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Metabolites

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https://read.qxmd.com/read/30744112/maldi-tof-ms-analysis-in-the-identification-of-urine-proteomic-patterns-of-gestational-trophoblastic-disease
#1
Paulina Banach, Paweł Dereziński, Eliza Matuszewska, Jan Matysiak, Hubert Bochyński, Zenon J Kokot, Ewa Nowak-Markwitz
Gestational trophoblastic disease (GTD) is a group of highly aggressive, rare tumors. Human chorionic gonadotropin is a common biomarker used in the diagnosis and monitoring of GTD. To improve our knowledge of the pathology of GTD, we performed protein-peptide profiling on the urine of patients affected with gestational trophoblastic neoplasm (GTN). We analyzed urine samples from patients diagnosed with GTN ( n = 26) and from healthy pregnant and non-pregnant controls ( n = 17) using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS)...
February 9, 2019: Metabolites
https://read.qxmd.com/read/30736341/current-developments-in-%C3%A2%C2%B5mas-nmr-analysis-for-metabolomics
#2
REVIEW
Covadonga Lucas-Torres, Alan Wong
Analysis of microscopic specimens has emerged as a useful analytical application in metabolomics because of its capacity for characterizing a highly homogenous sample with a specific interest. The undeviating analysis helps to unfold the hidden activities in a bulk specimen and contributes to the understanding of the fundamental metabolisms in life. In NMR spectroscopy, micro(µ)-probe technology is well-established and -adopted to the microscopic level of biofluids. However, this is quite the contrary with specimens such as tissue, cell and organism...
February 6, 2019: Metabolites
https://read.qxmd.com/read/30736318/consistency-inconsistency-and-ambiguity-of-metabolite-names-in-biochemical-databases-used-for-genome-scale-metabolic-modelling
#3
Nhung Pham, Ruben G A van Heck, Jesse C J van Dam, Peter J Schaap, Edoardo Saccenti, Maria Suarez-Diez
Genome-scale metabolic models (GEMs) are manually curated repositories describing the metabolic capabilities of an organism. GEMs have been successfully used in different research areas, ranging from systems medicine to biotechnology. However, the different naming conventions (namespaces) of databases used to build GEMs limit model reusability and prevent the integration of existing models. This problem is known in the GEM community, but its extent has not been analyzed in depth. In this study, we investigate the name ambiguity and the multiplicity of non-systematic identifiers and we highlight the (in)consistency in their use in 11 biochemical databases of biochemical reactions and the problems that arise when mapping between different namespaces and databases...
February 6, 2019: Metabolites
https://read.qxmd.com/read/30717353/metabolomic-profiling-of-cerebral-palsy-brain-tissue-reveals-novel-central-biomarkers-and-biochemical-pathways-associated-with-the-disease-a-pilot-study
#4
Zeynep Alpay Savasan, Ali Yilmaz, Zafer Ugur, Buket Aydas, Ray O Bahado-Singh, Stewart F Graham
Cerebral palsy (CP) is one of the most common causes of motor disability in childhood, with complex and heterogeneous etiopathophysiology and clinical presentation. Understanding the metabolic processes associated with the disease may aid in the discovery of preventive measures and therapy. Tissue samples (caudate nucleus) were obtained from post-mortem CP cases ( n = 9) and age- and gender-matched control subjects ( n = 11). We employed a targeted metabolomics approach using both ¹H NMR and direct injection liquid chromatography-tandem mass spectrometry (DI/LC-MS/MS)...
February 2, 2019: Metabolites
https://read.qxmd.com/read/30717275/activation-studies-of-the-%C3%AE-carbonic-anhydrase-from-the-pathogenic-protozoan-entamoeba-histolytica-with-amino-acids-and-amines
#5
Silvia Bua, Susanna Haapanen, Marianne Kuuslahti, Seppo Parkkila, Claudiu T Supuran
The β-carbonic anhydrase (CA, EC 4.2.1.1) from the pathogenic protozoan Entamoeba histolytica , EhiCA, was investigated for its activation with a panel of natural and non-natural amino acids and amines. EhiCA was potently activated by D-His, D-Phe, D-DOPA, L- and D-Trp, L- and D-Tyr, 4-amino-L-Tyr, histamine and serotonin, with KA s ranging between 1.07 and 10.1 M. The best activator was D-Tyr (KA of 1.07 µM). L-Phe, L-DOPA, L-adrenaline, L-Asn, L-Asp, L-Glu and L-Gln showed medium potency activation, with KA s of 16...
