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Metabolomic analysis

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https://www.readbyqxmd.com/read/28221771/joint-bounding-of-peaks-across-samples-improves-differential-analysis-in-mass-spectrometry-based-metabolomics
#1
Leslie Myint, André Kleensang, Liang Zhao, Thomas Hartung, Kasper D Hansen
As mass spectrometry-based metabolomics becomes more widely used in biomedical research, it is important to revisit existing data analysis paradigms. Existing data preprocessing efforts have largely focused on methods which starts by extracting features separately from each sample, followed by a subsequent attempt to group features across samples to facilitate comparisons. We show that this preprocessing approach leads to unnecessary variability in peak quantifications that adversely impacts downstream analysis...
February 21, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28221024/imet-a-network-based-computational-tool-to-assist-in-the-annotation-of-metabolites-from-tandem-mass-spectra
#2
Antoni Aguilar-Mogas, Marta Sales-Pardo, Miriam Navarro, Roger Guimerà, Oscar Yanes
Structural annotation of metabolites relies mainly on tandem mass spectrometry (MS/MS) analysis. However, approximately 90% of the known metabolites reported in metabolomic databases do not have annotated spectral data from standards. This situation has fostered the development of computational tools that predict fragmentation patterns in silico and compare these to experimental MS/MS spectra. However, because such methods require the molecular structure of the detected compound to be available for the algorithm, the identification of novel metabolites in organisms relevant for biotechnological and medical applications remains a challenge...
February 21, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28221022/quantitative-13c-traces-of-glucose-fate-in-hepatitis-b-virus-infected-hepatocytes
#3
Qianfen Wan, Yulan Wang, Huiru Tang
Quantitative characterization of 13C-labeled metabolites is an important part of the stable isotope tracing method widely used in metabolic flux analysis. Due to long relaxation time and low sensitivity of 13C nuclei, direct measurement of 13C labeled metabolites using one dimensional 13C NMR often fails to meet the demand of metabolomics studies especially with large number of samples and metabolites having low abundance. Although HSQC-based 2D NMR methods have improved sensitivity with inversion detection, they are time-consuming thus unsuitable for high-throughput absolute quantification of 13C-labeled metabolites...
February 21, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28220994/positional-enrichment-by-proton-analysis-pepa-a-one-dimensional-1-h-nmr-approach-for-13-c-stable-isotope-tracer-studies-in-metabolomics
#4
Maria Vinaixa, Miguel A Rodríguez, Suvi Aivio, Jordi Capellades, Josep Gómez, Nicolau Canyellas, Travis H Stracker, Oscar Yanes
A novel metabolomics approach for NMR-based stable isotope tracer studies called PEPA is presented, and its performance validated using human cancer cells. PEPA detects the position of carbon label in isotopically enriched metabolites and quantifies fractional enrichment by indirect determination of (13) C-satellite peaks using 1D-(1) H-NMR spectra. In comparison with (13) C-NMR, TOCSY and HSQC, PEPA improves sensitivity, accelerates the elucidation of (13) C positions in labeled metabolites and the quantification of the percentage of stable isotope enrichment...
February 21, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28220901/distinct-signatures-of-dental-plaque-metabolic-byproducts-dictated-by-periodontal-inflammatory-status
#5
Akito Sakanaka, Masae Kuboniwa, Ei Hashino, Takeshi Bamba, Eiichiro Fukusaki, Atsuo Amano
Onset of chronic periodontitis is associated with an aberrant polymicrobial community, termed dysbiosis. Findings regarding its etiology obtained using high-throughput sequencing technique suggested that dysbiosis holds a conserved metabolic signature as an emergent property. The purpose of this study was to identify robust biomarkers for periodontal inflammation severity. Furthermore, we investigated disease-associated metabolic signatures of periodontal microbiota using a salivary metabolomics approach. Whole saliva samples were obtained from adult subjects before and after removal of supragingival plaque (debridement)...
February 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28219950/nutritional-modulation-of-mouse-and-human-liver-bud-growth-through-a-branched-amino-acid-metabolism
#6
Hiroyuki Koike, Ran-Ran Zhang, Yasuharu Ueno, Keisuke Sekine, Yun-Wen Zheng, Takanori Takebe, Hideki Taniguchi
Liver bud progenitors experience a transient amplification during early organ growth phase, yet the responsible mechanism was not fully understood. Collective evidence highlighted the specific requirements in stem cell metabolism for expanding organ progenitors during organogenesis and regeneration. Here, transcriptome analyses showed progenitors of mouse and human liver bud growth stage specifically expressed branched chain aminotransferase1 gene, a known breakdown enzyme of branched-chain amino acid (BCAA) for energy generation...
