Alterations in mitochondrial base editors enhance targeted editing efficiency for mouse model generation by Seongho Hong, Sol Pin Kim, Sanghun Kim, Soo Kyung Kang, Sungmo Jung, Yeji Oh, Seung Hee Choi, Su Bin Lee, Hou Cha, Jieun Kim, Jiyoung Bae, Jiyoon Park, Kyoungmi Kim, Chang Geun Choi, Soo-Ji Park, Do Hyun Kim, Lark Kyun Kim, Je Kyung Seong, Hyunji Lee

“…These enhancements significantly increased editing efficiency while preserving minimal off-target effects across the transcriptome. …”
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Molecular landscape of sex- and modality-specific exercise adaptation in human skeletal muscle through large-scale multi-omics integration by Macsue Jacques, Shanie Landen, Adam P. Sharples, Andrew Garnham, Ralf Schittenhelm, Joel Steele, Aino Heikkinen, Elina Sillanpää, Miina Ollikainen, James Broatch, Navabeh Zarekookandeh, Ola Hanson, Ola Ekström, Olof Asplund, Séverine Lamon, Sarah E. Alexander, Cassandra Smith, Carlie Bauer, Mary N. Woessner, Itamar Levinger, Andrew E. Teschendorff, Linn Gillberg, Ida Blom, Jørn Wulff Helge, Nicholas R. Harvey, Larisa M. Haupt, Lyn R. Griffiths, Atul S. Deshmukh, Kirsi H. Pietiläinen, Päivi Piirilä, Robert A.E. Seaborne, Marie Klevjer, Anja Bye, Ulrik Wisløff, Bernadette Jones-Freeman, Nir Eynon

“…Summary: We investigated the molecular mechanisms of exercise adaptations in human muscle by integrating genome, methylome, transcriptome, and proteome data from over 1,000 participants (2,340 muscle samples). …”
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Study on factors affecting fruit development of seedless ponkan cultivar Huagan No.4 by LIU Chenglang, LI Gangqiu, LI Shunxin, WEI Ranran, LU Yan, CHENG Chao, TANG Zheng, LIU Baoyan, YE Junli, CHAI Lijun, DENG Xiuxin, XIE Zongzhou

“…The GA3 content of HG2 peaked at 2.27 ng·g-1 on 25 DAF, while the GA3 content of HG4 was only 0.90 ng·g-1, with significant differences. …”
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Acyl CoA-binding protein in brown adipose tissue acts as a negative regulator of adaptive thermogenesis by Albert Blasco-Roset, Tania Quesada-López, Alberto Mestres-Arenas, Joan Villarroya, Francisco J. Godoy-Nieto, Rubén Cereijo, Celia Rupérez, Ditte Neess, Nils J. Færgeman, Marta Giralt, Anna Planavila, Francesc Villarroya

“…Objective: Defective activity of brown adipose tissue (BAT) is linked to obesity and cardiometabolic diseases. While much is known regarding the biological signals that trigger BAT thermogenesis, relatively little is known about the repressors that may impair BAT function in physiological and pathological settings. …”
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EIF4A3 Promotes Muscle Atrophy and Aging by Inhibiting the FAK Pathway Through NEDD9 mRNA Destabilization by Qian Li, Xiaohang Yin, Wensi Wan, Yi Zhou, Siqi Wang, Yuwei Yan, Jingying Chen, Xinyi Ren, Junli Gao, Yuying Chen, Yanan Zhang, Caiyue Cui, Emeli Chatterjee, Guoping Li, Ming Wu, Yan Zhang, Dongchao Lu, Tingting Yang, Yongjun Zheng, Jin Li

“…Methods Single‐cell transcriptome analysis and western blot were employed to analyse EJC expression in muscle atrophy. …”
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An immune-focused supplemental alignment pipeline captures information missed from dominant single-cell RNA-seq analyses, including allele-specific MHC-I regulation by Sebastian Benjamin, GW McElfresh, Maanasa Kaza, Gregory J. Boggy, Benjamin Varco-Merth, Benjamin Varco-Merth, Sohita Ojha, Shana Feltham, William Goodwin, William Goodwin, Candice Nkoy, Candice Nkoy, Derick Duell, Derick Duell, Andrea Selseth, Tyler Bennett, Aaron Barber-Axthelm, Nicole N. Haese, Nicole N. Haese, Helen Wu, Courtney Waytashek, Carla Boyle, Jeremy V. Smedley, Jeremy V. Smedley, Caralyn S. Labriola, Caralyn S. Labriola, Michael K. Axthelm, Michael K. Axthelm, R. Keith Reeves, R. Keith Reeves, Daniel N. Streblow, Daniel N. Streblow, Jonah B. Sacha, Jonah B. Sacha, Afam A. Okoye, Afam A. Okoye, Scott G. Hansen, Scott G. Hansen, Louis J. Picker, Louis J. Picker, Benjamin N. Bimber, Benjamin N. Bimber

