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Alberto Gil de la Fuente, Joanna Godzien, Mariano Fernández López, Francisco J Rupérez, Coral Barbas, Abraham Otero
CEU Mass Mediator (CMM) is an on-line tool for aiding researchers when performing metabolite annotation. Its database is comprised of 279,318 real compounds integrated from several metabolomic databases including Human Metabolome Database (HMDB), KEGG and LipidMaps and 672,042 simulated compounds from MINE. In addition, CMM scores the annotations which matched the query parameters using 122 rules based on expert knowledge. This knowledge, obtained from the Centre for Metabolomics and Bioanalysis (CEMBIO) and from a literature review, enables CMM expert system to automatically extract evidence to support or refute the annotations by checking relationships among them...
February 23, 2018: Journal of Pharmaceutical and Biomedical Analysis
Annarita Falanga, Flavia A Mercurio, Antonietta Siciliano, Lucia Lombardi, Stefania Galdiero, Marco Guida, Giovanni Libralato, Marilisa Leone, Emilia Galdiero
This study evaluated the effect of QDs functionalized with the antimicrobial peptide indolicidin on oxidative stress and metabolomics profiles of Daphnia magna across three generations (F0, F1, and F2). Exposing D. magna to sub-lethal concentrations of the complex QDs-indolicidin, a normal survival of daphnids was observed from F0 to F2, but a delay of first brood, fewer broods per female, a decrease of length of about 50% compared to control. In addition, QDs-indolicidin induced a significantly higher production of reactive oxygen species (ROS) gradually in each generation and an impairment of enzymes response to oxidative stress such as superoxide dismutase (SOD), catalase (CAT) and glutathione transferase (GST)...
March 8, 2018: Aquatic Toxicology
Charalampos S Siristatidis, Eleni Sertedaki, Dennis Vaidakis, Christos Varounis, Marialena Trivella
BACKGROUND: In order to overcome the low effectiveness of assisted reproductive technologies (ART) and the high incidence of multiple births, metabolomics is proposed as a non-invasive method to assess oocyte quality, embryo viability, and endometrial receptivity, and facilitate a targeted subfertility treatment. OBJECTIVES: To evaluate the effectiveness and safety of metabolomic assessment of oocyte quality, embryo viability, and endometrial receptivity for improving live birth or ongoing pregnancy rates in women undergoing ART, compared to conventional methods of assessment...
March 16, 2018: Cochrane Database of Systematic Reviews
Nicholette D Palmer, Hayrettin Okut, Fang-Chi Hsu, Maggie C Y Ng, Yii-Der Ida Chen, Mark O Goodarzi, Kent D Taylor, Jill M Norris, Carlos Lorenzo, Jerome I Rotter, Richard N Bergman, Carl D Langefeld, Lynne E Wagenknecht, Donald W Bowden
Context: Metabolomics provides a biochemical fingerprint which, when coupled with clinical phenotypes, can provide insight into physiological processes and disease. Objective: Survey metabolites associated with dynamic and basal measures of glucose homeostasis. Design: Analysis of 733 serum metabolites from the Insulin Resistance Atherosclerosis Family Study. Setting: Community-based. Participants: 1111 Mexican Americans...
March 13, 2018: Journal of Clinical Endocrinology and Metabolism
Thomas Lange, Kathrin Budde, Georg Homuth, Gabi Kastenmüller, Anna Artati, Jan Krumsiek, Henry Völzke, Jerzy Adamski, Astrid Petersmann, Uwe Völker, Matthias Nauck, Nele Friedrich, Maik Pietzner
Objective: Thyroid hormones are ubiqiutiously involved in human metabolism. However, the precise molecular patterns associated with alterations in thyroid hormones levels remain to be explored in detail. A number of recent studies took great advantage of metabolomics profiling to outline metabolic actions of thyroid hormones in humans. Methods: Among 952 participants of the Study of Health in Pomerania data on serum free thyroxine (FT4) and thyrotropin (TSH) as well as comprehensive (non-)targeted metabolomics data of plasma and urine samples were available...
