Detecting gene copy number alterations by Oncomine Comprehensive genomic profiling in a comparative study on FFPE tumor samples by Fabio Bozzi, Elena Conca, Marco Silvestri, Gianpaolo Dagrada, Alice Ardore, Donata Penso, Daniele Lorenzini, Chiara Costanza Volpi, Desirè Viola Trupia, Adele Busico, Iolanda Capone, Federica Perrone, Elena Tamborini, Andrea Vingiani, Luca Agnelli, Giancarlo Pruneri

Get full text

The hypolipidemic effect of MI-883, the combined CAR agonist/ PXR antagonist, in diet-induced hypercholesterolemia model by Jan Dusek, Ivana Mejdrová, Klára Dohnalová, Tomas Smutny, Karel Chalupsky, Maria Krutakova, Josef Skoda, Azam Rashidian, Ivona Pavkova, Kryštof Škach, Jana Hricová, Michaela Chocholouskova, Lucie Smutna, Rajamanikkam Kamaraj, Miloš Hroch, Martin Leníček, Stanislav Mičuda, Dirk Pijnenburg, Rinie van Beuningen, Michal Holčapek, Libor Vítek, Magnus Ingelman-Sundberg, Oliver Burk, Thales Kronenberger, Radim Nencka, Petr Pavek

“…Through comprehensive analyses utilizing lipidomics, bile acid metabolomics, and transcriptomics in humanized PXR-CAR-CYP3A4/3A7 mice fed high-fat and high-cholesterol diets, we demonstrate that MI-883 significantly reduces plasma cholesterol levels and enhances fecal bile acid excretion. …”
Get full text

Disruption of Energy Metabolism and Reactive Oxygen Species Homeostasis in Honglian Type-Cytoplasmic Male Sterility (HL-CMS) Rice Pollen by Wang Mingyue, Zhao Weibo, Feng Xiaoya, Chen Yi, Li Junhao, Fu Jinmei, Yan Yingchun, Chu Zhaohui, Huang Wenchao

“…Transmission electron microscopy was employed to observe mitochondrial morphological changes at the microspore stage, revealing significant mitochondrial alterations, characterized by the formation of 'large spherical mitochondria', occurred at the binucleate stage in the YA line. Additionally, metabolomics analysis revealed decreased levels of metabolites associated with the carbohydrate and flavonoid pathways. …”
Get full text

Nrf2/cyclooxygenase 2 signaling in Cr(VI)-induced carcinogenesis by Lei Zhao, Yi-Fang Wang, Andrea Adamcakova-Dodd, Peter S. Thorne, Ranakul Islam, Ke Jian Liu, Fei Chen, Jia Luo, Ling-Zhi Liu

“…To address this question, we employed a mouse model exposed to Cr(VI) through intranasal instillation of particulate zinc chromate (ZnCrO4) for 12 weeks. Metabolomics and RNA-seq assays revealed enhanced activity of the arachidonic acid (AA)/eicosanoid metabolism pathway in lung tissues from mice exposed to Cr(VI). …”
Get full text

Impact of sleep deprivation on colon cancer: Unraveling the KynA-P4HA2-HIF-1α axis in tumor lipid metabolism and metastasis by Zuojie Peng, Jia Song, Wenzhong Zhu, Haijun Bao, Yuan Hu, Yongping Shi, Xukai Cheng, Mi Jiang, Feifei Fang, Jinhuang Chen, Xiaogang Shu

“…Subsequently, mice feces were collected for untargeted metabolomics to screen and identify the key mediator, Kynurenic acid (KynA). …”
Get full text

A study on the differences in the gut microbiota and metabolism between male and female mice in different stress periods by Yajun Qiao, Yajun Qiao, Yajun Qiao, Juan Guo, Qi Xiao, Jianv Wang, Jianv Wang, Xingfang Zhang, Xingfang Zhang, Xinxin Liang, Xinxin Liang, Lixin Wei, Lixin Wei, Hongtao Bi, Tingting Gao, Tingting Gao

“…Microbial diversity analysis and metabolomics were performed on collected mouse feces. …”
Get full text

Multi-omics unveils strain-specific neuroactive metabolite production linked to inflammation modulation by Bacteroides and their extracellular vesicles by Basit Yousuf, Walid Mottawea, Galal Ali Esmail, Nazila Nazemof, Nour Elhouda Bouhlel, Emmanuel Njoku, Yingxi Li, Xu Zhang, Zoran Minic, Riadh Hammami

