Enhanced production of indole-3-acetic acid by a genetically modified strain of Pseudomonas fluorescens CHA0 affects root growth of cucumber but does not improve protection of the plant against Pythium root rot

The biocontrol strain CHA0 of Pseudomonas fluorescens produces small amounts of indole-3-acetic acid via the tryptophan side chain oxidase and the tryptophan transaminase pathways. A recombinant plasmid (pME3468) expressing the tryptophan monooxygenase pathway was introduced into strain CHA0; this resulted in elevated synthesis of indole-3-acetic acid in vitro, especially after addition of -tryptophan. In natural soil, strain CHA0/pME3468 increased fresh root weight of cucumber by 17-36%, compared to the effect of strain CHA0; root colonization was about 106 cells per g of root. However, both strains gave similar protection of cucumber against Pythium ultimum. In autoclaved soil, at 6×107 cells per g of root, strain CHA0 stimulated growth of roots and shoots, whereas strain CHA0/pME3468 caused root stunting and strong reduction of plant weight. These results are in agreement with the known effects of exogenous indole-3-acetic acid on plant roots and suggest that in the system examined, indole-3-acetic acid does not contribute to the biocontrol properties of strain CHA0.

Peroxisomal beta-oxidation--a metabolic pathway with multiple functions.

Fatty acid degradation in most organisms occurs primarily via the beta-oxidation cycle. In mammals, beta-oxidation occurs in both mitochondria and peroxisomes, whereas plants and most fungi harbor the beta-oxidation cycle only in the peroxisomes. Although several of the enzymes participating in this pathway in both organelles are similar, some distinct physiological roles have been uncovered. Recent advances in the structural elucidation of numerous mammalian and yeast enzymes involved in beta-oxidation have shed light on the basis of the substrate specificity for several of them. Of particular interest is the structural organization and function of the type 1 and 2 multifunctional enzyme (MFE-1 and MFE-2), two enzymes evolutionarily distant yet catalyzing the same overall enzymatic reactions but via opposite stereochemistry. New data on the physiological roles of the various enzymes participating in beta-oxidation have been gathered through the analysis of knockout mutants in plants, yeast and animals, as well as by the use of polyhydroxyalkanoate synthesis from beta-oxidation intermediates as a tool to study carbon flux through the pathway. In plants, both forward and reverse genetics performed on the model plant Arabidopsis thaliana have revealed novel roles for beta-oxidation in the germination process that is independent of the generation of carbohydrates for growth, as well as in embryo and flower development, and the generation of the phytohormone indole-3-acetic acid and the signal molecule jasmonic acid.

Gas emission during laparoscopic colorectal surgery using a bipolar vessel sealing device: A pilot study on four patients.

BACKGROUND: Dissection during laparoscopic surgery produces smoke containing potentially toxic substances. The aim of the present study was to analyze smoke samples produced during laparoscopic colon surgery using a bipolar vessel sealing device (LigaSuretrade mark). METHODS: Four consecutive patients undergoing left-sided colectomy were enrolled in this pilot study. Smoke was produced by the use of LigaSuretrade mark. Samples (5,5l) were evacuated from the pneumoperitoneum in a closed system into a reservoir. Analysis was performed with CO2-laser-based photoacoustic spectroscopy and confirmed by a Fourier-transform infrared spectrum. The detected spectra were compared to the available spectra of known toxins. RESULTS: Samples from four laparoscopic sigmoid resections were analyzed. No relevant differences were noted regarding patient and operation characteristics. The gas samples were stable over time proven by congruent control measurements as late as 24 h after sampling. The absorption spectra differed considerably between the patients. One broad absorption line at 100 ppm indicating H2O and several unknown molecules were detected. With a sensitivity of alpha min ca 10-5 cm-1 no known toxic substances like phenol or indole were identified. CONCLUSION: The use of a vessel sealing device during laparoscopic surgery does not produce known toxic substances in relevant quantity. Further studies are needed to identify unknown molecules and to analyze gas emission under various conditions.

A one-year monitoring of nicotine use in sport: frontier between potential performance enhancement and addiction issues.