March 12, 2018: Journal of Clinical Endocrinology and Metabolism
Qiong Wu, Huan Zhang, Jia-Rong Ding, Zhan-Ying Hong, Hao Wu, Zhen-Yu Zhu, Zhi-Yong Guo, Yi-Feng Chai
As one of the most troublesome complications in patients with chronic renal disease, the etiology of uremic pruritus remains unknown, and the current therapeutic approaches are limited and unsatisfactory. To identify potential biomarkers for improving diagnosis and treatment and obtain a better understanding of the pathogenesis of uremic pruritus, we compared serum metabolome profiles of severe uremic pruritus (HUP) patients with mild uremic pruritus (LUP) patients using ultraperformance liquid chromatography-quadruple time-of-flight mass spectrometry (UPLC-QTOF MS)...
2018: BioMed Research International
Fariba Tayyari, G A Nagana Gowda, Olufunmilayo F Olopade, Richard Berg, Howard H Yang, Maxwell P Lee, Wilfred F Ngwa, Suresh K Mittal, Daniel Raftery, Sulma I Mohammed
Breast cancer, a heterogeneous disease with variable pathophysiology and biology, is classified into four major subtypes. While hormonal- and antibody-targeted therapies are effective in the patients with luminal and HER-2 subtypes, the patients with triple-negative breast cancer (TNBC) subtype do not benefit from these therapies. The incidence rates of TNBC subtype are higher in African-American women, and the evidence indicates that these women have worse prognosis compared to women of European descent. The reasons for this disparity remain unclear but are often attributed to TNBC biology...
February 20, 2018: Oncotarget
Yong Li, Peggy Sekula, Matthias Wuttke, Judith Wahrheit, Birgit Hausknecht, Ulla T Schultheiss, Wolfram Gronwald, Pascal Schlosser, Sara Tucci, Arif B Ekici, Ute Spiekerkoetter, Florian Kronenberg, Kai-Uwe Eckardt, Peter J Oefner, Anna Köttgen
Background The kidneys have a central role in the generation, turnover, transport, and excretion of metabolites, and these functions can be altered in CKD. Genetic studies of metabolite concentrations can identify proteins performing these functions. Methods We conducted genome-wide association studies and aggregate rare variant tests of the concentrations of 139 serum metabolites and 41 urine metabolites, as well as their pairwise ratios and fractional excretions in up to 1168 patients with CKD. Results After correction for multiple testing, genome-wide significant associations were detected for 25 serum metabolites, two urine metabolites, and 259 serum and 14 urinary metabolite ratios...
March 15, 2018: Journal of the American Society of Nephrology: JASN
Chuan-Xing Li, Craig E Wheelock, C Magnus Sköld, Åsa M Wheelock
Rationale: COPD represents an umbrella diagnosis caused by a multitude of underlying mechanisms, and molecular sub-phenotyping is needed to facilitate the development of molecular diagnostic/prognostic tools and efficacious treatments. Objectives: To investigate whether multi-omics integration improves the accuracy of molecular classification of COPD in small cohorts. Measurements and Results: Nine omics data-blocks (mRNA, miRNA, proteomes, metabolomes) collected from several anatomical locations from 52 female subjects were integrated by similarity network fusion (SNF)...
March 15, 2018: European Respiratory Journal: Official Journal of the European Society for Clinical Respiratory Physiology
Konstantinos C Tsolis, Evridiki-Pandora Tsare, Georgia Orfanoudaki, Tobias Busche, Katerina Kanaki, Reshmi Ramakrishnan, Frederic Rousseau, Joost Schymkowitz, Christian Rückert, Jörn Kalinowski, Jozef Anné, Spyridoula Karamanou, Maria I Klapa, Anastassios Economou
BACKGROUND: Members of the genus Streptomyces are Gram-positive bacteria that are used as important cell factories to produce secondary metabolites and secrete heterologous proteins. They possess some of the largest bacterial genomes and thus proteomes. Understanding their complex proteomes and metabolic regulation will improve any genetic engineering approach. RESULTS: Here, we performed a comprehensive annotation of the subcellular localization of the proteome of Streptomyces lividans TK24 and developed the Subcellular Topology of Polypeptides in Streptomyces database (SToPSdb) to make this information widely accessible...
