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Sample records for metabolite profiling identifies

  1. Metabolite profiling identifies candidate markers reflecting the clinical adaptations associated with Roux-en-Y gastric bypass surgery.

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    David M Mutch

    Full Text Available BACKGROUND: Roux-en-Y gastric bypass (RYGB surgery is associated with weight loss, improved insulin sensitivity and glucose homeostasis, and a reduction in co-morbidities such as diabetes and coronary heart disease. To generate further insight into the numerous metabolic adaptations associated with RYGB surgery, we profiled serum metabolites before and after gastric bypass surgery and integrated metabolite changes with clinical data. METHODOLOGY AND PRINCIPAL FINDINGS: Serum metabolites were detected by gas and liquid chromatography-coupled mass spectrometry before, and 3 and 6 months after RYGB in morbidly obese female subjects (n = 14; BMI = 46.2+/-1.7. Subjects showed decreases in weight-related parameters and improvements in insulin sensitivity post surgery. The abundance of 48% (83 of 172 of the measured metabolites changed significantly within the first 3 months post RYGB (p<0.05, including sphingosines, unsaturated fatty acids, and branched chain amino acids. Dividing subjects into obese (n = 9 and obese/diabetic (n = 5 groups identified 8 metabolites that differed consistently at all time points and whose serum levels changed following RYGB: asparagine, lysophosphatidylcholine (C18:2, nervonic (C24:1 acid, p-Cresol sulfate, lactate, lycopene, glucose, and mannose. Changes in the aforementioned metabolites were integrated with clinical data for body mass index (BMI and estimates for insulin resistance (HOMA-IR. Of these, nervonic acid was significantly and negatively correlated with HOMA-IR (p = 0.001, R = -0.55. CONCLUSIONS: Global metabolite profiling in morbidly obese subjects after RYGB has provided new information regarding the considerable metabolic alterations associated with this surgical procedure. Integrating clinical measurements with metabolomics data is capable of identifying markers that reflect the metabolic adaptations following RYGB.

  2. Metabolite Profiling Identified Methylerythritol Cyclodiphosphate Efflux as a Limiting Step in Microbial Isoprenoid Production

    Science.gov (United States)

    Zhou, Kang; Zou, Ruiyang; Stephanopoulos, Gregory; Too, Heng-Phon

    2012-01-01

    Isoprenoids are natural products that are all derived from isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). These precursors are synthesized either by the mevalonate (MVA) pathway or the 1-Deoxy-D-Xylulose 5-Phosphate (DXP) pathway. Metabolic engineering of microbes has enabled overproduction of various isoprenoid products from the DXP pathway including lycopene, artemisinic acid, taxadiene and levopimaradiene. To date, there is no method to accurately measure all the DXP metabolic intermediates simultaneously so as to enable the identification of potential flux limiting steps. In this study, a solid phase extraction coupled with ultra performance liquid chromatography mass spectrometry (SPE UPLC-MS) method was developed. This method was used to measure the DXP intermediates in genetically engineered E. coli. Unexpectedly, methylerythritol cyclodiphosphate (MEC) was found to efflux when certain enzymes of the pathway were over-expressed, demonstrating the existence of a novel competing pathway branch in the DXP metabolism. Guided by these findings, ispG was overexpressed and was found to effectively reduce the efflux of MEC inside the cells, resulting in a significant increase in downstream isoprenoid production. This study demonstrated the necessity to quantify metabolites enabling the identification of a hitherto unrecognized pathway and provided useful insights into rational design in metabolic engineering. PMID:23133596

  3. Metabolite profiling identified methylerythritol cyclodiphosphate efflux as a limiting step in microbial isoprenoid production.

    Directory of Open Access Journals (Sweden)

    Kang Zhou

    Full Text Available Isoprenoids are natural products that are all derived from isopentenyl diphosphate (IPP and dimethylallyl diphosphate (DMAPP. These precursors are synthesized either by the mevalonate (MVA pathway or the 1-Deoxy-D-Xylulose 5-Phosphate (DXP pathway. Metabolic engineering of microbes has enabled overproduction of various isoprenoid products from the DXP pathway including lycopene, artemisinic acid, taxadiene and levopimaradiene. To date, there is no method to accurately measure all the DXP metabolic intermediates simultaneously so as to enable the identification of potential flux limiting steps. In this study, a solid phase extraction coupled with ultra performance liquid chromatography mass spectrometry (SPE UPLC-MS method was developed. This method was used to measure the DXP intermediates in genetically engineered E. coli. Unexpectedly, methylerythritol cyclodiphosphate (MEC was found to efflux when certain enzymes of the pathway were over-expressed, demonstrating the existence of a novel competing pathway branch in the DXP metabolism. Guided by these findings, ispG was overexpressed and was found to effectively reduce the efflux of MEC inside the cells, resulting in a significant increase in downstream isoprenoid production. This study demonstrated the necessity to quantify metabolites enabling the identification of a hitherto unrecognized pathway and provided useful insights into rational design in metabolic engineering.

  4. Targeted Serum Metabolite Profiling Identifies Metabolic Signatures in Patients with Alzheimer's Disease, Normal Pressure Hydrocephalus and Brain Tumor

    DEFF Research Database (Denmark)

    Orešič, Matej; Anderson, Gabriella; Mattila, Ismo

    2018-01-01

    ) and brain tumors (BT). Blood samples were collected from 27 NPH and 20 BT patients. The profiles of 21 metabolites were examined. Additionally, data from 37 AD patients and 46 controls from a previous study were analyzed together with the newly acquired data. No differences in 2,4-DHB were found across AD...

  5. Metabolite Profiling of Red Sea Corals

    KAUST Repository

    Ortega, Jovhana Alejandra

    2016-12-01

    Looking at the metabolite profile of an organism provides insights into the metabolomic state of a cell and hence also into pathways employed. Little is known about the metabolites produced by corals and their algal symbionts. In particular, corals from the central Red Sea are understudied, but interesting study objects, as they live in one of the warmest and most saline environments and can provide clues as to the adjustment of corals to environmental change. In this study, we applied gas chromatography – mass spectrometry (GC–MS) metabolite profiling to analyze the metabolic profile of four coral species and their associated symbionts: Fungia granulosa, Acropora hemprichii, Porites lutea, and Pocillopora verrucosa. We identified and quantified 102 compounds among primary and secondary metabolites across all samples. F. granulosa and its symbiont showed a total of 59 metabolites which were similar to the 51 displayed by P. verrucosa. P. lutea and A. hemprichii both harbored 40 compounds in conjunction with their respective isolated algae. Comparing across species, 28 metabolites were exclusively present in algae, while 38 were exclusive to corals. A principal component and cluster analyses revealed that metabolite profiles clustered between corals and algae, but each species harbored a distinct catalog of metabolites. The major classes of compounds were carbohydrates and amino acids. Taken together, this study provides a first description of metabolites of Red Sea corals and their associated symbionts. As expected, the metabolites of coral hosts differ from their algal symbionts, but each host and algal species harbor a unique set of metabolites. This corroborates that host-symbiont species pairs display a fine-tuned complementary metabolism that provide insights into the specific nature of the symbiosis. Our analysis also revealed aquatic pollutants, which suggests that metabolite profiling might be used for monitoring pollution levels and assessing

  6. Metabolite profiles of common Stemphylium species

    DEFF Research Database (Denmark)

    Andersen, Birgitte; Solfrizzo, Michelle; Visconti, Angelo

    1995-01-01

    Thirty-three isolates of Stemphylium spp. have been analysed for their metabolite profiles. Five metabolites, stemphylin, stemphyloxin II, stemphyperylenol, stemphol and a stemphol related compound, have been detected by high-performance liquid chromatography and thin-layer chromatography...

  7. Profiling and Identification of the Metabolites of Evodiamine in Rats ...

    African Journals Online (AJOL)

    linear ion trap Orbitrap mass spectrometer (UPLC-LTQ-Orbitrap) method to profile and identify the metabolites of evodiamine in ... Keywords: Evodiamine, Ultra–performance liquid chromatography with linear ion trap-Orbitrap,. Hydroxyevodiamine ..... janthinellum and its application for metabolite identification in rat urine.

  8. Metabolites of cannabidiol identified in human urine.

    Science.gov (United States)

    Harvey, D J; Mechoulam, R

    1990-03-01

    1. Urine from a dystonic patient treated with cannabidiol (CBD) was examined by g.l.c.-mass spectrometry for CBD metabolites. Metabolites were identified as their trimethylsilyl (TMS), [2H9]TMS, and methyl ester/TMS derivatives and as the TMS derivatives of the product of lithium aluminium deuteride reduction. 2. Thirty-three metabolites were identified in addition to unmetabolized CBD, and a further four metabolites were partially characterized. 3. The major metabolic route was hydroxylation and oxidation at C-7 followed by further hydroxylation in the pentyl and propenyl groups to give 1"-, 2"-, 3"-, 4"- and 10-hydroxy derivatives of CBD-7-oic acid. Other metabolites, mainly acids, were formed by beta-oxidation and related biotransformations from the pentyl side-chain and these were also hydroxylated at C-6 or C-7. The major oxidized metabolite was CBD-7-oic acid containing a hydroxyethyl side-chain. 4. Two 8,9-dihydroxy compounds, presumably derived from the corresponding epoxide were identified. 5. Also present were several cyclized cannabinoids including delta-6- and delta-1-tetrahydrocannabinol and cannabinol. 6. This is the first metabolic study of CBD in humans; most observed metabolic routes were typical of those found for CBD and related cannabinoids in other species.

  9. De-novo RNA sequencing and metabolite profiling to identify genes involved in anthocyanin biosynthesis in Korean black raspberry (Rubus coreanus Miquel.

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    Tae Kyung Hyun

    Full Text Available The Korean black raspberry (Rubus coreanus Miquel, KB on ripening is usually consumed as fresh fruit, whereas the unripe KB has been widely used as a source of traditional herbal medicine. Such a stage specific utilization of KB has been assumed due to the changing metabolite profile during fruit ripening process, but so far molecular and biochemical changes during its fruit maturation are poorly understood. To analyze biochemical changes during fruit ripening process at molecular level, firstly, we have sequenced, assembled, and annotated the transcriptome of KB fruits. Over 4.86 Gb of normalized cDNA prepared from fruits was sequenced using Illumina HiSeq™ 2000, and assembled into 43,723 unigenes. Secondly, we have reported that alterations in anthocyanins and proanthocyanidins are the major factors facilitating variations in these stages of fruits. In addition, up-regulation of F3'H1, DFR4 and LDOX1 resulted in the accumulation of cyanidin derivatives during the ripening process of KB, indicating the positive relationship between the expression of anthocyanin biosynthetic genes and the anthocyanin accumulation. Furthermore, the ability of RcMCHI2 (R. coreanus Miquel chalcone flavanone isomerase 2 gene to complement Arabidopsis transparent testa 5 mutant supported the feasibility of our transcriptome library to provide the gene resources for improving plant nutrition and pigmentation. Taken together, these datasets obtained from transcriptome library and metabolic profiling would be helpful to define the gene-metabolite relationships in this non-model plant.

  10. De-novo RNA sequencing and metabolite profiling to identify genes involved in anthocyanin biosynthesis in Korean black raspberry (Rubus coreanus Miquel).

    Science.gov (United States)

    Hyun, Tae Kyung; Lee, Sarah; Rim, Yeonggil; Kumar, Ritesh; Han, Xiao; Lee, Sang Yeol; Lee, Choong Hwan; Kim, Jae-Yean

    2014-01-01

    The Korean black raspberry (Rubus coreanus Miquel, KB) on ripening is usually consumed as fresh fruit, whereas the unripe KB has been widely used as a source of traditional herbal medicine. Such a stage specific utilization of KB has been assumed due to the changing metabolite profile during fruit ripening process, but so far molecular and biochemical changes during its fruit maturation are poorly understood. To analyze biochemical changes during fruit ripening process at molecular level, firstly, we have sequenced, assembled, and annotated the transcriptome of KB fruits. Over 4.86 Gb of normalized cDNA prepared from fruits was sequenced using Illumina HiSeq™ 2000, and assembled into 43,723 unigenes. Secondly, we have reported that alterations in anthocyanins and proanthocyanidins are the major factors facilitating variations in these stages of fruits. In addition, up-regulation of F3'H1, DFR4 and LDOX1 resulted in the accumulation of cyanidin derivatives during the ripening process of KB, indicating the positive relationship between the expression of anthocyanin biosynthetic genes and the anthocyanin accumulation. Furthermore, the ability of RcMCHI2 (R. coreanus Miquel chalcone flavanone isomerase 2) gene to complement Arabidopsis transparent testa 5 mutant supported the feasibility of our transcriptome library to provide the gene resources for improving plant nutrition and pigmentation. Taken together, these datasets obtained from transcriptome library and metabolic profiling would be helpful to define the gene-metabolite relationships in this non-model plant.

  11. Plasma Metabolite Profiles in Response to Chronic Exercise.

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    Brennan, Andrea M; Benson, Mark; Morningstar, Jordan; Herzig, Matthew; Robbins, Jeremy; Gerszten, Robert E; Ross, Robert

    2018-03-05

    High throughput profiling of metabolic status (metabolomics) allows for the assessment of small-molecule metabolites that may participate in exercise-induced biochemical pathways and corresponding cardiometabolic risk modification. We sought to describe the changes in a diverse set of plasma metabolite profiles in patients undergoing chronic exercise training and assess the relationship between metabolites and cardiometabolic response to exercise. A secondary analysis was performed in 216 middle-aged abdominally obese men and women ([mean (SD)], 52.4 (8.0) years) randomized into one of four groups varying in exercise amount and intensity for 6 months duration: high amount high intensity, high amount low intensity, low amount low intensity, and control. 147 metabolites were profiled by liquid chromatography-tandem mass spectrometry. No significant differences in metabolite changes between specific exercise groups were observed; therefore, subsequent analyses were collapsed across exercise groups. There were no significant differences in metabolite changes between the exercise and control groups after 24 weeks at a Bonferroni-adjusted statistical significance (p < 3.0 x 10). Seven metabolites changed in the exercise group compared to the control group at p < 0.05. Changes in several metabolites from distinct metabolic pathways were associated with change in cardiometabolic risk traits, and three baseline metabolite levels predicted changes in cardiometabolic risk traits. Metabolomic profiling revealed no significant plasma metabolite changes between exercise compared to control after 24-weeks at Bonferroni significance. However, we identified circulating biomarkers that were predictive or reflective of improvements in cardiometabolic traits in the exercise group.

  12. Differences between human plasma and serum metabolite profiles.

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    Zhonghao Yu

    Full Text Available BACKGROUND: Human plasma and serum are widely used matrices in clinical and biological studies. However, different collecting procedures and the coagulation cascade influence concentrations of both proteins and metabolites in these matrices. The effects on metabolite concentration profiles have not been fully characterized. METHODOLOGY/PRINCIPAL FINDINGS: We analyzed the concentrations of 163 metabolites in plasma and serum samples collected simultaneously from 377 fasting individuals. To ensure data quality, 41 metabolites with low measurement stability were excluded from further analysis. In addition, plasma and corresponding serum samples from 83 individuals were re-measured in the same plates and mean correlation coefficients (r of all metabolites between the duplicates were 0.83 and 0.80 in plasma and serum, respectively, indicating significantly better stability of plasma compared to serum (p = 0.01. Metabolite profiles from plasma and serum were clearly distinct with 104 metabolites showing significantly higher concentrations in serum. In particular, 9 metabolites showed relative concentration differences larger than 20%. Despite differences in absolute concentration between the two matrices, for most metabolites the overall correlation was high (mean r = 0.81±0.10, which reflects a proportional change in concentration. Furthermore, when two groups of individuals with different phenotypes were compared with each other using both matrices, more metabolites with significantly different concentrations could be identified in serum than in plasma. For example, when 51 type 2 diabetes (T2D patients were compared with 326 non-T2D individuals, 15 more significantly different metabolites were found in serum, in addition to the 25 common to both matrices. CONCLUSIONS/SIGNIFICANCE: Our study shows that reproducibility was good in both plasma and serum, and better in plasma. Furthermore, as long as the same blood preparation procedure is

  13. Metabonomics identifies serum metabolite markers of colorectal cancer.

    Science.gov (United States)

    Tan, Binbin; Qiu, Yunping; Zou, Xia; Chen, Tianlu; Xie, Guoxiang; Cheng, Yu; Dong, Taotao; Zhao, Linjing; Feng, Bo; Hu, Xiaofang; Xu, Lisa X; Zhao, Aihua; Zhang, Menghui; Cai, Guoxiang; Cai, Sanjun; Zhou, Zhanxiang; Zheng, Minhua; Zhang, Yan; Jia, Wei

    2013-06-07

    Recent studies suggest that biofluid-based metabonomics may identify metabolite markers promising for colorectal cancer (CRC) diagnosis. We report here a follow-up replication study, after a previous CRC metabonomics study, aiming to identify a distinct serum metabolic signature of CRC with diagnostic potential. Serum metabolites from newly diagnosed CRC patients (N = 101) and healthy subjects (N = 102) were profiled using gas chromatography time-of-flight mass spectrometry (GC-TOFMS) and ultraperformance liquid chromatography quadrupole time-of-flight mass spectrometry (UPLC-QTOFMS). Differential metabolites were identified with statistical tests of orthogonal partial least-squares-discriminant analysis (VIP > 1) and the Mann-Whitney U test (p partial least-squares-discriminant analysis (OPLS-DA) in a learning sample set of 62 CRC patients and 62 matched healthy controls. This established model was able to correctly assign the rest of the samples to the CRC or control groups in a validation set of 39 CRC patients and 40 healthy controls. Consistent with our findings from the previous study, we observed a distinct metabolic signature in CRC patients including tricarboxylic acid (TCA) cycle, urea cycle, glutamine, fatty acids, and gut flora metabolism. Our results demonstrated that a panel of serum metabolite markers is of great potential as a noninvasive diagnostic method for the detection of CRC.

  14. SPE-NMR metabolite sub-profiling of urine

    NARCIS (Netherlands)

    Jacobs, D.M.; Spiesser, L.; Garnier, M.; Roo, de N.; Dorsten, van F.; Hollebrands, B.; Velzen, van E.; Draijer, R.; Duynhoven, van J.P.M.

    2012-01-01

    NMR-based metabolite profiling of urine is a fast and reproducible method for detection of numerous metabolites with diverse chemical properties. However, signal overlap in the (1)H NMR profiles of human urine may hamper quantification and identification of metabolites. Therefore, a new method has

  15. Metabolite Depletion Affects Flux Profiling of Cell Lines

    DEFF Research Database (Denmark)

    Nilsson, A.; Haanstra, J. R.; Teusink, B.

    2018-01-01

    Quantifying the rate of consumption and release of metabolites (i.e., flux profiling) has become integral to the study of cancer. The fluxes as well as the growth of the cells may be affected by metabolite depletion during cultivation.......Quantifying the rate of consumption and release of metabolites (i.e., flux profiling) has become integral to the study of cancer. The fluxes as well as the growth of the cells may be affected by metabolite depletion during cultivation....

  16. Profiling and Distribution of Metabolites of Procyanidin B2 in Mice by UPLC-DAD-ESI-IT-TOF-MSn Technique

    OpenAIRE

    Xiao, Ying; Hu, Zhongzhi; Yin, Zhiting; Zhou, Yiming; Liu, Taiyi; Zhou, Xiaoli; Chang, Dawei

    2017-01-01

    The metabolite profiles and distributions of procyanidin B2 were qualitatively described using UPLC-DAD-ESI-IT-TOF-MSn without help of reference standards, and a possible metabolic pathway was proposed in the present study. Summarily, 53 metabolites (24 new metabolites) were detected as metabolites of procyanidin B2, and 45 of them were tentatively identified. Twenty seven metabolites were assigned as similar metabolites of (−)-epicatechin by scission of the flavanol interflavanic bond C4–C8,...

  17. Identifying diseases-related metabolites using random walk.

    Science.gov (United States)

    Hu, Yang; Zhao, Tianyi; Zhang, Ningyi; Zang, Tianyi; Zhang, Jun; Cheng, Liang

    2018-04-11

    Metabolites disrupted by abnormal state of human body are deemed as the effect of diseases. In comparison with the cause of diseases like genes, these markers are easier to be captured for the prevention and diagnosis of metabolic diseases. Currently, a large number of metabolic markers of diseases need to be explored, which drive us to do this work. The existing metabolite-disease associations were extracted from Human Metabolome Database (HMDB) using a text mining tool NCBO annotator as priori knowledge. Next we calculated the similarity of a pair-wise metabolites based on the similarity of disease sets of them. Then, all the similarities of metabolite pairs were utilized for constructing a weighted metabolite association network (WMAN). Subsequently, the network was utilized for predicting novel metabolic markers of diseases using random walk. Totally, 604 metabolites and 228 diseases were extracted from HMDB. From 604 metabolites, 453 metabolites are selected to construct the WMAN, where each metabolite is deemed as a node, and the similarity of two metabolites as the weight of the edge linking them. The performance of the network is validated using the leave one out method. As a result, the high area under the receiver operating characteristic curve (AUC) (0.7048) is achieved. The further case studies for identifying novel metabolites of diabetes mellitus were validated in the recent studies. In this paper, we presented a novel method for prioritizing metabolite-disease pairs. The superior performance validates its reliability for exploring novel metabolic markers of diseases.

  18. Metabolite Profiles of Male and Female Humboldt Penguins

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    Jeffrey M. Levengood

    2015-10-01

    Full Text Available We examined 185 metabolites in 30 adult Humboldt Penguins (Spheniscus humboldti nesting at the Punta San Juan Marine Protected Area, Peru, in order to examine gender differences in metabolome profiles, particularly those involved in metabolism and energetics. The majority of the compounds identified were fatty (26% of total identified compounds, organic (19%, and amino (16% acids. We were able to differentiate male and female penguins with 96.6% accuracy on the basis of 12 metabolites, most of which are involved in lipid and carbohydrate metabolism. These included 2-oxoglutarate, erythronic acid, GABA, mannitol, sedoheptulose 7-phosphate, and serine and six metabolites present in higher concentrations in females compared to males (2-aminoadipic acid, O-phosphorylethanolamine, glycerol 2-phosphate, glycerol 3-phosphate, pantothenic acid, and creatinine. Of these, 2-oxoglutarate and glycerol 3-phosphate were key metabolites distinguishing gender. Our results indicated that male and female Humboldt Penguins were characterized by differing metabolic states. Such differences could be important to individual and brood survival in times of environmental stress.

  19. Characterizing Exposures of Fish to Wastewater Treatment Plant Effluent: An Integrated Metabolite and Lipid Profiling Approach

    Science.gov (United States)

    Metabolite and lipid profiling are well established techniques for studying chemical-induced alterations to normal biological function in numerous organisms. These techniques have been used successfully to identify biomarkers of chemical exposure, screen for chemical potency, or ...

  20. Metabolite profiles and the risk of developing diabetes

    OpenAIRE

    T J Wang; M G Larson; R S Vasan; S Cheng; E P Rhee; E McCabe; G D Lewis; C S Fox; P F Jacques; C Fernandez; C J ODonnell; S A Carr; V K Mootha; J C Florez; A Souza

    2011-01-01

    Emerging technologies allow the high-throughput profiling of metabolic status from a blood specimen (metabolomics). We investigated whether metabolite profiles could predict the development of diabetes. Among 2,422 normoglycemic individuals followed for 12 years, 201 developed diabetes. Amino acids, amines, and other polar metabolites were profiled in baseline specimens using liquid chromatography-tandem mass spectrometry. Cases and controls were matched for age, body mass index and fasting g...

  1. Profiling and Distribution of Metabolites of Procyanidin B2 in Mice by UPLC-DAD-ESI-IT-TOF-MSn Technique

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    Ying Xiao

    2017-05-01

    Full Text Available The metabolite profiles and distributions of procyanidin B2 were qualitatively described using UPLC-DAD-ESI-IT-TOF-MSn without help of reference standards, and a possible metabolic pathway was proposed in the present study. Summarily, 53 metabolites (24 new metabolites were detected as metabolites of procyanidin B2, and 45 of them were tentatively identified. Twenty seven metabolites were assigned as similar metabolites of (−-epicatechin by scission of the flavanol interflavanic bond C4–C8, including 16 aromatic metabolites, 5 conjugated metabolites, 3 ring-cleavage metabolites, and 2 phenylvalerolactone metabolites. Additionally, 14 metabolites were conjugates of free procyanidin B2, comprising 9 methylation metabolites, 8 sulfation metabolites, 5 hydration metabolites, 2 hydroxylation metabolites, 1 hydrogenation metabolites, and 1 glucuronidation metabolites. The results of metabolite distributions in organs indicated that the conjugated reaction of free procyanidin B2 mainly occurred in liver and diversified metabolites forms were observed in small intestine. The metabolic components of procyanidin B2 identified in mice provided useful information for further study of the bioactivity and mechanism of its action.

  2. Application of a new procedure for liquid chromatography/mass spectrometry profiling of plasma amino acid-related metabolites and untargeted shotgun proteomics to identify mechanisms and biomarkers of calcific aortic stenosis.

    Science.gov (United States)

    Olkowicz, Mariola; Debski, Janusz; Jablonska, Patrycja; Dadlez, Michal; Smolenski, Ryszard T

    2017-09-29

    Calcific aortic valve stenosis (CAS) increasingly affects our ageing population, but the mechanisms of the disease and its biomarkers are not well established. Recently, plasma amino acid-related metabolite (AA) profiling has attracted attention in studies on pathology and development of biomarkers of cardiovascular diseases, but has not been studied in CAS. To evaluate the potential relationship between CAS and AA metabolome, a new ion-pairing reversed-phase liquid chromatography-tandem mass spectrometry (IP-RPLC-MS/MS) method has been developed and validated for simultaneous determination of 43 AAs in plasma of stenotic patients and age-matched control subjects. Furthermore, untargeted mass spectrometry-based proteomic analysis and confirmatory ELISA assays were performed. The method developed offered high accuracy (intra-assay imprecision averaged 4.4% for all compounds) and sensitivity (LOQ within 0.01-0.5μM). We found that 22 AAs and three AA ratios significantly changed in the CAS group as compared to control. The most pronounced differences were observed in urea cycle-related AAs and branched-chain AA (BCAA)-related AAs. The contents of asymmetric dimethylarginine (ADMA) and its monomethylated derivative (NMMA) were increased by 30-64% with CAS. The arginine/ADMA and Fischer's ratios as well as arginine, homoarginine, ADMA, symmetric dimethylarginine, hydroxyproline, betaine and 3-methylhistidine correlated with cardiac function-related parameters and concomitant systemic factors in the CAS patients. The results of proteomic analysis were consistent with involvement of inflammation, lipid abnormalities, hemostasis and extracellular matrix remodeling in CAS. In conclusion, changes in plasma AA profile and protein pattern that we identified in CAS provide information relevant to pathomechanisms and may deliver new biomarkers of the disease. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. Alterations of urinary metabolite profile in model diabetic nephropathy

    Energy Technology Data Exchange (ETDEWEB)

    Stec, Donald F. [Vanderbilt Institute of Chemical Biology, Vanderbilt University Medical Center, Nashville, TN 37232 (United States); Wang, Suwan; Stothers, Cody [Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232 (United States); Avance, Josh [Berea College, 1916 CPO, Berea, KY 40404 (United States); Denson, Deon [Choctaw Central High School, Philadelphia, MS 39350 (United States); Harris, Raymond [Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232 (United States); Voziyan, Paul, E-mail: paul.voziyan@vanderbilt.edu [Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232 (United States)

    2015-01-09

    Highlights: • {sup 1}H NMR spectroscopy was employed to study urinary metabolite profile in diabetic mouse models. • Mouse urinary metabolome showed major changes that are also found in human diabetic nephropathy. • These models can be new tools to study urinary biomarkers that are relevant to human disease. - Abstract: Countering the diabetes pandemic and consequent complications, such as nephropathy, will require better understanding of disease mechanisms and development of new diagnostic methods. Animal models can be versatile tools in studies of diabetic renal disease when model pathology is relevant to human diabetic nephropathy (DN). Diabetic models using endothelial nitric oxide synthase (eNOS) knock-out mice develop major renal lesions characteristic of human disease. However, it is unknown whether they can also reproduce changes in urinary metabolites found in human DN. We employed Type 1 and Type 2 diabetic mouse models of DN, i.e. STZ-eNOS{sup −/−} C57BLKS and eNOS{sup −/−} C57BLKS db/db, with the goal of determining changes in urinary metabolite profile using proton nuclear magnetic resonance (NMR). Six urinary metabolites with significantly lower levels in diabetic compared to control mice have been identified. Specifically, major changes were found in metabolites from tricarboxylic acid (TCA) cycle and aromatic amino acid catabolism including 3-indoxyl sulfate, cis-aconitate, 2-oxoisocaproate, N-phenyl-acetylglycine, 4-hydroxyphenyl acetate, and hippurate. Levels of 4-hydroxyphenyl acetic acid and hippuric acid showed the strongest reverse correlation to albumin-to-creatinine ratio (ACR), which is an indicator of renal damage. Importantly, similar changes in urinary hydroxyphenyl acetate and hippurate were previously reported in human renal disease. We demonstrated that STZ-eNOS{sup −/−} C57BLKS and eNOS{sup −/−} C57BLKS db/db mouse models can recapitulate changes in urinary metabolome found in human DN and therefore can be

  4. Alterations of urinary metabolite profile in model diabetic nephropathy

    International Nuclear Information System (INIS)

    Stec, Donald F.; Wang, Suwan; Stothers, Cody; Avance, Josh; Denson, Deon; Harris, Raymond; Voziyan, Paul

    2015-01-01

    Highlights: • 1 H NMR spectroscopy was employed to study urinary metabolite profile in diabetic mouse models. • Mouse urinary metabolome showed major changes that are also found in human diabetic nephropathy. • These models can be new tools to study urinary biomarkers that are relevant to human disease. - Abstract: Countering the diabetes pandemic and consequent complications, such as nephropathy, will require better understanding of disease mechanisms and development of new diagnostic methods. Animal models can be versatile tools in studies of diabetic renal disease when model pathology is relevant to human diabetic nephropathy (DN). Diabetic models using endothelial nitric oxide synthase (eNOS) knock-out mice develop major renal lesions characteristic of human disease. However, it is unknown whether they can also reproduce changes in urinary metabolites found in human DN. We employed Type 1 and Type 2 diabetic mouse models of DN, i.e. STZ-eNOS −/− C57BLKS and eNOS −/− C57BLKS db/db, with the goal of determining changes in urinary metabolite profile using proton nuclear magnetic resonance (NMR). Six urinary metabolites with significantly lower levels in diabetic compared to control mice have been identified. Specifically, major changes were found in metabolites from tricarboxylic acid (TCA) cycle and aromatic amino acid catabolism including 3-indoxyl sulfate, cis-aconitate, 2-oxoisocaproate, N-phenyl-acetylglycine, 4-hydroxyphenyl acetate, and hippurate. Levels of 4-hydroxyphenyl acetic acid and hippuric acid showed the strongest reverse correlation to albumin-to-creatinine ratio (ACR), which is an indicator of renal damage. Importantly, similar changes in urinary hydroxyphenyl acetate and hippurate were previously reported in human renal disease. We demonstrated that STZ-eNOS −/− C57BLKS and eNOS −/− C57BLKS db/db mouse models can recapitulate changes in urinary metabolome found in human DN and therefore can be useful new tools in

  5. Metabolite profiling of the carnivorous pitcher plants Darlingtonia and Sarracenia.

    Directory of Open Access Journals (Sweden)

    Hannu Hotti

    Full Text Available Sarraceniaceae is a New World carnivorous plant family comprising three genera: Darlingtonia, Heliamphora, and Sarracenia. The plants occur in nutrient-poor environments and have developed insectivorous capability in order to supplement their nutrient uptake. Sarracenia flava contains the alkaloid coniine, otherwise only found in Conium maculatum, in which its biosynthesis has been studied, and several Aloe species. Its ecological role and biosynthetic origin in S. flava is speculative. The aim of the current research was to investigate the occurrence of coniine in Sarracenia and Darlingtonia and to identify common constituents of both genera, unique compounds for individual variants and floral scent chemicals. In this comprehensive metabolic profiling study, we looked for compound patterns that are associated with the taxonomy of Sarracenia species. In total, 57 different Sarracenia and D. californica accessions were used for metabolite content screening by gas chromatography-mass spectrometry. The resulting high-dimensional data were studied using a data mining approach. The two genera are characterized by a large number of metabolites and huge chemical diversity between different species. By applying feature selection for clustering and by integrating new biochemical data with existing phylogenetic data, we were able to demonstrate that the chemical composition of the species can be explained by their known classification. Although transcriptome analysis did not reveal a candidate gene for coniine biosynthesis, the use of a sensitive selected ion monitoring method enabled the detection of coniine in eight Sarracenia species, showing that it is more widespread in this genus than previously believed.

  6. Metabolite profiling of the carnivorous pitcher plants Darlingtonia and Sarracenia.

    Science.gov (United States)

    Hotti, Hannu; Gopalacharyulu, Peddinti; Seppänen-Laakso, Tuulikki; Rischer, Heiko

    2017-01-01

    Sarraceniaceae is a New World carnivorous plant family comprising three genera: Darlingtonia, Heliamphora, and Sarracenia. The plants occur in nutrient-poor environments and have developed insectivorous capability in order to supplement their nutrient uptake. Sarracenia flava contains the alkaloid coniine, otherwise only found in Conium maculatum, in which its biosynthesis has been studied, and several Aloe species. Its ecological role and biosynthetic origin in S. flava is speculative. The aim of the current research was to investigate the occurrence of coniine in Sarracenia and Darlingtonia and to identify common constituents of both genera, unique compounds for individual variants and floral scent chemicals. In this comprehensive metabolic profiling study, we looked for compound patterns that are associated with the taxonomy of Sarracenia species. In total, 57 different Sarracenia and D. californica accessions were used for metabolite content screening by gas chromatography-mass spectrometry. The resulting high-dimensional data were studied using a data mining approach. The two genera are characterized by a large number of metabolites and huge chemical diversity between different species. By applying feature selection for clustering and by integrating new biochemical data with existing phylogenetic data, we were able to demonstrate that the chemical composition of the species can be explained by their known classification. Although transcriptome analysis did not reveal a candidate gene for coniine biosynthesis, the use of a sensitive selected ion monitoring method enabled the detection of coniine in eight Sarracenia species, showing that it is more widespread in this genus than previously believed.

  7. Association between Metabolite Profiles, Metabolic Syndrome and Obesity Status

    Directory of Open Access Journals (Sweden)

    Bénédicte Allam-Ndoul

    2016-05-01

    Full Text Available Underlying mechanisms associated with the development of abnormal metabolic phenotypes among obese individuals are not yet clear. Our aim is to investigate differences in plasma metabolomics profiles between normal weight (NW and overweight/obese (Ov/Ob individuals, with or without metabolic syndrome (MetS. Mass spectrometry-based metabolite profiling was used to compare metabolite levels between each group. Three main principal components factors explaining a maximum of variance were retained. Factor 1’s (long chain glycerophospholipids metabolite profile score was higher among Ov/Ob with MetS than among Ov/Ob and NW participants without MetS. This factor was positively correlated to plasma total cholesterol (total-C and triglyceride levels in the three groups, to high density lipoprotein -cholesterol (HDL-C among participants without MetS. Factor 2 (amino acids and short to long chain acylcarnitine was positively correlated to HDL-C and negatively correlated with insulin levels among NW participants. Factor 3’s (medium chain acylcarnitines metabolite profile scores were higher among NW participants than among Ov/Ob with or without MetS. Factor 3 was negatively associated with glucose levels among the Ov/Ob with MetS. Factor 1 seems to be associated with a deteriorated metabolic profile that corresponds to obesity, whereas Factors 2 and 3 seem to be rather associated with a healthy metabolic profile.

  8. Temperament type specific metabolite profiles of the prefrontal cortex and serum in cattle.

    Directory of Open Access Journals (Sweden)

    Bodo Brand

    Full Text Available In the past decade the number of studies investigating temperament in farm animals has increased greatly because temperament has been shown not only to affect handling but also reproduction, health and economically important production traits. However, molecular pathways underlying temperament and molecular pathways linking temperament to production traits, health and reproduction have yet to be studied in full detail. Here we report the results of metabolite profiling of the prefrontal cortex and serum of cattle with distinct temperament types that were performed to further explore their molecular divergence in the response to the slaughter procedure and to identify new targets for further research of cattle temperament. By performing an untargeted comprehensive metabolite profiling, 627 and 1097 metabolite features comprising 235 and 328 metabolites could be detected in the prefrontal cortex and serum, respectively. In total, 54 prefrontal cortex and 51 serum metabolite features were indicated to have a high relevance in the classification of temperament types by a sparse partial least square discriminant analysis. A clear discrimination between fearful/neophobic-alert, interested-stressed, subdued/uninterested-calm and outgoing/neophilic-alert temperament types could be observed based on the abundance of the identified relevant prefrontal cortex and serum metabolites. Metabolites with high relevance in the classification of temperament types revealed that the main differences between temperament types in the response to the slaughter procedure were related to the abundance of glycerophospholipids, fatty acyls and sterol lipids. Differences in the abundance of metabolites related to C21 steroid metabolism and oxidative stress indicated that the differences in the metabolite profiles of the four extreme temperament types could be the result of a temperament type specific regulation of molecular pathways that are known to be involved in the

  9. Metabolite profiling of CHO cells: Molecular reflections of bioprocessing effectiveness

    NARCIS (Netherlands)

    Sellick, C.A.; Croxford, A.S.; Maqsood, A.R.; Stephens, G.M.; Westerhoff, H.V.; Goodacre, R.; Dickson, A.J.

    2015-01-01

    Whilst development of medium and feeds has provided major advances in recombinant protein production in CHO cells, the fundamental understanding is limited. We have applied metabolite profiling with established robust (GC-MS) analytics to define the molecular loci by which two yield-enhancing feeds

  10. NMR Spectroscopy Identifies Metabolites Translocated from Powdery Mildew Resistant Rootstocks to Susceptible Watermelon Scions.

    Science.gov (United States)

    Mahmud, Iqbal; Kousik, Chandrasekar; Hassell, Richard; Chowdhury, Kamal; Boroujerdi, Arezue F

    2015-09-16

    Powdery mildew (PM) disease causes significant loss in watermelon. Due to the unavailability of a commercial watermelon variety that is resistant to PM, grafting susceptible cultivars on wild resistant rootstocks is being explored as a short-term management strategy to combat this disease. Nuclear magnetic resonance-based metabolic profiles of susceptible and resistant rootstocks of watermelon and their corresponding susceptible scions (Mickey Lee) were compared to screen for potential metabolites related to PM resistance using multivariate principal component analysis. Significant score plot differences between the susceptible and resistant groups were revealed through Mahalanobis distance analysis. Significantly different spectral buckets and their corresponding metabolites (including choline, fumarate, 5-hydroxyindole-3-acetate, and melatonin) have been identified quantitatively using multivariate loading plots and verified by volcano plot analyses. The data suggest that these metabolites were translocated from the powdery mildew resistant rootstocks to their corresponding powdery mildew susceptible scions and can be related to PM disease resistance.

  11. Further insight into the latex metabolite profile of Ficus carica.

    Science.gov (United States)

    Oliveira, Andreia P; Silva, Luís R; Andrade, Paula B; Valentão, Patrícia; Silva, Branca M; Gonçalves, Rui F; Pereira, José A; Guedes de Pinho, Paula

    2010-10-27

    Latex is a sticky emulsion that exudes upon damage from specialized canals from several plants. It contains several biologically active compounds, such as phytosterols, fatty acids, and amino acids. In plants, these compounds are involved in the interaction between plants, insects, and the environment. Despite its chemical, biological, and ecological importance, Ficus carica latex is still poorly studied. To improve the knowledge on the metabolite profile of this matrix, a targeted metabolite analysis was performed in a representative sample from F. carica latex. Seven phytosterols were determined by gas chromatography-ion trap mass spectrometry (GC-ITMS) and high-performance liquid chromatography coupled to diode array detection (HPLC-DAD), with β-sitosterol and lupeol being the compounds present in higher concentrations (ca. 54 and 14%, respectively). A total of 18 fatty acids were characterized by GC-ITMS, being essentially represented by saturated fatty acids (ca. 86.4% of total fatty acids). A total of 13 free amino acids were also identified by high-performance liquid chromatography coupled to ultraviolet-visible spectroscopy (HPLC/UV-vis), and cysteine and tyrosine were the major ones (ca. 38.7 and 31.4%, respectively). In humans, phytosterols and some polyunsaturated fatty acids, such as linoleic acid, are known for their anticarcinogenic properties. With regard to amino acids, some of them, such as glycine, are neurotransmitters. Our results reveal the presence of a wide diversity of compounds, from distinct classes, in F. carica latex, possessing various potential pharmacological activities; thus, its biological potential appears to be worth further exploring.

  12. Biomarker Research in Parkinson's Disease Using Metabolite Profiling

    DEFF Research Database (Denmark)

    Havelund, Jesper F; Heegaard, Niels H H; Færgeman, Nils J K

    2017-01-01

    Biomarker research in Parkinson's disease (PD) has long been dominated by measuring dopamine metabolites or alpha-synuclein in cerebrospinal fluid. However, these markers do not allow early detection, precise prognosis or monitoring of disease progression. Moreover, PD is now considered a multifa......) and purine metabolism (uric acid) are also altered in most metabolite profiling studies in PD......., the potential as a biomarker and the significance of understanding the pathophysiology of PD. Many of the studies report alterations in alanine, branched-chain amino acids and fatty acid metabolism, all pointing to mitochondrial dysfunction in PD. Aromatic amino acids (phenylalanine, tyrosine, tryptophan...

  13. [Determination of the profiles of secondary metabolites characteristic of Alternaria strains isolated from tomato].

    Science.gov (United States)

    Benavidez Rozo, Martha Elizabeth; Patriarca, Andrea; Cabrera, Gabriela; Fernández Pinto, Virginia E

    2014-01-01

    Many Alternaria species have been studied for their ability to produce bioactive secondary metabolites, such as tentoxin (TEN), some of which have toxic properties. The main food contaminant toxins are tenuazonic acid, alternariol (AOH), alternariol monomethyl ether (AME), altenuene, and altertoxins i, ii and iii. To determine the profiles of secondary metabolites characteristic of Alternaria strains isolated from tomato for their chemotaxonomic classification. The profiles of secondary metabolites were determined by HPLC MS. The Alternaria isolates obtained from spoiled tomatoes belong, according to their morphological characteristics, to the species groups Alternaria alternata, Alternaria tenuissima and Alternaria arborescens, with A. tenuissima being the most frequent. The most frequent profiles of secondary metabolites belonging to the species groups A. alternata (AOH, AME, TEN), A. tenuissima (AOH, AME, TEN, tenuazonic acid) and A. arborescens (AOH, AME, TEN, tenuazonic acid) were determined, with some isolates of the latter being able to synthesize AAL toxins. Secondary metabolite profiles are a useful tool for the differentiation of small spored Alternaria isolates not easily identifiable by their morphological characteristics. Copyright © 2013 Revista Iberoamericana de Micología. Published by Elsevier Espana. All rights reserved.

  14. Rapid construction of metabolite biosensors using domain-insertion profiling

    Science.gov (United States)

    Nadler, Dana C.; Morgan, Stacy-Anne; Flamholz, Avi; Kortright, Kaitlyn E.; Savage, David F.

    2016-01-01

    Single-fluorescent protein biosensors (SFPBs) are an important class of probes that enable the single-cell quantification of analytes in vivo. Despite advantages over other detection technologies, their use has been limited by the inherent challenges of their construction. Specifically, the rational design of green fluorescent protein (GFP) insertion into a ligand-binding domain, generating the requisite allosteric coupling, remains a rate-limiting step. Here, we describe an unbiased approach, termed domain-insertion profiling with DNA sequencing (DIP-seq), that combines the rapid creation of diverse libraries of potential SFPBs and high-throughput activity assays to identify functional biosensors. As a proof of concept, we construct an SFPB for the important regulatory sugar trehalose. DIP-seq analysis of a trehalose-binding-protein reveals allosteric hotspots for GFP insertion and results in high-dynamic range biosensors that function robustly in vivo. Taken together, DIP-seq simultaneously accelerates metabolite biosensor construction and provides a novel tool for interrogating protein allostery. PMID:27470466

  15. Chemotaxonomy of Trichoderma spp. Using mass spectrometry-based metabolite profiling.

    Science.gov (United States)

    Kang, Daejung; Kim, Jiyoung; Choi, Jung Nam; Liu, Kwang-Hyeon; Lee, Choong Hwan

    2011-01-01

    In this study, seven Trichoderma species (33 strains) were classified using secondary metabolite profile-based chemotaxonomy. Secondary metabolites were analyzed by liquid chromatography-electrospray ionization tandem mass spectrometry (LC-ESI-MS-MS) and multivariate statistical methods. T. longibrachiatum and T. virens were independently clustered based on both internal transcribed spacer (ITS) sequence and secondary metabolite analyses. T. harzianum formed three subclusters in the ITS-based phylogenetic tree and two subclusters in the metabolitebased dendrogram. In contrast, T. koningii and T. atroviride strains were mixed in one cluster in the phylogenetic tree, whereas T. koningii was grouped in a different subcluster from T. atroviride and T. hamatum in the chemotaxonomic tree. Partial least-squares discriminant analysis (PLS-DA) was applied to determine which metabolites were responsible for the clustering patterns observed for the different Trichoderma strains. The metabolites were hetelidic acid, sorbicillinol, trichodermanone C, giocladic acid, bisorbicillinol, and three unidentified compounds in the comparison of T. virens and T. longibrachiatum; harzianic acid, demethylharzianic acid, homoharzianic acid, and three unidentified compounds in T. harzianum I and II; and koninginin B, E, and D, and six unidentified compounds in T. koningii and T. atroviride. The results of this study demonstrate that secondary metabolite profiling-based chemotaxonomy has distinct advantages relative to ITSbased classification, since it identified new Trichoderma clusters that were not found using the latter approach.

  16. An integrated strategy for in vivo metabolite profiling using high-resolution mass spectrometry based data processing techniques

    International Nuclear Information System (INIS)

    Guo, Jian; Zhang, Minli; Elmore, Charles S.; Vishwanathan, Karthick

    2013-01-01

    Graphical abstract: -- Highlights: •Profiling the metabolites of model compounds in rats using high resolution mass spectrometry based data processing techniques. •Demonstrating an integrated strategy in vivo metabolite profiling using data mining tools. •Unusual metabolites generated via thiazole-ring opening were characterized based on processed LC–MS.data. -- Abstract: An ongoing challenge of drug metabolite profiling is to detect and identify unknown or low-level metabolites in complex biological matrices. Here we present a generic strategy for metabolite detection using multiple accurate-mass-based data processing tools via the analysis of rat samples of two model drug candidates, AZD6280 and AZ12488024. First, the function of isotopic pattern recognition was proved to be highly effective in the detection of metabolites derived from [ 14 C]-AZD6280 that possesses a distinct isotopic pattern. The metabolites revealed using this approach were in excellent qualitative correlation to those observed in radiochromatograms. Second, the effectiveness of accurate mass based untargeted data mining tools such as background subtraction, mass defect filtering, or a data mining package (MZmine) used for metabolomic analysis in detection of metabolites of [ 14 C]-AZ12488024 in rat urine, feces, bile and plasma samples was examined and a total of 33 metabolites of AZ12488024 were detected. Among them, at least 16 metabolites were only detected by the aid of the data mining packages and not via radiochromatograms. New metabolic pathways such as S-oxidation and thiomethylation reactions occurring on the thiazole ring were proposed based on the processed data. The results of these experiments also demonstrated that accurate mass-based mass defect filtering (MDF) and data mining techniques used in metabolomics are complementary and can be valuable tools for delineating low-level metabolites in complex matrices. Furthermore, the application of distinct multiple data

  17. Quality assessment of ginseng by (1)H NMR metabolite fingerprinting and profiling analysis.

    Science.gov (United States)

    Lee, Eun-Jeong; Shaykhutdinov, Rustem; Weljie, Aalim M; Vogel, Hans J; Facchini, Peter J; Park, Sang-Un; Kim, Yong-Kyoung; Yang, Tae-Jin

    2009-08-26

    Metabolite profiling and fingerprint analysis by (1)H NMR spectroscopy were used to identify potential biomarkers capable of distinguishing different ginseng species, varieties, and commercial products with the aim of establishing quality control code protocol based on biochemical phenotype. Principal component (PC) analyses of (1)H NMR spectra reliably discriminated between the various ginseng samples, demonstrating the potential utility of metabolomics in the natural health products industry. Four Asian ginseng varieties separated along the PC1 and PC2 axes, and four different Korean ginseng products were divided into two groups by PC1. A strong separation was also revealed between Asian ginseng (Panax ginseng) and American ginseng (Panax quinquefolius). Glutamine, arginine, sucrose, malate, and myo-inositol were the major metabolites in ginseng samples tested in this study. Combined metabolite fingerprinting and profiling suggested that several compounds including glucose, fumarate, and various amino acids could serve as biomarkers for quality assurance in ginseng.

  18. Identifying metabolites related to nitrogen mineralisation using 1H NMR spectroscopy

    Science.gov (United States)

    . T McDonald, Noeleen; Graham, Stewart; Watson, Catherine; Gordon, Alan; Lalor, Stan; Laughlin, Ronnie; Elliott, Chris; . P Wall, David

    2015-04-01

    Exploring new analysis techniques to enhance our knowledge of the various metabolites within our soil systems is imperative. Principally, this knowledge would allow us to link key metabolites with functional influences on critical nutrient processes, such as the nitrogen (N) mineralisation in soils. Currently there are few studies that utilize proton nuclear magnetic resonance spectroscopy (1H NMR) to characterize multiple metabolites within a soil sample. The aim of this research study was to examine the effectiveness of 1H NMR for isolating multiple metabolites that are related to the mineralizable N (MN) capacity across a range of 35 Irish grassland soils. Soils were measured for MN using the standard seven day anaerobic incubation (AI-7). Additionally, soils were also analysed for a range of physio-chemical properties [e.g. total N, total C, mineral N, texture and soil organic matter (SOM)]. Proton NMR analysis was carried on these soils by extracting with 40% methanol:water, lyophilizing and reconstituting in deuterium oxide and recording the NMR spectra on a 400MHz Bruker AVANCE III spectrometer. Once the NMR data were spectrally processed and analysed using multivariate statistical analysis, seven metabolites were identified as having significant relationships with MN (glucose, trimethylamine, glutamic acid, serine, aspartic acid, 4-aminohippuirc acid and citric acid). Following quantification, glucose was shown to explain the largest percentage variability in MN (72%). These outcomes suggest that sources of labile carbon are essential in regulating N mineralisation and the capacity of plant available N derived from SOM-N pools in these soils. Although, smaller in concentration, the amino acids; 4-aminohippuirc acid, glutamic acid and serine also significantly (P<0.05) explained 43%, 27% and 19% of the variability in MN, respectively. This novel study highlights the effectiveness of using 1H NMR as a practical approach to profile multiple metabolites in

  19. Correlative analysis of metabolite profiling of Danggui Buxue Tang in rat biological fluids by rapid resolution LC-TOF/MS.

    Science.gov (United States)

    Li, Chang-Yin; Qi, Lian-Wen; Li, Ping

    2011-04-28

    In this work, the metabolite profiles of Danggui Buxue Tang (DBT) in rat bile and plasma were qualitatively described, and the possible metabolic pathways of DBT were subsequently proposed. Emphasis was put on correlative analysis of metabolite profiling in different biological fluids. After oral administration of DBT, bile and plasma samples were collected and pretreated by solid phase extraction. Rapid resolution liquid chromatography coupled to time-of-flight mass spectrometry (RRLC-TOFMS) was used for characterization of DBT-related compounds (parent compounds and metabolites) in biological matrices. A total of 142 metabolites were detected and tentatively identified from the drug-containing bile and plasma samples. Metabolite profiling shows that rat bile contained relatively more glutathione-derived conjugates, more saponins compounds and more diverse forms of metabolites than urine. The metabolite profile in plasma revealed that glucuronide conjugates of isoflavonoids, dimmers, acetylcysteine conjugates and parent form of phthalides, as well as saponin aglycones were the major circulating forms of DBT. Collectively, the metabolite profile analysis of DBT in different biological matrices provided a comprehensive understanding of the in vivo metabolic fates of constituents in DBT. Copyright © 2011 Elsevier B.V. All rights reserved.

  20. Comprehensive metabolite profiling of Sinorhizobium meliloti using gas chromatography-mass spectrometry.

    Science.gov (United States)

    Barsch, Aiko; Patschkowski, Thomas; Niehaus, Karsten

    2004-10-01

    A metabolite analysis of the soil bacterium Sinorhizobium meliloti was established as a first step towards a better understanding of the symbiosis with its host plant Medicago truncatula. A crucial step was the development of fast harvesting and extraction methods for the bacterial metabolites because of rapid changes in their composition. S. meliloti 1021 cell cultures grown in minimal medium were harvested by centrifugation, filtration or immediate freezing in liquid nitrogen followed by a lyophilisation step. Bacteria were lysed mechanically in methanol and hydrophilic compounds were analysed after methoxymation and silylisation via GC-MS. The different compounds were identified by comparison with the NIST 98 database and available standards. From about 200 peaks in each chromatogram 65 compounds have been identified so far. A comparison of the different extraction methods giving the metabolite composition revealed clear changes in several amino acids and amino acid precursor pools. A principal component analysis (PCA) was able to distinguish S. meliloti cells grown on different carbon sources based on their metabolite profile. A comparison of the metabolite composition of a S. meliloti leucine auxotrophic mutant with the wild type revealed a marked accumulation of 2-isopropylmalate in the mutant. Interestingly, the accumulated metabolite is not the direct substrate of the mutated enzyme, 3-isopropylmalate dehydrogenase, but the substrate of isopropylmalate isomerase, which acts one step further upstream in the biosynthetic pathway of leucine. This finding further emphasises the importance of integrating metabolic data into post-genomic research.

  1. 1H NMR- based metabolite profiling of tropane alkaloids in Duboisia spec.

    Directory of Open Access Journals (Sweden)

    Ullrich, Sophie Friederike

    2016-07-01

    Full Text Available Duboisia R.Br. (Solanaceae is the main source of the tropane alkaloid scopolamine, which is an important precursor of various active pharmaceutical ingredients due to its anticholinergic properties. As only little is known about the metabolite composition among the different species, NMRbased metabolic profiling was done in order to elucidate primary and secondary metabolism in Duboisia especially focusing on the tropane alkaloid pathway. For this purpose, plants of five different genotypes (Duboisia myoporoides, D. leichardtii and hybrids of D. myoporoides and D. leichhardtii were cultivated under strictly controlled conditions in climate chambers, leaf and root extracts were prepared and measured via 1H NMR. 14 different metabolites could be identified using 1D- and 2D-NMR techniques. Principal component analysis of the NMR data allowed a clear distinction between Duboisia hybrids and the wild types, which could be again subgrouped in D. myoporoides and D. leichhardtii, based on the metabolites identified.

  2. Antihepatotoxic Effect and Metabolite Profiling of Panicum turgidum Extract via UPLC-qTOF-MS

    Science.gov (United States)

    Farag, Mohamed A.; El Fishawy, Ahlam M.; El-Toumy, Sayed A.; Amer, Khadiga F.; Mansour, Ahmed M.; Taha, Hala E.

    2016-01-01

    Background: Panicum turgidum, desert grass, has not reported any detailed phytochemical or biological study as yet Objective: To establish P. turgidum secondary metabolite profile and to assess its antihepatotoxic effect Materials and Methods: Ultra-performance liquid chromatography (UPLC) coupled to quadrupole high-resolution time of flight mass spectrometry (qTOF-MS) was used for large-scale secondary metabolites profiling in P. turgidum extract, alongside assessing median lethal dose (LD50) and hepatoprotective effect against carbon tetrachloride (CCl4) intoxication Results: A total of 39 metabolites were identified with flavonoids as the major class present as O/C-glycosides of luteolin, apigenin, isorhamnetin and naringenin, most of which are first time to be reported in Panicum sp. Antihepatotoxic effect of P. turgidum crude extract was revealed via improving several biochemical marker levels and mitigation against oxidative stress in the serum and liver tissues, compared with CCl4 intoxicated group and further confirmed by histopathological examination. Conclusion: This study reveals that P. turgidum, enriched in C-flavonoids, presents a novel source of safe antihepatotoxic agents and further demonstrates the efficacy of UPLC-MS metabolomics in the field of natural products drug discovery. SUMMARY UPLC coupled to qTOF-MS was used for large scale secondary metabolites profiling in P. turgidum.A total of 39 metabolites were identified with flavonoids amounting as the major metabolite class.Anti-hepatotoxic effect of P. turgidum extract was revealed via several biochemical markers and histopathological examination.This study reveals that P. turgidum, enriched in C-flavonoids, present a novel source of antihepatotoxic agents. Abbreviations used: UPLC: Ultra-performance liquid chromatography (UPLC), LD50: median lethal dose, MDA: malondialdehyde, GSH: glutathione reductase, CAT: catalase, SOD: superoxide dismutase, ALT: alanine aminotransferase, AST: aspartate

  3. The effects of GA and ABA treatments on metabolite profile of germinating barley.

    Science.gov (United States)

    Huang, Yuqing; Cai, Shengguan; Ye, Lingzhen; Hu, Hongliang; Li, Chengdao; Zhang, Guoping

    2016-02-01

    Sugar degradation during grain germination is important for malt quality. In malting industry, gibberellin (GA) is frequently used for improvement of malting quality. In this study, the changes of metabolite profiles and starch-degrading enzymes during grain germination, and as affected by GA and abscisic acid (ABA) were investigated using two wild barley accessions XZ72 and XZ95. Totally fifty-two metabolites with known structures were detected and the change of metabolite during germination was time- and genotype dependent. Sugars and amino acids were the most dramatically changed compounds. Addition of GA enhanced the activities of starch-degrading enzymes, and increased most metabolites, especially sugars and amino acids, whereas ABA had the opposite effect. The effect varied with the barley accessions. The current study is the first attempt in investigating the effect of hormones on metabolite profiles in germinating barley grain, being helpful for identifying the factors affecting barley germination or malt quality. Copyright © 2015 Elsevier Ltd. All rights reserved.

  4. Interstitial Cystitis-Associated Urinary Metabolites Identified by Mass-Spectrometry Based Metabolomics Analysis

    Science.gov (United States)

    Kind, Tobias; Cho, Eunho; Park, Taeeun D.; Deng, Nan; Liu, Zhenqiu; Lee, Tack; Fiehn, Oliver; Kim, Jayoung

    2016-01-01

    This study on interstitial cystitis (IC) aims to identify a unique urine metabolomic profile associated with IC, which can be defined as an unpleasant sensation including pain and discomfort related to the urinary bladder, without infection or other identifiable causes. Although the burden of IC on the American public is immense in both human and financial terms, there is no clear diagnostic test for IC, but rather it is a disease of exclusion. Very little is known about the clinically useful urinary biomarkers of IC, which are desperately needed. Untargeted comprehensive metabolomic profiling was performed using gas-chromatography/mass-spectrometry to compare urine specimens of IC patients or health donors. The study profiled 200 known and 290 unknown metabolites. The majority of the thirty significantly changed metabolites before false discovery rate correction were unknown compounds. Partial least square discriminant analysis clearly separated IC patients from controls. The high number of unknown compounds hinders useful biological interpretation of such predictive models. Given that urine analyses have great potential to be adapted in clinical practice, research has to be focused on the identification of unknown compounds to uncover important clues about underlying disease mechanisms. PMID:27976711

  5. Secondary metabolite profiling of Alternaria dauci, A. porri, A. solani, and A. tomatophila

    DEFF Research Database (Denmark)

    Andersen, Birgitte; Dongo, Anita; Pryor, Barry M.

    2008-01-01

    Chemotaxonomy (secondary metabolite profiling) has been shown to be of great value in the classification and differentiation in Ascomycota. However, few studies have investigated the use of metabolite production for classification and identification purposes of plant pathogenic Alternaria species...

  6. Perceiving molecular evolution processes in Escherichia coli by comprehensive metabolite and gene expression profiling.

    Science.gov (United States)

    Vijayendran, Chandran; Barsch, Aiko; Friehs, Karl; Niehaus, Karsten; Becker, Anke; Flaschel, Erwin

    2008-04-10

    Evolutionary changes that are due to different environmental conditions can be examined based on the various molecular aspects that constitute a cell, namely transcript, protein, or metabolite abundance. We analyzed changes in transcript and metabolite abundance in evolved and ancestor strains in three different evolutionary conditions - excess nutrient adaptation, prolonged stationary phase adaptation, and adaptation because of environmental shift - in two different strains of bacterium Escherichia coli K-12 (MG1655 and DH10B). Metabolite profiling of 84 identified metabolites revealed that most of the metabolites involved in the tricarboxylic acid cycle and nucleotide metabolism were altered in both of the excess nutrient evolved lines. Gene expression profiling using whole genome microarray with 4,288 open reading frames revealed over-representation of the transport functional category in all evolved lines. Excess nutrient adapted lines were found to exhibit greater degrees of positive correlation, indicating parallelism between ancestor and evolved lines, when compared with prolonged stationary phase adapted lines. Gene-metabolite correlation network analysis revealed over-representation of membrane-associated functional categories. Proteome analysis revealed the major role played by outer membrane proteins in adaptive evolution. GltB, LamB and YaeT proteins in excess nutrient lines, and FepA, CirA, OmpC and OmpA in prolonged stationary phase lines were found to be differentially over-expressed. In summary, we report the vital involvement of energy metabolism and membrane-associated functional categories in all of the evolutionary conditions examined in this study within the context of transcript, outer membrane protein, and metabolite levels. These initial data obtained may help to enhance our understanding of the evolutionary process from a systems biology perspective.

  7. Intrathalline Metabolite Profiles in the Lichen Argopsis friesiana Shape Gastropod Grazing Patterns.

    Science.gov (United States)

    Gadea, Alice; Le Lamer, Anne-Cécile; Le Gall, Sophie; Jonard, Catherine; Ferron, Solenn; Catheline, Daniel; Ertz, Damien; Le Pogam, Pierre; Boustie, Joël; Lohézic-Le Devehat, Françoise; Charrier, Maryvonne

    2018-04-03

    Lichen-gastropod interactions generally focus on the potential deterrent or toxic role of secondary metabolites. To better understand lichen-gastropod interactions, a controlled feeding experiment was designed to identify the parts of the lichen Argopsis friesiana consumed by the Subantarctic land snail Notodiscus hookeri. Besides profiling secondary metabolites in various lichen parts (apothecia, cephalodia, phyllocladia and fungal axis of the pseudopodetium), we investigated potentially beneficial resources that snails can utilize from the lichen (carbohydrates, amino acids, fatty acids, polysaccharides and total nitrogen). Notodiscus hookeri preferred cephalodia and algal layers, which had high contents of carbohydrates, nitrogen, or both. Apothecia were avoided, perhaps due to their low contents of sugars and polyols. Although pseudopodetia were characterized by high content of arabitol, they were also rich in medullary secondary compounds, which may explain why they were not consumed. Thus, the balance between nutrients (particularly nitrogen and polyols) and secondary metabolites appears to play a key role in the feeding preferences of this snail.

  8. Spatial Mapping and Profiling of Metabolite Distributions during Germination.

    Science.gov (United States)

    Feenstra, Adam D; Alexander, Liza E; Song, Zhihong; Korte, Andrew R; Yandeau-Nelson, Marna D; Nikolau, Basil J; Lee, Young Jin

    2017-08-01

    Germination is a highly complex process by which seeds begin to develop and establish themselves as viable organisms. In this study, we utilize a combination of gas chromatography-mass spectrometry, liquid chromatography-fluorescence, and mass spectrometry imaging approaches to profile and visualize the metabolic distributions of germinating seeds from two different inbreds of maize ( Zea mays ) seeds, B73 and Mo17. Gas chromatography and liquid chromatography analyses demonstrate that the two inbreds are highly differentiated in their metabolite profiles throughout the course of germination, especially with regard to amino acids, sugar alcohols, and small organic acids. Crude dissection of the seed followed by gas chromatography-mass spectrometry analysis of polar metabolites also revealed that many compounds were highly sequestered among the various seed tissue types. To further localize compounds, matrix-assisted laser desorption/ionization mass spectrometry imaging was utilized to visualize compounds in fine detail in their native environments over the course of germination. Most notably, the fatty acyl chain-dependent differential localization of phospholipids and triacylglycerols was observed within the embryo and radicle, showing correlation with the heterogeneous distribution of fatty acids. Other interesting observations include unusual localization of ceramides on the endosperm/scutellum boundary and subcellular localization of ferulate in the aleurone. © 2017 American Society of Plant Biologists. All Rights Reserved.

  9. Metabolite profiling of human amniotic fluid by hyphenated nuclear magnetic resonance spectroscopy.

    Science.gov (United States)

    Graça, Gonçalo; Duarte, Iola F; J Goodfellow, Brian; Carreira, Isabel M; Couceiro, Ana Bela; Domingues, Maria do Rosário; Spraul, Manfred; Tseng, Li-Hong; Gil, Ana M

    2008-08-01

    The metabolic profiling of human amniotic fluid (HAF) is of potential interest for the diagnosis of disorders in the mother or the fetus. In order to build a comprehensive metabolite database for HAF, hyphenated NMR has been used, for the first time, for systematic HAF profiling. Experiments were carried out using reverse-phase (RP) and ion-exchange liquid chromatography (LC), in order to detect less and more polar compounds, respectively. RP-LC conditions achieved good separation of amino acids, some sugars, and xanthines. Subsequent NMR and MS analysis enabled the rapid identification of 30 compounds, including 3-methyl-2-oxovalerate and 4-aminohippurate identified in HAF for the first time, to our knowledge. Under ion-exchange LC conditions, a different set of 30 compounds was detected, including sugars, organic acids, several derivatives of organic acids, and amino acids. In this experiment, five compounds were identified for the first time in HAF: D-xylitol, amino acid derivatives (N-acetylalanine, N-acetylglycine, 2-oxoleucine), and isovalerate. The nonendogenous nature of some metabolites (caffeine, paraxanthine, D-xylitol, sorbitol) is discussed. Hyphenated NMR has allowed the rapid detection of approximately 60 metabolites in HAF, some of which are not detectable by standard NMR due to low abundance (microM) and signal overlap thus enabling an extended metabolite database to be built for HAF.

  10. Intracellular CHO Cell Metabolite Profiling Reveals Steady-State Dependent Metabolic Fingerprints in Perfusion Culture.

    Science.gov (United States)

    Karst, Daniel J; Steinhoff, Robert F; Kopp, Marie R G; Serra, Elisa; Soos, Miroslav; Zenobi, Renato; Morbidelli, Massimo

    2017-07-01

    Perfusion cell culture processes allow the steady-state culture of mammalian cells at high viable cell density, which is beneficial for overall product yields and homogeneity of product quality in the manufacturing of therapeutic proteins. In this study, the extent of metabolic steady state and the change of the metabolite profile between different steady states of an industrial Chinese hamster ovary (CHO) cell line producing a monoclonal antibody (mAb) was investigated in stirred tank perfusion bioreactors. Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) of daily cell extracts revealed more than a hundred peaks, among which 76 metabolites were identified by tandem MS (MS/MS) and high resolution Fourier transform ion cyclotron resonance (FT-ICR) MS. Nucleotide ratios (Uridine (U)-ratio, nucleotide triphosphate (NTP)-ratio and energy charge (EC)) and multivariate analysis of all features indicated a consistent metabolite profile for a stable culture performed at 40 × 10 6 cells/mL over 26 days of culture. Conversely, the reactor was operated continuously so as to reach three distinct steady states one after the other at 20, 60, and 40 × 10 6 cells/mL. In each case, a stable metabolite profile was achieved after an initial transient phase of approximately three days at constant cell density when varying between these set points. Clear clustering according to cell density was observed by principal component analysis, indicating steady-state dependent metabolite profiles. In particular, varying levels of nucleotides, nucleotide sugar, and lipid precursors explained most of the variance between the different cell density set points. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 33:879-890, 2017. © 2016 American Institute of Chemical Engineers.

  11. Spatio-Temporal Metabolite Profiling of the Barley Germination Process by MALDI MS Imaging.

    Directory of Open Access Journals (Sweden)

    Karin Gorzolka

    Full Text Available MALDI mass spectrometry imaging was performed to localize metabolites during the first seven days of the barley germination. Up to 100 mass signals were detected of which 85 signals were identified as 48 different metabolites with highly tissue-specific localizations. Oligosaccharides were observed in the endosperm and in parts of the developed embryo. Lipids in the endosperm co-localized in dependency on their fatty acid compositions with changes in the distributions of diacyl phosphatidylcholines during germination. 26 potentially antifungal hordatines were detected in the embryo with tissue-specific localizations of their glycosylated, hydroxylated, and O-methylated derivates. In order to reveal spatio-temporal patterns in local metabolite compositions, multiple MSI data sets from a time series were analyzed in one batch. This requires a new preprocessing strategy to achieve comparability between data sets as well as a new strategy for unsupervised clustering. The resulting spatial segmentation for each time point sample is visualized in an interactive cluster map and enables simultaneous interactive exploration of all time points. Using this new analysis approach and visualization tool germination-dependent developments of metabolite patterns with single MS position accuracy were discovered. This is the first study that presents metabolite profiling of a cereals' germination process over time by MALDI MSI with the identification of a large number of peaks of agronomically and industrially important compounds such as oligosaccharides, lipids and antifungal agents. Their detailed localization as well as the MS cluster analyses for on-tissue metabolite profile mapping revealed important information for the understanding of the germination process, which is of high scientific interest.

  12. Chemotaxonomic Metabolite Profiling of 62 Indigenous Plant Species and Its Correlation with Bioactivities

    Directory of Open Access Journals (Sweden)

    Sarah Lee

    2015-11-01

    Full Text Available Chemotaxonomic metabolite profiling of 62 indigenous Korean plant species was performed by ultrahigh performance liquid chromatography (UHPLC-linear trap quadrupole-ion trap (LTQ-IT mass spectrometry/mass spectrometry (MS/MS combined with multivariate statistical analysis. In partial least squares discriminant analysis (PLS-DA, the 62 species clustered depending on their phylogenetic family, in particular, Aceraceae, Betulaceae, and Fagaceae were distinguished from Rosaceae, Fabaceae, and Asteraceae. Quinic acid, gallic acid, quercetin, quercetin derivatives, kaempferol, and kaempferol derivatives were identified as family-specific metabolites, and were found in relatively high concentrations in Aceraceae, Betulaceae, and Fagaceae. Fagaceae and Asteraceae were selected based on results of PLS-DA and bioactivities to determine the correlation between metabolic differences among plant families and bioactivities. Quinic acid, quercetin, kaempferol, quercetin derivatives, and kaempferol derivatives were found in higher concentrations in Fagaceae than in Asteraceae, and were positively correlated with antioxidant and tyrosinase inhibition activities. These results suggest that metabolite profiling was a useful tool for finding the different metabolic states of each plant family and understanding the correlation between metabolites and bioactivities in accordance with plant family.

  13. Targeted and Untargeted Metabolic Profiling of Wild Grassland Plants identifies Antibiotic and Anthelmintic Compounds Targeting Pathogen Physiology, Metabolism and Reproduction

    OpenAIRE

    French, Katherine E.; Harvey, Joe; McCullagh, James S. O.

    2018-01-01

    Plants traditionally used by farmers to manage livestock ailments could reduce reliance on synthetic antibiotics and anthelmintics but in many cases their chemical composition is unknown. As a case study, we analyzed the metabolite profiles of 17 plant species and 45 biomass samples from agricultural grasslands in England using targeted and untargeted metabolite profiling by liquid-chromatography mass spectrometry. We identified a range of plant secondary metabolites, including 32 compounds w...

  14. Targeted and untargeted metabolic profiling of wild grassland plants identifies antibiotic and anthelmintic compounds targeting pathogen physiology, metabolism and reproduction

    OpenAIRE

    French, KE; Harvey, J; Mccullagh, J

    2018-01-01

    Plants traditionally used by farmers to manage livestock ailments could reduce reliance on synthetic antibiotics and anthelmintics but in many cases their chemical composition is unknown. As a case study, we analyzed the metabolite profiles of 17 plant species and 45 biomass samples from agricultural grasslands in England using targeted and untargeted metabolite profiling by liquid‐chromatography mass‐spectrometry. We identified a range of plant secondary metabolites, including 32 compounds w...

  15. Metabolite Profiling and Classification of DNA-Authenticated Licorice Botanicals

    Science.gov (United States)

    Simmler, Charlotte; Anderson, Jeffrey R.; Gauthier, Laura; Lankin, David C.; McAlpine, James B.; Chen, Shao-Nong; Pauli, Guido F.

    2015-01-01

    Raw licorice roots represent heterogeneous materials obtained from mainly three Glycyrrhiza species. G. glabra, G. uralensis, and G. inflata exhibit marked metabolite differences in terms of flavanones (Fs), chalcones (Cs), and other phenolic constituents. The principal objective of this work was to develop complementary chemometric models for the metabolite profiling, classification, and quality control of authenticated licorice. A total of 51 commercial and macroscopically verified samples were DNA authenticated. Principal component analysis and canonical discriminant analysis were performed on 1H NMR spectra and area under the curve values obtained from UHPLC-UV chromatograms, respectively. The developed chemometric models enable the identification and classification of Glycyrrhiza species according to their composition in major Fs, Cs, and species specific phenolic compounds. Further key outcomes demonstrated that DNA authentication combined with chemometric analyses enabled the characterization of mixtures, hybrids, and species outliers. This study provides a new foundation for the botanical and chemical authentication, classification, and metabolomic characterization of crude licorice botanicals and derived materials. Collectively, the proposed methods offer a comprehensive approach for the quality control of licorice as one of the most widely used botanical dietary supplements. PMID:26244884

  16. Fully Automated Trimethylsilyl (TMS) Derivatisation Protocol for Metabolite Profiling by GC-MS.

    Science.gov (United States)

    Zarate, Erica; Boyle, Veronica; Rupprecht, Udo; Green, Saras; Villas-Boas, Silas G; Baker, Philip; Pinu, Farhana R

    2016-12-29

    Gas Chromatography-Mass Spectrometry (GC-MS) has long been used for metabolite profiling of a wide range of biological samples. Many derivatisation protocols are already available and among these, trimethylsilyl (TMS) derivatisation is one of the most widely used in metabolomics. However, most TMS methods rely on off-line derivatisation prior to GC-MS analysis. In the case of manual off-line TMS derivatisation, the derivative created is unstable, so reduction in recoveries occurs over time. Thus, derivatisation is carried out in small batches. Here, we present a fully automated TMS derivatisation protocol using robotic autosamplers and we also evaluate a commercial software, Maestro available from Gerstel GmbH. Because of automation, there was no waiting time of derivatised samples on the autosamplers, thus reducing degradation of unstable metabolites. Moreover, this method allowed us to overlap samples and improved throughputs. We compared data obtained from both manual and automated TMS methods performed on three different matrices, including standard mix, wine, and plasma samples. The automated TMS method showed better reproducibility and higher peak intensity for most of the identified metabolites than the manual derivatisation method. We also validated the automated method using 114 quality control plasma samples. Additionally, we showed that this online method was highly reproducible for most of the metabolites detected and identified (RSD TMS method has been applied to analyse a large number of complex plasma samples. Furthermore, we found that this method was highly applicable for routine metabolite profiling (both targeted and untargeted) in any metabolomics laboratory.

  17. Fully Automated Trimethylsilyl (TMS Derivatisation Protocol for Metabolite Profiling by GC-MS

    Directory of Open Access Journals (Sweden)

    Erica Zarate

    2016-12-01

    Full Text Available Gas Chromatography-Mass Spectrometry (GC-MS has long been used for metabolite profiling of a wide range of biological samples. Many derivatisation protocols are already available and among these, trimethylsilyl (TMS derivatisation is one of the most widely used in metabolomics. However, most TMS methods rely on off-line derivatisation prior to GC-MS analysis. In the case of manual off-line TMS derivatisation, the derivative created is unstable, so reduction in recoveries occurs over time. Thus, derivatisation is carried out in small batches. Here, we present a fully automated TMS derivatisation protocol using robotic autosamplers and we also evaluate a commercial software, Maestro available from Gerstel GmbH. Because of automation, there was no waiting time of derivatised samples on the autosamplers, thus reducing degradation of unstable metabolites. Moreover, this method allowed us to overlap samples and improved throughputs. We compared data obtained from both manual and automated TMS methods performed on three different matrices, including standard mix, wine, and plasma samples. The automated TMS method showed better reproducibility and higher peak intensity for most of the identified metabolites than the manual derivatisation method. We also validated the automated method using 114 quality control plasma samples. Additionally, we showed that this online method was highly reproducible for most of the metabolites detected and identified (RSD < 20 and specifically achieved excellent results for sugars, sugar alcohols, and some organic acids. To the very best of our knowledge, this is the first time that the automated TMS method has been applied to analyse a large number of complex plasma samples. Furthermore, we found that this method was highly applicable for routine metabolite profiling (both targeted and untargeted in any metabolomics laboratory.

  18. Suppression of CCR impacts metabolite profile and cell wall composition in Pinus radiata tracheary elements.

    Science.gov (United States)

    Wagner, Armin; Tobimatsu, Yuki; Goeminne, Geert; Phillips, Lorelle; Flint, Heather; Steward, Diane; Torr, Kirk; Donaldson, Lloyd; Boerjan, Wout; Ralph, John

    2013-01-01

    Suppression of the lignin-related gene cinnamoyl-CoA reductase (CCR) in the Pinus radiata tracheary element (TE) system impacted both the metabolite profile and the cell wall matrix in CCR-RNAi lines. UPLC-MS/MS-based metabolite profiling identified elevated levels of p-coumaroyl hexose, caffeic acid hexoside and ferulic acid hexoside in CCR-RNAi lines, indicating a redirection of metabolite flow within phenylpropanoid metabolism. Dilignols derived from coniferyl alcohol such as G(8-5)G, G(8-O-4)G and isodihydrodehydrodiconiferyl alcohol (IDDDC) were substantially depleted, providing evidence for CCR's involvement in coniferyl alcohol biosynthesis. Severe CCR suppression almost halved lignin content in TEs based on a depletion of both H-type and G-type lignin, providing evidence for CCR's involvement in the biosynthesis of both lignin types. 2D-NMR studies revealed minor changes in the H:G-ratio and consequently a largely unchanged interunit linkage distribution in the lignin polymer. However, unusual cell wall components including ferulate and unsaturated fatty acids were identified in TEs by thioacidolysis, pyrolysis-GC/MS and/or 2D-NMR in CCR-RNAi lines, providing new insights into the consequences of CCR suppression in pine. Interestingly, CCR suppression substantially promoted pyrolytic breakdown of cell wall polysaccharides, a phenotype most likely caused by the incorporation of acidic compounds into the cell wall matrix in CCR-RNAi lines.

