Cette thèse aborde un point clé du couplage entre ces cycles: la dynamique des molécules azotées (AAs) des matières organiques du sol (MOS). Par des expériences d'incubation, nous avons estimé que les flux de biosynthèse des AAs par les micro-organismes du sol lors du processus de décomposition sont de l'ordre de 25% de la biomasse nouvellement formée. Le profil des AAs individuels biosynthétisés de novo est plus dépendant du type de sol que de la nature du substrat. Dans chaque sol, il est très similaire à celui des AAs des MOS. La biodégradation de matériaux végétaux marqués en 13C a révélé la transformation rapide des protéines végétales en matériaux microbiens. Ces résultats montrent que les AAs des MOS sont d'origine microbienne. Nous avons mesuré le renouvellement du C des AAs à long terme dans les horizons de surface de neuf sites présentant des végétations, climats et types de sol variés, en utilisant la technique de traçage par les abondances naturelles en 13C. L'âge moyen du carbone des AAs varie de 50 à 200 ans. Un modèle simple permet de discuter les hypothèses du recyclage des AAs des MOS par les micro-organismes. Les rapports isotopiques stables des AAs individuels ont été mesurés par chromatographie en phase gazeuse couplée à la spectrométrie de masse isotopique. À cette fin, nous avons développé une méthode d'étalonnage générique pour la détermination du rapport isotopique des composés spécifiques, par analyse de cultures microbiennes uniformément marquées. Au-delà des résultats présentés, l'étude apporte un large ensemble de données des AAs et examine les variations de l'abondance naturelle en 13C entre les AAs individuels. / We analyzed the coupled dynamics of C and N in Soil Organic Matter (SOM) through the dynamics of N-containing soil organic compounds (amino acids (AAs)) by tracing their carbon atoms. Stable isotope ratios of individual amino acids were measured by gas chromatography coupled with isotope ratio mass spectrometry. For this purpose, we developed a generic calibration method for compound-specific stable isotope ratio analysis, based on the analysis of uniformly labelled microbial cultures. We quantified the biosynthesis of AAs associated with the biodegradation process in four contrasted topsoils through short-term incubation experiments of 13C-labelled substrates. Amino acids-C accounts for ca. 25% of the newly-formed microbial biomass-C. The composition of the de novo biosynthesized individual amino acids was dependent on the soil type, and in each soil was similar to that of SOM amino acids. Biodegradation of 13C-labelled plant materials revealed the rapid conversion of plant proteins into microbial materials. These results together demonstrate that SOM amino acids are of microbial origin. We measured the dynamics of amino acids-C on the long term (decades to centuries) in nine sites using the natural 13C-labelling technique. On average, the age of AAs was equal or slightly inferior to that of bulk soil organic carbon, with mean ages ranging from 50 to 200 years. We built a conceptual model of AAs dynamics to discuss various hypotheses of AAs stabilization. Beyond these perspectives on C and N coupling in soil processes, the overall study brings a broad dataset of amino acids, as well as discuses variations of 13C natural abundance (δ13C) in-between individual amino acids.

No description available.

