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: 17 min 19 sec ago

Validation of a multi-analyte HPLC-DAD method for determination of uric acid, creatinine, homovanillic acid, niacinamide, hippuric acid, indole-3-acetic acid and 2-methylhippuric acid in human urine.

Wed, 08/07/2015 - 15:31
Validation of a multi-analyte HPLC-DAD method for determination of uric acid, creatinine, homovanillic acid, niacinamide, hippuric acid, indole-3-acetic acid and 2-methylhippuric acid in human urine. J Chromatogr B Analyt Technol Biomed Life Sci. 2015 Jun 24;998-999:40-44 Authors: Remane D, Grunwald S, Hoeke H, Mueller A, Roeder S, von Bergen M, Wissenbach DK Abstract During the last decades exposure sciences and epidemiological studies attracts more attention to unravel the mechanisms for the development of chronic diseases. According to this an existing HPLC-DAD method for determination of creatinine in urine samples was expended for seven analytes and validated. Creatinine, uric acid, homovanillic acid, niacinamide, hippuric acid, indole-3-acetic acid, and 2-methylhippuric acid were separated by gradient elution (formate buffer/methanol) using an Eclipse Plus C18 Rapid Resolution column (4.6mm×100mm). No interfering signals were detected in mobile phase. After injection of blank urine samples signals for the endogenous compounds but no interferences were detected. All analytes were linear in the selected calibration range and a non weighted calibration model was chosen. Bias, intra-day and inter-day precision for all analytes were below 20% for quality control (QC) low and below 10% for QC medium and high. The limits of quantification in mobile phase were in line with reported reference values but had to be adjusted in urine for homovanillic acid (45mg/L), niacinamide 58.5(mg/L), and indole-3-acetic acid (63mg/L). Comparison of creatinine data obtained by the existing method with those of the developed method showing differences from -120mg/L to +110mg/L with a mean of differences of 29.0mg/L for 50 authentic urine samples. Analyzing 50 authentic urine samples, uric acid, creatinine, hippuric acid, and 2-methylhippuric acid were detected in (nearly) all samples. However, homovanillic acid was detected in 40%, niacinamide in 4% and indole-3-acetic acid was never detected within the selected samples. PMID: 26151191 [PubMed - as supplied by publisher]

Metabolic dysregulation induced in Plasmodium falciparum by dihydroartemisinin and other front line antimalarial drugs.

Wed, 08/07/2015 - 15:31
Metabolic dysregulation induced in Plasmodium falciparum by dihydroartemisinin and other front line antimalarial drugs. J Infect Dis. 2015 Jul 6; Authors: Cobbold SA, Chua HH, Nijagal B, Creek DJ, Ralph SA, McConville MJ Abstract Detailed information on the mode of action of antimalarial drugs can be used to improve existing drugs, identify new drug targets and understand the basis of drug resistance. In this study we describe the use of a time-resolved, mass spectrometric-based metabolite profiling approach to map the metabolic perturbations induced by a panel of clinical antimalarial drugs and inhibitors on Plasmodium falciparum asexual blood stages. Drug-induced changes in metabolite levels in P. falciparum-infected erythrocytes were monitored over time using gas chromatography-mass spectrometry and liquid chromatography-mass spectrometry and changes in specific metabolic fluxes confirmed by non-stationary (13)C-glucose labelling. Dihydroartemisinin (DHA) was found to disrupt haemoglobin catabolism within one hour of exposure, resulting in a transient decrease in haemoglobin-derived peptides. Unexpectedly, DHA also disrupted pyrimidine biosynthesis resulting in increased (13)C-glucose flux towards malate production, potentially explaining the susceptibility of P. falciparum to DHA during early blood-stage development. Unique metabolic signatures were also found for atovaquone, chloroquine, proguanil, cycloguanil and methylene blue. We also show this approach can be used to identify the mode of action of novel antimalarials, such as the compound Torin 2, which we show here inhibits haemoglobin catabolism. PMID: 26150544 [PubMed - as supplied by publisher]

Cross-sectional examination of metabolites and metabolic phenotypes in uremia.

