Integrative Molecular Phenotyping
INTEGRATIVE MOLECULAR
PHENOTYPING
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY

PubMed

PubMed
NCBI: db=pubmed; Term=metabolomics
Updated: 3 min 53 sec ago

[Isolation and purification of seven catechin compounds from fresh tea leaves by semi-preparative liquid chromatography].

Sat, 27/01/2018 - 14:53
Related Articles [Isolation and purification of seven catechin compounds from fresh tea leaves by semi-preparative liquid chromatography]. Se Pu. 2017 Nov 08;35(11):1192-1197 Authors: Gong Z, Chen S, Gao J, Li M, Wang X, Lin J, Yu X Abstract An effective and simple method was established to simultaneously purify seven tea catechins (gallocatechin (GC), epigallocatechin (EGC), catechin (C), epigallocatechin-3-O-gallate (EGCG), epicatechin (EC), epigallocatechin-3-O-(3-O-methyl)-gallate (EGCG3"Me) and epicatechin-3-O-gallate (ECG)) from fresh tea leaves by semi-preparative high performance liquid chromatography (HPLC). Fresh leaves of Tieguanyin tea were successively extracted with methanol and chloroform. Then crude catechins were precipitated from the aqueous fraction of chloroform extraction by adding lead subacetate. Crude catechins were used for the isolation of the seven target catechin compounds by semi-preparative HPLC. Methanol-water and acetonitrile-water were sequentially used as mobile phases. After two rounds of semi-preparative HPLC, all target compounds were achieved with high purities (>90%). The proposed method was tested on two additional tea cultivars and showed similar results. This method demonstrated a simple and efficient strategy based on solvent extraction, ion precipitation and semi-preparative HPLC for the preparation of multiple catechins from tea leaves. PMID: 29372766 [PubMed - in process]

Exploring traditional aus-type rice for metabolites conferring drought tolerance.

Sat, 27/01/2018 - 14:53
Related Articles Exploring traditional aus-type rice for metabolites conferring drought tolerance. Rice (N Y). 2018 Jan 25;11(1):9 Authors: Casartelli A, Riewe D, Hubberten HM, Altmann T, Hoefgen R, Heuer S Abstract BACKGROUND: Traditional varieties and landraces belonging to the aus-type group of rice (Oryza sativa L.) are known to be highly tolerant to environmental stresses, such as drought and heat, and are therefore recognized as a valuable genetic resource for crop improvement. Using two aus-type (Dular, N22) and two drought intolerant irrigated varieties (IR64, IR74) an untargeted metabolomics analysis was conducted to identify drought-responsive metabolites associated with tolerance. RESULTS: The superior drought tolerance of Dular and N22 compared with the irrigated varieties was confirmed by phenotyping plants grown to maturity after imposing severe drought stress in a dry-down treatment. Dular and N22 did not show a significant reduction in grain yield compared to well-watered control plants, whereas the intolerant varieties showed a significant reduction in both, total spikelet number and grain yield. The metabolomics analysis was conducted with shoot and root samples of plants at the tillering stage at the end of the dry-down treatment. The data revealed an overall higher accumulation of N-rich metabolites (amino acids and nucleotide-related metabolites allantoin and uridine) in shoots of the tolerant varieties. In roots, the aus-type varieties were characterised by a higher reduction of metabolites representative of glycolysis and the TCA cycle, such as malate, glyceric acid and glyceric acid-3-phosphate. On the other hand, the oligosaccharide raffinose showed a higher fold increase in both, shoots and roots of the sensitive genotypes. The data further showed that, for certain drought-responsive metabolites, differences between the contrasting rice varieties were already evident under well-watered control conditions. CONCLUSIONS: The drought tolerance-related metabolites identified in the aus-type varieties provide a valuable set of protective compounds and an entry point for assessing genetic diversity in the underlying pathways for developing drought tolerant rice and other crops. PMID: 29372429 [PubMed]

Metabolomics diagnostic approach to mustard airway diseases: a preliminary study.

