PubMed

Related Articles BreathDx - molecular analysis of exhaled breath as a diagnostic test for ventilator-associated pneumonia: protocol for a European multicentre observational study. BMC Pulm Med. 2017 Jan 03;17(1):1 Authors: van Oort PM, Nijsen T, Weda H, Knobel H, Dark P, Felton T, Rattray NJ, Lawal O, Ahmed W, Portsmouth C, Sterk PJ, Schultz MJ, Zakharkina T, Artigas A, Povoa P, Martin-Loeches I, Fowler SJ, Bos LD, BreathDx Consortium Abstract BACKGROUND: The diagnosis of ventilator-associated pneumonia (VAP) remains time-consuming and costly, the clinical tools lack specificity and a bedside test to exclude infection in suspected patients is unavailable. Breath contains hundreds to thousands of volatile organic compounds (VOCs) that result from host and microbial metabolism as well as the environment. The present study aims to use breath VOC analysis to develop a model that can discriminate between patients who have positive cultures and who have negative cultures with a high sensitivity. METHODS/DESIGN: The Molecular Analysis of Exhaled Breath as Diagnostic Test for Ventilator-Associated Pneumonia (BreathDx) study is a multicentre observational study. Breath and bronchial lavage samples will be collected from 100 and 53 intubated and ventilated patients suspected of VAP. Breath will be analysed using Thermal Desorption - Gas Chromatography - Mass Spectrometry (TD-GC-MS). The primary endpoint is the accuracy of cross-validated prediction for positive respiratory cultures in patients that are suspected of VAP, with a sensitivity of at least 99% (high negative predictive value). DISCUSSION: To our knowledge, BreathDx is the first study powered to investigate whether molecular analysis of breath can be used to classify suspected VAP patients with and without positive microbiological cultures with 99% sensitivity. TRIAL REGISTRATION: UKCRN ID number 19086, registered May 2015; as well as registration at www.trialregister.nl under the acronym 'BreathDx' with trial ID number NTR 6114 (retrospectively registered on 28 October 2016). PMID: 28049457 [PubMed - in process]

Related Articles The Effect of Molecular Conformation on the Accuracy of Theoretical (1)H and (13)C Chemical Shifts Calculated by Ab Initio Methods for Metabolic Mixture Analysis. J Phys Chem B. 2016 Apr 14;120(14):3479-87 Authors: Chikayama E, Shimbo Y, Komatsu K, Kikuchi J Abstract NMR spectroscopy is a powerful method for analyzing metabolic mixtures. The information obtained from an NMR spectrum is in the form of physical parameters, such as chemical shifts, and construction of databases for many metabolites will be useful for data interpretation. To increase the accuracy of theoretical chemical shifts for development of a database for a variety of metabolites, the effects of sets of conformations (structural ensembles) and the levels of theory on computations of theoretical chemical shifts were systematically investigated for a set of 29 small molecules in the present study. For each of the 29 compounds, 101 structures were generated by classical molecular dynamics at 298.15 K, and then theoretical chemical shifts for 164 (1)H and 123 (13)C atoms were calculated by ab initio quantum chemical methods. Six levels of theory were used by pairing Hartree-Fock, B3LYP (density functional theory), or second order Møller-Plesset perturbation with 6-31G or aug-cc-pVDZ basis set. The six average fluctuations in the (1)H chemical shift were ±0.63, ± 0.59, ± 0.70, ± 0.62, ± 0.75, and ±0.66 ppm for the structural ensembles, and the six average errors were ±0.34, ± 0.27, ± 0.32, ± 0.25, ± 0.32, and ±0.25 ppm. The results showed that chemical shift fluctuations with changes in the conformation because of molecular motion were larger than the differences between computed and experimental chemical shifts for all six levels of theory. In conclusion, selection of an appropriate structural ensemble should be performed before theoretical chemical shift calculations for development of an accurate database for a variety of metabolites. PMID: 26963288 [PubMed - indexed for MEDLINE]

