PubMed

Related Articles Modulating the direction of carbon flow in Escherichia coli to improve L-tryptophan production by inactivating the global regulator FruR. J Biotechnol. 2016 Jun 10; Authors: Liu L, Duanabd X, Wu J Abstract The fructose repressor (FruR) affects carbon flux through the central metabolic pathways of E. coli. In this study, L-tryptophan production in Escherichia coli FB-04 was improved by knocking out the fruR gene, thereby inactivating FruR. This fruR knockout strain, E. coli FB-04(ΔfruR), not only exhibited higher growth efficiency, it also showed substantially improved L-tryptophan production. L-tryptophan production by E. coli FB-04(ΔfruR) and L-tryptophan yield per glucose were increased by 62.5% and 52.4%, respectively, compared with the parent E. coli FB-04. Metabolomics analysis showed that the fruR knockout significantly enhances metabolic flow through glycolysis, the pentose phosphate pathway and the TCA cycle, increasing levels of critical precursors and substrates for L-tryptophan biosynthesis. These results indicate that fruR deletion should enhance L-tryptophan production and improve the efficiency of carbon source utilization independent of genetic background. PMID: 27297546 [PubMed - as supplied by publisher]

Related Articles A Subset of Protective γ9δ2 T cells is Activated by Novel Mycobacterial Lipid Components. Infect Immun. 2016 Jun 13; Authors: Xia M, Hesser DC, De P, Sakala IG, Spencer CT, Kirkwood JS, Abate G, Chatterjee D, Dobos KM, Hoft DF Abstract γ9δ2 T cells provide a natural bridge between innate and adaptive immunity, rapidly and potently respond to pathogen infection in mucosal tissues, and are prominently induced by both tuberculosis (TB) infection and bacillus Calmette Guérin (BCG) vaccination. Mycobacteria-expanded γ9δ2 T cells represent only a subset of the phosphoantigen (IPP and HMBPP)-responsive γ9δ2 T cells, expressing an oligoclonal set of TCR sequences which more efficiently recognize and inhibit intracellular Mycobacterium tuberculosis (Mtb) infection. Based on this premise, we have been searching for Mtb antigens specifically capable of inducing a unique subset of mycobacteria-protective γ9δ2 T cells. Our screening strategy includes the identification of Mtb fractions that expand γ9δ2 T cells with biological functions capable of inhibiting intracellular mycobacteria replication. Chemical treatments of Mtb whole lysates (WL) ruled out protein, nucleic acid and nonpolar lipids as the Mtb antigens inducing protective γ9δ2 T cells. Mild acid hydrolysis, which transforms complex carbohydrate to monomeric residues, abrogated the specific activity of Mtb whole cell lysate, suggesting that a polysaccharide was required for biological activity. Extraction of MtbWL with chloroform: methanol: water (10:10:3) resulted in a polar lipid fraction with highly enriched specific activity; this activity was further enriched by silica gel chromatography. A combination of Mass Spectrometry and Nuclear Magnetic Resonance analysis of bioactive fractions indicated that 6-O-methyl-glucose containing lipopolysaccharides (mGLP) are predominant components present in this active fraction. These results have important implications for the development of new immunotherapeutic approaches for prevention/treatment of TB. PMID: 27297390 [PubMed - as supplied by publisher]

Related Articles Metabolic connectivity mapping reveals effective connectivity in the resting human brain. Proc Natl Acad Sci U S A. 2016 Jan 12;113(2):428-33 Authors: Riedl V, Utz L, Castrillón G, Grimmer T, Rauschecker JP, Ploner M, Friston KJ, Drzezga A, Sorg C Abstract Directionality of signaling among brain regions provides essential information about human cognition and disease states. Assessing such effective connectivity (EC) across brain states using functional magnetic resonance imaging (fMRI) alone has proven difficult, however. We propose a novel measure of EC, termed metabolic connectivity mapping (MCM), that integrates undirected functional connectivity (FC) with local energy metabolism from fMRI and positron emission tomography (PET) data acquired simultaneously. This method is based on the concept that most energy required for neuronal communication is consumed postsynaptically, i.e., at the target neurons. We investigated MCM and possible changes in EC within the physiological range using "eyes open" versus "eyes closed" conditions in healthy subjects. Independent of condition, MCM reliably detected stable and bidirectional communication between early and higher visual regions. Moreover, we found stable top-down signaling from a frontoparietal network including frontal eye fields. In contrast, we found additional top-down signaling from all major clusters of the salience network to early visual cortex only in the eyes open condition. MCM revealed consistent bidirectional and unidirectional signaling across the entire cortex, along with prominent changes in network interactions across two simple brain states. We propose MCM as a novel approach for inferring EC from neuronal energy metabolism that is ideally suited to study signaling hierarchies in the brain and their defects in brain disorders. PMID: 26712010 [PubMed - indexed for MEDLINE]

