Integrative Molecular Phenotyping
INTEGRATIVE MOLECULAR
PHENOTYPING
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY

PubMed

PubMed
NCBI: db=pubmed; Term=metabolomics
Updated: 1 hour 29 min ago

Physiological and metabolomic analysis of Issatchenkia orientalis MTY1 with multiple tolerance for cellulosic bioethanol production.

Sun, 27/08/2017 - 12:30
Physiological and metabolomic analysis of Issatchenkia orientalis MTY1 with multiple tolerance for cellulosic bioethanol production. Biotechnol J. 2017 Aug 26;: Authors: Seong YJ, Lee HJ, Lee JE, Kim S, Lee DY, Kim KH, Park YC Abstract Yeast with multiple tolerance onto harsh conditions has a number of advantages for bioethanol production. In this study, an alcohol yeast of Issatchenkia orientalis MTY1 was isolated in a Korean winery and its multiple tolerance against high temperature and acidic conditions was characterized in microaerobic batch cultures and by metabolomic analysis. In a series of batch cultures using 100 g/L glucose, I. orientalis MTY1 possessed wider growth ranges at pH 2-8 and 30-45 oC than a conventional yeast of Saccharomyces cerevisiae D452-2. Moreover, I. orientalis MTY1 showed higher cell growth and ethanol productivity in the presence of acetic acid or furfural than S. cerevisiae D452-2. I. orientalis MTY1 produced 41.4 g/L ethanol with 1.5 g/L-h productivity at 42 °C and pH 4.2 in the presence of 4 g/L acetic acid, whereas a thermo-tolerant yeast of Kluyvermyces marxianus ATCC36907 didn't grow. By metabolomics by GC-TOF MS and statistical analysis of 125 metabolite peaks, it was revealed that the thermo-tolerance of I. orientalis MTY1 might be ascribed to higher contents of unsaturated fatty acids, purines and pyrimidines than S. cerevisiae D452-2. Conclusively, I. orientalis MTY1 could be a potent workhorse with multiple tolerance against harsh conditions considered in cellulosic bioethanol production. PMID: 28843023 [PubMed - as supplied by publisher]

Distinct metabolomic signature in cerebrospinal fluid in early parkinson's disease.

Sun, 27/08/2017 - 12:30
Distinct metabolomic signature in cerebrospinal fluid in early parkinson's disease. Mov Disord. 2017 Aug 26;: Authors: Trezzi JP, Galozzi S, Jaeger C, Barkovits K, Brockmann K, Maetzler W, Berg D, Marcus K, Betsou F, Hiller K, Mollenhauer B Abstract OBJECTIVE: The purpose of this study was to profile cerebrospinal fluid (CSF) from early-stage PD patients for disease-related metabolic changes and to determine a robust biomarker signature for early-stage PD diagnosis. METHODS: By applying a non-targeted and mass spectrometry-driven approach, we investigated the CSF metabolome of 44 early-stage sporadic PD patients yet without treatment (DeNoPa cohort). We compared all detected metabolite levels with those measured in CSF of 43 age- and gender-matched healthy controls. After this analysis, we validated the results in an independent PD study cohort (Tübingen cohort). RESULTS: We identified that dehydroascorbic acid levels were significantly lower and fructose, mannose, and threonic acid levels were significantly higher (P < .05) in PD patients when compared with healthy controls. These changes reflect pathological oxidative stress responses, as well as protein glycation/glycosylation reactions in PD. Using a machine learning approach based on logistic regression, we successfully predicted the origin (PD patients vs healthy controls) in a second (n = 18) as well as in a third and completely independent validation set (n = 36). The biomarker signature is composed of the three markers-mannose, threonic acid, and fructose-and allows for sample classification with a sensitivity of 0.790 and a specificity of 0.800. CONCLUSION: We identified PD-specific metabolic changes in CSF that were associated with antioxidative stress response, glycation, and inflammation. Our results disentangle the complexity of the CSF metabolome to unravel metabolome changes related to early-stage PD. The detected biomarkers help understanding PD pathogenesis and can be applied as biomarkers to increase clinical diagnosis accuracy and patient care in early-stage PD. © 2017 International Parkinson and Movement Disorder Society. PMID: 28843022 [PubMed - as supplied by publisher]

Gut Microbiota and Atherosclerosis.

