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Metabolomics: Official Journal of the Metabolomic Society

Sanaya Bamji-Stocke, Victor van Berkel, Donald M Miller, Hermann B Frieboes
INTRODUCTION: Lung cancer continues to be the leading cause of cancer-related mortality worldwide. Early detection has proven essential to extend survival. Genomic and proteomic advances have provided impetus to the effort dedicated to detect and diagnose the disease at an earlier stage. Recently, the study of metabolites associated with tumor formation and progression has inaugurated the era of cancer metabolomics to aid in this effort. OBJECTIVES: This review summarizes recent work regarding novel metabolites with the potential to serve as biomarkers for early lung tumor detection, evaluation of disease progression, and prediction of patient outcomes...
June 2018: 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
Traci L Parry, Joseph W Starnes, Sara K O'Neal, James R Bain, Michael J Muehlbauer, Aubree Honcoop, Amro Ilaiwy, Peter Christopher, Cam Patterson, Monte S Willis
Introduction: The effects of exercise on the heart and its resistance to disease are well-documented. Recent studies have identified that exercise-induced resistance to arrhythmia is due to the preservation of mitochondrial membrane potential. Objectives: To identify novel metabolic changes that occur parallel to these mitochondrial alterations, we performed non-targeted metabolomics analysis on hearts from sedentary and exercise-trained rats challenged with isolated heart ischemia-reperfusion injury (I/R)...
January 2018: Metabolomics: Official Journal of the Metabolomic Society
Pei Han, Yong Huang, Yumin Xie, Wu Yang, Wenying Xiang, Peter J Hylands, Cristina Legido-Quigley
Introduction: In spite of advances in antibiotics, urinary tract infection (UTI) is still among the most common reasons for antibiotic medication worldwide. Persicaria capitata (Buch.-Ham. ex D. Don) H.Gross ( P. capitata ) is a herbal medicine used by the Miao people in China to treat UTI. However studies of its mechanism are challenging, owing to the complexity of P. capitata with multiple constituents acting on multiple metabolic pathways. Objective: The objective of this study was to explore the working mechanism of P...
2018: Metabolomics: Official Journal of the Metabolomic Society
Sang Youl Rhee, Eun Sung Jung, Hye Min Park, Su Jin Jeong, Kiyoung Kim, Suk Chon, Seung-Young Yu, Jeong-Taek Woo, Choong Hwan Lee
Introduction: Diabetic patients with a long disease duration usually accompanied complication such as diabetic retinopathy, but in some patients had no complication. Objectives: We analyzed differences in plasma metabolites according to the presence or absence of diabetic retinopathy (DR) in type 2 diabetic (T2D) patients with disease duration ≥ 15 years. Methods: A cohort of 183 T2D patients was established. Their biospecimens and clinical information were collected in accordance with the guidelines of the National Biobank of Korea, and the Korean Diabetes Association...
2018: Metabolomics: Official Journal of the Metabolomic Society
Daniel Morvan, Aicha Demidem
Introduction: Elucidating molecular alterations due to mitochondrial Complex I (CI) mutations may help to understand CI deficiency (CID), not only in mitochondriopathies but also as it is caused by drugs or associated to many diseases. Objectives: CID metabolic expression was investigated in Leber's hereditary optic neuropathy (LHON) caused by an inherited mutation of CI. Methods: NMR-based metabolomics analysis was performed in intact skin fibroblasts from LHON patients...
2018: Metabolomics: Official Journal of the Metabolomic Society
Marta Michalczuk, Beata Urban, Tadeusz Porowski, Anna Wasilewska, Alina Bakunowicz-Łazarczyk
Introduction: Citrate is an old metabolite which is best known for the role in the Krebs cycle. Citrate is widely used in many branches of medicine. In ophthalmology citrate is considered as a therapeutic agent and an useful diagnostic tool-biomarker. Objectives: To summarize the published literature on citrate usage in the leading causes of blindness and highlight the new possibilities for this old metabolite. Methods: We conducted a systematic search of the scientific literature about citrate usage in ophthalmology up to January 2018...
2018: Metabolomics: Official Journal of the Metabolomic Society
Edoardo Saccenti, Age K Smilde, José Camacho
Introduction: Modern omics experiments pertain not only to the measurement of many variables but also follow complex experimental designs where many factors are manipulated at the same time. This data can be conveniently analyzed using multivariate tools like ANOVA-simultaneous component analysis (ASCA) which allows interpretation of the variation induced by the different factors in a principal component analysis fashion. However, while in general only a subset of the measured variables may be related to the problem studied, all variables contribute to the final model and this may hamper interpretation...
2018: Metabolomics: Official Journal of the Metabolomic Society
David Broadhurst, Royston Goodacre, Stacey N Reinke, Julia Kuligowski, Ian D Wilson, Matthew R Lewis, Warwick B Dunn
Background: Quality assurance (QA) and quality control (QC) are two quality management processes that are integral to the success of metabolomics including their application for the acquisition of high quality data in any high-throughput analytical chemistry laboratory. QA defines all the planned and systematic activities implemented before samples are collected, to provide confidence that a subsequent analytical process will fulfil predetermined requirements for quality. QC can be defined as the operational techniques and activities used to measure and report these quality requirements after data acquisition...
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
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