  19. Secondary metabolite profiling of Curcuma species grown at different locations using GC/TOF and UPLC/Q-TOF MS.

    Science.gov (United States)

    Lee, Jueun; Jung, Youngae; Shin, Jeoung-Hwa; Kim, Ho Kyoung; Moon, Byeong Cheol; Ryu, Do Hyun; Hwang, Geum-Sook

    2014-07-04

    Curcuma, a genus of rhizomatous herbaceous species, has been used as a spice, traditional medicine, and natural dye. In this study, the metabolite profile of Curcuma extracts was determined using gas chromatography-time of flight mass spectrometry (GC/TOF MS) and ultrahigh-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC/Q-TOF MS) to characterize differences between Curcuma aromatica and Curcuma longa grown on the Jeju-do or Jin-do islands, South Korea. Previous studies have performed primary metabolite profiling of Curcuma species grown in different regions using NMR-based metabolomics. This study focused on profiling of secondary metabolites from the hexane extract of Curcuma species. Principal component analysis (PCA) and partial least-squares discriminant analysis (PLS-DA) plots showed significant differences between the C. aromatica and C. longa metabolite profiles, whereas geographical location had little effect. A t-test was performed to identify statistically significant metabolites, such as terpenoids. Additionally, targeted profiling using UPLC/Q-TOF MS showed that the concentration of curcuminoids differed depending on the plant origin. Based on these results, a combination of GC- and LC-MS allowed us to analyze curcuminoids and terpenoids, the typical bioactive compounds of Curcuma, which can be used to discriminate Curcuma samples according to species or geographical origin.

  20. Secondary Metabolite Profiling of Curcuma Species Grown at Different Locations Using GC/TOF and UPLC/Q-TOF MS

    Directory of Open Access Journals (Sweden)

    Jueun Lee

    2014-07-01

    Full Text Available Curcuma, a genus of rhizomatous herbaceous species, has been used as a spice, traditional medicine, and natural dye. In this study, the metabolite profile of Curcuma extracts was determined using gas chromatography-time of flight mass spectrometry (GC/TOF MS and ultrahigh-performance liquid chromatography–quadrupole time-of-flight mass spectrometry (UPLC/Q-TOF MS to characterize differences between Curcuma aromatica and Curcuma longa grown on the Jeju-do or Jin-do islands, South Korea. Previous studies have performed primary metabolite profiling of Curcuma species grown in different regions using NMR-based metabolomics. This study focused on profiling of secondary metabolites from the hexane extract of Curcuma species. Principal component analysis (PCA and partial least-squares discriminant analysis (PLS-DA plots showed significant differences between the C. aromatica and C. longa metabolite profiles, whereas geographical location had little effect. A t-test was performed to identify statistically significant metabolites, such as terpenoids. Additionally, targeted profiling using UPLC/Q-TOF MS showed that the concentration of curcuminoids differed depending on the plant origin. Based on these results, a combination of GC- and LC-MS allowed us to analyze curcuminoids and terpenoids, the typical bioactive compounds of Curcuma, which can be used to discriminate Curcuma samples according to species or geographical origin.

  1. A new hydroxytyrosol metabolite identified in human plasma: hydroxytyrosol acetate sulphate.

    Science.gov (United States)

    Rubió, Laura; Macià, Alba; Valls, Rosa M; Pedret, Anna; Romero, Maria-Paz; Solà, Rosa; Motilva, Maria-José

    2012-09-15

    We report progress in the study of olive oil phenolic metabolites in humans and identify a new hydroxytyrosol metabolite called hydroxytyrosol acetate sulphate, which was determined using tandem MS, after ingestion of 30 ml of olive oil with a high phenolic content (500 mg/kg oil), reaching a maximum concentration of 1.63 μM. In order to understand and explain the generation of this metabolite, two different pathways are proposed. Copyright © 2012 Elsevier Ltd. All rights reserved.

  2. Ultrahigh Pressure Processing Produces Alterations in the Metabolite Profiles of Panax ginseng.

    Science.gov (United States)

    Lee, Mee Youn; Singh, Digar; Kim, Sung Han; Lee, Sang Jun; Lee, Choong Hwan

    2016-06-22

    Ultrahigh pressure (UHP) treatments are non-thermal processing methods that have customarily been employed to enhance the quality and productivity of plant consumables. We aimed to evaluate the effects of UHP treatments on ginseng samples (white ginseng: WG; UHP-treated WG: UWG; red ginseng: RG; UHP-treated RG: URG; ginseng berries: GB; and UHP-treated GB: UGB) using metabolite profiling based on ultrahigh performance liquid chromatography-linear trap quadrupole-ion trap-tandem mass spectrometry (UHPLC-LTQ-IT-MS/MS) and gas chromatography time-of-flight mass spectrometry (GC-TOF-MS). Multivariate data analyses revealed a clear demarcation among the GB and UGB samples, and the phenotypic evaluations correlated the highest antioxidant activities and the total phenolic and flavonoid compositions with the UGB samples. Overall, eight amino acids, seven organic acids, seven sugars and sugar derivatives, two fatty acids, three notoginsenosides, three malonylginsenosides, and three ginsenosides, were identified as significantly discriminant metabolites between the GB and UGB samples, with relatively higher proportions in the latter. Ideally, these metabolites can be used as quality biomarkers for the assessment of ginseng products and our results indicate that UHP treatment likely led to an elevation in the proportions of total extractable metabolites in ginseng samples.

  3. Metabolite Profiles of Lactic Acid Bacteria in Grass Silage▿

    OpenAIRE

    Broberg, Anders; Jacobsson, Karin; Ström, Katrin; Schnürer, Johan

    2007-01-01

    The metabolite production of lactic acid bacteria (LAB) on silage was investigated. The aim was to compare the production of antifungal metabolites in silage with the production in liquid cultures previously studied in our laboratory. The following metabolites were found to be present at elevated concentrations in silos inoculated with LAB strains: 3-hydroxydecanoic acid, 2-hydroxy-4-methylpentanoic acid, benzoic acid, catechol, hydrocinnamic acid, salicylic acid, 3-phenyllactic acid, 4-hydro...

  4. Untargeted metabolomic profiling plasma samples of patients with lung cancer for searching significant metabolites by HPLC-MS method

    Science.gov (United States)

    Dementeva, N.; Ivanova, K.; Kokova, D.; Kurzina, I.; Ponomaryova, A.; Kzhyshkowska, J.

    2017-09-01

    Lung cancer is one of the most common types of cancer leading to death. Consequently, the search and the identification of the metabolites associated with the risk of developing cancer are very valuable. For the purpose, untargeted metabolic profiling of the plasma samples collected from the patients with lung cancer (n = 100) and the control group (n = 100) was conducted. After sample preparation, the plasma samples were analyzed using LC-MS method. Biostatistics methods were applied to pre-process the data for elicitation of dominating metabolites which responded to the difference between the case and the control groups. At least seven significant metabolites were evaluated and annotated. The most part of identified metabolites are connected with lipid metabolism and their combination could be useful for follow-up studies of lung cancer pathogenesis.

  5. Nutrient Intake Is Associated with Longevity Characterization by Metabolites and Element Profiles of Healthy Centenarians.

    Science.gov (United States)

    Cai, Da; Zhao, Shancang; Li, Danlei; Chang, Fang; Tian, Xiangxu; Huang, Guohong; Zhu, Zhenjun; Liu, Dong; Dou, Xiaowei; Li, Shubo; Zhao, Mouming; Li, Quanyang

    2016-09-19

    The relationships between diet and metabolites as well as element profiles in healthy centenarians are important but remain inconclusive. Therefore, to test the interesting hypothesis that there would be distinctive features of metabolites and element profiles in healthy centenarians, and that these would be associated with nutrient intake; the short chain fatty acids (SCFAs), total bile acids and ammonia in feces, phenol, p -cresol, uric acid, urea, creatinine and ammonia in urine, and element profiles in fingernails were determined in 90 healthy elderly people, including centenarians from Bama county (China)-a famous longevous region-and elderly people aged 80-99 from the longevous region and a non-longevous region. The partial least squares-discriminant analysis was used for pattern recognition. As a result, the centenarians showed a distinct metabolic pattern. Seven characteristic components closely related to the centenarians were identified, including acetic acid, total SCFA, Mn, Co, propionic acid, butyric acid and valeric acid. Their concentrations were significantly higher in the centenarians group ( p < 0.05). Additionally, the dietary fiber intake was positively associated with butyric acid contents in feces ( r = 0.896, p < 0.01), and negatively associated with phenol in urine ( r = -0.326, p < 0.01). The results suggest that the specific metabolic pattern of centenarians may have an important and positive influence on the formation of the longevity phenomenon. Elevated dietary fiber intake should be a path toward health and longevity.

  6. Nutrient Intake Is Associated with Longevity Characterization by Metabolites and Element Profiles of Healthy Centenarians

    Directory of Open Access Journals (Sweden)

    Da Cai

    2016-09-01

    Full Text Available The relationships between diet and metabolites as well as element profiles in healthy centenarians are important but remain inconclusive. Therefore, to test the interesting hypothesis that there would be distinctive features of metabolites and element profiles in healthy centenarians, and that these would be associated with nutrient intake; the short chain fatty acids (SCFAs, total bile acids and ammonia in feces, phenol, p-cresol, uric acid, urea, creatinine and ammonia in urine, and element profiles in fingernails were determined in 90 healthy elderly people, including centenarians from Bama county (China—a famous longevous region—and elderly people aged 80–99 from the longevous region and a non-longevous region. The partial least squares-discriminant analysis was used for pattern recognition. As a result, the centenarians showed a distinct metabolic pattern. Seven characteristic components closely related to the centenarians were identified, including acetic acid, total SCFA, Mn, Co, propionic acid, butyric acid and valeric acid. Their concentrations were significantly higher in the centenarians group (p < 0.05. Additionally, the dietary fiber intake was positively associated with butyric acid contents in feces (r = 0.896, p < 0.01, and negatively associated with phenol in urine (r = −0.326, p < 0.01. The results suggest that the specific metabolic pattern of centenarians may have an important and positive influence on the formation of the longevity phenomenon. Elevated dietary fiber intake should be a path toward health and longevity.

  7. Global metabolite profiling of synovial fluid for the specific diagnosis of rheumatoid arthritis from other inflammatory arthritis.

    Directory of Open Access Journals (Sweden)

    Sooah Kim

    Full Text Available Currently, reliable biomarkers that can be used to distinguish rheumatoid arthritis (RA from other inflammatory diseases are unavailable. To find possible distinctive metabolic patterns and biomarker candidates for RA, we performed global metabolite profiling of synovial fluid samples. Synovial fluid samples from 38 patients with RA, ankylosing spondylitis, Behçet's disease, and gout were analyzed by gas chromatography/time-of-flight mass spectrometry (GC/TOF MS. Orthogonal partial least-squares discriminant and hierarchical clustering analyses were performed for the discrimination of RA and non-RA groups. Variable importance for projection values were determined, and the Wilcoxon-Mann-Whitney test and the breakdown and one-way analysis of variance were conducted to identify potential biomarkers for RA. A total of 105 metabolites were identified from synovial fluid samples. The score plot of orthogonal partial least squares discriminant analysis showed significant discrimination between the RA and non-RA groups. The 20 metabolites, including citrulline, succinate, glutamine, octadecanol, isopalmitic acid, and glycerol, were identified as potential biomarkers for RA. These metabolites were found to be associated with the urea and TCA cycles as well as fatty acid and amino acid metabolism. The metabolomic analysis results demonstrated that global metabolite profiling by GC/TOF MS might be a useful tool for the effective diagnosis and further understanding of RA.

  8. Establishing the Secondary Metabolite Profile of the Marine Fungus: Tolypocladium geodes sp. MF458 and Subsequent Optimisation of Bioactive Secondary Metabolite Production.

    Science.gov (United States)

    Kebede, Bethlehem; Wrigley, Stephen K; Prashar, Anjali; Rahlff, Janina; Wolf, Markus; Reinshagen, Jeanette; Gribbon, Philip; Imhoff, Johannes F; Silber, Johanna; Labes, Antje; Ellinger, Bernhard

    2017-03-23

    As part of an international research project, the marine fungal strain collection of the Helmholtz Centre for Ocean Research (GEOMAR) research centre was analysed for secondary metabolite profiles associated with anticancer activity. Strain MF458 was identified as Tolypocladium geodes , by internal transcribed spacer region (ITS) sequence similarity and its natural product production profile. By using five different media in two conditions and two time points, we were able to identify eight natural products produced by MF458. As well as cyclosporin A ( 1 ), efrapeptin D ( 2 ), pyridoxatin ( 3 ), terricolin A ( 4 ), malettinins B and E ( 5 and 6 ), and tolypocladenols A1/A2 ( 8 ), we identified a new secondary metabolite which we termed tolypocladenol C ( 7 ). All compounds were analysed for their anticancer potential using a selection of the NCI60 cancer cell line panel, with malettinins B and E ( 5 and 6 ) being the most promising candidates. In order to obtain sufficient quantities of these compounds to start preclinical development, their production was transferred from a static flask culture to a stirred tank reactor, and fermentation medium development resulted in a nearly eight-fold increase in compound production. The strain MF458 is therefore a producer of a number of interesting and new secondary metabolites and their production levels can be readily improved to achieve higher yields.

  9. Metabolite profiling of somatic embryos of Cyclamen persicum in comparison to zygotic embryos, endosperm and testa

    Directory of Open Access Journals (Sweden)

    Traud eWinkelmann

    2015-08-01

    Full Text Available Somatic embryogenesis has been shown to be an efficient in vitro plant regeneration system for many crops such as the important ornamental plant Cyclamen persicum, for which this regeneration pathway of somatic embryogenesis is of interest for the vegetative propagation of parental lines as well as elite plants. However, somatic embryogenesis is not commercially used in many crops due to several unsolved problems, such as malformations, asynchronous development, deficiencies in maturation and germination of somatic embryos. In contrast, zygotic embryos in seeds develop and germinate without abnormalities in most cases. Instead of time-consuming and labor-intensive experiments involving tests of different in vitro culture conditions and plant growth regulator supplements, we follow a more directed approach. Zygotic embryos served as a reference and were compared to somatic embryos in metabolomic analyses allowing the future optimization of the in vitro system. The aims of this study were to detect differences in the metabolite profiles of torpedo stage somatic and zygotic embryos of C. persicum. Moreover, major metabolites in endosperm and testa were identified and quantified.Two sets of extracts of two to four biological replicates each were analyzed. In total 52 metabolites were identified and quantified in the different tissues. One of the most significant differences between somatic and zygotic embryos was that the proline concentration in the zygotic embryos was about 40 times higher than that found in somatic embryos. Epicatechin, a scavenger for reactive oxygen species, was found in highest abundance in the testa. Sucrose, the most abundant metabolite was detected in significantly higher concentrations in zygotic embryos. Also, a yet unknown trisaccharide, was significantly enriched in zygotic embryos.

  10. Metabolite profiling at the cellular and subcellular level reveals metabolites associated with salinity tolerance in sugar beet.

    Science.gov (United States)

    Hossain, M Sazzad; Persicke, Marcus; ElSayed, Abdelaleim Ismail; Kalinowski, Jörn; Dietz, Karl-Josef

    2017-12-16

    Sugar beet is among the most salt-tolerant crops. This study aimed to investigate the metabolic adaptation of sugar beet to salt stress at the cellular and subcellular levels. Seedlings were grown hydroponically and subjected to stepwise increases in salt stress up to 300 mM NaCl. Highly enriched fractions of chloroplasts were obtained by non-aqueous fractionation using organic solvents. Total leaf metabolites and metabolites in chloroplasts were profiled at 3 h and 14 d after reaching the maximum salinity stress of 300 mM NaCl. Metabolite profiling by gas chromatography-mass spectrometry (GC-MS) resulted in the identification of a total of 83 metabolites in leaves and chloroplasts under control and stress conditions. There was a lower abundance of Calvin cycle metabolites under salinity whereas there was a higher abundance of oxidative pentose phosphate cycle metabolites such as 6-phosphogluconate. Accumulation of ribose-5-phosphate and ribulose-5-phosphate coincided with limitation of carbon fixation by ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). Increases in glycolate and serine levels indicated that photorespiratory metabolism was stimulated in salt-stressed sugar beet. Compatible solutes such as proline, mannitol, and putrescine accumulated mostly outside the chloroplasts. Within the chloroplast, putrescine had the highest relative level and probably assisted in the acclimation of sugar beet to high salinity stress. The results provide new information on the contribution of chloroplasts and the extra-chloroplast space to salinity tolerance via metabolic adjustment in sugar beet. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  11. Plasma, urine and ligament tissue metabolite profiling reveals potential biomarkers of ankylosing spondylitis using NMR-based metabolic profiles.

    Science.gov (United States)

    Wang, Wei; Yang, Gen-Jin; Zhang, Ju; Chen, Chen; Jia, Zhen-Yu; Li, Jia; Xu, Wei-Dong

    2016-10-22

    they were also probably associated with immune regulation. Our work demonstrates that the potential biomarkers that were identified appeared to have diagnostic value for AS and deserve to be further investigated. In addition, this work also suggests that the metabolomic profiling approach is a promising screening tool for the diagnosis of patients with AS.

  12. Profil Metabolit Hormon Estrogen dan Progesteron Feses selama Kebuntingan serta Pola Kelahiran Rusa Sambar (Cervus unicolor)

    OpenAIRE

    Sitepu, Sukma Aditya

    2012-01-01

    Sukma Aditya Sitepu, 2012. Profile of Estrogen and Progesterone Hormone Metabolites Feces during Gestation and Pattern Birth of Sambar Deer (Cervus unicolor), under supervised by Dr. Ir. Ristika Handarini, MP and Prof. Dr. Ir. Sayed Umar, MS. Sampling by non invasive methode is used for wildlife, but for the domesticating animals that are still be used when experiencing difficulties in blood sampling. The aim of this study was to observe metabolites profiles of estrogen and progesterone ho...

  13. Arsenate Impact on the Metabolite Profile, Production, and Arsenic Loading of Xylem Sap in Cucumbers (Cucumis sativus L.).

    Science.gov (United States)

    Uroic, M Kalle; Salaün, Pascal; Raab, Andrea; Feldmann, Jörg

    2012-01-01

    Arsenic uptake and translocation studies on xylem sap focus generally on the concentration and speciation of arsenic in the xylem. Arsenic impact on the xylem sap metabolite profile and its production during short term exposure has not been reported in detail. To investigate this, cucumbers were grown hydroponically and arsenate (As(V)) and DMA were used for plant treatment for 24 h. Total arsenic and arsenic speciation in xylem sap was analyzed including a metabolite profiling under As(V) stress. Produced xylem sap was quantified and absolute arsenic transported was determined. As(V) exposure had a significant impact on the metabolite profile of xylem sap. Four m/z values corresponding to four compounds were up-regulated, one compound down-regulated by As(V) exposure. The compound down-regulated was identified to be isoleucine. Furthermore, As(V) exposure had a significant influence on sap production, leading to a reduction of up to 96% sap production when plants were exposed to 1000 μg kg(-1) As(V). No difference to control plants was observed when plants were exposed to 1000 μg kg(-1) DMA. Absolute arsenic amount in xylem sap was the lowest at high As(V) exposure. These results show that As(V) has a significant impact on the production and metabolite profile of xylem sap. The physiological importance of isoleucine needs further attention.

  14. Multicomponent Analysis of the Differential Induction of Secondary Metabolite Profiles in Fungal Endophytes.

    Science.gov (United States)

    González-Menéndez, Víctor; Pérez-Bonilla, Mercedes; Pérez-Victoria, Ignacio; Martín, Jesús; Muñoz, Francisca; Reyes, Fernando; Tormo, José R; Genilloud, Olga

    2016-02-18

    Small molecule histone deacetylase (HDAC) and DNA methyltransferase (DNMT) inhibitors are commonly used to perturb the production of fungal metabolites leading to the induction of the expression of silent biosynthetic pathways. Several reports have described the variable effects observed in natural product profiles in fungi treated with HDAC and DNMT inhibitors, such as enhanced chemical diversity and/or the induction of new molecules previously unknown to be produced by the strain. Fungal endophytes are known to produce a wide variety of secondary metabolites (SMs) involved in their adaptation and survival within higher plants. The plant-microbe interaction may influence the expression of some biosynthetic pathways, otherwise cryptic in these fungi when grown in vitro. The aim of this study was to setup a systematic approach to evaluate and identify the possible effects of HDAC and DNMT inhibitors on the metabolic profiles of wild type fungal endophytes, including the chemical identification and characterization of the most significant SMs induced by these epigenetic modifiers.

  15. Multicomponent Analysis of the Differential Induction of Secondary Metabolite Profiles in Fungal Endophytes

    Directory of Open Access Journals (Sweden)

    Víctor González-Menéndez

    2016-02-01

    Full Text Available Small molecule histone deacetylase (HDAC and DNA methyltransferase (DNMT inhibitors are commonly used to perturb the production of fungal metabolites leading to the induction of the expression of silent biosynthetic pathways. Several reports have described the variable effects observed in natural product profiles in fungi treated with HDAC and DNMT inhibitors, such as enhanced chemical diversity and/or the induction of new molecules previously unknown to be produced by the strain. Fungal endophytes are known to produce a wide variety of secondary metabolites (SMs involved in their adaptation and survival within higher plants. The plant-microbe interaction may influence the expression of some biosynthetic pathways, otherwise cryptic in these fungi when grown in vitro. The aim of this study was to setup a systematic approach to evaluate and identify the possible effects of HDAC and DNMT inhibitors on the metabolic profiles of wild type fungal endophytes, including the chemical identification and characterization of the most significant SMs induced by these epigenetic modifiers.

  16. Comparative Metabolite Profiling of Triterpenoid Saponins and Flavonoids in Flower Color Mutations of Primula veris L.

    Science.gov (United States)

    Apel, Lysanne; Kammerer, Dietmar R.; Stintzing, Florian C.; Spring, Otmar

    2017-01-01

    Primula veris L. is an important medicinal plant with documented use for the treatment of gout, headache and migraine reaching back to the Middle Ages. Triterpenoid saponins from roots and flowers are used in up-to-date phytotherapeutic treatment of bronchitis and colds due to their expectorant and secretolytic effects. In addition to the wild type plants with yellow petals, a red variant and an intermediate orange form of Primula veris L. have recently been found in a natural habitat. The secondary metabolite profiles of roots, leaves and flowers of these rare variants were investigated and compared with the wild type metabolome. Two flavonoids, six flavonoid glycosides, four novel methylated flavonoid glycosides, five anthocyanins and three triterpenoid saponins were identified in alcoholic extracts from the petals, leaves and roots of the three variants by high performance liquid chromatography (HPLC)-diode array detection (DAD)/mass spectrometry (MSn) analyses. Anthocyanins were detected in the petals of the red and orange variety, but not in the wild type. No other effects on the metabolite profiles of the three varieties have been observed. The possibility is discussed that a regulatory step of the anthocyanin biosynthetic pathway may have been affected by mutation thus triggering color polymorphism in the petals. PMID:28098796

  17. Analysis of hypoxia and hypoxia-like states through metabolite profiling.

    Directory of Open Access Journals (Sweden)

    Julie E Gleason

    Full Text Available In diverse organisms, adaptation to low oxygen (hypoxia is mediated through complex gene expression changes that can, in part, be mimicked by exposure to metals such as cobalt. Although much is known about the transcriptional response to hypoxia and cobalt, little is known about the all-important cell metabolism effects that trigger these responses.Herein we use a low molecular weight metabolome profiling approach to identify classes of metabolites in yeast cells that are altered as a consequence of hypoxia or cobalt exposures. Key findings on metabolites were followed-up by measuring expression of relevant proteins and enzyme activities. We find that both hypoxia and cobalt result in a loss of essential sterols and unsaturated fatty acids, but the basis for these changes are disparate. While hypoxia can affect a variety of enzymatic steps requiring oxygen and heme, cobalt specifically interferes with diiron-oxo enzymatic steps for sterol synthesis and fatty acid desaturation. In addition to diiron-oxo enzymes, cobalt but not hypoxia results in loss of labile 4Fe-4S dehydratases in the mitochondria, but has no effect on homologous 4Fe-4S dehydratases in the cytosol. Most striking, hypoxia but not cobalt affected cellular pools of amino acids. Amino acids such as aromatics were elevated whereas leucine and methionine, essential to the strain used here, dramatically decreased due to hypoxia induced down-regulation of amino acid permeases.These studies underscore the notion that cobalt targets a specific class of iron proteins and provide the first evidence for hypoxia effects on amino acid regulation. This research illustrates the power of metabolite profiling for uncovering new adaptations to environmental stress.

  18. Authentication of Zanthoxylum Species Based on Integrated Analysis of Complete Chloroplast Genome Sequences and Metabolite Profiles.

    Science.gov (United States)

    Lee, Hyeon Ju; Koo, Hyun Jo; Lee, Jonghoon; Lee, Sang-Choon; Lee, Dong Young; Giang, Vo Ngoc Linh; Kim, Minjung; Shim, Hyeonah; Park, Jee Young; Yoo, Ki-Oug; Sung, Sang Hyun; Yang, Tae-Jin

    2017-11-29

    We performed chloroplast genome sequencing and comparative analysis of two Rutaceae species, Zanthoxylum schinifolium (Korean pepper tree) and Z. piperitum (Japanese pepper tree), which are medicinal and culinary crops in Asia. We identified more than 837 single nucleotide polymorphisms and 103 insertions/deletions (InDels) based on a comparison of the two chloroplast genomes and developed seven DNA markers derived from five tandem repeats and two InDel variations that discriminated between Korean Zanthoxylum species. Metabolite profile analysis pointed to three metabolic groups, one with Korean Z. piperitum samples, one with Korean Z. schinifolium samples, and the last containing all the tested Chinese Zanthoxylum species samples, which are considered to be Z. bungeanum based on our results. Two markers were capable of distinguishing among these three groups. The chloroplast genome sequences identified in this study represent a valuable genomics resource for exploring diversity in Rutaceae, and the molecular markers will be useful for authenticating dried Zanthoxylum berries in the marketplace.

  19. Volatile metabolites profiling of a Chinese mangrove endophytic ...

    African Journals Online (AJOL)

    Pestalotiopsis JCM2A4, an endophytic fungus originally isolated from leaves of the Chinese mangrove plant Rhizophora mucronata, produces a mixture of volatile metabolites. As determined by gas chromatography and gas chromatography/mass spectrometry (GC/GC-MS), 18 compounds representing all of the hexane ...

  20. Metabolite profiling and quantification of phytochemicals in potato extracts using ultra-high-performance liquid chromatography-mass spectrometry.

    Science.gov (United States)

    Chong, Esther Swee Lan; McGhie, Tony K; Heyes, Julian A; Stowell, Kathryn M

    2013-12-01

    Potatoes contain a diverse range of phytochemicals which have been suggested to have health benefits. Metabolite profiling and quantification were conducted on plant extracts made from a white potato cultivar and 'Urenika', a purple potato cultivar traditionally consumed by New Zealand Maori. There is limited published information regarding the metabolite profile of Solanum tuberosum cultivar 'Urenika'. Using ultra-high- performance liquid chromatography-mass spectrometry (UHPLC-MS), a total of 31 compounds were identified and quantified in the potato extracts. The majority of the compounds were identified for the first time in 'Urenika'. These compounds include several types of anthocyanins, hydroxycinnamic acid (HCA) derivatives, and hydroxycinnamic amides (HCAA). Six classes of compounds, namely organic acids, amino acids, HCA, HCAA, flavonols and glycoalkaloids, were present in both extracts but quantities varied between the two extracts. The unknown plant metabolites in both potato extracts were assigned with molecular formulae and identified with high confidence. Quantification of the metabolites was achieved using a number of appropriate standards. High-resolution mass spectrometry data critical for accurate identification of unknown phytochemicals were achieved and could be added to potato or plant metabolomic database. © 2013 Society of Chemical Industry.

  1. GC-MS based metabolite profiling of five Bulgarian Fumaria species

    Directory of Open Access Journals (Sweden)

    Radka Z. Vrancheva

    2014-12-01

    Full Text Available The aim of this study was profiling of primary metabolites of five Bulgarian Fumaria species (F. officinalis L., F. thuretii Boiss., F. kralikii Jord., F. rostellata Knaf. and F. schrammii Velen. by GC-MS analyses. In polar fractions ten carbohydrates, one polyol, ten amino acids and six organic acids were identified. Apolar (lipid fractions showed the presence of four free fatty acids, two esters of fatty acids with glycerol and two fatty alcohols. Sucrose and fructose were in the highest relative concentrations of identified carbohydrates. Citric acid was the dominant organic acid in polar fractions of five Fumaria species. Predominant compounds in lipid fractions were palmitic acid and 1-stearoyl-glycerol. Principal component analysis (PCA of GC-MS data of polar and apolar fractions of five Bulgarian Fumaria species differentiates them in two groups (F. officinalis and F. thuretii; F. rostellata and F. schrammii, respectively, while F. kralikii had phythochemical similarity with plants of both distinguished groups. The obtained results of PCA of primary metabolites could be proposed as chemotaxonomic markers for plants of the genus Fumaria.

  2. Penicillium strains isolated from Slovak grape berries taxonomy assessment by secondary metabolite profile.

    Science.gov (United States)

    Santini, Antonello; Mikušová, Petra; Sulyok, Michael; Krska, Rudolf; Labuda, Roman; Srobárová, Antónia

    2014-11-01

    The secondary metabolite profiles of microfungi of the genus Penicillium isolated from samples of grape berries collected in two different phases during two vegetative seasons in Slovakia is described to assess the taxonomy. Three Slovak vine regions have been selected for this study, based on their climatic differences and national economic importance. Cultures of microfungi isolated from berries were incubated on different selective media for macro and micromorphology identification. The species Penicillium brevicompactum, Penicillium crustosum, Penicillium chrysogenum, Penicillium expansum, Penicillium palitans and Penicillium polonicum were identified according to growth and morphology. The related strains were found to produce a broad spectrum of fungal metabolites, including roquefortine C, chaetoglobosin A, penitrem A, cyclopeptin, cyclopenin, viridicatin, methylviridicatin, verrucofortine, secalonic acid D, cyclopiazonic acid, fumigaclavine and mycophenolic acid. Chemotaxonomy was performed using high-performance liquid chromatography (HPLC) and mass spectrometry (MS). Dried grape berries were also analyzed allowing to assess the presence of patulin, roquefortine C and penicillic acid; this last one has been identified in dried berries but not in vitro.

  3. Global Profiling of Various Metabolites in Platycodon grandiflorum by UPLC-QTOF/MS.

    Science.gov (United States)

    Lee, Jae Won; Ji, Seung-Heon; Kim, Geum-Soog; Song, Kyung-Sik; Um, Yurry; Kim, Ok Tae; Lee, Yi; Hong, Chang Pyo; Shin, Dong-Ho; Kim, Chang-Kug; Lee, Seung-Eun; Ahn, Young-Sup; Lee, Dae-Young

    2015-11-09

    In this study, a method of metabolite profiling based on UPLC-QTOF/MS was developed to analyze Platycodon grandiflorum. In the optimal UPLC, various metabolites, including major platycosides, were separated well in 15 min. The metabolite extraction protocols were also optimized by selecting a solvent for use in the study, the ratio of solvent to sample and sonication time. This method was used to profile two different parts of P. grandiflorum, i.e., the roots of P. grandiflorum (PR) and the stems and leaves of P. grandiflorum (PS), in the positive and negative ion modes. As a result, PR and PS showed qualitatively and quantitatively different metabolite profiles. Furthermore, their metabolite compositions differed according to individual plant samples. These results indicate that the UPLC-QTOF/MS-based profiling method is a good tool to analyze various metabolites in P. grandiflorum. This metabolomics approach can also be applied to evaluate the overall quality of P. grandiflorum, as well as to discriminate the cultivars for the medicinal plant industry.

  4. Steroid receptor profiling of vinclozolin and its primary metabolites

    International Nuclear Information System (INIS)

    Molina-Molina, Jose-Manuel; Hillenweck, Anne; Jouanin, Isabelle; Zalko, Daniel; Cravedi, Jean-Pierre; Fernandez, Mariana-Fatima; Pillon, Arnaud; Nicolas, Jean-Claude; Olea, Nicolas; Balaguer, Patrick

    2006-01-01

    Several pesticides and fungicides commonly used to control agricultural and indoor pests are highly suspected to display endocrine-disrupting effects in animals and humans. Endocrine disruption is mainly caused by the interference of chemicals at the level of steroid receptors: it is now well known that many of these chemicals can display estrogenic effects and/or anti-androgenic effects, but much less is known about the interaction of these compounds with other steroid receptors. Vinclozolin, a dicarboximide fungicide, like its primary metabolites 2-[[(3,5-dichlorophenyl)-carbamoyl]oxy]-2-methyl-3-butenoic acid (M1), and 3',5'-dichloro-2-hydroxy-2-methylbut-3-enanilide (M2), is known to bind androgen receptor (AR). Although vinclozolin and its metabolites were characterized as anti-androgens, relatively little is known about their effects on the function of the progesterone (PR), glucocorticoid (GR), mineralocorticoid (MR) or estrogen receptors (ERα and ERβ). Objectives of the study were to determine the ability of vinclozolin and its two primary metabolites to activate AR, PR, GR, MR and ER. For this purpose, we used reporter cell lines bearing luciferase gene under the control of wild type or chimeric Gal4 fusion AR, PR, GR, MR or ERs. We confirmed that all three were antagonists for AR, whereas only M2 was found a partial agonist. Interestingly, M2 was also a PR, GR and MR antagonist (MR >> PR > GR) while vinclozolin was an MR and PR antagonist. Vinclozolin, M1 and M2 were agonists for both ERs with a lower affinity for ERβ. Although the potencies of the fungicide and its metabolites are low when compared to natural ligands, their ability to act via more than one mechanism and the potential for additive or synergistic effect must be taken into consideration in the risk assessment process

  5. The use of secondary metabolite profiling in chemotaxonomy of filamentous fungi.

    Science.gov (United States)

    Frisvad, Jens C; Andersen, Birgitte; Thrane, Ulf

    2008-02-01

    A secondary metabolite is a chemical compound produced by a limited number of fungal species in a genus, an order, or even phylum. A profile of secondary metabolites consists of all the different compounds a fungus can produce on a given substratum and includes toxins, antibiotics and other outward-directed compounds. Chemotaxonomy is traditionally restricted to comprise fatty acids, proteins, carbohydrates, or secondary metabolites, but has sometimes been defined so broadly that it also includes DNA sequences. It is not yet possible to use secondary metabolites in phylogeny, because of the inconsistent distribution throughout the fungal kingdom. However, this is the very quality that makes secondary metabolites so useful in classification and identification. Four groups of organisms are particularly good producers of secondary metabolites: plants, fungi, lichen fungi, and actinomycetes, whereas yeasts, protozoa, and animals are less efficient producers. Therefore, secondary metabolites have mostly been used in plant and fungal taxonomy, whereas chemotaxonomy has been neglected in bacteriology. Lichen chemotaxonomy has been based on few biosynthetic families (chemosyndromes), whereas filamentous fungi have been analysed for a wide array of terpenes, polyketides, non-ribosomal peptides, and combinations of these. Fungal chemotaxonomy based on secondary metabolites has been used successfully in large ascomycete genera such as Alternaria, Aspergillus, Fusarium, Hypoxylon, Penicillium, Stachybotrys, Xylaria and in few basidiomycete genera, but not in Zygomycota and Chytridiomycota.

  6. Profiling of plasma metabolites in canine oral melanoma using gas chromatography-mass spectrometry.

    Science.gov (United States)

    Kawabe, Mifumi; Baba, Yuta; Tamai, Reo; Yamamoto, Ryohei; Komori, Masayuki; Mori, Takashi; Takenaka, Shigeo

    2015-08-01

    Malignant melanoma is one of the most common and aggressive tumors in the oral cavity of dog. The tumor has a poor prognosis, and methods for diagnosis and prediction of prognosis after treatment are required. Here, we examined metabolite profiling using gas chromatography-mass spectrometry (GC-MS) for development of a discriminant model for evaluation of prognosis. Metabolite profiles were evaluated in healthy and melanoma plasma samples using orthogonal projection to latent structure using discriminant analysis (OPLS-DA). Cases that were predicted to be healthy using the OPLS discriminant model had no advanced lesions after radiation therapy. These results indicate that metabolite profiling may be useful in diagnosis and prediction of prognosis of canine malignant melanoma.

  7. Metabolic Profiling and Antioxidant Assay of Metabolites from Three Radish Cultivars (Raphanus sativus

    Directory of Open Access Journals (Sweden)

    Chang Ha Park

    2016-01-01

    Full Text Available A total of 13 anthocyanins and 33 metabolites; including organic acids, phenolic acids, amino acids, organic compounds, sugar acids, sugar alcohols, and sugars, were profiled in three radish cultivars by using high-performance liquid chromatography (HPLC and gas chromatography time-of-flight mass spectrometry (GC-TOFMS-based metabolite profiling. Total phenolics and flavonoids and their in vitro antioxidant activities were assessed. Pelargonidins were found to be the major anthocyanin in the cultivars studied. The cultivar Man Tang Hong showed the highest level of anthocyanins (1.89 ± 0.07 mg/g, phenolics (0.0664 ± 0.0033 mg/g and flavonoids (0.0096 ± 0.0004 mg/g. Here; the variation of secondary metabolites in the radishes is described, as well as their association with primary metabolites. The low-molecular-weight hydrophilic metabolite profiles were subjected to principal component analysis (PCA, hierarchical clustering analysis (HCA, Pearson’s correlation analysis. PCA fully distinguished the three radish cultivars tested. The polar metabolites were strongly correlated between metabolites that participate in the TCA cycle. The chemometrics results revealed that TCA cycle intermediates and free phenolic acids as well as anthocyanins were higher in the cultivar Man Tang Hong than in the others. Furthermore; superoxide radical scavenging activities and 1,1-diphenyl-2-picrylhydrazyl (DPPH radical scavenging were investigated to elucidate the antioxidant activity of secondary metabolites in the cultivars. Man Tang Hong showed the highest superoxide radical scavenging activity (68.87% at 1000 μg/mL, and DPPH activity (20.78%, followed by Seo Ho and then Hong Feng No. 1. The results demonstrate that GC-TOFMS-based metabolite profiling, integrated with chemometrics, is an applicable method for distinguishing phenotypic variation and determining biochemical reactions connecting primary and secondary metabolism. Therefore; this study might

  8. Metabolite Profiling of Italian Tomato Landraces with Different Fruit Types

    Directory of Open Access Journals (Sweden)

    Svetlana eBaldina

    2016-05-01

    Full Text Available Increased interest towards traditional tomato varieties is fueled by the need to rescue desirable organoleptic traits and to improve the quality of fresh and processed tomatoes in the market. In addition, the phenotypic and genetic variation preserved in tomato landraces represents a means to understand the genetic basis of traits related to health and organoleptic aspects and improve them in modern varieties. To establish a framework for this approach, we studied the content of several metabolites in a panel of Italian tomato landraces categorized into three broad fruit type classes (flattened/ribbed, pear/oxheart, round/elongate. Three modern hybrids, corresponding to the three fruit shape typologies, were included as reference. Red ripe fruits were morphologically characterized and biochemically analyzed for their content in glycoalkaloids, phenols, amino acids and Amadori products. The round/elongate types showed a higher content in glycoalkaloids, whereas flattened types had higher levels of phenolic compounds. Flattened tomatoes were also rich in total amino acids and in particular in glutamic acid. Multivariate analysis of amino acid content clearly separated the three classes of fruit types. Making allowance of the very low number of genotypes, phenotype-marker relationships were analyzed after retrieving single nucleotide polymorphisms (SNPs among the landraces available in the literature. Sixty-six markers were significantly associated with the studied traits. The positions of several of these SNPs showed correspondence with already described genomic regions and QTLs supporting the reliability of the association. Overall the data indicated that significant changes in quality-related metabolites occur depending on the genetic background in traditional tomato germplasm, frequently according to specific fruit shape categories. Such a variability is suitable to harness association mapping for metabolic quality traits using this germplasm

  9. Consumption of pasteurized human lysozyme transgenic goats' milk alters serum metabolite profile in young pigs.

    Science.gov (United States)

    Brundige, Dottie R; Maga, Elizabeth A; Klasing, Kirk C; Murray, James D

    2010-08-01

    Nutrition, bacterial composition of the gastrointestinal tract, and general health status can all influence the metabolic profile of an organism. We previously demonstrated that feeding pasteurized transgenic goats' milk expressing human lysozyme (hLZ) can positively impact intestinal morphology and modulate intestinal microbiota composition in young pigs. The objective of this study was to further examine the effect of consuming hLZ-containing milk on young pigs by profiling serum metabolites. Pigs were placed into two groups and fed a diet of solid food and either control (non-transgenic) goats' milk or milk from hLZ-transgenic goats for 6 weeks. Serum samples were collected at the end of the feeding period and global metabolite profiling was performed. For a total of 225 metabolites (160 known, 65 unknown) semi-quantitative data was obtained. Levels of 18 known and 4 unknown metabolites differed significantly between the two groups with the direction of change in 13 of the 18 known metabolites being almost entirely congruent with improved health status, particularly in terms of the gastrointestinal tract health and immune response, with the effects of the other five being neutral or unknown. These results further support our hypothesis that consumption of hLZ-containing milk is beneficial to health.

  10. Characteristic differences in metabolite profile in male and female ...

    Indian Academy of Sciences (India)

    2012-10-30

    Oct 30, 2012 ... male and female plants. The recently developed Direct Analysis in Real Time Mass. Spectroscopy (DARTMS) is a fast, reliable high-throughput technique which is emerging as an accepted metabolic profil- ing tool. Some of the recent examples of applications of are direct analysis of curcumin, caffeine, ...

  11. Metabolite profiling, antioxidant and antibacterial activities of Brazilian propolis

    NARCIS (Netherlands)

    Bittencourt, M.L.F.; Ribeiro, Paulo R.; Franco, R.L.P.; Hilhorst, H.W.M.; Castro, de R.D.; Fernandez, L.G.

    2015-01-01

    The production of propolis by honeybees results from a selective collection of exudates from various plant species and present many potentialities in the pharmaceutical industry. The objective of this study was to investigate the chemical profile of Brazilian propolis, as well as their in vitro

  12. Application of metabolite profiling and antioxidant activity in ...

    African Journals Online (AJOL)

    This paper investigates the effect of processing and extraction method on chemical profiles and antioxidant activity of Malaysian stingless bee propolis. High Performance Thin Layer Chromatography (HPTLC) analysis in combination with chemometric shows that some of the compounds were degraded or not detected in ...

  13. Effects of Different Salt Treatments on the Fermentation Metabolites and Bacterial Profiles of Kimchi.

    Science.gov (United States)

    Kim, Dong Wook; Kim, Bo-Min; Lee, Hyeon-Jeong; Jang, Gwang-Ju; Song, Seong Hwa; Lee, Jae-In; Lee, Sang Bong; Shim, Jae Min; Lee, Kang Wook; Kim, Jeong Hwan; Ham, Kyung-Sik; Chen, Feng; Kim, Hyun-Jin

    2017-05-01

    The effects of purified salt (PS) and mineral-rich sea salt (MRS), both with different mineral profiles, on kimchi fermentation were studied using a culture-dependent 16S rRNA sequencing technique and mass-based metabolomic analysis. The different mineral profiles in the fermentation medium caused changes in the bacterial profiles of the 2 kimchi products. An increase of Leuconostoc species in MRS-kimchi decreased the Lactobacillus/Leuconostoc ratio, which led to changes in metabolites (including sugars, amino acids, organic acids, lipids, sulfur compounds, and terpenoids) associated with kimchi quality. Although further studies on the relationship between these salt types and kimchi fermentation are needed, these results suggested that the MRS treatment had positively affected the changes of the kimchi mineral contents, bacterial growth, and metabolite profiles, which are linked to kimchi quality. © 2017 Institute of Food Technologists®.

  14. Nontargeted metabolite profiles and sensory properties of strawberry cultivars grown both organically and conventionally.

    Science.gov (United States)

    Kårlund, Anna; Hanhineva, Kati; Lehtonen, Marko; Karjalainen, Reijo O; Sandell, Mari

    2015-01-28

    Strawberry (Fragaria × ananassa Duch.) contains many secondary metabolites potentially beneficial for human health, and several of these compounds contribute to strawberry sensory properties, as well. In this study, three strawberry cultivars grown both conventionally and organically were subjected to nontargeted metabolite profiling analysis with LC-qTOF-ESI-MS and to descriptive sensory evaluation by a trained panel. Combined metabolome and sensory data (PLS model) revealed that 79% variation in the metabolome explained 88% variation in the sensory profiles. Flavonoids and condensed and hydrolyzable tannins determined the orosensory properties, and fatty acids contributed to the odor attributes of strawberry. Overall, the results indicated that the chemical composition and sensory quality of strawberries grown in different cultivation systems vary mostly according to cultivar. Organic farming practices may enhance the accumulation of some plant metabolites in specific strawberry genotypes. Careful cultivar selection is a key factor for the improvement of nutritional quality and marketing value of organic strawberries.

  15. Metabolite profiling of Arabidopsis thaliana (L.) plants transformed with an antisense chalcone synthase gene

    DEFF Research Database (Denmark)

    Le Gall, G.; Metzdorff, Stine Broeng; Pedersen, Jan W.

    2005-01-01

    A metabolite profiling study has been carried out on Arabidopsis thaliana (L.) Heynh. ecotype Wassilewskija and a series of transgenic lines of the ecotype transformed with a CHS (chalcone synthase) antisense construct. Compound identifications by LC/MS and H-1 NMR are discussed. The glucosinolate...

  16. Prediction of Clinically Relevant Safety Signals of Nephrotoxicity through Plasma Metabolite Profiling

    Directory of Open Access Journals (Sweden)

    W. B. Mattes

    2013-01-01

    Full Text Available Addressing safety concerns such as drug-induced kidney injury (DIKI early in the drug pharmaceutical development process ensures both patient safety and efficient clinical development. We describe a unique adjunct to standard safety assessment wherein the metabolite profile of treated animals is compared with the MetaMap Tox metabolomics database in order to predict the potential for a wide variety of adverse events, including DIKI. To examine this approach, a study of five compounds (phenytoin, cyclosporin A, doxorubicin, captopril, and lisinopril was initiated by the Technology Evaluation Consortium under the auspices of the Drug Safety Executive Council (DSEC. The metabolite profiles for rats treated with these compounds matched established reference patterns in the MetaMap Tox metabolomics database indicative of each compound’s well-described clinical toxicities. For example, the DIKI associated with cyclosporine A and doxorubicin was correctly predicted by metabolite profiling, while no evidence for DIKI was found for phenytoin, consistent with its clinical picture. In some cases the clinical toxicity (hepatotoxicity, not generally seen in animal studies, was detected with MetaMap Tox. Thus metabolite profiling coupled with the MetaMap Tox metabolomics database offers a unique and powerful approach for augmenting safety assessment and avoiding clinical adverse events such as DIKI.

  17. Metabolite profile of cerebrospinal fluid in patients with spina bifida: a proton magnetic resonance spectroscopy study.

    Science.gov (United States)

    Pal, Kamalesh; Sharma, Uma; Gupta, D K; Pratap, Akshay; Jagannathan, N R

    2005-02-01

    The present study was carried out to assess the metabolic differences between cerebrospinal fluid samples of patients with spina bifida and age-matched control individuals. To study the metabolite profile of cerebrospinal fluid of patients with spina bifida using proton magnetic resonance spectroscopy, compare the levels of metabolites with controls, establish correlation of underlying neuronal dysfunction with metabolic changes in patients with spina bifida, and evaluate the potential use of this technique as an additional tool for diagnostic assessment. Combination of embryopathy, stretching, ischemia, compression, and trauma is responsible for cord dysfunction in spina bifida. Changes in neuronal metabolism leads to changes in the local milieu of cerebrospinal fluid in the cord. Change in metabolite profile of cerebrospinal fluid in spina bifida in terms of increase in products of anaerobic metabolism, nerve membrane integrity, and nerve ischemia has not yet been studied. Cerebrospinal fluid obtained from patients and control individuals were characterized using various one- and two-dimensional proton magnetic resonance spectroscopy techniques. Concentration of various metabolites was calculated using the area under the nuclear magnetic resonance peak. Statistically significantly higher levels of lactate, choline, glycerophosphocholine, acetate, and alanine in the cerebrospinal fluid of patients with spina bifida was observed compared with control individuals. Significantly higher levels of metabolites were observed in patients with spina bifida, representing a state of nerve ischemia, anaerobic metabolism, and disruption of neuronal membrane.

  18. Profiling of external metabolites during production of hantavirus nucleocapsid protein with recombinant Saccharomyces cerevisiae.

    Science.gov (United States)

    Antoniukas, Linas; Grammel, Hartmut; Sasnauskas, Kestutis; Reichl, Udo

    2008-03-01

    Recombinant strains of Saccharomyces cerevisiae, producing hantavirus Puumala nucleocapsid protein for diagnostics and as a candidate vaccine were analyzed for uptake and excretion of intermediary metabolites during process optimization studies of fed-batch bioreactor cultures. Concentrations of glucose, maltose, galactose, pyruvate, acetaldehyde, ethanol, acetate, succinate and formaldehyde (used as a selection agent) were measured in the culture medium in order to find a metabolite pattern, indicative for the physiological state of the producer culture. When the inducer galactose was employed as a growth substrate, the metabolite profile of recombinant yeast cells was different from those of the non-recombinant original strain which excreted considerable amounts of metabolites with this substrate. In contrast, galactose-induced heterologous gene expression was indicated by the absence of excreted intermediary metabolites, except succinate. A model strain expressing a GFP fusion of hantavirus nucleocapsid protein differed in the excretion of metabolites from strains without GFP. In addition, the influence of alkali ions, employed for pH control is also demonstrated.

  19. Metabolite profiling of wheat grains (Triticum aestivum L.) from organic and conventional agriculture.

    Science.gov (United States)

    Zörb, Christian; Langenkämper, Georg; Betsche, Thomas; Niehaus, Karsten; Barsch, Aiko

    2006-10-18

    In some European community countries up to 8% of the agricultural area is managed organically. The aim was to obtain a metabolite profile for wheat (Triticum aestivum L.) grains grown under comparable organic and conventional conditions. These conditions cannot be found in plant material originating from different farms or from products purchased in supermarkets. Wheat grains from a long-term biodynamic, bioorganic, and conventional farming system from the harvest 2003 from Switzerland were analyzed. The presented data show that using a high throughput GC-MS technique, it was possible to determine relative levels of a set of 52 different metabolites including amino acids, organic acids, sugars, sugar alcohols, sugar phosphates, and nucleotides from wheat grains. Within the metabolites from all field trials, there was at the most a 50% reduction comparing highest and lowest mean values. The statistical analysis of the data shows that the metabolite status of the wheat grain from organic and mineralic farming did not differ in concentrations of 44 metabolites. This result indicates no impact or a small impact of the different farming systems. In consequence, we did not detect extreme differences in metabolite composition and quality of wheat grains.

  20. Metabolite Profiling of Peppers of Various Colors Reveals Relationships Between Tocopherol, Carotenoid, and Phytosterol Content.

    Science.gov (United States)

    Kim, Tae Jin; Choi, Jaehyuk; Kim, Kil Won; Ahn, Soon Kil; Ha, Sun-Hwa; Choi, Yongsoo; Park, Nam Il; Kim, Jae Kwang

    2017-12-01

    Peppers are widely consumed in Korea; the varietal development of peppers with increased content of beneficial plant metabolites is, therefore, of considerable interest. This requires a comprehensive understanding of the metabolic profile of pepper plants and the factors affecting this profile. To this end, we determined the content of various metabolites, such as hydrophilic and lipophilic compounds, phenolic acids, carotenoids, and capsaicinoids in peppers of various colors (green, red, pale green, and violet peppers) and in a high-pungency (green) pepper. We also performed principal component analysis (PCA), Pearson's correlation analysis, and hierarchical clustering analysis (HCA) to determine the relationships among these metabolites in peppers. PCA results indicated no significant variances among the 3 sample replicates. The HCA showed correlations between the metabolites resulting from common or closely linked biosynthesis pathways. Our results showed that carotenoids correlated positively with tocopherols and negatively with phytosterols; our findings also indicated a close relationship between the methylerythritol 4-phosphate and mevalonic acid biosynthesis pathways, providing evidence in favor of an earlier hypothesis regarding crosstalk across the chloroplast membrane. We, thus, demonstrate that metabolic profiling combined with multivariate analysis is a useful tool for analyzing metabolic networks. A total of 71 metabolites were measured in 5 peppers of different colors. The metabolic profiling with multivariate analysis revealed that tocopherol content had a positive correlation with the carotenoid content and a negative correlation with the phytosterol content. The results of this study may help in breeding programs to produce new germplasm with enhanced nutritional quality. © 2017 Institute of Food Technologists®.

  1. Use of mass spectrometry fingerprinting to identify urinary metabolites after consumption of specific foods.

    Science.gov (United States)

    Lloyd, Amanda J; Favé, Gaëlle; Beckmann, Manfred; Lin, Wanchang; Tailliart, Kathleen; Xie, Long; Mathers, John C; Draper, John

    2011-10-01

    The lack of robust biological markers of dietary exposure hinders the quantitative understanding of causal relations between diet and health. We aimed to develop an efficient procedure to discover metabolites in urine that may have future potential as biomarkers of acute exposure to foods of high public health importance. Twenty-four participants were provided with a test breakfast in which the cereal component of a standardized breakfast was replaced by 1 of 4 foods of high public health importance; 1.5-, 3-, and 4.5-h postprandial urine samples were collected. Flow infusion electrospray-ionization mass spectrometry followed by supervised multivariate data analysis was used to discover signals resulting from consumption of each test food. Fasted-state urine samples provided a universal comparator for food biomarker lead discovery in postprandial urine. The filtering of data features associated with consumption of the common components of the standardized breakfast improved discrimination models and readily identified metabolites that showed consumption of specific test foods. A combination of trimethylamine-N-oxide and 1-methylhistidine was associated with salmon consumption. Novel ascorbate derivatives were discovered in urine after consumption of either broccoli or raspberries. Sulphonated caffeic acid and sulphonated methyl-epicatechin concentrations increased dramatically after consumption of raspberries. This biomarker lead discovery strategy can identify urinary metabolites associated with acute exposure to individual foods. Future studies are required to validate the specificity and utility of potential biomarkers in an epidemiologic context.

  2. Identifying User Profiles from Statistical Grouping Methods

    Directory of Open Access Journals (Sweden)

    Francisco Kelsen de Oliveira

    2018-02-01

    Full Text Available This research aimed to group users into subgroups according to their levels of knowledge about technology. Statistical hierarchical and non-hierarchical clustering methods were studied, compared and used in the creations of the subgroups from the similarities of the skill levels with these users’ technology. The research sample consisted of teachers who answered online questionnaires about their skills with the use of software and hardware with educational bias. The statistical methods of grouping were performed and showed the possibilities of groupings of the users. The analyses of these groups allowed to identify the common characteristics among the individuals of each subgroup. Therefore, it was possible to define two subgroups of users, one with skill in technology and another with skill with technology, so that the partial results of the research showed two main algorithms for grouping with 92% similarity in the formation of groups of users with skill with technology and the other with little skill, confirming the accuracy of the techniques of discrimination against individuals.

  3. Metabolite Profiling in Withania somnifera Roots Hydroalcoholic Extract Using LC/MS, GC/MS and NMR Spectroscopy.

    Science.gov (United States)

    Trivedi, Mahendra Kumar; Panda, Parthasarathi; Sethi, Kalyan Kumar; Jana, Snehasis

    2017-03-01

    Ashwagandha (Withania somnifera) is a very well-known herbal medicine and it was well studied for its active metabolites throughout the World. Although, nearly 40 withanolides were isolated from W. somnifera root extract, still there is remaining unidentified metabolites due to very low abundance and geographical variation. Advanced separation technology with online identification by mass and nuclear magnetic resonance (NMR) are nowadays used to find out the new compounds in the crude herbal extract. This article described the metabolite profiling of ashwagandha root hydroalcoholic extract using ultra-performance liquid chromatography coupled with a positive ion electrospray ionization tandem mass spectrometry through gas chromatography mass spectrometry (GC/MS) and NMR spectroscopy. A total of 43 possible withanolides was identified and proposed their structures based on the mass of molecular and fragment ions. GC/MS and NMR analysis indicated the presence of several known withanolides including withaferin A, withanolide D, withanoside IV or VI, withanolide sulfoxide, etc. To the best of our knowledge, dihydrowithanolide D at m/z 473 (t R 7.86 min) and ixocarpalactone A at m/z 505 (t R 8.43 min) were first time identified in the ashwagandha root hydroalcoholic extract. The current study that described the identification of withanolides with summarized literature review might be helpful for designing the experiment to identify of the new chemical constituents in Withania species. © 2017 Wiley-VHCA AG, Zurich, Switzerland.

  4. Differential metabolite profiles during fruit development in high-yielding oil palm mesocarp.

    Directory of Open Access Journals (Sweden)

    Huey Fang Teh

    Full Text Available To better understand lipid biosynthesis in oil palm mesocarp, in particular the differences in gene regulation leading to and including de novo fatty acid biosynthesis, a multi-platform metabolomics technology was used to profile mesocarp metabolites during six critical stages of fruit development in comparatively high- and low-yielding oil palm populations. Significantly higher amino acid levels preceding lipid biosynthesis and nucleosides during lipid biosynthesis were observed in a higher yielding commercial palm population. Levels of metabolites involved in glycolysis revealed interesting divergence of flux towards glycerol-3-phosphate, while carbon utilization differences in the TCA cycle were proven by an increase in malic acid/citric acid ratio. Apart from insights into the regulation of enhanced lipid production in oil palm, these results provide potentially useful metabolite yield markers and genes of interest for use in breeding programmes.

  5. Correlation between species-specific metabolite profiles and bioactivities of blueberries (Vaccinium spp.).

    Science.gov (United States)

    Lee, Sarah; Jung, Eun Sung; Do, Seon-Gil; Jung, Ga-Young; Song, Gwanpil; Song, Jung-Min; Lee, Choong Hwan

    2014-03-05

    Metabolite profiling of three blueberry species (Vaccinium bracteatum Thunb., V. oldhamii Miquel., and V. corymbosum L.) was performed using gas chromatography-time-of-flight-mass spectrometry (GC-TOF-MS) and ultraperformance liquid chromatography-quadrupole-time-of-flight-mass spectrometry (UPLC-Q-TOF-MS) combined multivariate analysis. Partial least-squares discriminant analysis clearly showed metabolic differences among species. GC-TOF-MS analysis revealed significant differences in amino acids, organic acids, fatty acids, sugars, and phenolic acids among the three blueberry species. UPLC-Q-TOF-MS analysis indicated that anthocyanins were the major metabolites distinguishing V. bracteatum from V. oldhamii. The contents of anthocyanins such as glycosides of cyanidin were high in V. bracteatum, while glycosides of delphinidin, petunidin, and malvidin were high in V. oldhamii. Antioxidant activities assessed using ABTS and DPPH assays showed the greatest activity in V. oldhamii and revealed the highest correlation with total phenolic, total flavonoid, and total anthocyanin contents and their metabolites.

  6. Promising Metabolite Profiles in the Plasma and CSF of Early Clinical Parkinson's Disease

    Directory of Open Access Journals (Sweden)

    Daniel Stoessel

    2018-03-01

    Full Text Available Parkinson's disease (PD shows high heterogeneity with regard to the underlying molecular pathogenesis involving multiple pathways and mechanisms. Diagnosis is still challenging and rests entirely on clinical features. Thus, there is an urgent need for robust diagnostic biofluid markers. Untargeted metabolomics allows establishing low-molecular compound biomarkers in a wide range of complex diseases by the measurement of various molecular classes in biofluids such as blood plasma, serum, and cerebrospinal fluid (CSF. Here, we applied untargeted high-resolution mass spectrometry to determine plasma and CSF metabolite profiles. We semiquantitatively determined small-molecule levels (≤1.5 kDa in the plasma and CSF from early PD patients (disease duration 0–4 years; n = 80 and 40, respectively, and sex- and age-matched controls (n = 76 and 38, respectively. We performed statistical analyses utilizing partial least square and random forest analysis with a 70/30 training and testing split approach, leading to the identification of 20 promising plasma and 14 CSF metabolites. These metabolites differentiated the test set with an AUC of 0.8 (plasma and 0.9 (CSF. Characteristics of the metabolites indicate perturbations in the glycerophospholipid, sphingolipid, and amino acid metabolism in PD, which underscores the high power of metabolomic approaches. Further studies will enable to develop a potential metabolite-based biomarker panel specific for PD.

  7. Effect of Solid Biological Waste Compost on the Metabolite Profile of Brassica rapa ssp. chinensis

    Directory of Open Access Journals (Sweden)

    Susanne Neugart

    2018-03-01

    Full Text Available Large quantities of biological waste are generated at various steps within the food production chain and a great utilization potential for this solid biological waste exists apart from the current main usage for the feedstuff sector. It remains unclear how the usage of biological waste as compost modulates plant metabolites. We investigated the effect of biological waste of the processing of coffee, aronia, and hop added to soil on the plant metabolite profile by means of liquid chromatography in pak choi sprouts. Here we demonstrate that the solid biological waste composts induced specific changes in the metabolite profiles and the changes are depending on the type of the organic residues and its concentration in soil. The targeted analysis of selected plant metabolites, associated with health beneficial properties of the Brassicaceae family, revealed increased concentrations of carotenoids (up to 3.2-fold and decreased amounts of glucosinolates (up to 4.7-fold as well as phenolic compounds (up to 1.5-fold.

  8. Monitoring the Modifications of the Vitreous Humor Metabolite Profile after Death: An Animal Model

    Directory of Open Access Journals (Sweden)

    Maria Francesca Rosa

    2015-01-01

    Full Text Available We applied a metabolomic approach to monitor the modifications occurring in goat vitreous humor (VH metabolite composition at different times (0, 6, 12, 18, and 24 hours after death. The 1H-NMR analysis of the VH samples was performed for the simultaneous determination of several metabolites (i.e., the metabolite profile representative of the VH status at different times. Spectral data were analyzed by Principal Component Analysis (PCA and by Orthogonal Projection to Latent Structures (OPLS regression technique. PCA and OPLS suggested that different spectral regions were involved in time-related changes. The major time-related compositional changes, here detected, were the increase of lactate, hypoxanthine, alanine, total glutathione, choline/phosphocholine, creatine, and myo-inositol and the decrease of glucose and 3-hydroxybutyrate. We attempted a speculative interpretation of the biological mechanisms underlying these changes. These results show that multivariate statistical approach, based on 1H NMR metabolite profiling, is a powerful tool for detecting ongoing differences in VH composition and may be applied to investigate several physiological and pathological conditions.

  9. Quantitative comparison and metabolite profiling of saponins in different parts of the root of Panax notoginseng.

    Science.gov (United States)

    Wang, Jing-Rong; Yau, Lee-Fong; Gao, Wei-Na; Liu, Yong; Yick, Pui-Wing; Liu, Liang; Jiang, Zhi-Hong

    2014-09-10

    Although both rhizome and root of Panax notoginseng are officially utilized as notoginseng in "Chinese Pharmacopoeia", individual parts of the root were differently used in practice. To provide chemical evidence for the differentiated usage, quantitative comparison and metabolite profiling of different portions derived from the whole root, as well as commercial samples, were carried out, showing an overall higher content of saponins in rhizome, followed by main root, branch root, and fibrous root. Ginsenoside Rb2 was proposed as a potential marker with a content of 0.5 mg/g as a threshold value for differentiating rhizome from other parts. Multivariate analysis of the metabolite profile further suggested 32 saponins as potential markers for the discrimination of different parts of notoginseng. Collectively, the study provided comprehensive chemical evidence for the distinct usage of different parts of notoginseng and, hence, is of great importance for the rational application and exploitation of individual parts of notoginseng.

  10. Combined mass spectrometry-based metabolite profiling of different pigmented rice (Oryza sativa L.) seeds and correlation with antioxidant activities.

    Science.gov (United States)

    Kim, Ga Ryun; Jung, Eun Sung; Lee, Sarah; Lim, Sun-Hyung; Ha, Sun-Hwa; Lee, Choong Hwan

    2014-09-29

    Nine varieties of pigmented rice (Oryza sativa L.) seeds that were black, red, or white were used to perform metabolite profiling by using ultra-performance liquid chromatography-quadrupole-time-of-flight mass spectrometry (UPLC-Q-TOF-MS) and gas chromatography (GC) TOF-MS, to measure antioxidant activities. Clear grouping patterns determined by the color of the rice seeds were identified in principle component analysis (PCA) derived from UPLC-Q-TOF-MS. Cyanidin-3-glucoside, peonidin-3-glucoside, proanthocyanidin dimer, proanthocyanidin trimer, apigenin-6-C-glugosyl-8-C-arabiboside, tricin-O-rhamnoside-O-hexoside, and lipids were identified as significantly different secondary metabolites. In PCA score plots derived from GC-TOF-MS, Jakwangdo (JKD) and Ilpoom (IP) species were discriminated from the other rice seeds by PC1 and PC2. Valine, phenylalanine, adenosine, pyruvate, nicotinic acid, succinic acid, maleic acid, malonic acid, gluconic acid, xylose, fructose, glucose, maltose, and myo-inositol were significantly different primary metabolites in JKD species, while GABA, asparagine, xylitol, and sucrose were significantly distributed in IP species. Analysis of antioxidant activities revealed that black and red rice seeds had higher activity than white rice seeds. Cyanidin-3-glucoside, peonidin-3-glucoside, proanthocyanidin dimers, proanthocyanidin trimers, and catechin were highly correlated with antioxidant activities, and were more plentiful in black and red rice seeds. These results are expected to provide valuable information that could help improve and develop rice-breeding techniques.

  11. Combined Mass Spectrometry-Based Metabolite Profiling of Different Pigmented Rice (Oryza sativa L. Seeds and Correlation with Antioxidant Activities

    Directory of Open Access Journals (Sweden)

    Ga Ryun Kim

    2014-09-01

    Full Text Available Nine varieties of pigmented rice (Oryza sativa L. seeds that were black, red, or white were used to perform metabolite profiling by using ultra-performance liquid chromatography-quadrupole-time-of-flight mass spectrometry (UPLC-Q-TOF-MS and gas chromatography (GC TOF-MS, to measure antioxidant activities. Clear grouping patterns determined by the color of the rice seeds were identified in principle component analysis (PCA derived from UPLC-Q-TOF-MS. Cyanidin-3-glucoside, peonidin-3-glucoside, proanthocyanidin dimer, proanthocyanidin trimer, apigenin-6-C-glugosyl-8-C-arabiboside, tricin-O-rhamnoside-O-hexoside, and lipids were identified as significantly different secondary metabolites. In PCA score plots derived from GC-TOF-MS, Jakwangdo (JKD and Ilpoom (IP species were discriminated from the other rice seeds by PC1 and PC2. Valine, phenylalanine, adenosine, pyruvate, nicotinic acid, succinic acid, maleic acid, malonic acid, gluconic acid, xylose, fructose, glucose, maltose, and myo-inositol were significantly different primary metabolites in JKD species, while GABA, asparagine, xylitol, and sucrose were significantly distributed in IP species. Analysis of antioxidant activities revealed that black and red rice seeds had higher activity than white rice seeds. Cyanidin-3-glucoside, peonidin-3-glucoside, proanthocyanidin dimers, proanthocyanidin trimers, and catechin were highly correlated with antioxidant activities, and were more plentiful in black and red rice seeds. These results are expected to provide valuable information that could help improve and develop rice-breeding techniques.

  12. TargetSearch - a Bioconductor package for the efficient preprocessing of GC-MS metabolite profiling data

    Directory of Open Access Journals (Sweden)

    Lisec Jan

    2009-12-01

    Full Text Available Abstract Background Metabolite profiling, the simultaneous quantification of multiple metabolites in an experiment, is becoming increasingly popular, particularly with the rise of systems-level biology. The workhorse in this field is gas-chromatography hyphenated with mass spectrometry (GC-MS. The high-throughput of this technology coupled with a demand for large experiments has led to data pre-processing, i.e. the quantification of metabolites across samples, becoming a major bottleneck. Existing software has several limitations, including restricted maximum sample size, systematic errors and low flexibility. However, the biggest limitation is that the resulting data usually require extensive hand-curation, which is subjective and can typically take several days to weeks. Results We introduce the TargetSearch package, an open source tool which is a flexible and accurate method for pre-processing even very large numbers of GC-MS samples within hours. We developed a novel strategy to iteratively correct and update retention time indices for searching and identifying metabolites. The package is written in the R programming language with computationally intensive functions written in C for speed and performance. The package includes a graphical user interface to allow easy use by those unfamiliar with R. Conclusions TargetSearch allows fast and accurate data pre-processing for GC-MS experiments and overcomes the sample number limitations and manual curation requirements of existing software. We validate our method by carrying out an analysis against both a set of known chemical standard mixtures and of a biological experiment. In addition we demonstrate its capabilities and speed by comparing it with other GC-MS pre-processing tools. We believe this package will greatly ease current bottlenecks and facilitate the analysis of metabolic profiling data.

  13. Metabolite Profiling of Maize Grain: Differentiation due to Genetics, Environment and Input System

    OpenAIRE

    Röhlig, Richard M.

    2011-01-01

    A metabolite profiling approach for maize (Zea mays) based on gas chromatography/mass spectrometry was applied to the simultaneous detection, identification and quantification of a broad spectrum of non-polar (fatty acid methyl esters, free fatty acids, fatty alcohols, sterols, hydrocarbons) and polar (sugars, sugar alcohols, organic and inorganic acids, amino acids, amines) constituents. The non-targeted method allowed the investigation of the influence of genetics (cultivar, genetic modific...

  14. 1H NMR- based metabolite profiling of tropane alkaloids in Duboisia spec.

    OpenAIRE

    Ullrich, Sophie Friederike; Rothauer, Andreas; Kayser, Oliver

    2016-01-01

    Duboisia R.Br. (Solanaceae) is the main source of the tropane alkaloid scopolamine, which is an important precursor of various active pharmaceutical ingredients due to its anticholinergic properties. As only little is known about the metabolite composition among the different species, NMRbased metabolic profiling was done in order to elucidate primary and secondary metabolism in Duboisia especially focusing on the tropane alkaloid pathway. For this purpose, plants of five different genotypes ...

  15. Quantitative Comparison and Metabolite Profiling of Saponins in Different Parts of the Root of Panax notoginseng

    OpenAIRE

    Wang, Jing-Rong; Yau, Lee-Fong; Gao, Wei-Na; Liu, Yong; Yick, Pui-Wing; Liu, Liang; Jiang, Zhi-Hong

    2014-01-01

    Although both rhizome and root of Panax notoginseng are officially utilized as notoginseng in ?Chinese Pharmacopoeia?, individual parts of the root were differently used in practice. To provide chemical evidence for the differentiated usage, quantitative comparison and metabolite profiling of different portions derived from the whole root, as well as commercial samples, were carried out, showing an overall higher content of saponins in rhizome, followed by main root, branch root, and fibrous ...

  16. Water and salinity stress in grapevines: early and late changes in transcript and metabolite profiles.

    Science.gov (United States)

    Cramer, Grant R; Ergül, Ali; Grimplet, Jerome; Tillett, Richard L; Tattersall, Elizabeth A R; Bohlman, Marlene C; Vincent, Delphine; Sonderegger, Justin; Evans, Jason; Osborne, Craig; Quilici, David; Schlauch, Karen A; Schooley, David A; Cushman, John C

    2007-04-01

    Grapes are grown in semiarid environments, where drought and salinity are common problems. Microarray transcript profiling, quantitative reverse transcription-PCR, and metabolite profiling were used to define genes and metabolic pathways in Vitis vinifera cv. Cabernet Sauvignon with shared and divergent responses to a gradually applied and long-term (16 days) water-deficit stress and equivalent salinity stress. In this first-of-a-kind study, distinct differences between water deficit and salinity were revealed. Water deficit caused more rapid and greater inhibition of shoot growth than did salinity at equivalent stem water potentials. One of the earliest responses to water deficit was an increase in the transcript abundance of RuBisCo activase (day 4), but this increase occurred much later in salt-stressed plants (day 12). As water deficit progressed, a greater number of affected transcripts were involved in metabolism, transport, and the biogenesis of cellular components than did salinity. Salinity affected a higher percentage of transcripts involved in transcription, protein synthesis, and protein fate than did water deficit. Metabolite profiling revealed that there were higher concentrations of glucose, malate, and proline in water-deficit-treated plants as compared to salinized plants. The metabolite differences were linked to differences in transcript abundance of many genes involved in energy metabolism and nitrogen assimilation, particularly photosynthesis, gluconeogenesis, and photorespiration. Water-deficit-treated plants appear to have a higher demand than salinized plants to adjust osmotically, detoxify free radicals (reactive oxygen species), and cope with photoinhibition.

  17. 1H NMR-based metabolite profiling of plasma in a rat model of chronic kidney disease.

    Directory of Open Access Journals (Sweden)

    Ju-Ae Kim

    Full Text Available Chronic kidney disease (CKD is characterized by the gradual loss of the kidney function to excrete wastes and fluids from the blood. (1H NMR-based metabolomics was exploited to investigate the altered metabolic pattern in rats with CKD induced by surgical reduction of the renal mass (i.e., 5/6 nephrectomy (5/6 Nx, particularly for identifying specific metabolic biomarkers associated with early of CKD. Plasma metabolite profiling was performed in CKD rats (at 4- or 8-weeks after 5/6 Nx compared to sham-operated rats. Principle components analysis (PCA, partial least squares-discriminant analysis (PLS-DA and orthogonal partial least squares-discriminant analysis (OPLS-DA score plots showed a significant separation between the groups. The resulting metabolic profiles demonstrated significantly increased plasma levels of organic anions, including citrate, β-hydroxybutyrate, lactate, acetate, acetoacetate, and formate in CKD. Moreover, levels of alanine, glutamine, and glutamate were significantly higher. These changes were likely to be associated with complicated metabolic acidosis in CKD for counteracting systemic metabolic acidosis or increased protein catabolism from muscle. In contrast, levels of VLDL/LDL (CH2n and N-acetylglycoproteins were decreased. Taken together, the observed changes of plasma metabolite profiles in CKD rats provide insights into the disturbed metabolism in early phase of CKD, in particular for the altered metabolism of acid-base and/or amino acids.

  18. Metabolite profiling of sheath blight disease resistance in rice: in the case of positive ion mode analysis by CE/TOF-MS

    Directory of Open Access Journals (Sweden)

    Woro Sri Suharti

    2016-04-01

    Full Text Available Rice sheath blight is an important disease caused by Rhizoctonia solani. The resistant and susceptible rice lines (32R and 29S, respectively showed different responses to R. solani infection in metabolite levels. The aim of this study was to characterize the metabolite levels in rice lines during R. solani infection using capillary electrophoresis equipped with time of flight mass spectrophotometry (CE/TOF-MS in positive ion mode. Hundred metabolites were identified and classified into six clusters by hierarchical cluster using Mass Profiler Professional software. Changes in metabolite level at inoculated 32R and 29S were mapped on branches of tricarboxylic acid and glycolysis pathway. Volcano plot successfully filtered the metabolites based on fold change and p-value. The volcano plot result showed that 10 metabolites were up and down regulated in inoculated 32R relative to 29S. One metabolite, chlorogenic acid, showed a positive response in 32R. Meanwhile, pipecolic acid showed as the highest magnitude of fold change and p-value significance level in 29S. In addition, eight amino acids; glutamate, γ-aminobutyric acid, glycine, histidine, phenylalanine, serine, tryptophan, and tyrosine showed increase in 29S after R. solani inoculation.

  19. GC-MS metabolic profiling of Cabernet Sauvignon and Merlot cultivars during grapevine berry development and network analysis reveals a stage- and cultivar-dependent connectivity of primary metabolites.

    Science.gov (United States)

    Cuadros-Inostroza, Alvaro; Ruíz-Lara, Simón; González, Enrique; Eckardt, Aenne; Willmitzer, Lothar; Peña-Cortés, Hugo

    Information about the total chemical composition of primary metabolites during grape berry development is scarce, as are comparative studies trying to understand to what extent metabolite modifications differ between cultivars during ripening. Thus, correlating the metabolic profiles with the changes occurring in berry development and ripening processes is essential to progress in their comprehension as well in the development of new approaches to improve fruit attributes. Here, the developmental metabolic profiling analysis across six stages from flowering to fully mature berries of two cultivars, Cabernet Sauvignon and Merlot, is reported at metabolite level. Based on a gas chromatography-mass spectrometry untargeted approach, 115 metabolites were identified and relative quantified in both cultivars. Sugars and amino acids levels show an opposite behaviour in both cultivars undergoing a highly coordinated shift of metabolite associated to primary metabolism during the stages involved in growth, development and ripening of berries. The changes are characteristic for each stage, the most pronounced ones occuring at fruit setting and pre-Veraison. They are associated to a reduction of the levels of metabolites present in the earlier corresponding stage, revealing a required catabolic activity of primary metabolites for grape berry developmental process. Network analysis revealed that the network connectivity of primary metabolites is stage- and cultivar-dependent, suggesting differences in metabolism regulation between both cultivars as the maturity process progresses. Furthermore, network analysis may represent an appropriate method to display the association between primary metabolites during berry developmental processes among different grapevine cultivars and for identifying potential biologically relevant metabolites.

  20. Alteration of the fecal microbiota and serum metabolite profiles in dogs with idiopathic inflammatory bowel disease

    Science.gov (United States)

    Minamoto, Yasushi; Otoni, Cristiane C; Steelman, Samantha M; Büyükleblebici, Olga; Steiner, Jörg M; Jergens, Albert E; Suchodolski, Jan S

    2015-01-01

    Idiopathic inflammatory bowel disease (IBD) is a common cause of chronic gastrointestinal (GI) disease in dogs. The combination of an underlying host genetic susceptibility, an intestinal dysbiosis, and dietary/environmental factors are suspected as main contributing factors in the pathogenesis of canine IBD. However, actual mechanisms of the host-microbe interactions remain elusive. The aim of this study was to compare the fecal microbiota and serum metabolite profiles between healthy dogs (n = 10) and dogs with IBD before and after 3 weeks of medical therapy (n = 12). Fecal microbiota and metabolite profiles were characterized by 454-pyrosequencing of 16 S rRNA genes and by an untargeted metabolomics approach, respectively. Significantly lower bacterial diversity and distinct microbial communities were observed in dogs with IBD compared to the healthy control dogs. While Gammaproteobacteria were overrepresented, Erysipelotrichia, Clostridia, and Bacteroidia were underrepresented in dogs with IBD. The functional gene content was predicted from the 16 S rRNA gene data using PICRUSt, and revealed overrepresented bacterial secretion system and transcription factors, and underrepresented amino acid metabolism in dogs with IBD. The serum metabolites 3-hydroxybutyrate, hexuronic acid, ribose, and gluconic acid lactone were significantly more abundant in dogs with IBD. Although a clinical improvement was observed after medical therapy in all dogs with IBD, this was not accompanied by significant changes in the fecal microbiota or in serum metabolite profiles. These results suggest the presence of oxidative stress and a functional alteration of the GI microbiota in dogs with IBD, which persisted even in the face of a clinical response to medical therapy. PMID:25531678

  1. Profile of urinary and fecal proanthocyanidin metabolites from common cinnamon (Cinnamomum zeylanicum L.) in rats.

    Science.gov (United States)

    Mateos-Martín, María Luisa; Pérez-Jiménez, Jara; Fuguet, Elisabet; Torres, Josep Lluís

    2012-04-01

    Cinnamon (Cinnamomum zeylanicum L.) bark is widely used as a spice and in traditional medicine. Its oligomeric and polymeric proanthocyanidins are believed to be partly responsible for the beneficial properties of the plant. We describe here the metabolic fate of cinnamon proanthocyanidins in the urine and feces of rats fed a suspension of the whole bark. The metabolites include ten mono-, di-, and tri- conjugated (epi)catechin phase II metabolites and more than 20 small phenolic acids from intestinal microbial fermentation. Some of these are sulfated conjugates. Feces contain intact (epi)catechin and dimers. This suggests that free radical scavenging species are in contact with the intestinal walls for hours after ingestion of cinnamon. The phenolic metabolite profile of cinnamon bark in urine is consistent with a mixture of proanthocyanidins that are depolymerized into their constitutive (epi)catechin units as well as cleaved into smaller phenolic acids during their transit along the intestinal tract, with subsequent absorption and conjugation into bioavailable metabolites. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Metabolite profiling of leek (Allium porrum L) cultivars by (1) H NMR and HPLC-MS.

