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https://www.readbyqxmd.com/read/29332245/reprogramming-the-metabolome-rescues-retinal-degeneration
#1
REVIEW
Karen Sophia Park, Christine L Xu, Xuan Cui, Stephen H Tsang
Metabolomics studies in the context of ophthalmology have largely focused on identifying metabolite concentrations that characterize specific retinal diseases. Studies involving mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy have shown that individuals suffering from retinal diseases exhibit metabolic profiles that markedly differ from those of control individuals, supporting the notion that metabolites may serve as easily identifiable biomarkers for specific conditions. An emerging branch of metabolomics resulting from biomarker studies, however, involves the study of retinal metabolic dysfunction as causes of degeneration...
January 13, 2018: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/29331744/urinary-metabolomics-study-the-mechanism-of-taohong-siwu-decoction-intervention-in-acute-blood-stasis-model-rats-based-on-liquid-chromatography-coupled-to-quadrupole-time-of-flight-mass-spectrometry
#2
Xiaosong Zhang, Pengling Li, Yongli Hua, Peng Ji, Wanling Yao, Qi Ma, Ziwen Yuan, Yanqiao Wen, Chaoxue Yang, Yanming Wei
Taohong Siwu Decoction (TSD) is a classic prescription in traditional Chinese medicine and is widely used to promote blood circulation to remove blood stasis. However, the effect mechanisms are not yet well understood. Here, a urinary metabolomic approach based on liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (LC/Q-TOF-MS) was conducted to explore the changes in the endogenous metabolites and to assess the integral efficacy of TSD on acute blood stasis model rats. Then, parameters for hemorheology and coagulation functions were detected...
January 2, 2018: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/29330793/hypoxia-induced-metabolomic-alterations-in-pancreatic-cancer-cells
#3
Venugopal Gunda, Sushil Kumar, Aneesha Dasgupta, Pankaj K Singh
Hypoxic conditions in the pancreatic tumor microenvironment lead to the stabilization of hypoxia-inducible factor-1 alpha (HIF-1α), which acts as the master regulator of cancer cell metabolism. HIF-1α-mediated metabolic reprogramming results in large-scale metabolite perturbations. Characterization of the metabolic intermediates and the corresponding metabolic pathways altered by HIF-1α would facilitate the identification of therapeutic targets for hypoxic microenvironments prevalent in pancreatic ductal adenocarcinoma and other solid tumors...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29330550/a-metabolomics-pilot-study-on-desmoid-tumors-and-novel-drug-candidates
#4
Kelly A Mercier, Mushriq Al-Jazrawe, Raymond Poon, Zachery Acuff, Benjamin Alman
Desmoid tumors (aggressive fibromatosis) are locally invasive soft tissue tumors that lack the ability to metastasize. There are no directed therapies or standard treatment plan, and chemotherapeutics, radiation, and surgery often have temporary effects. The majority of desmoid tumors are related to T41A and S45F mutations of the beta-catenin encoding gene (CTNNB1). Using broad spectrum metabolomics, differences were investigated between paired normal fibroblast and desmoid tumor cells from affected patients...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29330539/missing-value-imputation-approach-for-mass-spectrometry-based-metabolomics-data
#5
Runmin Wei, Jingye Wang, Mingming Su, Erik Jia, Shaoqiu Chen, Tianlu Chen, Yan Ni
Missing values exist widely in mass-spectrometry (MS) based metabolomics data. Various methods have been applied for handling missing values, but the selection can significantly affect following data analyses. Typically, there are three types of missing values, missing not at random (MNAR), missing at random (MAR), and missing completely at random (MCAR). Our study comprehensively compared eight imputation methods (zero, half minimum (HM), mean, median, random forest (RF), singular value decomposition (SVD), k-nearest neighbors (kNN), and quantile regression imputation of left-censored data (QRILC)) for different types of missing values using four metabolomics datasets...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29330507/uncovering-the-anticancer-mechanism-of-compound-kushen-injection-against-hcc-by-integrating-quantitative-analysis-network-analysis-and-experimental-validation
#6
Li Gao, Ke-Xin Wang, Yu-Zhi Zhou, Jian-Song Fang, Xue-Mei Qin, Guan-Hua Du
