Physiology and transcriptome of the polycyclic aromatic hydrocarbon-degrading Sphingomonas sp. LH128 after long-term starvation.

The survival, physiology and gene expression profile of the phenanthrene-degrading Sphingomonas sp. LH128 was examined after an extended period of complete nutrient starvation and compared with a non-starved population that had been harvested in exponential phase. After 6 months of starvation in an isotonic solution, only 5 % of the initial population formed culturable cells. Microscopic observation of GFP fluorescent cells, however, suggested that a larger fraction of cells (up to 80 %) were still alive and apparently had entered a viable but non-culturable (VBNC) state. The strain displayed several cellular and genetic adaptive strategies to survive long-term starvation. Flow cytometry, microscopic observation and fatty acid methyl ester (FAME) analysis showed a reduction in cell size, a change in cell shape and an increase in the degree of membrane fatty acid saturation. Transcriptome analysis showed decreased expression of genes involved in ribosomal protein biosynthesis, chromosomal replication, cell division and aromatic catabolism, increased expression of genes involved in regulation of gene expression and efflux systems, genetic translocations, and degradation of rRNA and fatty acids. Those phenotypic and transcriptomic changes were not observed after 4 h of starvation. Despite the starvation situation, the polycyclic aromatic hydrocarbon (PAH) catabolic activity was immediate upon exposure to phenanthrene. We conclude that a large fraction of cells maintain viability after an extended period of starvation apparently due to tuning the expression of a wide variety of cellular processes. Due to these survival attributes, bacteria of the genus Sphingomonas, like strain LH128, could be considered as suitable targets for use in remediation of nutrient-poor PAH-contaminated environments.

The nature of the Cr-C bond: direct estimation of aromaticity in Fischer carbenes

Report for the scientific sojourn at the the Philipps-Universität Marburg, Germany, from september to december 2007. For the first, we employed the Energy-Decomposition Analysis (EDA) to investigate aromaticity on Fischer carbenes as it is related through all the reaction mechanisms studied in my PhD thesis. This powerful tool, compared with other well-known aromaticity indices in the literature like NICS, is useful not only for quantitative results but also to measure the degree of conjugation or hyperconjugation in molecules. Our results showed for the annelated benzenoid systems studied here, that electron density is more concentrated on the outer rings than in the central one. The strain-induced bond localization plays a major role as a driven force to keep the more substituted ring as the less aromatic. The discussion presented in this work was contrasted at different levels of theory to calibrate the method and ensure the consistency of our results. We think these conclusions can also be extended to arene chemistry for explaining aromaticity and regioselectivity reactions found in those systems.In the second work, we have employed the Turbomole program package and density-functionals of the best performance in the state of art, to explore reaction mechanisms in the noble gas chemistry. Particularly, we were interested in compounds of the form H--Ng--Ng--F (where Ng (Noble Gas) = Ar, Kr and Xe) and we investigated the relative stability of these species. Our quantum chemical calculations predict that the dixenon compound HXeXeF has an activation barrier for decomposition of 11 kcal/mol which should be large enough to identify the molecule in a low-temperature matrix. The other noble gases present lower activation barriers and therefore are more labile and difficult to be observable systems experimentally.

In vitro evaluation of the activity of aromatic nitrocompounds against Trypanosoma cruzi

Fourteen compounds were evaluated for their activity against Trypanosoma cruzi blood stream forms at the concentration of 500 µg/ml. Six compounds were active and re-tested at lower concentrations.

Trichurid nematodes in ring-necked pheasants from backyard flocks of the State of Rio de Janeiro, Brazil: frequency and pathology