February 20, 2017: Development
https://www.readbyqxmd.com/read/28219798/integrative-hepatoprotective-efficacy-comparison-of-raw-and-vinegar-baked-radix-bupleuri-using-nuclear-magnetic-resonance-based-metabolomics
#7
Jie Xing, Hui-Min Sun, Jin-Ping Jia, Xue-Mei Qin, Zhen-Yu Li
Radix Bupleuri (RB), with a Chinese name Chaihu, is one of the most popular Traditional Chinese herbal drug. It can be baked with vinegar to afford vinegar-baked Radix Bupleuri (VBRB), which is used in Traditional Chinese Medicine (TCM) for liver diseases treatment. In the present study, nuclear magnetic resonance-based metabolomic approach was used to compare the liver protective effect of RB and two types of VBRBs, which were prepared by two kinds of vinegar. The contents of 14 metabolites in the liver of carbon tetrachloride (CCl4) treated mice were significantly altered in comparison with control group, and VBRB prepared by Shanxi vinegar showed best effect as revealed by the amount and regulatory degree of the perturbed metabolites...
February 7, 2017: Journal of Pharmaceutical and Biomedical Analysis
https://www.readbyqxmd.com/read/28218729/exhaled-breath-metabolomics-for-the-diagnosis-of-pneumonia-in-intubated-and-mechanically-ventilated-intensive-care-unit-icu-patients
#8
Pouline M P van Oort, Sanne de Bruin, Hans Weda, Hugo H Knobel, Marcus J Schultz, Lieuwe D Bos, On Behalf Of The Mars Consortium
The diagnosis of hospital-acquired pneumonia remains challenging. We hypothesized that analysis of volatile organic compounds (VOCs) in exhaled breath could be used to diagnose pneumonia or the presence of pathogens in the respiratory tract in intubated and mechanically-ventilated intensive care unit patients. In this prospective, single-centre, cross-sectional cohort study breath from mechanically ventilated patients was analysed using gas chromatography-mass spectrometry. Potentially relevant VOCs were selected with a p-value < 0...
February 19, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28217400/novel-plasma-biomarker-of-atenolol-induced-hyperglycemia-identified-through-a-metabolomics-genomics-integrative-approach
#9
Felipe A de Oliveira, Mohamed H Shahin, Yan Gong, Caitrin W McDonough, Amber L Beitelshees, John G Gums, Arlene B Chapman, Eric Boerwinkle, Stephen T Turner, Reginald F Frye, Oliver Fiehn, Rima Kaddurah-Daouk, Julie A Johnson, Rhonda M Cooper-DeHoff
INTRODUCTION: While atenolol is an effective antihypertensive agent, its use is also associated with adverse events including hyperglycemia and incident diabetes that may offset the benefits of blood pressure lowering. By combining metabolomic and genomic data acquired from hypertensive individuals treated with atenolol, it may be possible to better understand the pathways that most impact the development of an adverse glycemic state. OBJECTIVE: To identify biomarkers that can help predict susceptibility to blood glucose excursions during exposure to atenolol...
August 2016: Metabolomics: Open Access
https://www.readbyqxmd.com/read/28217037/lung-injury-induced-skeletal-muscle-wasting-in-aged-mice-is-linked-to-alterations-in-long-chain-fatty-acid-metabolism
#10
D Clark Files, Amro Ilaiwy, Traci L Parry, Kevin W Gibbs, Chun Liu, James R Bain, Osvaldo Delbono, Michael J Muehlbauer, Monte S Willis
INTRODUCTION: Older patients are more likely to acquire and die from acute respiratory distress syndrome (ARDS) and muscle weakness may be more clinically significant in older persons. Recent data implicate muscle ring finger protein 1 (MuRF1) in lung injury-induced skeletal muscle atrophy in young mice and identify an alternative role for MuRF1 in cardiac metabolism regulation through inhibition of fatty acid oxidation. OBJECTIVES: To develop a model of lung injury-induced muscle wasting in old mice and to evaluate the skeletal muscle metabolomic profile of adult and old acute lung injury (ALI) mice...
August 2016: Metabolomics: Official Journal of the Metabolomic Society
https://www.readbyqxmd.com/read/28216958/-1-h-nmr-based-serum-metabolomics-reveals-erythromycin-induced-liver-toxicity-in-albino-wistar-rats
#11
Atul Rawat, Durgesh Dubey, Anupam Guleria, Umesh Kumar, Amit K Keshari, Swati Chaturvedi, Anand Prakash, Sudipta Saha, Dinesh Kumar
INTRODUCTION: Erythromycin (ERY) is known to induce hepatic toxicity which mimics other liver diseases. Thus, ERY is often used to produce experimental models of drug-induced liver-toxicity. The serum metabolic profiles can be used to evaluate the liver-toxicity and to further improve the understanding of underlying mechanism. OBJECTIVE: To establish the serum metabolic patterns of Erythromycin induced hepatotoxicity in albino wistar rats using (1)H NMR based serum metabolomics...
