Comprendre l’émergence des maladies dans les agroécosystèmes nécessite d’étudier l’histoire évolutive des populations bactériennes associées aux plantes. L’objectif de ce travail était de déterminer les évènements évolutifsconduisant à l’émergence des lignées pathogènes ou pathovars dans l’espèce Xanthomonas arboricola. Une analyse de génétique des populations a été menée sur un panel de souches phytopathogènes et commensales et complétée par l’inférence des gains et pertes de facteurs de virulence. Cette espèce possède une structure de population épidémique ; les clones épidémiques ont émergé suite à l’acquisition de facteurs de virulence à partir d’un fond recombinant de souches commensales. Une analyse de génomique des populations et la reconstruction de scénarios de divergence entre ces clones et le réseau de souches recombinantes, a montré la persistance d’un flux de gènes asymétrique entre ces deux groupes, dans le sens souches pathogènes vers souches commensales. Enfin, l’histoire évolutive du principal facteur de virulence des Xanthomonas, le système de sécrétion de type 3, a été retracée au sein du genre, et a montré que celui-ci avait été acquis ancestralement puis perdu dans certaines souches commensales. En conclusion, l’ancêtre commun de X. arboricola possédait des facteurs de virulence et au sein des souches commensales, certaines ont perdu ces facteurs, tandis que d’autres ont conservé le répertoire ancestral. Ces dernières diffèrent peu de certains agents pathogènes, et pourraient représenter un risque pour de nouvelles émergences. Des travaux de génomique fonctionnelle permettraient de valider ces hypothèses. / Deciphering the evolutionary history of bacterial populations associated to plants is necessary to understand diseaseemergence in agroecosystems. The aim of this study is to unveil the evolutionary events responsible for pathogeniclineages or pathovar emergences in Xanthomonas arboricola. This species is composed of both plant pathogenic andcommensal strains Population genetics analyses and gain and loss inferences of virulence factors showed that X. arboricola exhibits an epidemic population structure, within which epidemic clones emerged from a recombinogenic background population following virulence factor acquisition. Population genomics and inference of divergence scenarii between epidemic clones and the network of recombinant strains showed persistence of homologous recombination along divergence of these two groups, with an asymmetric gene flux from pathogenic strains to commensal ones. Finally, evolutionary history of the type three secretion system (T3SS), the main virulence factor in Xanthomonas genus, was studied at genus scale and showed that T3SS was ancestrally acquired and lost in commensal strains. Altogether these analyses allowed us to show that the common ancestor of X.arboricola had virulence factors, and that within commensal strains, some lost these virulence factors whereas others kept the ancestral repertoire. These latter strains have a similar repertoire to that of some pathogenic strains, and could represent a risk for new disease emergence. Functional genomics could allow us to validate these hypotheses.

