Effects of fermentation residues on the melt processability and thermomechanical degradation of PHBV produced from cheese whey using mixed microbial cultures

"Available online 28 March 2016"

Proteomic analysis of nitrate-dependent acetone degradation by Alicycliphilus denitrificans strain BC

Alicycliphilus denitrificans strain BC grows anaerobically on acetone with nitrate as electron acceptor. Comparative proteomics of cultures of A. denitrificans strain BC grown on either acetone or acetate with nitrate was performed to study the enzymes involved in the acetone degradation pathway. In the proposed acetone degradation pathway, an acetone carboxylase converts acetone to acetoacetate, an AMP-dependent synthetase/ligase converts acetoacetate to acetoacetyl-CoA, and an acetyl-CoA acetyltransferase cleaves acetoacetyl-CoA to two acetyl-CoA. We also found a putative aldehyde dehydrogenase associated with acetone degradation. This enzyme functioned as a -hydroxybutyrate dehydrogenase catalyzing the conversion of surplus acetoacetate to -hydroxybutyrate that may be converted to the energy and carbon storage compound, poly--hydroxybutyrate. Accordingly, we confirmed the formation of poly-?-hydroxybutyrate in acetone-grown cells of strain BC. Our findings provide insight in nitrate-dependent acetone degradation that is activated by carboxylation of acetone. This will aid studies of similar pathways found in other microorganisms degrading acetone with nitrate or sulfate as electron acceptor.

Respuesta adaptativa y degradación de compuestos de amonio cuaternarios sintéticos por Pseudomonas putida. Adaptative answer and degradation of quaternary ammonium compounds by Pseudomonas putida.

El objetivo de este trabajo es caracterizar la respuesta de P. putida frente a condiciones ambientales adversas dadas por la presencia del detergente catiónico tetradeciltrimetilamonio (TDTMA). El objetivo final que se persigue es el de utilizar este microorganismo como vehículo en procesos de biorremediación. El proyecto comprende aspectos relacionados con la degradación y con la respuesta adaptativa que le permiten a P. putida tolerar altas concentraciones del biocida. La degradación de TDTMA por P. putida involucra una actividad monooxigenasa, que produce trimetilamina (TMA) y tetradecilalcanal. Parte de la TMA producida es demetilada, por una TMAdehidrogenasa (TMADH), e utilizada por la bacteria como fuente de nitrógeno y parte es acumulada intracelularmente, inhibiendo el crecimiento bacteriano. Considerando la importancia de las oxigenasas y dehidrogenasas en la transformación química de compuestos recalcitrantes, se identificarán los genes responsables de la actividad monooxigenasa y de la TMADH, se caracterizarán las enzimas, lo que permitirá conocer, además, datos evolutivos de las mismas. Teniendo en cuenta que la acumulación intracelular TMA conduce a la degradación parcial del detergente, efecto contrarrestado por la adición de aluminio (Al), se investigarán si otros factores nutricionales participan en el control de la degradación de TDMA por P. putida. Se investigará si el regulador global NtrC, que se activa en respuesta a limitación de nitrógeno, participa en el metabolismo de TDTMA. Se prevé construir mutantes en los genes que codifican para monoxigenasa y TMADH y analizar la respuesta de estas cepas frente al estrés ocasionado por TDTMA y Al. En este proyecto se postula además que los cambios a nivel de fosfolípidos (PL) de membrana son una estrategia de P. putida para sobrevivir en presencia del TDTMA. Para concluir si fosfatidilglicerol es el principal responsable de la adaptación de P. putida frente al estrés ocasionado por TDTMA, se pretenden obtener mutantes afectadas en la biosíntesis de novo de PL, particularmente en cardiolipina sintasa. Paralelamente se estudiará si fosfolipasa D participa en la respuesta, lo que permitirá asignar un rol a esta enzima en procesos de señalización análogos a los que ocurren en organismos eucariotas. En presencia de TDTMA y Al, P. putida responde aumentando el contenido de fosfatidilcolina y posiblemente este PL actúe como un reservorio temporario del ión. Identificar en P. putida los genes que codifican para las enzimas responsables de su biosíntesis, particularmente fosfatidilcolina sintasa y/o fosfolípido N-metiltranferasa, conducirá a conocer el mecanismo por el cual fosfatidilcolina estaría involucrada en la respuesta a Al.

