Cdkn1a silencing restores myoblast differentiation by inducing selective apoptosis in senescent cells by Sujin Kim, Bonsang Gu, Chan-Young So, Keren Esther Kristina Mantik, Seung-Hyun Jung, Sohee Moon, Dong-Ho Park, Hyo-Bum Kwak, Jinkyung Cho, Eun-Jeong Cho, Jae-Seon Lee, Ju-Hee Kang

“…Methods We performed transcriptomic analysis to identify genes related to aging-induced sarcopenia using 21 month-old Sprague–Dawley rats. …”
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Decoding mitochondrial stress genes in DCM: towards precision diagnosis and therapy by Bingbing Zhu, Hai Cheng, Jiawei Li, Yangyang Hu, Xiaoning Ge

“…Results The study identified five hub genes related to mitochondrial oxidative stress: VCL, ABCB1, JAK2, KDR, and NGF. Expression analysis revealed high levels of VCL, ABCB1, KDR, and NGF in the non-failing (NF) group, while JAK2 was elevated in the DCM group (p < 0.05). …”
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Cellular hierarchy framework based on single-cell and bulk RNA sequencing reveals fatty acid metabolic biomarker MYDGF as a therapeutic target for ccRCC by Ning Wang, Ziyu Xu, Lina Zhang, Lina Zhang, Yanfang Lu, Yanfang Lu, Yanliang Wang, Yanliang Wang, Lei Yan, Lei Yan, Huixia Cao, Huixia Cao, Limeng Wang, Limeng Wang, Fengmin Shao, Fengmin Shao

“…Through five distinct enrichment scoring methods and hdWGCNA analysis, we redefined a gene set related to increased FAM at the single-cell level. …”
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Induced pluripotent stem cell-derived mesenchymal stem cells (iMSCs) inhibit M1 macrophage polarization and reduce alveolar bone loss associated with periodontitis by Liang Chen, Yuanqing Liu, Chenhao Yu, Pei Cao, Yiming Ma, Yiran Geng, Yu Cai, Yong Zhang, Jia Liu, Yang Li, Qingxian Luan

“…Co-culture assays, cytokine analysis, reactive oxygen species (ROS) detection, transcriptomic analysis, flow cytometry, reverse transcription-quantitative polymerase chain reaction (RT-qPCR), and western blot analysis were performed to elucidate the underlying mechanisms. …”
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Candida albicans impacts carbohydrate metabolism of Enterococcus faecalis in interkingdom biofilms by Nicole de Mello Fiallos, Iriana J. Zanin dos Santos, Debra N. Brunson, Jessica K. Kajfasz, Lin Zeng, Rossana de Aguiar Cordeiro, José A. Lemos, Jacqueline Abranches

“…Mannose-PTS activity and glycerol quantification assays were conducted to investigate changes in carbohydrate metabolism.Results Transcriptomic analysis revealed 149 E. faecalis genes differentially expressed in dual-species biofilms. …”
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Thyroid‐Targeted Nano‐Bombs Empower HIFU for Graves' Disease by Binhao Wang, Zhuobing Yin, Xiangyue You, Hanwei Peng, Ying Jiang

“…Robust in vitro and in vivo results demonstrated that PSAPI is highly biocompatible, accumulates in the thyroid within 24 h after administration, and significantly potentiates the therapeutic efficacy of HIFU, resulting in markedly reduced inflammatory responses. Transcriptomic analysis revealed a cellular defense mechanism activated in PSAPI‐treated cells following HIFU irradiation, highlighting potential molecular targets for the future development of HIFU‐sensitizing agents. …”
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Role of riboflavin biosynthesis gene duplication and transporter in Aeromonas salmonicida virulence in marine teleost fish by Hajarooba Gnanagobal, Trung Cao, Ahmed Hossain, Ignacio Vasquez, Setu Chakraborty, Joy Chukwu-Osazuwa, Danny Boyce, María Jesus Espinoza, Víctor Antonio García-Angulo, Javier Santander

“…Likewise, ribN encodes a functional riboflavin importer. Transcriptomics analysis indicated that external riboflavin affected the expression of a relatively small number of genes, including a few involved in iron metabolism. ribB was downregulated in response to external riboflavin, suggesting negative feedback. …”
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Effects of environmental temperature on growth performance, muscle fiber structure, fatty acid composition, and gene expression in ducks by Ziyi Pan, Congcong Xu, Dongyue Sun, Xingda Yang, Rihong Guo, Zichun Dai, Fang Chen, Zhendan Shi, Shijia Ying