Related Articles Plants Possess a Cyclic Mitochondrial Metabolic Pathway similar to the Mammalian Metabolic Repair Mechanism Involving Malate Dehydrogenase and l-2-Hydroxyglutarate Dehydrogenase. Plant Cell Physiol. 2015 Sep;56(9):1820-30 Authors: Hüdig M, Maier A, Scherrers I, Seidel L, Jansen EE, Mettler-Altmann T, Engqvist MK, Maurino VG Abstract Enzymatic side reactions can give rise to the formation of wasteful and toxic products that are removed by metabolite repair pathways. In this work, we identify and characterize a mitochondrial metabolic repair mechanism in Arabidopsis thaliana involving malate dehydrogenase (mMDH) and l-2-hydroxyglutarate dehydrogenase (l-2HGDH). We analyze the kinetic properties of both A. thaliana mMDH isoforms, and show that they produce l-2-hydroxyglutarate (l-2HG) from 2-ketoglutarate (2-KG) at low rates in side reactions. We identify A. thaliana l-2HGDH as a mitochondrial FAD-containing oxidase that converts l-2HG back to 2-KG. Using loss-of-function mutants, we show that the electrons produced in the l-2HGDH reaction are transferred to the mitochondrial electron transport chain through the electron transfer protein (ETF). Thus, plants possess the biochemical components of an l-2HG metabolic repair system identical to that found in mammals. While deficiencies in the metabolism of l-2HG result in fatal disorders in mammals, accumulation of l-2HG in plants does not adversely affect their development under a range of tested conditions. However, orthologs of l-2HGDH are found in all examined genomes of viridiplantae, indicating that the repair reaction we identified makes an essential contribution to plant fitness in as yet unidentified conditions in the wild. PMID: 26203119 [PubMed - indexed for MEDLINE]

Related Articles Smoking-Associated Disordering of the Airway Basal Stem/Progenitor Cell Metabotype. Am J Respir Cell Mol Biol. 2016 Feb;54(2):231-40 Authors: Deeb RS, Walters MS, Strulovici-Barel Y, Chen Q, Gross SS, Crystal RG Abstract The airway epithelium is a complex pseudostratified multicellular layer lining the tracheobronchial tree, functioning as the primary defense against inhaled environmental contaminants. The major cell types of the airway epithelium include basal, intermediate columnar, ciliated, and secretory. Basal cells (BCs) are the proliferating stem/progenitor population that differentiate into the other specialized cell types of the airway epithelium during normal turnover and repair. Given that cigarette smoke delivers thousands of xenobiotics and high levels of reactive molecules to the lung epithelial surface, we hypothesized that cigarette smoke broadly perturbs BC metabolism. To test this hypothesis, primary airway BCs were isolated from healthy nonsmokers (n = 11) and healthy smokers (n = 7) and assessed by global metabolic profiling by liquid chromatography-mass spectrometry. The analysis identified 52 significant metabolites in BCs differentially expressed between smokers and nonsmokers (P < 0.05). These changes included metabolites associated with redox pathways, energy production, and inflammatory processes. Notably, BCs from smokers exhibited altered levels of the key enzyme cofactors/substrates nicotinamide adenine dinucleotide, flavin adenine dinucleotide, acetyl coenzyme A, and membrane phospholipid levels. Consistent with the high burden of oxidants in cigarette smoke, glutathione levels were diminished, whereas 3-nitrotyrosine levels were increased, suggesting that protection of airway epithelial cells against oxidative and nitrosative stress is significantly compromised in smoker BCs. It is likely that this altered metabotype is a reflection of, and likely contributes to, the disordered biology of airway BCs consequent to the stress cigarette smoking puts on the airway epithelium. PMID: 26161876 [PubMed - indexed for MEDLINE]