Sat, 27/01/2018 - 14:53
Related Articles Metabolomics diagnostic approach to mustard airway diseases: a preliminary study. Iran J Basic Med Sci. 2018 Jan;21(1):59-69 Authors: Ghoochani BFNM, Aliannejad R, Oskouie AA, Rezaei-Tavirani M, Kalantari S, Naseri MT, Baghban AA, Parastar H, Aliakbarzadeh G Abstract Objectives: This study aims to evaluate combined proton nuclear magnetic resonance (1H NMR) spectroscopy and gas chromatography-mass spectrometry (GC-MS) metabolic profiling approaches, for discriminating between mustard airway diseases (MADs) and healthy controls and for providing biochemical information on this disease. Materials and Methods: In the present study, analysis of serum samples collected from 17 MAD subjects and 12 healthy controls was performed using NMR. Of these subjects, 14 (8 patients and 6 controls) were analyzed by GC-MS. Then, their spectral profiles were subjected to principal component analysis (PCA) and orthogonal partial least squares regression discriminant analysis (OPLS-DA). Results: A panel of twenty eight metabolite biomarkers was generated for MADs, sixteen NMR-derived metabolites (3-methyl-2-oxovaleric acid, 3-hydroxyisobutyrate, lactic acid, lysine, glutamic acid, proline, hydroxyproline, dimethylamine, creatine, citrulline, choline, acetic acid, acetoacetate, cholesterol, alanine, and lipid (mainly VLDL)) and twelve GC-MS-derived metabolites (threonine, phenylalanine, citric acid, myristic acid, pentadecanoic acid, tyrosine, arachidonic acid, lactic acid, propionic acid, 3-hydroxybutyric acid, linoleic acid, and oleic acid). This composite biomarker panel could effectively discriminate MAD subjects from healthy controls, achieving an area under receiver operating characteristic curve (AUC) values of 1 and 0.79 for NMR and GC-MS, respectively. Conclusion: In the present study, a robust panel of twenty-eight biomarkers for detecting MADs was established. This panel is involved in three metabolic pathways including aminoacyl-tRNA biosynthesis, arginine, and proline metabolism, and synthesis and degradation of ketone bodies, and could differentiate MAD subjects from healthy controls with a higher accuracy. PMID: 29372038 [PubMed]

Spermidine in health and disease.

Sat, 27/01/2018 - 14:53
Related Articles Spermidine in health and disease. Science. 2018 Jan 26;359(6374): Authors: Madeo F, Eisenberg T, Pietrocola F, Kroemer G Abstract Interventions that delay aging and protect from age-associated disease are slowly approaching clinical implementation. Such interventions include caloric restriction mimetics, which are defined as agents that mimic the beneficial effects of dietary restriction while limiting its detrimental effects. One such agent, the natural polyamine spermidine, has prominent cardioprotective and neuroprotective effects and stimulates anticancer immunosurveillance in rodent models. Moreover, dietary polyamine uptake correlates with reduced cardiovascular and cancer-related mortality in human epidemiological studies. Spermidine preserves mitochondrial function, exhibits anti-inflammatory properties, and prevents stem cell senescence. Mechanistically, it shares the molecular pathways engaged by other caloric restriction mimetics: It induces protein deacetylation and depends on functional autophagy. Because spermidine is already present in daily human nutrition, clinical trials aiming at increasing the uptake of this polyamine appear feasible. PMID: 29371440 [PubMed - in process]

Multi-omics integration reveals the landscape of pro-metastasis metabolism in hepatocellular carcinoma.

Sat, 27/01/2018 - 14:53
Related Articles Multi-omics integration reveals the landscape of pro-metastasis metabolism in hepatocellular carcinoma. Mol Cell Proteomics. 2018 Jan 25;: Authors: Li Y, Zhuang H, Zhang X, Li Y, Liu Y, Yi X, Qin G, Wei W, Chen R Abstract The systematic investigation of gene mutation and expression is important to discover novel biomarkers and therapeutic targets in cancers. Here, we integrated genomics, transcriptomics, proteomics, and metabolomics to analyze three hepatocellular carcinoma (HCC) cell lines with differential metastatic potentials. The results revealed the profile of the pro-metastasis metabolism potentially associated with HCC metastasis. The multi-omic analysis identified 12 genes with variations at multiple levels from three metabolic pathways, including glycolysis, starch and sucrose metabolism, and glutathione metabolism. Furthermore, UDP-glucose pyrophosphorylase 2 (UGP2), was observed to be persistently up-regulated with increased metastatic potential. UGP2 overexpression promoted cell migration and invasion, and enhanced glycogenesis in vitro. The role of UGP2 in metastasis was further confirmed using a tumor xenograft mouse model. Taken together, the compendium of multi-omic data provides valuable insights to understand the roles of shifted cellular metabolism in HCC metastasis. PMID: 29371291 [PubMed - as supplied by publisher]

New insights into the catalytic mechanism of human glycine N-acyltransferase.

Sat, 27/01/2018 - 14:53
Related Articles New insights into the catalytic mechanism of human glycine N-acyltransferase. J Biochem Mol Toxicol. 2017 Nov;31(11): Authors: van der Sluis R, Ungerer V, Nortje C, A van Dijk A, Erasmus E Abstract Even though the glycine conjugation pathway was one of the first metabolic pathways to be discovered, this pathway remains very poorly characterized. The bi-substrate kinetic parameters of a recombinant human glycine N-acyltransferase (GLYAT, E.C. 2.3.1.13) were determined using the traditional colorimetric method and a newly developed HPLC-ESI-MS/MS method. Previous studies analyzing the kinetic parameters of GLYAT, indicated a random Bi-Bi and/or ping-pong mechanism. In this study, the hippuric acid concentrations produced by the GLYAT enzyme reaction were analyzed using the allosteric sigmoidal enzyme kinetic module. Analyses of the initial rate (v) against substrate concentration plots, produced a sigmoidal curve (substrate activation) when the benzoyl-CoA concentrations was kept constant, whereas the plot with glycine concentrations kept constant, passed through a maximum (substrate inhibition). Thus, human GLYAT exhibits mechanistic kinetic cooperativity as described by the Ferdinand enzyme mechanism rather than the previously assumed Michaelis-Menten reaction mechanism. PMID: 28759163 [PubMed - indexed for MEDLINE]

Dioxygenase-encoding AtDAO1 gene controls IAA oxidation and homeostasis in Arabidopsis.

