Influence of bioturbation on denitrification activity in Mediterranean coastal sediments:an in situ experimental approach

An in situ experiment was conducted in the French Mediterranean littoral (Gulf of Fos) from July 1993 to January 1994 using controls without macrofauna or natural sediments. After 1, 4 and 6 mo, sediment reworking and denitrification activities (natural and potential rates) were studied. The bacterial processes were stimulated by the bioturbating activity of the autochthonous infauna. The natural and potential denitrification rates were 160 and 280% higher, respectively, than in the controls. The increase of denitrification, occurring at different depths in the sediment with respect to time, was directly dependent on the macrofaunal activity

Influence of shellfish farming activities on nitrification, nitrate reduction to ammonium and denitrification at the water-sediment interface of the Thau lagoon, France

The seasonal patterns of nitrification, denitrification and dissimilatory ammonium production (DAP) rates were studied in the sediment of 2 stations in the Thau lagoon (south of France). The station ZA was located within the shellfish farming zone and thestation B was the reference site. A marked effect of shellfish farming on bacterial activities was observed. Spatial differences were associated with discrepancies in the organic content and the reduction state of sediments, i.e. highest reductive processes (denitrification and DAP) were noted in shellfish farming area, whereas the oxidative process (nitrification) was predominant outside the farming zone. At both stations, the DAP activity increased in September (autumn) concomitant with an increase of the C/N ratio in the sediment due to the sedimentation of the summer phytoplanktonic production. Nitrification and denitrification rates exhibited maxima in November (winter) corresponding to dissolved inorganic nitrogen inputs from the surrounding land. In the shellfish farming site, 98% of nitrate was reduced to NH4+ and 2% to N2O, showing that the most of the NO3- was reduced to ammonium and remained available for the ecosystem

Hydrocarbon influence on denitrification in bioturbated Mediterranean coastal sediments

An in situ experiment has been carried out inbioturbated Mediterranean coastal marine sediments (Gulfof Fos) in order to study the influence of hydrocarbons ondenitrification after 1, 4 and 6 months. In theabsence of hydrocarbons in the control sediments, the presenceof macrofauna stimulated denitrificationby 160%. This stimulation is induced by sediment reworkingthat favours both direct NO-3 supply fromthe water column and the penetration of O{2}, which in turnstimulated nitrification, the other source ofNO-3 in sediment. The presence of hydrocarbons in theexperimental sediments either stimulated orinhibited the denitrification. The denitrification response tothe presence of hydrocarbon is dependent onthe quantity of matter buried by the macrofauna activity. Insmall quantities, the organic matter relatedto hydrocarbons 120% enhanced the denitrification compared tothe controls. On the other hand, whenburied hydrocarbon concentrations were higher (>100 mgsaturated hydrocarbon fraction kg-1 drysediment), the denitrification was inhibited.On the basis of the results obtained, a descriptive model ofthe patterns of denitrification in relation to the presence ofmacrofauna and the distribution of hydrocarbons in sediments is proposed

Etude du métabolisme du mannitol chez l'algue brune modèle Ectocarpus siliculosus : caractérisation de l'enzyme clé mannitol-1-phosphate déshydrogénase.

Brown algae are multicellular photosynthetic organisms belonging to the stramenopile lineage and which are mainly found in the intertidal zone. One of their metabolic characteristics is to store carbon fixed by photosynthesis through the production of mannitol, a 6-carbon non-cyclic polyol. Synthesis and recycling of mannitol in these organisms occur through the mannitol cycle, which includes two steps for synthesis and two for recycling. Among brown algae, Ectocarpus siliculosus represents the model organisms to study different aspects of their biology. During the PhD thesis, three genes coding for the enzymes involved in the first step of the mannitol cycle, the mannitol-1-phosphate dehydrogenase (M1PDH), were studied (EsM1PDH1, EsM1PDH2, and EsM1PDH3). M1PDHs catalyze a reversible reaction between fructose-6-phosphate and mannitol-1-phosphate. One modified version of the EsM1PDH1 gene, coding for a N-terminal truncated protein in order to deleted a domain of unknown function, was overexpressed in the bacteria Escherichia coli. The truncated recombinant protein was purified and biochemically characterized, notably to determine kinetic parameters in both directions of the reversible reaction catalyzed by M1PDH. These results were completed by analysis of changes in expression of genes encoding enzymes involved in the mannitol cycle during the diurnal cycle. These observations contribute to increasing the understanding of a key metabolic pathway in brown algal physiology.Les algues brunes sont des organismes photosynthétiques multicellulaires, appartenant à la lignée des straménopiles, et dont l'habitat principal est la zone intertidale. Une de leurs caractéristiques métaboliques est d'utiliser le mannitol (polyalcool à six atomes de carbone) comme forme de stockage du carbone issu de la photosynthèse. Le métabolisme du mannitol chez ces organismes fait intervenir quatre enzymes, deux pour la synthèse et deux pour le recyclage, regroupées dans le cycle du mannitol. Parmi les algues brunes, Ectocarpus siliculosus est l'organisme modèle pour étudier différents aspects de leur biologie. Au cours de la thèse, trois gènes de cette algue codant pour les enzymes responsables de la première étape du cycle du mannitol, la mannitol-1-phosphate déshydrogénase (M1PDH), ont été étudiés (EsM1PDH1, EsM1PDH2, et EsM1PDH3). Les M1PDHs catalysent une réaction réversible entre le fructose-6-phosphate et le mannitol-1-phosphate. Une version du gène EsM1PDH, codant pour une protéine tronquée en N-terminal afin d'éliminer un domaine de fonction inconnue, a été surexprimée chez la bactérie Escherichia coli. La protéine recombinante tronquée a été purifiée et caractérisée au niveau biochimique, notamment pour déterminer ses paramètres cinétiques dans les deux sens de la réaction catalysée par les M1PDHs. Ces résultats ont été complétés par l'analyse de l'expression des gènes codant pour les enzymes du cycle du mannitol chez E. siliculosus au cours du cycle diurnal. L'ensemble de ces observations contribue à mieux comprendre une voie métabolique clé dans la physiologie des algues brunes