Related Articles Uncovering biologically significant lipid isomers with liquid chromatography, ion mobility spectrometry and mass spectrometry. Analyst. 2016 Mar 07;141(5):1649-59 Authors: Kyle JE, Zhang X, Weitz KK, Monroe ME, Ibrahim YM, Moore RJ, Cha J, Sun X, Lovelace ES, Wagoner J, Polyak SJ, Metz TO, Dey SK, Smith RD, Burnum-Johnson KE, Baker ES Abstract Understanding how biological molecules are generated, metabolized and eliminated in living systems is important for interpreting processes such as immune response and disease pathology. While genomic and proteomic studies have provided vast amounts of information over the last several decades, interest in lipidomics has also grown due to improved analytical technologies revealing altered lipid metabolism in type 2 diabetes, cancer, and lipid storage disease. Mass spectrometry (MS) measurements are currently the dominant approach for characterizing the lipidome by providing detailed information on the spatial and temporal composition of lipids. However, interpreting lipids' biological roles is challenging due to the existence of numerous structural and stereoisomers (i.e. distinct acyl chain and double-bond positions), which are often unresolvable using present approaches. Here we show that combining liquid chromatography (LC) and structurally-based ion mobility spectrometry (IMS) measurement with MS analyses distinguishes lipid isomers and allows insight into biological and disease processes. PMID: 26734689 [PubMed - indexed for MEDLINE]

Related Articles Cyclobenzaprine Raises ROS Levels in Leishmania infantum and Reduces Parasite Burden in Infected Mice. PLoS Negl Trop Dis. 2017 Jan 03;11(1):e0005281 Authors: Cunha-Júnior EF, Andrade-Neto VV, Lima ML, da Costa-Silva TA, Galisteo AJ, Abengózar MA, Barbas C, Rivas L, Almeida-Amaral EE, Tempone AG, Torres-Santos EC Abstract BACKGROUND: The leishmanicidal action of tricyclic antidepressants has been studied and evidences have pointed that their action is linked to inhibition of trypanothione reductase, a key enzyme in the redox metabolism of pathogenic trypanosomes. Cyclobenzaprine (CBP) is a tricyclic structurally related to the antidepressant amitriptyline, differing only by the presence of a double bond in the central ring. This paper describes the effect of CBP in experimental visceral leishmaniasis, its inhibitory effect in trypanothione reductase and the potential immunomodulatory activity. METHODOLOGY/PRINCIPAL FINDINGS: In vitro antileishmanial activity was determined in promastigotes and in L. infantum-infected macrophages. For in vivo studies, L. infantum-infected BALB/c mice were treated with CBP by oral gavage for five days and the parasite load was estimated. Trypanothione reductase activity was assessed in the soluble fraction of promastigotes of L. infantum. For evaluation of cytokines, L. infantum-infected macrophages were co-cultured with BALB/c splenocytes and treated with CBP for 48 h. The supernatant was analyzed for IL-6, IL-10, MCP-1, IFN-γ and TNF-α. CBP demonstrated an IC50 of 14.5±1.1μM and an IC90 of 74.5±1.2 μM in promastigotes and an IC50 of 12.6±1.05 μM and an IC90 of 28.7±1.3 μM in intracellular amastigotes. CBP also reduced the parasite load in L. infantum-infected mice by 40.4±10.3% and 66.7±10.5% in spleen at 24.64 and 49.28 mg/kg, respectively and by 85.6±5.0 and 89.3±4.8% in liver at 24.64 and 49.28mg/kg, after a short-term treatment. CBP inhibited the trypanothione reductase activity with a Ki of 86 ± 7.7 μM and increased the ROS production in promastigotes. CBP inhibited in 53% the production of IL-6 in infected macrophages co-culture. CONCLUSION/SIGNIFICANCE: To the best of our knowledge, this study is the first report of the in vivo antileishmanial activity of the FDA-approved drug CBP. Modulation of immune response and induction of oxidative stress in parasite seem to contribute to this efficacy. PMID: 28045892 [PubMed - as supplied by publisher]