    Science.gov (United States)

    Soininen, Tuula H; Jukarainen, Niko; Soininen, Pasi; Auriola, Seppo O K; Julkunen-Tiitto, Riitta; Oleszek, Wieslaw; Stochmal, Anna; Karjalainen, Reijo O; Vepsäläinen, Jouko J

    2014-01-01

    Leek (Allium ampeloprasum var. porrum) is consumed as a vegetable throughout the world. However, little is known about the metabolites of leek cultivars, especially those with potentially important beneficial properties for human health. We provide new information for the overall metabolite composition of several leek cultivars grown in Europe by using HPLC-MS and (1) H NMR. The use of a novel CTLS/NMR (constrained total-line-shape nuclear magnetic resonance) approach was found to be capable of reliable quantification, even with overlapping metabolite signals in the (1) H NMR of plant metabolites. Additionally, a new application for leek flavonoids was optimised for HPLC-MS. The total concentration of carbohydrates (glucose, fructose, kestose/nystose and sucrose) and nine amino acids varied by fourfold in leek juice from different cultivars, while the total concentrations of four organic acids were similar in all cultivars. All the quantified flavonols were kaempferol derivatives or quercetin derivatives and threefold differences in flavonol concentrations were detected between cultivars. In this study, various phytochemical profiles were determined for several leek cultivars by (1) H NMR spectroscopy with CTLS combined with HPLC-MS. The wide variation in bioactive compounds among commercial leek cultivars offers promising opportunities for breeders to raise the levels of important biochemical compounds in leek breeding lines, and also provides some objective measure for quality assurance for the leek industry. Copyright © 2014 John Wiley & Sons, Ltd.

  3. Dynamic Metabolite Profiling in an Archaeon Connects Transcriptional Regulation to Metabolic Consequences.

    Directory of Open Access Journals (Sweden)

    Horia Todor

    Full Text Available Previous work demonstrated that the TrmB transcription factor is responsible for regulating the expression of many enzyme-coding genes in the hypersaline-adapted archaeon Halobacterium salinarum via a direct interaction with a cis-regulatory sequence in their promoters. This interaction is abolished in the presence of glucose. Although much is known about the effects of TrmB at the transcriptional level, it remains unclear whether and to what extent changes in mRNA levels directly affect metabolite levels. In order to address this question, here we performed a high-resolution metabolite profiling time course during a change in nutrients using a combination of targeted and untargeted methods in wild-type and ΔtrmB strain backgrounds. We found that TrmB-mediated transcriptional changes resulted in widespread and significant changes to metabolite levels across the metabolic network. Additionally, the pattern of growth complementation using various purines suggests that the mis-regulation of gluconeogenesis in the ΔtrmB mutant strain in the absence of glucose results in low phosphoribosylpyrophosphate (PRPP levels. We confirmed these low PRPP levels using a quantitative mass spectrometric technique and found that they are associated with a metabolic block in de novo purine synthesis, which is partially responsible for the growth defect of the ΔtrmB mutant strain in the absence of glucose. In conclusion, we show how transcriptional regulation of metabolism affects metabolite levels and ultimately, phenotypes.

  4. Integrating milk metabolite profile information for the prediction of traditional milk traits based on SNP information for Holstein cows.

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    Nina Melzer

    Full Text Available In this study the benefit of metabolome level analysis for the prediction of genetic value of three traditional milk traits was investigated. Our proposed approach consists of three steps: First, milk metabolite profiles are used to predict three traditional milk traits of 1,305 Holstein cows. Two regression methods, both enabling variable selection, are applied to identify important milk metabolites in this step. Second, the prediction of these important milk metabolite from single nucleotide polymorphisms (SNPs enables the detection of SNPs with significant genetic effects. Finally, these SNPs are used to predict milk traits. The observed precision of predicted genetic values was compared to the results observed for the classical genotype-phenotype prediction using all SNPs or a reduced SNP subset (reduced classical approach. To enable a comparison between SNP subsets, a special invariable evaluation design was implemented. SNPs close to or within known quantitative trait loci (QTL were determined. This enabled us to determine if detected important SNP subsets were enriched in these regions. The results show that our approach can lead to genetic value prediction, but requires less than 1% of the total amount of (40,317 SNPs., significantly more important SNPs in known QTL regions were detected using our approach compared to the reduced classical approach. Concluding, our approach allows a deeper insight into the associations between the different levels of the genotype-phenotype map (genotype-metabolome, metabolome-phenotype, genotype-phenotype.

  5. Metabolite profiling of obese individuals before and after a one year weight loss program

    DEFF Research Database (Denmark)

    Geidenstam, N; Al-Majdoub, M; Ekman, M

    2017-01-01

    OBJECTIVE: We and others have previously characterized changes in circulating metabolite levels following diet-induced weight loss. Our aim was to investigate whether baseline metabolite levels and weight-loss-induced changes in these are predictive of or associated with changes in body mass index...... (BMI) and metabolic risk traits. METHODS: Serum metabolites were analyzed with gas and liquid chromatography/mass spectrometry in 91 obese individuals at baseline and after participating in a 1 year non-surgical weight loss program.ResultsA total of 137 metabolites were identified and semi......-quantified at baseline (BMI 42.7±5.8, mean±s.d.) and at follow-up (BMI 36.3±6.6). Weight-loss-induced modification was observed for levels of 57 metabolites in individuals with ⩾10% weight loss. Lower baseline levels of xylitol was predictive of a greater decrease in BMI (β=0.06, Pweight loss (odds ratio...

  6. Taxonomic Characterization and Secondary Metabolite Profiling of Aspergillus Section Aspergillus Contaminating Feeds and Feedstuffs

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    Mariana Greco

    2015-09-01

    Full Text Available Xerophilic fungal species of the genus Aspergillus are economically highly relevant due to their ability to grow on low water activity substrates causing spoilage of stored goods and animal feeds. These fungi can synthesize a variety of secondary metabolites, many of which show animal toxicity, creating a health risk for food production animals and to humans as final consumers, respectively. Animal feeds used for rabbit, chinchilla and rainbow trout production in Argentina were analysed for the presence of xerophilic Aspergillus section Aspergillus species. High isolation frequencies (>60% were detected in all the studied rabbit and chinchilla feeds, while the rainbow trout feeds showed lower fungal charge (25%. These section Aspergillus contaminations comprised predominantly five taxa. Twenty isolates were subjected to taxonomic characterization using both ascospore SEM micromorphology and two independent DNA loci sequencing. The secondary metabolite profiles of the isolates were determined qualitatively by HPLC-MS. All the isolates produced neoechinulin A, 17 isolates were positive for cladosporin and echinulin, and 18 were positive for neoechinulin B. Physcion and preechinulin were detected in a minor proportion of the isolates. This is the first report describing the detailed species composition and the secondary metabolite profiles of Aspergillus section Aspergillus contaminating animal feeds.

  7. Urinary Metabolite Profiles in Premature Infants Show Early Postnatal Metabolic Adaptation and Maturation

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    Sissel J. Moltu

    2014-05-01

    Full Text Available Objectives: Early nutrition influences metabolic programming and long-term health. We explored the urinary metabolite profiles of 48 premature infants (birth weight < 1500 g randomized to an enhanced or a standard diet during neonatal hospitalization. Methods: Metabolomics using nuclear magnetic resonance spectroscopy (NMR was conducted on urine samples obtained during the first week of life and thereafter fortnightly. Results: The intervention group received significantly higher amounts of energy, protein, lipids, vitamin A, arachidonic acid and docosahexaenoic acid as compared to the control group. Enhanced nutrition did not appear to affect the urine profiles to an extent exceeding individual variation. However, in all infants the glucogenic amino acids glycine, threonine, hydroxyproline and tyrosine increased substantially during the early postnatal period, along with metabolites of the tricarboxylic acid cycle (succinate, oxoglutarate, fumarate and citrate. The metabolite changes correlated with postmenstrual age. Moreover, we observed elevated threonine and glycine levels in first-week urine samples of the small for gestational age (SGA; birth weight < 10th percentile for gestational age as compared to the appropriate for gestational age infants. Conclusion: This first nutri-metabolomics study in premature infants demonstrates that the physiological adaptation during the fetal-postnatal transition as well as maturation influences metabolism during the breastfeeding period. Elevated glycine and threonine levels were found in the first week urine samples of the SGA infants and emerged as potential biomarkers of an altered metabolic phenotype.

  8. Plant secondary metabolite profiling evidences strain-dependent effect in the Azospirillum-Oryza sativa association.

    Science.gov (United States)

    Chamam, Amel; Sanguin, Hervé; Bellvert, Floriant; Meiffren, Guillaume; Comte, Gilles; Wisniewski-Dyé, Florence; Bertrand, Cédric; Prigent-Combaret, Claire

    2013-03-01

    Azospirillum is a plant growth-promoting rhizobacterium (PGPR) able to enhance growth and yield of cereals such as rice, maize and wheat. The growth-promoting ability of some Azospirillum strains appears to be highly specific to certain plant species and cultivars. In order to ascertain the specificity of the associative symbiosis between rice and Azospirillum, the physiological response of two rice cultivars, Nipponbare and Cigalon, inoculated with two rice-associated Azospirillum was analyzed at two levels: plant growth response and plant secondary metabolic response. Each strain of Azospirillum (Azospirillum lipoferum 4B isolated from Cigalon and Azospirillum sp. B510 isolated from Nipponbare) preferentially increased growth of the cultivar from which it was isolated. This specific effect is not related to a defect in colonization of host cultivar as each strain colonizes effectively both rice cultivars, either at the rhizoplane (for 4B and B510) and inside the roots (for B510). The metabolic profiling approach showed that, in response to PGPR inoculation, profiles of rice secondary metabolites were modified, with phenolic compounds such as flavonoids and hydroxycinnamic derivatives being the main metabolites affected. Moreover, plant metabolic changes differed according to Azospirillum strain×cultivar combinations; indeed, 4B induced major secondary metabolic profile modifications only on Cigalon roots, while B510, probably due to its endophytic feature, induced metabolic variations on shoots and roots of both cultivars, triggering a systemic response. Plant secondary metabolite profiling thereby evidences the specific interaction between an Azospirillum strain and its original host cultivar. Copyright © 2012 Elsevier Ltd. All rights reserved.

  9. Effect of metformin on plasma metabolite profile in the Copenhagen Insulin and Metformin Therapy (CIMT) trial

    DEFF Research Database (Denmark)

    Safai, N; Suvitaival, T; A, Ali

    2018-01-01

    treatment. Metabolites were measured by liquid chromatography-mass spectrometry at baseline and at 18-month follow-up and the data were analysed using a linear mixed-effect model. RESULTS: At baseline, participants who were on metformin before the trial (n = 312) had higher levels of leucine......AIM: Metformin is the first-line treatment for Type 2 diabetes. However, not all people benefit from this drug. Our aim was to investigate the effects of metformin on the plasma metabolome and whether the pretreatment metabolite profile can predict HbA1c outcome. METHODS: Post hoc analysis...... with placebo (n = 182). At baseline, participants on metformin treatment with the highest levels of carnitine C10:1 and leucine/isoleucine had the lowest HbA1c (P-interaction = 0.02 and 0.03, respectively). This association was not significant with HbA1c at follow-up. CONCLUSIONS: Metformin treatment...

  10. Factors influencing annual fecal testosterone metabolite profiles in captive male polar bears (Ursus maritimus).

    Science.gov (United States)

    Curry, E; Roth, T L; MacKinnon, K M; Stoops, M A

    2012-12-01

    The objectives of this study were to assess the effects of season, breeding activity, age and latitude on fecal testosterone metabolite concentrations in captive, adult male polar bears (Ursus maritimus). Fourteen polar bears from 13 North American zoos were monitored for 12-36 months, producing 25-year-long testosterone profiles. Results indicated that testosterone was significantly higher during the breeding season (early January through the end of May) compared with the non-breeding season with the highest concentrations excreted from early January through late March. Variations in excretion patterns were observed among individuals and also between years within an individual, with testosterone peaks closely associated with breeding activity. Results indicate that fecal testosterone concentrations are influenced by season, breeding activity and age, but not by latitude. This is the first report describing longitudinal fecal testosterone metabolite concentrations in individual adult male polar bears. © 2012 Blackwell Verlag GmbH.

  11. Different Polar Metabolites and Protein Profiles between High- and Low-Quality Japanese Ginjo Sake.

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    Kei Takahashi

    Full Text Available Japanese ginjo sake is a premium refined sake characterized by a pleasant fruity apple-like flavor and a sophisticated taste. Because of technical difficulties inherent in brewing ginjo sake, off-flavors sometimes occur. However, the metabolites responsible for off-flavors as well as those present or absent in higher quality ginjo sake remain uncertain. Here, the relationship between 202 polar chemical compounds in sake identified using capillary electrophoresis coupled with time-of-flight mass spectrometry and its organoleptic properties, such as quality and off-flavor, was examined. First, we found that some off-flavored sakes contained higher total amounts of metabolites than other sake samples. The results also identified that levels of 2-oxoglutaric acid and fumaric acid, metabolites in the tricarboxylic acid cycle, were highly but oppositely correlated with ginjo sake quality. Similarly, pyridoxine and pyridoxamine, co-enzymes for amino transferase, were also highly but oppositely correlated with ginjo sake quality. Additionally, pyruvic acid levels were associated with good quality as well. Compounds involved in the methionine salvage cycle, oxidative glutathione derivatives, and amino acid catabolites were correlated with low quality. Among off-flavors, an inharmonious bitter taste appeared attributable to polyamines. Furthermore, protein analysis displayed that a diversity of protein components and yeast protein (triosephosphate isomerase, TPI leakage was linked to the overall metabolite intensity in ginjo sake. This research provides insight into the relationship between sake components and organoleptic properties.

  12. Exploring the Impacts of Postharvest Processing on the Microbiota and Metabolite Profiles during Green Coffee Bean Production.

    Science.gov (United States)

    De Bruyn, Florac; Zhang, Sophia Jiyuan; Pothakos, Vasileios; Torres, Julio; Lambot, Charles; Moroni, Alice V; Callanan, Michael; Sybesma, Wilbert; Weckx, Stefan; De Vuyst, Luc

    2017-01-01

    The postharvest treatment and processing of fresh coffee cherries can impact the quality of the unroasted green coffee beans. In the present case study, freshly harvested Arabica coffee cherries were processed through two different wet and dry methods to monitor differences in the microbial community structure and in substrate and metabolite profiles. The changes were followed throughout the postharvest processing chain, from harvest to drying, by implementing up-to-date techniques, encompassing multiple-step metagenomic DNA extraction, high-throughput sequencing, and multiphasic metabolite target analysis. During wet processing, a cohort of lactic acid bacteria (i.e., Leuconostoc, Lactococcus, and Lactobacillus) was the most commonly identified microbial group, along with enterobacteria and yeasts (Pichia and Starmerella). Several of the metabolites associated with lactic acid bacterial metabolism (e.g., lactic acid, acetic acid, and mannitol) produced in the mucilage were also found in the endosperm. During dry processing, acetic acid bacteria (i.e., Acetobacter and Gluconobacter) were most abundant, along with Pichia and non-Pichia (Candida, Starmerella, and Saccharomycopsis) yeasts. Accumulation of associated metabolites (e.g., gluconic acid and sugar alcohols) took place in the drying outer layers of the coffee cherries. Consequently, both wet and dry processing methods significantly influenced the microbial community structures and hence the composition of the final green coffee beans. This systematic approach to dissecting the coffee ecosystem contributes to a deeper understanding of coffee processing and might constitute a state-of-the-art framework for the further analysis and subsequent control of this complex biotechnological process. Coffee production is a long process, starting with the harvest of coffee cherries and the on-farm drying of their beans. In a later stage, the dried green coffee beans are roasted and ground in order to brew a cup of coffee

  13. The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services

    Directory of Open Access Journals (Sweden)

    Hanspers Kristina

    2010-01-01

    Full Text Available Abstract Background Many complementary solutions are available for the identifier mapping problem. This creates an opportunity for bioinformatics tool developers. Tools can be made to flexibly support multiple mapping services or mapping services could be combined to get broader coverage. This approach requires an interface layer between tools and mapping services. Results Here we present BridgeDb, a software framework for gene, protein and metabolite identifier mapping. This framework provides a standardized interface layer through which bioinformatics tools can be connected to different identifier mapping services. This approach makes it easier for tool developers to support identifier mapping. Mapping services can be combined or merged to support multi-omics experiments or to integrate custom microarray annotations. BridgeDb provides its own ready-to-go mapping services, both in webservice and local database forms. However, the framework is intended for customization and adaptation to any identifier mapping service. BridgeDb has already been integrated into several bioinformatics applications. Conclusion By uncoupling bioinformatics tools from mapping services, BridgeDb improves capability and flexibility of those tools. All described software is open source and available at http://www.bridgedb.org.

  14. Analysis of Phenolic and Cyclic Compounds in Plants Using Derivatization Techniques in Combination with GC-MS-Based Metabolite Profiling

    Directory of Open Access Journals (Sweden)

    Jens Rohloff

    2015-02-01

    Full Text Available Metabolite profiling has been established as a modern technology platform for the description of complex chemical matrices and compound identification in biological samples. Gas chromatography coupled with mass spectrometry (GC-MS in particular is a fast and accurate method widely applied in diagnostics, functional genomics and for screening purposes. Following solvent extraction and derivatization, hundreds of metabolites from different chemical groups can be characterized in one analytical run. Besides sugars, acids, and polyols, diverse phenolic and other cyclic metabolites can be efficiently detected by metabolite profiling. The review describes own results from plant research to exemplify the applicability of GC-MS profiling and concurrent detection and identification of phenolics and other cyclic structures.

  15. Effect of Acinetobacter sp on metalaxyl degradation and metabolite profile of potato seedlings (Solanum tuberosum L.) alpha variety.

    Science.gov (United States)

    Zuno-Floriano, Fabiola G; Miller, Marion G; Aldana-Madrid, Maria L; Hengel, Matt J; Gaikwad, Nilesh W; Tolstikov, Vladimir; Contreras-Cortés, Ana G

    2012-01-01

    One of the most serious diseases in potato cultivars is caused by the pathogen Phytophthora infestans, which affects leaves, stems and tubers. Metalaxyl is a fungicide that protects potato plants from Phytophthora infestans. In Mexico, farmers apply metalaxyl 35 times during the cycle of potato production and the last application is typically 15 days before harvest. There are no records related to the presence of metalaxyl in potato tubers in Mexico. In the present study, we evaluated the effect of Acinetobacter sp on metalaxyl degradation in potato seedlings. The effect of bacteria and metalaxyl on the growth of potato seedlings was also evaluated. A metabolite profile analysis was conducted to determine potential molecular biomarkers produced by potato seedlings in the presence of Acinetobacter sp and metalaxyl. Metalaxyl did not affect the growth of potato seedlings. However, Acinetobacter sp strongly affected the growth of inoculated seedlings, as confirmed by plant length and plant fresh weights which were lower in inoculated potato seedlings (40% and 27%, respectively) compared to the controls. Acinetobacter sp also affected root formation. Inoculated potato seedlings showed a decrease in root formation compared to the controls. LC-MS/MS analysis of metalaxyl residues in potato seedlings suggests that Acinetobacter sp did not degrade metalaxyl. GC-TOF-MS platform was used in metabolic profiling studies. Statistical data analysis and metabolic pathway analysis allowed suggesting the alteration of metabolic pathways by both Acinetobacter sp infection and metalaxyl treatment. Several hundred metabolites were detected, 137 metabolites were identified and 15 metabolic markers were suggested based on statistical change significance found with PLS-DA analysis. These results are important for better understanding the interactions of putative endophytic bacteria and pesticides on plants and their possible effects on plant metabolism.

  16. Effect of Acinetobacter sp on metalaxyl degradation and metabolite profile of potato seedlings (Solanum tuberosum L. alpha variety.

    Directory of Open Access Journals (Sweden)

    Fabiola G Zuno-Floriano

    Full Text Available One of the most serious diseases in potato cultivars is caused by the pathogen Phytophthora infestans, which affects leaves, stems and tubers. Metalaxyl is a fungicide that protects potato plants from Phytophthora infestans. In Mexico, farmers apply metalaxyl 35 times during the cycle of potato production and the last application is typically 15 days before harvest. There are no records related to the presence of metalaxyl in potato tubers in Mexico. In the present study, we evaluated the effect of Acinetobacter sp on metalaxyl degradation in potato seedlings. The effect of bacteria and metalaxyl on the growth of potato seedlings was also evaluated. A metabolite profile analysis was conducted to determine potential molecular biomarkers produced by potato seedlings in the presence of Acinetobacter sp and metalaxyl. Metalaxyl did not affect the growth of potato seedlings. However, Acinetobacter sp strongly affected the growth of inoculated seedlings, as confirmed by plant length and plant fresh weights which were lower in inoculated potato seedlings (40% and 27%, respectively compared to the controls. Acinetobacter sp also affected root formation. Inoculated potato seedlings showed a decrease in root formation compared to the controls. LC-MS/MS analysis of metalaxyl residues in potato seedlings suggests that Acinetobacter sp did not degrade metalaxyl. GC-TOF-MS platform was used in metabolic profiling studies. Statistical data analysis and metabolic pathway analysis allowed suggesting the alteration of metabolic pathways by both Acinetobacter sp infection and metalaxyl treatment. Several hundred metabolites were detected, 137 metabolites were identified and 15 metabolic markers were suggested based on statistical change significance found with PLS-DA analysis. These results are important for better understanding the interactions of putative endophytic bacteria and pesticides on plants and their possible effects on plant metabolism.

  17. Microdialysis Sampling from Wound Fluids Enables Quantitative Assessment of Cytokines, Proteins, and Metabolites Reveals Bone Defect-Specific Molecular Profiles.

    Science.gov (United States)

    Förster, Yvonne; Schmidt, Johannes R; Wissenbach, Dirk K; Pfeiffer, Susanne E M; Baumann, Sven; Hofbauer, Lorenz C; von Bergen, Martin; Kalkhof, Stefan; Rammelt, Stefan

    2016-01-01

    Bone healing involves a variety of different cell types and biological processes. Although certain key molecules have been identified, the molecular interactions of the healing progress are not completely understood. Moreover, a clinical routine for predicting the quality of bone healing after a fracture in an early phase is missing. This is mainly due to a lack of techniques to comprehensively screen for cytokines, growth factors and metabolites at their local site of action. Since all soluble molecules of interest are present in the fracture hematoma, its in-depth assessment could reveal potential markers for the monitoring of bone healing. Here, we describe an approach for sampling and quantification of cytokines and metabolites by using microdialysis, combined with solid phase extractions of proteins from wound fluids. By using a control group with an isolated soft tissue wound, we could reveal several bone defect-specific molecular features. In bone defect dialysates the neutrophil chemoattractants CXCL1, CXCL2 and CXCL3 were quantified with either a higher or earlier response compared to dialysate from soft tissue wound. Moreover, by analyzing downstream adaptions of the cells on protein level and focusing on early immune response, several proteins involved in the immune cell migration and activity could be identified to be specific for the bone defect group, e.g. immune modulators, proteases and their corresponding inhibitors. Additionally, the metabolite screening revealed different profiles between the bone defect group and the control group. In summary, we identified potential biomarkers to indicate imbalanced healing progress on all levels of analysis.

  18. Family and academic performance: identifying high school student profiles

    Directory of Open Access Journals (Sweden)

    Alicia Aleli Chaparro Caso López

    2016-01-01

    Full Text Available The objective of this study was to identify profiles of high school students, based on variables related to academic performance, socioeconomic status, cultural capital and family organization. A total of 21,724 high school students, from the five municipalities of the state of Baja California, took part. A K-means cluster analysis was performed to identify the profiles. The analyses identified two clearly-defined clusters: Cluster 1 grouped together students with high academic performance and who achieved higher scores for socioeconomic status, cultural capital and family involvement, whereas Cluster 2 brought together students with low academic achievement, and who also obtained lower scores for socioeconomic status and cultural capital, and had less family involvement. It is concluded that the family variables analyzed form student profiles that can be related to academic achievement.

  19. Urinary metabolite profiling of flavonoids in Chinese volunteers after consumption of orange juice by UFLC-Q-TOF-MS/MS.

    Science.gov (United States)

    Zeng, Xuan; Su, Weiwei; Bai, Yang; Chen, Taobin; Yan, Zenghao; Wang, Jiawei; Su, Minmin; Zheng, Yuying; Peng, Wei; Yao, Hongliang

    2017-09-01

    The metabolism of flavonoids derived from orange juice in Chinese volunteers has not been well investigated. With the ultra-fast liquid chromatography-quadrupole-time-of-flight tandem mass spectrometry (UFLC-Q-TOF-MS/MS) system, orange juice-derived flavonoids, as well as metabolites contained in urine collected from healthy Chinese volunteers after consumption of 250mL orange juice, were systematically identified and quantified. Finally, a total of 9 flavonoids and 30 metabolites were detected. Obtained results revealed that flavonoids derived from orange juice underwent extensive phase II metabolism in human, mainly comprising glucuronidation and sulfation. The overall recovery of the primary flavonoid aglycones, i.e., naringenin and hesperetin, were both approximately equivalent 22% of intake, primarily occurred in 4-12h post consumption. Meanwhile, additional 35 phenolic catabolites were identified in urine collected post consumption. However, it is difficult to determine the exact amounts of phenolic catabolites derived from specific flavonoid due to the interference of diets and other flavonoids. This work would be valuable for the clarification of metabolic profiles for flavonoids in Chinese population. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. Metabolite Profiling of Wheat Seedlings Induced by Chitosan: Revelation of the Enhanced Carbon and Nitrogen Metabolism

    Directory of Open Access Journals (Sweden)

    Xiaoqian Zhang

    2017-11-01

    Full Text Available Chitosan plays an important role in regulating growth and eliciting defense in many plant species. However, the exact metabolic response of plants to chitosan is still not clear. The present study performed an integrative analysis of metabolite profiles in chitosan-treated wheat seedlings and further investigated the response of enzyme activities and transcript expression related to the primary carbon (C and nitrogen (N metabolism. Metabolite profiling revealed that chitosan could induce significant difference of organic acids, sugars and amino acids in leaves of wheat seedlings. A higher accumulation of sucrose content was observed after chitosan treatment, accompanied by an increase in sucrose phosphate synthase (SPS and fructose 1, 6-2 phosphatase (FBPase activities as well as an up-regulation of relative expression level. Several metabolites associated with tricarboxylic acid (TCA cycle, including oxaloacetate and malate, were also improved along with an elevation of phosphoenolpyruvate carboxylase (PEPC and pyruvate dehydrogenase (PDH activities. On the other hand, chitosan could also enhance the N reduction and N assimilation. Glutamate, aspartate and some other amino acids were higher in chitosan-treated plants, accompanied by the activation of key enzymes of N reduction and glutamine synthetase/glutamate synthase (GS/GOGAT cycle. Together, these results suggested a pleiotropic modulation of carbon and nitrogen metabolism in wheat seedlings induced by chitosan and provided a significant insight into the metabolic mechanism of plants in response to chitosan for the first time, and it would give a basic guidance for the future application of chitosan in agriculture.

  1. Gut flora profiling and fecal metabolite composition of colorectal cancer patients and healthy individuals.

    Science.gov (United States)

    Wang, Xiaoxue; Wang, Jianping; Rao, Benqiang; Deng, Li

    2017-06-01

    Colorectal cancer is one of the most common types of cancer in the world and its morbidity and mortality rates are increasing due to alterations to human lifestyle and dietary habits. The relationship between human gut flora and colorectal cancer has attracted increasing attention. In the present study, a metabolic fingerprinting technique that combined pyrosequencing with gas chromatography-mass spectrometry was utilized to compare the differences in gut flora profiling and fecal metabolites between healthy individuals and patients with colorectal cancer. The results demonstrated that there were no significant differences in the abundance and diversity of gut flora between healthy individuals and patients with colorectal cancer (P>0.05) and the dominant bacterial phyla present in the gut of both groups included Firmicutes , Bacteroidetes and Verrucomicrobia . At the bacterial strain/genus level, significant differences were observed in the relative abundance of 18 species of bacteria (Pflora profiling and metabolite composition. These findings suggest that gut flora disorder results in the alteration of bacterial metabolism, which may be associated with the pathogenesis of colorectal cancer. The results of the present study are useful as a foundation for further studies to elucidate a potential colorectal cancer diagnostic index and therapeutic targets.

  2. Spatial Mapping and Profiling of Metabolite Distributions during Germination1[OPEN

    Science.gov (United States)

    Feenstra, Adam D.; Song, Zhihong; Korte, Andrew R.

    2017-01-01

    Germination is a highly complex process by which seeds begin to develop and establish themselves as viable organisms. In this study, we utilize a combination of gas chromatography-mass spectrometry, liquid chromatography-fluorescence, and mass spectrometry imaging approaches to profile and visualize the metabolic distributions of germinating seeds from two different inbreds of maize (Zea mays) seeds, B73 and Mo17. Gas chromatography and liquid chromatography analyses demonstrate that the two inbreds are highly differentiated in their metabolite profiles throughout the course of germination, especially with regard to amino acids, sugar alcohols, and small organic acids. Crude dissection of the seed followed by gas chromatography-mass spectrometry analysis of polar metabolites also revealed that many compounds were highly sequestered among the various seed tissue types. To further localize compounds, matrix-assisted laser desorption/ionization mass spectrometry imaging was utilized to visualize compounds in fine detail in their native environments over the course of germination. Most notably, the fatty acyl chain-dependent differential localization of phospholipids and triacylglycerols was observed within the embryo and radicle, showing correlation with the heterogeneous distribution of fatty acids. Other interesting observations include unusual localization of ceramides on the endosperm/scutellum boundary and subcellular localization of ferulate in the aleurone. PMID:28634228

  3. Short communication: Practical issues in implementing volatile metabolite analysis for identifying mastitis pathogens

    NARCIS (Netherlands)

    Hettinga, K.A.; Bok, de F.A.M.; Lam, T.

    2015-01-01

    Several parameters for improving volatile metabolite analysis using headspace gas chromatography-mass spectrometry (GC-MS) analysis of volatile metabolites were evaluated in the framework of identification of mastitis-causing pathogens. Previous research showed that the results of such volatile

  4. Short communication : Practical issues in implementing volatile metabolite analysis for identifying mastitis pathogens

    NARCIS (Netherlands)

    Hettinga, Kasper A; de Bok, Frank A M; Lam, Theo J G M

    2015-01-01

    Several parameters for improving volatile metabolite analysis using headspace gas chromatography-mass spectrometry (GC-MS) analysis of volatile metabolites were evaluated in the framework of identification of mastitis-causing pathogens. Previous research showed that the results of such volatile

  5. An integrated structure- and system-based framework to identify new targets of metabolites and known drugs

    KAUST Repository

    Naveed, Hammad

    2015-08-18

    Motivation: The inherent promiscuity of small molecules towards protein targets impedes our understanding of healthy versus diseased metabolism. This promiscuity also poses a challenge for the pharmaceutical industry as identifying all protein targets is important to assess (side) effects and repositioning opportunities for a drug. Results: Here, we present a novel integrated structure- and system-based approach of drug-target prediction (iDTP) to enable the large-scale discovery of new targets for small molecules, such as pharmaceutical drugs, co-factors and metabolites (collectively called ‘drugs’). For a given drug, our method uses sequence order–independent structure alignment, hierarchical clustering, and probabilistic sequence similarity to construct a probabilistic pocket ensemble (PPE) that captures promiscuous structural features of different binding sites on known targets. A drug’s PPE is combined with an approximation of its delivery profile to reduce false positives. In our cross-validation study, we use iDTP to predict the known targets of eleven drugs, with 63% sensitivity and 81% specificity. We then predicted novel targets for these drugs—two that are of high pharmacological interest, the nuclear receptor PPARγ and the oncogene Bcl-2, were successfully validated through in vitro binding experiments. Our method is broadly applicable for the prediction of protein-small molecule interactions with several novel applications to biological research and drug development.

  6. Metabolite Profiling Reveals Developmental Inequalities in Pinot Noir Berry Tissues Late in Ripening.

    Science.gov (United States)

    Vondras, Amanda M; Commisso, Mauro; Guzzo, Flavia; Deluc, Laurent G

    2017-01-01

    Uneven ripening in Vitis vinifera is increasingly recognized as a phenomenon of interest, with substantial implications for fruit and wine composition and quality. This study sought to determine whether variation late in ripening (∼Modified Eichhorn-Lorenz stage 39) was associated with developmental differences that were observable as fruits within a cluster initiated ripening (véraison). Four developmentally distinct ripening classes of berries were tagged at cluster véraison, sampled at three times late in ripening, and subjected to untargeted HPLC-MS to measure variation in amino acids, sugars, organic acids, and phenolic metabolites in skin, pulp, and seed tissues separately. Variability was described using predominantly two strategies. In the first, multivariate analysis (Orthogonal Projections to Latent Structures-Discriminant Analysis, OPLS-DA) was used to determine whether fruits were still distinguishable per their developmental position at véraison and to identify which metabolites accounted for these distinctions. The same technique was used to assess changes in each tissue over time. In a second strategy and for each annotated metabolite, the variance across the ripening classes at each time point was measured to show whether intra-cluster variance (ICV) was growing, shrinking, or constant over the period observed. Indeed, berries could be segregated by OPLS-DA late in ripening based on their developmental position at véraison, though the four ripening classes were aggregated into two larger ripening groups. Further, not all tissues were dynamic over the period examined. Although pulp tissues could be segregated by time sampled, this was not true for seed and only moderately so for skin. Ripening group differences in seed and skin, rather than the time fruit was sampled, were better able to define berries. Metabolites also experienced significant reductions in ICV between single pairs of time points, but never across the entire experiment

  7. Influence of the RelA Activity on E. coli Metabolism by Metabolite Profiling of Glucose-Limited Chemostat Cultures

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    Sónia Carneiro

    2012-10-01

    Full Text Available Metabolite profiling of E. coli W3110 and the isogenic DrelA mutant cells was used to characterize the RelA-dependent stringent control of metabolism under different growth conditions. Metabolic profiles were obtained by gas chromatography–mass spectrometry (GC-MS analysis and revealed significant differences between E. coli strains grown at different conditions. Major differences between the two strains were assessed in the levels of amino acids and fatty acids and their precursor metabolites, especially when growing at the lower dilution rates, demonstrating differences in their metabolic behavior. Despite the fatty acid biosynthesis being the most affected due to the lack of the RelA activity, other metabolic pathways involving succinate, lactate and threonine were also affected. Overall, metabolite profiles indicate that under nutrient-limiting conditions the RelA-dependent stringent response may be elicited and promotes key changes in the E. coli metabolism.

  8. Protein Correlation Profiles Identify Lipid Droplet Proteins with High Confidence*

    Science.gov (United States)

    Krahmer, Natalie; Hilger, Maximiliane; Kory, Nora; Wilfling, Florian; Stoehr, Gabriele; Mann, Matthias; Farese, Robert V.; Walther, Tobias C.

    2013-01-01

    Lipid droplets (LDs) are important organelles in energy metabolism and lipid storage. Their cores are composed of neutral lipids that form a hydrophobic phase and are surrounded by a phospholipid monolayer that harbors specific proteins. Most well-established LD proteins perform important functions, particularly in cellular lipid metabolism. Morphological studies show LDs in close proximity to and interacting with membrane-bound cellular organelles, including the endoplasmic reticulum, mitochondria, peroxisomes, and endosomes. Because of these close associations, it is difficult to purify LDs to homogeneity. Consequently, the confident identification of bona fide LD proteins via proteomics has been challenging. Here, we report a methodology for LD protein identification based on mass spectrometry and protein correlation profiles. Using LD purification and quantitative, high-resolution mass spectrometry, we identified LD proteins by correlating their purification profiles to those of known LD proteins. Application of the protein correlation profile strategy to LDs isolated from Drosophila S2 cells led to the identification of 111 LD proteins in a cellular LD fraction in which 1481 proteins were detected. LD localization was confirmed in a subset of identified proteins via microscopy of the expressed proteins, thereby validating the approach. Among the identified LD proteins were both well-characterized LD proteins and proteins not previously known to be localized to LDs. Our method provides a high-confidence LD proteome of Drosophila cells and a novel approach that can be applied to identify LD proteins of other cell types and tissues. PMID:23319140

  9. Plasma and Serum Metabolite Association Networks: Comparability within and between Studies Using NMR and MS Profiling.

    Science.gov (United States)

    Suarez-Diez, Maria; Adam, Jonathan; Adamski, Jerzy; Chasapi, Styliani A; Luchinat, Claudio; Peters, Annette; Prehn, Cornelia; Santucci, Claudio; Spyridonidis, Alexandros; Spyroulias, Georgios A; Tenori, Leonardo; Wang-Sattler, Rui; Saccenti, Edoardo

    2017-07-07

    Blood is one of the most used biofluids in metabolomics studies, and the serum and plasma fractions are routinely used as a proxy for blood itself. Here we investigated the association networks of an array of 29 metabolites identified and quantified via NMR in the plasma and serum samples of two cohorts of ∼1000 healthy blood donors each. A second study of 377 individuals was used to extract plasma and serum samples from the same individual on which a set of 122 metabolites were detected and quantified using FIA-MS/MS. Four different inference algorithms (ARANCE, CLR, CORR, and PCLRC) were used to obtain consensus networks. The plasma and serum networks obtained from different studies showed different topological properties with the serum network being more connected than the plasma network. On a global level, metabolite association networks from plasma and serum fractions obtained from the same blood sample of healthy people show similar topologies, and at a local level, some differences arise like in the case of amino acids.

  10. Qualitative profiling and quantification of neonicotinoid metabolites in human urine by liquid chromatography coupled with mass spectrometry.

    Science.gov (United States)

    Taira, Kumiko; Fujioka, Kazutoshi; Aoyama, Yoshiko

    2013-01-01

    Neonicotinoid pesticides have been widely applied for the production of fruits and vegetables, and occasionally detected in conventionally grown produce. Thus oral exposure to neonicotinoid pesticides may exist in the general population; however, neonicotinoid metabolites in human body fluids have not been investigated comprehensively. The purpose of this study is the qualitative profiling and quantitative analysis of neonicotinoid metabolites in the human spot urine by liquid chromatography coupled with mass spectrometry (LC/MS). Human urine samples were collected from three patients suspected of subacute exposure to neonicotinoid pesticides. A qualitative profiling of urinary metabolites was performed using liquid chromatography/time-of-flight mass spectrometry (LC/TOFMS) with a database of nominal molecular weights of 57 known metabolites of three neonicotinoid pesticides (acetamiprid, Imidacloprid, and clothianidin), as well as the parent compounds. Then a quantitative analysis of selected urinary metabolites was performed using liquid chromatography/tandem mass spectrometry (LC/MS/MS) with a standard pesticide and metabolite, which were detected by the qualitative profiling. The result of qualitative profiling showed that seven metabolites, i.e. an acetamiprid metabolite, N-desmethyl-acetamiprid; three Imidacloprid metabolites, 5-hydroxy-Imidacloprid, 4,5-dihydroxy-imidacloprid, 4,5-dehydro-Imidacloprid; a common metabolite of acetamiprid and Imidacloprid, N-(6-chloronicotinoyl)-glycine; and two clothianidin metabolites, N-desmethyl-clothianidin, N-(2-(methylsulfanyl)thiazole-5-carboxyl)-glycine, as well as acetamiprid, were detected in the urine of three cases. The result of the quantitative analysis showed N-desmethyl-acetamiprid was determined in the urine of one case, which had been collected on the first visit, at a concentration of 3.2 ng/mL. This is the first report on the qualitative and quantitative detection of N-desmethyl-acetamiprid in the human

  11. Qualitative profiling and quantification of neonicotinoid metabolites in human urine by liquid chromatography coupled with mass spectrometry.

    Directory of Open Access Journals (Sweden)

    Kumiko Taira

    Full Text Available Neonicotinoid pesticides have been widely applied for the production of fruits and vegetables, and occasionally detected in conventionally grown produce. Thus oral exposure to neonicotinoid pesticides may exist in the general population; however, neonicotinoid metabolites in human body fluids have not been investigated comprehensively. The purpose of this study is the qualitative profiling and quantitative analysis of neonicotinoid metabolites in the human spot urine by liquid chromatography coupled with mass spectrometry (LC/MS. Human urine samples were collected from three patients suspected of subacute exposure to neonicotinoid pesticides. A qualitative profiling of urinary metabolites was performed using liquid chromatography/time-of-flight mass spectrometry (LC/TOFMS with a database of nominal molecular weights of 57 known metabolites of three neonicotinoid pesticides (acetamiprid, Imidacloprid, and clothianidin, as well as the parent compounds. Then a quantitative analysis of selected urinary metabolites was performed using liquid chromatography/tandem mass spectrometry (LC/MS/MS with a standard pesticide and metabolite, which were detected by the qualitative profiling. The result of qualitative profiling showed that seven metabolites, i.e. an acetamiprid metabolite, N-desmethyl-acetamiprid; three Imidacloprid metabolites, 5-hydroxy-Imidacloprid, 4,5-dihydroxy-imidacloprid, 4,5-dehydro-Imidacloprid; a common metabolite of acetamiprid and Imidacloprid, N-(6-chloronicotinoyl-glycine; and two clothianidin metabolites, N-desmethyl-clothianidin, N-(2-(methylsulfanylthiazole-5-carboxyl-glycine, as well as acetamiprid, were detected in the urine of three cases. The result of the quantitative analysis showed N-desmethyl-acetamiprid was determined in the urine of one case, which had been collected on the first visit, at a concentration of 3.2 ng/mL. This is the first report on the qualitative and quantitative detection of N-desmethyl-acetamiprid in

  12. Impact of nutrient excess and endothelial nitric oxide synthase on the plasma metabolite profile in mice

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    Brian E Sansbury

    2014-11-01

    Full Text Available An increase in calorie consumption is associated with the recent rise in obesity prevalence. However, our current understanding of the effects of nutrient excess on major metabolic pathways appears insufficient to develop safe and effective metabolic interventions to prevent obesity. Hence, we sought to identify systemic metabolic changes caused by nutrient excess and to determine how endothelial nitric oxide synthase (eNOS—which has anti-obesogenic properties—affects systemic metabolism by measuring plasma metabolites. Wild-type (WT and eNOS transgenic (eNOS-TG mice were placed on low fat or high fat diets for six weeks, and plasma metabolites were measured using an unbiased metabolomic approach. High fat feeding in WT mice led to significant increases in fat mass, which was associated with significantly lower plasma levels of 1,5-anhydroglucitol, lysophospholipids, 3-dehydrocarnitine, and bile acids, as well as branched chain amino acids (BCAAs and their metabolites. Plasma levels of several lipids including sphingomyelins, stearoylcarnitine, dihomo-linoleate and metabolites associated with oxidative stress were increased by high fat diet. In comparison with low fat-fed WT mice, eNOS-TG mice showed lower levels of several free fatty acids, but in contrast, the levels of bile acids, amino acids, and BCAA catabolites were increased. When placed on a high fat diet, eNOS overexpressing mice showed remarkably higher levels of plasma bile acids and elevated levels of plasma BCAAs and their catabolites compared with WT mice. Treatment with GW4064, an inhibitor of bile acid synthesis, decreased plasma bile acid levels but was not sufficient to reverse the anti-obesogenic effects of eNOS overexpression. These findings reveal unique metabolic changes in response to high fat diet and eNOS overexpression and suggest that the anti-obesity effects of eNOS are likely independent of changes in the bile acid pool.

  13. Genetics meets metabolomics: a genome-wide association study of metabolite profiles in human serum.

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    Christian Gieger

    2008-11-01

    Full Text Available The rapidly evolving field of metabolomics aims at a comprehensive measurement of ideally all endogenous metabolites in a cell or body fluid. It thereby provides a functional readout of the physiological state of the human body. Genetic variants that associate with changes in the homeostasis of key lipids, carbohydrates, or amino acids are not only expected to display much larger effect sizes due to their direct involvement in metabolite conversion modification, but should also provide access to the biochemical context of such variations, in particular when enzyme coding genes are concerned. To test this hypothesis, we conducted what is, to the best of our knowledge, the first GWA study with metabolomics based on the quantitative measurement of 363 metabolites in serum of 284 male participants of the KORA study. We found associations of frequent single nucleotide polymorphisms (SNPs with considerable differences in the metabolic homeostasis of the human body, explaining up to 12% of the observed variance. Using ratios of certain metabolite concentrations as a proxy for enzymatic activity, up to 28% of the variance can be explained (p-values 10(-16 to 10(-21. We identified four genetic variants in genes coding for enzymes (FADS1, LIPC, SCAD, MCAD where the corresponding metabolic phenotype (metabotype clearly matches the biochemical pathways in which these enzymes are active. Our results suggest that common genetic polymorphisms induce major differentiations in the metabolic make-up of the human population. This may lead to a novel approach to personalized health care based on a combination of genotyping and metabolic characterization. These genetically determined metabotypes may subscribe the risk for a certain medical phenotype, the response to a given drug treatment, or the reaction to a nutritional intervention or environmental challenge.

  14. The First Insight into the Metabolite Profiling of Grapes from Three Vitis vinifera L. Cultivars of Two Controlled Appellation (DOC Regions

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    António Teixeira

    2014-03-01

    Full Text Available The characterization of the metabolites accumulated in the grapes of specific cultivars grown in different climates is of particular importance for viticulturists and enologists. In the present study, the metabolite profiling of grapes from the cultivars, Alvarinho, Arinto and Padeiro de Basto, of two Portuguese Controlled Denomination of Origin (DOC regions (Vinho Verde and Lisboa was investigated by gas chromatography-coupled time-of-flight mass spectrometry (GC-TOF-MS and an amino acid analyzer. Primary metabolites, including sugars, organic acids and amino acids, and some secondary metabolites were identified. Tartaric and malic acids and free amino acids accumulated more in grapes from vines of the DOC region of Vinho Verde than DOC Lisboa, but a principal component analysis (PCA plot showed that besides the DOC region, the grape cultivar also accounted for the variance in the relative abundance of metabolites. Grapes from the cultivar, Alvarinho, were particularly rich in malic acid and tartaric acids in both DOC regions, but sucrose accumulated more in the DOC region of Vinho Verde.

  15. The first insight into the metabolite profiling of grapes from three Vitis vinifera L. cultivars of two controlled appellation (DOC) regions.

    Science.gov (United States)

    Teixeira, António; Martins, Viviana; Noronha, Henrique; Eiras-Dias, José; Gerós, Hernâni

    2014-03-10

    The characterization of the metabolites accumulated in the grapes of specific cultivars grown in different climates is of particular importance for viticulturists and enologists. In the present study, the metabolite profiling of grapes from the cultivars, Alvarinho, Arinto and Padeiro de Basto, of two Portuguese Controlled Denomination of Origin (DOC) regions (Vinho Verde and Lisboa) was investigated by gas chromatography-coupled time-of-flight mass spectrometry (GC-TOF-MS) and an amino acid analyzer. Primary metabolites, including sugars, organic acids and amino acids, and some secondary metabolites were identified. Tartaric and malic acids and free amino acids accumulated more in grapes from vines of the DOC region of Vinho Verde than DOC Lisboa, but a principal component analysis (PCA) plot showed that besides the DOC region, the grape cultivar also accounted for the variance in the relative abundance of metabolites. Grapes from the cultivar, Alvarinho, were particularly rich in malic acid and tartaric acids in both DOC regions, but sucrose accumulated more in the DOC region of Vinho Verde.

  16. Profiling contents of water-soluble metabolites and mineral nutrients to evaluate the effects of pesticides and organic and chemical fertilizers on tomato fruit quality.

    Science.gov (United States)

    Watanabe, Masami; Ohta, Yuko; Licang, Sun; Motoyama, Naoki; Kikuchi, Jun

    2015-02-15

    In this study, the contents of water-soluble metabolites and mineral nutrients were measured in tomatoes cultured using organic and chemical fertilizers, with or without pesticides. Mineral nutrients and water-soluble metabolites were determined by inductively coupled plasma-atomic emission spectrometry and (1)H nuclear magnetic resonance spectrometry, respectively, and results were analysed by principal components analysis (PCA). The mineral nutrient and water-soluble metabolite profiles differed between organic and chemical fertilizer applications, which accounted for 88.0% and 55.4%, respectively, of the variation. (1)H-(13)C-hetero-nuclear single quantum coherence experiments identified aliphatic protons that contributed to the discrimination of PCA. Pesticide application had little effect on mineral nutrient content (except Fe and P), but affected the correlation between mineral nutrients and metabolites. Differences in the content of mineral nutrients and water-soluble metabolites resulting from different fertilizer and pesticide applications probably affect tomato quality. Copyright © 2014 Elsevier Ltd. All rights reserved.

  17. Heat-stabilised rice bran consumption by colorectal cancer survivors modulates stool metabolite profiles and metabolic networks: a randomised controlled trial.

    Science.gov (United States)

    Brown, Dustin G; Borresen, Erica C; Brown, Regina J; Ryan, Elizabeth P

    2017-05-01

    Rice bran (RB) consumption has been shown to reduce colorectal cancer (CRC) growth in mice and modify the human stool microbiome. Changes in host and microbial metabolism induced by RB consumption was hypothesised to modulate the stool metabolite profile in favour of promoting gut health and inhibiting CRC growth. The objective was to integrate gut microbial metabolite profiles and identify metabolic pathway networks for CRC chemoprevention using non-targeted metabolomics. In all, nineteen CRC survivors participated in a parallel randomised controlled dietary intervention trial that included daily consumption of study-provided foods with heat-stabilised RB (30 g/d) or no additional ingredient (control). Stool samples were collected at baseline and 4 weeks and analysed using GC-MS and ultra-performance liquid chromatography-MS. Stool metabolomics revealed 93 significantly different metabolites in individuals consuming RB. A 264-fold increase in β-hydroxyisovaleroylcarnitine and 18-fold increase in β-hydroxyisovalerate exemplified changes in leucine, isoleucine and valine metabolism in the RB group. A total of thirty-nine stool metabolites were significantly different between RB and control groups, including increased hesperidin (28-fold) and narirutin (14-fold). Metabolic pathways impacted in the RB group over time included advanced glycation end products, steroids and bile acids. Fatty acid, leucine/valine and vitamin B6 metabolic pathways were increased in RB compared with control. There were 453 metabolites identified in the RB food metabolome, thirty-nine of which were identified in stool from RB consumers. RB consumption favourably modulated the stool metabolome of CRC survivors and these findings suggest the need for continued dietary CRC chemoprevention efforts.

  18. Host plant secondary metabolite profiling shows a complex, strain-dependent response of maize to plant growth-promoting rhizobacteria of the genus Azospirillum.

    Science.gov (United States)

    Walker, Vincent; Bertrand, Cédric; Bellvert, Floriant; Moënne-Loccoz, Yvan; Bally, René; Comte, Gilles

    2011-01-01

    Most Azospirillum plant growth-promoting rhizobacteria (PGPR) benefit plant growth through source effects related to free nitrogen fixation and/or phytohormone production, but little is known about their potential effects on plant physiology. These effects were assessed by comparing the early impacts of three Azospirillum inoculant strains on secondary metabolite profiles of two different maize (Zea mays) cultivars. After 10d of growth in nonsterile soil, maize methanolic extracts were analyzed by reverse-phase high-performance liquid chromatography (RP-HPLC) and secondary metabolites identified by liquid chromatography/mass spectrometry (LC/MS) and nuclear magnetic resonance (NMR). Seed inoculation resulted in increased shoot biomass (and also root biomass with one strain) of hybrid PR37Y15 but had no stimulatory effect on hybrid DK315. In parallel, Azospirillum inoculation led to major qualitative and quantitative modifications of the contents of secondary metabolites, especially benzoxazinoids, in the maize plants. These modifications depended on the PGPR strain×plant cultivar combination. Thus, Azospirillum inoculation resulted in early, strain-dependent modifications in the biosynthetic pathways of benzoxazine derivatives in maize in compatible interactions. This is the first study documenting a PGPR effect on plant secondary metabolite profiles, and suggests the establishment of complex interactions between Azospirillum PGPR and maize. © The Authors (2010). Journal compilation © New Phytologist Trust (2010).

  19. Serum metabolomic profiling in acute alcoholic hepatitis identifies multiple dysregulated pathways.

    Science.gov (United States)

    Rachakonda, Vikrant; Gabbert, Charles; Raina, Amit; Bell, Lauren N; Cooper, Sara; Malik, Shahid; Behari, Jaideep

    2014-01-01

    While animal studies have implicated derangements of global energy homeostasis in the pathogenesis of acute alcoholic hepatitis (AAH), the relevance of these findings to the development of human AAH remains unclear. Using global, unbiased serum metabolomics analysis, we sought to characterize alterations in metabolic pathways associated with severe AAH and identify potential biomarkers for disease prognosis. This prospective, case-control study design included 25 patients with severe AAH and 25 ambulatory patients with alcoholic cirrhosis. Serum samples were collected within 24 hours of the index clinical encounter. Global, unbiased metabolomics profiling was performed. Patients were followed for 180 days after enrollment to determine survival. Levels of 234 biochemicals were altered in subjects with severe AAH. Random-forest analysis, principal component analysis, and integrated hierarchical clustering methods demonstrated that metabolomics profiles separated the two cohorts with 100% accuracy. Severe AAH was associated with enhanced triglyceride lipolysis, impaired mitochondrial fatty acid beta oxidation, and upregulated omega oxidation. Low levels of multiple lysolipids and related metabolites suggested decreased plasma membrane remodeling in severe AAH. While most measured bile acids were increased in severe AAH, low deoxycholate and glycodeoxycholate levels indicated intestinal dysbiosis. Several changes in substrate utilization for energy homeostasis were identified in severe AAH, including increased glucose consumption by the pentose phosphate pathway, altered tricarboxylic acid (TCA) cycle activity, and enhanced peptide catabolism. Finally, altered levels of small molecules related to glutathione metabolism and antioxidant vitamin depletion were observed in patients with severe AAH. Univariable logistic regression revealed 15 metabolites associated with 180-day survival in severe AAH. Severe AAH is characterized by a distinct metabolic phenotype spanning

  20. Metabolite profiling of human colon carcinoma – deregulation of TCA cycle and amino acid turnover

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    Noske Aurelia

    2008-09-01

    Full Text Available Abstract Background Apart from genetic alterations, development and progression of colorectal cancer has been linked to influences from nutritional intake, hyperalimentation, and cellular metabolic changes that may be the basis for new diagnostic and therapeutic approaches. However, in contrast to genomics and proteomics, comprehensive metabolomic investigations of alterations in malignant tumors have rarely been conducted. Results In this study we investigated a set of paired samples of normal colon tissue and colorectal cancer tissue with gas-chromatography time-of-flight mass-spectrometry, which resulted in robust detection of a total of 206 metabolites. Metabolic phenotypes of colon cancer and normal tissues were different at a Bonferroni corrected significance level of p = 0.00170 and p = 0.00005 for the first two components of an unsupervised PCA analysis. Subsequent supervised analysis found 82 metabolites to be significantly different at p Conclusion This study demonstrates that metabolic profiling facilitates biochemical phenotyping of normal and neoplastic colon tissue at high significance levels and points to GC-TOF-based metabolomics as a new method for molecular pathology investigations.

  1. Genome-Wide Functional Profiling Reveals Genes Required for Tolerance to Benzene Metabolites in Yeast

    Science.gov (United States)

    North, Matthew; Tandon, Vickram J.; Thomas, Reuben; Loguinov, Alex; Gerlovina, Inna; Hubbard, Alan E.; Zhang, Luoping; Smith, Martyn T.; Vulpe, Chris D.

    2011-01-01

    Benzene is a ubiquitous environmental contaminant and is widely used in industry. Exposure to benzene causes a number of serious health problems, including blood disorders and leukemia. Benzene undergoes complex metabolism in humans, making mechanistic determination of benzene toxicity difficult. We used a functional genomics approach to identify the genes that modulate the cellular toxicity of three of the phenolic metabolites of benzene, hydroquinone (HQ), catechol (CAT) and 1,2,4-benzenetriol (BT), in the model eukaryote Saccharomyces cerevisiae. Benzene metabolites generate oxidative and cytoskeletal stress, and tolerance requires correct regulation of iron homeostasis and the vacuolar ATPase. We have identified a conserved bZIP transcription factor, Yap3p, as important for a HQ-specific response pathway, as well as two genes that encode putative NAD(P)H:quinone oxidoreductases, PST2 and YCP4. Many of the yeast genes identified have human orthologs that may modulate human benzene toxicity in a similar manner and could play a role in benzene exposure-related disease. PMID:21912624

  2. HPLC-ICP-MS compared with radiochemical detection for metabolite profiling of H-3-bromohexine in rat urine and faeces

    DEFF Research Database (Denmark)

    Jensen, B.P.; Gammelgaard, B.; Hansen, S.H.

    2005-01-01

    of detection of 1.3 ng of bromohexine on-column. This allowed ICP- MS detection of several minor metabolites that were not detected using radiochemical detection. Furthermore, metabolites that had lost the radioactive label were detected due to the bromine in the metabolites. As ICP- MS is also more selective......H-3-Bromohexine was dosed to rats as a model compound to allow comparison of HPLC-ICP-MS detection on bromine to radiochemical detection in an in vivo drug metabolism study. Metabolite profiles were obtained in urine and faeces extracts. No influence of the methanol gradient on the bromine response...... was observed in the range of 18 - 75% methanol. The sensitivity obtained by HPLC- ICP-MS was almost two orders of magnitude better than on-line H-3 radiochemical detection. For ICP- MS, the limit of detection was calculated to be 69 nM Br ( injection volume 100 mu l), corresponding to an absolute limit...

  3. A sex-specific metabolite identified in a marine invertebrate utilizing phosphorus-31 nuclear magnetic resonance.

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    Robert A Kleps

    Full Text Available Hormone level differences are generally accepted as the primary cause for sexual dimorphism in animal and human development. Levels of low molecular weight metabolites also differ between men and women in circulating amino acids, lipids and carbohydrates and within brain tissue. While investigating the metabolism of blue crab tissues using Phosphorus-31 Nuclear Magnetic Resonance, we discovered that only the male blue crab (Callinectes sapidus contained a phosphorus compound with a chemical shift well separated from the expected phosphate compounds. Spectra obtained from male gills were readily differentiated from female gill spectra. Analysis from six years of data from male and female crabs documented that the sex-specificity of this metabolite was normal for this species. Microscopic analysis of male and female gills found no differences in their gill anatomy or the presence of parasites or bacteria that might produce this phosphorus compound. Analysis of a rare gynandromorph blue crab (laterally, half male and half female proved that this sex-specificity was an intrinsic biochemical process and was not caused by any variations in the diet or habitat of male versus female crabs. The existence of a sex-specific metabolite is a previously unrecognized, but potentially significant biochemical phenomenon. An entire enzyme system has been synthesized and activated only in one sex. Unless blue crabs are a unique species, sex-specific metabolites are likely to be present in other animals. Would the presence or absence of a sex-specific metabolite affect an animal's development, anatomy and biochemistry?

  4. Profiling and identification of (-)-epicatechin metabolites in rats using ultra-high performance liquid chromatography coupled with linear trap-Orbitrap mass spectrometer.

    Science.gov (United States)

    Shang, Zhanpeng; Wang, Fei; Dai, Shengyun; Lu, Jianqiu; Wu, Xiaodan; Zhang, Jiayu

    2017-08-01

    (-)-Epicatechin (EC), an optical antipode of (+)-catechin (C), possesses many potential significant health benefits. However, the in vivo metabolic pathway of EC has not been clarified yet. In this study, an efficient strategy based on ultra-high performance liquid chromatography coupled with a linear ion trap-Orbitrap mass spectrometer was developed to profile and characterize EC metabolites in rat urine, faeces, plasma, and various tissues. Meanwhile, post-acquisition data-mining methods including high-resolution extracted ion chromatogram (HREIC), multiple mass defect filters (MMDFs), and diagnostic product ions (DPIs) were utilized to screen and identify EC metabolites from HR-ESI-MS 1 to ESI-MS n stage. Finally, a total of 67 metabolites (including parent drug) were tentatively identified based on standard substances, chromatographic retention times, accurate mass measurement, and relevant drug biotransformation knowledge. The results demonstrated that EC underwent multiple in vivo metabolic reactions including methylation, dehydration, hydrogenation, glucosylation, sulfonation, glucuronidation, ring-cleavage, and their composite reactions. Among them, methylation, dehydration, glucosylation, and their composite reactions were observed only occurring on EC when compared with C. Meanwhile, the distribution of these detected metabolites in various tissues including heart, liver, spleen, lung, kidney, and brain were respectively studied. The results demonstrated that liver and kidney were the most important organs for EC and its metabolites elimination. In conclusion, the newly discovered EC metabolites significantly expanded the understanding on its pharmacological effects and built the foundation for further toxicity and safety studies. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

  5. Identifying Twitter influencer profiles for health promotion in Saudi Arabia.

    Science.gov (United States)

    Albalawi, Yousef; Sixsmith, Jane

    2017-06-01

    New media platforms, such as Twitter, provide the ideal opportunity to positively influence the health of large audiences. Saudi Arabia has one of the highest number of Twitter users of any country, some of whom are very influential in setting agendas and contributing to the dissemination of ideas. Those opinion leaders, both individuals and organizations, influential in the new media environment have the potential to raise awareness of health issues, advocate for health and potentially instigate change at a social level. To realize the potential of the new media platforms for public health, the function of opinion leaders is key. This study aims to identify and profile the most influential Twitter accounts in Saudi Arabia. Multiple measures, including: number of followers and four influence scores, were used to evaluate Twitter accounts. The data were then filtered and analysed using ratio and percentage calculations to identify the most influential users. In total, 99 Saudi Twitter accounts were classified, resulting in the identification of 25 religious men/women, 16 traditional media, 14 sports related, 10 new media, 6 political, 6 company and 4 health accounts. The methods used to identify the key influential Saudi accounts can be applied to inform profile development of Twitter users in other countries. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  6. Metabolite profiles of Stachybotrys isolates from water-damaged buildings and their induction of inflammatory mediators and cytotoxicity in macrophages

    DEFF Research Database (Denmark)

    Nielsen, Kristian Fog; Huttunen, K.; Hyvarinen, A.

    2002-01-01

    The metabolite profiles of 20 Stachybotrys spp. isolates from Finnish water-damaged buildings were compared with their biological activities. Effects of purified compounds on cytotoxicity and production of inflammatory mediators such as nitric oxide, IL-6 and TNFalpha in murine RAW264.7 macrophage...

  7. Stable isotope N-phosphoryl amino acids labeling for quantitative profiling of amine-containing metabolites using liquid chromatography mass spectrometry.

    Science.gov (United States)

    Zhang, Shanshan; Shi, Jinwen; Shan, Changkai; Huang, Chengting; Wu, Yile; Ding, Rong; Xue, Yuhua; Liu, Wen; Zhou, Qiang; Zhao, Yufen; Xu, Pengxiang; Gao, Xiang

    2017-07-25

    Stable isotope chemical labeling liquid chromatography-mass spectrometry (LC-MS) is a powerful strategy for comprehensive metabolomics profiling, which can improve metabolites coverage and quantitative information for exploration of metabolic regulation in complex biological systems. In the current work, a novel stable isotope N-phosphoryl amino acids labeling strategy (SIPAL) has been successful developed for quantitative profiling of amine-containing metabolites in urine based on organic phosphorus chemistry. Two isotopic reagents, 16 O 2 - and 18 O 2 -N-diisopropyl phosphoryl l-alanine N-hydroxysuccinimide esters ( 16 O/ 18 O-DIPP-L-Ala-NHS), were firstly synthesized in high yields for labeling the amine-containing metabolites. The performance of SIPAL strategy was tested by analyzing standard samples including 20 l-amino acids, 10 d-amino acids and small peptides by using LC-MS. We observed highly efficient and selective labeling for SIPAL strategy within 15 min in a one-pot derivatization reaction under aqueous reaction conditions. The introduction of a neutral phosphate group at N-terminus can increase the proton affinity and overall hydrophobicity of targeted metabolites, leading to the better ionization efficiency in electrospray ionization processes and chromatographic separations of hydrophilic metabolites on reversed-phase column. Furthermore, the chiral metabolites, such as d-amino acids, could be converted to diastereomers after SIPAL and successfully separated on regular reversed-phase column. The chirality of labeled enantiomers can be determined by using different detection methods such as 31 P NMR, UV, and MS, demonstrating the potential application of SIPAL strategy. In addition, absolute quantification of chiral metabolites in biological samples can be easily achieved by using SIPAL strategy. For this purpose, urine samples collected from a healthy volunteer were analyzed by using LC-ESI-Orbitrap MS. Over 300 pairs of different amine

  8. Accessing biological actions of Ganoderma secondary metabolites by in silico profiling

    Science.gov (United States)

    Grienke, Ulrike; Kaserer, Teresa; Pfluger, Florian; Mair, Christina E.; Langer, Thierry; Schuster, Daniela; Rollinger, Judith M.

    2016-01-01

    The species complex around the medicinal fungus Ganoderma lucidum Karst. (Ganodermataceae) is widely known in traditional medicines as well as in modern applications such as functional food or nutraceuticals. A considerable number of publications reflects its abundance and variety in biological actions either provoked by primary metabolites such as polysaccharides or secondary metabolites such as lanostane-type triterpenes. However, due to this remarkable amount of information, a rationalization of the individual Ganoderma constituents to biological actions on a molecular level is quite challenging. To overcome this issue, a database was generated containing meta-information, i.e. chemical structures and biological actions of hitherto identified Ganoderma constituents (279). This was followed by a computational approach subjecting this 3D multi-conformational molecular dataset to in silico parallel screening against an in-house collection of validated structure- and ligand-based 3D pharmacophore models. The predictive power of the evaluated in silico tools and hints from traditional application fields served as criteria for the model selection. Thus, we focused on representative druggable targets in the field of viral infections (5) and diseases related to the metabolic syndrome (22). The results obtained from this in silico approach were compared to bioactivity data available from the literature to distinguish between true and false positives or negatives. 89 and 197 Ganoderma compounds were predicted as ligands of at least one of the selected pharmacological targets in the antiviral and the metabolic syndrome screening, respectively. Among them only a minority of individual compounds (around 10%) has ever been investigated on these targets or for the associated biological activity. Accordingly, this study discloses putative ligand target interactions for a plethora of Ganoderma constituents in the empirically manifested field of viral diseases and metabolic

  9. Characterization of differential cocaine metabolism in mouse and rat through metabolomics-guided metabolite profiling.

    Science.gov (United States)

    Yao, Dan; Shi, Xiaolei; Wang, Lei; Gosnell, Blake A; Chen, Chi

    2013-01-01

    Rodent animal models have been widely used for studying neurologic and toxicological events associated with cocaine abuse. It is known that the mouse is more susceptible to cocaine-induced hepatotoxicity (CIH) than the rat. However, the causes behind this species-dependent sensitivity to cocaine have not been elucidated. In this study, cocaine metabolism in the mouse and rat was characterized through LC-MS-based metabolomic analysis of urine samples and were further compared through calculating the relative abundance of individual cocaine metabolites. The results showed that the levels of benzoylecgonine, a major cocaine metabolite from ester hydrolysis, were comparable in the urine from the mice and rats treated with the same dose of cocaine. However, the levels of the cocaine metabolites from oxidative metabolism, such as N-hydroxybenzoylnorecgonine and hydroxybenzoylecgonine, differed dramatically between the two species, indicating species-dependent cocaine metabolism. Subsequent structural analysis through accurate mass analysis and LC-MS/MS fragmentation revealed that N-oxidation reactions, including N-demethylation and N-hydroxylation, are preferred metabolic routes in the mouse, while extensive aryl hydroxylation reactions occur in the rat. Through stable isotope tracing and in vitro enzyme reactions, a mouse-specific α-glucoside of N-hydroxybenzoylnorecgonine and a group of aryl hydroxy glucuronides high in the rat were identified and structurally elucidated. The differences in the in vivo oxidative metabolism of cocaine between the two rodent species were confirmed by the in vitro microsomal incubations. Chemical inhibition of P450 enzymes further revealed that different P450-mediated oxidative reactions in the ecgonine and benzoic acid moieties of cocaine contribute to the species-dependent biotransformation of cocaine.

  10. Characterization of D-3-hydroxybutyrylcarnitine (ketocarnitine): an identified ketosis-induced metabolite

    NARCIS (Netherlands)

    Soeters, Maarten R.; Serlie, Mireille J.; Sauerwein, Hans P.; Duran, Marinus; Ruiter, Jos P.; Kulik, Willem; Ackermans, Mariëtte T.; Minkler, Paul E.; Hoppel, Charles L.; Wanders, Ronald J. A.; Houten, Sander M.

    2012-01-01

    Hydroxybutyrylcarnitine (HB-carnitine) is a metabolite that has been associated with insulin resistance and type 2 diabetes mellitus. It is currently unknown whether HB-carnitine can be produced from D-3-hydroxybutyrate (D-3HB), a ketone body; but its formation from L-3-HB-CoA, a fatty acid

  11. Short communication: Practical issues in implementing volatile metabolite analysis for identifying mastitis pathogens.

    Science.gov (United States)

    Hettinga, Kasper A; de Bok, Frank A M; Lam, Theo J G M

    2015-11-01

    Several parameters for improving volatile metabolite analysis using headspace gas chromatography-mass spectrometry (GC-MS) analysis of volatile metabolites were evaluated in the framework of identification of mastitis-causing pathogens. Previous research showed that the results of such volatile metabolites analysis were comparable with those based on bacteriological culturing. The aim of this study was to evaluate the effect of several method changes on the applicability and potential implementation of this method in practice. The use of a relatively polar column is advantageous, resulting in a faster and less complex chromatographic setup with a higher resolving power yielding higher-quality data. Before volatile metabolite analysis is applied, a minimum incubation of 8h is advised, as reducing incubation time leads to less reliable pathogen identification. Application of GC-MS remained favorable compared with regular gas chromatography. The complexity and cost of a GC-MS system are such that this limits the application of the method in practice for identification of mastitis-causing pathogens. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  12. Molecular profiling identifies prognostic markers of stage IA lung adenocarcinoma.

    Science.gov (United States)

    Zhang, Jie; Shao, Jinchen; Zhu, Lei; Zhao, Ruiying; Xing, Jie; Wang, Jun; Guo, Xiaohui; Tu, Shichun; Han, Baohui; Yu, Keke

    2017-09-26

    We previously showed that different pathologic subtypes were associated with different prognostic values in patients with stage IA lung adenocarcinoma (AC). We hypothesize that differential gene expression profiles of different subtypes may be valuable factors for prognosis in stage IA lung adenocarcinoma. We performed microarray gene expression profiling on tumor tissues micro-dissected from patients with acinar and solid predominant subtypes of stage IA lung adenocarcinoma. These patients had undergone a lobectomy and mediastinal lymph node dissection at the Shanghai Chest Hospital, Shanghai, China in 2012. No patient had preoperative treatment. We performed the Gene Set Enrichment Analysis (GSEA) analysis to look for gene expression signatures associated with tumor subtypes. The histologic subtypes of all patients were classified according to the 2015 WHO lung Adenocarcinoma classification. We found that patients with the solid predominant subtype are enriched for genes involved in RNA polymerase activity as well as inactivation of the p53 pathway. Further, we identified a list of genes that may serve as prognostic markers for stage IA lung adenocarcinoma. Validation in the TCGA database shows that these genes are correlated with survival, suggesting that they are novel prognostic factors for stage IA lung adenocarcinoma. In conclusion, we have uncovered novel prognostic factors for stage IA lung adenocarcinoma using gene expression profiling in combination with histopathology subtyping.

  13. A high-resolution accurate mass (HR/AM) approach to identification, profiling and characterization of in vitro nefazodone metabolites using a hybrid quadrupole Orbitrap (Q-Exactive).

    Science.gov (United States)

    Perry, Simon J; Nász, Szilárd; Saeed, Mansoor

    2015-09-15

    This paper describes a strategy for the profiling and identification of metabolites based on chemical group classification using high-resolution accurate mass (HR/AM) full scan mass spectrometry (MS) and All-Ion fragmentation (AIF) MS 2 data. The proposed strategy uses a hybrid quadrupole Orbitrap (Q-Exactive) employing stepped normalised collision energy (NCE) at 35% and 80% to produce key chemically diagnostic product ions from full coverage of the product ion spectrum. This approach allows filtering of high-resolution AIF MS 2 data in order to identify parent-related compounds produced following incubation in rat liver microsomes (RLMs). An antidepressant drug, nefazodone (NEF), was selected as the model test compound to demonstrate the proposed workflow for metabolite profiling. This resulted in the identification of three indicative chemical groups within NEF: triazolone, phenoxy and chlorophenylpiperazine. High-resolution mass spectrometry provides increased specificity to distinguish between two characteristic product ion masses m/z 154.0975 (C 7 H 12 N 3 O) and 154.0419 (C 8 H 9 NCl), which are not fully resolved by spectrometers operating at nominal mass resolution, indicative of compounds containing the triazolone and chlorophenylpiperazine moieties, respectively. This post-acquisition processing strategy provides comprehensive detection and identification of high- and low-level metabolites from an 'all-in-one' analysis. This enables functional groups to be systematically traced across a wide range of metabolites, leading to the successful identification of 28 in vitro NEF-related metabolites. In our hands this approach has been applied to agrochemical environmental fate and dietary metabolism studies, as well as metabolomics and biomarker analysis. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

  14. Metabolite profiling reveals abiotic stress tolerance in Tn5 mutant of Pseudomonas putida.

    Directory of Open Access Journals (Sweden)

    Vasvi Chaudhry

    Full Text Available Pseudomonas is an efficient plant growth-promoting rhizobacteria (PGPR; however, intolerance to drought and high temperature limit its application in agriculture as a bioinoculant. Transposon 5 (Tn5 mutagenesis was used to generate a stress tolerant mutant from a PGPR Pseudomonas putida NBRI1108 isolated from chickpea rhizosphere. A mutant NBRI1108T, selected after screening of nearly 10,000 transconjugants, exhibited significant tolerance towards high temperature and drought. Southern hybridization analysis of EcoRI and XhoI restricted genomic DNA of NBRI1108T confirmed that it had a single Tn5 insertion. The metabolic changes in the polar and non-polar extracts of NBRI1108 and NBRI1108T were examined using 1H, 31P nuclear magnetic resonance (NMR spectroscopy and gas chromatography-mass spectrometry (GC-MS. Thirty six chemically diverse metabolites consisting of amino acids, fatty acids and phospholipids were identified and quantified. Insertion of Tn5 influenced amino acid and phospholipid metabolism and resulted in significantly higher concentration of aspartic acid, glutamic acid, glycinebetaine, glycerophosphatidylcholine (GPC and putrescine in NBRI1108T as compared to that in NBRI1108. The concentration of glutamic acid, glycinebetaine and GPC increased by 34%, 95% and 100%, respectively in the NBRI1108T as compared to that in NBRI1108. High concentration of glycerophosphatidylethanolamine (GPE and undetected GPC in NBRI1108 indicates that biosynthesis of GPE may have taken place via the methylation pathway of phospholipid biosynthesis. However, high GPC and low GPE concentration in NBRI1108T suggest that methylation pathway and phosphatidylcholine synthase (PCS pathway of phospholipid biosynthesis are being followed in the NBRI1108T. Application of multivariate principal component analysis (PCA on the quantified metabolites revealed clear variations in NBRI1108 and NBRI1108T in polar and non-polar metabolites. Identification of abiotic

  15. Comparison of trapping profiles between d-peptides and glutathione in the identification of reactive metabolites

    Directory of Open Access Journals (Sweden)

    Jaana E. Laine

    2015-01-01

    Full Text Available Qualitative trapping profile of reactive metabolites arising from six structurally different compounds was tested with three different d-peptide isomers (Peptide 1, gly–tyr–pro–cys–pro–his-pro; Peptide 2, gly–tyr–pro–ala–pro–his–pro; Peptide 3, gly–tyr–arg–pro–cys–pro–his–lys–pro and glutathione (GSH using mouse and human liver microsomes as the biocatalyst. The test compounds were classified either as clinically “safe” (amlodipine, caffeine, ibuprofen, or clinically as “risky” (clozapine, nimesulide, ticlopidine; i.e., associated with severe clinical toxicity outcomes. Our working hypothesis was as follows: could the use of short different amino acid sequence containing d-peptides in adduct detection confer any add-on value to that obtained with GSH? All “risky” agents’ resulted in the formation of several GSH adducts in the incubation mixture and with at least one peptide adduct with both microsomal preparations. Amlodipine did not form any adducts with any of the trapping agents. No GSH and peptide 2 and 3 adducts were found with caffeine, but with peptide 1 one adduct with human liver microsomes was detected. Ibuprofen produced one Peptide 1-adduct with human and mouse liver microsomes but not with GSH. In conclusion, GSH still remains the gold trapping standard for reactive metabolites. However, targeted d-peptides could provide additional information about protein binding potential of electrophilic agents, but their clinical significance needs to be clarified using a wider spectrum of chemicals together with other safety estimates.

  16. Antistaphylococcal activity and metabolite profiling of manuka honey (Leptospermum scoparium L.) after in vitro simulated digestion.

    Science.gov (United States)

    Mannina, Luisa; Sobolev, Anatoly P; Coppo, Erika; Di Lorenzo, Arianna; Nabavi, Seyed Mohammad; Marchese, Anna; Daglia, Maria

    2016-03-01

    The antistaphylococcal activity against methicillin-susceptible and -resistant Staphylococcus aureus and the metabolite profiling of manuka honey (MH) were investigated before and after in vitro simulated gastric (GD) and gastroduodenal (GDD) digestions. Undigested manuka honey showed antibacterial activity against all the tested strains, the GD sample showed no activity against S. aureus, and the GDD honey showed an antistaphylococcal activity, which was slightly reduced in comparison with the undigested sample. To explain these results, methylglyoxal (MGO), to which most of the antibacterial activity of MH is ascribed, was subjected to in vitro simulated GD and GDD. After digestion, MGO showed antibacterial activity at concentrations definitively higher than those registered in digested MH samples. These results showed that the antistaphylococcal activity registered after digestion cannot be ascribed to MGO. Thus metabolite analysis, carried out using an explorative untargeted NMR-based approach and a targeted RP-HPLC-PAD-ESI-MSn analysis focused on bio-active substances, was used to highlight the chemical modifications occurring from digestion. The results showed that (1) the level of MGO decreases and (2) the content of aromatic compounds, such as leptosin and methyl syringate, markers of manuka honey, was stable under gastric and gastroduodenal conditions, whereas (3) the levels of acetic and lactic acids increase in particular after gastroduodenal digestion, being 1.5 and 2.8 times higher in GDD-MH than in UND-MH, respectively. Overall, the results obtained from chemical analysis provide at least a partial explanation of the registered antibacterial activity observed after gastroduodenal digestion.

