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Metabolomic analysis

Raj Kumar Sharma, Kumudesh Mishra, Alvina Farooqui, Anu Behari, Vinay Kumar Kapoor, Neeraj Sinha
OBJECTIVE AND DESIGN: We present in this article (1)H nuclear magnetic resonance (NMR)-based metabolic approach to screen the serum metabolic alterations in human gallbladder inflammation with chronic cholecystitis (CC). MATERIAL/METHODS: Total of 71 human serum samples was divided into two groups, (n = 41, CC) and (n = 30 control). (1)H NMR metabolic profiling was carried out for investigation of metabolic alterations. Multivariate statistical analysis was applied for pattern recognition and identification of metabolites playing crucial role in gallbladder inflammation...
October 21, 2016: Inflammation Research: Official Journal of the European Histamine Research Society ... [et Al.]
Jiangshan Lian, Xiaofen Li, Yinyin Wang, Jianle Yang, Wei Liu, Jing Ma, Deying Chen, Lanjuan Li, Jianrong Huang
OBJECTIVE: The present study aims to compare serum metabolite alterations between acute-on-chronic liver failure (ACLF) and chronic liver failure (CLF), and find the specific biomarkers associated with the diseases. METHODS: Serum samples were collected from patients with ACLF (n=76) and CLF (n=56) as well as healthy individuals (n=20) and assayed by ultra-performance liquid chromatography mass spectrometry (UPLC-MS). The acquired data was analyzed using principal components analysis (PCA) and partial least squares discriminate analysis (PLS-DA)...
October 18, 2016: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
Christoph Nowak, Samira Salihovic, Andrea Ganna, Stefan Brandmaier, Taru Tukiainen, Corey D Broeckling, Patrik K Magnusson, Jessica E Prenni, Rui Wang-Sattler, Annette Peters, Konstantin Strauch, Thomas Meitinger, Vilmantas Giedraitis, Johan Ärnlöv, Christian Berne, Christian Gieger, Samuli Ripatti, Lars Lind, Nancy L Pedersen, Johan Sundström, Erik Ingelsson, Tove Fall
Insulin resistance (IR) and impaired insulin secretion contribute to type 2 diabetes and cardiovascular disease. Both are associated with changes in the circulating metabolome, but causal directions have been difficult to disentangle. We combined untargeted plasma metabolomics by liquid chromatography/mass spectrometry in three non-diabetic cohorts with Mendelian Randomization (MR) analysis to obtain new insights into early metabolic alterations in IR and impaired insulin secretion. In up to 910 elderly men we found associations of 52 metabolites with hyperinsulinemic-euglycemic clamp-measured IR and/or β-cell responsiveness (disposition index) during an oral glucose tolerance test...
October 2016: PLoS Genetics
Wei Zhang, M Can Gulersonmez, Thomas Hankemeier, Rawi Ramautar
In metabolomics, a wide range of analytical techniques is used for the global profiling of (endogenous) metabolites in complex samples. In this paper, a protocol is presented for the analysis of anionic and cationic metabolites in biological samples by capillary electrophoresis-mass spectrometry (CE-MS). CE is well-suited for the analysis of highly polar and charged metabolites as compounds are separated on the basis of their charge-to-size ratio. A recently developed sheathless interfacing design, i.e., a porous tip interface, is used for coupling CE to electrospray ionization (ESI) MS...
October 1, 2016: Journal of Visualized Experiments: JoVE
Silvia Dal Santo, Mauro Commisso, Erica D'Incà, Andrea Anesi, Matteo Stocchero, Sara Zenoni, Stefania Ceoldo, Giovanni B Tornielli, Mario Pezzotti, Flavia Guzzo
Terroir refers to the combination of environmental factors that affect the characteristics of crops such as grapevine (Vitis vinifera) according to particular habitats and management practices. This article shows how certain terroir signatures can be detected in the berry metabolome and transcriptome of the grapevine cultivar Corvina using multivariate statistical analysis. The method first requires an appropriate sampling plan. In this case study, a specific clone of the Corvina cultivar was selected to minimize genetic differences, and samples were collected from seven vineyards representing three different macro-zones during three different growing seasons...
