertility and seed development are essential for fruit quality and yield, while pod number per plant, seed number per pod, kernel weight, and seed size are indicators of peanut yield. In this study, metabolomic and RNA-seq analyses were conducted on the flowers and aerial pegs (aerpegs) of two peanut cultivars JNH3 (Jinonghei) and SLH (Silihong), respectively. Compared with SLH, JNH3 had 3840 up-regulated flower-specific differentially expressed genes (DEGs) and 5890 up-regulated aerpeg-specific DEGs. Compared with the JNH3 aerpegs, there were 4079 up-regulated variety-specific DEGs and 18 up-regulated differentially accumulated metabolites (DAMs) of JNH3 flowers, while there were 3732 up-regulated variety-specific DEGs and 48 up-regulated DAMs in SLH flowers. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the DEGs of JNH3 were associated with pollen germination and phenylalanine metabolism in flower and aerpeg tissues, respectively. In contrast, the DEGs of SLH were associated with protein degradation, amino acid metabolism, and DNA repair. However, there were significant differences in the lipids and lipid-like molecules between JNH3 flowers and SLH flowers. This investigation provides candidate genes and an experimental basis for the further improvement of high-quality and high-yield peanut varieties.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11942507/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729705","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Correction: Sadeghi et al. lncRNA-miRNA-mRNA ceRNA Network Involved in Sheep Prolificacy: An Integrated Approach. Genes 2022, 13, 1295.
IF 2.8 3区 生物学
Genes Pub Date : 2025-02-28 DOI: 10.3390/genes16030299
Masoumeh Sadeghi, Abolfazl Bahrami, Aliakbar Hasankhani, Hamed Kioumarsi, Reza Nouralizadeh, Sarah Ali Abdulkareem, Farzad Ghafouri, Herman W Barkema
{"title":"Correction: Sadeghi et al. lncRNA-miRNA-mRNA ceRNA Network Involved in Sheep Prolificacy: An Integrated Approach. <i>Genes</i> 2022, <i>13</i>, 1295.","authors":"Masoumeh Sadeghi, Abolfazl Bahrami, Aliakbar Hasankhani, Hamed Kioumarsi, Reza Nouralizadeh, Sarah Ali Abdulkareem, Farzad Ghafouri, Herman W Barkema","doi":"10.3390/genes16030299","DOIUrl":"10.3390/genes16030299","url":null,"abstract":"<p><p>In the original publication [...].</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11913319/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143648303","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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