Éditeur(s) : HAL CCSD American Society for Biochemistry and Molecular Biology
Résumé : International audience
The budding yeast Saccharomyces cerevisiae is a major model organism for important biological processes such as mitotic growth and meiotic development, it can be a human pathogen, and it is widely used in the food-, and biotechnology industries. Consequently, the genomes of numerous strains have been sequenced and a very large amount of RNA profiling data is available. Moreover, it has recently become possible to quantitatively analyze the entire yeast proteome; however, efficient and cost-effective high-throughput protein profiling remains a challenge. We report here a new approach to direct and label-free large-scale yeast protein identification using a tandem buffer system for protein extraction, two-step protein prefractionation and enzymatic digestion, and detection of peptides by iterative mass spectrometry. Our profiling study of diploid cells undergoing rapid mitotic growth identified 86% of the known proteins and its output was found to be widely concordant with genome-wide mRNA concentrations and DNA variations between yeast strains. This paves the way for comprehensive and straightforward yeast proteome profiling across a wide variety of experimental conditions.
ISSN: 1535-9476

hal-00682837
https://hal.archives-ouvertes.fr/hal-00682837
DOI : 10.1074/mcp.M111.012682
PUBMED : 21997732

Éditeur(s) : HAL CCSD
Résumé : International audience
MOTIVATION: Imaging mass spectrometry (IMS) is a maturating technique of molecular imaging. Confidence in the reproducible quality of IMS data is essential for its integration into routine use. However, the predominant method for assessing quality is visual examination, a time consuming, unstandardized and non-scalable approach. So far, the problem of assessing the quality has only been marginally addressed and existing measures do not account for the spatial information of IMS data. Importantly, no approach exists for unbiased evaluation of potential quality measures. RESULTS: We propose a novel approach for evaluating potential measures by creating a gold-standard set using collective expert judgements upon which we evaluated image-based measures. To produce a gold standard, we engaged 80 IMS experts, each to rate the relative quality between 52 pairs of ion images from MALDI-TOF IMS datasets of rat brain coronal sections. Experts' optional feedback on their expertise, the task and the survey showed that (i) they had diverse backgrounds and sufficient expertise, (ii) the task was properly understood, and (iii) the survey was comprehensible. A moderate inter-rater agreement was achieved with Krippendorff's alpha of 0.5. A gold-standard set of 634 pairs of images with accompanying ratings was constructed and showed a high agreement of 0.85. Eight families of potential measures with a range of parameters and statistical descriptors, giving 143 in total, were evaluated. Both signal-to-noise and spatial chaos-based measures performed highly with a correlation of 0.7 to 0.9 with the gold standard ratings. Moreover, we showed that a composite measure with the linear coefficients (trained on the gold standard with regularized least squares optimization and lasso) showed a strong linear correlation of 0.94 and an accuracy of 0.98 in predicting which image in a pair was of higher quality. AVAILABILITY AND IMPLEMENTATION: The anonymized data collected from the survey and the Matlab source code for data processing can be found at: https://github.com/alexandrovteam/IMS_quality. CONTACT: theodore.alexandrov@embl.de
Bioinformatics (Oxford, England)

hal-01163754
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01163754
DOI : 10.1093/bioinformatics/btv266
PUBMED : 26072506

Éditeur(s) : HAL CCSD IWA Publishing
Résumé : International audience
Anti-cancer drugs are an important class of pharmaceutical products. Methotrexate (MTX) is a folic acid antagonist used in high doses as antimetabolite in anti-cancer treatment as well as in low doses for the treatment of rheumatoid arthritis and adults' psoriasis. In the past, several anti-cancer drugs, including methotrexate, have been found in the environment. Their presence in water, especially if used for the production of drinking water, is even in low concentrations of particular interest, due to the risk to retrieve them in the consumed water and their high activity and grave effects. But prior to usage as drinking water, raw waters are treated and chlorination is a common practice in several countries. As such a treatment can lead to the formation of organochlorine in water, the study of the fate of MTX during chlorination in a batch trial was carried out. The reaction was monitored by dissolved organic carbon (DOC) and by fluorescence and UV spectroscopy. Investigation of by-products formed was done with liquid chromatography/mass spectrometry (LC/MS). Under the given experimental conditions, Methotrexate was eliminated rapidly (t1/2 around 21 min). However, DOC elimination was incomplete. Monitoring with LC-MS showed the formation of a monochlorinated transformation product of MTX. In silico analysis of the proposed transformation products for different carcinogenic, mutagenic and genotoxic endpoints with different software platforms provided no clear evidence that the possible transformation products after chlorination might be more toxic than the parent compound. However, since a number of alerts is altered after chlorination, it cannot be excluded that the toxicity of these transformation products might be modulated compared with the parent compound.
ISSN: 0043-1354

hal-01016617
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01016617
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01016617/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01016617/file/Monitoringsur methotrexate_final.pdf
DOI : 10.1016/j.watres.2014.03.008