Tobacco consumption is a global epidemic responsible for a vast burden of disease. With pharmacological properties sought-after by consumers and responsible for addiction issues, nicotine is the main reason of this phenomenon. Accordingly, smokeless tobacco products are of growing popularity in sport owing to potential performance enhancing properties and absence of adverse effects on the respiratory system. Nevertheless, nicotine does not appear on the 2011 World Anti-Doping Agency (WADA) Prohibited List or Monitoring Program by lack of a comprehensive large-scale prevalence survey. Thus, this work describes a one-year monitoring study on urine specimens from professional athletes of different disciplines covering 2010 and 2011. A method for the detection and quantification of nicotine, its major metabolites (cotinine, trans-3-hydroxycotinine, nicotine-N'-oxide and cotinine-N-oxide) and minor tobacco alkaloids (anabasine, anatabine and nornicotine) was developed, relying on ultra-high pressure liquid chromatography coupled to triple quadrupole mass spectrometry (UHPLC-TQ-MS/MS). A simple and fast dilute-and-shoot sample treatment was performed, followed by hydrophilic interaction chromatography-tandem mass spectrometry (HILIC-MS/MS) operated in positive electrospray ionization (ESI) mode with multiple reaction monitoring (MRM) data acquisition. After method validation, assessing the prevalence of nicotine consumption in sport involved analysis of 2185 urine samples, accounting for 43 different sports. Concentrations distribution of major nicotine metabolites, minor nicotine metabolites and tobacco alkaloids ranged from 10 (LLOQ) to 32,223, 6670 and 538 ng/mL, respectively. Compounds of interest were detected in trace levels in 23.0% of urine specimens, with concentration levels corresponding to an exposure within the last three days for 18.3% of samples. Likewise, hypothesizing conservative concentration limits for active nicotine consumption prior and/or during sport practice (50 ng/mL for nicotine, cotinine and trans-3-hydroxycotinine and 25 ng/mL for nicotine-N'-oxide, cotinine-N-oxide, anabasine, anatabine and nornicotine) revealed a prevalence of 15.3% amongst athletes. While this number may appear lower than the worldwide smoking prevalence of around 25%, focusing the study on selected sports highlighted more alarming findings. Indeed, active nicotine consumption in ice hockey, skiing, biathlon, bobsleigh, skating, football, basketball, volleyball, rugby, American football, wrestling and gymnastics was found to range between 19.0 and 55.6%. Therefore, considering the adverse effects of smoking on the respiratory tract and numerous health threats detrimental to sport practice at top level, likelihood of smokeless tobacco consumption for performance enhancement is greatly supported.

A hormonal regulatory module that provides flexibility to tropic responses.

Plants orient their growth depending on directional stimuli such as light and gravity, in a process known as tropic response. Tropisms result from asymmetrical accumulation of auxin across the responding organ relative to the direction of the stimulus, which causes differential growth rates on both sides of the organ. Here, we show that gibberellins (GAs) attenuate the gravitropic reorientation of stimulated hypocotyls of dark-grown Arabidopsis (Arabidopsis thaliana) seedlings. We show that the modulation occurs through induction of the expression of the negative regulator of auxin signaling INDOLE-3-ACETIC ACID INDUCIBLE19/MASSUGU2. The biological significance of this regulatory mechanism involving GAs and auxin seems to be the maintenance of a high degree of flexibility in tropic responses. This notion is further supported by observations that GA-deficient seedlings showed a much lower variance in the response to gravity compared to wild-type seedlings and that the attenuation of gravitropism by GAs resulted in an increased phototropic response. This suggests that the interplay between auxin and GAs may be particularly important for plant orientation under competing tropic stimuli.

Illicit drug profiling, reflection on statistical comparisons

This paper presents reflexions about statistical considerations on illicit drug profiling and more specifically about the calculation of threshold for determining of the seizure are linked or not. The specific case of heroin and cocaine profiling is presented with the necessary details on the target profiling variables (major alkaloids) selected and the analytical method used. Statistical approach to compare illicit drug seizures is also presented with the introduction of different scenarios dealing with different data pre-treatment or transformation of variables.The main aim consists to demonstrate the influence of data pre-treatment on the statistical outputs. A thorough study of the evolution of the true positive rate (TP) and the false positive rate (FP) in heroin and cocaine comparison is then proposed to investigate this specific topic and to demonstrate that there is no universal approach available and that the calculations have to be revaluate for each new specific application.

Central nervous system stimulants and sport practice.

BACKGROUND AND OBJECTIVES: Central nervous system (CNS) stimulants may be used to reduce tiredness and increase alertness, competitiveness, and aggression. They are more likely to be used in competition but may be used during training to increase the intensity of the training session. There are several potential dangers involving their misuse in contact sports. This paper reviews the three main CNS stimulants, ephedrine, amfetamine, and cocaine, in relation to misuse in sport. METHODS: Description of the pharmacology, actions, and side effects of amfetamine, cocaine, and ephedrine. RESULTS: CNS stimulants have psychotropic effects that may be perceived to be ergogenic. Some are prescription drugs, such as Ephedra alkaloids, and there are issues regarding their appropriate therapeutic use. Recently attention has been given to their widespread use by athletes, despite the lack of evidence regarding any ergogenic or real performance benefit, and their potentially serious side effects. Recreational drugs, some of which are illegal (cocaine, amfetamines), are commonly used by athletes and cause potential ergolytic effects. Overall, these drugs are important for their frequent use and mention in anti-doping laboratories statistics and the media, and their potentially serious adverse effects. CONCLUSIONS: Doping with CNS stimulants is a real public health problem and all sports authorities should participate in its prevention. Dissemination of information is essential to prevent doping in sport and to provide alternatives. Adequate training and education in this domain should be introduced.

Escherichia coli variants in periprosthetic joint infection: diagnostic challenges with sessile bacteria and sonication.

