Genes最新文献

{"title":"The Relevance of the Accurate Annotation of Micro and Long Non-Coding RNA Interactions for the Development of Therapies.","authors":"Simona Panni","doi":"10.3390/genes16030262","DOIUrl":"10.3390/genes16030262","url":null,"abstract":"<p><p>A large fraction of the human genome is transcribed in RNA molecules that do not encode for proteins but that do have a crucial role in regulating almost every level of gene expression and, thus, define the specific phenotype of each cell. These non-coding RNAs include well-characterized microRNAs and thousands of less-defined longer transcripts, named long non-coding RNAs. Both types markedly affect the onset and the progression of numerous pathologies, ranging from cancer to vascular and neuro-degenerative diseases. In recent years, a substantial effort has been made to design drugs targeting ncRNAs, and promising advancements have been produced from micro-RNA mimics and inhibitors. Each ncRNA controls several targets, and the overall effect of its inhibition or overexpression depends on the function of the set of genes it regulates. Therefore, in selecting the most appropriate target, and predicting the final outcome of ncRNA-based therapies, it is crucial to have and utilize detailed and accurate knowledge of their functional interactions. In this review, I recapitulate the principal resources which collect information on microRNA and lncRNA networks, focusing on the non-homogeneity of the data that result from disparate approaches. I highlight the role of RNA identifiers and interaction evidence standardization in helping the user to filter and integrate data derived from different databases in a reliable functional web of regulative relations.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11942133/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729643","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}

{"title":"Establishment and Molecular Characterization of a Human Stem Cell Line from a Primary Cell Culture Obtained from an Ectopic Calcified Lesion of a Tumoral Calcinosis Patient Carrying a Novel <i>GALNT3</i> Mutation.","authors":"Simone Donati, Gaia Palmini, Cinzia Aurilia, Irene Falsetti, Francesca Marini, Gianna Galli, Roberto Zonefrati, Teresa Iantomasi, Lorenzo Margheriti, Alessandro Franchi, Giovanni Beltrami, Laura Masi, Arcangelo Moro, Maria Luisa Brandi","doi":"10.3390/genes16030263","DOIUrl":"10.3390/genes16030263","url":null,"abstract":"<p><strong>Background/objectives: </strong>Tumoral calcinosis (TC) is an extremely rare inherited disease characterized by multilobulated, dense ectopic calcified masses, usually in the periarticular soft tissue regions. In a previous study, we isolated a primary cell line from an ectopic lesion of a TC patient carrying a previously undescribed <i>GALNT3</i> mutation. Here, we researched whether a stem cell (SC) subpopulation, which may play a critical role in TC progression, could be present within these lesions.</p><p><strong>Methods: </strong>A putative SC subpopulation was initially isolated by the sphere assay (marked as TC1-SC line) and characterized for its stem-like phenotype through several cellular and molecular assays, including colony forming unit assay, immunofluorescence staining for mesenchymal SC (MSC) markers, gene expression analyses for embryonic SC (ESC) marker genes, and multidifferentiation capacity. In addition, a preliminary expression pattern of osteogenesis-related pathways miRNAs and genes were assessed in the TC1-SC by quantitative Real-Time PCR (qPCR).</p><p><strong>Results: </strong>These cells were capable of differentiating into both the adipogenic and the osteogenic lineages. Moreover, they showed the presence of the MSC and ESC markers, confirmed respectively by using immunofluorescence and qualitative reverse transcriptase PCR (RT-PCR), and a good rate of clonogenic capacity. Finally, qPCR data revealed a signature of miRNAs (i.e., miR-21, miR-23a-3p, miR-26a, miR-27a-3p, miR-27b-3p, and miR-29b-3p) and osteogenic marker genes (i.e., <i>ALP</i>, <i>RUNX2</i>, <i>COLIA1</i>, <i>OPG</i>, <i>OCN</i>, and <i>CCN2</i>) characteristic for the established TC1-SC line.</p><p><strong>Conclusions: </strong>The establishment of this in vitro cell model system could advance the understanding of mechanisms underlying TC pathogenesis, thereby paving the way for the discovery of new diagnostic and novel gene-targeted therapeutic approaches for TC.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11942111/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729639","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}

