Age-related calcium signaling disturbance restricted cAMP metabolism and induced ovarian oxidation stress in laying ducks by Cheng-long Jin, Sheng-lin Wang, Shuang Wang, Ya-nan Zhang, Wei-guang Xia, Chang Zhang, Xue-bing Huang, Kai-chao Li, Chun-tian Zheng, Wei Chen

“…Then, according to RNA-Seq analysis, we detected those aged ducks displayed lower Ca concentration in the ovary, while Ca channel related gene expression was increased in GCs to maintain homeostasis. …”
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Galactin-8 DNA methylation mediates macrophage autophagy through the MAPK/mTOR pathway to alleviate atherosclerosis by Bing Xia, Yan-lin Lu, Jin Peng, Jing-wei Liang, Fang-qin Li, Jiu-yang Ding, Chang-wu Wan, Cui-yun Le, Jia-lin Dai, Jie-Wang, Bing Guo, Jiang Huang

“…However, the mechanism of GAL8 DNA methylation and gene expression in AS has not been elucidated, prompting us to carry out further research on it. …”
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Exploring the role of methylation-driven gene IFFO1 in pancreatic adenocarcinoma diagnosis, prognosis and cellular functions by XU Ziqi, HU Ruizhi, LI Junjian, WANG Hongxia, SANG Youzhou

“…Methods: mRNA expression data (TCGA-PAAD-mRNA), DNA methylation data (TCGA-PAAD-meth, GSE53051, PACA-AU) of PAAD and adjacent normal tissues, as well as DNA methylation data of healthy individuals’ blood (GSE69270), were obtained from the The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium (ICGC) and Gene Expression Omnibus (GEO) databases. By performing differential expression analysis combined with differential methylation analysis, we screened for MDG in PAAD. …”
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Genome-Wide Analysis, Characterization, and Expression Profile of the Basic Leucine Zipper Transcription Factor Family in Pineapple by Yanhui Liu, Mengnan Chai, Man Zhang, Qing He, Zhenxia Su, S. V. G. N. Priyadarshani, Liping Liu, Guanxi Dong, Yuan Qin

“…The study also analyzed the pineapple gene expression of bZIP genes in different tissues, organs, and developmental stages, as well as in abiotic stress responses. …”
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gga-miR-6634-5p Affects the proliferation and steroid hormone secretion of chicken (Gallus Gallus) granulosa cells by targeting MMP16 by Yixiang Tian, Xing Wu, Zihao Zhang, Yijie Li, Meng Hou, Ruirui Jiang, Donghua Li, Yanhua Zhang, Yulong Guo, Guoxi Li, Xiaojun Liu, Xiangtao Kang, Yadong Tian, Wenting Li, Yuetao Li

“…Furthermore, we found that MMP16 protein and gene expression can be down-regulated by gga-miR-6634-5p and demonstrated that MMP16 is a target gene of gga-miR-6634-5p by dual luciferase reporter assay (P < 0.05). …”
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Comparative Transcriptome Analyses Reveal the Mechanisms Underlying Waterlogging Tolerance in Barley by Juan Zhu, Haoxin Yin, Cong Cao, Chengqun Sun, Mengna Zhang, Yi Hong, Yuhang Zhang, Chao Lv, Baojian Guo, Feifei Wang, Rugen Xu

“…The results showed that 2209 and 2578 differentially expressed genes (DEGs) in Franklin and 1997 and 1709 DEGs in TamF169 were detected by comparing gene expression levels under control and waterlogging after 4 and 8 days, respectively, with 392 and 257 DEGs being specific to TamF169 after 4 and 8 days under waterlogging, respectively. …”
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BPZ inhibits early mouse embryonic development by disrupting maternal-to-zygotic transition and mitochondrial function by Zhiming Ding, Huilei Chen, Huiru Cheng, Caiyun Wu, Hongzhen Ruan, Bingjing Zhu, Ping Zhou, Zuying Xu, Huifen Xiang

“…RNA sequencing analysis has identified 593 differentially expressed genes as a result of BPZ exposure, highlighting considerable changes in early embryonic gene expression. Mechanistically, BPZ exposure inhibits the activation of the zygotic genome and impedes maternal mRNA degradation, thereby interfering with maternal-to-zygotic transition (MZT). …”
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Whole blood ratio of CDK1/CX3CR1 mRNA expression combined to lactate refines the prediction of ICU mortality in septic patients in the Sepsis-3 era: a proof-of-concept study by Marie-Angélique Cazalis, Marie-Angélique Cazalis, Louis Kreitmann, Louis Kreitmann, Guillaume Monneret, Guillaume Monneret, Alexandre Pachot, Alexandre Pachot, Karen Brengel-Pesce, Karen Brengel-Pesce, Jean-François Llitjos, Jean-François Llitjos, Jean-François Llitjos