Related Articles Kinesin-1 promotes post-Golgi trafficking of NCAM140 and NCAM180 to the cell surface. J Cell Sci. 2015 Aug 1;128(15):2816-29 Authors: Wobst H, Schmitz B, Schachner M, Diestel S, Leshchyns'ka I, Sytnyk V Abstract The neural cell adhesion molecule (NCAM, also known as NCAM1) is important during neural development, because it contributes to neurite outgrowth in response to its ligands at the cell surface. In the adult brain, NCAM is involved in regulating synaptic plasticity. The molecular mechanisms underlying delivery of NCAM to the neuronal cell surface remain poorly understood. We used a protein macroarray and identified the kinesin light chain 1 (KLC1), a component of the kinesin-1 motor protein, as a binding partner of the intracellular domains of the two transmembrane isoforms of NCAM, NCAM140 and NCAM180. KLC1 binds to amino acids CGKAGPGA within the intracellular domain of NCAM and colocalizes with kinesin-1 in the Golgi compartment. Delivery of NCAM180 to the cell surface is increased in CHO cells and neurons co-transfected with kinesin-1. We further demonstrate that the p21-activated kinase 1 (PAK1) competes with KLC1 for binding to the intracellular domain of NCAM and contributes to the regulation of the membrane insertion of NCAM. Our results indicate that NCAM is delivered to the cell surface through a kinesin-1-mediated transport mechanism in a PAK1-dependent manner. PMID: 26101351 [PubMed - indexed for MEDLINE]

Related Articles Metabolomic quality control of commercial Asian ginseng, and cultivated and wild American ginseng using (1)H NMR and multi-step PCA. J Pharm Biomed Anal. 2015 Oct 10;114:113-20 Authors: Zhao H, Xu J, Ghebrezadik H, Hylands PJ Abstract Ginseng, mainly Asian ginseng and American ginseng, is the most widely consumed herbal product in the world . However, the existing quality control method is not adequate: adulteration is often seen in the market. In this study, 31 batches of ginseng from Chinese stores were analyzed using (1)H NMR metabolite profiles together with multi-step principal component analysis. The most abundant metabolites, sugars, were excluded from the NMR spectra after the first principal component analysis, in order to reveal differences contributed by less abundant metabolites. For the first time, robust, distinctive and representative differences of Asian ginseng from American ginseng were found and the key metabolites responsible were identified as sucrose, glucose, arginine, choline, and 2-oxoglutarate and malate. Differences between wild and cultivated ginseng were identified as ginsenosides. A substitute cultivated American ginseng was noticed. These results demonstrated that the combination of (1)H NMR and PCA is effective in quality control of ginseng. PMID: 26037159 [PubMed - indexed for MEDLINE]