{"title":"Oncological Treatment Adverse Reaction Prediction: Development and Initial Validation of a Pharmacogenetic Model in Non-Small-Cell Lung Cancer Patients.","authors":"Concetta Cafiero, Raffaele Palmirotta, Canio Martinelli, Alessandra Micera, Luciano Giacò, Federica Persiani, Andrea Morrione, Cosimo Pastore, Claudia Nisi, Gabriella Modoni, Teresa Galeano, Tiziana Guarino, Ilaria Foggetti, Cecilia Nisticò, Antonio Giordano, Salvatore Pisconti","doi":"10.3390/genes16030265","DOIUrl":"10.3390/genes16030265","url":null,"abstract":"<p><p><b>Background/Objectives:</b> The accurate prediction of adverse drug reactions (ADRs) to oncological treatments still poses a clinical challenge. Chemotherapy is usually selected based on clinical trials that do not consider patient variability in ADR risk. Consequently, many patients undergo multiple treatments to find the appropriate medication or dosage, enhancing ADR risks and increasing the chance of discontinuing therapy. We first aimed to develop a pharmacogenetic model for predicting chemotherapy-induced ADRs in cancer patients (the ANTIBLASTIC DRUG MULTIPANEL PLATFORM) and then to assess its feasibility and validate this model in patients with non-small-cell lung cancer (NSCLC) undergoing oncological treatments. <b>Methods:</b> Seventy NSCLC patients of all stages that needed oncological treatment at our facility were enrolled, reflecting the typical population served by our institution, based on geographic and demographic characteristics. Treatments followed existing guidelines, and patients were continuously monitored for adverse reactions. We developed and used a multipanel platform based on 326 SNPs that we identified as strongly associated with response to cancer treatments. Subsequently, a network-based algorithm to link these SNPs to molecular and biological functions, as well as efficacy and adverse reactions to oncological treatments, was used. <b>Results:</b> Data and blood samples were collected from 70 NSCLC patients. A bioinformatic analysis of all identified SNPs highlighted five clusters of patients based on variant aggregations and the associated genes, suggesting potential susceptibility to treatment-related toxicity. We assessed the feasibility of the platform and technically validated it by comparing NSCLC patients undergoing the same course of treatment with or without ADRs against the cluster combination. An odds ratio analysis confirmed the correlation between cluster allocation and increased ADR risk, indicating specific treatment susceptibilities. <b>Conclusions:</b> The ANTIBLASTIC DRUG MULTIPANEL PLATFORM was easily applicable and able to predict ADRs in NSCLC patients undergoing oncological treatments. The application of this novel predictive model could significantly reduce adverse drug reactions and improve the rate of chemotherapy completion, enhancing patient outcomes and quality of life. Its potential for broader prescription management suggests significant treatment improvements in cancer patients.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11942520/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729704","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}

{"title":"Systematic Analysis of <i>Stay-Green</i> Genes in Six <i>Ipomoea</i> Species Reveals the Evolutionary Dynamics, Carotenoid and Anthocyanin Accumulation, and Stress Responses of Sweet Potato.","authors":"Zhidan Zuo, Huihui Ma, Longteng Li, Jialin Qian, Minghui Zhang, Xiang Li, Yeshun Sheng, Yuxin Wang","doi":"10.3390/genes16030266","DOIUrl":"10.3390/genes16030266","url":null,"abstract":"<p><strong>Background/objectives: </strong>Stay-green proteins (SGRs) play a vital role in regulating plant chlorophyll degradation and senescence. However, this gene family has not been explored in <i>Ipomoea</i> species and sweet potato.</p><p><strong>Methods: </strong>A total of 19 <i>SGR</i> family genes (<i>SGRs</i>) were identified using Basic Local Alignment Search Tool (BLAST) methods. The proteins' physiological properties, evolutionary and phylogenetic relationships, conserved domain and motifs, gene structures, collinearity, and promoter <i>cis</i>-elements were systematically analyzed. Moreover, expression patterns and protein interaction network analyses were performed for sweet potato.</p><p><strong>Results: </strong>In this study, we identified 19 <i>SGRs</i> in six <i>Ipomoea</i> species. These <i>SGRs</i> were divided into four subgroups according to their phylogenetic relationships. Domian analysis revealed that SGRs had the conserved \"stay-green\" domain. Gene structure analysis showed that <i>SGRs</i> had similar structures. The collinearity analysis revealed that the <i>SGRs</i> originated from two genes, with one gene undergoing duplication during evolution history; moreover, the <i>SGRs</i> experienced rearrangement throughout the evolutionary process in the <i>Ipomoea</i> species. <i>Cis</i>-elements related to pigment biosynthesis and hormone and stress responses were found. In addition, expression pattern analysis showed that <i>IbSGRs</i>, especially <i>IbSGR1</i>, <i>IbSGR2</i>, and <i>IbSGR3</i>, might play an important role in pigment accumulation. The <i>SGRs</i> could also respond to stress responses (i.e., cold, drought, and salt) and take part in hormone crosstalk (i.e., abscisic acid (ABA), methyl jasmonate (MeJA), salicylic acid (SA)).</p><p><strong>Conclusions: </strong>Taken together, the findings of this study provide new insights for further understanding the functions of <i>SGRs</i> and candidate genes for pigment accumulation and stress tolerance in sweet potatoes.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11941861/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729740","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}

