PubMed

Related Articles Gas Chromatography Coupled to Mass Spectrometry (GC-MS) to Study Metabolism in Cultured Cells. Adv Exp Med Biol. 2016;899:59-88 Authors: Grimm F, Fets L, Anastasiou D Abstract Cancer cells exhibit characteristic patterns of metabolic behaviour that can be exploited for therapeutic purposes. Conditions found within the tumour microenvironment, such as hypoxia and selective nutrient availability, are known to influence the metabolism of cancer and stromal cells. Understanding cancer metabolism requires the use of analytical methods that allow detection and quantification of many metabolites simultaneously. Gas chromatography-mass spectrometry (GC-MS) is a versatile method to quantify metabolite abundance and, in combination with stable isotope labelled compounds, can yield important insights into the activity of metabolic pathways in cancer cells. This chapter provides an overview of the use of GC-MS for metabolic analysis of adherent cancer cells with an emphasis on the technical background that should be taken into consideration when designing and executing GC-MS-based metabolomics experiments. PMID: 27325262 [PubMed - in process]

Related Articles Glucose Metabolism and AMPK Signaling Regulate Dopaminergic Cell Death Induced by Gene (α-Synuclein)-Environment (Paraquat) Interactions. Mol Neurobiol. 2016 Jun 20; Authors: Anandhan A, Lei S, Levytskyy R, Pappa A, Panayiotidis MI, Cerny RL, Khalimonchuk O, Powers R, Franco R Abstract While environmental exposures are not the single cause of Parkinson's disease (PD), their interaction with genetic alterations is thought to contribute to neuronal dopaminergic degeneration. However, the mechanisms involved in dopaminergic cell death induced by gene-environment interactions remain unclear. In this work, we have revealed for the first time the role of central carbon metabolism and metabolic dysfunction in dopaminergic cell death induced by the paraquat (PQ)-α-synuclein interaction. The toxicity of PQ in dopaminergic N27 cells was significantly reduced by glucose deprivation, inhibition of hexokinase with 2-deoxy-D-glucose (2-DG), or equimolar substitution of glucose with galactose, which evidenced the contribution of glucose metabolism to PQ-induced cell death. PQ also stimulated an increase in glucose uptake, and in the levels of glucose transporter type 4 (GLUT4) and Na(+)-glucose transporters isoform 1 (SGLT1) proteins, but only inhibition of GLUT-like transport with STF-31 or ascorbic acid reduced PQ-induced cell death. Importantly, while autophagy protein 5 (ATG5)/unc-51 like autophagy activating kinase 1 (ULK1)-dependent autophagy protected against PQ toxicity, the inhibitory effect of glucose deprivation on cell death progression was largely independent of autophagy or mammalian target of rapamycin (mTOR) signaling. PQ selectively induced metabolomic alterations and adenosine monophosphate-activated protein kinase (AMPK) activation in the midbrain and striatum of mice chronically treated with PQ. Inhibition of AMPK signaling led to metabolic dysfunction and an enhanced sensitivity of dopaminergic cells to PQ. In addition, activation of AMPK by PQ was prevented by inhibition of the inducible nitric oxide syntase (iNOS) with 1400W, but PQ had no effect on iNOS levels. Overexpression of wild type or A53T mutant α-synuclein stimulated glucose accumulation and PQ toxicity, and this toxic synergism was reduced by inhibition of glucose metabolism/transport and the pentose phosphate pathway (6-aminonicotinamide). These results demonstrate that glucose metabolism and AMPK regulate dopaminergic cell death induced by gene (α-synuclein)-environment (PQ) interactions. PMID: 27324791 [PubMed - as supplied by publisher]

