PubMed

Proteomic and metabolomic analysis of the carotenogenic yeast Xanthophyllomyces dendrorhous using different carbon sources. BMC Genomics. 2015 Apr 12;16(1):289 Authors: Martinez-Moya P, Niehaus K, Alcaíno J, Baeza M, Cifuentes V Abstract BACKGROUND: Astaxanthin is a potent antioxidant with increasing biotechnological interest. In Xanthophyllomyces dendrorhous, a natural source of this pigment, carotenogenesis is a complex process regulated through several mechanisms, including the carbon source. X. dendrorhous produces more astaxanthin when grown on a non-fermentable carbon source, while decreased astaxanthin production is observed in the presence of high glucose concentrations. In the present study, we used a comparative proteomic and metabolomic analysis to characterize the yeast response when cultured in minimal medium supplemented with glucose (fermentable) or succinate (non-fermentable). RESULTS: A total of 329 proteins were identified from the proteomic profiles, and most of these proteins were associated with carotenogenesis, lipid and carbohydrate metabolism, and redox and stress responses. The metabolite profiles revealed 92 metabolites primarily associated with glycolysis, the tricarboxylic acid cycle, amino acids, organic acids, sugars and phosphates. We determined the abundance of proteins and metabolites of the central pathways of yeast metabolism and examined the influence of these molecules on carotenogenesis. Similar to previous proteomic-stress response studies, we observed modulation of abundance from several redox, stress response, carbohydrate and lipid enzymes. Additionally, the accumulation of trehalose, absence of key ROS response enzymes, an increased abundance of the metabolites of the pentose phosphate pathway and tricarboxylic acid cycle suggested an association between the accumulation of astaxanthin and oxidative stress in the yeast. Moreover, we observed the increased abundance of late carotenogenesis enzymes during astaxanthin accumulation under succinate growth conditions. CONCLUSIONS: The use of succinate as a carbon source in X. dendrorhous cultures increases the availability of acetyl-CoA for the astaxanthin production compared with glucose, likely reflecting the positive regulation of metabolic enzymes of the tricarboxylic acid and glyoxylate cycles. The high metabolite level generated in this pathway could increase the cellular respiration rate, producing reactive oxygen species, which induces carotenogenesis. PMID: 25887121 [PubMed - as supplied by publisher]

Related Articles Quorum-Sensing Dysbiotic Shifts in the HIV-Infected Oral Metabiome. PLoS One. 2015;10(4):e0123880 Authors: Brown RE, Ghannoum MA, Mukherjee PK, Gillevet PM, Sikaroodi M Abstract We implemented a Systems Biology approach using Correlation Difference Probability Network (CDPN) analysis to provide insights into the statistically significant functional differences between HIV-infected patients and uninfected individuals. The analysis correlates bacterial microbiome ("bacteriome"), fungal microbiome ("mycobiome"), and metabolome data to model the underlying biological processes comprising the Human Oral Metabiome. CDPN highlights the taxa-metabolite-taxa differences between the cohorts that frequently capture quorum-sensing modifications that reflect communication disruptions in the dysbiotic HIV cohort. The results also highlight the significant role of cyclic mono and dipeptides as quorum-sensing (QS) mediators between oral bacteria and fungal genus. The developed CDPN approach allowed us to model the interactions of taxa and key metabolites, and hypothesize their possible contribution to the etiology of Oral Candidiasis (OC). PMID: 25886290 [PubMed - as supplied by publisher]

