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Metabolomics: Official Journal of the Metabolomic Society

Mahmoud Delphan, Tengda Lin, David B Liesenfeld, Johanna Nattenmüller, Jürgen T Böhm, Biljana Gigic, Nina Habermann, Lin Zielske, Petra Schrotz-King, Martin Schneider, Alexis Ulrich, Hans-Ulrich Kauczor, Cornelia M Ulrich, Jennifer Ose
Background: Branched-chain amino acids (BCAA) have been previously linked to survival in colorectal cancer (CRC) patients. It is unclear whether BCAAs are prognostic biomarkers or surrogate markers for energy balance. Objectives: We aimed to determine correlations of BCAAs with markers of energy balance over time and to investigate prognostic significance of BCAAs in CRC. Methods: We used urinary samples from newly diagnosed CRC patients [n=163; (stage I - IV)] from the ColoCare study in Heidelberg, Germany, collected at surgery (n=163), 6 (n=83) and 12 months follow-up (n=54)...
March 2018: Metabolomics: Official Journal of the Metabolomic Society
Kota Kera, Dennis D Fine, Daniel J Wherritt, Yoshiki Nagashima, Norimoto Shimada, Takeshi Ara, Yoshiyuki Ogata, Lloyd W Sumner, Hideyuki Suzuki
Introduction: Oxygen from carbon dioxide, water or molecular oxygen, depending on the responsible enzyme, can lead to a large variety of metabolites through chemical modification. Objectives: Pathway-specific labeling using isotopic molecular oxygen (18 O2 ) makes it possible to determine the origin of oxygen atoms in metabolites and the presence of biosynthetic enzymes (e.g., oxygenases). In this study, we established the basis of 18 O2 -metabolome analysis. Methods: 18 O2 labeled whole Medicago truncatula seedlings were prepared using 18 O2 -air and an economical sealed-glass bottle system...
2018: Metabolomics: Official Journal of the Metabolomic Society
Fuguang Xue, Xiaohua Pan, Linshu Jiang, Yuming Guo, Benhai Xiong
Introduction: Thiamine is known to attenuate high-concentrate diet induced subacute ruminal acidosis (SARA) in dairy cows, however, the underlying mechanisms remain unclear. Objectives: The major objective of this study was to investigate the metabolic mechanisms of thiamine supplementation on high-concentrate diet induced SARA. Methods: Six multiparous, rumen-fistulated Holstein cows were used in a replicated 3 × 3 Latin square design...
2018: Metabolomics: Official Journal of the Metabolomic Society
Oluwasola Lawal, Hugo Knobel, Hans Weda, Tamara M E Nijsen, Royston Goodacre, Stephen J Fowler
Introduction: Infections such as ventilator-associated pneumonia (VAP) can be caused by one or more pathogens. Current methods for identifying these pathogenic microbes often require invasive sampling, and can be time consuming, due to the requirement for prolonged cultural enrichment along with selective and differential plating steps. This results in delays in diagnosis which in such critically ill patients can have potentially life-threatening consequences. Therefore, a non-invasive and timely diagnostic method is required...
2018: Metabolomics: Official Journal of the Metabolomic Society
Andrey Smelter, Hunter N B Moseley
Introduction: The Metabolomics Workbench Data Repository is a public repository of mass spectrometry and nuclear magnetic resonance data and metadata derived from a wide variety of metabolomics studies. The data and metadata for each study is deposited, stored, and accessed via files in the domain-specific 'mwTab' flat file format. Objectives: In order to improve the accessibility, reusability, and interoperability of the data and metadata stored in 'mwTab' formatted files, we implemented a Python library and package...
2018: Metabolomics: Official Journal of the Metabolomic Society
Zoe M Matthews, Patrick J B Edwards, Ariane Kahnt, Mark G Collett, Jonathan C Marshall, Ashton C Partridge, Scott J Harrison, Karl Fraser, Mingshu Cao, Peter J Derrick
Introduction: Photosensitization is a common clinical sign in cows suffering from liver damage caused by the mycotoxin sporidesmin. This disease, called facial eczema (FE), is of major importance in New Zealand. Current techniques for diagnosing animals with subclinical sporidesmin-induced liver damage (i.e. without photosensitization) are nonspecific. In addition, little is known of the mechanisms involved in sporidesmin resistance, nor the early effects seen following low-dose sporidesmin intoxication...