February 1, 2019: Metabolites
https://read.qxmd.com/read/30717274/the-omics-window-into-nonalcoholic-fatty-liver-disease-nafld
#6
REVIEW
Lucia Carulli, Giulia Zanca, Filippo Schepis, Erica Villa
Nonalcoholic fatty liver disease (NAFLD) is a common cause of hepatic abnormalities worldwide. Nonalcoholic steatohepatitis (NASH) is part of the spectrum of NAFLD and leads to progressive liver disease, such as cirrhosis and hepatocellular carcinoma. In NASH patient, fibrosis represents the major predictor of liver-related mortality; therefore, it is important to have an early and accurate diagnosis of NASH. The current gold standard for the diagnosis of NASH is still liver biopsy. The development of biomarkers able to predict disease severity, prognosis, as well as response to therapy without the need for a biopsy is the focus of most up-to-date genomic, transcriptomic, proteomic, and metabolomic research...
February 1, 2019: Metabolites
https://read.qxmd.com/read/30717245/metabolic-alterations-in-male-sterile-potato-as-compared-to-male-fertile
#7
Maria Shishova, Roman Puzanskiy, Olga Gavrilova, Shamuhommed Kurbanniazov, Kirill Demchenko, Vladislav Yemelyanov, Galina Pendinen, Alexey Shavarda, Tatjana Gavrilenko
The common potato, Solanum tuberosum L., is the fourth most important agricultural crop worldwide. Until recently, vegetative propagation by tubers has been the main method of potato cultivation. A shift of interest to sexual potato reproduction by true botanical seeds is due to the appearance of a new hybrid seed breeding strategy whose successful application for many crop species has been supported by male sterility. This investigation was focused on the study of differences in the metabolite profiles of anthers at the mature pollen stage from male-fertile and male-sterile genotypes of S...
February 1, 2019: Metabolites
https://read.qxmd.com/read/30717187/crosstalk-between-metabolic-alterations-and-altered-redox-balance-in-ptc-derived-cell-lines
#8
Laura Tronci, Paola Caria, Daniela Virginia Frau, Sonia Liggi, Cristina Piras, Federica Murgia, Maria Laura Santoru, Monica Pibiri, Monica Deiana, Julian Leether Griffin, Roberta Vanni, Luigi Atzori
Background : Thyroid cancer is the most common endocrine malignancy, with papillary thyroid carcinoma (PTC) being the most common (85⁻90%) among all the different types of thyroid carcinomas. Cancer cells show metabolic alterations and, due to their rapid proliferation, an accumulation of reactive oxygen species, playing a fundamental role in cancer development and progression. Currently, the crosstalk among thyrocytes metabolism, redox balance and oncogenic mutations remain poorly characterized. The aim of this study was to investigate the interplay among metabolic alterations, redox homeostasis and oncogenic mutations in PTC-derived cells...
February 1, 2019: Metabolites
https://read.qxmd.com/read/30695998/metabolic-modeling-of-human-gut-microbiota-on-a-genome-scale-an-overview
#9
REVIEW
Partho Sen, Matej Orešič
There is growing interest in the metabolic interplay between the gut microbiome and host metabolism. Taxonomic and functional profiling of the gut microbiome by next-generation sequencing (NGS) has unveiled substantial richness and diversity. However, the mechanisms underlying interactions between diet, gut microbiome and host metabolism are still poorly understood. Genome-scale metabolic modeling (GSMM) is an emerging approach that has been increasingly applied to infer diet⁻microbiome, microbe⁻microbe and host⁻microbe interactions under physiological conditions...
January 28, 2019: Metabolites
https://read.qxmd.com/read/30691098/nmr-metabolomic-analysis-of-skeletal-muscle-heart-and-liver-of-hatchling-loggerhead-sea-turtles-caretta-caretta-experimentally-exposed-to-crude-oil-and-or-corexit
#10
Stasia A Bembenek-Bailey, Jennifer N Niemuth, Patricia D McClellan-Green, Matthew H Godfrey, Craig A Harms, Hanna Gracz, Michael K Stoskopf
We used nuclear magnetic spectroscopy (NMR) to evaluate the metabolic impacts of crude oil, Corexit 5900A, a dispersant, and a crude oil Corexit 5900A mixture exposure on skeletal muscle, heart, and liver physiology of hatchling loggerhead sea turtles ( Caretta caretta ). Tissue samples were obtained from 22 seven-day-old hatchlings after a four day cutaneous exposure to environmentally relevant concentrations of crude oil, Corexit 5900A, a combination of crude oil and Corexit 9500A, or a seawater control. We identified 38 metabolites in the aqueous extracts of the liver, and 30 metabolites in both the skeletal and heart muscle aqueous extracts, including organic acids/osmolytes, energy compounds, amino acids, ketone bodies, nucleosides, and nucleotides...