Les huiles essentielles extraites de plantes aromatiques, médicinales et à parfum, sont utilisées depuis des millénaires pour leurs propriétés médicinales ou olfactives. Pour des raisons de rentabilité, les distributeurs sont contraints à réduire leur coût au maximum et à commercialiser des huiles essentielles au plus bas prix. Certains ont recours à la fraude et proposent, des essences de qualité inférieure sous la dénomination produits naturels de haute qualité. Il existe des normes (AFNOR, pharmacopées) qui doivent être respectées. Mais leur seule application est souvent limitée. Cette étude a donc permis une nette amélioration du contrôle de la naturalité des huiles essentielles de citrus, et lavande. La connaissance des compositions moléculaires des volatiles et des polymethoxyflavones (citron), l'étude énantiomérique de molécules cibles telles que l'alpha-pinène, le sabinène (citrus), le linalol et l’acétate de linalyle (bergamote et lavande), les analyses isotopiques du carbone 13, deutérium, des linalol, acétate de linalyle (bergamote et lavande), citral, acétate de géranyle (citron) ainsi que les analyses isotopiques du deutérium et azote 15 du N-méthyle anthranilate de méthyle (mandarine) sont les analyses permettant la mise en évidence de nombreux types de fraudes. Pour une méthodologie efficace, les analyses en composante principale et discriminante ont été indispensables. Elles ont permis l’identification d’échantillons fraudés via l’étude des volatiles. Les analyses chirales et isotopiques permettent l'identification d'échantillon plus “ finement ” adultérés ou de mieux comprendre les processus de fraude / Essential oils extract from aromatics, medicinal and perfume plants, are used since ancient times for their medicinal or olfactory properties. They are quite expensive, and owing to the actual growing demand for getting high quality materials at lowest prices, fraudulent essential oils are frequently found on the market. In order to fight this problem, norms exist (AFNOR, pharmacopeas) which have to be respected. However those techniques are often limited. This work allowed great improves in the quality control of citrus and lavender essential oils. The knowledge of the chemical composition of volatiles and polymethoxy-flavones (lemon), of the chirale ratios of alpha-pinene, le sabinene (citrus), linalool et linalyl acetate (bergamot et lavender), isotope ratio analyses of carbon 13, deuterium, of linalool, linalyl acetate (bergamot et lavender), citral, geranyl acetate (lemon) as wall as isotope ratio analyses of deuterium of nitrogen 15 du Nmethyl anthranilate de methyl (mandarin) permitted the detection of various type of frauds. In order to have an efficient methodology, principal component and discriminant analyses have been proved indispensables. It allowed the identification of fraudulent samples via volatiles molecules study. Chirale analysis and isotope ratio highlight frauds on more “discrete” adulterated samples or a better understanding of adulteration’s process

The Encounters and Transformations in Iron Age Europe project (ENTRANS) aims to expand our knowledge regarding the nature and impact of cultural encounters during the European Iron Age. The study of ceramic vessels was included in the project, in order to further understand cultural practices in the south-east Alpine region. Organic residue analysis is an important tool in archaeological research for determining the presence of food and other organic substances associated with ceramic vessels. It has the potential to significantly improve our understanding of Iron Age societies and the interactions between them. This research focuses on the analysis of visible and absorbed organic residues from 377 ceramic vessels, from Late Bronze Age and Early Iron Age sites in Slovenia and Croatia, by gas-chromatography mass spectrometry. Two methods of lipid extraction were compared in a pilot study compressing 30 potsherds from Kaptol (solvent vs. acid extraction). This study revealed that more information was obtained by acid extraction, thus it was selected as the main method of extraction for this project. Differences between settlement, funerary and ritual sites were observed, suggesting that the vessels placed in the graves were not previously used or carried foodstuff with low lipid content, such as liquids and dry foods/cereals. Some types of residues were only identified in funerary vessels, specifically potential castor oil in Kaptol, mixed with other fats and oils. Lipid biomarkers and lipid ratios revealed significant differences between contexts and different sites, suggesting that the differences in cultural practices can also be identified in the use of ceramic vessels. Some residues were also sampled for gas-chromatography compound-specific isotope ratio mass spectrometry and bulk isotope analysis (only visible residues), which identified potential dairy fats in two potsherds from Poštela. The results were also compared with the contextual information, mainly the faunal remains, and the data obtained from the osteology and diet study preformed with individuals from the same area and chronology as the ceramic vessels. / Encounters and Transformations in Iron Age Europe Project (ENTRANS); Humanities in the European Research Area (HERA); Institute Life Sciences Research (ILSR) University of Bradford.

