Small RNA as global regulator of carbon catabolite repression in Pseudomonas aeruginosa.

In the metabolically versatile bacterium Pseudomonas aeruginosa, the RNA-binding protein Crc is involved in catabolite repression of a range of degradative genes, such as amiE (encoding aliphatic amidase). We found that a CA-rich sequence (termed CA motif) in the amiE translation initiation region was important for Crc binding. The small RNA CrcZ (407 nt) containing 5 CA motifs was able to bind the Crc protein with high affinity and to remove it from amiE mRNA in vitro. Overexpression of crcZ relieved catabolite repression in vivo, whereas a crcZ mutation pleiotropically prevented the utilization of several carbon sources. The sigma factor RpoN and the CbrA/CbrB two-component system, which is known to maintain a healthy carbon-nitrogen balance, were necessary for crcZ expression. During growth on succinate, a preferred carbon source, CrcZ expression was low, resulting in catabolite repression of amiE and other genes under Crc control. By contrast, during growth on mannitol, a poor carbon source, elevated CrcZ levels correlated with relief of catabolite repression. During growth on glucose, an intermediate carbon source, CrcZ levels and amiE expression were intermediate between those observed in succinate and mannitol media. Thus, the CbrA-CbrB-CrcZ-Crc system allows the bacterium to adapt differentially to various carbon sources. This cascade also regulated the expression of the xylS (benR) gene, which encodes a transcriptional regulator involved in benzoate degradation, in an analogous way, confirming this cascade's global role.

Towards storage and access of electronic theses: A proposal of its organisation for the Consortium of Catalan Libraries

Els objectius d'aquest informe són realitzar un estudi de la tècnica en la digitalització, l'emmagatzematge i l'accés a les tesis doctorals electròniques, per tal de fer una proposta d’organització al Consorci de Biblioteques Universitàries de Catalunya (CBUC). Actualment, tot i que existeixen diverses iniciatives a Europa, és als EUA on la digitalització de tesis doctorals s’ha desenvolupat més amb la creació de la Networked Digital Library for Theses and Dissertation (NDLTD), i ha estat qui ha definit els estàndards en aquest camp. En el següent informe es planteja i es recomana al CBUC l’adhesió institucional a l’NDLTD per poder gaudir de la seva experiència.

A double-quadrature radiofrequency coil design for proton-decoupled carbon-13 magnetic resonance spectroscopy in humans at 7T

Purpose Carbon-13 magnetic resonance spectroscopy (13C-MRS) is challenging because of the inherent low sensitivity of 13C detection and the need for radiofrequency transmission at the 1H frequency while receiving the 13C signal, the latter requiring electrical decoupling of the 13C and 1H radiofrequency channels. In this study, we added traps to the 13C coil to construct a quadrature-13C/quadrature-1H surface coil, with sufficient isolation between channels to allow simultaneous operation at both frequencies without compromise in coil performance. Methods Isolation between channels was evaluated on the bench by measuring all coupling parameters. The quadrature mode of the quadrature-13C coil was assessed using in vitro 23Na gradient echo images. The signal-to-noise ratio (SNR) was measured on the glycogen and glucose resonances by 13C-MRS in vitro, compared with that obtained with a linear-13C/quadrature-1H coil, and validated by 13C-MRS in vivo in the human calf at 7T. Results Isolation between channels was better than â^'30 dB. The 23Na gradient echo images indicate a region where the field is strongly circularly polarized. The quadrature coil provided an SNR enhancement over a linear coil of 1.4, in vitro and in vivo. Conclusion It is feasible to construct a double-quadrature 13C-1H surface coil for proton decoupled sensitivity enhanced 13C-NMR spectroscopy in humans at 7T. Magn Reson Med, 2014. © 2014 Wiley Periodicals, Inc.

Transcutaneous carbon dioxide and oxygen tension in newborn infants: reliability of a combined monitor of oxygen tension and carbon dioxide tension.