  17. Energetics and metabolite profiles during early flight in American robins (Turdus Migratorius).

    Science.gov (United States)

    Gerson, Alexander R; Guglielmo, Christopher G

    2013-10-01

    Although birds use fat as the primary fuel for migratory flights, carbohydrate and protein catabolism could be significant in the early stages of flight while pathways of fatty acid transport and oxidation are induced. The fuel mixture of long distance migrant birds can also be affected by the rate of water loss, where birds catabolize more protein to increase endogenous water production under dehydrating flight conditions. Despite many studies investigating flight metabolism, few have focused on the metabolic response to flight during the switchover to fat catabolism in migrants, and none have examined the effect of ambient conditions on fuel selection during early flight. We investigated the effect of water loss on the metabolic response to short duration flight in the American robin (Turdus migratorius). Birds were flown in a climatic wind tunnel and changes in body composition and plasma metabolites were measured. As flight duration increased, there was a gradual switchover from carbohydrate and protein catabolism to fat catabolism. Plasma metabolite profiles indicate that the mobilization of fat occurred within 20 min of initiating flight. Plasma glucose decreased and uric acid increased with flight duration. Ambient humidity did not affect fuel mixture. Thus, it seems that the utilization of fat may be delayed as migrants initiate flight. Short-hop migrants may exploit high rates of endogenous water production resulting from carbohydrate and protein catabolism early in flight to offset high water loss associated with low humidity. Rapid catabolism of lean body components at the start of a flight also reduces mass quickly, and may reduce energy costs.

  18. UV-B radiation modulates physiology and lipophilic metabolite profile in Olea europaea.

    Science.gov (United States)

    Celeste Dias, Maria; Pinto, Diana C G A; Correia, Carlos; Moutinho-Pereira, José; Oliveira, Helena; Freitas, Helena; Silva, Artur M S; Santos, Conceição

    2018-03-01

    Ultraviolet-B (UV-B) radiation plays an important role in plant photomorphogenesis. Whilst the morpho-functional disorders induced by excessive UV irradiation are well-known, it remains unclear how this irradiation modulates the metabolome, and which metabolic shifts improve plants' tolerance to UV-B. In this study, we use an important Mediterranean crop, Olea europaea, to decipher the impacts of enhanced UV-B radiation on the physiological performance and lipophilic metabolite profile. Young olive plants (cv. 'Galega Vulgar') were exposed for five days to UV-B biologically effective doses of 6.5 kJ m -2  d -1 and 12.4 kJ m -2 d -1 . Cell cycle/ploidy, photosynthesis and oxidative stress, as well as GC-MS metabolites were assessed. Both UV-B treatments impaired net CO 2 assimilation rate, transpiration rate, photosynthetic pigments, and RuBisCO activity, but 12.4 kJ m -2  d -1 also decreased the photochemical quenching (qP) and the effective efficiency of PSII (Φ PSII ). UV-B treatments promoted mono/triperpene pathways, while only 12.4 kJ m -2  d -1 increased fatty acids and alkanes, and decreased geranylgeranyl-diphosphate. The interplay between physiology and metabolomics suggests some innate ability of these plants to tolerate moderate UV-B doses (6.5 kJ m -2  d -1 ). Also their tolerance to higher doses (12.4 kJ m -2  d -1 ) relies on plants' metabolic adjustments, where the accumulation of specific compounds such as long-chain alkanes, palmitic acid, oleic acid and particularly oleamide (which is described for the first time in olive leaves) play an important protective role. This is the first study demonstrating photosynthetic changes and lipophilic metabolite adjustments in olive leaves under moderate and high UV-B doses. Copyright © 2018 Elsevier GmbH. All rights reserved.

  19. A diet rich in high-glucoraphanin broccoli interacts with genotype to reduce discordance in plasma metabolite profiles by modulating mitochondrial function123

    Science.gov (United States)

    Armah, Charlotte N; Traka, Maria H; Dainty, Jack R; Defernez, Marianne; Janssens, Astrid; Leung, Wing; Doleman, Joanne F; Potter, John F

    2013-01-01

    Background: Observational and experimental studies suggest that diets rich in cruciferous vegetables and glucosinolates may reduce the risk of cancer and cardiovascular disease (CVD). Objective: We tested the hypothesis that a 12-wk dietary intervention with high-glucoraphanin (HG) broccoli would modify biomarkers of CVD risk and plasma metabolite profiles to a greater extent than interventions with standard broccoli or peas. Design: Subjects were randomly assigned to consume 400 g standard broccoli, 400 g HG broccoli, or 400 g peas each week for 12 wk, with no other dietary restrictions. Biomarkers of CVD risk and 347 plasma metabolites were quantified before and after the intervention. Results: No significant differences in the effects of the diets on biomarkers of CVD risk were found. Multivariate analyses of plasma metabolites identified 2 discrete phenotypic responses to diet in individuals within the HG broccoli arm, differentiated by single nucleotide polymorphisms associated with the PAPOLG gene. Univariate analysis showed effects of sex (P broccoli arm, the consequence of the intervention was to reduce variation in lipid and amino acid metabolites, tricarboxylic acid (TCA) cycle intermediates, and acylcarnitines between the 2 PAPOLG genotypes. Conclusions: The metabolic changes observed with the HG broccoli diet are consistent with a rebalancing of anaplerotic and cataplerotic reactions and enhanced integration of fatty acid β-oxidation with TCA cycle activity. These modifications may contribute to the reduction in cancer risk associated with diets that are rich in cruciferous vegetables. This trial was registered at clinicaltrials.gov as NCT01114399. PMID:23964055

  20. 1H magnetic resonance spectroscopy metabolite profiles of neonatal rat hippocampus and brainstem regions following early postnatal exposure to intermittent hypoxia

    Science.gov (United States)

    Darnall, Robert A.; Chen, Xi; Nemani, Krishnamurthy V.; Sirieix, Chrystelle M.; Gimi, Barjor

    2017-03-01

    Most premature infants born at less than 30 weeks gestation are exposed to periods of mild intermittent hypoxia (IH) associated with apnea of prematurity and periodic breathing. In adults, IH associated with sleep apnea causes neurochemical and structural alterations in the brain. However, it is unknown whether IH in the premature infant leads to neurodevelopmental impairment. Quantification of biochemical markers that can precisely identify infants at risk of adverse neurodevelopmental outcome is essential. In vivo 1H magnetic resonance spectroscopy (1H MRS) facilitates the quantification of metabolites from distinct regions of the developing brain. We report the changes in metabolite profiles in the brainstem and hippocampal regions of developing rat brains, resulting from exposure to IH. Rat pups were chosen for study because there is rapid postnatal hippocampal development that occurs during the first 4 weeks in the developing rat brain, which corresponds to the first 2-3 postnatal years of development in humans. The brainstem was examined because of our interest in respiratory control disorders in the newborn and because of brainstem gliosis described in infants who succumb to Sudden Infant Death Syndrome (SIDS). Metabolite profiles were compared between hypoxia treated rat pups (n = 9) and normoxic controls (n = 6). Metabolite profiles were acquired using the Point-RESolved spectroscopy (PRESS) MRS sequence and were quantified using the TARQUIN software. There was a significant difference in the concentrations of creatine (p = 0.031), total creatine (creatine + phosphocreatine) (p = 0.028), and total choline (p = 0.001) in the brainstem, and glycine (p = 0.031) in the hippocampal region. The changes are consistent with altered cellular bioenergetics and metabolism associated with hypoxic insult.

  1. Volatiles and primary metabolites profiling in two Hibiscus sabdariffa (roselle) cultivars via headspace SPME-GC-MS and chemometrics.

    Science.gov (United States)

    Farag, Mohamed A; Rasheed, Dalia M; Kamal, Islam M

    2015-12-01

    Hibiscus sabdariffa (roselle) is a plant of considerable commercial importance worldwide as functional food due to its organic acids, mucilage, anthocyanins, macro and micro-nutrients content. Although Hibiscus flowers are emerging as very competitive targets for phytochemical studies, very little is known about their volatile composition and or aroma, such knowledge can be suspected to be relevant for understanding its olfactory and taste properties. To provide insight into Hibiscus flower aroma composition and for its future use in food and or pharmaceutical industry, volatile constituents from 2 cultivars grown in Egypt, viz. Aswan and Sudan-1 were profiled using solid-phase microextraction (SPME) coupled to GCMS. A total of 104 volatiles were identified with sugar and fatty acid derived volatiles amounting for the major volatile classes. To reveal for cultivar effect on volatile composition in an untargeted manner, multivariate data analysis was applied. Orthogonal projection to latent structures-discriminant analysis (OPLS-DA) revealed for 1-octen-3-ol versus furfural/acetic acid enrichment in Aswan and Sudan-1 cvs., respectively. Primary metabolites contributing to roselle taste and nutritional value viz. sugars and organic acids were profiled using GC-MS after silylation. The impact of probiotic bacteria on roselle infusion aroma profile was further assessed and revealed for the increase in furfural production with Lactobacillus plantarum inoculation and without affecting its anthocyanin content. This study provides the most complete map for volatiles, sugars and organic acids distribution in two Hibiscus flower cultivars and its fermented product. Copyright © 2015 Elsevier Ltd. All rights reserved.

  2. Metabolite profiling and volatiles of pineapple wine and vinegar obtained from pineapple waste.

    Science.gov (United States)

    Roda, Arianna; Lucini, Luigi; Torchio, Fabrizio; Dordoni, Roberta; De Faveri, Dante Marco; Lambri, Milena

    2017-08-15

    Vinegar is an inexpensive commodity, and economic considerations require that a relatively low-cost raw material be used for its production. An investigation into the use of a new, alternative substrate - pineapple waste - is described. This approach enables the utilization of the pineapple's (Ananas comosus) peels and core, which are usually discarded during the processing or consumption of the fruit. Using physical and enzymatic treatments, the waste was saccharified, and the resulting substrate was fermented with Saccharomyces cerevisiae for 7-10days under aerobic conditions at 25°C. This resulted in an alcohol yield of approximately 7%. The alcoholic medium was then used as a seed broth for acetic fermentation using Acetobacter aceti as the inoculum for approximately 30days at 32°C to obtain 5% acetic acid. Samples were analyzed at the beginning and end of the acetification cycle to assess the volatile and fixed compounds by GC-MS and UHPLC-QTOF-MS. The metabolomic analysis indicated that l-lysine, mellein, and gallic acid were significantly more concentrated in the pineapple vinegar than in the original wine. Higher alcohols, aldehydes, and ketones characterized the aroma of the final pineapple vinegar, whilst off-flavors were significantly reduced relative to the initial wine. This study is the first to highlight the metabolite profile of fruit vinegar with a slight floral aroma profile derived from pineapple waste. The potential to efficiently reduce the post-harvest losses of pineapple fruits by re-using them for products with added food values is also demonstrated. Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. Genetic engineering and metabolite profiling for overproduction of polyhydroxybutyrate in cyanobacteria.

    Science.gov (United States)

    Hondo, Sayaka; Takahashi, Masatoshi; Osanai, Takashi; Matsuda, Mami; Hasunuma, Tomohisa; Tazuke, Akio; Nakahira, Yoichi; Chohnan, Shigeru; Hasegawa, Morifumi; Asayama, Munehiko

    2015-11-01

    Genetic engineering and metabolite profiling for the overproduction of polyhydroxybutyrate (PHB), which is a carbon material in biodegradable plastics, were examined in the unicellular cyanobacterium Synechocystis sp. PCC 6803. Transconjugants harboring cyanobacterial expression vectors that carried the pha genes for PHB biosynthesis were constructed. The overproduction of PHB by the engineering cells was confirmed through microscopic observations using Nile red, transmission electron microscopy (TEM), or nuclear magnetic resonance (NMR). We successfully recovered PHB from transconjugants prepared from nitrogen-depleted medium without sugar supplementation in which PHB reached approximately 7% (w/w) of the dry cell weight, showing a value of 12-fold higher productivity in the transconjugant than that in the control strain. We also measured the intracellular levels of acetyl-CoA, acetoacetyl-CoA, and 3-hydroxybutyryl-CoA (3HB-CoA), which are intermediate products for PHB. The results obtained indicated that these products were absent or at markedly low levels when cells were subjected to the steady-state growth phase of cultivation under nitrogen depletion for the overproduction of bioplastics. Based on these results, efficient factors were discussed for the overproduction of PHB in recombinant cyanobacteria. Copyright © 2015 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  4. Differences between flocculating yeast and regular industrial yeast in transcription and metabolite profiling during ethanol fermentation

    Directory of Open Access Journals (Sweden)

    Lili Li

    2017-03-01

    Full Text Available Objectives: To improve ethanolic fermentation performance of self-flocculating yeast, difference between a flocculating yeast strain and a regular industrial yeast strain was analyzed by transcriptional and metabolic approaches. Results: The number of down-regulated (industrial yeast YIC10 vs. flocculating yeast GIM2.71 and up-regulated genes were 4503 and 228, respectively. It is the economic regulation for YIC10 that non-essential genes were down-regulated, and cells put more “energy” into growth and ethanol production. Hexose transport and phosphorylation were not the limiting-steps in ethanol fermentation for GIM2.71 compared to YIC10, whereas the reaction of 1,3-disphosphoglycerate to 3-phosphoglycerate, the decarboxylation of pyruvate to acetaldehyde and its subsequent reduction to ethanol were the most limiting steps. GIM2.71 had stronger stress response than non-flocculating yeast and much more carbohydrate was distributed to other bypass, such as glycerol, acetate and trehalose synthesis. Conclusions: Differences between flocculating yeast and regular industrial yeast in transcription and metabolite profiling will provide clues for improving the fermentation performance of GIM2.71.

  5. The use of secondary metabolite profiling in chemotaxonomy of filamentous fungi

    DEFF Research Database (Denmark)

    Frisvad, Jens Christian; Andersen, Birgitte; Thrane, Ulf

    2008-01-01

    distribution throughout the fungal kingdom. However, this is the very quality that makes secondary metabolites so useful in classification and identification. Four groups of organisms are particularly good producers of secondary metabolites: plants, fungi, lichen fungi, and actinomycetes, whereas yeasts...... have been analysed for a wide array of terpenes, polyketides, non-ribosomal peptides, and combinations of these. Fungal chemotaxonomy based on secondary metabolites has been used successfully in large ascomycete genera such as Alternaria, Aspergillus, Fusarium, Hypoxylon, Penicillium, Stachybotrys...

  6. Metabolite Profiles in Leaves and Spikes of Wheat under Constrasting Field-growing Environments Are Derived from Hyperspectral Readings

    Science.gov (United States)

    Vergara-Diaz, O.; Obata, T., Sr.; Kefauver, S. C.; Fernie, A., Sr.; Araus, J. L.

    2017-12-01

    The advance on metabolomics has led to a better understanding of plant-environment interactions and how the levels of specific metabolites may be used as indicators of plant performance. In cereals, the accumulation of certain metabolites -such as proline and sugars- has been related with water stress and drought tolerance/susceptibility, even revealing significant relationships with yield. On the other hand, recent studies relating plant biochemicals with spectral reflectance open the door to a deep assessment of plant status which would have implications on plant breeding and ecosystem studies. In this study, we investigated in durum wheat the relationship between the reflectance in the visible and near infrared regions (400-2500 µm wavelength) of the spectrum of the flag leaf, the ears and canopy levels with their respective metabolite profiles as well as its relationship with yield. To this aim, five durum wheat genotypes grown in four environments in the field were examined. PLS regression models indicated a strong determination of yield by using the spectrum of either leaves, ears and canopy. Additionally, grain yield was strongly predicted by the metabolite content of leaves and ears with multivariate regression analysis. Further preliminary results showed a promising performance of hyperspectral remote-proximal sensing for the calibration of plant metabolite content.

  7. Metabolite profiling of polyphenols in the Tunisian plant Tamarix aphylla (L.) Karst.

    Science.gov (United States)

    Mahfoudhi, Adel; Prencipe, Francesco Pio; Mighri, Zine; Pellati, Federica

    2014-10-01

    In this study, a detailed investigation on the composition of polyphenols of Tamarix aphylla (L.) Karst., consisting of phenolic acids and flavonoids, was carried out. In order to optimize the yield of secondary metabolites, three extraction techniques were compared, including dynamic maceration, ultrasound-assisted extraction and Soxhlet extraction. The latter technique provided the best results in terms of both recovery and selectivity, using ethyl acetate as extraction solvent for 2h. The analysis of T. aphylla polyphenols was performed by means of HPLC-UV/DAD, HPLC-ESI-MS and MS(2), using an ion trap mass analyzer. Phenolic acids and flavonoids were separated on an Ascentis C18 column (250mm×4.6mm I.D., 5μm), with a mobile phase composed of 0.1M formic acid in water and acetonitrile, under gradient elution. The proposed method was fully validated in agreement with ICH guidelines and then applied to the analysis of T. aphylla leaves and stems. A total of 14 phenolic compounds were characterized for the first time in this plant extracts by using UV, MS and MS(2) data. The amount of total phenolics was found to be 993.1±22.5μg/g in the leaves and 113.1±25.8μg/g in the stems, respectively. The most abundant constituents found in the leaves include ellagic acid (211.4±10.8μg/g), quercetin (125.7±4.7μg/g) and gallic acid (120.6±1.2μg/g), whereas those in the stems were ellagic acid (44.4±3.9μg/g), gallic acid (24.3±3.3μg/g) and kaempferol (16.3±1.6μg/g). The developed method can be considered a useful tool for the metabolite profiling of T. aphylla, which represents a potential source of bioactive compounds to be used in phytotherapy. Copyright © 2014 Elsevier B.V. All rights reserved.

  8. How does P affect photosynthesis and metabolite profiles of Eucalyptus globulus?

    Science.gov (United States)

    Warren, Charles R

    2011-07-01

    Phosphorus (P) has multiple effects on plant metabolism, but there are many unresolved questions especially for evergreen trees. For example, we do not know the general effects of P on metabolism, or if P affects photosynthesis via the internal conductance to CO(2) transfer from sub-stomatal cavities to chloroplast or amounts of Rubisco. This study investigates how P deficiency affects seedlings of the evergreen tree Eucalyptus globulus grown for 2.5 months with four nutrient solutions differing in P concentration. To determine why photosynthesis was affected by P supply, Rubisco was quantified by capillary electrophoresis, internal conductance was quantified from gas exchange and carbon isotope discrimination, and biochemical parameters of photosynthesis were estimated from A/C(c) responses. Additional insights into the effect of P on metabolism were provided by gas chromatography-mass spectrometry (GC-MS) metabolite profiling. Larger concentrations of P in the nutrient solution led to significantly faster rates of photosynthesis. There was no evidence that stomatal or internal conductances contributed to the effect of P supply on photosynthesis. The increase in photosynthesis with P supply was correlated with V(cmax), and amounts of P, phosphate and fructose 6-phosphate (6-P). Phosphorous supply affected approximately one-third of the 90 aqueous metabolites quantified by GC-MS, but the effect size was generally smaller than reported for experiments on herbaceous species. Phosphorus deficiency decreased concentrations of phosphate, glucose 6-P and fructose 6-P more than it decreased photosynthesis, suggesting faster turnover of smaller pools of phosphate and phosphorylated intermediates. The effect of P supply on most amino acids was small, with the exception of arginine and glutamine, which increased dramatically under P deficiency. P deficiency had small or non-significant effects on carbohydrates and organic acids of the tricarboxylic acid (TCA) cycle. The

  9. Non-targeted metabolite profiling highlights the potential of strawberry leaves as a resource for specific bioactive compounds.

    Science.gov (United States)

    Kårlund, Anna; Hanhineva, Kati; Lehtonen, Marko; McDougall, Gordon J; Stewart, Derek; Karjalainen, Reijo O

    2017-05-01

    The non-edible parts of horticultural crops, such as leaves, contain substantial amounts of valuable bioactive compounds which are currently only little exploited. For example, strawberry (Fragaria × ananassa) leaves may be a promising bioresource for diverse health-related applications. However, product standardization sets a real challenge, especially when the leaf material comes from varying cultivars. The first step towards better quality control of berry fruit leaf-based ingredients and supplements is to understand metabolites present and their stability in different plant cultivars, so this study surveyed the distribution of potentially bioactive strawberry leaf metabolites in six different strawberry cultivars. Non-targeted metabolite profiling analysis using LC/qTOF-ESI-MS with data processing via principal component analysis and k-means clustering analysis was utilized to examine differences and commonalities between the leaf metabolite profiles. Quercetin and kaempferol derivatives were the dominant flavonol groups in strawberry leaves. Previously described and novel caffeic and chlorogenic acid derivatives were among the major phenolic acids. In addition, ellagitannins were one of the distinguishing compound classes in strawberry leaves. In general, strawberry leaves also contained high levels of octadecatrienoic acid derivatives, precursors of valuable odour compounds. The specific bioactive compounds found in the leaves of different strawberry cultivars offer the potential for the selection of optimized leaf materials for added-value food and non-food applications. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

  10. Targeted and Untargeted Metabolic Profiling of Wild Grassland Plants identifies Antibiotic and Anthelmintic Compounds Targeting Pathogen Physiology, Metabolism and Reproduction.

    Science.gov (United States)

    French, Katherine E; Harvey, Joe; McCullagh, James S O

    2018-01-26

    Plants traditionally used by farmers to manage livestock ailments could reduce reliance on synthetic antibiotics and anthelmintics but in many cases their chemical composition is unknown. As a case study, we analyzed the metabolite profiles of 17 plant species and 45 biomass samples from agricultural grasslands in England using targeted and untargeted metabolite profiling by liquid-chromatography mass spectrometry. We identified a range of plant secondary metabolites, including 32 compounds with known antimicrobial/anthelmintic properties which varied considerably across the different plant samples. These compounds have been shown previously to target multiple aspects of pathogen physiology and metabolism in vitro and in vivo, including inhibition of quorum sensing in bacteria and egg viability in nematodes. The most abundant bioactive compounds were benzoic acid, myricetin, p-coumaric acid, rhamnetin, and rosmarinic acid. Four wild plants (Filipendula ulmaria (L.) Maxim., Prunella vulgaris L., Centuarea nigra L., and Rhinanthus minor L.) and two forage legumes (Medicago sativa L., Trifolium hybridium L.) contained high levels of these compounds. Forage samples from native high-diversity grasslands had a greater abundance of medicinal compounds than samples from agriculturally improved grasslands. Incorporating plants with antibiotic/anthelmintic compounds into livestock feeds may reduce global drug-resistance and preserve the efficacy of last-resort drugs.

  11. Solvent system selectivities in countercurrent chromatography using Salicornia gaudichaudiana metabolites as practical example with off-line electrospray mass-spectrometry injection profiling.

    Science.gov (United States)

    Costa, Fernanda das Neves; Jerz, Gerold; Figueiredo, Fabiana de Souza; Winterhalter, Peter; Leitão, Gilda Guimarães

    2015-03-13

    For the development of an efficient two-stage isolation process for high-speed countercurrent chromatography (HSCCC) with focus on principal metabolites from the ethyl acetate extract of the halophyte plant Salicornia gaudichaudiana, separation selectivities of two different biphasic solvent systems with similar polarities were evaluated using the elution and extrusion approach. Efficiency in isolation of target compounds is determined by the solvent system selectivity and their chronological use in multiple separation steps. The system n-hexane-ethyl acetate-methanol-water (0.5:6:0.5:6, v/v/v/v) resulted in a comprehensive separation of polyphenolic glycosides. The system n-hexane-n-butanol-water (1:1:2, v/v/v) was less universal but was highly efficient in the fractionation of positional isomers such as di-substituted cinnamic acid quinic acid derivatives. Multiple metabolite detection performed on recovered HSCCC tube fractions was done with rapid mass-spectrometry profiling by sequential off-line injections to electrospray mass-spectrometry (ESI-MS/MS). Selective ion traces of metabolites delivered reconstituted preparative HSCCC runs. Molecular weight distribution of target compounds in single HSCCC tube fractions and MS/MS fragment data were available. Chromatographic areas with strong co-elution effects and fractions of pure recoverable compounds were visualized. In total 11 metabolites have been identified and monitored. Result of this approach was a fast isolation protocol for S. gaudichaudiana metabolites using two solvent systems in a strategic sequence. The process could easily be scaled-up to larger lab-scale or industrial recovery. Copyright © 2015 Elsevier B.V. All rights reserved.

  12. Genome wide transcriptome profiling reveals differential gene expression in secondary metabolite pathway of Cymbopogon winterianus.

    Science.gov (United States)

    Devi, Kamalakshi; Mishra, Surajit K; Sahu, Jagajjit; Panda, Debashis; Modi, Mahendra K; Sen, Priyabrata

    2016-02-15

    Advances in transcriptome sequencing provide fast, cost-effective and reliable approach to generate large expression datasets especially suitable for non-model species to identify putative genes, key pathway and regulatory mechanism. Citronella (Cymbopogon winterianus) is an aromatic medicinal grass used for anti-tumoral, antibacterial, anti-fungal, antiviral, detoxifying and natural insect repellent properties. Despite of having number of utilities, the genes involved in terpenes biosynthetic pathway is not yet clearly elucidated. The present study is a pioneering attempt to generate an exhaustive molecular information of secondary metabolite pathway and to increase genomic resources in Citronella. Using high-throughput RNA-Seq technology, root and leaf transcriptome was analysed at an unprecedented depth (11.7 Gb). Targeted searches identified majority of the genes associated with metabolic pathway and other natural product pathway viz. antibiotics synthesis along with many novel genes. Terpenoid biosynthesis genes comparative expression results were validated for 15 unigenes by RT-PCR and qRT-PCR. Thus the coverage of these transcriptome is comprehensive enough to discover all known genes of major metabolic pathways. This transcriptome dataset can serve as important public information for gene expression, genomics and function genomics studies in Citronella and shall act as a benchmark for future improvement of the crop.

  13. Maternal Metabolomic Profile and Fetal Programming of Offspring Adiposity: Identification of Potentially Protective Lipid Metabolites.

    Science.gov (United States)

    Hellmuth, Christian; Lindsay, Karen L; Uhl, Olaf; Buss, Claudia; Wadhwa, Pathik D; Koletzko, Berthold; Entringer, Sonja

    2018-04-30

    The fetal programming paradigm posits that the origins of obesity can be traced, in part, to the intrauterine period of life. However, the mechanisms underlying fetal programming are not well understood, and few studies have measured offspring adiposity in the neonatal period. The aim of this study was to identify maternal metabolites, and their determinants, that are associated with neonatal adiposity. We applied a targeted metabolomics approach to analyze plasma samples collected across gestation from a well-characterized cohort of 253 pregnant women participating in a prospective study at the University of California, Irvine. Whole-body Dual X-Ray Absorptiometry (DXA) imaging of body composition was obtained in N = 121 newborns. Statistical models were adjusted for potential confounders and multiple testing. We identified six alkyl-linked phosphatidylcholines (PCae), containing fatty acid 20:4, that were significantly and negatively associated with neonatal body fat percentage. Factors indicating higher socioeconomic status, non-Hispanic ethnicity and higher non-esterified fatty acid percentages were positively associated with these PCae. The polyunsaturated fatty acid 20:4 contained in PCae may exert a beneficial effect with respect to future propensity for obesity development. Pre- and early-pregnancy factors are determinants of these PCae, highlighting the importance of addressing pre-conceptional conditions for fetal programming of newborn adiposity. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  14. Profiling contents of water-soluble metabolites and mineral nutrients to evaluate the effects of pesticides and organic and chemical fertilizers on tomato fruit quality

    OpenAIRE

    WATANABE, Masami; Ohta, Yuko; SUN, Li-Cang; Motoyama, Naoki; Kikuchi, Jun

    2015-01-01

    In this study, the contents of water-soluble metabolites and mineral nutrients were measured in tomatoes cultured using organic and chemical fertilizers, with or without pesticides. Mineral nutrients and water-soluble metabolites were determined by inductively coupled plasma-atomic emission spectrometry and 1H nuclear magnetic resonance spectrometry, respectively, and results were analyzed by principal components analysis (PCA). The mineral nutrient and water-soluble metabolite profiles diffe...

  15. Automatic untargeted metabolic profiling analysis coupled with Chemometrics for improving metabolite identification quality to enhance geographical origin discrimination capability.

    Science.gov (United States)

    Han, Lu; Zhang, Yue-Ming; Song, Jing-Jing; Fan, Mei-Juan; Yu, Yong-Jie; Liu, Ping-Ping; Zheng, Qing-Xia; Chen, Qian-Si; Bai, Chang-Cai; Sun, Tao; She, Yuan-Bin

    2018-03-16

    Untargeted metabolic profiling analysis is employed to screen metabolites for specific purposes, such as geographical origin discrimination. However, the data analysis remains a challenging task. In this work, a new automatic untargeted metabolic profiling analysis coupled with a chemometric strategy was developed to improve the metabolite identification results and to enhance the geographical origin discrimination capability. Automatic untargeted metabolic profiling analysis with chemometrics (AuMPAC) was used to screen the total ion chromatographic (TIC) peaks that showed significant differences among the various geographical regions. Then, a chemometric peak resolution strategy is employed for the screened TIC peaks. The retrieved components were further analyzed using ANOVA, and those that showed significant differences were used to build a geographical origin discrimination model by using two-way encoding partial least squares. To demonstrate its performance, a geographical origin discrimination of flaxseed samples from six geographical regions in China was conducted, and 18 TIC peaks were screened. A total of 19 significant different metabolites were obtained after the peak resolution. The accuracy of the geographical origin discrimination was up to 98%. A comparison of the AuMPAC, AMDIS, and XCMS indicated that AuMPACobtained the best geographical origin discrimination results. In conclusion, AuMPAC provided another method for data analysis. Copyright © 2018 Elsevier B.V. All rights reserved.

  16. Ecotype variability in growth and secondary metabolite profile in Moringa oleifera: impact of sulfur and water availability.

    Science.gov (United States)

    Förster, Nadja; Ulrichs, Christian; Schreiner, Monika; Arndt, Nick; Schmidt, Reinhard; Mewis, Inga

    2015-03-25

    Moringa oleifera is widely cultivated in plantations in the tropics and subtropics. Previous cultivation studies with M. oleifera focused primarily only on leaf yield. In the present study, the content of potentially health-promoting secondary metabolites (glucosinolates, phenolic acids, and flavonoids) were also investigated. Six different ecotypes were grown under similar environmental conditions to identify phenotypic differences that can be traced back to the genotype. The ecotypes TOT4880 (origin USA) and TOT7267 (origin India) were identified as having the best growth performance and highest secondary metabolite production, making them an ideal health-promoting food crop. Furthermore, optimal cultivation conditions-exemplarily on sulfur fertilization and water availability-for achieving high leaf and secondary metabolite yields were investigated for M. oleifera. In general, plant biomass and height decreased under water deficiency compared to normal cultivation conditions, whereas the glucosinolate content increased. The effects depended to a great extent on the ecotype.

  17. Profiling primaquine metabolites in primary human hepatocytes using UHPLC-QTOF-MS with 13C stable isotope labeling.

    Science.gov (United States)

    Avula, Bharathi; Tekwani, Babu L; Chaurasiya, Narayan D; Nanayakkara, N P Dhammika; Wang, Yan-Hong; Khan, Shabana I; Adelli, Vijender R; Sahu, Rajnish; Elsohly, Mahmoud A; McChesney, James D; Khan, Ikhlas A; Walker, Larry A

    2013-02-01

    Therapeutic efficiency and hemolytic toxicity of primaquine (PQ), the only drug available for radical cure of relapsing vivax malaria are believed to be mediated by its metabolites. However, identification of these metabolites has remained a major challenge apparently due to low quantities and their reactive nature. Drug candidates labeled with stable isotopes afford convenient tools for tracking drug-derived metabolites in complex matrices by liquid chromatography-tandem mass spectrometry (LC-MS-MS) and filtering for masses with twin peaks attributable to the label. This study was undertaken to identify metabolites of PQ from an in vitro incubation of a 1:1 w/w mixture of (13)C(6)-PQ/PQ with primary human hepatocytes. Acquity ultra-performance LC (UHPLC) was integrated with QTOF-MS to combine the efficiency of separation with high sensitivity, selectivity of detection and accurate mass determination. UHPLC retention time, twin mass peaks with difference of 6 (originating from (13)C(6)-PQ/PQ), and MS-MS fragmentation pattern were used for phenotyping. Besides carboxy-PQ (cPQ), formed by oxidative deamination of PQ to an aldehyde and subsequent oxidation, several other metabolites were identified: including PQ alcohol, predictably generated by oxidative deamination of PQ to an aldehyde and subsequent reduction, its acetate and the alcohol's glucuronide conjugate. Trace amounts of quinone-imine metabolites of PQ and cPQ were also detected which may be generated by hydroxylation of the PQ/cPQ quinoline ring at the 5-position and subsequent oxidation. These findings shed additional light on the human hepatic metabolism of PQ, and the method can be applied for identification of reactive PQ metabolites generated in vivo in preclinical and clinical studies. Copyright © 2013 John Wiley & Sons, Ltd.

  18. Integration of Traditional and Metabolomics Biomarkers Identifies Prognostic Metabolites for Predicting Responsiveness to Nutritional Intervention against Oxidative Stress and Inflammation

    Directory of Open Access Journals (Sweden)

    You Jin Kim

    2017-03-01

    Full Text Available Various statistical approaches can be applied to integrate traditional and omics biomarkers, allowing the discovery of prognostic markers to classify subjects into poor and good prognosis groups in terms of responses to nutritional interventions. Here, we performed a prototype study to identify metabolites that predict responses to an intervention against oxidative stress and inflammation, using a data set from a randomized controlled trial evaluating Korean black raspberry (KBR in sedentary overweight/obese subjects. First, a linear mixed-effects model analysis with multiple testing correction showed that four-week consumption of KBR significantly changed oxidized glutathione (GSSG, q = 0.027 level, the ratio of reduced glutathione (GSH to GSSG (q = 0.039 in erythrocytes, malondialdehyde (MDA, q = 0.006 and interleukin-6 (q = 0.006 levels in plasma, and seventeen NMR metabolites in urine compared with those in the placebo group. A subsequent generalized linear mixed model analysis showed linear correlations between baseline urinary glycine and N-phenylacetylglycine (PAG and changes in the GSH:GSSG ratio (p = 0.008 and 0.004 as well as between baseline urinary adenine and changes in MDA (p = 0.018. Then, receiver operating characteristic analysis revealed that a two-metabolite set (glycine and PAG had the strongest prognostic relevance for future interventions against oxidative stress (the area under the curve (AUC = 0.778. Leave-one-out cross-validation confirmed the accuracy of prediction (AUC = 0.683. The current findings suggest that a higher level of this two-metabolite set at baseline is useful for predicting responders to dietary interventions in subjects with oxidative stress and inflammation, contributing to the emergence of personalized nutrition.

  19. Liquid Chromatography-Mass Spectrometry-Based Rapid Secondary-Metabolite Profiling of Marine Pseudoalteromonas sp. M2

    Directory of Open Access Journals (Sweden)

    Woo Jung Kim

    2016-01-01

    Full Text Available The ocean is a rich resource of flora, fauna, and food. A wild-type bacterial strain showing confluent growth on marine agar with antibacterial activity was isolated from marine water, identified using 16S rDNA sequence analysis as Pseudoalteromonas sp., and designated as strain M2. This strain was found to produce various secondary metabolites including quinolone alkaloids. Using high-resolution mass spectrometry (MS and nuclear magnetic resonance (NMR analysis, we identified nine secondary metabolites of 4-hydroxy-2-alkylquinoline (pseudane-III, IV, V, VI, VII, VIII, IX, X, and XI. Additionally, this strain produced two novel, closely related compounds, 2-isopentylqunoline-4-one and 2-(2,3-dimetylbutylqunoline-4-(1H-one, which have not been previously reported from marine bacteria. From the metabolites produced by Pseudoalteromonas sp. M2, 2-(2,3-dimethylbutylquinolin-4-one, pseudane-VI, and pseudane-VII inhibited melanin synthesis in Melan-A cells by 23.0%, 28.2%, and 42.7%, respectively, wherein pseudane-VII showed the highest inhibition at 8 µg/mL. The results of this study suggest that liquid chromatography (LC-MS/MS-based metabolite screening effectively improves the efficiency of novel metabolite discovery. Additionally, these compounds are promising candidates for further bioactivity development.

  20. Proteomic profile of the Bradysia odoriphaga in response to the microbial secondary metabolite benzothiazole

    Science.gov (United States)

    Zhao, Yunhe; Cui, Kaidi; Xu, Chunmei; Wang, Qiuhong; Wang, Yao; Zhang, Zhengqun; Liu, Feng; Mu, Wei

    2016-01-01

    Benzothiazole, a microbial secondary metabolite, has been demonstrated to possess fumigant activity against Sclerotinia sclerotiorum, Ditylenchus destructor and Bradysia odoriphaga. However, to facilitate the development of novel microbial pesticides, the mode of action of benzothiazole needs to be elucidated. Here, we employed iTRAQ-based quantitative proteomics analysis to investigate the effects of benzothiazole on the proteomic expression of B. odoriphaga. In response to benzothiazole, 92 of 863 identified proteins in B. odoriphaga exhibited altered levels of expression, among which 14 proteins were related to the action mechanism of benzothiazole, 11 proteins were involved in stress responses, and 67 proteins were associated with the adaptation of B. odoriphaga to benzothiazole. Further bioinformatics analysis indicated that the reduction in energy metabolism, inhibition of the detoxification process and interference with DNA and RNA synthesis were potentially associated with the mode of action of benzothiazole. The myosin heavy chain, succinyl-CoA synthetase and Ca+-transporting ATPase proteins may be related to the stress response. Increased expression of proteins involved in carbohydrate metabolism, energy production and conversion pathways was responsible for the adaptive response of B. odoriphaga. The results of this study provide novel insight into the molecular mechanisms of benzothiazole at a large-scale translation level and will facilitate the elucidation of the mechanism of action of benzothiazole. PMID:27883048

  1. Chemometric analysis of the secondary metabolite profile of Yarrow (Achillea collina Becker ex Rchb. affected by phloem feeding Myzus persicae Sulzer aphids

    Directory of Open Access Journals (Sweden)

    Annamaria Giorgi

    2010-07-01

    Full Text Available Yarrow (Achillea collina Becker ex Rchb. has a high content of secondary metabolites including phenolic acids. Among them, hydroxycinnamic acid such as chlorogenic acid and its derivatives were found to be the most abundant ones. The phloem feeding Myzus persicae Sulzer was hypothesized to affect the contents of secondary metabolites and change the metabolite profile. A high-performance liquid chromatography technique (HPLC was used to evaluate whether there is a difference in the phenolic profile between aphid infested and non-infested yarrow leaves. M. persicae colonies composed of between 20 and 30 individuals were allowed to feed for 10 and 20 days. Preprocessing was carried out to standardize the procedures in order to obtain optimal separation of analytes, good chromatographic peak shape and robustness of the results. The methanol extracts of leaves were analyzed by means of HPLC, and the time series of peak areas obtained from each extract were evaluated through chemometric analyses. Results of the phenolic fingerprints showed a specific chromatographic profile with 58 peaks. An autoregression analysis demonstrated the absence of correlation. The discriminant analysis carried out with the data satisfying the assumption of the absence of collinearity showed a significant effect of phloem feeding on soluble phenolic compounds and identified two peaks that separate aphid infested from non-infested plants. The hydroxycinnamic acids widely found in A. collina leaves were not affected by M. persicae feeding. The results are the basis for the current studies aiming at the identification of chemical compounds that correspond to the peaks.

  2. Serum Metabolite Profiles Are Altered by Erlotinib Treatment and the Integrin α1-Null Genotype but Not by Post-Traumatic Osteoarthritis.

    Science.gov (United States)

    Mickiewicz, Beata; Shin, Sung Y; Pozzi, Ambra; Vogel, Hans J; Clark, Andrea L

    2016-03-04

    The risk of developing post-traumatic osteoarthritis (PTOA) following joint injury is high. Furthering our understanding of the molecular mechanisms underlying PTOA and/or identifying novel biomarkers for early detection may help to improve treatment outcomes. Increased expression of integrin α1β1 and inhibition of epidermal growth factor receptor (EGFR) signaling protect the knee from spontaneous OA; however, the impact of the integrin α1β1/EGFR axis on PTOA is currently unknown. We sought to determine metabolic changes in serum samples collected from wild-type and integrin α1-null mice that underwent surgery to destabilize the medial meniscus and were treated with the EGFR inhibitor erlotinib. Following (1)H nuclear magnetic resonance spectroscopy, we generated multivariate statistical models that distinguished between the metabolic profiles of erlotinib- versus vehicle-treated mice and the integrin α1-null versus wild-type mouse genotype. Our results show the sex-dependent effects of erlotinib treatment and highlight glutamine as a metabolite that counteracts this treatment. Furthermore, we identified a set of metabolites associated with increased reactive oxygen species production, susceptibility to OA, and regulation of TRP channels in α1-null mice. Our study indicates that systemic pharmacological and genetic factors have a greater effect on serum metabolic profiles than site-specific factors such as surgery.

  3. Serum metabolite profiles are altered by erlotinib treatment and the integrin α1-null genotype, but not by post traumatic osteoarthritis

    Science.gov (United States)

    Mickiewicz, Beata; Shin, Sung Y.; Pozzi, Ambra; Vogel, Hans J.; Clark, Andrea L.

    2016-01-01

    The risk of developing post traumatic osteoarthritis (PTOA) following joint injury is high. Furthering our understanding of the molecular mechanisms underlying PTOA and/or identifying novel biomarkers for early detection may help improve treatment outcomes. Increased expression of integrin α1β1 and inhibition of epidermal growth factor receptor (EGFR) signaling protect the knee from spontaneous OA, however the impact of the integrin α1β1/EGFR axis on PTOA is currently unknown. We sought to determine metabolic changes in serum samples collected from wild type and integrin α1-null mice that underwent surgery to destabilize the medial meniscus and were treated with the EGFR inhibitor erlotinib. Following 1H nuclear magnetic resonance spectroscopy we generated multivariate statistical models that distinguished between the metabolic profiles of erlotinib- versus vehicle-treated mice, and the integrin α1-null versus wild type mouse genotype. Our results show the sex dependent effects of erlotinib treatment and highlight glutamine as a metabolite that counteracts this treatment. Furthermore, we identified a set of metabolites associated with increased reactive oxygen species production, susceptibility to OA and regulation of TRP channels in α1-null mice. Our study indicates that systemic pharmacological and genetic factors have a greater effect on serum metabolic profiles than site specific factors such as surgery. PMID:26784366

  4. Profiling primaquine metabolites in primary human hepatocytes by UPLC-QTOF-MS with 13c stable isotope labeling

    Science.gov (United States)

    Primaquine (PQ) is an important antimalarial agent because of its activity against exoerythrocytic forms of Plasmodium spp. However, hemolytic anemia is a dose-limiting side effect of primaquine therapy that limits its widespread use. The major plasma metabolite identified in humans and animals, car...

  5. Raman spectroscopy applied to identify metabolites in urine of physically active subjects.

    Science.gov (United States)

    Moreira, Letícia Parada; Silveira, Landulfo; da Silva, Alexandre Galvão; Fernandes, Adriana Barrinha; Pacheco, Marcos Tadeu Tavares; Rocco, Débora Dias Ferraretto Moura

    2017-11-01

    Raman spectroscopy is a rapid and non-destructive technique suitable for biological fluids analysis. In this work, dispersive Raman spectroscopy has been employed as a rapid and nondestructive technique to detect the metabolites in urine of physically active subjects before and after vigorous 30min pedaling or running compared to sedentary subjects. For so, urine samples from 9 subjects were obtained before and immediately after physical activities and submitted to Raman spectroscopy (830nm excitation, 250mW laser power, 20s integration time) and compared to urine from 5 sedentary subjects. The Raman spectra of urine from sedentary showed peaks related to urea, creatinine, ketone bodies, phosphate and other nitrogenous compounds. These metabolic biomarkers presented peaks with different intensities in the urine of physically active individuals after exercises compared to before, measured by the intensity of selected peaks the Raman spectra, which means different concentrations after training. These peaks presented different intensity values for each subject before physical activity, also behaving differently compared to the post-training: some subjects presented increase while others decrease the intensity. Raman spectroscopy may allow the development of a rapid and non-destructive test for metabolic evaluation of the physical training in active and trained subjects using urine samples, allowing nutrition adjustment with the sport's performance. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. Metabolite profiling of red and white pitayas (Hylocereus polyrhizus and Hylocereus undatus) for comparing betalain biosynthesis and antioxidant activity.

    Science.gov (United States)

    Suh, Dong Ho; Lee, Sunmin; Heo, Do Yeon; Kim, Young-Suk; Cho, Somi Kim; Lee, Sarah; Lee, Choong Hwan

    2014-08-27

    Metabolite profiling of red and white pitayas (Hylocereus polyrhizus and Hylocereus undatus) was performed using gas chromatography-time-of-flight-mass spectrometry and ultraperformance liquid chromatography-quadrupole-time-of-flight-mass spectrometry with multivariate analysis. Different species and parts of pitayas (red peel, RP; white peel, WP; red flesh, RF; and white flesh, WF) were clearly separated by partial least-squares discriminate analysis. Furthermore, betalain-related metabolites, such as betacyanins and betaxanthins, or their precursors were described on the basis of their metabolites. The results of antioxidant activity tests [1,1-diphenyl-2-picrylhydrazyl (DPPH), 2,2'-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt (ABTS), and ferric reducing ability of plasma (FRAP)], total phenolic contents (TPC), total flavonoid contents (TFC), and total betacyanin contents (TBC) showed the following: RP ≥ WP > RF > WF. TPC, TFC, TBC, and betalain-related metabolites were higher in the peel than in the flesh and suggested to be the main contributors to antioxidant activity in pitayas. Therefore, peels as well as pulp of pitaya could beneficially help in the food industry.

  7. Profiling of external metabolites during production of hantavirus nucleocapsid protein with recombinant Saccharomyces cerevisiae

    OpenAIRE

    Antoniukas, Linas; Grammel, Hartmut; Sasnauskas, Kestutis; Reichl, Udo

    2007-01-01

    Recombinant strains of Saccharomyces cerevisiae, producing hantavirus Puumala nucleocapsid protein for diagnostics and as a candidate vaccine were analyzed for uptake and excretion of intermediary metabolites during process optimization studies of fed-batch bioreactor cultures. Concentrations of glucose, maltose, galactose, pyruvate, acetaldehyde, ethanol, acetate, succinate and formaldehyde (used as a selection agent) were measured in the culture medium in order to find a metabolite pattern,...

  8. Structural characterization and discrimination of Chinese medicinal materials with multiple botanical origins based on metabolite profiling and chemometrics analysis: Clematidis Radix et Rhizoma as a case study.

    Science.gov (United States)

    Guo, Lin-Xiu; Li, Rui; Liu, Ke; Yang, Jie; Li, Hui-Jun; Li, Song-Lin; Liu, Jian-Qun; Liu, Li-Fang; Xin, Gui-Zhong

    2015-12-18

    Traditional Chinese medicines (TCMs)-based products are becoming more and more popular over the world. To ensure the safety and efficacy, authentication of Chinese medicinal materials has been an important issue, especially for that with multiple botanical origins (one-to-multiple). Taking Clematidis Radix et Rhizoma (CRR) as a case study, we herein developed an integrated platform based on metabolite profiling and chemometrics analysis to characterize, classify, and predict the "one-to-multiple" herbs. Firstly, the predominant constituents, triterpenoid saponins, in three Clematis CRR were rapid characterized by a novel UPLC-QTOF/MS-based strategy, and a total of 49 triterpenoid saponins were identified. Secondly, metabolite profiling was performed by UPLC-QTOF/MS, and 4623 variables were extracted and aligned as dataset. Thirdly, by using pattern recognition analysis, a clear separation of the three Clematis CRR was achieved as well as a total number of 28 variables were screened as the valuable variables for discrimination. By matching with identified saponins, these 28 variables were corresponding to 10 saponins which were identified as marker compounds. Fourthly, based on the relative intensity of the marker compounds-related variables, genetic algorithm optimized support vector machines (GA-SVM) was employed to predict the species of CRR samples. The obtained model showed excellent prediction performance with a prediction accuracy of 100%. Finally, a heatmap visualization was employed for clarifying the distribution of identified saponins, which could be useful for phytochemotaxonomy study of Clematis herbs. These results indicated that our proposed platform was a powerful tool for chemical profiling and discrimination of herbs with multiple botanical origins, providing promising perspectives in tracking the formulation processes of TCMs products. Copyright © 2015 Elsevier B.V. All rights reserved.

  9. Metabolite profile of koji amazake and its lactic acid fermentation product by Lactobacillus sakei UONUMA.

    Science.gov (United States)

    Oguro, Yoshifumi; Nishiwaki, Toshikazu; Shinada, Ryota; Kobayashi, Kazuya; Kurahashi, Atsushi

    2017-08-01

    The koji amazake is a traditional sweet Japanese beverage. It has been consumed for over a thousand years in Japan; nonetheless, little is yet known of the ingredients in koji amazake. Therefore, this study aimed to analyze the metabolites of koji amazake using a metabolomics approach. Additionally, we reformed the flavor of koji amazake by lactic acid fermentation (LAF-amazake) using Lactobacillus sakei UONUMA, which was isolated from snow caverns. The purpose of this article is to identify the ingredients in these beverages. In LAF-amazake and koji amazake, sugars, amino acids, organic acids, and vitamin B complex were determined in the two beverages, and over 300 compounds were detected in total. Thirteen saccharides were identified including two unknown trisaccharides, and there were no differences in these between the two beverages. In LAF-amazake, lactic acid, vitamin B2 (riboflavin), B3 (nicotinic acid and nicotinamide), and B6 (pyridoxine) were significantly increased as compared to koji amazake, whereas malate and glutamine decreased. These results suggested that LAF, malolactic fermentation, and glutamine deamidation occurred simultaneously in LAF-amazake. L. sakei UONUMA strains produced these vitamins. Moreover, it was surprising that acetylcholine, a well-known neurotransmitter, was newly generated in LAF-amazake. Here, we have succeeded in reforming the flavor of koji amazake and obtained these metabolic data on the two beverages. The present study could provide useful basic information for promoting functional analyses of koji amazake and LAF-amazake for human health. Copyright © 2017 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  10. Urinary Metabolomic Profiling to Identify Potential Biomarkers for the Diagnosis of Behcet’s Disease by Gas Chromatography/Time-of-Flight−Mass Spectrometry

    Directory of Open Access Journals (Sweden)

    Joong Kyong Ahn

    2017-11-01

    Full Text Available Diagnosing Behcet’s disease (BD is challenging because of the lack of a diagnostic biomarker. The purposes of this study were to investigate distinctive metabolic changes in urine samples of BD patients and to identify urinary metabolic biomarkers for diagnosis of BD using gas chromatography/time-of-flight–mass spectrometry (GC/TOF−MS. Metabolomic profiling of urine samples from 44 BD patients and 41 healthy controls (HC were assessed using GC/TOF−MS, in conjunction with multivariate statistical analysis. A total of 110 urinary metabolites were identified. The urine metabolite profiles obtained from GC/TOF−MS analysis could distinguish BD patients from the HC group in the discovery set. The parameter values of the orthogonal partial least squared-discrimination analysis (OPLS-DA model were R2X of 0.231, R2Y of 0.804, and Q2 of 0.598. A biomarker panel composed of guanine, pyrrole-2-carboxylate, 3-hydroxypyridine, mannose, l-citrulline, galactonate, isothreonate, sedoheptuloses, hypoxanthine, and gluconic acid lactone were selected and adequately validated as putative biomarkers of BD (sensitivity 96.7%, specificity 93.3%, area under the curve 0.974. OPLS-DA showed clear discrimination of BD and HC groups by a biomarker panel of ten metabolites in the independent set (accuracy 88%. We demonstrated characteristic urinary metabolic profiles and potential urinary metabolite biomarkers that have clinical value in the diagnosis of BD using GC/TOF−MS.

  11. Urinary Metabolomic Profiling to Identify Potential Biomarkers for the Diagnosis of Behcet's Disease by Gas Chromatography/Time-of-Flight-Mass Spectrometry.

    Science.gov (United States)

    Ahn, Joong Kyong; Kim, Jungyeon; Hwang, Jiwon; Song, Juhwan; Kim, Kyoung Heon; Cha, Hoon-Suk

    2017-11-02

    Diagnosing Behcet's disease (BD) is challenging because of the lack of a diagnostic biomarker. The purposes of this study were to investigate distinctive metabolic changes in urine samples of BD patients and to identify urinary metabolic biomarkers for diagnosis of BD using gas chromatography/time-of-flight-mass spectrometry (GC/TOF-MS). Metabolomic profiling of urine samples from 44 BD patients and 41 healthy controls (HC) were assessed using GC/TOF-MS, in conjunction with multivariate statistical analysis. A total of 110 urinary metabolites were identified. The urine metabolite profiles obtained from GC/TOF-MS analysis could distinguish BD patients from the HC group in the discovery set. The parameter values of the orthogonal partial least squared-discrimination analysis (OPLS-DA) model were R ² X of 0.231, R ² Y of 0.804, and Q ² of 0.598. A biomarker panel composed of guanine, pyrrole-2-carboxylate, 3-hydroxypyridine, mannose, l-citrulline, galactonate, isothreonate, sedoheptuloses, hypoxanthine, and gluconic acid lactone were selected and adequately validated as putative biomarkers of BD (sensitivity 96.7%, specificity 93.3%, area under the curve 0.974). OPLS-DA showed clear discrimination of BD and HC groups by a biomarker panel of ten metabolites in the independent set (accuracy 88%). We demonstrated characteristic urinary metabolic profiles and potential urinary metabolite biomarkers that have clinical value in the diagnosis of BD using GC/TOF-MS.

  12. Effectiveness of different solid-phase microextraction fibres for differentiation of selected Madeira island fruits based on their volatile metabolite profile--identification of novel compounds.

    Science.gov (United States)

    Pereira, João; Pereira, Jorge; Câmara, José S

    2011-01-15

    A headspace solid-phase microextraction (HS-SPME) procedure based on five commercialised fibres (85 μm polyacrylate - PA, 100 μm polydimethylsiloxane - PDMS, 65 μm polydimethylsiloxane/divinylbenzene - PDMS/DVB, 70 μm carbowax/divinylbenzene - CW/DVB and 85 μm carboxen/polydimethylsiloxane - CAR/PDMS) is presented for the characterization of the volatile metabolite profile of four selected Madeira island fruit species, lemon (Citrus limon), kiwi (Actinidia deliciosa), papaya (Carica papaya L.) and Chickasaw plum (Prunus angustifolia). The isolation of metabolites was followed by thermal desorption gas chromatography-quadrupole mass spectrometry (GC-qMS) methodology. The performance of the target fibres was evaluated and compared. The SPME fibre coated with CW/DVB afforded the highest extraction efficiency in kiwi and papaya pulps, while in lemon and plum the same was achieved with PMDS/DVB fibre. This procedure allowed for the identification of 80 compounds, 41 in kiwi, 24 in plums, 23 in papaya and 20 in lemon. Considering the best extraction conditions, the most abundant volatiles identified in kiwi were the intense aldehydes and ethyl esters such as (E)-2-hexenal and ethyl butyrate, while in Chicasaw plum predominate 2-hexenal, 2-methyl-4-pentenal, hexanal, (Z)-3-hexenol and cyclohexylene oxide. The major compounds identified in the papaya pulp were benzyl isothiocyanate, linalool oxide, furfural, hydroxypropanone, linalool and acetic acid. Finally, lemon was shown to be the most divergent of the four fruits, being its aroma profile composed almost exclusively by terpens, namely limonene, γ-terpinene, o-cymene and α-terpinolene. Thirty two volatiles were identified for the first time in the fruit or close related species analysed and 14 volatiles are reported as novel volatile metabolites in fruits. This includes 5 new compounds in kiwi (2-cyclohexene-1,4-dione, furyl hydroxymethyl ketone, 4-hydroxydihydro-2(3H)-furanone, 5-acetoxymethyl-2-furaldehyde and

  13. The Use of NMR Metabolite Profiling and in vivo Hypoglycemic Assay for Comparison of Unfractionated Aqueous Leaf Extracts of Two Ocimum Species.

    Science.gov (United States)

    Casanova, Livia Marques; Espíndola-Netto, Jair Machado; Tinoco, Luzineide Wanderley; Sola-Penna, Mauro; Costa, Sônia Soares

    2016-06-01

    Ocimum basilicum and Ocimum gratissimum (Lamiaceae) are used to treat diabetes mellitus in Africa. In a previous work, we identified chicoric acid as a hypoglycemic substance in O. gratissimum. This study aims to compare the chemical metabolite profile and the hypoglycemic activity of unfractionated aqueous extracts from leaves of both Lamiaceae species. The metabolite composition of OB and OG decoctions (10% w/v) was analyzed using HPLC-DAD and NMR tools. Chicoric acid showed to be the major phenolic in both extracts, besides caftaric, caffeic, and rosmarinic acids; nevertheless, there is approximately three times more of this substance in OG. From 1D- and 2D-NMR analyses, 19 substances were identified in OB, while 12 in OG. The in vivo acute hypoglycemic activity of the extracts was assessed intraperitoneally in streptozotocin (STZ)-induced diabetic mice. The doses of 100 and 200 mg/kg of both extracts significantly reduced their glycemia, compared to controls (P Ocimum species by NMR. Our findings confirmed the potential of both species in DM treatment in spite of marked differences in their chemical composition. However, long-term studies are necessary in order to identify the most promising of the two species for the development of an herbal medicine. © 2016 Verlag Helvetica Chimica Acta AG, Zürich.

  14. Association between plasma metabolites and gene expression profiles in five porcine endocrine tissues

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    Bassols Anna

    2011-07-01

    Full Text Available Abstract Background Endocrine tissues play a fundamental role in maintaining homeostasis of plasma metabolites such as non-esterified fatty acids and glucose, the levels of which reflect the energy balance or the health status of animals. However, the relationship between the transcriptome of endocrine tissues and plasma metabolites has been poorly studied. Methods We determined the blood levels of 12 plasma metabolites in 27 pigs belonging to five breeds, each breed consisting of both females and males. The transcriptome of five endocrine tissues i.e. hypothalamus, adenohypophysis, thyroid gland, gonads and backfat tissues from 16 out of the 27 pigs was also determined. Sex and breed effects on the 12 plasma metabolites were investigated and associations between genes expressed in the five endocrine tissues and the 12 plasma metabolites measured were analyzed. A probeset was defined as a quantitative trait transcript (QTT when its association with a particular metabolic trait achieved a nominal P value Results A larger than expected number of QTT was found for non-esterified fatty acids and alanine aminotransferase in at least two tissues. The associations were highly tissue-specific. The QTT within the tissues were divided into co-expression network modules enriched for genes in Kyoto Encyclopedia of Genes and Genomes or gene ontology categories that are related to the physiological functions of the corresponding tissues. We also explored a multi-tissue co-expression network using QTT for non-esterified fatty acids from the five tissues and found that a module, enriched in hypothalamus QTT, was positioned at the centre of the entire multi-tissue network. Conclusions These results emphasize the relationships between endocrine tissues and plasma metabolites in terms of gene expression. Highly tissue-specific association patterns suggest that candidate genes or gene pathways should be investigated in the context of specific tissues.

  15. HdhQ111 Mice Exhibit Tissue Specific Metabolite Profiles that Include Striatal Lipid Accumulation.

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    Jeffrey B Carroll

    Full Text Available The HTT CAG expansion mutation causes Huntington's Disease and is associated with a wide range of cellular consequences, including altered metabolism. The mutant allele is expressed widely, in all tissues, but the striatum and cortex are especially vulnerable to its effects. To more fully understand this tissue-specificity, early in the disease process, we asked whether the metabolic impact of the mutant CAG expanded allele in heterozygous B6.HdhQ111/+ mice would be common across tissues, or whether tissues would have tissue-specific responses and whether such changes may be affected by diet. Specifically, we cross-sectionally examined steady state metabolite concentrations from a range of tissues (plasma, brown adipose tissue, cerebellum, striatum, liver, white adipose tissue, using an established liquid chromatography-mass spectrometry pipeline, from cohorts of 8 month old mutant and wild-type littermate mice that were fed one of two different high-fat diets. The differential response to diet highlighted a proportion of metabolites in all tissues, ranging from 3% (7/219 in the striatum to 12% (25/212 in white adipose tissue. By contrast, the mutant CAG-expanded allele primarily affected brain metabolites, with 14% (30/219 of metabolites significantly altered, compared to wild-type, in striatum and 11% (25/224 in the cerebellum. In general, diet and the CAG-expanded allele both elicited metabolite changes that were predominantly tissue-specific and non-overlapping, with evidence for mutation-by-diet interaction in peripheral tissues most affected by diet. Machine-learning approaches highlighted the accumulation of diverse lipid species as the most genotype-predictive metabolite changes in the striatum. Validation experiments in cell culture demonstrated that lipid accumulation was also a defining feature of mutant HdhQ111 striatal progenitor cells. Thus, metabolite-level responses to the CAG expansion mutation in vivo were tissue specific and

  16. Metabolite profiling of microfluidic cell culture conditions for droplet based screening

    DEFF Research Database (Denmark)

    Björk, Sara M.; Sjoström, Staffan L.; Svahn, Helene Andersson

    2015-01-01

    , such as directed evolution of yeast, as cell metabolic state directly affects production yields from cell factories. Here, we analyze glucose, pyruvate, ethanol, and glycerol, central metabolites in yeast glucose dissimilation to establish culture formats for screening of respiring as well as fermenting yeast...

  17. Focused Metabolite Profiling for Dissecting Cellular and Molecular Processes of Living Organisms in Space Environments

    Science.gov (United States)

    2008-01-01

    Regulatory control in biological systems is exerted at all levels within the central dogma of biology. Metabolites are the end products of all cellular regulatory processes and reflect the ultimate outcome of potential changes suggested by genomics and proteomics caused by an environmental stimulus or genetic modification. Following on the heels of genomics, transcriptomics, and proteomics, metabolomics has become an inevitable part of complete-system biology because none of the lower "-omics" alone provide direct information about how changes in mRNA or protein are coupled to changes in biological function. The challenges are much greater than those encountered in genomics because of the greater number of metabolites and the greater diversity of their chemical structures and properties. To meet these challenges, much developmental work is needed, including (1) methodologies for unbiased extraction of metabolites and subsequent quantification, (2) algorithms for systematic identification of metabolites, (3) expertise and competency in handling a large amount of information (data set), and (4) integration of metabolomics with other "omics" and data mining (implication of the information). This article reviews the project accomplishments.

  18. Profiling of secondary metabolite gene clusters regulated by LaeA in Aspergillus niger FGSC A1279 based on genome sequencing and transcriptome analysis.

    Science.gov (United States)

    Wang, Bin; Lv, Yangyong; Li, Xuejie; Lin, Yiying; Deng, Hai; Pan, Li

    The global regulator LaeA controls the production of many fungal secondary metabolites, possibly via chromatin remodeling. Here we aimed to survey the secondary metabolite profile regulated by LaeA in Aspergillus niger FGSC A1279 by genome sequencing and comparative transcriptomics between the laeA deletion (ΔlaeA) and overexpressing (OE-laeA) mutants. Genome sequencing revealed four putative polyketide synthase genes specific to FGSC A1279, suggesting that the corresponding polyketide compounds might be unique to FGSC A1279. RNA-seq data revealed 281 putative secondary metabolite genes upregulated in the OE-laeA mutants, including 22 secondary metabolite backbone genes. LC-MS chemical profiling illustrated that many secondary metabolites were produced in OE-laeA mutants compared to wild type and ΔlaeA mutants, providing potential resources for drug discovery. KEGG analysis annotated 16 secondary metabolite clusters putatively linked to metabolic pathways. Furthermore, 34 of 61 Zn 2 Cys 6 transcription factors located in secondary metabolite clusters were differentially expressed between ΔlaeA and OE-laeA mutants. Three secondary metabolite clusters (cluster 18, 30 and 33) containing Zn 2 Cys 6 transcription factors that were upregulated in OE-laeA mutants were putatively linked to KEGG pathways, suggesting that Zn 2 Cys 6 transcription factors might play an important role in synthesizing secondary metabolites regulated by LaeA. Taken together, LaeA dramatically influences the secondary metabolite profile in FGSC A1279. Copyright © 2017 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

  19. NMR Profiling of Metabolites in Larval and Juvenile Blue Mussels (Mytilus edulis) under Ambient and Low Salinity Conditions.

    Science.gov (United States)

    May, Melissa A; Bishop, Karl D; Rawson, Paul D

    2017-07-06

    Blue mussels ( Mytilus edulis ) are ecologically and economically important marine invertebrates whose populations are at risk from climate change-associated variation in their environment, such as decreased coastal salinity. Blue mussels are osmoconfomers and use components of the metabolome (free amino acids) to help maintain osmotic balance and cellular function during low salinity exposure. However, little is known about the capacity of blue mussels during the planktonic larval stages to regulate metabolites during osmotic stress. Metabolite studies in species such as blue mussels can help improve our understanding of the species' physiology, as well as their capacity to respond to environmental stress. We used 1D ¹H nuclear magnetic resonance (NMR) and 2D total correlation spectroscopy (TOCSY) experiments to describe baseline metabolite pools in larval (veliger and pediveliger stages) and juvenile blue mussels (gill, mantle, and adductor tissues) under ambient conditions and to quantify changes in the abundance of common osmolytes in these stages during low salinity exposure. We found evidence for stage- and tissue-specific differences in the baseline metabolic profiles of blue mussels, which reflect variation in the function and morphology of each larval stage or tissue type of juveniles. These differences impacted the utilization of osmolytes during low salinity exposure, likely stemming from innate physiological variation. This study highlights the importance of foundational metabolomic studies that include multiple tissue types and developmental stages to adequately evaluate organismal responses to stress and better place these findings in a broader physiological context.

  20. Metabolite profiles of nodulated alfalfa plants indicate that distinct stages of nodule organogenesis are accompanied by global physiological adaptations.

    Science.gov (United States)

    Barsch, Aiko; Tellström, Verena; Patschkowski, Thomas; Küster, Helge; Niehaus, Karsten

    2006-09-01

    An effective symbiosis between Sinorhizobium meliloti and its host plant Medicago sativa is dependent on a balanced physiological interaction enabling the microsymbiont to fix atmospheric nitrogen. Maintenance of the symbiotic interaction is regulated by still poorly understood control mechanisms. A first step toward a better understanding of nodule metabolism was the determination of characteristic metabolites for alfalfa root nodules. Furthermore, nodules arrested at different developmental stages were analyzed in order to address metabolic changes induced during the progression of nodule formation. Metabolite profiles of bacteroid-free pseudonodule extracts indicated that early nodule developmental processes are accompanied by photosynthate translocation but no massive organic acid formation. To determine metabolic adaptations induced by the presence of nonfixing bacteroids, nodules induced by mutant S. meliloti strains lacking the nitrogenase protein were analyzed. The bacteroids are unable to provide ammonium to the host plant, which is metabolically reflected by reduced levels of characteristic amino acids involved in ammonium fixation. Elevated levels of starch and sugars in Fix(-) nodules provide strong evidence that plant sanctions preventing a transformation from a symbiotic to a potentially parasitic interaction are not strictly realized via photosynthate supply. Instead, metabolic and gene expression data indicate that alfalfa plants react to nitrogen-fixation-deficient bacteroids with a decreased organic acid synthesis and an early induction of senescence. Noneffective symbiotic interactions resulting from plants nodulated by mutant rhizobia also are reflected in characteristic metabolic changes in leaves. These are typical for nitrogen deficiency, but also highlight metabolites potentially involved in sensing the N status.

  1. Metabolite profiling reveals novel multi-level cold responses in the diploid model Fragaria vesca (woodland strawberry).

    Science.gov (United States)

    Rohloff, Jens; Kopka, Joachim; Erban, Alexander; Winge, Per; Wilson, Robert C; Bones, Atle M; Davik, Jahn; Randall, Stephen K; Alsheikh, Muath K

    2012-05-01

    Winter freezing damage is a crucial factor in overwintering crops such as the octoploid strawberry (Fragaria × ananassa Duch.) when grown in a perennial cultivation system. Our study aimed at assessing metabolic processes and regulatory mechanisms in the close-related diploid model woodland strawberry (Fragaria vescaL.) during a 10-days cold acclimation experiment. Based on gas chromatography/time-of-flight-mass spectrometry (GC/TOF-MS) metabolite profiling of three F. vesca genotypes, clear distinctions could be made between leaves and non-photosynthesizing roots, underscoring the evolvement of organ-dependent cold acclimation strategies. Carbohydrate and amino acid metabolism, photosynthetic acclimation, and antioxidant and detoxification systems (ascorbate pathway) were strongly affected. Metabolic changes in F. vesca included the strong modulation of central metabolism, and induction of osmotically-active sugars (fructose, glucose), amino acids (aspartic acid), and amines (putrescine). In contrast, a distinct impact on the amino acid proline, known to be cold-induced in other plant systems, was conspicuously absent. Levels of galactinol and raffinose, key metabolites of the cold-inducible raffinose pathway, were drastically enhanced in both leaves and roots throughout the cold acclimation period of 10 days. Furthermore, initial freezing tests and multifaceted GC/TOF-MS data processing (Venn diagrams, independent component analysis, hierarchical clustering) showed that changes in metabolite pools of cold-acclimated F. vesca were clearly influenced by genotype. Copyright © 2012 Elsevier Ltd. All rights reserved.

  2. LC-MS-based metabolite profiling of methanolic extracts from the medicinal and aromatic species Mentha pulegium and Origanum majorana.

    Science.gov (United States)

    Taamalli, Amani; Arráez-Román, David; Abaza, Leila; Iswaldi, Ihsan; Fernández-Gutiérrez, Alberto; Zarrouk, Mokhtar; Segura-Carretero, Antonio

    2015-01-01

    There has been increasing interest dedicated to the phenolic compounds with a view to their antioxidant and healthy properties. Recent studies have focused on plants from the Lamiaceae family with special interest in phenolic compounds antioxidant potential. The metabolite profile of methanolic extracts from two Lamiacea medicinal plants was investigated. Mentha pulegium and Origanum majorana methanolic extracts were analysed using reversed-phase ultra-high-performance liquid chromatography (RP-UHPLC) coupled to electrospray ionisation quadrupole time-of-flight mass spectrometry (ESI-QTOF-MS) detection in the negative ion mode. A total of 85 metabolites were characterised from different families, such as organic acids and derivatives, amino acids and derivatives, nucleosides, phenolic compounds as well as other polar metabolites, by using the MS and MS/MS information provided by the QTOF-MS. However, the total phenols and flavonoids were also quantified spectrophotometrically and they registered higher amounts in Mentha pulegium than in Origanum majorana extract. Gallocatechin was the major compound in M. pulegium extract whereas quercetin dimethyl ether, jaceidin and dihydrokaempferide were the major ones in O. majorana extract. The distribution of phenolic compounds in the methanolic extract showed a variation among studied plants. Mentha pulegium can be considered as a source of gallocatechin. Copyright © 2015 John Wiley & Sons, Ltd.

  3. Environmental Factors Correlated with the Metabolite Profile of Vitis vinifera cv. Pinot Noir Berry Skins along a European Latitudinal Gradient.

    Science.gov (United States)

    Del-Castillo-Alonso, María Ángeles; Castagna, Antonella; Csepregi, Kristóf; Hideg, Éva; Jakab, Gabor; Jansen, Marcel A K; Jug, Tjaša; Llorens, Laura; Mátai, Anikó; Martínez-Lüscher, Johann; Monforte, Laura; Neugart, Susanne; Olejnickova, Julie; Ranieri, Annamaria; Schödl-Hummel, Katharina; Schreiner, Monika; Soriano, Gonzalo; Teszlák, Péter; Tittmann, Susanne; Urban, Otmar; Verdaguer, Dolors; Zipoli, Gaetano; Martínez-Abaigar, Javier; Núñez-Olivera, Encarnación

    2016-11-23

    Mature berries of Pinot Noir grapevines were sampled across a latitudinal gradient in Europe, from southern Spain to central Germany. Our aim was to study the influence of latitude-dependent environmental factors on the metabolite composition (mainly phenolic compounds) of berry skins. Solar radiation variables were positively correlated with flavonols and flavanonols and, to a lesser extent, with stilbenes and cinnamic acids. The daily means of global and erythematic UV solar radiation over long periods (bud break-veraison, bud break-harvest, and veraison-harvest), and the doses and daily means in shorter development periods (5-10 days before veraison and harvest) were the variables best correlated with the phenolic profile. The ratio between trihydroxylated and monohydroxylated flavonols, which was positively correlated with antioxidant capacity, was the berry skin variable best correlated with those radiation variables. Total flavanols and total anthocyanins did not show any correlation with radiation variables. Air temperature, degree days, rainfall, and aridity indices showed fewer correlations with metabolite contents than radiation. Moreover, the latter correlations were restricted to the period veraison-harvest, where radiation, temperature, and water availability variables were correlated, making it difficult to separate the possible individual effects of each type of variable. The data show that managing environmental factors, in particular global and UV radiation, through cultural practices during specific development periods, can be useful to promote the synthesis of valuable nutraceuticals and metabolites that influence wine quality.

  4. Using Profile Analysis via Multidimensional Scaling (PAMS) to identify core profiles from the WMS-III.

    Science.gov (United States)

    Frisby, Craig L; Kim, Se-Kang

    2008-03-01

    Profile Analysis via Multidimensional Scaling (PAMS) is a procedure for extracting latent core profiles in a multitest data set. The PAMS procedure offers several advantages compared with other profile analysis procedures. Most notably, PAMS estimates individual profile weights that reflect the degree to which an individual's observed profile approximates the shape and scatter of latent core profiles. The PAMS procedure was applied to index scores of nonreplicated participants from the standardization sample (N = 1,033) for the Wechsler Memory Scale--Third Edition (D. Tulsky, J. Zhu, & M. F. Ledbetter, 2002). PAMS extracted discrepant visual memory and auditory memory versus working memory core profiles for the complete 16- to 89-year-old sample and discrepant working memory and auditory memory versus working memory core profiles for the 75- to 89-year-old cohort. Implications for use of PAMS in future research are discussed.

  5. Metabolite Profiling of Diverse Rice Germplasm and Identification of Conserved Metabolic Markers of Rice Roots in Response to Long-Term Mild Salinity Stress.

    Science.gov (United States)

    Nam, Myung Hee; Bang, Eunjung; Kwon, Taek Yun; Kim, Yuran; Kim, Eun Hee; Cho, Kyungwon; Park, Woong June; Kim, Beom-Gi; Yoon, In Sun

    2015-09-11

    The sensitivity of rice to salt stress greatly depends on growth stages, organ types and cultivars. Especially, the roots of young rice seedlings are highly salt-sensitive organs that limit plant growth, even under mild soil salinity conditions. In an attempt to identify metabolic markers of rice roots responding to salt stress, metabolite profiling was performed by ¹H-NMR spectroscopy in 38 rice genotypes that varied in biomass accumulation under long-term mild salinity condition. Multivariate statistical analysis showed separation of the control and salt-treated rice roots and rice genotypes with differential growth potential. By quantitative analyses of ¹H-NMR data, five conserved salt-responsive metabolic markers of rice roots were identified. Sucrose, allantoin and glutamate accumulated by salt stress, whereas the levels of glutamine and alanine decreased. A positive correlation of metabolite changes with growth potential and salt tolerance of rice genotypes was observed for allantoin and glutamine. Adjustment of nitrogen metabolism in rice roots is likely to be closely related to maintain the growth potential and increase the stress tolerance of rice.

  6. Metabolite Profiling of Diverse Rice Germplasm and Identification of Conserved Metabolic Markers of Rice Roots in Response to Long-Term Mild Salinity Stress

    Directory of Open Access Journals (Sweden)

    Myung Hee Nam

    2015-09-01

    Full Text Available The sensitivity of rice to salt stress greatly depends on growth stages, organ types and cultivars. Especially, the roots of young rice seedlings are highly salt-sensitive organs that limit plant growth, even under mild soil salinity conditions. In an attempt to identify metabolic markers of rice roots responding to salt stress, metabolite profiling was performed by 1H-NMR spectroscopy in 38 rice genotypes that varied in biomass accumulation under long-term mild salinity condition. Multivariate statistical analysis showed separation of the control and salt-treated rice roots and rice genotypes with differential growth potential. By quantitative analyses of 1H-NMR data, five conserved salt-responsive metabolic markers of rice roots were identified. Sucrose, allantoin and glutamate accumulated by salt stress, whereas the levels of glutamine and alanine decreased. A positive correlation of metabolite changes with growth potential and salt tolerance of rice genotypes was observed for allantoin and glutamine. Adjustment of nitrogen metabolism in rice roots is likely to be closely related to maintain the growth potential and increase the stress tolerance of rice.

  7. Metabolite identification and pharmacokinetic profiling of PP242, an ATP-competitive inhibitor of mTOR using ultra high-performance liquid chromatography and mass spectrometry.

    Science.gov (United States)

    Rashid, Md Mamunur; Lee, Hyunbeom; Jung, Byung Hwa

    2018-01-01

    PP242 is a second generation novel selective ATP-competitive inhibitor of mTOR that displayed promising anti-cancer activity over several cancer types by inhibiting both the complexes of mTOR (mTORC1 and mTORC2). The purpose of this study is to identify the possible metabolites and to evaluate the pharmacokinetic profile of PP242 after a single oral administration to Sprague-Dawley (SD) rats. Two metabolites, including one phase I and one phase II, were identified by in vitro and in vivo studies using rat liver microsomes (RLMs) as well as rat plasma, urine and feces, respectively, through ultra high-performance liquid chromatography-linear ion trap quadrupole-orbitrap-mass spectrometry (UHPLC-LTQ-Orbitrap-MS). The major biotransformation pathways of PP242 were hydroxylation and glucuronide conjugation. Additionally, a simple and rapid quantification method was developed and validated. The method recovery was within 79.7-84.6%, whereas the matrix effect was 78.1-96.0% in all three quality control (QC) concentrations (low, medium and high) including the LLOQ. Other parameters showed acceptable results according to the US food and drug administration (FDA) guidelines for bioanalytical method validation. Afterwards, pharmacokinetic parameters were evaluated in rat plasma by successfully applying the validated method using liquid chromatography-tandem mass spectrometry (LC-MS/MS). After a single oral administration at a dose of 5mg/kg, the maximum plasma concentration (C max ) of PP242 was 0.17±0.08μg/mL, while the elimination was moderately fast (T 1/2 : 172.18±45.54min). All of the obtained information on the metabolite identification and pharmacokinetic parameter elucidation could facilitate the further development of PP242. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. Utilization of polar metabolite profiling in the comparison of juvenile wood and compression wood in loblolly pine (Pinus taeda).

    Science.gov (United States)

    Yeh, Ting-Feng; Morris, Cameron R; Goldfarb, Barry; Chang, Hou-Min; Kadla, John F

    2006-11-01

    Juvenile wood (JW) of conifers is often associated with compression wood (CW), with which it is sometimes believed to be identical. To determine whether JW and CW can be distinguished metabolically, we compared gas chromatographic profiles of 25 polar metabolites from rooted cuttings of a single loblolly pine (Pinus taeda L.) clone raised in controlled environment chambers and subject to three treatments: (1) grown erect with minimal wind sway (control); (2) swayed by wind from oscillating fans; and (3) with 30-cm growth increments successively bent at an angle of 45 degrees to the vertical. Profiles were compared by principal component analysis. Substantial increases in abundances of coniferin and p-glucocoumaryl alcohol separated immature JW-forming xylem tissues of the control trees from the CW-forming xylem of the bent and swayed trees.

