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Metabolites

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https://www.readbyqxmd.com/read/28294984/defining-the-baseline-and-oxidant-perturbed-lipidomic-profiles-of-daphnia-magna
#1
Nadine S Taylor, Thomas A White, Mark R Viant
Recent technological advancement has enabled the emergence of lipidomics as an important tool for assessing molecular stress, one which has yet to be assessed fully as an approach in an environmental toxicological context. Here we have applied a high-resolution, non-targeted, nanoelectrospray ionisation (nESI) direct infusion mass spectrometry (DIMS) technique to assess the effects of oxidative stress to Daphnia magna both in vitro (air exposure of daphniid extracts) and in vivo (Cu(2+) exposure). Multivariate and univariate statistical analyses were used to distinguish any perturbations including oxidation to the D...
March 15, 2017: Metabolites
https://www.readbyqxmd.com/read/28241496/the-role-of-sarcosine-uracil-and-kynurenic-acid-metabolism-in-urine-for-diagnosis-and-progression-monitoring-of-prostate-cancer
#2
Georgios Gkotsos, Christina Virgiliou, Ioanna Lagoudaki, Chrysanthi Sardeli, Nikolaos Raikos, Georgios Theodoridis, Georgios Dimitriadis
The aim of this pilot study is to evaluate sarcosine, uracil, and kynurenic acid in urine as potential biomarkers in prostate cancer detection and progression monitoring. Sarcosine, uracil, and kynurenic acid were measured in urine samples of 32 prostate cancer patients prior to radical prostatectomy, 101 patients with increased prostate-specific antigen prior to ultrasonographically-guided prostatic biopsy collected before and after prostatic massage, and 15 healthy volunteers (controls). The results were related to histopathologic data, Gleason score, and PSA (Prostate Specific Antigen)...
February 23, 2017: Metabolites
https://www.readbyqxmd.com/read/28241477/impact-of-exercise-and-aging-on-rat-urine-and-blood-metabolome-an-lc-ms-based-metabolomics-longitudinal-study
#3
Olga Deda, Helen G Gika, Ioannis Taitzoglou, Νikolaos Raikos, Georgios Theodoridis
Aging is an inevitable condition leading to health deterioration and death. Regular physical exercise can moderate the metabolic phenotype changes of aging. However, only a small number of metabolomics-based studies provide data on the effect of exercise along with aging. Here, urine and whole blood samples from Wistar rats were analyzed in a longitudinal study to explore metabolic alterations due to exercise and aging. The study comprised three different programs of exercises, including a life-long protocol which started at the age of 5 months and ended at the age of 21 months...
February 23, 2017: Metabolites
https://www.readbyqxmd.com/read/28216558/application-of-passive-sampling-to-characterise-the-fish-exometabolome
#4
Mark R Viant, Jessica Elphinstone Davis, Cathleen Duffy, Jasper Engel, Craig Stenton, Marion Sebire, Ioanna Katsiadaki
The endogenous metabolites excreted by organisms into their surrounding environment, termed the exometabolome, are important for many processes including chemical communication. In fish biology, such metabolites are also known to be informative markers of physiological status. While metabolomics is increasingly used to investigate the endogenous biochemistry of organisms, no non-targeted studies of the metabolic complexity of fish exometabolomes have been reported to date. In environmental chemistry, Chemcatcher(®) (Portsmouth, UK) passive samplers have been developed to sample for micro-pollutants in water...
February 14, 2017: Metabolites
https://www.readbyqxmd.com/read/28208794/qsrr-modeling-for-metabolite-standards-analyzed-by-two-different-chromatographic-columns-using-multiple-linear-regression
#5
Chrysostomi Zisi, Ioannis Sampsonidis, Stella Fasoula, Konstantinos Papachristos, Michael Witting, Helen G Gika, Panagiotis Nikitas, Adriani Pappa-Louisi
Modified quantitative structure retention relationships (QSRRs) are proposed and applied to describe two retention data sets: A set of 94 metabolites studied by a hydrophilic interaction chromatography system under organic content gradient conditions and a set of tryptophan and its major metabolites analyzed by a reversed-phase chromatographic system under isocratic as well as pH and/or simultaneous pH and organic content gradient conditions. According to the proposed modification, an additional descriptor is added to a conventional QSRR expression, which is the analyte retention time, tR(R), measured under the same elution conditions, but in a second chromatographic column considered as a reference one...
