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https://www.readbyqxmd.com/read/29324674/calcitriol-supplementation-causes-decreases-in-tumorigenic-proteins-and-different-proteomic-and-metabolomic-signatures-in-right-versus-left-sided-colon-cancer
#1
Monica M Schroll, Katelyn R Ludwig, Kerry M Bauer, Amanda B Hummon
Vitamin D deficiency is a common problem worldwide. In particular, it is an issue in the Northern Hemisphere where UVB radiation does not penetrate the atmosphere as readily. There is a correlation between vitamin D deficiency and colorectal cancer incidence and mortality. Furthermore, there is strong evidence that cancer of the ascending (right side) colon is different from cancer of the descending (left side) colon in terms of prognosis, tumor differentiation, and polyp type, as well as at the molecular level...
January 11, 2018: Metabolites
https://www.readbyqxmd.com/read/29324649/machine-learning-methods-for-analysis-of-metabolic-data-and-metabolic-pathway-modeling
#2
REVIEW
Miroslava Cuperlovic-Culf
Machine learning uses experimental data to optimize clustering or classification of samples or features, or to develop, augment or verify models that can be used to predict behavior or properties of systems. It is expected that machine learning will help provide actionable knowledge from a variety of big data including metabolomics data, as well as results of metabolism models. A variety of machine learning methods has been applied in bioinformatics and metabolism analyses including self-organizing maps, support vector machines, the kernel machine, Bayesian networks or fuzzy logic...
January 11, 2018: Metabolites
https://www.readbyqxmd.com/read/29300340/constraining-genome-scale-models-to-represent-the-bow-tie-structure-of-metabolism-for-13c-metabolic-flux-analysis
#3
Tyler W H Backman, David Ando, Jahnavi Singh, Jay D Keasling, Héctor García Martín
Determination of internal metabolic fluxes is crucial for fundamental and applied biology because they map how carbon and electrons flow through metabolism to enable cell function. 13 C Metabolic Flux Analysis ( 13 C MFA) and Two-Scale 13 C Metabolic Flux Analysis (2S- 13 C MFA) are two techniques used to determine such fluxes. Both operate on the simplifying approximation that metabolic flux from peripheral metabolism into central "core" carbon metabolism is minimal, and can be omitted when modeling isotopic labeling in core metabolism...
January 4, 2018: Metabolites
https://www.readbyqxmd.com/read/29295495/rethinking-the-combination-of-proton-exchanger-inhibitors-in-cancer-therapy
#4
REVIEW
Elisabetta Iessi, Mariantonia Logozzi, Davide Mizzoni, Rossella Di Raimo, Claudiu T Supuran, Stefano Fais
Microenvironmental acidity is becoming a key target for the new age of cancer treatment. In fact, while cancer is characterized by genetic heterogeneity, extracellular acidity is a common phenotype of almost all cancers. To survive and proliferate under acidic conditions, tumor cells up-regulate proton exchangers and transporters (mainly V-ATPase, Na⁺/H⁺ exchanger (NHE), monocarboxylate transporters (MCTs), and carbonic anhydrases (CAs)), that actively extrude excess protons, avoiding intracellular accumulation of toxic molecules, thus becoming a sort of survival option with many similarities compared with unicellular microorganisms...
December 23, 2017: Metabolites
https://www.readbyqxmd.com/read/29271872/methanol-generates-numerous-artifacts-during-sample-extraction-and-storage-of-extracts-in-metabolomics-research
#5
Claudia Sauerschnig, Maria Doppler, Christoph Bueschl, Rainer Schuhmacher
Many metabolomics studies use mixtures of (acidified) methanol and water for sample extraction. In the present study, we investigated if the extraction with methanol can result in artifacts. To this end, wheat leaves were extracted with mixtures of native and deuterium-labeled methanol and water, with or without 0.1% formic acid. Subsequently, the extracts were analyzed immediately or after storage at 10 °C, -20 °C or -80 °C with an HPLC-HESI-QExactive HF-Orbitrap instrument. Our results showed that 88 (8%) of the >1100 detected compounds were derived from the reaction with methanol and either formed during sample extraction or short-term storage...
December 22, 2017: Metabolites
https://www.readbyqxmd.com/read/29257083/dynamics-of-monoterpene-formation-in-spike-lavender-plants
#6
Isabel Mendoza-Poudereux, Erika Kutzner, Claudia Huber, Juan Segura, Isabel Arrillaga, Wolfgang Eisenreich
The metabolic cross-talk between the mevalonate (MVA) and the methylerythritol phosphate (MEP) pathways was analyzed in spike lavender (Lavandula latifolia Med) on the basis of 13CO₂-labelling experiments using wildtype and transgenic plants overexpressing the 3-hydroxy-3-methylglutaryl CoA reductase (HMGR), the first and key enzyme of the MVA pathway. The plants were labelled in the presence of 13CO₂ in a gas chamber for controlled pulse and chase periods of time. GC/MS and NMR analysis of 1,8-cineole and camphor, the major monoterpenes present in their essential oil, indicated that the C5-precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) of both monoterpenes are predominantly biosynthesized via the MEP pathway...
December 19, 2017: Metabolites
https://www.readbyqxmd.com/read/29258276/metabolomic-profiles-of-a-midge-procladius-villosimanus-kieffer-are-associated-with-sediment-contamination-in-urban-wetlands
#7
Katherine J Jeppe, Konstantinos A Kouremenos, Kallie R Townsend, Daniel F MacMahon, David Sharley, Dedreia L Tull, Ary A Hoffmann, Vincent Pettigrove, Sara M Long
Metabolomic techniques are powerful tools for investigating organism-environment interactions. Metabolite profiles have the potential to identify exposure or toxicity before populations are disrupted and can provide useful information for environmental assessment. However, under complex environmental scenarios, metabolomic responses to exposure can be distorted by background and/or organismal variation. In the current study, we use LC-MS (liquid chromatography-mass spectrometry) and GC-MS (gas chromatography-mass spectrometry) to measure metabolites of the midge Procladius villosimanus inhabiting 21 urban wetlands...
December 18, 2017: Metabolites
https://www.readbyqxmd.com/read/29186773/metabolic-perturbations-in-a-bacillus-subtilis-clpp-mutant-during-glucose-starvation
#8
(no author information available yet)
Proteolysis is essential for all living organisms to maintain the protein homeostasis and to adapt to changing environmental conditions. ClpP is the main protease in Bacillus subtilis, and forms complexes with different Clp ATPases. These complexes play crucial roles during heat stress, but also in sporulation or cell morphology. Especially enzymes of cell wall-, amino acid-, and nucleic acid biosynthesis are known substrates of the protease ClpP during glucose starvation. The aim of this study was to analyze the influence of a clpP mutation on the metabolism in different growth phases and to search for putative new ClpP substrates...
November 24, 2017: Metabolites
https://www.readbyqxmd.com/read/29156542/computational-approaches-for-integrative-analysis-of-the-metabolome-and-microbiome
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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