  9. Metabolite profiling of red and blue potatoes revealed cultivar and tissue specific patterns for anthocyanins and other polyphenols.

    Science.gov (United States)

    Oertel, Anne; Matros, Andrea; Hartmann, Anja; Arapitsas, Panagiotis; Dehmer, Klaus J; Martens, Stefan; Mock, Hans-Peter

    2017-08-01

    Metabolite profiling of tuber flesh and peel for selected colored potato varieties revealed cultivar and tissue specific profiles of anthocyanins and other polyphenols with variations in composition and concentration. Starchy tubers of Solanum tuberosum are a staple crop and food in many countries. Among cultivated potato varieties a huge biodiversity exists, including an increasing number of red and purple colored cultivars. This coloration relates to the accumulation of anthocyanins and is supposed to offer nutritional benefits possibly associated with the antioxidative capacity of anthocyanins. However, the anthocyanin composition and its relation to the overall polyphenol constitution in colored potato tubers have not been investigated closely. This study focuses on the phytochemical characterization of the phenolic composition of a variety of colored potato tubers, both for peel and flesh tissues. First, liquid chromatography (LC) separation coupled to UV and mass spectrometry (MS) detection of polyphenolic compounds of potato tubers from 57 cultivars was used to assign groups of potato cultivars differing in their anthocyanin and polyphenol profiles. Tissues from 19 selected cultivars were then analyzed by LC separation coupled to multiple reaction monitoring (MRM) to detect quantitative differences in anthocyanin and polyphenol composition. The measured intensities of 21 anthocyanins present in the analyzed potato cultivars and tissues could be correlated with the specific tuber coloration. Besides secondary metabolites well-known for potato tubers, the metabolic profiling led to the detection of two anthocyanins not described for potato tuber previously, which we tentatively annotated as pelargonidin feruloyl-xylosyl-glucosyl-galactoside and cyanidin 3-p-coumaroylrutinoside-5-glucoside. We detected significant correlations between some of the measured metabolites, as for example the negative correlation between the main anthocyanins of red and blue potato

  10. Diurnal Profiles of Melatonin Synthesis-Related Indoles, Catecholamines and Their Metabolites in the Duck Pineal Organ

    Directory of Open Access Journals (Sweden)

    Bogdan Lewczuk

    2014-07-01

    Full Text Available This study characterizes the diurnal profiles of ten melatonin synthesis-related indoles, the quantitative relations between these compounds, and daily variations in the contents of catecholamines and their metabolites in the domestic duck pineal organ. Fourteen-week-old birds, which were reared under a 12L:12D cycle, were killed at two-hour intervals. The indole contents were measured using HPLC with fluorescence detection, whereas the levels of catecholamines and their metabolites were measured using HPLC with electrochemical detection. All indole contents, except for tryptophan, showed significant diurnal variations. The 5-hydroxytryptophan level was approximately two-fold higher during the scotophase than during the photophase. The serotonin content increased during the first half of the photophase, remained elevated for approximately 10 h and then rapidly decreased in the middle of the scotophase. N-acetylserotonin showed the most prominent changes, with a more than 15-fold increase at night. The melatonin cycle demonstrated only an approximately 5-fold difference between the peak and nadir. The 5-methoxytryptamine content was markedly elevated during the scotophase. The 5-hydroxyindole acetic acid, 5-hydroxytryptophol, 5-methoxyindole acetic acid and 5-methoxytryptophol profiles were analogous to the serotonin rhythm. The norepinephrine and dopamine contents showed no significant changes. The DOPA, DOPAC and homovanillic acid levels were higher during the scotophase than during the photophase. Vanillylmandelic acid showed the opposite rhythm, with an elevated level during the daytime.

  11. Urinary Metabolite Profiles May be Predictive of Cognitive Performance Under Conditions of Acute Sleep Deprivation

    Science.gov (United States)

    2016-01-01

    Cognitive Performance Under Conditions of Acute Sleep Deprivation 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER Nicholas J...cognitive assessments as having a high tolerance (n=6) or low tolerance (n=6) to sleep deprivation could be classified separately with statistical...at early (0-12h) and late (28h) times during the 36-h sleep deprivation period. Man of these metabolites (11 of 20) appeared to be associated with

  12. Quality assessment of Polygonum cuspidatum and Polygonum multiflorum by 1H NMR metabolite fingerprinting and profiling analysis.

    Science.gov (United States)

    Frédérich, Michel; Wauters, Jean-Noël; Tits, Monique; Jason, Charlotte; de Tullio, Pascal; Van der Heyden, Yvan; Fan, Guorong; Angenot, Luc

    2011-01-01

    The quality assessment and control of traditional Chinese medicines (TCM) nowadays receives a great deal of attention worldwide and particularly in Europe with its increasing local use. Polygonum cuspidatum Siebold & Zucc. and Polygonum multiflorum Thunb. are two members of the Polygonaceae family, which are widely used as Chinese medicinal plants. The aim of this study was to achieve an overview of the quality of P. cuspidatum and P. multiflorum samples available on the Chinese market and to identify important metabolites for their discrimination, using (1)H NMR-based metabolomics. (1)H NMR and multivariate analysis techniques were applied to almost 60 plant samples collected in different places in China. Using (1)H NMR metabolomics, it was possible, without previous evaporation or separation steps, to obtain metabolic fingerprints to distinguish between the species. The important metabolites for discrimination were stilbene derivatives. Finally, a clear distinction between the two species was possible and the discriminant metabolites were identified. © Georg Thieme Verlag KG Stuttgart · New York.

  13. Dhurrin metabolism in the developing grain of Sorghum bicolor (L.) Moench investigated by metabolite profiling and novel clustering analyses of time-resolved transcriptomic data

    DEFF Research Database (Denmark)

    Nielsen, Lasse Janniche; Stuart, Peter; Pičmanová, Martina

    2016-01-01

    Background: The important cereal crop Sorghum bicolor (L.) Moench biosynthesize and accumulate the defensive compound dhurrin during development. Previous work has suggested multiple roles for the compound including a function as nitrogen storage/buffer. Crucial for this function is the endogenous...... analyses with the metabolite profiling, potential gene candidates of glutathione S-transferases, nitrilases and glycosyl transferases involved in these pathways were identified. The absence of dhurrin in the mature grain was replaced by a high content of proanthocyanidins. Cluster- and phylogenetic...... in these transformations and show that dhurrin in additionto its insect deterrent properties may serve as a storage form of reduced nitrogen. In the course of sorghum grainmaturation, proanthocyanidins replace dhurrin as a defense compound. The lack of cyanogenesis in the developingsorghum grain renders this a unique...

  14. Profil Hematologi dan Status Metabolit Darah Domba Garut yang Diberi Pakan Limbah Tauge pada Pagi atau Sore Hari (BLOOD HAEMATOLOGICAL PROFILE AND METABOLITE STATUS OF GARUT LAMB FED DIETS MUNG BEAN SPROUT WASTE IN THE MORNING OR EVENING

    Directory of Open Access Journals (Sweden)

    Sri Rahayu

    2017-04-01

    Full Text Available The aim of this study was to evaluate the effect of diet containing mung bean sprout waste (MBSW and feeding times on the hematological profiles and metabolite status of garut lambs. Experimental design used in this study was a factorial randomized block design with two factors of diet and two feeding times. Two factors of diets were 60% concentrate 1+40% natural grass and 60% concentrate 2+40% MBSW. Feeding times were in the morning (6:00-7:00 am or the evening (5:00-6:00 pm. The animals were reared in individual cages and fed with 5% DM/kg body weight/day. The hematological profiles of the goat were examined and analyzed with Anova. The results showed the treatment of rations significant effect on blood glucose, whereas feeding time very significant to glucose, erythrocytes and hemoglobin, and the interaction of both treatments significantly affect hemoglobin, hematocrit, and glucose level. Meanwhile,leukocytes, neutrophils, lymphocytes, neutrophils/lymphocyte ratio (N/L, urea-N, and blood cholesterol were not affected by the treatments and their interactions. But overall the number of erythrocytes 8.72-12.78x106/mm3, hemoglobin 7.6-10.02 g/dL, leukocytes 8.94-12.27x103/mm3, neutrophils 33.00-52.20%, lymphocytes 38.80-52.40%, N/L 0.78-1.66, glucose 41.94-54.24 mg/dL, urea-N 29.91-35.87 mg/dL, and blood cholesterol 24.57-30.28 mg/dL. These results suggest that diets containing 40% MBSW together with a morning or an evening feeding time did not cause disturbances in haematological profile and blood metabolite status of garut lamb. ABSTRAK Penelitian ini bertujuan untuk mengevaluasi efek ransum mengandung hijauan limbah tauge dan waktu pemberian yang berbeda terhadap profil hematologi dan status metabolit darah domba garut. Materi penelitian berupa 20 ekor domba garut berumur 6-7 bulan (bobot badan 15,42 ± 2,42 kg dipelihara selama tiga bulan dan dikandangkan secara individu serta diberi pakan sebanyak 5% bahan kering/kg berat badan

  15. Profiling convoluted single-dimension proton NMR spectra: a Plackett-Burman approach for assessing quantification error of metabolites in complex mixtures with application to cell culture.

    Science.gov (United States)

    Sokolenko, Stanislav; Blondeel, Eric J M; Azlah, Nada; George, Ben; Schulze, Steffen; Chang, David; Aucoin, Marc G

    2014-04-01

    Single-dimension hydrogen, or proton, nuclear magnetic resonance spectroscopy (1D-(1)H NMR) has become an attractive option for characterizing the full range of components in complex mixtures of small molecular weight compounds due to its relative simplicity, speed, spectral reproducibility, and noninvasive sample preparation protocols compared to alternative methods. One challenge associated with this method is the overlap of NMR resonances leading to "convoluted" spectra. While this can be mitigated through "targeted profiling", there is still the possibility of increased quantification error. This work presents the application of a Plackett-Burman experimental design for the robust estimation of precision and accuracy of 1D-(1)H NMR compound quantification in synthetic mixtures, with application to mammalian cell culture supernatant. A single, 20 sample experiment was able to provide a sufficient estimate of bias and variability at different metabolite concentrations. Two major sources of bias were identified: incorrect interpretation of singlet resonances and the quantification of resonances from protons in close proximity to labile protons. Furthermore, decreases in measurement accuracy and precision could be observed with decreasing concentration for a small fraction of the components as a result of their particular convolution patterns. Finally, the importance of a priori concentration estimates is demonstrated through the example of interpreting acetate metabolite trends from a bioreactor cultivation of Chinese hamster ovary cells expressing a recombinant antibody.

  16. Metabolite Profiling of Barley Grains Subjected to Water Stress: To Explain the Genotypic Difference in Drought-Induced Impacts on Malting Quality

    Directory of Open Access Journals (Sweden)

    Xiaojian Wu

    2017-09-01

    Full Text Available Grain weight and protein content will be reduced and increased, respectively, when barley is subjected to water stress after anthesis, consequently deteriorating the malt quality. However, such adverse impact of water stress differs greatly among barley genotypes. In this study, two Tibetan wild barley accessions and two cultivated varieties differing in water stress tolerance were used to investigate the genotypic difference in metabolic profiles during grain-filling stage under drought condition. Totally, 71 differently accumulated metabolites were identified, including organic acids, amino acids/amines, and sugars/sugar alcohols. Their relative contents were significantly affected by water stress for all genotypes and differed distinctly between the wild and cultivated barleys. The principal component analysis of metabolites indicated that the Tibetan wild barley XZ147 possessed a unique response to water stress. When subjected to water stress, the wild barley XZ147 showed the most increase of β-amylase activity among the four genotypes, as a result of its higher lysine content, less indole-3-acetic acid (IAA biosynthesis, more stable H2O2 homeostasis, and more up-regulation of BMY1 gene. On the other hand, XZ147 had the most reduction of β-glucan content under water stress than the other genotypes, which could be explained by the faster grain filling process and the less expression of β-glucan synthase gene GSL7. All these results indicated a great potential for XZ147 in barley breeding for improving water stress tolerance.

  17. Comparative metabolite profiling and fingerprinting of genus Passiflora leaves using a multiplex approach of UPLC-MS and NMR analyzed by chemometric tools.

    Science.gov (United States)

    Farag, Mohamed A; Otify, Asmaa; Porzel, Andrea; Michel, Camilia George; Elsayed, Aly; Wessjohann, Ludger A

    2016-05-01

    Passiflora incarnata as well as some other Passiflora species are reported to possess anxiolytic and sedative activity and to treat various CNS disorders. The medicinal use of only a few Passiflora species has been scientifically verified. There are over 400 species in the Passiflora genus worldwide, most of which have been little characterized in terms of phytochemical or pharmacological properties. Herein, large-scale multi-targeted metabolic profiling and fingerprinting techniques were utilized to help gain a broader insight into Passiflora species leaves' chemical composition. Nuclear magnetic resonance spectroscopy (NMR) and mass spectrometry (MS) spectra of extracted components derived from 17 Passiflora accessions and from different geographical origins were analyzed using multivariate data analyses. A total of 78 metabolites were tentatively identified, that is, 20 C-flavonoids, 8 O-flavonoids, 21 C, O-flavonoids, 2 cyanogenic glycosides, and 23 fatty acid conjugates, of which several flavonoid conjugates are for the first time to be reported in Passiflora spp. To the best of our knowledge, this study provides the most complete map for secondary metabolite distribution within that genus. Major signals in (1)H-NMR and MS spectra contributing to species discrimination were assigned to those of C-flavonoids including isovitexin-2″-O-xyloside, luteolin-C-deoxyhexoside-O-hexoside, schaftoside, isovitexin, and isoorientin. P. incarnata was found most enriched in C-flavonoids, justifying its use as an official drug within that genus. Compared to NMR, LC-MS was found more effective in sample classification based on genetic and/ or geographical origin as revealed from derived multivariate data analyses. Novel insight on metabolite candidates to mediate for Passiflora CNS sedative effects is also presented.

  18. Metabolic effects of influenza virus infection in cultured animal cells: Intra- and extracellular metabolite profiling

    Directory of Open Access Journals (Sweden)

    Genzel Yvonne

    2010-05-01

    Full Text Available Abstract Background Many details in cell culture-derived influenza vaccine production are still poorly understood and approaches for process optimization mainly remain empirical. More insights on mammalian cell metabolism after a viral infection could give hints on limitations and cell-specific virus production capacities. A detailed metabolic characterization of an influenza infected adherent cell line (MDCK was carried out based on extracellular and intracellular measurements of metabolite concentrations. Results For most metabolites the comparison of infected (human influenza A/PR/8/34 and mock-infected cells showed a very similar behavior during the first 10-12 h post infection (pi. Significant changes were observed after about 12 h pi: (1 uptake of extracellular glucose and lactate release into the cell culture supernatant were clearly increased in infected cells compared to mock-infected cells. At the same time (12 h pi intracellular metabolite concentrations of the upper part of glycolysis were significantly increased. On the contrary, nucleoside triphosphate concentrations of infected cells dropped clearly after 12 h pi. This behaviour was observed for two different human influenza A/PR/8/34 strains at slightly different time points. Conclusions Comparing these results with literature values for the time course of infection with same influenza strains, underline the hypothesis that influenza infection only represents a minor additional burden for host cell metabolism. The metabolic changes observed after12 h pi are most probably caused by the onset of apoptosis in infected cells. The comparison of experimental data from two variants of the A/PR/8/34 virus strain (RKI versus NIBSC with different productivities and infection dynamics showed comparable metabolic patterns but a clearly different timely behavior. Thus, infection dynamics are obviously reflected in host cell metabolism.

  19. Differentiation of Alternaria infectoria and Alternaria alternata based on morphology, metabolite profiles, and cultural characteristics

    DEFF Research Database (Denmark)

    Andersen, Birgitte; Thrane, Ulf

    1996-01-01

    Some small-spored species belonging to the genus Alternaria Nees have been studied according to their chemical, morphological, and cultural characteristics. A data matrix was constructed based on a combination of characters. Cluster analysis of the combined data set showed good resolution of two...... groups of small-spored Alternaria the Alternaria infectoria group and the Alternaria alternata group. Isolates in the A. infectoria group produced only unique metabolites of unknown identity, whereas all isolates in the A. alternata group produced alternariol and alternariol monomethyl ether. Furthermore...

  20. Utilizing relative potency factors (RPF) and threshold of toxicological concern (TTC) concepts to assess hazard and human risk assessment profiles of environmental metabolites: a case study.

    Science.gov (United States)

    Terry, C; Rasoulpour, R J; Knowles, S; Billington, R

    2015-03-01

    There is currently no standard paradigm for hazard and human risk assessment of environmental metabolites for agrochemicals. Using an actual case study, solutions to challenges faced are described and used to propose a generic concept to address risk posed by metabolites to human safety. A novel approach - built on the foundation of predicted human exposures to metabolites in various compartments (such as food and water), the threshold of toxicological concern (TTC) and the concept of comparative toxicity - was developed for environmental metabolites of a new chemical, sulfoxaflor (X11422208). The ultimate aim was to address the human safety of the metabolites with the minimum number of in vivo studies, while at the same time, ensuring that human safety would be considered addressed on a global regulatory scale. The third component, comparative toxicity, was primarily designed to determine whether the metabolites had the same or similar toxicity profiles to their parent molecule, and also to one another. The ultimate goal was to establish whether the metabolites had the potential to cause key effects - such as cancer and developmental toxicity, based on mode-of-action (MoA) studies - and to develop a relative potency factor (RPF) compared to the parent molecule. Collectively, the work presented here describes the toxicology programme developed for sulfoxaflor and its metabolites, and how it might be used to address similar future challenges aimed at determining the relevance of the metabolites from a human hazard and risk perspective. Sulfoxaflor produced eight environmental metabolites at varying concentrations in various compartments - soil, water, crops and livestock. The MoA for the primary effects of the parent molecule were elucidated in detail and a series of in silico, in vitro, and/or in vivo experiments were conducted on the environmental metabolites to assess relative potency of their toxicity profiles when compared to the parent. The primary metabolite

  1. Krebs cycle metabolite profiling for identification and stratification of pheochromocytomas/paragangliomas due to succinate dehydrogenase deficiency.

    Science.gov (United States)

    Richter, Susan; Peitzsch, Mirko; Rapizzi, Elena; Lenders, Jacques W; Qin, Nan; de Cubas, Aguirre A; Schiavi, Francesca; Rao, Jyotsna U; Beuschlein, Felix; Quinkler, Marcus; Timmers, Henri J; Opocher, Giuseppe; Mannelli, Massimo; Pacak, Karel; Robledo, Mercedes; Eisenhofer, Graeme

    2014-10-01

    Mutations of succinate dehydrogenase A/B/C/D genes (SDHx) increase susceptibility to development of pheochromocytomas and paragangliomas (PPGLs), with particularly high rates of malignancy associated with SDHB mutations. We assessed whether altered succinate dehydrogenase product-precursor relationships, manifested by differences in tumor ratios of succinate to fumarate or other metabolites, might aid in identifying and stratifying patients with SDHx mutations. PPGL tumor specimens from 233 patients, including 45 with SDHx mutations, were provided from eight tertiary referral centers for mass spectrometric analyses of Krebs cycle metabolites. Diagnostic performance of the succinate:fumarate ratio for identification of pathogenic SDHx mutations. SDH-deficient PPGLs were characterized by 25-fold higher succinate and 80% lower fumarate, cis-aconitate, and isocitrate tissue levels than PPGLs without SDHx mutations. Receiver-operating characteristic curves for use of ratios of succinate to fumarate or to cis-aconitate and isocitrate to identify SDHx mutations indicated areas under curves of 0.94 to 0.96; an optimal cut-off of 97.7 for the succinate:fumarate ratio provided a diagnostic sensitivity of 93% at a specificity of 97% to identify SDHX-mutated PPGLs. Succinate:fumarate ratios were higher in both SDHB-mutated and metastatic tumors than in those due to SDHD/C mutations or without metastases. Mass spectrometric-based measurements of ratios of succinate:fumarate and other metabolites in PPGLs offer a useful method to identify patients for testing of SDHx mutations, with additional utility to quantitatively assess functionality of mutations and metabolic factors responsible for malignant risk.

  2. A profile of carbohydrate metabolites in the fasting northern elephant seal.

    Science.gov (United States)

    Champagne, Cory D; Boaz, Segal M; Fowler, Melinda A; Houser, Dorian S; Costa, Daniel P; Crocker, Daniel E

    2013-06-01

    Northern elephant seals endure prolonged periods of food deprivation at multiple life-history stages and simultaneous with energetically costly activities-including reproduction and development. Most mammals decrease their energy expenditure while fasting, with simultaneous reductions in gluconeogenesis and circulating glucose concentration. Paradoxically, elephant seals maintain high rates of both energy expenditure and gluconeogenesis, and high blood glucose concentrations throughout fasting. We therefore characterized the suite of changes that occur in carbohydrate metabolites during fasting in northern elephant seals. Using a broad-based metabolomics platform we investigated fasting during two states-lactation in adult females and the post-weaning developmental period in pups. A total of 227 metabolites were detected in seal plasma; 31 associated with carbohydrate metabolism were analyzed in the present study. Several compounds showed similar responses during lactation and the post-weaning fast (e.g. glycerol and mesaconate) whereas other compounds displayed quite different abundances between groups (e.g. citrate and pyruvate). This work found that, while the changes that occur with fasting were frequently similar in lactating females and developing pups, the relative abundance of compounds often varied markedly. These differences suggest that the metabolic strategies used to endure prolonged fasts are influenced by life-history or nutrient constraints. Copyright © 2013 Elsevier Inc. All rights reserved.

  3. Quantitative metabolite profiling of edible onion species by NMR and HPLC-MS.

    Science.gov (United States)

    Soininen, Tuula H; Jukarainen, Niko; Auriola, Seppo O K; Julkunen-Tiitto, Riitta; Karjalainen, Reijo; Vepsäläinen, Jouko J

    2014-12-15

    Allium genus is a treasure trove of valuable bioactive compounds with potentially therapeutically important properties. This work utilises HPLC-MS and a constrained total-line-shape (CTLS) approach applied to (1)H NMR spectra to quantify metabolites present in onion species to reveal important inter-species differences. Extensive differences were detected between the sugar concentrations in onion species. Yellow onion contained the highest and red onion the lowest amounts of amino acids. The main flavonol-glucosides were quercetin 3,4'-diglucoside and quercetin 4'-glucoside. In general, the levels of flavonols were, higher in yellow onions than in red onions, and garlic and leek contained a lower amount of flavonols than the other Allium species. Our results highlight how (1)H NMR together with HPLC-MS can be useful in the quantification and the identification of the most abundant metabolites, representing an efficient means to pinpoint important functional food ingredients from Allium species. Copyright © 2014 Elsevier Ltd. All rights reserved.

  4. Proteomics Coupled with Metabolite and Cell Wall Profiling Reveal Metabolic Processes of a Developing Rice Stem Internode

    Energy Technology Data Exchange (ETDEWEB)

    Lin, Fan; Williams, Brad J.; Thangella, Padmavathi A. V.; Ladak, Adam; Schepmoes, Athena A.; Olivos, Hernando J.; Zhao, Kangmei; Callister, Stephen J.; Bartley, Laura E.

    2017-07-13

    Internodes of grass stems function in mechanical support, transport, and, in some species, are a major sink organ for carbon in the form of cell wall polymers. This study reports cell wall composition, proteomic and metabolite analyses of the rice elongating internode. Along eight segments of the second rice internode (internode II) at booting stage, cellulose, lignin, and xylose increase as a percentage of cell wall material from the younger to the older internode segments, indicating active cell wall synthesis. Liquid-chromatography tandem mass spectrometry (LC-MS/MS) of trypsin-digested peptides of size-fractionated proteins extracted from this internode at booting reveals 2547proteins with at least two unique peptides. The dataset includes many glycosyltransferases, acyltransferases, glycosyl hydrolases, cell wall-localized proteins, and protein kinases that have or may have functions in cell wall biosynthesis or remodeling. Phospho-enrichment of the internode II peptides identified 21 unique phosphopeptides belonging to 20 phosphoproteins including an LRR-III family receptor like kinase. GO over-representation and KEGG pathway analyses highlight the abundances of internode proteins involved in biosynthetic processes, especially the synthesis of secondary metabolites such as phenylpropanoids and flavonoids. LC-MS of hot methanol-extracted secondary metabolites from internode II at four stages (elongation, early mature, mature and post mature) indicates that secondary metabolites in stems are distinct from those of roots and leaves, and differ during stem maturation. This work fills a void of knowledge of proteomics and metabolomics data for grass stems, specifically for rice, and provides baseline knowledge for more detailed studies of cell wall synthesis and other biological processes during internode development, toward improving grass agronomic properties.

  5. Semi-automated knowledge discovery: identifying and profiling human trafficking

    Science.gov (United States)

    Poelmans, Jonas; Elzinga, Paul; Ignatov, Dmitry I.; Kuznetsov, Sergei O.

    2012-11-01

    We propose an iterative and human-centred knowledge discovery methodology based on formal concept analysis. The proposed approach recognizes the important role of the domain expert in mining real-world enterprise applications and makes use of specific domain knowledge, including human intelligence and domain-specific constraints. Our approach was empirically validated at the Amsterdam-Amstelland police to identify suspects and victims of human trafficking in 266,157 suspicious activity reports. Based on guidelines of the Attorney Generals of the Netherlands, we first defined multiple early warning indicators that were used to index the police reports. Using concept lattices, we revealed numerous unknown human trafficking and loverboy suspects. In-depth investigation by the police resulted in a confirmation of their involvement in illegal activities resulting in actual arrestments been made. Our human-centred approach was embedded into operational policing practice and is now successfully used on a daily basis to cope with the vastly growing amount of unstructured information.

  6. Metabolite profiling of phenolic and carotenoid contents in tomatoes after moderate-intensity pulsed electric field treatments.

    Science.gov (United States)

    Vallverdú-Queralt, Anna; Oms-Oliu, Gemma; Odriozola-Serrano, Isabel; Lamuela-Raventós, Rosa M; Martín-Belloso, Olga; Elez-Martínez, Pedro

    2013-01-01

    A metabolite profiling approach was used to study the effect of moderate-intensity pulsed electric field (MIPEF) treatments on the individual polyphenol and carotenoid contents of tomato fruit after refrigeration at 4°C for 24h. The MIPEF processing variables studied were electric field strength (from 0.4 to 2.0kV/cm) and number of pulses (from 5 to 30). Twenty four hours after MIPEF treatments, an increase was observed in hydroxycinnamic acids and flavanones, whereas flavonols, coumaric and ferulic acid-O-glucoside were not affected. Major changes were also observed for carotenoids, except for the 5-cis-lycopene isomer, which remain unchanged after 24h of MIPEF treatments. MIPEF treatments, conducted at 1.2kV/cm and 30 pulses, led to the greatest increases in chlorogenic (152%), caffeic acid-O-glucoside (170%) and caffeic (140%) acids. On the other hand, treatments at 1.2kV/cm and 5 pulses led to maximum increases of α-carotene, 9- and 13-cis-lycopene, which increased by 93%, 94% and 140%, respectively. Therefore, MIPEF could stimulate synthesis of secondary metabolites and contribute to production of tomatoes with high individual polyphenol and carotenoid contents. Copyright © 2012 Elsevier Ltd. All rights reserved.

  7. Metabolite profiling, antioxidant, and α-glucosidase inhibitory activities of germinated rice: nuclear-magnetic-resonance-based metabolomics study

    Directory of Open Access Journals (Sweden)

    Phaiwan Pramai

    2018-01-01

    Full Text Available In an attempt to profile the metabolites of three different varieties of germinated rice, specifically black (GBR, red, and white rice, a 1H-nuclear-magnetic-resonance-based metabolomics approach was conducted. Multivariate data analysis was applied to discriminate between the three different varieties using a partial least squares discriminant analysis (PLS-DA model. The PLS model was used to evaluate the relationship between chemicals and biological activities of germinated rice. The PLS-DA score plot exhibited a noticeable separation between the three rice varieties into three clusters by PC1 and PC2. The PLS model indicated that α-linolenic acid, γ-oryzanol, α-tocopherol, γ-aminobutyric acid, 3-hydroxybutyric acid, fumaric acid, fatty acids, threonine, tryptophan, and vanillic acid were significantly correlated with the higher bioactivities demonstrated by GBR that was extracted in 100% ethanol. Subsequently, the proposed biosynthetic pathway analysis revealed that the increased quantities of secondary metabolites found in GBR may contribute to its nutritional value and health benefits.

  8. Metabolite profiling, antioxidant, and α-glucosidase inhibitory activities of germinated rice: nuclear-magnetic-resonance-based metabolomics study.

    Science.gov (United States)

    Pramai, Phaiwan; Abdul Hamid, Nur Ashikin; Mediani, Ahmed; Maulidiani, Maulidiani; Abas, Faridah; Jiamyangyuen, Sudarat

    2018-01-01

    In an attempt to profile the metabolites of three different varieties of germinated rice, specifically black (GBR), red, and white rice, a 1 H-nuclear-magnetic-resonance-based metabolomics approach was conducted. Multivariate data analysis was applied to discriminate between the three different varieties using a partial least squares discriminant analysis (PLS-DA) model. The PLS model was used to evaluate the relationship between chemicals and biological activities of germinated rice. The PLS-DA score plot exhibited a noticeable separation between the three rice varieties into three clusters by PC1 and PC2. The PLS model indicated that α-linolenic acid, γ-oryzanol, α-tocopherol, γ-aminobutyric acid, 3-hydroxybutyric acid, fumaric acid, fatty acids, threonine, tryptophan, and vanillic acid were significantly correlated with the higher bioactivities demonstrated by GBR that was extracted in 100% ethanol. Subsequently, the proposed biosynthetic pathway analysis revealed that the increased quantities of secondary metabolites found in GBR may contribute to its nutritional value and health benefits. Copyright © 2017. Published by Elsevier B.V.

  9. De novo sequencing of Hypericum perforatum transcriptome to identify potential genes involved in the biosynthesis of active metabolites.

    Directory of Open Access Journals (Sweden)

    Miao He

    Full Text Available BACKGROUND: Hypericum perforatum L. (St. John's wort is a medicinal plant with pharmacological properties that are antidepressant, anti-inflammatory, antiviral, anti-cancer, and antibacterial. Its major active metabolites are hypericins, hyperforins, and melatonin. However, little genetic information is available for this species, especially that concerning the biosynthetic pathways for active ingredients. METHODOLOGY/PRINCIPAL FINDINGS: Using de novo transcriptome analysis, we obtained 59,184 unigenes covering the entire life cycle of these plants. In all, 40,813 unigenes (68.86% were annotated and 2,359 were assigned to secondary metabolic pathways. Among them, 260 unigenes are involved in the production of hypericin, hyperforin, and melatonin. Another 2,291 unigenes are classified as potential Type III polyketide synthase. Our BlastX search against the AGRIS database reveals 1,772 unigenes that are homologous to 47 known Arabidopsis transcription factor families. Further analysis shows that 10.61% (6,277 of these unigenes contain 7,643 SSRs. CONCLUSION: We have identified a set of putative genes involved in several secondary metabolism pathways, especially those related to the synthesis of its active ingredients. Our results will serve as an important platform for public information about gene expression, genomics, and functional genomics in H. perforatum.

  10. Physiological performance, secondary metabolite and expression profiling of genes associated with drought tolerance in Withania somnifera.

    Science.gov (United States)

    Sanchita; Singh, Ruchi; Mishra, Anand; Dhawan, Sunita S; Shirke, Pramod A; Gupta, Madan M; Sharma, Ashok

    2015-11-01

    Physiological, biochemical, and gene expression responses under drought stress were studied in Withania somnifera. Photosynthesis rate, stomatal conductance, transpiration rate, relative water content, chlorophyll content, and quantum yield of photosystems I and II (PSI and PSII) decreased in response to drought stress. Comparative expression of genes involved in osmoregulation, detoxification, signal transduction, metabolism, and transcription factor was analyzed through quantitative RT-PCR. The genes encoding 1-pyrroline-5-carboxylate synthetase (P5CS), glutathione S-transferase (GST), superoxide dismutase (SOD), serine threonine-protein kinase (STK), serine threonine protein phosphatase (PSP), aldehyde dehydrogenase (AD), leucoanthocyanidin dioxygenase/anthocyanin synthase (LD/AS), HSP, MYB, and WRKY have shown upregulation in response to drought stress condition in leaf tissues. Enhanced detoxification and osmoregulation along with increased withanolides production were also observed under drought stress. The results of this study will be helpful in developing stress-tolerant and high secondary metabolite yielding genotypes.

  11. Target metabolite and gene transcription profiling during the development of superficial scald in apple (Malus x domestica Borkh).

    Science.gov (United States)

    Busatto, Nicola; Farneti, Brian; Tadiello, Alice; Vrhovsek, Urska; Cappellin, Luca; Biasioli, Franco; Velasco, Riccardo; Costa, Guglielmo; Costa, Fabrizio

    2014-07-20

    Fruit quality features resulting from ripening processes need to be preserved throughout storage for economical reasons. However, during this period several physiological disorders can occur, of which superficial scald is one of the most important, due to the development of large brown areas on the fruit skin surface. This study examined the variation in polyphenolic content with the progress of superficial scald in apple, also with respect to 1-MCP, an ethylene competitor interacting with the hormone receptors and known to interfere with this etiology. The change in the accumulation of these metabolites was further correlated with the gene set involved in this pathway, together with two specific VOCs (Volatile Organic Compounds), α-farnesene and its oxidative form, 6-methyl-5-hepten-2-one. Metabolite profiling and qRT-PCR assay showed these volatiles are more heavily involved in the signalling system, while the browning coloration would seem to be due more to a specific accumulation of chlorogenic acid (as a consequence of the activation of MdPAL and MdC3H), and its further oxidation carried out by a polyphenol oxidase gene (MdPPO). In this physiological scenario, new evidence regarding the involvement of an anti-apoptotic regulatory mechanism for the compartmentation of this phenomenon in the skin alone was also hypothesized, as suggested by the expression profile of the MdDAD1, MdDND1 and MdLSD1 genes. The results presented in this work represent a step forward in understanding the physiological mechanisms of superficial scald in apple, shedding light on the regulation of the specific physiological cascade.

  12. Metabolomic analysis of 92 pulmonary embolism patients from a nested case-control study identifies metabolites associated with adverse clinical outcomes.

    Science.gov (United States)

    Zeleznik, O A; Poole, E M; Lindstrom, S; Kraft, P; Van Hylckama Vlieg, A; Lasky-Su, J A; Harrington, L B; Hagan, K; Kim, J; Parry, B A; Giordano, N; Kabrhel, C

    2018-03-01

    Essentials Risk-stratification often fails to predict clinical deterioration in pulmonary embolism (PE). First-ever high-throughput metabolomics analysis of risk-stratified PE patients. Changes in circulating metabolites reflect a compromised energy metabolism in PE. Metabolites play a key role in the pathophysiology and risk stratification of PE. Background Patients with acute pulmonary embolism (PE) exhibit wide variation in clinical presentation and outcomes. Our understanding of the pathophysiologic mechanisms differentiating low-risk and high-risk PE is limited, so current risk-stratification efforts often fail to predict clinical deterioration and are insufficient to guide management. Objectives To improve our understanding of the physiology differentiating low-risk from high-risk PE, we conducted the first-ever high-throughput metabolomics analysis (843 named metabolites) comparing PE patients across risk strata within a nested case-control study. Patients/methods We enrolled 92 patients diagnosed with acute PE and collected plasma within 24 h of PE diagnosis. We used linear regression and pathway analysis to identify metabolites and pathways associated with PE risk-strata. Results When we compared 46 low-risk with 46 intermediate/high-risk PEs, 50 metabolites were significantly different after multiple testing correction. These metabolites were enriched in the following pathways: tricarboxylic acid (TCA) cycle, fatty acid metabolism (acyl carnitine) and purine metabolism, (hypo)xanthine/inosine containing. Additionally, energy, nucleotide and amino acid pathways were downregulated in intermediate/high-risk PE patients. When we compared 28 intermediate-risk with 18 high-risk PE patients, 41 metabolites differed at a nominal P-value level. These metabolites were enriched in fatty acid metabolism (acyl cholines), and hemoglobin and porphyrin metabolism. Conclusion Our results suggest that high-throughput metabolomics can provide insight into the

  13. Metabolite profiling of ascidian Styela plicata using LC-MS with multivariate statistical analysis and their antitumor activity.

    Science.gov (United States)

    Palanisamy, Satheesh Kumar; Trisciuoglio, Daniela; Zwergel, Clemens; Del Bufalo, Donatella; Mai, Antonello

    2017-12-01

    To identify the metabolite distribution in ascidian, we have applied an integrated liquid chromatography- tandem mass spectrometry (LC-MS) metabolomics approach to explore and identify patterns in chemical diversity of invasive ascidian Styela plicata. A total of 71 metabolites were reported among these alkaloids, fatty acids and lipids are the most dominant chemical group. Multivariate statistical analysis, principal component analysis (PCA) showed a clear separation according to chemical diversity and taxonomic groups. PCA and partial least square discriminant analysis were applied to discriminate the chemical group of S. plicata crude compounds and classify the compounds with unknown biological activities. In this study, we reported for the first time that a partially purified methanol extract prepared from the ascidian S. plicata and Ascidia mentula possess antitumor activity against four tumor cell lines with different tumor histotype, such as HeLa (cervical carcinoma), HT29 (colon carcinoma), MCF-7 (breast carcinoma) and M14 (melanoma). S. plicata fraction SP-50 showed strong inhibition of cell proliferation and induced apoptosis in HeLa and HT29 cells, thus indicating S. plicata fraction SP-50 a potential lead compound for anticancer therapy. The molecular mechanism of action and chemotherapeutic potential of these ascidian unknown biomolecules need further research.

  14. Metabolite profiling of the fermentation process of "yamahai-ginjo-shikomi" Japanese sake.

    Science.gov (United States)

    Tatsukami, Yohei; Morisaka, Hironobu; Aburaya, Shunsuke; Aoki, Wataru; Kohsaka, Chihiro; Tani, Masafumi; Hirooka, Kiyoo; Yamamoto, Yoshihiro; Kitaoka, Atsushi; Fujiwara, Hisashi; Wakai, Yoshinori; Ueda, Mitsuyoshi

    2018-01-01

    Sake is a traditional Japanese alcoholic beverage prepared by multiple parallel fermentation of rice. The fermentation process of "yamahai-ginjo-shikomi" sake is mainly performed by three microbes, Aspergillus oryzae, Saccharomyces cerevisiae, and Lactobacilli; the levels of various metabolites fluctuate during the fermentation of sake. For evaluation of the fermentation process, we monitored the concentration of moderate-sized molecules (m/z: 200-1000) dynamically changed during the fermentation process of "yamahai-ginjo-shikomi" Japanese sake. This analysis revealed that six compounds were the main factors with characteristic differences in the fermentation process. Among the six compounds, four were leucine- or isoleucine-containing peptides and the remaining two were predicted to be small molecules. Quantification of these compounds revealed that their quantities changed during the month of fermentation process. Our metabolomic approach revealed the dynamic changes observed in moderate-sized molecules during the fermentation process of sake, and the factors found in this analysis will be candidate molecules that indicate the progress of "yamahai-ginjo-shikomi" sake fermentation.

  15. Profiling of urinary amino-carboxylic metabolites by in-situ heptafluorobutyl chloroformate mediated sample preparation and gas chromatography-mass spectrometry

    Czech Academy of Sciences Publication Activity Database

    Hušek, Petr; Švagera, Z.; Hanzlíková, D.; Řimnáčová, Lucie; Zahradníčková, Helena; Opekarová, Iva; Šimek, Petr

    2016-01-01

    Roč. 1443, April 22 (2016), s. 211-232 ISSN 0021-9673 R&D Projects: GA ČR GA13-18509S Institutional support: RVO:60077344 Keywords : metabolite profiling * metabolomics * urine Subject RIV: CE - Biochemistry Impact factor: 3.981, year: 2016 http://www.sciencedirect.com/science/article/pii/S0021967316302692

  16. Gender-dependent associations of metabolite profiles and body fat distribution in a healthy population with central obesity: Towards metabolomics diagnostics

    NARCIS (Netherlands)

    Szymańska, E.; Bouwman, J.; Strassburg, K.; Vervoort, J.; Kangas, A.J.; Soininen, P.; Ala-Korpela, M.; Westerhuis, J.; Duynhoven, J.P.M. van; Mela, D.J.; MacDonald, I.A.; Vreeken, R.J.; Smilde, A.K.; Jacobs, D.M.

    2012-01-01

    Obesity is a risk factor for cardiovascular diseases and type 2 diabetes especially when the fat is accumulated to central depots. Novel biomarkers are crucial to develop diagnostics for obesity and related metabolic disorders. We evaluated the associations between metabolite profiles (136 lipid

  17. Gender-dependent associations of metabolite profiles and body fat distribution in a healthy population with central obesity: towards metabolomics diagnostics

    NARCIS (Netherlands)

    Szymańska, E.; Bouwman, J.; Strassburg, K.; Vervoort, J.; Kangas, A.J.; Soininen, P.; Ala-Korpela, M.; Westerhuis, J.; van Duynhoven, J.P.M.; Mela, D.J.; Macdonald, I.A.; Vreeken, R.J.; Smilde, A.K.; Jacobs, D.M.

    2012-01-01

    Obesity is a risk factor for cardiovascular diseases and type 2 diabetes especially when the fat is accumulated to central depots. Novel biomarkers are crucial to develop diagnostics for obesity and related metabolic disorders. We evaluated the associations between metabolite profiles (136 lipid

  18. Gender-dependent associations of metabolite profiles and body fat distribution in a healthy population with central obesity: Towards metabolomics diagnostics

    NARCIS (Netherlands)

    Szymanska, E.; Bouwman, J.; Strassburg, K.; Vervoort, J.J.M.; Kangas, A.J.; Soininen, P.; Ala-Korpela, M.; Westerhuis, J.A.; Duynhoven, van J.P.M.; Mela, D.J.; Macdonald, I.A.; Vreeken, R.J.; Smilde, A.K.; Jacobs, D.M.

    2012-01-01

    Abstract Obesity is a risk factor for cardiovascular diseases and type 2 diabetes especially when the fat is accumulated to central depots. Novel biomarkers are crucial to develop diagnostics for obesity and related metabolic disorders. We evaluated the associations between metabolite profiles (136

  19. Lipophilic metabolite profiling of maize and sorghum seeds and seedlings, and their pest spotted stem borer larvae: a standardized GC-MS based approach.

    Science.gov (United States)

    Kumar, Sandeep; Dhillon, Mukesh K

    2015-03-01

    In order to better understand the biochemical interactions and to identify new biomarkers for plant resistance against insects, we proposed a suitable lipophilic profiling method for insects and their host plants. The critical components of GC-MS based analysis are: sample amount, extraction, derivatization, temperature gradient, run time, and identification of peaks. For lipophilic metabolite profiling of maize and sorghum, and their insect pest, spotted stem borer larvae, we recommend 100 mg sample weight for seeds and insect samples (whole insect body), and 200 mg for seedlings. Maize and sorghum seeds required less time for fat extraction in comparison to their seedlings and the pest fed on these seedlings. GC-MS was standardized for better separation and intensity of peaks using different temperature gradients in the range of 180-300 C. A total of 48 lipophilic compounds encompassing various classes based on their functional groups such as fatty acids, fatty alcohols, hydrocarbons, sterols and terpenoids, vitamin derivative, etc. were separated in the seedlings (30), seeds (14), and the pest (26) in the retention time range of 3.22 to 29.41 min. This method could be useful to study nutritional aspects of different field crops in relation to various stresses apart from the analysis of lipophilic compounds for better understanding of insect-plant interactions.

  20. Plasma stability-dependent circulation of acyl glucuronide metabolites in humans: how circulating metabolite profiles of muraglitazar and peliglitazar can lead to misleading risk assessment.

    Science.gov (United States)

    Zhang, Donglu; Raghavan, Nirmala; Wang, Lifei; Xue, Yongjun; Obermeier, Mary; Chen, Stephanie; Tao, Shiwei; Zhang, Hao; Cheng, Peter T; Li, Wenying; Ramanathan, Ragu; Yang, Zheng; Humphreys, W Griffith

    2011-01-01

    Muraglitazar and peliglitazar, two structural analogs differing by a methyl group, are dual peroxisome proliferator-activated receptor-α/γ activators. Both compounds were extensively metabolized in humans through acyl glucuronidation to form 1-O-β-acyl glucuronide (AG) metabolites as the major drug-related components in bile, representing at least 15 to 16% of the dose after oral administration. Peliglitazar AG was the major circulating metabolite, whereas muraglitazar AG was a very minor circulating metabolite in humans. Peliglitazar AG circulated at lower concentrations in animal species than in humans. Both compounds had a similar glucuronidation rate in UDP-glucuronic acid-fortified human liver microsomal incubations and a similar metabolism rate in human hepatocytes. Muraglitazar AG and peliglitazar AG were chemically synthesized and found to be similarly oxidized through hydroxylation and O-demethylation in NADPH-fortified human liver microsomal incubations. Peliglitazar AG had a greater stability than muraglitazar AG in incubations in buffer, rat, or human plasma (pH 7.4). Incubations of muraglitazar AG or peliglitazar AG in plasma produced more aglycon than acyl migration products compared with incubations in the buffer. These data suggested that the difference in plasma stability, not differences in intrinsic formation, direct excretion, or further oxidation of muraglitazar AG or peliglitazar AG, contributed to the observed difference in the circulation of these AG metabolites in humans. The study demonstrated the difficulty in doing risk assessment based on metabolite exposure in plasma because the more reactive muraglitazar AG would not have triggered a threshold of concern based on the recent U.S. Food and Drug Administration guidance on Metabolites in Safety Testing, whereas the more stable peliglitazar AG would have.

  1. Impacts of 17α-ethynylestradiol exposure on metabolite profiles of zebrafish (Danio rerio) liver cells

    Energy Technology Data Exchange (ETDEWEB)

    Teng, Quincy, E-mail: teng.quincy@epa.gov [National Exposure Research Laboratory, U.S. Environmental Protection Agency, 960 College Station Road, Athens, GA 30605 (United States); Ekman, Drew R., E-mail: ekman.drew@epa.gov [National Exposure Research Laboratory, U.S. Environmental Protection Agency, 960 College Station Road, Athens, GA 30605 (United States); Huang, Wenlin, E-mail: whuang2@ccny.cuny.edu [National Exposure Research Laboratory, U.S. Environmental Protection Agency, 960 College Station Road, Athens, GA 30605 (United States); Collette, Timothy W., E-mail: collette.tim@epa.gov [National Exposure Research Laboratory, U.S. Environmental Protection Agency, 960 College Station Road, Athens, GA 30605 (United States)

    2013-04-15

    Highlights: ► We apply NMR-based metabolomics to study responses of ZFL cells exposed to EE2. ► The metabolomics approach has capability to capture cellular response to exposure. ► The analysis provides detailed molecular information on chemical's mode of action. ► Cellular metabolomics may have application for screening chemical exposure/toxicity. -- Abstract: Endocrine disrupting chemicals (EDCs) that are frequently detected in bodies of water downstream from sewage treatment facilities can have adverse impacts on fish and other aquatic organisms. To properly assess risk(s) from EDCs, tools are needed that can establish linkages from chemical exposures to adverse outcomes. Traditional methods of testing chemical exposure and toxicity using experimental animals are excessively resource- and time-consuming. In line with EPA's goal of reducing animal use in testing, these traditional screening methods may not be sustainable in the long term, given the ever increasing number of chemicals that must be tested for safety. One of the most promising ways to reduce costs and increase throughput is to use cell cultures instead of experimental animals. In accordance with National Research Council's vision on 21st century toxicity testing, we have developed a cell culture-based metabolomics approach for this application. Using a zebrafish (Danio rerio) liver cell line (ZFL), we have applied NMR-based metabolomics to investigate responses of ZFL cells exposed to 17α-ethynylestradiol (EE2). This analysis showed that metabolite changes induced by EE2 exposure agree well with known impacts of estrogens on live fish. The results of this study demonstrate the potential of cell-based metabolomics to assess chemical exposure and toxicity for regulatory application.

  2. Abscisic acid metabolite profiling as indicators of plastic responses to drought in grasses from arid Patagonian Monte (Argentina).

    Science.gov (United States)

    Cenzano, Ana M; Masciarelli, O; Luna, M Virginia

    2014-10-01

    The identification of hormonal and biochemical traits that play functional roles in the adaptation to drought is necessary for the conservation and planning of rangeland management. The aim of this study was to evaluate the effects of drought on i) the water content (WC) of different plant organs, ii) the endogenous level of abscisic acid (ABA) and metabolites (phaseic acid-PA, dihydrophaseic acid-DPA and abscisic acid conjugated with glucose ester-ABA-GE), iii) the total carotenoid concentration and iv) to compare the traits of two desert perennial grasses (Pappostipa speciosa and Poa ligularis) with contrasting morphological and functional drought resistance traits and life-history strategies. Both species were subjected to two levels of gravimetric soil moisture (the highest near field capacity during autumn-winter and the lowest corresponding to summer drought). Drought significantly increased the ABA and DPA levels in the green leaves of P. speciosa and P. ligularis. Drought decreased ABA in the roots of P. speciosa while it increased ABA in the roots of P. ligularis. P. ligularis had the highest ABA level and WC in green leaves. While P. speciosa had the highest DPA levels in leaves. In conclusion, we found the highest ABA level in the mesophytic species P. ligularis and the lowest ABA level in the xerophytic species P. speciosa, revealing that the ABA metabolite profile in each grass species is a plastic response to drought resistance. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

  3. Identifying work setting profile factors from the Career Pathway Evaluation Program.

    Science.gov (United States)

    Schommer, Jon C; Sogol, Elliott M; Brown, Lawrence M

    2013-11-12

    To describe the work factors associated with 28 different career areas as reported by pharmacists who responded to the American Pharmacists Association (APhA) Career Pathway Evaluation Program for Pharmacy Professionals, 2012 Pharmacist Profile Survey. Data from the 1,119 completed survey instruments from the 2012 Pharmacist Profile Survey were analyzed. Exploratory factor analysis was used to identify the underlying factors that best represented respondents' work setting profiles. Eleven underlying factors were identified for the respondents' work setting profiles: patient care, application of clinical knowledge, innovation, stress, research, managerial responsibility, work schedule flexibility, job position flexibility, self-actualization, geographic location, and continuity of coworker relationships. Findings revealed variation for these underlying factors among career categories. Variation among pharmacist career types exists. The profiles constructed in this study describe the characteristics of various career paths and can be helpful for decisions regarding educational, experiential, residency, and certification training in pharmacist careers.

  4. Identifying Work Setting Profile Factors From the Career Pathway Evaluation Program

    Science.gov (United States)

    Sogol, Elliott M.; Brown, Lawrence M.

    2013-01-01

    Objectives. To describe the work factors associated with 28 different career areas as reported by pharmacists who responded to the American Pharmacists Association (APhA) Career Pathway Evaluation Program for Pharmacy Professionals, 2012 Pharmacist Profile Survey Methods. Data from the 1,119 completed survey instruments from the 2012 Pharmacist Profile Survey were analyzed. Exploratory factor analysis was used to identify the underlying factors that best represented respondents’ work setting profiles. Results. Eleven underlying factors were identified for the respondents’ work setting profiles: patient care, application of clinical knowledge, innovation, stress, research, managerial responsibility, work schedule flexibility, job position flexibility, self-actualization, geographic location, and continuity of coworker relationships. Findings revealed variation for these underlying factors among career categories. Conclusion. Variation among pharmacist career types exists. The profiles constructed in this study describe the characteristics of various career paths and can be helpful for decisions regarding educational, experiential, residency, and certification training in pharmacist careers. PMID:24249856

  5. Volatile metabolite profiling reveals the changes in the volatile compounds of new spontaneously generated loquat cultivars.

    Science.gov (United States)

    Besada, C; Sanchez, G; Gil, R; Granell, A; Salvador, A

    2017-10-01

    In recent years, the advantageous traits of three new loquat cultivars have drawn the attention of breeders and growers. All three have spontaneously arisen from the 'Algerie' cultivar: the new 'Xirlero' cultivar is a bud mutant of 'Algerie', while 'Amadeo' and 'Raúl' arose as chance seedlings. Following a non-targeted approach based on HS-SPME-GC-MS, the volatile compounds profile of the fruits from the new cultivars were obtained and compared to the original 'Algerie' cultivar. Carboxylic acids clearly dominated the volatile profile of all the loquat cultivars, but esters, aldehydes, ketones and alcohols were also predominant compounds. Interestingly when the bud mutant event did not lead to marked changes in the volatile compounds complement, pronounced changes in the volatile composition of chance seedling-generated cultivars 'Amadeo' and 'Raúl' were observed. 'Amadeo' fruits showed lower levels of 2-methyl butanoic acid and much higher levels of methylhexanoate, methylbutanoate and 2-hydroxy-5-methylacetophenone. The 'Raúl' cultivar also had a distinctive volatile profile characterised by high levels of C6-aldehydes, (E)-2-hexanal, 2-hexenal, (Z)-3-hexenal and hexanal, and several carotenoid-derived volatiles; e.g. 2-pentene-1,4-dione 1-(1,2,2-trimethylcyclopentyl), (S)-dihydroactinidiolide, isodurene, cis-geranyl acetone, β-damascenone, β-ionone, α-ionone and 3,4-dehydro-β-ionone. These changes in volatiles were associated with a more intense flavour in cultivars 'Amadeo' and 'Raúl', according to the sensory evaluation of the flavour intensity carried out by a semi-trained panel. A metabolomic correlation network analysis provided insights as to how volatiles were regulated, and revealed that the compounds modified in 'Amadeo' were uncoupled from the rest of the volatilome, while the volatiles modified in 'Raul' changed according to specific groups. To conclude, this work provides a holistic view of how the loquat volatilome was affected, and this

  6. Identifying Taiwanese University Students' Physics Learning Profiles and Their Role in Physics Learning Self-Efficacy

    Science.gov (United States)

    Lin, Tzung-Jin; Liang, Jyh-Chong; Tsai, Chin-Chung

    2015-08-01

    The main purposes of this study were to identify Taiwanese university students' physics learning profiles in terms of their critical conceptions of learning physics and to compare their physics learning self-efficacy with the different learning profiles. A total of 250 Taiwanese undergraduates who were majoring in physics participated in this study and were invited to complete two instruments, physics learning profile and physics learning self-efficacy (PLSE). The main results indicated that, first, the two instruments developed in this study had satisfactory validity and reliability. Second, three fundamental physics learning profiles, the reproductive, transitional, and constructive profiles, were characterized based on the cluster analysis. It is also evident that the three learning profiles demonstrated different levels of self-efficacy for the five PLSE dimensions. The students with a reproductive profile tended to possess the lowest PLSE across the five dimensions. The students with a transitional profile may possess higher confidence in higher-order cognitive skills and laboratory activities than those with a reproductive profile. However, only those with a constructive profile, highlighting a comprehensive understanding of physics knowledge/concepts as well as de-emphasizing physics learning as preparing for tests and calculating and practising tutorial problems, possessed stronger PLSE in applying what they learned to real-world contexts as well as in scientifically communicating with others.

  7. Metabolite profiling reveals a specific response in tomato to predaceous Chrysoperla carnea larvae and herbivore(s-predator interactions with the generalist pests Tetranychus urticae and Myzus persicae

    Directory of Open Access Journals (Sweden)

    Audrey Errard

    2016-08-01

    Full Text Available The spider mite Tetranychus urticae Koch and the aphid Myzus persicae (Sulzer both infest a number of economically significant crops, including tomato (Solanum lycopersicum. Although used for decades to control pests, the impact of green lacewing larvae Chrysoperla carnea (Stephens on plant biochemistry was not investigated. Here we used profiling methods and targeted analyses to explore the impact of the predator and herbivore(s-predator interactions on tomato biochemistry. Each pest and pest-predator combination induced a characteristic metabolite signature in the leaf and the fruit thus, the plant exhibited a systemic response. The treatments had a stronger impact on non-volatile metabolites including abscisic acid and amino acids in the leaves in comparison with the fruits. In contrast, the various biotic factors had a greater impact on the carotenoids in the fruits. We identified volatiles such as myrcene and α-terpinene which were induced by pest-predator interactions but not by single species, and we demonstrated the involvement of the phytohormone abscisic acid in tritrophic interactions for the first time. More importantly, C. carnea larvae alone impacted the plant metabolome, but the predator did not appear to elicit particular defense pathways on its own. Since the presence of both C. carnea larvae and pest individuals elicited volatiles which were shown to contribute to plant defense, C. carnea larvae could therefore contribute to the reduction of pest infestation, not only by its preying activity, but also by priming responses to generalist herbivores such as T. urticae and M. persicae. On the other hand, the use of C. carnea larvae alone did not impact carotenoids thus, was not prejudicial to the fruit quality. The present piece of research highlights the specific impact of predator and tritrophic interactions with green lacewing larvae, spider mites and aphids on different components of the tomato primary and secondary metabolism

  8. Metabolite Profiling Reveals a Specific Response in Tomato to Predaceous Chrysoperla carnea Larvae and Herbivore(s)-Predator Interactions with the Generalist Pests Tetranychus urticae and Myzus persicae.

    Science.gov (United States)

    Errard, Audrey; Ulrichs, Christian; Kühne, Stefan; Mewis, Inga; Mishig, Narantuya; Maul, Ronald; Drungowski, Mario; Parolin, Pia; Schreiner, Monika; Baldermann, Susanne

    2016-01-01

    The spider mite Tetranychus urticae Koch and the aphid Myzus persicae (Sulzer) both infest a number of economically significant crops, including tomato (Solanum lycopersicum). Although used for decades to control pests, the impact of green lacewing larvae Chrysoperla carnea (Stephens) on plant biochemistry was not investigated. Here, we used profiling methods and targeted analyses to explore the impact of the predator and herbivore(s)-predator interactions on tomato biochemistry. Each pest and pest-predator combination induced a characteristic metabolite signature in the leaf and the fruit thus, the plant exhibited a systemic response. The treatments had a stronger impact on non-volatile metabolites including abscisic acid and amino acids in the leaves in comparison with the fruits. In contrast, the various biotic factors had a greater impact on the carotenoids in the fruits. We identified volatiles such as myrcene and α-terpinene which were induced by pest-predator interactions but not by single species, and we demonstrated the involvement of the phytohormone abscisic acid in tritrophic interactions for the first time. More importantly, C. carnea larvae alone impacted the plant metabolome, but the predator did not appear to elicit particular defense pathways on its own. Since the presence of both C. carnea larvae and pest individuals elicited volatiles which were shown to contribute to plant defense, C. carnea larvae could therefore contribute to the reduction of pest infestation, not only by its preying activity, but also by priming responses to generalist herbivores such as T. urticae and M. persicae. On the other hand, the use of C. carnea larvae alone did not impact carotenoids thus, was not prejudicial to the fruit quality. The present piece of research highlights the specific impact of predator and tritrophic interactions with green lacewing larvae, spider mites, and aphids on different components of the tomato primary and secondary metabolism for the first

  9. Use of solid phase microextraction (SPME) for profiling the volatile metabolites produced by Glomerella cingulata.

    Science.gov (United States)

    Miyazawa, Mitsuo; Kimura, Minako; Yabe, Yoshito; Tsukamoto, Daisuke; Sakamoto, Masaya; Horibe, Isao; Okuno, Yoshiharu

    2008-01-01

    The profile of volatile organic compounds (VOCs) released from Glomerella cingulata using solid phase microextraction (SPME) with different fibers, Polydimethylsiloxane (PDMS), Polydimethylsiloxane/Divinylbenzene (PDMS/DVB), Carboxen/Polydimethylsiloxane (CAR/PDMS) and Divinylbenzene/Carboxen/Polydimethylsiloxane (DVB/CAR/PDMS), was investigated. C4-C6 aliphatic alcohols were the predominant fraction of VOCs isolated by CAR/PDMS fiber. Sesquiterpene hydrocarbons represented 20.3% of VOCs isolated by PDMS fiber. During the growth phase, Ochracin was produced in the large majority of VOCs. 3-Methylbutanol and phenylethyl alcohol were found in the log phase of it. Alcohols were found in cultures of higher age, while sesquiterpenes were found to be characteristic of initial growth stage of G. cingulata.

  10. Dynamic headspace solid-phase microextraction combined with one-dimensional gas chromatography-mass spectrometry as a powerful tool to differentiate banana cultivars based on their volatile metabolite profile.

    Science.gov (United States)

    Pontes, Marisela; Pereira, Jorge; Câmara, José S

    2012-10-15

    In this study the effect of the cultivar on the volatile profile of five different banana varieties was evaluated and determined by dynamic headspace solid-phase microextraction (dHS-SPME) combined with one-dimensional gas chromatography-mass spectrometry (1D-GC-qMS). This approach allowed the definition of a volatile metabolite profile to each banana variety and can be used as pertinent criteria of differentiation. The investigated banana varieties (Dwarf Cavendish, Prata, Maçã, Ouro and Platano) have certified botanical origin and belong to the Musaceae family, the most common genomic group cultivated in Madeira Island (Portugal). The influence of dHS-SPME experimental factors, namely, fibre coating, extraction time and extraction temperature, on the equilibrium headspace analysis was investigated and optimised using univariate optimisation design. A total of 68 volatile organic metabolites (VOMs) were tentatively identified and used to profile the volatile composition in different banana cultivars, thus emphasising the sensitivity and applicability of SPME for establishment of the volatile metabolomic pattern of plant secondary metabolites. Ethyl esters were found to comprise the largest chemical class accounting 80.9%, 86.5%, 51.2%, 90.1% and 6.1% of total peak area for Dwarf Cavendish, Prata, Ouro, Maçã and Platano volatile fraction, respectively. Gas chromatographic peak areas were submitted to multivariate statistical analysis (principal component and stepwise linear discriminant analysis) in order to visualise clusters within samples and to detect the volatile metabolites able to differentiate banana cultivars. The application of the multivariate analysis on the VOMs data set resulted in predictive abilities of 90% as evaluated by the cross-validation procedure. Copyright © 2012 Elsevier Ltd. All rights reserved.

  11. Profile of Serum Metabolites and Proteins of Broiler Breeders in Rearing Age

    Directory of Open Access Journals (Sweden)

    MS Rezende

    Full Text Available ABSTRACT The excellence of modern broiler production is based on the genetic improvement of broiler strains for high growth rate and high egg production, associated with technological developments in nutrition, management, and health. Over the last decades, the clinical biochemistry of broilers has been studied to determine serum biochemical component values; however, there are still many knowledge gaps on factors that determine changes in these values. In this study, the serum lipid and protein profiles of 4-week-old male and female Cobb broiler breeders were evaluated. Blood samples were collected on a commercial farm located in the city of Uberlândia, MG, Brazil. The following parameters were evaluated: total protein, albumin, globulin, albumin to globulin ratio (A/V, uric acid, urea, cholesterol, and triglyceride levels using an automatic analyzer. The results showed sex-specific biochemical patterns for most blood parameters evaluated. Moreover, the obtained values were different from those obtained in many published studies with broilers and commercial layers, stressing the need to develop further studies with chickens of different ages.

  12. Secondary Metabolite Profile, Antioxidant Capacity, and Mosquito Repellent Activity of Bixa orellana from Brazilian Amazon Region

    Directory of Open Access Journals (Sweden)

    Annamaria Giorgi

    2013-01-01

    Full Text Available The Brazilian flora was widely used as source of food and natural remedies to treat various diseases. Bixa orellana L. (Bixaceae, also known as annatto, urucù, or achiote, is a symbol for the Amazonian tribes that traditionally use its seeds as coloured ink to paint their bodies for religious ceremonies. The aim of this study was to investigate the volatile organic compounds (VOCs profile of B. orellana fresh fruits (in vivo sampled, dried seeds, wood, bark, and leaves analyzed with Headspace solid-phase microextraction coupled with gas chromatography and mass spectrometry. A screening on phenolic content (the Folin-Ciocalteu assay and antiradical activity (DPPH assay of seeds was also conducted. In addition, the repellent properties of seed extracts against Aedes aegypti L. were investigated. Volatile compounds detected in B. orellana samples consisted mainly of sesquiterpenes, monoterpenes, and arenes: α-humulene is the major volatile compound present in seed extracts followed by D-germacrene, γ-elemene, and caryophyllene. B. orellana proved to be a good source of antioxidants. Preliminary data on repellency against A. aegypti of three different dried seed extracts (hexane, ethanol, and ethanol/water indicated a significant skin protection activity. A protection of 90% and 73% for hexane and ethanol/water extracts was recorded.

  13. Biomarker discovery in biological specimens (plasma, hair, liver and kidney) of diabetic mice based upon metabolite profiling using ultra-performance liquid chromatography with electrospray ionization time-of-flight mass spectrometry.

    Science.gov (United States)

    Tsutsui, Haruhito; Maeda, Toshio; Min, Jun Zhe; Inagaki, Shinsuke; Higashi, Tatsuya; Kagawa, Yoshiyuki; Toyo'oka, Toshimasa

    2011-05-12

    The number of diabetic patients has recently been increasing worldwide. Diabetes is a multifactorial disorder based on environmental factors and genetic background. In many cases, diabetes is asymptomatic for a long period and the patient is not aware of the disease. Therefore, the potential biomarker(s), leading to the early detection and/or prevention of diabetes mellitus, are strongly required. However, the diagnosis of the prediabetic state in humans is a very difficult issue, because the lifestyle is variable in each person. Although the development of a diagnosis method in humans is the goal of our research, the extraction and structural identification of biomarker candidates in several biological specimens (i.e., plasma, hair, liver and kidney) of ddY strain mice, which undergo naturally occurring diabetes along with aging, were carried out based upon a metabolite profiling study. The low-molecular-mass compounds including metabolites in the biological specimens of diabetic mice (ddY-H) and normal mice (ddY-L) were globally separated by ultra-performance liquid chromatography (UPLC) using different reversed-phase columns (i.e., T3-C18 and HS-F5) and detected by electrospray ionization time-of-flight mass spectrometry (ESI-TOF-MS). The biomarker candidates related to diabetes mellitus were extracted from a multivariate statistical analysis, such as an orthogonal partial least-squares-discriminant analysis (OPLS-DA), followed by a database search, such as ChemSpider, KEGG and HMDB. Many metabolites and unknown compounds in each biological specimen were detected as the biomarker candidates related to diabetic mellitus. Among them, the elucidation of the chemical structures of several possible metabolites, including more than two biological specimens, was carried out along with the comparison of the tandem MS/MS analyses using authentic compounds. One metabolite was clearly identified as N-acetyl-L-leucine based upon the MS/MS spectra and the retention time on

  14. A new method to identify the foot of continental slope based on an integrated profile analysis

    Science.gov (United States)

    Wu, Ziyin; Li, Jiabiao; Li, Shoujun; Shang, Jihong; Jin, Xiaobin

    2017-06-01

    A new method is proposed to identify automatically the foot of the continental slope (FOS) based on the integrated analysis of topographic profiles. Based on the extremum points of the second derivative and the Douglas-Peucker algorithm, it simplifies the topographic profiles, then calculates the second derivative of the original profiles and the D-P profiles. Seven steps are proposed to simplify the original profiles. Meanwhile, multiple identification methods are proposed to determine the FOS points, including gradient, water depth and second derivative values of data points, as well as the concave and convex, continuity and segmentation of the topographic profiles. This method can comprehensively and intelligently analyze the topographic profiles and their derived slopes, second derivatives and D-P profiles, based on which, it is capable to analyze the essential properties of every single data point in the profile. Furthermore, it is proposed to remove the concave points of the curve and in addition, to implement six FOS judgment criteria.

  15. Metabolite profiling of Camellia sinensis by automated sequential, multidimensional gas chromatography/mass spectrometry reveals strong monsoon effects on tea constituents.

    Science.gov (United States)

    Kowalsick, Amanda; Kfoury, Nicole; Robbat, Albert; Ahmed, Selena; Orians, Colin; Griffin, Timothy; Cash, Sean B; Stepp, John Richard

    2014-11-28

    Seasonal variation in tea (Camellia sinensis (L.) Kuntze; Theaceae) chemistry was investigated using automated sequential, multidimensional gas chromatography/mass spectrometry (GC-GC/MS). Metabolite libraries were produced for teas harvested from the Bulang Mountains in Yunnan, China before and after the onset of the East Asian Monsoon. A total of 201 spring and 196 monsoon metabolites were identified, with 169 common and 59 seasonally unique compounds. An additional 163 metabolites were detected but their identity could not be confirmed. Spectral deconvolution of GC/MS data was used to measure the relative concentrations in the teas. Within each family individual metabolite concentrations increased, decreased and stayed the same. The major constituents in both teas were linalool (28%), geraniol (13%), α-terpineol (10%), hotrienol (4%) and nerol (3%). This work provides the foundation to monitor seasonal variations of tea chemistry. Copyright © 2014 Elsevier B.V. All rights reserved.

  16. Feed consumption, nutrient utilization and serum metabolite profile of captive blackbucks (Antelope cervicapra) fed diets varying in crude protein content.

    Science.gov (United States)

    Das, A; Katole, S; Kumar, A; Gupta, S P; Saini, M; Swarup, D

    2012-06-01

    A feeding trial was conducted to determine the optimum level of crude protein (CP) in the diet of captive blackbuck (Antelope cervicapra) in which feed consumption and nutrient utilization are maximal. Fifteen blackbucks (BW 25-34 kg) were distributed into three groups of five each in an experiment of 75-days duration including a digestion trial of 5-day collection period. All the animals were offered 200 g of concentrates and fresh maize fodder ad libitum. The overall CP content of the three respective diets was 6.9%, 10.4% and 12.7%. Blood samples were collected on the last day of the experiment. Intake and digestibility of CP increased (p consumption and nutrient intake were not significantly different among the groups. However, digestibilities of most of the nutrients were higher in the 10.4% CP diet than in the 6.9% CP diet. The endogenous loss of nitrogen was similar among the groups. Based on the endogenous losses, minimum N requirement was calculated to be 776 mg/kg BW(0.75) /day, and to meet this requirement, diet must contain at least 8.27% CP. Serum urea nitrogen concentration increased (p consumption and serum metabolite profile of blackbucks. © 2011 Blackwell Verlag GmbH.

  17. GC-MS based metabolite profiling implies three interdependent ways of ammonium assimilation in Medicago truncatula root nodules.

    Science.gov (United States)

    Barsch, Aiko; Carvalho, Helena G; Cullimore, Julie V; Niehaus, Karsten

    2006-12-15

    In symbiotic interaction with legume plants, bacteria termed Rhizobia can fix massive amounts of atmospheric nitrogen which is primarily provided in the form of ammonium to the host plants. Therefore, legume root nodules that house the symbiotic bacteria are ideally suited to study the process of primary ammonium assimilation. Here, we present a GC-MS based metabolite profiling analysis of Medicago truncatula root nodules (induced by the bacterium Sinorhizobium meliloti) before and after inhibition of glutamine synthetase (GS) by the chemical herbicide phosphinotricine. The primary role of GS in ammonium assimilation was revealed by drastically reduced levels of glutamine in phosphinotricine treated root nodules. In comparison to previous results of increased asparagine synthetase transcript and protein abundances in GS inhibited nodules the metabolic data revealed that decreased amounts of aspartate might preclude taking advantage of this elevated enzymatic activity. A potential role of glutamate dehydrogenase in ammonium assimilation was metabolically indicated 24 and 48 h after GS inhibition. Therefore, nodule ammonium assimilation might in principle involve three interdependent metabolic pathways which are adjusted to control basic nitrogen metabolism.

  18. Metabolite profiling and isolation of biologically active compounds from Scadoxus puniceus, a highly traded South African medicinal plant.

    Science.gov (United States)

    Naidoo, Devashan; Slavětínská, Lenka Poštová; Aremu, Adeyemi O; Gruz, Jiri; Biba, Ondrej; Doležal, Karel; Van Staden, Johannes; Finnie, Jeffrey F

    2017-12-11

    Scadoxus puniceus (Amaryllidaceae), a medicinal plant of high value in South Africa, is used as a component of a traditional herbal tonic prescribed to treat several ailments. Ultra-high performance liquid chromatography-tandem mass spectrometry quantified the phenolic compounds in different organs of S. puniceus. Gravity column chromatography was used to separate fractions and active compounds. The structure of these compounds was determined using 1D and 2D nuclear magnetic resonance and mass spectroscopic techniques. A microplate technique was used to determine the acetylcholinesterase inhibitory activity of the pure compounds. Metabolite profiling revealed a greater profusion of hydroxycinnamic acids (69.5%), as opposed to hydroxybenzoic acids (30.5%). Chlorogenic acid was the most abundant (49.6% of hydroxycinnamic acids) compound. In addition to chlorogenic acid, the study is the first to report the presence of sinapic, gallic, and m-hydroxybenzoic acids in the Amaryllidaceae. Chromatographic separation of S. puniceus led to the isolation of haemanthamine (1), haemanthidine (2), and a rare chlorinated amide, metolachlor (3), the natural occurrence of which is described for the first time. Haemanthamine, haemanthidine, and metolachlor displayed strong acetylcholinesterase inhibitory activity (IC 50 ; 23.1, 23.7, and 11.5 μM, respectively). These results substantiate the frequent use of S. puniceus as a medicinal plant and hold much promise for further pharmaceutical development. Copyright © 2017 John Wiley & Sons, Ltd.

  19. Metabolite and transcript profiling of berry skin during fruit development elucidates differential regulation between Cabernet Sauvignon and Shiraz cultivars at branching points in the polyphenol pathway.

    Science.gov (United States)

    Degu, Asfaw; Hochberg, Uri; Sikron, Noga; Venturini, Luca; Buson, Genny; Ghan, Ryan; Plaschkes, Inbar; Batushansky, Albert; Chalifa-Caspi, Vered; Mattivi, Fulvio; Delledonne, Massimo; Pezzotti, Mario; Rachmilevitch, Shimon; Cramer, Grant R; Fait, Aaron

    2014-07-26

    Grapevine berries undergo complex biochemical changes during fruit maturation, many of which are dependent upon the variety and its environment. In order to elucidate the varietal dependent developmental regulation of primary and specialized metabolism, berry skins of Cabernet Sauvignon and Shiraz were subjected to gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS) based metabolite profiling from pre-veraison to harvest. The generated dataset was augmented with transcript profiling using RNAseq. The analysis of the metabolite data revealed similar developmental patterns of change in primary metabolites between the two cultivars. Nevertheless, towards maturity the extent of change in the major organic acid and sugars (i.e. sucrose, trehalose, malate) and precursors of aromatic and phenolic compounds such as quinate and shikimate was greater in Shiraz compared to Cabernet Sauvignon. In contrast, distinct directional projections on the PCA plot of the two cultivars samples towards maturation when using the specialized metabolite profiles were apparent, suggesting a cultivar-dependent regulation of the specialized metabolism. Generally, Shiraz displayed greater upregulation of the entire polyphenol pathway and specifically higher accumulation of piceid and coumaroyl anthocyanin forms than Cabernet Sauvignon from veraison onwards. Transcript profiling revealed coordinated increased transcript abundance for genes encoding enzymes of committing steps in the phenylpropanoid pathway. The anthocyanin metabolite profile showed F3'5'H-mediated delphinidin-type anthocyanin enrichment in both varieties towards maturation, consistent with the transcript data, indicating that the F3'5'H-governed branching step dominates the anthocyanin profile at late berry development. Correlation analysis confirmed the tightly coordinated metabolic changes during development, and suggested a source-sink relation between the central and specialized

  20. In silico profiling for secondary metabolites from Lepidium meyenii (maca) by the pharmacophore and ligand-shape-based joint approach.

    Science.gov (United States)

    Yi, Fan; Tan, Xiao-Lei; Yan, Xin; Liu, Hai-Bo

    2016-01-01

    Lepidium meyenii Walpers (maca) is an herb known as a traditional nutritional supplement and widely used in Peru, North America, and Europe to enhance human fertility and treat osteoporosis. The secondary metabolites of maca, namely, maca alkaloids, macaenes, and macamides, are bioactive compounds, but their targets are undefined. The pharmacophore-based PharmaDB targets database screening joint the ligand shape similarity-based WEGA validation approach is proposed to predict the targets of these unique constituents and was performed using Discovery Studio 4.5 and PharmaDB. A compounds-targets-diseases network was established using Cytoscape 3.2. These suitable targets and their genes were calculated and analyzed using ingenuity pathway analysis and GeneMANIA. Certain targets were identified in osteoporosis (8 targets), prostate cancer (9 targets), and kidney diseases (11 targets). This was the first study to identify the targets of these bioactive compounds in maca for cardiovascular diseases (29 targets). The compound with the most targets (46) was an amide alkaloid (MA-24). In silico target fishing identified maca's traditional effects on treatment and prevention of osteoporosis, prostate cancer, and kidney diseases, and its potential function of treating cardiovascular diseases, as the most important of this herb's possible activities.

  1. Barriers Prevent Patient Access to Personalized Therapies Identified by Molecular Tumor Profiling of Gynecologic Malignancies

    Directory of Open Access Journals (Sweden)

    R. Tyler Hillman

    2015-05-01

    Full Text Available Objective. This study was designed to evaluate the ability of commercial molecular tumor profiling to discover actionable mutations and to identify barriers that might prevent patient access to personalized therapies. Methods. We conducted an IRB-approved retrospective review of 26 patients with gynecologic malignancies who underwent commercial tumor profiling at our institution during the first 18 months of test availability. Tumor profiles reported targeted therapies and clinical trials matched to patient-specific mutations. Data analysis consisted of descriptive statistics. Results. Most patients who underwent tumor profiling had serous epithelial ovarian, primary peritoneal, or fallopian tube carcinoma (46%. Patients underwent profiling after undergoing a median of two systemic therapies (range 0 to 13. A median of one targeted therapy was suggested per patient profile. Tumor profiling identified no clinically actionable mutations for seven patients (27%. Six patients sought insurance approval for a targeted therapy and two were declined (33%. One patient (4% received a targeted therapy and this was discontinued due to tumor progression. Conclusions. There are formidable barriers to targeted therapy for patients with gynecologic malignancies. These barriers include a dearth of FDA-approved targeted agents for gynecologic malignancies, lack of third party insurance coverage and limited geographic availability of clinical trials.

  2. Extending our tools and resources in the non-conventional industrial yeastXanthophyllomyces dendrorhousthrough the application of metabolite profiling methodologies.