Sun, 27/08/2017 - 12:30
Related Articles Gut Microbiota and Atherosclerosis. Curr Atheroscler Rep. 2017 Aug 25;19(10):39 Authors: Li DY, Tang WHW Abstract PURPOSE OF REVIEW: Studies in microbiota-mediated health risks have gained traction in recent years since the compilation of the Human Microbiome Project. No longer do we believe that our gut microbiota is an inert set of microorganisms that reside in the body without consequence. In this review, we discuss the recent findings which further our understanding of the connection between the gut microbiota and the atherosclerosis. RECENT FINDINGS: We evaluate studies which illustrate the current understanding of the relationship between infection, immunity, altered metabolism, and bacterial products such as immune activators or dietary metabolites and their contributions to the development of atherosclerosis. In particular, we critically examine rec ent clinical and mechanistic findings for the novel microbiota-dependent dietary metabolite, trimethylamine N-oxide (TMAO), which has been implicated in atherosclerosis. These discoveries are now becoming integrated with advances in microbiota profiling which enhance our ability to interrogate the functional role of the gut microbiome and develop strategies for targeted therapeutics. The gut microbiota is a multi-faceted system that is unraveling novel contributors to the development and progression of atherosclerosis. In this review, we discuss historic and novel contributors while highlighting the TMAO story mainly as an example of the various paths taken beyond deciphering microbial composition to elucidate downstream mechanisms that promote (or protect from) atherogenesis in the hopes of translating these findings from bench to bedside. PMID: 28842845 [PubMed - in process]

Advances in metabolome information retrieval: turning chemistry into biology. Part II: biological information recovery.

Sun, 27/08/2017 - 12:30
Related Articles Advances in metabolome information retrieval: turning chemistry into biology. Part II: biological information recovery. J Inherit Metab Dis. 2017 Aug 25;: Authors: Tebani A, Afonso C, Bekri S Abstract This work reports the second part of a review intending to give the state of the art of major metabolic phenotyping strategies. It particularly deals with inherent advantages and limits regarding data analysis issues and biological information retrieval tools along with translational challenges. This Part starts with introducing the main data preprocessing strategies of the different metabolomics data. Then, it describes the main data analysis techniques including univariate and multivariate aspects. It also addresses the challenges related to metabolite annotation and characterization. Finally, functional analysis including pathway and network strategies are discussed. The last section of this review is devoted to practical considerations and current challenges and pathways to bring metabolomics into clinical environments. PMID: 28842777 [PubMed - as supplied by publisher]

Glucose effectiveness, but not insulin sensitivity, is improved after short-term interval training in individuals with type 2 diabetes mellitus: a controlled, randomised, crossover trial.

Sun, 27/08/2017 - 12:30
Related Articles Glucose effectiveness, but not insulin sensitivity, is improved after short-term interval training in individuals with type 2 diabetes mellitus: a controlled, randomised, crossover trial. Diabetologia. 2017 Aug 25;: Authors: Karstoft K, Clark MA, Jakobsen I, Knudsen SH, van Hall G, Pedersen BK, Solomon TPJ Abstract AIMS/HYPOTHESIS: The role of glucose effectiveness (S G) in training-induced improvements in glucose metabolism in individuals with type 2 diabetes is unknown. The objectives and primary outcomes of this study were: (1) to assess the efficacy of interval walking training (IWT) and continuous walking training (CWT) on S G and insulin sensitivity (S I) in individuals with type 2 diabetes; and (2) to assess the association of changes in S G and S I with changes in glycaemic control. METHODS: Fourteen participants with type 2 diabetes underwent three trials (IWT, CWT and no training) in a crossover study. Exclusion criteria were exogenous insulin treatment, smoking, pregnancy, contraindications to structured physical activity and participation in recurrent training (>90 min/week). The trials were performed in a randomised order (computerised-generated randomisation). IWT and CWT consisted of ten supervised treadmill walking sessions, each lasting 60 min, over 2 weeks. IWT was performed as repeated cycles of 3 min slow walking and 3 min fast walking (aiming for 54% and 89% of [Formula: see text], respectively, which was measured during the last minute of each interval), and CWT was performed aiming for a moderate walking speed (73% of [Formula: see text]). A two-step (pancreatic and hyperinsulinaemic) hyperglycaemic clamp was implemented before and after each trial. All data were collected in a hospitalised setting. Neither participants nor assessors were blinded to the trial interventions. RESULTS: Thirteen individuals completed all procedures and were included in the analyses. IWT improved S G (mean ± SEM: 0.6 ± 0.1 mg kg(-1) min(-1), p < 0.05) but not S I (p > 0.05), whereas CWT matched for energy expenditure and time duration improved neither S G nor S I (both p > 0.05). Changes in S G, but not in S I, were associated with changes in mean (β = -0.62 ± 0.23, r (2) = 0.17, p < 0.01) and maximum (β = -1.18 ± 0.52, r (2) = 0.12, p < 0.05) glucose levels during 24 h continuous glucose monitoring. CONCLUSIONS/INTERPRETATION: Two weeks of IWT, but not CWT, improves S G but not S I in individuals with type 2 diabetes. Moreover, changes in S G are associated with changes in glycaemic control. Therefore, increased S G is likely an important mechanism by which training improves glycaemic control in individuals with type 2 diabetes. TRIAL REGISTRATION: ClinicalTrials.gov NCT02320526 FUNDING: CFAS is supported by a grant from TrygFonden. During the study period, the Centre of Inflammation and Metabolism (CIM) was supported by a grant from the Danish National Research Foundation (DNRF55). The study was further supported by grants from Diabetesforeningen, Augustinusfonden and Krista og Viggo Petersens Fond. CIM/CFAS is a member of DD2-the Danish Center for Strategic Research in Type 2 Diabetes (the Danish Council for Strategic Research, grant no. 09-067009 and 09-075724). PMID: 28842722 [PubMed - as supplied by publisher]