February 9, 2017: Metabolites
https://www.readbyqxmd.com/read/28165361/urine-and-serum-metabolomics-analyses-may-distinguish-between-stages-of-renal-cell-carcinoma
#6
Oluyemi S Falegan, Mark W Ball, Rustem A Shaykhutdinov, Phillip M Pieroraio, Farshad Farshidfar, Hans J Vogel, Mohamad E Allaf, Matthew E Hyndman
Renal cell carcinoma (RCC) is a heterogeneous disease that is usually asymptomatic until late in the disease. There is an urgent need for RCC specific biomarkers that may be exploited clinically for diagnostic and prognostic purposes. Preoperative fasting urine and serum samples were collected from patients with clinical renal masses and assessed with ¹H NMR and GCMS (gas chromatography-mass spectrometry) based metabolomics and multivariate statistical analysis. Alterations in levels of glycolytic and tricarboxylic acid (TCA) cycle intermediates were detected in RCC relative to benign masses...
February 3, 2017: Metabolites
https://www.readbyqxmd.com/read/28134772/effects-of-different-exercise-modes-on-the-urinary-metabolic-fingerprint-of-men-with-and-without-metabolic-syndrome
#7
Aikaterina Siopi, Olga Deda, Vasiliki Manou, Spyros Kellis, Ioannis Kosmidis, Despina Komninou, Nikolaos Raikos, Kosmas Christoulas, Georgios A Theodoridis, Vassilis Mougios
Exercise is important in the prevention and treatment of the metabolic syndrome (MetS), a cluster of risk factors that raises morbidity. Metabolomics can facilitate the optimization of exercise prescription. This study aimed to investigate whether the response of the human urinary metabolic fingerprint to exercise depends on the presence of MetS or exercise mode. Twenty-three sedentary men (MetS, n = 9, and Healthy, n = 14) completed four trials: resting, high-intensity interval exercise (HIIE), continuous moderate-intensity exercise (CME), and resistance exercise (RE)...
January 26, 2017: Metabolites
https://www.readbyqxmd.com/read/28134762/nmr-based-metabolic-profiling-of-field-grown-leaves-from-sugar-beet-plants-harbouring-different-levels-of-resistance-to-cercospora-leaf-spot-disease
#8
Yasuyo Sekiyama, Kazuyuki Okazaki, Jun Kikuchi, Seishi Ikeda
Cercospora leaf spot (CLS) is one of the most serious leaf diseases for sugar beet (Beta vulgaris L.) worldwide. The breeding of sugar beet cultivars with both high CLS resistance and high yield is a major challenge for breeders. In this study, we report the nuclear magnetic resonance (NMR)-based metabolic profiling of field-grown leaves for a subset of sugar beet genotypes harbouring different levels of CLS resistance. Leaves were collected from 12 sugar beet genotypes at four time points: seedling, early growth, root enlargement, and disease development stages...
January 26, 2017: Metabolites
https://www.readbyqxmd.com/read/28098776/distinguishing-benign-from-malignant-pancreatic-and-periampullary-lesions-using-combined-use-of-%C3%A2-h-nmr-spectroscopy-and-gas-chromatography-mass-spectrometry
#9
Yarrow J McConnell, Farshad Farshidfar, Aalim M Weljie, Karen A Kopciuk, Elijah Dixon, Chad G Ball, Francis R Sutherland, Hans J Vogel, Oliver F Bathe
Previous work demonstrated that serum metabolomics can distinguish pancreatic cancer from benign disease. However, in the clinic, non-pancreatic periampullary cancers are difficult to distinguish from pancreatic cancer. Therefore, to test the clinical utility of this technology, we determined whether any pancreatic and periampullary adenocarcinoma could be distinguished from benign masses and biliary strictures. Sera from 157 patients with malignant and benign pancreatic and periampullary lesions were analyzed using proton nuclear magnetic resonance (¹H-NMR) spectroscopy and gas chromatography-mass spectrometry (GC-MS)...