    Science.gov (United States)

    Alcalde, Eugenio; Fraser, Paul D

    2018-01-01

    Xanthophyllomyces dendrorhous is a non-conventional industrial yeast. It has the unique ability among yeasts to produce geranylgeranyl pyrophosphate derived terpenoids such as carotenoids and in particular the high value pigment astaxanthin. In order to fully exploit the industrial potential of Xanthophyllomyces using modern industrial biotechnology approaches the further development of "omic" resources in this organism are required to build on the now sequenced and annotated genome. To contribute to this goal, the present study has developed and implemented an efficient metabolite profiling system comprised of, quenching, extraction and associated GC-MS and UPLC analysis. Four quenching methods and five extraction methods compatible with GC-MS and UPLC profiling were tested and validated by analysing steady state metabolite changes of Xanthophyllomyces cultivated at laboratory scale in liquid shake culture at lag, exponential and early and late stationary phases. A customised Automated Mass Spectral Deconvolution and Identification System (AMDIS) library has been created for Xanthophyllomyces , over 400 compounds are present in the library of which 78 are detected and quantified routinely in polar and non-polar derived extracts. A preliminary biochemical network has been constructed. Over a standardised laboratory growth cycle, changes in metabolite levels have been determined to create reference point for future strain improvement approaches and the initial biochemical network construction. Correlation analysis has illustrated that astaxanthin formation correlates positively with different sectors of intermediary metabolism (e.g. the TCA cycle intermediates and amino acid formation), "short" saturated fatty acids and β-carotene, while other metabolites are reduced in response to astaxanthin production. These sectors of intermediary metabolism offer potential future targets for the manipulation resulting in the generation of strains with improved titres of given

  3. Profile of plasma and urine metabolites after the intake of almond [Prunus dulcis (Mill.) D.A. Webb] polyphenols in humans.

    Science.gov (United States)

    Urpi-Sarda, Mireia; Garrido, Ignacio; Monagas, María; Gómez-Cordovés, Carmen; Medina-Remón, Alexander; Andres-Lacueva, Cristina; Bartolomé, Begoña

    2009-11-11

    Nut skins are considered to be a rich source of polyphenols and may be partially responsible for the numerous health effects associated with nut consumption. However, more bioavailability studies of nut skin polyphenols are needed to understand the health effects derived from nut consumption. The aim of the present study was to determine the profiles of both phase II and microbial-derived phenolic metabolites in plasma and urine samples before and after the intake of almond skin polyphenols by healthy human subjects (n = 2). Glucuronide, O-methyl glucuronide, sulfate, and O-methyl sulfate derivatives of (epi)catechin, as well as the glucuronide conjugates of naringenin and glucuronide and sulfate conjugates of isorhamnetin, were detected in plasma and urine samples after consumption of almond skin polyphenols. The main microbial-derived metabolites of flavanols, such as 5-(dihydroxyphenyl)-gamma-valerolactone and 5-(hydroxymethoxyphenyl)-gamma-valerolactone, were also detected in their glucuronide and sulfate forms. In addition, numerous metabolites derived from further microbial degradation of hydroxyphenylvalerolactones, including hydroxyphenylpropionic, hydroxyphenylacetic, hydroxycinnamic, hydroxybenzoic, and hydroxyhippuric acids, registered major changes in urine after the consumption of almond skin polyphenols. The urinary excretion of these microbial metabolites was estimated to account for a larger proportion of the total polyphenol ingested than phase II metabolites of (epi)catechin, indicating the important role of intestinal bacteria in the metabolism of highly polymerized almond skin polyphenols. To the authors' knowledge this study constitutes the most complete report of the absorption of almond skin polyphenols in humans.

  4. Anionic metabolite profiling by capillary electrophoresis-mass spectrometry using a noncovalent polymeric coating. Orange juice and wine as case studies.

    Science.gov (United States)

    Acunha, Tanize; Simó, Carolina; Ibáñez, Clara; Gallardo, Alberto; Cifuentes, Alejandro

    2016-01-08

    In several metabolomic studies, it has already been demonstrated that capillary electrophoresis hyphenated to mass spectrometry (CE-MS) can detect an important group of highly polar and ionized metabolites that are overseen by techniques such as NMR, LC-MS and GC-MS, providing complementary information. In this work, we present a strategy for anionic metabolite profiling by CE-MS using a cationic capillary coating. The polymer, abbreviated as PTH, is composed of a poly-(N,N,N',N'-tetraethyldiethylenetriamine, N-(2-hydroxypropyl) methacrylamide, TEDETAMA-co-HPMA (50:50) copolymer. A CE-MS method based on PTH-coating was optimized for the analysis of a group of 16 standard anionic metabolites. Separation was achieved within 12min, with high separation efficiency (up to 92,000 theoretical plates per meter), and good repeatability, namely, relative standard deviation values for migration times and peak areas were below 0.2 and 2.1%, respectively. The optimized method allowed the detection of 87 metabolites in orange juice and 142 metabolites in red wine, demonstrating the good possibilities of this strategy for metabolomic applications. Copyright © 2015 Elsevier B.V. All rights reserved.

  5. Dissection of Trichoderma longibrachiatum-induced defense in onion (Allium cepa L.) against Fusarium oxysporum f. sp. cepa by target metabolite profiling.

    Science.gov (United States)

    Abdelrahman, Mostafa; Abdel-Motaal, Fatma; El-Sayed, Magdi; Jogaiah, Sudisha; Shigyo, Masayoshi; Ito, Shin-ichi; Tran, Lam-Son Phan

    2016-05-01

    Trichoderma spp. are versatile opportunistic plant symbionts that can cause substantial changes in the metabolism of host plants, thereby increasing plant growth and activating plant defense to various diseases. Target metabolite profiling approach was selected to demonstrate that Trichoderma longibrachiatum isolated from desert soil can confer beneficial agronomic traits to onion and induce defense mechanism against Fusarium oxysporum f. sp. cepa (FOC), through triggering a number of primary and secondary metabolite pathways. Onion seeds primed with Trichoderma T1 strain displayed early seedling emergence and enhanced growth compared with Trichoderma T2-treatment and untreated control. Therefore, T1 was selected for further investigations under greenhouse conditions, which revealed remarkable improvement in the onion bulb growth parameters and resistance against FOC. The metabolite platform of T1-primed onion (T1) and T1-primed onion challenged with FOC (T1+FOC) displayed significant accumulation of 25 abiotic and biotic stress-responsive metabolites, representing carbohydrate, phenylpropanoid and sulfur assimilation metabolic pathways. In addition, T1- and T1+FOC-treated onion plants showed discrete antioxidant capacity against 1,1-diphenyl-2-picrylhydrazyl (DPPH) compared with control. Our findings demonstrated the contribution of T. longibrachiatum to the accumulation of key metabolites, which subsequently leads to the improvement of onion growth, as well as its resistance to oxidative stress and FOC. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  6. Urinary Metabolite Profiling Offers Potential for Differentiation of Liver-Kidney Yin Deficiency and Dampness-Heat Internal Smoldering Syndromes in Posthepatitis B Cirrhosis Patients

    Directory of Open Access Journals (Sweden)

    Xiaoning Wang

    2015-01-01

    Full Text Available Zheng is the basic theory and essence of traditional Chinese medicine (TCM in diagnosing diseases. However, there are no biological evidences to support TCM Zheng differentiation. In this study we elucidated the biological alteration of cirrhosis with TCM “Liver-Kidney Yin Deficiency (YX” or “Dampness-Heat Internal Smoldering (SR” Zheng and the potential of urine metabonomics in TCM Zheng differentiation. Differential metabolites contributing to the intergroup variation between healthy controls and liver cirrhosis patients were investigated, respectively, and mainly participated in energy metabolism, gut microbiota metabolism, oxidative stress, and bile acid metabolism. Three metabolites, aconitate, citrate, and 2-pentendioate, altered significantly in YX Zheng only, representing the abnormal energy metabolism. Contrarily, hippurate and 4-pyridinecarboxylate altered significantly in SR Zheng only, representing the abnormalities of gut microbiota metabolism. Moreover, there were significant differences between two TCM Zhengs in three metabolites, glycoursodeoxycholate, cortolone-3-glucuronide, and L-aspartyl-4-phosphate, among all differential metabolites. Metabonomic profiling, as a powerful approach, provides support to the understanding of biological mechanisms of TCM Zheng stratification. The altered urinary metabolites constitute a panel of reliable biological evidence for TCM Zheng differentiation in patients with posthepatitis B cirrhosis and may be used for the potential biomarkers of TCM Zheng stratification.

  7. Accumulation profiles of parabens and their metabolites in fish, black bear, and birds, including bald eagles and albatrosses.

    Science.gov (United States)

    Xue, Jingchuan; Kannan, Kurunthachalam

    2016-09-01

    Although several studies have reported the ubiquitous occurrence of parabens in human specimens and the environment, little is known about the accumulation of these estrogenic chemicals in fish and birds. In this study, accumulation profiles of six parabens and their metabolites were determined in 254 tissue (including liver, kidney, egg, and plasma) samples from 12 species of fish and seven species of birds collected from inland, coastal, and remote aquatic ecosystems. In addition, liver and kidney tissues from black bears were analyzed. Methyl paraben (MeP) was found in a majority of the tissues, with the highest concentration (796ng/g (wet weight [wet wt])) found in the liver of a bald eagle from Michigan. 4-Hydroxy benzoate (HB) was the major metabolite, found in 91% of the tissue samples analyzed at concentrations as high as 68,600ng/g, wet wt, which was found in the liver of a white-tailed sea eagle from the Baltic Sea coast. The accumulation pattern of MeP and 4-HB varied, depending on the species. The mean concentrations of MeP measured in fishes from Michigan, New York, and Florida waters were <2.01 (fillet), 152 (liver), and 32.0 (liver) ng/g, wet wt, respectively, and the corresponding 4-HB concentrations were 39.5, 10,500, and 642ng/g, wet wt. The mean hepatic and renal concentrations of 4-HB in black bears were 1,720 and 1,330ng/g, wet wt, respectively. The concentrations of MeP and 4-HB were significantly positively correlated with each other in various tissues and species, which suggested a common source of exposure to these compounds in fish and birds. Trace concentrations of MeP and 4-HB also were found in the tissues of albatrosses from Midway Atoll, Northwestern Pacific Ocean, which suggested widespread distribution of these compounds in the marine environment. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. Influence of different proteolytic strains of Streptococcus thermophilus in co-culture with Lactobacillus delbrueckii subsp. bulgaricus on the metabolite profile of set-yoghurt.

    Science.gov (United States)

    Settachaimongkon, Sarn; Nout, M J Robert; Antunes Fernandes, Elsa C; Hettinga, Kasper A; Vervoort, Jacques M; van Hooijdonk, Toon C M; Zwietering, Marcel H; Smid, Eddy J; van Valenberg, Hein J F

    2014-05-02

    Proto-cooperation between Streptococcus thermophilus and Lactobacillus delbrueckii subsp. bulgaricus is one of the key factors that determine the fermentation process and final quality of yoghurt. In this study, the interaction between different proteolytic strains of S. thermophilus and L. delbrueckii subsp. bulgaricus was investigated in terms of microbial growth, acidification and changes in the biochemical composition of milk during set-yoghurt fermentation. A complementary metabolomics approach was applied for global characterization of volatile and non-volatile polar metabolite profiles of yoghurt associated with proteolytic activity of the individual strains in the starter cultures. The results demonstrated that only non-proteolytic S. thermophilus (Prt-) strain performed proto-cooperation with L. delbrueckii subsp. bulgaricus. The proto-cooperation resulted in significant higher populations of the two species, faster milk acidification, significant abundance of aroma volatiles and non-volatile metabolites desirable for a good organoleptic quality of yoghurt. Headspace SPME-GC/MS and (1)H NMR resulted in the identification of 35 volatiles and 43 non-volatile polar metabolites, respectively. Furthermore, multivariate statistical analysis allows discriminating set-yoghurts fermented by different types of starter cultures according to their metabolite profiles. Our finding underlines that selection of suitable strain combinations in yoghurt starters is important for achieving the best technological performance regarding the quality of product. Copyright © 2014 Elsevier B.V. All rights reserved.

  9. Comparing identified and statistically significant lipids and polar metabolites in 15-year old serum and dried blood spot samples for longitudinal studies: Comparing lipids and metabolites in serum and DBS samples

    Energy Technology Data Exchange (ETDEWEB)

    Kyle, Jennifer E. [Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland WA USA; Casey, Cameron P. [Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland WA USA; Stratton, Kelly G. [National Security Directorate, Pacific Northwest National Laboratory, Richland WA USA; Zink, Erika M. [Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland WA USA; Kim, Young-Mo [Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland WA USA; Zheng, Xueyun [Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland WA USA; Monroe, Matthew E. [Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland WA USA; Weitz, Karl K. [Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland WA USA; Bloodsworth, Kent J. [Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland WA USA; Orton, Daniel J. [Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland WA USA; Ibrahim, Yehia M. [Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland WA USA; Moore, Ronald J. [Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland WA USA; Lee, Christine G. [Department of Medicine, Bone and Mineral Unit, Oregon Health and Science University, Portland OR USA; Research Service, Portland Veterans Affairs Medical Center, Portland OR USA; Pedersen, Catherine [Department of Medicine, Bone and Mineral Unit, Oregon Health and Science University, Portland OR USA; Orwoll, Eric [Department of Medicine, Bone and Mineral Unit, Oregon Health and Science University, Portland OR USA; Smith, Richard D. [Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland WA USA; Burnum-Johnson, Kristin E. [Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland WA USA; Baker, Erin S. [Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland WA USA

    2017-02-05

    The use of dried blood spots (DBS) has many advantages over traditional plasma and serum samples such as smaller blood volume required, storage at room temperature, and ability for sampling in remote locations. However, understanding the robustness of different analytes in DBS samples is essential, especially in older samples collected for longitudinal studies. Here we analyzed DBS samples collected in 2000-2001 and stored at room temperature and compared them to matched serum samples stored at -80°C to determine if they could be effectively used as specific time points in a longitudinal study following metabolic disease. Four hundred small molecules were identified in both the serum and DBS samples using gas chromatograph-mass spectrometry (GC-MS), liquid chromatography-MS (LC-MS) and LC-ion mobility spectrometry-MS (LC-IMS-MS). The identified polar metabolites overlapped well between the sample types, though only one statistically significant polar metabolite in a case-control study was conserved, indicating degradation occurs in the DBS samples affecting quantitation. Differences in the lipid identifications indicated that some oxidation occurs in the DBS samples. However, thirty-six statistically significant lipids correlated in both sample types indicating that lipid quantitation was more stable across the sample types.

  10. A method to identify differential expression profiles of time-course gene data with Fourier transformation.

    Science.gov (United States)

    Kim, Jaehee; Ogden, Robert Todd; Kim, Haseong

    2013-10-18

    Time course gene expression experiments are an increasingly popular method for exploring biological processes. Temporal gene expression profiles provide an important characterization of gene function, as biological systems are both developmental and dynamic. With such data it is possible to study gene expression changes over time and thereby to detect differential genes. Much of the early work on analyzing time series expression data relied on methods developed originally for static data and thus there is a need for improved methodology. Since time series expression is a temporal process, its unique features such as autocorrelation between successive points should be incorporated into the analysis. This work aims to identify genes that show different gene expression profiles across time. We propose a statistical procedure to discover gene groups with similar profiles using a nonparametric representation that accounts for the autocorrelation in the data. In particular, we first represent each profile in terms of a Fourier basis, and then we screen out genes that are not differentially expressed based on the Fourier coefficients. Finally, we cluster the remaining gene profiles using a model-based approach in the Fourier domain. We evaluate the screening results in terms of sensitivity, specificity, FDR and FNR, compare with the Gaussian process regression screening in a simulation study and illustrate the results by application to yeast cell-cycle microarray expression data with alpha-factor synchronization.The key elements of the proposed methodology: (i) representation of gene profiles in the Fourier domain; (ii) automatic screening of genes based on the Fourier coefficients and taking into account autocorrelation in the data, while controlling the false discovery rate (FDR); (iii) model-based clustering of the remaining gene profiles. Using this method, we identified a set of cell-cycle-regulated time-course yeast genes. The proposed method is general and can be

  11. A metabolite-profiling approach to assess the uptake and metabolism of phenolic compounds from olive leaves in SKBR3 cells by HPLC-ESI-QTOF-MS.

    Science.gov (United States)

    Quirantes-Piné, R; Zurek, G; Barrajón-Catalán, E; Bäßmann, C; Micol, V; Segura-Carretero, A; Fernández-Gutiérrez, A

    2013-01-01

    Olive leaves, an easily available natural low-cost material, constitute a source of extracts with significant antitumor activity that inhibits cell proliferation in several breast-cancer-cell models. In this work, a metabolite-profiling approach has been used to assess the uptake and metabolism of phenolic compounds from an olive-leaf extract in the breast-cancer-cell line SKBR3 to evaluate the compound or compounds responsible for the cytotoxic activity. For this, the extract was firstly characterized quantitatively by high-performance liquid chromatography coupled to electrospray ionization-quadrupole time-of-flight mass spectrometry (HPLC-ESI-QTOF-MS). Then, SKBR3 cells were incubated with 200 μg/mL of the olive-leaf extract at different times (15 min, 1, 2, 24, and 48 h). A metabolite-profiling approach based on HPLC-ESI-QTOF-MS was used to determine the intracellular phenolic compounds, enabling the identification of 16 intact phenolic compounds from the extract and four metabolites derived from these compounds in the cell cytoplasm. The major compounds found within the cells were oleuropein, luteolin-7-O-glucoside and its metabolites luteolin aglycone and methyl-luteolin glucoside, as well as apigenin, and verbascoside. Neither hydroxytyrosol nor any of its metabolites were found within the cells at any incubation time. It is proposed that the major compounds responsible for the cytotoxic activity of the olive-leaf extract in SKBR3 cells are oleuropein and the flavones luteolin and apigenin, since these compounds showed high uptake and their antitumor activity has been previously reported. Copyright © 2012 Elsevier B.V. All rights reserved.

  12. Ultra performance liquid chromatography-mass spectrometry profiling of bile acid metabolites in biofluids: application to experimental toxicology studies.

    Science.gov (United States)

    Want, Elizabeth J; Coen, Muireann; Masson, Perrine; Keun, Hector C; Pearce, Jake T M; Reily, Michael D; Robertson, Donald G; Rohde, Cynthia M; Holmes, Elaine; Lindon, John C; Plumb, Robert S; Nicholson, Jeremy K

    2010-06-15

    We have developed an ultra performance liquid chromatography-mass spectrometry (UPLC-MS(E)) method to measure bile acids (BAs) reproducibly and reliably in biological fluids and have applied this approach for indications of hepatic damage in experimental toxicity studies. BAs were extracted from serum using methanol, and an Acquity HSS column coupled to a Q-ToF mass spectrometer was used to separate and identify 25 individual BAs within 5 min. Employing a gradient elution of water and acetonitrile over 21 min enabled the detection of a wide range of endogenous metabolites, including the BAs. The utilization of MS(E) allowed for characteristic fragmentation information to be obtained in a single analytical run, easily distinguishing glycine and taurine BA conjugates. The proportions of these conjugates were altered markedly in an experimental toxic state induced by galactosamine exposure in rats. Principally, taurine-conjugated BAs were greatly elevated ( approximately 50-fold from control levels), and were highly correlated to liver damage severity as assessed by histopathological scoring (r = 0.83), indicating their potential as a sensitive measure of hepatic damage. The UPLC-MS approach to BA analysis offers a sensitive and reproducible tool that will be of great value in exploring both markers and mechanisms of hepatotoxicity and can readily be extended to clinical studies of liver damage.

  13. Metabolite profiling with HPLC-ICP-MS as a tool for in vivo characterization of imaging probes.

    Science.gov (United States)

    Boros, Eszter; Pinkhasov, Omar R; Caravan, Peter

    2018-01-01

    Current analytical methods for characterizing pharmacokinetic and metabolic properties of positron emission tomography (PET) and single photon emission computed tomography (SPECT) probes are limited. Alternative methods to study tracer metabolism are needed. The study objective was to assess the potential of high performance liquid chromatography - inductively coupled plasma - mass spectrometry (HPLC-ICP-MS) for quantification of molecular probe metabolism and pharmacokinetics using stable isotopes. Two known peptide-DOTA conjugates were chelated with nat Ga and nat In. Limit of detection of HPLC-ICP-MS for 69 Ga and 115 In was determined. Rats were administered 50-150 nmol of Ga- and/or In-labeled probes, blood was serially sampled, and plasma analyzed by HPLC-ICP-MS using both reverse phase and size exclusion chromatography. The limits of detection were 0.16 pmol for 115 In and 0.53 pmol for 69 Ga. Metabolites as low as 0.001 %ID/g could be detected and transchelation products identified. Simultaneous administration of Ga- and In-labeled probes allowed the determination of pharmacokinetics and metabolism of both probes in a single animal. HPLC-ICP-MS is a robust, sensitive and radiation-free technique to characterize the pharmacokinetics and metabolism of imaging probes.

  14. Induced sclerotium formation exposes new bioactive metabolites from Aspergillus sclerotiicarbonarius

    DEFF Research Database (Denmark)

    Petersen, Lene Maj; Frisvad, Jens Christian; Knudsen, Peter Boldsen

    2015-01-01

    Sclerotia are known to be fungal survival structures, and induction of sclerotia may prompt production of otherwise undiscovered metabolites. Aspergillus sclerotiicarbonarius (IBT 28362) was investigated under sclerotium producing conditions, which revealed a highly altered metabolic profile. Four...... carbonarins; carbonarins I and J. We have identified the three latter as true sclerotial metabolites. All metabolites were tested for antifungal and antiinsectan activity, and sclerolizine and carbonarin I displayed antifungal activity against Candida albicans, while all four showed antiinsectan activity....... These results demonstrate induction of sclerotia as an alternative way of triggering otherwise silent biosynthetic pathways in filamentous fungi for the discovery of novel bioactive secondary metabolites....

  15. New biomarkers of coffee consumption identified by the non-targeted metabolomic profiling of cohort study subjects.

    Directory of Open Access Journals (Sweden)

    Joseph A Rothwell

    Full Text Available Coffee contains various bioactives implicated with human health and disease risk. To accurately assess the effects of overall consumption upon health and disease, individual intake must be measured in large epidemiological studies. Metabolomics has emerged as a powerful approach to discover biomarkers of intake for a large range of foods. Here we report the profiling of the urinary metabolome of cohort study subjects to search for new biomarkers of coffee intake. Using repeated 24-hour dietary records and a food frequency questionnaire, 20 high coffee consumers (183-540 mL/d and 19 low consumers were selected from the French SU.VI.MAX2 cohort. Morning spot urine samples from each subject were profiled by high-resolution mass spectrometry. Partial least-square discriminant analysis of multidimensional liquid chromatography-mass spectrometry data clearly distinguished high consumers from low via 132 significant (p-value<0.05 discriminating features. Ion clusters whose intensities were most elevated in the high consumers were annotated using online and in-house databases and their identities checked using commercial standards and MS-MS fragmentation. The best discriminants, and thus potential markers of coffee consumption, were the glucuronide of the diterpenoid atractyligenin, the diketopiperazine cyclo(isoleucyl-prolyl, and the alkaloid trigonelline. Some caffeine metabolites, such as 1-methylxanthine, were also among the discriminants, however caffeine may be consumed from other sources and its metabolism is subject to inter-individual variation. Receiver operating characteristics curve analysis showed that the biomarkers identified could be used effectively in combination for increased sensitivity and specificity. Once validated in other cohorts or intervention studies, these specific single or combined biomarkers will become a valuable alternative to assessment of coffee intake by dietary survey and finally lead to a better understanding of

  16. Metabolite Profiling of 14 Wuyi Rock Tea Cultivars Using UPLC-QTOF MS and UPLC-QqQ MS Combined with Chemometrics

    Directory of Open Access Journals (Sweden)

    Si Chen

    2018-01-01

    Full Text Available Wuyi Rock tea, well-recognized for rich flavor and long-lasting fragrance, is a premium subcategory of oolong tea mainly produced in Wuyi Mountain and nearby regions of China. The quality of tea is mainly determined by the chemical constituents in the tea leaves. However, this remains underexplored for Wuyi Rock tea cultivars. In this study, we investigated the leaf metabolite profiles of 14 major Wuyi Rock tea cultivars grown in the same producing region using UPLC-QTOF MS and UPLC-QqQ MS with data processing via principal component analysis and cluster analysis. Relative quantitation of 49 major metabolites including flavan-3-ols, proanthocyanidins, flavonol glycosides, flavone glycosides, flavonone glycosides, phenolic acid derivatives, hydrolysable tannins, alkaloids and amino acids revealed clear variations between tea cultivars. In particular, catechins, kaempferol and quercetin derivatives were key metabolites responsible for cultivar discrimination. Information on the varietal differences in the levels of bioactive/functional metabolites, such as methylated catechins, flavonol glycosides and theanine, offers valuable insights to further explore the nutritional values and sensory qualities of Wuyi Rock tea. It also provides potential markers for tea plant fingerprinting and cultivar identification.

  17. Metabolite Profiling of 14 Wuyi Rock Tea Cultivars Using UPLC-QTOF MS and UPLC-QqQ MS Combined with Chemometrics.

    Science.gov (United States)

    Chen, Si; Li, Meihong; Zheng, Gongyu; Wang, Tingting; Lin, Jun; Wang, Shanshan; Wang, Xiaxia; Chao, Qianlin; Cao, Shixian; Yang, Zhenbiao; Yu, Xiaomin

    2018-01-24

    Wuyi Rock tea, well-recognized for rich flavor and long-lasting fragrance, is a premium subcategory of oolong tea mainly produced in Wuyi Mountain and nearby regions of China. The quality of tea is mainly determined by the chemical constituents in the tea leaves. However, this remains underexplored for Wuyi Rock tea cultivars. In this study, we investigated the leaf metabolite profiles of 14 major Wuyi Rock tea cultivars grown in the same producing region using UPLC-QTOF MS and UPLC-QqQ MS with data processing via principal component analysis and cluster analysis. Relative quantitation of 49 major metabolites including flavan-3-ols, proanthocyanidins, flavonol glycosides, flavone glycosides, flavonone glycosides, phenolic acid derivatives, hydrolysable tannins, alkaloids and amino acids revealed clear variations between tea cultivars. In particular, catechins, kaempferol and quercetin derivatives were key metabolites responsible for cultivar discrimination. Information on the varietal differences in the levels of bioactive/functional metabolites, such as methylated catechins, flavonol glycosides and theanine, offers valuable insights to further explore the nutritional values and sensory qualities of Wuyi Rock tea. It also provides potential markers for tea plant fingerprinting and cultivar identification.

  18. The False-Profile View May Be Used to Identify Cam Morphology.

    Science.gov (United States)

    Hellman, Michael D; Mascarenhas, Randy; Gupta, Anil; Fillingham, Yale; Haughom, Bryan D; Salata, Michael J; Nho, Shane J

    2015-09-01

    To identify the accuracy of measuring the alpha angle on the false-profile, anteroposterior (AP), and 90° Dunn lateral views of the hip as compared with computed tomography (CT) scan findings. Forty patients were needed to have power greater than 80%. Forty-five consecutive patients undergoing hip arthroscopy were retrospectively reviewed with preoperative radial oblique CT reformatted scans and plain radiographs. Alpha angles were measured on plain radiographs (AP, 90° Dunn lateral, and false profile) and CT reformatted views. Abnormal alpha angles were considered greater than 50.5°. Two orthopaedic surgeons independently measured the images, and the results were compared between imaging modalities. The false-profile view was 60% sensitive and 89.0% specific for diagnosing cam deformities of the hip. All radiographs combined were 86% sensitive and 75% specific for diagnosing cam deformities. The false-profile view most strongly correlated with the 2-o'clock (R = 0.746, P = .001) and 3-o'clock (R = 0.698, P profile view. This study has proved that the false-profile view effectively characterizes cam deformity, especially anterior deformity at the 3-o'clock position. Measuring the alpha angle on the false-profile view appears to be reproducible. The false-profile view along with standing AP pelvis and 90° Dunn lateral views of the hip comprises a good screening radiographic series for patients presenting with symptoms of femoroacetabular impingement. Level III, diagnostic study. Copyright © 2015 Arthroscopy Association of North America. Published by Elsevier Inc. All rights reserved.

  19. Comparative Characterization of the Leaf Tissue of Physalis alkekengi and Physalis peruviana Using RNA-seq and Metabolite Profiling.

    Science.gov (United States)

    Fukushima, Atsushi; Nakamura, Michimi; Suzuki, Hideyuki; Yamazaki, Mami; Knoch, Eva; Mori, Tetsuya; Umemoto, Naoyuki; Morita, Masaki; Hirai, Go; Sodeoka, Mikiko; Saito, Kazuki

    2016-01-01

    The genus Physalis in the Solanaceae family contains several species of benefit to humans. Examples include P. alkekengi (Chinese-lantern plant, hôzuki in Japanese) used for medicinal and for decorative purposes, and P. peruviana , also known as Cape gooseberry, which bears an edible, vitamin-rich fruit. Members of the Physalis genus are a valuable resource for phytochemicals needed for the development of medicines and functional foods. To fully utilize the potential of these phytochemicals we need to understand their biosynthesis, and for this we need genomic data, especially comprehensive transcriptome datasets for gene discovery. We report the de novo assembly of the transcriptome from leaves of P. alkekengi and P. peruviana using Illumina RNA-seq technologies. We identified 75,221 unigenes in P. alkekengi and 54,513 in P. peruviana . All unigenes were annotated with gene ontology (GO), Enzyme Commission (EC) numbers, and pathway information from the Kyoto Encyclopedia of Genes and Genomes (KEGG). We classified unigenes encoding enzyme candidates putatively involved in the secondary metabolism and identified more than one unigenes for each step in terpenoid backbone- and steroid biosynthesis in P. alkekengi and P. peruviana . To measure the variability of the withanolides including physalins and provide insights into their chemical diversity in Physalis , we also analyzed the metabolite content in leaves of P. alkekengi and P. peruviana at five different developmental stages by liquid chromatography-mass spectrometry. We discuss that comprehensive transcriptome approaches within a family can yield a clue for gene discovery in Physalis and provide insights into their complex chemical diversity. The transcriptome information we submit here will serve as an important public resource for further studies of the specialized metabolism of Physalis species.

  20. Comparative characterization of the leaf tissue of Physalis alkekengi and Physalis peruviana using RNA-seq and metabolite profiling

    Directory of Open Access Journals (Sweden)

    Atsushi Fukushima

    2016-12-01

    Full Text Available The genus Physalis in the Solanaceae family contains several species of benefit to humans. Examples include Physalis alkekengi (Chinese-lantern plant, hōzuki in Japanese used for medicinal and for decorative purposes, and Physalis peruviana, also known as Cape gooseberry, which bears an edible, vitamin-rich fruit. Members of the Physalis genus are a valuable resource for phytochemicals needed for the development of medicines and functional foods. To fully utilize the potential of these phytochemicals we need to understand their biosynthesis, and for this we need genomic data, especially comprehensive transcriptome datasets for gene discovery. We report the de novo assembly of the transcriptome from leaves of P. alkekengi and P. peruviana using Illumina RNA-seq technologies. We identified 75,221 unigenes in P. alkekengi and 54,513 in P. peruviana. All unigenes were annotated with gene ontology (GO, Enzyme Commission (EC numbers, and pathway information from the Kyoto Encyclopedia of Genes and Genomes (KEGG. We classified unigenes encoding enzyme candidates putatively involved in the secondary metabolism and identified more than one unigenes for each step in terpenoid backbone- and steroid biosynthesis in P. alkekengi and P. peruviana. To measure the variability of the withanolides including physalins and provide insights into their chemical diversity of Physalis, we also analyzed the metabolite content in leaves of P. alkekengi and P. peruviana at 5 different developmental stages by liquid chromatography-mass spectrometry. We discuss that comprehensive transcriptome approaches within a family can yield a clue for gene discovery in Physalis and provide insights into their complex chemical diversity. The transcriptome information we submit here will serve as an important public resource for further studies of the specialized metabolism of Physalis species.

  1. Bacillus velezensis RC 218 as a biocontrol agent to reduce Fusarium head blight and deoxynivalenol accumulation: Genome sequencing and secondary metabolite cluster profiles.

    Science.gov (United States)

    Palazzini, Juan M; Dunlap, Christopher A; Bowman, Michael J; Chulze, Sofía N

    2016-11-01

    Bacillus subtilis RC 218 was originally isolated from wheat anthers as a potential antagonist of Fusarium graminearum, the causal agent of Fusarium head blight (FHB). It was demonstrated to have antagonist activity against the plant pathogen under in vitro and greenhouse assays. The current study extends characterizing B. subtilis RC 218 with a field study and genome sequencing. The field study demonstrated that B. subtilis RC 218 could reduce disease severity and the associated mycotoxin (deoxynivalenol) accumulation, under field conditions. The genome sequencing allowed us to accurately determine the taxonomy of the strain using a phylogenomic approach, which places it in the Bacillus velezensis clade. In addition, the draft genome allowed us to use bioinformatics to mine the genome for potential metabolites. The genome mining allowed us to identify 9 active secondary metabolites conserved by all B. velezensis strains and one additional secondary metabolite, the lantibiotic ericin, which is unique to this strain. This study represents the first confirmed production of ericin by a B. velezensis strain. The genome also allowed us to do a comparative genomics with its closest relatives and compare the secondary metabolite production of the publically available B. velezensis genomes. The results showed that the diversity in secondary metabolites of strains in the B. velezensis clade is driven by strains making different antibacterials. Copyright © 2016 Elsevier GmbH. All rights reserved.

  2. Large-scale metabolomic profiling identifies novel biomarkers for incident coronary heart disease.

    Directory of Open Access Journals (Sweden)

    Andrea Ganna

    2014-12-01

    Full Text Available Analyses of circulating metabolites in large prospective epidemiological studies could lead to improved prediction and better biological understanding of coronary heart disease (CHD. We performed a mass spectrometry-based non-targeted metabolomics study for association with incident CHD events in 1,028 individuals (131 events; 10 y. median follow-up with validation in 1,670 individuals (282 events; 3.9 y. median follow-up. Four metabolites were replicated and independent of main cardiovascular risk factors [lysophosphatidylcholine 18∶1 (hazard ratio [HR] per standard deviation [SD] increment = 0.77, P-value<0.001, lysophosphatidylcholine 18∶2 (HR = 0.81, P-value<0.001, monoglyceride 18∶2 (MG 18∶2; HR = 1.18, P-value = 0.011 and sphingomyelin 28∶1 (HR = 0.85, P-value = 0.015]. Together they contributed to moderate improvements in discrimination and re-classification in addition to traditional risk factors (C-statistic: 0.76 vs. 0.75; NRI: 9.2%. MG 18∶2 was associated with CHD independently of triglycerides. Lysophosphatidylcholines were negatively associated with body mass index, C-reactive protein and with less evidence of subclinical cardiovascular disease in additional 970 participants; a reverse pattern was observed for MG 18∶2. MG 18∶2 showed an enrichment (P-value = 0.002 of significant associations with CHD-associated SNPs (P-value = 1.2×10-7 for association with rs964184 in the ZNF259/APOA5 region and a weak, but positive causal effect (odds ratio = 1.05 per SD increment in MG 18∶2, P-value = 0.05 on CHD, as suggested by Mendelian randomization analysis. In conclusion, we identified four lipid-related metabolites with evidence for clinical utility, as well as a causal role in CHD development.

  3. Profile of an excellent nurse manager: identifying and developing health care team leaders.

    Science.gov (United States)

    Kallas, Kathryn D

    2014-01-01

    The purpose of this research was to identify the profile of an excellent nurse manager who can lead effective health care teams. Leadership attributes and competencies that characterize an excellent nurse manager and tools to identify them are lacking in the literature but are required to efficiently and effectively address the growing shortage of registered nurses (RNs) in health care team leadership roles and the critical linkage of these roles to patient outcomes. A profile of an excellent nurse manager was developed on the basis of the responses of nurse managers across the United States who had been identified as excellent or competent by chief nurse executive assessment or/and the Nurse Manager Ability, Leadership, and Support of Nurses staff survey to the Kouzes and Posner Leadership Practices Inventory: Self Instrument. Statistically significant distinctions exist between nurse managers who are excellent and those who are competent as assessed by the Five Practices of Exemplary Leadership, which together comprise the profile of an excellent nurse manager. The Kouzes and Posner Leadership Practices Inventory: Self Instrument can be used to identify, recruit, and develop RNs in the nurse manager role as excellent leaders of effective health care teams.

  4. Comparative evaluation of microbial diversity and metabolite profiles in doenjang, a fermented soybean paste, during the two different industrial manufacturing processes.

    Science.gov (United States)

    Lee, Sunmin; Lee, Sarah; Singh, Digar; Oh, Ji Young; Jeon, Eun Jung; Ryu, Hyung SeoK; Lee, Dong Wan; Kim, Beom Seok; Lee, Choong Hwan

    2017-04-15

    Two different doenjang manufacturing processes, the industrial process (IP) and the modified industrial process (mIP) with specific microbial assortments, were subjected to metabolite profiling using liquid chromatography-mass spectrometry (LC-MS) and gas chromatography time-of-flight mass spectrometry (GC-TOF-MS). The multivariate analyses indicated that both primary and secondary metabolites exhibited distinct patterns according to the fermentation processes (IP and mIP). Microbial community analysis for doenjang using denaturing gradient gel electrophoresis (DGGE), exhibited that both bacteria and fungi contributed proportionally for each step in the process viz., soybean, steaming, drying, meju fermentation, cooling, brining, and aging. Further, correlation analysis indicated that Aspergillus population was linked to sugar metabolism, Bacillus spp. with that of fatty acids, whereas Tetragenococcus and Zygosaccharomyces were found associated with amino acids. These results suggest that the components and quality of doenjang are critically influenced by the microbial assortments in each process. Copyright © 2016 Elsevier Ltd. All rights reserved.

  5. Metagenomic analysis and metabolite profiling of deep-sea sediments from the Gulf of Mexico following the Deepwater Horizon oil spill

    Directory of Open Access Journals (Sweden)

    Nikole Elizabeth Kimes

    2013-03-01

    Full Text Available Marine subsurface environments, such as deep-sea sediments, house abundant and diverse microbial communities that are believed to influence large-scale geochemical processes. These processes include the biotransformation and mineralization of numerous petroleum constituents. Thus, microbial communities in the Gulf of Mexico are thought to be responsible for the intrinsic bioremediation of crude oil released by the Deepwater Horizon (DWH oil spill. While hydrocarbon contamination is known to enrich for aerobic, oil-degrading bacteria in deep-seawater habitats, relatively little is known about the response of communities in deep-sea sediments, where low oxygen levels may hinder such a response. Here, we examined the hypothesis that increased hydrocarbon exposure results in an altered sediment microbial community structure that reflects the prospects for oil biodegradation under the prevailing conditions. We explore this hypothesis using metagenomic analysis and metabolite profiling of deep-sea sediment samples following the DWH oil spill. The presence of aerobic microbial communities and associated functional genes was consistent among all samples, whereas, a greater number of Deltaproteobacteria and anaerobic functional genes were found in sediments closest to the DWH blowout site. Metabolite profiling also revealed a greater number of putative metabolites in sediments surrounding the blowout zone relative to a background site located 127 km away. The mass spectral analysis of the putative metabolites revealed that alkylsuccinates remained below detection levels, but a homologous series of benzylsuccinates (with carbon chain lengths from 5 to 10 could be detected. Our findings suggest that increased exposure to hydrocarbons enriches for Deltaproteobacteria, which are known to be capable of anaerobic hydrocarbon metabolism. We also provide evidence for an active microbial community metabolizing aromatic hydrocarbons in deep-sea sediments of the

  6. Tissue Level Diet and Sex-by-Diet Interactions Reveal Unique Metabolite and Clustering Profiles Using Untargeted Liquid Chromatography-Mass Spectrometry on Adipose, Skeletal Muscle, and Liver Tissue in C57BL6/J Mice.

    Science.gov (United States)

    Wells, Ann; Barrington, William T; Dearth, Stephen; May, Amanda; Threadgill, David W; Campagna, Shawn R; Voy, Brynn H

    2018-03-02

    Dietary intervention is commonly used for weight loss or to improve health, as diet-induced obesity increases the risk of developing type 2 diabetes, hypertension, cardiovascular disease, stroke, osteoarthritis, and certain cancers. Various dietary patterns are associated with effects on health, yet little is known about the effects of diet at the tissue level. Using untargeted metabolomics, this study aimed to identify changes in water-soluble metabolites in C57BL/6J males and females fed one of five diets (Japanese, ketogenic, Mediterranean, American, and standard mouse chow) for 7 months. Metabolite abundance was examined in liver, skeletal muscle, and adipose tissue for sex, diet, and sex-by-diet interaction. Analysis of variance (ANOVA) suggests that liver tissue has the most metabolic plasticity under dietary changes compared with adipose and skeletal muscle. The ketogenic diet was distinguishable from other diets for both males and females according to partial least-squares discriminant analysis. Pathway analysis revealed that the majority of pathways affected play an important role in amino acid metabolism in liver tissue. Not surprisingly, amino acid profiles were affected by dietary patterns in skeletal muscle. Few metabolites were significantly altered in adipose tissue relative to skeletal muscle and liver tissue, indicating that it was largely stable, regardless of diet alterations. The results of this study revealed that the ketogenic diet had the largest effect on physiology, particularly for females. Furthermore, metabolomics analysis revealed that diet affects metabolites in a tissue-specific manner and that liver was most sensitive to dietary changes.

  7. Identifying the preferred subset of enzymatic profiles in nonlinear kinetic metabolic models via multiobjective global optimization and Pareto filters.

    Directory of Open Access Journals (Sweden)

    Carlos Pozo

    Full Text Available Optimization models in metabolic engineering and systems biology focus typically on optimizing a unique criterion, usually the synthesis rate of a metabolite of interest or the rate of growth. Connectivity and non-linear regulatory effects, however, make it necessary to consider multiple objectives in order to identify useful strategies that balance out different metabolic issues. This is a fundamental aspect, as optimization of maximum yield in a given condition may involve unrealistic values in other key processes. Due to the difficulties associated with detailed non-linear models, analysis using stoichiometric descriptions and linear optimization methods have become rather popular in systems biology. However, despite being useful, these approaches fail in capturing the intrinsic nonlinear nature of the underlying metabolic systems and the regulatory signals involved. Targeting more complex biological systems requires the application of global optimization methods to non-linear representations. In this work we address the multi-objective global optimization of metabolic networks that are described by a special class of models based on the power-law formalism: the generalized mass action (GMA representation. Our goal is to develop global optimization methods capable of efficiently dealing with several biological criteria simultaneously. In order to overcome the numerical difficulties of dealing with multiple criteria in the optimization, we propose a heuristic approach based on the epsilon constraint method that reduces the computational burden of generating a set of Pareto optimal alternatives, each achieving a unique combination of objectives values. To facilitate the post-optimal analysis of these solutions and narrow down their number prior to being tested in the laboratory, we explore the use of Pareto filters that identify the preferred subset of enzymatic profiles. We demonstrate the usefulness of our approach by means of a case study

  8. Identifying the preferred subset of enzymatic profiles in nonlinear kinetic metabolic models via multiobjective global optimization and Pareto filters.

    Science.gov (United States)

    Pozo, Carlos; Guillén-Gosálbez, Gonzalo; Sorribas, Albert; Jiménez, Laureano

    2012-01-01

    Optimization models in metabolic engineering and systems biology focus typically on optimizing a unique criterion, usually the synthesis rate of a metabolite of interest or the rate of growth. Connectivity and non-linear regulatory effects, however, make it necessary to consider multiple objectives in order to identify useful strategies that balance out different metabolic issues. This is a fundamental aspect, as optimization of maximum yield in a given condition may involve unrealistic values in other key processes. Due to the difficulties associated with detailed non-linear models, analysis using stoichiometric descriptions and linear optimization methods have become rather popular in systems biology. However, despite being useful, these approaches fail in capturing the intrinsic nonlinear nature of the underlying metabolic systems and the regulatory signals involved. Targeting more complex biological systems requires the application of global optimization methods to non-linear representations. In this work we address the multi-objective global optimization of metabolic networks that are described by a special class of models based on the power-law formalism: the generalized mass action (GMA) representation. Our goal is to develop global optimization methods capable of efficiently dealing with several biological criteria simultaneously. In order to overcome the numerical difficulties of dealing with multiple criteria in the optimization, we propose a heuristic approach based on the epsilon constraint method that reduces the computational burden of generating a set of Pareto optimal alternatives, each achieving a unique combination of objectives values. To facilitate the post-optimal analysis of these solutions and narrow down their number prior to being tested in the laboratory, we explore the use of Pareto filters that identify the preferred subset of enzymatic profiles. We demonstrate the usefulness of our approach by means of a case study that optimizes the

  9. Mass Balance, Metabolite Profile, and In Vitro-In Vivo Comparison of Clearance Pathways of Deleobuvir, a Hepatitis C Virus Polymerase Inhibitor

    Science.gov (United States)

    Chen, Lin-Zhi; Sabo, John P.; Philip, Elsy; Rowland, Lois; Mao, Yan; Latli, Bachir; Ramsden, Diane; Mandarino, Debra A.

    2014-01-01

    The pharmacokinetics, mass balance, and metabolism of deleobuvir, a hepatitis C virus (HCV) polymerase inhibitor, were assessed in healthy subjects following a single oral dose of 800 mg of [14C]deleobuvir (100 μCi). The overall recovery of radioactivity was 95.2%, with 95.1% recovered from feces. Deleobuvir had moderate to high clearance, and the half-life of deleobuvir and radioactivity in plasma were ∼3 h, indicating that there were no metabolites with half-lives significantly longer than that of the parent. The most frequently reported adverse events (in 6 of 12 subjects) were gastrointestinal disorders. Two major metabolites of deleobuvir were identified in plasma: an acyl glucuronide and an alkene reduction metabolite formed in the gastrointestinal (GI) tract by gut bacteria (CD 6168), representing ∼20% and 15% of the total drug-related material, respectively. Deleobuvir and CD 6168 were the main components in the fecal samples, each representing ∼30 to 35% of the dose. The majority of the remaining radioactivity found in the fecal samples (∼21% of the dose) was accounted for by three metabolites in which deleobuvir underwent both alkene reduction and monohydroxylation. In fresh human hepatocytes that form biliary canaliculi in sandwich cultures, the biliary excretion for these excretory metabolites was markedly higher than that for deleobuvir and CD 6168, implying that rapid biliary elimination upon hepatic formation may underlie the absence of these metabolites in circulation. The low in vitro clearance was not predictive of the observed in vivo clearance, likely because major deleobuvir biotransformation occurred by non-CYP450-mediated enzymes that are not well represented in hepatocyte-based in vitro models. PMID:25313217

  10. Development and validation of a DESI-HRMS/MS method for the fast profiling of esomeprazole and its metabolites in rat plasma: a pharmacokinetic study.

    Science.gov (United States)

    Rossi, Alessandra; Castrati, Luca; Colombo, Paolo; Flammini, Lisa; Barocelli, Elisabetta; Bettini, Ruggero; Elviri, Lisa

    2016-02-01

    The advances in pharmaceutical development and drug discovery impose the availability of reliable high-throughput screening methods for the rapid evaluation of drug metabolism and pharmacokinetic (PK) in biological samples. Here, a desorption electrospray mass spectrometry (DESI-MS) method has been developed and validated for the PK profiling of esomeprazole and its metabolites (5-hydroxyomeprazole and omeprazole sulfone) in rat plasma. Rats were treated with an esomeprazole solution (2.5 mg/mL) for endovenous administration and the analyte levels were profiled over 2 h after liquid-liquid extraction from plasma. MS and tandem mass spectrometry (MS/MS) experiments were performed by using a DESI-LTQ-Orbitrap XL instrument and an on-spot fixed time analysis on PMMA surfaces. Validation was performed for the esomeprazole. The DESI-MS/MS method exhibited for the esomepazole excellent sensitivity (limit of detection (LOD)=60 ng/mL), linearity (0.2-20 µg/mL concentration range; y=23848(±361)X, n=15; r(2) =0.987) and precision (RSD0.05). The data achieved demonstrated that the DESI-MS method is suitable for sensitive and fast profiling of a drug and its metabolites at the therapeutic concentration levels. Copyright © 2015 John Wiley & Sons, Ltd.

  11. Genomic profiling in Down syndrome acute lymphoblastic leukemia identifies histone gene deletions associated with altered methylation profiles

    Science.gov (United States)

    Loudin, Michael G.; Wang, Jinhua; Leung, Hon-Chiu Eastwood; Gurusiddappa, Sivashankarappa; Meyer, Julia; Condos, Gregory; Morrison, Debra; Tsimelzon, Anna; Devidas, Meenakshi; Heerema, Nyla A.; Carroll, Andrew J.; Plon, Sharon E.; Hunger, Stephen P.; Basso, Giuseppe; Pession, Andrea; Bhojwani, Deepa; Carroll, William L.; Rabin, Karen R.

    2014-01-01

    Patients with Down syndrome (DS) and acute lymphoblastic leukemia (ALL) have distinct clinical and biological features. Whereas most DS-ALL cases lack the sentinel cytogenetic lesions that guide risk assignment in childhood ALL, JAK2 mutations and CRLF2 overexpression are highly enriched. To further characterize the unique biology of DS-ALL, we performed genome-wide profiling of 58 DS-ALL and 68 non-Down syndrome (NDS) ALL cases by DNA copy number, loss of heterozygosity, gene expression, and methylation analyses. We report a novel deletion within the 6p22 histone gene cluster as significantly more frequent in DS-ALL, occurring in 11 DS (22%) and only two NDS cases (3.1%) (Fisher’s exact p = 0.002). Homozygous deletions yielded significantly lower histone expression levels, and were associated with higher methylation levels, distinct spatial localization of methylated promoters, and enrichment of highly methylated genes for specific pathways and transcription factor binding motifs. Gene expression profiling demonstrated heterogeneity of DS-ALL cases overall, with supervised analysis defining a 45-transcript signature associated with CRLF2 overexpression. Further characterization of pathways associated with histone deletions may identify opportunities for novel targeted interventions. PMID:21647151

  12. Early Assessment of Thiopurine Metabolites Identifies Patients at Risk of Thiopurine-induced Leukopenia in Inflammatory Bowel Disease.

    Science.gov (United States)

    Wong, Dennis R; Coenen, Marieke J H; Vermeulen, Sita H; Derijks, Luc J J; van Marrewijk, Corine J; Klungel, Olaf H; Scheffer, Hans; Franke, Barbara; Guchelaar, Henk-Jan; de Jong, Dirk J; Engels, Leopold G J B; Verbeek, André L M; Hooymans, Piet M

    2017-02-01

    Only a quarter of thiopurine-induced myelotoxicity in inflammatory bowel disease [IBD] patients is related to thiopurine S-methyltransferase deficiency. We determined the predictive value of 6-thioguanine nucleotide [6-TGN] and 6-methylmercaptopurine ribonucleotide [6-MMPR] concentrations 1 week after initiation [T1] for development of leukopenia during the first 8 weeks of thiopurine treatment. The study was performed in IBD patients starting thiopurine therapy as part of the Dutch randomized controlled TOPIC trial [ClinicalTrials.gov NCT00521950]. Blood samples for metabolite measurement were collected at T1. Leukopenia was defined by leukocyte counts of leukopenia who completed the 8 weeks on the stable dose were selected from the first 272 patients of the TOPIC trial. Thirty-two patients with, and 162 patients without leukopenia were analysed. T1 threshold 6-TGN concentrations of 213 pmol/8 × 10 8 erythrocytes and 3525 pmol/8 × 10 8 erythrocytes for 6-MMPR were defined: patients exceeding these values were at increased leukopenia risk (odds ratio [OR] 6.2 [95% CI: 2.8-13.8] and 5.9 [95% CI: 2.7-13.3], respectively). Leukopenia rates were higher in patients treated with mercaptopurine, compared with azathioprine (OR 7.3 [95% CI: 3.1-17.0]), and concurrent anti-TNF therapy (OR 5.1 [95% CI: 1.6-16.4]). Logistic regression analysis of thiopurine type, threshold concentrations, and concurrent anti-tumour necrosis factor [TNF] therapy revealed that elevations of both T1 6-TGN and 6-MMPR resulted in the highest risk for leukopenia, followed by exceeding only the T1 6-MMPR or 6-TGN threshold concentration (area under the curve 0.84 [95% CI: 0.76-0.92]). In ~80% of patients, leukopenia could be explained by T1 6-TGN and/or 6-MMPR elevations. Validation of the predictive model is needed before implementing in clinical practice. Copyright © 2016 European Crohn’s and Colitis Organisation (ECCO). Published by Oxford University Press. All rights reserved. For

  13. Rapid Inhibition Profiling in Bacillus subtilis to Identify the Mechanism of Action of New Antimicrobials.

    Science.gov (United States)

    Lamsa, Anne; Lopez-Garrido, Javier; Quach, Diana; Riley, Eammon P; Pogliano, Joe; Pogliano, Kit

    2016-08-19

    Increasing antimicrobial resistance has become a major public health crisis. New antimicrobials with novel mechanisms of action (MOA) are desperately needed. We previously developed a method, bacterial cytological profiling (BCP), which utilizes fluorescence microscopy to rapidly identify the MOA of antimicrobial compounds. BCP is based upon our discovery that cells treated with antibiotics affecting different metabolic pathways generate different cytological signatures, providing quantitative information that can be used to determine a compound's MOA. Here, we describe a system, rapid inhibition profiling (RIP), for creating cytological profiles of new antibiotic targets for which there are currently no chemical inhibitors. RIP consists of the fast, inducible degradation of a target protein followed by BCP. We demonstrate that degrading essential proteins in the major metabolic pathways for DNA replication, transcription, fatty acid biosynthesis, and peptidoglycan biogenesis in Bacillus subtilis rapidly produces cytological profiles closely matching that of antimicrobials targeting the same pathways. Additionally, RIP and antibiotics targeting different steps in fatty acid biosynthesis can be differentiated from each other. We utilize RIP and BCP to show that the antibacterial MOA of four nonsteroidal anti-inflammatory antibiotics differs from that proposed based on in vitro data. RIP is a versatile method that will extend our knowledge of phenotypes associated with inactivating essential bacterial enzymes and thereby allow for screening for molecules that inhibit novel essential targets.

  14. Metabolite Profiling during Fermentation of Makgeolli by the Wild Yeast Strain Saccharomyces cerevisiae Y98-5.

    Science.gov (United States)

    Kim, Hye Ryun; Kim, Jae-Ho; Ahn, Byung Hak; Bai, Dong-Hoon

    2014-12-01

    Makgeolli is a traditional Korean alcoholic beverage. The flavor of makgeolli is primarily determined by metabolic products such as free sugars, amino acids, organic acids, and aromatic compounds, which are produced during the fermentation of raw materials by molds and yeasts present in nuruk, a Korean fermentation starter. In this study, makgeolli was brewed using the wild yeast strain Saccharomyces cerevisiae Y98-5, and temporal changes in the metabolites during fermentation were analyzed by ultra-high-performance liquid chromatography-quadrupole-time-of-flight mass spectrometry. The resultant data were analyzed by partial least squares-discriminant analysis (PLS-DA). Various metabolites, including amino acids, organic acids, sugar alcohols, small peptides, and nucleosides, were obviously altered by increasing the fermentation period. Changes in these metabolites allowed us to distinguish among makgeolli samples with different fermentation periods (1, 2, 3, 6, 7, and 8 days) on a PLS-DA score plot. In the makgeolli brewed in this study, the amounts of tyrosine (463.13 µg/mL) and leucine (362.77 µg/mL) were high. Therefore, our results indicate that monitoring the changes in metabolites during makgeolli fermentation might be important for brewing makgeolli with good nutritional quality.

  15. Application of the ideal profile method to identify an ideal sufu for nonregular consumers.

    Science.gov (United States)

    Chen, Yan Ping; Chung, Hau Yin

    2018-02-06

    Sufu is a fermented soybean food with unique odor, flavor, and texture, which might not be appreciated by nonregular consumers. To identify the attributes that nonregular consumers appreciated, 12 commercial products bought from a Hong Kong market were tested by 113 consumers according to the ideal profile method (IPM), and rated on 22 attributes. Data provided from nonregular consumers were consistent at both panel and consumer levels. The predicted ideal profile received a higher hedonic score (7.0) than the tested products (6.0). Compared with commercial samples, the ideal sufu has low intensity in the attributes of fermented (aroma and flavor), moldy (aroma), and hard (texture), but high intensity in the soybean-like (aroma and flavor) and sesame oil-like (aroma and flavor) attributes. IPM could be used as an alternative approach to collect sensory profiles and preference data directly from consumers for product characterization. It could also be applied to identify the attributes that nonregular consumers appreciated. © 2018 Society of Chemical Industry. © 2018 Society of Chemical Industry.

  16. NMR-based metabolite profiling of human milk: A pilot study of methods for investigating compositional changes during lactation

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Junfang [Department of Chemistry, Umeå University (Sweden); Domellöf, Magnus [Department of Clinical Sciences, Pediatrics, Umeå University (Sweden); Zivkovic, Angela M. [Foods for Health Institute, University of California, Davis, CA (United States); Department of Nutrition, University of California, Davis, CA (United States); Larsson, Göran [Department of Medical Biochemistry and Biophysics, Unit of Research, Education and Development-Östersund, Umeå University (Sweden); Öhman, Anders, E-mail: anders.ohman01@umu.se [Department of Pharmacology and Clinical Neuroscience, Umeå University (Sweden); Nording, Malin L., E-mail: malin.nording@umu.se [Department of Chemistry, Umeå University (Sweden)

    2016-01-15

    Low-molecular-weight metabolites in human milk are gaining increasing interest in studies of infant nutrition. In the present study, the milk metabolome from a single mother was explored at different stages of lactation. Metabolites were extracted from sample aliquots using either methanol/water (MeOH/H{sub 2}O) extraction or ultrafiltration. Nuclear magnetic resonance (NMR) spectroscopy was used for metabolite identification and quantification, and multi- and univariate statistical data analyses were used to detect changes over time of lactation. Compared to MeOH/H{sub 2}O extraction, ultrafiltration more efficiently reduced the interference from lipid and protein resonances, thereby enabling the identification and quantification of 36 metabolites. The human milk metabolomes at the early (9–24 days after delivery) and late (31–87 days after delivery) stages of lactation were distinctly different according to multi- and univariate statistics. The late lactation stage was characterized by significantly elevated concentrations of lactose, choline, alanine, glutamate, and glutamine, as well as by reduced levels of citrate, phosphocholine, glycerophosphocholine, and N-acetylglucosamine. Our results indicate that there are significant compositional changes of the human milk metabolome also in different phases of the matured lactation stage. These findings complement temporal studies on the colostrum and transitional metabolome in providing a better understanding of the nutritional variations received by an infant. - Highlights: • 36 metabolites were simultaneously quantified in human milk by NMR. • Ultrafiltration more efficiently reduces interferences than MeOH/H{sub 2}O extraction. • Compositional changes of the human milk exist during the matured lactation stage.

  17. NMR-based metabolite profiling of human milk: A pilot study of methods for investigating compositional changes during lactation

    International Nuclear Information System (INIS)

    Wu, Junfang; Domellöf, Magnus; Zivkovic, Angela M.; Larsson, Göran; Öhman, Anders; Nording, Malin L.

    2016-01-01

    Low-molecular-weight metabolites in human milk are gaining increasing interest in studies of infant nutrition. In the present study, the milk metabolome from a single mother was explored at different stages of lactation. Metabolites were extracted from sample aliquots using either methanol/water (MeOH/H 2 O) extraction or ultrafiltration. Nuclear magnetic resonance (NMR) spectroscopy was used for metabolite identification and quantification, and multi- and univariate statistical data analyses were used to detect changes over time of lactation. Compared to MeOH/H 2 O extraction, ultrafiltration more efficiently reduced the interference from lipid and protein resonances, thereby enabling the identification and quantification of 36 metabolites. The human milk metabolomes at the early (9–24 days after delivery) and late (31–87 days after delivery) stages of lactation were distinctly different according to multi- and univariate statistics. The late lactation stage was characterized by significantly elevated concentrations of lactose, choline, alanine, glutamate, and glutamine, as well as by reduced levels of citrate, phosphocholine, glycerophosphocholine, and N-acetylglucosamine. Our results indicate that there are significant compositional changes of the human milk metabolome also in different phases of the matured lactation stage. These findings complement temporal studies on the colostrum and transitional metabolome in providing a better understanding of the nutritional variations received by an infant. - Highlights: • 36 metabolites were simultaneously quantified in human milk by NMR. • Ultrafiltration more efficiently reduces interferences than MeOH/H 2 O extraction. • Compositional changes of the human milk exist during the matured lactation stage.

  18. UPLC-MSE Profiling of Phytoplankton Metabolites: Application to the Identification of Pigments and Structural Analysis of Metabolites in Porphyridium purpureum

    Directory of Open Access Journals (Sweden)

    Camille Juin

    2015-04-01

    Full Text Available A fast and high-resolution UPLC-MSE analysis was used to identify phytoplankton pigments in an ethanol extract of Porphyridium purpureum (Pp devoid of phycobiliproteins. In a first step, 22 standard pigments were analyzed by UPLC-MSE to build a database including retention time and accurate masses of parent and fragment ions. Using this database, seven pigments or derivatives previously reported in Pp were unequivocally identified: β,β-carotene, chlorophyll a, zeaxanthin, chlorophyllide a, pheophorbide a, pheophytin a, and cryptoxanthin. Minor amounts of Divinyl chlorophyll a, a chemotaxonomic pigment marker for prochlorophytes, were also unequivocally identified using the database. Additional analysis of ionization and fragmentation patterns indicated the presence of ions that could correspond to hydroxylated derivatives of chlorophyll a and pheophytin a, produced during the ethanolic extraction, as well as previously described galactosyldiacylglycerols, the thylakoid coenzyme plastoquinone, and gracilamide B, a molecule previously reported in the red seaweed Gracillaria asiatica. These data point to UPLC-MSE as an efficient technique to identify phytoplankton pigments for which standards are available, and demonstrate its major interest as a complementary method for the structural elucidation of ionizable marine molecules.

  19. Effects of Developmental Stages and Reduced UVB and Low UV Conditions on Plant Secondary Metabolite Profiles in Pak Choi (Brassica rapa subsp. chinensis).

    Science.gov (United States)

    Heinze, Mandy; Hanschen, Franziska S; Wiesner-Reinhold, Melanie; Baldermann, Susanne; Gräfe, Jan; Schreiner, Monika; Neugart, Susanne

    2018-02-21

    Pak choi (Brassica rapa subsp. chinensis) is rich in secondary metabolites and contains numerous antioxidants, including flavonoids; hydroxycinnamic acids; carotenoids; chlorophylls; and glucosinolates, which can be hydrolyzed to epithionitriles, nitriles, or isothiocyanates. Here, we investigate the effect of reduced exposure to ultraviolet B (UVB) and UV (UVA and UVB) light at four different developmental stages of pak choi. We found that both the plant morphology and secondary metabolite profiles were affected by reduced exposure to UVB and UV, depending on the plant's developmental stage. In detail, mature 15- and 30-leaf plants had higher concentrations of flavonoids, hydroxycinnamic acids, carotenoids, and chlorophylls, whereas sprouts contained high concentrations of glucosinolates and their hydrolysis products. Dry weights and leaf areas increased as a result of reduced UVB and low UV. For the flavonoids and hydroxycinnamic acids in 30-leaf plants, less complex compounds were favored, for example, sinapic acid acylated kaempferol triglycoside instead of the corresponding tetraglycoside. Moreover, also in 30-leaf plants, zeaxanthin, a carotenoid linked to protection during photosynthesis, was increased under low UV conditions. Interestingly, most glucosinolates were not affected by reduced UVB and low UV conditions. However, this study underlines the importance of 4-(methylsulfinyl)butyl glucosinolate in response to UVA and UVB exposure. Further, reduced UVB and low UV conditions resulted in higher concentrations of glucosinolate-derived nitriles. In conclusion, exposure to low doses of UVB and UV from the early to late developmental stages did not result in overall lower concentrations of plant secondary metabolites.

  20. Urine and Serum Metabolite Profiling of Rats Fed a High-Fat Diet and the Anti-Obesity Effects of Caffeine Consumption

    Directory of Open Access Journals (Sweden)

    Hyang Yeon Kim

    2015-02-01

    Full Text Available In this study, we investigated the clinical changes induced by a high fat diet (HFD and caffeine consumption in a rat model. The mean body weight of the HFD with caffeine (HFDC-fed rat was decreased compared to that of the HFD-fed rat without caffeine. The levels of cholesterol, triglycerides (TGs, and free fatty acid, as well as the size of adipose tissue altered by HFD, were improved by caffeine consumption. To investigate the metabolites that affected the change of the clinical factors, the urine and serum of rats fed a normal diet (ND, HFD, and HFDC were analyzed using ultra performance liquid chromatography quadruple time-of-flight mass spectrometry (UPLC-Q-TOF-MS, gas chromatography (GC-TOF-MS, and linear trap quadruple mass spectrometry (LTQ-XL-MS combined with multivariate analysis. A total of 68 and 52 metabolites were found to be different in urine and serum, respectively. After being fed caffeine, some glucuronide-conjugated compounds, lysoPCs, CEs, DGs, TGs, taurine, and hippuric acid were altered compared to the HFD group. In this study, caffeine might potentially inhibit HFD-induced obesity and we suggest possible biomarker candidates using MS-based metabolite profiling.

  1. Profiling of phytohormones and their major metabolites in rice using binary solid-phase extraction and liquid chromatography-triple quadrupole mass spectrometry.

    Science.gov (United States)

    Cao, Zhao-Yun; Sun, Li-Hua; Mou, Ren-Xiang; Zhang, Lin-Ping; Lin, Xiao-Yan; Zhu, Zhi-Wei; Chen, Ming-Xue

    2016-06-17

    A high-throughput method was developed using liquid chromatography-triple quadrupole mass spectrometry (LC-MS/MS) for the profiling and quantification of 43 phytohormones and their major metabolites, including auxins, abscisic acid, jasmonic acid, salicylic acid, cytokinins and gibberellins in a single sample extract. Considerable matrix effects (MEs) were observed (with most ME values in the range of 29%-84%, but maximum MEs of more than 115%, even up to 206%, existed) in sample extracts for most of the compounds studied. The application of the proposed binary solid-phase extraction using polymer anion and polymer cation exchange resins, was performed to purify 25 acidic and 18 alkaline phytohormones and their major metabolites prior to the LC-MS/MS analysis, which markedly reduced the MEs to acceptable levels, with ME values in the range of ±15%. Moreover, all of the isomers of cytokinins and their metabolites were fully separated on a sub-2μm particle C18 reverse-phase column with the optimized mobile phase consisting of methanol and 5mM ammonium formate. The method showed good linearity for all 43 analytes with regression coefficients (R(2))>0.991. Limits of detection ranged from 0.19 to 7.57 fmol for auxin, gibberellins, abscisic acid and their metabolites, 29.7 fmol for jasmonic acid, 18.1 fmol for salicylic acid, and from 0.03 to 0.31 fmol for cytokinins and their metabolites. The mean recoveries for all of the analytes were from 70.7 to 118.5%, and the inter-day precisions (n=6) were less than 18.7%, with intra-day precisions (n=6) within 25.4%. Finally, 20 compounds were successfully quantified in rice sample profiles using the proposed method, which will greatly facilitate the understanding of hormone-related regulatory networks that influence rice growth and development. To our knowledge, there are limited reports that measure this level of phytohormone species in rice samples using a single analysis. Copyright © 2016 Elsevier B.V. All rights reserved.

  2. Metabolomic profiling to identify predictors of response to vitamin E for non-alcoholic steatohepatitis (NASH.

    Directory of Open Access Journals (Sweden)

    Jianfeng Cheng

    Full Text Available Vitamin E was recently shown to improve hepatic histology in a randomized controlled trial of pioglitazone or vitamin E for nonalcoholic steatohepatitis (PIVENS. The current study utilized samples collected in the PIVENS trial to identify: (1 baseline metabolomic profiles that could identify who would respond to vitamin E treatment and (2 end of treatment metabolomic profiles reflective of histologic improvement. A comprehensive analysis of metabolomics profiles (n = 547 quantified by mass spectrometry was performed in vitamin E responders (n = 16, vitamin E non-responders (n = 15, and placebo responders (n = 15. At baseline, phenyl-propionic acid (Odds ratio: 29.4, p<0.01, indole-propionic acid levels (Odds ratio: 16.2, p<0.01 were directly associated with a subsequent histologic response to vitamin E treatment whereas γ-carboxyethylhydroxychroman (CEHC levels were inversely related to histologic response. Adjusting for baseline values by analysis of covariance, the end of treatment levels of gamma-glutamyl leucine (Fold change: 0.82, p<0.02 and gamma-glutamyl valine (Fold change: 0.8, p<0.03 were significantly lower in vitamin E responders compared to non-responders. The levels of gamma-glutamyl transpeptidase were not significantly different across the two groups. Subjects receiving placebo who demonstrated a histologic improvement also demonstrated lower levels of gamma-glutamylated amino acids (leucine, valine and isoleucine compared to vitamin E non-responders. These data provide exploratory proof that there are measurable differences in the metabolic profile of subjects who are likely (vs unlikely to respond to vitamin E treatment for NASH and in those experiencing histologic improvement (vs no improvement on treatment and support further studies to validate these biomarkers.

  3. Comparative transcriptional profiling of the axolotl limb identifies a tripartite regeneration-specific gene program.

    Directory of Open Access Journals (Sweden)

    Dunja Knapp

    Full Text Available Understanding how the limb blastema is established after the initial wound healing response is an important aspect of regeneration research. Here we performed parallel expression profile time courses of healing lateral wounds versus amputated limbs in axolotl. This comparison between wound healing and regeneration allowed us to identify amputation-specific genes. By clustering the expression profiles of these samples, we could detect three distinguishable phases of gene expression - early wound healing followed by a transition-phase leading to establishment of the limb development program, which correspond to the three phases of limb regeneration that had been defined by morphological criteria. By focusing on the transition-phase, we identified 93 strictly amputation-associated genes many of which are implicated in oxidative-stress response, chromatin modification, epithelial development or limb development. We further classified the genes based on whether they were or were not significantly expressed in the developing limb bud. The specific localization of 53 selected candidates within the blastema was investigated by in situ hybridization. In summary, we identified a set of genes that are expressed specifically during regeneration and are therefore, likely candidates for the regulation of blastema formation.

  4. Identifying the ideal profile of French yogurts for different clusters of consumers.

    Science.gov (United States)

    Masson, M; Saint-Eve, A; Delarue, J; Blumenthal, D

    2016-05-01

    Identifying the sensory properties that affect consumer preferences for food products is an important feature of product development. Different methods, such as external preference mapping or partial least squares regression, are used to establish relationships between sensory data and consumer preferences and to identify sensory attributes that drive consumer preferences, by highlighting optimum products. Plain French yogurts were evaluated by a sensory profiling method performed by 12 trained judges. In parallel, 180 consumers were asked to score their overall liking and complete a cognitive restraint questionnaire. After hierarchical cluster analysis on the liking scores, preference mapping using a quadratic regression model was performed. Five clusters of consumers were identified as a function of different preference patterns. Contrary to our expectations, fat levels were not discriminating. For each cluster, the results of preference mapping enabled the identification of optimum products. A comparison of the 5 sensory profiles revealed numerous differences between key sensory attributes. For example, one consumer cluster had a strong preference for products perceived as very thick, grainy, but with a less flowing texture, less sticky, whey presence and color, in contrast to other clusters. In addition, each segment of consumers was characterized according to the results of the cognitive restraint questionnaire. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  5. TimeXNet: identifying active gene sub-networks using time-course gene expression profiles.

    Science.gov (United States)

    Patil, Ashwini; Nakai, Kenta

    2014-01-01

    Time-course gene expression profiles are frequently used to provide insight into the changes in cellular state over time and to infer the molecular pathways involved. When combined with large-scale molecular interaction networks, such data can provide information about the dynamics of cellular response to stimulus. However, few tools are currently available to predict a single active gene sub-network from time-course gene expression profiles. We introduce a tool, TimeXNet, which identifies active gene sub-networks with temporal paths using time-course gene expression profiles in the context of a weighted gene regulatory and protein-protein interaction network. TimeXNet uses a specialized form of the network flow optimization approach to identify the most probable paths connecting the genes with significant changes in expression at consecutive time intervals. TimeXNet has been extensively evaluated for its ability to predict novel regulators and their associated pathways within active gene sub-networks in the mouse innate immune response and the yeast osmotic stress response. Compared to other similar methods, TimeXNet identified up to 50% more novel regulators from independent experimental datasets. It predicted paths within a greater number of known pathways with longer overlaps (up to 7 consecutive edges) within these pathways. TimeXNet was also shown to be robust in the presence of varying amounts of noise in the molecular interaction network. TimeXNet is a reliable tool that can be used to study cellular response to stimuli through the identification of time-dependent active gene sub-networks in diverse biological systems. It is significantly better than other similar tools. TimeXNet is implemented in Java as a stand-alone application and supported on Linux, MS Windows and Macintosh. The output of TimeXNet can be directly viewed in Cytoscape. TimeXNet is freely available for non-commercial users.

  6. MR spectroscopy-based brain metabolite profiling in propionic acidaemia: metabolic changes in the basal ganglia during acute decompensation and effect of liver transplantation

    Directory of Open Access Journals (Sweden)

    McKiernan Patrick J

    2011-05-01

    Full Text Available Abstract Background Propionic acidaemia (PA results from deficiency of Propionyl CoA carboxylase, the commonest form presenting in the neonatal period. Despite best current management, PA is associated with severe neurological sequelae, in particular movement disorders resulting from basal ganglia infarction, although the pathogenesis remains poorly understood. The role of liver transplantation remains controversial but may confer some neuro-protection. The present study utilises quantitative magnetic resonance spectroscopy (MRS to investigate brain metabolite alterations in propionic acidaemia during metabolic stability and acute encephalopathic episodes. Methods Quantitative MRS was used to evaluate brain metabolites in eight children with neonatal onset propionic acidaemia, with six elective studies acquired during metabolic stability and five studies during acute encephalopathic episodes. MRS studies were acquired concurrently with clinically indicated MR imaging studies at 1.5 Tesla. LCModel software was used to provide metabolite quantification. Comparison was made with a dataset of MRS metabolite concentrations from a cohort of children with normal appearing MR imaging. Results MRI findings confirm the vulnerability of basal ganglia to infarction during acute encephalopathy. We identified statistically significant decreases in basal ganglia glutamate+glutamine and N-Acetylaspartate, and increase in lactate, during encephalopathic episodes. In white matter lactate was significantly elevated but other metabolites not significantly altered. Metabolite data from two children who had received liver transplantation were not significantly different from the comparator group. Conclusions The metabolite alterations seen in propionic acidaemia in the basal ganglia during acute encephalopathy reflect loss of viable neurons, and a switch to anaerobic respiration. The decrease in glutamine + glutamate supports the hypothesis that they are consumed to

  7. Comprehensive expression profiling of tumor cell lines identifies molecular signatures of melanoma progression.

    Directory of Open Access Journals (Sweden)

    Byungwoo Ryu

    2007-07-01

    Full Text Available Gene expression profiling has revolutionized our ability to molecularly classify primary human tumors and significantly enhanced the development of novel tumor markers and therapies; however, progress in the diagnosis and treatment of melanoma over the past 3 decades has been limited, and there is currently no approved therapy that significantly extends lifespan in patients with advanced disease. Profiling studies of melanoma to date have been inconsistent due to the heterogeneous nature of this malignancy and the limited availability of informative tissue specimens from early stages of disease.In order to gain an improved understanding of the molecular basis of melanoma progression, we have compared gene expression profiles from a series of melanoma cell lines representing discrete stages of malignant progression that recapitulate critical characteristics of the primary lesions from which they were derived. Here we describe the unsupervised hierarchical clustering of profiling data from melanoma cell lines and melanocytes. This clustering identifies two distinctive molecular subclasses of melanoma segregating aggressive metastatic tumor cell lines from less-aggressive primary tumor cell lines. Further analysis of expression signatures associated with melanoma progression using functional annotations categorized these transcripts into three classes of genes: 1 Upregulation of activators of cell cycle progression, DNA replication and repair (CDCA2, NCAPH, NCAPG, NCAPG2, PBK, NUSAP1, BIRC5, ESCO2, HELLS, MELK, GINS1, GINS4, RAD54L, TYMS, and DHFR, 2 Loss of genes associated with cellular adhesion and melanocyte differentiation (CDH3, CDH1, c-KIT, PAX3, CITED1/MSG-1, TYR, MELANA, MC1R, and OCA2, 3 Upregulation of genes associated with resistance to apoptosis (BIRC5/survivin. While these broad classes of transcripts have previously been implicated in the progression of melanoma and other malignancies, the specific genes identified within each class

  8. Metabolite profile of the tomato dwarf cultivar Micro-Tom and comparative response to saline and nutritional stresses with regard to a commercial cultivar.

    Science.gov (United States)

    Flores, Pilar; Hernández, Virginia; Hellín, Pilar; Fenoll, Jose; Cava, Juana; Mestre, Teresa; Martínez, Vicente

    2016-03-30

    The dwarf tomato variety Micro-Tom has been used as a plant model for studies of plant development. However, its response to environmental and agricultural factors has not been well studied. This work studies the phytochemical content of Micro-Tom tomato and its comparative response to saline and nutritional (N, K and Ca) stresses with regard to a commercial variety. The chromatographic profiles of Micro-Tom were similar to those of the commercial variety and the only differences appear to be the concentration of the components. In Micro-Tom, the concentrations of sugars and organic acids increased by salinity in a lesser extent than in Optima. Moreover, contrary to that observed in the commercial variety, phenolic compounds and vitamin C did not increase by salinity in the dwarf variety. However, both varieties increased similarly the concentrations of carotenoids under saline conditions. Finally, fruit yield and most primary and secondary metabolite concentrations in Micro-Tom were not affected by N, K or Ca limitation. The mutations leading to the dwarf phenotype did not greatly alter the metabolite profiles but studies using Micro-Tom as a plant model should consider the lower capacity for sugars and organic acids under saline conditions and the greater tolerance to nutrient limitation of the dwarf variety. © 2015 Society of Chemical Industry.

  9. Genome-Wide Expression Profiling of Five Mouse Models Identifies Similarities and Differences with Human Psoriasis

    Science.gov (United States)

    Swindell, William R.; Johnston, Andrew; Carbajal, Steve; Han, Gangwen; Wohn, Christian; Lu, Jun; Xing, Xianying; Nair, Rajan P.; Voorhees, John J.; Elder, James T.; Wang, Xiao-Jing; Sano, Shigetoshi; Prens, Errol P.; DiGiovanni, John; Pittelkow, Mark R.; Ward, Nicole L.; Gudjonsson, Johann E.

    2011-01-01

    Development of a suitable mouse model would facilitate the investigation of pathomechanisms underlying human psoriasis and would also assist in development of therapeutic treatments. However, while many psoriasis mouse models have been proposed, no single model recapitulates all features of the human disease, and standardized validation criteria for psoriasis mouse models have not been widely applied. In this study, whole-genome transcriptional profiling is used to compare gene expression patterns manifested by human psoriatic skin lesions with those that occur in five psoriasis mouse models (K5-Tie2, imiquimod, K14-AREG, K5-Stat3C and K5-TGFbeta1). While the cutaneous gene expression profiles associated with each mouse phenotype exhibited statistically significant similarity to the expression profile of psoriasis in humans, each model displayed distinctive sets of similarities and differences in comparison to human psoriasis. For all five models, correspondence to the human disease was strong with respect to genes involved in epidermal development and keratinization. Immune and inflammation-associated gene expression, in contrast, was more variable between models as compared to the human disease. These findings support the value of all five models as research tools, each with identifiable areas of convergence to and divergence from the human disease. Additionally, the approach used in this paper provides an objective and quantitative method for evaluation of proposed mouse models of psoriasis, which can be strategically applied in future studies to score strengths of mouse phenotypes relative to specific aspects of human psoriasis. PMID:21483750

  10. Transcriptional Profiling of Biofilm Regulators Identified by an Overexpression Screen in Saccharomyces cerevisiae

    Science.gov (United States)

    Cromie, Gareth A.; Tan, Zhihao; Hays, Michelle; Sirr, Amy; Jeffery, Eric W.; Dudley, Aimée M.