March 15, 2018: Microbial Cell Factories
Stacy A Voils, Mohamed H Shahin, Timothy J Garrett, Reginald F Frye
OBJECTIVE: Incidence of venous thromboembolism (VTE) in critically ill patients remains unacceptably high despite widespread use of thromboprophylaxis. A systems biology approach may be useful in understanding disease pathology and predicting response to treatment. Metabolite profile under specific environmental conditions provides the closest link to phenotype, but the relationship between metabolomics and risk of VTE in critically ill patients is unknown. In this study, metabolomics signatures are compared in patients with and without VTE...
March 8, 2018: Thrombosis Research
Feng Peng, Yingzi Liu, Chenjie He, Yi Kong, Qianying Ouyang, Xiaonv Xie, Tong Liu, Zhaoqian Liu, Jingbo Peng
Lung cancer is the common cause of cancer-related death worldwide. Platinum-based chemotherapy is the cornerstone of treatment for lung cancer. Platinum sensitivity is a major possibility for effective cancer treatment. In this study, several potential biomarkers were identified for evaluating and predicting the response to platinum-based chemotherapy. LC-MS-based metabolomics was performed on plasma samples from 43 lung cancer patients with different chemotherapy efficacy. By combing multivariate statistical analysis, pathway analysis with correlation analysis, 8 potential biomarkers were significantly associated with platinum chemotherapy response...
February 23, 2018: Journal of Pharmaceutical and Biomedical Analysis
Hailong Zhang, Longzhen Cui, Wen Liu, Zhenfeng Wang, Yang Ye, Xue Li, Huijuan Wang
Introduction: Gastric cancer (GC) is a malignant tumor worldwide. As primary pathway for metastasis, the lymphatic system is an important prognostic factor for GC patients. Although the metabolic changes of gastric cancer have been investigated in extensive studies, little effort focused on the metabolic profiling of lymph node metastasis (LNM)-positive or negative GC patients. Objectives: We performed1 H NMR spectrum of GC tissue samples with and without LNM to identify novel potential metabolic biomarkers in the process of LNM of GC...
2018: Metabolomics: Official Journal of the Metabolomic Society
Wenlong Zhou, Yan Yang, Liang Tang, Kai Cheng, Changkun Li, Huimin Wang, Minzhi Liu, Wei Wang
Acrolein (Acr) was used as a selection agent to improve the glutathione (GSH) overproduction of the prototrophic strain W303-1b/FGPPT . After two rounds of adaptive laboratory evolution (ALE), an unexpected result was obtained wherein identical GSH production was observed in the selected isolates. Then, a threshold selection mechanism of Acr-stressed adaption was clarified based on the formation of an Acr-GSH adduct, and a diffusion coefficient (0.36 ± 0.02 μmol·min-1 ·OD600 -1 ) was calculated. Metabolomic analysis was carried out to reveal the molecular bases that triggered GSH overproduction...
March 14, 2018: Scientific Reports
Muhammad Shahid, Nicole Gull, Austin Yeon, Eunho Cho, Jooeun Bae, Hyun Seok Yoon, Sungyong You, Hana Yoon, Minjung Kim, Benjamin P Berman, Jayoung Kim
Interstitial cystitis (IC) is a chronic urinary tract disease that is characterized by unpleasant sensations, such as persistent pelvic pain, in the absence of infection or other identifiable causes. We previously performed comprehensive metabolomics profiling of urine samples from IC patients using nuclear magnetic resonance and gas-chromatography/mass spectrometry and found that urinary α-oxoglutarate (α-OG), was significantly elevated. α-OG, a tricarboxylic acid (TCA) cycle intermediate, reportedly functions to suppress the proliferation of immortalized normal human bladder epithelial cells...
