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https://www.readbyqxmd.com/read/29786954/urinary-metabolites-predict-prolonged-duration-of-delayed-graft-function-in-dcd-kidney-transplant-recipients
#1
S Kostidis, J R Bank, D Soonawala, E Nevedomskaya, C van Kooten, O A Mayboroda, J W de Fijter
Extending kidney donor criteria, including donation after circulatory death (DCD), has resulted in increased rates of delayed graft function (DGF) and primary nonfunction. Here, we used Nuclear Magnetic Resonance (NMR) spectroscopy to analyze the urinary metabolome of DCD transplant recipients at multiple time points (days 10, 42, 180 and 360 after transplantation). The aim was to identify markers that predict prolonged duration of functional DGF (fDGF). Forty-seven metabolites were quantified and their levels were evaluated in relation to fDGF...
May 22, 2018: American Journal of Transplantation
https://www.readbyqxmd.com/read/29786832/the-primary-active-components-antioxidant-properties-and-differential-metabolite-profiles-of-radish-sprouts-raphanus-sativus-l-upon-domestic-storage-analysis-of-nutritional-quality
#2
Ru Li, Yi Zhu
BACKGROUND: This study aimed to analyze the nutritional quality of radish sprouts (Raphanus sativus L.) upon domestic short-term storage. We stored fresh radish sprouts at 25±1°C and at 4±1°C for 12 h, detected phenolic substances, glucosinolates, isothiocyanates, vitamin C, and various antioxidant and abiotic stress-related factors. We investigated nutrient-related metabolic differences and associated pathways and postharvest treatment effects on nutritional quality via metabolomics analysis...
May 21, 2018: Journal of the Science of Food and Agriculture
https://www.readbyqxmd.com/read/29786797/nmr-based-prostate-cancer-metabolomics
#3
Leslie R Euceda, Maria K Andersen, May-Britt Tessem, Siver A Moestue, Maria T Grinde, Tone F Bathen
Prostate cancer is the second most common malignancy, and the fifth leading cause of cancer-related death among men, worldwide. A major unsolved clinical challenge in prostate cancer is the ability to accurately distinguish indolent cancer types from the aggressive ones. Reprogramming of metabolism is now a widely accepted hallmark of cancer development, where cancer cells must be able to convert nutrients to biomass while maintaining energy production. Metabolomics is the large-scale study of small molecules, commonly known as metabolites, within cells, biofluids, tissues, or organisms...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29786646/metabolic-reprogramming-by-3-iodothyronamine-t1am-a-new-perspective-to-reverse-obesity-through-co-regulation-of-sirtuin-4-and-6-expression
#4
Fariba M Assadi-Porter, Hannah Reiland, Martina Sabatini, Leonardo Lorenzini, Vittoria Carnicelli, Micheal Rogowski, Ebru S Selen Alpergin, Marco Tonelli, Sandra Ghelardoni, Alessandro Saba, Riccardo Zucchi, Grazia Chiellini
Obesity is a complex disease associated with environmental and genetic factors. 3-Iodothyronamine (T1AM) has revealed great potential as an effective weight loss drug. We used metabolomics and associated transcriptional gene and protein expression analysis to investigate the tissue specific metabolic reprogramming effects of subchronic T1AM treatment at two pharmacological daily doses (10 and 25 mg/kg) on targeted metabolic pathways. Multi-analytical results indicated that T1AM at 25 mg/kg can act as a novel master regulator of both glucose and lipid metabolism in mice through sirtuin-mediated pathways...
May 22, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29786565/modelling-non-alcoholic-fatty-liver-disease-in-human-hepatocyte-like-cells
#5
Marcus J Lyall, Jessy Cartier, John P Thomson, Kate Cameron, Jose Meseguer-Ripolles, Eoghan O'Duibhir, Dagmara Szkolnicka, Baltasar Lucendo Villarin, Yu Wang, Giovanny Rodriguez Blanco, Warwick B Dunn, Richard R Meehan, David C Hay, Amanda J Drake
Non-alcoholic fatty liver disease (NAFLD) is the most common cause of liver disease in developed countries. An in vitro NAFLD model would permit mechanistic studies and enable high-throughput therapeutic screening. While hepatic cancer-derived cell lines are a convenient, renewable resource, their genomic, epigenomic and functional alterations mean their utility in NAFLD modelling is unclear. Additionally, the epigenetic mark 5-hydroxymethylcytosine (5hmC), a cell lineage identifier, is rapidly lost during cell culture, alongside expression of the Ten-eleven-translocation ( TET ) methylcytosine dioxygenase enzymes, restricting meaningful epigenetic analysis...
