PubMed

Related Articles Negative prognostic value of high levels of intracellular poly (ADP-ribose) in non-small cell lung cancer. Ann Oncol. 2015 Sep 19; Authors: Michels J, Adam J, Goubar A, Obrist F, Damotte D, Robin A, Alifano M, Vitale I, Olaussen KA, Girard P, Cremer I, Castedo M, Soria JC, Kroemer G Abstract BACKGROUND: Cisplatin-resistant non-small cell lung cancer (NSCLC) cells are often characterized by alterations in vitamin B-related metabolic processes, including the overexpression and hyperactivation of poly(ADP-ribose) polymerase 1 (PARP1) and the down-regulation of pyridoxal kinase (PDXK), correlating with elevated apoptosis resistance. Low PDXK expression is an established negative prognostic factor in NSCLC. PATIENTS AND METHODS: We determined by immunohistochemistry the expression of PARP1 and the level of its product, poly(ADP-ribose) (PAR) in two independent cohorts of patients with resected NSCLC. RESULTS: Intratumoral high levels (above median) of PAR (but not PARP1 protein levels) had a negative prognostic impact in both the training (92 stage I subjects) and validation (133 stage I and II subjects) cohorts, as determined by univariate and multivariate analyses. The simultaneous assessment of PAR and PDXK protein levels improved risk stratification. CONCLUSION: NSCLC patients with high intratumoral PARP1 activity (i.e., elevated PAR levels above median) and low PDXK expression (below median) had, a dismal prognosis, while patients with low PARP1 activity and high PDXK expression had a favourable outcome. Altogether, these results underscore the clinical potential and possible therapeutic relevance of these biomarkers. PMID: 26387143 [PubMed - as supplied by publisher]

Systematic analysis of rice (Oryza sativa) metabolic responses to herbivory. Plant Cell Environ. 2015 Sep 19; Authors: Alamgir KM, Hojo Y, Christeller JT, Fukumoto K, Isshiki R, Shinya T, Baldwin IT, Galis I Abstract Plants defend against attack from herbivores by direct and indirect defense mechanisms mediated by the accumulation of phytoalexins and release of volatile signals, respectively. While the defensive arsenals of some plants, such as tobacco and Arabidopsis are well known, most of rice's (Oryza sativa) defense metabolites and their effectiveness against herbivores remain uncharacterized. Here, we used a non-biased metabolomics approach to identify many novel herbivory-regulated metabolic signatures in rice. Most were up-regulated by herbivore attack while only a few were suppressed. Two of the most prominent up-regulated signatures were characterized as phenolamides (PAs), p-coumaroylputrescine and feruloylputrescine. PAs accumulated in response to attack by both chewing insects, i.e. feeding of the lawn armyworm (Spodoptera mauritia) and the rice skipper (Parnara guttata) larvae, and the attack of the sucking insect, the brown planthopper (Nilaparvata lugens, BPH). In bioassays, BPH insects feeding on 15% sugar solution containing p-coumaroylputrescine or feruloylputrescine, at concentrations similar to those elicited by heavy BPH attack in rice, had a higher mortality compared to those feeding on sugar diet alone. Our results highlight PAs as a rapidly expanding new group of plant defense metabolites that are elicited by herbivore attack, and deter herbivores in rice and other plants. PMID: 26386366 [PubMed - as supplied by publisher]

RhizoFlowCell system reveals early effects of micropollutants on aquatic plant rhizosphere. Environ Pollut. 2015 Sep 16;207:205-210 Authors: Mynampati KC, Lee YJ, Wijdeveld A, Reuben S, Samavedham L, Kjelleberg S, Swarup S Abstract In aquatic systems, one of the non-destructive ways to quantify toxicity of contaminants to plants is to monitor changes in root exudation patterns. In aquatic conditions, monitoring and quantifying such changes are currently challenging because of dilution of root exudates in water phase and lack of suitable instrumentation to measure them. Exposure to pollutants would not only change the plant exudation, but also affect the microbial communities that surround the root zone, thereby changing the metabolic profiles of the rhizosphere. This study aims at developing a device, the RhizoFlowCell, which can quantify metabolic response of plants, as well as changes in the microbial communities, to give an estimate of the stress to which the rhizosphere is exposed. The usefulness of RhizoFlowCell is demonstrated using naphthalene as a test pollutant. Results show that RhizoFlowCell system is useful in quantifying the dynamic metabolic response of aquatic rhizosphere to determine ecosystem health. PMID: 26386206 [PubMed - as supplied by publisher]

