PubMed

Metabolic Consequences of Infection of Grapevine (Vitis vinifera L.) cv. "Modra frankinja" with Flavescence Dorée Phytoplasma. Front Plant Sci. 2016;7:711 Authors: Prezelj N, Covington E, Roitsch T, Gruden K, Fragner L, Weckwerth W, Chersicola M, Vodopivec M, Dermastia M Abstract Flavescence dorée, caused by the quarantine phytoplasma FDp, represents the most devastating of the grapevine yellows diseases in Europe. In an integrated study we have explored the FDp-grapevine interaction in infected grapevines of cv. "Modra frankinja" under natural conditions in the vineyard. In FDp-infected leaf vein-enriched tissues, the seasonal transcriptional profiles of 14 genes selected from various metabolic pathways showed an FDp-specific plant response compared to other grapevine yellows and uncovered a new association of the SWEET17a vacuolar transporter of fructose with pathogens. Non-targeted metabolome analysis from leaf vein-enriched tissues identified 22 significantly changed compounds with increased levels during infection. Several metabolites corroborated the gene expression study. Detailed investigation of the dynamics of carbohydrate metabolism revealed significant accumulation of sucrose and starch in the mesophyll of FDp-infected leaves, as well as significant up-regulation of genes involved in their biosynthesis. In addition, infected leaves had high activities of ADP-glucose pyrophosphorylase and, more significantly, sucrose synthase. The data support the conclusion that FDp infection inhibits phloem transport, resulting in accumulation of carbohydrates and secondary metabolites that provoke a source-sink transition and defense response status. PMID: 27242887 [PubMed]

Abiotic Stress Tolerance of Charophyte Green Algae: New Challenges for Omics Techniques. Front Plant Sci. 2016;7:678 Authors: Holzinger A, Pichrtová M Abstract Charophyte green algae are a paraphyletic group of freshwater and terrestrial green algae, comprising the classes of Chlorokybophyceae, Coleochaetophyceae, Klebsormidiophyceae, Zygnematophyceae, Mesostigmatophyceae, and Charo- phyceae. Zygnematophyceae (Conjugating green algae) are considered to be closest algal relatives to land plants (Embryophyta). Therefore, they are ideal model organisms for studying stress tolerance mechanisms connected with transition to land, one of the most important events in plant evolution and the Earth's history. In Zygnematophyceae, but also in Coleochaetophyceae, Chlorokybophyceae, and Klebsormidiophyceae terrestrial members are found which are frequently exposed to naturally occurring abiotic stress scenarios like desiccation, freezing and high photosynthetic active (PAR) as well as ultraviolet (UV) irradiation. Here, we summarize current knowledge about various stress tolerance mechanisms including insight provided by pioneer transcriptomic and proteomic studies. While formation of dormant spores is a typical strategy of freshwater classes, true terrestrial groups are stress tolerant in vegetative state. Aggregation of cells, flexible cell walls, mucilage production and accumulation of osmotically active compounds are the most common desiccation tolerance strategies. In addition, high photophysiological plasticity and accumulation of UV-screening compounds are important protective mechanisms in conditions with high irradiation. Now a shift from classical chemical analysis to next-generation genome sequencing, gene reconstruction and annotation, genome-scale molecular analysis using omics technologies followed by computer-assisted analysis will give new insights in a systems biology approach. For example, changes in transcriptome and role of phytohormone signaling in Klebsormidium during desiccation were recently described. Application of these modern approaches will deeply enhance our understanding of stress reactions in an unbiased non-targeted view in an evolutionary context. PMID: 27242877 [PubMed]

