Decoding Flavonoid Metabolism for Nutritional Enhancement: A Transcriptome–Metabolome Integration Study of Biosynthesis in Edible <i>Chrysanthemum indicum</i> L. by Chengxiang Wang, Yong Su, Min Wei, Qiaosheng Guo, Qingjun Zou, Tao Wang

“…Transcriptomics identified 43 differentially expressed enzyme genes, with key regulators <i>FNSII</i>, <i>F3′H</i>, and <i>F3H</i> showing expression patterns correlating with metabolite profiles. …”
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Identification and Characterization of Flavonoid Biosynthetic Gene Families in <i>Paeonia</i> Species and Their Roles in Stamen Petalization of <i>Paeonia lactiflora</i> by Yanyi Zheng, Yongming Fan, Xiang Ji, Xiaopei Wu

“…To further investigate the role of these genes in stamen petalization of <i>P. lactiflora</i>, expression profiling analyses were performed on ‘Fen Yu Nu’ (normal stamens) and ‘Lian Tai’ (petaloid stamens) cultivars using transcriptomic data released previously. Three quercetin-related genes revealed distinct stage-specific patterns in ‘Fen Yu Nu’ and ‘Lian Tai’. …”
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Transcriptome analysis reveals nutrient deprivation reduces nitrate content in lettuce (Lactuca sativa var. ramosa Hort.) and enhances nitrogen metabolism by Yingying Zhang, Xuena Liu, Shikai La, Mingjiao Wang, Xu Hu, Ainong Shi, Jinghua Guo, Lingdi Dong

“…These results suggest that lettuce responds to nutrient deprivation by activating nitrate transport and antioxidant pathways to reduce nitrate levels and enhance nitrogen use efficiency.DiscussionThis study provides a foundation for optimizing pre-harvest strategies to improve lettuce quality and identifies candidate genes (e.g., NRT2.5, LOX) for breeding low-nitrate varieties suited for nitrogen-limited environments.…”
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An environmental isolate of Pseudomonas, 20EI1, reduces Aspergillus flavus growth in an iron-dependent manner and alters secondary metabolism by Elizabeth M. Wyman, W. Scott Grayburn, Matthew K. Gilbert, Matthew D. Lebar, Jessica M. Lohmar, Jeffrey W. Cary, Thomas J. C. Sauters, Antonis Rokas, Ana M. Calvo

“…To further elucidate the nature of this bacterial-fungal interaction, we also performed chemical and transcriptomics analyses.ResultsIn the present study, Pseudomonas spp., 20EI1 was able to reduce the growth of A. flavus. …”
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Transcriptomic analysis elucidates the enhanced skeletal muscle mass, reduced fat accumulation, and metabolically benign liver in human follistatin-344 transgenic pigs by Ke-ren LONG, Xiao-kai LI, Ruo-wei ZHANG, Yi-ren GU, Min-jie DU, Xiang-yang XING, Jia-xiang DU, Miao-miao MAI, Jing WANG, Long JIN, Qian-zi TANG, Si-lu HU, Ji-deng MA, Xun WANG, Deng-ke PAN, Ming-zhou LI

“…Together, these results provide new insights into the molecular mechanisms underlying the phenotypic changes in pig.…”
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Novel metabolic subtypes in IDH-mutant gliomas: implications for prognosis and therapy by Peng Wang, Jiayi Wang, Zheng Fang, Qiaodong Chen, Ying Zhang, Xiaoguang Qiu, Zhaoshi Bao

“…This study aims to identify transcriptomic metabolic subtypes and associated immune microenvironment differences to better understand survival variability and potential therapeutic targets in IDH-mutant glioma. …”
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RNA-seq data of pig placenta and endometrium during late gestationFAANG by Sarah Maman-Haddad, Laure Gress, Amandine Suin, Nathalie Vialaneix, Agnès Bonnet

