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Metabolites

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https://www.readbyqxmd.com/read/28878200/a-protocol-for-generating-and-exchanging-genome-scale-metabolic-resource-allocation-models
#1
Alexandra-M Reimers, Henning Lindhorst, Steffen Waldherr
In this article, we present a protocol for generating a complete (genome-scale) metabolic resource allocation model, as well as a proposal for how to represent such models in the systems biology markup language (SBML). Such models are used to investigate enzyme levels and achievable growth rates in large-scale metabolic networks. Although the idea of metabolic resource allocation studies has been present in the field of systems biology for some years, no guidelines for generating such a model have been published up to now...
September 6, 2017: Metabolites
https://www.readbyqxmd.com/read/28878168/metabolomics-analysis-of-urine-samples-from-children-after-acetaminophen-overdose
#2
Laura K Schnackenberg, Jinchun Sun, Sudeepa Bhattacharyya, Pritmohinder Gill, Laura P James, Richard D Beger
Acetaminophen (APAP), a commonly used over-the-counter analgesic, accounts for approximately fifty percent of the cases of acute liver failure (ALF) in the United States due to overdose, with over half of those unintentional. Current clinical approaches for assessing APAP overdose rely on identifying the precise time of overdose and quantitating acetaminophen alanine aminotransferase (ALT) levels in peripheral blood. Novel specific and sensitive biomarkers may provide additional information regarding patient status post overdose...
September 6, 2017: Metabolites
https://www.readbyqxmd.com/read/28841195/recommendations-for-improving-identification-and-quantification-in-non-targeted-gc-ms-based-metabolomic-profiling-of-human-plasma
#3
Hanghang Wang, Michael J Muehlbauer, Sara K O'Neal, Christopher B Newgard, Elizabeth R Hauser, James R Bain, Svati H Shah
The field of metabolomics as applied to human disease and health is rapidly expanding. In recent efforts of metabolomics research, greater emphasis has been placed on quality control and method validation. In this study, we report an experience with quality control and a practical application of method validation. Specifically, we sought to identify and modify steps in gas chromatography-mass spectrometry (GC-MS)-based, non-targeted metabolomic profiling of human plasma that could influence metabolite identification and quantification...
August 25, 2017: Metabolites
https://www.readbyqxmd.com/read/28832555/impact-of-soil-warming-on-the-plant-metabolome-of-icelandic-grasslands
#4
Albert Gargallo-Garriga, Marta Ayala-Roque, Jordi Sardans, Mireia Bartrons, Victor Granda, Bjarni D Sigurdsson, Niki I W Leblans, Michal Oravec, Otmar Urban, Ivan A Janssens, Josep Peñuelas
Climate change is stronger at high than at temperate and tropical latitudes. The natural geothermal conditions in southern Iceland provide an opportunity to study the impact of warming on plants, because of the geothermal bedrock channels that induce stable gradients of soil temperature. We studied two valleys, one where such gradients have been present for centuries (long-term treatment), and another where new gradients were created in 2008 after a shallow crustal earthquake (short-term treatment). We studied the impact of soil warming (0 to +15 °C) on the foliar metabolomes of two common plant species of high northern latitudes: Agrostis capillaris, a monocotyledon grass; and Ranunculus acris, a dicotyledonous herb, and evaluated the dependence of shifts in their metabolomes on the length of the warming treatment...
August 23, 2017: Metabolites
https://www.readbyqxmd.com/read/28829385/extracellular-microbial-metabolomics-the-state-of-the-art
#5
REVIEW
Farhana R Pinu, Silas G Villas-Boas
Microorganisms produce and secrete many primary and secondary metabolites to the surrounding environment during their growth. Therefore, extracellular metabolites provide important information about the changes in microbial metabolism due to different environmental cues. The determination of these metabolites is also comparatively easier than the extraction and analysis of intracellular metabolites as there is no need for cell rupture. Many analytical methods are already available and have been used for the analysis of extracellular metabolites from microorganisms over the last two decades...