Metabolomic Analysis Reveals Vitamin D-induced Decrease in Polyol Pathway and Subtle Modulation of Glycolysis in HEK293T Cells.

Sun, 27/08/2017 - 12:30
Related Articles Metabolomic Analysis Reveals Vitamin D-induced Decrease in Polyol Pathway and Subtle Modulation of Glycolysis in HEK293T Cells. Sci Rep. 2017 Aug 25;7(1):9510 Authors: Santos GC, Zeidler JD, Pérez-Valencia JA, Sant'Anna-Silva ACB, Da Poian AT, El-Bacha T, Almeida FCL Abstract We combined (1)H NMR metabolomics with functional and molecular biochemical assays to describe the metabolic changes elicited by vitamin D in HEK293T, an embryonic proliferative cell line adapted to high-glucose concentrations. Activation of the polyol pathway, was the most important consequence of cell exposure to high glucose concentration, resembling cells exposed to hyperglycemia. Vitamin D induced alterations in HEK293T cells metabolism, including a decrease in sorbitol, glycine, glutamate, guanine. Vitamin D modulated glycolysis by increasing phosphoglycerate mutase and decreasing enolase activities, changing carbon fate without changing glucose consumption, lactate export and Krebs cycle. The decrease in sorbitol intracellular concentration seems to be related to vitamin D regulated redox homeostasis and protection against oxidative stress, and helped maintaining the high proliferative phenotype, supported by the decrease in glycine and guanine and orotate concentration and increase in choline and phosphocholine concentration. The decrease in orotate and guanine indicated an increased biosynthesis of purine and pyrimidines. Vitamin D elicited metabolic alteration without changing cellular proliferation and mitochondrial respiration, but reclaiming reductive power. Our study may contribute to the understanding of the metabolic mechanism of vitamin D upon exposure to hyperglycemia, suggesting a role of protection against oxidative stress. PMID: 28842639 [PubMed - in process]

Probing the genome-scale metabolic landscape of Bordetella pertussis, the causative agent of whooping cough.

Sun, 27/08/2017 - 12:30
Related Articles Probing the genome-scale metabolic landscape of Bordetella pertussis, the causative agent of whooping cough. Appl Environ Microbiol. 2017 Aug 25;: Authors: Branco Dos Santos F, Olivier BG, Boele J, Smessaert V, De Rop P, Krumpochova P, Klau GW, Giera M, Dehottay P, Teusink B, Goffin P Abstract Whooping cough is a highly-contagious respiratory disease caused by Bordetella pertussis. Despite vaccination, its incidence has been rising alarmingly, and yet, the physiology of B. pertussis remains poorly understood. We combined genome-scale metabolic reconstruction, a novel optimization algorithm and experimental data to probe the full metabolic potential of this pathogen, using strain Tohama I as a reference. Experimental validation showed that B. pertussis secretes a significant proportion of nitrogen as arginine and purine nucleosides, which may contribute to modulation of the host response. We also found that B. pertussis can be unexpectedly versatile, being able to metabolize many compounds while displaying minimal nutrient requirements. It can grow without cysteine - using inorganic sulfur sources such as thiosulfate - and it can grow on organic acids such as citrate or lactate as sole carbon sources, providing in vivo demonstration that its TCA cycle is functional. Although the metabolic reconstruction of eight additional strains indicates that the structural genes underlying this metabolic flexibility are widespread, experimental validation suggests a role of strain-specific regulatory mechanisms in shaping metabolic capabilities. Among five alternative strains tested, three were shown to grow on substrate combinations requiring a functional TCA cycle, but only one could use thiosulfate. Finally, the metabolic model was used to rationally design growth media with over two-fold improvements in pertussis toxin production. This study thus provides novel insights into B. pertussis physiology, and highlights the potential, but also limitations of models solely based on metabolic gene content.IMPORTANCE The metabolic capabilities of Bordetella pertussis - the causative agent of whooping cough - were investigated from a systems-level perspective. We constructed a comprehensive genome-scale metabolic model for B. pertussis, and challenged its predictions experimentally. This systems approach shed light on new potential host-microbe interactions, and allowed to rationally design novel growth media with over two-fold improvements in pertussis toxin production. Most importantly, we also uncovered the potential for metabolic flexibility of B. pertussis (significantly larger range of substrates than previously alleged; novel active pathways allowing growth in minimal, nearly mineral nutrient combinations where only the carbon source must be organic), although our results also highlight the importance of strain-specific regulatory determinants in shaping metabolic capabilities. Deciphering the underlying regulatory mechanisms appears crucial for a comprehensive understanding of B. pertussis's lifestyle and the epidemiology of whooping cough. The contribution of metabolic models in this context will require the extension of the genome-scale metabolic model to integrate this regulatory dimension. PMID: 28842544 [PubMed - as supplied by publisher]

