Biology and pathogenicity of "Chlamydia"- related organisms

Abstract : This thesis investigates the pathogenicity and biology of Parachlamydia acanthamoebae and other obligate intracellular bacteria related to chlamydiae. All these Chlamydia-like organisms replicate in amoebae. Some evolved to resist to macrophages and represent possible new agents of respiratory tract infection. Using serological and molecular approaches, we showed that Parachlamydia acanthameobae likely plays a role as an etiological agent of pneumonia [1,2]. We also showed that Parachlamydia was able to enter and survive within pneumocytes and lung fibroblasts [3]. Moreover, we developed an animal model of lung infection in mice, which fulfilled the third and fourth Koch postulate [4]. Given the likely role of Parachlamydia in pneumonia, we studied its antibiotic susceptibility. We showed that Chlamydia-related organisms were resistant to quinolones, mainly due to mutations in the QRDR of gyrA [5]. To have tools to investigate the role of other Chlamydia-related bacteria in pneumonia, we developed immunofluorescence assays and assessed the rate of serological cross-reactivity between all these Chlamydia-related bacteria [6]. We also developed new diagnostic specific PCRs [2,7] and sequenced additional genes that are useful for both taxonomic and diagnostic purposes [8]. Then, we applied these serological and molecular approaches to patients with and without respiratory tract infections. This led to the identification of a possible role of Protochlamydia naegleriophila [7] and of Waddlia chondrophila in pneumonia [1]. A significant part of the thesis also investigated interactions of Parachlamydia with macrophages [9] and the host range of Chlamydia-related bacteria [10]. In conclusion, there are growing body of evidence supporting the role of Chlamydia-like organisms as agents of pneumonia. Further studies are needed to precise their pathogenic role in this setting. The diagnostic tools developed during this thesis will be useful to investigate the role of these strict intracellular bacteria in other diseases in both humans and animals [11,12]. Résumé : Le but de cette thèse est de déterminer le rôle pathogène de Parachlamydia et des bactéries apparentées aux Chlamydia ainsi que d'étudier leur biologie. Parachlamydia acanthamoebae est une bactérie intracellulaire apparentée aux Chlamydia, et qui est résistante non seulement aux amibes mais aussi aux macrophages. Par une approche sérologique et moléculaire, nous avons montré que les bactéries apparentées aux Chlamydia jouent probablement un rôle comme agent de pneumonie [1,2]. De plus, nous avons démontré que P. acanthameobae est capable d'entrer et de survivre dans les pneumocytes et fibroblastes pulmonaires [3]. Nous avons ensuite développé un modèle animal remplissant les troisième et quatrième postulats de Koch [4]. Nous avons aussi démontré que les bactéries apparentées aux Chlamydia sont résistantes aux quinolones, en raison de mutations dans la région QRDR de gyrA [5]. Afin de mieux déterminer le rôle pathogène de ces bactéries, nous avons mis au point des techniques d' immunofluorescence et déterminé la cross-réaction sérologique entre les différentes bactéries apparentées aux Chlamydia [6]. Différentes PCR diagnostiques ont aussi été développées [2,7] et des gènes supplémentaires ont été séquencés, qui seront utiles à la taxonomie ainsi qu'au développement de nouvelles méthodes diagnostiques [8]. Ces méthodes ont été appliquées à des échantillons provenant de patient avec ou sans pneumonie et ont permis l'identification du possible rôle pathogène de Protochlamydia naegleriophila [7] et de Waddlia chondrophila [1]. L'interaction de Parachlamydia avec les macrophages [9] et la permissivité de différentes cellules aux bactéries apparentées aux Chlamydia [10] ont également été étudiés dans le cadre de cette thèse. En conclusion, plusieurs nouveaux éléments viennent renforcer l'hypothèse que les bactéries apparentées aux Chlamydia sont des agents de pneumonies. Cependant, d'autres études doivent être menées pour confirmer leur rôle dans cette maladie. Les méthodes diagnostiques développées ici seront très utiles pour déterminer le rôle pathogène de ces bactéries chez les humains et animaux [11,12]

Lymphatic vascular morphogenesis in development, physiology, and disease.