    2017-01-01

    Biofilm formation by microorganisms is a major cause of recurring infections and removal of biofilms has proven to be extremely difficult given their inherent drug resistance . Understanding the biological processes that underlie biofilm formation is thus extremely important and could lead to the development of more effective drug therapies, resulting in better infection outcomes. Using the yeast Saccharomyces cerevisiae as a biofilm model, overexpression screens identified DIG1, SFL1, HEK2, TOS8, SAN1, and ROF1/YHR177W as regulators of biofilm formation. Subsequent RNA-seq analysis of biofilm and nonbiofilm-forming strains revealed that all of the overexpression strains, other than DIG1 and TOS8, were adopting a single differential expression profile, although induced to varying degrees. TOS8 adopted a separate profile, while the expression profile of DIG1 reflected the common pattern seen in most of the strains, plus substantial DIG1-specific expression changes. We interpret the existence of the common transcriptional pattern seen across multiple, unrelated overexpression strains as reflecting a transcriptional state, that the yeast cell can access through regulatory signaling mechanisms, allowing an adaptive morphological change between biofilm-forming and nonbiofilm states. PMID:28673928

  11. Perturbational Profiling of Metabolites in Patient Fibroblasts Implicates α-Aminoadipate as a Potential Biomarker for Bipolar Disorder

    Science.gov (United States)

    Huang, Joanne H.; Berkovitch, Shaunna S.; Iaconelli, Jonathan; Watmuff, Bradley; Park, Hyoungjun; Chattopadhyay, Shrikanta; McPhie, Donna; Öngür, Dost; Cohen, Bruce M.; Clish, Clary B.; Karmacharya, Rakesh

    2016-01-01

    Many studies suggest the presence of aberrations in cellular metabolism in bipolar disorder. We studied the metabolome in bipolar disorder to gain insight into cellular pathways that may be dysregulated in bipolar disorder and to discover evidence of novel biomarkers. We measured polar and nonpolar metabolites in fibroblasts from subjects with bipolar I disorder and matched healthy control subjects, under normal conditions and with two physiologic perturbations: low-glucose media and exposure to the stress-mediating hormone dexamethasone. Metabolites that were significantly different between bipolar and control subjects showed distinct separation by principal components analysis methods. The most statistically significant findings were observed in the perturbation experiments. The metabolite with the lowest p value in both the low-glucose and dexamethasone experiments was α-aminoadipate, whose intracellular level was consistently lower in bipolar subjects. Our study implicates α-aminoadipate as a possible biomarker in bipolar disorder that manifests under cellular stress. This is an intriguing finding given the known role of α-aminoadipate in the modulation of kynurenic acid in the brain, especially as abnormal kynurenic acid levels have been implicated in bipolar disorder. PMID:27606323

  12. Metabolite Profiling of Eastern Teaberry (Gaultheria procumbens L. Lipophilic Leaf Extracts with Hyaluronidase and Lipoxygenase Inhibitory Activity

    Directory of Open Access Journals (Sweden)

    Piotr Michel

    2017-03-01

    Full Text Available The phytochemical profile and anti-inflammatory activity of Gaultheria procumbens dry lipophilic leaf extracts were evaluated. Forty compounds were identified by GC-MS, representing 86.36% and 81.97% of the petroleum ether (PE and chloroform (CHE extracts, respectively, with ursolic acid (28.82%, oleanolic acid (10.11%, methyl benzoate (10.03%, and methyl salicylate (6.88% dominating in CHE, and methyl benzoate (21.59%, docosane (18.86%, and octacosane (11.72% prevailing in PE. Three components of CHE were fully identified after flash chromatography isolation and spectroscopic studies as (6S,9R-vomifoliol (4.35%, 8-demethyl-latifolin (1.13%, and 8-demethylsideroxylin (2.25%. Hyaluronidase and lipoxygenase inhibitory activity was tested for CHE (IC50 = 282.15 ± 10.38 μg/mL and 899.97 ± 31.17 μg/mL, respectively, PE (IC50 = 401.82 ± 16.12 μg/mL and 738.49 ± 15.92 μg/mL, and nine of the main constituents versus heparin (IC50 = 366.24 ± 14.72 μg/mL and indomethacin (IC50 = 92.60 ± 3.71 μg/mL as positive controls. With the best activity/concentration relationships, ursolic and oleanolic acids were recommended as analytical markers for the extracts and plant material. Seasonal variation of both markers following foliar development was investigated by UHPLC-PDA. The highest levels of ursolic (5.36–5.87 mg/g DW of the leaves and oleanolic (1.14–1.26 mg/g DW acids were observed between August and October, indicating the optimal season for harvesting.

  13. Profiling of engineering hotspots identifies an allosteric CRISPR-Cas9 switch.

    Science.gov (United States)

    Oakes, Benjamin L; Nadler, Dana C; Flamholz, Avi; Fellmann, Christof; Staahl, Brett T; Doudna, Jennifer A; Savage, David F

    2016-06-01

    The clustered, regularly interspaced, short palindromic repeats (CRISPR)-associated protein Cas9 from Streptococcus pyogenes is an RNA-guided DNA endonuclease with widespread utility for genome modification. However, the structural constraints limiting the engineering of Cas9 have not been determined. Here we experimentally profile Cas9 using randomized insertional mutagenesis and delineate hotspots in the structure capable of tolerating insertions of a PDZ domain without disruption of the enzyme's binding and cleavage functions. Orthogonal domains or combinations of domains can be inserted into the identified sites with minimal functional consequence. To illustrate the utility of the identified sites, we construct an allosterically regulated Cas9 by insertion of the estrogen receptor-α ligand-binding domain. This protein showed robust, ligand-dependent activation in prokaryotic and eukaryotic cells, establishing a versatile one-component system for inducible and reversible Cas9 activation. Thus, domain insertion profiling facilitates the rapid generation of new Cas9 functionalities and provides useful data for future engineering of Cas9.

  14. Methods for simultaneously identifying coherent local clusters with smooth global patterns in gene expression profiles

    Directory of Open Access Journals (Sweden)

    Lee Yun-Shien

    2008-03-01

    Full Text Available Abstract Background The hierarchical clustering tree (HCT with a dendrogram 1 and the singular value decomposition (SVD with a dimension-reduced representative map 2 are popular methods for two-way sorting the gene-by-array matrix map employed in gene expression profiling. While HCT dendrograms tend to optimize local coherent clustering patterns, SVD leading eigenvectors usually identify better global grouping and transitional structures. Results This study proposes a flipping mechanism for a conventional agglomerative HCT using a rank-two ellipse (R2E, an improved SVD algorithm for sorting purpose seriation by Chen 3 as an external reference. While HCTs always produce permutations with good local behaviour, the rank-two ellipse seriation gives the best global grouping patterns and smooth transitional trends. The resulting algorithm automatically integrates the desirable properties of each method so that users have access to a clustering and visualization environment for gene expression profiles that preserves coherent local clusters and identifies global grouping trends. Conclusion We demonstrate, through four examples, that the proposed method not only possesses better numerical and statistical properties, it also provides more meaningful biomedical insights than other sorting algorithms. We suggest that sorted proximity matrices for genes and arrays, in addition to the gene-by-array expression matrix, can greatly aid in the search for comprehensive understanding of gene expression structures. Software for the proposed methods can be obtained at http://gap.stat.sinica.edu.tw/Software/GAP.

  15. Profiling of engineering hotspots identifies an allosteric CRISPR-Cas9 switch

    Science.gov (United States)

    Oakes, Benjamin L; Nadler, Dana C.; Flamholz, Avi; Fellmann, Christof; Staahl, Brett T.; Doudna, Jennifer A.; Savage, David F.

    2016-01-01

    The CRISPR-associated protein Cas9 from Streptococcus pyogenes is an RNA-guided DNA endonuclease with widespread utility for genome modification. However, the structural constraints limiting the engineering of Cas9 have not been determined. Here we experimentally profile Cas9 using randomized insertional mutagenesis and delineate hotspots in the structure capable of tolerating insertions of a PDZ domain without disrupting the enzyme’s binding and cleavage functions. Orthogonal domains or combinations of domains can be inserted into the identified sites with minimal functional consequence. To illustrate the utility of the identified sites, we construct an allosterically regulated Cas9 by insertion of the Estrogen Receptor α Ligand Binding Domain. This protein displayed robust, ligand-dependent activation in prokaryotic and eukaryotic cells, establishing a versatile one-component system for inducible and reversible Cas9 activation. Thus, domain insertion profiling facilitates the rapid generation of new Cas9 functionalities and provides useful data for future engineering of Cas9. PMID:27136077

  16. Preparative mass-spectrometry profiling of bioactive metabolites in Saudi-Arabian propolis fractionated by high-speed countercurrent chromatography and off-line atmospheric pressure chemical ionization mass-spectrometry injection.

    Science.gov (United States)

    Jerz, Gerold; Elnakady, Yasser A; Braun, André; Jäckel, Kristin; Sasse, Florenz; Al Ghamdi, Ahmad A; Omar, Mohamed O M; Winterhalter, Peter

    2014-06-20

    Propolis is a glue material collected by honeybees which is used to seal cracks in beehives and to protect the bee population from infections. Propolis resins have a long history in medicinal use as a natural remedy. The multiple biological properties are related to variations in their chemical compositions. Geographical settings and availability of plant sources are important factors for the occurrence of specific natural products in propolis. A propolis ethylacetate extract (800mg) from Saudi Arabia (Al-Baha region) was separated by preparative scale high-speed countercurrent chromatography (HSCCC) using a non-aqueous solvent system n-hexane-ACN (1:1, v/v). For multiple metabolite detection, the resulting HSCCC-fractions were sequentially injected off-line into an atmospheric pressure chemical ionization mass-spectrometry (APCI-MS/MS) device, and a reconstituted mass spectrometry profile of the preparative run was visualized by selected ion traces. Best ion-intensities for detected compounds were obtained in the negative APCI mode and monitored occurring co-elution effects. HSCCC and successive purification steps resulted in the isolation and characterization of various bioactive natural products such as (12E)- and (12Z)-communic acid, sandaracopimaric acid, (+)-ferruginol, (+)-totarol, and 3β-acetoxy-19(29)-taraxasten-20a-ol using EI-, APCI-MS and 1D/2D-NMR. Cycloartenol-derivatives and triterpene acetates were isolated in mixtures and elucidated by EI-MS and 1D-NMR. Free fatty acids, and two labdane fatty acid esters were identified by APCI-MS/MS. In total 19 metabolites have been identified. The novel combination of HSCCC fractionation, and APCI-MS-target-guided molecular mass profiling improve efficiency of lead-structure identification. Copyright © 2014 Elsevier B.V. All rights reserved.

  17. Mass spectrometric characterization of urinary metabolites of the selective androgen receptor modulator S-22 to identify potential targets for routine doping controls.

    Science.gov (United States)

    Thevis, Mario; Thomas, Andreas; Möller, Ines; Geyer, Hans; Dalton, James T; Schänzer, Wilhelm

    2011-08-15

    Drugs that promote anabolic processes with limited undesirable effects are of considerable therapeutic interest; some notable examples include those for the treatment of cancer cachexia and muscle-wasting diseases. Anabolic properties are not only therapeutically beneficial to critically ill and debilitated patients, but are also desirable to athletes seeking artificial enhancements in endurance, strength and accelerated recovery. The use of anabolic agents in the clinical setting is being reconsidered with the emergence of a new class of drugs referred to as SARMs (selective androgen receptor modulators). SARMs have the potential to complement or even replace anabolic androgenic steroidal use with the benefit of a reduction of the undesirable side effects associated with steroid administration alone. Arylpropionamide-based SARMs such as andarine (S-4) and S-22 have shown promising therapeutic properties and have attracted the interest of elite and amateur athletes despite the absence of clinical approval, and evidence for trafficking and misuse in sport has been obtained by doping control authorities. In this communication, the elucidation of urinary metabolites of the SARM drug candidate S-22 is compared with earlier in vitro metabolism studies. Following oral administration of illicit S-22, urine samples were collected after 62 and 135 h and analyzed for the active drug and its major metabolic products. Liquid chromatography interfaced with high-resolution/high-accuracy (tandem) mass spectrometry was used to identify and/or confirm the predicted target analytes for sports drug testing purposes. S-22 was detected in both specimens accompanied by its glucuronic acid conjugate. This was the B-ring hydroxylated derivative of S-22 plus the corresponding glucuronide (with the phase-II metabolites being the more abundant analytes). In addition, the samples collected 62 h post-administration also contained the phase-I metabolite hydroxylated at the methyl residue (C-20

  18. Expression profiling of rainbow trout testis development identifies evolutionary conserved genes involved in spermatogenesis

    Directory of Open Access Journals (Sweden)

    Esquerré Diane

    2009-11-01

    Full Text Available Abstract Background Spermatogenesis is a late developmental process that involves a coordinated expression program in germ cells and a permanent communication between the testicular somatic cells and the germ-line. Current knowledge regarding molecular factors driving male germ cell proliferation and differentiation in vertebrates is still limited and mainly based on existing data from rodents and human. Fish with a marked reproductive cycle and a germ cell development in synchronous cysts have proven to be choice models to study precise stages of the spermatogenetic development and the germ cell-somatic cell communication network. In this study we used 9K cDNA microarrays to investigate the expression profiles underlying testis maturation during the male reproductive cycle of the trout, Oncorhynchus mykiss. Results Using total testis samples at various developmental stages and isolated spermatogonia, spermatocytes and spermatids, 3379 differentially expressed trout cDNAs were identified and their gene activation or repression patterns throughout the reproductive cycle were reported. We also performed a tissue-profiling analysis and highlighted many genes for which expression signals were restricted to the testes or gonads from both sexes. The search for orthologous genes in genome-sequenced fish species and the use of their mammalian orthologs allowed us to provide accurate annotations for trout cDNAs. The analysis of the GeneOntology terms therefore validated and broadened our interpretation of expression clusters by highlighting enriched functions that are consistent with known sequential events during male gametogenesis. Furthermore, we compared expression profiles of trout and mouse orthologs and identified a complement of genes for which expression during spermatogenesis was maintained throughout evolution. Conclusion A comprehensive study of gene expression and associated functions during testis maturation and germ cell differentiation in

  19. Gene expression profiling in whole blood identifies distinct biological pathways associated with obesity

    Directory of Open Access Journals (Sweden)

    Gorman Shelby A

    2010-12-01

    Full Text Available Abstract Background Obesity is reaching epidemic proportions and represents a significant risk factor for cardiovascular disease, diabetes, and cancer. Methods To explore the relationship between increased body mass and gene expression in blood, we conducted whole-genome expression profiling of whole blood from seventeen obese and seventeen well matched lean subjects. Gene expression data was analyzed at the individual gene and pathway level and a preliminary assessment of the predictive value of blood gene expression profiles in obesity was carried out. Results Principal components analysis of whole-blood gene expression data from obese and lean subjects led to efficient separation of the two cohorts. Pathway analysis by gene-set enrichment demonstrated increased transcript levels for genes belonging to the "ribosome", "apoptosis" and "oxidative phosphorylation" pathways in the obese cohort, consistent with an altered metabolic state including increased protein synthesis, enhanced cell death from proinflammatory or lipotoxic stimuli, and increased energy demands. A subset of pathway-specific genes acted as efficient predictors of obese or lean class membership when used in Naive Bayes or logistic regression based classifiers. Conclusion This study provides a comprehensive characterization of the whole blood transcriptome in obesity and demonstrates that the investigation of gene expression profiles from whole blood can inform and illustrate the biological processes related to regulation of body mass. Additionally, the ability of pathway-related gene expression to predict class membership suggests the feasibility of a similar approach for identifying clinically useful blood-based predictors of weight loss success following dietary or surgical interventions.

  20. Transcriptional profiling identifies physicochemical properties of nanomaterials that are determinants of the in vivo pulmonary response.

    Science.gov (United States)

    Halappanavar, Sabina; Saber, Anne Thoustrup; Decan, Nathalie; Jensen, Keld Alstrup; Wu, Dongmei; Jacobsen, Nicklas Raun; Guo, Charles; Rogowski, Jacob; Koponen, Ismo K; Levin, Marcus; Madsen, Anne Mette; Atluri, Rambabu; Snitka, Valentinas; Birkedal, Renie K; Rickerby, David; Williams, Andrew; Wallin, Håkan; Yauk, Carole L; Vogel, Ulla

    2015-03-01

    We applied transcriptional profiling to elucidate the mechanisms associated with pulmonary responses to titanium dioxide (TiO2 ) nanoparticles (NPs) of different sizes and surface coatings, and to determine if these responses are modified by NP size, surface area, surface modification, and embedding in paint matrices. Adult C57BL/6 mice were exposed via single intratracheal instillations to free forms of TiO2 NPs (10, 20.6, or 38 nm in diameter) with different surface coatings, or TiO2 NPs embedded in paint matrices. Controls were exposed to dispersion medium devoid of NPs. TiO2 NPs were characterized for size, surface area, chemical impurities, and agglomeration state in the exposure medium. Pulmonary transcriptional profiles were generated using microarrays from tissues collected one and 28 d postexposure. Property-specific pathway effects were identified. Pulmonary protein levels of specific inflammatory cytokines and chemokines were confirmed by ELISA. The data were collapsed to 659 differentially expressed genes (P ≤ 0.05; fold change ≥ 1.5). Unsupervised hierarchical clustering of these genes revealed that TiO2 NPs clustered mainly by postexposure timepoint followed by particle type. A pathway-based meta-analysis showed that the combination of smaller size, large deposited surface area, and surface amidation contributes to TiO2 NP gene expression response. Embedding of TiO2 NP in paint dampens the overall transcriptional effects. The magnitude of the expression changes associated with pulmonary inflammation differed across all particles; however, the underlying pathway perturbations leading to inflammation were similar, suggesting a generalized mechanism-of-action for all TiO2 NPs. Thus, transcriptional profiling is an effective tool to determine the property-specific biological/toxicity responses induced by nanomaterials. © 2014 Wiley Periodicals, Inc.

  1. Metabolite Profiling Reveals the Effect of Dietary Rubus coreanus Vinegar on Ovariectomy-Induced Osteoporosis in a Rat Model.

    Science.gov (United States)

    Lee, Mee Youn; Kim, Hyang Yeon; Singh, Digar; Yeo, Soo Hwan; Baek, Seong Yeol; Park, Yoo Kyoung; Lee, Choong Hwan

    2016-01-26

    The study was aimed at exploring the curative effects of Rubus coreanus (RC) vinegar against postmenopausal osteoporosis by using ovariectomized rats as a model. The investigations were performed in five groups: sham, ovariectomized (OVX) rats without treatment, low-dose RC vinegar (LRV)-treated OVX rats, high-dose RC vinegar (HRV)-treated OVX rats and alendronate (ALEN)-treated OVX rats. The efficacy of RC vinegar was evaluated using physical, biochemical, histological and metabolomic parameters. Compared to the OVX rats, the LRV and HRV groups showed positive effects on the aforementioned parameters, indicating estrogen regulation. Plasma metabolome analysis of the groups using gas chromatography-time of flight mass spectrometry (GC-TOF-MS) and ultra-performance liquid chromatography quadrupole-TOF-MS (UPLC-Q-TOF-MS) with multivariate analysis revealed 19 and 16 metabolites, respectively. Notably, the levels of butyric acid, phenylalanine, glucose, tryptophan and some lysophosphatidylcholines were marginally increased in RC vinegar-treated groups compared to OVX. However, the pattern of metabolite levels in RC vinegar-treated groups was found similar to ALEN, but differed significantly from that in sham group. The results highlight the prophylactic and curative potential of dietary vinegar against postmenopausal osteoporosis. RC vinegar could be an effective natural alternative for the prevention of postmenopausal osteoporosis.

  2. Quantitative determination of five metabolites of aspirin by UHPLC-MS/MS coupled with enzymatic reaction and its application to evaluate the effects of aspirin dosage on the metabolic profile.

    Science.gov (United States)

    Li, Jian-Ping; Guo, Jian-Ming; Shang, Er-Xin; Zhu, Zhen-Hua; Liu, Yang; Zhao, Bu-Chang; Zhao, Jing; Tang, Zhi-Shu; Duan, Jin-Ao

    2017-05-10

    Acetylsalicylic acid (Aspirin, ASA) is a famous drug for cardiovascular diseases in recent years. Effects of ASA dosage on the metabolic profile have not been fully understood. The purpose of our study is to establish a rapid and reliable method to quantify ASA metabolites in biological matrices, especially for glucuronide metabolites whose standards are not commercially available. Then we applied this method to evaluate the effects of ASA dosage on the metabolic and excretion profile of ASA metabolites in rat urine. Salicylic acid (SA), gentisic acid (GA) and salicyluric acid (SUA) were determined directly by UHPLC-MS/MS, while salicyl phenolic glucuronide (SAPG) and salicyluric acid phenolic glucuronide (SUAPG) were quantified indirectly by measuring the released SA and SUA from SAPG and SUAPG after β-glucuronidase digestion. SUA and SUAPG were the major metabolites of ASA in rat urine 24h after ASA administration, which accounted for 50% (SUA) and 26% (SUAPG). When ASA dosage was increased, the contributions dropped to 32% and 18%, respectively. The excretion of other three metabolites (GA, SA and SAPG) however showed remarkable increases by 16%, 6% and 4%, respectively. In addition, SUA and SUAPG were mainly excreted in the time period of 12-24h, while GA was excreted in the earlier time periods (0-4h and 4-8h). SA was mainly excreted in the time period of 0-4h and 12-24h. And the excretion of SAPG was equally distributed in the four time periods. We went further to show that the excretion of five metabolites in rat urine was delayed when ASA dosage was increased. In conclusion, we have developed a rapid and sensitive method to determine the five ASA metabolites (SA, GA, SUA, SAPG and SUAPG) in rat urine. We showed that ASA dosage could significantly influence the metabolic and excretion profile of ASA metabolites in rat urine. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. Identifying at-risk profiles and protective factors for problem gambling: A longitudinal study across adolescence and early adulthood.

    Science.gov (United States)

    Allami, Youssef; Vitaro, Frank; Brendgen, Mara; Carbonneau, René; Tremblay, Richard E

    2018-03-19

    Past studies have identified various risk and protective factors for problem gambling (PG). However, no study has examined the interplay between these factors using a combination of person-centered and variable-centered approaches embedded within a longitudinal design. The present study aimed to (a) identify distinct profiles in early adolescence based on a set of risk factors commonly associated with PG (impulsivity, depression, anxiety, drug-alcohol use, aggressiveness, and antisociality), (b) explore the difference in reported gambling problems between these profiles during midadolescence and early adulthood, and (c) identify family- and peer-related variables that could operate as protective or compensatory factors in this context. Two samples were used: (a) a population sample (N = 1,033) living in low socioeconomic-status neighborhoods and (b) a population sample (N = 3,017) representative of students attending Quebec schools. Latent profile analyses were conducted to identify at-risk profiles based on individual risk factors measured at age 12 years. Negative binomial regression models were estimated to compare profiles in terms of their reported gambling problems at ages 16 and 23. Finally, family- and peer-related variables measured at age 14 were included to test their protective or compensatory role with respect to the link between at-risk profiles and gambling problems. Four profiles were identified: well-adjusted, internalizing, externalizing, and comorbid. Compared to the well-adjusted profile, the externalizing and comorbid profiles reported more gambling problems at ages 16 and 23, but the internalizing profile did not differ significantly. Various protective and compensatory factors emerged for each profile at both time points. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

  4. Identifying 'unhealthy' food advertising on television: a case study applying the UK Nutrient Profile model.

    Science.gov (United States)

    Jenkin, Gabrielle; Wilson, Nick; Hermanson, Nicole

    2009-05-01

    To evaluate the feasibility of the UK Nutrient Profile (NP) model for identifying 'unhealthy' food advertisements using a case study of New Zealand television advertisements. Four weeks of weekday television from 15.30 hours to 18.30 hours was videotaped from a state-owned (free-to-air) television channel popular with children. Food advertisements were identified and their nutritional information collected in accordance with the requirements of the NP model. Nutrient information was obtained from a variety of sources including food labels, company websites and a national nutritional database. From the 60 h sample of weekday afternoon television, there were 1893 advertisements, of which 483 were for food products or retailers. After applying the NP model, 66 % of these were classified as advertising high-fat, high-salt and high-sugar (HFSS) foods; 28 % were classified as advertising non-HFSS foods; and the remaining 2 % were unclassifiable. More than half (53 %) of the HFSS food advertisements were for 'mixed meal' items promoted by major fast-food franchises. The advertising of non-HFSS food was sparse, covering a narrow range of food groups, with no advertisements for fresh fruit or vegetables. Despite the NP model having some design limitations in classifying real-world televised food advertisements, it was easily applied to this sample and could clearly identify HFSS products. Policy makers who do not wish to completely restrict food advertising to children outright should consider using this NP model for regulating food advertising.

  5. MicroRNA Expression Profiling Identifies Molecular Diagnostic Signatures for Anaplastic Large Cell Lymphoma

    DEFF Research Database (Denmark)

    Liu, Cuiling; Iqbal, Javeed; Teruya-Feldstein, Julie

    2013-01-01

    Anaplastic large-cell lymphomas (ALCLs) encompass at least 2 systemic diseases distinguished by the presence or absence of anaplastic lymphoma kinase (ALK) expression. We performed genome-wide microRNA (miRNA) profiling on 33 ALK-positive (ALK[+]) ALCLs, 25 ALK-negative (ALK[-]) ALCLs, 9......) that differentiates ALK(-) ALCL from other PTCLs. Our in vitro studies identified a set of 32 miRNAs associated with ALK expression. Of these, the miR-17∼92 cluster and its paralogues were also highly expressed in ALK(+) ALCL and may represent important downstream effectors of the ALK oncogenic pathway....... angioimmunoblastic T-cell lymphomas, 11 peripheral T-cell lymphomas not otherwise specified (PTCLNOS), and normal T cells, and demonstrated that ALCLs express many of the miRNAs that are highly expressed in normal T cells with the prominent exception of miR-146a. Unsupervised hierarchical clustering demonstrated...

  6. Identification of discriminant proteins through antibody profiling, methods and apparatus for identifying an individual

    Science.gov (United States)

    Thompson, Vicki S; Lacey, Jeffrey A; Gentillon, Cynthia A; Apel, William A

    2015-03-03

    A method for determining a plurality of proteins for discriminating and positively identifying an individual based from a biological sample. The method may include profiling a biological sample from a plurality of individuals against a protein array including a plurality of proteins. The protein array may include proteins attached to a support in a preselected pattern such that locations of the proteins are known. The biological sample may be contacted with the protein array such that a portion of antibodies in the biological sample reacts with and binds to the proteins forming immune complexes. A statistical analysis method, such as discriminant analysis, may be performed to determine discriminating proteins for distinguishing individuals. Proteins of interest may be used to form a protein array. Such a protein array may be used, for example, to compare a forensic sample from an unknown source with a sample from a known source.

  7. Integrated genomic and gene expression profiling identifies two major genomic circuits in urothelial carcinoma.

    Directory of Open Access Journals (Sweden)

    David Lindgren

    Full Text Available Similar to other malignancies, urothelial carcinoma (UC is characterized by specific recurrent chromosomal aberrations and gene mutations. However, the interconnection between specific genomic alterations, and how patterns of chromosomal alterations adhere to different molecular subgroups of UC, is less clear. We applied tiling resolution array CGH to 146 cases of UC and identified a number of regions harboring recurrent focal genomic amplifications and deletions. Several potential oncogenes were included in the amplified regions, including known oncogenes like E2F3, CCND1, and CCNE1, as well as new candidate genes, such as SETDB1 (1q21, and BCL2L1 (20q11. We next combined genome profiling with global gene expression, gene mutation, and protein expression data and identified two major genomic circuits operating in urothelial carcinoma. The first circuit was characterized by FGFR3 alterations, overexpression of CCND1, and 9q and CDKN2A deletions. The second circuit was defined by E3F3 amplifications and RB1 deletions, as well as gains of 5p, deletions at PTEN and 2q36, 16q, 20q, and elevated CDKN2A levels. TP53/MDM2 alterations were common for advanced tumors within the two circuits. Our data also suggest a possible RAS/RAF circuit. The tumors with worst prognosis showed a gene expression profile that indicated a keratinized phenotype. Taken together, our integrative approach revealed at least two separate networks of genomic alterations linked to the molecular diversity seen in UC, and that these circuits may reflect distinct pathways of tumor development.

  8. Genome-wide DNA methylation profile analysis identifies differentially methylated loci associated with ankylosis spondylitis.

    Science.gov (United States)

    Hao, Jiangcan; Liu, Yang; Xu, Jiawen; Wang, Wenyu; Wen, Yan; He, Awen; Fan, Qianrui; Guo, Xiong; Zhang, Feng

    2017-07-25

    Ankylosing spondylitis (AS) is a chronic rheumatic and autoimmune disease. Little is known about the potential role of DNA methylation in the pathogenesis of AS. This study was undertaken to explore the potential role of DNA methylation in the genetic mechanism of AS. In this study, we compared the genome-wide DNA methylation profiles of peripheral blood mononuclear cells (PBMCs) between five AS patients and five healthy subjects, using the Illumina Infinium HumanMethylation450 BeadChip. Quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR) was performed to validate the relevance of the identified differentially methylated genes for AS, using another independent sample of five AS patients and five healthy subjects. Compared with healthy controls, we detected 1915 differentially methylated CpG sites mapped to 1214 genes. The HLA-DQB1 gene achieved the most significant signal (cg14323910, adjusted P = 1.84 × 10 -6 , β difference = 0.5634) for AS. Additionally, the CpG site cg04777551 of HLA-DQB1 presented a suggestive association with AS (adjusted P = 1.46 × 10 -3 , β difference = 0.3594). qRT-PCR observed that the mRNA expression level of HLA-DQB1 in AS PBMCs was significantly lower than that in healthy control PBMCs (ratio = 0.48 ± 0.10, P pathway enrichment analysis of differentially methylated genes identified four GO terms and 10 pathways for AS, functionally related to antigen dynamics and function. Our results demonstrated the altered DNA methylation profile of AS and implicated HLA-DQB1 in the development of AS.

  9. GC-MS Metabolite Profiling of Extreme Southern Pinot noir Wines: Effects of Vintage, Barrel Maturation, and Fermentation Dominate over Vineyard Site and Clone Selection.

    Science.gov (United States)

    Schueuermann, Claudia; Khakimov, Bekzod; Engelsen, Søren Balling; Bremer, Phil; Silcock, Patrick

    2016-03-23

    Wine is an extremely complex beverage that contains a multitude of volatile and nonvolatile compounds. This study investiged the effect of vineyard site and grapevine clone on the volatile profiles of commercially produced Pinot noir wines from central Otago, New Zealand. Volatile metabolites in Pinot noir wines produced from five grapevine clones grown on six vineyard sites in close proximity, over two consecutive vintages, were surveyed using gas chromatography-mass spectrometry (GC-MS). The raw GC-MS data were processed using parallel factor analysis (PARAFAC2), and final metabolite data were analyzed by principal component analysis (PCA). Winemaking conditions, vintage, and barrel maturation were found to be the most dominant factors. The effects of vineyard site and clone were mostly vintage dependent. Although four compounds including β-citronellol, homovanillyl alcohol, N-(3-methylbutyl)acetamide, and N-(2-phenylethyl)acetamide discriminated the vineyard sites independent of vintage, Pinot noir wines from different clones were only partially discriminated by PCA, and marker compound selection remained challenging.

  10. Identifying patterns in treatment response profiles in acute bipolar mania: a cluster analysis approach

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    Houston John P

    2008-07-01

    Full Text Available Abstract Background Patients with acute mania respond differentially to treatment and, in many cases, fail to obtain or sustain symptom remission. The objective of this exploratory analysis was to characterize response in bipolar disorder by identifying groups of patients with similar manic symptom response profiles. Methods Patients (n = 222 were selected from a randomized, double-blind study of treatment with olanzapine or divalproex in bipolar I disorder, manic or mixed episode, with or without psychotic features. Hierarchical clustering based on Ward's distance was used to identify groups of patients based on Young-Mania Rating Scale (YMRS total scores at each of 5 assessments over 7 weeks. Logistic regression was used to identify baseline predictors for clusters of interest. Results Four distinct clusters of patients were identified: Cluster 1 (n = 64: patients did not maintain a response (YMRS total scores ≤ 12; Cluster 2 (n = 92: patients responded rapidly (within less than a week and response was maintained; Cluster 3 (n = 36: patients responded rapidly but relapsed soon afterwards (YMRS ≥ 15; Cluster 4 (n = 30: patients responded slowly (≥ 2 weeks and response was maintained. Predictive models using baseline variables found YMRS Item 10 (Appearance, and psychosis to be significant predictors for Clusters 1 and 4 vs. Clusters 2 and 3, but none of the baseline characteristics allowed discriminating between Clusters 1 vs. 4. Experiencing a mixed episode at baseline predicted membership in Clusters 2 and 3 vs. Clusters 1 and 4. Treatment with divalproex, larger number of previous manic episodes, lack of disruptive-aggressive behavior, and more prominent depressive symptoms at baseline were predictors for Cluster 3 vs. 2. Conclusion Distinct treatment response profiles can be predicted by clinical features at baseline. The presence of these features as potential risk factors for relapse in patients who have responded to treatment

  11. Amyloid β42 peptide is toxic to non-neural cells in Drosophila yielding a characteristic metabolite profile and the effect can be suppressed by PI3K

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    Mercedes Arnés

    2017-11-01

    Full Text Available The human Aβ42 peptide is associated with Alzheimer's disease through its deleterious effects in neurons. Expressing the human peptide in adult Drosophila in a tissue- and time-controlled manner, we show that Aβ42 is also toxic in non-neural cells, neurosecretory and epithelial cell types in particular. This form of toxicity includes the aberrant signaling by Wingless morphogen leading to the eventual activation of Caspase 3. Preventing Caspase 3 activation by means of p53 keeps epithelial cells from elimination but maintains the Aβ42 toxicity yielding more severe deleterious effects to the organism. Metabolic profiling by nuclear magnetic resonance (NMR of adult flies at selected ages post Aβ42 expression onset reveals characteristic changes in metabolites as early markers of the pathological process. All morphological and most metabolic features of Aβ42 toxicity can be suppressed by the joint overexpression of PI3K.

  12. HPLC-PAD-atmospheric pressure chemical ionization-MS metabolite profiling of cytotoxic carotenoids from the echinoderm Marthasterias glacialis (spiny sea-star).

    Science.gov (United States)

    Ferreres, Federico; Pereira, David M; Gil-Izquierdo, Angel; Valentão, Patrícia; Botelho, João; Mouga, Teresa; Andrade, Paula B

    2010-08-01

    An HPLC-PAD-atmospheric pressure chemical ionization-MS metabolite profiling analysis was conducted on the marine echinoderm Marthasterias glacialis (spiny sea-star). Bio-guided purification of the methanolic extract led to the isolation of several carotenoids, namely zeaxanthin, astaxanthin and lutein. These compounds were characterized using both UV-Vis characteristics and MS spectra interpretation. No previous works addressed the MS analysis of carotenoids present in this organism. The purified carotenoid fraction displayed a strong cell proliferation inhibition against rat basophilic leukemia RBL-2H3 (IC(25)=268 microg/mL) cancer cell line. Against healthy V79 (rat lung fibroblasts (IC(25)=411 microg/mL)) cell line, however, toxicity was lower, as it is desired for anti-cancer molecules. This study suggests that M. glacialis may constitute a good source of bioactive compounds that can be used as lead compounds for the pharmaceutical industry.

  13. New metabolites of hongdenafil, homosildenafil and hydroxyhomosildenafil.

    Science.gov (United States)

    Yeo, Miseon; Park, Yujin; Lee, Heesang; Choe, Sanggil; Baek, Seung-Hoon; Kim, Hye Kyung; Pyo, Jae Sung

    2018-02-05

    Recently, illegal sildenafil analogues have emerged, causing serious social issues. In spite of the importance of sildenafil analogues, their metabolic profiles or clinical effects have not been reported yet. In this study, new metabolites of illegal sildenafil analogues such as hongdenafil, homosildenafil, and hydroxyhomosildenafil were determined using liquid chromatography quadrupole-time of flight mass spectrometry (LC-Q-TOF-MS) and tandem mass spectrometry (LC-Q-TOF-MS/MS). To prepare metabolic samples, in vitro and in vivo studies were performed. For in vivo metabolites analysis, urine and feces samples of rats treated with sildenafil analogues were analyzed. For in vitro metabolites analysis, human liver microsomes incubated with sildenafil analogues were extracted and analyzed. All metabolites were characterized by LC-Q-TOF-MS and LC-Q-TOF-MS/MS. As a result, five, six, and seven metabolites were determined in hongdenafil, homosildenafil, and hydroxyhomosildenafil treated samples, respectively. These results could be applied to forensic science and other analytical fields. Moreover, these newly identified metabolites could be used as fundamental data to determine the side effect and toxicity of illegal sildenafil analogues. Copyright © 2017 Elsevier B.V. All rights reserved.

  14. Comparing cancer vs normal gene expression profiles identifies new disease entities and common transcriptional programs in AML patients

    DEFF Research Database (Denmark)

    Rapin, Nicolas; Bagger, Frederik Otzen; Jendholm, Johan

    2014-01-01

    Gene expression profiling has been used extensively to characterize cancer, identify novel subtypes, and improve patient stratification. However, it has largely failed to identify transcriptional programs that differ between cancer and corresponding normal cells and has not been efficient in iden......-karyotype AML, which allowed for the generation of a highly prognostic survival signature. Collectively, our CvN method holds great potential as a tool for the analysis of gene expression profiles of cancer patients....

  15. Comparative expression profiling identifies differential roles for Myogenin and p38α MAPK signaling in myogenesis.

    Science.gov (United States)

    Liu, Qi-Cai; Zha, Xiao-Hui; Faralli, Hervé; Yin, Hang; Louis-Jeune, Caroline; Perdiguero, Eusebio; Pranckeviciene, Erinija; Muñoz-Cànoves, Pura; Rudnicki, Michael A; Brand, Marjorie; Perez-Iratxeta, Carol; Dilworth, F Jeffrey

    2012-12-01

    Skeletal muscle differentiation is mediated by a complex gene expression program requiring both the muscle-specific transcription factor Myogenin (Myog) and p38α MAPK (p38α) signaling. However, the relative contribution of Myog and p38α to the formation of mature myotubes remains unknown. Here, we have uncoupled the activity of Myog from that of p38α to gain insight into the individual roles of these proteins in myogenesis. Comparative expression profiling confirmed that Myog activates the expression of genes involved in muscle function. Furthermore, we found that in the absence of p38α signaling, Myog expression leads to the down-regulation of genes involved in cell cycle progression. Consistent with this, the expression of Myog is sufficient to induce cell cycle exit. Interestingly, p38α-defective, Myog-expressing myoblasts fail to form multinucleated myotubes, suggesting an important role for p38α in cell fusion. Through the analysis of p38α up-regulated genes, the tetraspanin CD53 was identified as a candidate fusion protein, a role confirmed both ex vivo in primary myoblasts, and in vivo during myofiber regeneration in mice. Thus, our study has revealed an unexpected role for Myog in mediating cell cycle exit and has identified an essential role for p38α in cell fusion through the up-regulation of CD53.

  16. Transcriptome sequencing in pediatric acute lymphoblastic leukemia identifies fusion genes associated with distinct DNA methylation profiles.

    Science.gov (United States)

    Marincevic-Zuniga, Yanara; Dahlberg, Johan; Nilsson, Sara; Raine, Amanda; Nystedt, Sara; Lindqvist, Carl Mårten; Berglund, Eva C; Abrahamsson, Jonas; Cavelier, Lucia; Forestier, Erik; Heyman, Mats; Lönnerholm, Gudmar; Nordlund, Jessica; Syvänen, Ann-Christine

    2017-08-14

    Structural chromosomal rearrangements that lead to expressed fusion genes are a hallmark of acute lymphoblastic leukemia (ALL). In this study, we performed transcriptome sequencing of 134 primary ALL patient samples to comprehensively detect fusion transcripts. We combined fusion gene detection with genome-wide DNA methylation analysis, gene expression profiling, and targeted sequencing to determine molecular signatures of emerging ALL subtypes. We identified 64 unique fusion events distributed among 80 individual patients, of which over 50% have not previously been reported in ALL. Although the majority of the fusion genes were found only in a single patient, we identified several recurrent fusion gene families defined by promiscuous fusion gene partners, such as ETV6, RUNX1, PAX5, and ZNF384, or recurrent fusion genes, such as DUX4-IGH. Our data show that patients harboring these fusion genes displayed characteristic genome-wide DNA methylation and gene expression signatures in addition to distinct patterns in single nucleotide variants and recurrent copy number alterations. Our study delineates the fusion gene landscape in pediatric ALL, including both known and novel fusion genes, and highlights fusion gene families with shared molecular etiologies, which may provide additional information for prognosis and therapeutic options in the future.

  17. Transcriptome sequencing in pediatric acute lymphoblastic leukemia identifies fusion genes associated with distinct DNA methylation profiles

    Directory of Open Access Journals (Sweden)

    Yanara Marincevic-Zuniga

    2017-08-01

    Full Text Available Abstract Background Structural chromosomal rearrangements that lead to expressed fusion genes are a hallmark of acute lymphoblastic leukemia (ALL. In this study, we performed transcriptome sequencing of 134 primary ALL patient samples to comprehensively detect fusion transcripts. Methods We combined fusion gene detection with genome-wide DNA methylation analysis, gene expression profiling, and targeted sequencing to determine molecular signatures of emerging ALL subtypes. Results We identified 64 unique fusion events distributed among 80 individual patients, of which over 50% have not previously been reported in ALL. Although the majority of the fusion genes were found only in a single patient, we identified several recurrent fusion gene families defined by promiscuous fusion gene partners, such as ETV6, RUNX1, PAX5, and ZNF384, or recurrent fusion genes, such as DUX4-IGH. Our data show that patients harboring these fusion genes displayed characteristic genome-wide DNA methylation and gene expression signatures in addition to distinct patterns in single nucleotide variants and recurrent copy number alterations. Conclusion Our study delineates the fusion gene landscape in pediatric ALL, including both known and novel fusion genes, and highlights fusion gene families with shared molecular etiologies, which may provide additional information for prognosis and therapeutic options in the future.

  18. Transcript profiling of Elf5+/- mammary glands during pregnancy identifies novel targets of Elf5.

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    Renee L Rogers

    Full Text Available BACKGROUND: Elf5, an epithelial specific Ets transcription factor, plays a crucial role in the pregnancy-associated development of the mouse mammary gland. Elf5(-/- embryos do not survive, however the Elf5(+/- mammary gland displays a severe pregnancy-associated developmental defect. While it is known that Elf5 is crucial for correct mammary development and lactation, the molecular mechanisms employed by Elf5 to exert its effects on the mammary gland are largely unknown. PRINCIPAL FINDINGS: Transcript profiling was used to investigate the transcriptional changes that occur as a result of Elf5 haploinsufficiency in the Elf5(+/- mouse model. We show that the development of the mouse Elf5(+/- mammary gland is delayed at a transcriptional and morphological level, due to the delayed increase in Elf5 protein in these glands. We also identify a number of potential Elf5 target genes, including Mucin 4, whose expression, is directly regulated by the binding of Elf5 to an Ets binding site within its promoter. CONCLUSION: We identify novel transcriptional targets of Elf5 and show that Muc4 is a direct target of Elf5, further elucidating the mechanisms through which Elf5 regulates proliferation and differentiation in the mammary gland.

  19. The profiling and identification of chemical components, prototypes and metabolites of Run-zao-zhi-yang capsule in rat plasma, urine and bile by an UPLC-Q-TOF/MSE -based high throughput strategy.

    Science.gov (United States)

    Lin, Shan; Yue, Xinyi; Ouyang, Danwei; Li, Quan; Yang, Peiming

    2018-04-12

    Run-zao-zhi-yang (RZZY) capsule, a traditional Chinese medicine formula (TCMF), has been popularly used for the treatment of dermatitis and eczema. However, few studies have been carried out on RZZY and its metabolites. In this study, we developed a three-step strategy to rapidly characterize the chemical constituents and metabolites of RZZY by using ultra high performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry. A total of 41 chemical components were characterized from RZZY. Among which, there are 11 flavonoids, six alkaloids, six stilbene glycosides, five anthraquinones and 13 other compounds. In addition, 18 prototypes and 35 metabolites were detected in rat plasma, urine and bile. This study offers an applicable approach for high throughput profiling and identification of chemical components and metabolites derived from TCMF in vivo, and also provides essential data for exploring bioactive ingredients and action mechanisms of RZZY. This article is protected by copyright. All rights reserved.

  20. Transcriptome profiling of whole blood cells identifies PLEK2 and C1QB in human melanoma.

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    Yuchun Luo

    Full Text Available Developing analytical methodologies to identify biomarkers in easily accessible body fluids is highly valuable for the early diagnosis and management of cancer patients. Peripheral whole blood is a "nucleic acid-rich" and "inflammatory cell-rich" information reservoir and represents systemic processes altered by the presence of cancer cells.We conducted transcriptome profiling of whole blood cells from melanoma patients. To overcome challenges associated with blood-based transcriptome analysis, we used a PAXgene™ tube and NuGEN Ovation™ globin reduction system. The combined use of these systems in microarray resulted in the identification of 78 unique genes differentially expressed in the blood of melanoma patients. Of these, 68 genes were further analyzed by quantitative reverse transcriptase PCR using blood samples from 45 newly diagnosed melanoma patients (stage I to IV and 50 healthy control individuals. Thirty-nine genes were verified to be differentially expressed in blood samples from melanoma patients. A stepwise logit analysis selected eighteen 2-gene signatures that distinguish melanoma from healthy controls. Of these, a 2-gene signature consisting of PLEK2 and C1QB led to the best result that correctly classified 93.3% melanoma patients and 90% healthy controls. Both genes were upregulated in blood samples of melanoma patients from all stages. Further analysis using blood fractionation showed that CD45(- and CD45(+ populations were responsible for the altered expression levels of PLEK2 and C1QB, respectively.The current study provides the first analysis of whole blood-based transcriptome biomarkers for malignant melanoma. The expression of PLEK2, the strongest gene to classify melanoma patients, in CD45(- subsets illustrates the importance of analyzing whole blood cells for biomarker studies. The study suggests that transcriptome profiling of blood cells could be used for both early detection of melanoma and monitoring of patients

  1. Comprehensive Analysis of Gene Expression Profiles of Sepsis-Induced Multiorgan Failure Identified Its Valuable Biomarkers.

    Science.gov (United States)

    Wang, Yumei; Yin, Xiaoling; Yang, Fang

    2018-02-01

    Sepsis is an inflammatory-related disease, and severe sepsis would induce multiorgan dysfunction, which is the most common cause of death of patients in noncoronary intensive care units. Progression of novel therapeutic strategies has proven to be of little impact on the mortality of severe sepsis, and unfortunately, its mechanisms still remain poorly understood. In this study, we analyzed gene expression profiles of severe sepsis with failure of lung, kidney, and liver for the identification of potential biomarkers. We first downloaded the gene expression profiles from the Gene Expression Omnibus and performed preprocessing of raw microarray data sets and identification of differential expression genes (DEGs) through the R programming software; then, significantly enriched functions of DEGs in lung, kidney, and liver failure sepsis samples were obtained from the Database for Annotation, Visualization, and Integrated Discovery; finally, protein-protein interaction network was constructed for DEGs based on the STRING database, and network modules were also obtained through the MCODE cluster method. As a result, lung failure sepsis has the highest number of DEGs of 859, whereas the number of DEGs in kidney and liver failure sepsis samples is 178 and 175, respectively. In addition, 17 overlaps were obtained among the three lists of DEGs. Biological processes related to immune and inflammatory response were found to be significantly enriched in DEGs. Network and module analysis identified four gene clusters in which all or most of genes were upregulated. The expression changes of Icam1 and Socs3 were further validated through quantitative PCR analysis. This study should shed light on the development of sepsis and provide potential therapeutic targets for sepsis-induced multiorgan failure.

  2. Fatty acid metabolites in rapidly proliferating breast cancer.

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    Joseph T O'Flaherty

    Full Text Available Breast cancers that over-express a lipoxygenase or cyclooxygenase are associated with poor survival possibly because they overproduce metabolites that alter the cancer's malignant behaviors. However, these metabolites and behaviors have not been identified. We here identify which metabolites among those that stimulate breast cancer cell proliferation in vitro are associated with rapidly proliferating breast cancer.We used selective ion monitoring-mass spectrometry to quantify in the cancer and normal breast tissue of 27 patients metabolites that stimulate (15-, 12-, 5-hydroxy-, and 5-oxo-eicosatetraenoate, 13-hydroxy-octadecaenoate [HODE] or inhibit (prostaglandin [PG]E2 and D2 breast cancer cell proliferation. We then related their levels to each cancer's proliferation rate as defined by its Mib1 score.13-HODE was the only metabolite strongly, significantly, and positively associated with Mib1 scores. It was similarly associated with aggressive grade and a key component of grade, mitosis, and also trended to be associated with lymph node metastasis. PGE2 and PGD2 trended to be negatively associated with these markers. No other metabolite in cancer and no metabolite in normal tissue had this profile of associations.Our data fit a model wherein the overproduction of 13-HODE by 15-lipoxygenase-1 shortens breast cancer survival by stimulating its cells to proliferate and possibly metastasize; no other oxygenase-metabolite pathway, including cyclooxygenase-PGE2/D2 pathways, uses this specific mechanism to shorten survival.

  3. Long non-coding RNA expression profiles in gallbladder carcinoma identified using microarray analysis.

    Science.gov (United States)

    Wang, Jiwen; Liu, Han; Shen, Xiaokun; Wang, Yueqi; Zhang, Dexiang; Shen, Sheng; Suo, Tao; Pan, Hongtao; Ming, Yue; Ding, Kan; Liu, Houbao

    2017-05-01

    Gallbladder carcinoma (GBC) is the most common biliary tract cancer and exhibits poor patient prognosis. Previous studies have identified that long non-coding RNAs (lncRNAs) serve important regulatory roles in cancer biology. Alterations in lncRNAs are associated with several types of cancer. However, the contribution of lncRNAs to GBC remains unclear. To investigate the lncRNAs that are potentially involved in GBC, lncRNA profiles were identified in three pairs of human GBC and corresponding peri-carcinomatous tissue samples using microarray analysis. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was used to validate the microarray data. In order to elucidate potential functions, Gene Ontology, Kyoto Encyclopedia of Genes and Genomes analysis, and network analysis were used to determine relevant signaling pathways. Abundant RNA probes were used, and 1,758 lncRNAs and 1,254 mRNAs were detected to be differentially expressed by the microarray. Compared with para-carcinoma tissue, numerous lncRNAs were markedly upregulated or downregulated in GBC. The results demonstrated that the lncRNAs that were downregulated in GBC were more numerous compared with the lncRNAs that were upregulated. Among them, RP11-152P17.2-006 was the most upregulated, whereas CTA-941F9.9 was the most downregulated. The RT-qPCR results were consistent with the microarray data. Pathway analysis indicated that five pathways corresponded to the differentially expressed transcripts. It was demonstrated that lncRNA expression in GBC was markedly altered, and a series of novel lncRNAs associated with GBC were identified. The results of the present study suggest that the functions of lncRNAs are important in GBC development and progression.

  4. Systematic enrichment analysis of gene expression profiling studies identifies consensus pathways implicated in colorectal cancer development

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    Jesús Lascorz

    2011-01-01

    Full Text Available Background: A large number of gene expression profiling (GEP studies on colorectal carcinogenesis have been performed but no reliable gene signature has been identified so far due to the lack of reproducibility in the reported genes. There is growing evidence that functionally related genes, rather than individual genes, contribute to the etiology of complex traits. We used, as a novel approach, pathway enrichment tools to define functionally related genes that are consistently up- or down-regulated in colorectal carcinogenesis. Materials and Methods: We started the analysis with 242 unique annotated genes that had been reported by any of three recent meta-analyses covering GEP studies on genes differentially expressed in carcinoma vs normal mucosa. Most of these genes (218, 91.9% had been reported in at least three GEP studies. These 242 genes were submitted to bioinformatic analysis using a total of nine tools to detect enrichment of Gene Ontology (GO categories or Kyoto Encyclopedia of Genes and Genomes (KEGG pathways. As a final consistency criterion the pathway categories had to be enriched by several tools to be taken into consideration. Results: Our pathway-based enrichment analysis identified the categories of ribosomal protein constituents, extracellular matrix receptor interaction, carbonic anhydrase isozymes, and a general category related to inflammation and cellular response as significantly and consistently overrepresented entities. Conclusions: We triaged the genes covered by the published GEP literature on colorectal carcinogenesis and subjected them to multiple enrichment tools in order to identify the consistently enriched gene categories. These turned out to have known functional relationships to cancer development and thus deserve further investigation.

  5. Genome-wide methylation profiling identifies hypermethylated biomarkers in high-grade cervical intraepithelial neoplasia.

    Science.gov (United States)

    Lendvai, Ágnes; Johannes, Frank; Grimm, Christina; Eijsink, Jasper J H; Wardenaar, René; Volders, Haukeline H; Klip, Harry G; Hollema, Harry; Jansen, Ritsert C; Schuuring, Ed; Wisman, G Bea A; van der Zee, Ate G J

    2012-11-01

    Epigenetic modifications, such as aberrant DNA promoter methylation, are frequently observed in cervical cancer. Identification of hypermethylated regions allowing discrimination between normal cervical epithelium and high-grade cervical intraepithelial neoplasia (CIN2/3), or worse, may improve current cervical cancer population-based screening programs. In this study, the DNA methylome of high-grade CIN lesions was studied using genome-wide DNA methylation screening to identify potential biomarkers for early diagnosis of cervical neoplasia. Methylated DNA Immunoprecipitation (MeDIP) combined with DNA microarray was used to compare DNA methylation profiles of epithelial cells derived from high-grade CIN lesions with normal cervical epithelium. Hypermethylated differentially methylated regions (DMRs) were identified. Validation of nine selected DMRs using BSP and MSP in cervical tissue revealed methylation in 63.2-94.7% high-grade CIN and in 59.3-100% cervical carcinomas. QMSP for the two most significant high-grade CIN-specific methylation markers was conducted exploring test performance in a large series of cervical scrapings. Frequency and relative level of methylation were significantly different between normal and cancer samples. Clinical validation of both markers in cervical scrapings from patients with an abnormal cervical smear confirmed that frequency and relative level of methylation were related with increasing severity of the underlying CIN lesion and that ROC analysis was discriminative. These markers represent the COL25A1 and KATNAL2 and their observed increased methylation upon progression could intimate the regulatory role in carcinogenesis. In conclusion, our newly identified hypermethylated DMRs represent specific DNA methylation patterns in high-grade CIN lesions and are candidate biomarkers for early detection.

  6. Methylation profiling in individuals with uniparental disomy identifies novel differentially methylated regions on chromosome 15

    Science.gov (United States)

    Sharp, Andrew J.; Migliavacca, Eugenia; Dupre, Yann; Stathaki, Elisavet; Sailani, Mohammad Reza; Baumer, Alessandra; Schinzel, Albert; Mackay, Deborah J.; Robinson, David O.; Cobellis, Gilda; Cobellis, Luigi; Brunner, Han G.; Steiner, Bernhard; Antonarakis, Stylianos E.

    2010-01-01

    The maternal and paternal genomes possess distinct epigenetic marks that distinguish them at imprinted loci. In order to identify imprinted loci, we used a novel method, taking advantage of the fact that uniparental disomy (UPD) provides a system that allows the two parental chromosomes to be studied independently. We profiled the paternal and maternal methylation on chromosome 15 using immunoprecipitation of methylated DNA and hybridization to tiling oligonucleotide arrays. Comparison of six individuals with maternal versus paternal UPD15 revealed 12 differentially methylated regions (DMRs). Putative DMRs were validated by bisulfite sequencing, confirming the presence of parent-of-origin-specific methylation marks. We detected DMRs associated with known imprinted genes within the Prader-Willi/Angelman syndrome region, such as SNRPN and MAGEL2, validating this as a method of detecting imprinted loci. Of the 12 DMRs identified, eight were novel, some of which are associated with genes not previously thought to be imprinted. These include a site within intron 2 of IGF1R at 15q26.3, a gene that plays a fundamental role in growth, and an intergenic site upstream of GABRG3 that lies within a previously defined candidate region conferring an increased maternal risk of psychosis. These data provide a map of parent-of-origin-specific epigenetic modifications on chromosome 15, identifying DNA elements that may play a functional role in the imprinting process. Application of this methodology to other chromosomes for which UPD has been reported will allow the systematic identification of imprinted sites throughout the genome. PMID:20631049

  7. Functional profiling of microtumors to identify cancer associated fibroblast-derived drug targets.

    Science.gov (United States)

    Horman, Shane R; To, Jeremy; Lamb, John; Zoll, Jocelyn H; Leonetti, Nicole; Tu, Buu; Moran, Rita; Newlin, Robbin; Walker, John R; Orth, Anthony P

    2017-11-21

    Recent advances in chemotherapeutics highlight the importance of molecularly-targeted perturbagens. Although these therapies typically address dysregulated cancer cell proteins, there are increasing therapeutic modalities that take into consideration cancer cell-extrinsic factors. Targeting components of tumor stroma such as vascular or immune cells has been shown to represent an efficacious approach in cancer treatment. Cancer-associated fibroblasts (CAFs) exemplify an important stromal component that can be exploited in targeted therapeutics, though their employment in drug discovery campaigns has been relatively minimal due to technical logistics in assaying for CAF-tumor interactions. Here we report a 3-dimensional multi-culture tumor:CAF spheroid phenotypic screening platform that can be applied to high-content drug discovery initiatives. Using a functional genomics approach we systematically profiled 1,024 candidate genes for CAF-intrinsic anti-spheroid activity; identifying several CAF genes important for development and maintenance of tumor:CAF co-culture spheroids. Along with previously reported genes such as WNT, we identify CAF-derived targets such as ARAF and COL3A1 upon which the tumor compartment depends for spheroid development. Specifically, we highlight the G-protein-coupled receptor OGR1 as a unique CAF-specific protein that may represent an attractive drug target for treating colorectal cancer. In vivo , murine colon tumor implants in OGR1 knockout mice displayed delayed tumor growth compared to tumors implanted in wild type littermate controls. These findings demonstrate a robust microphysiological screening approach for identifying new CAF targets that may be applied to drug discovery efforts.

  8. Targeted metabolite profile of food bioactive compounds by Orbitrap high resolution mass spectrometry: The 'FancyTiles' approach

    NARCIS (Netherlands)

    Troise, A.D.; Ferracane, R.; Palermo, M.; Fogliano, V.

    2014-01-01

    In this paper a new targeted metabolic profile approach using Orbitrap high resolution mass spectrometry was described. For each foodmatrix various classes of bioactive compounds and some specificmetabolites of interest were selected on the basis of the existing knowledge creating an easy-to-read

  9. Prostaglandin F2 alpha metabolite and progesterone profiles in post-partum cows with retained foetal membranes.

    Science.gov (United States)

    Bekana, M; Odensvik, K; Kindahl, H

    1996-01-01

    Post-partum prostaglandin release and resumption of cyclical ovarian activities were studied in 11 Swedish dairy cows with retained foetal membranes (RFM), leaving the RFM untreated. The main PGF2 alpha metabolite, 15-ketodihydro-PGF2 alpha, was measured in blood plasma collected twice daily during the first 50-60 days after delivery. Progesterone was monitored from all morning samples to evaluate the resumption of ovarian activity. The plasma levels of 15-ketodihydro-PGF2 alpha were arbitrarily considered to be significantly elevated between 6-24 days when they exceeded the mean basal value + 2 standard deviations. Comparison between this duration in days of the post-partum PGF2 alpha release and the time required for the completion of uterine involution, placental shedding and last day of post-partum clinical signs showed no significant relations. However, prior to a final decrease below a line of significance of 233-590 pmol/l, pronounced sustained and pulsatile release of PGF2 alpha occurred in relation to the increased frequency of the bacteriological findings. These additional periods of PGF2 alpha release were described as the "total" duration of post-partum release, and were found to be positively correlated with the time required for uterine involution from the stand point of rectal palpation (p < 0.05), while a tendency towards a positive relationship existed for the last day post-partum of clinical signs (p = 0.11). Progesterone analysis revealed resumption of ovarian activity and the first ovulation occurred between 19-29 days in 70% of the cows. The levels of the PGF2 alpha metabolite were again high at the time of luteolysis, thus terminating the luteal phase in the ovulating animals. Thus, it is seen that non-removal of the RFM or the resultant intrauterine infection do not prolong the duration of the immediate post-partum release of PGF2 alpha as compared to normal animals. However, a second release is associated with the increased frequency of

  10. Biocontrol of Bacterial Leaf Blight of Rice and Profiling of Secondary Metabolites Produced by Rhizospheric Pseudomonas aeruginosa BRp3

    Science.gov (United States)

    Yasmin, Sumera; Hafeez, Fauzia Y.; Mirza, Muhammad S.; Rasul, Maria; Arshad, Hafiz M. I.; Zubair, Muhammad; Iqbal, Mazhar

    2017-01-01

    Xanthomonas oryzae pv. oryzae (Xoo) is widely prevalent and causes Bacterial Leaf Blight (BLB) in Basmati rice grown in different areas of Pakistan. There is a need to use environmentally safe approaches to overcome the loss of grain yield in rice due to this disease. The present study aimed to develop inocula, based on native antagonistic bacteria for biocontrol of BLB and to increase the yield of Super Basmati rice variety. Out of 512 bacteria isolated from the rice rhizosphere and screened for plant growth promoting determinants, the isolate BRp3 was found to be the best as it solubilized 97 μg/ mL phosphorus, produced 30 μg/mL phytohormone indole acetic acid and 15 mg/ L siderophores in vitro. The isolate BRp3 was found to be a Pseudomonas aeruginosa based on 16S rRNA gene sequencing (accession no. HQ840693). This bacterium showed antagonism in vitro against different phytopathogens including Xoo and Fusarium spp. Strain BRp3 showed consistent pathogen suppression of different strains of BLB pathogen in rice. Mass spectrometric analysis detected the production of siderophores (1-hydroxy-phenazine, pyocyanin, and pyochellin), rhamnolipids and a series of already characterized 4-hydroxy-2-alkylquinolines (HAQs) as well as novel 2,3,4-trihydroxy-2-alkylquinolines and 1,2,3,4-tetrahydroxy-2-alkylquinolines in crude extract of BRp3. These secondary metabolites might be responsible for the profound antibacterial activity of BRp3 against Xoo pathogen. Another contributing factor toward the suppression of the pathogen was the induction of defense related enzymes in the rice plant by the inoculated strain BRp3. When used as an inoculant in a field trial, this strain enhanced the grain and straw yields by 51 and 55%, respectively, over non-inoculated control. Confocal Laser Scanning Microscopy (CLSM) used in combination with immunofluorescence marker confirmed P. aeruginosa BRp3 in the rice rhizosphere under sterilized as well as field conditions. The results provide

  11. Biocontrol of Bacterial Leaf Blight of Rice and Profiling of Secondary Metabolites Produced by Rhizospheric Pseudomonas aeruginosa BRp3

    Directory of Open Access Journals (Sweden)

    Sumera Yasmin

    2017-09-01

    Full Text Available Xanthomonas oryzae pv. oryzae (Xoo is widely prevalent and causes Bacterial Leaf Blight (BLB in Basmati rice grown in different areas of Pakistan. There is a need to use environmentally safe approaches to overcome the loss of grain yield in rice due to this disease. The present study aimed to develop inocula, based on native antagonistic bacteria for biocontrol of BLB and to increase the yield of Super Basmati rice variety. Out of 512 bacteria isolated from the rice rhizosphere and screened for plant growth promoting determinants, the isolate BRp3 was found to be the best as it solubilized 97 μg/ mL phosphorus, produced 30 μg/mL phytohormone indole acetic acid and 15 mg/ L siderophores in vitro. The isolate BRp3 was found to be a Pseudomonas aeruginosa based on 16S rRNA gene sequencing (accession no. HQ840693. This bacterium showed antagonism in vitro against different phytopathogens including Xoo and Fusarium spp. Strain BRp3 showed consistent pathogen suppression of different strains of BLB pathogen in rice. Mass spectrometric analysis detected the production of siderophores (1-hydroxy-phenazine, pyocyanin, and pyochellin, rhamnolipids and a series of already characterized 4-hydroxy-2-alkylquinolines (HAQs as well as novel 2,3,4-trihydroxy-2-alkylquinolines and 1,2,3,4-tetrahydroxy-2-alkylquinolines in crude extract of BRp3. These secondary metabolites might be responsible for the profound antibacterial activity of BRp3 against Xoo pathogen. Another contributing factor toward the suppression of the pathogen was the induction of defense related enzymes in the rice plant by the inoculated strain BRp3. When used as an inoculant in a field trial, this strain enhanced the grain and straw yields by 51 and 55%, respectively, over non-inoculated control. Confocal Laser Scanning Microscopy (CLSM used in combination with immunofluorescence marker confirmed P. aeruginosa BRp3 in the rice rhizosphere under sterilized as well as field conditions. The

  12. Metabolomic analysis identifies differentially produced oral metabolites, including the oncometabolite 2-hydroxyglutarate, in patients with head and neck squamous cell carcinoma

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    Pranab K. Mukherjee

    2017-06-01

    Conclusions: Oral metabolites related to energy metabolism were elevated in HNSCC, and acylcarnitine and 2HG may have potential as non-invasive biomarkers. Further validation in clinical studies is warranted.

  13. Histochemical screening, metabolite profiling and expression analysis reveal Rosaceae roots as the site of flavan-3-ol biosynthesis.

    Science.gov (United States)

    Hoffmann, T; Friedlhuber, R; Steinhauser, C; Tittel, I; Skowranek, K; Schwab, W; Fischer, T C

    2012-01-01

    Histochemical screening of 30 Rosaceae genera representing all classic subfamilies demonstrated flavan-3-ols (catechins) as general secondary metabolites in roots of Rosaceae. Semi-quantitative LC-MS analyses confirmed the presence of catechin, epicatechin and various dimeric flavan-3-ols (also representing higher polymeric proanthocyanidins) as prominent polyphenols in root tips of Fragaria (strawberry), Malus (apple), Rosa (rose), Pyrus (pear) and Prunus (plum). Distinct patterns of flavan-3-ol distribution at the cellular level were found in strawberry (Fragaria × ananassa) and apple (Malus × domestica) root tips. The calyptras (root caps) showed the most prominent flavan-3-ol staining for these two genera. Border cells of Fragaria and Malus, as first demonstrated here for Rosaceae, were also found to contain flavan-3-ols. Transcript analyses with cDNA demonstrated root expression of known flavonoid genes expressed in the respective fruits and leaves. Primarily, this proves in situ biosynthesis of flavan-3-ols in these roots. Knowledge of the distinct cellular distribution patterns and their in situ biosynthesis in roots provides a basis for analysis of the functional roles of Rosaceae root flavan-3-ols. © 2011 German Botanical Society and The Royal Botanical Society of the Netherlands.

  14. Automated Comparative Metabolite Profiling of Large LC-ESIMS Data Sets in an ACD/MS Workbook Suite Add-in, and Data Clustering on a New Open-Source Web Platform FreeClust.

    Science.gov (United States)

    Božičević, Alen; Dobrzyński, Maciej; De Bie, Hans; Gafner, Frank; Garo, Eliane; Hamburger, Matthias

    2017-12-05

    The technological development of LC-MS instrumentation has led to significant improvements of performance and sensitivity, enabling high-throughput analysis of complex samples, such as plant extracts. Most software suites allow preprocessing of LC-MS chromatograms to obtain comprehensive information on single constituents. However, more advanced processing needs, such as the systematic and unbiased comparative metabolite profiling of large numbers of complex LC-MS chromatograms remains a challenge. Currently, users have to rely on different tools to perform such data analyses. We developed a two-step protocol comprising a comparative metabolite profiling tool integrated in ACD/MS Workbook Suite, and a web platform developed in R language designed for clustering and visualization of chromatographic data. Initially, all relevant chromatographic and spectroscopic data (retention time, molecular ions with the respective ion abundance, and sample names) are automatically extracted and assembled in an Excel spreadsheet. The file is then loaded into an online web application that includes various statistical algorithms and provides the user with tools to compare and visualize the results in intuitive 2D heatmaps. We applied this workflow to LC-ESIMS profiles obtained from 69 honey samples. Within few hours of calculation with a standard PC, honey samples were preprocessed and organized in clusters based on their metabolite profile similarities, thereby highlighting the common metabolite patterns and distributions among samples. Implementation in the ACD/Laboratories software package enables ulterior integration of other analytical data, and in silico prediction tools for modern drug discovery.

  15. Distribution of Penicillium commune isolates in cheese dairies mapped using secondary metabolite profiles, morphotypes, RAPD and AFLP fingerprinting

    DEFF Research Database (Denmark)

    Lund, Flemming; Nielsen, A.B.; Skouboe, P.

    2003-01-01

    ) and amplified fragment length polymorphism, (AFLP). For a sub-set of 272 P. commune isolates RAPD analysis generated 33 RAPD groups whereas AFLP profiling revealed 55 AFLP groups. This study conclusively showed that the discriminatory power of AFLP was high compared to RAPD and that AFLP fingerprinting matched...... morphotyping, P. commune isolates with identical profiles using all four typing techniques were interpreted as closely related isolates with a common origin and the distribution of these isolates in the processing environment indicated possible contamination points in the cheese dairies. The coating process...... and unpacking of cheeses with growth of P. commune seemed to cause the contamination problems. Several identical P. commune isolates remained present in the processing environment for more than 7 years in both dairies....

  16. Integrated genomics identifies five medulloblastoma subtypes with distinct genetic profiles, pathway signatures and clinicopathological features.

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    Marcel Kool

    Full Text Available BACKGROUND: Medulloblastoma is the most common malignant brain tumor in children. Despite recent improvements in cure rates, prediction of disease outcome remains a major challenge and survivors suffer from serious therapy-related side-effects. Recent data showed that patients with WNT-activated tumors have a favorable prognosis, suggesting that these patients could be treated less intensively, thereby reducing the side-effects. This illustrates the potential benefits of a robust classification of medulloblastoma patients and a detailed knowledge of associated biological mechanisms. METHODS AND FINDINGS: To get a better insight into the molecular biology of medulloblastoma we established mRNA expression profiles of 62 medulloblastomas and analyzed 52 of them also by comparative genomic hybridization (CGH arrays. Five molecular subtypes were identified, characterized by WNT signaling (A; 9 cases, SHH signaling (B; 15 cases, expression of neuronal differentiation genes (C and D; 16 and 11 cases, respectively or photoreceptor genes (D and E; both 11 cases. Mutations in beta-catenin were identified in all 9 type A tumors, but not in any other tumor. PTCH1 mutations were exclusively identified in type B tumors. CGH analysis identified several fully or partly subtype-specific chromosomal aberrations. Monosomy of chromosome 6 occurred only in type A tumors, loss of 9q mostly occurred in type B tumors, whereas chromosome 17 aberrations, most common in medulloblastoma, were strongly associated with type C or D tumors. Loss of the inactivated X-chromosome was highly specific for female cases of type C, D and E tumors. Gene expression levels faithfully reflected the chromosomal copy number changes. Clinicopathological features significantly different between the 5 subtypes included metastatic disease and age at diagnosis and histology. Metastatic disease at diagnosis was significantly associated with subtypes C and D and most strongly with subtype E

  17. Root constituents of Lactuca sibirica and a comparison of metabolite profiles of L. sibirica and L. tatarica

    Directory of Open Access Journals (Sweden)

    Wanda Kisiel

    2011-01-01

    Full Text Available Nine known sesquiterpene lactones, including four lactucin-type guaianolides, four costuslactone-type guaianolides and one germacranolide, were isolated from roots of Lactuca sibirica (Asteraceae, six of which were glycoside derivatives. The chemosystematic significance of the compounds is discussed in the context of sesquiterpenoids present in roots of the closely related species Lactuca tatarica. A comparison of sesquiterpene lactone profiles indicate that the species can be differentiated on the basis of their germacranolide glycoside compositions.

  18. Analysis of the retinal gene expression profile after hypoxic preconditioning identifies candidate genes for neuroprotection

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    Wenzel Andreas

    2008-02-01

    Full Text Available Abstract Background Retinal degeneration is a main cause of blindness in humans. Neuroprotective therapies may be used to rescue retinal cells and preserve vision. Hypoxic preconditioning stabilizes the transcription factor HIF-1α in the retina and strongly protects photoreceptors in an animal model of light-induced retinal degeneration. To address the molecular mechanisms of the protection, we analyzed the transcriptome of the hypoxic retina using microarrays and real-time PCR. Results Hypoxic exposure induced a marked alteration in the retinal transcriptome with significantly different expression levels of 431 genes immediately after hypoxic exposure. The normal expression profile was restored within 16 hours of reoxygenation. Among the differentially regulated genes, several candidates for neuroprotection were identified like metallothionein-1 and -2, the HIF-1 target gene adrenomedullin and the gene encoding the antioxidative and cytoprotective enzyme paraoxonase 1 which was previously not known to be a hypoxia responsive gene in the retina. The strongly upregulated cyclin dependent kinase inhibitor p21 was excluded from being essential for neuroprotection. Conclusion Our data suggest that neuroprotection after hypoxic preconditioning is the result of the differential expression of a multitude of genes which may act in concert to protect visual cells against a toxic insult.

  19. Multiplatform molecular profiling identifies potentially targetable biomarkers in malignant phyllodes tumors of the breast.

    Science.gov (United States)

    Gatalica, Zoran; Vranic, Semir; Ghazalpour, Anatole; Xiu, Joanne; Ocal, Idris Tolgay; McGill, John; Bender, Ryan P; Discianno, Erin; Schlum, Aaron; Sanati, Souzan; Palazzo, Juan; Reddy, Sandeep; Pockaj, Barbara

    2016-01-12

    Malignant phyllodes tumor is a rare breast malignancy with sarcomatous overgrowth and with limited effective treatment options for recurrent and metastatic cases. Recent clinical trials indicated a potential for anti-angiogenic, anti-EGFR and immunotherapeutic approaches for patients with sarcomas, which led us to investigate these and other targetable pathways in malignant phyllodes tumor of the breast. Thirty-six malignant phyllodes tumors (including 8 metastatic tumors with two cases having matched primary and metastatic tumors) were profiled using gene sequencing, gene copy number analysis, whole genome expression, and protein expression. Whole genome expression analysis demonstrated consistent over-expression of genes involved in angiogenesis including VEGFA, Angiopoietin-2, VCAM1, PDGFRA, and PTTG1. EGFR protein overexpression was observed in 26/27 (96%) of cases with amplification of the EGFR gene in 8/24 (33%) cases. Two EGFR mutations were identified including EGFRvIII and a presumed pathogenic V774M mutation, respectively. The most common pathogenic mutations included TP53 (50%) and PIK3CA (15%). Cases with matched primary and metastatic tumors harbored identical mutations in both sites (PIK3CA/KRAS and RB1 gene mutations, respectively). Tumor expression of PD-L1 immunoregulatory protein was observed in 3/22 (14%) of cases. Overexpression of molecular biomarkers of increased angiogenesis, EGFR and immune checkpoints provides novel targeted therapy options in malignant phyllodes tumors of the breast.

  20. Expression profiling feline peripheral blood monocytes identifies a transcriptional signature associated with type two diabetes mellitus.

    Science.gov (United States)

    O'Leary, Caroline A; Sedhom, Mamdouh; Reeve-Johnson, Mia; Mallyon, John; Irvine, Katharine M

    2017-04-01

    Diabetes mellitus is a common disease of cats and is similar to type 2 diabetes (T2D) in humans, especially with respect to the role of obesity-induced insulin resistance, glucose toxicity, decreased number of pancreatic β-cells and pancreatic amyloid deposition. Cats have thus been proposed as a valuable translational model of T2D. In humans, inflammation associated with adipose tissue is believed to be central to T2D development, and peripheral blood monocytes (PBM) are important in the inflammatory cascade which leads to insulin resistance and β-cell failure. PBM may thus provide a useful window to study the pathogenesis of diabetes mellitus in cats, however feline monocytes are poorly characterised. In this study, we used the Affymetrix Feline 1.0ST array to profile peripheral blood monocytes from 3 domestic cats with T2D and 3 cats with normal glucose tolerance. Feline monocytes were enriched for genes expressed in human monocytes, and, despite heterogeneous gene expression, we identified a T2D-associated expression signature associated with cell cycle perturbations, DNA repair and the unfolded protein response, oxidative phosphorylation and inflammatory responses. Our data provide novel insights into the feline monocyte transcriptome, and support the hypothesis that inflammatory monocytes contribute to T2D pathogenesis in cats as well as in humans. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Clonal analyses and gene profiling identify genetic biomarkers of human brown and white preadipocyte thermogenic potential

    Science.gov (United States)

    Xue, Ruidan; Lynes, Matthew D.; Dreyfuss, Jonathan M.; Shamsi, Farnaz; Schulz, Tim J.; Zhang, Hongbin; Huang, Tian Lian; Townsend, Kristy L.; Li, Yiming; Takahashi, Hirokazu; Weiner, Lauren S.; White, Andrew P.; Lynes, Maureen S.; Rubin, Lee L.; Goodyear, Laurie J.; Cypess, Aaron M.; Tseng, Yu-Hua

    2015-01-01

    Targeting brown adipose tissue (BAT) content or activity has therapeutic potential for treating obesity and the metabolic syndrome by increasing energy expenditure. Both inter- and intra-individual differences contribute to heterogeneity in human BAT and potentially to differential thermogenic capacity in human populations. Here, we demonstrated the generated clones of brown and white preadipocytes from human neck fat of four individuals and characterized their adipogenic differentiation and thermogenic function. Combining an uncoupling protein 1(UCP1) reporter system and expression profiling, we defined novel sets of gene signatures in human preadipocytes that could predict the thermogenic potential of the cells once they were maturated in culture. Knocking out the positive UCP1 regulators identified by this approach, PREX1 and EDNRB in brown preadipocytes using CRISPR/Cas9 markedly abolished the high level of UCP1 in brown adipocytes differentiated from the preadipocytes. Finally, we were able to prospectively isolate adipose progenitors with great thermogenic potential using cell surface marker CD29. These data provide new insights into the cellular heterogeneity in human fat and offer the identification of possible biomarkers of thermogenically competent preadipocytes. PMID:26076036

  2. New genes associated with rheumatoid arthritis identified by gene expression profiling.

    Science.gov (United States)

    Wang, H; Guo, J; Jiang, J; Wu, W; Chang, X; Zhou, H; Li, Z; Zhao, J

    2017-06-01

    In this study, we aimed to find new genes associated with rheumatoid arthritis (RA) so that more comprehensive genes would be used for monitoring and/or diagnosing patients. Illumina digital gene expression profiling was applied in two sample types - peripheral blood mononuclear cells (PBMCs) and synovial cells to compare the gene expression pattern between 17 patients with RA and three control groups (six osteoarthritis patients, three ankylosing spondylitis patients and 17 healthy controls). Bioinformatics was performed on pathway analysis and protein-protein interaction networks. Four novel genes from PBMCs - DHRS3, TTC38, SAP30BP and LPIN2 - were found to be associated with RA and further confirmed through quantitative real-time polymerase chain reaction. Five new differentially expressed genes (EPYC, LIFR, GLDN, TADA3 and ZNRF3) found in synovial cells were not confirmed. Pathway analyses revealed 10 significantly enriched pathways, and a protein-protein interaction network analysis showed that four novel PBMC-derived genes were connected to previously reported genes by four intermediate genes. Therefore, we proposed that four newly identified PBMC-derived genes could be integrated with previously reported RA-associated genes to monitor and/or diagnose RA. © 2017 John Wiley & Sons Ltd.