Evaluación de la degradación del suelo en agroecosistemas del centro-sur de Córdoba mediante indicadores e índices. Assessment of soil degradation in agroecosystems of central-southern Córdoba by means of indicators and indices

Las actividades agropecuarias ejercen diferentes presiones sobre los recursos naturales. Esto ha llevado, en algunas áreas, a un deterioro del suelo que provoca un impacto sobre la sustentabilidad en los sistemas agropecuarios. Para evaluar la degradación del suelo se han propuesto listas de indicadores, sin embargo, se carece de una herramienta metodológica robusta, adaptada a las condiciones edafoclimáticas regionales. Además, existe una demanda de productores e instituciones interesados en orientar acciones para preservar el suelo. El objetivo de este proyecto es evaluar la degradación física, química y biológica de los suelos en agroecosistemas del centro-sur de Córdoba. Por ello se propone desarrollar una herramienta metodológica que consiste en un set de indicadores físicos, químicos y biológicos, con valores umbrales, integrados en índices de degradación, que asistan a los agentes tomadores de decisiones y productores, en la toma de decisiones respecto de la degradación del suelo. El área de trabajo será una región agrícola del centro-sur de Córdoba con más de 100 años de agricultura. La metodología comienza con la caracterización del uso del territorio y sistemas de manejo, su clasificación y la obtención de mapas base de usos y manejos, mediante sensores remotos y encuestas. Se seleccionarán sitios de muestreo mediante una metodología semi-dirigida usando un SIG, asegurando un mínimo de un punto de muestreo por unidad de mapeo. Se elegirán sitios de referencia lo más cercano a una condición natural. Los indicadores a evaluar surgen de listas propuestas en trabajos previos del grupo, seleccionados en base a criterios internacionales y a adecuados a suelos de la región. Se usarán indicadores núcleo y complementarios. Para la obtención de umbrales, se usarán por un lado valores provenientes de la bibliografía y por otro, umbrales generados a partir de la distribución estadística del indicador en suelos de referencia. Para estandarizar cada indicador se definirá una función de transformación. Luego serán ponderarán mediante análisis estadísticos mulivariados e integrados en índices de degradación física, química y biológica, y un índice general de degradación. El abordaje concluirá con el desarrollo de dos instrumentos para la toma de decisiones: uno a escala regional, que consistirá en mapas de degradación en base a unidades cartográficas ambientales, de uso del territorio y de sistemas de manejo y otro a escala predial que informará sobre la degradación del suelo de un lote en particular, en comparación con suelos de referencia. Los actores interesados contarán con herramientas robustas para la toma de decisiones respecto de la degradación del suelo tanto a escala regional como local. Agricultural activities exert different pressures on natural resources. In some areas this has led to soil degradation and has an impact on agricultural sustainability. To assess soil degradation a robust methodological tool, adapted to regional soil and climatic conditions, is lacking. In addition, there is a demand from farmers and institutions interested in direct actions to preserve the soil. The objective of this project is to assess physical, chemical and biological soil degradation in agroecosystems of Córdoba. We propose to develop a tool that consists of a set of physical, chemical and biological indicators, with threshold values, integrated in soil degradation indices. The study area is a region with more than 100 years of agriculture. The methodology begins with the characterization of land use and management systems and the obtaining of base maps by means of remote sensing and survey. Sampling sites will be selected through a semi-directed methodology using GIS, ensuring at least one sampling point by mapping unit. Reference sites will be chosen as close to a natural condition. The proposed indicators emerge from previous works of the group, selected based on international standards and appropriate for the local soils. To obtain the thresholds, we will use, by one side, values from the literature, and by the other, values generated from the statistical distribution of the indicator in the reference soils. To standardize indicators transformation functions will be defined. Indicators will be weighted by mans of multivariate analysis and integrated in soil degradation indices. The approach concluded with the development of two instruments for decision making: a regional scale one, consisting in degradation maps based on environmental, land use and management systems mapping units; and an instrument at a plot level which will report on soil degradation of a particular plot compared to reference soils.

Degradación de efluentes de las industrias del cuero y textil mediante procesos fotocatalíticos heterogéneos empleando la luz solar. Degradation of effluents from the leather and textile industries through heterogeneous photocatalytic processes using sunlight.