We evaluated a new combined sensor for monitoring transcutaneous carbon dioxide tension (PtcCO2) and oxygen tension (PtcO2) in 20 critically ill newborn infants. Arterial oxygen tension (PaO2) ranged from 16 to 126 torr and arterial carbon dioxide tension (PaCO2) from 14 to 72 torr. Linear correlation analysis (100 paired values) of PtcO2 versus PaO2 showed an r value of 0.75 with a regression equation of PtcO2 = 8.59 + 0.905 (PaO2), while PtcCO2 versus PaCO2 revealed a correlation coefficient of r = 0.89 with an equation of PtcCO2 = 2.53 + 1.06 (PaCO2). The bias between PaO2 and PtcO2 was -2.8 with a precision of +/- 16.0 torr (range, -87 to +48 torr). The bias between PaCO2 and PtcCO2 was -5.1 with a precision of +/- 7.3 torr (range, -34 to +8 torr). The transcutaneous sensor detected 83% of hypoxia (PaO2 less than 45 torr), 75% of hyperoxia (PaO2 greater than 90 torr), 45% of hypocapnia (PaCO2 less than 35 torr), and 96% of hypercapnia (PaCO2 greater than 45 torr). We conclude that the reliability of the combined transcutaneous PO2 and PCO2 monitor in sick neonates is good for detecting hypercapnia, fair for hypoxia and hyperoxia, but poor for hypocapnia. It is an improvement in that it spares available skin surface and requires less handling, but it appears to be slightly less accurate than the single electrodes.

Efecto de los usos del suelo en la emisión de dióxido de carbono del suelo a la atmósfera en un agroecosistema semiárido del Valle del Ebro

Los cambios en los usos del suelo han contribuido de manera importante al incremento de gases de efecto invernadero en la atmósfera, especialmente de dióxido de carbono, aumentando sus emisiones desde 1970 en un 80%. Estos cambios causan la alteración de los suelos provocando un impacto sobre el ciclo del carbono, aumentando las tasas de descomposición de la fracción orgánica creando así un flujo de CO2 a la atmosfera. Entre las recomendaciones del Panel Intergubernamental de expertos sobre el Cambio Climático (IPCC, en inglés), y contemplado en el Protocolo de Kyoto, se encuentra el proceso de secuestro de carbono en suelos, que implica la eliminación del CO2 atmosférico por parte de las plantas y su almacenamiento como materia orgánica del suelo. Para poder favorecer dicho proceso, en un determinado tipo de ecosistema, es fundamental conocer cuáles son los factores que gobiernan la respiración del suelo y el impacto que tienen los diferentes usos en la emisión de CO2. En el presente trabajo se han estudiado 4 usos del suelo representativos del secano aragonés: un monocultivo de cebada en siembra directa (NT), un suelo abandonado labrado (AC), un suelo abandonado no alterado (AU) y un suelo forestal (FR) con el objetivo de conocer sus tasas de respiración, la influencia de diferentes parámetros edáficos en ellas, y proponer cambios en el uso del suelo que ayuden a mitigar estas emisiones. Además, se ha dedicado un apartado para conocer cómo influyen diferentes técnicas de fertilización nitrogenada (mineral y orgánica) en la respiración de un monocultivo de cebada en siembra directa. En cuanto a los usos, los resultados obtenidos tanto in situ como en laboratorio muestran una mayor respiración en AC, siendo los valores más bajos los de NT y FR. Una de las principales conclusiones es que la supresión del laboreo y del periodo de barbecho largo, así como la conversión de tierras abandonadas y marginales a cultivos y zonas forestales se presentan en este tipo de ecosistemas como prácticas de secuestro de carbono. En el estudio de aplicación de fertilizantes, no se observó ningún cambio en la respiración del suelo después de la aplicación de nitrógeno mineral. En cambio, el suelo fertilizado con purín sí que mostró picos de emisión durante las siguientes horas a la incorporación de éste, debido fundamentalmente a su alto contenido de carbono lábil.

Soil water storage in an upland forest after selective logging in Central Amazonia

Soil water storage of Central Amazonian soil profiles in upland forest plots subjected to selective logging (in average, 8 trees or 34, 3 m³ of timber per hectare were removed) was measured in four layers, down to a depth of 70 cm. The study lasted 27-months and was divided in two phases: measurements were carried out nearly every week during the first 15 months; in the following year, five intensive periods of measurements were performed. Five damage levels were compared: (a) control (undisturbed forest plot); (b) centre of the clearing/gap; (c) edge of the gap; (d) edge of the remaining forest; and (e) remaining forest. The lowest values for water storage were found in the control (296 ± 19.1 mm), while the highest were observed (333 ± 25.8 mm) in the centre of the gap, during the dry period. In the older gaps (7.5-8.5 year old), soil water storage was similar to the remaining and the control forest, indicating a recovery of hydric soil properties to nearly the levels prior to selective logging.