October 5, 2016: Journal of Visualized Experiments: JoVE
John J Guardiola, Juliane I Beier, K Cameron Falkner, Benjamin Wheeler, Craig James McClain, Matt Cave
BACKGROUND: Occupational vinyl chloride (VC) exposures have been associated with toxicant-associated steatohepatitis and liver cancer. Metabolomics has been used to clarify mode of action in drug-induced liver injury but has not been performed following VC exposures. METHODS: Plasma samples from 17 highly exposed VC workers without liver cancer and 27 unexposed healthy volunteers were obtained for metabolite extraction and GC/MS and LC/MS(2) analysis. Following ion identification/quantification, Ingenuity pathway analysis was performed...
October 17, 2016: Toxicology and Applied Pharmacology
Nabil Killiny
Orange jasmine, Murraya paniculata and curry leaf tree, Bergera koenegii are alternative hosts for Diaphorina citri, the vector of Candidatus Liberibacter asiaticus (CLas), the pathogen of huanglongbing (HLB) in citrus. D. citri feeds on the phloem sap where CLas grows. It has been shown that orange jasmine was a better host than curry leaf tree to D. citri. In addition, CLas can infect orange jasmine but not curry leaf tree. Here, we compared the phloem sap composition of these two plants to the main host, Valencia sweet orange, Citrus sinensis...
October 20, 2016: Plant Signaling & Behavior
Ulrike Glaubitz, Xia Li, Sandra Schaedel, Alexander Erban, Ronan Sulpice, Joachim Kopka, Dirk K Hincha, Ellen Zuther
Transcript and metabolite profiling were performed on leaves from six rice cultivars under high night temperature (HNT) condition. Six genes were identified as central for HNT response encoding proteins involved in transcription regulation, signal transduction, protein-protein interactions, jasmonate response, and the biosynthesis of secondary metabolites. Sensitive cultivars showed specific changes in transcript abundance including abiotic stress responses, changes of cell wall related genes, of ABA signaling and secondary metabolism...
October 20, 2016: Plant, Cell & Environment
Yongbo Bao, Xiao Liu, Weiwei Zhang, Jianping Cao, Wei Li, Chenghua Li, Zhihua Lin
Clam, a filter-feeding lamellibranch mollusk, is capable to accumulate high levels of trace metals and has therefore become a model for investigation the mechanism of heavy metal toxification. In this study, the effects of cadmium were characterized in the gills of Tegillarca granosa during a 96-hour exposure course using integrated metabolomic and proteomic approaches. Neurotoxicity and disturbances in energy metabolism were implicated according to the metabolic responses after Cd exposure, and eventually affected the osmotic function of gill tissue...
October 20, 2016: Scientific Reports
Nurkhalida Kamal, Christina V Viegelmann, Carol J Clements, RuAngelie Edrada-Ebel
Fungal endophytes offer diverse and unique secondary metabolites, making these organisms potential sources of promising drug leads. The application of high-resolution-liquid chromatography mass spectrometry and nuclear magnetic resonance-based metabolomics to fungal endophytes is practical in terms of dereplication studies and the mining of bioactive compounds. In this paper, we report the application of metabolomics in parallel with anti-trypanosomal assays to determine the ideal conditions for the medium-scale fermentation of the endophyte Lasiodiplodia theobromae...