“…IntroductionRNA sequencing (RNA-seq) can measure whole transcriptome gene expression from tissues or even individual cells, providing a powerful tool to study the immune response. …”
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Genome-wide identification and expression analysis of growth-regulating factor (GRF) and GRF-interacting factor (GIF) gene families in Castanea mollissima by WANG Xiangyu, TIAN Yujuan, LI Yun, WANG Dongsheng, WANG Xuan, GUO Chunlei, LIU Jing, ZHANG Hai’e, ZHANG Jingzheng, YU Liyang

“…The collinear analysis between Chinese chestnut and five other representative species (Arabidopsis thaliana, Quercus, Vitis vinifera, Oryza sativa, and Zea mays) suggested that the GRF and GIF families might have undergone independent duplication events after the differentiation between dicotyledonous and monocotyledonous plants. Transcriptome data analysis showed that CmGRF3 and CmGIF2 were consistently highly expressed in female flowers, while almost not in male flowers (FPKM<1). …”
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Multi-omics landscape of alternative splicing in diffuse midline glioma reveals immune- and neural-driven subtypes with implications for spliceosome-targeted therapy by Chaxian Liu, Chaxian Liu, Chaxian Liu, Chaxian Liu, Chaxian Liu, Yue Liu, Yue Liu, Yue Liu, Yue Liu, Yue Liu, Hao Lin, Hao Lin, Hao Lin, Hao Lin, Hao Lin, Chufan Zhang, Chufan Zhang, Chufan Zhang, Bilong Zhang, Bilong Zhang, Bilong Zhang, Haikun Song, Haikun Song, Haikun Song, Xiaomin Fan, Yi Lyu, Hui Yang, Hui Yang, Hui Yang, Hui Yang, Hui Yang, Ying Mao, Ying Mao, Ying Mao, Ying Mao

“…Given its potential impact on gene regulation and tumor progression, a comprehensive analysis of alternative splicing could provide novel insights into targeted or immune therapeutic strategies, complementing existing transcriptomic studies of DMG.MethodsTo investigate the alternative splicing landscape of DMG, we performed transcriptome sequencing (RNA-seq) on patient-derived H3WT and H3K27-altered DMG cell lines, integrating these data with RNA-seq and single-cell transcriptomic (scRNA-seq) datasets from published sources. …”
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Prognostic Biomarkers for Papillary Thyroid Cancer: Reducing Overtreatment, Improving Clinical Efficiency, and Enhancing Patient Experience by Oliver F Bathe MD, MSc, Cynthia Stretch PhD

“…In contrast, transcriptomic profiling has emerged as a powerful tool for identifying aggressive PTC subtypes with greater precision. …”
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The Tumor-Associated Calcium Signal Transducer 2 (TACSTD2) oncogene is upregulated in cystic epithelial cells revealing a potential new target for polycystic kidney disease. by Abigail O Smith, William Tyler Frantz, Kenley M Preval, Yvonne J K Edwards, Craig J Ceol, Julie A Jonassen, Gregory J Pazour

“…Polycystic kidney disease (PKD) is an important cause of kidney failure, but treatment options are limited. While later stages of the disease have been extensively studied, mechanisms driving the initial conversion of kidney tubules into cysts are not understood. …”
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Comparative evaluation of immunomodulatory cytokines for oncolytic therapy based on a high-efficient platform for oHSV1 reconstruction by Yingzheng Gao, Yufang Zou, Changjing Wu, Juan Tao, Zuqing Nie, Jinyuan Yan, Pengfei Wang, Xinwei Huang