Related Articles Population pharmacokinetic modeling of the Qishe pill in three major traditional Chinese medicine-defined constitutional types of healthy Chinese subjects: study protocol for a randomized controlled trial. Trials. 2015;16(1):64 Authors: Sun YL, Hou T, Liu SF, Zhang ZL, Zhang N, Yao M, Yang L, Shi Q, Cui XJ, Wang YJ Abstract BACKGROUND: High incidences of neck pain morbidity are challenging in various situations for populations based on their demographic, physiological and pathological characteristics. Chinese proprietary herbal medicines, as Complementary and Alternative Medicine (CAM) products, are usually developed from well-established and long-standing recipes formulated as tablets or capsules. However, good quantification and strict standardization are still needed for implementation of individualized therapies. The Qishe pill was developed and has been used clinically since 2009. The Qishe pill's personalized medicine should be documented and administered to various patients according to the ancient TCM system, a classification of personalized constitution types, established to determine predisposition and prognosis to diseases as well as therapy and life-style administration. Therefore, we describe the population pharmacokinetic profile of the Qishe pill and compare its metabolic rate in the three major constitution types (Qi-Deficiency, Yin-Deficiency and Blood-Stasis) to address major challenges to individualized standardized TCM. METHODS/DESIGN: Healthy subjects (N = 108) selected based on constitutional types will be assessed, and standardized pharmacokinetic protocol will be used for assessing demographic, physiological, and pathological data. Laboratory biomarkers will be evaluated and blood samples collected for pharmacokinetics(PK) analysis and second-generation gene sequencing. In single-dose administrations, subjects in each constitutional type cohort (N = 36) will be randomly divided into three groups to receive different Qishe pill doses (3.75, 7.5 and 15 grams). Multiomics, including next generation sequencing, metabolomics, and proteomics, will complement the Qishe pill's multilevel assessment, with cytochrome P450 genes as targets. In a comparison with the general population, a systematic population pharmacokinetic (PopPK) model for the Qishe pill will be established and verified. TRIAL REGISTRATION: This study is registered at ClinicalTrials.gov, NCT02294448 .15 November 2014. PMID: 25885543 [PubMed - as supplied by publisher]

Related Articles MRM-Ion Pair Finder: a systematic approach to transform non-targeted mode to pseudo-targeted mode for metabolomics study based on liquid chromatography-mass spectrometry. Anal Chem. 2015 Apr 17; Authors: Luo P, Dai W, Yin P, Zeng Z, Kong H, Zhou L, Wang X, Chen S, Lu X, Xu G Abstract Pseudo-targeted metabolic profiling is a novel strategy combining the advantages of both targeted and untargeted methods. The strategy obtains metabolites and their product ions from Q-TOF MS by information-dependent acquisition (IDA), then picks targeted ion-pair and measures them on a triple-quadrupole MS by multiple reaction monitoring (MRM). The picking of ion pairs from thousands of candidates is the most time-consuming step of pseudo-targeted strategy. Herein, a systematic and automated approach and software (MRM-Ion Pair Finder) were developed to acquire characteristic MRM ion pairs by precursor ions alignment, MS2 spectrum extraction and reduction, characteristic product ion selection, and ion fusion. To test the reliability of the approach, a mixture of 15 metabolite standards was firstly analyzed and the representative ion pairs were correctly picked out, then pooled serum samples were further studied and the results were confirmed by the manual selection. Finally, a comparison with a commercial peak alignment software was performed, a good characteristic ion coverage of metabolites was obtained. As a proof of concept, the proposed approach was applied to a metabolomics study of liver cancer, 854 metabolite ion pairs were defined in the positive ion mode from serum. Our approach provides a high throughput method which is reliable to acquire MRM ion pairs for pseudo-targeted metabolomics with improved metabolite coverage and facilitate more reliable biomarkers discoveries. PMID: 25884293 [PubMed - as supplied by publisher]