2018: Metabolomics: Official Journal of the Metabolomic Society
Lenin D Sarabia, Berin A Boughton, Thusitha Rupasinghe, Allison M L van de Meene, Damien L Callahan, Camilla B Hill, Ute Roessner
Introduction: Mass spectrometry imaging (MSI) is a technology that enables the visualization of the spatial distribution of hundreds to thousands of metabolites in the same tissue section simultaneously. Roots are below-ground plant organs that anchor plants to the soil, take up water and nutrients, and sense and respond to external stresses. Physiological responses to salinity are multifaceted and have predominantly been studied using whole plant tissues that cannot resolve plant salinity responses spatially...
2018: Metabolomics: Official Journal of the Metabolomic Society
Elizabeth A Scoville, Margaret M Allaman, Caroline T Brown, Amy K Motley, Sara N Horst, Christopher S Williams, Tatsuki Koyama, Zhiguo Zhao, Dawn W Adams, Dawn B Beaulieu, David A Schwartz, Keith T Wilson, Lori A Coburn
Introduction: Biomarkers are needed in inflammatory bowel disease (IBD) to help define disease activity and identify underlying pathogenic mechanisms. We hypothesized that serum metabolomics, which produces unique metabolite profiles, can aid in this search. Objectives: The aim of this study was to characterize serum metabolomic profiles in patients with IBD, and to assess for differences between patients with ulcerative colitis (UC), Crohn's disease (CD), and non- IBD subjects...
January 2018: Metabolomics: Official Journal of the Metabolomic Society
Daqiang Pan, Caroline Lindau, Simon Lagies, Nils Wiedemann, Bernd Kammerer
Introduction: Subcellular compartmentalization enables eukaryotic cells to carry out different reactions at the same time, resulting in different metabolite pools in the subcellular compartments. Thus, mutations affecting the mitochondrial energy metabolism could cause different metabolic alterations in mitochondria compared to the cytoplasm. Given that the metabolite pool in the cytosol is larger than that of other subcellular compartments, metabolic profiling of total cells could miss these compartment-specific metabolic alterations...
2018: Metabolomics: Official Journal of the Metabolomic Society
Lifeng Ye, Maria De Iorio, Timothy M D Ebbels
Introduction: To aid the development of better algorithms for [Formula: see text]H NMR data analysis, such as alignment or peak-fitting, it is important to characterise and model chemical shift changes caused by variation in pH. The number of protonation sites, a key parameter in the theoretical relationship between pH and chemical shift, is traditionally estimated from the molecular structure, which is often unknown in untargeted metabolomics applications. Objective: We aim to use observed NMR chemical shift titration data to estimate the number of protonation sites for a range of urinary metabolites...
2018: Metabolomics: Official Journal of the Metabolomic Society
Sonia Liggi, Christine Hinz, Zoe Hall, Maria Laura Santoru, Simone Poddighe, John Fjeldsted, Luigi Atzori, Julian L Griffin
Introduction: Data processing is one of the biggest problems in metabolomics, given the high number of samples analyzed and the need of multiple software packages for each step of the processing workflow. Objectives: Merge in the same platform the steps required for metabolomics data processing. Methods: KniMet is a workflow for the processing of mass spectrometry-metabolomics data based on the KNIME Analytics platform. Results: The approach includes key steps to follow in metabolomics data processing: feature filtering, missing value imputation, normalization, batch correction and annotation...
2018: Metabolomics: Official Journal of the Metabolomic Society
Anita Rácz, Filip Andrić, Dávid Bajusz, Károly Héberger
Introduction: Contemporary metabolomic fingerprinting is based on multiple spectrometric and chromatographic signals, used either alone or combined with structural and chemical information of metabolic markers at the qualitative and semiquantitative level. However, signal shifting, convolution, and matrix effects may compromise metabolomic patterns. Recent increase in the use of qualitative metabolomic data, described by the presence (1) or absence (0) of particular metabolites, demonstrates great potential in the field of metabolomic profiling and fingerprint analysis...
2018: Metabolomics: Official Journal of the Metabolomic Society
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 performed 1 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
Parastoo Fazelzadeh, Roland W J Hangelbroek, Peter J Joris, Casper G Schalkwijk, Diederik Esser, Lydia Afman, Thomas Hankemeier, Doris M Jacobs, Velitchka V Mihaleva, Sander Kersten, John van Duynhoven, Mark V Boekschoten
Introduction: The response to dietary challenges has been proposed as a more accurate measure of metabolic health than static measurements performed in the fasted state. This has prompted many groups to explore the potential of dietary challenge tests for assessment of diet and lifestyle induced shifts in metabolic phenotype. Objectives: We examined whether the response to a mixed-meal challenge could provide a readout for a weight loss (WL)-induced phenotype shift in abdominally obese male subjects...