Wed, 08/07/2015 - 15:31
Cross-sectional examination of metabolites and metabolic phenotypes in uremia. BMC Nephrol. 2015;16(1):98 Authors: Kalim S, Clish CB, Deferio JJ, Ortiz G, Moffet AS, Gerszten RE, Thadhani R, Rhee EP Abstract BACKGROUND: Although metabolomic approaches have begun to document numerous changes that arise in end stage renal disease (ESRD), how these alterations relate to established metabolic phenotypes in uremia is unknown. METHODS: In 200 incident hemodialysis patients we used partial least squares discriminant analysis to identify which among 166 metabolites could best discriminate individuals with or without diabetes, and across tertiles of body mass index, serum albumin, total cholesterol, and systolic blood pressure. RESULTS: Our data do not recapitulate metabolomic signatures of diabetes and obesity identified among individuals with normal renal function (e.g. elevations in branched chain and aromatic amino acids) and highlight several potential markers of diabetes status specific to ESRD, including xanthosine-5-phosphate and vanillylmandelic acid. Further, our data identify significant associations between elevated tryptophan and long-chain acylcarnitine levels and both decreased total cholesterol and systolic blood pressure in ESRD. Higher tryptophan levels were also associated with higher serum albumin levels, but this may reflect tryptophan's significant albumin binding. Finally, an examination of the uremic retention solutes captured by our platform in relation to 24 clinical phenotypes provides a framework for investigating mechanisms of uremic toxicity. CONCLUSIONS: In sum, these studies leveraging metabolomic and metabolic phenotype data acquired in a well-characterized ESRD cohort demonstrate striking differences from metabolomics studies in the general population, and may provide clues to novel functional pathways in the ESRD population. PMID: 26149577 [PubMed - as supplied by publisher]

Metabolomic Responses of Human Hepatocytes to Emodin, Aristolochic Acid, and Triptolide: Chemicals Purified from Traditional Chinese Medicines.

Wed, 08/07/2015 - 15:31
Metabolomic Responses of Human Hepatocytes to Emodin, Aristolochic Acid, and Triptolide: Chemicals Purified from Traditional Chinese Medicines. J Biochem Mol Toxicol. 2015 Jul 7; Authors: Liu X, Liu Y, Cheng M, Xiao H Abstract The present study was undertaken to investigate the metabolic responses of human liver cells HL-7702 on chemicals purified from traditional Chinese medicine: emodin, triptolide, and aristolochic acid. Cytotoxicity tests demonstrated a dose-dependent toxic effect of emodin, triptolide, and aristolochic acid on HL7702 cells for 48 h. Emodin (14 μM), aristolochic acid (12 μg/mL), or triptolide (18 nM) was individually administrated to HL7702 and cell samples were collected after 48 h for metabolites extraction and analysis. Pattern recognition analysis reflected the significant difference in metabolic profiles between chemical-treated groups and the control group. Finally, eight metabolites including N1 -acetylspermidine, Glu Gly, N-undecanoylglycine, C16 sphinganine, sphinganine, glutathione, l-palmitoylcarnitine, and elaidic carnitine were detected as potential common biomarkers. Three pathways including sphinganine metabolism, fatty acid oxidation, and oxidative stress were identified. Our findings indicated that metabolomics would be an efficient approach to understand the molecular mechanism of hepatotoxicity induced by chemicals. PMID: 26149242 [PubMed - as supplied by publisher]

Shedding metabo'light' on the search for sepsis biomarkers.

Wed, 08/07/2015 - 15:31
Shedding metabo'light' on the search for sepsis biomarkers. Crit Care. 2015;19(1):277 Authors: Dos Santos CC Abstract The clinical presentation of severe infection with generalized inflammation is similar, if not identical, to systemic inflammation induced by sterile tissue injury. Novel models and unbiased technologies are urgently needed for biomarker identification and disease profiling in sepsis. Here we briefly review the article of Kamisoglu and colleagues in this issue of Critical Care on comparing metabolomics data from different studies to assess whether responses elicited by endotoxin recapitulate, at least in part, those seen in clinical sepsis. PMID: 26148483 [PubMed - as supplied by publisher]

Glyoxylate, a new marker metabolite of type 2 diabetes.