The present investigation is related to the frequency of infection and to the gross and microscopic lesions associated to the presence of trichurid worms in 50 ring-necked pheasants (Phasianus colchicus) from backyard flocks in the state of Rio de Janeiro, Brazil. In the investigated birds, the overall infection rate was of 74%, with the presence of Eucoleus perforans with 72% of prevalence and 21.2 of mean intensity, in the esophageal and crop mucosa and rarely in the junction of the proventriculus and esophagus, E. annulatus with 2% and 3 in the crop mucosa, Capillaria phasianina, with 12% and 4.3 in the cecum and small intestine and Baruscapillaria obsignata, for the first time referred in this host, with 2% and 1 in the small intestine. Clinical signs were absent. The gross lesions observed in the crop and esophagus of 14 (38.9%) pheasants parasitized with E. perforans were thickening, small nodules, congestion, and petechial haemorrhages in the mucosa. These birds presented a mean infection of 37.5 and a range of infection of 10-82. The microscopic lesions revealed chronic esophagitis with diffuse inflammatory process in the lamina propria characterized mostly by a mononuclear cell infiltrate and also with the presence of granulocytes. In the case of the parasitism of pheasants with C. phasianina, the gross lesions were absent; microscopic lesions were characterized by chronic typhlitis with mononuclear infiltrate. Gross and microscopic lesions were absent in the pheasants parasitized with E. annulatus and B. obsignata.

Prevention of the renarrowing of coronary arteries using drug-eluting stents in the perioperative period: an update.

The management of patients scheduled for surgery with a coronary stent, and receiving 1 or more antiplatelet drugs, has many controversies. The premature discontinuation of antiplatelet drugs substantially increases the risk of stent thrombosis (ST), myocardial infarction, and cardiac death, and surgery under an altered platelet function could also lead to an increased risk of bleeding in the perioperative period. Because of the conflict in the recommendations, this article reviews the current antiplatelet protocols after positioning a coronary stent, the evidence of increased risk of ST associated with the withdrawal of antiplatelet drugs and increased bleeding risk associated with its maintenance, the different perioperative antiplatelet protocols when patients are scheduled for surgery or need an urgent operation, and the therapeutic options if excessive bleeding occurs.

Study of chemical modification of alkaline lignin by the glyoxalation reaction

In this study, glyoxalated alkaline lignins with a non-volatile and non-toxic aldehyde, which can be obtained from several natural resources, namely glyoxal, were prepared and characterized for its use in wood adhesives. The preparation method consisted of the reaction of lignin with glyoxal under an alkaline medium. The influence of reaction conditions such as the molar ratio of sodium hydroxide-to-lignin and reaction time were studied relative to the properties of the prepared adducts. The analytical techniques used were FTIR and 1H-NMR spectroscopies, gel permeation chromatography (GPC), differential scanning calorimetry (DSC), and thermogravimetric analysis (TGA). Results from both the FTIR and 1H-NMR spectroscopies showed that the amount of introduced aliphatic hydroxyl groups onto the lignin molecule increased with increasing reaction time and reached a maximum value at 10 h, and after they began to decrease. The molecular weights remained unchanged until 10 h of reaction time, and then started to increase, possibly due to the repolymerization reactions. DSC analysis showed that the glass transition temperature (Tg) decreased with the introduction of glyoxal onto the lignin molecule due to the increase in free volume of the lignin molecules. TGA analysis showed that the thermal stability of glyoxalated lignin is not influenced and remained suitable for wood adhesives. Compared to the original lignin, the improved lignin is reactive and a suitable raw material for adhesive formula

Double-tagged fluorescent bacterial bioreporter for the study of polycyclic aromatic hydrocarbon diffusion and bioavailability.

Bacterial degradation of polycyclic aromatic hydrocarbons (PAHs), ubiquitous contaminants from oil and coal, is typically limited by poor accessibility of the contaminant to the bacteria. In order to measure PAH availability in complex systems, we designed a number of diffusion-based assays with a double-tagged bacterial reporter strain Burkholderia sartisoli RP037-mChe. The reporter strain is capable of mineralizing phenanthrene (PHE) and induces the expression of enhanced green fluorescent protein (eGFP) as a function of the PAH flux to the cell. At the same time, it produces a second autofluorescent protein (mCherry) in constitutive manner. Quantitative epifluorescence imaging was deployed in order to record reporter signals as a function of PAH availability. The reporter strain expressed eGFP proportionally to dosages of naphthalene or PHE in batch liquid cultures. To detect PAH diffusion from solid materials the reporter cells were embedded in 2 cm-sized agarose gel patches, and fluorescence was recorded over time for both markers as a function of distance to the PAH source. eGFP fluorescence gradients measured on known amounts of naphthalene or PHE served as calibration for quantifying PAH availability from contaminated soils. To detect reporter gene expression at even smaller diffusion distances, we mixed and immobilized cells with contaminated soils in an agarose gel. eGFP fluorescence measurements confirmed gel patch diffusion results that exposure to 2-3 mg lampblack soil gave four times higher expression than to material contaminated with 10 or 1 (mg PHE) g(-1).