Related Articles Development of a transplantable glioma tumour model from genetically engineered mice: MRI/MRS/MRSI characterisation. J Neurooncol. 2016 Jun 21; Authors: Ciezka M, Acosta M, Herranz C, Canals JM, Pumarola M, Candiota AP, Arús C Abstract The initial aim of this study was to generate a transplantable glial tumour model of low-intermediate grade by disaggregation of a spontaneous tumour mass from genetically engineered models (GEM). This should result in an increased tumour incidence in comparison to GEM animals. An anaplastic oligoastrocytoma (OA) tumour of World Health Organization (WHO) grade III was obtained from a female GEM mouse with the S100β-v-erbB/inK4a-Arf (+/-) genotype maintained in the C57BL/6 background. The tumour tissue was disaggregated; tumour cells from it were grown in aggregates and stereotactically injected into C57BL/6 mice. Tumour development was followed using Magnetic Resonance Imaging (MRI), while changes in the metabolomics pattern of the masses were evaluated by Magnetic Resonance Spectroscopy/Spectroscopic Imaging (MRS/MRSI). Final tumour grade was evaluated by histopathological analysis. The total number of tumours generated from GEM cells from disaggregated tumour (CDT) was 67 with up to 100 % penetrance, as compared to 16 % in the local GEM model, with an average survival time of 66 ± 55 days, up to 4.3-fold significantly higher than the standard GL261 glioblastoma (GBM) tumour model. Tumours produced by transplantation of cells freshly obtained from disaggregated GEM tumour were diagnosed as WHO grade III anaplastic oligodendroglioma (ODG) and OA, while tumours produced from a previously frozen sample were diagnosed as WHO grade IV GBM. We successfully grew CDT and generated tumours from a grade III GEM glial tumour. Freezing and cell culture protocols produced progression to grade IV GBM, which makes the developed transplantable model qualify as potential secondary GBM model in mice. PMID: 27324642 [PubMed - as supplied by publisher]

Related Articles Multimode gradient high performance liquid chromatography mass spectrometry method applicable to metabolomics and environmental monitoring. J Chromatogr A. 2016 Jun 5; Authors: Ammann AA, Suter MJ Abstract Metabolomics or environmental investigations generate samples containing very large numbers of small molecular weight analytes. A single mode chromatographic separation excludes a substantial part of such complex analyte mixtures. For instance, a reversed-phase separation would not retain ionic species, resulting in a correspondingly huge front peak. To address this problem, we used two commercially available mixed-mode ion-exchange reversed-phase columns (WAX-1 and WCX-1) in sequence in a novel multimode separation method. After trapping hydrophobics on a C18-trap in loop position, hydrophilics passing the trap are separated by a simultaneous gradient for HILIC, anion and cation exchange chromatography. This gradient ends in a washout phase with a high percentage of water, the correct starting conditions for a reversed-phase gradient eluting hydrophobics from the trap in a second step of the run. Amino acids (9), organic acids (2), sugars (8), fatty acid derived compounds (11), antioxidants (4), miscellanea (6) and xenobiotics (4) were analyzed. Compounds were separated after a single sample injection during a 50min run. Lipids derived small fatty acids up to a chain length of 12 carbons were also accessible within this run time. PMID: 27324626 [PubMed - as supplied by publisher]

Related Articles Characterization of the Plasmodium falciparum and P. berghei glycerol 3-phosphate acyltransferase involved in FASII fatty acid utilization in the malaria parasite apicoplast. Cell Microbiol. 2016 Jun 20; Authors: Shears MJ, MacRae JI, Mollard V, Goodman CD, Sturm A, Orchard LM, Llinás M, McConville MJ, Botté CY, McFadden GI Abstract Malaria parasites can synthesize fatty acids via a type II fatty acid synthesis (FASII) pathway located in their apicoplast. The FASII pathway has been pursued as an anti-malarial drug target, but surprisingly little is known about its role in lipid metabolism. Here we characterize the apicoplast glycerol 3-phosphate acyltransferase that acts immediately downstream of FASII in human (Plasmodium falciparum) and rodent (P. berghei) malaria parasites and investigate how this enzyme contributes to incorporating FASII fatty acids into precursors for membrane lipid synthesis. Apicoplast targeting of the P. falciparum and P. berghei enzymes are confirmed by fusion of the N-terminal targeting sequence to GFP and 3' tagging of the full length protein. Activity of the P. falciparum enzyme is demonstrated by complementation in mutant bacteria, and critical residues in the putative active site identified by site-directed mutagenesis. Genetic disruption of the P. falciparum enzyme demonstrates it is dispensable in blood stage parasites, even in conditions known to induce FASII activity. Disruption of the P. berghei enzyme demonstrates it is dispensable in blood and mosquito stage parasites, and only essential for development in the late liver stage, consistent with the requirement for FASII in rodent models. However, the P. berghei mutant liver stage phenotype is found to only partially phenocopy loss of FASII, suggesting newly made fatty acids can take multiple pathways out of the apicoplast and so giving new insight into the role of FASII and apicoplast glycerol 3-phosphate acyltransferase in malaria parasites. PMID: 27324409 [PubMed - as supplied by publisher]

