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https://www.readbyqxmd.com/read/28335577/gc-ms-metabolomic-analysis-to-reveal-the-metabolites-and-biological-pathways-involved-in-the-developmental-stages-and-tissue-response-of-panax-ginseng
#1
Jia Liu, Yang Liu, Yu Wang, Ann Abozeid, Yuan-Gang Zu, Xiao-Ning Zhang, Zhong-Hua Tang
Ginsenosides, the major compounds present in ginseng, are known to have numerous physiological and pharmacological effects. The physiological processes, enzymes and genes involved in ginsenoside synthesis in P. ginseng have been well characterized. However, relatively little information is known about the dynamic metabolic changes that occur during ginsenoside accumulation in ginseng. To explore this topic, we isolated metabolites from different tissues at different growth stages, and identified and characterized them by using gas chromatography coupled with mass spectrometry (GC-MS)...
March 21, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28335448/a-community-multi-omics-approach-towards-the-assessment-of-surface-water-quality-in-an-urban-river-system
#2
David J Beale, Avinash V Karpe, Warish Ahmed, Stephen Cook, Paul D Morrison, Christopher Staley, Michael J Sadowsky, Enzo A Palombo
A multi-omics approach was applied to an urban river system (the Brisbane River (BR), Queensland, Australia) in order to investigate surface water quality and characterize the bacterial population with respect to water contaminants. To do this, bacterial metagenomic amplicon-sequencing using Illumina next-generation sequencing (NGS) of the V5-V6 hypervariable regions of the 16S rRNA gene and untargeted community metabolomics using gas chromatography coupled with mass spectrometry (GC-MS) were utilized. The multi-omics data, in combination with fecal indicator bacteria (FIB) counts, trace metal concentrations (by inductively coupled plasma mass spectrometry (ICP-MS)) and in-situ water quality measurements collected from various locations along the BR were then used to assess the health of the river ecosystem...
March 14, 2017: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/28335386/revisiting-the-metabolism-and-bioactivation-of-ketoconazole-in-human-and-mouse-using-liquid-chromatography-mass-spectrometry-based-metabolomics
#3
Ju-Hyun Kim, Won-Gu Choi, Sangkyu Lee, Hye Suk Lee
Although ketoconazole (KCZ) has been used worldwide for 30 years, its metabolic characteristics are poorly described. Moreover, the hepatotoxicity of KCZ limits its therapeutic use. In this study, we used liquid chromatography-mass spectrometry-based metabolomics to evaluate the metabolic profile of KCZ in mouse and human and identify the mechanisms underlying its hepatotoxicity. A total of 28 metabolites of KCZ, 11 of which were novel, were identified in this study. Newly identified metabolites were classified into three categories according to the metabolic positions of a piperazine ring, imidazole ring, and N-acetyl moiety...
March 13, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28335380/vitamin-e-nicotinate
#4
REVIEW
Kimbell R Duncan, Yuichiro J Suzuki
Vitamin E refers to a family of compounds that function as lipid-soluble antioxidants capable of preventing lipid peroxidation. Naturally occurring forms of vitamin E include tocopherols and tocotrienols. Vitamin E in dietary supplements and fortified foods is often an esterified form of α-tocopherol, the most common esters being acetate and succinate. The vitamin E esters are hydrolyzed and converted into free α-tocopherol prior to absorption in the intestinal tract. Because its functions are relevant to many chronic diseases, vitamin E has been extensively studied in respect to a variety of diseases as well as cosmetic applications...
March 13, 2017: Antioxidants (Basel, Switzerland)
https://www.readbyqxmd.com/read/28335378/bioavailability-of-microencapsulated-iron-from-fortified-bread-assessed-using-piglet-model
#5
Malgorzata A Bryszewska, Luca Laghi, Augusta Zannoni, Andrea Gianotti, Francesca Barone, Danielle L Taneyo Saa, Maria L Bacci, Domenico Ventrella, Monica Forni
The aim of this study was to investigate the influence of oral iron supplementation, in the form of fortified breads, on the growth performance, health, iron status parameters, and fecal metabolome of anemic piglets. A study was conducted on 24 hybrid (Large White × Landrace × Duroc) piglets. From day 44, the post-natal 12 piglets were supplemented with 100 g of one of two experimental breads, each fortified with 21 mg of ferrous sulphate, either encapsulated or not. After one week of oral supplementation, hematological parameters (hematocrit value, hemoglobin, and red blood cells) showed statistically significant differences (p ≤ 0...