Sat, 27/01/2018 - 14:53
Related Articles Dioxygenase-encoding AtDAO1 gene controls IAA oxidation and homeostasis in Arabidopsis. Proc Natl Acad Sci U S A. 2016 09 27;113(39):11016-21 Authors: Porco S, Pěnčík A, Rashed A, Voß U, Casanova-Sáez R, Bishopp A, Golebiowska A, Bhosale R, Swarup R, Swarup K, Peňáková P, Novák O, Staswick P, Hedden P, Phillips AL, Vissenberg K, Bennett MJ, Ljung K Abstract Auxin represents a key signal in plants, regulating almost every aspect of their growth and development. Major breakthroughs have been made dissecting the molecular basis of auxin transport, perception, and response. In contrast, how plants control the metabolism and homeostasis of the major form of auxin in plants, indole-3-acetic acid (IAA), remains unclear. In this paper, we initially describe the function of the Arabidopsis thaliana gene DIOXYGENASE FOR AUXIN OXIDATION 1 (AtDAO1). Transcriptional and translational reporter lines revealed that AtDAO1 encodes a highly root-expressed, cytoplasmically localized IAA oxidase. Stable isotope-labeled IAA feeding studies of loss and gain of function AtDAO1 lines showed that this oxidase represents the major regulator of auxin degradation to 2-oxoindole-3-acetic acid (oxIAA) in Arabidopsis Surprisingly, AtDAO1 loss and gain of function lines exhibited relatively subtle auxin-related phenotypes, such as altered root hair length. Metabolite profiling of mutant lines revealed that disrupting AtDAO1 regulation resulted in major changes in steady-state levels of oxIAA and IAA conjugates but not IAA. Hence, IAA conjugation and catabolism seem to regulate auxin levels in Arabidopsis in a highly redundant manner. We observed that transcripts of AtDOA1 IAA oxidase and GH3 IAA-conjugating enzymes are auxin-inducible, providing a molecular basis for their observed functional redundancy. We conclude that the AtDAO1 gene plays a key role regulating auxin homeostasis in Arabidopsis, acting in concert with GH3 genes, to maintain auxin concentration at optimal levels for plant growth and development. PMID: 27651491 [PubMed - indexed for MEDLINE]

Maternal and fetal genomes interplay through phosphoinositol 3-kinase(PI3K)-p110α signaling to modify placental resource allocation.

Sat, 27/01/2018 - 14:53
Related Articles Maternal and fetal genomes interplay through phosphoinositol 3-kinase(PI3K)-p110α signaling to modify placental resource allocation. Proc Natl Acad Sci U S A. 2016 10 04;113(40):11255-11260 Authors: Sferruzzi-Perri AN, López-Tello J, Fowden AL, Constancia M Abstract Pregnancy success and life-long health depend on a cooperative interaction between the mother and the fetus in the allocation of resources. As the site of materno-fetal nutrient transfer, the placenta is central to this interplay; however, the relative importance of the maternal versus fetal genotypes in modifying the allocation of resources to the fetus is unknown. Using genetic inactivation of the growth and metabolism regulator, Pik3ca (encoding PIK3CA also known as p110α, α/+), we examined the interplay between the maternal genome and the fetal genome on placental phenotype in litters of mixed genotype generated through reciprocal crosses of WT and α/+ mice. We demonstrate that placental growth and structure were impaired and associated with reduced growth of α/+ fetuses. Despite its defective development, the α/+ placenta adapted functionally to increase the supply of maternal glucose and amino acid to the fetus. The specific nature of these changes, however, depended on whether the mother was α/+ or WT and related to alterations in endocrine and metabolic profile induced by maternal p110α deficiency. Our findings thus show that the maternal genotype and environment programs placental growth and function and identify the placenta as critical in integrating both intrinsic and extrinsic signals governing materno-fetal resource allocation. PMID: 27621448 [PubMed - indexed for MEDLINE]

Untargeted saliva metabonomics study of breast cancer based on ultra performance liquid chromatography coupled to mass spectrometry with HILIC and RPLC separations.