The lymphatic vasculature constitutes a highly specialized part of the vascular system that is essential for the maintenance of interstitial fluid balance, uptake of dietary fat, and immune response. Recently, there has been an increased awareness of the importance of lymphatic vessels in many common pathological conditions, such as tumor cell dissemination and chronic inflammation. Studies of embryonic development and genetically engineered animal models coupled with the discovery of mutations underlying human lymphedema syndromes have contributed to our understanding of mechanisms regulating normal and pathological lymphatic morphogenesis. It is now crucial to use this knowledge for the development of novel therapies for human diseases.

The amphioxus genome illuminates vertebrate origins and cephalochordate biology.

Cephalochordates, urochordates, and vertebrates evolved from a common ancestor over 520 million years ago. To improve our understanding of chordate evolution and the origin of vertebrates, we intensively searched for particular genes, gene families, and conserved noncoding elements in the sequenced genome of the cephalochordate Branchiostoma floridae, commonly called amphioxus or lancelets. Special attention was given to homeobox genes, opsin genes, genes involved in neural crest development, nuclear receptor genes, genes encoding components of the endocrine and immune systems, and conserved cis-regulatory enhancers. The amphioxus genome contains a basic set of chordate genes involved in development and cell signaling, including a fifteenth Hox gene. This set includes many genes that were co-opted in vertebrates for new roles in neural crest development and adaptive immunity. However, where amphioxus has a single gene, vertebrates often have two, three, or four paralogs derived from two whole-genome duplication events. In addition, several transcriptional enhancers are conserved between amphioxus and vertebrates--a very wide phylogenetic distance. In contrast, urochordate genomes have lost many genes, including a diversity of homeobox families and genes involved in steroid hormone function. The amphioxus genome also exhibits derived features, including duplications of opsins and genes proposed to function in innate immunity and endocrine systems. Our results indicate that the amphioxus genome is elemental to an understanding of the biology and evolution of nonchordate deuterostomes, invertebrate chordates, and vertebrates.

Neuroscience robotics to investigate multisensory integration and bodily awareness.

Humans experience the self as localized within their body. This aspect of bodily self-consciousness can be experimentally manipulated by exposing individuals to conflicting multisensory input, or can be abnormal following focal brain injury. Recent technological developments helped to unravel some of the mechanisms underlying multisensory integration and self-location, but the neural underpinnings are still under investigation, and the manual application of stimuli resulted in large variability difficult to control. This paper presents the development and evaluation of an MR-compatible stroking device capable of presenting moving tactile stimuli to both legs and the back of participants lying on a scanner bed while acquiring functional neuroimaging data. The platform consists of four independent stroking devices with a travel of 16-20 cm and a maximum stroking velocity of 15 cm/s, actuated over non-magnetic ultrasonic motors. Complemented with virtual reality, this setup provides a unique research platform allowing to investigate multisensory integration and its effects on self-location under well-controlled experimental conditions. The MR-compatibility of the system was evaluated in both a 3 and a 7 Tesla scanner and showed negligible interference with brain imaging. In a preliminary study using a prototype device with only one tactile stimulator, fMRI data acquired on 12 healthy participants showed visuo-tactile synchrony-related and body-specific modulations of the brain activity in bilateral temporoparietal cortex.

Biologie oxydative et implications cliniques du peroxynitrite [Oxidative biology and clinical implications of peroxynitrite]

Peroxynitrite is a strong biological oxidant formed from the reaction between two free radicals, superoxide and nitric oxide. It inflicts serious damages to most biomolecules, including proteins, lipids and nucleic acids, either through direct oxidation or through the secondary generation of highly reactive free radicals. When such damage reaches a critical threshold, cells eventually die by necrosis or apoptosis. An excessive production of peroxynitrite is instrumental in the development of organ damage and dysfunction in conditions such as circulatory shock and ischemia-reperfusion. In such circumstances, various synthetic metalloporphyrins, able to degrade peroxynitrite, disclose important beneficial effects in animal models, and might therefore represent novel pharmacological agents in the future.

Hypocretin (orexin) biology and the pathophysiology of narcolepsy with cataplexy.

