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Raúl González-Domínguez, Ana Sayago, Ángeles Fernández-Recamales
Direct mass spectrometry-based metabolomics has been widely employed in recent years to characterize the metabolic alterations underlying Alzheimer's disease development and progression. This high-throughput approach presents great potential for fast and simultaneous fingerprinting of a vast number of metabolites, which can be applied to multiple biological matrices including serum/plasma, urine, cerebrospinal fluid and tissues. In this review article, we present the main advantages and drawbacks of metabolomics based on direct mass spectrometry compared with conventional analytical techniques, and provide a comprehensive revision of the literature on the use of these tools in the investigation of Alzheimer's disease...
September 18, 2018: Metabolites
Clément Frainay, Emma L Schymanski, Steffen Neumann, Benjamin Merlet, Reza M Salek, Fabien Jourdan, Oscar Yanes
The use of mass spectrometry-based metabolomics to study human, plant and microbial biochemistry and their interactions with the environment largely depends on the ability to annotate metabolite structures by matching mass spectral features of the measured metabolites to curated spectra of reference standards. While reference databases for metabolomics now provide information for hundreds of thousands of compounds, barely 5% of these known small molecules have experimental data from pure standards. Remarkably, it is still unknown how well existing mass spectral libraries cover the biochemical landscape of prokaryotic and eukaryotic organisms...
September 15, 2018: Metabolites
Massimo S Fiandaca, Thomas J Gross, Thomas M Johnson, Michele T Hu, Samuel Evetts, Richard Wade-Martins, Kian Merchant-Borna, Jeffrey Bazarian, Amrita K Cheema, Mark Mapstone, Howard J Federoff
The etiologic basis for sporadic forms of neurodegenerative diseases has been elusive but likely represents the product of genetic predisposition and various environmental factors. Specific gene-environment interactions have become more salient owing, in part, to the elucidation of epigenetic mechanisms and their impact on health and disease. The linkage between traumatic brain injury (TBI) and Parkinson's disease (PD) is one such association that currently lacks a mechanistic basis. Herein, we present preliminary blood-based metabolomic evidence in support of potential association between TBI and PD...
September 7, 2018: Metabolites
Abu Hanifah, Awang Maharijaya, Sastia P Putri, Walter A Laviña
Eggplant is one of the most widely cultivated vegetables in the world and has high biodiversity in terms of fruit shape, size, and color. Therefore, fruit morphology and nutrient content become important considerations for both consumers and breeders who develop new eggplant-based products. To gain insight on the diversity of eggplant metabolites, twenty-one eggplant accessions were analyzed by untargeted metabolomics using GC-MS and LC-MS. The dataset of eggplant fruit morphologies, and metabolites specific to different eggplant fruit accessions were used for correlation analysis...
September 1, 2018: Metabolites
Hajime Sato, Masanobu Uchiyama, Kazuki Saito, Mami Yamazaki
Lys-derived alkaloids widely distributed in plant kingdom have received considerable attention and have been intensively studied; however, little is known about their biosynthetic mechanisms. In terms of the skeleton formation, for example, of quinolizidine alkaloid biosynthesis, only the very first two steps have been identified and the later steps remain unknown. In addition, there is no available information on the number of enzymes and reactions required for their skeletal construction. The involvement of the Δ 1 -piperideine dimerization has been proposed for some of the Lys-derived alkaloid biosyntheses, but no enzymes for this dimerization reaction have been reported to date; moreover, it is not clear whether this dimerization reaction proceeds spontaneously or enzymatically...
August 31, 2018: Metabolites
Helena U Zacharias, Michael Altenbuchinger, Wolfram Gronwald
In this review, we summarize established and recent bioinformatic and statistical methods for the analysis of NMR-based metabolomics. Data analysis of NMR metabolic fingerprints exhibits several challenges, including unwanted biases, high dimensionality, and typically low sample numbers. Common analysis tasks comprise the identification of differential metabolites and the classification of specimens. However, analysis results strongly depend on the preprocessing of the data, and there is no consensus yet on how to remove unwanted biases and experimental variance prior to statistical analysis...
August 28, 2018: Metabolites
Ville Mikael Koistinen, Andreia Bento da Silva, László Abrankó, Dorrain Low, Rocio Garcia Villalba, Francisco Tomás Barberán, Rikard Landberg, Otto Savolainen, Inmaculada Alvarez-Acero, Sonia de Pascual-Teresa, Christof Van Poucke, Conceição Almeida, Lucie Petrásková, Kateřina Valentová, Stephanie Durand, Wiesław Wiczkowski, Dorota Szawara-Nowak, Raúl González-Domínguez, Rafael Llorach, Cristina Andrés-Lacueva, Anna-Marja Aura, Tuulikki Seppänen-Laakso, Kati Hanhineva, Claudine Manach, Maria Rosário Bronze
Bioactive compounds present in plant-based foods, and their metabolites derived from gut microbiota and endogenous metabolism, represent thousands of chemical structures of potential interest for human nutrition and health. State-of-the-art analytical methodologies, including untargeted metabolomics based on high-resolution mass spectrometry, are required for the profiling of these compounds in complex matrices, including plant food materials and biofluids. The aim of this project was to compare the analytical coverage of untargeted metabolomics methods independently developed and employed in various European platforms...