Related Articles A dynamic pathway analysis approach reveals a limiting futile cycle in N-acetylglucosamine overproducing Bacillus subtilis. Nat Commun. 2016;7:11933 Authors: Liu Y, Link H, Liu L, Du G, Chen J, Sauer U Abstract Recent advances in genome engineering have further widened the gap between our ability to implement essentially any genetic change and understanding the impact of these changes on cellular function. We lack efficient methods to diagnose limiting steps in engineered pathways. Here, we develop a generally applicable approach to reveal limiting steps within a synthetic pathway. It is based on monitoring metabolite dynamics and simplified kinetic modelling to differentiate between putative causes of limiting product synthesis during the start-up phase of the pathway with near-maximal rates. We examine the synthetic N-acetylglucosamine (GlcNAc) pathway in Bacillus subtilis and find none of the acetyl-, amine- or glucose-moiety precursors to limit synthesis. Our dynamic metabolomics approach predicts an energy-dissipating futile cycle between GlcNAc6P and GlcNAc as the primary problem in the pathway. Deletion of the responsible glucokinase more than doubles GlcNAc productivity by restoring healthy growth of the overproducing strain. PMID: 27324299 [PubMed - in process]

Related Articles Investigating the early metabolic fingerprint of celiac disease - a prospective approach. J Autoimmun. 2016 Jun 17; Authors: Kirchberg FF, Werkstetter KJ, Uhl O, Auricchio R, Castillejo G, Korponay-Szabo IR, Polanco I, Ribes-Koninckx C, Vriezinga SL, Koletzko B, Mearin ML, Hellmuth C Abstract OBJECTIVES AND STUDY: In the development of Celiac Disease (CD) both genetic and environmental factors play a crucial role. The Human Leukocyte Antigen (HLA)-DQ2 and HLA-DQ8 loci are strongly related to the disease and are necessary but not sufficient for the development of CD. Therefore, increasing interest lies in examining the mechanisms of CD onset from the early beginning. Differences in serum and urine metabolic profiles between healthy individuals and CD patients have been reported previously. We aimed to investigate if the metabolic pathways were already altered in young, 4 month old infants, preceding the CD diagnosis. METHODS: Serum samples were available for 230 four month old infants of the PreventCD project, a multicenter, randomized, double-blind, dietary intervention study. All children were positive for HLA-DQ2 and/or HLA-DQ8 and had at least one first-degree relative diagnosed with CD. Amino acids were quantified after derivatization with liquid chromatography - tandem mass spectrometry (MS/MS) and polar lipid concentrations (acylcarnitines, lysophosphatidylcholines, phosphatidylcholines, and sphingomyelins) were determined with direct infusion MS/MS. We investigated the association of the metabolic profile with (1) the development of CD up to the age of 8 years (yes/no), (2) with HLA-risk groups, (3) with the age at CD diagnosis, using linear mixed models and cox proportional hazards models. Gender, intervention group, and age at blood withdrawal were included as potential confounder. RESULTS: By the end of 2014, thirty-three out of the 230 children (14%) were diagnosed with CD according to the ESPGHAN criteria. Median age at diagnosis was 3.4 years (IQR, 2.4-5.2). Testing each metabolite for a difference in the mean between healthy and CD children, we (1) could not identify a discriminant analyte or a pattern pointing towards an altered metabolism (Bonferroni corrected P > 0.05 for all). Metabolite concentrations (2) did not differ across the HLA-risk groups. When investigating the age at diagnosis using (3) survival models, we found no evidence for an association between the metabolic profile and the risk of a later CD diagnosis. CONCLUSION: The metabolic profile at 4 months of age was not predictive for the development of CD up to the age of 8 years. Our results suggest that metabolic pathways reflected in serum are affected only later in life and that the HLA-genotype does not influence the serum metabolic profile in young infants before introduction of solid food. PMID: 27323936 [PubMed - as supplied by publisher]