Related Articles Metabolomics and proteomics technologies to explore the herbal preparation affecting metabolic disorders using high resolution mass spectrometry. Mol Biosyst. 2017 Jan 03;: Authors: Zhang A, Zhou X, Zhao H, Zou S, Ma CW, Liu Q, Sun H, Liu L, Wang X Abstract An integrative metabolomics and proteomics approach can provide novel insights in the understanding of biological systems. We have integrated proteome and metabolome data sets for a holistic view of the molecular mechanisms in disease. Using quantitative iTRAQ-LC-MS/MS proteomics coupled with UPLC-Q-TOF-HDMS based metabolomics, we determined the protein and metabolite expression changes in the kidney-yang deficiency syndrome (KYDS) rat model and further investigated the intervention effects of the Jinkui Shenqi Pill (JSP). The VIP-plot of the orthogonal PLS-DA (OPLS-DA) was used for discovering the potential biomarkers to clarify the therapeutic mechanisms of JSP in treating KYDS. The results showed that JSP can alleviate the kidney impairment induced by KYDS. Sixty potential biomarkers, including 5-l-glutamyl-taurine, phenylacetaldehyde, 4,6-dihydroxyquinoline, and xanthurenic acid etc., were definitely up- or down-regulated. The regulatory effect of JSP on the disturbed metabolic pathways was proved by the established metabonomic method. Using pathway analyses, we identified the disturbed metabolic pathways such as taurine and hypotaurine metabolism, pyrimidine metabolism, tyrosine metabolism, tryptophan metabolism, histidine metabolism, steroid hormone biosynthesis, etc. Furthermore, using iTRAQ-based quantitative proteomics analysis, seventeen differential proteins were identified and significantly altered by the JSP treatment. These proteins appear to be involved in Wnt, chemokine, PPAR, and MAPK signaling pathways, etc. Functional pathway analysis revealed that most of the proteins were found to play a key role in the regulation of metabolism pathways. Bioinformatics analysis with the IPA software found that these differentially-expressed moleculars had a strong correlation with the α-adrenergic signaling, FGF signaling, etc. Our data indicate that high-throughput metabolomics and proteomics can provide an insight on the herbal preparations affecting the metabolic disorders using high resolution mass spectrometry. PMID: 28045158 [PubMed - as supplied by publisher]

Related Articles Vitamin D insufficiency in the first 6 months of infancy and challenge-proven IgE-mediated food allergy at 1 year of age: a case-cohort study. Allergy. 2017 Jan 02;: Authors: Molloy J, Koplin JJ, Allen KJ, Tang ML, Collier F, Carlin JB, Saffery R, Burgner D, Ranganathan S, Dwyer T, Ward AC, Moreno-Betancur M, Clarke M, Ponsonby AL, Vuillermin P, BIS investigator group Abstract BACKGROUND: Ecological evidence suggests vitamin D insufficiency (VDI) due to lower ambient ultraviolet radiation (UVR) exposure may be a risk factor for IgE-mediated food allergy. However there are no studies relating directly measured VDI during early infancy to subsequent challenge-proven food allergy. OBJECTIVE: To prospectively investigate the association between VDI during infancy and challenge-proven food allergy at 1 year. METHODS: In a birth cohort (n=1074), we used a case-cohort design to compare 25-hydroxy-vitamin-D3 (25(OH)D3 ) levels among infants with food allergy versus a random subcohort (n=274). The primary exposures were VDI (25(OH)D3 <50 nmol/L) at birth and 6 months of age. Ambient UVR and time in the sun were combined to estimate UVR exposure dose. IgE-mediated food allergy status at 1 year was determined by formal challenge. Binomial regression was used to examine associations between VDI, UVR exposure dose and food allergy, and investigate potential confounding. RESULTS: Within the random subcohort VDI was present in 45% (105/233) of newborns and 24% (55/227) of infants at 6 months. Food allergy prevalence at 1 year was 7.7% (61/786) and 6.5% (53/808) were egg allergic. There was no evidence of an association between VDI at either birth (aRR 1.25, 95% CI 0.70-2.22) or 6 months (aRR 0.93, 95% CI 0.41-2.14) and food allergy at 1 year. CONCLUSIONS: There was no evidence that VDI during the first 6 months of infancy is a risk factor for food allergy at 1 year of age. These findings primarily relate to egg allergy and larger studies are required. This article is protected by copyright. All rights reserved. PMID: 28042676 [PubMed - as supplied by publisher]