Wed, 08/07/2015 - 15:31
Related Articles Glyoxylate, a new marker metabolite of type 2 diabetes. J Diabetes Res. 2014;2014:685204 Authors: Nikiforova VJ, Giesbertz P, Wiemer J, Bethan B, Looser R, Liebenberg V, Ruiz Noppinger P, Daniel H, Rein D Abstract Type 2 diabetes (T2D) is characterized by a variety of metabolic impairments that are closely linked to nonenzymatic glycation reactions of proteins and peptides resulting in advanced glycation end-products (AGEs). Reactive aldehydes derived from sugars play an important role in the generation of AGEs. Using metabolite profiling to characterize human plasma from diabetic versus nondiabetic subjects we observed in a recent study that the reactive aldehyde glyoxylate was increased before high levels of plasma glucose, typical for a diabetic condition, could be measured. Following this observation, we explored the relevance of increased glyoxylate in diabetic subjects and in diabetic C57BLKS/J-Lepr (db/db (-/-)) mice in the pathophysiology of diabetes. A retrospective study using samples of long-term blood donors revealed that glyoxylate levels unlike glucose levels became significantly elevated up to 3 years prior to diabetes diagnosis (difference to control P = 0.034). Elevated glyoxylate levels impact on newly identified mechanisms linking hyperglycemia and AGE production with diabetes-associated complications such as diabetic nephropathy. Glyoxylate in its metabolic network may serve as an early marker in diabetes diagnosis with predictive qualities for associated complications and as potential to guide the development of new antidiabetic therapies. PMID: 25525609 [PubMed - indexed for MEDLINE]

Radiosensitization by a novel Bcl-2 and Bcl-XL inhibitor S44563 in small-cell lung cancer.

Wed, 08/07/2015 - 15:31
Related Articles Radiosensitization by a novel Bcl-2 and Bcl-XL inhibitor S44563 in small-cell lung cancer. Cell Death Dis. 2014;5:e1423 Authors: Loriot Y, Mordant P, Dugue D, Geneste O, Gombos A, Opolon P, Guegan J, Perfettini JL, Pierre A, Berthier LK, Kroemer G, Soria JC, Depil S, Deutsch E Abstract Radiotherapy has a critical role in the treatment of small-cell lung cancer (SCLC). The effectiveness of radiation in SCLC remains limited as resistance results from defects in apoptosis. In the current study, we investigated whether using the Bcl-2/Bcl-XL inhibitor S44563 can enhance radiosensitivity of SCLC cells in vitro and in vivo. In vitro studies confirmed that S44563 caused SCLC cells to acquire hallmarks of apoptosis. S44563 markedly enhanced the sensitivity of SCLC cells to radiation, as determined by a clonogenic assay. The combination of S44563 and cisplatin-based chemo-radiation showed a significant tumor growth delay and increased overall survival in mouse xenograft models. This positive interaction was greater when S44563 was given after the completion of the radiation, which might be explained by the radiation-induced overexpression of anti-apoptotic proteins secondary to activation of the NF-κB pathway. These data underline the possibility of combining IR and Bcl-2/Bcl-XL inhibition in the treatment of SCLC as they underscore the importance of administering conventional and targeted therapies in an optimal sequence. PMID: 25232677 [PubMed - indexed for MEDLINE]

Molecular and physiological stages of priming: how plants prepare for environmental challenges.

Wed, 08/07/2015 - 15:31
Related Articles Molecular and physiological stages of priming: how plants prepare for environmental challenges. Plant Cell Rep. 2014 Dec;33(12):1935-49 Authors: Gamir J, Sánchez-Bel P, Flors V Abstract Being sessile organisms, plants must respond to various challenges in the environment. The priming process consists of three clear stages. The first stage includes all the cellular changes in the absence of the challenge so-called pre-challenge priming stage. These changes are expected to be rather subtle, affecting the preparation of the plant to properly manage subsequent responses to pathogens with no major fitness costs. Most of the research that has been conducted at this stage has been dedicated to the study of changes in gene expression and protein phosphorylation. However, the metabolic changes that occur during the pre-challenge priming stage are poorly understood. The second stage affects the early to late stages of the defence response, which occurs after the interaction with a pathogen has been established. Most studies involving priming are dedicated to the molecular events that take place during this stage. Most studies have shown that defence priming is strongly hormonally regulated; however, there is also evidence of the involvement of phenolic derivative compounds and many other secondary metabolites, leading to stronger and faster plant responses. The third priming phase ranges from long lasting defence priming to trans-generational acquired resistance. Long-term metabolic transitions, that occur in the offspring of primed plants, remain to be elucidated. Here we review existing information in the literature that relates to the metabolic changes that occur during all three defence priming stages and highlight the metabolic transitions that are associated with the stimulation of priming and the characteristics of the pathogens whenever possible. PMID: 25113544 [PubMed - indexed for MEDLINE]