July 5, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/29785738/mass-spectrometry-for-characterization-of-homologous-piperidine-alkaloids-and-their-activity-as-acetylcholinesterase-inhibitors
#6
Thamires R Freitas, Amanda Danuello, Claudio Viegas Júnior, Vanderlan S Bolzani, Marcos Pivatto
RATIONALE: Piperidine alkaloids from Senna spectabilis constitute a rare class of natural products with several biological activities. However, the absence of chromophores makes their structural elucidation by conventional methods a great challenge. In this context, mass spectrometry emerges as a powerful tool for metabolomics studies. METHODS: The piperidine alkaloids (-)-cassine and (-)-spectaline and the semisynthetic derivatives (-)-3-O-acetylcassine and (-)-3-O-acetylspectaline were investigated by electrospray ionization tandem mass spectrometry (ESI-MS/MS) in the positive mode and electron ionization mass spectrometry (EI-MS)...
May 22, 2018: Rapid Communications in Mass Spectrometry: RCM
https://www.readbyqxmd.com/read/29785207/promiscuous-activities-of-heterologous-enzymes-lead-to-unintended-metabolic-rerouting-in-saccharomyces-cerevisiae-engineered-to-assimilate-various-sugars-from-renewable-biomass
#7
Eun Ju Yun, Eun Joong Oh, Jing-Jing Liu, Sora Yu, Dong Hyun Kim, Suryang Kwak, Kyoung Heon Kim, Yong-Su Jin
Background: Understanding the global metabolic network, significantly perturbed upon promiscuous activities of foreign enzymes and different carbon sources, is crucial for systematic optimization of metabolic engineering of yeast Saccharomyces cerevisiae . Here, we studied the effects of promiscuous activities of overexpressed enzymes encoded by foreign genes on rerouting of metabolic fluxes of an engineered yeast capable of assimilating sugars from renewable biomass by profiling intracellular and extracellular metabolites...
2018: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/29785073/scale-free-networks-in-metabolomics
#8
Hema Sekhar Reddy Rajula, Matteo Mauri, Vassilios Fanos
Metabolomics is an expanding discipline in biology. It is the process of portraying the phenotype of a cell, tissue or species organism using a comprehensive set of metabolites. Therefore, it is of interest to understand complex systems such as metabolomics using a scale-free topology. Genetic networks and the World Wide Web (WWW) are described as networks with complex topology. Several large networks have vertex connectivity that goes beyond a scale-free power-law distribution. It is observed that (a) networks expand constantly by the addition of recent vertices, and (b) recent vertices attach preferentially to sites that are already well connected...
2018: Bioinformation
https://www.readbyqxmd.com/read/29784957/metabolic-reprogramming-in-leaf-lettuce-grown-under-different-light-quality-and-intensity-conditions-using-narrow-band-leds
#9
Kazuyoshi Kitazaki, Atsushi Fukushima, Ryo Nakabayashi, Yozo Okazaki, Makoto Kobayashi, Tetsuya Mori, Tomoko Nishizawa, Sebastian Reyes-Chin-Wo, Richard W Michelmore, Kazuki Saito, Kazuhiro Shoji, Miyako Kusano
Light-emitting diodes (LEDs) are an artificial light source used in closed-type plant factories and provide a promising solution for a year-round supply of green leafy vegetables, such as lettuce (Lactuca sativa L.). Obtaining high-quality seedlings using controlled irradiation from LEDs is critical, as the seedling health affects the growth and yield of leaf lettuce after transplantation. Because key molecular pathways underlying plant responses to a specific light quality and intensity remain poorly characterised, we used a multi-omics-based approach to evaluate the metabolic and transcriptional reprogramming of leaf lettuce seedlings grown under narrow-band LED lighting...
May 21, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29784955/integration-of-large-scale-data-for-extraction-of-integrated-arabidopsis-root-cell-type-specific-models
#10
Michael Scheunemann, Siobhan M Brady, Zoran Nikoloski
Plant organs consist of multiple cell types that do not operate in isolation, but communicate with each other to maintain proper functions. Here, we extract models specific to three developmental stages of eight root cell types or tissue layers in Arabidopsis thaliana based on a state-of-the-art constraint-based modeling approach with all publicly available transcriptomics and metabolomics data from this system to date. We integrate these models into a multi-cell root model which we investigate with respect to network structure, distribution of fluxes, and concordance to transcriptomics and proteomics data...
