Combining Genomics and Metabolomics for the Discovery of Regulatory Genes and Their Use in Metabolic Engineering to Produce ‘Healthy Foods’

Plants often accumulate their natural products to relatively low levels, so there is a lot of interest in breeding or engineering plants that produce higher levels. It has been shown that the most effective way to increase the accumulation of secondary metabolites is to increase the activity of genes that regulate the activity of the biosynthetic pathways that make different natural products. Regulatory genes of this type encode proteins called transcription factors. The biggest bottleneck in using this strategy to develop plants that accumulate significantly higher levels of important natural products is that not many transcription factors regulating secondary metabolism have yet been identified at the molecular level. Genes encoding transcription factors can be identified from model plants with sequenced genomes. The ability of such genes to regulate metabolism can be assayed by examination of mutants (reverse genetics) and by investigating the metabolic effects of high levels of expression of the genes. The combined techniques of metabolic fingerprinting and metabolite profiling of mutant and transgenic plants are allowing us to identify new genes encoding transcription factors controlling secondary metabolism, that can be used as tools for engineering natural product accumulatio

Skeletal muscle metabolomics and blood biochemistry analysis reveal metabolic changes associated with dietary amino acid supplementation in dairy calves

The effects of different amino acid (AA) supplementations of milk protein-based milk replacers in pre-ruminant calves from 3 days to 7 weeks of age were studied. Animals were divided into 4 groups: Ctrl) Control group fed with milk protein-based milk replacer without supplementation; GP) supplementation with 0.1% glycine and 0.3% proline; FY) supplementation with 0.2% phenylalanine and 0.2% tyrosine; MKT) supplementation with 0.62% lysine, 0.22% methionine and 0.61% threonine. For statistical analysis, t-test was used to compare AA-supplemented animals to the Ctrl group. At week 7, body weight and average daily gain (ADG) were measured and blood samples and skeletal muscle biopsies were taken. Blood biochemistry analytes related to energy metabolism were determined and it was shown that MKT group had higher serum creatinine and higher plasma concentration of three supplemented AAs as well as arginine compared with the Ctrl group. GP group had similar glycine/proline plasma concentration compared with the other groups while in FY group only plasma phenylalanine concentration was higher compared with Control. Although the AA supplementations in the GP and FY groups did not affect average daily gain and metabolic health profile from serum, the metabolome analysis from skeletal muscle biopsy revealed several differences between the GP-FY groups and the Ctrl-MKT groups, suggesting a metabolic adaptation especially in GP and FY groupsinfo:eu-repo/semantics/publishedVersio

Raw NMR data for "NMR based metabolomic analysis of the physiological role of the electron-bifurcating FeFe-hydrogenase Hnd in Solidesulfovibrio fructosivorans under pyruvate fermentation"

This dataset contains raw NMR spectra used for the metabolomics study published in "NMR based metabolomic analysis of the physiological role of the electron-bifurcating FeFe-hydrogenase Hnd in Solidesulfovibrio fructosivorans under pyruvate fermentation". Proton NMR spectra of culture medium and cell pellets, from WT and HndD-deleted Solidesulfovibrio fructosivorans strains, grown under pyruvate fermentation condition, were recorded using liquid-state and HRMAS NMR spectroscopy, respectively.THIS DATASET IS ARCHIVED AT DANS/EASY, BUT NOT ACCESSIBLE HERE. TO VIEW A LIST OF FILES AND ACCESS THE FILES IN THIS DATASET CLICK ON THE DOI-LINK ABOV

Method of toxicological evaluation, method of toxicological screening and associated system

The present invention relates to a method of toxicological evaluation of a candidate substance on at least one tissue or organ, characterized in that it comprises the steps of: (a) obtaining a bioartificial tissue or organ by simulation or modelling of the metabolic activity of said tissue or organ by at least one bioreactor; (b) exposure of said bioartificial tissue or organ to said substance; (c) observation of the metabolic response of the bioartificial tissue or organ and acquisition without a priori of an associated multidimensional data set; (d) identification by means of a method of multivariate statistical analysis of the components of the multidimensional data set which are quantitatively correlated with predetennined variables; (e) generation of a predictive model on the basis of the components of the data set that are actually retained; (f) testing of the predictive nature of said model by at least one statistical method of estimating reliability; (g) identification of the metabolic response of the bioartificial tissue or organ in the fonn of biomarkers associated with the components of the data set that are adopted for the model. The present invention also relates to a method of toxicological screening and to a system for this purpose

Toward the Reliable Diagnosis of Indeterminate Thyroid Lesions: A HRMAS NMR-Based Metabolomics Case of Study

Cytological analysis of thyroid nodules detected using ultrasound-guided fine-needle aspiration technique is an efficient method for the diagnosis of well-differenciated tumors such as papillary thyroid carcinoma. However, for between 10 to 30% of all the nodules, the cytological analysis based on fine-needle aspiration biopsies leads to an 'indeterminated' identification. Consequently, a surgical excision is then necessary for a definite histological diagnosis of the lesions, resulting in 85% of the patient with indeterminated nodules undergoing unnecessary surgery since their tumor is finally diagnosed as benign. In this work, we discuss how HRMAS H-1 NMR-based metabolomics could be a complementary tool for the diagnosis of these elusive cases. We first showed that our approach was able to discriminate clearly any types of thyroid lesions from healthy tissues. Then we proceeded to demonstrate that the information produced by H-1 HRMAS NMR spectra differentiate tumors according to their malignancy grade, even when they belong to the 'indeterminate' category. Analysis of the discriminating spectral area in this last case points out toward a possible increase of phenylalanine, taurine, and lactate and a decrease of choline and choline derivatives, myo- and scyllo-inositol in the malignant tumors compared to the benign ones.11633173325Universita Italo-franceseANR [ANR-08-BLAN-273, ANR-2011- JS08-014-01]Region PACA [APO-G 2009]ANR [ANR-08-BLAN-273, ANR-2011- JS08-014-01]Region PACA [APO-G 2009

