Stochastic demethylation and redundant epigenetic suppressive mechanisms generate highly heterogeneous responses to pharmacological DNA methyltransferase inhibition by Mie K. Jakobsen, Sofie Traynor, Aaraby Y. Nielsen, Christina Dahl, Mette Staehr, Simon T. Jakobsen, Maria S. Madsen, Rasmus Siersbaek, Mikkel G. Terp, Josefine B. Jensen, Christina B. Pedersen, Anup Shrestha, Jonathan R. Brewer, Pascal H. G. Duijf, Odd L. Gammelgaard, Henrik J. Ditzel, Alexei F. Kirkin, Per Guldberg, Morten F. Gjerstorff

“…Methods In this study, we used cancer/testis antigen genes as a model for methylation-dependent gene expression to examine the activity of DNA methyltransferase inhibitors and their potential synergistic effect with histone deacetylase inhibitors at the single-cancer cell level. …”
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Identification of RNA Editing Sites Reveals Functional Modifications with the Addition of Methionine to the Daily Rations of Yaks by Shiyu Wu, Xinrui Liu, Yaxin Liu, Shikai Wang, Wei Peng, Ming Zhang, Binglin Yue, Hui Wang, Jikun Wang, Jincheng Zhong, Fang Sun, Yixi Kangzhu, Jiabo Wang

“…This provides further understanding of the mechanism of yak muscle tissue and regulation of gene expression after the addition of methionine to daily rations.…”
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Response of YPM x Ross 708 male broilers to diets containing varying inclusions of phytase, calcium butyrate, and bacitracin methylene disalicylate during the grower and finisher p... by Joseph P. Gulizia, Zubair Khalid, Maria T. Terra-Long, Jose I. Vargas, Jose R. Hernandez, Wilmer J. Pacheco, James T. Krehling, Kenneth S. Macklin, William A. Dozier, III, Klint W. McCafferty, Ruediger Hauck

“…Jejunum wall and cecal content samples were collected on d 28 and 42 to assess jejunum villus height (VH), crypt depth, tight-junction and mucin gene expression, cecal microbiome diversity, and predicted bacterial metabolic pathways. …”
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Assessing Heat Resistance and Selecting Heat-Resistant Individuals of Largemouth Bass (<i>Micropterus salmoides</i>) with Tiered Thermal Exposure by Haijie Chen, Hui Qiao, Zhicheng Xv, Guili Song, Shuning Liu, Cheng Luo, Yong Long, Shimei Lin

“…To correlate the changes in tissue structure and gene expression with the heat resistance, a new batch of LMB juveniles (average body weight 23.66 ± 6.98 g) were subjected to tiered heat exposure. …”
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A missense variant in the SOX5 gene (c.221C > T) is associated with intellectual disability by Xiujuan Yang, Zhongzhi Gan, Xiaoling Guo, Xiang Huang, Juan Liu, Yingchun Zheng, Xiaoqiang Zhou, Jingli Lian, Yue Liu, Tingting Yang, Chao Li, Fenying Chen, Fei He, Xiangmin Xu, Yasi Zhou, Qian Liu, Xingkun Yang, Fu Xiong

“…Western blots and QPCR were employed to assess gene expression and protein stability. Flow cytometry was utilized to compare the cell cycle dynamics between wild-type and mutant cells. …”
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CHOLINE TRANSPORTER-RELATED 4 (CTR4) Is Involved in Drought and Saline Tolerance in Rice by Yu Shicong, Luo Ruxian, Zheng Shuqin, Ning Jing, Shi Yuanzhu, Guo Daiming, Jia Liangmeng, Wang Sen, Xiao Guizong, Guo Pengwang, Li Yang, Ma Xiaoding

“…Moreover, lipid synthesis gene expression was down-regulated in CTR4 mutants, potentially exacerbating membrane permeability defects and further compromising stress resistance. …”
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Deletion of sphingosine 1-phosphate receptor 1 in myeloid cells reduces hepatic inflammatory macrophages and attenuates MASH by Gopanandan Parthasarathy, Nanditha Venkatesan, Guneet Singh Sidhu, Myeong Jun Song, Chieh-Yu Liao, Fanta Barrow, Amy Mauer, Tejasav Sehrawat, Yasuhiko Nakao, P. Vineeth Daniel, Debanjali Dasgupta, Kevin Pavelko, Xavier S. Revelo, Harmeet Malhi