Éditeur(s) : HAL CCSD Wiley Open Access
Résumé : International audience
Plant responses to natural enemies include formation of secondary metabolites acting as direct or indirect defenses. Volatile terpenes represent one of the most diverse groups of secondary metabolites. We aimed to explore evolutionary patterns of volatile terpene emission. We measured the composition of damage-induced volatile terpenes from 202 Amazonian tree species, spanning the angiosperm phylogeny. Volatile terpenes were extracted with solid-phase micro extraction and desorbed in a gas chromatography–mass spectrometry for compound identification. The chemical diversity of the terpene blend showed a strong phylogenetic signal as closely related species emitted a similar number of compounds. Closely related species also tended to have compositionally similar blends, although this relationship was weak. Meanwhile, the ability to emit a given compound showed no significant phylogenetic signal for 200 of 286 compounds, indicating a high rate of diversification in terpene synthesis and/or great variability in their expression. Three lineages (Magnoliales, Laurales, and Sapindales) showed exceptionally high rates of terpene diversification. Of the 70 compounds found in >10% of their species, 69 displayed significant correlated evolution with at least one other compound. These results provide insights into the complex evolutionary history of volatile terpenes in angiosperms, while highlighting the need for further research into this important class of compounds.
ISSN: 2045-7758

Droits : http://creativecommons.org/licenses/by/
hal-01296640
http://hal.upmc.fr/hal-01296640
http://hal.upmc.fr/hal-01296640/document
http://hal.upmc.fr/hal-01296640/file/ece31810.pdf
DOI : 10.1002/ece3.1810

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The behaviour of the four Ra isotopes (measured by gamma spectrometry) and 222Rn (measured with an AlphaGUARD ionisation chamber) has been investigated in NaCl-rich thermal waters of Balaruc-les-Bains on the Mediterranean coast (South of France). This study allows identification of the deep thermal water signature and reveals the influence of seawater or karst water inflows on Ra isotopes and 222Rn. The deep thermal water has 226Ra and 222Rn activities of 840 and 1900 mBq/l, respectively, a (228Ra/226Ra) activity ratio of 0.59, and low (224Ra/228Ra) and (223Ra/226Ra) ratios of 0.67 and 0.025, respectively. Several arguments suggest a dominant role of radioactive decay for short-lived Ra isotopes and Rn during the relatively rapid ascent of thermal water through wide open fractures and drains. The low (223Ra/226Ra) ratio constrains the maximum ascent velocity of thermal water to 8-10 m/h. Seawater inflow into the hydrothermal system results in an enrichment in short-lived Ra isotopes and 222Rn. The high (223Ra/226Ra) ratio (0.23) suggests that 223Ra, 224Ra and 222Rn produced by alpha-recoil in the upper-Jurassic limestone are entrained by seawater percolation through the coastal basement, due to active pumping in one of the near shore production well. This process would be enhanced by a low water/rock ratio (i.e. in a low-porosity, micro-fractured limestone). Mixing of this enriched seawater with thermal water induces barite precipitation with co-precipitation of a large fraction of Ra. Short-lived Ra isotopes may thus be useful tracers of seawater flux towards the continent. Conversely, the inflow and mixing of karst groundwater result in a general dilution of all dissolved elements, only a small enrichment in 224Ra and 223Ra, but a large enrichment in 222Rn (up to 26 Bq/l). The combination of Ra isotopes and 222Rn data provides a good way to trace the dynamics of different water masses along coastal areas.
ISSN: 0016-7037

hal-00795512
https://hal.archives-ouvertes.fr/hal-00795512
DOI : 10.1016/j.gca.2012.09.010

