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Metabolites

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https://www.readbyqxmd.com/read/29156542/computational-approaches-for-integrative-analysis-of-the-metabolome-and-microbiome
#1
REVIEW
Jasmine Chong, Jianguo Xia
The study of the microbiome, the totality of all microbes inhabiting the host or an environmental niche, has experienced exponential growth over the past few years. The microbiome contributes functional genes and metabolites, and is an important factor for maintaining health. In this context, metabolomics is increasingly applied to complement sequencing-based approaches (marker genes or shotgun metagenomics) to enable resolution of microbiome-conferred functionalities associated with health. However, analyzing the resulting multi-omics data remains a significant challenge in current microbiome studies...
November 18, 2017: Metabolites
https://www.readbyqxmd.com/read/29144418/nmr-based-identification-of-metabolites-in-polar-and-non-polar-extracts-of-avian-liver
#2
Fariba Fathi, Antonio Brun, Katherine H Rott, Paulo Falco Cobra, Marco Tonelli, Hamid R Eghbalnia, Enrique Caviedes-Vidal, William H Karasov, John L Markley
Metabolites present in liver provide important clues regarding the physiological state of an organism. The aim of this work was to evaluate a protocol for high-throughput NMR-based analysis of polar and non-polar metabolites from a small quantity of liver tissue. We extracted the tissue with a methanol/chloroform/water mixture and isolated the polar metabolites from the methanol/water layer and the non-polar metabolites from the chloroform layer. Following drying, we re-solubilized the fractions for analysis with a 600 MHz NMR spectrometer equipped with a 1...
November 16, 2017: Metabolites
https://www.readbyqxmd.com/read/29144383/monitoring-for-response-to-antineoplastic-drugs-the-potential-of-a-metabolomic-approach
#3
REVIEW
Jodi Rattner, Oliver F Bathe
For most cancers, chemotherapeutic options are rapidly expanding, providing the oncologist with substantial choices. Therefore, there is a growing need to select the best systemic therapy, for any individual, that effectively halts tumor progression with minimal toxicity. Having the capability to predict benefit and to anticipate toxicity would be ideal, but remains elusive at this time. An alternative approach is an adaptive approach that involves close observation for treatment response and emergence of resistance...
November 16, 2017: Metabolites
https://www.readbyqxmd.com/read/29137184/cell-type-specific-metabolic-flux-analysis-a-challenge-for-metabolic-phenotyping-and-a-potential-solution-in-plants
#4
Merja T Rossi, Monika Kalde, Chaiyakorn Srisakvarakul, Nicholas J Kruger, R George Ratcliffe
Stable isotope labelling experiments are used routinely in metabolic flux analysis (MFA) to determine the metabolic phenotype of cells and tissues. A complication arises in multicellular systems because single cell measurements of transcriptomes, proteomes and metabolomes in multicellular organisms suggest that the metabolic phenotype will differ between cell types. In silico analysis of simulated metabolite isotopomer datasets shows that cellular heterogeneity confounds conventional MFA because labelling data averaged over multiple cell types does not necessarily yield averaged flux values...
November 13, 2017: Metabolites
https://www.readbyqxmd.com/read/29137180/metabolomic-modularity-analysis-mma-to-quantify-human-liver-perfusion-dynamics
#5
Gautham Vivek Sridharan, Bote Bruinsma, Shyam Sundhar Bale, Anandh Swaminathan, Nima Saeidi, Martin L Yarmush, Korkut Uygun
Large-scale -omics data are now ubiquitously utilized to capture and interpret global responses to perturbations in biological systems, such as the impact of disease states on cells, tissues, and whole organs. Metabolomics data, in particular, are difficult to interpret for providing physiological insight because predefined biochemical pathways used for analysis are inherently biased and fail to capture more complex network interactions that span multiple canonical pathways. In this study, we introduce a nov-el approach coined Metabolomic Modularity Analysis (MMA) as a graph-based algorithm to systematically identify metabolic modules of reactions enriched with metabolites flagged to be statistically significant...