The diagnostic yield of prosthetic joint-associated infection is hampered by the phenotypic change of bacteria into a sessile and resistant form, also called biofilm. With sonication, adherent bacteria can be dislodged from the prosthesis. Species identification may be difficult because of their variations in phenotypic appearance and biochemical reaction. We have studied the phenotypic, genotypic, and biochemical properties of Escherichia coli variants isolated from a periprosthetic joint infection. The strains were collected from synovial fluid, periprosthetic tissue, and fluid from the explanted and sonicated prosthesis. Isolates from synovial fluid revealed a normal phenotype, whereas a few variants from periprosthetic tissue and all isolates from sonication fluid showed different morphological features (including small-colony variants). All isolates from sonication fluid were beta-galactosidase negative and nonmotile; most were indole negative. Because of further variations in biochemical properties, species identification was false or not possible in 50% of the isolates included in this study. In contrast to normal phenotypes, variants were resistant to aminoglycosides. Typing of the isolates using pulsed-field gel electrophoresis yielded nonidentical banding patterns, but all strains were assigned to the same clonal origin when compared with 207 unrelated E. coli isolates. The bacteria were repeatedly passaged on culture media and reanalyzed. Thereafter, most variants reverted to normal phenotype and regained their motility and certain biochemical properties. In addition, some variants displayed aminoglycoside susceptibility after reversion. Sonication of an explanted prosthesis allows insight into the lifestyle of bacteria in biofilms. Since sonication fluid also reveals dislodged sessile forms, species identification of such variants may be misleading.

A one-year monitoring of nicotine use in sport: frontier between potential performance enhancement and addiction issues

Tobacco consumption is a global epidemic responsible for a vast burden of disease. With pharmacological properties sought-after by consumers and responsible for addiction issues, nicotine is the main reason of this phenomenon. Accordingly, smokeless tobacco products are of growing popularity in sport owing to potential performance enhancing properties and absence of adverse effects on the respiratory system. Nevertheless, nicotine does not appear on the 2011 World Anti-Doping Agency (WADA) Prohibited List or Monitoring Program by lack of a comprehensive large-scale prevalence survey. Thus, this work describes a one-year monitoring study on urine specimens from professional athletes of different disciplines covering 2010 and 2011. A method for the detection and quantification of nicotine, its major metabolites (cotinine, trans-3-hydroxycotinine, nicotine-N′-oxide and cotinine-N-oxide) and minor tobacco alkaloids (anabasine, anatabine and nornicotine) was developed, relying on ultra-high pressure liquid chromatography coupled to triple quadrupole mass spectrometry (UHPLC-TQ-MS/MS). A simple and fast dilute-and-shoot sample treatment was performed, followed by hydrophilic interaction chromatography-tandem mass spectrometry (HILIC-MS/MS) operated in positive electrospray ionization (ESI) mode with multiple reaction monitoring (MRM) data acquisition. After method validation, assessing the prevalence of nicotine consumption in sport involved analysis of 2185 urine samples, accounting for 43 different sports. Concentrations distribution of major nicotine metabolites, minor nicotine metabolites and tobacco alkaloids ranged from 10 (LLOQ) to 32,223, 6670 and 538 ng/mL, respectively. Compounds of interest were detected in trace levels in 23.0% of urine specimens, with concentration levels corresponding to an exposure within the last three days for 18.3% of samples. Likewise, hypothesizing conservative concentration limits for active nicotine consumption prior and/or during sport practice (50 ng/mL for nicotine, cotinine and trans-3-hydroxycotinine and 25 ng/mL for nicotine-N′-oxide, cotinine-N-oxide, anabasine, anatabine and nornicotine) revealed a prevalence of 15.3% amongst athletes. While this number may appear lower than the worldwide smoking prevalence of around 25%, focusing the study on selected sports highlighted more alarming findings. Indeed, active nicotine consumption in ice hockey, skiing, biathlon, bobsleigh, skating, football, basketball, volleyball, rugby, American football, wrestling and gymnastics was found to range between 19.0 and 55.6%. Therefore, considering the adverse effects of smoking on the respiratory tract and numerous health threats detrimental to sport practice at top level, likelihood of smokeless tobacco consumption for performance enhancement is greatly supported.

A phase I clinical and pharmacological study evaluating vinflunine in combination with doxorubicin as first line treatment in metastatic breast cancer.

Vinfunine (VFL) is a novel bifluorinated tubulin-targeted agent of the vinca alkaloids class active in advanced stage breast cancer. We conducted a phase I study combining VFL with doxorubicin (DXR) to define the recommended dose (RD), safety, pharmacokinetic (PK) interaction and efficacy. Two schedules (day 1 every 3 weeks; days 1 and 8 every 3 weeks) were investigated as first line chemotherapy in metastatic breast cancer patients. Thirty-two patients received a total of 162 cycles of the VFL-DXR combination (median 6). The RDs were VFL 250 mg/m(2)/DXR 40 mg/m(2) every 3 weeks for schedule 1 and VFL 120 mg/m(2)/DXR 25 mg/m(2) days 1 and 8 every 3 weeks for schedule 2. The main dose-limiting toxicity was neutropenia. The most frequent non-hematological adverse events were nausea, fatigue, constipation, vomiting, anorexia, stomatitis and dyspnea. Objective response rate was reached in 47.1% of the patients. No PK interaction was observed. VFL-DXR combination is feasible with manageable toxicity. The antitumor activity was promising and supports further evaluation.

