Genes & genomics最新文献

{"title":"Aneusomaty in glyphosate-resistant Amaranthus palmeri and its hybrid with Amaranthus tuberculatus.","authors":"Yoonha Ju, Rajendran Sathishraj, Bikram S Gill, Dal-Hoe Koo","doi":"10.1007/s13258-025-01662-7","DOIUrl":"https://doi.org/10.1007/s13258-025-01662-7","url":null,"abstract":"<p><strong>Background: </strong>Glyphosate [N-(phosphonomethyl) Glycine], commonly known as Roundup, is one of the most widely used herbicides for controlling crop weeds. However, its extensive use has led to the rapid evolution of glyphosate-resistant (GR) weed populations, often via amplification of the target gene EPSPS (5-enolpyruvylshikimate-3-phosphate synthase), sometimes accompanied by chromosomal abnormalities.</p><p><strong>Objective: </strong>This study investigates the occurrence and characteristics of aneusomaty in GR Amaranthus palmeri and its interspecific hybrids with A. tuberculatus.</p><p><strong>Methods: </strong>Fluorescence in situ hybridization (FISH) was used to cytologically characterize glyphosate resistance and aneusomaty in A. palmeri.</p><p><strong>Results: </strong>Aneusomaty was observed in GR A. palmeri and its hybrids with A. tuberculatus. Root tips from a single GR A. palmeri plant exhibited two distinct chromosome numbers: 2n = 34 and 2n = 68. Similarly, F1 hybrid root tips [A. tuberculatus (2n = 32) x A. palmeri (2n = 34)] displayed 2n = 33 and 2n = 66. The pseudo F₂ plants, apomictically derived from F₁ hybrids, consistently showed 2n = 50 chromosomes. FISH targeting 5 S rDNA loci, was used to distinguish the genomes of A. palmeri and A. tuberculatus in the F₁ and pseudo F₂ plants. The pseudo F₂ plants (2n = 50) contained the diploid chromosome set of A. palmeri (2n = 34) and the haploid chromosome set of A. tuberculatus (n = 16). Notably, these sporadic chromosome duplications occurred only in glyphosate-resistant (GR) plants and were absent in glyphosate-sensitive (GS) plants.</p><p><strong>Conclusion: </strong>Our results suggest that aneusomaty-related increases in chromosome numbers during the sporophytic phase may facilitate EPSPS gene duplication, offering a previously unrecognized mechanism contributing to glyphosate resistance in A. palmeri.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":""},"PeriodicalIF":1.6,"publicationDate":"2025-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144707324","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction: Expression of lncRNA NEAT1 in endometriosis and its biological functions in ectopic endometrial cells as mediated via miR-124-3p.","authors":"Donglan Yuan, Dandan Zhu, Boyu Yin, Hongshan Ge, Yinling Zhao, Aihua Huang, Xiaosu Wang, Xiuhong Cao, Nan Xia, Hua Qian","doi":"10.1007/s13258-025-01651-w","DOIUrl":"https://doi.org/10.1007/s13258-025-01651-w","url":null,"abstract":"","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":""},"PeriodicalIF":1.6,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144659074","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction: the role of miRNA-624-5p in congenital hypothyroidism and its molecular mechanism by targeting SIRT1.","authors":"Wanli Wu, Xuying Cao, Yuhong Wang","doi":"10.1007/s13258-025-01652-9","DOIUrl":"https://doi.org/10.1007/s13258-025-01652-9","url":null,"abstract":"","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":""},"PeriodicalIF":1.6,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144659075","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hierarchical structural component model for pathway analysis of multinomial phenotypes.","authors":"Md Kamruzzaman, Taewan Goo, Taesung Park","doi":"10.1007/s13258-025-01655-6","DOIUrl":"https://doi.org/10.1007/s13258-025-01655-6","url":null,"abstract":"","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":""},"PeriodicalIF":1.6,"publicationDate":"2025-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144553315","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"De novo somatic mosaicisms of INF2 and TRPV4 in patients with Charcot-Marie-Tooth disease.","authors":"Ah Jin Lee, Sumaira Kanwal, Manisha Awasthi, Byung-Ok Choi, Ki Wha Chung","doi":"10.1007/s13258-025-01643-w","DOIUrl":"10.1007/s13258-025-01643-w","url":null,"abstract":"<p><strong>Background: </strong>Somatic mosaicism is caused by a postzygotic de novo mutation. It is a very rare genetic event, and mosaic cases have been reported only very limitedly among Korean patients with peripheral neuropathies, including Charcot-Marie-Tooth disease (CMT) so far.</p><p><strong>Objective: </strong>This study was performed to identify and characterize somatic mosaicism in Korean families with CMT.