“…Transcriptomic profiling revealed divergent immune modulation: OV-IL15Fu enriched T cell/NK cytotoxicity pathways, OV-IFNG amplified cytokine/chemokine signaling, and OV-GMCSF paradoxically enhanced myeloid recruitment while inhibiting MHC-II pathways. …”
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Coordinated regulation of core and accessory genes in the multipartite genome of Sinorhizobium fredii. by Jian Jiao, Meng Ni, Biliang Zhang, Ziding Zhang, J Peter W Young, Ting-Fung Chan, Wen Xin Chen, Hon-Ming Lam, Chang Fu Tian

“…Condition-dependent transcriptomes exhibited adaptive transcriptional changes in pangenome subsets shared by the two strains, while strain-dependent transcriptomes were enriched with accessory genes on the chromid. …”
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Flexible integration of spatial and expression information for precise spot embedding via ZINB-based graph-enhanced autoencoder by Jiacheng Leng, Jiating Yu, Ling-Yun Wu, Hongyang Chen

“…Some regions have intact and clear boundaries, while others exhibit blurred boundaries with high intra-domain expression similarity. …”
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The effect of non-linear signal in classification problems using gene expression. by Benjamin J Heil, Jake Crawford, Casey S Greene

“…Those building predictive models from transcriptomic data are faced with two conflicting perspectives. …”
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Japanese encephalitis virus-associated human microglia induce cell death of human microvascular endothelial cells in receptor-independent infection by Isabelle Fellay, Pauline Blanc, Alexey Larionov, Léa Schlunke, Léa Schlunke, Luis Filgueira, Nils Lannes

“…While the CX3CR1-CX3CL1 axis was inefficient in blocking virus rescue and protecting endothelial cell from cell death, transcriptomics analysis identified Tumour Necrosis Factor-related apoptosis inducing ligand and receptors as potential key player leading to endothelial cell death.DiscussionOverall, our findings demonstrate that human microvascular endothelial cells supply virus propagation and Japanese encephalitis virus-associated microglia greatly contribute to endothelial cell death, an important component of the blood brain barrier integrity. …”
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Neural representation of cytokines by vagal sensory neurons by Tomás S. Huerta, Adrian C. Chen, Saher Chaudhry, Aisling Tynan, Timothy Morgan, Kicheon Park, Richard Adamovich-Zeitlin, Bilal Haider, Jian Hua Li, Mitali Nagpal, Stavros Zanos, Valentin A. Pavlov, Michael Brines, Theodoros P. Zanos, Sangeeta S. Chavan, Kevin J. Tracey, Eric H. Chang

“…In male mice with induced colitis, inflammation increased the baseline activity of these neurons but decreased responsiveness to specific cytokines, reflecting altered neural excitability. Transcriptomic analysis of vagal ganglia from colitis mice revealed downregulation of cytokine signaling pathways, while neuronal activity pathways were upregulated. …”
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Chromosome number variation and phylogenetic divergence of East Asian Cirsium sect. Onotrophe subsect. Nipponocirsium (Compositae), with a new species from Taiwan by Chih-Yi Chang, Pei-Chun Liao, Hsy-Yu Tzeng, Junko Kusumi, Zhi-Hui Su, Yen-Hsueh Tseng

“…Cirsium pengii diverged around 0.47 Myr, while tetraploid species C. kawakamii and C. tatakaense diverged around 0.35 Myr. …”
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Differential behavior responses and genetic alteration underpinning exercise effectiveness in stress-susceptible mice by Dong-Joo Hwang, Ji-Eun Kim, Joon-Yong Cho, Jung-Hoon Koo, Yongchul Jang, Tae-Kyung Kim

“…These findings suggest that while VWR can mitigates multiple behavior symptoms in stress-susceptible mice, its effectiveness is modulated by distinct biological mechanisms. …”
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Multi-modal investigation reveals pathogenic features of diverse DDX3X missense mutations. by Federica Mosti, Mariah L Hoye, Carla F Escobar-Tomlienovich, Debra L Silver

“…Amongst ~200 mutations identified to date, half are missense. While DDX3X loss of function is known to impair neural cell fate, how the landscape of missense mutations impacts neurodevelopment is almost entirely unknown. …”
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Immune Characters and Plasticity of the Sentinel Lymph Node in Colorectal Cancer Patients by Xiaoyun Li, Jingling Tang, Hang Du, Xinjun Wang, Liyun Wu, Pingsheng Hu, Hua Zhang, Ruyi Zhang, Yuan Yang

“…SNs are shown to be in an immune active state in vivo, while highly expressing inhibitory cytokines and suppressive markers. …”
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