Related Articles Oxidized phosphatidylcholines suggest oxidative stress in patients with medium-chain acyl-CoA dehydrogenase deficiency. Talanta. 2015 Jul 1;139:62-6 Authors: Najdekr L, Gardlo A, Mádrová L, Friedecký D, Janečková H, Correa ES, Goodacre R, Adam T Abstract Inborn errors of metabolism encompass a large group of diseases caused by enzyme deficiencies and are therefore amenable to metabolomics investigations. Medium chain acyl-CoA dehydrogenase deficiency (MCADD) is a defect in β-oxidation of fatty acids, and is one of the most well understood disorders. We report here the use of liquid chromatography-mass spectrometry (LC-MS) based untargeted metabolomics and targeted flow injection analysis-tandem mass spectrometry (FIA-TMS) that lead to discovery of novel compounds of oxidative stress. Dry blood spots of controls (n=25) and patient samples (n=25) were extracted by methanol/water (1/1, v/v) and these supernatants were analyzed by LC-MS method with detection by an Orbitrap Elite MS. Data were processed by XCMS and CAMERA followed by dimension reduction methods. Patients were clearly distinguished from controls in PCA. S-plot derived from OPLS-DA indicated that medium-chain acylcarnitines (octanoyl, decenoyl and decanoyl carnitines) as well as three phosphatidylcholines (PC(16:0,9:0(COOH))), PC(18:0,5:0(COOH)) and PC(16:0,8:0(COOH)) were important metabolites for differentiation between patients and healthy controls. In order to biologically validate these discriminatory molecules as indicators for oxidative stress, a second cohort of individuals were analyzed, including MCADD (n=25) and control (n=250) samples. These were measured by a modified newborn screening method using FIA-TMS (API 4000) in MRM mode. Calculated p-values for PC(16:0,9:0(COOH)), PC(18:0,5:0(COOH)) and PC(16:0,8:0(COOH)) were 1.927×10(-14), 2.391×10(-15) and 3.354×10(-15) respectively. These elevated oxidized phospholipids indeed show an increased presence of oxidative stress in MCADD patients as one of the pathophysiological mechanisms of the disease. PMID: 25882409 [PubMed - in process]

Related Articles A gas chromatography-mass spectrometry based study on serum metabolomics in rats chronically poisoned with hydrogen sulfide. J Forensic Leg Med. 2015 May;32:59-63 Authors: Deng M, Zhang M, Huang X, Ma J, Hu L, Lin G, Wang X Abstract Hydrogen sulfide poisoning is a common occupational hazard, whose mortality and incidence rates are first and second, respectively, among occupational poisoning incidents in China. The main target organs of its toxicity are in the central nervous system and respiratory system. However, there are currently no specific direct tests that can be used to diagnose poisoned patients. In this study, we developed a serum metabonomic method using orthogonal partial least squares-discriminate analysis (OPLS-DA), based on gas chromatography-mass spectrometry (GC/MS) to evaluate the effect of chronic poisoning by hydrogen sulfide in rats. The OPLS-DA data demonstrated that the model group (n = 60) differed significantly from the control group (n = 30), suggesting that the metabolic profiles of the two groups are markedly different. Alterations in the levels of some metabolites such as citrate, galactose, lactate, mannose, inositol, urea, phosphate, alanine and valine were detected by OPLS-DA analysis. We observed changes in metabolic pathways including lipid metabolism, energy metabolism and amino metabolism in the model group. Our results indicate that GC/MS-based metabonomic methods may provide novel detection means for chronic hydrogen sulfide poisoning. PMID: 25882152 [PubMed - in process]