</p><p><strong>Methods: </strong>Genetic causes were identified by whole exome sequencing (WES) and a subsequent filtering process of the variants. The level of mosaicism for the de novo somatic mutations was determined by counting altered sequences from approximately 100 colonies/mutation and the ratio of altered sequences per total reads at the mutation site using the WES data.</p><p><strong>Results: </strong>We observed two cases of somatic mosaicism in different families with CMT: p.Cys104Tyr in INF2 (male with CMT1) and p.Ser729Arg in TRPV4 (female with CMT2). The approximate levels of mosaicism were determined to be 24% and 30% in the blood, respectively. A man with the INF2 mutation showed very mild symptoms, while a woman with the TRPV4 mutation showed severe clinical phenotypes. The INF2 mutation is specifically considered a case of gonadal mosaicism. In addition, we confirmed that the p.Cys104Tyr in INF2 is associated with the CMT1 phenotype without focal segmental glomerulosclerosis (FSGS).</p><p><strong>Conclusion: </strong>This study may be the first or second report for the INF2 and TRPV4 mosaicism. The degrees of the phenotypic severity for the mosaic mutations probably depend on the mutation sites and the levels of mosaicism in the affected tissues. This study suggests that somatic mosaicism may contribute to inter- or intra-familial phenotypic heterogeneity.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"797-806"},"PeriodicalIF":1.6,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143997365","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of Zonula occludens-1 (ZO-1) tight junction protein on tumor characteristics in human ovarian cancer cells.","authors":"Hyung Joon Yoon, Do-Ye Kim, Hyojin An, Min-Hye Kim, Seongsoo Choi, Eun-Ji Ko, Heungyeol Kim, Ji Young Lee, Wan Kyu Eo, Min Young Kim, Ki Hyung Kim, Hee-Jae Cha","doi":"10.1007/s13258-025-01649-4","DOIUrl":"10.1007/s13258-025-01649-4","url":null,"abstract":"<p><strong>Background: </strong>Ovarian cancer is among the most lethal malignancies affecting women, largely due to its asymptomatic progression in early stages, rapid advancement, and high mortality rate. Tight junction protein 1 (TJP1), also known as Zonula occludens-1 (ZO-1), plays a critical role in epithelial and endothelial cell integrity by regulating paracellular permeability. Additionally, ZO-1 is involved in cell-cell communication networks, influencing cellular proliferation, differentiation, and metastasis. While previous studies have demonstrated the significance of ZO-1 in tumorigenesis and cancer progression, its precise mechanistic role remains to be fully elucidated.</p><p><strong>Objective: </strong>This study aims to investigate the functional role of ZO-1 in human ovarian cancer cells to provide a molecular perspective on its impact on tumor progression.</p><p><strong>Methods: </strong>Human ovarian cancer cell lines SNU119 and SKOV3 were utilized. ZO-1 knockout (KO) was achieved using the Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR-associated protein 9 (CRISPR-Cas9) system in combination with single-guide RNA (sgRNA) targeting ZO-1. Hygromycin B selection was employed to establish stable ZO-1 KO SNU119 and ZO-1 KO SKOV3 cell lines. The successful knockout of ZO-1 was confirmed at both the transcript and protein levels via real-time quantitative PCR (RT-qPCR) and Western blotting. Functional assays, including cell proliferation, migration, and invasion assays, were conducted to assess the effects of ZO-1 KO on key tumor-associated characteristics.</p><p><strong>Results: </strong>CRISPR-Cas9-mediated ZO-1 KO in SNU119 and SKOV3 ovarian cancer cell lines resulted in a significant reduction of ZO-1 expression at both the transcript and protein levels. The loss of ZO-1 led to a disruption of cell-cell junctions. Functionally, ZO-1 KO cells exhibited reduced proliferation, whereas cell migration and invasion were significantly enhanced, suggesting a shift toward a more aggressive phenotype.</p><p><strong>Conclusion: </strong>The findings indicate that ZO-1 KO in ovarian cancer cells suppresses cell proliferation while promoting migratory and invasive properties, hallmarks of tumor progression. These results underscore the complex role of ZO-1 in ovarian cancer and highlight the need for further investigation into its broader regulatory impact on oncogenic pathways.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"867-875"},"PeriodicalIF":1.6,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144142440","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular cloning, expression analysis, and functional characterization of Intelectin-1 from Chinese giant salamanders (Andrias davidianus).","authors":"Haolin Mo, Kexin Liu, Xiaoran An, Yongqing Chen, Jiajia Yu, Huixia Yu, Mingxing Yao, Weijia Song, Yang Li, Lixin Wang","doi":"10.1007/s13258-025-01630-1","DOIUrl":"10.1007/s13258-025-01630-1","url":null,"abstract":"<p><strong>Background: </strong>Intelectin (ITLN) plays a pivotal role in innate immunity, inflammatory responses, and tumor progression. However, its physiological roles in caudate amphibians, such as Andrias davidianus, remain elusive.