August 22, 2017: Metabolites
https://www.readbyqxmd.com/read/28800113/biomarker-research-in-parkinson-s-disease-using-metabolite-profiling
#6
REVIEW
Jesper F Havelund, Niels H H Heegaard, Nils J K Færgeman, Jan Bert Gramsbergen
Biomarker research in Parkinson's disease (PD) has long been dominated by measuring dopamine metabolites or alpha-synuclein in cerebrospinal fluid. However, these markers do not allow early detection, precise prognosis or monitoring of disease progression. Moreover, PD is now considered a multifactorial disease, which requires a more precise diagnosis and personalized medication to obtain optimal outcome. In recent years, advanced metabolite profiling of body fluids like serum/plasma, CSF or urine, known as "metabolomics", has become a powerful and promising tool to identify novel biomarkers or "metabolic fingerprints" characteristic for PD at various stages of disease...
August 11, 2017: Metabolites
https://www.readbyqxmd.com/read/28792436/special-issue-cancer-metabolism
#7
EDITORIAL
Madhu Basetti
This special issue is designed to present the latest research findings and developments in the field of cancer metabolism. Cancer is a complex disease and a common term used for more than 100 diseases, whereas metabolism describes a labyrinth of complex biochemical pathways in the cell. It is essential to understand metabolism in the context of cancer for the early detection of disease biomarkers and to find proper targets for potential treatments. The articles presented in this issue cover metabolic aspects of brain tumours, breast tumours, paraganglioma, and the metabolic activity of tumour suppressor gene p53...
August 9, 2017: Metabolites
https://www.readbyqxmd.com/read/28786928/exercise-induced-alterations-in-skeletal-muscle-heart-liver-and-serum-metabolome-identified-by-non-targeted-metabolomics-analysis
#8
Joseph W Starnes, Traci L Parry, Sara K O'Neal, James R Bain, Michael J Muehlbauer, Aubree Honcoop, Amro Ilaiwy, Peter M Christopher, Cam Patterson, Monte S Willis
BACKGROUND: The metabolic and physiologic responses to exercise are increasingly interesting, given that regular physical activity enhances antioxidant capacity, improves cardiac function, and protects against type 2 diabetes. The metabolic interactions between tissues and the heart illustrate a critical cross-talk we know little about. METHODS: To better understand the metabolic changes induced by exercise, we investigated skeletal muscle (plantaris, soleus), liver, serum, and heart from exercise trained (or sedentary control) animals in an established rat model of exercise-induced aerobic training via non-targeted GC-MS metabolomics...
August 8, 2017: Metabolites
https://www.readbyqxmd.com/read/28788107/volatile-metabolites-emission-by-in-vivo-microalgae-an-overlooked-opportunity
#9
REVIEW
Komandoor E Achyuthan, Jason C Harper, Ronald P Manginell, Matthew W Moorman
Fragrances and malodors are ubiquitous in the environment, arising from natural and artificial processes, by the generation of volatile organic compounds (VOCs). Although VOCs constitute only a fraction of the metabolites produced by an organism, the detection of VOCs has a broad range of civilian, industrial, military, medical, and national security applications. The VOC metabolic profile of an organism has been referred to as its 'volatilome' (or 'volatome') and the study of volatilome/volatome is characterized as 'volatilomics', a relatively new category in the 'omics' arena...
July 31, 2017: Metabolites
https://www.readbyqxmd.com/read/28758940/non-targeted-metabolomics-analysis-of-golden-retriever-muscular-dystrophy-affected-muscles-reveals-alterations-in-arginine-and-proline-metabolism-and-elevations-in-glutamic-and-oleic-acid-in-vivo
#10
Muhammad Abdullah, Joe N Kornegay, Aubree Honcoop, Traci L Parry, Cynthia J Balog-Alvarez, Sara K O'Neal, James R Bain, Michael J Muehlbauer, Christopher B Newgard, Cam Patterson, Monte S Willis
BACKGROUND: Like Duchenne muscular dystrophy (DMD), the Golden Retriever Muscular Dystrophy (GRMD) dog model of DMD is characterized by muscle necrosis, progressive paralysis, and pseudohypertrophy in specific skeletal muscles. This severe GRMD phenotype includes moderate atrophy of the biceps femoris (BF) as compared to unaffected normal dogs, while the long digital extensor (LDE), which functions to flex the tibiotarsal joint and serves as a digital extensor, undergoes the most pronounced atrophy...
