Network analysis combined with genome-wide association study helps identification of genes related to amino acid contents in soybean by Kyujung Van, Sungwoo Lee, M. A. Rouf Mian, Leah K. McHale

“…For Approach II, the individual AAs were grouped by five families according to their metabolic pathways and were examined based on the sum, ratios, and interactions of AAs within the same biochemical family. …”
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Inhibition of programmed cell death by melanoma cell subpopulations reveals mechanisms of melanoma metastasis and potential therapeutic targets by Yuepeng An, Fu Zhao, Hongling Jia, Siyu Meng, Ziwei Zhang, Shuxiao Li, Jiusi Zhao

“…Through analyzing metabolic pathways, stemness genes, and transcription factors (TFs) among cells in different phases (G1, G2/M, and S) as well as between primary and metastatic foci cells, we investigated the specific mechanisms underlying melanoma metastasis. …”
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Effect of different diets on the fatty acid composition of buffalo bulk milk by Sebastiana Failla, Giuliano Palocci, Michela Contò, Gianluca Renzi, Chiara Evangelista, Loredana Basiricò, Umberto Bernabucci

“…The feeds supplied attended all metabolic pathways, and in particular, linseed and grass could enrich the milk with functional compounds. …”
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The Metabolome Characteristics of Aerobic Endurance Development in Adolescent Male Rowers Using Polarized and Threshold Model: An Original Research by Fanming Kong, Miaomiao Zhu, Xinliang Pan, Li Zhao, Sanjun Yang, Jinyuan Zhuo, Cheng Peng, Dongkai Li, Jing Mi

“…The THR and POL groups had 46 shared differential metabolites before and after the intervention, primarily enriched in sphingolipid metabolism, glutathione metabolism, and glycine, serine, and threonine metabolism pathways. Nine unique differential metabolites were identified in the THR group, mainly enriched in pyruvate metabolism, glycine, serine, and threonine metabolism, glutathione metabolism, and sphingolipid metabolism. …”
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Integrative bioinformatic approach reveals novel melatonin-related biomarkers for Alzheimer’s disease by Hua-xiong Zhang, Dilmurat Hamit, Qing Li, Xiao Hu, San-feng Li, Fu Xu, Ming-yuan Wang, Guo-qing Bao, Hong-yan Li

“…Furthermore, gene set enrichment analysis, immune infiltration analysis and correlation analysis with metabolic pathways were conducted, as well as construction of a regulator network and molecular docking. …”
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Transcriptomic and metabolomic analysis of recalcitrant phosphorus solubilization mechanisms in Trametes gibbosa by Yulan Chen, Akasha Farooq, XieLuyao Wei, Leitao Qin, Yong Wang, Lingzi Zhang, Quanju Xiang, Ke Zhao, Xiumei Yu, Qiang Chen, Xue Gao, Tashi Nyima, Petri Penttinen, Yunfu Gu

“…Transcriptomic and metabolomic analysis revealed that different phosphorus sources altered metabolic pathways such as galactose metabolism, glyoxylate and dicarboxylic acid metabolism, and ascorbate and aldolate metabolism. …”
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Impacts of alfalfa nutrient concentrate on pellet physical attributes, growth performance, metabolism and nutritional quality of rainbow trout, Oncorhynchus mykiss by Hu Chen, Patrick C. Blaufuss, Dong-Fang Deng, Fabio Casu, Emma K. Kraco, Brian Shepherd, Wendy M. Sealey, Aaron M. Watson, Matthew F. Digman, Deborah A. Samac

“…Significant changes were observed in liver metabolism including tricarboxylic acid cycle, amino acid and energy metabolism pathways in fish fed the 20% ANC diet versus the 0% ANC diet (P < 0.05). …”
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Gut dysbiosis is associated with difficult-to-treat rheumatoid arthritis by Patricia Ruiz-Limón, Patricia Ruiz-Limón, Patricia Ruiz-Limón, Natalia Mena-Vázquez, Natalia Mena-Vázquez, Isabel Moreno-Indias, Isabel Moreno-Indias, Isabel Moreno-Indias, Jose Manuel Lisbona-Montañez, Jose Manuel Lisbona-Montañez, Jose Manuel Lisbona-Montañez, Arkaitz Mucientes, Arkaitz Mucientes, Sara Manrique-Arija, Sara Manrique-Arija, Sara Manrique-Arija, Rocío Redondo-Rodriguez, Rocío Redondo-Rodriguez, Laura Cano-García, Laura Cano-García, Francisco J. Tinahones, Francisco J. Tinahones, Francisco J. Tinahones, Francisco J. Tinahones, Antonio Fernández-Nebro, Antonio Fernández-Nebro, Antonio Fernández-Nebro