“…We aimed to: (a) identify and validate an mRNA biomarker signature whose association with all-cause intensive care unit (ICU) mortality is consistent at several timepoints; and (b) evaluate how this mRNA signature could be used in association with lactate levels for predictive and prognostic enrichment in sepsis.MethodsWe conducted a gene expression analysis study at two timepoints (day 1 and day 2–3 following ICU admission) using microarray data from adult septic patients to identify candidate biomarkers predictive of all-cause ICU mortality. …”
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Effects of pyrazosulfuron-ethyl on caudal fin regeneration in zebrafish larvae by Chenkai Ge, Zhijun Ye, Weitao Hu, Jingrong Tang, Huimin Li, Fasheng Liu, Xinjun Liao, Jianjun Chen, Shouhua Zhang, Zigang Cao

“…Pyrazosulfuron-ethyl exposure resulted in the decreased number of neutrophils and macrophages, and the downregulation of immune related gene expression levels during caudal fin. Using LPS to activate inflammation can effectively rescue the fin regeneration defects induced by pyrazosulfuron-ethyl. …”
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Comparative functional analysis of a new CDR1-like ABC transporter gene in multidrug resistance and virulence between Magnaporthe oryzae and Trichophyton mentagrophytes by Jing Wang, Chenwen Xiao, Shuang Liang, Muhammad Noman, Yingying Cai, Zhen Zhang, Xueming Zhu, Rongyao Chai, Haiping Qiu, Zhongna Hao, Yanli Wang, Jiaoyu Wang, Guolian Bao, Guochang Sun, Fucheng Lin

“…MoCdr1 and TmCdr1 are conserved in structures and functions, and both involved in drug resistance and pathogenicity by analogously regulating gene expression levels related to transporter activity, MAPK signaling pathway, and metabolic processes. …”
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Identification of biomarkers for the diagnosis of type 2 diabetes mellitus with metabolic associated fatty liver disease by bioinformatics analysis and experimental validation by Guiling Wu, Guiling Wu, Sihui Wu, Sihui Wu, Tian Xiong, Tian Xiong, Tian Xiong, You Yao, You Yao, Yu Qiu, Yu Qiu, Yu Qiu, Liheng Meng, Cuihong Chen, Xi Yang, Xi Yang, Xi Yang, Xinghuan Liang, Yingfen Qin

“…Therefore, we aimed to identify potential biomarkers for diagnosing both conditions.MethodsWe performed differential expression analysis and weighted gene correlation network analysis (WGCNA) on publicly available data on the two diseases in the Gene Expression Omnibus database to find genes related to both conditions. …”
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Outer retina micro-inflammation is driven by T cell responses prior to retinal degeneration in early age-related macular degeneration by Lucas Stürzbecher, Lucas Stürzbecher, Lucas Stürzbecher, Lucas Stürzbecher, Hendrik Bartolomaeus, Hendrik Bartolomaeus, Hendrik Bartolomaeus, Hendrik Bartolomaeus, Theda U. P. Bartolomaeus, Theda U. P. Bartolomaeus, Theda U. P. Bartolomaeus, Theda U. P. Bartolomaeus, Sylvia Bolz, Andjela Sekulic, Marius Ueffing, Marius Ueffing, Simon J. Clark, Simon J. Clark, Simon J. Clark, Nadine Reichhart, Sergio Crespo-Garcia, Nicola Wilck, Nicola Wilck, Nicola Wilck, Nicola Wilck, Olaf Strauß

“…Furthermore, flow cytometry and gene expression analysis were used on ocular and splenic tissues of Cx3cr1GFP/GFP and C57BL/6J mice at 8 and 12 months of age to characterize the dynamics of local and systemic T cell populations.ResultsWe show the presence of memory T cells such as CD45RO+ cells in the choroid and retina of patients with AMD with a peak of abundance in early stages of AMD. …”
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Construction of a prognostic model for gastric cancer based on immune infiltration and microenvironment, and exploration of MEF2C gene function by Si-yu Wang, Yu-xin Wang, Lu-shun Guan, Ao Shen, Run-jie Huang, Shu-qiang Yuan, Yu-long Xiao, Li-shuai Wang, Dan Lei, Yin Zhao, Chuan Lin, Chang-ping Wang, Zhi-ping Yuan

“…Methods Transcriptome sequence data of GC was obtained from The Cancer Genome Atlas (TCGA), the Gene Expression Omnibus (GEO) and PRJEB25780 cohort for subsequent immune infiltration analysis, immune microenvironment analysis, consensus clustering analysis and feature selection for definition and classification of gene M and N. …”
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Single-cell multiomics reveal divergent effects of DNMT3A- and TET2-mutant clonal hematopoiesis in inflammatory response by Wazim Mohammed Ismail, Jenna A. Fernandez, Moritz Binder, Terra L. Lasho, Minsuk Kim, Susan M. Geyer, Amelia Mazzone, Christy M. Finke, Abhishek A. Mangaonkar, Jeong-Heon Lee, Liguo Wang, Kwan Hyun Kim, Vernadette A. Simon, Fariborz Rakhshan Rohakthar, Amik Munankarmy, Seul Kee Byeon, Susan M. Schwager, Jonathan J. Harrington, Melissa R. Snyder, Keith D. Robertson, Akhilesh Pandey, Eric D. Wieben, Nicholas Chia, Alexandre Gaspar-Maia, Mrinal M. Patnaik