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : International audience
Mantle cell lymphoma (MCL) is a hematologic neoplasm characterised by the t(11;14)(q13;q32) translocation leading to aberrant cyclin D1 expression. The cell functions of cyclin D1 depend on its partners and/or subcellular distribution, resulting in different oncogenic properties. We observed the accumulation of cyclin D1 in the cytoplasm of a subset of MCL cell lines and primary cells. In primary cells, this cytoplasmic distribution was correlated with a more frequent blastoid phenotype. We performed immunoprecipitation assays and mass spectrometry on enriched cytosolic fractions from two cell lines. The cyclin D1 interactome was found to include several factors involved in adhesion, migration and invasion. We found that the accumulation of cyclin D1 in the cytoplasm was associated with higher levels of migration and invasiveness. We also showed that MCL cells with high cytoplasmic levels of cyclin D1 engrafted more rapidly into the bone marrow, spleen, and brain in immunodeficient mice. Both migration and invasion processes, both in vivo and in vitro, were counteracted by the exportin 1 inhibitor KPT-330, which retains cyclin D1 in the nucleus. Our data reveal a role of cytoplasmic cyclin D1 in the control of MCL cell migration and invasion, and as a true operator of MCL pathogenesis.
ISSN: 2045-2322

hal-01635754
https://hal.archives-ouvertes.fr/hal-01635754
DOI : 10.1038/s41598-017-14222-1
PUBMED : 29066743

Éditeur(s) : HAL CCSD Mineralogical Society of America
Résumé : International audience
Wadsleyites with various iron contents were synthesized at ~12-14 GPa and 1400 °C under oxidizing and hydrous conditions in coexistence with enstatite. The samples were studied using micro-X-ray absorption near edge structure (XANES) and micro-Mössbauer spectroscopy to determine the ferric iron contents in polyphasic samples and secondary ion mass spectrometry (SIMS) to determine the water concentrations. XANES and Mössbauer analyses show that ferric iron content increases with increasing total iron content, and reaches a maximum of ~30% Fe3+/Fetotal. Two XANES results were cross-checked by Mössbauer analysis and both methods are in reasonable agreement. The use of Fourier transform infrared spectroscopy reveals a new protonation scheme in wadsleyite, with a significant proportion of protons associated with the high-frequency band at 3611 cm−1 and a new band located at 3500 cm−1. The intensity of these two bands is higher for Fe3+-rich wadsleyite. SIMS analyses show that water contents in wadsleyite vary from 4500 to 9400 ppm H2O by weight. Pyroxene water contents range from 790 to 1600 ppm wt H2O. The concentration of water in both phases decreases with increasing iron content. The partition coefficient of water between wadsleyite and pyroxene varies between 5 and 9 and increases with increasing Fe-number of wadsleyite [i.e., XFe/(XFe + XMg) × 100 ratio]. The divalent cation concentrations (i.e., Mg2+ + Fe2+), the Si as well as the H content in wadsleyite decrease with increasing Fe3+ content, indicating an incorporation mechanism via substitution into the metal (Me = Mg2+ and Fe2+) and Si sites with a ratio of 5/3 for (Fe3++H+):Me and of 5/1 for (Fe3++H+):Si, similarly as in the dry system. Thus, coupled substitution of Fe3+ and H+ does not affect the incorporation mechanism of Fe3+, but does affect the location of H+, which is partly incorporated at tetrahedral edges forming [FeSi′-(OH)o*]X neutral defects substituting for Si. In this model 25% of the ferric iron occupies the tetrahedral sites.
ISSN: 0003-004X

hal-00758071
https://hal.archives-ouvertes.fr/hal-00758071
DOI : 10.2138/am.2012.3869

Éditeur(s) : HAL CCSD MDPI
Résumé : International audience
Lead in childhood is well known to be associated with poor neurodevelopment. As part of a study on maternal anemia and offspring neurodevelopment, we analyzed blood lead level (BLL) with no prior knowledge of lead exposure in 225 mothers and 685 offspring 1 to 2 years old from Allada, a semi-rural area in Benin, sub-Saharan Africa, between May 2011 and May 2013. Blood samples were analyzed by inductively coupled plasma mass spectrometry. Environmental assessments in households and isotopic ratio measurements were performed for eight children with BLL extgreater 100 µg/L. High lead levels (BLL extgreater 50 µg/L) were found in 44% of mothers and 58% of children. The median BLL was 55.1 (interquartile range 39.2-85.0) and 46.6 (36.5-60.1) µg/L, respectively. Maternal BLL was associated with offspring's consumption of piped water and animals killed by ammunition. Children's BLL was associated with presence of paint chips in the house and consumption of animals killed by ammunition. In this population, with 98% of children still breastfed, children's BLL was highly associated with maternal BLL on multivariate analyses. Environmental measures and isotopic ratios supported these findings. Offspring may be highly exposed to lead in utero and probably via breastfeeding in addition to lead paint exposure
ISSN: 1660-4601

hal-01296778
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01296778
DOI : 10.3390/ijerph13030316
PUBMED : 26978384