Sat, 27/01/2018 - 14:53
Related Articles Untargeted saliva metabonomics study of breast cancer based on ultra performance liquid chromatography coupled to mass spectrometry with HILIC and RPLC separations. Talanta. 2016 Sep 01;158:351-60 Authors: Zhong L, Cheng F, Lu X, Duan Y, Wang X Abstract Breast cancer (BC) is not only the most frequently diagnosed cancer, but also the leading cause of cancer death among women worldwide. This study aimed to screen the potential salivary biomarkers for breast cancer diagnosis, staging, and biomarker discovery. For the first time, a UPLC-MS based method along with multivariate data analysis, was proposed for the global saliva metabonomics analysis and diagnosis of BC, which used both hydrophilic interaction chromatography (HILIC) and reversed-phase liquid chromatography (RPLC) separations and operated in both positive (ESI+) and negative (ESI-) ionization modes. On account of different polarities of endogenous metabolites, this method was established to overcome the boundedness of a single chromatographic approach. As a result, 18 potential metabolites for diagnosing BC were identified. A nonparametric Mann-Whitney U test, heat map, and the receiver operating characteristic (ROC) were exploited to analyze the data with the purpose of evaluating the predictive power of the 18 biomarkers. Significant differences (P<0.05) were disclosed in terms of the levels of the 18 potential biomarkers between BC patients and healthy controls (HC). Among the 18 biomarkers, three up-regulated metabolites, LysoPC (18:1), LysoPC (22:6) and MG (0:0/14:0/0:0) displayed the area under the curve (AUC) values of 0.920, 0.920 and 0.929, respectively, indicating the high accuracy of this method to predict BC. In this study, an integrated metabonomics analysis in human saliva for identifying potential biomarkers to diagnose and stage BC was successfully eastablished, which was non-invasive, reliable, low-cost, and simple. The HILIC was demonstrated to be essential for a comprehensive saliva metabonomics profiling as well as RPLC separation. This saliva metabonomics technique may provide new insight into the discovery and identification of diagnostic biomarkers for BC. PMID: 27343615 [PubMed - indexed for MEDLINE]

Unravelling the in vivo regulation and metabolic role of the alternative oxidase pathway in C3 species under photoinhibitory conditions.

Sat, 27/01/2018 - 14:53
Related Articles Unravelling the in vivo regulation and metabolic role of the alternative oxidase pathway in C3 species under photoinhibitory conditions. New Phytol. 2016 Oct;212(1):66-79 Authors: Florez-Sarasa I, Ribas-Carbo M, Del-Saz NF, Schwahn K, Nikoloski Z, Fernie AR, Flexas J Abstract The mitochondrial alternative oxidase pathway (AOP) has been suggested to act as a sink for excess reducing power generated in the chloroplast under high-light (HL) stress and thus may reduce photoinhibition. The aim of this study was to compare different species to investigate the in vivo regulation and role of AOP under HL stress. The in vivo activities of AOP (νalt ) and the cytochrome oxidase pathway, chlorophyll fluorescence, metabolite profiles, alternative oxidase (AOX) capacity and protein amount were determined in leaves of five C3 species under growth light and after HL treatment. Differences in respiration and metabolite levels were observed among species under growth light conditions. The HL response of νalt was highly species dependent, correlated with the AOP capacity and independent of AOX protein content. Nevertheless, significant correlations were observed between νalt , levels of key metabolites and photosynthetic parameters. The results show that the species-specific response of νalt is caused by the differential post-translational regulation of AOX. Significant correlations between respiration, metabolites and photosynthetic performance across species suggest that AOP may permit stress-related amino acid synthesis, whilst maintaining photosynthetic activity under HL stress. PMID: 27321208 [PubMed - indexed for MEDLINE]

Comparative metabolomic analysis reveals a reactive oxygen species-dominated dynamic model underlying chilling environment adaptation and tolerance in rice.

Sat, 27/01/2018 - 14:53
Related Articles Comparative metabolomic analysis reveals a reactive oxygen species-dominated dynamic model underlying chilling environment adaptation and tolerance in rice. New Phytol. 2016 Sep;211(4):1295-310 Authors: Zhang J, Luo W, Zhao Y, Xu Y, Song S, Chong K Abstract Cold, a major environmental stress for plants, has been studied intensively for decades. Its response system has been revealed, especially at the transcriptional level. The mechanisms underlying recovery growth and environmental adaptation, however, remain unknown. Taking advantage of a naturally existing system, two subspecies of Asian cultivated rice (Oryza sativa) with significant divergence in chilling tolerance, we analyzed representative japonica and indica varieties, Nipponbare and 93-11, using comparative metabolomic analysis at six time points covering chilling treatment and recovery. In total, 223 known metabolites were detected. During chilling treatment, significant biochemical changes were centered on antioxidation. During recovery, a wide-ranging chilling response was observed. Large-scale amino acid accumulation occurred, consistent with the appearance of chilling injury. At the mid-treatment stage, the accumulation of antioxidation-related compounds appeared earlier in Nipponbare than in 93-11, consistent with the higher reactive oxygen species (ROS) levels in japonica vs indica varieties. A significant contribution of ROS-mediated gene regulation, rather than the C-repeat binding factor/dehydration-responsive-element binding factor (CBF/DREB) regulon, to the more vigorous transcriptional stress response in Nipponbare was revealed by RNA-seq. Accordingly, during recovery, the induction of stress-tolerant-related metabolites was more active in the chilling-tolerant variety Nipponbare. Senescence-related compounds accumulated only in the chilling-sensitive variety 93-11. Our study uncovers the dynamic metabolic models underlying chilling response and recovery, and reveals a ROS-dominated rice adaptation mechanism to low-temperature environments. PMID: 27198693 [PubMed - indexed for MEDLINE]

Brain and blood metabolite signatures of pathology and progression in Alzheimer disease: A targeted metabolomics study.