Long-distance wound signalling in arabidopsis

The leaves of all plants use elaborate and inducible defence systems to protect themselves. A wide variety of such defences are known and they include defence chemicals such as alkaloids, phenolics and terpenes, physical structures ranging from fibre cells to silica deposits, and a wide variety of defence proteins many of which target digestive processes in herbivores. It has long been known that the defence responses of plants under attack by insects are not restricted to the site of attack. Instead, if a leaf is damaged, defence can be triggered in other parts of the plant body, for example in distal leaves or even in roots and flowers. This raises the question of what are the organ-to-organ signals that coordinate this process. Several hypotheses have been proposed. These include the long-distance transfer of chemical signals through the plant vasculature, hydraulic signals that may transit through the xylem, and electrical signals that would move through living tissues such as the phloem. Much evidence for each of these scenarios has been published. In this thesis we took advantage of the fact that many plant defence responses are regulated by a signal transduction pathway based on a molecule called jasmonic acid. We used this molecule, one of its derivatives (jasmonoyl-isoleucine), and some of the genes it regulates as markers. Using these we investigated the possible role of the electrical signals in the leaf- to-leaf activation of the jasmonate pathway. We found that feeding insects stimulate easily detected electrical activity in the leaves of Arabidopsis thaliana and we used non-invasive surface electrodes to record this activity. This approach showed that jasmonate pathway activity and the electrical activity provoked by mechanical wounding occurred within identical spatial boundaries. Measurements of the apparent speed of surface potentials agreed well with previous velocity estimates for the speed of leaf-to-leaf signals that activate the jasmonate pathway. Using this knowledge we were able to investigate the effects of current injection into Arabidopsis leaves. This resulted in the strong expression of many jasmonate-regulated genes. All these results showed that electrical activity and the activation of jasmonate signalling were highly correlated. In order to test for possible causal links between the two processes, we conducted a small-scale reverse genetic screen on a series of T-DNA insertion mutants in ion channel genes and in other genes encoding proteins such as proton pumps. This screen, which was based on surface potential measurements, revealed that mutations in genes related to ionotropic glutamate receptors in animals had impaired electrical activity after wounding. Combining mutation of two of these glutamate-receptor-like genes in a double mutant reduced the response of leaves to current injection. When a leaf of this double mutant was wounded it failed to transmit a long-distance signal to a distal leaf. This result distinguished the double mutant from the wild-type plant and provides the first genetic evidence that electrical signalling is necessary to coordinate defence responses between organs in plants. - Les feuilles des plantes disposent de systèmes de défense inductibles très élaborés. Un grand nombre de ces systèmes de défenses sont connus et sont basés sur des composés chimiques comme les alcaloïdes, les composés phénoliques ou les terpènes, des systèmes physiques allant de la production de cellules fibreuses aux cristaux de silice ainsi qu'un grand nombre de protéines de défense ciblant le processus digestif des herbivores. Il est connu dépuis longtemps que la réponse défensive de la plante face à l'attaque pas un insecte n'est pas seulement localisée au niveau de la zone d'attaque. A la place, si une feuille est attaquée, les systèmes de défense peuvent être activés ailleurs dans la plante, comme par exemple dans d'autres feuilles, les racines ou même les fleurs. Ces observations soulèvent la question de la nature des signaux d'organes à organes qui régulent ces systèmes. Plusieurs hypothèses ont été formulées; une ou plusieures molécules pourraient être véhiculées dans la plante grâce au système vasculaire, un signal hydraulique transmis au travers du xylème ou encore des signaux électriques transmis par les cellules comme dans le phloème par exemple. De nombreuses études ont été publiées sur ces différentes hypothèses. Dans ce travail de thèse, nous avons choisi d'utiliser à notre avantage le fait que de nombreuses réponses de défense de la plante sont régulées par une même voie de signalisation utilisant l'acide jasmonique. Nous avons utilisé comme marqueurs cette molécule, un de ses dérivés (le jasmonoyl-isoleucine) ainsi que certains des gènes que l'acide jasmonique régule. Nous avons alors testé l'implication de la transmission de signaux électriques dans l'activation de la voie du jasmonate de feuille à feuille. Nous avons découvert que les insectes qui se nourrissent de feuilles d'Arabidopsis thaliana activent un signal électrique que nous avons pu mesurer grâce à une technique non invasive d'électrodes de surface. Les enregistrements ont montré que la génération de signaux électriques et l'activation de la voie du jasmonate avaient lieu aux mêmes endroits. La mesure de la vitesse de déplacement des impulsions électriques correspond aux estimations faites concernant l'activation de la voie du jasmonate. Grâce à cela, nous avons pu tester l'effet d'injection de courant électrique dans les feuilles d'Arabidopsis. La conséquence a été une forte expression de nombreux gènes de la voie du jasmonate, suggérant une forte corrélation entre l'activité électrique et l'activation de la voie du jasmonate. Afin de tester le lien de cause entre ces deux phénomènes, nous avons entrepris un criblage génétique sur une série de mutants d'insertion à l'ADN-T dans des gènes de canaux ioniques et d'autres gènes d'intérêt comme les gènes des pompes à protons. Ce criblage, basé sur la mesure de potentiels de surface, a permis de montrer que plusieurs mutations de gènes liés aux récepteurs au glutamate ionotropique présentent une baisse drastique de leurs activités électriques après une blessure mécanique des feuilles par rapport au type sauvage. Par la combinaison de deux mutations de ces récepteurs au glutamate en un double mutant, on obtient une réponse à la stimulation électrique encore plus faible. Quand une feuille du double mutant est blessée, elle est incapable de transmettre un signal à longue distance vers une feuille éloignée. Ce résultat permet de distinguer le double mutant de la plante sauvage et amène la première preuve génétique que l'activité électrique est nécessaire pour coordonner les réponses de défense entre les organes chez les plantes.