Nontargeted metabolomic analysis and "Commercial-homophyletic" comparison-induced biomarkers verification for the systematic chemical differentiation of five different parts of Panax ginseng. J Chromatogr A. 2016 May 13; Authors: Qiu S, Yang WZ, Yao CL, Qiu ZD, Shi XJ, Zhang JX, Hou JJ, Wang QR, Wu WY, Guo DA Abstract A key segment in authentication of herbal medicines is the establishment of robust biomarkers that embody the intrinsic metabolites difference independent of the growing environment or processing technics. We present a strategy by nontargeted metabolomics and "Commercial-homophyletic" comparison-induced biomarkers verification with new bioinformatic vehicles, to improve the efficiency and reliability in authentication of herbal medicines. The chemical differentiation of five different parts (root, leaf, flower bud, berry, and seed) of Panax ginseng was illustrated as a case study. First, an optimized ultra-performance liquid chromatography/quadrupole time-of-flight-MS(E) (UPLC/QTOF-MS(E)) approach was established for global metabolites profiling. Second, UNIFI™ combined with search of an in-house library was employed to automatically characterize the metabolites. Third, pattern recognition multivariate statistical analysis of the MS(E) data of different parts of commercial and homophyletic samples were separately performed to explore potential biomarkers. Fourth, potential biomarkers deduced from commercial and homophyletic root and leaf samples were cross-compared to infer robust biomarkers. Fifth, discriminating models by artificial neutral network (ANN) were established to identify different parts of P. ginseng. Consequently, 164 compounds were characterized, and 11 robust biomarkers enabling the differentiation among root, leaf, flower bud, and berry, were discovered by removing those structurally unstable and possibly processing-related ones. The ANN models using the robust biomarkers managed to exactly discriminate four different parts and root adulterant with leaf as well. Conclusively, biomarkers verification using homophyletic samples conduces to the discovery of robust biomarkers. The integrated strategy facilitates authentication of herbal medicines in a more efficient and more intelligent manner. PMID: 27240945 [PubMed - as supplied by publisher]

Use of metabolomics and lipidomics to evaluate the hypocholestreolemic effect of Proanthocyanidins from grape seed in a pig model. Mol Nutr Food Res. 2016 May 31; Authors: Quifer-Rada P, Choy YY, Calvert CC, Waterhouse AL, Lamuela-Raventos RM Abstract SCOPE: This work aims to evaluate changes in the fecal metabolomic profile due to grape seed extract (GSE) intake by untargeted and targeted analysis using high resolution mass spectrometry in conjunction with multivariate statistics. METHODS AND RESULTS: An intervention study with six crossbred female pigs was performed. The pigs followed a standard diet for 3 days, then they were fed with a supplemented diet containing 1% (w/w) of MegaNatural® Gold grape seed extract for 6 days. Fresh pig fecal samples were collected daily. A combination of untargeted high resolution mass spectrometry, multivariate analysis (PLS-DA), data-dependent MS/MS scan and accurate mass database matching was used to measure the effect of the treatment on fecal composition. The resultant PLS-DA models showed a good discrimination among classes with great robustness and predictability. A total of 14 metabolites related to the GSE consumption were identified including biliary acid, dicarboxylic fatty acid, cholesterol metabolites, purine metabolites, and eicosanoid metabolites among others. Moreover, targeted metabolomics using GC-MS showed that cholesterol and its metabolites fecal excretion was increased due to the proanthocyanidins from grape seed extract. CONCLUSION: The results show that oligomeric procyanidins from GSE modifies bile acid and steroid excretion, which could exert a hypocholesterolemic effect. This article is protected by copyright. All rights reserved. PMID: 27240545 [PubMed - as supplied by publisher]

Related Articles Investigation of Host-Gut Microbiota Modulation of Therapeutic Outcome. Drug Metab Dispos. 2015 Oct;43(10):1619-31 Authors: Yip LY, Chan EC Abstract A broader understanding of factors underlying interindividual variation in pharmacotherapy is important for our pursuit of "personalized medicine." Based on knowledge gleaned from the investigation of human genetics, drug-metabolizing enzymes, and transporters, clinicians and pharmacists are able to tailor pharmacotherapies according to the genotype of patients. However, human host factors only form part of the equation that accounts for heterogeneity in therapeutic outcome. Notably, the gut microbiota possesses wide-ranging metabolic activities that expand the metabolic functions of the human host beyond that encoded by the human genome. In this review, we first illustrate the mechanisms in which gut microbes modulate pharmacokinetics and therapeutic outcome. Second, we discuss the application of metabonomics in deciphering the complex host-gut microbiota interaction in pharmacotherapy. Third, we highlight an integrative approach with particular mention of the investigation of gut microbiota using culture-based and culture-independent techniques to complement the investigation of the host-gut microbiota axes in pharmaceutical research. PMID: 25979259 [PubMed - indexed for MEDLINE]