November 13, 2017: Metabolites
https://www.readbyqxmd.com/read/29137138/metabolic-profile-of-the-cellulolytic-industrial-actinomycete-thermobifida-fusca
#6
Niti Vanee, J Paul Brooks, Stephen S Fong
Actinomycetes have a long history of being the source of numerous valuable natural products and medicinals. To expedite product discovery and optimization of biochemical production, high-throughput technologies can now be used to screen the library of compounds present (or produced) at a given time in an organism. This not only facilitates chemical product screening, but also provides a comprehensive methodology to the study cellular metabolic networks to inform cellular engineering. Here, we present some of the first metabolomic data of the industrial cellulolytic actinomycete Thermobifida fusca generated using LC-MS/MS...
November 11, 2017: Metabolites
https://www.readbyqxmd.com/read/29137134/an-overview-of-the-bacterial-carbonic-anhydrases
#7
REVIEW
Claudiu T Supuran, Clemente Capasso
Bacteria encode carbonic anhydrases (CAs, EC 4.2.1.1) belonging to three different genetic families, the α-, β-, and γ-classes. By equilibrating CO₂ and bicarbonate, these metalloenzymes interfere with pH regulation and other crucial physiological processes of these organisms. The detailed investigations of many such enzymes from pathogenic and non-pathogenic bacteria afford the opportunity to design both novel therapeutic agents, as well as biomimetic processes, for example, for CO₂ capture. Investigation of bacterial CA inhibitors and activators may be relevant for finding antibiotics with a new mechanism of action...
November 11, 2017: Metabolites
https://www.readbyqxmd.com/read/29104224/parameters-of-the-endocannabinoid-system-as-novel-biomarkers-in-sepsis-and-septic-shock
#8
REVIEW
J Daniel Lafreniere, Christian Lehmann
Sepsis represents a dysregulated immune response to infection, with a continuum of severity progressing to septic shock. This dysregulated response generally follows a pattern by which an initial hyperinflammatory phase is followed by a state of sepsis-associated immunosuppression. Major challenges in improving sepsis care include developing strategies to ensure early and accurate identification and diagnosis of the disease process, improving our ability to predict outcomes and stratify patients, and the need for novel sepsis-specific treatments such as immunomodulation...
November 1, 2017: Metabolites
https://www.readbyqxmd.com/read/29064436/modelling-of-hydrophilic-interaction-liquid-chromatography-stationary-phases-using-chemometric-approaches
#9
Meritxell Navarro-Reig, Elena Ortiz-Villanueva, Romà Tauler, Joaquim Jaumot
Metabolomics is a powerful and widely used approach that aims to screen endogenous small molecules (metabolites) of different families present in biological samples. The large variety of compounds to be determined and their wide diversity of physical and chemical properties have promoted the development of different types of hydrophilic interaction liquid chromatography (HILIC) stationary phases. However, the selection of the most suitable HILIC stationary phase is not straightforward. In this work, four different HILIC stationary phases have been compared to evaluate their potential application for the analysis of a complex mixture of metabolites, a situation similar to that found in non-targeted metabolomics studies...
October 24, 2017: Metabolites
https://www.readbyqxmd.com/read/29065530/analysis-of-intracellular-metabolites-from-microorganisms-quenching-and-extraction-protocols
#10
REVIEW
Farhana R Pinu, Silas G Villas-Boas, Raphael Aggio
Sample preparation is one of the most important steps in metabolome analysis. The challenges of determining microbial metabolome have been well discussed within the research community and many improvements have already been achieved in last decade. The analysis of intracellular metabolites is particularly challenging. Environmental perturbations may considerably affect microbial metabolism, which results in intracellular metabolites being rapidly degraded or metabolized by enzymatic reactions. Therefore, quenching or the complete stop of cell metabolism is a pre-requisite for accurate intracellular metabolite analysis...
October 23, 2017: Metabolites
https://www.readbyqxmd.com/read/29048351/bacterial-substrate-transformation-tracked-by-stable-isotope-guided-nmr-metabolomics-application-in-a-natural-aquatic-microbial-community
#11
Mario Uchimiya, Yuuri Tsuboi, Kengo Ito, Yasuhiro Date, Jun Kikuchi
The transformation of organic substrates by heterotrophic bacteria in aquatic environments constitutes one of the key processes in global material cycles. The development of procedures that would enable us to track the wide range of organic compounds transformed by aquatic bacteria would greatly improve our understanding of material cycles. In this study, we examined the applicability of nuclear magnetic resonance spectroscopy coupled with stable-isotope labeling to the investigation of metabolite transformation in a natural aquatic bacterial community...