Related Articles 1 H NMR-based Metabolomics Study for Identifying Urinary Biomarkers and Perturbed Metabolic Pathways Associated with Severity of IgA Nephropathy: A Pilot Study. Magn Reson Chem. 2017 Jan 01;: Authors: Kalantari S, Nafar M, Samavat S, Parvin M Abstract The severity of IgA nephropathy (IgAN), the most common primary glomerulonephritis, is judged on the basis of histologic and clinical features. A limited number of studies have considered molecular signature of IgAN for this issue and no reliable biomarkers have been presented non-invasively for use in patient evaluations. This study aims to identify metabolite markers excreted in the urine and impaired pathways that are associated with a known marker of severity (proteinuria) to predict mild and severe stages of IgAN. Urine samples were analysed using nuclear magnetic resonance (NMR) from biopsy-proven IgA nephropathy patients at mild and severe stages. Multivariate statistical analysis and pathway analysis were performed. The most changed metabolites were acetoacetate, Hypotaurine, homocysteine, L-Kynurenine and phenylalanine. Nine metabolites were positively correlated with proteinuria, including mesaconic acid, trans-cinnamic acid, fumaric acid, 5-thymidylic acid, anthranilic acid, indole, deoxyguanosine triphosphate, 13-cis-retinoic acid and nicotinamide riboside while three metabolites were negatively correlated with proteinuria including acetoacetate, hypotaurine and hexanal 'phenylalanine metabolism' was the most significant pathway which was impaired in severe stage in comparison to mild stage of IgA nephropathy. This study indicates that NMR is a versatile technique that is capable of detecting metabolite biomarkers in combination with advanced multivariate statistical analysis. PMID: 28042675 [PubMed - as supplied by publisher]

Related Articles Magic Angle Spinning NMR Metabolomics. Metabolomics (Los Angel). 2016 Jun;6(2): Authors: Hu JZ PMID: 28042496 [PubMed]

Related Articles The Chlamydia trachomatis Inclusion Membrane Protein CpoS Counteracts STING-Mediated Cellular Surveillance and Suicide Programs. Cell Host Microbe. 2016 Dec 28;: Authors: Sixt BS, Bastidas RJ, Finethy R, Baxter RM, Carpenter VK, Kroemer G, Coers J, Valdivia RH Abstract Evading cell death is critical for Chlamydia to maintain a replicative niche, but the underlying mechanisms are unknown. We screened a library of Chlamydia mutants for modulators of cell death. Inactivation of the inclusion membrane protein CpoS (Chlamydia promoter of survival) induced rapid apoptotic and necrotic death in infected cells. The protection afforded by CpoS is limited to the inclusion in which it resides, indicating that it counteracts a spatially restricted pro-death signal. CpoS-deficient Chlamydia induced an exacerbated type I interferon response that required the host cGAS/STING/TBK1/IRF3 signaling pathway. Disruption of STING, but not cGAS or IRF3, attenuated cell death, suggesting that STING mediates Chlamydia-induced cell death independent of its role in regulating interferon responses. CpoS-deficient strains are attenuated in their ability to propagate in cell culture and are cleared faster from the murine genital tract, highlighting the importance of CpoS for Chlamydia pathogenesis. PMID: 28041929 [PubMed - as supplied by publisher]

Related Articles Comparative "Omics" of the Fusarium fujikuroi Species Complex Highlights Differences in Genetic Potential and Metabolite Synthesis. Genome Biol Evol. 2016 Dec 31;8(11):3574-3599 Authors: Niehaus EM, Münsterkötter M, Proctor RH, Brown DW, Sharon A, Idan Y, Oren-Young L, Sieber CM, Novák O, Pěnčík A, Tarkowská D, Hromadová K, Freeman S, Maymon M, Elazar M, Youssef SA, El-Shabrawy ES, Shalaby AB, Houterman P, Brock NL, Burkhardt I, Tsavkelova EA, Dickschat JS, Galuszka P, Güldener U, Tudzynski B Abstract Species of the Fusarium fujikuroi species complex (FFC) cause a wide spectrum of often devastating diseases on diverse agricultural crops, including coffee, fig, mango, maize, rice, and sugarcane. Although species within the FFC are difficult to distinguish by morphology, and their genes often share 90% sequence similarity, they can differ in host plant specificity and life style. FFC species can also produce structurally diverse secondary metabolites (SMs), including the mycotoxins fumonisins, fusarins, fusaric acid, and beauvericin, and the phytohormones gibberellins, auxins, and cytokinins. The spectrum of SMs produced can differ among closely related species, suggesting that SMs might be determinants of host specificity. To date, genomes of only a limited number of FFC species have been sequenced. Here, we provide draft genome sequences of three more members of the FFC: a single isolate of F. mangiferae, the cause of mango malformation, and two isolates of F. proliferatum, one a pathogen of maize and the other an orchid endophyte. We compared these genomes to publicly available genome sequences of three other FFC species. The comparisons revealed species-specific and isolate-specific differences in the composition and expression (in vitro and in planta) of genes involved in SM production including those for phytohormome biosynthesis. Such differences have the potential to impact host specificity and, as in the case of F. proliferatum, the pathogenic versus endophytic life style. PMID: 28040774 [PubMed - in process]