Éditeur(s) : HAL CCSD Taylor & Francis
Résumé : International audience
Humans may be exposed via their environment to multiple chemicals as a consequence of human activities and use of synthetic products. Little knowledge is routinely generated on the hazards of these chemical mixtures. The metabolomic approach is widely used to identify metabolic pathways modified by diseases, drugs, or exposures to toxicants. This review, based on the state of the art of the current applications of metabolomics in environmental health, attempts to determine whether metabolomics might constitute an original approach to the study of associations between multiple, low-dose environmental exposures in humans. Studying the biochemical consequences of complex environmental exposures is a challenge demanding the development of careful experimental and epidemiological designs, in order to take into account possible confounders associated with the high level of interindividual variability induced by different lifestyles. The choices of populations studied, sampling and storage procedures, statistical tools used, and system biology need to be considered. Suggestions for improved experimental and epidemiological designs are described. Evidence indicates that metabolomics may be a powerful tool in environmental health in the identification of both complex exposure biomarkers directly in human populations and modified metabolic pathways, in an attempt to improve understanding the underlying environmental causes of diseases. Nevertheless, the validity of biomarkers and relevancy of animal-to-human extrapolation remain key challenges that need to be properly explored.
ISSN: 1093-7404

hal-00976116
https://hal-univ-rennes1.archives-ouvertes.fr/hal-00976116
https://hal-univ-rennes1.archives-ouvertes.fr/hal-00976116/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-00976116/file/Potential_input_from_metabolomics_accepted.pdf
DOI : 10.1080/10937404.2013.860318

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
Unravelling the detailed pressure–temperature–time-deformation (P–T–t-D) evolution of magmatic and metamorphic rocks provides essential insights into the timing and duration of partial melting and related plutonism during crustal flow and migmatitic dome formation. The Montagne Noire Axial Zone (MNAZ) is a migmatitic dome located within the Variscan orogen in the southern French Massif Central. The timing of the main thermal event that was responsible for intense partial melting is still highly debated. In this study we present new laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) age data on micaschists, migmatites and granites that clarify the P–T–t-D evolution of the MNAZ. Structurally controlled samples were collected in order to constrain the timing of metamorphism, migmatization and plutonism regarding the main structural pattern D1, D2 and D3. D1 and D2 correspond to nappe stacking and dextral transpression, respectively. D3 is related to vertical shortening and coaxial thinning with a preferential NE–SW- to E–W-directed stretching. LA-ICP-MS analyses on the syntectonic Anglès, Soulié and Martys granites yielded U–Th/Pb monazite ages of 305 ± 1.5, 306 ± 1.9 and 314 ± 2 Ma, respectively. Five migmatitic rocks sampled in the eastern and central Espinouse area yielded in situ ages ranging between 312 ± 2 and 301 ± 2 Ma. Along the dome envelope, two garnet–staurolite-bearing micaschists near Saint-Pons-de-Thomières village gave in situ U–Th–Pb ages of 312.1 ± 2.1 and 309.0 ± 3.1 Ma. A fine-grained gneiss with a D3 fabrics in the eastern dome envelope yield a 208Pb/232Th mean age at 305.7 ± 3.9 Ma. All ages obtained in this study for the micaschists, migmatites and granites range between 315 and 301 Ma. We interpret this time span as the record of the high thermal event responsible for intense crustal partial melting within the lower and middle crust. The onset of partial melting occurred at ca. 315 Ma that marked the beginning of transpressional deformation D2. Based on structural and petrological studies, our new U–Th–Pb results suggest that (1) partial melting may have started at ca. 315 Ma and lasted 15–10 Myr and (2) D2 et D3 developed between 315 and 300 Ma and were synchronous. D1 deformation ended at 315 Ma. The onset and duration of D1 related to nappe stacking and crustal thickening is still uncertain.
ISSN: 1437-3254

hal-01526942
https://hal.archives-ouvertes.fr/hal-01526942
DOI : 10.1007/s00531-016-1417-x