Related Articles Analytical pitfalls and challenges in clinical metabolomics. Bioanalysis. 2016 Jun 21; Authors: Kohler I, Verhoeven A, Derks RJ, Giera M Abstract Metabolomics-based strategies have become an integral part of modern clinical research, allowing for a better understanding of pathophysiological conditions and disease mechanisms, as well as providing innovative tools for more adequate diagnostic and prognosis approaches. Metabolomics is considered an essential tool in precision medicine, which aims for personalized prevention and tailor-made treatments. Nevertheless, multiple pitfalls may be encountered in clinical metabolomics during the entire workflow, hampering the quality of the data and, thus, the biological interpretation. This review describes the challenges underlying metabolomics-based experiments, discussing step by step the potential pitfalls of the analytical process, including study design, sample collection, storage, as well as preparation, chromatographic and electrophoretic separation, detection and data analysis. Moreover, it offers practical solutions and strategies to tackle these challenges, ensuring the generation of high-quality data. PMID: 27323646 [PubMed - as supplied by publisher]

Related Articles Single- versus Multiple-Pest Infestation Affects Differently the Biochemistry of Tomato (Solanum lycopersicum 'Ailsa Craig'). J Agric Food Chem. 2015 Nov 25;63(46):10103-11 Authors: Errard A, Ulrichs C, Kühne S, Mewis I, Drungowski M, Schreiner M, Baldermann S Abstract Tomato is susceptible to pest infestations by both spider mites and aphids. The effects of each individual pest on plants are known, whereas multiple-pest infestations have received little interest. We studied the effects of single- versus multiple-pest infestation by Tetranychus urticae and Myzus persicae on tomato biochemistry (Solanum lycopersicum) by combining a metabolomic approach and analyses of carotenoids using UHPLC-ToF-MS and volatiles using GC-MS. Plants responded differently to aphids and mites after 3 weeks of infestation, and a multiple infestation induced a specific metabolite composition in plants. In addition, we showed that volatiles emissions differed between the adaxial and abaxial leaf epidermes and identified compounds emitted particularly in response to a multiple infestation (cyclohexadecane, dodecane, aromadendrene, and β-elemene). Finally, the carotenoid concentrations in leaves and stems were more affected by multiple than single infestations. Our study highlights and discusses the interplay of biotic stressors within the terpenoid metabolism. PMID: 26507319 [PubMed - indexed for MEDLINE]