The effects of polycyclic aromatic hydrocarbons and heavy metals on terrestrial annelids in urban soils

The effect of soil contamination by polycyclic aromatic hydrocarbons (PAH) and heavy metals on earthworms and enchytraeids was studied in urban parks, in Brno, Czech Republic. In spring and autumn 2007, annelids were collected and soil samples taken in lawns along transects, at three different distances (1, 5 and 30 m) from streets with heavy traffic. In both seasons, two parks with two transects each were sampled. Earthworms were collected using the electrical octet method. Enchytraeids were extracted by the wet funnel method from soil cores. All collected annelids were counted and identified. Basic chemical parameters and concentrations of 16 PAH, Cd, Cu, Pb, and Zn were analysed from soil from each sampling point. PAH concentrations were rather low, decreasing with the distance from the street in spring but not in autumn. Heavy metal concentrations did not decrease significantly with increasing distance. Annelid densities did not significantly differ between distances, although there was a trend of increase in the number of earthworms with increasing distance. There were no significant correlations between soil content of PAH or heavy metals and earthworm or enchytraeid densities. Earthworm density and biomass were negatively correlated with soil pH; and enchytraeid density was positively correlated with soil phosphorus.

Transjugular liver biopsy: prospective evaluation of the angle formed between the hepatic veins and the vena cava main axis and modification of a semi-automated biopsy device in cases of an unfavorable angle.

In cases of transjugular liver biopsies, the venous angle formed between the chosen hepatic vein and the vena cava main axis in a frontal plane can be large, leading to technical difficulties. In a prospective study including 139 consecutive patients who underwent transjugular liver biopsy using the Quick-Core biopsy set, the mean venous angle was equal to 49.6 degrees. For 21.1% of the patients, two attempts at hepatic venous catheterization failed because the venous angle was too large, with a mean of 69.7 degrees. In all of these patients, manual reshaping of the distal curvature of the stiffening metallic cannula, by forming a new mean angle equal to 48 degrees , allowed successful completion of the procedure in less than 10 min.