“…The data generated from this analysis provides a complete transcriptional profile of the feto-maternal interface during late gestation. …”
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Integrated analysis of microRNA and mRNA interactions regulating fecundity in the ovaries of two distinct sheep breeds by Salsabeel Yousuf, Waqar Afzal Malik, Hui Feng, Tianyi Liu, Lingli Xie, Xiangyang Miao

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Identification and validation of reference genes for qRT-PCR analyses under different experimental conditions in Dendrobium nobile by Kaijie Li, Xianfen Deng, Yao Wu, Jinling Li, Mingjin Huang, Chunli Luo, Hualei Wang, Hongchang Liu, Dandan Li

“…In this study, eight genes were selected as the candidate RGs based on the transcriptome data from different tissues of D. nobile. …”
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BrGSTF12, an anthocyanin-related glutathione S-transferase gene, is essential for light-induced anthocyanin accumulation in zicaitai (Brassica Rapa Var. purpuraria) by Mei Fu, Guihua Li, Mengting Lu, Shizheng Jiang, Umer Karamat, Imran Khan, Juxian Guo

“…Bioinformatics approaches were employed to predict and identify potential genes involved in the sequestration of anthocyanins in Zicaitai (Brassica rapa var. purpuraria) utilizing data from the transcriptome database. Results In this study 0-hour light (dark) and 8-hour light treatments of Zicaitai were examined using transcriptome analysis. …”
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Melatonin-induced Bacillus tequilensis enhanced the disease resistance of Camellia oleifera against anthracnose by modulating cell wall and phenylpropanoid metabolism by Aiting Zhou, Aiting Zhou, Huiqin Zhou, Huiqin Zhou, Ruiqi Peng, Ruiqi Peng, Di Liu, Di Liu, Jianrong Wu, Jianrong Wu, Jia Deng, Jia Deng, Fang Wang, Fang Wang

“…Furthermore, we analyzed the impact of MT-DZY 6715 on the anatomical features of C. oleifera leaves using histological sectioning. Additionally, transcriptome and enzymatic assays were employed to assess the expression of secondary metabolism-related genes and the activity of cell wall-degrading enzymes.ResultsThe application of MT-DZY 6715 effectively controls the growth of C. siamense, markedly reducing the incidence of C. oleifera anthracnose and delaying the spread of pathogens on the leaves. …”
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Herpes simplex virus-induced upregulation of inflammatory cytokines in human gingival fibroblasts by Yu Zhang, Kalam Lo, Chunmei Wang, Guoliang Zhou, Xiping Feng, Jing Ni, Xi Chen

“…The present study used RNA sequencing to investigate the transcriptomes of human gingival fibroblasts (HGFs) following HSV-1 infection from the early to late stages (12–72 h). …”
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Gut microbiota contribute to high-altitude adaptation in tree sparrows by Tingbei Bo, Gang Song, Mengru Zhang, Xiaoming Xu, Jundong Duan, Huishang She, Yun Fang, Wenting Li, Jing Wen, Jingsong Liu, Dehua Wang, Fumin Lei

“…Therefore, we employed a multidisciplinary approach combining amplicon sequencing, transcriptome analysis, and fecal microbiota transplantation (FMT) to investigate the functional role of gut microbiota in high-altitude tree sparrows across different seasons. …”
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Whole-transcriptome sequencing reveals the global molecular responses and ceRNA regulatory network involved in programmed cell death of rice cultivars zyk639 and zyk-lm by Haipeng Zhang, Han Zheng, Weifang Liang, Junjie Zhang, Hongyu Zhao, Jianzhong Li, Yujie Zhou, Liujie Xie, Chulang Yu, Binfeng Dai, Liequan Zhong, Fan Hou, Chengyu Wang, Jianping Chen, Yong Yang