Metabolic responses to Lactobacillus plantarum contamination or bacteriophage treatment in Saccharomyces cerevisiae using a GC-MS-based metabolomics approach. World J Microbiol Biotechnol. 2015 Sep 18; Authors: Cui FX, Zhang RM, Liu HQ, Wang YF, Li H Abstract Bacteriophage can be used as a potential alternative agent for controlling Lactobacillus plantarum contamination during bioethanol production. However, how Saccharomyces cerevisiae respond against contaminative L. plantarum or added bacteriophage remains to be fully understood. In this study, gas chromatography-mass spectrometry and a multivariate analysis were employed to investigate the intracellular biochemical changes in S. cerevisiae cells that were elicited by L. plantarum contamination or bacteriophage treatment. The intracellular metabolite profiles originating from different groups were unique and could be distinguished with the aid of principal component analysis. Moreover, partial least-squares-discriminant analysis revealed a group classification and pairwise discrimination, and 13 differential metabolites with variable importance in the projection value greater than 1 were identified. The metabolic relevance of these compounds in the response of S. cerevisiae to L. plantarum contamination or bacteriophage treatment was discussed. Besides generating lactic acid and competing for nutrients or living space, L. plantarum contamination might also inhibit the growth of S. cerevisiae through regulating the glycolysis in S. cerevisiae. Moreover, increased concentrations of monounsaturated fatty acids secondary to bacteriophage treatment might lead to more membrane fluidity and promote the cell viability of S. cerevisiae. PMID: 26385547 [PubMed - as supplied by publisher]

Vaginal microbiome and metabolome highlight specific signatures of bacterial vaginosis. Eur J Clin Microbiol Infect Dis. 2015 Sep 18; Authors: Vitali B, Cruciani F, Picone G, Parolin C, Donders G, Laghi L Abstract In this study, we sought to find novel bacterial and metabolic hallmarks for bacterial vaginosis (BV). We studied the vaginal microbiome and metabolome of vaginal fluids from BV-affected patients (n = 43) and healthy controls (n = 37) by means of an integrated approach based on quantitative polymerase chain reaction (qPCR) and proton nuclear magnetic resonance ((1)H-NMR). The correlations between the clinical condition and vaginal bacterial communities were investigated by principal component analysis (PCA). To define the metabolomics signatures of BV, 100 discriminant analysis by projection on latent structure (PLS-DA) models were calculated. Bacterial signatures distinguishing the health condition and BV were identified by qPCR. Lactobacillus crispatus strongly featured the healthy vagina, while increased concentrations of Prevotella, Atopobium and Mycoplasma hominis specifically marked the infection. (1)H-NMR analysis has led to the identification and quantification of 17 previously unreported molecules. BV was associated with changes in the concentration of metabolites belonging to the families of amines, organic acids, short chain fatty acids, amino acids, nitrogenous bases and monosaccharides. In particular, maltose, kynurenine and NAD(+) primarily characterised the healthy status, while nicotinate, malonate and acetate were the best metabolic hallmarks of BV. This study helps to better understand the role of the vaginal microbiota and metabolome in the development of BV infection. We propose a molecular approach for the diagnosis of BV based on quantitative detection in the vaginal fluids of Atopobium, Prevotella and M. hominis, and nicotinate, malonate and acetate by combining qPCR and (1)H-NMR. PMID: 26385347 [PubMed - as supplied by publisher]

Metabolic responses of the isopod Porcellionides pruinosus to nickel exposure assessed by (1)H NMR metabolomics. J Proteomics. 2015 Sep 15; Authors: Ferreira NG, Saborano R, Morgado R, Cardoso DN, Rocha CM, Soares AM, Loureiro S, Duarte IF PMID: 26385004 [PubMed - as supplied by publisher]