Factors promoting the exposure to bioaerosols among crop workers

Introduction. Agricultural workers are among the professional groups most at risk of developing acute or chronic respiratory problems. Despite this fact, the etiology of these occupational diseases is poorly known, even in important sectors of agriculture such as the crops sector. Cereals can be colonized by a large number of fungal species throughout the plants' growth, but also during grain storage. Some of these fungi deliver toxins that can have a serious impact on human health when they are ingested via wheat products. Although International and European legislation on contaminants in food, including mycotoxins, include measures to ensure protection of public health by setting down the maximum levels for certain contaminants, the risks associated with the inhalation of such molecules during grain handling remains poorly documented. Goal of study. This project's objective was to characterize worker exposure to pathogenic, irritative or allergenic microorganisms and to identify the abiotic or biotic factors that reduce the growth of these microorganisms in crops. Indeed, the proliferation of microorganisms on wheat is dependent on temperature, rainfall and human disturbance (e.g. usage of tillage, addition of fungicides). A change in the concentration of these microorganisms in the substrate will directly result in a change in the concentration of aerosolized particles of the same microorganisms. Therefore, the exposure of worker to bioaérosols will also change. The Vaud region of Switzerland is a perfect region for conduct such a project as weather conditions vary and agricultural land management programs are divers at a small geographic scale. Methods. Bioaerosols and wheat dust have been sampled during wheat harvesting of summer 2010 at 100 sites uniformly distributed in the Vaud region that are representative of the different agriculture practices. Personal exposure has been evaluated for different wheat related activities: harvesting, grain unload, baling straw, the cleaning of harvesters and silos. Aerosols have been sampled at a rate of 2L/min between 15 min to 4 hours (t) on a 5m PVC filter for estimating the total dust inhaled, on gelatine filter for the identification and quantification of molds, and on a 0.45um polycarbonate filter for endotoxin quantification. Altitude, temperature and annual average rainfall were considered for each site. The physical and chemical characteristics of soils were determined using the methods in effect at Sol Council (Nyon). Total dust has been quantified following NIOSH 0500 method. Reactive endotoxine activity has been determined with Limulus Amebocyte Lysate Assay. All molds have been identified by the pyrosequencing of ITS2 amplicons generated from bioaerosol or wheat dust genomic DNA. Results & Conclusions. Our results confirm the previous quantitative data on the worker exposure to wheat dust. In addition, they show that crop workers are systematically exposed to complex mixtures of allergens, irritants or cytotoxic components. The novelty of our study is the systematic detection of molds such as Fusarium - that is a mycotoxins producer - in the bioaerosols. The results are interpreted by taking in account the agriculture practice, the Phosphorus : Carbon : Nitrogen ratio of the soil, the altitude and the average of rainy days per year.

Fermentative 2-carbon metabolism produces carcinogenic levels of acetaldehyde in Candida albicans.

Acetaldehyde is a carcinogenic product of alcohol fermentation and metabolism in microbes associated with cancers of the upper digestive tract. In yeast acetaldehyde is a by-product of the pyruvate bypass that converts pyruvate into acetyl-Coenzyme A (CoA) during fermentation. The aims of our study were: (i) to determine the levels of acetaldehyde produced by Candida albicans in the presence of glucose in low oxygen tension in vitro; (ii) to analyse the expression levels of genes involved in the pyruvate-bypass and acetaldehyde production; and (iii) to analyse whether any correlations exist between acetaldehyde levels, alcohol dehydrogenase enzyme activity or expression of the genes involved in the pyruvate-bypass. Candida albicans strains were isolated from patients with oral squamous cell carcinoma (n = 5), autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED) patients with chronic oral candidosis (n = 5), and control patients (n = 5). The acetaldehyde and ethanol production by these isolates grown under low oxygen tension in the presence of glucose was determined, and the expression of alcohol dehydrogenase (ADH1 and ADH2), pyruvate decarboxylase (PDC11), aldehyde dehydrogenase (ALD6) and acetyl-CoA synthetase (ACS1 and ACS2) and Adh enzyme activity were analysed. The C. albicans isolates produced high levels of acetaldehyde from glucose under low oxygen tension. The acetaldehyde levels did not correlate with the expression of ADH1, ADH2 or PDC11 but correlated with the expression of down-stream genes ALD6 and ACS1. Significant differences in the gene expressions were measured between strains isolated from different patient groups. Under low oxygen tension ALD6 and ACS1, instead of ADH1 or ADH2, appear the most reliable indicators of candidal acetaldehyde production from glucose.