Potential Neurotoxicity of Prenatal Exposure to Sevoflurane on Offspring: Metabolomics Investigation on Neurodevelopment and Underlying Mechanism.

Sun, 27/08/2017 - 12:30
Related Articles Potential Neurotoxicity of Prenatal Exposure to Sevoflurane on Offspring: Metabolomics Investigation on Neurodevelopment and Underlying Mechanism. Int J Dev Neurosci. 2017 Aug 22;: Authors: Jiang J, Li S, Wang Y, Xiao X, Jin Y, Wang Y, Yang Z, Yan S, Li Y Abstract Repeated or prolonged anesthesia to pregnant women disturbs neurodevelopment of developing infants, but its mechanism has not been elaborated absolutely. This study was conducted to investigate the mechanism of potential neurotoxicity on their offspring generation after sevoflurane anesthesia in adult animals during pregnancy based on metabolomics. 16 pregnant rats were equally assigned to sevoflurane group and control group, and serum samples were collected from their 7-day-old offspring for metabolomics analysis using ultra performance liquid chromatography coupled to time-of-flight mass spectrometry. Principal component analysis and partial least squares-discriminate analysis were used for pattern recognition, and pathway analysis was performed by MetaboAnalyst platform. 29 metabolites were discovered as neurotoxicity related-biomarkers, among which S-Adenosylmethioninamine was inhibited dramatically after sevoflurane exposure. Prenatal exposure to sevoflurane led to a significant reduction in S-Adenosylmethionine level, as shown by enzyme-linked immunosorbent assay. Pathway analysis highlighted that prenatal exposure to sevoflurane induced alteration in arginine/proline metabolism, cysteine/methionine metabolism, and so on. The most important altered metabolic pathway was arginine/proline metabolism. This study suggests that abnormal methylation and disturbed arginine/proline metabolism may crucially contribute to the mechanism with neurotoxicity on offspring generation after sevoflurane anesthesia in adult animals during pregnancy, and dietary supplement of S-Adenosylmethionine and modulating arginine/proline metabolism may be the potential therapeutic targets for protecting neurodevelopment from detrimental effects of prenatal exposure to inhalational anesthetics. PMID: 28842206 [PubMed - as supplied by publisher]

Analysis of multiple mass spectrometry images from different Phaseolus vulgaris samples by multivariate curve resolution.

Sun, 27/08/2017 - 12:30
Related Articles Analysis of multiple mass spectrometry images from different Phaseolus vulgaris samples by multivariate curve resolution. Talanta. 2017 Dec 01;175:557-565 Authors: Bedia C, Tauler R, Jaumot J Abstract A new procedure based on the simultaneous analysis of multiple mass spectrometry images using multivariate curve resolution is presented in this work. Advantages of the application of the proposed approach are shown for three cases of plant studies demonstrating its potential usefulness in metabolomics studies, particularly in lipidomics. In the first dataset, a three stage germination time course process of green bean seeds is presented. The second example is a dose-response study where the stem bases of a non-exposed plant are compared to those of plants exposed to increasing concentrations of the pesticide chlorpyrifos. Finally, the third study is the simultaneous analysis of several sequential transversal and longitudinal cuts of the same green bean plant stem segment. The analysis of these three examples required the comprehensive adaptation of different chemometric methodologies including data compression by selection of the regions of interest (ROI strategy), appropriate data normalization and baseline correction, all of them before MCR-ALS simultaneous image analysis of multiple samples and post processing of the achieved results. MCR-ALS resolved components provided spatial information about the changes in the spatial composition and distribution of the different lipids on the surface of the investigated samples. These results enabled the identification of single lipids and the clustering of those lipids that behaved similarly in the different images simultaneously analyzed. The proposed strategy for MSI analysis represents a step forward in the simultaneous analysis of multiple sets of images providing an improved recovery of both spatial and structural information in environmental and biomedical studies. PMID: 28842033 [PubMed - in process]

Metabolic control of immune system activation in rheumatic diseases.