Compound Kushen Injection (CKI) is a Traditional Chinese Medicine (TCM) preparation that has been clinically used in China to treat various types of solid tumours. Although several studies have revealed that CKI can inhibit the proliferation of hepatocellular carcinoma (HCC) cell lines, the active compounds, potential targets and pathways involved in these effects have not been systematically investigated. Here, we proposed a novel idea of "main active compound-based network pharmacology" to explore the anti-cancer mechanism of CKI...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29330424/metagenomic-and-metabolomic-analyses-unveil-dysbiosis-of-gut-microbiota-in-chronic-heart-failure-patients
#7
Xiao Cui, Lei Ye, Jing Li, Ling Jin, Wenjie Wang, Shuangyue Li, Minghui Bao, Shouling Wu, Lifeng Li, Bin Geng, Xin Zhou, Jian Zhang, Jun Cai
Previous studies suggested a possible gut microbiota dysbiosis in chronic heart failure (CHF). However, direct evidence was lacking. In this study, we investigated the composition and metabolic patterns of gut microbiota in CHF patients to provide direct evidence and comprehensive understanding of gut microbiota dysbiosis in CHF. We enrolled 53 CHF patients and 41 controls. Metagenomic analyses of faecal samples and metabolomic analyses of faecal and plasma samples were then performed. We found that the composition of gut microbiota in CHF was significantly different from controls...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29329654/uhplc-ltq-orbitrap-based-metabolomics-coupled-with-metabolomics-pathway-analysis-method-for-exploring-the-protection-mechanism-of-kudiezi-injection-in-a-rat-anti-ischemic-cerebral-reperfusion-damage-model
#8
Si-Yi Liu, Wei Cai, Fei Wang, Ying Liu, Zhan-Peng Shang, Xiu-Ping Zhang, Zi-Jian Wang, Jian-Qiu Lu, Jia-Yu Zhang
Kudiezi injection has been used extensively in the treatment of cerebrovascular and cardiovascular diseases. However, its therapeutic effects and underlying mechanism of action are not fully understood. The aim of the present study was to clarify the protective mechanisms of Kudiezi injection on cerebral ischemic injury, using metabolomics methods. Middle cerebral artery occlusion (MCAO) was introduced in rats to build the cerebral ischemic damage. UHPLC-LTQ-Orbitrap-based analytical method was established for analysis of the metabolites...
December 2017: Chinese Journal of Natural Medicines
https://www.readbyqxmd.com/read/29329102/arsenic-exposure-from-drinking-water-and-urinary-metabolomics-associations-and-long-term-reproducibility-in-bangladesh-adults
#9
Fen Wu, Liang Chi, Hongyu Ru, Faruque Parvez, Vesna Slavkovich, Mahbub Eunus, Alauddin Ahmed, Tariqul Islam, Muhammad Rakibuz-Zaman, Rabiul Hasan, Golam Sarwar, Joseph H Graziano, Habibul Ahsan, Kun Lu, Yu Chen
BACKGROUND: Chronic exposure to inorganic arsenic from drinking water has been associated with a host of cancer and noncancer diseases. The application of metabolomics in epidemiologic studies may allow researchers to identify biomarkers associated with arsenic exposure and its health effects. OBJECTIVE: Our goal was to evaluate the long-term reproducibility of urinary metabolites and associations between reproducible metabolites and arsenic exposure. METHODS: We studied samples and data from 112 nonsmoking participants (58 men and 54 women) who were free of any major chronic diseases and who were enrolled in the Health Effects of Arsenic Longitudinal Study (HEALS), a large prospective cohort study in Bangladesh...
January 12, 2018: Environmental Health Perspectives
https://www.readbyqxmd.com/read/29328914/rewiring-of-the-fruit-metabolome-in-tomato-breeding
#10
Guangtao Zhu, Shouchuang Wang, Zejun Huang, Shuaibin Zhang, Qinggang Liao, Chunzhi Zhang, Tao Lin, Mao Qin, Meng Peng, Chenkun Yang, Xue Cao, Xu Han, Xiaoxuan Wang, Esther van der Knaap, Zhonghua Zhang, Xia Cui, Harry Klee, Alisdair R Fernie, Jie Luo, Sanwen Huang
Humans heavily rely on dozens of domesticated plant species that have been further improved through intensive breeding. To evaluate how breeding changed the tomato fruit metabolome, we have generated and analyzed a dataset encompassing genomes, transcriptomes, and metabolomes from hundreds of tomato genotypes. The combined results illustrate how breeding globally altered fruit metabolite content. Selection for alleles of genes associated with larger fruits altered metabolite profiles as a consequence of linkage with nearby genes...