The carbon-isotope shift at the Permian/ Triassic boundary in the southern Alps is gradual

Carbon isotope ratios in marine carbonate rocks have been shown to shift at some of the time boundaries associated with extinction events; for example, Cretaceous/Tertiary and Ordovician/ Silurian. The Permian/Triassic boundary, the greatest extinction event of the Phanerozoic, is also marked by a large d13C depletion. New carbon isotope results from sections in the southern Alps show that this depletion did not actually represent a single event, but was a complex change that spanned perhaps a million years during the late Permian and early Triassic. These results suggest that the Permian/Triassic (P/Tr) extinction may have been in part gradual and in part 'stepwise', but was not in any case a single catastrophic event.

Audit report on the Iowa Petroleum Underground Storage Tank Board (UST Board) for the year ended June 30, 2009

Audit report on the Iowa Petroleum Underground Storage Tank Board (UST Board) for the year ended June 30, 2009

PROTEOMICS OF OXIDATIVE LESIONS OCCURRING DURING TRANSFUSION-PURPOSED STORAGE OF ERYTHROCYTE CONCENTRATES

Erythrocyte concentrates (ECs) are the major labile blood product being transfused worldwide, aiming at curing anemia of diverse origins. In Switzerland, ECs are stored at 4 °C up to 42 days in saline-adenine-glucose-mannitol (SAGM). Such storage induces cellular lesions, altering red blood cells (RBCs) metabolism, protein content and rheological properties. A hot debate exists regarding the impact of the storage lesions, thus the age of ECs on transfusion-related clinical adverse outcomes. Several studies tend to show that poorer outcomes occur in patients receiving older blood products. However, no clear association was demonstrated up to date. While metabolism and early rheological changes are reversible through transfusion of the blood units, oxidized proteins cannot be repaired, and it is likely such irreversible damages would affect the quality of the blood product and the efficiency of the transfusion. In vivo, RBCs are constantly exposed to oxygen fluxes, and are thus well equipped to deal with oxidative challenges. Moreover, functional 20S proteasome complexes allow for recognition and proteolysis of fairly oxidized protein, and some proteins can be eliminated from RBCs by the release of microvesicles. The present PhD thesis is involved in a global research project which goal is to characterize the effect of processing and storage on the quality of ECs. Assessing protein oxidative damages during RBC storage is of major importance to understand the mechanisms of aging of stored RBCs. To this purpose, redox proteomic-based investigations were conducted here. In a first part, cysteine oxidation and protein carbonylation were addressed via 2D-DIGE and derivatization-driven immunodetection approaches, respectively. Then, the oxidized sub- proteomes were characterized through LC-MS/MS identification of proteins in spots of interest (cysteine oxidation) or affinity-purified carbonylated proteins. Gene ontology annotation allowed classifying targets of oxidation according to their molecular functions. In a third part, the P20S activity was evaluated throughout the storage period of ECs, and its susceptibility to highly oxidized environment was investigated. The potential defensive role of microvesiculation was also addressed through the quantification of eliminated carbonylated proteins. We highlighted distinct protein groups differentially affected by cysteine oxidation, either reversibly or irreversibly. In addition, soluble extracts showed a decrease in carbonylation at the beginning of the storage and membrane extracts revealed increasing carbonylation after 4 weeks of storage. Engaged molecular functions revealed that antioxidant (AO) are rather reversibly oxidized at their cysteine residue(s), but are irreversibly oxidized through carbonylation. In the meantime, the 20S proteasome activity is decreased by around 40 % at the end of the storage period. Incubation of fresh RBCs extracts with exogenous oxidized proteins showed a dose-dependent and protein-dependent inhibitory effect. Finally, we proved that the release of microvesicles allows the elimination of increasing quantities of carbonylated proteins. Taken together, these results revealed an oxidative pathway model of RBCs storage, on which further investigation towards improved storage conditions will be based. -- Les concentrés érythrocytaires (CE) sont le produit sanguin le plus délivré au monde, permettant de traiter différentes formes d'anémies. En Suisse, les CE sont stocké à 4 °C pendant 42 jours dans une solution saline d'adénine, glucose et mannitol (SAGM). Une telle conservation induit des lésions de stockage qui altèrent le métabolisme, les protéines et les propriétés rhéologique du globule rouge (GR). Un débat important concerne l'impact du temps de stockage des CE sur les risques de réaction transfusionnelles, certaines études tentant de démontrer que des transfusions de sang vieux réduiraient l'espérance de vie des patients. Cependant, aucune association concrète n'a été prouvée à ce jour. Alors que les modifications du métabolisme et changement précoces des propriétés rhéologiques sont réversibles suite à la transfusion du CE, les protéines oxydées ne peuvent être réparées, et il est probable que de telles lésions affectent la qualité et l'efficacité des produits sanguins. In vivo, les GR sont constamment exposés à l'oxygène, et sont donc bien équipés pour résister aux lésions oxydatives. De plus, les complexes fonctionnels de proteasome 20S reconnaissent et dégradent les protéines modérément oxydées, et certaines protéines peuvent être éliminées par les microparticules. Cette thèse de doctorat est imbriquée dans un projet de recherche global ayant pour objectif la caractérisation des effets de la préparation et du stockage sur la qualité des GR. Evaluer les dommages oxydatifs du GR pendant le stockage est primordial pour comprendre les mécanismes de vieillissement des produits sanguin. Dans ce but, des recherches orientées redoxomique ont été conduites. Dans une première partie, l'oxydation des cystéines et la carbonylation des protéines sont évaluées par électrophorèse bidimensionnelle différentielle et par immunodétection de protéines dérivatisées. Ensuite, les protéines d'intérêt ainsi que les protéines carbonylées, purifiées par affinité, sont identifiées par spectrométrie de masse en tandem. Les protéines cibles de l'oxydation sont classées selon leur fonction moléculaire. Dans une troisième partie, l'activité protéolytique du protéasome 20S est suivie durant la période de stockage. L'impact du stress oxydant sur cette activité a été évalué en utilisant des protéines exogènes oxydées in vitro. Le potentiel rôle défensif de la microvesiculation a également été étudié par la quantification des protéines carbonylées éliminées. Dans ce travail, nous avons observé que différents groupes de protéines sont affectés par l'oxydation réversible ou irréversible de leurs cystéines. De plus, une diminution de la carbonylation en début de stockage dans les extraits solubles et une augmentation de la carbonylation après 4 semaines dans les extraits membranaires ont été montrées. Les fonctions moléculaires engagées par les protéines altérées montrent que les défenses antioxydantes sont oxydées de façon réversible sur leurs résidus cystéines, mais sont également irréversiblement carbonylées. Pendant ce temps, l'activité protéolytique du protéasome 20S décroit de 40 % en fin de stockage. L'incubation d'extraits de GR en début de stockage avec des protéines oxydées exogènes montre un effet inhibiteur « dose-dépendant » et « protéine-dépendant ». Enfin, les microvésicules s'avèrent éliminer des quantités croissantes de protéines carbonylées. La synthèse de ces résultats permet de modéliser une voie oxydative du stockage des GRs, à partir de laquelle de futures recherches seront menées avec pour but l'amélioration des conditions de stockage.