March 13, 2017: Nutrients
https://www.readbyqxmd.com/read/28334329/metabolomics-of-pichia-pastoris-impact-of-buffering-conditions-on-the-kinetics-and-nature-of-metabolite-loss-during-quenching
#6
Matthias Mattanovich, Hannes Rußmayer, Theresa Scharl-Hirsch, Verena Puxbaum, Jonas Burgard, Diethard Mattanovich, Stephan Hann
Mass spectrometry based metabolomic profiling is a powerful strategy to quantify the concentrations of numerous primary metabolites in parallel. To avoid distortion of metabolite concentrations, quenching is applied to stop the cellular metabolism instantly. For yeasts, cold methanol quenching is accepted to be the most suitable method to stop metabolism, while keeping the cells intact for separation from the supernatant. During this treatment, metabolite loss may occur while the cells are suspended in the quenching solution...
March 15, 2017: FEMS Yeast Research
https://www.readbyqxmd.com/read/28334295/metccs-predictor-a-web-server-for-predicting-collision-cross-section-values-of-metabolites-in-ion-mobility-mass-spectrometry-based-metabolomics
#7
Zhiwei Zhou, Xin Xiong, Zheng-Jiang Zhu
Summary: In metabolomics, rigorous structural identification of metabolites presents a challenge for bioinformatics. The use of collision cross-section (CCS) values of metabolites derived from ion mobility-mass spectrometry effectively increases the confidence of metabolite identification, but this technique suffers from the limit number of available CCS values. Currently, there is no software available for rapidly generating the metabolites' CCS values. Here, we developed the first web server, namely, MetCCS Predictor, for predicting CCS values...
March 11, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28333921/bioenergetics-based-modeling-of-plasmodium-falciparum-metabolism-reveals-its-essential-genes-nutritional-requirements-and-thermodynamic-bottlenecks
#8
Anush Chiappino-Pepe, Stepan Tymoshenko, Meriç Ataman, Dominique Soldati-Favre, Vassily Hatzimanikatis
Novel antimalarial therapies are urgently needed for the fight against drug-resistant parasites. The metabolism of malaria parasites in infected cells is an attractive source of drug targets but is rather complex. Computational methods can handle this complexity and allow integrative analyses of cell metabolism. In this study, we present a genome-scale metabolic model (iPfa) of the deadliest malaria parasite, Plasmodium falciparum, and its thermodynamics-based flux analysis (TFA). Using previous absolute concentration data of the intraerythrocytic parasite, we applied TFA to iPfa and predicted up to 63 essential genes and 26 essential pairs of genes...
March 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28333226/exploring-the-human-microbiome-from-multiple-perspectives-factors-altering-its-composition-and-function
#9
David Rojo, Celia Méndez-García, Beata Anna Raczkowska, Rafael Bargiela, Andrés Moya, Manuel Ferrer, Coral Barbas
Our microbiota presents peculiarities and characteristics that may be altered by multiple factors. The degree and consequences of these alterations depend on the nature, strength and duration of the perturbations as well as the structure and stability of each microbiota. The aim of this review is to sketch a very broad picture of the factors commonly influencing different body sites, and which have been associated with alterations in the human microbiota in terms of composition and function. To do so, first, a graphical representation of bacterial, fungal and archaeal genera reveals possible associations among genera affected by different factors...