Related Articles Mitophagy-driven mitochondrial rejuvenation regulates stem cell fate. Aging (Albany NY). 2016 Jun 13; Authors: Vazquez-Martin A, Van den Haute C, Cufí S, Corominas-Faja B, Cuyàs E, Lopez-Bonet E, Rodriguez-Gallego E, Fernández-Arroyo S, Joven J, Baekelandt V, Menendez JA Abstract Our understanding on how selective mitochondrial autophagy, or mitophagy, can sustain the archetypal properties of stem cells is incomplete. PTEN-induced putative kinase 1 (PINK1) plays a key role in the maintenance of mitochondrial morphology and function and in the selective degradation of damaged mitochondria by mitophagy. Here, using embryonic fibroblasts fromPINK1 gene-knockout (KO) mice, we evaluated whether mitophagy is a causal mechanism for the control of cell-fate plasticity and maintenance of pluripotency. Loss of PINK1-dependent mitophagy was sufficient to dramatically decrease the speed and efficiency of induced pluripotent stem cell (iPSC) reprogramming. Mitophagy-deficient iPSC colonies, which were characterized by a mixture of mature and immature mitochondria, seemed unstable, with a strong tendency to spontaneously differentiate and form heterogeneous populations of cells. Although mitophagy-deficient iPSC colonies normally expressed pluripotent markers, functional monitoring of cellular bioenergetics revealed an attenuated glycolysis in mitophagy-deficient iPSC cells. Targeted metabolomics showed a notable alteration in numerous glycolysis- and TCA-related metabolites in mitophagy-deficient iPSC cells, including a significant decrease in the intracellular levels of α-ketoglutarate -a key suppressor of the differentiation path in stem cells. Mitophagy-deficient iPSC colonies exhibited a notably reduced teratoma-initiating capacity, but fully retained their pluripotency and multi-germ layer differentiation capacity in vivo. PINK1-dependent mitophagy pathway is an important mitochondrial switch that determines the efficiency and quality of somatic reprogramming. Mitophagy-driven mitochondrial rejuvenation might contribute to the ability of iPSCs to suppress differentiation by directing bioenergetic transition and metabolome remodeling traits. These findings provide new insights into how mitophagy might influence the stem cell decisions to retain pluripotency or differentiate in tissue regeneration and aging, tumor growth, and regenerative medicine. PMID: 27295498 [PubMed - as supplied by publisher]

Related Articles Metabolomics as a Challenging Approach for Medicinal Chemistry and Personalized Medicine. J Med Chem. 2016 Jun 13; Authors: Frederich M, Pirotte B, Fillet M, De Tullio P Abstract "Omics" sciences have been developed to provide a holistic point of view of biology and to better understand the complexity of an organism as a whole. These systems biology approaches can be examined at different levels, starting from the most fundamental, i.e., the genome, and finishing with the most functional, i.e., the metabolome. Similar to how genomics is applied to the exploration of DNA, metabolomics is the qualitative and quantitative study of metabolites. This emerging field is clearly linked to genomics, transcriptomics and proteomics. In addition, metabolomics provides a unique and direct vision of the functional outcome of an organism's activities that are required for it to survive, grow and respond to internal and external stimuli or stress, e.g., pathologies and drugs. The links between metabolic changes, patient phenotype, physiological and/or pathological status and treatment are now well established and have opened a new area for the application of metabolomics in the drug discovery process and in personalized medicine. PMID: 27295417 [PubMed - as supplied by publisher]

Related Articles Integration of multi-omics data for prediction of phenotypic traits using random forest. BMC Bioinformatics. 2016;17(Suppl 5):180 Authors: Acharjee A, Kloosterman B, Visser RG, Maliepaard C Abstract BACKGROUND: In order to find genetic and metabolic pathways related to phenotypic traits of interest, we analyzed gene expression data, metabolite data obtained with GC-MS and LC-MS, proteomics data and a selected set of tuber quality phenotypic data from a diploid segregating mapping population of potato. In this study we present an approach to integrate these ~ omics data sets for the purpose of predicting phenotypic traits. This gives us networks of relatively small sets of interrelated ~ omics variables that can predict, with higher accuracy, a quality trait of interest. RESULTS: We used Random Forest regression for integrating multiple ~ omics data for prediction of four quality traits of potato: tuber flesh colour, DSC onset, tuber shape and enzymatic discoloration. For tuber flesh colour beta-carotene hydroxylase and zeaxanthin epoxidase were ranked first and forty-fourth respectively both of which have previously been associated with flesh colour in potato tubers. Combining all the significant genes, LC-peaks, GC-peaks and proteins, the variation explained was 75 %, only slightly more than what gene expression or LC-MS data explain by themselves which indicates that there are correlations among the variables across data sets. For tuber shape regressed on the gene expression, LC-MS, GC-MS and proteomics data sets separately, only gene expression data was found to explain significant variation. For DSC onset, we found 12 significant gene expression, 5 metabolite levels (GC) and 2 proteins that are associated with the trait. Using those 19 significant variables, the variation explained was 45 %. Expression QTL (eQTL) analyses showed many associations with genomic regions in chromosome 2 with also the highest explained variation compared to other chromosomes. Transcriptomics and metabolomics analysis on enzymatic discoloration after 5 min resulted in 420 significant genes and 8 significant LC metabolites, among which two were putatively identified as caffeoylquinic acid methyl ester and tyrosine. CONCLUSIONS: In this study, we made a strategy for selecting and integrating multiple ~ omics data using random forest method and selected representative individual peaks for networks based on eQTL, mQTL or pQTL information. Network analysis was done to interpret how a particular trait is associated with gene expression, metabolite and protein data. PMID: 27295212 [PubMed - as supplied by publisher]

