PubMed

Related Articles Cyclic diGMP regulates production of sortase substrates of Clostridium difficile and their surface exposure through ZmpI protease-mediated cleavage. J Biol Chem. 2015 Oct 2;290(40):24453-69 Authors: Peltier J, Shaw HA, Couchman EC, Dawson LF, Yu L, Choudhary JS, Kaever V, Wren BW, Fairweather NF Abstract In Gram-positive pathogens, surface proteins may be covalently anchored to the bacterial peptidoglycan by sortase, a cysteine transpeptidase enzyme. In contrast to other Gram-positive bacteria, only one single sortase enzyme, SrtB, is conserved between strains of Clostridium difficile. Sortase-mediated peptidase activity has been reported in vitro, and seven potential substrates have been identified. Here, we demonstrate the functionality of sortase in C. difficile. We identify two sortase-anchored proteins, the putative adhesins CD2831 and CD3246, and determine the cell wall anchor structure of CD2831. The C-terminal PPKTG sorting motif of CD2831 is cleaved between the threonine and glycine residues, and the carboxyl group of threonine is amide-linked to the side chain amino group of diaminopimelic acid within the peptidoglycan peptide stem. We show that CD2831 protein levels are elevated in the presence of high intracellular cyclic diGMP (c-diGMP) concentrations, in agreement with the control of CD2831 expression by a c-diGMP-dependent type II riboswitch. Low c-diGMP levels induce the release of CD2831 and presumably CD3246 from the surface of cells. This regulation is mediated by proteolytic cleavage of CD2831 and CD3246 by the zinc metalloprotease ZmpI, whose expression is controlled by a type I c-diGMP riboswitch. These data reveal a novel regulatory mechanism for expression of two sortase substrates by the secondary messenger c-diGMP, on which surface anchoring is dependent. PMID: 26283789 [PubMed - indexed for MEDLINE]

Related Articles Metabolic profiling of antioxidants constituents in Artemisia selengensis leaves. Food Chem. 2015 Nov 1;186:123-32 Authors: Zhang L, Tu ZC, Wang H, Fu ZF, Wen QH, Fan D Abstract This study aimed to evaluate the antioxidant potential of Artemisia selengensis Turcz (AST) leaves, a byproduct when processing AST stalk, and identify the antioxidant constituents by using HPLC-QTOF-MS(2). The total phenolics content (TPC), total flavonoids content (TFC) and antioxidant abilities of fractions resulted from the successively partition of chloroform, ethyl acetate and n-butanol were compared. Ethyl acetate fraction (EAF) exhibited the highest TFC (65.44 mg QuE/g fraction), n-butanol fraction (nBuF) showed the highest TPC (384.78 mg GAE/g fraction) and the best DPPH scavenging ability, ABTS(+) scavenging ability and reducing power. Totally, 57 compounds were identified or tentatively identified in nBuF and EAF, 40 of them were reported in AST for the first time. The major constituents in EAF were flavonoids, and the major constituents in nBuF were phenolic acids and organic acids. Thus, AST leaves might be a potential low-cost resource of natural antioxidants. PMID: 25976801 [PubMed - indexed for MEDLINE]

Related Articles Metabonomic Study of the Effects of Acanthopanax senticosus on Peripheral System of Rats. Planta Med. 2015 Jun;81(9):722-32 Authors: Zhang SN, Li XZ, Liu SM, Lu F Abstract Acanthopanax senticosus is extensively used to treat various nervous and cerebrovascular diseases in traditional medicinal systems in China and Russia. Ultrahigh-performance liquid chromatography-quadrupole time-of-flight-mass spectrometry coupled with pattern recognition methods was used to investigate the effects of A. senticosus on the peripheral system in rats. The analysis of possible pathways influenced by A. senticosus was performed with MetaboAnalyst and Cytoscape software. After treatment with A. senticosus, 21 modulated metabolites in heart tissue, 20 in liver tissue, 14 in spleen tissue, 17 in lung tissue, 16 in kidney tissue, and 12 in a serum sample were identified and considered potential biomarkers of A. senticosus treatments. The regulation of some endogenous metabolites by A. senticosus could be beneficial for the treatment of several peripheral system diseases, such as hypertension, cancer, and oxidative stress, etc. However, there were also some upregulated endogenous metabolites producing potential toxicity to the peripheral system. A metabonomic analysis revealed that protection and toxicity coexisted in the effects of A. senticosus on the peripheral system, which may be a practical guide for its safe use and beneficial to the expansion of its application. PMID: 25922912 [PubMed - indexed for MEDLINE]