El creciente desarrollo de la industria del cuero y textil en nuestro país, y específicamente en la provincia de Córdoba, ha hecho resurgir en los ultimos años una problemática aún no resuelta que es la elevada contaminación de los recursos hídricos. En ambas industrias, la operación de teñido involucra principalmente colorantes de tipo azoico los cuales son "no biodegradables" y se fragmentan liberando aminas aromáticas cancerígenas. Para abordar esta problemática, la fotocatálisis heterogénea aparece como una nueva tecnología que permitiría la completa mineralización de estos colorantes. A través de radiación y un fotocatalizador sólido adecuado se pueden generan radicales libres eficientes para la oxidación de materia orgánica (colorantes) en medio acuoso. En este sentido, se proponen tamices moleculares mesoporosos modificados con metales de transición (MT) como fotocatalizadores potencialmente aptos para la degradación de estos contaminantes. El propósito principal de este proyecto es el diseño, síntesis, caracterización y evaluación de materiales mesoporosos que presenten actividad fotocatalítica ya sea mediante la modificación de su estructura con diversos metales fotosensibles y/o empleándolos como soporte de óxido de titanio. Se pretende evaluar estos materiales en la degradación de colorantes intentando desplazar su fotosensibilidad hacia la radiación visible para desarrollar nuevas tecnologías con menor impacto ambiental y mayor aprovechamiento de la energía solar. Para ello se sintetizarán materiales del tipo MCM-41 modificados con distintos MT tales como Fe, Cr, Co, Ni y Zn mediante incorporación directa del ión metálico o impregnación. Al mismo tiempo, tanto estos últimos materiales como el MCM-41 silíceo serán empleados como soporte de TiO2. Sus propiedades fisicoquímicas se caracterizarán mediante distintas técnicas instrumentales y su actividad fotocatalítica se evaluará en la degradación de colorantes azoicos bajo radiación visible. Se seleccionará el catalizador más eficiente y se estudiarán los diversos factores que afectan el proceso de fotodegradación. Así mismo, el análisis de la concentración del colorante y los productos presentes en el medio en función del tiempo de reacción permitirá inferir sobre la cinética de la decoloración y postular posibles mecanismos de fotodegradación. Con esta propuesta se espera contribuír al desarrollo de un sector industrial importante en nuestra provincia como es el de las industrias del cuero y textil, mediante la generación de nuevas tecnologías que empleen la energía solar para la degradación de sus efluentes (colorantes). En este sentido, se espera desarrollar nuevos materiales optimizados para lograr la mayor eficiencia fotocatalítica. Esto conduciría entonces hacia la remediación de un problema ambiental de alto impacto tanto para nuestra provincia y nuestro país como para la población mundial, como es la contaminación de los recursos hídricos. Finalmente, con este proyecto se contribuirá a la formación de dos doctorandos y un maestrando, cuyos temas de tesis están vinculados con nuestro objeto de estudio. The increasing development of the textile and leather industries in our country, and specifically in Córdoba, has revived an unresolved problem that is the high contamination of water resources. In both industries, the dyeing involves mainly type azoic dyes which are not biodegradable and break releasing carcinogenic aromatic amines. Heterogeneous photocatalysis appears as a new technology that would allow the complete mineralization of these pollutants. Through radiation and a suitable solid it is possible to generate free radicals for efficient oxidation of organic matter (dyes) in aqueous medium. In this respect, mesoporous molecular sieves modified with transition metals are proposed as potential photocatalysts. The main purpose of this project is the synthesis of mesoporous materials having photocatalytic activity for the degradation of dyes. We will try to move their photosensitivity to visible radiation to develop new technologies with lower environmental impact and greater use of solar energy. Materials MCM-41 modified with metals (Fe, Cr, Co, Ni and Zn) will be synthesized by direct incorporation or impregnation. These materials and the siliceous MCM-41 will be then employed as support of TiO2. The materials will be evaluated in the photocatalytic degradation of azoic dyes under visible radiation. The influence of different factors on the photodegradation proccess will be studied. Kinetic studies will be carried out and a possible reaction way will be proposed. Thus, this work will contribute to the advancement of an important industrial sector and the remediation of an environmental problem with high impact for our province and our country. Moreover, this proyect will contribute to the development of two doctoral tesis and one magister tesis which are vinculated with our study subject.

mRNA metabolism: nonsense mediated mRNA decay as a tool for gene therapy and the role of human DIS3L2 in transcript degradation

Tese de mestrado em Biologia Humana e Ambiente, apresentada à Universidade de Lisboa, através da Faculdade de Ciências, 2015

Tumor necrosis factor (TNF) signaling, but not TWEAK (TNF-like weak inducer of apoptosis)-triggered cIAP1 (cellular inhibitor of apoptosis protein 1) degradation, requires cIAP1 RING dimerization and E2 binding.