A crescente incidência de disfunções metabólicas, como resistência à insulina e diabetes mellitus tipo 2 (T2DM), está correlacionada com a elevação da ocorrência de obesidade e sobrepeso. Em busca da melhora da saúde e de um corpo ideal segundo os padrões estéticos propagados atualmente, um número cada vez maior de indivíduos adere às dietas da moda que prometem rápida redução do peso corporal, ao invés de adotar uma alimentação balanceada e a prática regular de exercícios físicos. Uma dieta bastante divulgada e até recomendada por profissionais da saúde é o jejum intermitente (JI), que consiste em alternar períodos de jejum de até 24 horas com períodos de ingestão alimentar. Diversos estudos experimentais têm relatado alterações metabólicas em consequência do JI, como modificações da glicemia e da tolerância à glicose, porém, os resultados encontrados na literatura são conflitantes e, além disso, o impacto do jejum intermitente, em longo prazo, sobre as ilhotas pancreáticas ainda não foi devidamente elucidado. Desta forma, o presente estudo teve como objetivo caracterizar os impactos de doze semanas de JI em ratas Wistar. Para tal, ratas Wistar com 30 dias de idade foram distribuídas aleatoriamente em dois grupos: controle, com livre acesso à ração balanceada; e jejum intermitente, submetido a 24 horas de jejum intercalado com 24 horas de livre acesso à ração balanceada. Foi observado que os animais submetidos ao JI, apresentaram menor ganho de peso corporal, redução do comprimento da tíbia e da distância naso-anal, e alteração da composição corporal, incluindo diminuição da massa muscular e aumento do tecido adiposo. Em média, o consumo de ração do grupo JI foi menor, porém, no dia que era disponibilizado alimento, os animais apresentaram hiperfagia o que resultou em grande aumento das dimensões do estômago. O jejum intermitente reduziu os valores plasmáticos do colesterol total, triglicérides, LDL, HDL e glicemia, e aumentou a concentração basal da insulina plasmática, bem como a secreção da insulina após o estímulo com glicose. Foi observada redução significativa da massa de ilhotas pancreáticas e aumento da porcentagem de células dispersas de ilhotas em apoptose. Ainda nas células dispersas de ilhotas pancreáticas, houve aumento do conteúdo de espécies reativas de oxigênio mitocondrial e total, e do peróxido de hidrogênio (H2O2), além de aumento da expressão do sistema antioxidante. Assim, nossos dados sugerem que esse protocolo estudado de 24 horas de jejum intercalados com 24 horas de alimentação à vontade não seja saudável em longo prazo. Mais estudos em longo prazo são necessários para investigar qual seria o melhor protocolo de jejum intermitente de forma a reduzir os efeitos colaterais e melhorar a saúde, para então o JI ser considerado uma boa alternativa para perda e manutenção do peso. / The increasing incidence of metabolic dysfunctions, such as insulin resistance and type 2 diabetes mellitus (T2DM), is correlated with increased occurrence of obesity and overweight. In pursuit of improved health and an ideal body according to today\'s aesthetic standards, an increasing number of individuals adhere to fad diets that promise a rapid reduction of body weight, instead of adopting a balanced diet and regular practice of physical exercises. A well-publicized diet and even recommended by health professionals is intermittent fasting (IF), which consists of alternating fasting periods of up to 24 hours with periods of food intake. Several experimental studies have reported metabolic changes as a consequence of IF, such as changes in glucose and glucose tolerance, but the results found in the literature are conflicting and, in addition, the impact of intermittent fasting in the long term on pancreatic islets has not yet been properly elucidated. Thus, the present study aimed to characterize the effects of twelve-week IF on Wistar rats. For this, 30-day-old Wistar rats were randomly assigned to two groups: control, with free access to balanced chow; and intermittent fasting, subjected to 24-hour fast intercalated with 24 hours of free access to the balanced chow. It was observed that the animals submitted to IF presented lower body weight gain, reduced tibia length and naso-anal distance, and altered body composition, including decreased muscle mass and increased adipose tissue. On average, the dietary intake of the IF group was lower, but on the day that food was available, the animals presented hyperphagia which resulted in a large increase in the stomach size. Intermittent fasting reduced plasma levels of total cholesterol, triglycerides, LDL, HDL, and glycaemia, and increased basal plasmatic insulin level, as well as insulin secretion after stimulation with glucose. We observed significant reduction in pancreatic islet mass and increase in percentage of islet-dispersed cells in apoptosis. Still in islet-dispersed cells, there was an increase in mitochondrial and total reactive oxygen species content, and of hydrogen peroxide (H2O2), in addition to an increase in expression of antioxidant system. Thus, our data suggest that this protocol of 24-hour fasting intercalated with 24-hour feed at will is not healthy in the long run. More long-term studies are needed to investigate the best intermittent fasting protocol in order to reduce side effects and improve health, so IF be considered a good alternative for weight loss and maintenance.

The development of microarray technology has provided an unprecedented wealth of data on gene expression in various tissue and cell types. Few studies have, however, taken full advantage of these data by selecting and then extensively characterising the functions of particular genes chosen from these microarray datasets. In this study, after analysing differentially-regulated genes revealed by microarray analysis of human mast cells activated via Fc??RI cross-linking, we chose two promising gene candidates for further research, A20 and Gem. Our group??s extensive gene expression database of major leukocytes showed that both A20 and Gem were up-regulated in other leukocyte types, and yet neither of these genes has been extensively explored in mast cells or in the immune system prior to our study. In order to investigate the first of these genes selected for further study, A20, we utilised both A20-deficient mast cells and mast cells in which A20 was over-expressed. Our findings establish for the first time that A20 is an important regulator of mast cell inflammatory responses to both LPS and Fc??RI cross-linking, and that it plays a novel role in mast cell proliferation. Our study of the second gene chosen for investigation, Gem, was conducted in a Gemdeficient mouse model developed by our group. In this study, we investigated the effect of Gem deficiency in two key immune cell types, macrophages and T-cells, complementing the work of a previous group member who investigated Gem deficiency in mast cells. Our results clearly exclude a role for Gem in macrophage and T-cell effector responses, and further establish that Gem is dispensable for in vivo inflammatory responses in models of delayed-type hypersensitivity and allergic airway inflammation. In addition to these findings, and given that the physiological role of Gem was not yet understood prior to our study, we extended our investigation to explore a potential function for Gem in the metabolic system. Using Gem-deficient mice, we found that Gem is necessary for insulin secretion from pancreatic islets. These findings confirm the potential for microarray expression data to reveal excellent gene candidates for further research and functional characterisation.