L'influence du style parental et d'autres facteurs familiaux sur le processus de développement de l'autodétermination des élèves handicapés ou en difficulté d'adaptation ou d'apprentissage : perceptions de la mère

Le présent projet de recherche s'intéresse au processus de développement de l'autodétermination des adolescents de 12 à 21 ans, scolarisés, et classés « élèves handicapés ou en difficulté d'adaptation ou d'apprentissage » (EHDAA). Il s'adresse plus particulièrement aux attitudes et pratiques éducatives parentales et à certains facteurs en lien avec les caractéristiques de la famille pouvant influencer ce processus. Cette recherche vient cerner les caractéristiques, la dynamique et le fonctionnement des environnements familiaux, qui sont généralement associés aux jeunes présentant un niveau d'autodétermination égal ou supérieur à la moyenne. Plus précisément, il documente le .ou les types d'attitudes et pratiques parentales les plus fréquemment adoptées par les mères des jeunes dotés d'un tel niveau d'autodétermination. Dans cette recherche l'auteure donne la parole aux mères, puisqu'un des objectifs est d'explorer la perception de ces dernières quant aux divers aspects pouvant influencer le développement de l'autodétermination de l'enfant. Le cadre théorique de ce mémoire vise à approfondir les connaissances au sujet des styles parentaux déjà reconnus dans la littérature, soit les styles autoritaire, démocratique, désengagé et permissif, qui se déclinent en deux dimensions essentielles, soit le niveau de sensibilité ou d'engagement du parent et celui du contrôle qu'il exerce sur l'enfant. Il vise également à pousser plus loin les connaissances en regard de ce qui est contributif au développement de l'autodétermination chez un individu. Ce projet s'inscrit dans les orientations ministérielles qui favorisent le développement de l'expertise, notamment celle concernant les pratiques professionnelles axées sur le développement des capacités des personnes présentant des incapacités (Ministère de la Santé et des Services sociaux, 2001; p. 76). Une révision des programmes, approches et façons de dispenser et organiser les services aux EHDAA et à leur famille, est toujours actuelle. De nouvelles données en regard des conditions favorables au développement de cette clientèle s'avèrent indiquées. Toutefois, l'analyse des résultats obtenus n'a pu démontrer que l'adoption du style parental démocratique favorise le développement de l'autodétermination, tel que nous le pensions. Nous avons cependant constaté qu'il existe un lien manifeste entre l'estime de soi que le jeune a de lui-même et son niveau d'autodétermination. Il a également été observé qu'au niveau des facteurs familiaux, le statut socio-économique et la scolarité de la mère auraient une influence sur le développement de l'autodétermination. Finalement, d'autres facteurs d'influence, tel le réseau social du jeune, ont pu être identifiés comme jouant un rôle dans le développement de l'autodétermination des jeunes ayant fait partie de l'étude.\ud ______________________________________________________________________________ \ud MOTS-CLÉS DE L’AUTEUR : attitudes parentales, autodétermination, difficulté d'adaptation/d'apprentissage, pratiques parentales, style parental

Pressure-Retaining Sampler and High-Pressure Systems to Study Deep-Sea Microbes Under in situ Conditions