“…Transcriptomic analysis revealed 544 differentially expressed genes (DEGs) primarily associated with the Cell Cycle, Cell Replication, and PPAR signaling pathways, with key genes cell division cycle 45 (CDC45), chromatin licensing and DNA replication factor 1 (CDT1), and others identified through protein-protein interaction (PPI) network analysis as crucial for temperature regulation of muscle fiber structure and fatty acid composition, particularly within the significantly enriched cell cycle pathway. …”
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A deep learning model to predict glioma recurrence using integrated genomic and clinical data by Jessica A. Patricoski-Chavez, Seema Nagpal, Ritambhara Singh, Jeremy L. Warner, Ece D. Gamsiz Uzun

“…The prognosis varies considerably; patients with low-grade gliomas (LGGs) have 5-year survival rates of up to 80%, while patients with higher-grade gliomas (HGGs) often experience rates below 5%. …”
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Low-intensity laser exposure enhances rice (Oryza sativa L.) growth through physio-biochemical regulation, transcriptional modulation, and microbiome alteration by Yetong Qi, Yumeng Lei, Temoor Ahmed, Feng Cheng, Kangqi Lei, Han Yang, Hayssam M. Ali, Zhitao Li, Xingjiang Qi

“…Transmission electron microscopy showed improved chloroplast structure, correlating with enhanced photosynthetic efficiency. Transcriptomic analysis identified 623 differentially expressed genes, with significant enrichment in pathways related to photosynthesis, carbon metabolism, and hormone signaling. …”
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Multi-omics exploration of CAV1+ tumor epithelial subcelltype in oral squamous cell carcinoma and its impact on the immune microenvironment by Yan’an Shi, Yiting Shao, Bin Xia, Wenying Yang, Yan Wang, Lifu Yu, Yonghui Zhang

“…Results Our findings indicate that the CAV1+ epithelial subcelltype (CAV1+EIP) exhibits the highest copy number variation scores, significantly correlating with poor patient prognosis. Analysis of specific transcription factors reveals that high expression of LHX1 and ATF1 is associated with malignant features, while IGF2BP1, a target gene of these transcription factors, shows a negative correlation with immune regulatory pathways. …”
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Animal Wellness: The Power of Multiomics and Integrative Strategies by Ratan Kumar Choudhary, Sunil Kumar B. V., Chandra Sekhar Mukhopadhyay, Neeraj Kashyap, Vishal Sharma, Nisha Singh, Sina Salajegheh Tazerji, Roozbeh Kalantari, Pouneh Hajipour, Yashpal Singh Malik

“…Multiomic approaches, including phenomics, genomics, epigenomics, metabolomics, proteomics, transcriptomics, microbiomics, and metaproteomics, are widely employed to assess and enhance animal health. …”
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Breed-specific differences of gut microbiota and metabolomic insights into fat deposition and meat quality in Chinese Songliao Black Pig and Large White × Landrace Pig Breeds by Suthar Teerath Kumar, Yunpeng Zhang, Qi Zhang, Riaz Muhammad Azeem, Zhang Jing, Li Pan, Wu-Sheng Sun, Yuan Zhao, Shu-Min Zhang

“…Results Microbiome analysis revealed that Fibrobacter, Unidentified_Peptostreptococcaceae, Sutterella, and Unidentifed_Rickettsiales were enriched in SBP, while Ruminococcus, Corynebacterium, and Streptococcaceae in LWLDP. …”
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Neuro-immune communication at the core of craving-associated brain structural network reconfiguration in methamphetamine users by Yanyao Du, Jiaqi Zhang, Dan Cao, Wenhan Yang, Jin Li, Deying Li, Ming Song, Zhengyi Yang, Jun Zhang, Tianzi Jiang, Jun Liu