<p>Diabetes mellitus is a bihormonal disorder with hyperglycemia due to deficiency of insulin and hypersecretion of glucagon. To improve diabetes treatment it is important to clarify the signal transduction of glucagon secretion. The cytoplasmic Ca²⁺ concentration ([Ca²⁺]_i), an important determinant of hormone secretion, and the membrane potential were recorded in individual mouse α-cells. Glucagon and insulin secretion were measured from mouse islets and glucagon secretion from hamster glucagonoma cells. Glucose inhibited glucagon secretion from islets and glucagonoma cells with maximal effect at 7 mM, indicating a direct action on the α-cells. High concentrations of glucose paradoxically stimulated glucagon secretion. Whereas glucose inhibition of glucagon release was associated with lowering of [Ca²⁺]_i, stimulation of secretion at high glucose concentrations was Ca²⁺-independent. Adrenaline, which is a potent stimulator of glucagon secretion, increased [Ca²⁺]_i by α₁- and β-adrenergic mechanisms involving mobilization of intracellular Ca²⁺ from the endoplasmic reticulum (ER) and influx of the ion across the plasma membrane. Ca²⁺ mobilization could be attributed to generation of inositol 1,4,5-trisphosphate and cAMP, and influx occurred through voltage-dependent L-type channels activated by a depolarizing store-operated current. Glucose hyperpolarized the α-cells and inhibited adrenaline-induced [Ca²⁺]_i signalling. At 3 mM, glucose had a pronounced stimulatory effect on Ca²⁺ sequestration in the ER, shutting off store-operated Ca²⁺ influx. The α-cells express ATP-regulated K⁺ channels but pharmacological blockade of these channels neither interfered with the hyperpolarizing and [Ca²⁺]_ilowering effects of glucose nor with the inhibition of glucagon secretion. In contrast, activation of the depolarizing store-operated mechanism prevented glucose-induced, hyperpolarization, lowering of [Ca²⁺]_i and inhibition of glucagon secretion. It is proposed that adrenaline stimulation and glucose inhibition of glucagon release involve modulation of a store-operated depolarizing current. The U-shaped dose response relationship for glucose-regulated glucagon secretion may explain the hyperglucagonemia in diabetes.</p>

Due to the emergence and dissemination of multidrug resistance, bacterial pathogens have been causing a serious public health problem in recent years. To address the existing drug resistant problem, there is an urgent need to find new antimicrobials, especially those against drug-resistant bacteria. SecA is the central component of Sec-dependent secretion pathway, which is responsible for the secretion of many essential proteins as well as many toxins and virulence factors. Two SecA homologues are indentified in some important Gram-positive pathogens. SecA1 is involved in general secretion pathway and essential for viability, whereas SecA2 contribute to secretion of specific virulence factors. The high conservation among a wide range of bacteria and no human counterpart make SecA homologues attractive targets for exploring novel antimicrobials. We hypothesize that inhibition of these SecA homologues could reduce virulence, inhibit bacteria growth, and kill bacteria. SecA1 and SecA2 from four different species were cloned, purified, and characterized. All these SecA homologues show ATPase activities, thus screening ATPase inhibitors might help to develop new antimicrobials. In this study, three structurally different classes of SecA inhibitors were developed and optimized: 1) Rose Bengal (RB) and RB analogs derived from systematical dissection RB and Structure-Activity relationship (SAR) study; 2) pyrimidine analogs derived from virtual screening based on the ATP binding pocket of EcSecA and SAR study; and 3) bistriazole analogs derived from random screening and SAR study. Several potent SecA inhibitors show promising enzymatic inhibition against SecA homologues as well as bacteriostatic and bactericidal effects. Two major efflux pumps of S. aureus, NorA and MepA, have little negative effect on the antimicrobial activities of SecA inhibitors, suggesting that targeting SecA could by-pass efflux pumps. Moreover, these inhibitors impair the secretion of important toxins of S. aureus and B. anthracis, indicating the inhibition of in vivo SecA function could reduce virulence. Target identification assays confirm that these inhibitors could directly bind to SecA homologues, and specifically identify SecA from whole cell lysate of E. coli and S. aureus, suggesting that these inhibitors are really targeting on SecA. These studies validate that SecA is a good target for development antimicrobials.