“…The factors associated with D2T RA were inflammatory activity according to DAS28-ESR (HR, 2.649; p = 0.013), prednisone (HR, 3.794; p = 0.008), and the Firmicutes/Bacteroidetes ratio (HR, 0.288; p = 0.033).ConclusionThe composition of the gut microbiota of patients with D2T RA differed from that of E2T RA patients, as did the metabolic pathways.…”
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Growth of microbes in competitive lifestyles promotes increased ARGs in soil microbiota: insights based on genetic traits by Zishu Liu, Xiangwu Yao, Chengyi Chen, Yuxiang Zhao, Chifei Dong, Lingtao Sun, Junxian Zhao, Baofeng Zhang, Zhendi Yu, Dongqing Cheng, Lizhong Zhu, Baolan Hu

“…Moreover, optimizations in energy production and conversion, alongside a streamlining of bypass metabolic pathways, further boost the growth of ARGs in sub-inhibitory antibiotic conditions. …”
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<i>METTL3</i> and <i>FTO</i> Regulate Heat Stress Response in Hu Sheep Through Lipid Metabolism via m6A Modification by Bowen Chen, Chao Yuan, Tingting Guo, Jianbin Liu, Zengkui Lu

“…Transcriptome and metabolome analyses showed that lipid deposition heat stress had significant effects on the linoleic acid, linolenic acid, glycerophospholipid, and arachidonic acid metabolic pathways in hepatocytes. After <i>METTL3</i> knockdown, the m6A methylation level decreased, but the difference was not significant (<i>p</i> > 0.05), the <i>FABP4</i> and <i>Accα</i> expression levels increased, and the <i>HSP60</i>, <i>HSP70</i>, and <i>HSP110</i> expression levels decreased significantly. …”
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Diversity and Functional Insights into Endophytic Fungi in Halophytes from West Ordos Desert Ecosystems by Xingzhe Wang, Yan Zhang, Jingpeng Li, Yiteng Ding, Xiaodan Ma, Peng Zhang, Haijing Liu, Jie Wei, Yuying Bao

“…Functional predictions indicated that endophytic fungi play important roles in metabolic pathways such as nucleotide biosynthesis, carbohydrate degradation, and lipid metabolism, which may enhance plant survival in saline–alkaline and arid environments. …”
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To construct and validate a risk score model of angiogenesis-related genes to predict the prognosis of hepatocellular carcinoma by Duangui Gao, Yuan Lu, Tianpeng Jiang, Qinghong Duan, Zhi Huang

“…The GSVA analysis suggested that the predicted high-risk population showed higher activity in the purine, pyrimidine, and riboflavin metabolic pathways. Compared with the low-risk group, the tumor microenvironment in the high-risk group showed a reduction in the number of cells promoting anti-tumor immunity and an increase in the number of cells inhibiting anti-tumor immunity, as well as a reduction in overall immune infiltration and matrix components. …”
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Identification of Potential Diagnostic Biomarkers of Carotid Atherosclerosis in Obese Populations by Wu X, Pan J, Pan X, Kang J, Ren J, Huang Y, Gong L, Li Y

“…Finally, high-fat diet-fed C57BL/6J ApoE−/− mice were used for in vivo validation.Results: MMP9, PLA2G7, and SPP1 as regulators of the immune infiltration microenvironment in OB patients with CAS, and stratified CAS samples into subtypes with differences in metabolic pathways based on OB classification. Enrichment analysis indicated abnormalities in immune and inflammatory responses, the calcium signaling, and lipid response in obese CAS patients. …”
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Effect of different diets on the fatty acid compo- sition of buffalo bulk milk by Sebastiana Failla, Giuliano Palocci, Michela Contò, Gianluca Renzi, Chiara Evangelista, Loredana Basiricò, Umberto Bernabucci

“…The feeds supplied attend all metabolic pathways, and in particular, linseed and grass could enrich the milk with nutraceuticals. …”
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Efferocytosis-related gene IL33 predicts prognosis and immune response and mediates proliferation and migration in vitro and in vivo of breast cancer by Xiao He, Xianjie Cheng, Zhun Zhang, Lanhui Chen, Changjun Xie, Mengjie Tang

“…The enrichment of metabolic pathways within the detected clusters was evaluated using gene set variation analysis (GSVA) and gene set enrichment analysis (GSEA). …”
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Comparative Genomics Reveals Evidence of the Genome Reduction and Metabolic Potentials of <i>Aliineobacillus hadale</i> Isolated from Challenger Deep Sediment of the Mariana Trench by Shaofeng Yang, Jie Liu, Yang Liu, Weichao Wu, Jiahua Wang, Yuli Wei