January 13, 2017: Metabolites
https://www.readbyqxmd.com/read/28036063/fully-automated-trimethylsilyl-tms-derivatisation-protocol-for-metabolite-profiling-by-gc-ms
#10
Erica Zarate, Veronica Boyle, Udo Rupprecht, Saras Green, Silas G Villas-Boas, Philip Baker, Farhana R Pinu
Gas Chromatography-Mass Spectrometry (GC-MS) has long been used for metabolite profiling of a wide range of biological samples. Many derivatisation protocols are already available and among these, trimethylsilyl (TMS) derivatisation is one of the most widely used in metabolomics. However, most TMS methods rely on off-line derivatisation prior to GC-MS analysis. In the case of manual off-line TMS derivatisation, the derivative created is unstable, so reduction in recoveries occurs over time. Thus, derivatisation is carried out in small batches...
December 29, 2016: Metabolites
https://www.readbyqxmd.com/read/28009836/metabolomics-with-nuclear-magnetic-resonance-spectroscopy-in-a-drosophila-melanogaster-model-of-surviving-sepsis
#11
Veli Bakalov, Roland Amathieu, Mohamed N Triba, Marie-Jeanne Clément, Laura Reyes Uribe, Laurence Le Moyec, Ata Murat Kaynar
Patients surviving sepsis demonstrate sustained inflammation, which has been associated with long-term complications. One of the main mechanisms behind sustained inflammation is a metabolic switch in parenchymal and immune cells, thus understanding metabolic alterations after sepsis may provide important insights to the pathophysiology of sepsis recovery. In this study, we explored metabolomics in a novel Drosophila melanogaster model of surviving sepsis using Nuclear Magnetic Resonance (NMR), to determine metabolite profiles...
December 21, 2016: Metabolites
https://www.readbyqxmd.com/read/27983674/current-and-future-perspectives-on-the-structural-identification-of-small-molecules-in-biological-systems
#12
REVIEW
Daniel A Dias, Oliver A H Jones, David J Beale, Berin A Boughton, Devin Benheim, Konstantinos A Kouremenos, Jean-Luc Wolfender, David S Wishart
Although significant advances have been made in recent years, the structural elucidation of small molecules continues to remain a challenging issue for metabolite profiling. Many metabolomic studies feature unknown compounds; sometimes even in the list of features identified as "statistically significant" in the study. Such metabolic "dark matter" means that much of the potential information collected by metabolomics studies is lost. Accurate structure elucidation allows researchers to identify these compounds...
December 15, 2016: Metabolites
https://www.readbyqxmd.com/read/27941694/quantification-of-microbial-phenotypes
#13
REVIEW
Verónica S Martínez, Jens O Krömer
Metabolite profiling technologies have improved to generate close to quantitative metabolomics data, which can be employed to quantitatively describe the metabolic phenotype of an organism. Here, we review the current technologies available for quantitative metabolomics, present their advantages and drawbacks, and the current challenges to generate fully quantitative metabolomics data. Metabolomics data can be integrated into metabolic networks using thermodynamic principles to constrain the directionality of reactions...
December 9, 2016: Metabolites
https://www.readbyqxmd.com/read/27929385/the-metabolic-implications-of-glucocorticoids-in-a-high-fat-diet-setting-and-the-counter-effects-of-exercise
#14
REVIEW
Emily C Dunford, Michael C Riddell
Glucocorticoids (GCs) are steroid hormones, naturally produced by activation of the hypothalamic-pituitary-adrenal (HPA) axis, that mediate the immune and metabolic systems. Synthetic GCs are used to treat a number of inflammatory conditions and diseases including lupus and rheumatoid arthritis. Generally, chronic or high dose GC administration is associated with side effects such as steroid-induced skeletal muscle loss, visceral adiposity, and diabetes development. Patients who are taking exogenous GCs could also be more susceptible to poor food choices, but the effect that increasing fat consumption in combination with elevated exogenous GCs has only recently been investigated...
December 5, 2016: Metabolites
https://www.readbyqxmd.com/read/27916960/detection-of-volatile-metabolites-derived-from-garlic-allium-sativum-in-human-urine
#15
Laura Scheffler, Yvonne Sauermann, Anja Heinlein, Constanze Sharapa, Andrea Buettner
The metabolism and excretion of flavor constituents of garlic, a common plant used in flavoring foods and attributed with several health benefits, in humans is not fully understood. Likewise, the physiologically active principles of garlic have not been fully clarified to date. It is possible that not only the parent compounds present in garlic but also its metabolites are responsible for the specific physiological properties of garlic, including its influence on the characteristic body odor signature of humans after garlic consumption...