Physiological changes due to mild cooling in healthy lean males of white Caucasian and South Asian descent: a metabolomics study. Arch Biochem Biophys. 2015 Sep 15; Authors: Nahon KJ, Boon MR, Bakker LE, Prehn C, Adamski J, Jazet IM, van Dijk KW, Rensen PC, Mook-Kanamori DO Abstract During mild cold exposure, non-shivering thermogenesis increases to maintain core body temperature by increasing utilization of substrates, especially fatty acids (FA), ultimately affecting lipid-associated metabolites. We aimed to investigate whether mild cooling induces changes in other metabolites and whether this response differs between white Caucasians and South Asians, who have a disadvantageous metabolic phenotype. 12 lean male Dutch white Caucasians and 12 matched Dutch South Asians were exposed to mild cold. Before and after 100 minutes exposure, serum samples were collected for analysis of 163 metabolites and 27 derived parameters using high throughput metabolomics. The overall response to mild cooling between both ethnicities was not different, therefore the data were pooled. After Bonferroni correction, mild cooling significantly changed 44 of 190 (23%) metabolic parameters. Specifically, cooling increased 19 phosphatidylcholine (PC) species, only those containing very long chain FAs, and increased the total class of PC containing mono-unsaturated FAs (+12.5%). Furthermore, cooling increased 10 sphingomyelin species as well as the amino acids glutamine (+18.7%), glycine (+11.6%) and histidine (+10.6%), and decreased short-chain (C3 and C4) acylcarnitines (-17.1% and -19.4%, respectively). In conclusion, mild cooling elicits substantial effects on serum metabolites in healthy males, irrespective of white Caucasian or South Asian ethnicity. PMID: 26384768 [PubMed - as supplied by publisher]

Related Articles Exploring the Process of Energy Generation in Pathophysiology by Targeted Metabolomics: Performance of a Simple and Quantitative Method. J Am Soc Mass Spectrom. 2015 Sep 17; Authors: Riera-Borrull M, Rodríguez-Gallego E, Hernández-Aguilera A, Luciano F, Ras R, Cuyàs E, Camps J, Segura-Carretero A, Menendez JA, Joven J, Fernández-Arroyo S Abstract Abnormalities in mitochondrial metabolism and regulation of energy balance contribute to human diseases. The consequences of high fat and other nutrient intake, and the resulting acquired mitochondrial dysfunction, are essential to fully understand common disorders, including obesity, cancer, and atherosclerosis. To simultaneously and noninvasively measure and quantify indirect markers of mitochondrial function, we have developed a method based on gas chromatography coupled to quadrupole-time of flight mass spectrometry and an electron ionization interface, and validated the system using plasma from patients with peripheral artery disease, human cancer cells, and mouse tissues. This approach was used to increase sensibility in the measurement of a wide dynamic range and chemical diversity of multiple intermediate metabolites used in energy metabolism. We demonstrate that our targeted metabolomics method allows for quick and accurate identification and quantification of molecules, including the measurement of small yet significant biological changes in experimental samples. The apparently low process variability required for its performance in plasma, cell lysates, and tissues allowed a rapid identification of correlations between interconnected pathways. Our results suggest that delineating the process of energy generation by targeted metabolomics can be a valid surrogate for predicting mitochondrial dysfunction in biological samples. Importantly, when used in plasma, targeted metabolomics should be viewed as a robust and noninvasive source of biomarkers in specific pathophysiological scenarios. Graphical Abstract ᅟ. PMID: 26383735 [PubMed - as supplied by publisher]

Related Articles Changes in Brain Metallome/Metabolome Pattern due to a Single i.v. Injection of Manganese in Rats. PLoS One. 2015;10(9):e0138270 Authors: Neth K, Lucio M, Walker A, Zorn J, Schmitt-Kopplin P, Michalke B Abstract Exposure to high concentrations of Manganese (Mn) is known to potentially induce an accumulation in the brain, leading to a Parkinson related disease, called manganism. Versatile mechanisms of Mn-induced brain injury are discussed, with inactivation of mitochondrial defense against oxidative stress being a major one. So far, studies indicate that the main Mn-species entering the brain are low molecular mass (LMM) compounds such as Mn-citrate. Applying a single low dose MnCl2 injection in rats, we observed alterations in Mn-species pattern within the brain by analysis of aqueous brain extracts by size-exclusion chromatography-inductively coupled plasma mass spectrometry (SEC-ICP-MS). Additionally, electrospray ionization-ion cyclotron resonance-Fourier transform-mass spectrometry (ESI-ICR/FT-MS) measurement of methanolic brain extracts revealed a comprehensive analysis of changes in brain metabolisms after the single MnCl2 injection. Major alterations were observed for amino acid, fatty acid, glutathione, glucose and purine/pyrimidine metabolism. The power of this metabolomic approach is the broad and detailed overview of affected brain metabolisms. We also correlated results from the metallomic investigations (Mn concentrations and Mn-species in brain) with the findings from metabolomics. This strategy might help to unravel the role of different Mn-species during Mn-induced alterations in brain metabolism. PMID: 26383269 [PubMed - as supplied by publisher]