“…Genomic analysis reveals a streamlined genome in the organism, characterized by a significant loss of orthologous genes, including those involved in cytochrome c synthesis, aromatic compound degradation, and polyhydroxybutyrate (PHB) synthesis, which suggests its adaptation to low oxygen levels and oligotrophic conditions through alternative metabolic pathways. In addition, the reduced number of paralogous genes in strain Lsc_1132^T, together with its high protein-coding gene density, may further contribute to streamlining its genome and enhancing its genomic efficiency. …”
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Niacin alters ruminal microbial composition and metabolites in sheep fed a high-concentrate diet by Zhiqiang Cheng, Jiancheng Liu, Yingying Yu, Wentao Liu, Xiaobin Li, Fengming Li, Changjiang Zang, Kailun Yang

“…The concentrations of NH3-N (p &lt; 0.01), propionate (p &lt; 0.01), and butyrate (p &lt; 0.05) in the NA group were significantly higher than those in the CON group. (3) Compared to the CON group, the ruminal pyruvate content in the NA group was significantly increased at 0 h before feeding (p &lt; 0.05), and lactic acid (p &lt; 0.05) was significantly decreased at 1 and 3 h after feeding, lactate dehydrogenase activities was significantly decreased (p &lt; 0.01) at 3 and 5 h after feeding. (4) The number of specific operational taxonomic units (OTUs) in the CON and NA groups were 26 and 37, respectively, for a total of 1,178 OTUs; principal coordinate analysis (R2 = 0.172, p-value = 0.007) and non-metric multidimensional scaling (stress = 0.1646) results showed that the two groups of samples were significantly separated. (5) The species distribution bar graph shows that at the phylum level, the relative abundances of Bacteroidetes, Firmicutes, and Proteobacteria were 43.70, 36.25, and 12.77%, respectively. (6) Orthogonal projection to latent structure-discriminant analysis results showed that the two groups of samples were clearly separated in the positive and negative ionization modes, with R2Y and Q2Y values of 0.705, 0.857, 0.695, and 0.28, respectively. There were 72 metabolic pathways, mainly citric acid cycle, pyruvate metabolism, and cysteine and methionine metabolism. (7) Correlation analysis showed that a number of microorganisms (such as Succinivibrio and Prevotella) and differential metabolites (such as L-malic acid, propionic acid, succinic acid, and pyruvic acid) participated in tricarboxylic acid cycle metabolism. …”
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Genome-Wide Comprehensive Identification and In Silico Characterization of Lectin Receptor-Like Kinase Gene Family in Barley (Hordeum vulgare L.) by Fee Faysal Ahmed, Farah Sumaiya Dola, Md Shohel Ul Islam, Fatema Tuz Zohra, Nasrin Akter, Shaikh Mizanur Rahman, Md. Abdur Rauf Sarkar

“…Exploration of gene ontology (GO) enrichment indicated that the identified HvlecRLK genes are associated with various cellular processes, metabolic pathways, defense mechanisms, kinase activity, catalytic activity, ion binding, and other essential pathways. …”
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Characterizing tumor biology and immune microenvironment in high-grade serous ovarian cancer via single-cell RNA sequencing: insights for targeted and personalized immunotherapy st... by Fu Zhao, Fu Zhao, Xiaojing Jiang, Yumeng Li, Tianjiao Huang, Zhikai Xiahou, Wenyang Nie, Qian Li

“…The C2 subtype was also associated with various metabolic pathways, such as glycolysis and riboflavin metabolism, as well as programmed cell death processes. …”
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The protective effects of Levilactobacillus brevis FZU0713 on lipid metabolism and intestinal microbiota in hyperlipidemic rats by Xiaoyun Fan, Qing Zhang, Weiling Guo, Qi Wu, Jinpeng Hu, Wenjian Cheng, Xucong Lü, Pingfan Rao, Li Ni, Youting Chen, Lijiao Chen

“…Furthermore, liver metabolomics analysis demonstrated that L. brevis FZU0713 had a significant regulatory effect on the composition of liver metabolites in hyperlipidemic rats, especially the levels of some important biomarkers involved in the metabolic pathways of arachidonic acid metabolism, primary bile acid biosynthesis, amino sugar and nucleotide sugar metabolism, taurine and hypotaurine metabolism, biosynthesis of unsaturated fatty acid, fructose and mannose metabolism, tyrosine metabolism, etc. …”
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