January 26, 2019: Metabolites
https://read.qxmd.com/read/30682824/the-methoxylated-highly-conjugated-c-40-carotenoids-spirilloxanthin-and-anhydrorhodovibrin-can-be-separated-using-high-performance-liquid-chromatography-with-safe-and-environmentally-friendly-solvents
#11
Caroline Autenrieth, Robin Ghosh
High performance liquid chromatography (HPLC) is a frequently used technique in carotenoid research. So far, however, little attention has been paid to the fact that many of the organic solvents used in HPLC separation of highly apolar C40 carotenoids impose a significant threat to both health (especially for women) and the general laboratory environment. Here, we developed a solvent combination capable of allowing high-resolution HPLC separation of the C40 carotenoid, spirilloxanthin, and all of its biosynthetic precursors beginning with phytoene, using relatively safe, environmentally friendly solvents...
January 24, 2019: Metabolites
https://read.qxmd.com/read/30678289/hr-mas-nmr-based-quantitative-metabolomics-in-breast-cancer
#12
REVIEW
Mikheil Gogiashvili, Jessica Nowacki, Roland Hergenröder, Jan G Hengstler, Jörg Lambert, Karolina Edlund
High resolution magic-angle spinning (HR-MAS) nuclear magnetic resonance (NMR) spectroscopy is increasingly used for profiling of breast cancer tissue, delivering quantitative information for approximately 40 metabolites. One unique advantage of the method is that it can be used to analyse intact tissue, thereby requiring only minimal sample preparation. Importantly, since the method is non-destructive, it allows further investigations of the same specimen using for instance transcriptomics. Here, we discuss technical aspects critical for a successful analysis - including sample handling, measurement conditions, pulse sequences for one- and two dimensional analysis, and quantification methods - and summarize available studies, with a focus on significant associations of metabolite levels with clinically relevant parameters...
January 22, 2019: Metabolites
https://read.qxmd.com/read/30669322/gc-ms-metabolomics-reveals-distinct-profiles-of-low-and-high-grade-bladder-cancer-cultured-cells
#13
Daniela Rodrigues, Joana Pinto, Ana Margarida Araújo, Carmen Jerónimo, Rui Henrique, Maria de Lourdes Bastos, Paula Guedes de Pinho, Márcia Carvalho
Previous studies have shown that metabolomics can be a useful tool to better understand the mechanisms of carcinogenesis; however, alterations in biochemical pathways that lead to bladder cancer (BC) development have hitherto not been fully investigated. In this study, gas chromatography-mass spectrometry (GC-MS)-based metabolomics was applied to unveil the metabolic alterations between low-grade and high-grade BC cultured cell lines. Multivariable analysis revealed a panel of metabolites responsible for the separation between the two tumorigenic cell lines...
January 18, 2019: Metabolites
https://read.qxmd.com/read/30669279/a-metabolomic-study-of-the-variability-of-the-chemical-composition-of-commonly-consumed-coffee-brews
#14
Joseph A Rothwell, Erikka Loftfield, Roland Wedekind, Neal Freedman, Callie Kambanis, Augustin Scalbert, Rashmi Sinha
Coffee drinking has been associated with a lower risk of certain chronic diseases and overall mortality. Its effects on disease risk may vary according to the type of coffee brew consumed and its chemical composition. We characterized variations in the chemical profiles of 76 coffee brew samples representing different brew methods, roast levels, bean species, and caffeine types, either prepared or purchased from outlets in Rockville, Maryland, United States of America. Samples were profiled using liquid chromatography coupled with high-resolution mass spectrometry, and the main sources of chemical variability identified by the principal component partial R-square multivariable regression were found to be brew methods (Rpartial ² = 36%)...
January 18, 2019: Metabolites
https://read.qxmd.com/read/30654443/1d-spikelet-projections-from-heteronuclear-2d-nmr-data-permitting-1d-chemometrics-while-preserving-2d-dispersion
#15
Maryam Tabatabaei Anaraki, Wolfgang Bermel, Rudraksha Dutta Majumdar, Ronald Soong, Myrna Simpson, Martine Monnette, André J Simpson
Nuclear magnetic resonance (NMR) spectroscopy is a powerful tool for the non-targeted metabolomics of intact biofluids and even living organisms. However, spectral overlap can limit the information that can be obtained from 1D 1H NMR. For example, magnetic susceptibility broadening in living organisms prevents any metabolic information being extracted from solution-state 1D 1H NMR. Conversely, the additional spectral dispersion afforded by 2D 1H-13C NMR allows a wide range of metabolites to be assigned in-vivo in 13C enriched organisms, as well as a greater depth of information for biofluids in general...