January 11, 2018: Cell
https://www.readbyqxmd.com/read/29327330/microbiome-analysis-and-omics-studies-of-microbial-denitrification-processes-in-wastewater-treatment-recent-advances
#11
REVIEW
Lili Miao, Zhipei Liu
Nitrogen pollution is an increasingly severe worldwide problem because of drainage of nitrogen-containing wastewater and intensive application of nitrogen-containing fertilizers. Denitrification, a key process in nitrogen cycles, is commonly employed for nitrogen removal in engineered wastewater treatment systems. Biological denitrification is performed by denitrifying microbes (bacteria) that use nitrate as terminal electron acceptor. Better understanding the functions of diverse microbial populations in denitrification-based wastewater treatment systems, and the interactions of these populations with operating environments, is essential for improving both treatment performance and system stability...
January 9, 2018: Science China. Life Sciences
https://www.readbyqxmd.com/read/29327263/proton-pump-inhibitors-increase-the-susceptibility-of-mice-to-oral-infection-with-enteropathogenic-bacteria
#12
Eiichiro Yasutomi, Namiko Hoshi, Soichiro Adachi, Takafumi Otsuka, Lingling Kong, Yuna Ku, Haruka Yamairi, Jun Inoue, Tsukasa Ishida, Daisuke Watanabe, Makoto Ooi, Masaru Yoshida, Tomoya Tsukimi, Shinji Fukuda, Takeshi Azuma
BACKGROUND AND AIMS: Proton pump inhibitors (PPIs) are among the most frequently prescribed medications. Side effects including an increased risk of intestinal infections have been reported. It is assumed that PPIs can increase susceptibility to enteropathogens; however, the underlying mechanisms are unknown. Here in this study, we explored whether Lansoprazole (Laz), one of the PPIs, increases the susceptibility to enteropathogens, and further investigated the mechanism of it. METHODS: Mice were administered Laz intraperitoneally once daily and orally infected with Citrobacter rodentium (C...
January 11, 2018: Digestive Diseases and Sciences
https://www.readbyqxmd.com/read/29327126/antipyretic-effect-of-herba-ephedrae-ramulus-cinnamomi-herb-pair-on-yeast-induced-pyrexia-rats-a-metabolomics-study
#13
Xiao-Ming Wang, Wen-Jie Xu, Liang-Kui Xu, Shuai Song, Xue-Feng Xing, Jia-Bo Luo
OBJECTIVE: To investigate the antipyretic mechanism of Herba Ephedrae (Eph)-Ramulus Cinnamomi (RC) herb pair on yeast-induced pyrexia in rats. METHODS: Totally 30 qualifified male SD rats were randomly assigned to the normal control (NC) group, the pyrexia model (model) group, the Eph, RC and Eph-RC treatment groups by a random digital table, 6 rats in each group. Each rat received a 20% aqueous suspension of yeast (10 mL/kg) except the NC group. The 3 treatment groups were administered 8...
January 9, 2018: Chinese Journal of Integrative Medicine
https://www.readbyqxmd.com/read/29326050/a-defined-medium-for-leishmania-culture-allows-definition-of-essential-amino-acids
#14
Archana Nayak, Snezhana Akpunarlieva, Michael Barrett, Richard Burchmore
Axenic culture of Leishmania is generally performed in rich, serum-supplemented media which sustain robust growth over multiple passages. The use of such undefined media, however, obscures proteomic analyses and confounds the study of metabolism. We have established a simple, defined culture medium that supports the sustained growth of promastigotes over multiple passages and which yields parasites that have similar infectivity to macrophages to parasites grown in a conventional semi-defined medium. We have exploited this medium to investigate the amino acid requirements of promastigotes in culture and have found that phenylalanine and tryptophan are essential for viability in culture, while the absence of arginine, leucine, lysine, and valine results in significantly impaired, almost negligible growth...
January 8, 2018: Experimental Parasitology
https://www.readbyqxmd.com/read/29325475/investigation-of-the-mechanisms-of-genkwa-flos-hepatotoxicity-by-a-cell-metabolomics-strategy-combined-with-serum-pharmacology-in-hl-7702-liver-cells
#15
Zhipeng Wang, Yuanyuan Zhang, Quanli Liu, Linjia Sun, Mingming Lv, Peipei Yu, Xiaohui Chen
1. To investigate Genkwa Flos hepatotoxicity, a cell metabolomics strategy combined with serum pharmacology was performed on human HL-7702 liver cells in this study. 2. Firstly, cell viability and biochemical indicators were determined and the cell morphology was observed to confirm the cell injury and develop a cell hepatotoxicity model. Then, with the help of cell metabolomics based on UPLC-MS, the Genkwa Flos group samples were completely separated from the blank group samples in the score plots and seven upregulated as well as two down-regulated putative biomarkers in the loading plot were identified and confirmed...