Fri, 26/01/2018 - 14:14
Related Articles Brain and blood metabolite signatures of pathology and progression in Alzheimer disease: A targeted metabolomics study. PLoS Med. 2018 Jan;15(1):e1002482 Authors: Varma VR, Oommen AM, Varma S, Casanova R, An Y, Andrews RM, O'Brien R, Pletnikova O, Troncoso JC, Toledo J, Baillie R, Arnold M, Kastenmueller G, Nho K, Doraiswamy PM, Saykin AJ, Kaddurah-Daouk R, Legido-Quigley C, Thambisetty M Abstract BACKGROUND: The metabolic basis of Alzheimer disease (AD) is poorly understood, and the relationships between systemic abnormalities in metabolism and AD pathogenesis are unclear. Understanding how global perturbations in metabolism are related to severity of AD neuropathology and the eventual expression of AD symptoms in at-risk individuals is critical to developing effective disease-modifying treatments. In this study, we undertook parallel metabolomics analyses in both the brain and blood to identify systemic correlates of neuropathology and their associations with prodromal and preclinical measures of AD progression. METHODS AND FINDINGS: Quantitative and targeted metabolomics (Biocrates AbsoluteIDQ [identification and quantification] p180) assays were performed on brain tissue samples from the autopsy cohort of the Baltimore Longitudinal Study of Aging (BLSA) (N = 44, mean age = 81.33, % female = 36.36) from AD (N = 15), control (CN; N = 14), and "asymptomatic Alzheimer's disease" (ASYMAD, i.e., individuals with significant AD pathology but no cognitive impairment during life; N = 15) participants. Using machine-learning methods, we identified a panel of 26 metabolites from two main classes-sphingolipids and glycerophospholipids-that discriminated AD and CN samples with accuracy, sensitivity, and specificity of 83.33%, 86.67%, and 80%, respectively. We then assayed these 26 metabolites in serum samples from two well-characterized longitudinal cohorts representing prodromal (Alzheimer's Disease Neuroimaging Initiative [ADNI], N = 767, mean age = 75.19, % female = 42.63) and preclinical (BLSA) (N = 207, mean age = 78.68, % female = 42.63) AD, in which we tested their associations with magnetic resonance imaging (MRI) measures of AD-related brain atrophy, cerebrospinal fluid (CSF) biomarkers of AD pathology, risk of conversion to incident AD, and trajectories of cognitive performance. We developed an integrated blood and brain endophenotype score that summarized the relative importance of each metabolite to severity of AD pathology and disease progression (Endophenotype Association Score in Early Alzheimer's Disease [EASE-AD]). Finally, we mapped the main metabolite classes emerging from our analyses to key biological pathways implicated in AD pathogenesis. We found that distinct sphingolipid species including sphingomyelin (SM) with acyl residue sums C16:0, C18:1, and C16:1 (SM C16:0, SM C18:1, SM C16:1) and hydroxysphingomyelin with acyl residue sum C14:1 (SM (OH) C14:1) were consistently associated with severity of AD pathology at autopsy and AD progression across prodromal and preclinical stages. Higher log-transformed blood concentrations of all four sphingolipids in cognitively normal individuals were significantly associated with increased risk of future conversion to incident AD: SM C16:0 (hazard ratio [HR] = 4.430, 95% confidence interval [CI] = 1.703-11.520, p = 0.002), SM C16:1 (HR = 3.455, 95% CI = 1.516-7.873, p = 0.003), SM (OH) C14:1 (HR = 3.539, 95% CI = 1.373-9.122, p = 0.009), and SM C18:1 (HR = 2.255, 95% CI = 1.047-4.855, p = 0.038). The sphingolipid species identified map to several biologically relevant pathways implicated in AD, including tau phosphorylation, amyloid-β (Aβ) metabolism, calcium homeostasis, acetylcholine biosynthesis, and apoptosis. Our study has limitations: the relatively small number of brain tissue samples may have limited our power to detect significant associations, control for heterogeneity between groups, and replicate our findings in independent, autopsy-derived brain samples. CONCLUSIONS: We present a novel framework to identify biologically relevant brain and blood metabolites associated with disease pathology and progression during the prodromal and preclinical stages of AD. Our results show that perturbations in sphingolipid metabolism are consistently associated with endophenotypes across preclinical and prodromal AD, as well as with AD pathology at autopsy. Sphingolipids may be biologically relevant biomarkers for the early detection of AD, and correcting perturbations in sphingolipid metabolism may be a plausible and novel therapeutic strategy in AD. PMID: 29370177 [PubMed - in process]

Targeted metabolomic analysis of 33 amino acids and biogenic amines in human urine by ion-pairing HPLC-MS/MS: biomarkers for tacrolimus nephrotoxicity after renal transplantation.