Signal transduction is a crucial event that enables cells to sense and respond to cues from their immediate environment. Guanylyl cyclase C (GC-C) is a member of the family of receptor guanylyl cyclases. GC-C is a single transmembrane protein that responds to its ligands by the production of the second messenger cGMP. The guanylin family of peptides, (including the bacterially produced heat-stable enterotoxin ST) is the ligand for GC-C, elevates intracellular cGMP levels and activates downstream pathways. GC-C regulates the cystic fibrosis transmembrane conductance regulator (CFTR) by inducing phosphorylation by protein kinase G, resulting in chloride ion and fluid efflux. GC-C also regulates cell cycle progression through cGMP-gated Ca2+ channels. These functions are seen in the intestinal epithelium, the primary site for GC-C expression. GC-C as a molecule has been studied in detail, but its functioning in the context of other signaling pathways remains unknown. The aim of the present investigation was to understand the regulation of signal transduction by GC-C and its cross-talk with other signaling pathways operating in the cell. Molecular events that commonly connect components in a signaling pathway are protein phosphorylation and protein-protein interaction. These two aspects are explored in this thesis. The possibility of tyrosine phosphorylation of GC-C has been explored earlier in our laboratory. In vitro studies indicated that the residue Tyr820 was a site for phosphorylation by the Src family of non-receptor tyrosine kinases and those studies also suggested that phosphorylated Tyr820 could bind to the SH2 domain of Src. We generated a nonphosphorylatable mutant of GC-C, GC-CY820F, and a phosphomimetic mutant GC-CY820E to study the effect of phosphorylation of Tyr820, on the functioning of GC-C. A stable cell line of HEK293:GC-CY820F cells was generated and compared with HEK293:GC-CWT. Dose response to ST in the two cell lines showed that cGMP accumulation by GC-CY820F was greater than that of GC-CWT, although the EC50 remained unchanged. The phosphomimetic GC-CY820E mutant receptor was non-responsive to ST. Further in HEK293 cells, phosphorylation of GC-CWT by constitutively active v-Src resulted in decreased ST stimulation and this effect of v-Src was reduced with GC-CY820F. Inhibition of ST stimulation brought about by v-Src required catalytically active Src, as the kinase inactive v-SrcK295R did not inhibit ST stimulation. These results were corroborated by in vitro studies by using the recombinant catalytic domain of GC-C expressed in insect cells and by phosphorylation using a purified kinase, Hck. Observations suggested that phosphorylation of Tyr820 in the catalytic domain of GC-C compromises the guanylyl cyclase activity of GC-C. T84 and Caco-2 colon carcinoma cells endogenously express GC-C. The effect of tyrosine phosphorylation of GC-C was studied by using HgCl2, a known activator of Src kinases, and by the inhibition of protein tyrosine phosphatases using pervanadate, an irreversible inhibitor. Both these ways of achieving increased tyrosine phosphorylation resulted in decreased ST-stimulated cGMP production by GC-C, as suggested from v-Src transfection studies. This decrease was reversed by using a Src kinase specific inhibitor PP2, confirming the role of Src kinases in the inhibition of GC-C activity. Interestingly, in Caco-2 cells that differentiate in culture, the effect of pervanadate on the inhibition of ST-stimulated GC-C activation was dependent on the differentiation stage. Crypt-like cells showed higher inhibition with pervanadate. As they matured into villus-like cells, the effect of pervanadate on GC-C activation was gradually lost. This effect also correlated with a decrease in the expression of Lck, suggesting that in the context of the intestine there could be differential regulation of tyrosine phosphorylation of GC-C along the crypt-villus axis. Intestinal ligated loop assays