Metabolic Effect of Estrogen Receptor Agonists on Breast Cancer Cells in the Presence or Absence of Carbonic Anhydrase Inhibitors. Metabolites. 2016;6(2) Authors: Belkaid A, Čuperlović-Culf M, Touaibia M, Ouellette RJ, Surette ME Abstract Metabolic shift is one of the major hallmarks of cancer development. Estrogen receptor (ER) activity has a profound effect on breast cancer cell growth through a number of metabolic changes driven by its effect on transcription of several enzymes, including carbonic anhydrases, Stearoyl-CoA desaturase-1, and oncogenes including HER2. Thus, estrogen receptor activators can be expected to lead to the modulation of cell metabolism in estrogen receptor positive cells. In this work we have investigated the effect of 17β-estradiol, an ER activator, and ferulic acid, a carbonic anhydrase inhibitor, as well as ER activator, in the absence and in the presence of the carbonic anhydrase inhibitor acetazolamide on the metabolism of MCF7 cells and MCF7 cells, stably transfected to express HER2 (MCF7HER2). Metabolic profiles were studied using 1D and 2D metabolomic Nuclear Magnetic Resonance (NMR) experiments, combined with the identification and quantification of metabolites, and the annotation of the results in the context of biochemical pathways. Overall changes in hydrophilic metabolites were largest following treatment of MCF7 and MC7HER2 cells with 17β-estradiol. However, the carbonic anhydrase inhibitor acetazolamide had the largest effect on the profile of lipophilic metabolites. PMID: 27240414 [PubMed - as supplied by publisher]

Association between Metabolite Profiles, Metabolic Syndrome and Obesity Status. Nutrients. 2016;8(6) Authors: Allam-Ndoul B, Guénard F, Garneau V, Cormier H, Barbier O, Pérusse L, Vohl MC Abstract 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. PMID: 27240400 [PubMed - as supplied by publisher]

Metabolomic Profiling of Bradyrhizobium diazoefficiens-Induced Root Nodules Reveals Both Host Plant-Specific and Developmental Signatures. Int J Mol Sci. 2016;17(6) Authors: Lardi M, Murset V, Fischer HM, Mesa S, Ahrens CH, Zamboni N, Pessi G Abstract Bradyrhizobium diazoefficiens is a nitrogen-fixing endosymbiont, which can grow inside root-nodule cells of the agriculturally important soybean and other host plants. Our previous studies described B. diazoefficiens host-specific global expression changes occurring during legume infection at the transcript and protein level. In order to further characterize nodule metabolism, we here determine by flow injection-time-of-flight mass spectrometry analysis the metabolome of (i) nodules and roots from four different B. diazoefficiens host plants; (ii) soybean nodules harvested at different time points during nodule development; and (iii) soybean nodules infected by two strains mutated in key genes for nitrogen fixation, respectively. Ribose (soybean), tartaric acid (mungbean), hydroxybutanoyloxybutanoate (siratro) and catechol (cowpea) were among the metabolites found to be specifically elevated in one of the respective host plants. While the level of C4-dicarboxylic acids decreased during soybean nodule development, we observed an accumulation of trehalose-phosphate at 21 days post infection (dpi). Moreover, nodules from non-nitrogen-fixing bacteroids (nifA and nifH mutants) showed specific metabolic alterations; these were also supported by independent transcriptomics data. The alterations included signs of nitrogen limitation in both mutants, and an increased level of a phytoalexin in nodules induced by the nifA mutant, suggesting that the tissue of these nodules exhibits defense and stress reactions. PMID: 27240350 [PubMed - as supplied by publisher]