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Impact of life adversity and gene expression on psychiatric symptoms in children and adolescents: findings from the Brazilian high risk cohort study by Vanessa Kiyomi Ota, Vanessa Kiyomi Ota, Vanessa Kiyomi Ota, Vanessa Kiyomi Ota, Adrielle Martins Oliveira, Adrielle Martins Oliveira, Adrielle Martins Oliveira, Amanda Victória Gomes Bugiga, Amanda Victória Gomes Bugiga, Amanda Victória Gomes Bugiga, Helena B. Conceição, Pedro Alexandre Favoretto Galante, Paula Fontes Asprino, Julia Luiza Schäfer, Julia Luiza Schäfer, Mauricio Scopel Hoffmann, Mauricio Scopel Hoffmann, Mauricio Scopel Hoffmann, Mauricio Scopel Hoffmann, Mauricio Scopel Hoffmann, Rodrigo Bressan, Rodrigo Bressan, Rodrigo Bressan, Elisa Brietzke, Gisele Gus Manfro, Gisele Gus Manfro, Rodrigo Grassi-Oliveira, Ary Gadelha, Ary Gadelha, Luis Augusto Rohde, Luis Augusto Rohde, Luis Augusto Rohde, Luis Augusto Rohde, Euripedes Constantino Miguel, Euripedes Constantino Miguel, Pedro Mario Pan, Pedro Mario Pan, Pedro Mario Pan, Marcos Leite Santoro, Marcos Leite Santoro, Marcos Leite Santoro, Giovanni Abrahao Salum, Giovanni Abrahao Salum, Giovanni Abrahao Salum, Carolina Muniz Carvalho, Carolina Muniz Carvalho, Carolina Muniz Carvalho, Sintia Iole Belangero, Sintia Iole Belangero, Sintia Iole Belangero, Sintia Iole Belangero

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Weighted Gene Co-Expression Network Analysis Identifies Hub Genes Governing Resistance to <i>Fusarium oxysporum</i> f. sp. <i>niveum</i> in Watermelon (<i>Citrullus lanatus</i>) by Chen Zhang, Xufeng Fang, Jing Zhang, Xinying Wang, Zhao Liu, Shusen Liu, Zhengfeng Song, Peng Gao, Feishi Luan

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Integrated transcriptomic and metabolomic analyses reveal tissue-specific accumulation and expression patterns of monoterpene glycosides, gallaglycosides, and flavonoids in Paeonia... by Pan Xu, Jinghui Li, Cuiting Chen, Jing Chen, Meiping Yang, Huimin Deng, Xuechun Jiang, Kelang Lou, Xiaojun Wu, Rubing Chen, Yijuan Hu, Weiqing Liang, Jinbao Pu

“…Results Metabolomic and transcriptome profiling revealed tissue-specific patterns of metabolite accumulation and gene expression. …”
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A Novel Research Paradigm for Sarcopenia of Limb Muscles: Lessons From the Perpetually Working Diaphragm's Anti‐Aging Mechanisms by Enhui Li, Rui Wang, Yanli Li, Xiang Zan, Shufen Wu, Yiru Yin, Xiaorong Yang, Litian Yin, Yu Zhang, Jianguo Li, Xin Zhao, Ce Zhang

“…Critically, the potential endogenous anti‐aging mechanisms of DIA that may provide new insights into the mechanisms of sarcopenia in limb muscles remain scarce. …”
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Integrated spatial omics of metabolic reprogramming and the tumor microenvironment in pancreatic cancer by Hao Wu, Qiyao Zhang, Zhen Cao, Hongtao Cao, Mengwei Wu, Mengdi Fu, Tingping Huang, Xianlin Han, Xiaoyan Chang, Ziwen Liu

“…Spatial transcriptomics identified distinct pathological regions, which were further characterized using single-cell transcriptomic data and pathologist annotations. …”
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Tumor-derived colorectal cancer organoids induce a unique Treg cell population by directing CD4+ T cell differentiation by Sonia Aristin Revilla, Cynthia L. Frederiks, Stefan Prekovic, Enric Mocholi, Onno Kranenburg, Paul J. Coffer

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