Related Articles Drug metabolism and disposition diversity of Ranunculales phytometabolites: A systems perspective. Expert Opin Drug Metab Toxicol. 2016 Jun 13; Authors: Hao DC, Yang L Abstract INTRODUCTION: Although investigations in metabolism and pharmacokinetics of Ranunculales phytometabolites are booming, data obtained from human and animal studies have not been summarized as a whole to outline current trends and to predict future development. AREAS COVERED: Here, we highlight the current knowledge, as well as the challenges around the DMPK (drug metabolism and pharmacokinetics) associated concerns in streamlining drug research and therapeutic use of Ranunculales phytometabolites. Data from various in vivo and in vitro models are classified and discussed. DMPK characteristics of Ranunculales phytometabolites are summarized and presented according to the phylogenetic relationship of families and genera. This review also presents an overview of the complex interaction between drug metabolizing enzymes/transporters and phytochemicals, as well as of the most advanced approaches in the relevant field. EXPERT OPINION: Since species-specific differences in DMPK exist, data obtained from animal studies may not be sufficient to predict drug metabolism reactions in humans. Omics-based methodologies (genomics, epigenomics, transcriptomics, proteomics, microbiomics, and metabolomics) should be used to enhance the reliability of DMPK prediction. The fluorescent probes may bridge the gap between conventional models and in vivo clinical studies in humans and provide a consistent basis for DMPK assay development. PMID: 27295138 [PubMed - as supplied by publisher]

Related Articles An Evaluation of 1-Deoxynojirimycin Oral Administration in Eri Silkworm through Fat Body Metabolomics Based on (1) H Nuclear Magnetic Resonance. Biomed Res Int. 2016;2016:4676505 Authors: Wen CW, Lin XD, Dong MJ, Deng MJ Abstract 1-Deoxynojirimycin (DNJ), the main hypoglycemic constituent in mulberry (Morus alba) latex, has been extensively researched. Although there is considerable interest in the biological effects of DNJ, the roles of 1-deoxynojirimycin (DNJ) in glycometabolism and energy metabolism in insects have received little attention. In this paper, (1)H nuclear magnetic resonance ((1)H NMR) based metabonomic was performed to study the effects of the oral supplementation of 0.25% DNJ, 0.5% DNJ, latex, and the mixture of 0.5% DNJ and latex (1 : 1) on the fat body glycometabolism and energy metabolism of the fourth-instar larvae of Eri silkworms, Samia cynthia ricini. Metabolic pattern recognition analysis (partial least square-discriminant analysis, PLS-DA) of fat body extracts indicated that the groups of 0.25% DNJ, 0.5% DNJ, latex, and the mixture of 0.5% DNJ and latex (1 : 1) were significantly different from the control group. Further, compared to the control group, the metabolites levels of lactate, trehalose, succinate, malate, and fumarate were remarkably changed in experimental groups, which were involved in glycolysis, hydrolysis of trehalose, and tricarboxylic acid (TCA) cycle. Our results indicate that DNJ has a positive impact on the reverse energy metabolism of Eri silkworms and metabonomic analysis based on NMR can be used as a tool to identify potential biomarkers. PMID: 27294120 [PubMed - in process]

