Lung Tissue Extracellular Vesicles-Mediated Delivery of miR-128-3p as a Novel Mechanism of Acute Lung Inflammation by Deng W, Zhu X, Li H, Hu P, Qian K, Liu F

“…This study combines transcriptomic profiling and functional validation to reveal how Lung Ti-EVs mediate macrophage polarization through miRNA-dependent NLRP3 inflammasome activation.Methods: We established a sepsis mouse model, extracted and characterized lung tissue-derived EVs, performed high-throughput transcriptome sequencing and bioinformatics analysis. …”
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Application of root exudates derived from peanut/maize intercropping system promotes peanut growth and yield via modulating nitrogen turnover processes by Tong Si, Lijian Yang, Jinhao Lu, Yimin Lin, Xiaona Yu, Xiaojun Zhang, Xiaoxia Zou

“…Sucrose (SUC) and myo-inositol (MI) were significantly declined while oxalic acid (OA) was dramatically enriched compared with peanut monoculture. …”
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Unsupervised evaluation of pre-trained DNA language model embeddings by Raghav Awasthi, Gayan Samuditha Mend Mend Arachchige, Xiaofeng Zhu

“…However, they have struggled with tasks such as learning individual-level personal transcriptome variation, highlighting the need for robust evaluation approaches. …”
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Molecular Adjuvant Potential of <i>GCSF</i> and <i>MCSF</i> in Starry Flounder Challenged with <i>Streptococcus parauberis</i> by Min-Young Sohn, Gyoungsik Kang, Kyung-Ho Kim, Ha-Jeong Son, Chan-Il Park

“…Phylogenetic analysis confirmed high evolutionary conservation with other marine species. …”
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FgUbiH Is Essential for Vegetative Development, Energy Metabolism, and Antioxidant Activity in <i>Fusarium graminearum</i> by Jinwen Ge, Huanchen Zhai, Lei Tang, Shuaibing Zhang, Yangyong Lv, Pingan Ma, Shan Wei, Yu Zhou, Xiaofu Wu, Yang Lei, Fengguang Zhao, Yuansen Hu

“…Using a <i>FgUbiH</i> deletion mutant, we observed reduced hyphal growth, conidial production, germination, toxin synthesis, and pathogenicity compared to the wild-type. A transcriptome analysis indicated <i>FgUbiH</i>’s involvement in regulating carbohydrate and amino acid metabolism. …”
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Amblyostatin-1, the first salivary cystatin with host immunomodulatory and anti-inflammatory properties from the Neotropical tick Amblyomma sculptum, vector of Brazilian spotted fe... by Wilson Santos Molari, Mohamed Amine Jmel, Mohamed Amine Jmel, Josiane Betim Assis, Alan Frazão-Silva, Júlia Moura Bernardi, Gretta Huamanrayme, José María Medina, Eliane Esteves, Solange Cristina Antão, Gabriel Cerqueira Alves Costa, Aparecida Sadae Tanaka, Aparecida Sadae Tanaka, Andréa Cristina Fogaça, Andréa Cristina Fogaça, Zdenek Franta, Lucas Tirloni, Michalis Kotsyfakis, Michalis Kotsyfakis, Anderson Sá-Nunes, Anderson Sá-Nunes

“…Thus, this study aims to describe and characterize the most expressed member of the cystatin family identified in Amblyomma sculptum salivary transcriptome, named Amblyostatin-1. MethodsBioinformatic tools were employed for in silico analysis of the Amblyostatin-1 sequence and structure. …”
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Human alveolar macrophage response to Mycobacterium tuberculosis: immune characteristics underlying large inter-individual variability by Wolfgang Sadee, Ian H. Cheeseman, Audrey Papp, Maciej Pietrzak, Michal Seweryn, Xiaofei Zhou, Shili Lin, Amanda M. Williams, Mark D. Wewers, Heather M. Curry, Hao Zhang, Hong Cai, Carine Kunsevi-Kilola, Happy Tshivhula, Gerhard Walzl, Blanca I. Restrepo, Léanie Kleynhans, Katharina Ronacher, Yufeng Wang, Eusondia Arnett, Abul K. Azad, Larry S. Schlesinger