Related Articles ¹H NMR based serum metabolic profiles associated with pathological progression of pancreatic islet β cell tumor in Rip1-Tag2 mice. Int J Biol Sci. 2015;11(5):595-603 Authors: Yang Y, Liu Y, Zheng L, Zhang Q, Gu Q, Wang L, Wang L Abstract Pancreatic islet β cell tumor is the most common islet cell tumor. A well-characterized tumor progression in Rip1-Tag2 mice undergoes five stages, involving normal, hyperplasia, angiogenic islets, tumorigenesis and invasive carcinoma. (1)H NMR based metabonomics was applied to identify potential biomarkers for monitoring pancreatic islet β cell tumor progression in Rip1-Tag2 mice. Multivariate analysis results showed the serum metabonome at hyperplasia stage shared the similar characteristics with the ones at normal stage as a result of slight proliferation of pancreatic islet β cells. At angiogenic islets stage, the up-regulated glycolysis, disturbed choline and phospholipid metabolism composed the metabolic signature. In addition to the changes mentioned above, several metabolites were identified as early biomarkers for tumorigenesis, including increased methionine, citrate and choline, and reduced acetate, taurine and glucose, which suggested the activated energy and amino acid metabolism. All the changes were aggravated at invasive carcinoma stage, coupled with notable changes in alanine, glutamate and glycine. Moreover, the distinct metabolic phenotype was found associated with the implanting of SV40 large T antigen in Rip1-Tag2 mice. The combined metabolic and multivariate statistics approach provides a robust method for screening the biomarkers of disease progression and examining the association between gene and metabolism. PMID: 25892966 [PubMed - indexed for MEDLINE]

Related Articles How to measure metabolic fluxes: a taxonomic guide for (13)C fluxomics. Curr Opin Biotechnol. 2015 Aug;34:82-90 Authors: Niedenführ S, Wiechert W, Nöh K Abstract Metabolic reaction rates (fluxes) contribute fundamentally to our understanding of metabolic phenotypes and mechanisms of cellular regulation. Stable isotope-based fluxomics integrates experimental data with biochemical networks and mathematical modeling to 'measure' the in vivo fluxes within an organism that are not directly observable. In recent years, (13)C fluxomics has evolved into a technology with great experimental, analytical, and mathematical diversity. This review aims at establishing a unified taxonomy by means of which the various fluxomics methods can be compared to each other. By linking the developed modeling approaches to recent studies, their challenges and opportunities are put into perspective. The proposed classification serves as a guide for scientific 'travelers' who are striving to resolve research questions with the currently available (13)C fluxomics toolset. PMID: 25531408 [PubMed - indexed for MEDLINE]

Related Articles Metabolic profiling study on potential toxicity and immunotoxicity-biomarker discovery in rats treated with cyclophosphamide using HPLC-ESI-IT-TOF-MS. Biomed Chromatogr. 2015 May;29(5):768-76 Authors: Li J, Lin W, Lin W, Xu P, Zhang J, Yang H, Ling X Abstract Despite the recent advances in understanding toxicity mechanism of cyclophosphamide (CTX), the development of biomarkers is still essential. CTX-induced immunotoxicity in rats by a metabonomics approach was investigated using high-performance liquid chromatography coupled with ion trap time-of-flight mass spectrometry (HPLC-ESI-IT-TOF-MS). The rats were orally administered CTX (30 mg/kg/day) for five consecutive days, and on the fifth day samples of urine, thymus and spleen were collected and analyzed. A significant difference in metabolic profiling was observed between the CTX-treated group and the control group by partial least squares-discriminant analysis (PLS-DA), which indicated that metabolic disturbances of immunotoxicity in CTX-treated rats had occurred. One potential biomarker in spleen, three in urine and three in thymus were identified. It is suggested that the CTX-toxicity mechanism may involve the modulation of tryptophan metabolism, phospholipid metabolism and energy metabolism. This research can help to elucidate the CTX-influenced pathways at a low dose and can further help to indicate the patients' pathological status at earlier stages of toxicological progression after drug administration. PMID: 25322901 [PubMed - indexed for MEDLINE]