Cellular inhibitor of apoptosis (cIAP) proteins, cIAP1 and cIAP2, are important regulators of tumor necrosis factor (TNF) superfamily (SF) signaling and are amplified in a number of tumor types. They are targeted by IAP antagonist compounds that are undergoing clinical trials. IAP antagonist compounds trigger cIAP autoubiquitylation and degradation. The TNFSF member TWEAK induces lysosomal degradation of TRAF2 and cIAPs, leading to elevated NIK levels and activation of non-canonical NF-kappaB. To investigate the role of the ubiquitin ligase RING domain of cIAP1 in these pathways, we used cIAP-deleted cells reconstituted with cIAP1 point mutants designed to interfere with the ability of the RING to dimerize or to interact with E2 enzymes. We show that RING dimerization and E2 binding are required for IAP antagonists to induce cIAP1 degradation and protect cells from TNF-induced cell death. The RING functions of cIAP1 are required for full TNF-induced activation of NF-kappaB, however, delayed activation of NF-kappaB still occurs in cIAP1 and -2 double knock-out cells. The RING functions of cIAP1 are also required to prevent constitutive activation of non-canonical NF-kappaB by targeting NIK for proteasomal degradation. However, in cIAP double knock-out cells TWEAK was still able to increase NIK levels demonstrating that NIK can be regulated by cIAP-independent pathways. Finally we show that, unlike IAP antagonists, TWEAK was able to induce degradation of cIAP1 RING mutants. These results emphasize the critical importance of the RING of cIAP1 in many signaling scenarios, but also demonstrate that in some pathways RING functions are not required.

Environmental Degradation and the Limits to LOV

We show how consumers’ environmental concerns may limit ‘love of variety’ (LOV) and be reflected in consumers decisions. We investigate how the impact of environmental degradation on LOV influences demand and optimal product variety, and how a pollution tax on firms might be used to improve upon the market outcome and increase welfare.

Morphological features of collagen degradation in advanced hepatic schistosomiasis of man

Optical and electron microscopical evidences of focal matrix degradation were frequently seen in liver sections taken from patients with periportal ("pipe-stem") fibrosis caused by schistosomiasis mansoni. Besides present of focal areas of rarefaction, fragmentation and dispersion of collagen fibers, the enlargend portal spaces also showed hyperplasia of elastic tisue and disarray of smooth muscle fibers following the destrution of portal vein branches. Ultrastructural cahnges represented by focal lytic and/or electron dense alterations of colagen fibrils were similar to those first seen in experimental material and designated as "chronic collagen degradation". Elastin and related microfibrils were also affected by focal condensation, fragmentation, distorsion and dissolution. Schistosome eggs were scanty in the tissue sections examined. Matrix degradation represented involuting changes related to the progressive diminution of parasite aggression, which occurs spontaneously with age or after cure by chemotherapy. Changes of focal matrix degradation now being described represent the basic morphological counterpart of periportal fibrosis involution documented clinically, especially by ultrasonography, in patients with hepatosplenic schistosomiasis submitted to curative chemotherapy.

Mutation analysis of the different tfd genes for degradation of chloroaromatic compounds in Ralstonia eutropha JMP134.