{"title":"Transcriptome Analysis of Environmental Adaptation of Largemouth Bass (<i>Micropterus salmonides</i>).","authors":"Yuao Wang, Huan Li, Chuan Li, Weibin Tang, Yanchao Wang, Hongxia Hou","doi":"10.3390/genes16030267","DOIUrl":"10.3390/genes16030267","url":null,"abstract":"<p><strong>Background/objectives: </strong>The largemouth bass (<i>Micropterus salmonides</i>) is a farmed fish of significant economic value, and studying its adaptability is crucial for enhancing the economic benefits of aquaculture. The largemouth bass changes gene expression pattern to rapidly adapt to environmental changes and maintain normal physiological function.</p><p><strong>Methods: </strong>In this study, largemouth bass from two distinct environmental backgrounds-Huzhou and Xingtai-were used as experimental materials, and they have significantly different breeding conditions. Comparative transcriptomics was used to analyze the gene expression patterns in largemouth bass from both backgrounds.</p><p><strong>Results: </strong>In the female, there were 1678 differentially expressed genes, of which 541 were upregulated and 1137 were downregulated. Meanwhile, in the male, there were 1287 differentially expressed genes, including 542 upregulated genes and 745 downregulated genes. The differentially expressed genes were mainly enriched in biological processes such as metabolic process, biological regulation, response to stimulus, developmental process, signaling, reproduction and immune system process. The enriched pathways included carbon metabolism, glycolysis/gluconeogenesis, purine metabolism, biosynthesis of amino acids, starch and sucrose metabolism, fructose and mannose metabolism, pyrimidine metabolism, MAPK signaling pathway, spliceosome, protein processing in the endoplasmic reticulum, ribosome biogenesis in eukaryotes, etc. Conclusions: We speculated that largemouth bass in Xingtai may adapt to the environment by downregulating metabolism- and reproduction-related genes and altering the expression of immune-related genes. Our study provided molecular evidence for the adaptation research of largemouth bass and provided a scientific basis for optimizing largemouth bass breeding technology.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11942557/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729709","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}

{"title":"Metabolomic and Transcriptomic Analyses of Flavonoid Biosynthesis in <i>Dendrobium devonianum</i> Flowers.","authors":"Yue Li, Yawen Wu, Ran Pu, Xuejiao Li, Tian Bai, Nengbo Li, Ying Zhou, Jingli Zhang","doi":"10.3390/genes16030264","DOIUrl":"10.3390/genes16030264","url":null,"abstract":"<p><strong>Background: </strong><i>Dendrobium devonianum</i> is a traditional Chinese medicinal herb with notable ornamental and medicinal value.</p><p><strong>Methods: </strong>In this study, transcriptomic and metabolomic approaches were employed to investigate gene expression and secondary metabolite changes during four developmental stages of <i>D. devonianum</i> flowers.</p><p><strong>Results: </strong>Metabolomic analysis identified 1186 distinct metabolites, with flavonoid compounds being the most abundant category (213 types). Transcriptomic analysis revealed 31 differentially expressed genes associated with flavonoid biosynthesis and flavonoid and flavonol biosynthesis pathways. Among these, key genes regulating flavonol synthesis, including <i>F3H</i> (Unigene0077194) and <i>FLS</i> (Unigene0062137), exhibited high expression levels in the early developmental stage (S1).</p><p><strong>Conclusions: </strong>Flavonoids serve as the major active components in <i>D. devonianum</i> flowers, exhibiting a wide range of pharmacological properties. This study provides valuable insights into the molecular mechanisms driving flavonoid accumulation in <i>D. devonianum</i>, offering a foundation for further functional studies and applications in ornamental and medicinal plant research.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11942320/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729654","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}