“…The HAM RNA transcriptome following infection revealed thousands of differentially expressed (DE) genes and differential secretion of 25/27 proteins. …”
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Genetically supported causal genes for rheumatoid arthritis: Mendelian randomization and co‐localization analyses by Yuanyuan Niu, Fan Su, Simin Chen, Jingnan Wang, Shuoyang Zhang, Ruiru Li, Yu Kuang, Liuqin Liang, Youjun Xiao, Hanshi Xu

“…Results At a Bonferroni significance level of p < 2.70 × 10−6, the Mendelian randomization analysis revealed that 20 genes increased the risk of RA, while 16 genes showed a marginally protective effect. …”
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Epigenetic dynamics in meniscus cell migration and its zonal dependency in response to inflammatory conditions by Yize Zhang, Ellen Y. Zhang, Catherine Cheung, Yuna Heo, Bat-Ider Tumenbayar, Se-Hwan Lee, Yongho Bae, Su Chin Heo

“…Interestingly, TNF-α differentially alters histone modifications, particularly H3K27me3, between the cell types. Transcriptome analysis showed significant gene expression changes with inner cells more affected than outer cells. …”
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ALDH18A1 has carcinogenic functions and regulates alternative splicing events of DNA repair-related genes in esophageal carcinoma cells by Wang Yongkang, Maimaiti Yisireyili, Kelimu Abudureyimu, Atsushi Enomoto

“…In addition, we performed an overlap analysis between the genes bound by ALDH18A1 and RASGs and found 339 bound RASGs. …”
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MiR-21-5p enhances differentiation and mitigates oleic acid-induced lipid droplet accumulation in C2C12 myoblasts by targeting FBXO11 by Yi Li, Jiayuan Fang, Yingying Jiao, Qinchuan Lv, Xingyu Xiao, Shuo Zheng, Xi Chen, Jie Song, Xunming Zhang, Libo Zhang, Ze Ma, Changhong Li, Linlin Hao

“…Methods The role of miR-21-5p in the proliferation and differentiation of myofibroblasts and intracellular lipid accumulation was analyzed using bioinformatics, CCK-8 assay, quantitative real-time polymerase chain reaction, immunoblotting, immunofluorescence staining, and Oil Red O staining. Results The analysis of porcine BodyMap transcriptome data revealed differential expression of miRNA 21-5p in skeletal muscle and adipose tissue. …”
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Expression of sex-related genes and effects of dmrt1 siRNA-silencing on sex differentiation in juvenile yellow perch by Ding-Kun Xie, Han-Ping Wang, Rafidah Othman, Hong Yao, Paul O’Bryant, Dean Rapp

“…Transcriptome analysis showed that dmrt1 were mainly expressed in gonad tissue with their levels being significantly higher in the male groups respectively comparing to each other; foxl2 was dominantly expressed in gonads showing a significantly higher expression in big female groups than the male and small female groups. cyp19a1 was dominantly expressed in gonads, while cyp19a2 was dominantly expressed in brain, and both female groups exhibiting a significantly higher expression than the male groups. sox9a was mainly expressed in brain and gonad tissue with the male groups displaying a significantly higher expression in gonad than the female groups. …”
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Genome characterization of a newly discovered grapevine leafroll-associated virus S, in the genus ampelovirus by high-throughput sequencing by Malyaj R. Prajapati, Nitika Gupta, Mailem Yazing Shimray, Jayesh Gehlot, Abhinav Tiwari, Pooja Thapa, Damini Diksha, Somnath Kadappa Holkar, Pallavi Jagannath Mahajan, Sujoy Saha, Virendra Kumar Baranwal, Susheel Kumar Sharma