Ralstonia eutropha JMP134 possesses two sets of similar genes for degradation of chloroaromatic compounds, tfdCDEFB (in short: tfdI cluster) and tfdDII CII EII FII BII (tfdII cluster). The significance of two sets of tfd genes for the organism has long been elusive. Here, each of the tfd genes in the two clusters on the original plasmid pJP4 was replaced by double recombination with a gene fragment in which a kanamycin resistance gene was inserted into the respective tfd gene's reading frame. The insertion mutants were all tested for growth on 2,4-dichlorophenoxyacetic acid (2,4-D), 2-methyl-4-chlorophenoxyacetic acid (MCPA), and 3-chlorobenzoate (3-CBA). None of the tfdDII CII EII FII BII genes appeared to be essential for growth on 2,4-D or on 3-CBA. Mutations in tfdC, tfdD and tfdF also did not abolish but only retarded growth on 2,4-D, indicating that they were redundant to some extent as well. Of all tfd genes tested, only tfdE and tfdB were absolutely essential, and interruption of those two reading frames abolished growth on 2,4-D, 3-CBA ( tfdE only), and MCPA completely. Interestingly, strains with insertion mutations in the tfdI cluster and those in tfdDII, tfdCII, tfdEII and tfdBII were severely effected in their growth on MCPA, compared to the wild-type. This indicated that not only the tfdI cluster but also the tfdII cluster has an essential function for R. eutropha during growth on MCPA. In contrast, insertion mutation of tfdDII resulted in better growth of R. eutropha JMP134 on 3-CBA, which is most likely due to the prevention of toxic metabolite production in the absence of TfdDII activity.

Dibenzofuran degradation by Sphingomonas wittichii RW1 under environmental stresses