The discovery of hypocretins (orexins) and their causal implication in narcolepsy is the most important advance in sleep research and sleep medicine since the discovery of rapid eye movement sleep. Narcolepsy with cataplexy is caused by hypocretin deficiency owing to destruction of most of the hypocretin-producing neurons in the hypothalamus. Ablation of hypocretin or hypocretin receptors also leads to narcolepsy phenotypes in animal models. Although the exact mechanism of hypocretin deficiency is unknown, evidence from the past 20 years strongly favours an immune-mediated or autoimmune attack, targeting specifically hypocretin neurons in genetically predisposed individuals. These neurons form an extensive network of projections throughout the brain and show activity linked to motivational behaviours. The hypothesis that a targeted immune-mediated or autoimmune attack causes the specific degeneration of hypocretin neurons arose mainly through the discovery of genetic associations, first with the HLA-DQB1*06:02 allele and then with the T-cell receptor α locus. Guided by these genetic findings and now awaiting experimental testing are models of the possible immune mechanisms by which a specific and localised brain cell population could become targeted by T-cell subsets. Great hopes for the identification of new targets for therapeutic intervention in narcolepsy also reside in the development of patient-derived induced pluripotent stem cell systems.

La biologie moléculaire est-elle utile au praticien [Is molecular biology useful to the practitioner?]

The relative importance of molecular biology in clinical practice is often underestimated. However, numerous procedures in clinical diagnosis and new therapeutic drugs have resulted from basic molecular research. Furthermore, understanding of the physiological and physiopathological mechanisms underlying several human diseases has been improved by the results of basic molecular research. For example, cloning of the gene encoding leptin has provided spectacular insights into the understanding of the mechanisms involved in the control of food intake and body weight maintenance in man. In cystic fibrosis, the cloning and identification of several mutations in the gene encoding the chloride channel transmembrane regulator (CFTR) have resolved several important issues in clinical practice: cystic fibrosis constitutes a molecular defect of a single gene. There is a strong correlation between the clinical manifestations or the severity of the disease (phenotype) with the type of mutations present in the CFTR gene (genotype). More recently, identification of mutations in the gene encoding a subunit of the renal sodium channel in the Liddle syndrome has provided important insight into the physiopathological understanding of mechanisms involved in this form of hereditary hypertension. Salt retention and secondary high blood pressure are the result of constitutive activation of the renal sodium channel by mutations in the gene encoding the renal sodium channel. It is speculated that less severe mutations in this channel could result in a less severe form of hypertension which may correspond to patients suffering from high blood pressure with low plasma renin activity. Several tools, most notably PCR, are derived from molecular research and are used in everyday practice, i.e. in prenatal diagnosis and in the diagnosis of several infectious diseases including tuberculosis and hepatitis. Finally, the production of recombinant proteins at lower cost and with fewer side effects is used in everyday clinical practice. Gene therapy remains an extraordinary challenge in correcting severe hereditary or acquired diseases. The use of genetically modified animal cell lines producing growth factors, insulin or erythropoetin, which are subsequently encapsulated and transferred to man, represents an attractive approach for gene therapy.

ENFIN--A European network for integrative systems biology.

Integration of biological data of various types and the development of adapted bioinformatics tools represent critical objectives to enable research at the systems level. The European Network of Excellence ENFIN is engaged in developing an adapted infrastructure to connect databases, and platforms to enable both the generation of new bioinformatics tools and the experimental validation of computational predictions. With the aim of bridging the gap existing between standard wet laboratories and bioinformatics, the ENFIN Network runs integrative research projects to bring the latest computational techniques to bear directly on questions dedicated to systems biology in the wet laboratory environment. The Network maintains internally close collaboration between experimental and computational research, enabling a permanent cycling of experimental validation and improvement of computational prediction methods. The computational work includes the development of a database infrastructure (EnCORE), bioinformatics analysis methods and a novel platform for protein function analysis FuncNet.