Identified metabolic signature for assessing red blood cell unit quality is associated with endothelial damage markers and clinical outcomes. Transfusion. 2016 Jan 8; Authors: Bordbar A, Johansson PI, Paglia G, Harrison SJ, Wichuk K, Magnusdottir M, Valgeirsdottir S, Gybel-Brask M, Ostrowski SR, Palsson S, Rolfsson O, Sigurjónsson OE, Hansen MB, Gudmundsson S, Palsson BO Abstract BACKGROUND: There has been interest in determining whether older red blood cell (RBC) units have negative clinical effects. Numerous observational studies have shown that older RBC units are an independent factor for patient mortality. However, recently published randomized clinical trials have shown no difference of clinical outcome for patients receiving old or fresh RBCs. An overlooked but essential issue in assessing RBC unit quality and ultimately designing the necessary clinical trials is a metric for what constitutes an old or fresh RBC unit. STUDY DESIGN AND METHODS: Twenty RBC units were profiled using quantitative metabolomics over 42 days of storage in SAGM with 3- to 4-day time intervals. Metabolic pathway usage during storage was assessed using systems biology methods. The detected time intervals of the metabolic states were compared to clinical outcomes. RESULTS: Using multivariate statistics, we identified a nonlinear decay process exhibiting three distinct metabolic states (Days 0-10, 10-17, and 17-42). Hematologic variables traditionally measured in the transfusion setting (e.g., pH, hemolysis, RBC indices) did not distinguish these three states. Systemic changes in pathway usage occurred between the three states, with key pathways changing in both magnitude and direction. Finally, an association was found between the time periods of the metabolic states with the clinical outcomes of more than 280,000 patients in the country of Denmark transfused over the past 15 years and endothelial damage markers in healthy volunteers undergoing autologous transfusions. CONCLUSION: The state of RBC metabolism may be a better indicator of cellular quality than traditional hematologic variables. PMID: 26749434 [PubMed - as supplied by publisher]

Implication of Metabolomic profiles to wide thermoneutral zone in Mongolian gerbils (Meriones unguiculatus). Integr Zool. 2016 Jan 9; Authors: Shi Y, Wang D Abstract Mongolian gerbils (Meriones unguiculatus) have evolved a wide thermoneutral zone (26.5-38.9 ºC) and high upper critical temperature, and appear to have a high tolerance for heat exposure. Here, we use a metabolomic approach to measure global metabolite profiles for gerbils between lower (27 ºC) and upper critical temperatures (38 ºC) to investigate the role of metabolomic characterization in maintaining basal metabolic rates within a wide thermoneutral zone. We found that in serum and liver, 14 and 19 metabolites were significantly altered, respectively. In the aerobic respiration-related tricarboxylic cycle (TCA), five intermediates (isocitric acid, cis-aconitic acid, α-ketoglutaric acid, fumaric acid and malic acid) were increased in serum in 38 ºC animals; however, no such increase was found in the liver. A stable level of hepatic TCA cycle intermediates may be related to the steady state of aerobic respiration at 38 ºC. Metabolomic results also revealed that acute heat exposure caused increased oxidative stress and low molecular weight antioxidants in Mongolian gerbils. Increased methionine and 2-hydroxybutyrate suggest an accelerated synthesis of glutathione. Increased urate and its precursors, inosine and hypoxanthine, were detected at 38 ºC. Glucuronate, threonate and oxalate involved in ascorbate synthesis and degradation were increased in serum at 38 ºC. In conclusion, although dramatic metabolomic variation was found, a stable hepatic TCA cycle may contribute to maintaining a constant basal metabolic rate within a wide thermoneutral zone in Mongolian gerbils. This article is protected by copyright. All rights reserved. PMID: 26749160 [PubMed - as supplied by publisher]