Related Articles Integrated isotope-assisted metabolomics and (13)C metabolic flux analysis reveals metabolic flux redistribution for high glucoamylase production by Aspergillus niger. Microb Cell Fact. 2015;14(1):147 Authors: Lu H, Liu X, Huang M, Xia J, Chu J, Zhuang Y, Zhang S, Noorman H Abstract BACKGROUND: Aspergillus niger is widely used for enzyme production and achievement of high enzyme production depends on the comprehensive understanding of cell's metabolic regulation mechanisms. RESULTS: In this paper, we investigate the metabolic differences and regulation mechanisms between a high glucoamylase-producing strain A. niger DS03043 and its wild-type parent strain A. niger CBS513.88 via an integrated isotope-assisted metabolomics and (13)C metabolic flux analysis approach. We found that A. niger DS03043 had higher cell growth, glucose uptake, and glucoamylase production rates but lower oxalic acid and citric acid secretion rates. In response to above phenotype changes, A. niger DS03043 was characterized by an increased carbon flux directed to the oxidative pentose phosphate pathway in contrast to reduced flux through TCA cycle, which were confirmed by consistent changes in pool sizes of metabolites. A higher ratio of ATP over AMP in the high producing strain might contribute to the increase in the PP pathway flux as glucosephosphate isomerase was inhibited at higher ATP concentrations. A. niger CBS513.88, however, was in a higher redox state due to the imbalance of NADH regeneration and consumption, resulting in the secretion of oxalic acid and citric acid, as well as the accumulation of intracellular OAA and PEP, which may in turn result in the decrease in the glucose uptake rate. CONCLUSIONS: The application of integrated metabolomics and (13)C metabolic flux analysis highlights the regulation mechanisms of energy and redox metabolism on flux redistribution in A. niger. Graphical abstract An integrated isotope-assisted metabolomics and (13)C metabolic flux analysis was was firstly systematically performed in A. niger. In response to enzyme production, the metabolic flux in A. niger DS03043 (high-producing) was redistributed, characterized by an increased carbon flux directed to the oxidative pentose phosphate pathway as well as an increased pool size of pentose. The consistency in (13)C metabolic flux analysis and metabolites quantification indicated that an imbalance of NADH formation and consumption led to the accumulation and secretion of organic acids in A. niger CBS513.88 (wild-type). PMID: 26383080 [PubMed - as supplied by publisher]

Related Articles Learning from other diseases: protection and pathology in chronic fungal infections. Semin Immunopathol. 2015 Sep 17; Authors: Zelante T, Pieraccini G, Scaringi L, Aversa F, Romani L Abstract Fungal commensals coexist in a complex milieu of bacteria within the human body. An increased understanding of the importance of microbiota in shaping the host's immune and metabolic activities has rendered fungal interactions with their hosts more complex than previously appreciated. Metagenomics has revealed the complex interactions between fungal and bacterial commensals that, either directly or through the participation of the host immune system, impact on immune homeostasis at mucosal surfaces that, in turn, lead to secondary fungal infections. Metabolomics has captured the dialogue between the mammalian host and its microbiota. It appears that the host tryptophan catabolic enzyme, indoleamine 2,3-dioxygenase 1 (IDO1) plays a dominant role in the interplay between tryptophan catabolism by microbial communities, the host's own pathway of metabolite production, and the activation of the aryl hydrocarbon receptor (AhR)/IL-22 axis, eventually impacting on mucosal immune homeostasis and host/fungal symbiosis. Thus, the regulatory loop involving AhR and IDO1 may be exploited for the development of multi-pronged host- and microbiota-directed therapeutic approaches for mucosal and systemic fungal diseases. PMID: 26382631 [PubMed - as supplied by publisher]