Related Articles Integration of proteomics and metabolomics to elucidate metabolic adaptation in Leishmania. J Proteomics. 2016 Dec 28;: Authors: Akpunarlieva S, Weidt S, Lamasudin D, Naula C, Henderson D, Barrett M, Burgess K, Burchmore R Abstract Leishmania parasites multiply and develop in the gut of a sand fly vector in order to be transmitted to a vertebrate host. During this process they encounter and exploit various nutrients, including sugars, and amino and fatty acids. We have previously generated a mutant Leishmania line that is deficient in glucose transport and which displays some biologically important phenotypic changes such as reduced growth in axenic culture, reduced biosynthesis of hexose-containing virulence factors, increased sensitivity to oxidative stress, and dramatically reduced parasite burden in both insect vector and macrophage host cells. Here we report the generation and integration of proteomic and metabolomic approaches to identify molecular changes that may explain these phenotypes. Our data suggest changes in pathways of glycoconjugate production and redox homeostasis, which likely represent adaptations to the loss of sugar uptake capacity and explain the reduced virulence of this mutant in sand flies and mammals. Our data contribute to understanding the mechanisms of metabolic adaptation in Leishmania and illustrate the power of integrated proteomic and metabolomic approaches to relate biochemistry to phenotype. SIGNIFICANCE: This paper reports the application of comparative proteomic and metabolomic approaches to reveal the molecular basis for important phenotypic changes Leishmania parasites that are deficient in glucose uptake. Leishmania cause a very significant disease burden across the world and there are few effective drugs available for control. This work shows that proteomics and metabolomics can produce complementary data that advance understanding of parasite metabolism and highlight potential new targets for chemotherapy. PMID: 28040509 [PubMed - as supplied by publisher]

Related Articles Exhaled breath condensate analysis from intubated newborns by nano-HPLC coupled to high resolution MS. J Chromatogr B Analyt Technol Biomed Life Sci. 2016 Dec 23;: Authors: Kononikhin AS, Starodubtseva NL, Chagovets VV, Ryndin AY, Burov AA, Popov IA, Bugrova AE, Dautov RA, Tokareva AO, Podurovskaya YL, Ionov OV, Frankevich VE, Nikolaev EN, Sukhikh GT Abstract Invasiveness of examination and therapy methods is a serious problem for intensive care and nursing of premature infants. Exhaled breath condensate (EBC) is the most attractive biofluid for non-invasive methods development in neonatology for monitoring the status of intubated infants. The aim of the study was to propose an approach for EBC sampling and analysis from mechanically ventilated neonates. EBC collection system with good reproducibility of sampling was demonstrated. Discovery-based proteomic and metabolomic studies were performed using nano-HPLC coupled to high resolution MS. Label-free semi-quantitative data were compared for intubated neonates with congenital pneumonia (12 infants) and left-sided congenital diaphragmatic hernia (12 infants) in order to define disease-specific features. Totally 119 proteins and 164 metabolites were found. A number of proteins and metabolites that can act as potential biomarkers of respiratory diseases were proposed and require further validation. PMID: 28040456 [PubMed - as supplied by publisher]