Sat, 26/08/2017 - 14:51
Metabolic control of immune system activation in rheumatic diseases. Arthritis Rheumatol. 2017 Aug 25;: Authors: Perl A Abstract Metabolic pathways exert profound influence over the development of unicellular and multi-cellular organisms. Engagement of antigen receptors and co-stimulatory molecules, growth factors, hormones, cytokines, environmental factors, and other regulatory cues shape the development of the immune system by reprogramming of metabolic gene expression in a cell type-specific manner. In fact, the heterogeneity of cells both within the innate and adaptive immune systems depends on the supply of metabolites that allow for lineage-specific differentiation. This review integrates recent discoveries in metabolomics and genetics with immunological pathways of pathogenesis to delineate checkpoints for diagnosis and targets for treatment in rheumatic diseases. This article is protected by copyright. All rights reserved. PMID: 28841779 [PubMed - as supplied by publisher]

Earwax metabolomics: An innovative pilot metabolic profiling study for assessing metabolic changes in ewes during periparturition period.

Sat, 26/08/2017 - 14:51
Earwax metabolomics: An innovative pilot metabolic profiling study for assessing metabolic changes in ewes during periparturition period. PLoS One. 2017;12(8):e0183538 Authors: Shokry E, Pereira J, Marques Júnior JG, da Cunha PHJ, Noronha Filho ADF, da Silva JA, Fioravanti MCS, de Oliveira AE, Antoniosi Filho NR Abstract Important metabolic changes occur during transition period of late pregnancy and early lactation to meet increasing energy demands of the growing fetus and for milk production. The aim of this investigation is to present an innovative and non-invasive tool using ewe earwax sample analysis to assess the metabolic profile in ewes during late pregnancy and early lactation. In this work, earwax samples were collected from 28 healthy Brazilian Santa Inês ewes divided into 3 sub-groups: 9 non-pregnant ewes, 6 pregnant ewes in the last 30 days of gestation, and 13 lactating ewes ≤ 30 days postpartum. Then, a range of metabolites including volatile organic compounds (VOC), amino acids (AA), and minerals were profiled and quantified in the samples by applying headspace gas chromatography/mass spectrometry, high performance liquid chromatography/tandem mass spectrometry, and inductively coupled plasma-optical emission spectrometry, respectively. As evident in our results, significant changes were observed in the metabolite profile of earwax between the studied groups where a remarkable elevation was detected in the levels of non-esterified fatty acids, alcohols, ketones, and hydroxy urea in the VOC profile of samples obtained from pregnant and lactating ewes. Meanwhile, a significant decrease was detected in the levels of 9 minerals and 14 AA including essential AA (leucine, phenyl alanine, lysine, isoleucine, threonine, valine), conditionally essential AA (arginine, glycine, tyrosine, proline, serine), and a non-essential AA (alanine). Multivariate analysis using robust principal component analysis and hierarchical cluster analysis was successfully applied to discriminate the three study groups using the variations of metabolites in the two stress states (pregnancy and lactation) from the healthy non-stress condition. The innovative developed method was successful in evaluating pre- and post-parturient metabolic changes using earwax and can in the future be applied to recognize markers for diagnosis, prevention, and intervention of pregnancy complications in ewes. PMID: 28841695 [PubMed - in process]

Toxicological effects of tris(2-chloropropyl) phosphate in human hepatic cells.

Sat, 26/08/2017 - 14:51
Toxicological effects of tris(2-chloropropyl) phosphate in human hepatic cells. Chemosphere. 2017 Aug 22;187:88-96 Authors: Li F, Wang L, Ji C, Wu H, Zhao J, Tang J Abstract Organophosphate flame retardants (OPFRs) are widely used as flame retardants which are ubiquitous in various environment media. As many of OPFRs are toxic and persistent, concerns have been raised in regards to their environmental impact. In this study, the toxicological effects of tris(2-chloropropyl) phosphate (TCPP) in human L02 cells was investigated by cell proliferation and apoptosis, oxidative stress, metabolomic and proteomic responses as well as gene expressions related to apoptosis. Results showed that TCPP did not significantly affect the L02 cell apoptosis, however, a significant increase of ROS production was observed in L02 cells with TCPP treatment compared with that in control group (p < 0.05). The expression levels of Bcl-2 family-encoding genes (Bax, Hrk and Bax/Bcl-2) were up-regulated significantly in 10(-4) M group (p < 0.05). Metabolomic and proteomic responses indicated that TCPP mainly caused disturbance in cell growth/division and gene expression, energy and material metabolism, signal transduction, defense and cytoskeleton, which was further confirmed by the western blot analysis. PMID: 28841435 [PubMed - as supplied by publisher]

High-throughput LC-MS method for the rapid characterization of multiple chemical constituents and metabolites of Da-Bu-Yin-Wan.