Related Articles Activation of surrogate death receptor signaling triggers peroxynitrite-dependent execution of cisplatin-resistant cancer cells. Cell Death Dis. 2015;6:e1926 Authors: Seah S, Low IC, Hirpara JL, Sachaphibulkij K, Kroemer G, Brenner C, Pervaiz S Abstract Platinum-based drugs remain as the cornerstone of cancer chemotherapy; however, development of multidrug resistance presents a therapeutic challenge. This study aims at understanding the molecular mechanisms underlying resistance to cisplatin and unraveling surrogate signaling networks that could revert sensitivity to apoptosis stimuli. We made use of three different sets of cell lines, A549 and H2030 non-small-cell lung cancer (NSCLC) and A2780 ovarian cancer cells and their cisplatin-resistant variants. Here we report that cisplatin-resistant cell lines displayed a multidrug-resistant phenotype. Changes in mitochondrial metabolism and defective mitochondrial signaling were unraveled in the resistant cells. More interestingly, a marked increase in sensitivity of the resistant cells to death receptor-induced apoptosis, in particular TRAIL (TNF-related apoptosis-inducing ligand)-mediated execution, was observed. Although this was not associated with an increase in gene transcription, a significant increase in the localization of TRAIL death receptor, DR4, to the lipid raft subdomains of plasma membrane was detected in the resistant variants. Furthermore, exposure of cisplatin-resistant cells to TRAIL resulted in upregulation of inducible nitric oxide synthase (iNOS) and increase in nitric oxide (NO) production that triggered the generation of peroxynitrite (ONOO(-)). Scavenging ONOO(-) rescued cells from TRAIL-induced apoptosis, thereby suggesting a critical role of ONOO(-) in TRAIL-induced execution of cisplatin-resistant cells. Notably, preincubation of cells with TRAIL restored sensitivity of resistant cells to cisplatin. These data provide compelling evidence for employing strategies to trigger death receptor signaling as a second-line treatment for cisplatin-resistant cancers. PMID: 26492363 [PubMed - indexed for MEDLINE]

21 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results: metabolomics These pubmed results were generated on 2016/06/21PubMed comprises more than 24 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

Time-resolved NMR metabolomics of plant cells based on a microfluidic chip. J Plant Physiol. 2016 Jun 10;200:28-34 Authors: Maisch J, Kreppenhofer K, Büchler S, Merle C, Sobich S, Görling B, Luy B, Ahrens R, Guber AE, Nick P Abstract The plant secondary metabolism generates numerous compounds harbouring pharmaceutical activity. In plants, these compounds are typically formed by different and specialised cell types that have to interact constituting a metabolic process chain. This interactivity impedes biotechnological production of secondary compounds, because cell differentiation is suppressed under the conditions of a batch bio-fermenter. We present a novel strategy to address this limitation using a biomimetic approach, where we simulate the situation in a real tissue by a microfluidic chamber system, where plant cells can be integrated into a process flow. We show that walled cells of the plant model tobacco BY-2 can be successfully cultivated in this system and that physiological parameters (such as cell viability, mitotic index and division synchrony) can be preserved over several days. The microfluidic design allows to resolve dynamic changes of specific metabolites over different stages of culture development. These results serve as proof-of-principle that a microfluidic organisation of cultivated plant cells can mimic the metabolic flows in a real plant tissue. PMID: 27318870 [PubMed - as supplied by publisher]

Global metabolite analysis of the land snail Theba pisana hemolymph during active and aestivated states. Comp Biochem Physiol Part D Genomics Proteomics. 2016 Jun 6;19:25-33 Authors: Bose U, Centurion E, Hodson MP, Shaw PN, Storey KB, Cummins SF Abstract The state of metabolic dormancy has fascinated people for hundreds of years, leading to research exploring the identity of natural molecular components that may induce and maintain this state. Many animals lower their metabolism in response to high temperatures and/or arid conditions, a phenomenon called aestivation. The biological significance for this is clear; by strongly suppressing metabolic rate to low levels, animals minimize their exposure to stressful conditions. Understanding blood or hemolymph metabolite changes that occur between active and aestivated animals can provide valuable insights relating to those molecular components that regulate hypometabolism in animals, and how they afford adaptation to their different environmental conditions. In this study, we have investigated the hemolymph metabolite composition from the land snail Theba pisana, a remarkably resilient mollusc that displays an annual aestivation period. Using LC-MS-based metabolomics analysis, we have identified those hemolymph metabolites that show significant changes in relative abundance between active and aestivated states. We show that certain metabolites, including some phospholipids [e.g. LysoPC(14:0)], and amino acids such as l-arginine and l-tyrosine, are present at high levels within aestivated snails. Further investigation of our T. pisana RNA-sequencing data elucidated the entire repertoire of phospholipid-synthesis genes in the snail digestive gland, as a precursor towards future comparative investigation between the genetic components of aestivating and non-aestivating species. In summary, we have identified a large number of metabolites that are elevated in the hemolymph of aestivating snails, supporting their role in protecting against heat or desiccation. PMID: 27318654 [PubMed - as supplied by publisher]