May 21, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29784925/acrylamide-acute-neurotoxicity-in-adult-zebrafish
#11
Melissa Faria, Tamar Ziv, Cristian Gómez-Canela, Shani Ben-Lulu, Eva Prats, Karen Adriana Novoa-Luna, Arie Admon, Benjamin Piña, Romà Tauler, Leobardo Manuel Gómez-Oliván, Demetrio Raldúa
Acute exposure to acrylamide (ACR), a type-2 alkene, may lead to a ataxia, skeletal muscles weakness and numbness of the extremities in human and laboratory animals. In the present manuscript, ACR acute neurotoxicity has been characterized in adult zebrafish, a vertebrate model increasingly used in human neuropharmacology and toxicology research. At behavioral level, ACR-treated animals exhibited "depression-like" phenotype comorbid with anxiety behavior. At transcriptional level, ACR induced down-regulation of regeneration-associated genes and up-regulation of oligodendrocytes and reactive astrocytes markers, altering also the expression of genes involved in the presynaptic vesicle cycling...
May 21, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29784908/integration-of-multi-omics-data-and-deep-phenotyping-enables-prediction-of-cytokine-responses
#12
Olivier B Bakker, Raul Aguirre-Gamboa, Serena Sanna, Marije Oosting, Sanne P Smeekens, Martin Jaeger, Maria Zorro, Urmo Võsa, Sebo Withoff, Romana T Netea-Maier, Hans J P M Koenen, Irma Joosten, Ramnik J Xavier, Lude Franke, Leo A B Joosten, Vinod Kumar, Cisca Wijmenga, Mihai G Netea, Yang Li
The immune response to pathogens varies substantially among people. Whereas both genetic and nongenetic factors contribute to interperson variation, their relative contributions and potential predictive power have remained largely unknown. By systematically correlating host factors in 534 healthy volunteers, including baseline immunological parameters and molecular profiles (genome, metabolome and gut microbiome), with cytokine production after stimulation with 20 pathogens, we identified distinct patterns of co-regulation...
May 21, 2018: Nature Immunology
https://www.readbyqxmd.com/read/29784392/simultaneous-detection-of-multiple-inherited-metabolic-diseases-using-gc-ms-urinary-metabolomics-by-chemometrics-multi-class-classification-strategies
#13
Qin Yang, Lu Xu, Li-Juan Tang, Jiang-Tao Yang, Ben-Qing Wu, Nan Chen, Jian-Hui Jiang, Ru-Qin Yu
Metabonomics has been widely used in disease diagnosis and clinically practical methods often require the detection of multi-class bio-samples. In this work, multi-class classification methods were investigated to simultaneously discriminate among 6 inherited metabolic diseases (IMDs) and the normal instances using gas chromatography-mass spectrometry (GC-MS) of urine samples. Two common multi-class classification strategies, one-against-all (OAA) and one-against-one (OAO) were compared and enhanced using a novel ensemble classification strategy (ECS), which developed a set of sequential sub-classifiers by fusion of OAA and OAO and made the final classification decisions using softmax function...
August 15, 2018: Talanta
https://www.readbyqxmd.com/read/29784310/effects-of-fermented-milk-treatment-on-microbial-population-and-metabolomic-outcomes-in-a-three-stage-semi-continuous-culture-system
#14
Kwang Hyun Cha, Eun Ha Lee, Hyo Shin Yoon, Jae Ho Lee, Joo Yun Kim, Kyungsu Kang, Jin-Soo Park, Jong Beom Jin, GwangPyo Ko, Cheol-Ho Pan
We investigated the impact of a fermented milk product on gut microbiota and their metabolism in 3 different conditions of the colon with a systemic viewpoint. An in vitro semi-continuous anaerobic cultivation was used to assess the colon compartment-specific influence of fermented milk, followed by a multiomics approach combining 16S rDNA amplicon sequencing and nuclear magnetic resonance (NMR) spectroscopy. The microbiome profiling and metabolomic features were significantly different across three colon compartments and after fermented milk treatment...
October 15, 2018: Food Chemistry
https://www.readbyqxmd.com/read/29783758/investigation-of-daphnia-magna-sub-lethal-exposure-to-organophosphate-esters-in-the-presence-of-dissolved-organic-matter-using-%C3%A2-h-nmr-based-metabolomics
#15
Vera Kovacevic, André J Simpson, Myrna J Simpson
Organophosphate esters (OPEs) are frequently detected in aquatic environments. Hydrophobic OPEs with high octanol-water partition coefficients (Log KOW ) will likely sorb to dissolved organic matter (DOM) and consequently alter OPE bioavailability and sub-lethal toxicity. ¹H nuclear magnetic resonance (NMR)-based metabolomics was used to evaluate how DOM (5 mg organic carbon/L) alters the metabolic response of Daphnia magna exposed to sub-lethal concentrations of three individual OPEs with varying hydrophobicity...