Sat, 26/08/2017 - 14:51
High-throughput LC-MS method for the rapid characterization of multiple chemical constituents and metabolites of Da-Bu-Yin-Wan. J Sep Sci. 2017 Aug 25;: Authors: Li X, Sun H, Zhang A, Liu Z, Zou D, Song Y, Liu L, Wang X Abstract Traditional Chinese medicine is the clinical experience accumulated by Chinese people against diseases. Da-Bu-Yin-Wan is a famous traditional Chinese medicine formula consisting of Phellodendri amurensis Rupr., Anemarrhenae asphodeloides Bge., Radix Rehmanniae Preparata and Chinemys reevesii. In this study, ultra high performance liquid chromatography equipped with electrospray ionization quadrupole time-of-flight high-definition mass spectrometry with the controlled software of Masslynx (V4.1) was established for comprehensive screen and identified the chemical constituents and serum metabolites of Da-Bu-Yin-Wan in vivo and in vitro. Consequently, 70 peaks in the methanol extract from Da-Bu-Yin-Wan and 38 peaks absorbed into rat blood were characterized. The 70 constituents in vitro included alkaloids, flavonoids, polysaccharide, limonoids, flavonoid, etc. And the 38 constituents were consists of 22 absorbed prototype and 16 metabolites of Da-Bu-Yin-Wan absorbed in vivo. We fully clarified the chemical constituents of Da-Bu-Yin-Wan and provided a scientific strategy for screening and characterization the chemical constituents and metabolites of traditional Chinese medicine in vitro and in vivo. This article is protected by copyright. All rights reserved. PMID: 28841261 [PubMed - as supplied by publisher]

Recommendations for Improving Identification and Quantification in Non-Targeted, GC-MS-Based Metabolomic Profiling of Human Plasma.

Sat, 26/08/2017 - 14:51
Recommendations for Improving Identification and Quantification in Non-Targeted, GC-MS-Based Metabolomic Profiling of Human Plasma. Metabolites. 2017 Aug 25;7(3): Authors: Wang H, Muehlbauer MJ, O'Neal SK, Newgard CB, Hauser ER, Bain JR, Shah SH Abstract The field of metabolomics as applied to human disease and health is rapidly expanding. In recent efforts of metabolomics research, greater emphasis has been placed on quality control and method validation. In this study, we report an experience with quality control and a practical application of method validation. Specifically, we sought to identify and modify steps in gas chromatography-mass spectrometry (GC-MS)-based, non-targeted metabolomic profiling of human plasma that could influence metabolite identification and quantification. Our experimental design included two studies: (1) a limiting-dilution study, which investigated the effects of dilution on analyte identification and quantification; and (2) a concentration-specific study, which compared the optimal plasma extract volume established in the first study with the volume used in the current institutional protocol. We confirmed that contaminants, concentration, repeatability and intermediate precision are major factors influencing metabolite identification and quantification. In addition, we established methods for improved metabolite identification and quantification, which were summarized to provide recommendations for experimental design of GC-MS-based non-targeted profiling of human plasma. PMID: 28841195 [PubMed]

Untargeted metabolomic analysis and pathway discovery in perinatal asphyxia and hypoxic-ischaemic encephalopathy.

Sat, 26/08/2017 - 14:51
Untargeted metabolomic analysis and pathway discovery in perinatal asphyxia and hypoxic-ischaemic encephalopathy. J Cereb Blood Flow Metab. 2017 Jan 01;:271678X17726502 Authors: Denihan NM, Kirwan JA, Walsh BH, Dunn WB, Broadhurst DI, Boylan GB, Murray DM Abstract Elucidating metabolic effects of hypoxic-ischaemic encephalopathy (HIE) may reveal early biomarkers of injury and new treatment targets. This study uses untargeted metabolomics to examine early metabolic alterations in a carefully defined neonatal population. Infants with perinatal asphyxia who were resuscitated at birth and recovered (PA group), those who developed HIE (HIE group) and healthy controls were all recruited at birth. Metabolomic analysis of cord blood was performed using direct infusion FT-ICR mass spectrometry. For each reproducibly detected metabolic feature, mean fold differences were calculated HIE vs. controls (ΔHIE) and PA vs. controls (ΔPA). Putative metabolite annotations were assigned and pathway analysis was performed. Twenty-nine putatively annotated metabolic features were significantly different in ΔPA after false discovery correction ( q < 0.05), with eight of these also significantly altered in ΔHIE. Altered putative metabolites included; melatonin, leucine, kynurenine and 3-hydroxydodecanoic acid which differentiated between infant groups (ΔPA and ΔHIE); and D-erythrose-phosphate, acetone, 3-oxotetradecanoic acid and methylglutarylcarnitine which differentiated across severity grades of HIE. Pathway analysis revealed ΔHIE was associated with a 50% and 75% perturbation of tryptophan and pyrimidine metabolism, respectively. We have identified perturbed metabolic pathways and potential biomarkers specific to PA and HIE, which measured at birth, may help direct treatment. PMID: 28840775 [PubMed - as supplied by publisher]

Chemical Composition and Antioxidant, Antinociceptive, and Anti-inflammatory Activities of Four Amazonian Byrsonima Species.