{"title":"Etiologies of Early-Onset Hearing Impairment in Rwanda.","authors":"Esther Uwibambe, Leon Mutesa, Charles Muhizi, Isaie Ncogoza, Elvis Twumasi Aboagye, Norbert Dukuze, Samuel M Adadey, Carmen DeKock, Ambroise Wonkam","doi":"10.3390/genes16030257","DOIUrl":"10.3390/genes16030257","url":null,"abstract":"<p><p><b>Background:</b> Over three-quarters of the people living with hearing impairment (HI) live in low- and middle-income countries. However, Rwanda has limited data on the clinical profile of HI. <b>Aim:</b> We used community-based nationwide recruitment of participants to determine the etiology of early-onset (<7 years of age) HI in Rwanda. <b>Methods:</b> Participants were included after clinical examination, including audiological assessment by pure tone audiometry and/or auditory brainstem response. DNA was extracted from peripheral blood, and the entire coding region of <i>GJB2</i> was interrogated using Sanger sequencing. Multiplex PCR and Sanger sequencing were used to analyze the prevalence of the <i>GJB6</i>-D3S1830 deletion. <b>Results:</b> The participants were recruited from seven inclusive schools, one university teaching hospital, and four independent communities nationwide. We reviewed the clinical histories of 422 individuals affected by early-onset HI from 348 families and found that 21.18% (<i>n</i> = 89/422) was linked to early childhood meningitis infection while 51.23% (<i>n</i> = 216/422) was categorized as unknown HI etiology. Because of putative genetic causes, 82/348 (23.6%) families were reviewed and identified for genetic testing. Within the 82 families with potential genetic causes, 122 individuals were affected by HI, and 205 were unaffected. The male/female ratio of those enrolled for genetic investigations was 0.79 (<i>n</i> = 145/182). The mean age of diagnosis of HI was 4.3 ± 2.6 years. Most cases (89.36%, <i>n</i> = 109/122) reviewed were prelingual. Pedigree analysis suggested autosomal recessive inheritance in 46.3% (<i>n</i> = 38/82) of families. Most HI participants from familial cases had nonsyndromic HI (94.2%, <i>n</i> = 115/122). Waardenburg syndrome was found in three participants out of seven participants who presented with syndromic HI, while three other participants manifested signs of Usher syndrome and one with suspected Noonan syndrome. Molecular analysis did not find pathogenic variants in <i>GJB2</i> or <i>GJB6</i>-D3S1830 deletion in any of the probands tested (<i>n</i> = 27/122; 22.13%) or 100 non-affected control participants. <b>Conclusions:</b> This study revealed an overall late diagnosis (mean at 4.3 years) of HI in Rwanda. Most cases were of unknown origin or putative environmental origin (76.4%), with meningitis predominating as the acquired cause of early-onset HI. Among cases of putative genetic etiology, nonsyndromic HI accounted for the large majority (94.2%). However, <i>GJB2</i> and <i>GJB6</i> pathogenic variants were not identified in the screened proportion of the cohort. This study calls for the implementation of neonatal hearing screening as well as reinforcement of immunization programs to reduce the burden of acquired early-onset HI in Rwanda. Additional genomic studies, ideally using exome sequencing for familial cases, are needed.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11941765/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729641","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}

{"title":"ACT2.6: Global Gene Coexpression Network in <i>Arabidopsis thaliana</i> Using WGCNA.","authors":"Vasileios L Zogopoulos, Konstantinos Papadopoulos, Apostolos Malatras, Vassiliki A Iconomidou, Ioannis Michalopoulos","doi":"10.3390/genes16030258","DOIUrl":"10.3390/genes16030258","url":null,"abstract":"<p><strong>Background/objectives: </strong>Genes with similar expression patterns across multiple samples are considered coexpressed, and they may participate in similar biological processes or pathways. Gene coexpression networks depict the degree of similarity between the expression profiles of all genes in a set of samples. Gene coexpression tools allow for the prediction of functional gene partners or the assignment of roles to genes of unknown function. Weighted Gene Correlation Network Analysis (WGCNA) is an R package that provides a multitude of functions for constructing and analyzing a weighted or unweighted gene coexpression network.</p><p><strong>Methods: </strong>Previously preprocessed, high-quality gene expression data of 3500 samples of Affymetrix microarray technology from various tissues of the <i>Arabidopsis thaliana</i> plant model species were used to construct a weighted gene coexpression network, using WGCNA.</p><p><strong>Results: </strong>The gene dendrogram was used as the basis for the creation of a new <i>Arabidopsis</i> coexpression tool (ACT) version (ACT2.6). The dendrogram contains 21,273 leaves, each one corresponding to a single gene. Genes that are clustered in the same clade are coexpressed. WGCNA grouped the genes into 27 functional modules, all of which were positively or negatively correlated with specific tissues.</p><p><strong>Discussion: </strong>Genes known to be involved in common metabolic pathways were discovered in the same module. By comparing the current ACT version with the previous one, it was shown that the new version outperforms the old one in discovering the functional connections between gene partners. ACT2.6 is a major upgrade over the previous version and a significant addition to the collection of public gene coexpression tools.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11942487/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729608","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}

