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https://www.readbyqxmd.com/read/29783758/investigation-of-daphnia-magna-sub-lethal-exposure-to-organophosphate-esters-in-the-presence-of-dissolved-organic-matter-using-%C3%A2-h-nmr-based-metabolomics
#1
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
https://www.readbyqxmd.com/read/29772713/genetic-optimization-algorithm-for-metabolic-engineering-revisited
#2
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
https://www.readbyqxmd.com/read/29757993/profiling-redox-and-energy-coenzymes-in-whole-blood-tissue-and-cells-using-nmr-spectroscopy
#3
REVIEW
G A Nagana Gowda
Coenzymes of cellular redox reactions and cellular energy, as well as antioxidants mediate biochemical reactions fundamental to the functioning of all living cells. Conventional analysis methods lack the opportunity to evaluate these important redox and energy coenzymes and antioxidants in a single step. Major coenzymes include redox coenzymes: NAD⁺ (oxidized nicotinamide adenine dinucleotide), NADH (reduced nicotinamide adenine dinucleotide), NADP⁺ (oxidized nicotinamide adenine dinucleotide phosphate) and NADPH (reduced nicotinamide adenine dinucleotide phosphate); energy coenzymes: ATP (adenosine triphosphate), ADP (adenosine diphosphate) and AMP (adenosine monophosphate); and antioxidants: GSSG (oxidized glutathione) and GSH (reduced glutathione)...
May 14, 2018: Metabolites
https://www.readbyqxmd.com/read/29748461/software-tools-and-approaches-for-compound-identification-of-lc-ms-ms-data-in-metabolomics
#4
REVIEW
Ivana Blaženović, Tobias Kind, Jian Ji, Oliver Fiehn
The annotation of small molecules remains a major challenge in untargeted mass spectrometry-based metabolomics. We here critically discuss structured elucidation approaches and software that are designed to help during the annotation of unknown compounds. Only by elucidating unknown metabolites first is it possible to biologically interpret complex systems, to map compounds to pathways and to create reliable predictive metabolic models for translational and clinical research. These strategies include the construction and quality of tandem mass spectral databases such as the coalition of MassBank repositories and investigations of MS/MS matching confidence...
May 10, 2018: Metabolites
https://www.readbyqxmd.com/read/29724022/adenosine-5-triphosphate-metabolism-in-red-blood-cells-as-a-potential-biomarker-for-post-exercise-hypotension-and-a-drug-target-for-cardiovascular-protection
#5
REVIEW
Pollen K Yeung, Shyam Sundar Kolathuru, Sheyda Mohammadizadeh, Fatemeh Akhoundi, Brett Linderfield
The importance of adenosine and ATP in regulating many biological functions has long been recognized, especially for their effects on the cardiovascular system, which may be used for management of hypertension and cardiometabolic diseases. In response to ischemia and cardiovascular injury, ATP is broken down to release adenosine. The effect of adenosine is very short lived because it is rapidly taken up by erythrocytes (RBCs), myocardial and endothelial cells, and also rapidly catabolized to oxypurine metabolites...
May 2, 2018: Metabolites
https://www.readbyqxmd.com/read/29690607/lipidomic-profiling-of-murine-macrophages-treated-with-fatty-acids-of-varying-chain-length-and-saturation-status
#6
Kevin Huynh, Gerard Pernes, Natalie A Mellett, Peter J Meikle, Andrew J Murphy, Graeme I Lancaster
Macrophages are abundant within adipose tissue depots where they are exposed to fatty acids, leading to lipid accumulation. Herein, we have determined the effects of various fatty acids on the macrophage lipidome. Using targeted mass-spectrometry, we were able to detect 641 individual lipid species in primary murine macrophages treated with a variety of saturated fatty acids and an un-saturated fatty acid, either alone or in combination. The most pronounced effects were observed for the long-chain saturated fatty acid palmitate, which increased the total abundance of numerous classes of lipids...