Ultrastructural analysis of neuronal plasticity in the adult mouse

ABSTRACT Adult neuronal plasticity is a term that corresponds to a set of biological mechanisms allowing a neuronal circuit to respond and adapt to modifications of the received inputs. Mystacial whiskers of the mouse are the starting point of a major sensory pathway that provides the animal with information from its immediate environment. Through whisking, information is gathered that allows the animal to orientate itself and to recognize objects. This sensory system is crucial for nocturnal behaviour during which vision is not of much use. Sensory information of the whiskers are sent via brainstem and thalamus to the primary somatosensory area (S1) of the cerebral cortex in a strictly topological manner. Cell bodies in the layer N of S 1 are arranged in ring forming structures called barrels. As such, each barrel corresponds to the cortical representation in layer IV of a single whisker follicle. This histological feature allows to identify with uttermost precision the part of the cortex devoted to a given whisker and to study modifications induced by different experimental conditions. The condition used in the studies of my thesis is the passive stimulation of one whisker in the adult mouse for a period of 24 hours. It is performed by glueing a piece of metal on one whisker and placing the awake animal in a cage surrounded by an electromagnetic coil that generates magnetic field burst inducing whisker movement at a given frequency during 24 hours. I analysed the ultrastructure of the barrel corresponding the stimulated whisker using serial sections electron microscopy and computer-based three-dimensional reconstructions; analysis of neighbouring, unstimulated barrels as well as those from unstimulated mice served as control. The following elements were structurally analyzed: the spiny dendrites, the axons of excitatory as well as inhibitory cells, their connections via synapses and the astrocytic processes. The density of synapses and spines is upregulated in a barrel corresponding to a stimulated whisker. This upregulation is absent in the BDNF heterozygote mice, indicating that a certain level of activity-dependent released BDNF is required for synaptogenesis in the adult cerebral cortex. Synpaptogenesis is correlated with a modification of the astrocytes that place themselves in closer vicinity of the excitatory synapses on spines. Biochemical analysis revealed that the astrocytes upregulate the expression of transporters by which they internalise glutamate, the neurotransmitter responsible for the excitatory response of cortical neurons. In the final part of my thesis, I show that synaptogenesis in the stimulated barrel is due to the increase in the size of excitatory axonal boutons that become more frequently multisynaptic, whereas the inhibitory axons do not change their morphology but form more synapses with spines apposed to them. Taken together, my thesis demonstrates that all the cellular elements present in the neuronal tissue of the adult brain contribute to activity-dependent cortical plasticity and form part of a mechanism by which the animal responds to a modified sensory experience. Throughout life, the neuronal circuit keeps the faculty to adapt its function. These adaptations are partially transitory but some aspects remain and could be the structural basis of a memory trace in the cortical circuit. RESUME La plasticité neuronale chez l'adulte désigne un ensemble de mécanismes biologiques qui permettent aux circuits neuronaux de répondre et de s'adapter aux modifications des stimulations reçues. Les vibrisses des souris sont un système crucial fournissant des informations sensorielles au sujet de l'environnement de l'animal. L'information sensorielle collectée par les vibrisses est envoyée via le tronc cérébral et le thalamus à l'aire sensorielle primaire (S 1) du cortex cérébral en respectant strictement la somatotopie. Les corps cellulaires dans la couche IV de S 1 sont organisés en anneaux délimitant des structures nommées tonneaux. Chaque tonneau reçoit l'information d'une seule vibrisse et l'arrangement des tonneaux dans le cortex correspond à l'arrangement des vibrisses sur le museau de la souris. Cette particularité histologique permet de sélectionner avec certitude la partie du cortex dévolue à une vibrisse et de l'étudier dans diverses conditions. Le paradigme expérimental utilisé dans cette thèse est la stimulation passive d'une seule vibrisse durant 24 heures. Pour ce faire, un petit morceau de métal est collé sur une vibrisse et la souris est placée dans une cage entourée d'une bobine électromagnétique générant un champ qui fait vibrer le morceau de métal durant 24 heures. Nous analysons l'ultrastructure du cortex cérébral à l'aide de la microscopie électronique et des coupes sériées permettant la reconstruction tridimensionnelle à l'aide de logiciels informatiques. Nous observons les modifications des structures présentes : les dendrites épineuses, les axones des cellules excitatrices et inhibitrices, leurs connections par des synapses et les astrocytes. Le nombre de synapses et d'épines est augmenté dans un tonneau correspondant à une vibrisse stimulée 24 heures. Basé sur cela, nous montrons dans ces travaux que cette réponse n'est pas observée dans des souris hétérozygotes BDNF+/-. Cette neurotrophine sécrétée en fonction de l'activité neuronale est donc nécessaire pour la synaptogenèse. La synaptogenèse est accompagnée d'une modification des astrocytes qui se rapprochent des synapses excitatrices au niveau des épines dendritiques. Ils expriment également plus de transporteurs chargés d'internaliser le glutamate, le neurotransmetteur responsable de la réponse excitatrice des neurones. Nous montrons aussi que les axones excitateurs deviennent plus larges et forment plus de boutons multi-synaptiques à la suite de la stimulation tandis que les axones inhibiteurs ne changent pas de morphologie mais forment plus de synapses avec des épines apposées à leur membrane. Tous les éléments analysés dans le cerveau adulte ont maintenu la capacité de réagir aux modifications de l'activité neuronale et répondent aux modifications de l'activité permettant une constante adaptation à de nouveaux environnements durant la vie. Les circuits neuronaux gardent la capacité de créer de nouvelles synapses. Ces adaptations peuvent être des réponses transitoires aux stimuli mais peuvent aussi laisser une trace mnésique dans les circuits.