The pelagic realm of the dark ocean is characterized by high hydrostatic pressure, low temperature, high-inorganic nutrients, and low organic carbon concentrations. Measurements of metabolic activities of bathypelagic bacteria are often underestimated due to the technological limitations in recovering samples and maintaining them under in situ environmental conditions. Moreover, most of the pressure-retaining samplers, developed by a number of different labs, able to maintain seawater samples at in situ pressure during recovery have remained at the prototype stage, and therefore not available to the scientific community. In this paper, we will describe a ready-to-use pressure-retaining sampler, which can be adapted to use on a CTD-carousel sampler. As well as being able to recover samples under in situ high pressure (up to 60 MPa) we propose a sample processing in equi-pressure mode. Using a piloted pressure generator, we present how to perform sub-sampling and transfer of samples in equi-pressure mode to obtain replicates and perform hyperbaric experiments safely and efficiently (with <2% pressure variability). As proof of concept, we describe a field application (prokaryotic activity measurements and incubation experiment) with samples collected at 3,000m-depth in the Mediterranean Sea. Sampling, sub-sampling, transfer, and incubations were performed under in situ high pressure conditions and compared to those performed following decompression and incubation at atmospheric pressure. Three successive incubations were made for each condition using direct dissolved-oxygen concentration measurements to determine the incubation times. Subsamples were collected at the end of each incubation to monitor the prokaryotic diversity, using 16S-rDNA/rRNA high-throughput sequencing. Our results demonstrated that oxygen consumption by prokaryotes is always higher under in situ conditions than after decompression and incubation at atmospheric pressure. In addition, over time, the variations in the prokaryotic community composition and structure are seen to be driven by the different experimental conditions. Finally, within samples maintained under in situ high pressure conditions, the active (16S rRNA) prokaryotic community was dominated by sequences affiliated with rare families containing piezophilic isolates, such as Oceanospirillaceae or Colwelliaceae. These results demonstrate the biological importance of maintaining in situ conditions during and after sampling in deep-sea environments

Aerobic and Anaerobic Metabolism of 6,10,14-Trimethylpentadecan-2-one by a Denitrifying-bacterium Isolated from Marine Environments

This report describes the metabolism of 6,10,14-trimethylpentadecan-2-one by a denitrifying bacterium (Marinobacter sp. strain CAB) isolated from marine sediments. Under aerobic and denitrifying conditions, this strain efficiently degraded this ubiquitous isoprenoid ketone. Several bacterial metabolites, 4,8,12-trimethyltridecan-1-ol, 4,8,12-trimethyltridecanal, 4,8,12-trimethyltridecanoic acid, Z-3,7-dimethylocten-2-oic acid,Z-3,7, 11-trimethyldodecen-2-oic acid, and 6,10,14-trimethylpentadecan-2-ol, were formally identified, and different pathways were proposed to explain the formation of such isoprenoid compounds

High quality copy number and genotype data from FFPE samples using Molecular Inversion Probe (MIP) microarrays

BACKGROUND:A major challenge facing DNA copy number (CN) studies of tumors is that most banked samples with extensive clinical follow-up information are Formalin-Fixed Paraffin Embedded (FFPE). DNA from FFPE samples generally underperforms or suffers high failure rates compared to fresh frozen samples because of DNA degradation and cross-linking during FFPE fixation and processing. As FFPE protocols may vary widely between labs and samples may be stored for decades at room temperature, an ideal FFPE CN technology should work on diverse sample sets. Molecular Inversion Probe (MIP) technology has been applied successfully to obtain high quality CN and genotype data from cell line and frozen tumor DNA. Since the MIP probes require only a small (~40 bp) target binding site, we reasoned they may be well suited to assess degraded FFPE DNA. We assessed CN with a MIP panel of 50,000 markers in 93 FFPE tumor samples from 7 diverse collections. For 38 FFPE samples from three collections we were also able to asses CN in matched fresh frozen tumor tissue.RESULTS:Using an input of 37 ng genomic DNA, we generated high quality CN data with MIP technology in 88% of FFPE samples from seven diverse collections. When matched fresh frozen tissue was available, the performance of FFPE DNA was comparable to that of DNA obtained from matched frozen tumor (genotype concordance averaged 99.9%), with only a modest loss in performance in FFPE.CONCLUSION:MIP technology can be used to generate high quality CN and genotype data in FFPE as well as fresh frozen samples.This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at [email protected]

Discovery and functional prioritization of Parkinson's disease candidate genes from large-scale whole exome sequencing.

BACKGROUND: Whole-exome sequencing (WES) has been successful in identifying genes that cause familial Parkinson's disease (PD). However, until now this approach has not been deployed to study large cohorts of unrelated participants. To discover rare PD susceptibility variants, we performed WES in 1148 unrelated cases and 503 control participants. Candidate genes were subsequently validated for functions relevant to PD based on parallel RNA-interference (RNAi) screens in human cell culture and Drosophila and C. elegans models. RESULTS: Assuming autosomal recessive inheritance, we identify 27 genes that have homozygous or compound heterozygous loss-of-function variants in PD cases. Definitive replication and confirmation of these findings were hindered by potential heterogeneity and by the rarity of the implicated alleles. We therefore looked for potential genetic interactions with established PD mechanisms. Following RNAi-mediated knockdown, 15 of the genes modulated mitochondrial dynamics in human neuronal cultures and four candidates enhanced α-synuclein-induced neurodegeneration in Drosophila. Based on complementary analyses in independent human datasets, five functionally validated genes-GPATCH2L, UHRF1BP1L, PTPRH, ARSB, and VPS13C-also showed evidence consistent with genetic replication. CONCLUSIONS: By integrating human genetic and functional evidence, we identify several PD susceptibility gene candidates for further investigation. Our approach highlights a powerful experimental strategy with broad applicability for future studies of disorders with complex genetic etiologies