A 1H-NMR Based Study on Hemolymph Metabolomics in Eri Silkworm after Oral Administration of 1-Deoxynojirimycin.

Tue, 07/07/2015 - 13:54
A 1H-NMR Based Study on Hemolymph Metabolomics in Eri Silkworm after Oral Administration of 1-Deoxynojirimycin. PLoS One. 2015;10(7):e0131696 Authors: Deng MJ, Lin XD, Lin QT, Wen DF, Zhang ML, Wang XQ, Gao HC, Xu JP Abstract We aimed to investigate whether 1-deoxynojirimycin (DNJ) modulates glycometabolism and has toxicity in Eri silkworm (Samia cynthia ricini, Saturniidae). In this paper, hemolymph metabolites were used to explore metabolic changes after oral administration of DNJ or mulberry latex and to characterize the biological function of DNJ at the metabolic and systemic levels. Hemolymph samples were collected from fourth-instar larvae of Eri silkworm and ex-vivo high-resolution 1H nuclear magnetic resonance (NMR) spectra were acquired from the collected hemolymph samples. Then the obtained spectra were analyzed by principal component analysis (PCA) and independent-samples t-test. Metabolic pattern recognition analysis of hemolymph samples indicated that the groups of 0.25% DNJ, latex, and the mixture of 0.5% DNJ and latex (1:1) were significantly different from the control group. Moreover, compared to the control group, the groups of 0.25% DNJ, latex, and the mixture of 0.5% DNJ and latex (1:1) showed the decreased levels of citrate, succinate, fumarate, malate, and glutamine in hemolymph, the groups of 0.25% DNJ and the mixture of 0.5% DNJ and latex (1:1) showed the increased levels of trehalose and lactate. In addition, mulberry leaves exude latex was highly toxic to Eri silkworm because rich unidentified high-molecular-weight factor (s) acted as toxic substances. In our results, latex caused 20 deaths among 50 fourth-instar larvae of Eri silkmoth, but DNJ or the mixture did not caused death. All these results suggest that DNJ has a positive impact on the reverse glycometabolism by modulating glycometabolism and inhibiting glucogenesis and energy metabolism. DNJ is a secure substance as a single-ingredient antidiabetic medicine due to its nontoxicity and bioactivity. PMID: 26148185 [PubMed - as supplied by publisher]

Data Normalization of (1)H-NMR Metabolite Fingerprinting Datasets in the Presence of Unbalanced Metabolite Regulation.

Tue, 07/07/2015 - 13:54
Data Normalization of (1)H-NMR Metabolite Fingerprinting Datasets in the Presence of Unbalanced Metabolite Regulation. J Proteome Res. 2015 Jul 6; Authors: Hochrein J, Zacharias HU, Taruttis F, Samol C, Engelmann JC, Spang R, Oefner PJ, Gronwald W Abstract Data normalization is an essential step in NMR-based metabolomics. Conducted properly, it improves data quality and removes unwanted biases. The choice of the appropriate normalization method is critical and depends on the inherent properties of the dataset in question. In particular, the presence of unbalanced metabolic regulation, where the different specimens and cohorts under investigation do not contain approximately equal shares of up- and down-regulated features, may strongly influence data normalization. Here, we demonstrate the suitability of the Shapiro-Wilk-Test to detect such unbalanced regulation. Next, employing a Latin-square design consisting of eight metabolites spiked into a urine specimen at eight different known concentrations, we show that commonly used normalization and scaling methods fail to retrieve true metabolite concentrations in the presence of increasing amounts of glucose added to simulate unbalanced regulation. However, by learning the normalization parameters on a subset of non-regulated features only, Linear Baseline Normalization, Probabilistic Quotient Normalization and Variance Stabilization Normalization were found to account well for different dilutions of the samples without distorting the true spike-in levels even in the presence of marked unbalanced metabolic regulation. Finally, the methods described were applied successfully to a real world example of unbalanced regulation, namely a set of plasma specimens collected from patients with and without acute kidney injury after cardiac surgery with cardiopulmonary bypass use. PMID: 26147738 [PubMed - as supplied by publisher]

Serum metabolomics in animal models and human disease.