October 19, 2016: Planta Medica
Mie Rostved Rasmussen, Kirstine Lykke Nielsen, Mia Roest Laursen, Camilla Bak Nielsen, Pia Svendsen, Henrik Dimke, Erik Ilsø Christensen, Mogens Johannsen, Søren Kragh Moestrup
Loss-of-function mutations in the transmembrane ABCC6 transport protein cause pseudoxanthoma elasticum - an ectopic, metabolic mineralization disorder affecting the skin, eye and vessels. ABCC6 is assumed to mediate efflux of one or several small molecule compounds from the liver cytosol to the circulation. Untargeted metabolomics using liquid chromatography mass spectrometry was employed to inspect liver cytosolic extracts from mice with targeted disruption of the Abcc6 gene. Absence of the ABCC6 protein induced an altered profile of metabolites in the liver causing accumulation of compounds as more features were upregulated than downregulated in ABCC6-deficient mice...
October 19, 2016: Journal of Proteome Research
Seu Ping Guiraud, Ivan Montoliu, Laeticia Da Silva, Loïc Dayon, Antonio Núñez Galindo, John Corthésy, Martin Kussmann, Francois-Pierre Martin
The methionine cycle is a key pathway contributing to the regulation of human health, with well-established involvement in cardiovascular diseases and cognitive function. Changes in one-carbon cycle metabolites have also been associated with mild cognitive decline, vascular dementia, and Alzheimer's disease. Today, there is no single analytical method to monitor both metabolites and co-factors of the methionine cycle. To address this limitation, we here report for the first time a new method for the simultaneous quantitation of 17 metabolites in the methionine cycle, which are homocysteic acid, taurine, serine, cysteine, glycine, homocysteine, riboflavin, methionine, pyridoxine, cystathionine, pyridoxamine, S-adenosylhomocysteine, S-adenosylmethionine, betaine, choline, dimethylglycine, and 5-methyltetrahydrofolic acid...
October 18, 2016: Analytical and Bioanalytical Chemistry
Yunpeng Wang, Lei Chen, Weiwen Zhang
BACKGROUND: 3-hydroxypropionic acid (3-HP) is an important platform chemical with a wide range of applications. In our previous study, the biosynthetic pathway of 3-HP was constructed and optimized in cyanobacterium Synechocystis sp. PCC 6803, which led to 3-HP production directly from CO2 at a level of 837.18 mg L(-1) (348.8 mg/g dry cell weight). As the production and accumulation of 3-HP in cells affect cellular metabolism, a better understanding of cellular responses to 3-HP synthesized internally in Synechocystis will be important for further increasing 3-HP productivity in cyanobacterial chassis...
2016: Biotechnology for Biofuels
Eugenio Baraldi, Giuseppe Giordano, Matteo Stocchero, Laura Moschino, Patrizia Zaramella, Maria Rosa Tran, Silvia Carraro, Roberto Romero, Maria Teresa Gervasi
OBJECTIVE: Bronchopulmonary dysplasia (BPD) is a serious complication associated with preterm birth. A growing body of evidence suggests a role for prenatal factors in its pathogenesis. Metabolomics allows simultaneous characterization of low molecular weight compounds and may provide a picture of such a complex condition. The aim of this study was to evaluate whether an unbiased metabolomic analysis of amniotic fluid (AF) can be used to investigate the risk of spontaneous preterm delivery (PTD) and BPD development in the offspring...
2016: PloS One
Sanad Alonezi, Jonans Tusiimire, Jennifer Wallace, Mark J Dufton, John A Parkinson, Louise C Young, Carol J Clements, Jin Kyu Park, Jong Woon Jeon, Valerie A Ferro, David G Watson
In the present study, liquid chromatography-mass spectrometry (LC-MS) was employed to characterise the metabolic profiles of two human ovarian cancer cell lines A2780 (cisplatin-sensitive) and A2780CR (cisplatin-resistant) in response to their exposure to melittin, a cytotoxic peptide from bee venom. In addition, the metabolomics data were supported by application of Biolog microarray technology to examine the utilisation of carbon sources by the two cell lines. Data extraction with MZmine 2.14 and database searching were applied to provide metabolite lists...