The Acetyl Group Buffering Action of Carnitine Acetyltransferase Offsets Macronutrient-Induced Lysine Acetylation of Mitochondrial Proteins. Cell Rep. 2015 Dec 30; Authors: Davies MN, Kjalarsdottir L, Thompson JW, Dubois LG, Stevens RD, Ilkayeva OR, Brosnan MJ, Rolph TP, Grimsrud PA, Muoio DM Abstract Lysine acetylation (AcK), a posttranslational modification wherein a two-carbon acetyl group binds covalently to a lysine residue, occurs prominently on mitochondrial proteins and has been linked to metabolic dysfunction. An emergent theory suggests mitochondrial AcK occurs via mass action rather than targeted catalysis. To test this hypothesis, we performed mass spectrometry-based acetylproteomic analyses of quadriceps muscles from mice with skeletal muscle-specific deficiency of carnitine acetyltransferase (CrAT), an enzyme that buffers the mitochondrial acetyl-CoA pool by converting short-chain acyl-CoAs to their membrane permeant acylcarnitine counterparts. CrAT deficiency increased tissue acetyl-CoA levels and susceptibility to diet-induced AcK of broad-ranging mitochondrial proteins, coincident with diminished whole body glucose control. Sub-compartment acetylproteome analyses of muscles from obese mice and humans showed remarkable overrepresentation of mitochondrial matrix proteins. These findings reveal roles for CrAT and L-carnitine in modulating the muscle acetylproteome and provide strong experimental evidence favoring the nonenzymatic carbon pressure model of mitochondrial AcK. PMID: 26748706 [PubMed - as supplied by publisher]

A role for GIBBERELLIN 2-OXIDASE6 and gibberellins in regulating nectar production. Mol Plant. 2015 Dec 31; Authors: Wiesen LB, Bender RL, Paradis T, Larson A, Perera MA, Nikolau BJ, Olszewski NE, Carter CJ Abstract The secretion of floral nectar is tightly regulated by both developmental and temporal cues. Auxin and jasmonic acid were previously reported as having roles in regulating nectar production; however, the effects other phytohormones on this process are unknown. Here we report a role for gibberellins (GAs) in controlling nectar production in Arabidopsis thaliana. Specifically, we demonstrate that GA 2-OXIDASE6 (GA2ox6) is expressed in mature, secretory nectaries, and three independent ga2ox6 mutants display significant decreases in nectar production. On the other hand, overexpression of GA2ox6 in nectaries increases nectar output. These results suggest that elevated GA negatively impacts nectary function. This hypothesis is supported by the finding that known mutants with enhanced GA signaling also display a decrease in total nectar production, and that nectar output is restored to near wild-type levels in ga2ox6 flowers treated with the GA synthesis inhibitor paclobutrazol. Further, ga2ox6 flowers display a downregulation in the expression of genes involved in nectar production, as well as a significant decrease in the nectary auxin response. Cumulatively, these results strongly suggest that GA negatively regulates nectary function via control of the auxin response pathway. PMID: 26748313 [PubMed - as supplied by publisher]

Histo-blood group glycans in the context of personalized medicine. Biochim Biophys Acta. 2015 Dec 31; Authors: Dotz V, Wuhrer M Abstract BACKGROUND: A subset of histo-blood group antigens including ABO and Lewis are oligosaccharide structures which may be conjugated to lipids or proteins. They are known to be important recognition motifs not only in the context of blood transfusions, but also in infection and cancer development. SCOPE OF REVIEW: Current knowledge on the molecular background and the implication of histo-blood group glycans in the prevention and therapy of infectious and non-communicable diseases, such as cancer and cardiovascular disease, is presented. MAJOR CONCLUSIONS: Glycan-based histo-blood groups are associated with intestinal microbiota composition, the risk of various diseases as well as therapeutic success of, e.g., vaccination. Their potential as prebiotic or anti-microbial agents, as disease biomarkers and vaccine targets should be further investigated in future studies. For this, recent and future technological advancements will be of particular importance, especially with regard to the unambiguous structural characterization of the glycan portion in combination with information on the protein and lipid carriers of histo-blood group-active glycans in large cohorts. GENERAL SIGNIFICANCE: Histo-blood group glycans have a unique linking position in the complex network of genes, oncodevelopmental biological processes, and disease mechanisms. Thus, they are highly promising targets for novel approaches in the field of personalized medicine. PMID: 26748235 [PubMed - as supplied by publisher]

