KDM3A and KDM3B regulate alternative splicing in mouse pluripotent stem cells by Caleb M. Dillingham, Harshini Cormaty, Ellen C. Morgan, Andrew I. Tak, Dakarai E. Esgdaille, Paul L. Boutz, Rupa Sridharan

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Early in vivo target genes in human immune cells highlight vitamin D’s role in antioxidant defense by Tanya Tripathi, Carsten Carlberg, Carsten Carlberg

“…Peripheral blood mononuclear cells (PBMCs) were collected immediately before and at 4, 24, and 48 hours post-supplementation for transcriptome-wide differential gene expression analysis.ResultsWe identified 570 genes significantly responsive to vitamin D3 (p < 0.05) at one or more timepoints. …”
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Transcriptional time-course analysis during ash dieback infection revealed different responses in tolerant and susceptible Fraxinus excelsior genotypes by Víctor Chano, Renata Callegari Ferrari, Tania Domínguez-Flores, Karuna Shrestha, Barbara Fussi, Hannes Seidel, Oliver Gailing, Katharina B. Budde

“…We performed RNA-sequencing to study the transcriptomic response to the disease in four ash genotypes (ADB-tolerant FAR3 and FS36, and ADB-susceptible UW1 and UW2), during a time-course of 7, 14, 21, and 28 days post-inoculation, including mock-inoculated trees as control samples for each sampling time point. …”
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Temporally resolved single-cell RNA sequencing reveals protective and pathological responses during herpes simplex virus CNS infection by Xiangning Ding, Xin Lai, Ida H. Klaestrup, Sara R. N. Jensen, Morten M. Nielsen, Kasper Thorsen, Marina Romero-Ramos, Yonglun Luo, Lin Lin, Line S. Reinert, Søren R. Paludan

“…Abstract Background Herpes Simplex Virus 1 (HSV-1) is a neurotropic virus causing encephalitis and post-infectious complications. Infections can induce a range of acute, subacute, and progressing brain disease, and in recent years it has emerged that immune responses are involved in the pathogenesis of these diseases. …”
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Advanced omics approaches in liver transplant settings: current applications and future prospectives by Huijuan Wang, Huijuan Wang, Huijuan Wang, Yifeng Zhou, Lu Yu, Lu Yu, Lu Yu, Zhengtao Liu, Zhengtao Liu, Zhengtao Liu, Zhengtao Liu, Shusen Zheng, Shusen Zheng, Shusen Zheng, Shusen Zheng, Shusen Zheng

“…Specifically, we focus on key immune cells involved in LT, with an emphasis on post-transplant immune responses and ischemia-reperfusion injury (IRI), as revealed by scRNA-seq and ST. …”
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Functional Characterization of <i>MaSPL8</i> Reveals Its Different Roles in Biotic and Abiotic Stress Responses in Mulberry by Longyan Zheng, Wenhao Zhang, Liuqing Wei, Mengqi Li, Li Liu

“…Downregulation of <i>MaSPL8</i> via virus-induced gene silencing (VIGS) resulted in more susceptibility to <i>Ciboria shiraiana</i> infection, but significantly enhanced resistance to drought and salt stress, as evidenced by reduced oxidative damage, elevated proline accumulation, and increased antioxidant enzyme activities. Transcriptomic profiling of <i>MaSPL8</i>-silenced plants revealed enrichment of differentially expressed genes (DEGs) in brassinosteroid biosynthesis, jasmonic acid metabolism, and oxidative stress responses, suggesting hormone signaling interplay. …”
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N  6-methyladenosine modifications stabilize phosphate starvation response–related mRNAs in plant adaptation to nutrient-deficient stress by Kai Liu, Xiaojia Wang, Jingyi Wang, Shuman Wang, Haiyan Bai, Weiguo Dong, Lulu Qiao, Qiongli Jin, Zhonghui Zhang, Guan-Zheng Luo, Zhiye Wang

“…Abstract N 6 -methyladenosine (m6A), an abundant internal mRNA modification, is induced by various stress conditions and post-transcriptionally regulates gene expression. …”
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Neddylation status determines the therapeutic sensitivity of tyrosine kinase inhibitors in chronic myeloid leukemia by Congyi Zhang, Yikai Yao, Qiuting Qian, Xiongyu Han, Yunkun Lu, Xinyi Jiang, Hongqiang Cheng, Xue Zhang, Ying Chi, Yuehai Ke, Peng Xiao

“…Hence, our study offers new insights into the post-translational modification (PTM)-mediated drug resistance, and highlights the potential clinical benefits of neddylation agonists in improving the responsiveness of BCR::ABL1 TKIs in CML.…”
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Arginine-Mediated Liver Immune Regulation and Antioxidant Defense in Largemouth Bass (<i>Micropterus salmoides</i>): Multi-Omics Insights into Metabolic Remodeling During <i>Nocard... by Yu-Long Sun, Shuai-Liang Zhang, Feng-Feng Zhou, Yuan-Xin Qian, Yang He, Run-Zhe Zhang, Fen Dong, Qiang Chen, Han-Ying Xu, Ji-Teng Wang, Yu-Ting Deng, Tao Han

“…The level of mRNA expression of immune-related genes in the liver was significantly increased 2 days post-infection. Moreover, the combined analysis of transcriptome and metabolome showed that <i>N. seriolae</i> infection markedly affected liver metabolism, including glutathione metabolism, arginine and proline metabolism, arachidonic acid metabolism, as well as starch and sucrose metabolism. …”
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Deciphering the role of acetylation-related gene NAT10 in colon cancer progression and immune evasion: implications for overcoming drug resistance by Xuancheng Zhou, Xun Sang, Lai Jiang, Shengke Zhang, Chenglu Jiang, Yuheng Gu, Yipin Fu, Guanhu Yang, Jieyin Zhang, Hao Chi, Binbin Wang, Xiaolin Zhong