Fri, 26/01/2018 - 14:14
Related Articles Targeted metabolomic analysis of 33 amino acids and biogenic amines in human urine by ion-pairing HPLC-MS/MS: biomarkers for tacrolimus nephrotoxicity after renal transplantation. Biomed Chromatogr. 2018 Jan 25;: Authors: Xia T, Fu S, Wang Q, Wen Y, Chan SA, Zhu S, Gao S, Tao X, Zhang F, Chen W Abstract BACKGROUND: Calcineurin inhibitors (CNIs) nephrotoxicity especially for the widely applicable tacrolimus has become a major concern in post-transplant immunosuppression. Multi-parametric amino acid metabolomics is instrumental for biomarker identification of tacrolimus (Tac) nephrotoxicity, for which specific quantitative methods is highlighted as a premise. METHODS: This article presented a targeted metabolomic assay to quantify 33 amino acids and biogenic amines in human urine by high performance liquid chromatography coupled with tandem mass spectrometry (HPLC-MS/MS). Chromatographic separation was carried out on an Agilent Zorbax SB-C18 column (3.0 mm×150 mm, 5 μm) with addition of an ion-pairing agent in the mobile phase, and MS/MS detection was achieved in both the positive and negative multiple reaction monitoring (MRM) mode. RESULTS: Good correlation coefficients (r2 >0.98) were obtained for most analytes. Intra- and inter- day precision, stability, carryover and incurred sample reanalysis met with the acceptance criteria of the FDA Guidance (2001). Analysis on urine from healthy volunteers and renal transplantation patients with Tac nephrotoxicity confirmed symmetric dimethylarginine (SDMA) and serine (Ser) as biomarker at kidney injury, with AUC values of 0.95 and 0.81 in ROC analysis, respectively. Additionally, SDMA exhibited a tight correlation with serum creatinine, and was therefore indicative of renal function. CONCLUSIONS: The targeted metabolomic assay was time and cost prohibitive for amino acid analysis in human urine, facilitating the biomarker identification of Tac nephrotoxicity. PMID: 29369388 [PubMed - as supplied by publisher]

The Role of Mitochondrial DNA (mtDNA) in the Development of Diabetic Retinopathy (DR): A Systematic Review.

Fri, 26/01/2018 - 14:14
Related Articles The Role of Mitochondrial DNA (mtDNA) in the Development of Diabetic Retinopathy (DR): A Systematic Review. Med Hypothesis Discov Innov Ophthalmol. 2017;6(2):30-38 Authors: Sarhangi N, Khatami F, Keshtkar A, Heshmat R, Atlasi R, Mohammadamoli M Abstract Diabetic Retinopathy (DR) is the most prevalent health problem, which is influenced by environmental and genetic factors with an increasing prevalence. The current systematic review is focused on mtDNA modification, including polymorphism and mutation/deletion, with a direct effect on DR.This systematic search was initially done through PubMed, Cochrane, EMBASE, SCOPUS, and Web of Science without a restriction on the years of publication. The terms searched included ''mtDNA'', ''mitochondrial DNA'', ''diabetes'', ''diabetic'', ''retina'', and ''diabetic retinopathy''. Animal, cohort, cross-sectional, and in vitro studies, as well as case series, case reports, review articles, and Letters to Editor were excluded from this research.From 1528 resulting searched articles, only 12papers were finally chosen as the case-control studies considering mtDNA gene and DR. Actually, of these 12 articles, 8 studies were concerned with mtDNA polymorphisms (UCP1, UCP2, ROMO-1, and Mn-SOD) and 4 articles were related to mtDNA mutation (A3243G mutation in tRNALeu(UUR) gene and mtDNA deletion (ΔmtDNA 4977)).Some conflicting results were found between the selected genetic modifications of mtDNA, such as Mn-SOD, UCP1, ΔmtDNA 4977, tRNALeu (UUR), and ROMO-1.Finally, A3243G mutation in the tRNALeu (UUR) gene and rs660339 and V16A polymorphisms of UCP2 and Mn-SOD genes were respectively considered as the most important factors in the pathogenesis of DR. PMID: 29367932 [PubMed]

A comparison of sample preparation methods for extracting volatile organic compounds (VOCs) from equine faeces using HS-SPME.