Related Articles Cardiomyopathy and Worsened Ischemic Heart Failure in SM22-α Cre-Mediated Neuropilin-1 Null Mice: Dysregulation of PGC1α and Mitochondrial Homeostasis. Arterioscler Thromb Vasc Biol. 2015 Apr 16; Authors: Wang Y, Cao Y, Yamada S, Thirunavukkarasu M, Nin V, Joshi M, Rishi MT, Bhattacharya S, Camacho-Pereira J, Sharma AK, Shameer K, Kocher JP, Sanchez JA, Wang E, Hoeppner LH, Dutta SK, Leof EB, Shah V, Claffey KP, Chini E, Simons M, Terzic A, Maulik N, Mukhopadhyay D Abstract OBJECTIVE: Neuropilin-1 (NRP-1) is a multidomain membrane receptor involved in angiogenesis and development of neuronal circuits, however, the role of NRP-1 in cardiovascular pathophysiology remains elusive. APPROACH AND RESULTS: In this study, we first observed that deletion of NRP-1 induced peroxisome proliferator-activated receptor γ coactivator 1α in cardiomyocytes and vascular smooth muscle cells, which was accompanied by dysregulated cardiac mitochondrial accumulation and induction of cardiac hypertrophy- and stress-related markers. To investigate the role of NRP-1 in vivo, we generated mice lacking Nrp-1 in cardiomyocytes and vascular smooth muscle cells (SM22-α-Nrp-1 KO), which exhibited decreased survival rates, developed cardiomyopathy, and aggravated ischemia-induced heart failure. Mechanistically, we found that NRP-1 specifically controls peroxisome proliferator-activated receptor γ coactivator 1 α and peroxisome proliferator-activated receptor γ in cardiomyocytes through crosstalk with Notch1 and Smad2 signaling pathways, respectively. Moreover, SM22-α-Nrp-1 KO mice exhibited impaired physical activities and altered metabolite levels in serum, liver, and adipose tissues, as demonstrated by global metabolic profiling analysis. CONCLUSIONS: Our findings provide new insights into the cardioprotective role of NRP-1 and its influence on global metabolism. PMID: 25882068 [PubMed - as supplied by publisher]

Related Articles Metabolite profiles in heart failure: looking for unique signatures in a heterogeneous syndrome. J Am Coll Cardiol. 2015 Apr 21;65(15):1521-4 Authors: Wang TJ, Gupta DK PMID: 25881933 [PubMed - in process]

Related Articles Metabolic Disturbances Identified in Plasma Are Associated With Outcomes in Patients With Heart Failure: Diagnostic and Prognostic Value of Metabolomics. J Am Coll Cardiol. 2015 Apr 21;65(15):1509-20 Authors: Cheng ML, Wang CH, Shiao MS, Liu MH, Huang YY, Huang CY, Mao CT, Lin JF, Ho HY, Yang NI Abstract BACKGROUND: Identification of novel biomarkers is needed to improve the diagnosis and prognosis of heart failure (HF). Metabolic disturbance is remarkable in patients with HF. OBJECTIVES: This study sought to assess the diagnostic and prognostic values of metabolomics in HF. METHODS: Mass spectrometry-based profiling of plasma metabolites was performed in 515 participants; the discovery phase study enrolled 51 normal control subjects and 183 HF patients, and the validation study enrolled 63 control subjects and 218 patients with stage C HF. Another independent group of 32 patients with stage C HF who recovered to New York Heart Association functional class I at 6 and 12 months was profiled as the "recovery" group. RESULTS: A panel of metabolites, including histidine, phenylalanine, spermidine, and phosphatidylcholine C34:4, has a diagnostic value similar to B-type natriuretic peptide (BNP). In the recovery group, the values of this panel significantly improved at 6 and 12 months. To evaluate the prognostic values, events were defined as the combined endpoints of death or HF-related re-hospitalization. A metabolite panel, which consisted of the asymmetric methylarginine/arginine ratio, butyrylcarnitine, spermidine, and the total amount of essential amino acids, provided significant prognostic values (p < 0.0001) independent of BNP and traditional risk factors. The prognostic value of the metabolite panel was better than that of BNP (area under the curve of 0.85 vs. 0.74 for BNP) and Kaplan-Meier curves (log rank: 17.5 vs. 9.95). These findings were corroborated in the validation study. CONCLUSIONS: Metabolomics demonstrate powerful diagnostic value in estimating HF-related metabolic disturbance. The profile of metabolites provides better prognostic value versus conventional biomarkers. PMID: 25881932 [PubMed - in process]