Metabolic Fingerprinting to Assess the Impact of Salinity on Carotenoid Content in Developing Tomato Fruits. Int J Mol Sci. 2016;17(6) Authors: Van Meulebroek L, Hanssens J, Steppe K, Vanhaecke L Abstract As the presence of health-promoting substances has become a significant aspect of tomato fruit appreciation, this study investigated nutrient solution salinity as a tool to enhance carotenoid accumulation in cherry tomato fruit (Solanum lycopersicum L. cv. Juanita). Hereby, a key objective was to uncover the underlying mechanisms of carotenoid metabolism, moving away from typical black box research strategies. To this end, a greenhouse experiment with five salinity treatments (ranging from 2.0 to 5.0 decisiemens (dS) m(-1)) was carried out and a metabolomic fingerprinting approach was applied to obtain valuable insights on the complicated interactions between salinity treatments, environmental conditions, and the plant's genetic background. Hereby, several hundreds of metabolites were attributed a role in the plant's salinity response (at the fruit level), whereby the overall impact turned out to be highly depending on the developmental stage. In addition, 46 of these metabolites embraced a dual significance as they were ascribed a prominent role in carotenoid metabolism as well. Based on the specific mediating actions of the retained metabolites, it could be determined that altered salinity had only marginal potential to enhance carotenoid accumulation in the concerned tomato fruit cultivar. This study invigorates the usefulness of metabolomics in modern agriculture, for instance in modeling tomato fruit quality. Moreover, the metabolome changes that were caused by the different salinity levels may enclose valuable information towards other salinity-related plant processes as well. PMID: 27240343 [PubMed - as supplied by publisher]

Quantitative analysis of amino acids and acylcarnitines combined with untargeted metabolomics using ultra-high performance liquid chromatography and quadrupole time-of-flight mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci. 2016 May 14;1027:40-49 Authors: Roy C, Tremblay PY, Bienvenu JF, Ayotte P Abstract Metabolomics is an "omic" technique being increasingly used in epidemiological and clinical studies. We developed a method combining untargeted metabolomics with the quantitative determination of eight amino acids (AA) and eight acylcarnitines (AC) in plasma using ultra-high pressure liquid chromatography (UHPLC), electrospray ionization (ESI) and quadrupole time-of-flight mass spectrometry (QTOFMS). Separation of metabolites is performed by ion-pair reverse phase UHPLC using a HSS T3 column (2.1×100mm, 100Å, 1.8μm particle size) and formic acid-ammonium acetate-heptafluorobutyric acid in water and formic acid-ammonium acetate in methanol as mobile phases. Metabolite identification and quantification are achieved using a QTOFMS operating in ESI-positive and full-scan mode along with MS(E) acquisition of fragmentation patterns. Targeted metabolites are quantified using the appropriate labeled standards and include branched-chain AA (leucine, isoleucine, valine), aromatic AA (phenylalanine, tyrosine) as well as acetylcarnitine and propionylcarnitine, which have been identified as biomarkers of future cardiometabolic disease risk. The inter-day precision (relative standard deviation) for the targeted method was <15% for all but one metabolite and accuracy (bias) of amino acids ranged from 0.5% to 13.9% using SRM 1950 as the external standard. Untargeted metabolomics in 30 plasma samples from the general Canadian population revealed 5018 features, of which 48 metabolites were identified using the MZmine 2.19 software including 23 by our in-house library that comprises 671 annotated metabolites. SRM 1950 analysis revealed 11,684 features, among which 154 metabolites were identified. Our method is currently applied in several epidemiological studies to better characterize cardiometabolic diseases and identify new biomarkers for disease prevention. PMID: 27240302 [PubMed - as supplied by publisher]

