Applications of liquid chromatography coupled to mass spectrometry-based metabolomics in clinical chemistry and toxicology: A review.

International audienceThe metabolome is the set of small molecular mass organic compounds found in a given biological media. It includes all organic substances naturally occurring from the metabolism of the studied living organism, except biological polymers, but also xenobiotics and their biotransformation products. The metabolic fingerprints of biofluids obtained by mass spectrometry (MS) or nuclear magnetic resonance (NMR)-based methods contain a few hundreds to thousands of signals related to both genetic and environmental contributions. Metabolomics, which refers to the untargeted quantitative or semi-quantitative analysis of the metabolome, is a promising tool for biomarker discovery. Although proof-of-concept studies by metabolomics-based approaches in the field of toxicology and clinical chemistry have initially been performed using NMR, the use of liquid chromatography hyphenated to mass spectrometry (LC/MS) has increased over the recent years, providing complementary results to those obtained with other approaches. This paper reviews and comments the input of LC/MS in this field. We describe here the overall process of analysis, review some seminal papers in the field and discuss the perspectives of metabolomics for the biomonitoring of exposure and diagnosis of diseases

vHOG, a multispecies vertebrate ontology of homologous organs groups

Motivation: Most anatomical ontologies are species-specific, whereas a framework for comparative studies is needed. We describe the vertebrate Homologous Organs Groups ontology, vHOG, used to compare expression patterns between species. Results: vHOG is a multispecies anatomical ontology for the vertebrate lineage. It is based on the HOGs used in the Bgee database of gene expression evolution. vHOG version 1.4 includes 1184 terms, follows OBO principles and is based on the Common Anatomy Reference Ontology (CARO). vHOG only describes structures with historical homology relations between model vertebrate species. The mapping to species-specific anatomical ontologies is provided as a separate file, so that no homology hypothesis is stated within the ontology itself. Each mapping has been manually reviewed, and we provide support codes and references when available. Availability and implementation: vHOG is available from the Bgee download site (http://bgee.unil.ch/), as well as from the OBO Foundry and the NCBO Bioportal websites. Contact: [email protected]; [email protected]

Development of an electrospray-mass spectral database for annotating metabolomics datasets: application to the analysis of the adult human urinary metabolome

Metabolomics opens new perspectives for biomarker discovery in the field of nutrition and heath, and also in the development of system biology. The metabolic profiles of biofluids obtained by mass spectrometry or nuclear magnetic resonance contain a few hundreds to thousands of signals. However, a major part of this information remains unknown, or at least not characterized in the analytical systems, thus hampering the obtention of biologically meaningfull data. In this context, we here report on the development of an electrospray (ESI) spectral database for the annotation of high resolution mass spectrometry based metabolomics data sets and on its application to the analysis of urine samples from a cohort of healthy volunteers

Damages and matter ejection during HVI on brittle structures: implications for space environment

The population of space debris is suspected to grow on earth’s orbits. This might be due to self generation processes occurring when an object impacts a satellite’s surface. As brittle materials, widely used for large solar arrays, are particularly sensitive to HVI in terms of damage and matter ejection, they might play an important role in debris generation. This paper focuses on HVI on thin brittle targets like Hubble silicon solar cells. Simulated and in-situ Front back impacts on both HST-CS and simple SiO2 targets were analyzed. Ejected volume and fragments were collected and filmed to characterize potential secondary debris. A mechanical analysis of damages due to the multilayered structure of solar cells as well as Ls-Dyna SPH calculations have also been performed and are compared to experimental results to assess predictions capabilities of the SPH code

Estimation of transmission parameters of a fluoroquinolone-resistant Escherichia coli strain between pigs in experimental conditions