Fri, 26/01/2018 - 14:14
Related Articles A comparison of sample preparation methods for extracting volatile organic compounds (VOCs) from equine faeces using HS-SPME. Metabolomics. 2018;14(2):19 Authors: Hough R, Archer D, Probert C Abstract Introduction: Disturbance to the hindgut microbiota can be detrimental to equine health. Metabolomics provides a robust approach to studying the functional aspect of hindgut microorganisms. Sample preparation is an important step towards achieving optimal results in the later stages of analysis. The preparation of samples is unique depending on the technique employed and the sample matrix to be analysed. Gas chromatography mass spectrometry (GCMS) is one of the most widely used platforms for the study of metabolomics and until now an optimised method has not been developed for equine faeces. Objectives: To compare a sample preparation method for extracting volatile organic compounds (VOCs) from equine faeces. Methods: Volatile organic compounds were determined by headspace solid phase microextraction gas chromatography mass spectrometry (HS-SPME-GCMS). Factors investigated were the mass of equine faeces, type of SPME fibre coating, vial volume and storage conditions. Results: The resultant method was unique to those developed for other species. Aliquots of 1000 or 2000 mg in 10 ml or 20 ml SPME headspace were optimal. From those tested, the extraction of VOCs should ideally be performed using a divinylbenzene-carboxen-polydimethysiloxane (DVB-CAR-PDMS) SPME fibre. Storage of faeces for up to 12 months at - 80 °C shared a greater percentage of VOCs with a fresh sample than the equivalent stored at - 20 °C. Conclusions: An optimised method for extracting VOCs from equine faeces using HS-SPME-GCMS has been developed and will act as a standard to enable comparisons between studies. This work has also highlighted storage conditions as an important factor to consider in experimental design for faecal metabolomics studies. PMID: 29367839 [PubMed]

Ginseng polysaccharides enhanced ginsenoside Rb1 and microbial metabolites exposure through enhancing intestinal absorption and affecting gut microbial metabolism.

Fri, 26/01/2018 - 14:14
Related Articles Ginseng polysaccharides enhanced ginsenoside Rb1 and microbial metabolites exposure through enhancing intestinal absorption and affecting gut microbial metabolism. J Ethnopharmacol. 2018 Jan 20;: Authors: Shen H, Gao X, Li T, Jing W, Han B, Jia Y, Hu N, Yan Z, Li S, Yan R Abstract ETHNOPHARMACOLOGICAL RELEVANCE: Polysaccharides and small molecules commonly co-exist in decoction of traditional Chinese medicines (TCMs). Our previous study outlined that ginseng polysaccharides (GP) could interact with co-existing ginsenosides to produce synergistic effect in an over-fatigue and acute cold stress model via gut microbiota involved mechanisms. AIM OF THE STUDY: This study aimed to verify the interactions by examining the impact of GP on oral pharmacokinetics of ginsenoside Rb1 (Rb1), the dominant protopanoxadiol (PPD)-type ginsenoside in Ginseng, on a dextran sulphate sodium (DSS) induced experimental colitis model which was characterized by gut dysbiosis, and to delineate the underlying mechanisms in vitro. MATERIALS AND METHODS: Rats received drinking water (normal group), 5% DSS (UC group), or 5% DSS plus daily oral administration of GP (GP group) for 7 days and fecal samples were collected on day -3, 0 and 6. On day 7 all animals received an oral dosage of Rb1 and blood samples were withdrawn for pharmacokinetic study. The in vitro metabolism of Rb1 with gut microbiota from normal and UC rats and the transport of Rb1 across Caco-2 cell monolayer were carried out in presence/absence of GP. Rb1 and its bacterial metabolites ginsenoside Rd (Rd), ginsenoside F2 (F2), Compound K (CK) and PPD were determined using LC-MS/MS. Total and target bacteria in fecal samples were determined by using 16S rRNA-based RT-PCR. β-Glucosidase activity was determined by measuring 4-nitrophenol formed from 4-nitrophenyl-β-D-glucopyranoside hydrolysis. RESULTS: DSS induction did not alter AUC0-t and Cmax of Rb1, which, however, were doubled together with elevated AUC0-t of the metabolites, in particular Rd and CK, in GP group. GP influenced the microbial composition and showed a prebiotic-like effect. Accordingly, GP treatment could partially restore the β-glucosidase activity which was reduced by DSS induction. The presence of GP resulted in quicker microbial metabolism of Rb1 and higher Rd formation in first 8h of incubation, while the impact on F2 and CK formation/conversion became obvious after 8h. More interestingly, GP slightly stimulated Caco-2 cell growth and facilitated Rb1 transport across the Caco-2 monolayer in both directions, increasing the Papp of Rb1 from 10-7cm/s to 10-6cm/s. CONCLUSIONS: GP alleviated DSS-induced colitis-like symptoms and enhanced the systemic exposure of Rb1 through enhancing microbial deglycosylation and intestinal epithelial absorption of Rb1. These findings further demonstrated the important role of gut microbiota in the multifaceted action of polysaccharides in the holistic actions of traditional decoction of TCMs. PMID: 29366768 [PubMed - as supplied by publisher]

Microbe participation in aroma production during soy sauce fermentation.