February 25, 2017: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/28332841/effects-of-diet-quality-and-psychosocial-stress-on-the-metabolic-profiles-of-mice
#10
Tatsuhiko Goto, Shozo Tomonaga, Atsushi Toyoda
There has been an increasing interest in relationship between stress and diet. To address this relationship, we evaluated an animal model of depression: male C57BL/6J mice subjected to subchronic mild social defeat stress (sCSDS) for 10 consecutive days using male ICR mice under two different calorie-adjusted diets conditions-non-purified (MF) and semi-purified (AIN) diets made from natural and chemical ingredients mainly, respectively. Our previous study indicates diet quality and purity affect stress susceptibility in sCSDS mice...
March 23, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28332056/allelopathic-interference-of-alfalfa-medicago-sativa-l-genotypes-to-annual-ryegrass-lolium-rigidum
#11
Hasan Muhammad Zubair, James E Pratley, G A Sandral, A Humphries
Alfalfa (Medicago sativa L.) genotypes at varying densities were investigated for allelopathic impact using annual ryegrass (Lolium rigidum) as the target species in a laboratory bioassay. Three densities (15, 30, and 50 seedlings/beaker) and 40 alfalfa genotypes were evaluated by the equal compartment agar method (ECAM). Alfalfa genotypes displayed a range of allelopathic interference in ryegrass seedlings, reducing root length from 5 to 65%. The growth of ryegrass decreased in response to increasing density of alfalfa seedlings...
March 22, 2017: Journal of Plant Research
https://www.readbyqxmd.com/read/28330782/preparative-two-dimensional-separations-involving-liquid-liquid-chromatography
#12
Léa Marlot, Karine Faure
The increasing performances of analytical techniques, especially two-dimensional liquid chromatography hyphenated with highly sensitive detectors, allow discovery of new targeted compounds in highly complex samples, whether biomarkers in environmental effluents, natural metabolomes in natural products or unknown impurities in synthetic chemical process. While structural identification can usually be achieved through mass spectrometry and databases, it can be useful to confirm the potential structure via NMR analysis and/or to obtain standard reference material for quantitative purposes, incentive for the production of μg to mg of new target compounds...
March 18, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/28330772/erratum-to-cessation-of-biomechanical-stretch-model-of-c2c12-cells-modelsmyocyte-atrophy-and-anaplerotic-changes-in-metabolism-usingnon-targeted-metabolomics-analysisamro-int-j-biochem-cell-biol-2016-80-92
#13
Amro Ilaiwy, Megan T Quintana, James R Bain, Michael J Muehlbauer, David I Brown, William E Stansfield, Monte S Willis
No abstract text is available yet for this article.
March 19, 2017: International Journal of Biochemistry & Cell Biology
https://www.readbyqxmd.com/read/28330265/isolation-and-characterization-of-plant-synergistic-bacteria-capable-of-degrading-xenobiotics-from-oil-spillage-sites
#14
Indranil De, Sarika Gupta
Oil spillage sites primarily contain various types of hydrocarbons, such as linear chain, polycyclic, and aromatic compounds, posing several detrimental effects on plants. Results from our previous study showed an alteration of various metabolomic parameters, indirectly resulting in an observable decline of growth in the mung seedlings upon incubation with phenol, toluene, xylene, and hexane. This study evaluates the role of these compounds upon plant growth and focusses to mitigate the effect of the same, using some isolated plant synergistic bacteria...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28329151/caloric-restriction-and-rapamycin-differentially-alter-energy-metabolism-in-yeast
#15
Kyung-Mi Choi, Seok-Jin Hong, Jan M van Deursen, Sooah Kim, Kyoung Heon Kim, Cheol-Koo Lee
Rapamycin (RM), a drug that inhibits the mechanistic target of rapamycin (mTOR) pathway and responds to nutrient availability, seemingly mimics the effects of caloric restriction (CR) on healthy life span. However, the extent of the mechanistic overlap between RM and CR remains incompletely understood. Here, we compared the impact of CR and RM on cellular metabolic status. Both regimens maintained intracellular ATP through the chronological aging process and showed enhanced mitochondrial capacity. Comparative transcriptome analysis showed that CR had a stronger impact on global gene expression than RM...