Related Articles Metabolomics and lipidomics analyses by (1)H nuclear magnetic resonance of schizophrenia patient serum reveal potential peripheral biomarkers for diagnosis. Schizophr Res. 2016 Dec 28;: Authors: Tasic L, Pontes JG, Carvalho MS, Cruz G, Dal Mas C, Sethi S, Pedrini M, Rizzo LB, Zeni-Graiff M, Asevedo E, Lacerda AL, Bressan RA, Poppi RJ, Brietzke E, Hayashi MA Abstract Using (1)H NMR-based metabolomics in association to chemometrics analysis, we analyzed here the metabolic differences between schizophrenia patients (SCZ) compared to healthy controls (HCs). HCs and SCZ patients underwent clinical interview using the Structured Clinical Interview for DSM Disorders (SCID). SCZ patients were further assessed by Positive and Negative Syndrome Scale (PANSS), Calgary Depression Scale, Global Assessment of Functioning Scale (GAF), and Clinical Global Impressions Scale (CGI). Using the principal component analysis (PCA) and supervised partial least-squares discriminate analysis (PLS-DA) in obtained NMR data, a clear group separation between HCs and SCZ patients was achieved. Interestingly, all metabolite compounds identified as exclusively present in the SCZ group, except for the gamma-aminobutyric acid (GABA), were never previously associated with mental disorders. Although the initial perception of an absence of obvious biological link among the different key molecules exclusively observed in each group, and no identification of any specific pathway yet, the present work represents an important contribution for the identification of potential biomarkers to inform diagnosis, as it was possible to completely separate the affected SCZ patients from HCs, with no outliers or exceptions. In addition, the data presented here reinforced the role of the modulation of glycolysis pathway and the loss of GABA interneuron/hyperglutamate hypothesis in SCZ. PMID: 28040324 [PubMed - as supplied by publisher]

Related Articles The Role of CD44 in Glucose Metabolism in Prostatic Small Cell Neuroendocrine Carcinoma. Mol Cancer Res. 2016 Apr;14(4):344-53 Authors: Li W, Cohen A, Sun Y, Squires J, Braas D, Graeber TG, Du L, Li G, Li Z, Xu X, Chen X, Huang J Abstract UNLABELLED: While prostatic adenocarcinomas are relatively indolent, some patients with advanced adenocarcinomas recur with small cell neuroendocrine carcinoma which is highly aggressive and lethal. Because glycolysis is a feature of malignancy and the degree of glycolysis generally correlates with tumor aggressiveness, we wanted to compare the metabolic differences and the molecular mechanisms involved between the two tumor types. In this study, and based on previous characterization, LNCaP and PC-3 prostate cancer cell lines were selected as models of prostatic adenocarcinoma and small cell neuroendocrine carcinoma, respectively. In addition to measuring glucose consumption, lactate secretion, and reactive oxygen species (ROS) levels, we performed metabolic profiling in these two model systems. The role of CD44 was studied by RNAi and lentivirus-mediated overexpression. Expression of key enzymes in glycolysis was studied using human tissue microarrays containing benign prostate, adenocarcinoma, and small cell neuroendocrine carcinoma. Results showed that glycolytic features of PC-3 cells were higher than that of LNCaP cells. PFKFB4 was overexpressed in human small cell carcinoma tissue versus adenocarcinoma tissue. CD44 regulated glucose metabolism, intracellular ROS, and cell proliferation in PC-3 cells. Inhibition of CD44 also sensitized PC-3 cells to carboplatin. In conclusion, this study suggests different pathways of glucose metabolism contribute to the disparate biologic behaviors of these two tumor types. IMPLICATIONS: CD44 is an important regulator of glucose metabolism in small cell neuroendocrine carcinoma and may be an important therapeutic target. PMID: 26832214 [PubMed - indexed for MEDLINE]