Tue, 07/07/2015 - 13:54
Serum metabolomics in animal models and human disease. Curr Opin Clin Nutr Metab Care. 2015 Jul 2; Authors: James EL, Parkinson EK Abstract PURPOSE OF REVIEW: The aim of this study is to highlight some recent uses of serum metabolomics in human and animal studies. The main themes are the importance of understanding the underlying variation in human metabolism and the use of serum metabolomics in disease profiling. RECENT FINDINGS: Several studies have attempted to use serum metabolomics to develop noninvasive biomarkers of disease and/or track the consequences of nutritional and genetic interventions. Many advances have been made with common changes being identified in ageing, the menopause and cancer but several problems of interpretation have emerged from these studies. These include the small sample sizes in most human studies and the differences between human and rodent metabolomes. However, a metabolic screen of over 1000 'healthy' humans (the Humsermet project) has highlighted many variables that may be used to refine the interpretation and design of previous and future human studies alike, in addition to data mining. SUMMARY: Some common serum metabolome alterations have been identified but many inconsistencies remain. The construction of a human serum metabolome database should be informative in the design of future human and animal model studies. PMID: 26147529 [PubMed - as supplied by publisher]

Energy Metabolism Disorder as a Contributing Factor of Rheumatoid Arthritis: A Comparative Proteomic and Metabolomic Study.

Tue, 07/07/2015 - 13:54
Energy Metabolism Disorder as a Contributing Factor of Rheumatoid Arthritis: A Comparative Proteomic and Metabolomic Study. PLoS One. 2015;10(7):e0132695 Authors: Yang XY, Zheng KD, Lin K, Zheng G, Zou H, Wang JM, Lin YY, Chuka CM, Ge RS, Zhai W, Wang JG Abstract OBJECTIVES: To explore the pathogenesis of rheumatoid arthritis (RA), the different metabolites were screened in synovial fluid by metabolomics. METHODS: Synovial fluid from 25 RA patients and 10 normal subjects were analyzed by GC/TOF MS analysis so as to give a broad overview of synovial fluid metabolites. The metabolic profiles of RA patients and normal subjects were compared using multivariate statistical analysis. Different proteins were verified by qPCR and western blot. Different metabolites were verified by colorimetric assay kit in 25 inactive RA patients, 25 active RA patients and 20 normal subjects. The influence of hypoxia-inducible factor (HIF)-1α pathway on catabolism was detected by HIF-1α knockdown. RESULTS: A subset of 58 metabolites was identified, in which the concentrations of 7 metabolites related to energy metabolism were significantly different as shown by importance in the projection (VIP) (VIP≥1) and Student's t-test (p<0.05). In the 7 metabolites, the concentration of glucose was decreased, and the concentration of lactic acid was increased in the synovial fluid of RA patients than normal subjects verified by colorimetric assay Kit. Receiver operator characteristic (ROC) analysis shows that the concentration of glucose and lactic acid in synovial fluid could be used as dependable biomarkers for the diagnosis of active RA, provided an AUC of 0.906 and 0.922. Sensitivity and specificity, which were determined by cut-off points, reached 84% and 96% in sensitivity and 95% and 85% in specificity, respectively. The verification of different proteins identified in our previous proteomic study shows that the enzymes of anaerobic catabolism were up-regulated (PFKP and LDHA), and the enzymes of aerobic oxidation and fatty acid oxidation were down-regulated (CS, DLST, PGD, ACSL4, ACADVL and HADHA) in RA patients. The expression of HIF-1α and the enzymes of aerobic oxidation and fatty acid oxidation were decreased and the enzymes of anaerobic catabolism were increased in FLS cells after HIF-1α knockdown. CONCLUSION: It was found that enhanced anaerobic catabolism and reduced aerobic oxidation regulated by HIF pathway are newly recognized factors contributing to the progression of RA, and low glucose and high lactic acid concentration in synovial fluid may be the potential biomarker of RA. PMID: 26147000 [PubMed - as supplied by publisher]

First-Trimester Serum Acylcarnitine Levels to Predict Preeclampsia: A Metabolomics Approach.