Genome reconstruction and comparative genomics of pneumocystis jirovecii

Pneumocystis jirovecii is a fungus belonging to a basal lineage of the Ascomycotina, the Taphrinomycotina subphylum. It is a parasite specific to humans that dwells primarily in the lung and can cause severe pneumonia in individuals with debilitated immune system. Despite its clinical importance, many aspects of its biology remain poorly understood, at least in part because of the lack of a continuous in vitro cultivation system. The present thesis consists in the genome reconstruction and comparative genomics of P. jirovecii. It is made of three parts: (i) the de novo sequencing of P. jirovecii genome starting from a single broncho- alveolar lavage fluid of a single patient (ii) the de novo sequencing of the genome of the plant pathogen Taphrina deformans, a fungus closely related to P. jirovecii, and (iii) the genome scale comparison of P. jirovecii to other Taphrinomycotina members. Enrichment in P. jirovecii cells by immuno-precipitation, whole DNA random amplification, two complementary high throughput DNA sequencing methods, and in silico sorting and assembly of sequences were used for the de novo reconstruction of P. jirovecii genome from the microbiota of a single clinical specimen. An iterative ad hoc pipeline as well as numerical simulations was used to recover P. jirovecii sequences while purging out contaminants and assembly or amplification chimeras. This strategy produced a 8.1 Mb assembly, which encodes 3,898 genes. Homology searches, mapping on biochemical pathways atlases, and manual validations revealed that this genome lacks (i) most of the enzymes dedicated to the amino acids biosyntheses, and (ii) most virulence factors observed in other fungi, e.g. the glyoxylate shunt pathway and specific peptidases involved in the degradation of the host cell membrane. The same analyses applied to the available genomic sequences from Pneumocystis carinii the species infecting rats and Pneumocystis murina the species infecting mice revealed the same deficiencies. The genome sequencing of T. deformans yielded a 13 Mb assembly, which encodes 5,735 genes. T. deformans possesses enzymes involved plant cell wall degradation, secondary metabolism, the glyoxylate cycle, detoxification, sterol biosynthesis, as well as the biosyntheses of plant hormones such as abscisic acid or indole-3-acetic acid. T. deformans also harbors gene subsets that have counterparts in plant saprophytes or pathogens, which is consistent with its alternate saprophytic and pathogenic lifestyles. Mating genes were also identified. The homothallism of this fungus suggests a mating-type switching mechanism. Comparative analyses indicated that 81% of P. jirovecii genes are shared with eight other Taphrinomycotina members, including T. deformans, P. carinii and P. murina. These genes are mostly involved in housekeeping activities. The genes specific to the Pneumocystis genus represent 8%, and are involved in RNA metabolism and signaling. The signaling is known to be crucial for interaction of Pneumocystis spp with their environment. Eleven percent are unique to P. jirovecii and encode mostly proteins of unknown function. These genes in conjunction with other ones (e.g. the major surface glycoproteins) might govern the interaction of P. jirovecii with its human host cells, and potentially be responsible of the host specificity. P. jirovecii exhibits a reduced genome in size with a low GC content, and most probably scavenges vital compounds such as amino acids and cholesterol from human lungs. Consistently, its genome encodes a large set of transporters (ca. 22% of its genes), which may play a pivotal role in the acquisition of these compounds. All these features are generally observed in obligate parasite of various kingdoms (bacteria, protozoa, fungi). Moreover, epidemiological studies failed to evidence a free-living form of the fungus and Pneumocystis spp were shown to co-evolved with their hosts. Given also the lack of virulence factors, our observations strongly suggest that P. jirovecii is an obligate parasite specialized in the colonization of human lungs, and which causes disease only in individuals with compromised immune system. The same conclusion is most likely true for all other Pneumocystis spp in their respective mammalian host. - Pneumocystis jirovecii est un champignon appartenant à ine branche basale des Ascomycotina, le sous-embranchement des Taphrinomycotina. C'est un parasite spécifique aux humains qui réside principalement dans les poumons, et qui peut causer des pneumonies sévères chez des individus ayant un