“…Liver injury and inflammation were determined by histological and gene expression analyses. Intrahepatic leukocyte populations were analyzed by mass cytometry and immunohistochemistry. …”
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Genes Involved in the Transcriptional Regulation of Pluripotency Are Expressed in Malignant Tumors of the Uterine Cervix and Can Induce Tumorigenic Capacity in a Nontumorigenic Cel... by Graciela Ruiz, Heriberto A. Valencia-González, Delia Pérez-Montiel, Felipe Muñoz, Rodolfo Ocadiz-Delgado, Jorge Fernández-Retana, Carlos Pérez-Plasencia, Osbaldo Reséndis-Antonio, Patricio Gariglio, Alejandro García-Carrancá

“…To determine their contribution to cell transformation, we analyzed the gene expression profiles of these transcription factors in cervical cancer samples and found that they are preferentially expressed in the tumor component. …”
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Contribution of cuproptosis and immune-related genes to idiopathic pulmonary fibrosis disease by Chengji Jin, Jia Li, Qiaoyu Li, Lipeng Zhang, Shaomao Zheng, Qiong Feng, Yongjie Li, Yu Zheng, Qiuli Nie, Jin Liang, Jing Wang, Jing Wang

“…Additionally, multiple bioinformatics analyses were employed to identify immune-related biomarkers associated with the diagnosis of IPF, offering valuable insights for future treatment strategies.MethodsFour microarray datasets were selected from the Gene Expression Omnibus (GEO) collection for screening. …”
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Artemisinin supplementation in concentrated cottonseed protein basal diets enhances growth, antioxidant capacity, intestinal immunity and microbiota in hybrid grouper (Epinephelus... by Ling Pan, Qi Wang, Weikang Li, Xiaohui Dong, Shiwei Xie, Beiping Tan, Hongyu Liu, Yan Wang

“…In the artemisinin-treated groups, significant alterations in gene expression were observed, including a marked upregulation of interleukin-8, tumor necrosis factor-α, and toll-like receptor-2 (P < 0.05); however, the expression of tumor necrosis factor-β and toll-like receptor-1 was significantly downregulated (P < 0.05), suggesting that artemisinin may mitigate intestinal inflammatory injury. …”
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Exploring biomarkers and molecular mechanisms of Type 2 diabetes mellitus promotes colorectal cancer progression based on transcriptomics by Simin Luo, Yuhong Zhu, Zhanli Guo, Chuan Zheng, Xi Fu, Fengming You, Xueke Li

“…COX11 was the key gene for co-morbidities: in tumor tissues, COX11 expression was significantly higher than that in normal colon tissues. However, COX11 gene expression was significantly lower in patients with comorbidities than in patients without T2DM in tumor tissue. …”
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NF-κB/AP-1-Targeted Inhibition of Macrophage-Mediated Inflammatory Responses by Depigmenting Compound AP736 Derived from Natural 1,3-Diphenylpropane Skeleton by Van Thai Ha, Heung Soo Beak, Eunji Kim, Kwang-Soo Baek, Muhammad Jahangir Hossen, Woo Seok Yang, Yong Kim, Jun Ho Kim, Sungjae Yang, Jeong-Hwan Kim, Yung Hyup Joo, Chang Seok Lee, Joonho Choi, Hong-Ju Shin, Sungyoul Hong, Song Seok Shin, Jae Youl Cho

“…The effects of AP736 on various inflammatory events such as nitric oxide (NO)/prostaglandin (PG) E2 production, inflammatory gene expression, phagocytic uptake, and morphological changes were examined in RAW264.7 cells. …”
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Exploring the molecular basis of efficient feed utilization in low residual feed intake slow-growing ducks based on breast muscle transcriptome by Lei Wu, Zhong Zhuang, Wenqian Jia, Yongpeng Li, Yijia Lu, Minghong Xu, Hao Bai, Zhixiu Wang, Guobin Chang, Yong Jiang

“…There were significant differences in gene expression between LRFI and HRFI ducks, with 102 upregulated and 258 downregulated genes, which were enriched in the PPAR signaling pathway, adipocytokine signaling pathway, actin cytoskeleton regulation, ECM-receptor interaction, and focal adhesion. …”
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RatDEGdb: a knowledge base of differentially expressed genes in the rat as a model object in biomedical research by I. V. Chadaeva, S. V. Filonov, K. A. Zolotareva, B. M. Khandaev, N. I. Ershov, N. L. Podkolodnyy, R. V. Kozhemyakina, D. A. Rasskazov, A. G. Bogomolov, E. Yu. Kondratyuk, N. V. Klimova, S. G. Shikhevich, M. A.  Ryazanova, L. A. Fedoseeva, О. Е. Redina, О. S. Kozhevnikova, N. A. Stefanova, N. G. Kolosova, A. L. Markel, M. P. Ponomarenko, Yu. D. Oshchepkov