“…Background: Transcriptome data obtained from plant samples often contain significant numbers of reads originating from viral genomes, which are typically co-isolated during the RNA extraction process. …”
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Mechanisms of sorafenib-induced cardiotoxicity: ER stress induces upregulation of ATF3, leading to downregulation of NDUFS1 expression and mitochondrial dysfunction by Ming Yan, Ming Yan, Ming Yan, Cheng Peng, Cheng Peng, Xueyan Lang, Xueyan Lang, Yilan Li, Yilan Li, Yao Zhang, Yao Zhang

“…Further enrichment analysis identified several related pathways, while RT-PCR and immunoblotting confirmed ATF3 upregulation in H9C2 cells. …”
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A Rare Frameshift Mutation of in <i>CmACS7</i> Alters Ethylene Biosynthesis and Determines Fruit Morphology in Melon (<i>Cucumis melo</i> L.) by Jiyang Zhou, Xiaobing Ma, Qianqian Deng, Zhicong Zhong, Xuefei Ning, Li Zhong, Xianliang Zhang, Xianlei Wang

“…A genetic diversity analysis of public melon germplasm resources indicated that while the CmACS7^{A57V/frameshift} mutation accounts for only 0.5% of the germplasm, it is strongly correlated with the round fruit phenotype and is important for breeding in Xinjiang. …”
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Silicon and iron co-application modulates cadmium accumulation and cell wall composition in tomato seedlings by Xiaoting Zhou, Ruihan Xia, Jiayi Zhong, Xiaoru Liu, Tian Xia, Yunxin Tang, Qianke Yang, Encai Bao, Kai Cao, Qiang Chen, Zhongqun He

“…Based on transcriptome KEGG differential enrichment analysis, CSF vs Cd phenylpropane synthesis pathway and pectin metabolism gene expression were up-regulated and down-regulated, respectively, suggesting that the application of Si and Fe may remodel the cell wall and enhance Cd fixation by alleviating excessive cellular lignification as well as sustaining pectin methyl esterification. …”
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SSL5-AnxA5 Fusion Protein Constructed Based on Human Atherosclerotic Plaque scRNA-Seq Data Preventing the Binding of Apoptotic Endothelial Cells, Platelets, and Inflammatory Cells by Yifei Zhao, Xingyu He, Teng Hu, Tianli Xia, Fangyang Huang, Changming Li, Yiming Li, Fei Chen, Mao Chen, Jun Ma, Yong Peng

“…<b>Methods:</b> The scRNA-seq data were extracted from the Gene Expression Omnibus (GEO) database. Single-cell transcriptome analysis results and cell–cell communication were analyzed to identify the ACS and SAP cell clusters and elucidate the intercellular communication differences. …”
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Genome-Wide Identification of the <i>DOG1</i> Gene Family in Pepper (<i>Capsicum annuum</i>) and Its Expression Profiles During Seed Germination by Zhichao Zhao, Jingbo Sun, Feng Zhang, Chunjuan Dong

“…Expression profile analysis using transcriptome data revealed that <i>CaDOG1</i> genes were differentially expressed across various tissues and developmental stages, with notable involvement in flowers and seeds. …”
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First Indonesian Nasopharyngeal Cancer Whole Epigenome Sequencing Identify Tumour Suppressor CpG Methylation by Handoko, Adham M, Rachmadi L, Tobing DL, Asmarinah A, Fadilah F, Dai W, Lee AWM, Gondhowiardjo SA

“…DNA was extracted, sequenced using Oxford Nanopore technology, and aligned to the GRCh38 human reference genome. Methylation analysis was performed using modkit and statistical analysis with R software. …”
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Role and mechanism of tigecycline in delaying the resistance of Klebsiella pneumoniae to polymyxin B by inhibiting cpxR by ZHANG Huanhuan, ZHANG Huanhuan, FENG Wei, HUA Shangjun

“…Transcriptomic and proteomic analyses indicated that in strain 686K·R, the expression levels of the PhoP/Q two-component system, lipopolysaccharide (LPS) modification enzymes, and efflux pump systems were significantly up-regulated (|Log2FC|≥2, P<0.0001), while TGC co-administration markedly inhibited these expression changes. …”
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