Related Articles NMR/MS Translator for the Enhanced Simultaneous Analysis of Metabolomics Mixtures by NMR Spectroscopy and Mass Spectrometry: Application to Human Urine. J Proteome Res. 2015 Apr 17; Authors: Bingol K, Bruschweiler R Abstract A novel metabolite identification strategy is presented for the combined NMR/MS analysis of complex metabolite mixtures. The approach first identifies metabolite candidates from 1D or 2D NMR spectra by NMR database query, which is followed by the determination of the masses (m/z) of their possible ions, adducts, fragments, and characteristic isotope distributions. The expected m/z ratios are then compared with the MS spectrum for the direct assignment of those signals of the mass spectrum that contain information about the same metabolites as the NMR spectra. In this way, the mass spectrum can be assigned with very high confidence and it provides at the same time validation of the NMR-derived metabolites. The method was first demonstrated on a model mixture and it was then applied to human urine collected from a pool of healthy individuals. A number of metabolites could be detected that had not been reported previously further extending the list of known urine metabolites. The new analysis approach, which is termed NMR/MS Translator, is fully automated and takes only few seconds on a computer workstation. The NMR/MS Translator synergistically uses the power of NMR and MS enhancing the accuracy and efficiency of the identification of those metabolites compiled in databases. PMID: 25881480 [PubMed - as supplied by publisher]

Related Articles 1H nuclear magnetic resonance-based metabolomic study on efficacy of Qingrehuatan decoction against abundant phlegm-heat syndrome in young adults with essential hypertension. J Tradit Chin Med. 2015 Feb;35(1):28-35 Authors: Feng X, Yang Z, Chu Y, Du B, Su M, Li Y, Wang Y, Jiang C, Hu Y Abstract OBJECTIVE: To observe the influence of Qingrehuatan decoction (QRHT) on serum metabolic profile in young essential hypertension (YEH) patients with abundant phlegm-heat syndrome and provide a basis for treatment with the decoction. METHODS: Twelve male YEH patients were randomly selected and serum samples were collected for examination before and after 4 weeks of the treatment with QRHT. Twelve healthy males were randomly selected and their serum samples were collected as a control. All serum samples were detected using metabolomic technology with 1H nuclear magnetic resonance. Differences in metabolites were studied by principal component analysis and partial least squares-discriminate analysis, which produced scores and loadings plots. RESULTS: After 4 weeks of treatment, serum substances could be distinguished between the YEH patients with abundant phlegm-heat syndrome and the control patients. The specific serum endog- enous metabolites tended to improve after the treatment. QRHT can appropriately increase the levels of glucose, lactic acid, citric acid, high-density lipoprotein, phosphatidylcholine, glycerophosphate choline, hydroxybutyrate, alanine, and glutamate. QRHT could also decrease the levels of low-density lipoprotein/very low-density lipoprotein, lipids, N-acetyl glycoprotein, and O-acetyl glycoprotein. CONCLUSION: QRHT can effectively ameliorate metabolic disorders in YEH Patients with abundant phlegm-heat syndrome. 1H NMR-based metabolomic technology can provide an objective basis for the treatment of YEH patients with abundant phlegm-heat syndrome using QRHT. PMID: 25842725 [PubMed - indexed for MEDLINE]

Related Articles [Metabolic profiling for characteristics of Trichoderma from buried soils]. Tsitologiia. 2014;56(6):445-9 Authors: Tukhbatova RI, Morozova IuA, Alimova FK Abstract Previously, 135 strains of Trichoderma isolated from buried soils of Tatarstan have been identified as T. asperellum, T. viride, T. atroviride, T. harzianum, T. hamatum, T. citrinoviride and T. longibrachiatum. At this stage, the biochemical analysis of the strains was carried out using the Biolog system, which being a simple screening test enables rapid preparation of strains based on 95 substrates. We have revealed that each species has only a specific substrate utilisation profile. Biochemical analysis provides a large amount of information that can then be used for optimization of biotechnological processes, in particular, the selection of effective nutrient media. PMID: 25696984 [PubMed - indexed for MEDLINE]

16 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 2015/04/17PubMed 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.