système immunitaire déficient. En dépit de son importance clinique, de nombreux aspects de sa biologie demeurent,largement méconnus, au moins en partie à cause de l'absence d'un système de culture in vitro continu. Cette thèse traite de la reconstruction du génome et de la génomique comparative de P. jirovecii. Elle comporte trois parties: (i) le séquençage de novo du génome de P. jirovecii à partir d'un lavage broncho-alvéolaire provenant d'un seul patient, (ii) le séquençage de novo du génome d'un champignon pathogène de plante Taphrina deformans qui est phylogénétiquement proche de P. jirovecii, et (iii) la comparaison du génome de P. jirovecii à celui d'autres membres du sous-embranchement des Taphrinomycotina. Un enrichissement en cellules de P. jirovecii par immuno-précipitation, une amplification aléatoire des molécules d'ADN, deux méthodes complémentaires de séquençage à haut débit, un tri in silico et un assemblage des séquences ont été utilisés pour reconstruire de novo le génome de P. jirovecii à partir du microbiote d'un seul échantillon clinique. Un pipeline spécifique ainsi que des simulations numériques ont été utilisés pour récupérer les séquences de P. jirovecii tout en éliminant les séquences contaminants et les chimères d'amplification ou d'assemblage. Cette stratégie a produit un assemblage de 8.1 Mb, qui contient 3898 gènes. Les recherches d'homologies, de cartographie des voies métaboliques et des validations manuelles ont révélé que ce génome est dépourvu (i) de la plupart des enzymes dédiées à la biosynthèse des acides aminés, et (ii) de la plupart des facteurs de virulence observés chez d'autres champignons, par exemple, le cycle du glyoxylate ainsi que des peptidases spécifiques impliquées dans la dégradation de la membrane de la cellule hôte. Les analyses appliquées aux données génomiques disponibles de Pneumocystis carinii, l'espèce infectant les rats, et de Pneumocystis murina, l'espèce infectant les souris, ont révélé les mêmes déficiences. Le séquençage du génome de T. deformans a généré un assemblage de 13.3 Mb qui contient 5735 gènes. T. deformans possède les gènes codant pour les enzymes impliquées dans la dégradation des parois cellulaires des plantes, le métabolisme secondaire, le cycle du glyoxylate, la détoxification, la biosynthèse des stérols ainsi que la biosynthèse d'hormones de plantes telles que l'acide abscissique ou l'acide indole 3-acétique. T. deformans possède également des sous-ensembles de gènes présents exclusivement chez des saprophytes ou des pathogènes de plantes, ce qui est consistent avec son mode de vie alternatif saprophyte et pathogène. Des gènes impliqués dans la conjugaison ont été identifiés. L'homothallisme de ce champignon suggère mécanisme de permutation du type conjuguant. Les analyses comparatives ont démontré que 81% des gènes de P. jirovecii sont présent chez les autres membres du sous-embranchement des Taphrinomycotina. Ces gènes sont essentiellement impliqués dans le métabolisme basai. Les gènes spécifiques au genre Pneumocystis représentent 8%, et sont impliqués dans le métabolisme de l'ARN et la signalisation. La signalisation est connue pour être cruciale pour l'interaction des espèces de Pneumocystis avec leur environnement. Les gènes propres à P. jirovecii représentent 11% et codent en majorité pour des protéines dont la fonction est inconnue. Ces gènes en conjonction avec d'autres (par exemple, les glycoprotéines de surface), pourraient être déterminants dans l'interaction de P. jirovecii avec les cellules de l'hôte humain, et être potentiellement responsable de la spécificité d'hôte. P. jirovecii possède un génome de taille réduite à faible pourcentage en GC et récupère très probablement des composés vitaux comme les acides aminés et le cholestérol à partir des poumons humains. De manière consistante, son génome code pour de nombreux transporteurs (22% de ses gènes), qui pourraient jouer un rôle essentiel dans l'acquisition de ces composés. Ces caractéristiques sont généralement observées chez les parasites obligatoires de plusieurs règnes (bactéries, protozoaires, champignons). De plus, les études épidémiologiques n'ont pas réussi à prouver l'existence d'ime forme vivant librement du champignon. Etant donné également l'absence de facteurs de virulence, nos observations suggèrent que P. jirovecii est un parasite obligatoire spécialisé dans la colonisation des poumons humains, ne causant une maladie que chez des individus ayant un système immunitaire compromis. La même conclusion est très probablement applicable à toutes les autres espèces de Pneumocystis dans leur hôte mammifère respectif.