Numerical analysis of wave-induced fluid flow effects on seismic data: Application to monitoring of CO2 storage at the Sleipner Field

In this work we analyze how patchy distributions of CO2 and brine within sand reservoirs may lead to significant attenuation and velocity dispersion effects, which in turn may have a profound impact on surface seismic data. The ultimate goal of this paper is to contribute to the understanding of these processes within the framework of the seismic monitoring of CO2 sequestration, a key strategy to mitigate global warming. We first carry out a Monte Carlo analysis to study the statistical behavior of attenuation and velocity dispersion of compressional waves traveling through rocks with properties similar to those at the Utsira Sand, Sleipner field, containing quasi-fractal patchy distributions of CO2 and brine. These results show that the mean patch size and CO2 saturation play key roles in the observed wave-induced fluid flow effects. The latter can be remarkably important when CO2 concentrations are low and mean patch sizes are relatively large. To analyze these effects on the corresponding surface seismic data, we perform numerical simulations of wave propagation considering reservoir models and CO2 accumulation patterns similar to the CO2 injection site in the Sleipner field. These numerical experiments suggest that wave-induced fluid flow effects may produce changes in the reservoir's seismic response, modifying significantly the main seismic attributes usually employed in the characterization of these environments. Consequently, the determination of the nature of the fluid distributions as well as the proper modeling of the seismic data constitute important aspects that should not be ignored in the seismic monitoring of CO2 sequestration problems.