Related Articles A robust and efficient method for estimating enzyme complex abundance and metabolic flux from expression data. Comput Biol Chem. 2015 Sep 1; Authors: Barker BE, Sadagopan N, Wang Y, Smallbone K, Myers CR, Xi H, Locasale JW, Gu Z Abstract A major theme in constraint-based modeling is unifying experimental data, such as biochemical information about the reactions that can occur in a system or the composition and localization of enzyme complexes, with high-throughput data including expression data, metabolomics, or DNA sequencing. The desired result is to increase predictive capability and improve our understanding of metabolism. The approach typically employed when only gene (or protein) intensities are available is the creation of tissue-specific models, which reduces the available reactions in an organism model, and does not provide an objective function for the estimation of fluxes. We develop a method, flux assignment with LAD (least absolute deviation) convex objectives and normalization (FALCON), that employs metabolic network reconstructions along with expression data to estimate fluxes. In order to use such a method, accurate measures of enzyme complex abundance are needed, so we first present an algorithm that addresses quantification of complex abundance. Our extensions to prior techniques include the capability to work with large models and significantly improved run-time performance even for smaller models, an improved analysis of enzyme complex formation, the ability to handle large enzyme complex rules that may incorporate multiple isoforms, and either maintained or significantly improved correlation with experimentally measured fluxes. FALCON has been implemented in MATLAB and ATS, and can be downloaded from: https://github.com/bbarker/FALCON. ATS is not required to compile the software, as intermediate C source code is available. FALCON requires use of the COBRA Toolbox, also implemented in MATLAB. PMID: 26381164 [PubMed - as supplied by publisher]

Related Articles Metabolic youth in middle age - predicting ageing in Caenorhabditis elegans using metabolomics. J Proteome Res. 2015 Sep 18; Authors: Davies SK, Bundy JG, Leroi AM Abstract Many mutations and allelic variants are known that influence the rate at which animals age. But when in life do such variants diverge from normal patterns of ageing? And is this divergence visible in their physiologies? To investigate these questions we have used 1H NMR spectroscopy to study how the metabolome of the nematode Caenorhabditis elegans changes as it grows older. We identify a series of metabolic changes that, collectively, predict the age of wild-type worms. We then show that long-lived mutant daf-2(m41) worms are metabolically youthful compared to wild-type worms - but that this relative youth only appears in middle age. Finally, we show that metabolic age predicts the timing and magnitude of differences in age-specific mortality between these strains. Thus the future mortality of these two genotypes can be predicted long before most of the worms die. PMID: 26381038 [PubMed - as supplied by publisher]

Related Articles Non-invasive assessment of in-vitro embryo quality to improve transfer success. Reprod Biomed Online. 2015 Aug 12; Authors: Rødgaard T, Heegaard PM, Callesen H Abstract Although IVF has been performed routinely for many years to help couples with fertility problems and in relation to modern breeding of farm animals, pregnancy rates after transfer to a recipient have not improved during the last decade. Early prediction of the viability of in-vitro developed embryos before the transfer to a recipient still remains challenging. Presently, the predominant non-invasive technique for selecting viable embryos is based on morphology, where parameters such as rates of cleavage and blastocyst formation as well as developmental kinetics are evaluated mostly subjectively. The simple morphological approach is, however, inadequate for the prediction of embryo quality, and several studies have focused on developing new non-invasive methods using molecular approaches based particularly on proteomics, metabolomics and most recently small non-coding RNA, including microRNA. This review outlines the potential of several non-invasive in-vitro methods based on analysis of spent embryo culture medium. PMID: 26380864 [PubMed - as supplied by publisher]