“…Using untargeted and targeted metabolomics, we identified key neurotransmitter-related or precursor metabolites, including GABA, l-tryptophan, 5-HTP, normelatonin, kynurenic acid, l-tyrosine, and norepinephrine, in a strain- and media-specific manner, with GABA (1–2 mM) being the most abundant. …”
Get full text

Dihydroquercetin attenuated Prevotella copri-caused intestinal injury by modulating gut microbiota and bile acids in weaned piglets by Long Wang, Ruizhi Hu, Siqi Ma, Xizi Yang, Jiatai Gong, Hongkun Xiang, Mingkun Shi, Xupeng Yuan, Liang Chen, Hongfu Zhang, Bie Tan, Xi He, Jianhua He, Shusong Wu

“…Intestinal flora analysis showed that P. copri increased the relative abundance of Prevotella (P = 0.026) and Eubacterium coprostanoligenes group (P < 0.001), but decreased the relative abundance of Lachnospiraceae NK4A136 group (P < 0.001), while supplementation of DHQ reduced the relative abundance of Prevotella (P = 0.026). Metabolomics results indicated that P. copri enhanced the content of 12-OH bile acid, but decreased the contents of glycodeoxycholic acid (GDCA) and glycochenodeoxycholic acid (GCDCA) (P < 0.001), while DHQ reduced the 12-OH bile acid content (P < 0.001) and increased the GDCA content (P = 0.020). …”
Get full text

Attentional dysfunction arises from right frontocentral and occipital network connectivity in Parkinson's disease by Isobel Timothea French, Kuo-Hsuan Chang, Wei-Kuang Liang, Wen-Sheng Chang, Yen-Shi Lo, Yi-Ru Wang, Mei-Ling Cheng, Norden E. Huang, Hsiu-Chuan Wu, Siew-Na Lim, Chiung-Mei Chen, Chi-Hung Juan

Get full text

Spireoside Controls Blast Disease by Disrupting Membrane Integrity of Magnaporthe oryzae by Xu Liting, He Kaiwei, Guo Chunyu, Quan Cantao, Ma Yahuan, Zhang Wei, Ren Lifen, Wang Long, Song Li, Ouyang Qing, Yin Junjie, Zhu Xiaobo, Tang Yongyan, He Min, Chen Xuewei, Li Weitao

“…Following metabolomic analysis, we identified nine flavonoids that were differentially accumulated and are considered potential candidates for disease control. …”
Get full text

Fecal microbiota transplantation modulates jejunal host-microbiota interface in weanling piglets by Shankumar Mooyottu, Muhammed Shafeekh Muyyarikkandy, Farnaz Yousefi, Ganwu Li, Orhan Sahin, Eric Burrough, Joy Scaria, Brett Sponseller, Alejandro Ramirez

“…Prior FMT treatment in the context of ETEC infection indicated a potential protective role, as evidenced by a significant shift in microbial diversity and metabolomic compositions and decreased diarrhea severity even though no effect on pathogen shedding was evident. …”
Get full text

Integrated multi-omics analysis reveals the underlying molecular mechanism for the neurotoxicity of triclosan in zebrafish by Shasha Zhao, Yuhang Ling, Baohua Zhang, Danting Wang, Limei Sun

“…Transcriptomics indicated that immune- and metabolism-related gene expression patterns were severely disturbed by TCS. Metabolomic analysis revealed 82 distinct metabolites in adult zebrafish exposed to TCS. …”
Get full text

Reshaping lipid metabolism with long-term alternate day feeding in type 2 diabetes mice by Eleni Beli, Yuanqing Yan, Leni Moldovan, Todd A. Lydic, Preethi Krishman, Sarah A. Tersey, Yaqian Duan, Tatiana E. Salazar, James M. Dominguez, Dung V. Nguyen, Abigail Cox, Sergio Li Calzi, Craig Beam, Raghavendra G. Mirmira, Carmella Evans-Molina, Julia V. Busik, Maria B. Grant

“…We demonstrated using lipidomic, microbiome, metabolomic and liver transcriptomic studies that chronic IF improved carbohydrate utilization and glucose homeostasis without weight loss and reduced white adipose tissue inflammation and significantly impacted lipid metabolism in the liver. …”
Get full text