Study of the regulation of antifungal activity in plant-associated pseudomas fluorescens

RésuméEn agriculture d'énormes pertes sont causées par des champignons telluriques pathogènes tels que Thielaviopsis, Fusarium, Gaeumannomyces et Rhizoctonia ou encore l'oomycète Pythium. Certaines bactéries dites bénéfiques, comme Pseudomonas fluorescens, ont la capacité de protéger les plantes de ces pathogènes par la colonisation de leur racines, par la production de métabolites secondaires possédants des propriétés antifongiques et par l'induction des mécanismes de défenses de la plante colonisée. P. fluorescens CHAO, une bactérie biocontrôle isolée d'un champ de tabac à Payerne, a la faculté de produire un large spectre de métabolites antifongiques, en particulier le 2,4- diacétylphloroglucinol (DAPG), la pyolutéorine (PLT), le cyanure d'hydrogène (HCN), la pyrrolnitrine (PRN) ainsi que des chélateurs de fer.La plante, par sécrétion racinaire, produit des rhizodéposites, source de carbone et d'azote, qui profitent aux populations bactériennes vivant dans la rhizosphere. De plus, certains stresses biotiques et abiotiques modifient cette sécrétion racinaire, en terme quantitatif et qualitatif. De leur côté, les bactéries bénéfiques, améliorent, de façon direct et/ou indirect, la croissance de la plante hôte. De nombreux facteurs biotiques et abiotiques sont connus pour réguler la production de métabolites secondaires chez les bactéries. Des études récentes ont démontré l'importance de la communication entre la plante et les bactéries bénéfiques afin que s'établisse une interaction profitant à chacun des deux partis. Il est ainsi vraisemblable que les populations bactériennes associées aux racines soient capables d'intégrer ces signaux et d'adapter spécifiquement leur comportement en conséquence.La première partie de ce travail de thèse a été la mise au point d'outils basés sur la cytométrie permettant de mesurer l'activité antifongique de cellules bactériennes individuelles dans un environnent naturel, les racines des plantes. Nous avons démontré, grâce à un double marquage aux protéines autofluorescentes GFP et mCherry, que les niveaux d'expression des gènes impliqués dans la biosynthèse des substances antifongiques DAPG, PLT, PRN et HCN ne sont pas les mêmes dans des milieux de cultures liquides que sur les racines de céréales. Par exemple, l'expression de pltA (impliqué dans la biosynthèse du PLT) est quasiment abolie sur les racines de blé mais atteint un niveau relativement haut in vitro. De plus cette étude a mis en avant l'influence du génotype céréalien sur l'expression du gène phlA qui est impliqué dans la biosynthèse du DAPG.Une seconde étude a révélé la communication existant entre une céréale (orge) infectée par le pathogène tellurique Pythium ultimum et P. fluorescens CHAO. Un système de partage des racines nous a permis de séparer physiquement le pathogène et la bactérie bénéfique sur la plante. Cette méthode a donné la possibilité d'évaluer l'effet systémique, causé par l'attaque du pathogène, de la plante sur la bactérie biocontrôle. En effet, l'infection par le phytopathogène modifie la concentration de certains composés phénoliques dans les exsudats racinaires stimulant ainsi l'expression de phi A chez P.fluorescens CHAO.Une troisième partie de ce travail focalise sur l'effet des amibes qui sont des micro-prédateurs présents dans la rhizosphere. Leur présence diminue l'expression des gènes impliqués dans la biosynthèse du DAPG, PLT, PRN et HCN chez P.fluorescens CHAO, ceci en culture liquide et sur des racines d'orge. De plus, des molécules provenant du surnageant d'amibes, influencent l'expression des gènes requis pour la biosynthèse de ces antifongiques. Ces résultats illustrent que les amibes et les bactéries de la rhizosphere ont développé des stratégies pour se reconnaître et adapter leur comportement.La dernière section de ce travail est consacrée à l'acide indole-acétique (LA.A), une phytohormone connue pour son effet stimulateur sur phlA. Une étude moléculaire détaillée nous a démontré que cet effet de l'IAA est notamment modulé par une pompe à efflux (FusPl) et de son régulateur transcriptionnel (MarRl). De plus, les gènes fusPl et marRl sont régulés par d'autres composés phénoliques tels que le salicylate (un signal végétal) et l'acide fusarique (une phytotoxine du pathogène Fusarium).En résumé, ce travail de thèse illustre la complexité des interactions entre les eucaryotes et procaryotes de la rhizosphère. La reconnaissance mutuelle et l'instauration d'un dialogue moléculaire entre une plante hôte et ses bactéries bénéfiques associées? sont indispensables à la survie des deux protagonistes et semblent être hautement spécifiques.SummaryIn agriculture important crop losses result from the attack of soil-borne phytopathogenic fungi, including Thielaviopsis, Fusarium, Gaeumannomyces and Rhizoctonia, as well as from the oomycete Pythium. Certain beneficial microorganisms of the rhizosphere, in particular Pseudomonas fluorescens, have the ability to protect plants against phytopathogens by the intense colonisation of roots, by the production of antifungal exoproducts, and by induction of plant host defences. P. fluorescens strain CHAO, isolated from a tobacco field near Payerne, produces a large array of antifungal exoproducts, including 2,4-diacetylphloroglucinol (DAPG), pyoluteorin (PLT), hydrogen cyanide (HCN), pyrrolnitrin (PRN) and iron chelators. Plants produce rhizodeposites via root secretion and these represent a relevant source of carbon and nitrogen for rhizosphere microorganisms. Various biotic and abiotic stresses influence the quantity and the quality of released exudates. One the other hand, beneficial bacteria directly or indirectly promote plant growth. Biotic and abiotic factors regulate exoproduct production in biocontrol microorganisms. Recent studies have highlighted the importance of communication in establishing a fine-tuned mutualist interaction between plants and their associated beneficial bacteria. Bacteria may be able to integrate rhizosphere signals and adapt subsequently their behaviour.In a first part of the thesis, we developed a new method to monitor directly antifungal activity of individual bacterial cells in a natural environment, i.e. on roots of crop plants. We were able to demonstrate, via a dual-labelling system involving green and red fluorescent proteins (GFP, mCherry) and FACS-based flow cytometry, that expression levels of biosynthetic genes for the antifungal compounds DAPG, PLT, PRN, and HCN are highly different in liquid culture and on roots of cereals. For instance, expression of pltA (involved in PLT biosynthesis) was nearly abolished on wheat roots whereas it attained a relatively high level under in vitro conditions. In addition, we established the importance of the cereal genotype in the expression of phi A (involved in DAPG biosynthesis) in P. fluorescens CHAO.A second part of this work highlighted the systemic communication that exists between biocontrol pseudomonads and plants following attack by a root pathogen. A split-root system, allowing physical separation between the soil-borne oomycete pathogen Phytium ultimum and P. fluorescens CHAO on barley roots, was set up. Root infection by the pathogen triggered a modification of the concentration of certain phenolic root exudates in the healthy root part, resulting in an induction ofphlA expression in P. fluorescens CHAO.Amoebas are micro-predators of the rhizosphere that feed notably on bacteria. In the third part of the thesis, co-habitation of Acanthamoeba castellanii with P. fluorescens CHAO in culture media and on barley roots was found to significantly reduce bacterial expression of genes involved in the biosynthesis of DAPG, PLT, HCN and PRN. Interestingly, molecular cues present in supernatant of A. castelanii induced the expression of these antifungal genes. These findings illustrate the strategies of mutual recognition developed by amoeba and rhizosphere bacteria triggering responses that allow specific adaptations of their behaviour.The last section of the work focuses on indole-3-acetic acid (IAA), a phytohormone that stimulates the expression of phi A. A detailed molecular study revealed that the IAA-mediated effect on phi A is notably modulated by an efflux pump (FusPl) and its transcriptional regulator (MarRl). Remarkably, transcription of fusPl and marRl was strongly upregulated in presence of other phenolic compounds such as salicylate (a plant signal) and fusaric acid (a phytotoxin of the pathogenic fungus Fusarium).To sum up, this work illustrates the great complexity of interactions between eukaryotes and prokaryotes taking place in the rhizosphere niche. The mutual recognition and the establishment of a molecular cross-talk between the host plant and its associated beneficial bacteria are essential for the survival of the two partners and these interactions appear to be highly specific.