NMR-based metabolomic analysis of Haliotis diversicolor exposed to thermal and hypoxic stresses. Sci Total Environ. 2015 Dec 31;545-546:280-288 Authors: Lu J, Shi Y, Wang S, Chen H, Cai S, Feng J Abstract Haliotis diversicolor is a commercially important cultured shellfish. It is also an important marine model organism for environmental science. High temperature accompanied with hypoxia frequently induces diseases or even death to abalones. In present study, (1)H NMR spectroscopy together with pattern recognition methods was used to investigate the responses of muscle and gill of H. diversicolor to thermal and hypoxic stresses. It was found that obvious gender-, time- and tissue-specific metabolic responses were induced by thermal and hypoxic stresses. In combination with the changes of H. diversicolor in physiological features, the dual-modal stresses were suggested to mainly cause the disturbance in energy metabolism and osmotic balance in muscle and gill tissues with different mechanisms. Further, the corresponding correlation networks and metabolic pathways derived from the characteristic metabolites were used to assess the major metabolic functions of these characteristic metabolites. These findings shed some lights on the metabolic influences of environmental stresses on marine organisms. PMID: 26747992 [PubMed - as supplied by publisher]

Serum metabolomics strategy for understanding pharmacological effects of ShenQi pill acting on kidney yang deficiency syndrome. J Chromatogr B Analyt Technol Biomed Life Sci. 2015 Dec 19; Authors: Nan Y, Zhou X, Liu Q, Zhang A, Guan Y, Lin S, Kong L, Han Y, Wang X Abstract Kidney yang deficiency syndrome, a diagnostic pattern in Chinese medicine, is similar with clinical features of the glucocorticoid withdrawal syndrome. The aim of this present study was to explore low molecular mass differentiating metabolites between control group and model group of kidney yang deficiency rats induced with corticosterone as well as the therapeutic effect of Shen Qi Pill, a classic traditional Chinese medicine formula for treating Kidney yang deficiency syndrome in China. This study utilized ultra-performance liquid chromatography coupled with electrospray ionization synapt quadrupole time-of-flight high definition mass spectrometry (UPLC/ESI-SYNAPT-QTOF-HDMS) to identify the underlying biomarkers for clarifying mechanism of Shen Qi Pill in treating Kidney yang deficiency syndrome based on metabolite profiling of the serum samples and in conjunction with multivariate and pathway analysis. Meanwhile, blood biochemistry assay and histopathology were examined to identify specific changes in the model group rats. Distinct changes in the pattern of metabolites were observed by UPLC-HDMS. The changes in metabolic profiling were restored to their baseline values after treatment with Shen Qi Pill according to the combined with a principal component analysis (PCA) score plots. Altogether, the current metabolomics approach based on UPLC-HDMS and orthogonal projection to latent structures discriminate analysis (OPLS-DA) demonstrated 27 ions (18 in the negative mode, 9 in the positive mode, 17 ions restored by Shen Qi Pill). These results indicated that effectiveness of Shen Qi Pill in Kidney yang deficiency syndrome rats induced a substantial change in the metabolic profiles by regulating the biomarkers and adjusting the metabolic disorder. It suggested that the metabolomics approach was a powerful approach for elucidation of pathologic changes of Chinese medicine syndrome and action mechanisms of traditional Chinese medicine. PMID: 26747643 [PubMed - as supplied by publisher]