October 2016: Journal of Pharmacy & Bioallied Sciences
https://www.readbyqxmd.com/read/28215548/identification-of-highly-sensitive-biomarkers-that-can-aid-the-early-detection-of-pancreatic-cancer-using-gc-ms-ms-based-targeted-metabolomics
#12
Yuichi Hirata, Takashi Kobayashi, Shin Nishiumi, Kodai Yamanaka, Takashi Nakagawa, Seiji Fujigaki, Takao Iemoto, Makoto Kobayashi, Takuji Okusaka, Shoji Nakamori, Masashi Shimahara, Takaaki Ueno, Akihiko Tsuchida, Naohiro Sata, Tatsuya Ioka, Yohichi Yasunami, Tomoo Kosuge, Takashi Kaneda, Takao Kato, Kazuhiro Yagihara, Shigeyuki Fujita, Tesshi Yamada, Kazufumi Honda, Takeshi Azuma, Masaru Yoshida
BACKGROUND: To improve prognosis of pancreatic cancer (PC) patients, the discovery of more reliable biomarkers for the early detection is desired. METHODS: Blood samples were collected by 2 independent groups. The 1st set was included 55 early PC and 58 healthy volunteers (HV), and the 2nd set was included 16 PC and 16HV. The 16 targeted metabolites were quantitatively analyzed by gas chromatography/tandem mass spectrometry together with their corresponding stable isotopes...
February 16, 2017: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/28215546/analysis-of-human-serum-metabolome-for-potential-biomarkers-identification-of-erosive-oral-lichen-planus
#13
Xu-Yan YangG, Shuai-Nan Zhang, Xu-Zhao Li, Yu Wang, Xiao-Dong Yin
BACKGROUND: Oral lichen planus (OLP) is a chronic auto-inflammatory mucositis and potentially oral premalignant lesion. Erosive OLP patients display the higher canceration rate as compared to the patients with non-erosive OLP. Identification of the potential biomarkers associated with erosive OLP may help to investigate the disease pathogenesis and to improve clinical treatment. METHODS: Ultra-performance liquid chromatography-quadrupole time-of-flight-mass spectrometry (UPLC-QTOF-MS) combined with pattern recognition approaches were integrated to acquire differentially expressed metabolites for the pathways analysis and elucidate mechanisms of disease...
February 16, 2017: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/28215068/comprehensive-ms-and-solid-state-nmr-metabolomic-profiling-reveals-molecular-variations-in-native-periderms-from-four-solanum-tuberosum-potato-cultivars
#14
Wenlin Huang, Olga Serra, Keyvan Dastmalchi, Liqing Jin, Lijia Yang, Ruth E Stark
The potato (Solanum tuberosum L.) ranks third in worldwide consumption among food crops. Whereas disposal of potato peels poses significant challenges for the food industry, secondary metabolites in these tissues are also bioactive and essential to crop development. The diverse primary and secondary metabolites reported in whole tubers and wound-healing tissues prompted a comprehensive profiling study of native periderms from four cultivars with distinctive skin morphologies and commercial food uses. Polar and nonpolar soluble metabolites were extracted concurrently, analyzed chromatographically, and characterized with mass spectrometry; the corresponding solid interfacial polymeric residue was examined by solid-state 13C NMR...
February 18, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28214354/long-chain-unsaturated-fatty-acids-as-possible-important-metabolites-for-primary-angle-closure-glaucoma-based-on-targeted-metabolomic-analysis
#15
Shengzhong Rong, Yang Li, Yue Guan, Lili Zhu, Qiang Zhou, Mucong Gao, Hongzhi Pan, Lina Zou, Dong Chang
Primary angle-closure glaucoma (PACG) is a severe chronic neurodegenerative disease in Asia. Identification of important metabolites associated with PACG is crucial for early intervention and advancing knowledge of the disease mechanism. We applied gas chromatography-mass spectrometry (GC-MS) for targeted metabolomic analysis on serum samples from thirty-eight newly diagnosed PACG patients and forty-eight controls. Palmitoleic acid (PA), linoleic acid (LA), gamma-linolenic acid (GLA) and arachidonic acid (ARA) were identified as important metabolites associated with PACG...