March 8, 2017: Journals of Gerontology. Series A, Biological Sciences and Medical Sciences
https://www.readbyqxmd.com/read/28328083/oral-iron-supplementation-potential-implications-for-the-gut-microbiome-and-metabolome-in-patients-with-ckd
#16
Guus A M Kortman, Dorien Reijnders, Dorine W Swinkels
Patients with chronic kidney disease (CKD) and loss of kidney function are at increased risk for morbidity and mortality. The risks of CKD are attributed to "uremia," an increased concentration of uremic retention solutes (toxins) in the plasma. Recently, a colo-renal axis became clearly apparent and uremia has been associated with an altered gut microbiome composition and metabolism. There is a high prevalence of anemia in patients with CKD, for which patients are often treated with oral or intravenous iron...
March 22, 2017: Hemodialysis International
https://www.readbyqxmd.com/read/28328075/role-of-amino-acids-in-rheumatoid-arthritis-studied-by-metabolomics
#17
Min He, Amy C Harms, Eduard van Wijk, Mei Wang, Ruud Berger, Slavik Koval, Thomas Hankemeier, Jan van der Greef
BACKGROUND: Rheumatoid arthritis (RA) is a complex, chronic autoimmune disease characterized by various inflammatory symptoms, including joint swelling, joint pain, and both structural and functional joint damage. The most commonly used animal model for studying RA is mice with collagen-induced arthritis (CIA); the wide use of this model is due primarily to many similarities with RA in human patients. Metabolomics is used increasingly in biological studies for diagnosing disease and for predicting and evaluating drug interventions, as a large number of disease-associated metabolites can be analyzed and interpreted from a biological perspective...
March 22, 2017: International Journal of Rheumatic Diseases
https://www.readbyqxmd.com/read/28327092/metax-a-flexible-and-comprehensive-software-for-processing-metabolomics-data
#18
Bo Wen, Zhanlong Mei, Chunwei Zeng, Siqi Liu
BACKGROUND: Non-targeted metabolomics based on mass spectrometry enables high-throughput profiling of the metabolites in a biological sample. The large amount of data generated from mass spectrometry requires intensive computational processing for annotation of mass spectra and identification of metabolites. Computational analysis tools that are fully integrated with multiple functions and are easily operated by users who lack extensive knowledge in programing are needed in this research field...
March 21, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28327077/regional-muscle-tissue-saturation-is-an-indicator-of-global-inadequate-circulation-during-cardiopulmonary-bypass-a-randomized-porcine-study-using-muscle-intestinal-and-brain-tissue-metabolomics
#19
Sisse Anette Thomassen, Benedict Kjærgaard, Preben Sørensen, Jan Jesper Andreasen, Anders Larsson, Bodil Steen Rasmussen
BACKGROUND: Muscle tissue saturation (StO2) measured with near-infrared spectroscopy has generally been considered a measurement of the tissue microcirculatory condition. However, we hypothesized that StO2 could be more regarded as a fast and reliable measure of global than of regional circulatory adequacy and tested this with muscle, intestinal and brain metabolomics at normal and two levels of low cardiopulmonary bypass blood flow rates in a porcine model. METHODS: Twelve 80 kg pigs were connected to normothermic cardiopulmonary bypass with a blood flow of 60 mL/kg/min for one hour, reduced randomly to 47...
April 2017: Perfusion
https://www.readbyqxmd.com/read/28325553/metabolomics-through-the-lens-of-precision-cardiovascular-medicine
#20
REVIEW
Sin Man Lam, Yuan Wang, Bowen Li, Jie Du, Guanghou Shui
Metabolomics, which targets at the extensive characterization and quantitation of global metabolites from both endogenous and exogenous sources, has emerged as a novel technological avenue to advance the field of precision medicine principally driven by genomics-oriented approaches. In particular, metabolomics has revealed the cardinal roles that the environment exerts in driving the progression of major diseases threatening public health. Herein, the existent and potential applications of metabolomics in two key areas of precision cardiovascular medicine will be critically discussed: 1) the use of metabolomics in unveiling novel disease biomarkers and pathological pathways; 2) the contribution of metabolomics in cardiovascular drug development...
March 8, 2017: Journal of Genetics and Genomics, Yi Chuan Xue Bao
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