October 19, 2017: Metabolites
https://www.readbyqxmd.com/read/28991180/robust-regression-analysis-of-gcms-data-reveals-differential-rewiring-of-metabolic-networks-in-hepatitis-b-and-c-patients
#12
Cedric Simillion, Nasser Semmo, Jeffrey R Idle, Diren Beyoğlu
About one in 15 of the world's population is chronically infected with either hepatitis virus B (HBV) or C (HCV), with enormous public health consequences. The metabolic alterations caused by these infections have never been directly compared and contrasted. We investigated groups of HBV-positive, HCV-positive, and uninfected healthy controls using gas chromatography-mass spectrometry analyses of their plasma and urine. A robust regression analysis of the metabolite data was conducted to reveal correlations between metabolite pairs...
October 8, 2017: Metabolites
https://www.readbyqxmd.com/read/28976938/exometabolomic-analysis-of-cross-feeding-metabolites
#13
Andrea Lubbe, Benjamin P Bowen, Trent Northen
Microbial consortia have the potential to perform complex, industrially important tasks. The design of microbial consortia requires knowledge of the substrate preferences and metabolic outputs of each member, to allow understanding of potential interactions such as competition and beneficial metabolic exchange. Here, we used exometabolite profiling to follow the resource processing by a microbial co-culture of two biotechnologically relevant microbes, the bacterial cellulose degrader Cellulomonas fimi, and the oleaginous yeast Yarrowia lipolytica...
October 4, 2017: Metabolites
https://www.readbyqxmd.com/read/28937622/specificities-of-human-hepatocellular-carcinoma-developed-on-non-alcoholic-fatty-liver-disease-in-absence-of-cirrhosis-revealed-by-tissue-extracts-%C3%A2-h-nmr-spectroscopy
#14
Camille Teilhet, Daniel Morvan, Juliette Joubert-Zakeyh, Anne-Sophie Biesse, Bruno Pereira, Sylvie Massoulier, Pierre Dechelotte, Denis Pezet, Emmanuel Buc, Géraldine Lamblin, Michel Peoc'h, Jack Porcheron, Marie-Paule Vasson, Armando Abergel, Aicha Demidem
There is a rising incidence of non-alcoholic fatty liver disease (NAFLD) as well as of the frequency of Hepato-Cellular Carcinoma (HCC) associated with NAFLD. To seek for putative metabolic pathways specific of the NAFLD etiology, we performed comparative metabolomics between HCC associated with NAFLD and HCC associated with cirrhosis. The study included 28 pairs of HCC tissue versus distant Non-Tumoral Tissue (NTT) collected from patients undergoing hepatectomy. HCC was associated with cirrhosis (n = 9), normal liver (n = 6) and NAFLD (n = 13)...
September 22, 2017: Metabolites
https://www.readbyqxmd.com/read/28926956/carbonic-anhydrase-inhibition-and-the-management-of-hypoxic-tumors
#15
REVIEW
Claudiu T Supuran
Hypoxia and acidosis are salient features of many tumors, leading to a completely different metabolism compared to normal cells. Two of the simplest metabolic products, protons and bicarbonate, are generated by the catalytic activity of the metalloenzyme carbonic anhydrase (CA, EC 4.2.1.1), with at least two of its isoforms, CA IX and XII, mainly present in hypoxic tumors. Inhibition of tumor-associated CAs leads to an impaired growth of the primary tumors, metastases and reduces the population of cancer stem cells, leading thus to a complex and beneficial anticancer action for this class of enzyme inhibitors...
September 16, 2017: Metabolites
https://www.readbyqxmd.com/read/28878200/a-protocol-for-generating-and-exchanging-genome-scale-metabolic-resource-allocation-models
#16
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
#17
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
#18
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
#19
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
#20
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
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