</p><p><strong>Objective: </strong>A proto-type of intelectin (AdITLN1) from A. davidianus was characterized, following which an AdITLN1 homology model was generated to analyze its expression profiles and functional characterizations.</p><p><strong>Methods: </strong>The intelectin1 gene (AdITLN1) was cloned, and its evolutionary relationship with ITLN1 from other species was explored. Additionally, a homology model was generated using Molecular Operating Environment (MOE) software, and the active binding pocket of AdITLN1 was identified. Infections with Aeromonas hydrophila were conducted to analyze changes in ITLN1 transcript levels in liver tissue. Finally, recombinant A. davidianus ITLN1 protein (rAdITLN1) was synthesized using prokaryotic expression, and its bacterial agglutination activity and impact on macrophage phagocytosis were examined.</p><p><strong>Results: </strong>Multiple sequence alignment and phylogenetic analysis indicated that AdITLN1 shared the closest evolutionary relationship with amphibians, with its structure being similar to that of human intelectin1 and Xenopus Embryonic Epidermal Lectin. Moreover, AdITLN1 mRNA was expressed in a wide range of tissues and was significantly up-regulated post-A. hydrophila infection. Meanwhile, the AdITLN1 protein was successfully expressed and purified in Escherichia coli (E. coli) BL21 (DE3). The recombinant AdITLN1 (rAdITLN1) displayed strong agglutination activity against different Gram-negative and Gram-positive bacteria. Lastly, The phagocytosis of rAdITLN1-treated E. coli by macrophages was significantly enhanced.</p><p><strong>Conclusion: </strong>The results of the present study demonstrated that AdITLN1 was a multifunctional immune protein with potent immunomodulatory activity. This study offers valuable insights into disease control in giant salamanders and the conservation of natural resources.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"843-853"},"PeriodicalIF":1.6,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143656904","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of genetic signatures of positive selection in apes linked to life-history trait adaptations.","authors":"Yoo-Rim Roh, Kiejung Park, Young Jun An, Hyung-Soon Yim, Jung-Hyun Lee","doi":"10.1007/s13258-025-01647-6","DOIUrl":"10.1007/s13258-025-01647-6","url":null,"abstract":"<p><strong>Background: </strong>Apes, including humans, exhibit distinctive life history traits such as increased brain mass, delayed sexual maturity, and extended longevity compared to non-ape primates. These pronounced interspecific differences likely arise from underlying genetic architecture. However, the molecular mechanisms contributing to these traits remain largely unknown.</p><p><strong>Objective: </strong>This study aims to identify genetic factors under positive selection that may have contributed to the evolution of ape-specific life history traits, particularly extended longevity.</p><p><strong>Methods: </strong>Comparative genomic analyses were performed between 7 ape species and 22 non-ape primate taxa to identify positively selected genes (PSGs). Functional enrichment analyses were conducted to determine the biological processes associated with these PSGs. Additionally, expression analyses were carried out to assess tissue-specific patterns and their potential roles in neurodevelopment and systemic homeostasis.</p><p><strong>Results: </strong>A total of 143 PSGs were idetntified, showing significant enrichment in biological processes including homeostatic regulation, protein complex assembly, and G protein-coupled receptor signaling pathways. Among these, ADCY5, PRKCB, and IL2 were of particular interest due to their established roles in longevity-associated mechanisms. Expression analyses revealed tissue-specific patterns suggesting potential involvement in brain evolution, neurodevelopment, and glucose homeostasis.</p><p><strong>Conclusion: </strong>This study provides molecular insights into the genetic mechanisms underlying longevity in apes and highlights key biological processes that may have contributed to the evolution of ape-specific life history traits. These findings enhance our understanding of how positive selection has shaped complex phenotypes, particularly extended lifespan, in the ape lineage.