  3. Cytokeratin Profiles Identify Diagnostic Signatures in Colorectal Cancer Using Multiplex Analysis of Tissue Microarrays

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    Thomas Knösel

    2006-01-01

    Full Text Available Background and aims: Recent cDNA expression profiling analyses indicate that within specific organ cancers Cytokeratins (CKs dysregulation may identify subgroups with distinct biological phenotypes. Our objectives in this study were (1 to test whether cytokeratins were also distinct on the protein level, (2 to evaluate these biomarkers in a series of well-characterised CRCs, (3 to apply hierarchical cluster analysis to immunohistochemical data. Methods: Tissue microarrays (TMA comprising 468 CRC specimens from 203 patients were constructed to evaluate CK5, CK7, CK8, CK13, CK14, CK16, CK17, CK18, CK19 and CK20. In total, 2919 samples were analyzed. Results: Unsupervised hierarchical clustering discovered subgroups represented by reduced CK8 and CK20 expression, that differed by a shorter patients survival. The evaluation of the specific biomarkers by Kaplan–Meier analysis showed that reduced CK8 expression (p < 0.01 was significantly associated with shorter patients’ survival, but was not an independent factor correlated with tumour stage (pT, grading (G and nodal stage (pN. Conclusions: Reduced coexpression of CK8 and CK20 may indicate an epithelial-mesenchymal transition (EMT representing an important step in the development of more aggressive CRCs. In addition, multiplex analysis of TMAs together with immunohistochemistry (IHC supplemented by hierarchical clustering are a useful, promising and very powerful tool for the identification of tumour subgroups with diagnostic and prognostic signatures.

  4. Transcriptome profiling of the goose (Anser cygnoides ovaries identify laying and broodiness phenotypes.

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    Qi Xu

    Full Text Available BACKGROUND: The geese have strong broodiness and poor egg performance. These characteristics are the key issues that hinder the goose industry development. Yet little is known about the mechanisms responsible for follicle development due to lack of genomic resources. Hence, studies based on high-throughput sequencing technologies are needed to produce a comprehensive and integrated genomic resource and to better understand the biological mechanisms of goose follicle development. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we performed de novo transcriptome assembly and gene expression analysis using short-read sequencing technology (Illumina. We obtained 67,315,996 short reads of 100 bp, which were assembled into 130,514 unique sequences by Trinity strategy (mean size = 753 bp. Based on BLAST results with known proteins, these analyses identified 52,642 sequences with a cut-off E-value above 10(-5. Assembled sequences were annotated with gene descriptions, gene ontology and clusters of orthologous group terms. In addition, we investigated the transcription changes during the goose laying/broodiness period using a tag-based digital gene expression (DGE system. We obtained a sequencing depth of over 4.2 million tags per sample and identified a large number of genes associated with follicle development and reproductive biology including cholesterol side-chain cleavage enzyme gene and dopamine beta-hydroxylas gene. We confirm the altered expression levels of the two genes using quantitative real-time PCR (qRT-PCR. CONCLUSIONS/SIGNIFICANCE: The obtained goose transcriptome and DGE profiling data provide comprehensive gene expression information at the transcriptional level that could promote better understanding of the molecular mechanisms underlying follicle development and productivity.

  5. Serum proteome profiling identifies novel and powerful markers of cystic fibrosis liver disease.

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    Timo Rath

    Full Text Available BACKGROUND AND AIMS: Cystic Fibrosis associated liver disease (CFLD develops in approximately 30% of CF patients. However, routine sensitive diagnostic tools for CFLD are lacking. Within this study, we aimed to identify new experimental biomarkers for the detection of CFLD. METHODS: 45 CF patients were included in the study and received transient elastography. Differential regulation of 220 different serum proteins was assessed in a subgroup of patients with and without CFLD. Most interesting candidate proteins were further quantified and validated by ELISA in the whole patient cohort. To assess a potential relation of biomarker expression to the degree of hepatic fibrosis, serum biomarkers were further determined in 18 HCV patients where liver histology was available. RESULTS: 43 serum proteins differed at least 2-fold in patients with CFLD compared to those without liver disease as identified in proteome profiling. In ELISA quantifications, TIMP-4 and Endoglin were significantly up-regulated in patients with CFLD as diagnosed by clinical guidelines or increased liver stiffness. Pentraxin-3 was significantly decreased in patients with CFLD. Serum TIMP-4 and Endoglin showed highest values in HCV patients with liver cirrhosis compared to those with fibrosis but without cirrhosis. At a cut-off value of 6.3 kPa, transient elastography compassed a very high diagnostic accuracy and specificity for the detection of CFLD. Among the biomarkers, TIMP-4 and Endoglin exhibited a high diagnostic accuracy for CFLD. Diagnostic sensitivities and negative predictive values were increased when elastography and TIMP-4 and Endoglin were combined for the detection of CFLD. CONCLUSIONS: Serum TIMP-4 and Endoglin are increased in CFLD and their expression correlates with hepatic staging. Determination of TIMP-4 and Endoglin together with transient elastography can increase the sensitivity for the non-invasive diagnosis of CFLD.

  6. Transcriptional profile analysis of RPGRORF15 frameshift mutation identifies novel genes associated with retinal degeneration.

    Science.gov (United States)

    Genini, Sem; Zangerl, Barbara; Slavik, Julianna; Acland, Gregory M; Beltran, William A; Aguirre, Gustavo D

    2010-11-01

    To identify genes and molecular mechanisms associated with photoreceptor degeneration in a canine model of XLRP caused by an RPGR exon ORF15 microdeletion. Methods. Expression profiles of mutant and normal retinas were compared by using canine retinal custom cDNA microarrays. qRT-PCR, Western blot analysis, and immunohistochemistry (IHC) were applied to selected genes, to confirm and expand the microarray results. At 7 and 16 weeks, respectively, 56 and 18 transcripts were downregulated in the mutant retinas, but none were differentially expressed (DE) at both ages, suggesting the involvement of temporally distinct pathways. Downregulated genes included the known retina-relevant genes PAX6, CHML, and RDH11 at 7 weeks and CRX and SAG at 16 weeks. Genes directly or indirectly active in apoptotic processes were altered at 7 weeks (CAMK2G, NTRK2, PRKCB, RALA, RBBP6, RNF41, SMYD3, SPP1, and TUBB2C) and 16 weeks (SLC25A5 and NKAP). Furthermore, the DE genes at 7 weeks (ELOVL6, GLOD4, NDUFS4, and REEP1) and 16 weeks (SLC25A5 and TARS2) are related to mitochondrial functions. qRT-PCR of 18 genes confirmed the microarray results and showed DE of additional genes not on the array. Only GFAP was DE at 3 weeks of age. Western blot and IHC analyses also confirmed the high reliability of the transcriptomic data. Several DE genes were identified in mutant retinas. At 7 weeks, a combination of nonclassic anti- and proapoptosis genes appear to be involved in photoreceptor degeneration, whereas at both 7 and 16 weeks, the expression of mitochondria-related genes indicates that they may play a relevant role in the disease process.

  7. Global Fitness Profiling Identifies Arsenic and Cadmium Tolerance Mechanisms in Fission Yeast

    Directory of Open Access Journals (Sweden)

    Lan Guo

    2016-10-01

    Full Text Available Heavy metals and metalloids such as cadmium [Cd(II] and arsenic [As(III] are widespread environmental toxicants responsible for multiple adverse health effects in humans. However, the molecular mechanisms underlying metal-induced cytotoxicity and carcinogenesis, as well as the detoxification and tolerance pathways, are incompletely understood. Here, we use global fitness profiling by barcode sequencing to quantitatively survey the Schizosaccharomyces pombe haploid deletome for genes that confer tolerance of cadmium or arsenic. We identified 106 genes required for cadmium resistance and 110 genes required for arsenic resistance, with a highly significant overlap of 36 genes. A subset of these 36 genes account for almost all proteins required for incorporating sulfur into the cysteine-rich glutathione and phytochelatin peptides that chelate cadmium and arsenic. A requirement for Mms19 is explained by its role in directing iron–sulfur cluster assembly into sulfite reductase as opposed to promoting DNA repair, as DNA damage response genes were not enriched among those required for cadmium or arsenic tolerance. Ubiquinone, siroheme, and pyridoxal 5′-phosphate biosynthesis were also identified as critical for Cd/As tolerance. Arsenic-specific pathways included prefoldin-mediated assembly of unfolded proteins and protein targeting to the peroxisome, whereas cadmium-specific pathways included plasma membrane and vacuolar transporters, as well as Spt–Ada–Gcn5-acetyltransferase (SAGA transcriptional coactivator that controls expression of key genes required for cadmium tolerance. Notable differences are apparent with corresponding screens in the budding yeast Saccharomyces cerevisiae, underscoring the utility of analyzing toxic metal defense mechanisms in both organisms.

  8. An update on sORFs.org: a repository of small ORFs identified by ribosome profiling.

    Science.gov (United States)

    Olexiouk, Volodimir; Van Criekinge, Wim; Menschaert, Gerben

    2018-01-04

    sORFs.org (http://www.sorfs.org) is a public repository of small open reading frames (sORFs) identified by ribosome profiling (RIBO-seq). This update elaborates on the major improvements implemented since its initial release. sORFs.org now additionally supports three more species (zebrafish, rat and Caenorhabditis elegans) and currently includes 78 RIBO-seq datasets, a vast increase compared to the three that were processed in the initial release. Therefore, a novel pipeline was constructed that also enables sORF detection in RIBO-seq datasets comprising solely elongating RIBO-seq data while previously, matching initiating RIBO-seq data was necessary to delineate the sORFs. Furthermore, a novel noise filtering algorithm was designed, able to distinguish sORFs with true ribosomal activity from simulated noise, consequently reducing the false positive identification rate. The inclusion of other species also led to the development of an inner BLAST pipeline, assessing sequence similarity between sORFs in the repository. Building on the proof of concept model in the initial release of sORFs.org, a full PRIDE-ReSpin pipeline was now released, reprocessing publicly available MS-based proteomics PRIDE datasets, reporting on true translation events. Next to reporting those identified peptides, sORFs.org allows visual inspection of the annotated spectra within the Lorikeet MS/MS viewer, thus enabling detailed manual inspection and interpretation. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  9. Effect of fertilisation and harvest period on polar metabolites of Calendula oficcinalis

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    Eduardo Felipe Alves Fernandes

    Full Text Available The present study evaluated the chemical profile of polar extracts of Calendula officinalis L., Asteraceae, that were grown under different cultivation conditions: chemical fertilisation, organic fertilisation and mulching. Furthermore, we investigated metabolite variations during plant development by comparing the metabolites from harvested plants at 60 and 120 days after planting. We used HPLC-DAD-MS/MS to tentatively identify metabolites. In total, we identified seven known compounds: five flavonoid glycosides and two caffeoylquinic acids derivatives. There were no statistically significant differences in the expression of metabolites from plants grown under the examined soil treatments. However, five substances varied according to harvest time, suggesting that the biosynthesis of polar metabolites of Calendula officinalis is not affected by changes in soil composition. Therefore, this plant could represent a source for phytomedicines with a constant content of polar metabolites.

  10. Identified ankle extensor and flexor motoneurons display different firing profiles in the neonatal rat

    DEFF Research Database (Denmark)

    Cotel, Florence; Antri, Myriam; Barthe, Jean-Yves

    2009-01-01

    population of flexor motoneurons solely exhibited the type II profile, characterized by a frequency-current (F-I) relationship with a clockwise hysteresis. In contrast, in addition to this type II profile, the other three profiles of repetitive firing (type I, III and IV) were observed in extensor...... postnatal development, a significant part of the population of extensor motoneurons, but not flexors, are able to produce self-sustained discharges known to involve the activation of persistent inward currents....

  11. Contribution towards a Metabolite Profile of the Detoxification of Benzoic Acid through Glycine Conjugation: An Intervention Study.

    Science.gov (United States)

    Irwin, Cindy; van Reenen, Mari; Mason, Shayne; Mienie, Lodewyk J; Westerhuis, Johan A; Reinecke, Carolus J

    2016-01-01

    Benzoic acid is widely used as a preservative in food products and is detoxified in humans through glycine conjugation. Different viewpoints prevail on the physiological significance of the glycine conjugation reaction and concerns have been raised on potential public health consequences following uncontrolled benzoic acid ingestion. We performed a metabolomics study which used commercial benzoic acid containing flavored water as vehicle for designed interventions, and report here on the controlled consumption of the benzoic acid by 21 cases across 6 time points for a total of 126 time points. Metabolomics data from urinary samples analyzed by nuclear magnetic resonance spectroscopy were generated in a time-dependent cross-over study. We used ANOVA-simultaneous component analysis (ASCA), repeated measures analysis of variance (RM-ANOVA) and unfolded principal component analysis (unfolded PCA) to supplement conventional statistical methods to uncover fully the metabolic perturbations due to the xenobiotic intervention, encapsulated in the metabolomics tensor (three-dimensional matrices having cases, spectral areas and time as axes). Identification of the biologically important metabolites by the novel combination of statistical methods proved the power of this approach for metabolomics studies having complex data structures in general. The study disclosed a high degree of inter-individual variation in detoxification of the xenobiotic and revealed metabolic information, indicating that detoxification of benzoic acid through glycine conjugation to hippuric acid does not indicate glycine depletion, but is supplemented by ample glycine regeneration. The observations lend support to the view of maintenance of glycine homeostasis during detoxification. The study indicates also that time-dependent metabolomics investigations, using designed interventions, provide a way of interpreting the variation induced by the different factors of a designed experiment-an approach with

  12. Use of latent profile analysis to identify eating disorder phenotypes in an adult Australian twin cohort.

    Science.gov (United States)

    Wade, Tracey D; Crosby, Ross D; Martin, Nicholas G

    2006-12-01

    The relationships among the different eating disorders that exist in the community are poorly understood, especially for residual disorders in which bingeing or purging occurs in the absence of other behaviors. To examine a community sample for the number of mutually exclusive weight and eating profiles. Data regarding lifetime eating disorder symptoms and weight range were submitted to a latent profile analysis. Profiles were compared regarding personality, current eating and weight, retrospectively reported life events, and lifetime depressive psychopathology. Longitudinal study among female twins from the Australian Twin Registry in whom eating was assessed by a telephone interview. A community sample of 1002 twins (individuals) who had participated in earlier waves of data collection. Number and clinical character of latent profiles. The best fit was a 5-profile solution with women who were (1) of normal weight with few lifetime eating disorders (4.3%), (2) overweight (10.6% had a lifetime eating disorder), (3) underweight and generally had no eating disorders except for 5.3% who had restricting anorexia nervosa, (4) of low to normal weight (89.0% had a lifetime eating disorder), and (5) obese (37.0% had a lifetime eating disorder). Each profile contained more than 1 type of lifetime eating disorder except for the third profile. Women in the first and third profiles had the best functioning, with women in the fourth and fifth profiles having similarly poorer functioning. The women in the fourth group had a symptom profile distinctive from the other 4 groups in terms of severity; they were also more likely to have had lifetime major depression and suicidality. Lifetime weight ranges and the severity of eating disorder symptoms affected clustering more than the type of eating disorder symptom.

  13. Carbon and nitrogen isotopic signatures and nitrogen profile to identify adulteration in organic fertilizers.

    Science.gov (United States)

    Verenitch, Sergei; Mazumder, Asit

    2012-08-29

    Recently it has been shown that stable isotopes of nitrogen can be used to discriminate between organic and synthetic fertilizers, but the robustness of the approach is questionable. This work developed a comprehensive method that is far more robust in identifying an adulteration of organic nitrogen fertilizers. Organic fertilizers of various types (manures, composts, blood meal, bone meal, fish meal, products of poultry and plant productions, molasses and seaweed based, and others) available on the North American market were analyzed to reveal the most sensitive criteria as well as their quantitative ranges, which can be used in their authentication. Organic nitrogen fertilizers of known origins with a wide δ(15)N range between -0.55 and 28.85‰ (n = 1258) were characterized for C and N content, δ(13)C, δ(15)N, viscosity, pH, and nitrogen profile (urea, ammonia, organic N, water insoluble N, and NO3). A statistically significant data set of characterized unique organic nitrogen fertilizers (n = 335) of various known origins has been assembled. Deliberately adulterated samples of different types of organic fertilizers mixed with synthetic fertilizers at a wide range of proportions have been used to develop the quantitative critical characteristics of organic fertilizers as the key indicators of their adulteration. Statistical analysis based on the discriminant functions of the quantitative critical characteristics of organic nitrogen fertilizers from 14 different source materials revealed a very high average rate of correct classification. The developed methodology has been successfully used as a source identification tool for numerous commercial nitrogen fertilizers available on the North American market.

  14. Profiling G protein-coupled receptors of Fasciola hepatica identifies orphan rhodopsins unique to phylum Platyhelminthes.

    Science.gov (United States)

    McVeigh, Paul; McCammick, Erin; McCusker, Paul; Wells, Duncan; Hodgkinson, Jane; Paterson, Steve; Mousley, Angela; Marks, Nikki J; Maule, Aaron G

    2018-02-05

    G protein-coupled receptors (GPCRs) are established drug targets. Despite their considerable appeal as targets for next-generation anthelmintics, poor understanding of their diversity and function in parasitic helminths has thwarted progress towards GPCR-targeted anti-parasite drugs. This study facilitates GPCR research in the liver fluke, Fasciola hepatica, by generating the first profile of GPCRs from the F. hepatica genome. Our dataset describes 147 high confidence GPCRs, representing the largest cohort of GPCRs, and the largest set of in silico ligand-receptor predictions, yet reported in any parasitic helminth. All GPCRs fall within the established GRAFS nomenclature; comprising three glutamate, 135 rhodopsin, two adhesion, five frizzled, one smoothened, and one secretin GPCR. Stringent annotation pipelines identified 18 highly diverged rhodopsins in F. hepatica that maintained core rhodopsin signatures, but lacked significant similarity with non-flatworm sequences, providing a new sub-group of potential flukicide targets. These facilitated identification of a larger cohort of 76 related sequences from available flatworm genomes, representing new members of existing groups (PROF1/Srfb, Rho-L, Rho-R, Srfa, Srfc) of flatworm-specific rhodopsins. These receptors imply flatworm specific GPCR functions, and/or co-evolution with unique flatworm ligands, and could facilitate the development of exquisitely selective anthelmintics. Ligand binding domain sequence conservation relative to deorphanised rhodopsins enabled high confidence ligand-receptor matching of seventeen receptors activated by acetylcholine, neuropeptide F/Y, octopamine or serotonin. RNA-Seq analyses showed expression of 101 GPCRs across various developmental stages, with the majority expressed most highly in the pathogenic intra-mammalian juvenile parasites. These data identify a broad complement of GPCRs in F. hepatica, including rhodopsins likely to have key functions in neuromuscular control and

  15. Profiling G protein-coupled receptors of Fasciola hepatica identifies orphan rhodopsins unique to phylum Platyhelminthes

    Directory of Open Access Journals (Sweden)

    Paul McVeigh

    2018-04-01

    Full Text Available G protein-coupled receptors (GPCRs are established drug targets. Despite their considerable appeal as targets for next-generation anthelmintics, poor understanding of their diversity and function in parasitic helminths has thwarted progress towards GPCR-targeted anti-parasite drugs. This study facilitates GPCR research in the liver fluke, Fasciola hepatica, by generating the first profile of GPCRs from the F. hepatica genome. Our dataset describes 147 high confidence GPCRs, representing the largest cohort of GPCRs, and the largest set of in silico ligand-receptor predictions, yet reported in any parasitic helminth. All GPCRs fall within the established GRAFS nomenclature; comprising three glutamate, 135 rhodopsin, two adhesion, five frizzled, one smoothened, and one secretin GPCR. Stringent annotation pipelines identified 18 highly diverged rhodopsins in F. hepatica that maintained core rhodopsin signatures, but lacked significant similarity with non-flatworm sequences, providing a new sub-group of potential flukicide targets. These facilitated identification of a larger cohort of 76 related sequences from available flatworm genomes, representing new members of existing groups (PROF1/Srfb, Rho-L, Rho-R, Srfa, Srfc of flatworm-specific rhodopsins. These receptors imply flatworm specific GPCR functions, and/or co-evolution with unique flatworm ligands, and could facilitate the development of exquisitely selective anthelmintics. Ligand binding domain sequence conservation relative to deorphanised rhodopsins enabled high confidence ligand-receptor matching of seventeen receptors activated by acetylcholine, neuropeptide F/Y, octopamine or serotonin. RNA-Seq analyses showed expression of 101 GPCRs across various developmental stages, with the majority expressed most highly in the pathogenic intra-mammalian juvenile parasites. These data identify a broad complement of GPCRs in F. hepatica, including rhodopsins likely to have key functions in

  16. Comprehensive profiling of mercapturic acid metabolites from dietary acrylamide as short-term exposure biomarkers for evaluation of toxicokinetics in rats and daily internal exposure in humans using isotope dilution ultra-high performance liquid chromatography tandem mass spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Yu [Department of Food Science and Nutrition, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, Zhejiang (China); Zhejiang Key Laboratory for Agro-Food Processing, Zhejiang R & D Center for Food Technology and Equipment, Fuli Institute of Food Science, Zhejiang University, Hangzhou 310058, Zhejiang (China); Wang, Qiao; Cheng, Jun [Department of Food Science and Nutrition, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, Zhejiang (China); Zhang, Jingshun; Xu, Jiaojiao [Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, Zhejiang (China); Ren, Yiping, E-mail: renyiping@263.net [Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, Zhejiang (China)

    2015-09-24

    Mercapturic acid metabolites from dietary acrylamide are important short-term exposure biomarkers for evaluating the in vivo toxicity of acrylamide. Most of studies have focused on the measurement of two metabolites, N-acetyl-S-(2-carbamoylethyl)-L-cysteine (AAMA) and N-acetyl-S-(2-carbamoyl-2-hydroxyethyl)-L-cysteine (GAMA). Thus, the comprehensive profile of acrylamide urinary metabolites cannot be fully understood. We developed an isotope dilution ultra-high performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) method for the simultaneous determination of all four mercapturic acid adducts of acrylamide and its primary metabolite glycidamide under the electroscopy ionization negative (ESI-) mode in the present study. The limit of detection (LOD) and limit of quantification (LOQ) of the analytes ranged 0.1–0.3 ng/mL and 0.4–1.0 ng/mL, respectively. The recovery rates with low, intermediate and high spiking levels were calculated as 95.5%–105.4%, 98.2%–114.0% and 92.2%–108.9%, respectively. Acceptable within-laboratory reproducibility (RSD < 7.0%) substantially supported the use of current method for robust analysis. Rapid pretreatment procedures and short run time (8 min per sample) ensured good efficiency of metabolism profiling, indicating a wide application for investigating short-term internal exposure of dietary acrylamide. Our proposed UHPLC-MS/MS method was successfully applied to the toxicokinetic study of acrylamide in rats. Meanwhile, results of human urine analysis indicated that the levels of N-acetyl-S-(2-carbamoylethyl)-L-cysteine-sulfoxide (AAMA-sul), which did not appear in the mercapturic acid metabolites in rodents, were more than the sum of GAMA and N-acetyl-S-(1-carbamoyl-2-hydroxyethyl)-L-cysteine (iso-GAMA). Thus, AAMA-sul may alternatively become a specific biomarker for investigating the acrylamide exposure in humans. Current proposed method provides a substantial methodology support for comprehensive

  17. Comprehensive profiling of mercapturic acid metabolites from dietary acrylamide as short-term exposure biomarkers for evaluation of toxicokinetics in rats and daily internal exposure in humans using isotope dilution ultra-high performance liquid chromatography tandem mass spectrometry

    International Nuclear Information System (INIS)

    Zhang, Yu; Wang, Qiao; Cheng, Jun; Zhang, Jingshun; Xu, Jiaojiao; Ren, Yiping

    2015-01-01

    Mercapturic acid metabolites from dietary acrylamide are important short-term exposure biomarkers for evaluating the in vivo toxicity of acrylamide. Most of studies have focused on the measurement of two metabolites, N-acetyl-S-(2-carbamoylethyl)-L-cysteine (AAMA) and N-acetyl-S-(2-carbamoyl-2-hydroxyethyl)-L-cysteine (GAMA). Thus, the comprehensive profile of acrylamide urinary metabolites cannot be fully understood. We developed an isotope dilution ultra-high performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) method for the simultaneous determination of all four mercapturic acid adducts of acrylamide and its primary metabolite glycidamide under the electroscopy ionization negative (ESI-) mode in the present study. The limit of detection (LOD) and limit of quantification (LOQ) of the analytes ranged 0.1–0.3 ng/mL and 0.4–1.0 ng/mL, respectively. The recovery rates with low, intermediate and high spiking levels were calculated as 95.5%–105.4%, 98.2%–114.0% and 92.2%–108.9%, respectively. Acceptable within-laboratory reproducibility (RSD < 7.0%) substantially supported the use of current method for robust analysis. Rapid pretreatment procedures and short run time (8 min per sample) ensured good efficiency of metabolism profiling, indicating a wide application for investigating short-term internal exposure of dietary acrylamide. Our proposed UHPLC-MS/MS method was successfully applied to the toxicokinetic study of acrylamide in rats. Meanwhile, results of human urine analysis indicated that the levels of N-acetyl-S-(2-carbamoylethyl)-L-cysteine-sulfoxide (AAMA-sul), which did not appear in the mercapturic acid metabolites in rodents, were more than the sum of GAMA and N-acetyl-S-(1-carbamoyl-2-hydroxyethyl)-L-cysteine (iso-GAMA). Thus, AAMA-sul may alternatively become a specific biomarker for investigating the acrylamide exposure in humans. Current proposed method provides a substantial methodology support for comprehensive

  18. A comparative study on volatile metabolites profile of Dracaena cochinchinensis (Lour.) S.C. Chen xylem with and without resin using GC-MS.

    Science.gov (United States)

    Teng, Zhongqiu; Zhang, Mei; Meng, Shiying; Dai, Rongji; Meng, Weiwei; Deng, Yulin; Huang, Luqi

    2015-11-01

    Dragon's blood is a famous traditional Chinese medicine produced from source plants under bio- or abio-stress. Dracaena cochinchinensis (Lour.) S.C. Chen xylem (DX) is one of the most important sources of the medicine. In this work, a GC-MS method was developed for analysis of the n-hexane extracts of DX with resin (DXR) and without resin (DXW). The repeatability of the method was also investigated for a metabolite comparative study of the different xylems. About 80 components were detected, 26 of which were identified in both DXR and DXN. Three sesquiterpenes (τ-cadinol, τ-muurolon and α-cadinol) were first discovered in Dracaena cochinchinensis (Lour.) S.C. Chen. The chromatographs of the two plant materials were compared and differences of compounds were found. It showed that phytosterols showed a dramatic rise in content, and sesquiterpenes were found to be synthesized in DXR. Copyright © 2015 John Wiley & Sons, Ltd.

  19. Quantifying biochemical quality parameters in carrots (Daucus carota L.) - FT-Raman spectroscopy as efficient tool for rapid metabolite profiling.

    Science.gov (United States)

    Krähmer, Andrea; Böttcher, Christoph; Rode, Andrea; Nothnagel, Thomas; Schulz, Hartwig

    2016-12-01

    Application of FT-Raman spectroscopy for simultaneous quantification of carotenoids, carbohydrates, polyacetylenes and phenylpropanoids with high bioactive potential was investigated in storage roots of Daucus carota. Within single FT-Raman experiment carbohydrates, carotenoids, and polyacetylenes could be reliably quantified with high coefficients of determination of R(2)>0.91. The most abundant individual representatives of each compound class could be quantified with comparably high quality resulting in R(2)=0.97 and 0.96 for α-carotene and β-carotene, in R(2)=0.90 for falcarindiol (FaDOH), R(2)=0.99, 0.98 and 0.96 for fructose, glucose and sucrose. In contrast, application of FT-Raman spectroscopy for quantification of two laserine-type phenylpropanoids was investigated but failed due to low concentration and Raman response. Furthermore, evaluation of metabolic profiles by principle component analysis (PCA) revealed metabolic variety of carrot root composition depending on root color and botanical relationship. Copyright © 2016 Elsevier Ltd. All rights reserved.

  20. Profiling olfactory stem cells from living patients identifies miRNAs relevant for autism pathophysiology.

    Science.gov (United States)

    Nguyen, Lam Son; Lepleux, Marylin; Makhlouf, Mélanie; Martin, Christelle; Fregeac, Julien; Siquier-Pernet, Karine; Philippe, Anne; Feron, François; Gepner, Bruno; Rougeulle, Claire; Humeau, Yann; Colleaux, Laurence

    2016-01-01

    Autism spectrum disorders (ASD) are a group of neurodevelopmental disorders caused by the interaction between genetic vulnerability and environmental factors. MicroRNAs (miRNAs) are key posttranscriptional regulators involved in multiple aspects of brain development and function. Previous studies have investigated miRNAs expression in ASD using non-neural cells like lymphoblastoid cell lines (LCL) or postmortem tissues. However, the relevance of LCLs is questionable in the context of a neurodevelopmental disorder, and the impact of the cause of death and/or post-death handling of tissue likely contributes to the variations observed between studies on brain samples. miRNA profiling using TLDA high-throughput real-time qPCR was performed on miRNAs extracted from olfactory mucosal stem cells (OMSCs) biopsied from eight patients and six controls. This tissue is considered as a closer tissue to neural stem cells that could be sampled in living patients and was never investigated for such a purpose before. Real-time PCR was used to validate a set of differentially expressed miRNAs, and bioinformatics analysis determined common pathways and gene targets. Luciferase assays and real-time PCR analysis were used to evaluate the effect of miRNAs misregulation on the expression and translation of several autism-related transcripts. Viral vector-mediated expression was used to evaluate the impact of miRNAs deregulation on neuronal or glial cells functions. We identified a signature of four miRNAs (miR-146a, miR-221, miR-654-5p, and miR-656) commonly deregulated in ASD. This signature is conserved in primary skin fibroblasts and may allow discriminating between ASD and intellectual disability samples. Putative target genes of the differentially expressed miRNAs were enriched for pathways previously associated to ASD, and altered levels of neuronal transcripts targeted by miR-146a, miR-221, and miR-656 were observed in patients' cells. In the mouse brain, miR-146a, and miR-221

  1. Defensive Armor of Potato Tubers: Nonpolar Metabolite Profiling, Antioxidant Assessment, and Solid-State NMR Compositional Analysis of Suberin-Enriched Wound-Healing Tissues.

    Science.gov (United States)

    Dastmalchi, Keyvan; Kallash, Linda; Wang, Isabel; Phan, Van C; Huang, Wenlin; Serra, Olga; Stark, Ruth E

    2015-08-05

    The cultivation, storage, and distribution of potato tubers are compromised by mechanical damage and suboptimal healing. To investigate wound-healing progress in cultivars with contrasting russeting patterns, metabolite profiles reported previously for polar tissue extracts were complemented by GC/MS measurements for nonpolar extracts and quantitative (13)C NMR of interfacial solid suspensions. Potential marker compounds that distinguish cultivar type and wound-healing time point included fatty acids, fatty alcohols, alkanes, glyceryl esters, α,ω-fatty diacids, and hydroxyfatty acids. The abundant long-chain fatty acids in nonpolar extracts and solids from the smooth-skinned Yukon Gold cultivar suggested extensive suberin biopolymer formation; this hypothesis was supported by high proportions of arenes, alkenes, and carbonyl groups in the solid and among the polar markers. The absence of many potential marker classes in nonpolar Atlantic extracts and interfacial solids suggested a limited extent of suberization. Modest scavenging activities of all nonpolar extracts indicate that the majority of antioxidants produced in response to wounding are polar.

  2. Metabolite Damage and Metabolite Damage Control in Plants

    Energy Technology Data Exchange (ETDEWEB)

    Hanson, Andrew D. [Horticultural Sciences Department and; Henry, Christopher S. [Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois 60439, email:; Computation Institute, University of Chicago, Chicago, Illinois 60637; Fiehn, Oliver [Genome Center, University of California, Davis, California 95616, email:; de Crécy-Lagard, Valérie [Microbiology and Cell Science Department, University of Florida, Gainesville, Florida 32611, email: ,

    2016-04-29

    It is increasingly clear that (a) many metabolites undergo spontaneous or enzyme-catalyzed side reactions in vivo, (b) the damaged metabolites formed by these reactions can be harmful, and (c) organisms have biochemical systems that limit the buildup of damaged metabolites. These damage-control systems either return a damaged molecule to its pristine state (metabolite repair) or convert harmful molecules to harmless ones (damage preemption). Because all organisms share a core set of metabolites that suffer the same chemical and enzymatic damage reactions, certain damage-control systems are widely conserved across the kingdoms of life. Relatively few damage reactions and damage-control systems are well known. Uncovering new damage reactions and identifying the corresponding damaged metabolites, damage-control genes, and enzymes demands a coordinated mix of chemistry, metabolomics, cheminformatics, biochemistry, and comparative genomics. This review illustrates the above points using examples from plants, which are at least as prone to metabolite damage as other organisms.

  3. Polymerase specific error rates and profiles identified by single molecule sequencing.

    Science.gov (United States)

    Hestand, Matthew S; Van Houdt, Jeroen; Cristofoli, Francesca; Vermeesch, Joris R

    2016-01-01

    DNA polymerases have an innate error rate which is polymerase and DNA context specific. Historically the mutational rate and profiles have been measured using a variety of methods, each with their own technical limitations. Here we used the unique properties of single molecule sequencing to evaluate the mutational rate and profiles of six DNA polymerases at the sequence level. In addition to accurately determining mutations in double strands, single molecule sequencing also captures direction specific transversions and transitions through the analysis of heteroduplexes. Not only did the error rates vary, but also the direction specific transitions differed among polymerases. Copyright © 2016 Elsevier B.V. All rights reserved.

  4. Discovering metabolic indices for early detection of squash (Cucurbita maxima) storage quality using GC-MS-based metabolite profiling.

    Science.gov (United States)

    Okazaki, K; Kimura, Y; Sugiyama, K; Kami, D; Nakamura, T; Oka, N

    2016-04-01

    Squash (Cucubita maxima) cultivars with good storage qualities are needed for breeding to improve poor crop supply during winter in Japan. We measured changes in squash constituents during different storage periods to identify compounds that were suitable to be used as indices of storage quality. Principal components analysis of compounds at 1-5 months after harvest showed that PC1 scores were lower for cultivars with a higher rather than lower SQ (storage quality) ranks. Partial least-squares regression analysis was performed using the peak areas of all compounds identified from the 15 cultivars at 1 month after harvest as explanation variables and SQ as the target variable. Variable influence on projection scores and rank correlation coefficients were higher for arabinose and xylose, which showed less temporal change during the storage period; hence, they were considered to be suitable indicators for storage evaluation. These data will be useful for future studies aiming to improve storage quality of squash. Copyright © 2015 Elsevier Ltd. All rights reserved.

  5. Antioxidant and metabolite profiling of North American and neotropical blueberries using LC-TOF-MS and multivariate analyses.

    Science.gov (United States)

    Ma, Chunhui; Dastmalchi, Keyvan; Flores, Gema; Wu, Shi-Biao; Pedraza-Peñalosa, Paola; Long, Chunlin; Kennelly, Edward J

    2013-04-10

    There are many neotropical blueberries, and recent studies have shown that some have even stronger antioxidant activity than the well-known edible North American blueberries. Antioxidant marker compounds were predicted by applying multivariate statistics to data from LC-TOF-MS analysis and antioxidant assays of 3 North American blueberry species (Vaccinium corymbosum, Vaccinium angustifolium, and a defined mixture of Vaccinium virgatum with V. corymbosum) and 12 neotropical blueberry species (Anthopterus wardii, Cavendishia grandifolia, Cavendishia isernii, Ceratostema silvicola, Disterigma rimbachii, Macleania coccoloboides, Macleania cordifolia, Macleania rupestris, Satyria boliviana, Sphyrospermum buxifolium, Sphyrospermum cordifolium, and Sphyrospermum ellipticum). Fourteen antioxidant markers were detected, and 12 of these, including 7 anthocyanins, 3 flavonols, 1 hydroxycinnamic acid, and 1 iridoid glycoside, were identified. This application of multivariate analysis to bioactivity and mass data can be used for identification of pharmacologically active natural products and may help to determine which neotropical blueberry species will be prioritized for agricultural development. Also, the compositional differences between North American and neotropical blueberries were determined by chemometric analysis, and 44 marker compounds including 16 anthocyanins, 15 flavonoids, 7 hydroxycinnamic acid derivatives, 5 triterpene glycosides, and 1 iridoid glycoside were identified.

  6. Metabolite profiling of flavonols and in vitro antioxidant activity of young shoots of wild Humulus lupulus L. (hop).

    Science.gov (United States)

    Maietti, Annalisa; Brighenti, Virginia; Bonetti, Gianpiero; Tedeschi, Paola; Prencipe, Francesco Pio; Benvenuti, Stefania; Brandolini, Vincenzo; Pellati, Federica

    2017-08-05

    Humulus lupulus L., commonly named hop, is well-known for its sedative and estrogenic activity. While hop cones are widely characterized, only few works have been carried out on the young shoots of this plant. In the light of this, the aim of this study was to identify for the first time the flavonoids present in young hop shoots and to compare the composition of samples harvested from different locations in Northern Italy with their antioxidant activity. The samples were extracted by means of dynamic maceration with methanol. The HPLC-UV/DAD, HPLC-ESI-MS and MS 2 analysis were carried out by using an Ascentis C 18 column (250×4.6mm I.D., 5μm), with a mobile phase composed of 0.1M formic acid in both water and acetonitrile, under gradient elution. Quercetin and kaempferol glycosides were the main compounds identified and quantified in hop shoot extracts. Total flavonols ranged from 2698±185 to 517±48μg/g (fresh weight). The antioxidant activity was determined by means of the radical scavenging activity assay against diphenylpicrylhydrazyl (DPPH) and by using a photochemiluscence assay with a Photochem ® apparatus. The results showed that hop shoots represent a new source of flavonols; therefore, they can be useful for a possible incorporation in the diet as a functional food or applied in the nutraceutical ambit. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. High-throughput metabolic profiling of diverse green Coffea arabica beans identified tryptophan as a universal discrimination factor for immature beans.

    Science.gov (United States)

    Setoyama, Daiki; Iwasa, Keiko; Seta, Harumichi; Shimizu, Hiroaki; Fujimura, Yoshinori; Miura, Daisuke; Wariishi, Hiroyuki; Nagai, Chifumi; Nakahara, Koichi

    2013-01-01

    The maturity of green coffee beans is the most influential determinant of the quality and flavor of the resultant coffee beverage. However, the chemical compounds that can be used to discriminate the maturity of the beans remain uncharacterized. We herein analyzed four distinct stages of maturity (immature, semi-mature, mature and overripe) of nine different varieties of green Coffea arabica beans hand-harvested from a single experimental field in Hawaii. After developing a high-throughput experimental system for sample preparation and liquid chromatography-mass spectrometry (LC-MS) measurement, we applied metabolic profiling, integrated with chemometric techniques, to explore the relationship between the metabolome and maturity of the sample in a non-biased way. For the multivariate statistical analyses, a partial least square (PLS) regression model was successfully created, which allowed us to accurately predict the maturity of the beans based on the metabolomic information. As a result, tryptophan was identified to be the best contributor to the regression model; the relative MS intensity of tryptophan was higher in immature beans than in those after the semi-mature stages in all arabica varieties investigated, demonstrating a universal discrimination factor for diverse arabica beans. Therefore, typtophan, either alone or together with other metabolites, may be utilized for traders as an assessment standard when purchasing qualified trading green arabica bean products. Furthermore, our results suggest that the tryptophan metabolism may be tightly linked to the development of coffee cherries and/or beans.

  8. High-throughput metabolic profiling of diverse green Coffea arabica beans identified tryptophan as a universal discrimination factor for immature beans.

    Directory of Open Access Journals (Sweden)

    Daiki Setoyama

    Full Text Available The maturity of green coffee beans is the most influential determinant of the quality and flavor of the resultant coffee beverage. However, the chemical compounds that can be used to discriminate the maturity of the beans remain uncharacterized. We herein analyzed four distinct stages of maturity (immature, semi-mature, mature and overripe of nine different varieties of green Coffea arabica beans hand-harvested from a single experimental field in Hawaii. After developing a high-throughput experimental system for sample preparation and liquid chromatography-mass spectrometry (LC-MS measurement, we applied metabolic profiling, integrated with chemometric techniques, to explore the relationship between the metabolome and maturity of the sample in a non-biased way. For the multivariate statistical analyses, a partial least square (PLS regression model was successfully created, which allowed us to accurately predict the maturity of the beans based on the metabolomic information. As a result, tryptophan was identified to be the best contributor to the regression model; the relative MS intensity of tryptophan was higher in immature beans than in those after the semi-mature stages in all arabica varieties investigated, demonstrating a universal discrimination factor for diverse arabica beans. Therefore, typtophan, either alone or together with other metabolites, may be utilized for traders as an assessment standard when purchasing qualified trading green arabica bean products. Furthermore, our results suggest that the tryptophan metabolism may be tightly linked to the development of coffee cherries and/or beans.

  9. Whole-genome sequencing and comprehensive molecular profiling identify new driver mutations in gastric cancer

    NARCIS (Netherlands)

    Wang, Kai; Yuen, Siu Tsan; Xu, Jiangchun; Lee, Siu Po; Yan, Helen H N; Shi, Stephanie T; Siu, Hoi Cheong; Deng, Shibing; Chu, Kent Man; Law, Simon; Chan, Kok Hoe; Chan, Annie S Y; Tsui, Wai Yin; Ho, Siu Lun; Chan, Anthony K W; Man, Jonathan L K; Foglizzo, Valentina; Ng, Man Kin; Chan, April S; Ching, Yick Pang; Cheng, Grace H W; Xie, Tao; Fernandez, Julio; Li, Vivian S W; Clevers, Hans; Rejto, Paul A; Mao, Mao; Leung, Suet Yi

    Gastric cancer is a heterogeneous disease with diverse molecular and histological subtypes. We performed whole-genome sequencing in 100 tumor-normal pairs, along with DNA copy number, gene expression and methylation profiling, for integrative genomic analysis. We found subtype-specific genetic and

  10. Transcriptional profiling identifies physicochemical properties of nanomaterials that are determinants of the in vivo pulmonary response

    DEFF Research Database (Denmark)

    Halappanavar, Sabina; Saber, Anne Thoustrup; Decan, Nathalie

    2015-01-01

    We applied transcriptional profiling to elucidate the mechanisms associated with pulmonary responses to titanium dioxide (TiO2) nanoparticles (NPs) of different sizes and surface coatings, and to determine if these responses are modified by NP size, surface area, surface modification, and embeddi...

  11. Use of NMR metabolomic plasma profiling methodologies to identify illicit growth-promoting administrations

    NARCIS (Netherlands)

    Graham, S.F.; Ruiz Aracama, A.; Lommen, A.; Cannizzo, F.T.; Biolatti, B.; Elliott, C.T.; Mooney, M.H.

    2012-01-01

    Detection of growth-promoter use in animal production systems still proves to be an analytical challenge despite years of activity in the field. This study reports on the capability of NMR metabolomic profiling techniques to discriminate between plasma samples obtained from cattle treated with

  12. Qualitatively and quantitatively comparing secondary metabolites in three medicinal parts derived from Poria cocos (Schw.) Wolf using UHPLC-QTOF-MS/MS-based chemical profiling.

    Science.gov (United States)

    Zhu, Lixia; Xu, Jun; Zhang, Shijin; Wang, Rujing; Huang, Qing; Chen, Hubiao; Dong, Xiaoping; Zhao, Zhongzhen

    2018-02-20

    Poria cocos (Schw.) Wolf, is a fungus that grows on dead pine roots, producing a solid white sclerotium (fruiting body). Three parts of the sclerotium are commonly used in traditional Chinese medicine, namely, the epidermis, known as Poria Cutis or fulingpi in Chinese; the middle part, known as Poria or baifuling; and the sclerotium with some host attached, known as fushen. For fushen, the hostwood is the inner part, known as fushenmu. The epidermis, middle part and middle-plus-inner parts have long been used for different syndromes or diseases, but the differences in their chemistry have not been established. In this study, ultra-performance liquid chromatography-quadrupole/time-of-flight mass spectrometry (UHPLC-QTOF-MS/MS) was used to explore the differences of secondary metabolites in these three botanical parts of Poria cocos. In 13 batches of samples, a total of 147 chromatographic peaks were unequivocally or tentatively identified. Of these, 15 peaks were common to all three parts (the epidermis, middle, and inner part), while the rest were found in only one or two of the parts. Meanwhile, dissimilarities among the chemical compositions of three botanical parts were further investigated by principal component analysis (PCA), and supervised orthogonal partial least squares-discriminate analysis (OPLS-DA). Eight major bioactive triterpene acids that played important roles in differentiating the epidermis, middle and inner part were simultaneously quantified using the extracting ion mode of UHPLC-QTOF-MS/MS. The quantitative results showed that the analytes accumulated mostly in the epidermis and inner part, with the least accumulation in the middle part. This systematic information on the differences in secondary metabolites in the three botanical regions of Poria cocos provides a factual chemical basis not only for discrimination in therapeutic practice but also for quality evaluation of Poria cocos. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. Laser microdissection and cryogenic nuclear magnetic resonance spectroscopy: an alliance for cell type-specific metabolite profiling.

    Science.gov (United States)

    Hölscher, D; Schneider, B

    2007-02-01

    Laser microdissection was used as a tool to harvest secretory cavities (SC) from leaves of Dilatris pillansii Barker (Haemodoraceae) and from leaves and flowers of herbarium specimens of Dilatris corymbosa Berg. and Dilatris viscosa L. Cryogenic (1)H NMR spectroscopy and HPLC analysis of microdissected samples indicated specific accumulation of methoxyphenylphenalenones in the SC. The structures of two novel and a known natural product in the secretory tissue were confirmed by comparison with authentic compounds isolated from rhizomes and roots from which further phenylphenalenones and phenylphenalenone glucosides were isolated and identified by spectroscopic methods. How it will be possible to use the LMD technique to localize natural products in specific plant cell populations is also discussed.

  14. Comparative evaluation of ICP sample introduction systems to be used in the metabolite profiling of chlorine-containing pharmaceuticals via HPLC-ICP-MS.

    Science.gov (United States)

    Klencsár, Balázs; Sánchez, Carlos; Balcaen, Lieve; Todolí, José; Lynen, Frederic; Vanhaecke, Frank

    2018-05-10

    A systematic evaluation of four different ICP sample introduction systems to be used in the context of metabolite profiling of chlorine-containing pharmaceuticals via HPLC-ICP-MS was carried out using diclofenac and its major metabolite, 4'-hydroxy-diclofenac, as model compounds. The strict requirements for GMP validation of chromatographic methods in the pharmaceutical industry were adhered to in this context. The final aim of this investigation is an extension of the applicability and validatability of HPLC-ICP-MS in the field of pharmaceutical R&D. Five different gradient programmes were tested while the baseline peak width (w b ), peak capacity (P), USP tailing factor (A s ) and USP signal-to-noise ratio (USP S/N) were determined as major indicators of the chromatographic performance and the values obtained were compared to the corresponding FDA recommendations (if applicable). Four different ICP-MS sample introductions systems were investigated involving two units typically working at higher flow rates (∼1.0 mL min -1 ) and another two systems working at lower flow rates (∼0.1 mL min -1 ). Optimal conditions with potential for applicability under GMP conditions were found at a mobile phase flow rate of 1.0 mL min -1 by using a pneumatic micro-flow LC nebulizer mounted onto a Peltier-cooled cyclonic spray chamber cooled to -1 °C for sample introduction. Under these conditions, HPLC-ICP-MS provided a chromatographic performance similar to that of HPLC with UV detection. The peak shape (USP tailing factor = 1.1-1.4) was significantly improved compared to that obtained with the Peltier-cooled Scott-type spray chamber. Two alternative sample introduction systems - a POINT ® and a High-Temperature Torch-Integrated Sample Introduction System (hTISIS) - were also tested at a flow rate of 0.1 mL min -1 using a chromatographic column with 1.0 mm ID. Although these systems allowed the peak shape to be improved compared to that obtained with

  15. Utilization of IκB–EGFP Chimeric Gene as an Indicator to Identify Microbial Metabolites with NF-κB Inhibitor Activity

    Directory of Open Access Journals (Sweden)

    Lin Yu-Ling

    2010-10-01

    Full Text Available Abstract NF-κB regulates several important expressions, such as cytokine release, anti-apoptosis, adhesion molecule expression, and cell cycle processing. Several NF-κB inhibitors have been discovered as an anti-tumor or anti-inflammatory drug. The activity of NF-κB transcription factor is negatively regulated by IκB binding. In this study, IκB assay system was established and IκB–EGFP fusion protein was used as an indicator to monitor the effects of substances on the IκB degradation. The results indicated that the chosen hydroquinone could inhibit the IκB degradation and cause the cell de-attachment from the bottom of culture plate. In addition, this system could also monitor the IκB degradation of microbial metabolite of natural mixtures of propolis. Thus, the IκB assay system may be a good system for drug discovery related to microbial metabolite.

  16. Utilization of IκB–EGFP Chimeric Gene as an Indicator to Identify Microbial Metabolites with NF-κB Inhibitor Activity

    Directory of Open Access Journals (Sweden)

    Chen Yen-Shun

    2010-01-01

    Full Text Available Abstract NF-κB regulates several important expressions, such as cytokine release, anti-apoptosis, adhesion molecule expression, and cell cycle processing. Several NF-κB inhibitors have been discovered as an anti-tumor or anti-inflammatory drug. The activity of NF-κB transcription factor is negatively regulated by IκB binding. In this study, IκB assay system was established and IκB–EGFP fusion protein was used as an indicator to monitor the effects of substances on the IκB degradation. The results indicated that the chosen hydroquinone could inhibit the IκB degradation and cause the cell de-attachment from the bottom of culture plate. In addition, this system could also monitor the IκB degradation of microbial metabolite of natural mixtures of propolis. Thus, the IκB assay system may be a good system for drug discovery related to microbial metabolite.

  17. Metabolites of Siamenoside I and Their Distributions in Rats

    Directory of Open Access Journals (Sweden)

    Xue-Rong Yang

    2016-01-01

    Full Text Available Siamenoside I is the sweetest mogroside that has several kinds of bioactivities, and it is also a constituent of Siraitiae Fructus, a fruit and herb in China. Hitherto the metabolism of siamenoside I in human or animals remains unclear. To reveal its metabolic pathways, a high-performance liquid chromatography-electrospray ionization-ion trap-time of flight-multistage mass spectrometry (HPLC-ESI-IT-TOF-MSn method was used to profile and identify its metabolites in rats. Altogether, 86 new metabolites were identified or tentatively identified, and 23 of them were also new metabolites of mogrosides. In rats, siamenoside I was found to undergo deglycosylation, hydroxylation, dehydrogenation, deoxygenation, isomerization, and glycosylation reactions. Among them, deoxygenation, pentahydroxylation, and didehydrogenation were novel metabolic reactions of mogrosides. The distributions of siamenoside I and its 86 metabolites in rat organs were firstly reported, and they were mainly distributed to intestine, stomach, kidney, and brain. The most widely distributed metabolite was mogroside IIIE. In addition, eight metabolites were bioactive according to literature. These findings would help to understand the metabolism and effective forms of siamenoside I and other mogrosides in vivo.

  18. Targeting high-performance liquid chromatography-high-resolution mass spectrometry-solid-phase extraction-nuclear magnetic resonance analysis with high-resolution radical scavenging profiles - bioactive secondary metabolites from the endophytic fungus Penicillium namyslowskii

    DEFF Research Database (Denmark)

    Wubshet, Sileshi Gizachew; Nyberg, Nils; Tejesvi, Mysore V.

    2013-01-01

    The high-resolution radical scavenging profile of an extract of the endophytic fungus Penicillium namyslowskii was used to target analysis by high-performance liquid chromatography-high-resolution mass spectrometry-solid-phase extraction-nuclear magnetic resonance spectroscopy, i.e., HPLC......-HRMS-SPE-NMR, for identification of anti-oxidative secondary metabolites. This revealed the two chromatographic peaks with the highest relative response in the radical scavenging profile to be griseophenone C and peniprequinolone. The HPLC-HRMS-SPE-NMR analysis was performed in the tube-transfer mode using a cryogenically cooled...... NMR probe designed for 1.7-mm NMR tubes. To further explore the potential of the above HPLC-HRMS-SPE-NMR platform for analysis of endophytic extracts, six peaks displaying no radical scavenging activity were also analyzed. This allowed unambiguous identification of six metabolites, i...

  19. Personality Profiles Identify Depressive Symptoms over Ten Years? A Population-Based Study

    Directory of Open Access Journals (Sweden)

    Kim Josefsson

    2011-01-01

    Full Text Available Little is known about the relationship between temperament and character inventory (TCI profiles and depressive symptoms. Personality profiles are useful, because personality traits may have different effects on depressive symptoms when combined with different combinations of other traits. Participants were from the population-based Young Finns study with repeated measurements in 1997, 2001, and 2007 (=1402 to 1902. TCI was administered in 1997 and mild depressive symptoms (modified Beck’s depression inventory, BDI were reported in 1997, 2001, and 2007. BDI-II was also administered in 2007. We found that high harm avoidance and low self-directedness related strongly to depressive symptoms. In addition, sensitive (NHR and fanatical people (ScT were especially vulnerable to depressive symptoms. high novelty seeking and reward dependence increased depressive symptoms when harm avoidance was high. These associations were very similar in cross-sectional and longitudinal analysis. Personality profiles help in understanding the complex associations between depressive symptoms and personality.

  20. High speed rail and coastal tourism: Identifying passenger profiles and travel behaviour.

    Science.gov (United States)

    Gutiérrez, Aaron; Ortuño, Armando

    2017-01-01

    In this paper, we characterise tourists most likely to visit a coastal destination by high-speed rail (HSR). Our data came from a survey conducted among HSR passengers during 2014's high season (July and August) at Spain's Camp de Tarragona and Alicante Stations, each of which is near a mass tourism destination on the Mediterranean coast: the Costa Daurada and the Costa Blanca, respectively. We used responses to the survey, which presented binary discrete-choice situations, to construct a database necessary for a logistic regression model that allowed us to examine how passenger profile, trip characteristics, and stay conditions influenced the use of HSR services on visits to each coastal destination. Results highlighted significant differences in the profiles of tourists who arrived at each destination by HSR and, in turn, that no specific tourist profile is associated with HSR, even for two stations that serve sunny beach destinations. Among its implications, to analyse travellers that HSR can attract, it is vital to consider the specific characteristics of each destination and its current market.

  1. Metabolite profiling using liquid chromatography/quadrupole time-of-flight mass spectrometry for the identification of a suitable marker and target matrix of griseofulvin use in bovines.

    Science.gov (United States)

    Tarbin, J A; Fussell, R J

    2013-06-30

    Griseofulvin is an antifungal agent with potential for misuse in food-producing animals. Little is known about its metabolism in ruminants and hence what are suitable marker residues and target matrices for monitoring purposes. Tissues harvested from cattle treated with the antifungal agent griseofulvin were screened using liquid chromatography coupled to positive and negative electrospray ionization (ESI) quadrupole time-of-flight mass spectrometry (qToFMS) operated in ToF mode. Twenty-five possible metabolites were detected across all tissue types, but two isomeric compounds with accurate masses corresponding to loss of a methyl group from parent griseofulvin were considered to be the best candidate markers. Data from fragmentation experiments enabled a tentative assignment of the structures of the two compounds as 4-demethylgriseofulvin and 6-demethylgriseofulvin. These assignments were confirmed by matching the product ion spectra of incurred residues to those of custom synthesized reference standards. 4-Demethyl- and 6-demethylgriseofulvin have been identified as potential marker compounds of griseofulvin use in cattle. Liver was identified as the target matrix. Hair was shown to have potential for non-invasive testing. © Crown copyright 2013. Reproduced with the permission of Her Majesty's Stationery Office. Published by John Wiley & Sons, Ltd.

  2. Mutagenic azide metabolite is azidoalanine

    International Nuclear Information System (INIS)

    Owais, W.M.; Rosichan, J.L.; Ronald, R.C.; Kleinhofs, A.; Nilan, R.A.

    1981-01-01

    Sodium axide produces high mutation rates in a number of species. Azide mutagenicity is mediated through a metabolite in barley and bacteria. Many studies showed that azide affects the L-cysteine biosynthesis pathway. Cell-free extracts of Salmonella typhimurium convert azide and O-acetylserine to the mutagenic metabolite. O-acetylserine sulfhydrylase was identified as the enzyme responsible for the metabolite biosynthesis. To confirm the conclusion that the azide metabolite is formed through the β-substitution pathway of L-cysteine, we radioactively labeled the azide metabolite using 14 C-labeled precursors. Moreover, the mutagenic azide metabolite was purified and identified as azidoalanine based on mass spectroscopy and elemental analysis. 26 refs., 3 figs., 1 tab

  3. Detection of characteristic metabolites of Aspergillus fumigatus and Candida species using ion mobility spectrometry-metabolic profiling by volatile organic compounds.

    Science.gov (United States)

    Perl, Thorsten; Jünger, Melanie; Vautz, Wolfgang; Nolte, Jürgen; Kuhns, Martin; Borg-von Zepelin, Margarete; Quintel, Michael

    2011-11-01

    Volatile metabolites of Aspergillus fumigatus and Candida species can be detected by gas chromatography/mass spectrometry (GC/MS). A multi-capillary column - ion mobility spectrometer (MCC-IMS) was used in this study to assess volatile organic compounds (VOCs) in the headspace above A. fumigatus and the four Candida species Candida albicans, Candida parapsilosis, Candida glabrata and Candida tropicalis in an innovative approach, validated for A. fumigatus and C. albicans by GC/MS analyses. For the detection of VOCs, a special stainless steel measurement chamber for the microbial cultures was used. The gas outlet was either attached to MCC-IMS or to adsorption tubes (Tenax GR) for GC/MS measurements. Isoamyl alcohol, cyclohexanone, 3-octanone and phenethylalcohol can be described as discriminating substances by means of GC/MS. With MCC-IMS, the results for 3-octanone and phenethylalcohol are concordant and additionally to GC/MS, ethanol and two further compounds (p_0642_1/p_683_1 and p_705_3) can be described. Isoamyl alcohol and cyclohexanone were not properly detectable with MCC-IMS. The major advantage of the MCC-IMS system is the feasibility of rapid analysis of complex gas mixtures without pre-concentration or preparation of samples and regardless of water vapour content in an online setup. Discrimination of fungi on genus level of the investigated germs by volatile metabolic profile and therefore detection of VOC is feasible. However, a further discrimination on species level for Candida species was not possible. © 2011 Blackwell Verlag GmbH.

  4. Metabolite profiles reveal energy failure and impaired beta-oxidation in liver of mice with complex III deficiency due to a BCS1L mutation.

    Directory of Open Access Journals (Sweden)

    Heike Kotarsky

    Full Text Available BACKGROUND & AIMS: Liver is a target organ in many mitochondrial disorders, especially if the complex III assembly factor BCS1L is mutated. To reveal disease mechanism due to such mutations, we have produced a transgenic mouse model with c.232A>G mutation in Bcs1l, the causative mutation for GRACILE syndrome. The homozygous mice develop mitochondrial hepatopathy with steatosis and fibrosis after weaning. Our aim was to assess cellular mechanisms for disease onset and progression using metabolomics. METHODS: With mass spectrometry we analyzed metabolite patterns in liver samples obtained from homozygotes and littermate controls of three ages. As oxidative stress might be a mechanism for mitochondrial hepatopathy, we also assessed H(2O(2 production and expression of antioxidants. RESULTS: Homozygotes had a similar metabolic profile at 14 days of age as controls, with the exception of slightly decreased AMP. At 24 days, when hepatocytes display first histopathological signs, increases in succinate, fumarate and AMP were found associated with impaired glucose turnover and beta-oxidation. At end stage disease after 30 days, these changes were pronounced with decreased carbohydrates, high levels of acylcarnitines and amino acids, and elevated biogenic amines, especially putrescine. Signs of oxidative stress were present in end-stage disease. CONCLUSIONS: The findings suggest an early Krebs cycle defect with increases of its intermediates, which might play a role in disease onset. During disease progression, carbohydrate and fatty acid metabolism deteriorate leading to a starvation-like condition. The mouse model is valuable for further investigations on mechanisms in mitochondrial hepatopathy and for interventions.

  5. Transcriptional and Cytokine Profiles Identify CXCL9 as a Biomarker of Disease Activity in Morphea.

    Science.gov (United States)

    O'Brien, Jack C; Rainwater, Yevgeniya Byekova; Malviya, Neeta; Cyrus, Nika; Auer-Hackenberg, Lorenz; Hynan, Linda S; Hosler, Gregory A; Jacobe, Heidi T

    2017-08-01

    IFN-related pathways have not been studied in morphea, and biomarkers are needed. We sought to characterize morphea serum cytokine imbalance and IFN-related gene expression in blood and skin to address this gap by performing a case-control study of 87 participants with morphea and 26 healthy control subjects. We used multiplexed immunoassays to determine serum cytokine concentrations, performed transcriptional profiling of whole blood and lesional morphea skin, and used double-staining immunohistochemistry to determine the cutaneous cellular source of CXCL9. We found that CXCL9 was present at increased concentrations in morphea serum (P morphea skin (fold change = 30.6, P = 0.006), and preliminary transcriptional profiling showed little evidence for IFN signature in whole blood. Double-staining immunohistochemistry showed CXCL9 co-localized with CD68 + dermal macrophages. In summary, inflammatory morphea is characterized by T helper type 1 cytokine imbalance in serum, particularly CXCL9, which is associated with disease activity. CXCL9 expression in lesional macrophages implicates the skin as the source of circulating cytokines. CXCL9 is a promising biomarker of disease activity in morphea. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  6. Effect of alcohol fermented feed on lactating performance, blood metabolites, milk Fatty Acid profile and cholesterol content in holstein lactating cows.

    Science.gov (United States)

    Li, X Z; Park, B K; Yan, C G; Choi, J G; Ahn, J S; Shin, J S

    2012-11-01

    A feeding experiment with 40 lactating Holstein cows and 4 dietary treatments was conducted to investigate supplementation with different levels of alcohol fermented feed to the TMR on lactating performance, blood metabolites, milk fatty acid profile and cholesterol concentration of blood and milk. Forty Holstein lactating cows (106±24 d post-partum; mean±SD) were distributed into four groups and randomly assigned to one of four treatments with each containing 10 cows per treatment. The treatment supplemented with TMR (DM basis) as the control (CON), and CON mixed with alcohol-fermented feeds (AFF) at a level of 5%, 10% and 15% of the TMR as T1, T2 and T3, respectively. Dry matter intake and milk yield were not affected by supplementation of AFF. An increased 4% FCM in the milk occurred in cows fed T3 diet compared with CON, while T1 and T2 diets decreased 4% FCM in a dose dependent manner. Supplementation of AFF increased the concentration of albumin, total protein (TP), ammonia, and high density lipoprotein-cholesterol in serum compared with CON. In contrast, supplementation with AFF clearly decreased concentration of blood urea nitrogen (BUN) and total cholesterol (TC) compare with CON. AFF supplementation increased the proportion of C18:1n9 and C18:2n6 compared to CON. A decrease in the concentration of saturated fatty acid (SFA) for T1, T2 and T3 resulted in an increased unsaturated fatty acid (USFA) to SFA ratio compared to CON. Concentration of cholesterol in milk fat was reduced in proportion to the supplemental level of AFF. Feeding a diet supplemented with a moderate level AFF to lactating cows could be a way to alter the feed efficiency and fatty acid profile of milk by increasing potentially human consumer healthy fatty acid without detrimental effects on feed intake and milk production. A substantially decreased cholesterol proportion in milk induced by supplementation AFF suggests that alcohol fermented feed may improve milk cholesterol levels

  7. Effect of Alcohol Fermented Feed on Lactating Performance, Blood Metabolites, Milk Fatty Acid Profile and Cholesterol Content in Holstein Lactating Cows

    Directory of Open Access Journals (Sweden)

    X. Z. Li

    2012-11-01

    Full Text Available A feeding experiment with 40 lactating Holstein cows and 4 dietary treatments was conducted to investigate supplementation with different levels of alcohol fermented feed to the TMR on lactating performance, blood metabolites, milk fatty acid profile and cholesterol concentration of blood and milk. Forty Holstein lactating cows (106±24 d post-partum; mean±SD were distributed into four groups and randomly assigned to one of four treatments with each containing 10 cows per treatment. The treatment supplemented with TMR (DM basis as the control (CON, and CON mixed with alcohol-fermented feeds (AFF at a level of 5%, 10% and 15% of the TMR as T1, T2 and T3, respectively. Dry matter intake and milk yield were not affected by supplementation of AFF. An increased 4% FCM in the milk occurred in cows fed T3 diet compared with CON, while T1 and T2 diets decreased 4% FCM in a dose dependent manner. Supplementation of AFF increased the concentration of albumin, total protein (TP, ammonia, and high density lipoprotein-cholesterol in serum compared with CON. In contrast, supplementation with AFF clearly decreased concentration of blood urea nitrogen (BUN and total cholesterol (TC compare with CON. AFF supplementation increased the proportion of C18:1n9 and C18:2n6 compared to CON. A decrease in the concentration of saturated fatty acid (SFA for T1, T2 and T3 resulted in an increased unsaturated fatty acid (USFA to SFA ratio compared to CON. Concentration of cholesterol in milk fat was reduced in proportion to the supplemental level of AFF. Feeding a diet supplemented with a moderate level AFF to lactating cows could be a way to alter the feed efficiency and fatty acid profile of milk by increasing potentially human consumer healthy fatty acid without detrimental effects on feed intake and milk production. A substantially decreased cholesterol proportion in milk induced by supplementation AFF suggests that alcohol fermented feed may improve milk cholesterol

  8. Determination of AM-2201 metabolites in urine and comparison with JWH-018 abuse.

    Science.gov (United States)

    Jang, Moonhee; Yang, Wonkyung; Shin, Ilchung; Choi, Hyeyoung; Chang, Hyejin; Kim, Eunmi

    2014-03-01

    With respect to the continuous emergence of new synthetic cannabinoids on the market since 2008, evaluation of the metabolism of these compounds and the development of analytical methods for the detection of these drugs including their respective metabolites in biological fluids have become essential. Other than JWH-018 or JWH-073, AM-2201 is one of the frequently identified synthetic cannabinoids in Korea. Recently, in our laboratory, several JWH-018 metabolites have been detected in some urine samples obtained from subjects who were arrested for the possession of herbal mixtures containing only AM-2201 or from those who confessed AM-2201 abuse. In the present study, we identified major urinary metabolites of AM-2201 and several metabolites of JWH-018, i.e., N-5-hydroxylated and carboxylated metabolites from rats administered AM-2201 and found that the metabolic profile in rats was similar to those in human subjects in this study. Analytical results of the urine samples from suspects who had a considerable possibility of AM-2201 or JWH-018 intake were also compared to distinguish between AM-2201 and JWH-018 abuse. The presence of 6-indole hydroxylated metabolites of each drug and N-4-hydroxy metabolite of AM-2201 was found to contribute to the decisive differences in the metabolic patterns of the two drugs. In addition, the concentration ratio of the N-(5-hydroxypentyl) metabolite to the N-(4-hydroxypentyl) metabolite of JWH-018 may be used as a criterion to differentiate between AM-2201 and JWH-018 abuse.

  9. Proteomic profiling of human plasma exosomes identifies PPARγ as an exosome-associated protein

    International Nuclear Information System (INIS)

    Looze, Christopher; Yui, David; Leung, Lester; Ingham, Matthew; Kaler, Maryann; Yao, Xianglan; Wu, Wells W.; Shen Rongfong; Daniels, Mathew P.; Levine, Stewart J.

    2009-01-01

    Exosomes are nanovesicles that are released from cells as a mechanism of cell-free intercellular communication. Only a limited number of proteins have been identified from the plasma exosome proteome. Here, we developed a multi-step fractionation scheme incorporating gel exclusion chromatography, rate zonal centrifugation through continuous sucrose gradients, and high-speed centrifugation to purify exosomes from human plasma. Exosome-associated proteins were separated by SDS-PAGE and 66 proteins were identified by LC-MS/MS, which included both cellular and extracellular proteins. Furthermore, we identified and characterized peroxisome proliferator-activated receptor-γ (PPARγ), a nuclear receptor that regulates adipocyte differentiation and proliferation, as well as immune and inflammatory cell functions, as a novel component of plasma-derived exosomes. Given the important role of exosomes as intercellular messengers, the discovery of PPARγ as a component of human plasma exosomes identifies a potential new pathway for the paracrine transfer of nuclear receptors.

  10. Phylogenetic & Physiological Profiling of Microbial Communities of Contaminated Soils/Sediments: Identifying Microbial consortia...

    Energy Technology Data Exchange (ETDEWEB)

    Terence L. Marsh

    2004-05-26

    The goals of this study were: (1) survey the microbial community in soil samples from a site contaminated with heavy metals using new rapid molecular techniques that are culture-independent; (2) identify phylogenetic signatures of microbial populations that correlate with metal ion contamination; and (3) cultivate these diagnostic strains using traditional as well as novel cultivation techniques in order to identify organisms that may be of value in site evaluation/management or bioremediation.

  11. Gene expression profiles in human and mouse primary cells provide new insights into the differential actions of vitamin D3 metabolites

    DEFF Research Database (Denmark)

    Tuohimaa, Pentti; Wang, Jing-Huan; Khan, Sofia

    2013-01-01

    prostate stromal P29SN cells (hP29SN), which convert 25(OH)D3 into 1α,25(OH)2D3 by 1α-hydroxylase (encoded by the gene CYP27B1), displayed regulation of 164, 171, and 175 genes by treatment with 1α,25(OH)2D3, 25(OH)D3, and 24R,25(OH)2D3, respectively. Mouse primary Cyp27b1 knockout fibroblasts (mCyp27b1...... (-/-)), which lack 1α-hydroxylation, displayed regulation of 619, 469, and 66 genes using the same respective treatments. The number of shared genes regulated by two metabolites is much lower in hP29SN than in mCyp27b1 (-/-). By using DAVID Functional Annotation Bioinformatics Microarray Analysis tools......1α,25-Dihydroxyvitamin D3 (1α,25(OH)2D3) had earlier been regarded as the only active hormone. The newly identified actions of 25-hydroxyvitamin D3 (25(OH)D3) and 24R,25-dihydroxyvitamin D3 (24R,25(OH)2D3) broadened the vitamin D3 endocrine system, however, the current data are fragmented...

  12. Identifying and profiling scholastic cheaters: their personality, cognitive ability, and motivation.

    Science.gov (United States)

    Williams, Kevin M; Nathanson, Craig; Paulhus, Delroy L

    2010-09-01

    Despite much research, skepticism remains over the possibility of profiling scholastic cheaters. However, several relevant predictor variables and newer diagnostic tools have been overlooked. We remedy this deficit with a series of three studies. Study 1 was a large-scale survey of a broad range of personality predictors of self-reported cheating. Significant predictors included the Dark Triad (Machiavellianism, narcissism, psychopathy) as well as low agreeableness and low conscientiousness. Only psychopathy remained significant in a multiple regression. Study 2 replicated this pattern using a naturalistic, behavioral indicator of cheating, namely, plagiarism as indexed by the Internet service Turn-It-In. Poor verbal ability was also an independent predictor. Study 3 examined possible motivational mediators of the association between psychopathy and cheating. Unrestrained achievement and moral inhibition were successful mediators whereas fear of punishment was not. Practical implications for researchers and educators are discussed. PsycINFO Database Record (c) 2010 APA, all rights reserved.

  13. Proteomic profiling of Mycobacterium tuberculosis identifies nutrient-starvation-responsive toxin-antitoxin systems

    DEFF Research Database (Denmark)

    Albrethsen, Jakob; Agner, Jeppe; Piersma, Sander R

    2013-01-01

    In order to successfully enter the latent stage, Mycobacterium tuberculosis must adapt to conditions such as nutrient limitation and hypoxia. In vitro models that mimic latent infection are valuable tools for describing the changes in metabolism that occur when the bacterium exists in a non......-growing form. We used two complementary proteomic approaches, label-free LC-MS/MS analysis and two-dimensional difference gel electrophoresis, to determine the proteome profile of extracellular proteins from M. tuberculosis cultured under nutrient starvation. Through the label-free LC-MS/MS analysis......, significant differences in the overall metabolism during nutrient starvation were detected. Notably, members of the toxin-antitoxin systems were present in larger quantities in nutrient-starved cultures, supporting a role for these global modules as M. tuberculosis switches its metabolism into dormancy...

  14. Expression profiling of S. pombe acetyltransferase mutants identifies redundant pathways of gene regulation

    Directory of Open Access Journals (Sweden)

    Wright Anthony PH

    2010-01-01

    Full Text Available Abstract Background Histone acetyltransferase enzymes (HATs are implicated in regulation of transcription. HATs from different families may overlap in target and substrate specificity. Results We isolated the elp3+ gene encoding the histone acetyltransferase subunit of the Elongator complex in fission yeast and characterized the phenotype of an Δelp3 mutant. We examined genetic interactions between Δelp3 and two other HAT mutants, Δmst2 and Δgcn5 and used whole genome microarray analysis to analyze their effects on gene expression. Conclusions Comparison of phenotypes and expression profiles in single, double and triple mutants indicate that these HAT enzymes have overlapping functions. Consistent with this, overlapping specificity in histone H3 acetylation is observed. However, there is no evidence for overlap with another HAT enzyme, encoded by the essential mst1+ gene.

  15. Identifying measures to balance the risk profile of the Tihange 2 NPP

    International Nuclear Information System (INIS)

    D'Eer, A.M.; Monniez, J.J.

    2001-01-01

    In Belgium, each Nuclear Power Plant is subject to a periodic safety reassessment. In this context, it was found to be desirable to perform a Probabilistic Safety Assessment (PSA) in support of the ten yearly back-fitting process. The Tihange 2 NPP is a 3-loop PWR having a thermal capacity of 2905 MW. Analysis of the plant's risk profile shows that implementing feasible measures for improvement of the shutdown risk, would be beneficial. This is because a configuration leading to significant risk, namely cold pressurization when the residual heat removal system is lost during reduced primary inventory, thus can be avoided. As a result the risk between reactor shutdown and power operation will be balanced. The presentation describes the lessons learnt regarding the Tihange 2 shutdown PSA model and the expected benefits following implementation of one of the proposed measures. (author)

  16. Morphine metabolites

    DEFF Research Database (Denmark)

    Christrup, Lona Louring

    1997-01-01

    , morphine-3-glucuronide (M3G) and morphine-6-glucuronide (M6G) are the major metabolites of morphine. The metabolism of morphine occurs not only in the liver, but may also take place in the brain and the kidneys. The glucuronides are mainly eliminated via bile and urine. Glucuronides as a rule...... are considered as highly polar metabolites unable to cross the blood-brain barrier. Although morphine glucuronidation has been demonstrated in human brain tissue, the capacity is very low compared to that of the liver, indicating that the M3G and M6G concentrations observed in the cerebrospinal fluid (CSF) after...

  17. Students' Conceptual Knowledge and Process Skills in Civic Education: Identifying Cognitive Profiles and Classroom Correlates

    Science.gov (United States)

    Zhang, Ting; Torney-Purta, Judith; Barber, Carolyn

    2012-01-01

    In 2 related studies framed by social constructivism theory, the authors explored a fine-grained analysis of adolescents' civic conceptual knowledge and skills and investigated them in relation to factors such as teachers' qualifications and students' classroom experiences. In Study 1 (with about 2,800 U.S. students), the authors identified 4…

  18. Can LASSI Score Profiles Help Identify Postsecondary Students with Underlying Reading Problems?

    Science.gov (United States)

    Hewlett, Maureen G.; Boonstra, Jacqui; Bell, James H.; Zumbo, Bruno D.

    2000-01-01

    Investigates whether scores on the Learning and Study Skills Inventory (LASSI) could be used to identify postsecondary students who had deficiencies in reading comprehension and vocabulary as measured by the Nelson-Denny Reading Test (NDRT). Finds that participants who obtained low percentile rankings on vocabulary and comprehension were most…

  19. Phenolic metabolites of anthocyanins following a dietary intervention study in post-menopausal women.

    Science.gov (United States)

    de Ferrars, Rachel M; Cassidy, Aedín; Curtis, Peter; Kay, Colin D

    2014-03-01

    Numerous studies feeding anthocyanin-rich foods report limited bioavailability of the parent anthocyanins. The present study explores the identity and concentration of the phenolic metabolites of anthocyanins in humans. Anthocyanin metabolites were quantified in samples collected from a previously conducted 12-wk elderberry intervention study in healthy post-menopausal women. Individual 1-, 2- and 3-h post-bolus urine samples and pooled plasma samples following acute (single bolus) and chronic (12-wk supplementation) anthocyanin consumption (500 mg/day) were analysed using HPLC-ESI-MS/MS. Twenty-eight anthocyanin metabolites were identified in urine and 21 in plasma (including sulfates of vanillic, protocatechuic and benzoic acid). Phenolic metabolites reached peak concentrations of 1237 nM in plasma, while anthocyanin conjugates only reached concentrations of 34 nM. Similarly, in urine, phenolic metabolites were detected at concentrations of 33,185 ± 2549 nM/mM creatinine, while anthocyanin conjugates reached concentrations of 548 ± 219 nM/mM creatinine. There was no evidence that chronic exposure had any impact on either the profile or quantity of metabolites recovered relative to acute exposure. An extensive range of phenolic metabolites of anthocyanin was identified following elderberry consumption in humans, including 11 novel metabolites, which were identified at much higher concentrations than their parent compounds. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Proteomic profiling of Plasmodium sporozoite maturation identifies new proteins essential for parasite development and infectivity

    DEFF Research Database (Denmark)

    Lasonder, Edwin; Janse, Chris J; van Gemert, Geert-Jan

    2008-01-01

    Plasmodium falciparum sporozoites that develop and mature inside an Anopheles mosquito initiate a malaria infection in humans. Here we report the first proteomic comparison of different parasite stages from the mosquito -- early and late oocysts containing midgut sporozoites, and the mature...... whose annotation suggest an involvement in sporozoite maturation, motility, infection of the human host and associated metabolic adjustments. Analyses of proteins identified in the P. falciparum sporozoite proteomes by orthologous gene disruption in the rodent malaria parasite, P. berghei, revealed...... three previously uncharacterized Plasmodium proteins that appear to be essential for sporozoite development at distinct points of maturation in the mosquito. This study sheds light on the development and maturation of the malaria parasite in an Anopheles mosquito and also identifies proteins that may...