Early changes in apoplast composition associated with defence and disease in interactions between Phaseolus vulgaris and the halo blight pathogen Pseudomonas syringae pv. phaseolicola. Plant Cell Environ. 2016 May 30; Authors: O'Leary BM, Neale HC, Geilfus CM, Jackson RW, Arnold DL, Preston GM Abstract The apoplast is the arena in which endophytic pathogens such as Pseudomonas syringae grow and interact with plant cells. Using metabolomic and ion analysis techniques, this study shows how the composition of Phaseolus vulgaris leaf apoplastic fluid changes during the first six hours of compatible and incompatible interactions with two strains of Pseudomonas syringae pv. phaseolicola (Pph) that differ in the presence of the genomic island PPHGI-1. Leaf inoculation with the avirulent island-carrying strain Pph 1302A elicited effector-triggered immunity (ETI) and resulted in specific changes in apoplast composition, including increases in conductivity, pH, citrate, γ-aminobutyrate (GABA) and K(+) , that are linked to the onset of plant defence responses. Other apoplastic changes, including increases in Ca(2+) , Fe(2/3+) Mg(2+) , sucrose, β-cyanoalanine and several amino acids, occurred to a relatively similar extent in interactions with both Pph 1302A and the virulent, island-less strain Pph RJ3. Metabolic footprinting experiments established that Pph preferentially metabolizes malate, glucose and glutamate, but excludes certain other abundant apoplastic metabolites, including citrate and GABA, until preferred metabolites are depleted. These results demonstrate that Pph is well-adapted to the leaf apoplast metabolic environment and that loss of PPHGI-1 enables Pph to avoid changes in apoplast composition linked to plant defences. PMID: 27239727 [PubMed - as supplied by publisher]

Metabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic Variation. mSystems. 2016 Jan-Feb;1(1) Authors: Noecker C, Eng A, Srinivasan S, Theriot CM, Young VB, Jansson JK, Fredricks DN, Borenstein E Abstract Multiple molecular assays now enable high-throughput profiling of the ecology, metabolic capacity, and activity of the human microbiome. However, to date, analyses of such multi-omic data typically focus on statistical associations, often ignoring extensive prior knowledge of the mechanisms linking these various facets of the microbiome. Here, we introduce a comprehensive framework to systematically link variation in metabolomic data with community composition by utilizing taxonomic, genomic, and metabolic information. Specifically, we integrate available and inferred genomic data, metabolic network modeling, and a method for predicting community-wide metabolite turnover to estimate the biosynthetic and degradation potential of a given community. Our framework then compares variation in predicted metabolic potential with variation in measured metabolites' abundances to evaluate whether community composition can explain observed shifts in the community metabolome, and to identify key taxa and genes contributing to the shifts. Focusing on two independent vaginal microbiome data sets, each pairing 16S community profiling with large-scale metabolomics, we demonstrate that our framework successfully recapitulates observed variation in 37% of metabolites. Well-predicted metabolite variation tends to result from disease-associated metabolism. We further identify several disease-enriched species that contribute significantly to these predictions. Interestingly, our analysis also detects metabolites for which the predicted variation negatively correlates with the measured variation, suggesting environmental control points of community metabolism. Applying this framework to gut microbiome data sets reveals similar trends, including prediction of bile acid metabolite shifts. This framework is an important first step toward a system-level multi-omic integration and an improved mechanistic understanding of the microbiome activity and dynamics in health and disease. IMPORTANCE: Studies characterizing both the taxonomic composition and metabolic profile of various microbial communities are becoming increasingly common, yet new computational methods are needed to integrate and interpret these data in terms of known biological mechanisms. Here, we introduce an analytical framework to link species composition and metabolite measurements, using a simple model to predict the effects of community ecology on metabolite concentrations and evaluating whether these predictions agree with measured metabolomic profiles. We find that a surprisingly large proportion of metabolite variation in the vaginal microbiome can be predicted based on species composition (including dramatic shifts associated with disease), identify putative mechanisms underlying these predictions, and evaluate the roles of individual bacterial species and genes. Analysis of gut microbiome data using this framework recovers similar community metabolic trends. This framework lays the foundation for model-based multi-omic integrative studies, ultimately improving our understanding of microbial community metabolism. PMID: 27239563 [PubMed - as supplied by publisher]