Related Articles [Investigation of Evolution Rules of Phlegm and Blood Stasis Syndrome in Hyperlipidemia and Ath- erosclerosis by NMR-based Metabolic Profiling and Metabonomic Approaches]. Zhongguo Zhong Xi Yi Jie He Za Zhi. 2015 Jul;35(7):823-33 Authors: Zhang L, Zhang Q, You Y, Zhou MX, Wang LH, Chen HB, Yan XZ, Liu XZ, Liu WH Abstract OBJECTIVE: To explore evolution rules of phlegm and blood stasis syndrome ( PBSS) in hyperlipidemia and atherosclerosis (AS) using NMR-based metabolic profiling and metabonomic approaches based on formulas corresponding to syndrome. METHODS: Totally 150 SD rats were divided into the normal group, the model group, the Erchen Decoction (ED) group, the Xuefu Zhuyu Decoction (XZD) group, the Lipitor group, 30 in each group. The hyperlipidemia and AS rat model was duplicated by suturing carotid artery, injecting vitamin D3, and feeding with high fat diet. ED and XZD were used as drug probes. Blood samples were withdrawn at week 2, 4, and 8 after modeling. Blood lipids, blood rheology, histopathology and metabolomics were detected and analyzed. Results Results of blood lipids and pathology showed hyperlipidemia and early AS rat models were successfully established. At week 2 after modeling, levels of total cholesterol (TC) and low-density lipoprotein cholesterol (LDL-C) significantly increased, which reached the peak at week 4 and maintained at higher levels at week 8. ED exerted obvious effect in improving TC and LDL-C levels of early models, while XZD could greatly improve levels of TC and LDL-C of late models. Rheological results showed at week 2, there was no significant difference in whole blood viscosity, plasma viscosity, or hematocrit between the model group and the normal group (P > 0.05). At week 4 partial hemorheological indicators (such as plasma viscosity) were abnormal. Till week 8 whole blood viscosity, plasma viscosity, and hematocrit were significantly abnormal (P <0. 05, P < 0.01). As time went by, whole blood viscosity, plasma viscosity, and hematocrit showed gradual increasing tendency in the ED group, while they showed gradual decreasing tendency in the XZD group. Results of metabonomics showed significant difference in spectra of metabolites between the normal group and the model group. As modeling time was prolonged, contents of acetyl glucoprotein and glucose in the model group increased in late stage, which was in. line with results of blood lipids and hemorheology. ED showed more obvious effect in early and mid-term modeling (at week 2 and 4), and increased contents of partial metabolites (such as choline, phosphatidyl choline, glycerophosphocholine), but these changes in the XZD group were consistent with those of the model group. In late modeling (at week 8) XZD showed more obvious effect in improving contents of lactic acid, acetyl glycoprotein, LDL, creatine, choline, and glucose. CONCLUSIONS: ED and XZD not only showed regulatory effects on lipid disorders, but also could improve dysbolism of Chos. In formulas corresponding to syndrome, damp-phlegm was main pathogenesis of hyperlipidema and AS in early and mid stages. Blood stasis syndrome began to occur along with it progressed. Phlegm can result in blood stasis and intermingles with stasis. Phlegm turbidity runs through the whole process. PMID: 26380446 [PubMed - in process]

Related Articles [Optimization and application of targeted LC-MS metabolomic analyses in photosynthetic cyanobacteria]. Sheng Wu Gong Cheng Xue Bao. 2015 Apr;31(4):577-90 Authors: Niu X, Zhang X, Yu X, Su Y, Chen L, Zhang W Abstract To accurately analyze metabolites in industry-important photosynthetic microbes, LC-MS based metabolomics protocol needs to be optimized specifically for individual species. In this study, an LC-MS based metabolomics method was optimized for cyanobacterium Synechocystis sp. PCC 6803. With the optimized extraction, liquid chromatographic and mass spectral parameters, the method was capable of detecting 24 important metabolites related to central carbohydrate and energy metabolism in Synechocystis sp. PCC 6803. The study laid an important foundation for the metabolomics analysis of cyanobacteria. PMID: 26380414 [PubMed - in process]

Related Articles Prospects of breeding high-quality rice using post-genomic tools. Theor Appl Genet. 2015 Aug;128(8):1449-66 Authors: Anacleto R, Cuevas RP, Jimenez R, Llorente C, Nissila E, Henry R, Sreenivasulu N Abstract KEY MESSAGE: The holistic understanding derived from integrating grain quality and sensory research outcomes in breeding high-quality rice in the light of post-genomics resources has been synthesized. Acceptance of new rice genotypes by producers and consumers hinges not only on their potential for higher yield but recent emphasis has also been on premium-value genotypes that have the ability to satisfy consumer preferences for grain quality. This review article provides insights into how to link grain quality attributes and sensory perception to support breeding superior rice varieties. Recent advances in quality profiling and omics technologies have provided efficient approaches to identify the key genes and biochemical markers involved in rice quality traits. Emphasis has been given to the upcoming area of holistic understanding of grain quality and attributes derived from sensory evaluation to leverage integrative gene discovery strategies that enable breeding programs to efficiently tap the huge genetic diversity in rice for novel genes that enhance rice food quality. PMID: 25993897 [PubMed - indexed for MEDLINE]