Systems Biology Analysis Merging Phenotype, Metabolomic and Genomic Data Identifies Non-SMC Condensin I Complex, Subunit G (NCAPG) and Cellular Maintenance Processes as Major Contributors to Genetic Variability in Bovine Feed Efficiency. PLoS One. 2015;10(4):e0124574 Authors: Widmann P, Reverter A, Weikard R, Suhre K, Hammon HM, Albrecht E, Kuehn C Abstract Feed efficiency is a paramount factor for livestock economy. Previous studies had indicated a substantial heritability of several feed efficiency traits. In our study, we investigated the genetic background of residual feed intake, a commonly used parameter of feed efficiency, in a cattle resource population generated from crossing dairy and beef cattle. Starting from a whole genome association analysis, we subsequently performed combined phenotype-metabolome-genome analysis taking a systems biology approach by inferring gene networks based on partial correlation and information theory approaches. Our data about biological processes enriched with genes from the feed efficiency network suggest that genetic variation in feed efficiency is driven by genetic modulation of basic processes relevant to general cellular functions. When looking at the predicted upstream regulators from the feed efficiency network, the Tumor Protein P53 (TP53) and Transforming Growth Factor beta 1 (TGFB1) genes stood out regarding significance of overlap and number of target molecules in the data set. These results further support the hypothesis that TP53 is a major upstream regulator for genetic variation of feed efficiency. Furthermore, our data revealed a significant effect of both, the Non-SMC Condensin I Complex, Subunit G (NCAPG) I442M (rs109570900) and the Growth /differentiation factor 8 (GDF8) Q204X (rs110344317) loci, on residual feed intake and feed conversion. For both loci, the growth promoting allele at the onset of puberty was associated with a negative, but favorable effect on residual feed intake. The elevated energy demand for increased growth triggered by the NCAPG 442M allele is obviously not fully compensated for by an increased efficiency in converting feed into body tissue. As a consequence, the individuals carrying the NCAPG 442M allele had an additional demand for energy uptake that is reflected by the association of the allele with increased daily energy intake as observed in our study. PMID: 25875852 [PubMed - as supplied by publisher]

A Four-Compartment Metabolomics Analysis of the Liver, Muscle, Serum, and Urine Response to Polytrauma with Hemorrhagic Shock following Carbohydrate Prefeed. PLoS One. 2015;10(4):e0124467 Authors: Witowski N, Lusczek E, Determan C, Lexcen D, Mulier K, Ostrowski B, Beilman G Abstract OBJECTIVE: Hemorrhagic shock accompanied by injury represents a major physiologic stress. Fasted animals are often used to study hemorrhagic shock (with injury). A fasted state is not guaranteed in the general human population. The objective of this study was to determine if fed animals would exhibit a different metabolic profile in response to hemorrhagic shock with trauma when compared to fasted animals. METHODS: Proton (1H) NMR spectroscopy was used to determine concentrations of metabolites from four different compartments (liver, muscle, serum, urine) taken at defined time points throughout shock/injury and resuscitation. PLS-DA was performed and VIP lists established for baseline, shock and resuscitation (10 metabolites for each compartment at each time interval) on metabolomics data from surviving animals. RESULTS: Fed status prior to the occurrence of hemorrhagic shock with injury alters the metabolic course of this trauma and potentially affects mortality. The death rate for CPF animals is higher than FS animals (47 vs 28%). The majority of deaths occur post-resuscitation suggesting reperfusion injury. The metabolomics response to shock reflects priorities evident at baseline. FS animals raise the baseline degree of proteolysis to provide additional amino acids for energy production while CPF animals rely on both glucose and, to a lesser extent, amino acids. During early resuscitation levels of metabolites associated with energy production drop, suggesting diminished demand. CONCLUSIONS: Feeding status prior to the occurrence of hemorrhagic shock with injury alters the metabolic course of this trauma and potentially affects mortality. The response to shock reflects metabolic priorities at baseline. PMID: 25875111 [PubMed - as supplied by publisher]