July 29, 2017: Metabolites
https://www.readbyqxmd.com/read/28714878/integrated-metabolomics-assessment-of-human-dried-blood-spots-and-urine-strips
#11
Jeremy Drolet, Vladimir Tolstikov, Brian A Williams, Bennett P Greenwood, Collin Hill, Vivek K Vishnudas, Rangaprasad Sarangarajan, Niven R Narain, Michael A Kiebish
(1) Background: Interest in the application of metabolomics toward clinical diagnostics development and population health monitoring has grown significantly in recent years. In spite of several advances in analytical and computational tools, obtaining a sufficient number of samples from patients remains an obstacle. The dried blood spot (DBS) and dried urine strip (DUS) methodologies are a minimally invasive sample collection method allowing for the relative simplicity of sample collection and minimal cost...
July 15, 2017: Metabolites
https://www.readbyqxmd.com/read/28684716/nmr-profiling-of-metabolites-in-larval-and-juvenile-blue-mussels-mytilus-edulis-under-ambient-and-low-salinity-conditions
#12
Melissa A May, Karl D Bishop, Paul D Rawson
Blue mussels (Mytilus edulis) are ecologically and economically important marine invertebrates whose populations are at risk from climate change-associated variation in their environment, such as decreased coastal salinity. Blue mussels are osmoconfomers and use components of the metabolome (free amino acids) to help maintain osmotic balance and cellular function during low salinity exposure. However, little is known about the capacity of blue mussels during the planktonic larval stages to regulate metabolites during osmotic stress...
July 6, 2017: Metabolites
https://www.readbyqxmd.com/read/28640228/development-and-validation-of-a-high-throughput-mass-spectrometry-based-urine-metabolomic-test-for-the-detection-of-colonic-adenomatous-polyps
#13
Lu Deng, David Chang, Rae R Foshaug, Roman Eisner, Victor K Tso, David S Wishart, Richard N Fedorak
Background: Colorectal cancer is one of the leading causes of cancer deaths worldwide. The detection and removal of the precursors to colorectal cancer, adenomatous polyps, is the key for screening. The aim of this study was to develop a clinically scalable (high throughput, low cost, and high sensitivity) mass spectrometry (MS)-based urine metabolomic test for the detection of adenomatous polyps. Methods: Prospective urine and stool samples were collected from 685 participants enrolled in a colorectal cancer screening program to undergo colonoscopy examination...
June 22, 2017: Metabolites
https://www.readbyqxmd.com/read/28640223/non-targeted-metabolomics-analysis-of-the-effects-of-tyrosine-kinase-inhibitors-sunitinib-and-erlotinib-on-heart-muscle-liver-and-serum-metabolism-in-vivo
#14
Brian C Jensen, Traci L Parry, Wei Huang, Amro Ilaiwy, James R Bain, Michael J Muehlbauer, Sara K O'Neal, Cam Patterson, Gary L Johnson, Monte S Willis
Background: More than 90 tyrosine kinases have been implicated in the pathogenesis of malignant transformation and tumor angiogenesis. Tyrosine kinase inhibitors (TKIs) have emerged as effective therapies in treating cancer by exploiting this kinase dependency. The TKI erlotinib targets the epidermal growth factor receptor (EGFR), whereas sunitinib targets primarily vascular endothelial growth factor receptor (VEGFR) and platelet-derived growth factor receptor (PDGFR).TKIs that impact the function of non-malignant cells and have on- and off-target toxicities, including cardiotoxicities...
June 22, 2017: Metabolites
https://www.readbyqxmd.com/read/28635678/evaluation-of-classifier-performance-for-multiclass-phenotype-discrimination-in-untargeted-metabolomics
#15
Patrick J Trainor, Andrew P DeFilippis, Shesh N Rai
Statistical classification is a critical component of utilizing metabolomics data for examining the molecular determinants of phenotypes. Despite this, a comprehensive and rigorous evaluation of the accuracy of classification techniques for phenotype discrimination given metabolomics data has not been conducted. We conducted such an evaluation using both simulated and real metabolomics datasets, comparing Partial Least Squares-Discriminant Analysis (PLS-DA), Sparse PLS-DA, Random Forests, Support Vector Machines (SVM), Artificial Neural Network, k-Nearest Neighbors (k-NN), and Naïve Bayes classification techniques for discrimination...