Antibiotic-Induced Alterations of the Gut Microbiota Alter Secondary Bile Acid Production and Allow for Clostridium difficile Spore Germination and Outgrowth in the Large Intestine. mSphere. 2016 Jan-Feb;1(1) Authors: Theriot CM, Bowman AA, Young VB Abstract It is hypothesized that the depletion of microbial members responsible for converting primary bile acids into secondary bile acids reduces resistance to Clostridium difficile colonization. To date, inhibition of C. difficile growth by secondary bile acids has only been shown in vitro. Using targeted bile acid metabolomics, we sought to define the physiologically relevant concentrations of primary and secondary bile acids present in the murine small and large intestinal tracts and how these impact C. difficile dynamics. We treated mice with a variety of antibiotics to create distinct microbial and metabolic (bile acid) environments and directly tested their ability to support or inhibit C. difficile spore germination and outgrowth ex vivo. Susceptibility to C. difficile in the large intestine was observed only after specific broad-spectrum antibiotic treatment (cefoperazone, clindamycin, and vancomycin) and was accompanied by a significant loss of secondary bile acids (deoxycholate, lithocholate, ursodeoxycholate, hyodeoxycholate, and ω-muricholate). These changes were correlated to the loss of specific microbiota community members, the Lachnospiraceae and Ruminococcaceae families. Additionally, physiological concentrations of secondary bile acids present during C. difficile resistance were able to inhibit spore germination and outgrowth in vitro. Interestingly, we observed that C. difficile spore germination and outgrowth were supported constantly in murine small intestinal content regardless of antibiotic perturbation, suggesting that targeting growth of C. difficile will prove most important for future therapeutics and that antibiotic-related changes are organ specific. Understanding how the gut microbiota regulates bile acids throughout the intestine will aid the development of future therapies for C. difficile infection and other metabolically relevant disorders such as obesity and diabetes. IMPORTANCE Antibiotics alter the gastrointestinal microbiota, allowing for Clostridium difficile infection, which is a significant public health problem. Changes in the structure of the gut microbiota alter the metabolome, specifically the production of secondary bile acids. Specific bile acids are able to initiate C. difficile spore germination and also inhibit C. difficile growth in vitro, although no study to date has defined physiologically relevant bile acids in the gastrointestinal tract. In this study, we define the bile acids C. difficile spores encounter in the small and large intestines before and after various antibiotic treatments. Antibiotics that alter the gut microbiota and deplete secondary bile acid production allow C. difficile colonization, representing a mechanism of colonization resistance. Multiple secondary bile acids in the large intestine were able to inhibit C. difficile spore germination and growth at physiological concentrations and represent new targets to combat C. difficile in the large intestine. PMID: 27239562 [PubMed]

Expression of protocadherin gamma in skeletal muscle tissue is associated with age and muscle weakness. J Cachexia Sarcopenia Muscle. 2016 Feb 2; Authors: Hangelbroek RW, Fazelzadeh P, Tieland M, Boekschoten MV, Hooiveld GJ, van Duynhoven JP, Timmons JA, Verdijk LB, de Groot LC, van Loon LJ, Müller M Abstract BACKGROUND: The skeletal muscle system plays an important role in the independence of older adults. In this study we examine differences in the skeletal muscle transcriptome between healthy young and older subjects and (pre-)frail older adults. Additionally, we examine the effect of resistance-type exercise training on the muscle transcriptome in healthy older subjects and (pre-)frail older adults. METHODS: Baseline transcriptome profiles were measured in muscle biopsies collected from 53 young, 73 healthy older subjects, and 61 frail older subjects. Follow-up samples from these frail older subjects (31 samples) and healthy older subjects (41 samples) were collected after 6 months of progressive resistance-type exercise training. Frail older subjects trained twice per week and the healthy older subjects trained three times per week. RESULTS: At baseline genes related to mitochondrial function and energy metabolism were differentially expressed between older and young subjects, as well as between healthy and frail older subjects. Three hundred seven genes were differentially expressed after training in both groups. Training affected expression levels of genes related to extracellular matrix, glucose metabolism ,and vascularization. Expression of genes that were modulated by exercise training was indicative of muscle strength at baseline. Genes that strongly correlated with strength belonged to the protocadherin gamma gene cluster (r = -0.73). CONCLUSION: Our data suggest significant remaining plasticity of ageing skeletal muscle to adapt to resistance-type exercise training. Some age-related changes in skeletal muscle gene expression appear to be partially reversed by prolonged resistance-type exercise training. The protocadherin gamma gene cluster may be related to muscle denervation and re-innervation in ageing muscle. PMID: 27239416 [PubMed - as supplied by publisher]