Chronical sleep interruption-induced cognitive decline assessed by a metabolomics method. Behav Brain Res. 2015 Dec 30; Authors: Feng L, Wu HW, Song GQ, Lu C, Li YH, Qu LN, Chen SG, Liu XM, Chang Q Abstract Good sleep is necessary for optimal health, especially for mental health. Insomnia, sleep deprivation will make your ability to learn and memory impaired. Nevertheless, the underlying pathophysiological mechanism of sleep disorders-induced cognitive decline is still largely unknown. In this study, the sleep deprivation of animal model was induced by chronical sleep interruption (CSI), the behavioral tests, biochemical index determinations, and a liquid chromatography-mass spectrometry (LC-MS) based serum metabolic profiling analysis were performed to explore the effects of CSI on cognitive function and the underlying mechanisms. After 14-days CSI, the cognitive function of the mice was evaluated by new objects preference (NOP) task and temporal order judgment (TOJ) task. Serum corticosterone (CORT), and brain Malondialdehyde (MDA), Superoxide Dismutase (SOD), and Catalase (CAT) levels were determined by ELISA kits. Data were analyzed by Principal Component Analysis (PCA), Partial Least Squares project to latent structures-Discriminant Analysis (PLS-DA), and Student's t-test. We found that the cognitive function of the mice was significantly affected by CSI. Besides, levels of CORT and MDA were higher, and SOD and CAT were lower in CSI mice than those of control. Obvious body weight loss of CSI mice was also observed. Thirteen potential serum biomarkers including choline, valine, uric acid, allantoic acid, carnitines, and retinoids were identified. Affected metabolic pathways involve metabolism of purine, retinoid, lipids, and amino acid. These results showed that CSI can damage the cognitive performance notably. The cognitive decline may ascribe to excessive oxidative stress and a series of disturbed metabolic pathways. PMID: 26747207 [PubMed - as supplied by publisher]

UHPLC/Q-TOFMS-based metabolomics for the characterization of cold and hot properties of Chinese Materia Medica. J Ethnopharmacol. 2015 Dec 30; Authors: Wang Y, Zhou S, Wang M, Liu S, Hu Y, He C, Li P, Wan JB Abstract ETHNOPHARMACOLOGICAL RELEVANCE: The cold/hot property of Chinese materia medica (CMM) and the application of its corresponding knowledge in the diagnosis, differentiation and treatment of diseases have been considered to be the extremely important part of traditional Chinese medicine (TCM). As highly abstracted TCM theory, the cold/hot property of CMMs is still not fully understood and remains to be elucidated by systems biology approach. The cold and hot properties of CMM are mainly defined by the response of the body to a given CMM. Metabolomics, is a promising systems biology method to profile entire endogenous metabolites and monitor their fluctuations related to an exogenous stimulus. Thus, a metabolomics approach was applied to characterize the cold and hot properties of CMMs. MATERIAL AND METHODS: Mice were intragastrically administered three selected cold property CMMs (i.e., Rheum palmatum L., radix et rhizoma; Coptis chinensis Franch, rhizome and Scutellaria baicalensis Georgi, radix) and three hot property TCMMs (i.e., Cinnamomum cassia (L.) J. Presl, cortex; Zingiber officinale Roscoe, rhizoma and Evodia rutaecarpa (Juss.) Benth., fructus) once daily for one week. The comprehensive metabolome changes in the plasma of mice after treatment with cold or hot property CMMs were characterized by ultra-high performance liquid chromatography/time of flight mass spectrometry (UHPLC/Q-TOF-MS), and the potential biomarkers related to cold and hot properties of CMM were explored. RESULTS: Metabolites perturbation in plasma occurs after treatment of cold CMMs and hot CMMs in mice, and 15 and 16 differential biomarkers were identified to be associated with the cold and hot properties of CMMs, respectively. Among them, LPC (18:0), LPC (18:1), LPC (20:4) and LPC (20:5) showed decreased trends in the cold property CMM treated groups, but increased in the hot property CMM treated groups. CONCLUSIONS: There is a strong connection between the cold/hot property of CMMs and lysophosphatidylcholines metabolism. This study offers new insight into CMM properties and their clinical application. PMID: 26747020 [PubMed - as supplied by publisher]