June 21, 2017: Metabolites
https://www.readbyqxmd.com/read/28629182/magnetic-resonance-spectroscopy-for-detection-of-2-hydroxyglutarate-as-a-biomarker-for-idh-mutation-in-gliomas
#16
REVIEW
Thomas Leather, Michael D Jenkinson, Kumar Das, Harish Poptani
Mutations in the isocitrate dehydrogenase (IDH)1/2 genes are highly prevalent in gliomas and have been suggested to play an important role in the development and progression of the disease. Tumours harbouring these mutations exhibit a significant alteration in their metabolism resulting in the aberrant accumulation of the oncometabolite 2-hydroxygluarate (2-HG). As well as being suggested to play an important role in tumour progression, 2-HG may serve as a surrogate indicator of IDH status through non-invasive detection using magnetic resonance spectroscopy (MRS)...
June 19, 2017: Metabolites
https://www.readbyqxmd.com/read/28629125/metabolomic-profiling-of-bile-acids-in-clinical-and-experimental-samples-of-alzheimer-s-disease
#17
Xiaobei Pan, Christopher T Elliott, Bernadette McGuinness, Peter Passmore, Patrick G Kehoe, Christian Hölscher, Paula L McClean, Stewart F Graham, Brian D Green
Certain endogenous bile acids have been proposed as potential therapies for ameliorating Alzheimer's disease (AD) but their role, if any, in the pathophysiology of this disease is not currently known. Given recent evidence of bile acids having protective and anti-inflammatory effects on the brain, it is important to establish how AD affects levels of endogenous bile acids. Using LC-MS/MS, this study profiled 22 bile acids in brain extracts and blood plasma from AD patients (n = 10) and age-matched control subjects (n = 10)...
June 17, 2017: Metabolites
https://www.readbyqxmd.com/read/28608848/furanoterpene-diversity-and-variability-in-the-marine-sponge-spongia-officinalis-from-untargeted-lc-ms-ms-metabolomic-profiling-to-furanolactam-derivatives
#18
Cléa Bauvais, Natacha Bonneau, Alain Blond, Thierry Pérez, Marie-Lise Bourguet-Kondracki, Séverine Zirah
The Mediterranean marine sponge Spongia officinalis has been reported as a rich source of secondary metabolites and also as a bioindicator of water quality given its capacity to concentrate trace metals. In this study, we evaluated the chemical diversity within 30 S. officinalis samples collected over three years at two sites differentially impacted by anthropogenic pollutants located near Marseille (South of France). Untargeted liquid chromatography-mass spectrometry (LC-MS) metabolomic profiling (C18 LC, ESI-Q-TOF MS) combined with XCMS Online data processing and multivariate statistical analysis revealed 297 peaks assigned to at least 86 compounds...
June 13, 2017: Metabolites
https://www.readbyqxmd.com/read/28594380/effects-of-obesity-on-pro-oxidative-conditions-and-dna-damage-in-liver-of-dmba-induced-mammary-carcinogenesis-models
#19
Stepan Melnyk, Soheila Korourian, Joseph W Levy, Oleksandra Pavliv, Teresa Evans, Reza Hakkak
The prevalence of the overweight and obesity is on the rise worldwide. Obesity can increase the risk of certain cancers and liver steatosis development. Previously, we reported that obesity increased liver steatosis in a mammary tumor model, but little is known about the effects of obesity in the liver in regard to global DNA methylation, DNA damage, and oxidative/nitrosative stress. Using a mammary tumor model, we investigated the effects of obesity on oxidative stress and DNA reaction. Five-week-old lean and obese female rats were used...
June 8, 2017: Metabolites
https://www.readbyqxmd.com/read/28590405/breast-tissue-metabolism-by-magnetic-resonance-spectroscopy
#20
REVIEW
Naranamangalam R Jagannathan, Uma Sharma
Metabolic alterations are known to occur with oncogenesis and tumor progression. During malignant transformation, the metabolism of cells and tissues is altered. Cancer metabolism can be studied using advanced technologies that detect both metabolites and metabolic activities. Identification, characterization, and quantification of metabolites (metabolomics) are important for metabolic analysis and are usually done by nuclear magnetic resonance (NMR) or by mass spectrometry. In contrast to the magnetic resonance imaging that is used to monitor the tumor morphology during progression of the disease and during therapy, in vivo NMR spectroscopy is used to study and monitor tumor metabolism of cells/tissues by detection of various biochemicals or metabolites involved in various metabolic pathways...
June 7, 2017: Metabolites
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