“…Craving-associated structural alterations (CSA) were investigated through multivariate group comparisons and biological relevance analysis. The neural mechanisms underlying CSA were elucidated using transcriptomic and neurochemical analyses. …”
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Immunomodulatory effects of intratumoral cowpea mosaic virus and calreticulin nanoparticles in canine tumors: early results by Akansha Singh, Jessica Fernanda Affonso de Oliveira, Jessica Fernanda Affonso de Oliveira, Jessica Fernanda Affonso de Oliveira, Jessica Schrader, Deepan Kishore, Sri Vidhya Chandrasekar, Steven Fiering, Nicole F. Steinmetz, Nicole F. Steinmetz, Nicole F. Steinmetz, Nicole F. Steinmetz, Nicole F. Steinmetz, Nicole F. Steinmetz, Nicole F. Steinmetz, Nicole F. Steinmetz, Ashish Ranjan

“…Endpoints included serum cytokine analysis, tumor transcriptomics via NanoString, immune cell profiling in blood and tumor biopsies, and efficacy assessment using RECIST criteria.ResultCPMV exhibited an icosahedral shape (~30 nm), while CRT-NP were spherical (~300 nm). …”
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Interaction between post-tumor inflammation and vascular smooth muscle cell dysfunction in sepsis-induced cardiomyopathy by Rui Liu, Lina Jia, Lin Yu, Detian Lai, Qingzhu Li, Bingyu Zhang, Enwei Guo, Kailiang Xu, Qiancheng Luo

“…BackgroundSepsis-induced cardiomyopathy (SIC) presents a critical complication in cancer patients, contributing notably to heart failure and elevated mortality rates. While its clinical relevance is well-documented, the intricate molecular mechanisms that link sepsis, tumor-driven inflammation, and cardiac dysfunction remain inadequately explored. …”
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Recombinant serralysin metalloproteases D enhances the intracellular replication of infectious bovine rhinotracheitis virus by Longfei Yan, Yanran Li, Jiancheng Qi, Li Ren, Xueke Zhou, Liping Gou, Zhicai Zuo

“…Quantification of IBRV gB gene copy numbers using fluorescence quantification PCR (FQ-PCR) revealed that rSPD promotes viral replication during the intracellular stage, without affecting viral adsorption, entry, or directly interacting with viral particles. The transcriptomic analysis further demonstrated that rSPD suppresses innate immune responses while amplifying inflammatory pathways in IBRV-infected MDBK cells. …”
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GPD1L downregulation in colorectal cancer: a novel obesity-related biomarker linking metabolic dysregulation to tumor progression by Feng Zhu, Feng Zhu, Huiyuan Li, Huiyuan Li, Hongzhang Liu, Hongzhang Liu, Yusheng Wang, Yusheng Wang

“…Following GPD1L quantification via qPCR, selected cell models underwent pcDNA3.1-GPD1L transfection for functional characterization. Then Western blot analysis was used to explore its possible mechanism.ResultsComparative analysis revealed a marked elevation of GPD1L expression in non-neoplastic tissues relative to tumor specimens (P&lt;0.001). …”
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Bile acids enhance fat metabolism and skeletal muscle development in Zhijiang duck by modulating gut microbiota by Liang Chen, Zhizhong Zhang, Wei Deng, Guitao Jiang, Deming Xie, Aizhi Cao

“…Additionally, BA increased (P < 0.05) the cross-sectional area of breast muscle fibers, total bile acid content, and levels of insulin-like growth factors 1/2 (IGF1/2). Transcriptomic analysis further revealed that BA significantly upregulated (P < 0.05) the levels of PPARα, CPT1α, NR1H4, and CETP in breast muscle. 16S rRNA analysis showed a significant increase (P < 0.05) in the relative abundances of genera Enorma, [Eubacterium nodatum group], Rikenellaceae RC9 gut group, and SP3-e08. …”
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SHED-derived exosome-mimetics promotes rotator cuff tendon-bone healing via macrophage immunomodulation through NF-κB suppression and autophagy activation by Yanwei He, Junzhe Sheng, Fashun Liu, Fangqi Li, Shihao Lu, Wenbo Chen, Li Yang, Peng Zhou, Zan Chen, Shiyi Chen, Zhiwen Luo, Junming Sun

“…In vivo, GM@PDA&EMs reduced M1 macrophage infiltration, enhanced osteocalcin and VEGF expression, and improved biomechanical strength. Transcriptomic analysis of macrophages revealed SHED-EMs suppressed NF-κB signaling, while subsequent experiments demonstrated autophagy activation (increased LC3II/I, decreased P62) and reduced inflammation (lower TNF-α/iNOS). …”
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