Influence of the Melissa officinalis Leaf Extract on Long-Term Memory in Scopolamine Animal Model with Assessment of Mechanism of Action. Evid Based Complement Alternat Med. 2016;2016:9729818 Authors: Ozarowski M, Mikolajczak PL, Piasecka A, Kachlicki P, Kujawski R, Bogacz A, Bartkowiak-Wieczorek J, Szulc M, Kaminska E, Kujawska M, Jodynis-Liebert J, Gryszczynska A, Opala B, Lowicki Z, Seremak-Mrozikiewicz A, Czerny B Abstract Melissa officinalis (MO, English: lemon balm, Lamiaceae), one of the oldest and still most popular aromatic medicinal plants, is used in phytomedicine for the prevention and treatment of nervous disturbances. The aim of our study was to assess the effect of subchronic (28-fold) administration of a 50% ethanol extract of MO leaves (200 mg/kg, p.o.) compared with rosmarinic acid (RA, 10 mg/kg, p.o.) and huperzine A (HU, 0.5 mg/kg, p.o.) on behavioral and cognitive responses in scopolamine-induced rats. The results were linked with acetylcholinesterase (AChE), butyrylcholinesterase (BuChE), and beta-secretase (BACE-1) mRNA levels and AChE and BuChE activities in the hippocampus and frontal cortex of rats. In our study, MO and HU, but not RA, showed an improvement in long-term memory. The results were in line with mRNA levels, since MO produced a decrease of AChE mRNA level by 52% in the cortex and caused a strong significant inhibition of BACE1 mRNA transcription (64% in the frontal cortex; 50% in the hippocampus). However, the extract produced only an insignificant inhibition of AChE activity in the frontal cortex. The mechanisms of MO action are probably more complicated, since its role as a modulator of beta-secretase activity should be taken into consideration. PMID: 27239217 [PubMed]

An improved pseudotargeted metabolomics approach using multiple ion monitoring with time-staggered ion lists based on ultra-high performance liquid chromatography/quadrupole time-of-flight mass spectrometry. Anal Chim Acta. 2016 Jul 13;927:82-8 Authors: Wang Y, Liu F, Li P, He C, Wang R, Su H, Wan JB Abstract Pseudotargeted metabolomics is a novel strategy integrating the advantages of both untargeted and targeted methods. The conventional pseudotargeted metabolomics required two MS instruments, i.e., ultra-high performance liquid chromatography/quadrupole-time- of-flight mass spectrometry (UHPLC/Q-TOF MS) and UHPLC/triple quadrupole mass spectrometry (UHPLC/QQQ-MS), which makes method transformation inevitable. Furthermore, the picking of ion pairs from thousands of candidates and the swapping of the data between two instruments are the most labor-intensive steps, which greatly limit its application in metabolomic analysis. In the present study, we proposed an improved pseudotargeted metabolomics method that could be achieved on an UHPLC/Q-TOF/MS instrument operated in the multiple ion monitoring (MIM) mode with time-staggered ion lists (tsMIM). Full scan-based untargeted analysis was applied to extract the target ions. After peak alignment and ion fusion, a stepwise ion picking procedure was used to generate the ion lists for subsequent single MIM and tsMIM. The UHPLC/Q-TOF tsMIM MS-based pseudotargeted approach exhibited better repeatability and a wider linear range than the UHPLC/Q-TOF MS-based untargeted metabolomics method. Compared to the single MIM mode, the tsMIM significantly increased the coverage of the metabolites detected. The newly developed method was successfully applied to discover plasma biomarkers for alcohol-induced liver injury in mice, which indicated its practicability and great potential in future metabolomics studies. PMID: 27237840 [PubMed - in process]