April 23, 2018: Metabolites
https://www.readbyqxmd.com/read/29690538/adipose-tissue-lactate-clearance-but-not-blood-lactate-clearance-is-associated-with-clinical-outcome-in-sepsis-or-septic-shock-during-the-post-resuscitation-period
#7
Ioannis Ilias, Sofia Apollonatou, Dimitra-Argyro Vassiliadi, Nikitas Nikitas, Maria Theodorakopoulou, Argyris Diamantakis, Anastasia Kotanidou, Ioanna Dimopoulou
No study has directly measured tissue lactate clearance in patients with sepsis during the post-resuscitation period. In this study we aimed to assess in ICU patients with sepsis ( n = 32) or septic shock ( n = 79)—during the post-resuscitation phase—the relative kinetics of blood/tissue lactate clearances and to examine whether these are associated with outcome. We measured serially—over a 48-h period—blood and adipose tissue interstitial fluid lactate levels (with microdialysis) and we calculated lactate clearance...
April 21, 2018: Metabolites
https://www.readbyqxmd.com/read/29642378/pasture-feeding-changes-the-bovine-rumen-and-milk-metabolome
#8
Tom F O'Callaghan, Rosa Vázquez-Fresno, Arnau Serra-Cayuela, Edison Dong, Rupasri Mandal, Deirdre Hennessy, Stephen McAuliffe, Pat Dillon, David S Wishart, Catherine Stanton, R Paul Ross
The purpose of this study was to examine the effects of two pasture feeding systems-perennial ryegrass (GRS) and perennial ryegrass and white clover (CLV)-and an indoor total mixed ration (TMR) system on the (a) rumen microbiome; (b) rumen fluid and milk metabolome; and (c) to assess the potential to distinguish milk from different feeding systems by their respective metabolomes. Rumen fluid was collected from nine rumen cannulated cows under the different feeding systems in early, mid and late lactation, and raw milk samples were collected from ten non-cannulated cows in mid-lactation from each of the feeding systems...
April 6, 2018: Metabolites
https://www.readbyqxmd.com/read/29570652/gc-ms-based-metabolomics-and-nmr-spectroscopy-investigation-of-food-intake-biomarkers-for-milk-and-cheese-in-serum-of-healthy-humans
#9
Alessia Trimigno, Linda Münger, Gianfranco Picone, Carola Freiburghaus, Grégory Pimentel, Nathalie Vionnet, François Pralong, Francesco Capozzi, René Badertscher, Guy Vergères
The identification and validation of food intake biomarkers (FIBs) in human biofluids is a key objective for the evaluation of dietary intake. We report here the analysis of the GC-MS and 1H-NMR metabolomes of serum samples from a randomized cross-over study in 11 healthy volunteers having consumed isocaloric amounts of milk, cheese, and a soy drink as non-dairy alternative. Serum was collected at baseline, postprandially up to 6 h, and 24 h after consumption. A multivariate analysis of the untargeted serum metabolomes, combined with a targeted analysis of candidate FIBs previously reported in urine samples from the same study, identified galactitol, galactonate, and galactono-1,5-lactone (milk), 3-phenyllactic acid (cheese), and pinitol (soy drink) as candidate FIBs for these products...
March 23, 2018: Metabolites
https://www.readbyqxmd.com/read/29561812/carbonic-anhydrases-and-metabolism
#10
EDITORIAL
Claudiu T Supuran
Although the role of carbonic anhydrases (CAs, EC 4.2.1.1) in metabolism is well-established, pharmacological applications of this phenomenon started to be considered only recently. In organisms all over the phylogenetic tree, the seven CA genetic families known to date are involved in biosynthetic processes and pH modulation, which may influence metabolism in multiple ways, with both processes being amenable to pharmacologic intervention. CA inhibitors possess antiobesity action directly by inhibiting lipogenesis, whereas the hypoxic tumor metabolism is highly controlled by the transmembrane isoforms CA IX and XII, which contribute to the acidic extracellular environment of tumors and supply bicarbonate for their high proliferation rates...
March 21, 2018: Metabolites
https://www.readbyqxmd.com/read/29558381/identification-of-an-epoxide-metabolite-of-lycopene-in-human-plasma-using-13-c-labeling-and-qtof-ms
#11
Morgan J Cichon, Nancy E Moran, Ken M Riedl, Steven J Schwartz, Steven K Clinton
The carotenoid lycopene is a bioactive component of tomatoes and is hypothesized to reduce risk of several chronic diseases, such as prostate cancer. The metabolism of lycopene is only beginning to be understood and some studies suggest that metabolites of lycopene may be partially responsible for bioactivity associated with the parent compound. The detection and characterization of these compounds in vivo is an important step in understanding lycopene bioactivity. The metabolism of lycopene likely involves both chemical and enzymatic oxidation...