Tue, 07/07/2015 - 13:54
First-Trimester Serum Acylcarnitine Levels to Predict Preeclampsia: A Metabolomics Approach. Dis Markers. 2015;2015:857108 Authors: Koster MP, Vreeken RJ, Harms AC, Dane AD, Kuc S, Schielen PC, Hankemeier T, Berger R, Visser GH, Pennings JL Abstract Objective. To expand the search for preeclampsia (PE) metabolomics biomarkers through the analysis of acylcarnitines in first-trimester maternal serum. Methods. This was a nested case-control study using serum from pregnant women, drawn between 8 and 14 weeks of gestational age. Metabolites were measured using an UPLC-MS/MS based method. Concentrations were compared between controls (n = 500) and early-onset- (EO-) PE (n = 68) or late-onset- (LO-) PE (n = 99) women. Metabolites with a false discovery rate <10% for both EO-PE and LO-PE were selected and added to prediction models based on maternal characteristics (MC), mean arterial pressure (MAP), and previously established biomarkers (PAPPA, PLGF, and taurine). Results. Twelve metabolites were significantly different between EO-PE women and controls, with effect levels between -18% and 29%. For LO-PE, 11 metabolites were significantly different with effect sizes between -8% and 24%. Nine metabolites were significantly different for both comparisons. The best prediction model for EO-PE consisted of MC, MAP, PAPPA, PLGF, taurine, and stearoylcarnitine (AUC = 0.784). The best prediction model for LO-PE consisted of MC, MAP, PAPPA, PLGF, and stearoylcarnitine (AUC = 0.700). Conclusion. This study identified stearoylcarnitine as a novel metabolomics biomarker for EO-PE and LO-PE. Nevertheless, metabolomics-based assays for predicting PE are not yet suitable for clinical implementation. PMID: 26146448 [PubMed - as supplied by publisher]

What was old is new again: using the host response to diagnose infectious disease.

Tue, 07/07/2015 - 13:54
What was old is new again: using the host response to diagnose infectious disease. Expert Rev Mol Diagn. 2015 Jul 4;:1-16 Authors: Ko ER, Yang WE, McClain MT, Woods CW, Ginsburg GS, Tsalik EL Abstract A century of advances in infectious disease diagnosis and treatment changed the face of medicine. However, challenges continue to develop including multi-drug resistance, globalization that increases pandemic risks and high mortality from severe infections. These challenges can be mitigated through improved diagnostics, focusing on both pathogen discovery and the host response. Here, we review how 'omics' technologies improve sepsis diagnosis, early pathogen identification and personalize therapy. Such host response diagnostics are possible due to the confluence of advanced laboratory techniques (e.g., transcriptomics, metabolomics, proteomics) along with advanced mathematical modeling such as machine learning techniques. The road ahead is promising, but obstacles remain before the impact of such advanced diagnostic modalities is felt at the bedside. PMID: 26145249 [PubMed - as supplied by publisher]

Ferroptosis in p53-dependent oncosuppression and organismal homeostasis.

Tue, 07/07/2015 - 13:54
Ferroptosis in p53-dependent oncosuppression and organismal homeostasis. Cell Death Differ. 2015 Aug;22(8):1237-8 Authors: Galluzzi L, Bravo-San Pedro JM, Kroemer G PMID: 26143748 [PubMed - in process]

Application of CE-MS to a metabonomics study of human urine from cigarette smokers and non-smokers.