Response and Defense Mechanisms of Taxus chinensis leaves under UV-A Radiation are Revealed Using Comparative Proteomics and Metabolomics Analyses. Plant Cell Physiol. 2016 Jun 18; Authors: Zheng W, Komatsu S, Zhu W, Zhang L, Li X, Cui L, Tian J Abstract Taxus chinensis var. mairei is an endemic species to southeastern China and one of the natural sources for the anticancer medicine paclitaxel. To investigate the molecular response and defense mechanisms of T. chinensis leaves to enhanced ultraviolet-A (UV-A) radiation, gel-free/label-free and gel-based proteomics and GC-MS analyses were performed. The transmission electron microscopy results indicated damage on chloroplast under UV-A radiation. Proteomics analyses in leaves and chloroplast showed that photosynthesis-, glycolysis-, secondary metabolism-, stress-, and protein synthesis, degradation, and activation- related systems were mainly changed under UV-A radiation. Forty-seven PS II proteins and six PS I proteins were identified changed in leaves and chloroplast under UV-A treatment. It indicated that PS II was more sensitive to UV-A than PS I as UV-A light target. Enhanced glycolysis, with four glycolysis-related key enzymes increased, provided precursors for secondary metabolism. The 1-deoxy-D-xylulose-5-phosphate reductoisomerase and 4-hydroxy-3-methylbut-2-enyl diphosphate reductase were identified significantly increased during UV-A radiation, which resulted in paclitaxel enhancement. Additionally, mRNA expression levels of genes involved in the paclitaxel biosynthetic pathway indicated a down-regulation under UV-A irradiation and up-regulation in dark incubation. These results reveal that a short-term high dose of UV-A radiation could stimulate the plant stress defense system and paclitaxel production. PMID: 27318281 [PubMed - as supplied by publisher]

Metabolic and biochemical changes in streptozotocin induced obese-diabetic rats treated with Phyllanthus niruri extract. J Pharm Biomed Anal. 2016 Jun 4;128:302-312 Authors: Mediani A, Abas F, Maulidiani M, Khatib A, Tan CP, Ismail IS, Shaari K, Ismail A, Lajis NH Abstract Herbal medicine has been proven to be an effective therapy offering a variety of benefits, such as moderate reduction in hypoglycemia, in the treatment and prevention of obesity and diabetes. Phyllanthus niruri has been used as a treatment for diabetes mellitus. Herein, the induction of type 2 diabetes in Sprague-Dawley rats was achieved by a low dose of streptozotocin (STZ) (25mg/kgbw). Here, we evaluated the in vivo antidiabetic properties of two concentrations (250 and 500mg/kg bw) of P. niruri via metabolomics approach. The administration of 500mg/kgbw of P. niruri extract caused the metabolic disorders of obese diabetic rats to be improved towards the normal state. The extract also clearly decreased the serum glucose level and improved the lipid profile in obese diabetic rats. The results of this study may contribute towards better understanding the molecular mechanism of this medicinal plant in managing diabetes mellitus. PMID: 27318080 [PubMed - as supplied by publisher]