Related Articles Using the knowns to discover the unknowns: MS-based dereplication uncovers structural diversity in 17-hydroxygeranyllinalool diterpene glycoside production in the Solanaceae. Plant J. 2016 Feb;85(4):561-77 Authors: Heiling S, Khanal S, Barsch A, Zurek G, Baldwin IT, Gaquerel E Abstract Exploring the diversity of plant secondary metabolism requires efficient methods to obtain sufficient structural insights to discriminate previously known from unknown metabolites. De novo structure elucidation and confirmation of known metabolites (dereplication) remain a major bottleneck for mass spectrometry-based metabolomic workflows, and few systematic dereplication strategies have been developed for the analysis of entire compound classes across plant families, partly due to the complexity of plant metabolic profiles that complicates cross-species comparisons. 17-hydroxygeranyllinalool diterpene glycosides (HGL-DTGs) are abundant defensive secondary metabolites whose malonyl and glycosyl decorations are induced by jasmonate signaling in the ecological model plant Nicotiana attenuata. The multiple labile glycosidic bonds of HGL-DTGs result in extensive in-source fragmentation (IS-CID) during ionization. To reconstruct these IS-CID clusters from profiling data and identify precursor ions, we applied a deconvolution algorithm and created an MS/MS library from positive-ion spectra of purified HGL-DTGs. From this library, 251 non-redundant fragments were annotated, and a workflow to characterize leaf, flower and fruit extracts of 35 solanaceous species was established. These analyses predicted 105 novel HGL-DTGs that were restricted to Nicotiana, Capsicum and Lycium species. Interestingly, malonylation is a highly conserved step in HGL-DTG metabolism, but is differentially affected by jasmonate signaling among Nicotiana species. This MS-based workflow is readily applicable for cross-species re-identification/annotation of other compound classes with sufficient fragmentation knowledge, and therefore has the potential to support hypotheses regarding secondary metabolism diversification. PMID: 26749139 [PubMed - indexed for MEDLINE]

Related Articles Metabolomics Book. 2012 02 10Authors: Roessner U Abstract Inflammation is a normal and extraordinarily important component of responses to infection and injury. The cardinal features of swelling, redness, stiffness and increasing temperature are strong indicators of the significant changes in tissue metabolism and the ingress of immune cells into the tissues. The increase in blood flow which underlies many of these changes may result in changes to the supply of nutrients and in particular the level of oxygen in the tissues. Inward migration of immune cells, which is also enabled by the increased blood flow, will put further stress on the metabolic environment of the tissues. The activity of macrophages and neutrophils in clearing infection and repairing tissue damage also have significant metabolic consequences particularly because of the production of cytokines and cytotoxic molecules such as reactive oxygen species and reactive nitrogen species, which are required to kill invading organisms. Production of these molecules will consume considerable quantities of oxygen, ATP and NADPH. These antimicrobial agents put considerable stress on host cells in the surrounding and distal tissues and can lead to significant loss of protective metabolites such as glutathione. Most infections and traumatic injuries are cleared or repaired relatively rapidly and metabolic homoeostasis is soon restored. However, there is a broad range of inflammatory diseases which involve chronic activation of the immune system and, as a result, chronic persistent inflammation. We have been studying the metabolic consequences of chronic inflammatory diseases with the aim of identifying metabolic fingerprints which may provide clues about why the localised tissue disease persists. For example, why in rheumatoid arthritis does persistent inflammation lead to widespread cartilage and joint destruction? However, the metabolic consequences of chronic inflammation are much more widespread than the localised disease and can lead on to important comorbidities such as accelerated atherosclerosis and cardiovascular disease. Metabolomic analysis may be able to distinguish between localised and systemic metabolic consequences of inflammation and provide novel targets for therapeutic intervention in these important human diseases. PMID: 28045482

Related Articles A fully validated GC-TOF-MS method for the quantification of fatty acids revealed alterations in the metabolic profile of fatty acids after smoking cessation. J Chromatogr B Analyt Technol Biomed Life Sci. 2016 Dec 23;1041-1042:141-150 Authors: Goettel M, Niessner R, Pluym N, Scherer G, Scherer M Abstract We developed and validated an efficient and robust method for the simultaneous quantification of 44 fatty acid species in human plasma via GC-TOF-MS. The method is characterized by its robustness, accuracy and precision covering a wide range of fatty acid species with various saturation degrees including short chain fatty acids (beginning with FA 4:0) and long chain fatty acids (up to FA 32:0). The fatty acids were methylated prior to analyses and subsequently detected as fatty acid methyl esters by means of GC-TOF-MS. A highly substituted polar column allowed the separation of geometrical and positional isomers of fatty acid species. The method was applied to plasma samples of a strictly diet controlled clinical smoking cessation study including 39 smokers followed over the course of three months after having quit. Statistical significant alterations within the fatty acid profile were observed when comparing the baseline (subjects still smoking) with one week, one month and three months of smoking cessation. After 3 months of smoking cessation, a partial recovery of alterations in the fatty acid profile evoked by smoking was observed. In conclusion, the developed fatty acid profiling method using GC-TOF-MS has proven as a reliable tool for the quantitative determination of 44 individual fatty acid species within clinical studies. PMID: 28039811 [PubMed - as supplied by publisher]