Tue, 07/07/2015 - 13:54
Related Articles Application of CE-MS to a metabonomics study of human urine from cigarette smokers and non-smokers. Bioanalysis. 2014 Oct;6(20):2733-49 Authors: Garcia-Perez I, Lindon JC, Minet E Abstract BACKGROUND: Novel biomarkers of exposure and early adverse effects are needed for comparative studies of combustible and non-combustible tobacco products for regulatory authority evaluation. Metabolic biomarkers reflect both gene and environmental effects. RESULTS: CE-MS has been applied to human urine samples from non-smokers and smokers of cigarettes at two tar levels. Validated chemometric models were able to separate smokers from non-smokers, with discrimination mainly based on the presence of nicotine metabolites. With these removed, it still proved possible to discriminate smokers from non-smokers with models now based on endogenous metabolites. The biochemical relevance of these biomarkers is discussed. CONCLUSION: This proof-of-principle metabonomics study illustrates the potential of CE-MS to discover novel biomarkers in urine from tobacco users. PMID: 25413705 [PubMed - indexed for MEDLINE]

An integrated "omics" approach to the characterization of maize (Zea mays L.) mutants deficient in the expression of two genes encoding cytosolic glutamine synthetase.

Tue, 07/07/2015 - 13:54
Related Articles An integrated "omics" approach to the characterization of maize (Zea mays L.) mutants deficient in the expression of two genes encoding cytosolic glutamine synthetase. BMC Genomics. 2014;15:1005 Authors: Amiour N, Imbaud S, Clément G, Agier N, Zivy M, Valot B, Balliau T, Quilleré I, Tercé-Laforgue T, Dargel-Graffin C, Hirel B Abstract BACKGROUND: To identify the key elements controlling grain production in maize, it is essential to have an integrated view of the responses to alterations in the main steps of nitrogen assimilation by modification of gene expression. Two maize mutant lines (gln1.3 and gln1.4), deficient in two genes encoding cytosolic glutamine synthetase, a key enzyme involved in nitrogen assimilation, were previously characterized by a reduction of kernel size in the gln1.4 mutant and by a reduction of kernel number in the gln1.3 mutant. In this work, the differences in leaf gene transcripts, proteins and metabolite accumulation in gln1.3 and gln1.4 mutants were studied at two key stages of plant development, in order to identify putative candidate genes, proteins and metabolic pathways contributing on one hand to the control of plant development and on the other to grain production. RESULTS: The most interesting finding in this study is that a number of key plant processes were altered in the gln1.3 and gln1.4 mutants, including a number of major biological processes such as carbon metabolism and transport, cell wall metabolism, and several metabolic pathways and stress responsive and regulatory elements. We also found that the two mutants share common or specific characteristics across at least two or even three of the "omics" considered at the vegetative stage of plant development, or during the grain filling period. CONCLUSIONS: This is the first comprehensive molecular and physiological characterization of two cytosolic glutamine synthetase maize mutants using a combined transcriptomic, proteomic and metabolomic approach. We find that the integration of the three "omics" procedures is not straight forward, since developmental and mutant-specific levels of regulation seem to occur from gene expression to metabolite accumulation. However, their potential use is discussed with a view to improving our understanding of nitrogen assimilation and partitioning and its impact on grain production. PMID: 25410248 [PubMed - indexed for MEDLINE]

Roles of rhizobial symbionts in selenium hyperaccumulation in Astragalus (Fabaceae).

Tue, 07/07/2015 - 13:54
Related Articles Roles of rhizobial symbionts in selenium hyperaccumulation in Astragalus (Fabaceae). Am J Bot. 2014 Nov;101(11):1895-905 Authors: Alford ÉR, Lindblom SD, Pittarello M, Freeman JL, Fakra SC, Marcus MA, Broeckling C, Pilon-Smits EA, Paschke MW Abstract PREMISE OF THE STUDY: Are there dimensions of symbiotic root interactions that are overlooked because plant mineral nutrition is the foundation and, perhaps too often, the sole explanation through which we view these relationships? In this paper we investigate how the root nodule symbiosis in selenium (Se) hyperaccumulator and nonaccumulator Astragalus species influences plant selenium (Se) accumulation. METHODS: In greenhouse studies, Se was added to nodulated and nonnodulated hyperaccumulator and nonaccumulator Astragalus plants, followed by investigation of nitrogen (N)-Se relationships. Selenium speciation was also investigated, using x-ray microprobe analysis and liquid chromatography-mass spectrometry (LC-MS). KEY RESULTS: Nodulation enhanced biomass production and Se to S ratio in both hyperaccumulator and nonaccumulator plants. The hyperaccumulator contained more Se when nodulated, while the nonaccumulator contained less S when nodulated. Shoot [Se] was positively correlated with shoot N in Se-hyperaccumulator species, but not in nonhyperaccumulator species. The x-ray microprobe analysis showed that hyperaccumulators contain significantly higher amounts of organic Se than nonhyperaccumulators. LC-MS of A. bisulcatus leaves revealed that nodulated plants contained more γ-glutamyl-methylselenocysteine (γ-Glu-MeSeCys) than nonnodulated plants, while MeSeCys levels were similar. CONCLUSIONS: Root nodule mutualism positively affects Se hyperaccumulation in Astragalus. The microbial N supply particularly appears to contribute glutamate for the formation of γ-Glu-MeSeCys. Our results provide insight into the significance of symbiotic interactions in plant adaptation to edaphic conditions. Specifically, our findings illustrate that the importance of these relationships are not limited to alleviating macronutrient deficiencies. PMID: 25366855 [PubMed - indexed for MEDLINE]