Ambient Mass Spectrometry Imaging Metabolomics Method Provides Novel Insights into Action Mechanism of Drug Candidate. Anal Chem. 2015 Apr 15; Authors: He J, Luo Z, Huang L, He J, Chen Y, Rong X, Jia S, Tang F, Wang X, Zhang R, Zhang J, Shi JG, Abliz Z Abstract Elucidation of mechanism of action for drug candidates is fundamental to drug development, and is strongly facilitated by metabolomics. Herein, we developed an imaging metabolomics method based on air flow assisted desorption electrospray ionization mass spectrometry imaging (AFADESI-MSI) under ambient condition. This method was sub-sequently applied to simultaneously profile a novel anti-insomnia drug candidate, N6-(4-hydroxybenzyl)-adenosine (NHBA), and various endogenous metabolites in rat whole-body tissue sections after administration of NHBA. The principle component analysis (PCA) represented by an intuitive color-coding scheme based on hyperspectral imaging revealed in situ molecular profiling alterations in response to stimulation of NHBA, which are in a very low intensity and hidden in massive interferential peaks. We found that the abundance of six endogenous metabolites changed after drug administration. The spatiotemporal distribution indicated that five altered molecules, including neurotransmitter gamma-aminobutyric acid, neurotransmitter precursors choline and glycerophosphocholine, energy metabolism-related molecules adenosine (an endogenous sleep factor) and creatine, are closely associated with insomnia or other neurological disorders. These findings not only provide insights into deeply understanding on the mechanism of action of NHBA, but also demonstrate that the AFADESI-MSI-based imaging metabolomics is a powerful technique to investigate the molecular mechanism of drug action, especially for drug candidates with multi-target or undefined target in the preclinical study stage. PMID: 25874739 [PubMed - as supplied by publisher]

Metaproteomics of complex microbial communities in biogas plants. Microb Biotechnol. 2015 Apr 15; Authors: Heyer R, Kohrs F, Reichl U, Benndorf D Abstract Production of biogas from agricultural biomass or organic wastes is an important source of renewable energy. Although thousands of biogas plants (BGPs) are operating in Germany, there is still a significant potential to improve yields, e.g. from fibrous substrates. In addition, process stability should be optimized. Besides evaluating technical measures, improving our understanding of microbial communities involved into the biogas process is considered as key issue to achieve both goals. Microscopic and genetic approaches to analyse community composition provide valuable experimental data, but fail to detect presence of enzymes and overall metabolic activity of microbial communities. Therefore, metaproteomics can significantly contribute to elucidate critical steps in the conversion of biomass to methane as it delivers combined functional and phylogenetic data. Although metaproteomics analyses are challenged by sample impurities, sample complexity and redundant protein identification, and are still limited by the availability of genome sequences, recent studies have shown promising results. In the following, the workflow and potential pitfalls for metaproteomics of samples from full-scale BGP are discussed. In addition, the value of metaproteomics to contribute to the further advancement of microbial ecology is evaluated. Finally, synergistic effects expected when metaproteomics is combined with advanced imaging techniques, metagenomics, metatranscriptomics and metabolomics are addressed. PMID: 25874383 [PubMed - as supplied by publisher]

Metabolomic profiling in tomato reveals diel compositional changes in fruit affected by source-sink relationships. J Exp Bot. 2015 Apr 11; Authors: Bénard C, Bernillon S, Biais B, Osorio S, Maucourt M, Ballias P, Deborde C, Colombié S, Cabasson C, Jacob D, Vercambre G, Gautier H, Rolin D, Génard M, Fernie AR, Gibon Y, Moing A Abstract A detailed study of the diurnal compositional changes was performed in tomato (Solanum lycopersicum cv. Moneymaker) leaves and fruits. Plants were cultivated in a commercial greenhouse under two growth conditions: control and shaded. Expanding fruits and the closest mature leaves were harvested during two different day/night cycles (cloudy or sunny day). High-throughput robotized biochemical phenotyping of major compounds, as well as proton nuclear magnetic resonance and mass spectrometry metabolomic profiling, were used to measure the contents of about 70 metabolites in the leaves and 60 metabolites in the fruits, in parallel with ecophysiological measurements. Metabolite data were processed using multivariate, univariate, or clustering analyses and correlation networks. The shaded carbon-limited plants adjusted their leaf area, decreased their sink carbon demand and showed subtle compositional modifications. For source leaves, several metabolites varied along a diel cycle, including those directly linked to photosynthesis and photorespiration. These metabolites peaked at midday in both conditions and diel cycles as expected. However, transitory carbon storage was limited in tomato leaves. In fruits, fewer metabolites showed diel fluctuations, which were also of lower amplitude. Several organic acids were among the fluctuating metabolites. Diel patterns observed in leaves and especially in fruits differed between the cloudy and sunny days, and between the two conditions. Relationships between compositional changes in leaves and fruits are in agreement with the fact that several metabolic processes of the fruit appeared linked to its momentary supply of sucrose. PMID: 25873655 [PubMed - as supplied by publisher]