Fri, 26/01/2018 - 14:14
Related Articles Microbe participation in aroma production during soy sauce fermentation. J Biosci Bioeng. 2018 Jan 20;: Authors: Harada R, Yuzuki M, Ito K, Shiga K, Bamba T, Fukusaki E Abstract Soy sauce is a traditional Japanese fermented seasoning that contains various constituents such as amino acids, organic acids, and volatiles that are produced during the long fermentation process. Although studies regarding the correlation between microbes and aroma constituents have been performed, there are no reports about the influences of the microbial products, such as lactic acid, acetic acid, and ethanol, during fermentation. Because it is known that these compounds contribute to microbial growth and to changes in the constituent profile by altering the moromi environment, understanding the influence of these compounds is important. Metabolomics, the comprehensive study of low molecular weight metabolites, is a promising strategy for the deep understanding of constituent contributions to food characteristics. Therefore, the influences of microbes and their products such as lactic acid, acetic acid, and ethanol on aroma profiles were investigated using gas chromatography/mass spectrometry (GC/MS)-based metabolic profiling. The presence of aroma constituents influenced by microbes and chemically influenced by lactic acid, acetic acid, and ethanol were proposed. Most of the aroma constituents were not produced by adding ethanol alone, confirming the participation of yeast in aroma production. It was suggested that lactic acid bacterium relates to a key aromatic compound, 2,5-dimethyl-4-hydroxy-3(2H)-furanone. However, most of the measured aroma constituents changed similarly in both samples with lactic acid bacterium and acids. Thus, it was clear that the effect of lactic acid and acetic acid on the aroma profile was significant. PMID: 29366719 [PubMed - as supplied by publisher]

Lipoprotein particle number and size distribution in apparently healthy spanish population according to sex and age, assessed by nuclear magnetic resonance.

Fri, 26/01/2018 - 14:14
Related Articles Lipoprotein particle number and size distribution in apparently healthy spanish population according to sex and age, assessed by nuclear magnetic resonance. Atherosclerosis. 2017 Aug;263:e86 Authors: Gil Serret M, Ibarretxe D, Plana N, Correig X, Masana L, Amigó N PMID: 29366250 [PubMed - in process]

Characterization of glycoprotein and lipoprotein profiles of rheumatoid arthritis (RA) patiens by 1H-nuclear magnetic resonance spectroscopy (1H-NMR).

Fri, 26/01/2018 - 14:14
Related Articles Characterization of glycoprotein and lipoprotein profiles of rheumatoid arthritis (RA) patiens by 1H-nuclear magnetic resonance spectroscopy (1H-NMR). Atherosclerosis. 2017 Aug;263:e121 Authors: Fuertes Martín R, Amigó Grau N, Carles Vallvé J, Paredes S, Taverner D, Masana L, Correig Blanchar X PMID: 29365495 [PubMed - in process]

Homeostatic control of metabolic and functional fitness of Treg cells by LKB1 signalling.

Fri, 26/01/2018 - 14:14
Related Articles Homeostatic control of metabolic and functional fitness of Treg cells by LKB1 signalling. Nature. 2017 08 31;548(7669):602-606 Authors: Yang K, Blanco DB, Neale G, Vogel P, Avila J, Clish CB, Wu C, Shrestha S, Rankin S, Long L, Kc A, Chi H Abstract Regulatory T cells (Treg cells) have a pivotal role in the establishment and maintenance of immunological self-tolerance and homeostasis. Transcriptional programming of regulatory mechanisms facilitates the functional activation of Treg cells in the prevention of diverse types of inflammatory responses. It remains unclear how Treg cells orchestrate their homeostasis and interplay with environmental signals. Here we show that liver kinase B1 (LKB1) programs the metabolic and functional fitness of Treg cells in the control of immune tolerance and homeostasis. Mice with a Treg-specific deletion of LKB1 developed a fatal inflammatory disease characterized by excessive TH2-type-dominant responses. LKB1 deficiency disrupted Treg cell survival and mitochondrial fitness and metabolism, but also induced aberrant expression of immune regulatory molecules including the negative co-receptor PD-1 and the TNF receptor superfamily proteins GITR and OX40. Unexpectedly, LKB1 function in Treg cells was independent of conventional AMPK signalling or the mTORC1-HIF-1α axis, but contributed to the activation of β-catenin signalling for the control of PD-1 and TNF receptor proteins. Blockade of PD-1 activity reinvigorated the ability of LKB1-deficient Treg cells to suppress TH2 responses and the interplay with dendritic cells primed by thymic stromal lymphopoietin. Thus, Treg cells use LKB1 signalling to coordinate their metabolic and immunological homeostasis and to prevent apoptotic and functional exhaustion, thereby orchestrating the balance between immunity and tolerance. PMID: 28847007 [PubMed - indexed for MEDLINE]

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