Related Articles Mitochondrial Dynamics Controls T Cell Fate through Metabolic Programming. Cell. 2016 Jun 8; Authors: Buck MD, O'Sullivan D, Klein Geltink RI, Curtis JD, Chang CH, Sanin DE, Qiu J, Kretz O, Braas D, van der Windt GJ, Chen Q, Huang SC, O'Neill CM, Edelson BT, Pearce EJ, Sesaki H, Huber TB, Rambold AS, Pearce EL Abstract Activated effector T (TE) cells augment anabolic pathways of metabolism, such as aerobic glycolysis, while memory T (TM) cells engage catabolic pathways, like fatty acid oxidation (FAO). However, signals that drive these differences remain unclear. Mitochondria are metabolic organelles that actively transform their ultrastructure. Therefore, we questioned whether mitochondrial dynamics controls T cell metabolism. We show that TE cells have punctate mitochondria, while TM cells maintain fused networks. The fusion protein Opa1 is required for TM, but not TE cells after infection, and enforcing fusion in TE cells imposes TM cell characteristics and enhances antitumor function. Our data suggest that, by altering cristae morphology, fusion in TM cells configures electron transport chain (ETC) complex associations favoring oxidative phosphorylation (OXPHOS) and FAO, while fission in TE cells leads to cristae expansion, reducing ETC efficiency and promoting aerobic glycolysis. Thus, mitochondrial remodeling is a signaling mechanism that instructs T cell metabolic programming. PMID: 27293185 [PubMed - as supplied by publisher]

Related Articles Evaluation of the Anti-inflammatory Effects of Volatile Oils from Processed Products of Angelica sinensis radix by GC-MS-Based Metabolomics. J Ethnopharmacol. 2016 Jun 9; Authors: Zhong LJ, Hua YL, Ji P, Yao WL, Zhang WQ, Li J, Wei YM Abstract ETHNOPHARMACOLOGICAL RELEVANCE: Roots of Angelica sinensis (Oliv.) Diels (AS) a commonly used herbal，always act as an anti-inflammatory drug in Chinese traditional therapy. In clinical use, AS is always processed before being used for the reason that processing can increase its therapeutic effect. Recent studies have shown that volatile oil of AS (VOAS), an important component in AS, has evident anti-inflammatory activities. AIM OF THE STUDY: In this study, our aim is to evaluate the anti-inflammatory effects of volatile oils from processed products of AS. MATERIALS AND METHODS: In this paper, volatile oils from stir-fried AS (C -VOAS), parched AS with alcohol (J-VOAS), parched AS with soil (T-VOAS), and parched AS with sesame oil (Y-VOAS) were applied to intervene the carrageenan-induced acute inflammation model rats. GC-MS based metabolomics was utilized to determine different metabolites in the inflammatory exudate and plasma samples. RESULTS: The results showed that VOASs could significantly inhibit the release of PGE2, HIS, 5-HT and TNF-α, among which C-VOAS and J-VOAS expressed better effect. Otherwise, 14 potential biomarkers were identified respectively in inflammatory exudate and plasma, which changed highly significantly (P<0.01) in C-VOAS and J-VOAS groups. CONCLUSIONS: We inferred that the anti-inflammatory effect of C-VOAS and J-VOAS were superior to other VOASs. PMID: 27292195 [PubMed - as supplied by publisher]

Related Articles ChEBI in 2016: Improved services and an expanding collection of metabolites. Nucleic Acids Res. 2016 Jan 4;44(D1):D1214-9 Authors: Hastings J, Owen G, Dekker A, Ennis M, Kale N, Muthukrishnan V, Turner S, Swainston N, Mendes P, Steinbeck C Abstract ChEBI is a database and ontology containing information about chemical entities of biological interest. It currently includes over 46,000 entries, each of which is classified within the ontology and assigned multiple annotations including (where relevant) a chemical structure, database cross-references, synonyms and literature citations. All content is freely available and can be accessed online at http://www.ebi.ac.uk/chebi. In this update paper, we describe recent improvements and additions to the ChEBI offering. We have substantially extended our collection of endogenous metabolites for several organisms including human, mouse, Escherichia coli and yeast. Our front-end has also been reworked and updated, improving the user experience, removing our dependency on Java applets in favour of embedded JavaScript components and moving from a monthly release update to a 'live' website. Programmatic access has been improved by the introduction of a library, libChEBI, in Java, Python and Matlab. Furthermore, we have added two new tools, namely an analysis tool, BiNChE, and a query tool for the ontology, OntoQuery. PMID: 26467479 [PubMed - indexed for MEDLINE]