The acinar salivary gland of the cockroach, Periplaneta americana, is innervated by dopaminergic and serotonergic nerve fibers. Stimulation of the glands by serotonin (5-hydroxytryptamine, 5-HT) results in the production of a protein-rich saliva, whereas stimulation by dopamine results in saliva that is protein-free. Thus, dopamine acts selectively on ion-transporting peripheral cells within the acini, and 5-HT acts on protein-producing central cells. We have investigated the pharmacology of the 5-HT-induced secretory activity of isolated salivary glands of P. americana by testing several 5-HT receptor agonists and antagonists. The effects of 5-HT can be mimicked by the non-selective 5-HT receptor agonist 5-methoxytryptamine. All tested agonists that display at least some receptor subtype specificity in mammals, i.e., 5-carboxamidotryptamine, (+/-)-8-OH-DPAT, (+/-)-DOI, and AS 19, were ineffective in stimulating salivary secretion. 5-HT-induced secretion can be blocked by the vertebrate 5-HT receptor antagonists methiothepin, cyproheptadine, and mianserin. Our pharmacological data indicate that the pharmacology of arthropod 5-HT receptors is remarkably different from that of their vertebrate counterparts. (C) 2007 Elsevier Ltd. All rights reserved.

Identification of modifiable risk factors for Alzheimer’s disease (AD) is crucial in order to diminish suffering from this devastating disease. The aim of this thesis was to investigate if different aspects of glucose metabolism, insulin, fatty-acid composition or other vascular risk factors predict the future development of AD and dementia. This thesis is based on the Uppsala Longitudinal Study of Adult Men (ULSAM) cohort, which started in 1970. A total of 2322 men at age 50 were examined with focus on vascular risk factors. The cohort was re-examined at ages 60, 71, 77, 82 and 88. Incident diagnoses of AD, vascular dementia, other dementias and cognitive impairment were assessed in 2005–2010. The risk of AD was increased in subjects with lower early insulin response measured with both an intravenous glucose tolerance test at 50 years and an oral glucose tolerance test at 71 years of age. The presence of vascular risk factors such as hypertension, obesity, hypercholesterolemia and smoking increased the risk of future vascular dementia but not of AD. Furthermore, saturated fatty acids at midlife were inversely associated with risk of AD. No evidence of a protective effect of omega-3 fatty acids against dementia was found. The susceptibility allele, APOE ε4, was the strongest individual risk factor. APOE ε4 carriers with vascular risk factors had the greatest risk of developing dementia. Low insulin response was a risk factor for AD mainly in APOE ε4 non-carriers. Disturbances in insulin and glucose metabolism, vascular risk factors and fatty acids are linked differentially to the pathogenesis of AD and vascular dementia. These observations should be considered when future clinical approaches are planned to prevent and postpone the onset of dementia. / ULSAM

Many bacteria live in close association with other organisms such as plants and animals, with important implications for both health and disease. This thesis investigates bacteria that are well adapted to live inside an animal host, and describes the molecular evolutionary processes underlying host-adaptation, based on bacterial genome comparisons. Insect-transmitted bacteria of the genus Bartonella infect the red blood cells of mammals, and we investigate host adaptation and genome evolution in this genus. In Bartonella, many host-interaction systems are encoded in a highly variable chromosomal segment previously shown to be amplified and packaged into bacteriophage particles. Among all genes imported into the Bartonella ancestor, we identify the short gene cluster encoding these phage particles as the most evolutionary conserved, indicating a strong selective advantage and a role in niche adaptation. We also provide an overview of the remarkable evolutionary dynamics of type IV and type V secretion systems, including a detailed analysis of the type IV secretion system trw. Our results highlight the importance of recombination and gene conversion in the evolution of host-adaptation systems, and reveal how these mutational mechanisms result in strikingly different outcomes depending on the selective constraints. In the insect endosymbionts Buchnera and Blochmannia, we show that genes frameshifted at poly(A) tracts can remain functional due to transcriptional slippage. Selection against poly(A) tracts is very inefficient in these genomes compared to other bacteria, and we discuss why this can lead to increased rates of gene loss. Using the human pathogen Helicobacter pylori as a model, we provide a deeper understanding of why highly expressed genes evolve slowly. This thesis emphasizes the power of using complete genome sequences to study evolutionary processes. In particular, we argue that knowledge about the complex evolution of duplicated gene segments is crucial to understand host adaptation in bacteria.