Omics Meets Metabolic Pathway Engineering. Cell Syst. 2016 May 26; Authors: Chen GQ Abstract A principled approach to integrating metabolomics, proteomics, and genome-scale metabolic modeling facilitaties rational pathway engineering of E. coli. PMID: 27237740 [PubMed - as supplied by publisher]

Comparison and Optimization of Methods for the Simultaneous Extraction of DNA, RNA, Proteins, and Metabolites. Anal Biochem. 2016 May 26; Authors: Vorreiter F, Richter S, Peter M, Baumann S, von Bergen M, Tomm JM Abstract The challenge of performing a time-resolved comprehensive analysis of molecular systems has led to the quest to optimize extraction methods. When the size of a biological sample is limited, there is demand for the simultaneous extraction of molecules representing the four areas of 'omics,' genomics, transcriptomics, proteomics, and metabolomics. Here,we optimized a protocol for the simultaneous extraction of RNA, proteins, and metabolites and a compared it to tow existing protocols.second for the concurrent recovery of DNA, RNA, and proteins and compared it to two existing protconducted a previouslty described method. Our optimisation comprised the addition of a methanol/chloroform metabolite purification before the separation of DNA/RNA and proteins. Extracted DNA, RNA, proteins, and metabolites were quantitatively and/or qualitatively analyzed. Of the three methods, only the newly developed protocol yielded all biomolecule classes of adequate quantity and quality. PMID: 27237373 [PubMed - as supplied by publisher]

Metabolic variations in different citrus rootstock cultivars associated with different responses to Huanglongbing. Plant Physiol Biochem. 2016 May 20;107:33-44 Authors: Albrecht U, Fiehn O, Bowman KD Abstract Huanglongbing (HLB) is one of the most destructive bacterial diseases of citrus. No resistant cultivars have been identified, although tolerance has been observed in the genus Poncirus and some of its hybrids with Citrus that are commonly used as rootstocks. In this study we exploited this tolerance by comparing five different tolerant hybrids with a cultivar that shows pronounced HLB sensitivity to discern potential contributing metabolic factors. Whole leaves of infected and non-infected greenhouse-grown seedlings were extracted and subjected to untargeted GC-TOF MS based metabolomics. After BinBase data filtering, 342 (experiment 1) and 650 (experiment 2) unique metabolites were quantified, of which 122 and 195, respectively, were assigned by chemical structures. The number of metabolites found to be differently regulated in the infected state compared with the non-infected state varied between the cultivars and was largest (166) in the susceptible cultivar Cleopatra mandarin (Citrus reticulata) and lowest (3) in the tolerant cultivars US-897 (C. reticulata 'Cleopatra' × Poncirus trifoliata) and US-942 (C. reticulata 'Sunki' × P. trifoliata) from experiment 2. Tolerance to HLB did not appear to be associated with accumulation of higher amounts of protective metabolites in response to infection. Many metabolites were found in higher concentrations in the tolerant cultivars compared with susceptible Cleopatra mandarin and may play important roles in conferring tolerance to HLB. Lower availability of specific sugars necessary for survival of the pathogen may also be a contributing factor in the decreased disease severity observed for these cultivars. PMID: 27236226 [PubMed - as supplied by publisher]

Discrimination and quantification of true biological signals in LC-MS-based metabolomics analysis. Mol Plant. 2016 May 25; Authors: Duan L, Molnár I, Snyder JH, Shen GA, Qi X PMID: 27235546 [PubMed - as supplied by publisher]