Understanding developmental and adaptive cues in pine through metabolite profiling and co-expression network analysis. J Exp Bot. 2015 Apr 1; Authors: Cañas RA, Canales J, Muñoz-Hernández C, Granados JM, Ávila C, García-Martín ML, Cánovas FM Abstract Conifers include long-lived evergreen trees of great economic and ecological importance, including pines and spruces. During their long lives conifers must respond to seasonal environmental changes, adapt to unpredictable environmental stresses, and co-ordinate their adaptive adjustments with internal developmental programmes. To gain insights into these responses, we examined metabolite and transcriptomic profiles of needles from naturally growing 25-year-old maritime pine (Pinus pinaster L. Aiton) trees over a year. The effect of environmental parameters such as temperature and rain on needle development were studied. Our results show that seasonal changes in the metabolite profiles were mainly affected by the needles' age and acclimation for winter, but changes in transcript profiles were mainly dependent on climatic factors. The relative abundance of most transcripts correlated well with temperature, particularly for genes involved in photosynthesis or winter acclimation. Gene network analysis revealed relationships between 14 co-expressed gene modules and development and adaptation to environmental stimuli. Novel Myb transcription factors were identified as candidate regulators during needle development. Our systems-based analysis provides integrated data of the seasonal regulation of maritime pine growth, opening new perspectives for understanding the complex regulatory mechanisms underlying conifers' adaptive responses. Taken together, our results suggest that the environment regulates the transcriptome for fine tuning of the metabolome during development. PMID: 25873654 [PubMed - as supplied by publisher]

Assessing the translational landscape of myogenic differentiation by ribosome profiling. Nucleic Acids Res. 2015 Apr 14; Authors: de Klerk E, Fokkema IF, Thiadens KA, Goeman JJ, Palmblad M, den Dunnen JT, von Lindern M, 't Hoen PA Abstract The formation of skeletal muscles is associated with drastic changes in protein requirements known to be safeguarded by tight control of gene transcription and mRNA processing. The contribution of regulation of mRNA translation during myogenesis has not been studied so far. We monitored translation during myogenic differentiation of C2C12 myoblasts, using a simplified protocol for ribosome footprint profiling. Comparison of ribosome footprints to total RNA showed that gene expression is mostly regulated at the transcriptional level. However, a subset of transcripts, enriched for mRNAs encoding for ribosomal proteins, was regulated at the level of translation. Enrichment was also found for specific pathways known to regulate muscle biology. We developed a dedicated pipeline to identify translation initiation sites (TISs) and discovered 5333 unannotated TISs, providing a catalog of upstream and alternative open reading frames used during myogenesis. We identified 298 transcripts with a significant switch in TIS usage during myogenesis, which was not explained by alternative promoter usage, as profiled by DeepCAGE. Also these transcripts were enriched for ribosomal protein genes. This study demonstrates that differential mRNA translation controls protein expression of specific subsets of genes during myogenesis. Experimental protocols, analytical workflows, tools and data are available through public repositories (http://lumc.github.io/ribosome-profiling-analysis-framework/). PMID: 25873627 [PubMed - as supplied by publisher]