Recommendations and Standardization of Biomarker Quantification Using NMR-based Metabolomics with Particular Focus on Urinary Analysis. J Proteome Res. 2016 Jan 8; Authors: Emwas AH, Roy R, McKay RT, Ryan D, Brennan L, Tenori L, Luchinat C, Gao X, Zeri AC, Gowda GA, Raftery D, Steinbeck C, Salek RM, Wishart DS Abstract NMR-based metabolomics has shown considerable promise in disease diagnosis and biomarker discovery because it allows one to non-destructively identify and quantify large numbers of novel metabolite biomarkers in both biofluids and tissues. Indeed, precise metabolite quantification is a necessary prerequisite to move any chemical biomarker or biomarker panel from the lab into the clinic. Among the many biofluids (urine, serum, plasma, cerebrospinal fluid and saliva) commonly used for disease diagnosis and prognosis, urine has several advantages. It is abundant, sterile, easily obtained, needs little sample preparation and does not require any invasive medical procedures for collection. Furthermore, urine captures and concentrates many "unwanted" or "undesirable" compounds throughout the body, thereby providing a rich source of potentially useful disease biomarkers. However, the incredible variation in urine chemical concentrations due to effects such as gender, age, diet, life style, health conditions, and physical activity make the analysis of urine and the identification of useful urinary biomarkers by NMR quite challenging. In this review, we discuss a number of the most significant issues regarding NMR-based urinary metabolomics with a specific emphasis on metabolite quantification for disease biomarker applications. We also propose a number of data collection and instrumental recommendations regarding NMR pulse sequences, acceptable acquisition parameter ranges, relaxation effects on quantitation, proper handling of instrumental differences, as well as recommendations regarding sample preparation and biomarker assessment. PMID: 26745651 [PubMed - as supplied by publisher]

Aberrant purine metabolism in allergic asthma revealed by plasma metabolomics. J Pharm Biomed Anal. 2015 Dec 17;120:181-189 Authors: Yu M, Cui FX, Jia HM, Zhou C, Yang Y, Zhang HW, Ding G, Zou ZM Abstract Asthma is a disease characterized by chronic relapsing airways, and its etiology remains incompletely understood. To better understand the metabolic phenotypes of asthma, we investigated a plasma metabolic signature associated with allergic asthma in ovalbumin (OVA)-sensitized mice by using ultra high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF/MS). Sixteen metabolites were characterized as potential pathological biomarkers related to asthma. Among them, 6 (dodecanoic acid (P1), myristic acid (P2), phytosphingosine (P3), sphinganine (P4), inosine (P13) and taurocholic acid (P15)) were first reported to have potential relevance in the pathogenesis of experimental asthma. The identified potential biomarkers were involved in 6 metabolic pathways and achieved the most entire metabolome contributing to the formation of allergic asthma. Purine metabolism was the most prominently influenced in OVA-induced asthma mice according to the metabolic pathway analysis (MetPA), suggesting that significantly changes in inflammatory responses in the pathophysiologic process of asthma. The metabolites of purine metabolism, especially uric acid (P12) and inosine (P13), may denote their potential as targeted biomarkers related to experimental asthma. The decreased plasma uric acid (P12) suggested that inflammation responses of allergic asthma inhibited the activity of xanthine oxidase in purine metabolism, and manifested the severity of asthma exacerbation. The increased level of inosine (P13) suggests that inflammatory cells induce adenosine triphosphate (ATP) breakdown, resulting in excessive expression of adenosine deaminase (ADA) in the formation of allergic asthma. These findings provided a novel perspective on the metabolites signatures related to allergic asthma, which provided us with new insights into the pathogenesis of asthma, and the discovery of targets for clinical diagnosis and treatment. PMID: 26744988 [PubMed - as supplied by publisher]

The ratio of phosphatidylcholines to lysophosphatidylcholines in plasma differentiates healthy controls from patients with Alzheimer's disease and mild cognitive impairment. Alzheimers Dement (Amst). 2015 Sep 2;1(3):295-302 Authors: Klavins K, Koal T, Dallmann G, Marksteiner J, Kemmler G, Humpel C Abstract BACKGROUND: Metabolomic processes have been identified as being strongly linked to the development of Alzheimer's disease (AD). Thus, lipid metabolites appear to be highly useful as diagnostic substrates for the diagnosis of AD and mild cognitive impairment (MCI) in plasma. METHODS: We analyzed plasma samples from controls (n = 35), MCI (n = 33), and AD patients (n = 43) using the AbsoluteIDQ p180 Kit (Biocrates Life Sciences), which included quantitative analysis of 40 acylcarnitines, 21 amino acids, 19 biogenic amines, 15 sphingolipids, 90 glycerophospholipids, and sum of hexoses. RESULTS: We found that individual lipid metabolites can differentiate controls from MCI and AD with relevant significance. However, the ratio between PC aa C34:4 and lysoPC a C18:2 differentiates controls from MCI (P = .0000007) and from AD (P = .0000009) with greater significance. CONCLUSIONS: The results provide evidence that the ratio of these two lipid metabolites is useful for diagnosing MCI and AD with an accuracy of 82%-85%. PMID: 26744734 [PubMed - as supplied by publisher]