January 16, 2019: Metabolites
https://read.qxmd.com/read/30650532/univariate-statistical-analysis-as-a-guide-to-%C3%A2-h-nmr-spectra-signal-assignment-by-visual-inspection
#16
Chenglin Zhu, Beatrice Vitali, Gilbert Donders, Carola Parolin, Yan Li, Luca Laghi
In Proton Nuclear Magnetic Resonance (¹H-NMR) spectroscopy, the signals assignment procedure is normally conducted by visual inspection of the spectra, by taking advantage of the innate predisposition of human eye for pattern recognition. In the case of untargeted metabolomics investigations on food and body fluids, the complexity of the spectra may lead the user to overlook signals, independently from their biological relevance. Here, we describe a four steps procedure that is designed to guide signals assignment task by visual inspection...
January 15, 2019: Metabolites
https://read.qxmd.com/read/30646552/serum-amino-acids-in-association-with-prevalent-and-incident-type-2-diabetes-in-a-chinese-population
#17
Yonghai Lu, Yeli Wang, Xu Liang, Li Zou, Choon Nam Ong, Jian-Min Yuan, Woon-Puay Koh, An Pan
We aimed to simultaneously examine the associations of both essential and non-essential amino acids with both prevalent and incident type 2 diabetes in a Chinese population. A case-control study was nested within the Singapore Chinese Health Study. Participants included 144 cases with prevalent and 160 cases with incident type 2 diabetes and 304 controls. Cases and controls were individually matched on age, sex, and date of blood collection. Baseline serum levels of 9 essential and 10 non-essential amino acids were measured using liquid chromatography tandem mass spectrometry...
January 14, 2019: Metabolites
https://read.qxmd.com/read/30641988/rapid-cerebral-metabolic-shift-during-neonatal-sepsis-is-attenuated-by-enteral-colostrum-supplementation-in-preterm-pigs
#18
Masoumeh Alinaghi, Ping-Ping Jiang, Anders Brunse, Per Torp Sangild, Hanne Christine Bertram
Sepsis, the clinical manifestation of serious infection, may disturb normal brain development, especially in preterm infants with an immature brain. We hypothesized that neonatal sepsis induces systemic metabolic alterations that rapidly affect metabolic signatures in immature brain and cerebrospinal fluid (CSF). Cesarean-delivered preterm pigs systemically received 10⁸ CFU/kg Staphylococcus epidermidis (SE) and were provided total parenteral nutrition ( n = 9) or enteral supplementation with bovine colostrum ( n = 10) and compared with uninfected pigs receiving parenteral nutrition ( n = 7)...
January 11, 2019: Metabolites
https://read.qxmd.com/read/30641898/direct-infusion-based-metabolomics-identifies-metabolic-disease-in-patients-dried-blood-spots-and-plasma
#19
Hanneke A Haijes, Marcel Willemsen, Maria Van der Ham, Johan Gerrits, Mia L Pras-Raves, Hubertus C M T Prinsen, Peter M Van Hasselt, Monique G M De Sain-van der Velden, Nanda M Verhoeven-Duif, Judith J M Jans
In metabolic diagnostics, there is an emerging need for a comprehensive test to acquire a complete view of metabolite status. Here, we describe a non-quantitative direct-infusion high-resolution mass spectrometry (DI-HRMS) based metabolomics method and evaluate the method for both dried blood spots (DBS) and plasma. 110 DBS of 42 patients harboring 23 different inborn errors of metabolism (IEM) and 86 plasma samples of 38 patients harboring 21 different IEM were analyzed using DI-HRMS. A peak calling pipeline developed in R programming language provided Z-scores for ~1875 mass peaks corresponding to ~3835 metabolite annotations (including isomers) per sample...
January 11, 2019: Metabolites
https://read.qxmd.com/read/30634493/alteration-of-metabolic-pathways-in-osteoarthritis
#20
REVIEW
Guangju Zhai
Sir Archibald Edward Garrod, who pioneered the field of inborn errors of metabolism and first elucidated the biochemical basis of alkaptonuria over 100 years ago, suggested that inborn errors of metabolism were "merely extreme examples of variations of chemical behavior which are probably everywhere present in minor degrees, just as no two individuals of a species are absolutely identical in bodily structure neither are their chemical processes carried out on exactly the same lines", and that this "chemical individuality [confers] predisposition to and immunities from various mishaps which are spoken of as diseases"...
January 9, 2019: Metabolites
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