Concentrative nucleoside transporter 1 (hCNT1) promotes phenotypic changes relevant to tumor biology in a translocation independent manner

Nucleoside transporters (NTs) mediate the uptake of nucleosides and nucleobases across the plasma membrane, mostly for salvage purposes. The canonical NTs belong to two gene families, SLC29 and SLC28. The former encode equilibrative nucleoside transporter proteins (ENTs), which mediate the facilitative diffusion of natural nucleosides with broad selectivity, whereas the latter encode concentrative nucleoside transporters (CNTs), which are sodium-coupled and show high affinity for substrates with variable selectivity. These proteins are expressed in most cell types, exhibiting apparent functional redundancy. This might indicate that CNTs play specific roles in the physiology of the cell beyond nucleoside salvage. Here, we addressed this possibility using adenoviral vectors to restore tumor cell expression of hCNT1 or a polymorphic variant (hCNT1S546P) lacking nucleoside translocation ability. We found that hCNT1 restoration in pancreatic cancer cells significantly altered cell-cycle progression and phosphorylation status of key signal-transducing kinases, promoted poly-(ADP ribose) polymerase hyperactivation and cell death, and reduced tumor growth and cell migration. Importantly, the translocation-defective transporter triggered these same effects on cell physiology. These data predict a novel and totally unexpected biological role for the nucleoside transporter protein hCNT1 that appears to be independent of its role as mediator of nucleoside uptake by cells, thereby suggesting a transceptor function. Cell Death & Disease Anastasis Stephanou Receiving Editor Cell Death & Disease 19th Apr 2013 Dr Perez-Torras Av/ Diagonal 643. Edif. Prevosti, Pl -1 Barcelona 08028 Spain RE: Manuscript CDDIS-13-0136R, 'CDDIS-13-0136R' Dear Dr Perez-Torras, It is a pleasure to inform you that your manuscript has been evaluated at the editorial level and has now been officially accepted for publication in Cell Death & Disease, pending you meet the following editorial requirements: 1) the list of the abbreviations is missing please include Could you send us the revised text as word file via e-mail and we will proceed and transfer the paper onto our typesetters. Please download, print, sign, and return the Licence to Publish Form using the link below. This must be returned via FAX to ++ 39 06 7259 6977 before your manuscript can be published:

Animal modelling for inherited central vision loss.

Disease-causing variants of a large number of genes trigger inherited retinal degeneration leading to photoreceptor loss. Because cones are essential for daylight and central vision such as reading, mobility, and face recognition, this review focuses on a variety of animal models for cone diseases. The pertinence of using these models to reveal genotype/phenotype correlations and to evaluate new therapeutic strategies is discussed. Interestingly, several large animal models recapitulate human diseases and can serve as a strong base from which to study the biology of disease and to assess the scale-up of new therapies. Examples of innovative approaches will be presented such as lentiviral-based transgenesis in pigs and adeno-associated virus (AAV)-gene transfer into the monkey eye to investigate the neural circuitry plasticity of the visual system. The models reported herein permit the exploration of common mechanisms that exist between different species and the identification and highlighting of pathways that may be specific to primates, including humans.

Molecular biology of the kallikrein-kinin system: from structure to function

The participation of the kallikrein-kinin system, comprising the serine proteases kallikreins, the protein substrates kininogens and the effective peptides kinins, in some pathological processes like hypertension and cardiovascular diseases is still a matter of controversy. The use of different experimental set-ups in concert with the development of potent and specific inhibitors and antagonists for the system has highlighted its importance but the results still lack conclusivity. Over the last few years, transgenic and gene-targeting technologies associated with molecular biology tools have provided specific information about the elusive role of the kallikrein-kinin system in the control of blood pressure and electrolyte homeostasis. cDNA and genomic sequences for kinin receptors B2 and B1 from different species were isolated and shown to encode G-protein-coupled receptors and the structure and pharmacology of the receptors were characterized. Transgenic animals expressing an overactive kallikrein-kinin system were established to study the cardiovascular effects of these alterations and the results of these investigations further corroborate the importance of this system in the maintenance of normal blood pressure. Knockout animals for B2 and B1 receptors are available and their analysis also points to the role of these receptors in cardiovascular regulation and inflammatory processes. In this paper the most recent and relevant genetic animal models developed for the study of the kallikrein-kinin system are reviewed, and the advances they brought to the understanding of the biological role of this system are discussed.