Thriving of hyperthermophilic microbial communities from a deep-sea sulfidic hydrothermal chimney under electrolithoautotrophic conditions with nitrate as electron acceptor

Abstract Recent studies have shown the presence of an abiotic electrical current across the walls of deep-sea hydrothermal chimneys, allowing the growth of electroautotrophic microbial communities. To understand the role of the different phylogenetic groups and metabolisms involved, this study focused on an electrotrophic enrichment, with nitrate as electron acceptor. The biofilm density, the community composition, the organic products released, and the electrical consumption were monitored by FISH confocal microscopy, qPCR, Metabarcoding, MNR and potentiostat measurements. A statistic analysis by PCA showed the correlation between the different parameters in 3 distinct temporal phases. The Archaeoglobales have been shown to play a key role in the development of the community, as first colonizers and producing pyruvate, therefor used as organic source for heterotrophs. Some Thermococcales showed the ability to perform electrofermentation of this pyruvate into acetate and H 2 . Finally, through subcultures of the community, we showed the development of a larger biodiversity over time. This observed phenomenon could explain the biodiversity development in hydrothermal context where energy sources are transient and unstable

Toward the Reliable Diagnosis of Indeterminate Thyroid Lesions: A HRMAS NMR-Based Metabolomics Case of Study

Cytological analysis of thyroid nodules detected using ultrasound-guided fine-needle aspiration technique is an efficient method for the diagnosis of well-differenciated tumors such as papillary thyroid carcinoma. However, for between 10 to 30% of all the nodules, the cytological analysis based on fine-needle aspiration biopsies leads to an "indeterminated" identification. Consequently, a surgical excision is then necessary for a definite histological diagnosis of the lesions, resulting in 85% of the patient with indeterminated nodules undergoing unnecessary surgery since their tumor is finally diagnosed as benign. In this work, we discuss how HRMAS H-1 NMR-based metabolomics could be a complementary tool for the diagnosis of these elusive cases. We first showed that our approach was able to discriminate clearly any types of thyroid lesions from healthy tissues. Then we proceeded to demonstrate that the information produced by H-1 HRMAS NMR spectra differentiate tumors according to their malignancy grade, even when they belong to the "indeterminate" category. Analysis of the discriminating spectral area in this last case points out toward a possible increase of phenylalanine, taurine, and lactate and a decrease of choline and choline derivatives, myo- and scyllo-inositol in the malignant tumors compared to the benign ones

Metabolomics approach to thyroid nodules: A high-resolution magic-angle spinning nuclear magnetic resonance-based study

Background Proton magnetic resonance spectroscopy of operative specimens has been reported to successfully differentiate normal tissue from malignant thyroid tissue. We used a new high-resolution magnetic resonance spectroscopy technique for the differentiation of benign and malignant thyroid neoplasms. Methods Histological specimens from 72 patients undergoing a total thyroidectomy were processed into a 4-mm ZrO2 high-resolution magic angle spinning (HRMAS) rotor with 5 μL of D2O. A Bruker Avance spectrometer operating at 400 MHz for the 1H frequency and equipped with a 1H/13C/31P HRMAS probe was used. Results Normal and neoplastic thyroid tissues could be discriminated from each other by different relative concentrations of several amino acids and lipids, as well as benign and malignant neoplasms, that differed in terms of a greater lactate and taurine and a lesser lipid choline, phosphocholine, myo-inositol, and scyllo-inositol levels in malignant samples. A statistical analysis with a receiver operating characteristic curve revealed that 77% of the samples were accurately predicted. Similar results were obtained with specimens obtained from ex vivo aspirates. Conclusion A further development of this project will be to use the metabolomics approach on specimens obtained from aspirates in vivo after the resolution of technical problems attributable to possible contamination

Metabolomics approach to thyroid nodules: A high-resolution magic-angle spinning nuclear magnetic resonance-based study

Background. Proton magnetic resonance spectroscopy of operative specimens has been reported to successfully differentiate normal tissue from malignant thyroid tissue. We used a new high-resolution magnetic resonance spectroscopy technique for the differentiation of benign and malignant thyroid neoplasms. Methods. Histological specimens from 72 patients undergoing a total thyroidectomy were processed into a 4-mm ZrO2 high-resolution magic angle spinning (HRMAS) rotor with 5 mu L of D2O. A Bruker Avance spectrometer operating at 400 MHz for the H-1 frequency and equipped with a H-1/C-13/P-31 HRMAS probe was used. Results. Normal and neoplastic thyroid tissues could be discriminated from each other by different relative concentrations of several amino acids and lipids, as well as benign and malignant neoplasms, that differed in terms of a greater lactate and taurine and a lesser lipid choline, phosphocholine, myoinositol, and scyllo-inositol levels in malignant samples. A statistical analysis with a receiver operating characteristic curve revealed. that 77% of the samples were accurately predicted. Similar results were obtained with specimens obtained from ex vivo aspirates. Conclusion. A further development of this project will be to use the metabolomics approach on specimens obtained from aspirates in vivo after the resolution of technical problems attributable to possible contamination. (Surgery 2012;152:1118-24.)152611181124Universite Franco-Italienn