Sphingomonas wittichii is a gram-negative Alpha-proteobacterium, capable of degrading xenobiotic compounds such as dibenzofuran (DBF), dibenzo-p-dioxin, carbazole, 2-hydroxybiphenyl or nitro diphenyl ether herbicides. The metabolism of strain RW1 has been the subject of previous studies and a number of genes involved in DBF degradation have been characterized. It is known that RW1 posseses a unique initial DBF dioxygenase (encoded by the dxnAl gene) that catalyzes the first step in the degradation pathway. None of the organisms known to be able to degrade DBF have a similar dioxygenase, the closest match being the DBF dioxygenase from Rhodococcus sp. with an overall amino acid similarity of 45%. Genes participating in the conversion of the metabolite salicylate via the ortho-cleavage pathway to TCA cycle intermediates were identified as well. Apart from this scarce information, however, there is a lack of global knowledge on the genes that are involved in DBF degradation by strain RW1 and the influence of environmental stresses on DBF-dependent global gene expression. A global analysis is necessary, because it may help to better understand the behaviour of the strain under field conditions and suggest improvements for the current bioaugmentation practice. Chapter 2 describes the results of whole-genome analysis to characterize the genes involved in DBF degradation by RW1. Micro-array analysis allowed us to detect differences in gene transcription when strain RW1 was exposed to DBF. This was complemented by ultra-high throughput sequencing of mutants no longer capable of growing on salicylate and DBF. Some of the genes of the ortho-cleavage pathway were induced 2 to 4 times in the presence of DBF, as well as the initial DBF dioxygenase. However two gene clusters, named 4925 and 5102 were induced up to 19 times in response to DBF induction. The cluster 4925 is putatively participating in a meta-cleavage pathway while the cluster 5102 might be part of a gentisate pathway. The three pathways, ortho-cleavage, meta-cleavage and gentisate pathway seem to be active in parallel when strain RW1 is exposed to DBF, presenting evidence for a redundancy of genes for DBF degradation in the genome of RW1. Chapter 3 focuses on exploiting genetic tools to construct bioreporters representative for DBF degradation in RW1. A set of basic tools for genetic manipulation in Sphingomonas wittichii RW1 was tested and optimized. Both plasmids and mini-transposons were evaluated for their ability to be maintained in RW1 with or without antibiotic selection pressure, and for their ability to lead to fluorescent protein expression in strain RW1 from a constitutive promoter. Putative promoter regions of three of the previously found DBF-induced genes (Swit_4925, Swit_5102 and Swit_4897-dxnAl) were then used to construct eg/^-bioreporters in RW1. Chapter 4 describes the use of the constructed RW1-based bioreporter strains for examining the expression of the DBF degradation pathway genes under microcosm conditions. The bioreporter strains were first exposed to different carbon sources in liquid culture to calibrate the egfp induction. Contrary to our expectations from micro-array analysis only the construct with the promoter from gene cluster 4925 responded to DBF, whereas the other two constructs did not show specific induction with DBF. The response from the bioreporters was subsequently tested for sensitivity to water stress, given that this could have an important impact in soils. Exposure to liquid cultures with decreasing water potential, achieved by NaCl or PEG addition to the growth media, showed that eGFP expression in RW1 from the promoter regions 4925 and 5102 was not directly influenced by water stress, but only through an overall reduction in growth rate. In contrast, expression of eGFP from the dxnAl or an uspA promoter was also directly dependent on the extent of water stress. The RW1 with the 4925 construct was subsequently used in soil microcosms to evaluate DBF bioavailability to the cells in presence or absence of native microbiota or other contaminated material. We found that RW1 could grow on DBF added to soil, but bioreporter expression suggested that competition with native microbiota for DBF intermediates may limit its ability to proliferate to a maximum. Chapter 5 describes the results from the experiments carried out to more specifically detect genes of RW1 that might be implicated in water stress resistance. Hereto we created transposon mutagenesis libraries in RW1, either with a classical mini-Tn5 or with a variant that would express egfp when the transposon would insert in a gene induced under water stress. Classical mutant libraries were screened by replica plating under high and low water stress conditions (achieved by adding NaCl to the agar medium). In addition, we screened for smaller microcolonies formed by mutants in agarose beads that could be analized with flow cytometry. A number of mutants impaired to grow on NaCl-supplemented media were recovered and the transposon insertion sites sequenced. In a second procedure we screened by flow cytometry for mutants with a higher eGFP production after exposure to growth medium with higher NaCl concentrations. Mutants from both libraries rarely overlapped. Discovered gene functions of the transposon insertions pointed to compatible solute synthesis (glutamate and proline), cell membrane synthesis and modification of cell membrane composition. The results obtained in the present study give us a more complete picture of the mechanisms of DBF degradation by S. wittichii RW1, how it reacts to different DBF availability and how the DBF catabolic activity may be affected by the conditions found in contaminated environments. - Sphingomonas wittichii est une alpha-protéobactérie gram-négative, capable de dégrader des composés xénobiotiques tels que le dibenzofurane (DBF), la dibenzo-p-dioxine, le carbazole, le 2-hydroxybiphényle ou les herbicides dérivés du nitro-diphényléther. Le métabolisme de la souche RW1 a fait l'objet d'études antérieures et un certain nombre de gènes impliqués dans la dégradation du DBF ont été caractérisés. Il est connu que RW1 possède