October 13, 2016: Metabolites
Emiko Sato, Yukako Tsunokuni, Tomofumi Fushima, Manami Kaneko, Ritsumi Saito, Akiyo Sekimoto, Daisuke Saigusa, Sadayoshi Ito, Hiroshi Sato, Nobuyuki Takahashi
OBJECTIVE: Preeclampsia (PE) is pregnancy-induced hypertension with proteinuria, and is often associated with fetal growth restriction (FGR). PE is a leading cause of maternal morbidity and mortality. Although alterations in circulating angiogenic factors are pathogenic, the details of pathological mechanisms of PE remain to be elucidated. We investigated changes in metabolites in a mouse model of PE induced by overproducing soluble fms-like tyrosine kinase 1 (sFlt-1) to elucidate the pathological conditions of PE by metabolomics analysis...
September 2016: Journal of Hypertension
Valentina Di Gialleonardo, Sui Seng Tee, Hannah N Aldeborgh, Vesselin Z Miloushev, Lidia S Cunha, George D Sukenick, Kayvan R Keshari
Nuclear magnetic resonance (NMR) spectroscopy is used in metabolomics to perform quantitative profiling of low-molecular weight compounds from biological specimens. The measurement of endogenous metabolites using NMR can identify new metabolic biomarkers in physiological and pathological conditions, and assess treatment response. In this study we present a rapid approach to indirectly quantify 13C enriched molecules using one-dimensional (1D) 1H NMR. We demonstrate this approach using isotopically labeled [1,6-13C]glucose and in 4 different cell lines...
October 17, 2016: Analytical Chemistry
Luisa Matos Do Canto, Catalin Marian, Rency S Varghese, Jaeil Ahn, Patricia A Da Cunha, Shawna Willey, Mary Sidawy, Janice D Rone, Amrita K Cheema, George Luta, Mohammad R Nezami Ranjbar, Habtom W Ressom, Bassem R Haddad
Identification of new biomarkers for breast cancer remains critical in order to enhance early detection of the disease and improve its prognosis. Towards this end, we performed an untargeted metabolomic analysis of breast ductal fluid using an ultra-performance liquid chromatography coupled with a quadrupole time-of-light (UPLC-QTOF) mass spectrometer. We investigated the metabolomic profiles of breast tumors using ductal fluid samples collected by ductal lavage (DL). We studied fluid from both the affected breasts and the unaffected contralateral breasts (as controls) from 43 women with confirmed unilateral breast cancer...
October 13, 2016: International Journal of Oncology
Joseph W Zabinski, Gonzalo Garcia-Vargas, Marisela Rubio-Andrade, Rebecca C Fry, Jacqueline MacDonald Gibson
Dose-response functions used in regulatory risk assessment are based on studies of whole organisms and fail to incorporate genetic and metabolomic data. Bayesian belief networks (BBNs) could provide a powerful framework for incorporating such data, but no prior research has examined this possibility. To address this gap, we develop a BBN-based model predicting birthweight at gestational age from arsenic exposure via drinking water and maternal metabolic indicators using a cohort of 200 pregnant women from an arsenic-endemic region of Mexico...
May 10, 2016: Environmental Science & Technology Letters
Fausto Carnevale Neto, Alan C Pilon, Denise M Selegato, Rafael T Freire, Haiwei Gu, Daniel Raftery, Norberto P Lopes, Ian Castro-Gamboa
Dereplication based on hyphenated techniques has been extensively applied in plant metabolomics, thereby avoiding re-isolation of known natural products. However, due to the complex nature of biological samples and their large concentration range, dereplication requires the use of chemometric tools to comprehensively extract information from the acquired data. In this work we developed a reliable GC-MS-based method for the identification of non-targeted plant metabolites by combining the Ratio Analysis of Mass Spectrometry deconvolution tool (RAMSY) with Automated Mass Spectral Deconvolution and Identification System software (AMDIS)...
2016: Frontiers in Molecular Biosciences
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