Hepatic encephalopathy in ICU: cerebrospinal fluid metabolomics highlights alteration of multiple metabolic pathways representing new potential therapeutic targets. Intensive Care Med Exp. 2015 Dec;3(Suppl 1):A690 Authors: Weiss N, Colsch B, Isnard F, Attala S, Amador M, Lamari F, Sedel F, Junot C, Thabut D, Brain Liver Pitie-Salpetriere Study Group (BLIPS) PMID: 27290266 [PubMed - as supplied by publisher]

Gas chromatography-mass spectrometry metabolomics of goat milk with different polymorphism at the αS1-casein genotype locus. J Dairy Sci. 2016 Jun 8; Authors: Caboni P, Murgia A, Porcu A, Demuru M, Pulina G, Nudda A Abstract Hyphenated gas chromatography-mass spectrometry (GC-MS) and multivariate data analysis techniques were used to uncover milk metabolite differences in different αS1-casein genotypes of goats. By a discriminant GC-MS metabolomics approach, we characterized milk polar metabolites of 28 goats. Animals were selected on the basis of their genotypes as 7 goats classified heterozygous for weak or null alleles, 5 for the genotype EE, 9 for the genotypes AE and BE, and finally 7 for the strong genotype AA. Low molecular weight polar metabolite profile was tightly related to the different goat genotypes, milk production, and protein levels. Results of multivariate statistical analysis of GC-MS data demonstrate that different heterozygous and homozygous genotypes expressed different metabolites such as citric and aconitic acid for the strong allele class with different sugars and polyols for the weak class. PMID: 27289154 [PubMed - as supplied by publisher]

Primary HCMV Infection in Pregnancy from Classic Data towards Metabolomics: an Exploratory analysis. Clin Chim Acta. 2016 Jun 8; Authors: Fattuoni C, Palmas F, Noto A, Barberini L, Mussap M, Grapov D, Dessì A, Casu M, Casanova A, Furione M, Arossa A, Spinillo A, Baldanti F, Fanos V, Zavattoni M Abstract BACKGROUND: Human cytomegalovirus (HCMV) is one of the most frequent risk of viral infections during pregnancy. The aim of this study was to evaluate the metabolic profile in amniotic fluid (AF) samples obtained from HCMV-infected, and uninfected fetuses in order to elucidate changes in metabolic pathways during congenital HCMV infection and to recognize new potential diagnostic and/or prognostic biomarkers. METHODS: A retrospective cohort study was conducted on 63 pregnant women: 20 contracted primary HCMV infection during pregnancy and, subsequently, transmitted the virus to the fetus (transmitters); 20 contracted the infection without transmitting the virus to the fetus (non-transmitters); 23 who underwent amniocentesis for cytogenetic-based diagnosis were considered controls. Metabolomics analysis was performed by using the hyphenated technique Gas chromatography-mass spectrometry (GC-MS) followed by a multivariate statistical approach. Four PLS-DA models were generated: controls vs. transmitters; controls vs. non-transmitters; transmitters vs. non-transmitters; and asymptomatic infected vs. symptomatic infected newborns. Subsequently, these models were exploited for network mapping. RESULTS: Compared with controls, HCMV transmitters showed significantly increased levels in glutamine, glycine, serine, pyruvic acid, threonine, threonic acid, and cystine; conversely, unknown U1715 and U1804, glutamic acid, U1437, fructose, sugar-like A203003 and A203005, and tyrosine levels were found decreased. In non-transmitters, glutamine, serine, glycine, threonic acid, threonine, 1-monostearin, urea, and cystine were found increased, while sorbitol, unknown U1804, sugar-like A203003, U1751, xylitol, leucine and fructose were decreased. The comparison between transmitters and non-transmitters did not produce a statistically significant model. Unlike controls' profile, a common feature of HCMV infected subjects (transmitters and non-transmitters) was the activation of glutamine-glutamate and pyrimidine metabolic pathways. In addition, a clusterization for asymptomatic vs. symptomatic outcome was also observed due to alteration of fatty acids biosynthesis. CONCLUSIONS: Metabolomics approach could highlight the significant modification of maternal and placental status during HCMV infection for both transmitter and non-transmitter subjects. A further separation was observed for asymptomatic vs. symptomatic HCMV congenital infections model. Therefore, metabolomics may be a promising tool to improve the accuracy of an early diagnosis, and the management of HCMV pregnancy-related infections. PMID: 27288986 [PubMed - as supplied by publisher]