Staphylococcus aureus methicillin resistance detected by HPLC-MS/MS targeted metabolic profiling. J Chromatogr B Analyt Technol Biomed Life Sci. 2016 Jun 3; Authors: Schelli K, Rutowski J, Roubidoux J, Zhu J Abstract Recently, novel bioanalytical methods, such as NMR and mass spectrometry based metabolomics approaches, have started to show promise in providing rapid, sensitive and reproducible detection of Staphylococcus aureus antibiotic resistance. Here we performed a proof-of-concept study focused on the application of HPLC-MS/MS based targeted metabolic profiling for detecting and monitoring the bacterial metabolic profile changes in response to sub-lethal levels of methicillin exposure. One hundred seventy-seven targeted metabolites from over 20 metabolic pathways were specifically screened and one hundred and thirty metabolites from in vitro bacterial tests were confidently detected from both methicillin susceptible and methicillin resistant Staphylococcus aureus (MSSA and MRSA, respectively). The metabolic profiles can be used to distinguish the isogenic pairs of MSSA strains from MRSA strains, without or with sub-lethal levels of methicillin exposure. In addition, better separation between MSSA and MRSA strains can be achieved in the latter case using principal component analysis (PCA). Metabolite data from isogenic pairs of MSSA and MRSA strains were further compared without and with sub-lethal levels of methicillin exposure, with metabolic pathway analyses additionally performed. Both analyses suggested that the metabolic activities of MSSA strains were more susceptible to the perturbation of the sub-lethal levels of methicillin exposure compared to the MRSA strains. PMID: 27316783 [PubMed - as supplied by publisher]

Related Articles Biotransformation and metabolic profile of caudatin-2,6-dideoxy-3-O-methy-β-d-cymaropyranoside with human intestinal microflora by liquid chromatography quadrupole time-of-flight mass spectrometry. Biomed Chromatogr. 2015 Nov;29(11):1715-23 Authors: Zhang W, Peng YR, Ding YF Abstract In our previous studies, caudatin-2,6-dideoxy-3-O-methy-β-d- cymaropyranoside (CDMC) was for the first time isolated from Cynanchum auriculatum Royle ex Wightand and was reported to possess a wide range of biological activities. However, the routes and metabolites of CDMC produced by intestinal bacteria are not well understood. In this study, ultra-performance liquid chromatography/quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS) technique combined with Metabolynx(TM) software was applied to analyze metabolites of CDMC by human intestinal bacteria. The incubated samples collected for 48 h in an anaerobic incubator and extracted with ethyl acetate were analyzed by UPLC-Q-TOF-MS within 12 min. Eight metabolites were identified based on MS and MS/MS data. The results indicated that hydrolysis, hydrogenation, demethylation and hydroxylation were the major metabolic pathways of CDMC in vitro. Seven strains of bacteria including Bacillus sp. 46, Enterococcus sp. 30 and sp. 45, Escherichia sp. 49A, sp. 64, sp. 68 and sp. 75 were further identified using 16S rRNA gene sequencing owing to their relatively strong metabolic capacity toward CDMC. The present study provides important information about metabolic routes of CDMC and the roles of different intestinal bacteria in the metabolism of CDMC. Moreover, those metabolites might influence the biological effect of CDMC in vivo, which affects the clinical effects of this medicinal plant. PMID: 26018801 [PubMed - indexed for MEDLINE]

Multi-omics Frontiers in Algal Research: Techniques and Progress to Explore Biofuels in the Postgenomics World. OMICS. 2016 Jun 17; Authors: Rai V, Karthikaichamy A, Das D, Noronha S, Wangikar PP, Srivastava S Abstract Current momentum of microalgal research rests extensively in tapping the potential of multi-omics methodologies in regard to sustainable biofuels. Microalgal biomass is fermented to bioethanol; while lipids, particularly triacylglycerides (TAGs), are transesterified to biodiesels. Biodiesel has emerged as an ideal biofuel candidate; hence, its commercialization and use are increasingly being emphasized. Abiotic stresses exaggerate TAG accumulation, but the precise mechanisms are yet to be known. More recently, comprehensive multi-omics studies in microalgae have emerged from the biofuel perspective. Genomics and transcriptomics of microalgae have provided crucial leads and basic understanding toward lipid biosynthesis. Proteomics and metabolomics are now complementing "algal omics" and offer precise functional insights into the attendant static and dynamic physiological contexts. Indeed, the field has progressed from shotgun to targeted approaches. Notably, targeted proteomics studies in microalga are not yet reported. Several multi-omics tools and technologies that may be used to dig deeper into the microalgal physiology are examined and highlighted in this review. The article therefore aims to both introduce various available high-throughput biotechnologies and applications of "omics" in microalgae, and enlists a compendium of the emerging cutting edge literature. We suggest that a strategic and thoughtful combination of data streams from different omics platforms can provide a system-wide overview. The algal omics warrants closer attention in the future, with a view to technical, economic, and societal impacts that are anticipated in the current postgenomics era. PMID: 27315140 [PubMed - as supplied by publisher]