Antimicrobial resistance is of primary importance regarding public and animal health issues. Persistence and spread of resistant strains within a population contribute to the maintenance of a reservoir and lead to treatment failure. An experimental trial was carried out to study the horizontal transmission of a fluoroquinolone-resistant Escherichia coli strain from inoculated to naïve pigs. All naïve contact pigs had positive counts of fluoroquinolone-resistant E. coli after only two days of contact. Moreover, re-infections of inoculated pigs caused by newly contaminated animals were suspected. A maximum likelihood method, based on a susceptible-infectious-susceptible (SIS) model, was used to determine the transmission parameters. Two transmission levels were identified depending on the quantity of bacteria shed by infected individuals: (i) low-shedders with bacterial counts of resistant E. coli in the faeces between 5*103 and 106 CFU/g (βL = 0.41 [0.27; 0.62]), (ii) high shedders with bacterial counts above 106 CFU/g (βH = 0.98 [0.59; 1.62]). Hence, transmission between animals could be pivotal in explaining the persistence of resistant bacteria within pig herds

Preferential Entry of Botulinum Neurotoxin A Hc Domain through Intestinal Crypt Cells and Targeting to Cholinergic Neurons of the Mouse Intestine

Botulism, characterized by flaccid paralysis, commonly results from botulinum neurotoxin (BoNT) absorption across the epithelial barrier from the digestive tract and then dissemination through the blood circulation to target autonomic and motor nerve terminals. The trafficking pathway of BoNT/A passage through the intestinal barrier is not yet fully understood. We report that intralumenal administration of purified BoNT/A into mouse ileum segment impaired spontaneous muscle contractions and abolished the smooth muscle contractions evoked by electric field stimulation. Entry of BoNT/A into the mouse upper small intestine was monitored with fluorescent HcA (half C-terminal domain of heavy chain) which interacts with cell surface receptor(s). We show that HcA preferentially recognizes a subset of neuroendocrine intestinal crypt cells, which probably represent the entry site of the toxin through the intestinal barrier, then targets specific neurons in the submucosa and later (90–120 min) in the musculosa. HcA mainly binds to certain cholinergic neurons of both submucosal and myenteric plexuses, but also recognizes, although to a lower extent, other neuronal cells including glutamatergic and serotoninergic neurons in the submucosa. Intestinal cholinergic neuron targeting by HcA could account for the inhibition of intestinal peristaltism and secretion observed in botulism, but the consequences of the targeting to non-cholinergic neurons remains to be determined

La filiacion y la fecundacion "in vitro"

Las tecnicas de reproduccion asistida no solo representan una solucion para ayudar a superar problemas de esterilidad, sino que su practica conlleva problemas eticos y juridicos. Esta Tesis analiza los problemas que plantea la fecundacion "in vitro", desde el punto de vista de la filiacion, para determinar la paternidad y maternidad cuando se utilizan los gametos de la pareja o de un tercero. Desde este punto de vista, se estudian la situacion juridica del tercero -llamado donante- y de las madres subrogadas, asi como las acciones de filiacion Tambien se examina la problematica que plantea la congelacion de semen y embriones, al poder un hombre engendrar un hijo despues de muerto. Entre las fuentes que se analizan estan los principales informes extranjeros que han estudiado la problematica de estas tecnicas, asi como el Informe especial de..

Nat Genet

The function of the majority of genes in the mouse and human genomes remains unknown. The mouse embryonic stem cell knockout resource provides a basis for the characterization of relationships between genes and phenotypes. The EUMODIC consortium developed and validated robust methodologies for the broad-based phenotyping of knockouts through a pipeline comprising 20 disease-oriented platforms. We developed new statistical methods for pipeline design and data analysis aimed at detecting reproducible phenotypes with high power. We acquired phenotype data from 449 mutant alleles, representing 320 unique genes, of which half had no previous functional annotation. We captured data from over 27,000 mice, finding that 83% of the mutant lines are phenodeviant, with 65% demonstrating pleiotropy. Surprisingly, we found significant differences in phenotype annotation according to zygosity. New phenotypes were uncovered for many genes with previously unknown function, providing a powerful basis for hypothesis generation and further investigation in diverse systems.Comment in : Genetic differential calculus. [Nat Genet. 2015] Comment in : Scaling up phenotyping studies. [Nat Biotechnol. 2015