August 24, 2018: Metabolites
Markus Rotter, Stefan Brandmaier, Marcela Covic, Katarzyna Burek, Johannes Hertel, Martina Troll, Erik Bader, Jonathan Adam, Cornelia Prehn, Birgit Rathkolb, Martin Hrabe de Angelis, Hans Jörgen Grabe, Hannelore Daniel, Thomas Kantermann, Volker Harth, Thomas Illig, Dirk Pallapies, Thomas Behrens, Thomas Brüning, Jerzy Adamski, Heiko Lickert, Sylvia Rabstein, Rui Wang-Sattler
Night shift work can have a serious impact on health. Here, we assess whether and how night shift work influences the metabolite profiles, specifically with respect to different chronotype classes. We have recruited 100 women including 68 nurses working both, day shift and night shifts for up to 5 consecutive days and collected 3640 spontaneous urine samples. About 424 waking-up urine samples were measured using a targeted metabolomics approach. To account for urine dilution, we applied three methods to normalize the metabolite values: creatinine-, osmolality- and regression-based normalization...
August 21, 2018: Metabolites
Jatin Nandania, Gopal Peddinti, Alberto Pessia, Meri Kokkonen, Vidya Velagapudi
The use of metabolomics profiling to understand the metabolism under different physiological states has increased in recent years, which created the need for robust analytical platforms. Here, we present a validated method for targeted and semiquantitative analysis of 102 polar metabolites that cover major metabolic pathways from 24 classes in a single 17.5-min assay. The method has been optimized for a wide range of biological matrices from various organisms, and involves automated sample preparation and data processing using an inhouse developed R-package...
August 5, 2018: Metabolites
Simone Circi, Cinzia Ingallina, Silvia Vista, Donatella Capitani, Andrea Di Vecchia, Genesio Leonardi, Giovanni D'Achille, Luigi Centauri, Federica Camin, Luisa Mannina
An analytical approach including Panel Test, Isotope Ratio Mass Spectrometry (IRMS) and Nuclear Magnetic Resonance (NMR) spectroscopy was proposed to characterize Italian " Colline Pontine " PDO olive oils (40 samples) of two consecutive crop years. Our approach has evidenced the high quality of these olive oils. Only 6 of 40 olive oils samples were defined as " defective " by the official Panel Test due to the detection of negative sensory attributes. The low variability of isotopic data monitored by IRMS confirmed that the olive oil samples all came from a limited geographical area...
July 28, 2018: Metabolites
Nadine S Taylor, Alex Gavin, Mark R Viant
Chemical risk assessment remains entrenched in chronic toxicity tests that set safety thresholds based on animal pathology or fitness. Chronic tests are resource expensive and lack mechanistic insight. Discovering a chemical's mode-of-action can in principle provide predictive molecular biomarkers for a toxicity endpoint. Furthermore, since molecular perturbations precede pathology, early-response molecular biomarkers may enable shorter, more resource efficient testing that can predict chronic animal fitness...
July 23, 2018: Metabolites
Preeti Purwaha, Franklin Gu, Danthasinghe Waduge Badrajee Piyarathna, Theckelnaycke Rajendiran, Anindita Ravindran, Angela R Omilian, Sao Jiralerspong, Gokul Das, Carl Morrison, Christine Ambrosone, Cristian Coarfa, Nagireddy Putluri, Arun Sreekumar
The reprogramming of lipid metabolism is a hallmark of many cancers that has been shown to promote breast cancer progression. While several lipid signatures associated with breast cancer aggressiveness have been identified, a comprehensive lipidomic analysis specifically targeting the triple-negative subtype of breast cancer (TNBC) may be required to identify novel biomarkers and therapeutic targets for this most aggressive subtype of breast cancer that still lacks effective therapies. In this current study, our global LC-MS-based lipidomics platform was able to measure 684 named lipids across 15 lipid classes in 70 TNBC tumors...
July 13, 2018: Metabolites
Teresa W-M Fan, Salim S El-Amouri, Jessica K A Macedo, Qing Jun Wang, Huan Song, Teresa Cassel, Andrew N Lane
Conventional two-dimensional (2D) cell cultures are grown on rigid plastic substrates with unrealistic concentration gradients of O₂, nutrients, and treatment agents. More importantly, 2D cultures lack cell⁻cell and cell⁻extracellular matrix (ECM) interactions, which are critical for regulating cell behavior and functions. There are several three-dimensional (3D) cell culture systems such as Matrigel, hydrogels, micropatterned plates, and hanging drop that overcome these drawbacks but they suffer from technical challenges including long spheroid formation times, difficult handling for high throughput assays, and/or matrix contamination for metabolic studies...