Sat, 26/08/2017 - 14:51
Related Articles Chemical Composition and Antioxidant, Antinociceptive, and Anti-inflammatory Activities of Four Amazonian Byrsonima Species. Phytother Res. 2017 Aug 25;: Authors: Guilhon-Simplicio F, Machado TM, do Nascimento LF, Souza RDS, Koolen HHF, da Silva FMA, Acho LDR, Dos Santos ARS, Cos P, Pereira MM, Lima ES Abstract Species of the Byrsonima genus are widely used in Brazil, especially for the treatment of gastrointestinal disorders. However, species from the Amazonian region are still poorly studied. Thus, we studied the antioxidant, antinociceptive, and anti-inflammatory activities of for Amazonian species, Byrsonima crispa, Byrsonima duckeana, Byrsonima garcibarrigae, and Byrsonima incarnata. Phenolic composition was determined by chemical and chromatographic methods. The aqueous extracts were evaluated in DPPH(•) , ABTS(+•) , and superoxide (O2(•-) ) tests, LPS-activated macrophage assay, and formalin test. All species contained a high phenolic and flavonoid content. We identified 15 phenolic compounds, including phenolic acids, hydroxycinnamic acids, flavonoids, and catechins. The extracts showed high antioxidant activity and were more active than quercetin at inhibiting nitric oxide release in the LPS-activated macrophage assay. B. duckeana and B. garcibarrigae showed higher in vivo antinociceptive and anti-inflammatory activities. B. garcibarrigae presented significant effect on the early phase of the formalin test, pointing to an antinociceptive mechanism distinct from traditional anti-inflammatory medicines. In conclusion, the pharmacological potential of these species is closely related to their flavonoid-rich chemical composition, which seems to act through antioxidant mechanisms. Copyright © 2017 John Wiley & Sons, Ltd. PMID: 28840624 [PubMed - as supplied by publisher]

Advances in metabolome information retrieval: turning chemistry into biology. Part I: analytical chemistry of the metabolome.

Sat, 26/08/2017 - 14:51
Related Articles Advances in metabolome information retrieval: turning chemistry into biology. Part I: analytical chemistry of the metabolome. J Inherit Metab Dis. 2017 Aug 24;: Authors: Tebani A, Afonso C, Bekri S Abstract Metabolites are small molecules produced by enzymatic reactions in a given organism. Metabolomics or metabolic phenotyping is a well-established omics aimed at comprehensively assessing metabolites in biological systems. These comprehensive analyses use analytical platforms, mainly nuclear magnetic resonance spectroscopy and mass spectrometry, along with associated separation methods to gather qualitative and quantitative data. Metabolomics holistically evaluates biological systems in an unbiased, data-driven approach that may ultimately support generation of hypotheses. The approach inherently allows the molecular characterization of a biological sample with regard to both internal (genetics) and environmental (exosome, microbiome) influences. Metabolomics workflows are based on whether the investigator knows a priori what kind of metabolites to assess. Thus, a targeted metabolomics approach is defined as a quantitative analysis (absolute concentrations are determined) or a semiquantitative analysis (relative intensities are determined) of a set of metabolites that are possibly linked to common chemical classes or a selected metabolic pathway. An untargeted metabolomics approach is a semiquantitative analysis of the largest possible number of metabolites contained in a biological sample. This is part I of a review intending to give an overview of the state of the art of major metabolic phenotyping technologies. Furthermore, their inherent analytical advantages and limits regarding experimental design, sample handling, standardization and workflow challenges are discussed. PMID: 28840392 [PubMed - as supplied by publisher]

Antisense oligonucleotide and thyroid hormone conjugates for obesity treatment.