Related Articles Detection of reactive metabolites using isotope-labeled glutathione trapping and simultaneous neutral loss and precursor ion scanning with ultra-high-pressure liquid chromatography triple quadruple mass spectrometry. Anal Chem. 2015 Apr 7;87(7):3646-54 Authors: Huang K, Huang L, van Breemen RB Abstract Metabolic activation of drugs to electrophilic species is responsible for over 60% of black box warnings and drug withdrawals from the market place in the United States. Reactive metabolite trapping using glutathione (GSH) and analysis using high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) or HPLC with high resolution mass spectrometry (mass defect filtering) have enabled screening for metabolic activation to become routine during drug development. However, current MS-based approaches cannot detect all GSH conjugates present in complex mixtures, especially those present in extracts of botanical dietary supplements. To overcome these limitations, a fast triple quadrupole mass spectrometer-based approach was developed that can detect positively and negatively charged GSH conjugates in a single analysis without the need for advanced knowledge of the elemental compositions of potential conjugates and while avoiding false positives. This approach utilized UHPLC instead of HPLC to shorten separation time and enhance sensitivity, incorporated stable-isotope labeled GSH to avoid false positives, and used fast polarity switching electrospray MS/MS to detect GSH conjugates that form positive and/or negative ions. The general new method was then used to test the licorice dietary supplement Glycyrrhiza glabra, which was found to form multiple GSH conjugates upon metabolic activation. Among the GSH conjugates found in the licorice assay were conjugates with isoliquiritigenin and glabridin, which is an irreversible inhibitor of cytochrome P450 enzymes. PMID: 25774910 [PubMed - indexed for MEDLINE]

Related Articles Non-protein amino acids in Australian acacia seed: implications for food security and recommended processing methods to reduce djenkolic acid. Food Chem. 2015 Jul 15;179:109-15 Authors: Boughton BA, Reddy P, Boland MP, Roessner U, Yates P Abstract Seed of Australian acacia species, Acacia colei, Acacia elecantha, Acacia torulosa, Acacia turmida and Acacia saligna, were analysed for the presence of toxic non-protein amino acids and the levels of essential amino acids. Amines were derivatised with 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate before analysis using liquid chromatography electrospray ionisation triple quadrupole mass spectrometry (LC-ESI-QQQ-MS). Multiple reaction monitoring (MRM) with optimised transitions and collision energies for each analyte were employed. The known nephrotoxic compound djenkolic acid was found to be present at elevated levels in all species tested. The lowest levels were in A. colei (0.49% w/w) and the highest in A. saligna (1.85% w/w). Observed levels of djenkolic acid are comparable to measured and reported levels found in the djenkol bean. Subsequent testing of seed processing methods showed djenkolic acid levels can be significantly reduced by over 90% by dry roasting at 180 °C rendering the seed safe for human consumption. PMID: 25722145 [PubMed - indexed for MEDLINE]

Related Articles An efficient TOF-SIMS image analysis with spatial correlation and alternating non-negativity-constrained least squares. Bioinformatics. 2015 Mar 1;31(5):753-60 Authors: Aram P, Shen L, Pugh JA, Vaidyanathan S, Kadirkamanathan V Abstract MOTIVATION: Advances in analytical instrumentation towards acquiring high-resolution images of mass spectrometry constantly demand efficient approaches for data analysis. This is particularly true of time-of-flight secondary ion mass spectrometry imaging where recent advances enable acquisition of high-resolution data in multiple dimensions. In many applications, the distribution of different species from a sampled surface is spatially continuous in nature and a model that incorporates the spatial correlation across the surface would be preferable to estimations at discrete spatial locations. A key challenge here is the capability to analyse the high-resolution multidimensional data to extract relevant information reliably and efficiently. RESULTS: We propose a framework based on alternating non-negativity-constrained least squares which accounts for the spatial correlation across the sample surface. The proposed method also decouples the computational complexity of the estimation procedure from the image resolution, which significantly reduces the processing time. We evaluate the performance of the algorithm with biochemical image datasets generated from mixture of metabolites. PMID: 25452330 [PubMed - indexed for MEDLINE]