Multi-omics analysis reveals the mechanism for galactose metabolism in mutant Streptococcus thermophilus IMAU20551Y by Jiahui Tai, Haimin Hu, Jinhui Liu, Wenhui Lu, Tong Dan

“…In a previous study, a mutant of S. thermophilus IMAU20551Y was obtained by N-methyl-N′-nitro-N-nitrosoguanidine (NTG) mutagenesis in which key enzymes related to galactose metabolism were significantly changed compared with the wild type. β-galactosidase and galactokinase activity were higher in the mutant while glucokinase and pyruvate kinase activities were significantly decreased compared with the wild type. …”
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Melatonin-induced Bacillus tequilensis enhanced the disease resistance of Camellia oleifera against anthracnose by modulating cell wall and phenylpropanoid metabolism by Aiting Zhou, Aiting Zhou, Huiqin Zhou, Huiqin Zhou, Ruiqi Peng, Ruiqi Peng, Di Liu, Di Liu, Jianrong Wu, Jianrong Wu, Jia Deng, Jia Deng, Fang Wang, Fang Wang

“…Furthermore, MT-DZY 6715 treatment enhanced leaf thickness, palisade mesophyll, as well as elevated the ratio of palisade mesophyll to spongy mesophyll (PS) and tissue compactness (CTR), while simultaneously decreasing tissue looseness (SR). …”
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Multi-omics interpretation of how lysophospholipids regulate hepatic lipid metabolism and immunity in hybrid grouper (♀Epinephelus fuscoguttatus × ♂Epinephelus Lanceolatu) fed high... by Hongjin Deng, Jiacheng Zhang, Weixing Liang, Beiping Tan, Shuyan Chi

“…The mRNA expression of major histocompatibility complex class II molecule and interleukin-10 genes were significantly higher in the L0.1 group than in the L0 group (P < 0.05), while the mRNA expression of interleukin-6 and interferon-γ genes in the L0 group was significantly higher than those in the L0.1 group (P < 0.05).The transcriptome and metabolome data showed that the critical genes such as lipoprotein lipase and fatty acid synthase, as well as metabolites such as taurine and docosahexaenoic acid were enriched in the lipid metabolism pathway. …”
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The Hedyotis diffusa chromosome-level genome and multi-omics analysis provide new insights into the iridoids biosynthetic pathway by Pengyu Chen, Pengyu Chen, Zhuang Huang, Zhuang Huang, Mingzhu Yin, Yu-xin Wen, Yu-xin Wen, Qi Jiang, Qi Jiang, Ping Huang, Rui Qian, Rui Qian, Xing Hong, Xing Hong, Kaojiang Zhu, Kaojiang Zhu, Benjiang Xiao, Benjiang Xiao, Meng Chen, Meng Chen, Shihao Li, Shihao Li, Fang Huang, Lin-tao Han, Lin-tao Han

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A Novel Research Paradigm for Sarcopenia of Limb Muscles: Lessons From the Perpetually Working Diaphragm's Anti‐Aging Mechanisms by Enhui Li, Rui Wang, Yanli Li, Xiang Zan, Shufen Wu, Yiru Yin, Xiaorong Yang, Litian Yin, Yu Zhang, Jianguo Li, Xin Zhao, Ce Zhang

“…Methods Treadmill and grip tests assessed limb muscle function, while a lung function system evaluated respiratory function in both adult (6‐month‐old) and old (22‐month‐old) mice. …”
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Longitudinal profiling of host response and oropharyngeal respiratory microbiome reveals dynamic alterations during recovery from community-acquired pneumonia by Lizhe Hong, Lijun Suo, Kang Chang, Hongyun Cao, Jiahui Luan, Fuxin Zhang, Xiaofeng Yu, Xiaohui Zou, Bo Liu, Bin Cao

“…CAP increased the relative abundance of Streptococcus, Veillonella, and Peptostreptococcus, while decreasing that of Haemophilus, Neisseria, and Porphyromonas. …”
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Case Report: FAP+ fibroblasts and SPP1+ macrophages in SMARCA2-deficient while SMARCA4-preserved poorly differentiated lung adenocarcinoma: two case reports and multi-omics analysi... by Zhaoxuan Wang, Junying Wang, Shengmin Wang, Weijiao Xu, Yixiang Zhang

“…Furthermore, we perform a comprehensive multi-omics analysis of the transcriptomic cohort GSE31210 (n=226), the proteomic cohort from the study by Chen et al. …”
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Multi-omics whole-genome characterization of the copy number landscape of metastatic pancreatic ductal adenocarcinoma by James T. Topham, Joanna M. Karasinska, Andrew Metcalfe, Hassan A. Ali, Steve E. Kalloger, Maya Kevorkova, Emma Titmuss, Gian Luca Negri, Sandra E. Spencer, Gun Ho Jang, Grainne M. O’Kane, Richard A. Moore, Andrew J. Mungall, Jonathan M. Loree, Faiyaz Notta, Julie M. Wilson, Oliver F. Bathe, Patricia A. Tang, Rachel Goodwin, Gregg B. Morin, Jennifer J. Knox, Steven Gallinger, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, Daniel J. Renouf, David F. Schaeffer

“…Summary: Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive disease with limited therapeutic options. While genome profiling has benefitted clinical decision-making in many cancer types, PDAC remains among the most lethal solid cancers and has relatively few clinically actionable molecular targets. …”
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Dying occurs as a defined molecular progression in Drosophila rather than as nonspecific physiological collapse by Andrew W. Scott, Andrew P.K. Wodrich, Hitesh S. Chaouhan, Arvind K. Shukla, Kory Johnson, Philip G. McQueen, Edward Giniger

