Comparative energy metabolism in red and white muscles of juvenile yellowfin tuna, Thunnus albacore by Zhiyuan Lu, Zhiyuan Lu, Qian Li, Edwine Yongo, Juan Xiao, Zhiqiang Guo, Zhiqiang Guo

“…Functional enrichment analysis demonstrated significant association of red muscle DEGs with oxidative phosphorylation, tricarboxylic acid cycle, and fatty acid β-oxidation, while white muscle preferentially enriched glycolysis/gluconeogenesis pathways. …”
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Involvement of dysregulated RNA binding protein and alternative splicing regulatory networks in diabetic nephropathy from type 2 albuminuric cohorts by Yu Wang, Jingjing Zhang, Qian Tang

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High spatial resolution gene expression profiling and characterization of neuroblasts migrating in the peri-injured cortex using photo-isolation chemistry by Takuya Miyamoto, Kazuya Kuboyama, Mizuki Honda, Mizuki Honda, Yasuyuki Ohkawa, Shinya Oki, Shinya Oki, Kazunobu Sawamoto, Kazunobu Sawamoto

“…Gene Ontology analysis revealed that in neuroblasts migrating in the peri-injured cortex, expression of genes involved in regulating migration direction and preventing cell death was upregulated, while the expression of genes involved in cell proliferation and maintenance of the immature state was downregulated. …”
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Selenium Alleviates Low-Temperature Stress in Rice by Regulating Metabolic Networks and Functional Genes by Naixin Liu, Qingtao Yu, Baicui Chen, Chengxin Li, Fanshan Bu, Jingrui Li, Xianlong Peng, Yuncai Lu

“…Se treatment also increased the activities of antioxidant enzymes, including catalase (CAT), superoxide dismutase (SOD), and peroxidase (POD), by 25.2%, 42.7%, and 33.3%, respectively, and upregulated flavonoids, soluble sugars, cysteine (Cys), glutathione (GSH), and oxidized glutathione (GSSG). Transcriptome analysis revealed that ColdSe1 treatment upregulated genes associated with amino and nucleotide sugar metabolism, glutathione metabolism, and fructose and mannose metabolism. …”
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Single-cell sequencing and spatial transcriptomics reveal the evolution of glucose metabolism in hepatocellular carcinoma and identify G6PD as a potential therapeutic target by Deyang Xi, Deyang Xi, Yinshuang Yang, Jiayi Guo, Jiayi Guo, Mengjiao Wang, Mengjiao Wang, Xuebing Yan, Chunyang Li

“…Pseudotime analysis was performed on the single-cell data, while ST data was used to analyze spatial metabolic activity. …”
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Optimal Vase Solution for <i>Gerbera hybrida</i> Cut Flower Keeping Fresh by Activating SA and Cytokinin Signaling and Scavenging Reactive Oxygen Species by Chaoshui Xia, Yiyang Cao, Weixin Gan, Huifeng Lin, Huayang Li, Fazhuang Lin, Zhenhong Lu, Weiting Chen

“…Further, transcriptome GO-enrichment and physiological analysis showed that the OS might extend VL of Gerbera cut flowers by scavenging reactive oxygen species, including by activating the expression of genes related to oxidoreductase activity and the activities of antioxidant-system-related enzymes catalase (CAT), peroxidase (POD), ascorbate peroxidase (APX), and superoxide dismutase (SOD), while decreasing the malondialdehyde (MDA) content. …”
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Genomic, Transcriptomic and Suspect/Non‐Target Screening Analyses Reveal the Role of CYP450s in the Degradation of Imazalil and Delineate Its Transformation Pathway by Cladosporium... by Christina V. Papazlatani, Sotirios Vasileiadis, Eleni I. Panagopoulou, Dimitrios E. Damalas, Panagiotis A. Karas, Evdoxia Gerovasileiou, Nikolaos S. Thomaidis, Dimitrios G. Karpouzas

“…Here we describe the genetic network utilised by the fungus to degrade IMZ and its detailed transformation. Genomic and transcriptomic analysis of C. herbarum pointed to the involvement of strongly upregulated CYP450s in IMZ degradation, as further verified by cessation of its biodegradation by CYP450 inhibitors. …”
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Achievements and prospects of applying high-throughput sequencing techniques to potato genetics and breeding by I. V. Bykova, N. A. Shmakov, D. A. Afonnikov, A. V. Kochetov, E. K. Khlestkina

“…This information should prove useful while planning comparative assays of potato transcriptome or application of DNA-markers. …”
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FGSE02, a Novel Secreted Protein in <i>Fusarium graminearum</i> FG-12, Leads to Cell Death in Plant Tissues and Modulates Fungal Virulence by Zhigang Hao, Lei Pan, Jiaqing Xu, Chengxuan Yu, Jianqiang Li, Laixin Luo

“…Here, we combined transcriptome analysis and functional validation to identify virulence-associated genes in <i>Fusarium graminearum</i> during fungi infection. …”
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Evaluation of Drought Tolerance and Trehalose Response in <i>Auricularia heimuer</i> by Jian Sun, Fangjie Yao, Lixin Lu, Youmin Zhang, Ming Fang, Xiaoxu Ma, Kaisheng Shao, Xu Sun