in rats demonstrated that ST-induced fluid accumulation in the intestine was abrogated on pervanadate treatment. Reduction in this fluid accumulation by pervanadate was not observed with 8-Br-cGMP, a cell permeable analogue of cGMP. This indicated that tyrosine phosphorylation of proteins is important for ST-induced fluid accumulation, and perhaps pervanadate modulates this by phosphorylation of GC-C, thereby causing a reduction in fluid accumulation. Earlier in vitro studies on Src-SH2 binding from the laboratory had suggested the possibility of activation of Src family kinases by GC-C. The activation status of Src kinases was monitored by using phosphorylation-state specific antibody, pSFK416. ST stimulation in T84 cells increased Tyr416 phosphorylation of Src kinases in a time dependent manner, indicating that Src kinases are activated downstream of GC-C. This activation of Src kinases was also seen with the endogenous ligand of GC-C, uroguanylin. Interestingly, 8-Br-cGMP a cell permeable analogue of cGMP that is known to mimic other cellular effects of GC-C, namely Cl-secretion and cell cycle progression, did not activate Src kinases, suggesting that the mechanism of Src kinase activation by GC-C could be independent of cGMP. Binding affinities of Src, Lck, Fyn and Yes SH2 domains to Tyr820 phosphorylated GCC peptide were in the nM range, indicating a high affinity of interaction. In vitro GST-SH2 pull down experiments suggested that phosphorylation of Tyr820 in full length GC-C allows interaction of GC-C to the SH2 domain of Src. These studies suggest a dual cross-talk between Src kinases and GC-C; Src phosphorylation inhibits GC-C signaling and stimulation of GC-C by its ligands activates Src kinases. Interaction of proteins containing SH2 and SH3 domains are commonly found in signaling molecules. In accordance with the observation that there are three PXXP motifs in GCC, many SH3 domains could interact with GC-C. GC-C appears to show a preference to bind the SH3 domains of Fyn, Hck, Abl tyrosine kinases, Grb2 and Crk adaptor proteins, the α-subunit of P85 PI3 kinase, PLC-γ and cortactin to various extents. The SH3 domains of spectrin and Nck did not show any detectable interaction with GC-C. In SH3 pull-down assays, the N-terminal SH3 domain of Crk, CrkSH3 (N), bound GC-C maximally, suggesting that Crk is a good candidate for interaction with GC-C. By overlay analysis, the region of GC-C that binds CrkSH3 (N) was narrowed down to the catalytic domain of GC-C containing a ‘PGLP’ motif. Mutations were generated in GC-C at this site to generate GC-CP916Q and GC-CW918R. These mutations compromised the binding of full length receptor to CrkSH3 (N). In cells, CrkII and GC-C co-transfection inhibited the ST stimulation of GC-C. A CrkII mutant, that has compromised binding through its SH3 domain, did not inhibit the activity of GC-C. CrkII from T84 cells co-immunoprecipitated with GC-C and interestingly, the phosphorylated form of CrkII did not, indicating that GC-C - Crk interaction could be regulated by the phosphorylation of Crk. In summary, this study places GC-C, in the context of tyrosine kinase signaling pathway and interaction with the adaptor protein Crk. These studies suggest that GC-C signal transduction can be altered by cross-talk with other signaling events in the cell. Reversible phosphorylation of tyrosine residues inhibits the activity of GC-C, and this is mediated by Src family kinases. Src kinases themselves are activated on stimulation of GC-C by its ligands, possibly because of SH2 domain interaction with GC-C. Association of Crk by its SH3 domain regulates GC-C functioning primarily by inhibiting ST-stimulated cGMP production. This opens up the possibility of GC-C signaling through a multimeric complex involving other binding partners of Crk, and these cross-talks involving GC-C with the two proto-oncogenes, Src and Crk, might have far reaching consequences in the regulation of cellular functions.