March 14, 2018: Scientific Reports
Nanako Kanno, Katsumi Matsuura, Shin Haruta
Purple photosynthetic bacteria utilize light energy for growth. We previously demonstrated that light energy contributed to prolonging the survival of multiple purple bacteria under carbon-starved conditions. In order to clarify the effects of illumination on metabolic states under carbon-starved, non-growing conditions, we herein compared the metabolic profiles of starved cells in the light and dark using the purple bacterium, Rhodopseudomonas palustris. The metabolic profiles of starved cells in the light were markedly different from those in the dark...
March 13, 2018: Microbes and Environments
Adam J Chicco, Catherine H Le, Erich Gnaiger, Hans C Dreyer, Jonathan B Muyskens, Angelo D'Alessandro, Travis Nemkov, Austin D Hocker, Jessica E Prenni, Lisa M Wolfe, Nathan M Sindt, Andrew T Lovering, Andrew W Subudhi, Robert C Roach
Metabolic responses to hypoxia play important roles in cell survival strategies and disease pathogenesis in humans.  However, the homeostatic adjustments that balance changes in energy supply and demand to maintain organismal function under chronic low oxygen conditions remain incompletely understood, making it difficult to distinguish adaptive from maladaptive responses in hypoxia-related pathologies.  We integrated metabolomic and proteomic profiling with mitochondrial respirometry and blood gas analyses to comprehensively define the physiological responses of skeletal muscle energy metabolism to 16 days of high-altitude hypoxia (5260 m) in healthy volunteers from the AltitudeOmics project...
March 14, 2018: Journal of Biological Chemistry
Jessica N R Peoples, Timmi Maxmillian, Quynh Le, Sergiy M Nadtochiy, Paul S Brookes, George A Porter, Victor L Davidson, Steven N Ebert
Cardiac energy demands during early embryonic periods are sufficiently met through glycolysis, but as development proceeds, oxidative phosphorylation in mitochondria becomes increasingly vital. Adrenergic hormones are known to stimulate metabolism in adult mammals and are essential for embryonic development, but relatively little is known about their effects on metabolism in the embryonic heart.  Here, we show that embryos lacking adrenergic stimulation have approximately 10-fold less cardiac ATP compared to littermate controls...
March 14, 2018: Journal of Biological Chemistry
Zixing Dong, Xiaoling Chen, Ke Cai, Zhixin Chen, Hongbin Wang, Peng Jin, Xiaoguang Liu, Kugenthiren Permaul, Suren Singh, Zhengxiang Wang
Due to its high protein secretion capacity, simple nutritional requirements and the GRAS (generally regarded as safe) status, Bacillus licheniformis is widely used as a host for the industrial production of enzymes, antibiotics and peptides. However, as compared with its close relative B. subtilis , little is known about physiology and stress responses of B. licheniformis . To explore its temperature-stress metabolome, strains B. licheniformis ATCC 14580 and B186, with respective optimal growth temperatures of 42°C and 50°C, were cultured at 42°C, 50°C and 60°C and their corresponding metabolic profiles determined by gas chromatography/mass spectrometry (GC/MS) and multivariate statistical analyses...
March 15, 2018: Journal of Microbiology and Biotechnology
Shiho Fujisaka, Julian Avila-Pacheco, Marion Soto, Aleksandar Kostic, Jonathan M Dreyfuss, Hui Pan, Siegfried Ussar, Emrah Altindis, Ning Li, Lynn Bry, Clary B Clish, C Ronald Kahn
Diet, genetics, and the gut microbiome are determinants of metabolic status, in part through production of metabolites by the gut microbiota. To understand the mechanisms linking these factors, we performed LC-MS-based metabolomic analysis of cecal contents and plasma from C57BL/6J, 129S1/SvImJ, and 129S6/SvEvTac mice on chow or a high-fat diet (HFD) and HFD-treated with vancomycin or metronidazole. Prediction of the functional metagenome of gut bacteria by PICRUSt analysis of 16S sequences revealed dramatic differences in microbial metabolism...
March 13, 2018: Cell Reports
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