“…Using single-cell multiomics sequencing, we identify cell-specific gene expression changes associated with DNMT3A mutations, along with significant epigenomic deregulation affecting enhancer accessibility, resulting in overexpression of interleukin-32 (IL-32), a proinflammatory cytokine that can result in inflammasome activation in monocytes and macrophages. …”
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Nanostructured lipid carriers based mRNA vaccine leads to a T cell–inflamed tumour microenvironment favourable for improving PD-1/PD-L1 blocking therapy and long-term immunity in a... by Carole Fournier, Marion Mercey-Ressejac, Valentin Derangère, Amal Al Kadi, David Rageot, Christine Charrat, Alexis Leroy, Julien Vollaire, Véronique Josserand, Marie Escudé, Séverine Escaich, François Ghiringhelli, Thomas Decaens, Fabrice P. Navarro, Evelyne Jouvin-Marche, Patrice N. Marche

“…A profound intratumoral remodelling of the innate and adaptive immunity in association with an increase in the gene expression of chemokines (Cxcl10, Cxcl11, Cxcl9) involved in CD8+ T cell attraction were observed in immunised mice. …”
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Peptide P2 targeting Vibrio parahaemolyticus PirB toxins blocks the cytotoxic effects to shrimp Litopenaeus vannamei by Xin Zhang, Ting Chen, Chunhua Ren, Yanhong Wang, Xiao Jiang, Jiasheng Huang, Bo Ma, Boxiang Zhu, Jiayue Yin, Chaoqun Hu, Peng Luo

“…The receptor candidates for PirB were genome-wide identified and selected based on gene expression profiles, and the biological function of Lv-APN1 was confirmed through RNAi. …”
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Bridging animal models and humans: neuroimaging as intermediate phenotypes linking genetic or stress factors to anhedonia by Huiling Guo, Yao Xiao, Shuai Dong, Jingyu Yang, Pengfei Zhao, Tongtong Zhao, Aoling Cai, Lili Tang, Juan Liu, Hui Wang, Ruifang Hua, Rongxun Liu, Yange Wei, Dandan Sun, Zhongchun Liu, Mingrui Xia, Yong He, Yankun Wu, Tianmei Si, Fay Y. Womer, Fuqiang Xu, Yanqing Tang, Jie Wang, Weixiong Zhang, Xizhe Zhang, Fei Wang

“…In contrast, the stress animal-like subtype did not show changes in genetic risk scores but exhibited enriched risk gene expression in somatic and endocrine tissues, along with mitochondrial dysfunction in the antioxidant stress system. …”
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Evaluating metagenomics and targeted approaches for diagnosis and surveillance of viruses by Sarah Buddle, Leysa Forrest, Naomi Akinsuyi, Luz Marina Martin Bernal, Tony Brooks, Cristina Venturini, Charles Miller, Julianne R. Brown, Nathaniel Storey, Laura Atkinson, Timothy Best, Sunando Roy, Sian Goldsworthy, Sergi Castellano, Peter Simmonds, Heli Harvala, Tanya Golubchik, Rachel Williams, Judith Breuer, Sofia Morfopoulou, Oscar Enrique Torres Montaguth

“…However, the application of robust thresholds standardized results between taxonomic classifiers. Host gene expression analysis is optimal with untargeted Illumina sequencing but possible with both the CVRP and ONT. …”
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Multi-omics analysis reveals the interplay between intratumoral bacteria and glioma by Ting Li, Zhanyi Zhao, Meichang Peng, Lu Zhang, Cheng Wang, Feiyang Luo, Meiqin Zeng, Kaijian Sun, Zhencheng Fang, Yunhao Luo, Yugu Xie, Cui Lv, Jiaxuan Wang, Jian-Dong Huang, Hongwei Zhou, Haitao Sun

“…Our findings shed light on the intricate interplay between intratumoral bacteria and glioma.IMPORTANCEOur study adopted a multi-omics approach to unravel the impact of intratumoral microbes on neuron-related gene expression through bacteria-associated metabolites. …”
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Collagen deposition in lung parenchyma driven by depletion of interstitial Lyve-1+ macrophages prevents cigarette smoke-induced emphysema and loss of airway function by Yinebeb Mezgebu Dagnachew, Yinebeb Mezgebu Dagnachew, Yinebeb Mezgebu Dagnachew, Hwee Ying Lim, Hwee Ying Lim, Liao Wupeng, Liao Wupeng, Sheau Yng Lim, Sheau Yng Lim, Sheng Jie Natalie Lim, Sheng Jie Natalie Lim, Chung Hwee Thiam, Chung Hwee Thiam, Shu Wen Tan, Shu Wen Tan, Joan Lau Joo Eng, Joan Lau Joo Eng, Dan Mei, Syaza Hazwany Mohammad Azhar, Wei Siong Ong, Qi Hui Caris Tan, Wai-Shiu Fred Wong, Wai-Shiu Fred Wong, Wai-Shiu Fred Wong, Veronique Angeli, Veronique Angeli

“…A decrease in MMP-9 gene expression and proteolytic activity together with an increase in Col1a1, Timp-3 and Lox expression accompanied the collagen alterations. …”
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