The survival of the any living organism depends on its availability to communicate, and a breakdown of cellular signaling can have dire consequences such as uncontrolled cellular proliferations or even cell death. Environmental cues or ligands are perceived by cognate receptors, expressed primarily on the cell surface, and transmitted to the interior of the cell to elicit a response. This universal phenomenon is termed as signal transduction. During this process, second messengers such as cyclic nucleotides, cAMP and cGMP, are produced which serve to amplify the signal. Cyclic GMP is emerging as a universal second messenger, and is found in both prokaryotes and eukaryotes. It is synthesized from GTP by the action of guanylyl cyclases. Vertebrate guanylyl cyclases are of two forms, soluble and membrane-associated. Soluble guanylyl cyclases are heterodimeric enzymes which are activated by nitic oxide. Membrane-associated guanylyl cyclases on the other hand are homodimeric enzymes that act as receptors for divers polypeptide ligands. In mammals, there are seven isoforms of receptors guanylyl cyclase, GC-A through GC-G. These recptors have a highly conseved modular domin organization with an N-terminal extracellular domain, a single transmembrane domain and a C- terminal intra cellular regions. The intracellular region contains a juxtamembrane domain followed by a protein-kinase domain, a linker region and a catalytic guanylyl cyclase domain. The coordinated actions of these domains ensure fine tuned-regulations of the catalytic domain. Guanylyl cyclase-C (GC-C) is a member of the membrane-bound guanylyl cyclases. GC-C is predominantely present in the intestine, on the apical surface of epithelial cells, but has also been detected in the rat epididymis. In the intestine it serves as the guanylin, uroguanylin and lymphoguanylin which are the endogenous peptide ligands, while heat- stable entrotoxins (ST) peptides secreted by enterotoxigenic E.coil, are exogenic ligands. Activation of GC-C by these ligands results in an increase in intracellular cGMP levels, which then activates cGMP-dependent protein kinase and cross-activates protein kinase A. In turn, these activated kinases phosphorylate and active the cystic fibrosis transmembrane conductance regulator (CFTR), resulting in chloride and water secretion into the intestine lumen, thus regulating salt and water homeostasis in the intestine. ST peptide has a greater affinity for GC-C than the endogenous ligands and activation of GC-C by ST results in masiive fluid and ion efflux from the intestine cells from which manifests as Travelers’ Diarrhea. The GC-C mediated cGMP signal transduction pathway also maintains intestinal crypt-villus axis homeostatis by exerting a cytostatic effect on the epithelial cells, there by regulating their turn over. Over the years multiple mechanisms of regulation of GC-C activity has been identified including allosteric controlled by various domains in the receptor and phosphorylation-mediated regulation of guanylyl cyclase activity. The current study describes aspects of the regulation of GC-C by gycosylation, and also reports the molecular phenotypes of a naturally occurring mutation in GC-C causes sever diarrhea in affected individuals. GC-C is expressed as a differentially glycosylated protein (130k Da and 145kDa). While both forms bind with equal affinity, only one the 145 kDa form is activated by its ligands. It is this higher glycosylated form which is selectively downregulated in the process of decensitization of GC-C in colomn carcinoma cells (Caco2). Give the critical role gycosylation plays in protein folding, trafficking, receptor activity and mediating protein inter actions, its influence on GC-C was analysed.

No / RATIONALE: The carbon isotopic characterisation of ruminant lipids associated with ceramic vessels has been crucial for elucidating the origins and changing nature of pastoral economies. delta(13)C values of fatty acids extracted from potsherds are commonly compared with those from the dairy and carcass fats of modern domesticated animals to determine vessel use. However, the processing of wild ruminant products in pottery, such as deer, is rarely considered despite the presence of several different species on many prehistoric sites. To address this issue, the carbon isotope range of fatty acids from a number of red deer (Cervus elaphus) tissues, a species commonly encountered in the European archaeological record, was investigated. METHODS: Lipids were extracted from 10 modern red deer tissues obtained from the Slowinski National Park (Poland). Fatty acids were fractionated, methylated and analysed by gas chromatography/combustion/isotope ratio mass spectrometry (GCCIRMS). The delta(13)C values of n-octadecanoic acid and n-hexadecanoic acid, and the difference between these values (Delta(13)C), were compared with those from previously published ruminant fats. RESULTS: Nine of the ten deer carcass fats measured have Delta(13)C values of less than -3.3 per thousand, the threshold previously used for classifying dairy products. Despite considerable overlap, dairy fats from domesticated ruminants with Delta(13)C values less than -4.3 per thousand are still distinguishable. CONCLUSIONS: The finding has implications for evaluating pottery use and early pastoralism. The processing of deer tissues and our revised criteria should be considered, especially where there is other archaeological evidence for their consumption.