“…RatDEGdb, a knowledge base of the differentially expressed genes (DEGs) of the rat as a model object in biomedical research is a collection of published data on gene expression in rat strains simulating arterial hypertension, age-related diseases, psychopathological conditions and other human afflictions. …”
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Identification of EARS2 as a Potential Biomarker with Diagnostic, Prognostic, and Therapeutic Implications in Colorectal Cancer by Wang L, Deng X, Tang J, Gong Y, Bu S, Li Z, Liao B, Ding Y, Dai T, Liao Y, Li Y

“…This study identifies key genes associated with lactic acid metabolism and explore their impact on CRC.Patients and Methods: This study utilized data from The Cancer Genome Atlas, Gene Expression Omnibus, other public databases, and our institutional resources. …”
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High lipid diet can keep liver health but cause muscle oxidative stress of triploid rainbow trout treated with acute hypoxic challenge by Changye Li, Buying Han, Guoliang Sun, Haining Tian, Zezhong Wu, Changzhong Li, Yuqiong Meng, Rui Ma

“…The results showed that 1) HL diet significantly increased plasma lactate dehydrogenase, glucose, total cholesterol, high and low density lipoprotein cholesterol levels, but decreased alanine aminotransferase level (P < 0.05). 2) HL diet did not affect hepatic malondialdehyde (MDA) content (P > 0.05), while it significantly increased MDA content in the plasma and muscle (P < 0.05). Antioxidant gene expression in the liver were upregulated, but some genes expression in the muscle were downregulated in the HL group. 3) HL diet significantly increased inflammatory and immune genes expression in the liver and muscle (P < 0.05), and the increase is more pronounced in the muscle. 4) HL diet activated lipolysis, autophagy and gluconeogenesis related genes expression, but inhibited lipid synthesis and glycolysis related genes expression. …”
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Advancements in noninvasive techniques for transplant rejection: from biomarker detection to molecular imaging by Yuan Song, Yihui Wang, Wenyuan Wang, Yuji Xie, Junmin Zhang, Jing Liu, Qiaofeng Jin, Wenqian Wu, He Li, Jing Wang, Li Zhang, Yali Yang, Tang Gao, Mingxing Xie

“…For example, donor-derived cell-free DNA (dd-cfDNA) is highly sensitive in detecting early graft injury, whereas gene expression profiling effectively excludes moderate-to-severe acute rejection (AR). …”
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DNA Methylation and Transcriptome Profiling Reveal the Role of the Antioxidant Pathway and Lipid Metabolism in <i>Plectropomus leopardus</i> Skin Color Formation by Yang Liu, Linna Wang, Zhentong Li, Linlin Li, Tangtang Ding, Shuai Chen, Pengfei Duan, Xinyi Wang, Yishu Qiu, Xiaoyu Ding, Yongsheng Tian

“…To dissect the regulatory mechanisms underlying the red skin trait in <i>P. leopardus</i>, gene expression and DNA methylation modifications were compared between red and black skin tissues after astaxanthin treatment. …”
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Generation of Insulin-Producing Cells from Canine Adipose Tissue-Derived Mesenchymal Stem Cells by Takahiro Teshima, Keiji Okamoto, Kazuho Dairaku, Tomokazu Nagashima, Masaki Michishita, Ryohei Suzuki, Hirotaka Matsumoto, Hidekazu Koyama

“…Canine IPCs also showed gene expression typical for pancreatic beta cells and increased insulin secretion in response to glucose stimulation. …”
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Characterization and functional analysis of conserved non-coding sequences among poaceae: insights into gene regulation and phenotypic variation in maize by Yi Luo, Hang Zhai, Xiu Zhong, Bo Yang, Yang Xu, Tianhong Liu, Qi Wang, Yang Zhou, Yan Mao, Yaxi Liu, Qi Tang, Yanli Lu, Yao Wang, Jie Xu

“…Conclusions In summary, we identified and characterized CNS in maize through genomic comparative analysis, which provides valuable insights into their potential regulatory effects on gene expression and phenotypic variation.…”
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