Bacteria of the genus Bartonella infect the red blood cells of a wide range of wild and domestic mammals and are transmitted between hosts by blood-sucking insects. Although most Bartonella infections are asymptomatic, the genus contains several human pathogens. In this work, host adaptation and host switches in Bartonella have been studied from a genomic perspective, with special focus on the acquisition and evolution of genes involved in host interactions. As part of this study, the complete genome of B. grahamii isolated from a Swedish wood mouse was sequenced. A genus-wide comparison revealed that rodent-associated Bartonella species, which have rarely been associated with human disease, have the largest genomes and the largest number of host-adaptability genes. Analysis of known and putative genes for host interactions identified several families of autotransporters as horizontally transferred to the Bartonella ancestor, with a possible role both during early host adaptation and subsequent host shifts. In B. grahamii, the association of a gene transfer agent (GTA) and phage-derived run-off replication of a large genomic segment was demonstrated for the first time. Among all acquisitions to the Bartonella ancestor, the only well conserved gene clusters are those that encode the GTA and contain the origin of the run-off replication. This conservation, along with a high density of host-adaptability genes in the amplified region suggest that the GTA provides a strong selective advantage, possibly by increasing recombination frequencies of host-adaptability genes, thereby facilitating evasion of the host immune system and colonization of new hosts. B. grahamii displays stronger geographic pattern and higher recombination frequencies than the cat-associated B. henselae, probably caused by different lifestyles and/or population sizes of the hosts. The genomic diversity of B. grahamii is markedly lower in Europe and North America than in Asia, possibly an effect of reduced host variability in these areas following the latest ice age.

<p><italic>Chlamydia<italic> <italic>trachomatis<italic> remains a highly relevant clinical pathogen as it is the causative agent of the most commonly reported sexually transmitted disease in the western hemisphere, and the most common cause of infectious blindness in the developing world. As an obligate intracellular pathogen, <italic>Chlamydia<italic> employs a vast assay of virulence proteins to hijack and remodel the host cellular machinery to facilitate its growth and dissemination. Besides delivering effector proteins into the host cytoplasm via a conserved type III secretion machinery, Chlamydia encodes components of multiple secretion systems, such as type II and IV. Chapter 3 of this document describes the secretion, processing and localization of two putative autotransporters (Pls1 and Pls2) and their involvement in inclusion expansion.</p><p> </p><p>In recent years, many new chlamydial effector proteins have been described. CPAF (Chlamydial Protease-like Activity Factor) is a secreted serine protease that is emerging as a central virulence protein: it is proposed to play a central role in <italic>Chlamydia<italic> pathogenesis by cleaving proteins involved in antigen-presentation, apoptosis and cytoskeletal re-arrangements. However, the functional significance of CPAF remains elusive due to the lack of specific inhibitors and <italic>Chlamydia<italic> mutants. The body of work presented herein demonstrates that in addition to targeting host proteins, CPAF cleaves a subset of early chlamydial effector proteins, including Inc-proteins that reside on the nascent pathogenic vacuole ("inclusion"). The design and development of a CPAF-specific inhibitory peptide demonstrates that these chlamydial effector proteins are true targets of CPAF. This peptide reversed the cleavage of bacterial targets by CPAF both in an in vitro cleavage assay and during infection, indicating that these effectors are bona fide targets. Inhibition of CPAF activity also revealed that this protease regulates multiple facets of chlamydial pathogenesis. CPAF inhibition in infected epithelial cells led to the complete dismantling of the inclusion, secretion of pro-inflammatory cytokines and engagement of an inflammasome-dependent programmed cell death pathway. While fibroblasts defective in various inflammasome components were resistant to <italic>Chlamydia<italic>-induced cell death, inclusion integrity and bacterial replication was still compromised upon CPAF inhibition, indicating that loss of inclusion integrity was not a consequence of caspase-1 activation. Overall, these findings revealed that CPAF, in addition to regulating host function, directly modulates the activity of secreted effectors and early Inc-proteins. Furthermore, we establish that CPAF is an essential virulence factor that is required to maintain the integrity of the inclusion and prevent the engagement of innate immune programmed cell death pathways in infected epithelial cells. CPAF activity thus remains a compelling mechanism by which intracellular pathogens employ proteolytic events to modify the host environment.</p> / Dissertation