July 10, 2018: Metabolites
Bertrand Rochat, Rayane Mohamed, Pierre-Edouard Sottas
Today’s high-resolution mass spectrometers (HRMS) allow bioanalysts to perform untargeted/global determinations that can reveal unexpected compounds or concentrations in a patient’s sample. This could be performed for preliminary diagnosis attempts when usual diagnostic processes and targeted determinations fail. We have evaluated an untargeted diagnostic screening (UDS) procedure. UDS is a metabolome analysis that compares one sample (e.g., a patient) with control samples (a healthy population)...
June 15, 2018: Metabolites
Garth L Maker, Tobias Green, Ian Mullaney, Robert D Trengove
Methamphetamine is an illicit psychostimulant drug that is linked to a number of diseases of the nervous system. The downstream biochemical effects of its primary mechanisms are not well understood, and the objective of this study was to investigate whether untargeted metabolomic analysis of an in vitro model could generate data relevant to what is already known about this drug. Rat B50 neuroblastoma cells were treated with 1 mM methamphetamine for 48 h, and both intracellular and extracellular metabolites were profiled using gas chromatography⁻mass spectrometry...
June 7, 2018: Metabolites
Morteza Abdoli, Murat Bozdag, Andrea Angeli, Claudiu T Supuran
A series of benzamides incorporating 4-sulfamoyl moieties were obtained by reacting 4-sulfamoyl benzoic acid with primary and secondary amines and amino acids. These sulfonamides were investigated as inhibitors of the metalloenzyme carbonic anhydrase (CA, EC The human (h) isoforms hCA II, VII, and IX were inhibited in the low nanomolar or subnanomolar ranges, whereas hCA I was slightly less sensitive to inhibition (KI s of 5.3⁻334 nM). The β- and γ-class CAs from pathogenic bacteria and fungi, such as Vibrio cholerae and Malassezia globosa , were inhibited in the micromolar range by the sulfonamides reported in the paper...
June 1, 2018: Metabolites
Niccolò Chiaramonte, Maria Novella Romanelli, Elisabetta Teodori, Claudiu T Supuran
Carbonic anhydrases (CAs) are a superfamily of metalloenzymes widespread in all life, classified into seven genetically different families (α⁻θ). These enzymes catalyse the reversible hydration of carbonic anhydride (CO₂), generating bicarbonate (HCO₃- ) and protons (H⁺). Fifteen isoforms of human CA (hCA I⁻XV) have been isolated, their presence being fundamental for the regulation of many physiological processes. In addition, overexpression of some isoforms has been associated with the outbreak or progression of several diseases...
May 24, 2018: Metabolites
Monica Bastawrous, Amy Jenne, Maryam Tabatabaei Anaraki, André J Simpson
Part review, part perspective, this article examines the applications and potential of in-vivo Nuclear Magnetic Resonance (NMR) for understanding environmental toxicity. In-vivo NMR can be applied in high field NMR spectrometers using either magic angle spinning based approaches, or flow systems. Solution-state NMR in combination with a flow system provides a low stress approach to monitor dissolved metabolites, while magic angle spinning NMR allows the detection of all components (solutions, gels and solids), albeit with additional stress caused by the rapid sample spinning...
May 24, 2018: Metabolites
Vera Kovacevic, André J Simpson, Myrna J Simpson
Organophosphate esters (OPEs) are frequently detected in aquatic environments. Hydrophobic OPEs with high octanol-water partition coefficients (Log KOW ) will likely sorb to dissolved organic matter (DOM) and consequently alter OPE bioavailability and sub-lethal toxicity. ¹H nuclear magnetic resonance (NMR)-based metabolomics was used to evaluate how DOM (5 mg organic carbon/L) alters the metabolic response of Daphnia magna exposed to sub-lethal concentrations of three individual OPEs with varying hydrophobicity...
May 19, 2018: Metabolites
Tobias B Alter, Lars M Blank, Birgitta E Ebert
To date, several independent methods and algorithms exist for exploiting constraint-based stoichiometric models to find metabolic engineering strategies that optimize microbial production performance. Optimization procedures based on metaheuristics facilitate a straightforward adaption and expansion of engineering objectives, as well as fitness functions, while being particularly suited for solving problems of high complexity. With the increasing interest in multi-scale models and a need for solving advanced engineering problems, we strive to advance genetic algorithms, which stand out due to their intuitive optimization principles and the proven usefulness in this field of research...
May 16, 2018: Metabolites
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