Evaluation of taste quality of Keemun congou black tea during ripening and the effect of this quality on antioxidant capacity and in vitro inhibition of α-amylase and α-glucosidase... by Wenjing Huang, Zhibin Ye, Yida Wu, Tianzi Yu, Wei Zhao, Zihao Qi, Yanqun Jiang, Qiuyan Liu, Guofu Lu, Jingming Ning

“…In this study, taste was quantitatively evaluated by using sensory and biomimetic electrodes and by employing metabolomic techniques. The results revealed that the content of polyphenols was greatly affected by ripening, catechins and flavonoids reduced by 63.5 % and 9.2 %, respectively, and theaflavins increased by 14.6 %, thereby attenuating the bitterness and astringency of the tea infusion while enhancing its sweetness and mellowness. …”
Get full text

Effects of pesticide dichlorvos on liver injury in rats and related toxicity mechanisms by Pengcheng Zhang, Zixian Zhou, Jiaqi Yao, Yuhong Jiang, Hang Lei, Zhijun Xie, Juan Li, Xianlin Zhao, Lv Zhu, Meihua Wan, Ling Liu, Wenfu Tang

“…RNA sequencing and metabolomic analyses revealed that the pathways affected by DDVP exposure in hepatocytes include ABC transporters and amino acid biosynthesis processes. …”
Get full text

Multi-omic spatial effects on high-resolution AI-derived retinal thickness by V. E. Jackson, Y. Wu, R. Bonelli, J. P. Owen, L. W. Scott, S. Farashi, Y. Kihara, M. L. Gantner, C. Egan, K. M. Williams, B. R. E. Ansell, A. Tufail, A. Y. Lee, M. Bahlo

“…Analysis of common genomic variants, metabolomic, blood and immune biomarkers, disease PheCodes and genetic scores across a fine-scale macular thickness grid, reveals multiple novel genetic loci including four on the X chromosome; retinal thinning associated with many systemic disorders including multiple sclerosis; and multiple associations to correlated metabolites that cluster spatially in the retina. …”
Get full text

Unlocking biological complexity: the role of machine learning in integrative multi-omics by Ravindra Kumar, Rajrani Ruhel, Andre J. van Wijnen

“…Integrative multi-omics approaches use multi-layered datasets such as genomic, transcriptomic, proteomic, and metabolomic data to understand biological processes much more comprehensively compared to the single-omics analysis and to provide a comprehensive view of cellular and molecular processes. …”
Get full text

Increased distribution of carbon metabolic flux during de novo cytidine biosynthesis via attenuation of the acetic acid metabolism pathway in Escherichia coli by Tong Ye, Wei Ding, Zhengxu An, Haojie Zhang, Xiaobo Wei, Junnan Xu, Huiyan Liu, Haitian Fang

“…Transcriptomic and metabolomic analyses revealed that impairing the acetic acid metabolic pathway in E. coli effectively redirected carbon flux toward cytidine biosynthesis, yielding a 5.26-fold reduction in acetate metabolism and an 11.56-fold increase in cytidine production. …”
Get full text

Xiaohua Funing decoction ameliorates non-alcoholic fatty liver disease by modulating the gut microbiota and bile acids by Jindong Zhao, Jindong Zhao, Yan Li

“…Furthermore, metagenomic sequencing and BA metabolomic analyses were performed.ResultsCompared to the Con group, the Mod group presented significant differences in body and liver weights; serum total cholesterol (TC) and triglyceride (TG) levels; and liver TG, TC, and bile salt hydrolase levels (p &lt; 0.05 or p &lt; 0.01). …”
Get full text

Application of the DEB-TKTD model with multi-omics data: Prediction of life history traits of Chinese mitten crab (Eriocheir sinensis) under different salinities by Hanzun Zhang, Shipeng Dong, Hongwei Shan, Chao Yang, Fang Wang

“…Subsequently, tissues including the eyestalk, posterior gill, hepatopancreas, and ovary were sampled from crabs in both the freshwater control group and the 18 ‰ salinity treatment group for transcriptional and metabolomic analysis. The omics data were used to ascertain the physiological mode of action (pMoA) affected by salinity in the crabs. …”
Get full text