“…The tested strains were classified into the following four categories according to their membership function values: the first category consisted of the highly drought-tolerant strain A; the second consisted of the drought-tolerant strains A127 and C; the third consisted of the moderately drought-tolerant strains A124, A14, A386, A462, A184, A496, A125, and B; and the fourth consisted of the drought-sensitive strains A356 and A508. Transcriptome analysis was performed on C before and after drought stress treatment, and 1762 differentially expressed genes (DEGs) were obtained, including 798 up- and 964 down-regulated genes. …”
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Network Pharmacology and Transcriptomics Reveal the Mechanism of GuaLouQuMaiWan in Treatment of Type 2 Diabetes and Its Active Small Molecular Compound by Jiahao Feng, Yuheng Zhou, Li Liao, Liping Yu, Ping Yuan, Jun Zhang

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A comprehensive RNA virome identified in the oyster Magallana gigas reveals the intricate network of virus sharing between seawater and mollusks by Shuang Wu, Yimin Ni, Shuling Yan, Yongxin Yu, Yongjie Wang

“…M. hongkongensis has been found to harbor the most diverse viruses found in M. gigas, while 37 and 25 newly identified RNA viruses in oysters were discovered in an octopus meta-transcriptome and seawater virome, respectively. …”
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Integrating whole-genome re-sequencing and transcriptome data to reveal the molecular mechanism of TBX5 gene regulating feathered feet in Guangxi native chickens by Zhuliang Yang, Yongcui Liu, Jintang Luo, Cong Xiao, Hong Yuan, Wenya Du, Xiurong Yang

“…This study combined whole-genome re-sequencing (WGS) data, transcriptomic analysis, and cellular experiments to investigate the genetic basis of feathered feet in Guangxi native chickens. …”
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Methylation and gene expression patterns in adamantinomatous craniopharyngioma highlight a panel of genes associated with disease progression-free survival by Junier Marrero-Gutiérrez, Ana Carolina Bueno, Ana Carolina Bueno, Clarissa Silva Martins, Rui Milton Patrício Silva-Júnior, Antônio Carlos dos Santos, Marcelo Volpon Santos, Luiz Eduardo Wildemberg, Ximene Lima da Silva Antunes, Monica R. Gadelha, Ayrton Custodio Moreira, Ricardo Zorzetto Nicoliello Vêncio, Sonir Roberto R. Antonini, Margaret de Castro

“…IntroductionOver the past decade, advancements in next-generation sequencing have significantly enhanced our understanding of the molecular pathogenesis of adamantinomatous craniopharyngiomas (ACP).ObjectiveThis study integrated methylome and transcriptome analyses in ACP samples to explore the potential interplay between DNA methylation and RNA expression signatures for diagnostic and prognostic applications in ACP patients.MethodsThis cross-sectional study evaluated clinicopathological features, DNA methylation, and gene expression profiles in 15 patients with ACP (33% women, age range: 3–55 years, 53% diagnosed before 18 years) treated at Ribeirao Preto Medical School, University of São Paulo.ResultsMultidimensional scaling and principal component analysis identified two distinct clusters (ACP-A: n=9, ACP-B: n=6) with consistent composition across DNA methylation and gene expression profiles. …”
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Metabolite differences and molecular mechanism between dehiscent and indehiscent capsule of mature sesame by Yinping Zhang, Ruirui Chen, Yujun Liu, Shuwen Xu, Shuguang Gao, Haiyang Zhang, Hongmei Miao, Lingling Qin, Xiangyu Zhou, Kiran Thakur, Cheng Li, Juan Li, Pengcheng Wei, Zhao-Jun Wei

“…Using comparative metabolome and transcriptome analysis, this work investigated the molecular regulation and enrichment pathways in two sesame types of indehiscent capsule WanZhi28 (ND) and dehiscent capsule WanZhi2 (WZ2). …”
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MicroRNA transcriptome of skeletal muscle during yak development reveals that miR-652 regulates myoblasts differentiation and survival by targeting ISL1 by Xue-lan ZHOU, Xian GUO, Chun-nian LIANG, Min CHU, Xiao-yun WU, Ping YAN

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Dietary Tannic Acid Promotes Growth Performance and Resistance Against <i>Aeromonas hydrophila</i> Infection by Improving the Antioxidative Capacity and Intestinal Health in the Ch... by Liqin Ji, Yisen Shangguan, Chen Chen, Chengqing Wei, Junxian Zhu, Xiaoyou Hong, Xiaoli Liu, Xinping Zhu, Wei Li

“…Additionally, 1–4 g/kg of TA improved the T-SOD, CAT, and GSH-Px activities during infection, while 2 g/kg of dietary TA enhanced the richness and diversity of the microbiota, for example, by increasing Actinobacteria but inhibiting Firmicutes. …”
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CD9, a novel potential biomarker of sarcopenia by Lin Yin, Na Li, Peirong Bai, Shasha Wu, Xuena Wang, Bin Lu

“…The combined omics analysis identified 8 key genes, while the experiments verified that only CD9 significantly decreased in sarcopenia. …”
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Prediction of hub genes in pulpal inflammation and regeneration using autoencoders and a generative AI approach by Pradeep K. Yadalam, Jogikalmat Krithikadatta, Prabhu M. Natarajan, Carlos M. Ardila

“…Abstract Pulpal inflammation and regeneration are crucial for enhancing endodontic treatment outcomes. Transcriptomic studies highlight the involvement of proinflammatory cytokines, NF-κB signaling, and stem cell activity. …”
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Decoding aging in the heart via single cell dual omics of non-cardiomyocytes by Yiran Song, Li Wang, Haofei Wang, Hong Ma, Jun Xu, Jiandong Liu, Li Qian

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