une unique dioxygénase DBF initiale (codée par le gène dxnAl) qui catalyse la première étape de la voie de dégradation. Aucun des organismes connus pour être capables de dégrader le DBF n'a de dioxygénase similaire. L'enzyme la plus proche étant la DBF dioxygénase de Rhodococcus sp. avec 45% d'acides aminés conservés. Les gènes qui participent à la transformation du salicylate en métabolites intermédiaires du cycle de Krebs par la voie ort/io-cleavage ont aussi été identifiés. Outre ces informations lacunaires, il y a un manque de connaissances sur l'ensemble des gènes impliqués dans la dégradation du DBF par la souche RW1 ainsi que l'effet des stress environnementaux sur l'expression génétique globale, en présence du DBF. Une analyse globale est nécessaire, car elle peut aider à mieux comprendre le comportement de la souche dans les conditions de terrain et de proposer des améliorations pour l'utilisation de la bio-augmentation comme technique de bio-remédiation. Le chapitre 2 décrit les résultats de l'analyse du génome pour caractériser les gènes impliqués dans la dégradation du DBF par RW1. Une analyse de micro-arrays nous a permis de détecter des différences dans la transcription des gènes lorsque la souche RW1 a été exposée au DBF. L'analyse a été complétée par le criblage à ultra-haut débit de mutants qui n'étaient plus capables de croître avec le salicylate ou le DBF comme seule source de carbone. Certains des gènes de la voie ortho-cleavage, dont la DBF dioxygénase initiale, ont xî été induits 2 à 4 fois, en présence du DBF. Cependant, deux groupes de gènes, nommés 4925 et 5102 ont été induits jusqu'à 19 fois en réponse au DBF. Le cluster 4925 participe probablement dans une voie de meta-cleavage tandis que le cluster 5102 pourrait faire partie d'une voie du gentisate. Les trois voies, ortho-cleavage, meta-cleavage et la voie du gentisate semblent être activées en parallèle lorsque la souche RW1 est exposée au DBF, ce qui représente une redondance de voies pour la dégradation du DBF dans le génome de RW1. Le chapitre 3 se concentre sur l'exploitation des outils génétiques pour la construction de biorapporteurs de la dégradation du DBF par RW1. Un ensemble d'outils de base pour la manipulation génétique dans Sphingomonas wittichii RW1 a été testé et optimisé. Deux plasmides et mini-transposons ont été évalués pour leur capacité à être maintenu dans RW1 avec ou sans pression de sélection par des antibiotiques, et pour leur capacité à exprimer la protéine fluorescente verte (eGFP) dans la souche RW1. Les trois promoteurs des gènes Swit_4925, Swit_5102 et Swit_4897 (dxnAl), induits en réponse au DBF, ont ensuite été utilisés pour construire des biorapporteurs dans RW1. Le chapitre 4 décrit l'utilisation des souches biorapportrices construites pour l'analyse de l'expression des gènes de la voie de dégradation du DBF dans des microcosmes avec différents types de sols. Les souches biorapportrices ont d'abord été exposées à différentes sources de carbone en cultures liquides afin de calibrer l'induction de la eGFP. La construction avec le promoteur du gène 4925 a permis une réponse au DBF. Mais contrairement à nos attentes, basées sur les résultats de l'analyse des micro-arrays, les deux autres constructions n'ont pas montré d'induction spécifique au DBF. La réponse des biorapporteurs a ensuite été testée pour la sensibilité au stress hydrique, étant donné que cela pourrait avoir un impact important dans les microcosmes. La diminution du potentiel hydrique en culture liquide est obtenue par addition de NaCl ou de PEG au milieu de croissance. Nous avons montré que l'expression de la eGFP contrôlée par les promoteurs 4925 et 5102 n'était pas directement influencée par le stress hydrique, mais seulement par une réduction globale des taux de croissance. En revanche, l'expression de la eGFP dépendante des promoteurs dxnAl et uspA était aussi directement dépendante de l'ampleur du stress hydrique. La souche avec la construction 4925 a été utilisée par la suite dans des microcosmes avec différents types de sols pour évaluer la biodisponibilité du DBF en présence ou absence des microbes indigènes et d'autres composés contaminants. Nous avons constaté que RW1 pouvait se développer si le DBF a été ajouté au sol, mais l'expression de la eGFP par le biorapporteur suggère que la compétition avec la microbiota indigène pour les métabolites intermédiaires du DBF peut limiter sa capacité à proliférer de manière optimale. Le chapitre 5 décrit les résultats des expériences réalisées afin de détecter spécifiquement les gènes de RW1 qui pourraient être impliquées dans la résistance au stress hydrique. Ici on a crée des bibliothèques de mutants de RW1 par transposon, soit avec un mini-Tn5 classique ou avec une variante qui exprime la eGFP lorsque le transposon s'insère dans un gène induit par le stress hydrique. Les bibliothèques de mutants ont été criblées par la méthode classique de repiquage sur boîtes, dans des conditions de stress hydrique élevé (obtenu par l'addition de NaCl dans les boîtes). En outre, nous avons criblé des micro¬colonies dans des billes d'agarose qui ont pu être analysées par cytométrie de flux. Un certain nombre de mutants déficients à croître sur des milieux supplémentés avec du NaCl ont été isolés et les sites d'insertion du transposon séquencés. Dans une deuxième procédure nous avons criblé par cytométrie de flux des mutants avec une production de eGFP supérieure, après exposition à un milieu de croissance avec une concentration élevée de NaCl. Les mutants obtenus dans les deux bibliothèques n'étaient pas similaires. Les fonctions des gènes où se trouvent les insertions de transposons sont impliqués dans la synthèse de solutés compatibles (glutamate et de la proline), dans la synthèse de la membrane cellulaire et dans la modification de la composition de la membrane cellulaire. Les résultats obtenus dans la présente étude nous donnent une image plus complète des mécanismes de dégradation du DBF par S. wittichii RW1, comment cette souche réagit à la disponibilité du DBF et comment l'activité catabolique peut être affectée par les conditions rencontrées dans des environnements contaminés.