Precision medicine of aneurysmal subarachnoid hemorrhage, vasospasm and delayed cerebral ischemia. Expert Rev Neurother. 2016 Jun 17; Authors: Burrell C, Avalon NE, Siegel J, Pizzi M, Dutta T, Charlesworth MC, Freeman WD Abstract INTRODUCTION: Precision medicine is an emerging paradigm aimed at providing individualized prevention and treatment of diseases through understanding and leveraging patient-to-patient variation. Aneurysmal subarachnoid hemorrhage (aSAH) carries tremendous morbidity and mortality with subsequent cerebral vasospasm (CV) and delayed cerebral ischemia (DCI) proving devastating and unpredictable. The paucity of effective treatment or prevention measures for these conditions could potentially be improved through implementation of precision medicine. AREAS COVERED: This review presents the basic pathophysiology of CV and DCI, current treatment guidelines, and evidence for the use of precision medicine in the prediction and prevention of poor outcomes following aSAH. An extensive PubMed literature search was performed using keywords cerebral vasospasm or delayed cerebral ischemia and either biomarkers, precision medicine, metabolomics, proteomics, or genomics. Over 200 peer-reviewed articles were reviewed. The studies presented focus on biomarkers identified as predictive markers or therapeutic targets following aSAH. Expert Commentary: The array of novel biomarkers reviewed here, ranging from genotypes to metabolites, has been found to correlate with CV, DCI, and neurologic outcomes after aSAH. Though their practical use in the clinical management of aSAH is not well established, using these biomarkers as predictive tools or therapeutic targets demonstrates the potential of precision medicine in the treatment of aSAH. PMID: 27314601 [PubMed - as supplied by publisher]

Metabolomic Profiles of Aspergillus oryzae and Bacillus amyloliquefaciens During Rice Koji Fermentation. Molecules. 2016;21(6) Authors: Lee DE, Lee S, Jang ES, Shin HW, Moon BS, Lee CH Abstract Rice koji, used early in the manufacturing process for many fermented foods, produces diverse metabolites and enzymes during fermentation. Using gas chromatography time-of-flight mass spectrometry (GC-TOF-MS), ultrahigh-performance liquid chromatography linear trap quadrupole ion trap tandem mass spectrometry (UHPLC-LTQ-IT-MS/MS), and multivariate analysis we generated the metabolite profiles of rice koji produced by fermentation with Aspergillus oryzae (RK_AO) or Bacillus amyloliquefaciens (RK_BA) for different durations. Two principal components of the metabolomic data distinguished the rice koji samples according to their fermenter species and fermentation time. Several enzymes secreted by the fermenter species, including α-amylase, protease, and β-glucosidase, were assayed to identify differences in expression levels. This approach revealed that carbohydrate metabolism, serine-derived amino acids, and fatty acids were associated with rice koji fermentation by A. oryzae, whereas aromatic and branched chain amino acids, flavonoids, and lysophospholipids were more typical in rice koji fermentation by B. amyloliquefaciens. Antioxidant activity was significantly higher for RK_BA than for RK_AO, as were the abundances of flavonoids, including tricin, tricin glycosides, apigenin glycosides, and chrysoeriol glycosides. In summary, we have used MS-based metabolomics and enzyme activity assays to evaluate the effects of using different microbial species and fermentation times on the nutritional profile of rice koji. PMID: 27314317 [PubMed - as supplied by publisher]