January 11, 2018: Xenobiotica; the Fate of Foreign Compounds in Biological Systems
https://www.readbyqxmd.com/read/29325156/using-metabolomics-to-explore-the-role-of-postmenopausal-adiposity-in-breast-cancer-risk
#16
Jessica A Lasky-Su, Oana A Zeleznik, A Heather Eliassen
No abstract text is available yet for this article.
January 9, 2018: Journal of the National Cancer Institute
https://www.readbyqxmd.com/read/29325144/a-metabolomics-analysis-of-body-mass-index-and-postmenopausal-breast-cancer-risk
#17
Steven C Moore, Mary C Playdon, Joshua N Sampson, Robert N Hoover, Britton Trabert, Charles E Matthews, Regina G Ziegler
Background: Elevated body mass index (BMI) is associated with increased risk of postmenopausal breast cancer. The underlying mechanisms, however, remain elusive. Methods: In a nested case-control study of 621 postmenopausal breast cancer case participants and 621 matched control participants, we measured 617 metabolites in prediagnostic serum. We calculated partial Pearson correlations between metabolites and BMI, and then evaluated BMI-associated metabolites (Bonferroni-corrected α level for 617 statistical tests = P < 8...
January 9, 2018: Journal of the National Cancer Institute
https://www.readbyqxmd.com/read/29325019/deep-molecular-phenotypes-link-complex-disorders-and-physiological-insult-to-cpg-methylation
#18
Shaza B Zaghlool, Dennis O Mook-Kanamori, Sara Kader, Nisha Stephan, Anna Halama, Rudolf Engelke, Hina Sarwath, Eman K Al-Dous, Yasmin A Mohamoud, Werner Roemisch-Margl, Jerzy Adamski, Gabi Kastenmüller, Nele Friedrich, Alessia Visconti, Pei-Chien Tsai, Tim Spector, Jordana Bell, Mario Falchi, Annika Wahl, Melanie Waldenberger, Annette Peters, Christian Gieger, Maija Pezer, Gordan Lauc, Johannes Graumann, Joel A Malek, Karsten Suhre
Epigenetic regulation of cellular function provides a mechanism for rapid organismal adaptation to changes in health, lifestyle, and environment. Associations of cytosine-guanine di-nucleotide (CpG) methylation with clinical endpoints that overlap with metabolic phenotypes suggest a regulatory role for these CpG sites in the body's response to disease or environmental stress. We previously identified 20 CpG sites in an epigenome-wide association study (EWAS) with metabolomics that were also associated in recent EWASs with diabetes-, obesity-, and smoking-related endpoints...
January 8, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29324799/comprehensive-untargeted-metabolomics-of-lychnnophorinae-subtribe-asteraceae-vernonieae-in-a-phylogenetic-context
#19
Maria Elvira Poleti Martucci, Benoit Loeuille, José Rubens Pirani, Leonardo Gobbo-Neto
Members of the subtribe Lychnophorinae occur mostly within the Cerrado domain of the Brazilian Central Plateau. The relationships between its 11 genera, as well as between Lychnophorinae and other subtribes belonging to the tribe Vernonieae, have recently been investigated upon a phylogeny based on molecular and morphological data. We report the use of a comprehensive untargeted metabolomics approach, combining HPLC-MS and GC-MS data, followed by multivariate analyses aiming to assess the congruence between metabolomics data and the phylogenetic hypothesis, as well as its potential as a chemotaxonomic tool...
2018: PloS One
https://www.readbyqxmd.com/read/29324798/qualitative-metabolomics-profiling-of-serum-and-bile-from-dogs-with-gallbladder-mucocele-formation
#20
Jody L Gookin, Kyle G Mathews, John Cullen, Gabriela Seiler
Mucocele formation is characterized by secretion of abnormally thick mucus by the gallbladder epithelium of dogs that may cause obstruction of the bile duct or rupture of the gallbladder. The disease is increasingly recognized and is associated with a high morbidity and mortality. The cause of gallbladder mucocele formation in dogs is unknown. There is a strong breed predisposition and affected dogs have a high incidence of concurrent endocrinopathy or hyperlipidemia. These observations suggest a significant influence of both genetic and metabolic factors on disease pathogenesis...
2018: PloS One
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