Identification of novel factors during the establishment of the Casparian strip in the endodermis

Multicellular organisms rely on specialized tissues that allow for the controlled exchange of matter with their surrounding. In order to function properly, these tissues need to establish a tight connection between the individual cells to prevent uncontrolled passive diffusion across the extracellular space. In animals, these connections are called tight and adherens junctions and are a critical feature of epithelia. These connections, however, rely on direct protein-protein interaction of plasma membrane proteins of adjacent cells. Such a mechanism is not possible in plants due to the cell wall, which encases the individual cells. In order to absorb nutrients, while simultaneously preventing uncontrolled diffusion between cells, land plants have evolved the root endodermis, which is functionally equivalent to animal epithelia. Its cells are surrounded by a precisely localized and aligned, ring-like lignin deposition, called the Casparian strip, and therefore tightly connected between each other. Very little was known about the development of the endodermis and the Casparian strip until recently. In the meantime, however, we have identified a family of endodermis- specific proteins, the CASPs, which recruits extracellular proteins the specific Casparian strip membrane domain (CSD) to locally synthesize lignin in the cell wall. Yet, we hardly knew any specifics on how the CSD is initially defined and how the critically important CASPs are being recruited to it. We therefore conducted a forward genetic screen on the localization of CASPI-GFP in order to identify novel mutants, which lack a defined CSD. We identified 48 mutants, which fell into 15 different complementation groups. While some of the isolated genes had previously been identified through different approaches, nine novel genes, which had never been implicated in CSD development and maintenance, were identified. One of them, LORD OF THE RINGS 2 (.LOTR2) is described to greater detail in this work. LOTR2 encodes for EX070A1, a protein of the evolutionary conserved exocyst complex. This complex has frequently been implicated in various secretory processes across kingdoms. In Arabidopsis, it transiently defines the positioning of CASPI-GFP. We have performed a detailed analysis of the dynamics of EX070A1 and CASPI-GFP, including studies with other markers and propose a mechanism, by which the cytosolic EX070A1 transiently defines a plasma membrane domain to recruit transmembrane proteins, which then recruit extracellular enzymes for localized cell wall modification. Considering the ubiquitous expression of EX070A1, we think that this mechanism is potentially of importance not only for the endodermis and the Casparian strip but also for many other tissues, in which the cell wall becomes locally modified. In fact, many other tissues with secondary cell wall modifications contain proteins very similar to the CASPs. It will be interesting to see to which degree this mechanism is employed in other tissues. As for the endodermis, we have now identified the first gene, which is not specific to the endodermis but shows endodermis-specific dynamics. This might give us a better insight on how the plant modulates this ubiquitously present factor in a cell- or tissue-type specific manner. Considering the knowledge, mutants and tools, which are available to us for investigating the endodermis, the Casparian strip, the exocyst complex and EX070A1 might be just the right experimental system to address these questions. -- Les organismes multicellulaires dépendent des tissues spécialisé pour l'échange contrôlé entre eux et leur environnement. Pour leur bon fonctionnement, les cellules de ces tissus ont besoin d'être très étroitement assemblés afin de prévenir la diffusion non-contrôlée à travers l'espace extracellulaire. Chez les animaux, ces connexions sont appelées jonctions serrées et jonctions adhérentes. Ces jonctions dépendent des interactions directes entre les protéines des cellules voisines. Ceci n'est pas possible chez les plantes à cause de la paroi cellulaire qui recouvre chaque cellule individuellement. Pour absorber les nutriments et en même temps empêcher la diffusion non-contrôlé entre cellules, les plantes ont évolué 1'endoderme dans la racine, qui est fonctionnellement équivalent aux épithéliums des animaux. Les cellules de l'endoderme sont ceinturées par une déposition de lignine très précisément localisées comme un anneau et alignées entre les cellules, et qui, donc, connecte étroitement les cellules avoisinante: Le cadre de Caspary. Peu était connu sur le développement de l'endoderme et le cadre de Caspaiy jusqu'à il y a quelques années. Récemment, pourtant, nous avons