December 1, 2016: Metabolites
https://www.readbyqxmd.com/read/27845718/a-simple-method-for-measuring-carbon-13-fatty-acid-enrichment-in-the-major-lipid-classes-of-microalgae-using-gc-ms
#16
Sheik Nadeem Elahee Doomun, Stella Loke, Sean O'Callaghan, Damien L Callahan
A simple method for tracing carbon fixation and lipid synthesis in microalgae was developed using a combination of solid-phase extraction (SPE) and negative ion chemical ionisation gas chromatography mass spectrometry (NCI-GC-MS). NCI-GC-MS is an extremely sensitive technique that can produce an unfragmented molecular ion making this technique particularly useful for stable isotope enrichment studies. Derivatisation of fatty acids using pentafluorobenzyl bromide (PFBBr) allows the coupling of the high separation efficiency of GC and the measurement of unfragmented molecular ions for each of the fatty acids by single quadrupole MS...
November 11, 2016: Metabolites
https://www.readbyqxmd.com/read/27834866/staphylococcus-aureus-infection-reduces-nutrition-uptake-and-nucleotide-biosynthesis-in-a-human-airway-epithelial-cell-line
#17
Philipp Gierok, Manuela Harms, Karen Methling, Falko Hochgräfe, Michael Lalk
The Gram positive opportunistic human pathogen Staphylococcus aureus induces a variety of diseases including pneumonia. S. aureus is the second most isolated pathogen in cystic fibrosis patients and accounts for a large proportion of nosocomial pneumonia. Inside the lung, the human airway epithelium is the first line in defence with regard to microbial recognition and clearance as well as regulation of the immune response. The metabolic host response is, however, yet unknown. To address the question of whether the infection alters the metabolome and metabolic activity of airway epithelial cells, we used a metabolomics approach...
November 9, 2016: Metabolites
https://www.readbyqxmd.com/read/27827887/a-conversation-on-data-mining-strategies-in-lc-ms-untargeted-metabolomics-pre-processing-and-pre-treatment-steps
#18
Fidele Tugizimana, Paul A Steenkamp, Lizelle A Piater, Ian A Dubery
Untargeted metabolomic studies generate information-rich, high-dimensional, and complex datasets that remain challenging to handle and fully exploit. Despite the remarkable progress in the development of tools and algorithms, the "exhaustive" extraction of information from these metabolomic datasets is still a non-trivial undertaking. A conversation on data mining strategies for a maximal information extraction from metabolomic data is needed. Using a liquid chromatography-mass spectrometry (LC-MS)-based untargeted metabolomic dataset, this study explored the influence of collection parameters in the data pre-processing step, scaling and data transformation on the statistical models generated, and feature selection, thereafter...
November 3, 2016: Metabolites
https://www.readbyqxmd.com/read/27827849/metmatch-a-semi-automated-software-tool-for-the-comparison-and-alignment-of-lc-hrms-data-from-different-metabolomics-experiments
#19
Stefan Koch, Christoph Bueschl, Maria Doppler, Alexandra Simader, Jacqueline Meng-Reiterer, Marc Lemmens, Rainer Schuhmacher
Due to its unsurpassed sensitivity and selectivity, LC-HRMS is one of the major analytical techniques in metabolomics research. However, limited stability of experimental and instrument parameters may cause shifts and drifts of retention time and mass accuracy or the formation of different ion species, thus complicating conclusive interpretation of the raw data, especially when generated in different analytical batches. Here, a novel software tool for the semi-automated alignment of different measurement sequences is presented...
November 2, 2016: Metabolites
https://www.readbyqxmd.com/read/27801817/partial-least-squares-with-structured-output-for-modelling-the-metabolomics-data-obtained-from-complex-experimental-designs-a-study-into-the-y-block-coding
#20
Yun Xu, Howbeer Muhamadali, Ali Sayqal, Neil Dixon, Royston Goodacre
Partial least squares (PLS) is one of the most commonly used supervised modelling approaches for analysing multivariate metabolomics data. PLS is typically employed as either a regression model (PLS-R) or a classification model (PLS-DA). However, in metabolomics studies it is common to investigate multiple, potentially interacting, factors simultaneously following a specific experimental design. Such data often cannot be considered as a "pure" regression or a classification problem. Nevertheless, these data have often still been treated as a regression or classification problem and this could lead to ambiguous results...
October 28, 2016: Metabolites
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