May 19, 2018: Metabolites
https://www.readbyqxmd.com/read/29783739/sterol-composition-of-clinically-relevant-mucorales-and-changes-resulting-from-posaconazole-treatment
#16
Christoph Müller, Thomas Neugebauer, Patrizia Zill, Cornelia Lass-Flörl, Franz Bracher, Ulrike Binder
Mucorales are fungi with increasing importance in the clinics. Infections take a rapidly progressive course resulting in high mortality rates. The ergosterol biosynthesis pathway and sterol composition are of interest, since they are targeted by currently applied antifungal drugs. Nevertheless, Mucorales often exhibit resistance to these drugs, resulting in therapeutic failure. Here, sterol patterns of six clinically relevant Mucorales ( Lichtheimia corymbifera , Lichtheimia ramosa , Mucor circinelloides , Rhizomucor pusillus , Rhizopus arrhizus , and Rhizopus microsporus ) were analysed in a targeted metabolomics fashion after derivatization by gas chromatography-mass spectrometry...
May 19, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29783718/functional-genomics-approaches-to-studying-symbioses-between-legumes-and-nitrogen-fixing-rhizobia
#17
REVIEW
Martina Lardi, Gabriella Pessi
Biological nitrogen fixation gives legumes a pronounced growth advantage in nitrogen-deprived soils and is of considerable ecological and economic interest. In exchange for reduced atmospheric nitrogen, typically given to the plant in the form of amides or ureides, the legume provides nitrogen-fixing rhizobia with nutrients and highly specialised root structures called nodules. To elucidate the molecular basis underlying physiological adaptations on a genome-wide scale, functional genomics approaches, such as transcriptomics, proteomics, and metabolomics, have been used...
May 18, 2018: High-throughput
https://www.readbyqxmd.com/read/29783186/-1-h-nmr-and-uplc-ms-metabolomics-functional-tools-for-exploring-chemotypic-variation-in-sceletium-tortuosum-from-two-provinces-in-south-africa
#18
Jianping Zhao, Ikhlas A Khan, Sandra Combrinck, Maxleene Sandasi, Weiyang Chen, Alvaro M Viljoen
Sceletium tortuosum (Aizoaceae) is widely recognised for the treatment of stress, anxiety and depression, as well as for obsessive compulsive disorders. A comprehensive intraspecies chemotypic variation study, using samples harvested from two distinct regions of South Africa, was done using both proton nuclear magnetic resonance (1 H-NMR) spectroscopy of methanol extracts (N = 145) and ultra performance liquid chromatography-mass spectrometry (UPLC-MS) of acid/base extracts (N = 289). Chemometric analysis of the 1 H-NMR data indicated two main clusters that were region-specific (Northern Cape and Western Cape provinces)...
May 17, 2018: Phytochemistry
https://www.readbyqxmd.com/read/29783096/all-roads-lead-to-rome-towards-understanding-different-avenues-of-tolerance-to-huanglongbing-in-citrus-cultivars
#19
Nabil Killiny, Shelley E Jones, Yasser Nehela, Faraj Hijaz, Manjul Dutt, Frederick G Gmitter, Jude W Grosser
Citrus tolerance to huanglongbing could result from tolerance to the pathogen Candidatus Liberibacter asiaticus (CLas) and/or to its vector Diaphorina citri. Field observations and greenhouse-controlled studies showed that some citrus cultivars were more tolerant than others. However, the mechanism(s) behind the tolerance has not been determined yet. Using GC-MS, we investigated the volatile organic compounds (VOCs) and the non-volatile metabolite profiles of two tolerant citrus cultivars- Australian finger lime, 'LB8-9' Sugar Belle® mandarin hybrid, and a recently released mandarin hybrid 'Bingo'...
May 18, 2018: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/29782246/precision-medicine-and-radiogenomics-in-breast-cancer-new-approaches-toward-diagnosis-and-treatment
#20
Katja Pinker, Joanne Chin, Amy N Melsaether, Elizabeth A Morris, Linda Moy
Precision medicine is medicine optimized to the genotypic and phenotypic characteristics of an individual and, when present, his or her disease. It has a host of targets, including genes and their transcripts, proteins, and metabolites. Studying precision medicine involves a systems biology approach that integrates mathematical modeling and biology genomics, transcriptomics, proteomics, and metabolomics. Moreover, precision medicine must consider not only the relatively static genetic codes of individuals, but also the dynamic and heterogeneous genetic codes of cancers...
June 2018: Radiology
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