identifié une famille de protéines spécifiques à l'endoderme, les CASPs, qui définissent le domaine membranaire du cadre de Caspaiy (CSD). Les CASPs recrutent les protéines extracellulaires nécessaire à la synthèse du cadre de Caspary vers une région limité dans la paroi cellulaire. Pourtant, on connaît très peu les processus spécifiques concernant la définition initiale du CSD et comment les CASPs, qui ont une importance cruciale, sont recrutées vers ce domaine. Par conséquent nous avons mené un crible génétique sur la localisation du CASPI- GFP, qui sert comme marqueur pour le CSD. Notre but étant d'isoler de nouveaux mutants affectés dans l'établissement du CSD. Nous avons identifié 48 mutants, en 15 groupes de complémentation. Bien que certains des gènes isolés étaient déjà impliqué dans la formation du cadre de Caspary, neuf nouveaux gènes n'ayant jamais été impliqués dans le développement ou la maintenance du CSD ont pu être identifiés. Un de ces gènes, LORD OF THE RINGS2 (LOTR2) sera décrit plus en détail dans cette étude. LOTR2 code pour EX070A1, qui est une protéine, du complexe exocyste. Ce complexe de protéines a très bien été conservé au cours de l'évolution. Il était souvent impliqué dans plusieurs processus de sécrétion dans toutes les branches de la vie. Chez Arabidopsis, EX070A1 définit la position du CSD d'une façon transitoire et recrute CASP1- GFP. Nous avons mené une analyse détaillée des dynamiques d'EX070Al et CASPI-GFP ainsi que, des études avec des autres mutants. Nous proposons un mécanisme, d'après lequel EX070A1, recruté du cytosol, définit un domaine dans la membrane plasmique pour localiser des protéines transmembranaires, ces dernières ensuite recruteront des enzymes extracellulaires pour la modification locale de la paroi cellulaire. Vu qu'EX070A1 est exprimé dans toute dans la plante, nous pensons que ce mécanisme est potentiellement important non seulement pour l'endoderme et le cadre de Caspary, mais aussi pour les autres tissus où la paroi cellulaire doit être localement modifiée. En effet, plusieurs autres tissus contiennent des protéines très similaires aux CASPs. Il serait intéressant de voir à quelle dégrée ce mécanisme est également utilisé dans ces tissues. En ce qui concerne l'endoderme, nous avons maintenant identifié le premier gène qui n'est pas exprimé spécifiquement dans l'endoderme, mais qui montre tout de même une dynamique caractéristique dans ce tissu. Il serait intéressant de voir comment la plante peut moduler ce facteur omniprésent d'une façon spécifique. Vu les connaissances, les mutants et les outils qu'on a maintenant à notre disposition, l'endoderme et son cadre de Caspary, le complexe exocyste et EX070A1 sont probablement des bons systèmes expérimentaux pour étudier ces questions. -- Identification des nouveaux facteurs pendant l'établissement du cadre de Caspary dans l'endoderme. Lothar Kalmbach, Département de Biologie Moléculaire Végétale (DBMV), Université de Lausanne. Comme tous les autres organismes multicellulaires, les plantes terrestres dépendent de tissus spécialisés pour l'échange contrôlé avec leur environnement. Ces tissus sont importants pour l'absorption des nutriments mais également pour éviter l'influx de composés toxiques. Chez les plantes, ce tissu se trouve dans la racine. C'est l'endoderme. Grâce au cadre de Caspary, qui permet une forte connexion entre les cellules au niveau de leur paroi, l'endoderme empêche les éléments toxiques d'entrer dans le système vasculaire. Depuis quelques années, nous comprenons de plus en plus la nature et la biosynthèse, ainsi que les protéines impliquées dans l'ancrage des enzymes à la membrane plasmique. Nous n'avons eu, par contre, aucune idée sur le mécanisme qui d'abord définit cet endroit dans la membrane plasmique. Nous avons mené un crible génétique sur la localisation de CASPI-GFP, une protéine, qui recrute les enzymes extracellulaires pour la synthèse du cadre de Caspary. Nous avons identifié plusieurs nouveaux gènes qui sont impliqués dans l'intégrité du cadre de Caspary. L'un de ces gènes est EX070A1, qui est un facteur ayant un rôle important lors de la sécrétion des protéines dans tous les organismes eukaryotes. Ces mutants sont gravement affectés au niveau du cadre de Caspary, mais surtout ils ne sont plus capables de localiser CASPI-GFP. Nous avons suivi la dynamique d'EX070Al et de CASP1-GFP en combinaison avec d'autres marqueurs. Nous avons pu montrer que l'accumulation d'EX070Al est spécifique pour l'endoderme et essentielle pour bien localiser CASPI-GFP et donc, le cadre de Caspary. Ces résultats nous aident à mieux comprendre le développement de l'endoderme mais peuvent potentiellement aussi être utilisés pour étudier les modifications de la paroi cellulaire dans d'autres cellules de la plante.