{"title":"An Extensive Gap Junction Neural Network Modulates <i>Caenorhabditis elegans</i> Aversive Behavior.","authors":"Savannah E Sojka, Meredith J Ezak, Emily A Polk, Andrew P Bischer, Katherine E Neyland, Andrew P Wojtovich, Denise M Ferkey","doi":"10.3390/genes16030260","DOIUrl":"10.3390/genes16030260","url":null,"abstract":"<p><strong>Background/objectives: </strong><i>Caenorhabditis elegans</i> rely on sensory perception of environmental cues for survival in their native soil and compost habitats. These cues provide information about nutrient availability, mating partners, or predatory and hazardous beacons. In <i>C. elegans</i>, the two bilaterally-symmetric head sensory neurons termed ASH are the main detectors of aversive nociceptive signals. Through their downstream connections in the nervous system, ASH activation causes the animal to initiate backward locomotion to escape and avoid the harmful stimulus. Modulation of avoidance behavior allows for situation-appropriate sensitivity and response to stimuli. We previously reported a role for gap junctions in the transport of regulatory cGMP to the ASHs where it functions to dampen avoidance responses.</p><p><strong>Methods: </strong>Here, we used genetic mutants and a combination of cell-selective rescue and knockdown experiments to identify gap junction proteins (innexins) involved in modulating ASH-mediated nociceptive behavioral responses.</p><p><strong>Results: </strong>We have characterized six additional <i>C. elegans</i> innexins that have overlapping and distinct roles within this regulatory network: INX-7, INX-15, INX-16, INX-17, UNC-7, and UNC-9.</p><p><strong>Conclusions: </strong>This work expands our understanding of the extent to which ASH sensitivity can be tuned in a non-cell-autonomous manner.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11941935/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729625","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}

{"title":"Identification of Key Pathways and Candidate Genes Controlling Organ Size Through Transcriptome and Weighted Gene Co-Expression Network Analyses in Navel Orange Plants (<i>Citrus sinensis</i>).","authors":"Yi Lin, Jinghao Zheng, Qinyu Wan, Zhenmin Chen, Qiong Chen, Shubei Wan, Jianmei Chen","doi":"10.3390/genes16030259","DOIUrl":"10.3390/genes16030259","url":null,"abstract":"<p><p><b>Background/Objectives:</b> Organ size is a critical target trait in fruit-tree breeding programs, as it significantly impacts the economic value of plants by influencing their biomass, yield, and quality. Understanding the molecular mechanisms underlying organ size in citrus is essential for breeding new cultivars with superior fruit quality. <b>Methods:</b> In this study, we investigated the regulatory network involved in organ size using the <i>Citrus sinensis</i> 'Newhall' navel orange variety and its large-organ mutant, 'M25'. <b>Results:</b> Ploidy analysis indicated that the organ enlargement observed in 'M25' was not attributable to changes in chromosome ploidy. Furthermore, RNA sequencing of tender leaves and young fruits from both 'M25' and 'Newhall' oranges identified 1817 and 1605 differentially expressed genes (DEGs), respectively. Functional enrichment analysis revealed that these DEGs were enriched in pathways associated with organ size regulation, including those related to cell division, DNA replication, protein biosynthesis, plant hormone signal transduction, and cell wall metabolism. Weighted gene co-expression network analysis identified the grey 60 and orange modules as the key modules influencing organ enlargement; from these modules, we identified 51 and 35 hub genes, respectively. Combined homologous function annotation and expression analysis identified four transcription-factor-encoding hub genes (<i>Cs_ont_6g005380</i>, <i>Cs_ont_8g025330</i>, <i>Cs_ont_9g019400</i>, and <i>Cs_ont_9g008010</i>) as candidate genes potentially related to organ size. <b>Conclusions:</b> Among these, <i>Cs_ont_8g025330</i> (<i>CsMYB73</i>) was inferred to be the key gene influencing organ size through auxin and cytokinin regulation. These findings lay the foundation for further investigations of the regulatory mechanism of organ size in navel orange varieties.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11942113/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729675","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}