March 20, 2018: Metabolites
https://www.readbyqxmd.com/read/29562689/gc-ms-based-endometabolome-analysis-differentiates-prostate-cancer-from-normal-prostate-cells
#12
Ana Rita Lima, Ana Margarida Araújo, Joana Pinto, Carmen Jerónimo, Rui Henrique, Maria de Lourdes Bastos, Márcia Carvalho, Paula Guedes de Pinho
Prostate cancer (PCa) is an important health problem worldwide. Diagnosis and management of PCa is very complex because the detection of serum prostate specific antigen (PSA) has several drawbacks. Metabolomics brings promise for cancer biomarker discovery and for better understanding PCa biochemistry. In this study, a gas chromatography-mass spectrometry (GC-MS) based metabolomic profiling of PCa cell lines was performed. The cell lines include 22RV1 and LNCaP from PCa with androgen receptor (AR) expression, DU145 and PC3 (which lack AR expression), and one normal prostate cell line (PNT2)...
March 19, 2018: Metabolites
https://www.readbyqxmd.com/read/29534024/an-update-on-the-metabolic-roles-of-carbonic-anhydrases-in-the-model-alga-chlamydomonas-reinhardtii
#13
REVIEW
Ashok Aspatwar, Susanna Haapanen, Seppo Parkkila
Carbonic anhydrases (CAs) are metalloenzymes that are omnipresent in nature. CAs catalyze the basic reaction of the reversible hydration of CO₂ to HCO₃- and H⁺ in all living organisms. Photosynthetic organisms contain six evolutionarily different classes of CAs, which are namely: α-CAs, β-CAs, γ-CAs, δ-CAs, ζ-CAs, and θ-CAs. Many of the photosynthetic organisms contain multiple isoforms of each CA family. The model alga Chlamydomonas reinhardtii contains 15 CAs belonging to three different CA gene families...
March 13, 2018: Metabolites
https://www.readbyqxmd.com/read/29533993/nanoparticle-assisted-metabolomics
#14
REVIEW
Bo Zhang, Mouzhe Xie, Lei Bruschweiler-Li, Rafael Brüschweiler
Understanding and harnessing the interactions between nanoparticles and biological molecules is at the forefront of applications of nanotechnology to modern biology. Metabolomics has emerged as a prominent player in systems biology as a complement to genomics, transcriptomics and proteomics. Its focus is the systematic study of metabolite identities and concentration changes in living systems. Despite significant progress over the recent past, important challenges in metabolomics remain, such as the deconvolution of the spectra of complex mixtures with strong overlaps, the sensitive detection of metabolites at low abundance, unambiguous identification of known metabolites, structure determination of unknown metabolites and standardized sample preparation for quantitative comparisons...
March 13, 2018: Metabolites
https://www.readbyqxmd.com/read/29517989/coordinated-regulation-of-metabolic-transporters-and-migration-invasion-by-carbonic-anhydrase-ix
#15
REVIEW
Paul C McDonald, Mridula Swayampakula, Shoukat Dedhar
Hypoxia is a prominent feature of the tumor microenvironment (TME) and cancer cells must dynamically adapt their metabolism to survive in these conditions. A major consequence of metabolic rewiring by cancer cells in hypoxia is the accumulation of acidic metabolites, leading to the perturbation of intracellular pH (pHi) homeostasis and increased acidosis in the TME. To mitigate the potentially detrimental consequences of an increasingly hypoxic and acidic TME, cancer cells employ a network of enzymes and transporters to regulate pH, particularly the extracellular facing carbonic anhydrase IX (CAIX) and CAXII...