February 18, 2017: Biomedical Chromatography: BMC
https://www.readbyqxmd.com/read/28213610/prebiotic-inulin-type-fructans-induce-specific-changes-in-the-human-gut-microbiota
#16
Doris Vandeputte, Gwen Falony, Sara Vieira-Silva, Jun Wang, Manuela Sailer, Stephan Theis, Kristin Verbeke, Jeroen Raes
OBJECTIVE: Contrary to the long-standing prerequisite of inducing selective (ie, bifidogenic) effects, recent findings suggest that prebiotic interventions lead to ecosystem-wide microbiota shifts. Yet, a comprehensive characterisation of this process is still lacking. Here, we apply 16S rDNA microbiota profiling and matching (gas chromatography mass spectrometry) metabolomics to assess the consequences of inulin fermentation both on the composition of the colon bacterial ecosystem and faecal metabolites profiles...
February 17, 2017: Gut
https://www.readbyqxmd.com/read/28213261/a-method-for-the-analysis-of-sugars-in-biological-systems-using-reductive-amination-in-combination-with-hydrophilic-interaction-chromatography-and-high-resolution-mass-spectrometry
#17
Sami Bawazeer, Ali Muhsen Ali, Aliyah Alhawiti, Abedawn Khalaf, Colin Gibson, Jonans Tusiimire, David G Watson
Separation of sugar isomers extracted from biological samples is challenging because of their natural occurrence as alpha and beta anomers and, in the case of hexoses, in their pyranose and furanose forms. A reductive amination method was developed for the tagging of sugars with the aim of it becoming part of a metabolomics work flow. The best separation of the common hexoses (glucose, fructose, mannose and galactose) was achieved when (2)H5-aniline was used as the tagging reagent in combination with separation on a ZICHILIC column...
May 1, 2017: Talanta
https://www.readbyqxmd.com/read/28212624/understanding-the-response-to-endurance-exercise-using-a-systems-biology-approach-combining-blood-metabolomics-transcriptomics-and-mirnomics-in-horses
#18
Núria Mach, Yuliaxis Ramayo-Caldas, Allison Clark, Marco Moroldo, Céline Robert, Eric Barrey, Jesús Maria López, Laurence Le Moyec
BACKGROUND: Endurance exercise in horses requires adaptive processes involving physiological, biochemical, and cognitive-behavioral responses in an attempt to regain homeostasis. We hypothesized that the identification of the relationships between blood metabolome, transcriptome, and miRNome during endurance exercise in horses could provide significant insights into the molecular response to endurance exercise. For this reason, the serum metabolome and whole-blood transcriptome and miRNome data were obtained from ten horses before and after a 160 km endurance competition...
February 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28211897/metabolomic-tool-to-identify-soybean-glycine-max-l-merrill-germplasms-with-a-high-level-of-shade-tolerance-at-the-seedling-stage
#19
Jiang Liu, Baoyu Hu, Weiguo Liu, Wenting Qin, Haijun Wu, Jing Zhang, Caiqiong Yang, Juncai Deng, Kai Shu, Junbo Du, Feng Yang, Taiwen Yong, Xiaochun Wang, Wenyu Yang
The isoflavone profiles of seeds of various soybean genotypes with different levels of shade tolerance at the seedling stage were investigated. High-performance liquid chromatography (HPLC) was used to quantify 12 isoflavones, and the data were analyzed using a multivariate statistical analysis. Combined with field experimental data and an orthogonal partial least-squares discriminant analysis (OPLS-DA), several aglycones (genistein (GE), daidzein (DE), and glycitein (GLE)) were selected and identified as key compounds involved in the shade tolerance of soybean seedlings...
February 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28210249/feeding-a-high-concentration-diet-induces-unhealthy-alterations-in-the-composition-and-metabolism-of-ruminal-microbiota-and-host-response-in-a-goat-model
#20
Canfeng Hua, Jing Tian, Ping Tian, Rihua Cong, Yanwen Luo, Yali Geng, Shiyu Tao, Yingdong Ni, Ruqian Zhao
There is limited knowledge about the impact of long-term feeding a high-concentrate (HC) diet on rumen microbiota, metabolome, and host cell functions. In this study, a combination of mass spectrometry-based metabolomics techniques, 454 pyrosequencing of 16S rDNA genes, and RT-PCR was applied to evaluate the changes of ruminal microbiota composition, ruminal metabolites, and related genes expression in rumen epithelial cells of lactating goats received either a 35% concentrate diet or a 65% concentrate diet for 4 or 19 weeks, respectively...
2017: Frontiers in Microbiology
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