no / During the micro-excavation of the cauldrons, residues were identified which appeared different from the surrounding soil and metal corrosion products. Thirty-seven of these residues from nine cauldrons and two significant fragments of incomplete cauldrons were analysed by gas chromatography-mass spectrometry (GC-MS) along with two samples of soil from the micro-excavation for comparison. The aim of the analysis was to determine whether these residues contained any organic material related to the use of the cauldrons, specifically lipids (fats, waxes, resins etc.) from the preparation of food or drink. Two of the samples from the cauldrons were also sent for compound specific carbon stable isotope analysis by gas chromatography-combustion-isotope ratio mass spectrometry (GC-C-IRMS) to give a more precise identification of the residues.

No description available.

Guanylyl cyclase C (GC-C) is a member of particulate guanylyl cyclases, discovered primarily as the target of a family of heat stable enterotoxins (ST), produced by enterotoxigenic Escherichia coli (ETEC). ST is acknowledged as a prime cause of traveller’s diarrhea and the leading cause of child mortality under the age of 5 years in developing nations. The bacterial expression of ST peptides represents molecular mimicry where the pathogen has exploited a gastrointestinal tract-signaling pathway to disperse and propagate. GC-C is primarily expressed on the apical or the brush border membranes of intestinal epithelial cells. GC-C agonists elaborated in the gastrointestinal tract are a family of guanylin peptides, which are responsible for maintaining fluid-ion homeostasis, essential for normal gut physiology. The signal of liigand binding to the extracellular domain of GC-C is transduced to the catalytic guanylyl cyclase domain, which results in production of intracellular cGMP. The elevated levels of cGMP influence multiple downstream targets, which finally regulate ion-flux through the transporters present on the membrane of an enterocyte. The ST peptide, a GC-C superagonist, produces physiologically abnormal levels of cGMP that manifest as secretory diarrhea. The purview of GC-C misregulation was confined to the notion of its hyperactivation caused by ETEC infection and the ensuing diarrhea. Recently, two seminal studies widened the scope of pathologies associated with GC-C. Studies described point mutations in GUCY2C, which were associated with human disease. One study identified a Norwegian family whose members demonstrated a dominantly inherited syndrome of frequent diarrhea associated with hyperactive GC-C. Following this study, inactivating mutations in GC-C in a small Bedouin population was reported. The current study reports the molecular phenotypes associated with the first germ line mutations in GC-C that result in a severe form of congenital sodium diarrhea. Our collaborators from Austria (Thomas Muller & Andreas Janecke, Department of Pediatrics Innsbruck Medical University) communicated to us their study of patients who had clinical diagnosis of congenital sodium diarrhea, with proportionally high fecal sodium loss, metabolic acidosis and dehydration. Exome sequencing in a cohort of 6 unrelated patients revealed four heterozygous missense mutations in GC-C (R792S, L775P, K507E, N850D). Novel GC-C mutations were de novo spontaneous mutations with the carrier being the only affected family member in contrast to the previous two reports with familial history. Biochemical characterization revealed that the mutants (GC-CR792S, GC-CL775P) were constitutively active with GC-CR792S, GC-CK507E, and GC-CN850D showing further stimulation upon treatment with ST and guanylin family of peptides. Interestingly, there was no change in the binding affinities of the ligands for the mutant receptors compared to wild type. However, a significant decrease (ranging from 10-100 fold) in ligand EC50 for the mutant GC-C receptors was prominent. The in vitro assays suggested that the mutations occupying different domains of GC-C might have resulted in distinct structural consequences reflected in the repertoire of phenotypes that were observed. The results presented in this thesis illustrate the molecular basis of the severe form of congenital diarrhea associated with the GC-C gain-of-function mutations. This study has also elaborated our understanding of the regulation of GC-C activity by its various domains.