2018: Metabolomics: Official Journal of the Metabolomic Society
Marek J Noga, Ronald Zielman, Robin M van Dongen, Sabine Bos, Amy Harms, Gisela M Terwindt, Arn M J M van den Maagdenberg, Thomas Hankemeier, Michel D Ferrari
Introduction: Metabolic profiling of cerebrospinal fluid (CSF) is a promising technique for studying brain diseases. Measurements should reflect the in vivo situation, so ex vivo metabolism should be avoided. Objective: To investigate the effects of temperature (room temperature vs. 4 °C), centrifugation and ethanol, as anti-enzymatic additive during CSF sampling on concentrations of glutamic acid, glutamine and other endogenous amines. Methods: CSF samples from 21 individuals were processed using five different protocols...
2018: Metabolomics: Official Journal of the Metabolomic Society
Antonio Rosato, Leonardo Tenori, Marta Cascante, Pedro Ramon De Atauri Carulla, Vitor A P Martins Dos Santos, Edoardo Saccenti
Introduction: Metabolomics is a well-established tool in systems biology, especially in the top-down approach. Metabolomics experiments often results in discovery studies that provide intriguing biological hypotheses but rarely offer mechanistic explanation of such findings. In this light, the interpretation of metabolomics data can be boosted by deploying systems biology approaches. Objectives: This review aims to provide an overview of systems biology approaches that are relevant to metabolomics and to discuss some successful applications of these methods...
2018: Metabolomics: Official Journal of the Metabolomic Society
Abdul-Hamid Emwas, Edoardo Saccenti, Xin Gao, Ryan T McKay, Vitor A P Martins Dos Santos, Raja Roy, David S Wishart
1 H NMR spectra from urine can yield information-rich data sets that offer important insights into many biological and biochemical phenomena. However, the quality and utility of these insights can be profoundly affected by how the NMR spectra are processed and interpreted. For instance, if the NMR spectra are incorrectly referenced or inconsistently aligned, the identification of many compounds will be incorrect. If the NMR spectra are mis-phased or if the baseline correction is flawed, the estimated concentrations of many compounds will be systematically biased...
2018: Metabolomics: Official Journal of the Metabolomic Society
Eugenio Alcalde, Paul D Fraser
Introduction: Xanthophyllomyces dendrorhous is a non-conventional industrial yeast. It has the unique ability among yeasts to produce geranylgeranyl pyrophosphate derived terpenoids such as carotenoids and in particular the high value pigment astaxanthin. Objective: In order to fully exploit the industrial potential of Xanthophyllomyces using modern industrial biotechnology approaches the further development of "omic" resources in this organism are required to build on the now sequenced and annotated genome...
2018: Metabolomics: Official Journal of the Metabolomic Society
Rachel A Spicer, Christoph Steinbeck
Introduction: Data sharing is being increasingly required by journals and has been heralded as a solution to the 'replication crisis'. Objectives: (i) Review data sharing policies of journals publishing the most metabolomics papers associated with open data and (ii) compare these journals' policies to those that publish the most metabolomics papers. Methods: A PubMed search was used to identify metabolomics papers. Metabolomics data repositories were manually searched for linked publications...
2018: Metabolomics: Official Journal of the Metabolomic Society
Margaux Luck, Caroline Schmitt, Neila Talbi, Laurent Gouya, Cédric Caradeuc, Hervé Puy, Gildas Bertho, Nicolas Pallet
Introduction: Metabolomic profiling combines Nuclear Magnetic Resonance spectroscopy with supervised statistical analysis that might allow to better understanding the mechanisms of a disease. Objectives: In this study, the urinary metabolic profiling of individuals with porphyrias was performed to predict different types of disease, and to propose new pathophysiological hypotheses. Methods: Urine 1 H-NMR spectra of 73 patients with asymptomatic acute intermittent porphyria (aAIP) and familial or sporadic porphyria cutanea tarda (f/sPCT) were compared using a supervised rule-mining algorithm...
2018: Metabolomics: Official Journal of the Metabolomic Society
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