Sat, 26/08/2017 - 14:51
Related Articles Antisense oligonucleotide and thyroid hormone conjugates for obesity treatment. Sci Rep. 2017 Aug 24;7(1):9307 Authors: Cao Y, Matsubara T, Zhao C, Gao W, Peng L, Shan J, Liu Z, Yuan F, Tang L, Li P, Guan Z, Fang Z, Lu X, Huang H, Yang Q Abstract Using the principle of antibody-drug conjugates that deliver highly potent cytotoxic agents to cancer cells for cancer therapy, we here report the synthesis of antisense-oligonucleotides (ASO) and thyroid hormone T3 conjugates for obesity treatment. ASOs primarily target fat and liver with poor penetrance to other organs. Pharmacological T3 treatment increases energy expenditure and causes weight loss, but is contraindicated for obesity treatment due to systemic effects on multiple organs. We hypothesize that ASO-T3 conjugates may knock down target genes and enrich T3 action in fat and liver. Two established ASOs are tested. Nicotinamide N-methyltransferase (NNMT)-ASO prevents diet-induced obesity in mice. Apolipoprotein B (ApoB)-ASO is an FDA approved drug for treating familial hypercholesterolemia. NNMT-ASO and ApoB-ASO are chemically conjugated with T3 using a non-cleavable sulfo-SMCC linker. Both NNMT-ASO-T3 (NAT3) and ApoB-ASO-T3 (AAT3) enhance thyroid hormone receptor activity. Treating obese mice with NAT3 or AAT3 decreases adiposity and increases lean mass. ASO-T3 enhances white fat browning, decreases genes for fatty acid synthesis in liver, and shows limited effects on T3 target genes in heart and muscle. Furthermore, AAT3 augments LDL cholesterol-lowering effects of ApoB-ASO. Therefore, ASO and hormone/drug conjugation may provide a novel strategy for obesity and hyperlipidemia treatment. PMID: 28839185 [PubMed - in process]

Hydrogen sulfide modulates eukaryotic translation initiation factor 2α (eIF2α) phosphorylation status in the integrated stress-response pathway.

Sat, 26/08/2017 - 14:51
Related Articles Hydrogen sulfide modulates eukaryotic translation initiation factor 2α (eIF2α) phosphorylation status in the integrated stress-response pathway. J Biol Chem. 2017 Aug 11;292(32):13143-13153 Authors: Yadav V, Gao XH, Willard B, Hatzoglou M, Banerjee R, Kabil O Abstract Hydrogen sulfide (H2S) regulates various physiological processes, including neuronal activity, vascular tone, inflammation, and energy metabolism. Moreover, H2S elicits cytoprotective effects against stressors in various cellular models of injury. However, the mechanism of the signaling pathways mediating the cytoprotective functions of H2S is not well understood. We previously uncovered a heme-dependent metabolic switch for transient induction of H2S production in the trans-sulfuration pathway. Here, we demonstrate that increased endogenous H2S production or its exogenous administration modulates major components of the integrated stress response promoting a metabolic state primed for stress response. We show that H2S transiently increases phosphorylation of eukaryotic translation initiation factor 2 (eIF2α) resulting in inhibition of general protein synthesis. The H2S-induced increase in eIF2α phosphorylation was mediated at least in part by inhibition of protein phosphatase-1 (PP1c) via persulfidation at Cys-127. Overexpression of a PP1c cysteine mutant (C127S-PP1c) abrogated the H2S effect on eIF2α phosphorylation. Our data support a model in which H2S exerts its cytoprotective effect on ISR signaling by inducing a transient adaptive reprogramming of global mRNA translation. Although a transient increase in endogenous H2S production provides cytoprotection, its chronic increase such as in cystathionine β-synthase deficiency may pose a problem. PMID: 28637872 [PubMed - indexed for MEDLINE]

MLL2, Not MLL1, Plays a Major Role in Sustaining MLL-Rearranged Acute Myeloid Leukemia.

Sat, 26/08/2017 - 14:51
Related Articles MLL2, Not MLL1, Plays a Major Role in Sustaining MLL-Rearranged Acute Myeloid Leukemia. Cancer Cell. 2017 Jun 12;31(6):755-770.e6 Authors: Chen Y, Anastassiadis K, Kranz A, Stewart AF, Arndt K, Waskow C, Yokoyama A, Jones K, Neff T, Lee Y, Ernst P Abstract The MLL1 histone methyltransferase gene undergoes many distinct chromosomal rearrangements to yield poor-prognosis leukemia. The remaining wild-type allele is most commonly, but not always, retained. To what extent the wild-type allele contributes to leukemogenesis is unclear. Here we show, using rigorous, independent animal models, that endogenous MLL1 is dispensable for MLL-rearranged leukemia. Potential redundancy was addressed by co-deleting the closest paralog, Mll2. Surprisingly, Mll2 deletion alone had a significant impact on survival of MLL-AF9-transformed cells, and additional Mll1 loss further reduced viability and proliferation. We show that MLL1/MLL2 collaboration is not through redundancy, but regulation of distinct pathways. These findings highlight the relevance of MLL2 as a drug target in MLL-rearranged leukemia and suggest its broader significance in AML. PMID: 28609655 [PubMed - indexed for MEDLINE]

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