“…Recent studies highlight the significant role of post-transcriptional modifications like acetylation in cancer biology, affecting processes like gene transcription, metabolism, and tumor progression. …”
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Comparative gene expression analysis of Beauveria bassiana against Spodoptera frugiperda by Hamdy H. Aly, Yun Meng, Dun Wang

“…At 48 hours’ post-infection, genes involved in adhesion and cuticle penetration, such as serine/threonine-protein kinases (STPKs) and lipases, were upregulated, indicating adaptation to host invasion. …”
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Oxygen availability strongly affects chronological lifespan and thermotolerance in batch cultures of Saccharomyces cerevisiae by Markus M.M. Bisschops, Tim Vos, Rubén Martínez-Moreno, Pilar de la Torre Cortés, Jack T. Pronk, Pascale Daran-Lapujade

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Identification and analysis of major latex protein (MLP) family genes in Rosa chinensis responsive to Botrytis cinerea infection by RNA-seq approaches by Haoyuan Chen, Qingkui Li, Peilei Cheng, Taotao Yan, Chunlan Dong, Zhe Hou, Peihuang Zhu, Changbing Huang

“…Here we inoculated the resistant rose variety ‘Yellow Leisure Liness’ with B. cinerea to investigate its resistance mechanisms against gray mold disease. Through transcriptome sequencing, we identified 578 differentially expressed genes (DEGs) that were significantly upregulated at 24, 48, and 72 hours post-inoculation, with these genes significantly enriched for three defense response-related GO terms. …”
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Multi-Omics Analysis of <i>Curculio dieckmanni</i> (Coleoptera: Curculionidae) Larvae Reveals Host Responses to <i>Steinernema carpocapsae</i> Infection by Bin Wang, Fanyu Meng, Shiqi Song, Bin Xie, Shuxia Jia, Dongying Xiu, Xingpeng Li

“…To investigate the molecular responses of hazelnut weevil larvae to nematode infection, we employed integrated transcriptomic and proteomic analyses following infection by <i>S. carpocapsae</i>. …”
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Tumor gene expression signatures associated with outcome in large B−cell lymphoma treated with CD19-directed CAR T−cell therapy (axicabtagene ciloleucel) by Yuan Tian, Justin Budka, Frederick L. Locke, Jason R. Westin, Christina To, Gayatri Tiwari, Daqin Mao, Davide Bedognetti, Rhine R. Shen, Jorge Andrade, Simone Filosto

“…The 6-GES was reduced, whereas the 17-GES was elevated at progression post axi-cel, consistent with the notion that these signatures represent features relevant for response and resistance to CAR T-cell therapy.ConclusionOur transcriptomic analysis identified gene expression signatures potentially predictive of outcome with CD19-directed CAR T-cell therapy, and these findings are informative for risk stratification and development of next-generation products.…”
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Single-dose VSV-based vaccine protects cynomolgus macaques from disease after Taï Forest virus infection by Paige Fletcher, Kyle L. O’Donnell, Brianna M. Doratt, Delphine C. Malherbe, Chad S. Clancy, Joseph F. Rhoderick, Friederike Feldmann, Patrick W. Hanley, Thomas G. Ksiazek, Thomas W. Geisbert, Ilhem Messaoudi, Andrea Marzi

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Immune Suppression and Rapid Invasion of Nile Tilapia Gills Following an Acute Challenge by <i>Flavobacterium davisii</i> by Yingxuan Xu, Shifeng Wang, Yongcan Zhou, Zhenyu Xie, Bei Wang, Zhangding Zhao, Wenlong Cai, Peibo Wang, Weiliang Guo, Dongdong Zhang, Zhi Ye

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Enhanced early innate immunity and phagocytosis in grass carp (Ctenopharyngodon idella) induced by Aeromonas hydrophila fermentation broth during initial vaccine response by Xiaobo Yu, Qinglin Yang, Yanhong Jiang, Yanhong Li, Zhengli Wu

“…Moreover, in vivo studies revealed that the fermentation broth of A. hydrophila promoted cytophagocytosis in the blood leukocytes of grass carp by regulating the innate immune response during vaccine-induced immunity. This modulation conferred histopathological protection against early A. hydrophila infection within 7 days post-immunostimulation. …”
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The peripheral Atf3⁺ neuronal population is responsible for nerve regeneration at the early stage of nerve injury revealed by sin... by Liu Li, Chen Junhui, Yin Wen, Gao Po, Fan Yinghui, Wen Daxiang, Jiao Yingfu, Yu Weifeng

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Immunogenicity and Protective Efficacy of an mRNA Vaccine Targeting HSV-2 UL41 in Mice by Tangwei Mou, Yu Zhao, Jie Jia, Kai-Cheng Gao, Shao-You Li, Yi-Qun Kuang

“…Dendritic cell (DC) activation in spleen tissue was analyzed via transcriptome sequencing. Results: A comparison of the clinical, immunological, and pathological characteristics of the groups that were immunized with the UL41 mRNA vaccine and then infected with HSV2, along with the control groups, revealed that the vaccine elicited both cellular and humoral immunity, inhibited viral replication, suppressed the inflammatory response, and provided protective effects against the virus in vivo. …”
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