TWEAK-FN14 signaling induces lysosomal degradation of a cIAP1-TRAF2 complex to sensitize tumor cells to TNFalpha.

Synthetic inhibitor of apoptosis (IAP) antagonists induce degradation of IAP proteins such as cellular IAP1 (cIAP1), activate nuclear factor kappaB (NF-kappaB) signaling, and sensitize cells to tumor necrosis factor alpha (TNFalpha). The physiological relevance of these discoveries to cIAP1 function remains undetermined. We show that upon ligand binding, the TNF superfamily receptor FN14 recruits a cIAP1-Tnf receptor-associated factor 2 (TRAF2) complex. Unlike IAP antagonists that cause rapid proteasomal degradation of cIAP1, signaling by FN14 promotes the lysosomal degradation of cIAP1-TRAF2 in a cIAP1-dependent manner. TNF-like weak inducer of apoptosis (TWEAK)/FN14 signaling nevertheless promotes the same noncanonical NF-kappaB signaling elicited by IAP antagonists and, in sensitive cells, the same autocrine TNFalpha-induced death occurs. TWEAK-induced loss of the cIAP1-TRAF2 complex sensitizes immortalized and minimally passaged tumor cells to TNFalpha-induced death, whereas primary cells remain resistant. Conversely, cIAP1-TRAF2 complex overexpression limits FN14 signaling and protects tumor cells from TWEAK-induced TNFalpha sensitization. Lysosomal degradation of cIAP1-TRAF2 by TWEAK/FN14 therefore critically alters the balance of life/death signals emanating from TNF-R1 in immortalized cells.

Keratin degradation by dermatophytes relies on cysteine dioxygenase and a sulfite efflux pump.

Millions of people suffer from superficial infections caused by dermatophytes. Intriguingly, these filamentous fungi exclusively infect keratin-rich host structures such as hair, nails, and skin. Keratin is a hard, compact protein, and its utilization by dermatophytes for growth has long been discussed as a major virulence attribute. Here, we provide strong support for the hypothesis that keratin degradation is facilitated by the secretion of the reducing agent sulfite, which can cleave keratin-stabilizing cystine bonds. We discovered that sulfite is produced by dermatophytes from environmental cysteine, which at elevated concentrations is toxic for microbes and humans. We found that sulfite formation from cysteine relies on the key enzyme cysteine dioxygenase Cdo1. Sulfite secretion is supported by the sulfite efflux pump Ssu1. Targeted mutagenesis proved that dermatophyte mutants in either Cdo1 or Ssu1 were highly growth-sensitive to cysteine, and mutants in Ssu1 were specifically sensitive to sulfite. Most notably, dermatophyte mutants in Cdo1 and Ssu1 were specifically growth-defective on hair and nails. As keratin is rich in cysteine, our identified mechanism of cysteine conversion and sulfite efflux supports both cysteine and sulfite tolerance per se and progression of keratin degradation. These in vitro findings have implications for dermatophyte infection pathogenesis.

DNA degradation in avian faecal samples and feasibility of non-invasive genetic studies applied to threatened capercaillie populations

We evaluated the feasibility of using faeces as a non-invasively collected DNA source for the genetic study of an endangered bird population (capercaillie; Tetrao urogallus). We used a multitube approach, and for our panel of 11 microsatellites genotyping reliability was estimated at 98% with five repetitions. Experiments showed that free DNases in faecal material were the major cause of DNA degradation. Our results demonstrate that using avian faeces as a source of DNA, reliable microsatellite genotyping can be obtained with a reasonable number of PCR replicates.

Quantifying degradation rates of transmembrane receptor kinases.

Transmembrane receptor-kinases are widespread throughout eukaryotes and their activities are known to regulate all kinds of cellular responses in diverse organs and cell types. In order to guarantee the correct amplitude and duration of signals, receptor levels at the cellular surface need to be tightly controlled. The regulation of receptor degradation is the most direct way to achieve this and elaborate mechanisms are in place to control this process. Therefore, the rate of receptor degradation is a parameter of central importance for understanding the dynamics of a signal transduction cascade. Unfortunately, degradation of transmembrane receptors is a complicated multistep process that involves internalization from the plasma membrane, invagination into the lumen of endosomal compartments, and finally fusion with the vacuole for degradation by vacuolar proteases. Therefore, degradation should be measured in an as noninvasive way as possible, such as not to interfere with the complicated transport processes. Here, a method for minimally invasive, in vivo turn-over measurements in intact organs is provided. This technique was used for quantifying the turn-over rates of the Brassinosteroid receptor kinase BRI1 (BRASSINOSTEROID INSENSITIVE 1) in Arabidopsis thaliana root meristems. Pulse-chase expression of a fluorescently labeled BRI1 variant was used and its turn-over rate was determined by quantitative confocal microscopy. This method is well suited to measure turn-over of transmembrane kinases, but can evidently be extended to measure turn-over of any types of transmembrane proteins.