Oxygen-dependent regulation of c-di-GMP synthesis by SadC controls alginate production in Pseudomonas aeruginosa. Environ Microbiol. 2016 Jan 6; Authors: Schmidt A, Hammerbacher AS, Bastian M, Nieken KJ, Klockgether J, Merighi M, Lapouge K, Poschgan C, Kölle J, Acharya KR, Ulrich M, Tümmler B, Unden G, Kaever V, Lory S, Haas D, Schwarz S, Döring G Abstract Pseudomonas aeruginosa produces increased levels of alginate in response to oxygen-deprived conditions. The regulatory pathway(s) that links oxygen limitation to increased synthesis of alginate has remained elusive. In the present study, using immunofluorescence microscopy, we show that anaerobiosis-induced alginate production by planktonic PAO1 requires the diguanylate cyclase (DGC) SadC, previously identified as a regulator of surface-associated lifestyles. Furthermore, we found that the gene products of PA4330 and PA4331, located in a predicted operon with sadC, have a major impact on alginate production: Deletion of PA4330 (odaA, for oxygen-dependent alginate synthesis activator) caused an alginate production defect under anaerobic conditions whereas a PA4331 (odaI, for oxygen-dependent alginate synthesis inhibitor) deletion mutant produced alginate also in the presence of oxygen, which would normally inhibit alginate synthesis. Based on their sequence, OdaA and OdaI have predicted hydratase and dioxygenase reductase activity, respectively. Enzymatic assays using purified protein showed that unlike OdaA, which did not significantly affect DGC activity of SadC, OdaI inhibited c-di-GMP production by SadC. Our data indicate that SadC, OdaA and OdaI are components of a novel response pathway of P. aeruginosa that regulates alginate synthesis in an oxygen-dependent manner. PMID: 26743546 [PubMed - as supplied by publisher]

An integrated strategy to quantitatively differentiate chemome between Cistanche deserticola and C. tubulosa using high performance liquid chromatography-hybrid triple quadrupole-linear ion trap mass spectrometry. J Chromatogr A. 2015 Dec 21; Authors: Song Y, Song Q, Li J, Zhang N, Zhao Y, Liu X, Jiang Y, Tu P Abstract It is important to conduct large-scale detection, identification, and quantitation of metabolites in a given sample. Herein, a practical strategy was proposed to quantitatively compare the chemome between Cistanche deserticola (CD) and C. tubulosa (CT), which have been widely believed as the ideal edible and medicinal plants for conquering the deserts. The entire workflow was implemented on high performance liquid chromatography-hybrid triple quadrupole-linear ion trap mass spectrometer and consisted of three primary steps: (1) component detection and identification, various mass spectrometric approaches were applied to globally screen the chemical constituents, and structural elucidation was achieved by comparing with authentic compounds, analyzing MS(2) spectra, and referring to the literature along with accessible databases; (2) comprehensive relative quantitation, scheduled multiple reaction monitoring algorithm was introduced for relative quantitation of all detected ingredients; and (3) chemome comparison, the quantitative dataset was subjected for multivariate statistical analysis to carry out comparative study. A total of 513 metabolites were detected and relatively quantitated, and 379 ones were annotated. Betaine, Krebs cycle intermediates, phenylethanoid glycosides, and iridoids were picked out as the chemical markers being responsible for the discrimination of the chemical profiles between CD and CT. Above all, the quantitative chemome of CD and CT were exhaustively characterized and compared, which could advance their values concerning drug development, economics, and desertification control. The proposed strategy is expected as a reliable choice for widely targeted metabolomics of plants. PMID: 26742897 [PubMed - as supplied by publisher]