Related Articles What computational non-targeted mass spectrometry-based metabolomics can gain from shotgun proteomics. Curr Opin Biotechnol. 2016 Dec 28;43:141-146 Authors: Hamzeiy H, Cox J Abstract Computational workflows for mass spectrometry-based shotgun proteomics and untargeted metabolomics share many steps. Despite the similarities, untargeted metabolomics is lagging behind in terms of reliable fully automated quantitative data analysis. We argue that metabolomics will strongly benefit from the adaptation of successful automated proteomics workflows to metabolomics. MaxQuant is a popular platform for proteomics data analysis and is widely considered to be superior in achieving high precursor mass accuracies through advanced nonlinear recalibration, usually leading to five to ten-fold better accuracy in complex LC-MS/MS runs. This translates to a sharp decrease in the number of peptide candidates per measured feature, thereby strongly improving the coverage of identified peptides. We argue that similar strategies can be applied to untargeted metabolomics, leading to equivalent improvements in metabolite identification. PMID: 28039739 [PubMed - as supplied by publisher]

Related Articles Micafungin alters the amino acid, nucleic acid and central carbon metabolism of Candida albicans at subinhibitory concentrations: novel insights into mechanisms of action. J Antimicrob Chemother. 2016 Dec 30;: Authors: Katragkou A, Williams M, Sternberg S, Pantazatos D, Roilides E, Walsh TJ Abstract BACKGROUND: Echinocandins are an important class of antifungal agents in the treatment of invasive candidiasis. However, little is known about the metabolomic effects of echinocandins on Candida We therefore performed LC-high-resolution MS (LC-HRMS)-based metabolomics profiling of the response of Candida albicans cells to increasing concentrations of micafungin to determine the metabolic response of Candida to micafungin subinhibitory injury. METHODS: Isolates of C. albicans were cultured on nitrocellulose filters to mid-logarithmic phase of growth and micafungin (0-0.25 mg/L) was added. At mid-logarithmic phase, replicates were metabolically quenched. Intracellular metabolites were analysed by LC-HRMS. Changes in pool sizes of individual metabolites were analysed by Student's t-test adjusted for multiple hypothesis testing by Benjamini-Hochberg correction. Metabolites were ascribed by the Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways database. RESULTS: Among 3446 detected metabolites, 204 were identified by comparison against pure standard or comparison against a library of mass-retention-time pairs. Fifty had significantly altered abundances in response to increasing micafungin concentrations. Pool sizes of amino acids, nucleic acids and polyamine metabolism were significantly increased at subinhibitory concentrations, while exposure to inhibitory concentrations resulted in a precipitous decrease consistent with fungicidal activity. CONCLUSIONS: Micafungin induces a re-routing of metabolic pathways inhibiting protein synthesis and cell replication. These results shed light on new mechanisms of action of echinocandins. PMID: 28039272 [PubMed - as supplied by publisher]

Related Articles Recent Advances in Lipidomics: Analytical and Clinical Perspectives. Prostaglandins Other Lipid Mediat. 2016 Dec 27;: Authors: Sethi S, Brietzke E Abstract Lipidomics or lipid-profiling is a lipid-targeted metabolomics approach aiming at comprehensive analysis of lipids in biological systems. The extent of information in the genomic and proteomic fields is greater than that in the lipidomics field, because of the complex nature of lipids and the limitations of tools for analysis. Modern technological advances in mass spectrometry and chromatography have greatly improved the developments and applications of metabolic profiling of diverse lipids in complex biological samples. Lipidomics will not only provide insights into the specific functions of lipid species in health and disease, but will also identify potential biomarkers for establishing preventive or therapeutic programs for human diseases. In this review, emphasis is given to the current advances in lipidomics technologies and their applications in disease biomarker discovery, and its clinical application. The application of lipidomics in clinical studies may provide new insights into lipid profiling and pathophysiological mechanisms. We also discuss the lipidomics for the future perspectives and their potential problems. PMID: 28039059 [PubMed - as supplied by publisher]