March 8, 2018: Metabolites
https://www.readbyqxmd.com/read/29495652/carbonic-anhydrases-role-in-ph-control-and-cancer
#16
REVIEW
Mam Y Mboge, Brian P Mahon, Robert McKenna, Susan C Frost
The pH of the tumor microenvironment drives the metastatic phenotype and chemotherapeutic resistance of tumors. Understanding the mechanisms underlying this pH-dependent phenomenon will lead to improved drug delivery and allow the identification of new therapeutic targets. This includes an understanding of the role pH plays in primary tumor cells, and the regulatory factors that permit cancer cells to thrive. Over the last decade, carbonic anhydrases (CAs) have been shown to be important mediators of tumor cell pH by modulating the bicarbonate and proton concentrations for cell survival and proliferation...
February 28, 2018: Metabolites
https://www.readbyqxmd.com/read/29495309/identifying-biomarkers-of-wharton-s-jelly-mesenchymal-stromal-cells-using-a-dynamic-metabolic-model-the-cell-passage-effect
#17
Benoît Laflaquière, Gabrielle Leclercq, Chandarong Choey, Jingkui Chen, Sabine Peres, Caryn Ito, Mario Jolicoeur
Because of their unique ability to modulate the immune system, mesenchymal stromal cells (MSCs) are widely studied to develop cell therapies for detrimental immune and inflammatory disorders. However, controlling the final cell phenotype and determining immunosuppressive function following cell amplification in vitro often requires prolonged cell culture assays, all of which contribute to major bottlenecks, limiting the clinical emergence of cell therapies. For instance, the multipotent Wharton's Jelly mesenchymal stem/stromal cells (WJMSC), extracted from human umbilical cord, exhibit immunosuppressive traits under pro-inflammatory conditions, in the presence of interferon-γ (IFNγ), and tumor necrosis factor-α (TNFα)...
February 24, 2018: Metabolites
https://www.readbyqxmd.com/read/29495258/study-of-the-serum-metabolomic-profile-in-nonalcoholic-fatty-liver-disease-research-and-clinical-perspectives
#18
REVIEW
Stefano Gitto, Filippo Schepis, Pietro Andreone, Erica Villa
In recent years, metabolomics has attracted great scientific attention. The metabolomics methodology might permit a view into transitional phases between healthy liver and nonalcoholic steatohepatitis. Metabolomics can help to analyze the metabolic alterations that play a main role in the progression of nonalcoholic steatohepatitis. Lipid, glucose, amino acid, and bile acid metabolism should be widely studied to understand the complex pathogenesis of nonalcoholic steatohepatitis. The discovery of new biomarkers would be important for diagnosis and staging of liver disease as well as for the assessment of efficacy of new drugs...
February 24, 2018: Metabolites
https://www.readbyqxmd.com/read/29470400/ramp-a-comprehensive-relational-database-of-metabolomics-pathways-for-pathway-enrichment-analysis-of-genes-and-metabolites
#19
Bofei Zhang, Senyang Hu, Elizabeth Baskin, Andrew Patt, Jalal K Siddiqui, Ewy A Mathé
The value of metabolomics in translational research is undeniable, and metabolomics data are increasingly generated in large cohorts. The functional interpretation of disease-associated metabolites though is difficult, and the biological mechanisms that underlie cell type or disease-specific metabolomics profiles are oftentimes unknown. To help fully exploit metabolomics data and to aid in its interpretation, analysis of metabolomics data with other complementary omics data, including transcriptomics, is helpful...
February 22, 2018: Metabolites
https://www.readbyqxmd.com/read/29443915/quantification-of-stable-isotope-traces-close-to-natural-enrichment-in-human-plasma-metabolites-using-gas-chromatography-mass-spectrometry
#20
Lisa Krämer, Christian Jäger, Jean-Pierre Trezzi, Doris M Jacobs, Karsten Hiller
Currently, changes in metabolic fluxes following consumption of stable isotope-enriched foods are usually limited to the analysis of postprandial kinetics of glucose. Kinetic information on a larger diversity of metabolites is often lacking, mainly due to the marginal percentage of fully isotopically enriched plant material in the administered food product, and hence, an even weaker 13 C enrichment in downstream plasma metabolites. Therefore, we developed an analytical workflow to determine weak 13 C enrichments of diverse plasma metabolites with conventional gas chromatography-mass spectrometry (GC-MS)...
February 14, 2018: Metabolites
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