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Metabolites

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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
#1
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/28085025/acknowledgement-to-reviewers-of-metabolites-in-2016
#2
EDITORIAL
Metabolites Editorial Office
The editors of Metabolites would like to express their sincere gratitude to the following reviewers for assessing manuscripts in 2016. [...].
January 11, 2017: Metabolites
https://www.readbyqxmd.com/read/28036063/fully-automated-trimethylsilyl-tms-derivatisation-protocol-for-metabolite-profiling-by-gc-ms
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
https://www.readbyqxmd.com/read/27775610/prediction-detection-and-validation-of-isotope-clusters-in-mass-spectrometry-data
#14
Hendrik Treutler, Steffen Neumann
Mass spectrometry is a key analytical platform for metabolomics. The precise quantification and identification of small molecules is a prerequisite for elucidating the metabolism and the detection, validation, and evaluation of isotope clusters in LC-MS data is important for this task. Here, we present an approach for the improved detection of isotope clusters using chemical prior knowledge and the validation of detected isotope clusters depending on the substance mass using database statistics. We find remarkable improvements regarding the number of detected isotope clusters and are able to predict the correct molecular formula in the top three ranks in 92 % of the cases...
October 20, 2016: Metabolites
https://www.readbyqxmd.com/read/27775560/foodpro-a-web-based-tool-for-evaluating-covariance-and-correlation-nmr-spectra-associated-with-food-processes
#15
Eisuke Chikayama, Ryo Yamashina, Keiko Komatsu, Yuuri Tsuboi, Kenji Sakata, Jun Kikuchi, Yasuyo Sekiyama
Foods from agriculture and fishery products are processed using various technologies. Molecular mixture analysis during food processing has the potential to help us understand the molecular mechanisms involved, thus enabling better cooking of the analyzed foods. To date, there has been no web-based tool focusing on accumulating Nuclear Magnetic Resonance (NMR) spectra from various types of food processing. Therefore, we have developed a novel web-based tool, FoodPro, that includes a food NMR spectrum database and computes covariance and correlation spectra to tasting and hardness...
October 19, 2016: Metabolites
https://www.readbyqxmd.com/read/27754384/metabolomic-profiling-of-the-effects-of-melittin-on-cisplatin-resistant-and-cisplatin-sensitive-ovarian-cancer-cells-using-mass-spectrometry-and-biolog-microarray-technology
#16
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
https://www.readbyqxmd.com/read/27754354/analysis-of-mammalian-cell-proliferation-and-macromolecule-synthesis-using-deuterated-water-and-gas-chromatography-mass-spectrometry
#17
Victoria C Foletta, Michelle Palmieri, Joachim Kloehn, Shaun Mason, Stephen F Previs, Malcolm J McConville, Oliver M Sieber, Clinton R Bruce, Greg M Kowalski
Deuterated water (²H₂O), a stable isotopic tracer, provides a convenient and reliable way to label multiple cellular biomass components (macromolecules), thus permitting the calculation of their synthesis rates. Here, we have combined ²H₂O labelling, GC-MS analysis and a novel cell fractionation method to extract multiple biomass components (DNA, protein and lipids) from the one biological sample, thus permitting the simultaneous measurement of DNA (cell proliferation), protein and lipid synthesis rates...
October 13, 2016: Metabolites
https://www.readbyqxmd.com/read/27706102/the-redox-status-of-cancer-cells-supports-mechanisms-behind-the-warburg-effect
#18
Jorgelindo da Veiga Moreira, Minoo Hamraz, Mohammad Abolhassani, Erwan Bigan, Sabine Pérès, Loïc Paulevé, Marcel Levy Nogueira, Jean-Marc Steyaert, Laurent Schwartz
To better understand the energetic status of proliferating cells, we have measured the intracellular pH (pHi) and concentrations of key metabolites, such as adenosine triphosphate (ATP), nicotinamide adenine dinucleotide (NAD), and nicotinamide adenine dinucleotide phosphate (NADP) in normal and cancer cells, extracted from fresh human colon tissues. Cells were sorted by elutriation and segregated in different phases of the cell cycle (G0/G1/S/G2/M) in order to study their redox (NAD, NADP) and bioenergetic (ATP, pHi) status...
October 3, 2016: Metabolites
https://www.readbyqxmd.com/read/27706078/strategies-for-extending-metabolomics-studies-with-stable-isotope-labelling-and-fluxomics
#19
Anubhav Srivastava, Greg M Kowalski, Damien L Callahan, Peter J Meikle, Darren J Creek
This is a perspective from the peer session on stable isotope labelling and fluxomics at the Australian & New Zealand Metabolomics Conference (ANZMET) held from 30 March to 1 April 2016 at La Trobe University, Melbourne, Australia. This report summarizes the key points raised in the peer session which focused on the advantages of using stable isotopes in modern metabolomics and the challenges in conducting flux analyses. The session highlighted the utility of stable isotope labelling in generating reference standards for metabolite identification, absolute quantification, and in the measurement of the dynamic activity of metabolic pathways...
October 1, 2016: Metabolites
https://www.readbyqxmd.com/read/27706030/metabolomics-and-cheminformatics-analysis-of-antifungal-function-of-plant-metabolites
#20
Miroslava Cuperlovic-Culf, NandhaKishore Rajagopalan, Dan Tulpan, Michele C Loewen
Fusarium head blight (FHB), primarily caused by Fusarium graminearum, is a devastating disease of wheat. Partial resistance to FHB of several wheat cultivars includes specific metabolic responses to inoculation. Previously published studies have determined major metabolic changes induced by pathogens in resistant and susceptible plants. Functionality of the majority of these metabolites in resistance remains unknown. In this work we have made a compilation of all metabolites determined as selectively accumulated following FHB inoculation in resistant plants...
September 30, 2016: Metabolites
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