Metabolite signatures of exercise training in human skeletal muscle relate to mitochondrial remodelling and cardiometabolic fitness.

Tue, 07/07/2015 - 13:54
Related Articles Metabolite signatures of exercise training in human skeletal muscle relate to mitochondrial remodelling and cardiometabolic fitness. Diabetologia. 2014 Nov;57(11):2282-95 Authors: Huffman KM, Koves TR, Hubal MJ, Abouassi H, Beri N, Bateman LA, Stevens RD, Ilkayeva OR, Hoffman EP, Muoio DM, Kraus WE Abstract AIMS/HYPOTHESIS: Targeted metabolomic and transcriptomic approaches were used to evaluate the relationship between skeletal muscle metabolite signatures, gene expression profiles and clinical outcomes in response to various exercise training interventions. We hypothesised that changes in mitochondrial metabolic intermediates would predict improvements in clinical risk factors, thereby offering novel insights into potential mechanisms. METHODS: Subjects at risk of metabolic disease were randomised to 6 months of inactivity or one of five aerobic and/or resistance training programmes (n = 112). Pre/post-intervention assessments included cardiorespiratory fitness ([Formula: see text]), serum triacylglycerols (TGs) and insulin sensitivity (SI). In this secondary analysis, muscle biopsy specimens were used for targeted mass spectrometry-based analysis of metabolic intermediates and measurement of mRNA expression of genes involved in metabolism. RESULTS: Exercise regimens with the largest energy expenditure produced robust increases in muscle concentrations of even-chain acylcarnitines (median 37-488%), which correlated positively with increased expression of genes involved in muscle uptake and oxidation of fatty acids. Along with free carnitine, the aforementioned acylcarnitine metabolites were related to improvements in [Formula: see text], TGs and SI (R = 0.20-0.31, p < 0.05). Muscle concentrations of the tricarboxylic acid cycle intermediates succinate and succinylcarnitine (R = 0.39 and 0.24, p < 0.05) emerged as the strongest correlates of SI. CONCLUSIONS/INTERPRETATION: The metabolic signatures of exercise-trained skeletal muscle reflected reprogramming of mitochondrial function and intermediary metabolism and correlated with changes in cardiometabolic fitness. Succinate metabolism and the succinate dehydrogenase complex emerged as a potential regulatory node that intersects with whole-body insulin sensitivity. This study identifies new avenues for mechanistic research aimed at understanding the health benefits of physical activity. Trial registration ClinicalTrials.gov NCT00200993 and NCT00275145 Funding This work was supported by the National Heart, Lung, and Blood Institute (National Institutes of Health), National Institute on Aging (National Institutes of Health) and National Institute of Arthritis and Musculoskeletal and Skin Diseases (National Institutes of Health). PMID: 25091629 [PubMed - indexed for MEDLINE]

Immune infiltrate in cancer.

Mon, 06/07/2015 - 12:58
Immune infiltrate in cancer. Aging (Albany NY). 2015 Jun 25; Authors: Stoll G, Zitvogel L, Kroemer G PMID: 26143478 [PubMed - as supplied by publisher]

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