Quantitative functional neuroimaging of cerebral physiology in healthy aging

Les études d’imagerie par résonance magnétique fonctionnelle (IRMf) ont pour prémisse générale l’idée que le signal BOLD peut être utilisé comme un succédané direct de l’activation neurale. Les études portant sur le vieillissement cognitif souvent comparent directement l’amplitude et l’étendue du signal BOLD entre des groupes de personnes jeunes et âgés. Ces études comportent donc un a priori additionnel selon lequel la relation entre l’activité neurale et la réponse hémodynamique à laquelle cette activité donne lieu restent inchangée par le vieillissement. Cependant, le signal BOLD provient d’une combinaison ambiguë de changements de métabolisme oxydatif, de flux et de volume sanguin. De plus, certaines études ont démontré que plusieurs des facteurs influençant les propriétés du signal BOLD subissent des changements lors du vieillissement. L’acquisition d’information physiologiquement spécifique comme le flux sanguin cérébral et le métabolisme oxydatif permettrait de mieux comprendre les changements qui sous-tendent le contraste BOLD, ainsi que les altérations physiologiques et cognitives propres au vieillissement. Le travail présenté ici démontre l’application de nouvelles techniques permettant de mesurer le métabolisme oxydatif au repos, ainsi que pendant l’exécution d’une tâche. Ces techniques représentent des extensions de méthodes d’IRMf calibrée existantes. La première méthode présentée est une généralisation des modèles existants pour l’estimation du métabolisme oxydatif évoqué par une tâche, permettant de prendre en compte tant des changements arbitraires en flux sanguin que des changements en concentrations sanguine d’O2. Des améliorations en terme de robustesse et de précisions sont démontrées dans la matière grise et le cortex visuel lorsque cette méthode est combinée à une manipulation respiratoire incluant une composante d’hypercapnie et d’hyperoxie. Le seconde technique présentée ici est une extension de la première et utilise une combinaison de manipulations respiratoires incluant l’hypercapnie, l’hyperoxie et l’administration simultanée des deux afin d’obtenir des valeurs expérimentales de la fraction d’extraction d’oxygène et du métabolisme oxydatif au repos. Dans la deuxième partie de cette thèse, les changements vasculaires et métaboliques liés à l’âge sont explorés dans un groupe de jeunes et aînés, grâce au cadre conceptuel de l’IRMf calibrée, combiné à une manipulation respiratoire d’hypercapnie et une tâche modifiée de Stroop. Des changements de flux sanguin au repos, de réactivité vasculaire au CO2 et de paramètre de calibration M ont été identifiés chez les aînés. Les biais affectant les mesures de signal BOLD obtenues chez les participants âgés découlant de ces changements physiologiques sont de plus discutés. Finalement, la relation entre ces changements cérébraux et la performance dans la tâche de Stroop, la santé vasculaire centrale et la condition cardiovasculaire est explorée. Les résultats présentés ici sont en accord avec l’hypothèse selon laquelle une meilleure condition cardiovasculaire est associée à une meilleure fonction vasculaire centrale, contribuant ainsi à l’amélioration de la santé vasculaire cérébrale et cognitive.

Mécanismes moléculaires de l’hypertrophie vasculaire dans le modèle animal d’hypertension essentielle (SHR)