“…Summary: While we know much about aging, dying remains mysterious. …”
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Compositional variation in eye-infiltrating immune cells distinguishes human uveitis subtypes by Christian Concepcion, Yu Xia, Yulia Korshunova, Gregory W. Bligard, Amal Taylor, Michael A. Paley, Philip A. Ruzycki, Lynn M. Hassman

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Integrated spatial omics of metabolic reprogramming and the tumor microenvironment in pancreatic cancer by Hao Wu, Qiyao Zhang, Zhen Cao, Hongtao Cao, Mengwei Wu, Mengdi Fu, Tingping Huang, Xianlin Han, Xiaoyan Chang, Ziwen Liu

“…Spatial transcriptomics identified distinct pathological regions, which were further characterized using single-cell transcriptomic data and pathologist annotations. …”
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An exploratory study of high-throughput transcriptomic analysis reveals novel mRNA biomarkers for acute myocardial infarction using integrated methods by Fei Huang, Zongning Chen, Binjie Tan, Rong He, Xiaoyu Zhang, Yali Chen, Jinsong Gao, Bo Sun

“…Abstract Acute myocardial infarction (AMI) is a major contributor to cardiovascular-related mortality, and early diagnosis is crucial for effective treatment and better outcomes. While several biomarkers have been explored for AMI, there remains a need for reliable, non-invasive biomarkers that can accurately differentiate AMI patients from healthy individuals. …”
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Comparative transcriptome analysis reveals abscisic acid-induced bHLH transcription factors involved in saikosaponin biosynthesis in Bupleurum chinense DC by Han Wang, Shanqun Hu, Tong Li, Xuejie Qu, Jiaqi Zhang, Baoshun Wang, Yixuan Sun, Rui Cao, Yutong Yan, Ze Song, Xia’nan Zhang, Rong Luo, Yuru Tong, Changli Liu

“…BcbHLH3/4 exhibited transcriptional activation activity in the MYC_N domain, while molecular docking predicted 11th Arginine in the HLH domain as essential for G-box DNA binding. …”
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Transcriptome analyses of shell color and egg production traits between the uteruses of blue-green eggshell chickens and Hy-Line brown layers by Huanhuan Wang, Lei Zhang, Yinghui Wei, Hang Liu, Yanlu Wang, Ying Ge, Yuchun Pan

“…The up-regulated genes were CCR2, CCR8, CD40LG, IL18RAP, INHBA, and P2RY13, while the down-regulated genes were ABCA13, ADCY2, and GRM1. …”
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Prospective multicenter study identifying prognostic biomarkers and microbial profiles in severe CAP using BALF, blood mNGS, and PBMC transcriptomics by Wanmei Song, Qingyuan Yang, Hui Lv, Yingqi Lv, Yanshan Jiang, Jieming Qu, Yanan Li

“…These findings underscore the superiority of BALF mNGS over blood mNGS for pathogen detection, revealing microbial differences and transcriptomic alterations between mild and severe cases while identifying prognostic markers for SCAP treatment strategies.…”
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Stage-specific transcriptomic analysis reveals insights into the development, reproduction and biological function of allergens in the European house dust mite Dermatophagoides pte... by José Cristian Vidal-Quist, Félix Ortego, Bart N. Lambrecht, Stephane Rombauts, Pedro Hernández-Crespo

“…Results Analysis of differentially expressed genes (DEG) revealed that female-biased expression was the most prevalent profile (16% of genes), while males exhibited the highest fold-change differences. …”
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Integration of Transcriptomic Analysis, Network Pharmacology, and Experimental Validation Demonstrates Enhanced Muscle-Protective Effects of Ethanol Extract of Jakyak-Gamcho-Tang by Aeyung Kim, Minh Nhat Tran, A Yeong Lee, Heerim Yeo, Su-Jin Baek, No Soo Kim, Seongwon Cha, Sang-Min Park

“…This comprehensive investigation enabled a detailed assessment of the biological activities of both JGT-E and JGT-W. Transcriptomic analysis revealed that JGT-E significantly modulates key pathways involved in oxidative phosphorylation, mitochondrial biogenesis, and signaling cascades related to PGC-1α, mTORC1, and ERRα, while simultaneously inhibiting TGF-β-mediated muscle atrophic signaling. …”
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DeepGFT: identifying spatial domains in spatial transcriptomics of complex and 3D tissue using deep learning and graph Fourier transform by Shuli Sun, Jixin Liu, Guojun Li, Bingqiang Liu

“…Abstract The rapid advancements in spatially resolved transcriptomics (SRT) enable the characterization of gene expressions while preserving spatial information. …”
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Transcriptome Analysis Reveals the Molecular Mechanisms for Mycorrhiza-Enhanced Drought Tolerance in Maize by Regulating the Ca²⁺ Signaling Pathway by Qiaoming Zhang, Wenjing Yang, Miaomiao Wang, Junwei Chen, Zhaoran Zhang, Yanan Wei, Qingshan Chang, Minggui Gong

“…However, comprehensive transcriptome analysis to reveal the molecular mechanism of drought tolerance in the symbiotic process between AMF and maize is still limited. …”
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Transcriptomics assisted by metabolomics analysis provides insights into regulation mechanisms during carcinogenic process in a hydrodynamically transfected liver cancer model by Qi Zhang, Yongfeng Li, Xiaojing Cheng, Zhouxiang Liao, Sha Wen, Xuejing Huang, Zhenyu Song, Min He, Lichao Yang

“…By combining metabolomics-assisted transcriptomics assay, this research seeks to provide new insights into HCC development. …”
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