PPARbeta/delta regulates paneth cell differentiation via controlling the hedgehog signaling pathway.

BACKGROUND & AIMS: All 4 differentiated epithelial cell types found in the intestinal epithelium derive from the intestinal epithelial stem cells present in the crypt unit, in a process whose molecular clues are intensely scrutinized. Peroxisome proliferator-activated receptor beta (PPARbeta) is a nuclear hormone receptor activated by fatty acids and is highly expressed in the digestive tract. However, its function in intestinal epithelium homeostasis is understood poorly. METHODS: To assess the role of PPARbeta in the small intestinal epithelium, we combined various cellular and molecular approaches in wild-type and PPARbeta-mutant mice. RESULTS: We show that the expression of PPARbeta is particularly remarkable at the bottom of the crypt of the small intestine where Paneth cells reside. These cells, which have an important role in the innate immunity, are strikingly affected in PPARbeta-null mice. We then show that Indian hedgehog (Ihh) is a signal sent by mature Paneth cells to their precursors, negatively regulating their differentiation. Importantly, PPARbeta acts on Paneth cell homeostasis by down-regulating the expression of Ihh, an effect that can be mimicked by cyclopamine, a known inhibitor of the hedgehog signaling pathway. CONCLUSIONS: We unraveled the Ihh-dependent regulatory loop that controls mature Paneth cell homeostasis and its modulation by PPARbeta. PPARbeta currently is being assessed as a drug target for metabolic diseases; these results reveal some important clues with respect to the signals controlling epithelial cell fate in the small intestine.

A fluorescent peptide substrate for the surface metalloprotease of Leishmania.

A fluorescent oligopeptide substrate for the promastigote surface protease (PSP) of Leishmania was designed using the data reported for the substrate specificity of the enzyme (Bouvier, J., Schneider, P., Etges, R. J., and Bordier, C. 1990. Biochemistry 29, 10113-10119). The indole fluorescence of the tryptophan residue was efficiently quenched through resonance energy transfer by an N-terminal dansyl group located five amino acid residues away. The heptapeptide, dansyl-A-Y-L-K-K-W-V-NH2, was cleaved by PSP between the tyrosine and leucine residues with a kcat/Km ratio of 8.8 x 10(6) M-1sec-1. Hydrolysis by the enzyme results in a time-dependent increase of fluorescence intensity of 3.7-fold. Assays can be designed based on the tryptophan fluorescence at 360 nm or by individual product analyses using thin-layer chromatography. The synthetic substrate is readily cleaved by the metalloprotease at the surface of fixed promastigotes. The specificity and sensitivity of such internally quenched fluorescent peptide substrate will facilitate the identification of novel inhibitors for the enzyme and aid in detailed studies on its enzymology.