La voie de signalisation des phosphoinositides joue un rôle clé dans la régulation du tonus vasculaire. Plusieurs études rapportent une production endogène de l’angiotensin II (Ang II) et de l’endothéline-1 (ET-1) par les cellules musculaires lisses vasculaires (CMLVs) de rats spontanément hypertendus (spontaneously hypertensive rats : SHR). De plus, l’Ang II exogène induit son effet prohypertrophique sur les CMLVs selon un mécanisme dépendant de la protéine Gqα et de la PKCẟ. Cependant, le rôle de l’axe Gqα/PLCβ/PKCẟ dans l’hypertrophie des CMLVs provenant d’un modèle animal de l’hypertension artérielle n’est pas encore étudié. L’objectif principal de cette thèse est d’examiner le rôle de l’axe Gqα/PLCβ1 dans les mécanismes moléculaires de l’hypertrophie des CMLVs provenant d’un modèle animal d’hypertension artérielle essentielle (spontaneously hypertensive rats : SHR). Nos premiers résultats indiquent que contrairement aux CMLVs de SHR âgés de 12 semaines (absence d’hypertrophie cardiaque), les CMLVs de SHR âgés de 16 semaines (présence d’hypertrophie cardiaque) présentent une surexpression protéique endogène de Gqα et de PLCβ1 par rapport aux CMLVs de rats WKY appariés pour l’âge. L’inhibition du taux d’expression protéique de Gqα et de PLCβ1 par des siRNAs spécifiques diminue significativement le taux de synthèse protéique élevé dans les CMLVs de SHR. De plus, la surexpression endogène des Gqα et PLCβ1, l’hyperphosphorylation de la molécule ERK1/2 et le taux de synthèse protéique élevé dans les CMLVs de SHR de 16 semaines ont été atténués significativement par des antagonistes des récepteurs AT1 (losartan) et ETA (BQ123), mais pas par l’antagoniste du récepteur ETB (BQ788). L’inhibition pharmacologique des MAPKs par PD98059 diminue significativement la surexpression endogène de Gqα/PLCβ1 et le taux de synthèse protéique élevé dans les CMLVs de SHR. D’un côté, l’inhibition du stress oxydatif (par DPI, inhibiteur de la NAD(P)H oxidase, et NAC , molécule anti-oxydante), de la molécule c-Src (PP2) et des récepteurs de facteurs de croissance (AG1024 (inhibiteur de l’IGF1-R), AG1478 (inhibiteur de l’EGFR) et AG1295 (inhibiteur du PDGFR)) a permis d’atténuer significativement la surexpression endogène élevée de Gqα/PLCβ1 et l’hypertrophie des CMLVs de SHR. D’un autre côté, DPI, NAC et PP2 atténuent significativement l’hyperphosphorylation de la molécule c-Src, des RTKs (récepteurs à activité tyrosine kinase) et de la molécule ERK1/2. Dans une autre étude, nous avons aussi démontré que la PKCẟ montre une hyperphosphorylation en Tyr311 dans les CMLVs de SHR comparées aux CMLVs de WKY. La rottlerin, utilisée comme inhibiteur spécifique de la PKCẟ, inhibe significativement cette hyperphosphorylation en Tyr311 dépendamment de la concentration. L’inhibition de l’activité de la PKCẟ par la rottlerin a été aussi associée à une atténuation significative de la surexpression protéique endogène de Gqα/PLCβ1 et l’hypertrophie des CMLVs de SHR. De plus, l’inhibition pharmacologique de l’activité de la PKCẟ, en amont du stress oxydatif, a permis d’inhiber significativement l’activité de la NADPH, le taux de production élevée de l’ion superoxyde ainsi que l’hyperphosphorylation de la molécule ERK1/2, de la molécule c-Src et des RTKs. À notre surprise, nous avons aussi remarqué une surexpression protéique de l’EGFR et de l’IGF-1R dans les CMLVs de SHR à l’âge de 16 semaines. L’inhibition pharmacologique de l’activité de la PKCẟ, de la molécule c-Src et du stress oxydatif a permis d’inhiber significativement la surexpression protéique endogène de ces RTKs. De plus, l’inhibition de l’expression protéique de l’EGFR et de la molécule c-Src par des siRNA spécifiques atténue significativement le taux d’expression protéique élevé de Gqα et de PLCβ1 ainsi que le taux de synthèse protéique élevé dans les CMLVs de SHR. Des siRNAs spécifiques à la PKCẟ ont permis d’atténuer significativement le taux de synthèse protéique élevé dans les CMLVs de SHR et confirment le rôle important de la PKCẟ dans les mécanismes moléculaires de l’hypertrophie des CMLVs selon une voie dépendante du stress oxydatif. En conclusion, ces résultats suggèrent un rôle important de l’activation endogène de l’axe Gqα-PLCβ-PKCẟ dans le processus d’hypertrophie vasculaire selon un mécanisme impliquant une activation endogène des récepteurs AT1/ETa, de la molécule c-Src, du stress oxidatif, des RTKs et des MAPKs.