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"807-822"},"PeriodicalIF":1.6,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143980281","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Gene expression profile in ulcerative colitis patients: FOXO4, ALDOB, SLC26A3, SOD2 genes as potential biomarkers.","authors":"Yakup Ülger, Anıl Delik","doi":"10.1007/s13258-025-01625-y","DOIUrl":"10.1007/s13258-025-01625-y","url":null,"abstract":"<p><strong>Background: </strong>Ulcerative colitis (UC) is a complex, chronic inflammatory disease that primarily impacts the colon mucosa. One of the key pathological contributors to the development and progression of inflammatory bowel disease (IBD) is oxidative stress, which results in reactive oxygen species (ROS)-induced mucosal damage. This stress leads to dysfunction of the intestinal barrier.</p><p><strong>Objectives: </strong>The purpose of this study is to examine the expression levels of genes involved in various inflammatory pathways, including autophagy, unfolded protein response (UPR), ubiquitination, metabolic pathways, and immune responses in the colon mucosa of patients with UC.</p><p><strong>Material and methods: </strong>Patients diagnosed with UC at Çukurova University, Balcalı Hospital, Gastroenterology Department between December 2023 and January 2024 were included in this prospective study. A total of 40 participants were included in the study: 27 ulcerative colitis patients and 13 controls. To isolate high-quality RNA, colon biopsy material obtained during colonoscopy was immediately placed in stabilization solution and stored at - 80 degrees Celsius. The relative quantification of target gene mRNA was determined using a Light Cycler. Subsequently, differences in gene expression between patients and the control group were evaluated using the Mann-Whitney U and Kruskal-Wallis tests.</p><p><strong>Results: </strong>In our study, FOXO4 gene expression increased in UC patients during both active and remission phases compared to the control group. The high expression of this gene is associated with its role in inflammation and cell death processes. Additionally, the high expression of ALDOB and SLC26A genes is linked to increased inflammation and energy demand. Lastly, the elevated expression of the SOD2 gene can be considered a response to oxidative stress-related inflammatory processes in the disease.</p><p><strong>Conclusion: </strong>These findings propose that these genes could serve as potential biomarkers for genomic identification and understanding the pathogenesis of UC.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"833-842"},"PeriodicalIF":1.6,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143735756","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptomic analysis revealed that short-day treatment of seedlings promotes flowering in maize (Zea mays L.).","authors":"Chunlei Li, Hongquan Mao, Xiaoxue Fan, Meihui Yu, Xiaoming Yu","doi":"10.1007/s13258-025-01640-z","DOIUrl":"10.1007/s13258-025-01640-z","url":null,"abstract":"<p><strong>Background: </strong>In this study, blockage of transition from vegetative to reproductive growth was observed in short-day maize (Zea mays L.) varieties under long-day conditions.</p><p><strong>Methods: </strong>Two short-day varieties, namely, CML116 and CML493, were cultivated under long-day conditions at various time points of short-day treatments of seedlings. Notably, short-day treatment was started at the three-leaf stage and ended at the five- (5 L), seven- (7 L) and nine-leaf (9 L) stages. Moreover, transcriptomic analysis (RNA-seq) was carried out to examine the gene expression profiles.</p><p><strong>Results: </strong>The results of gene functional analysis showed that DEGs related to light stimulation and circadian rhythm had different expression patterns among various groups. Additionally, ZmCO, ZmSOC1, ZmFT and ZmHY5 acted as the key regulators of the transition process from vegetative to reproductive growth. Furthermore, the expression of most CO transcripts reached a peak at 5 L in both CML493 and CML116 but decreased in the subsequent short-day treatment.</p><p><strong>Conclusions: </strong>It is possible that accumulation of CO and FT at the seedling stage facilitated transition from vegetative to reproductive growth. In addition, long-day conditions were not conducive to the accumulation of CO and FT as well as their downstream target, SOC1. Moreover, accumulation of the HY5 protein promoted photomorphogenesis, which played a positive role in promoting the normal development of maize plants.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"855-866"},"PeriodicalIF":1.6,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143794731","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}