Metabolic signatures of Huntington's disease (HD): (1)H NMR analysis of the polar metabolome in post mortem human brain. Biochim Biophys Acta. 2016 Jun 8; Authors: Graham SF, Kumar PK, Bjorndahl T, Han B, Yilmaz A, Sherman E, Bahado-Singh RO, Wishart D, Mann D, Green BD Abstract Huntington's disease (HD) is an autosomal neurodegenerative disorder affecting approximately 5-10 persons per 100,000 worldwide. The pathophysiology of HD is not fully understood but the age of onset is known to be highly dependent on the number of CAG triplet repeats in the huntingtin gene. Using (1)H NMR spectroscopy this study biochemically profiled 39 brain metabolites in post-mortem striatum (n=14) and frontal lobe (n=14) from HD sufferers and controls (n=28). Striatum metabolites were more perturbed with 15 significantly affected in HD cases, compared with only 4 in frontal lobe (P<0.05; q<0.3). The metabolite which changed most overall was urea which decreased 3.25-fold in striatum (P<0.01). Four metabolites were consistently affected in both brain regions. These included the neurotransmitter precursors tyrosine and L-phenylalanine which were significantly depleted by 1.55-1.58-fold and 1.48-1.54-fold in striatum and frontal lobe, respectively (P=0.02-0.03). They also included L-leucine which was reduced 1.54-1.69-fold (P=0.04-0.09) and myo-inositol which was increased 1.26-1.37-fold (P<0.01). Logistic regression analyses performed with MetaboAnalyst demonstrated that data obtained from striatum produced models which were profoundly more sensitive and specific than those produced from frontal lobe. The brain metabolite changes uncovered in this first (1)H NMR investigation of human HD offer new insights into the disease pathophysiology. Further investigations of striatal metabolite disturbances are clearly warranted. PMID: 27288730 [PubMed - as supplied by publisher]

Amino Acids in a Targeted Versus a Non-Targeted Metabolomics LC-MS/MS Assay. Are the Results Consistent? Clin Biochem. 2016 Jun 8; Authors: Klepacki J, Klawitter J, Klawitter J, Karimpour-Fard A, Thurman J, Ingle G, Patel D, Christians U Abstract BACKGROUND: The results of plasma amino acid patterns in samples from kidney transplant patients with good and impaired renal function using a targeted LC-MS/MS amino acid assay and a non-targeted metabolomics assay were compared. METHODS: EDTA plasma samples were prospectively collected at baseline, 1, 2, 4 and 6months post-transplant (n=116 patients, n=398 samples). Each sample was analyzed using both a commercial amino acid LC-MS/MS assay and a non-targeted metabolomics assay also based on MS/MS ion transitions. The results of both assays were independently statistically analyzed to identify amino acids associated with estimated glomerular filtration rates using correlation and partial least squares- discriminant analysis. RESULTS: Although there was overlap between the results of the targeted and non-targeted metabolomics assays (tryptophan, 1-methyl histidine), there were also substantial inconsistencies, with the non-targeted assay resulting in more "hits" than the targeted assay. Without further verification of the hits detected by the non-targeted discovery assay, this would have led to different interpretation of the results. There were also false negative results when the non-targeted assay was used (hydroxy proline). Several of said discrepancies could be explained by loss of sensitivity during analytical runs for selected amino acids (serine and threonine), retention time shifts, signals above the range of linear detector response and integration of peaks not separated from background and interferences (aspartate) when the non-targeted metabolomics assay was used. CONCLUSIONS: Whenever assessment of a specific pathway such as amino acids is the focus of interest, a targeted seems preferable to a non-targeted metabolomics assay. PMID: 27288551 [PubMed - as supplied by publisher]