Comparative and functional genomics provide insights into the pathogenicity of dermatophytic fungi.

ABSTRACT: BACKGROUND: Millions of humans and animals suffer from superficial infections caused by a group of highly specialized filamentous fungi, the dermatophytes, which exclusively infect keratinized host structures. To provide broad insights into the molecular basis of the pathogenicity-associated traits, we report the first genome sequences of two closely phylogenetically related dermatophytes, Arthroderma benhamiae and Trichophyton verrucosum, both of which induce highly inflammatory infections in humans. RESULTS: 97% of the 22.5 megabase genome sequences of A. benhamiae and T. verrucosum are unambiguously alignable and collinear. To unravel dermatophyte-specific virulence-associated traits, we compared sets of potentially pathogenicity-associated proteins, such as secreted proteases and enzymes involved in secondary metabolite production, with those of closely related onygenales (Coccidioides species) and the mould Aspergillus fumigatus. The comparisons revealed expansion of several gene families in dermatophytes and disclosed the peculiarities of the dermatophyte secondary metabolite gene sets. Secretion of proteases and other hydrolytic enzymes by A. benhamiae was proven experimentally by a global secretome analysis during keratin degradation. Molecular insights into the interaction of A. benhamiae with human keratinocytes were obtained for the first time by global transcriptome profiling. Given that A. benhamiae is able to undergo mating, a detailed comparison of the genomes further unraveled the genetic basis of sexual reproduction in this species. CONCLUSIONS: Our results enlighten the genetic basis of fundamental and putatively virulence-related traits of dermatophytes, advancing future research on these medically important pathogens.

Retinal thickening in HLA-B27 associated acute anterior uveitis: evolution with time and association with severity of inflammatory activity.

Purpose: To describe the evolution of retinal thickness in eyes affected with acute anterior uveitis (AAU) in the course of follow-up and to assess its correlation with severity of inflammatory activity in the anterior chamber. Methods: Design: Prospective, cohort study Setting: Institutional study Patient population: 72 eyes (affected and fellow eyes) of 36 patients Observation procedure: Patients were followed daily until beginning of resolution of inflammatory activity and weekly thereafter. Optical coherence tomography and laser flare photometry were performed at each visit. Treatment consisted of topical corticosteroids Main outcome measures: Retinal thickness of affected eyes, difference in retinal thickness between affected and fellow eyes and their evolution in time, association between maximal retinal thickness and initial laser flare photometry. Results: Difference in retinal thickness between affected and fellow eyes became significant on average seven days from baseline and remained so through-out follow-up (p<0.001). There was a steep increase in retinal thickness of affected eyes followed by a progressive decrease after reaching a peak value. Maximal difference in retinal thickness between affected and fellow eyes was observed between 17 and 25 days from baseline and exhibited a strong, positive correlation with initial laser flare photometry values (p=0.015). Conclusions: Retinal thickness in eyes affected with AAU presents a steep increase over 3 to 4 weeks and then gradually decreases. Severity of inflammation at baseline predicts the amount of retinal thickening in affected eyes. A characteristic pattern of temporal response of retinal anatomy to inflammatory stimuli seems to arise.

What kind of relationships between the evolution of pain, beliefs and bio-psycho-social complexity after a locomotor traumatism?

Introduction: Pain and beliefs have an influence on the patient's course in rehabilitation, pain causes fears and fears influence pain perception. The aim of this study is to understand pain and beliefs evolutions during rehabilitation taking into account of bio-psycho-social complexity.Patients and methods: 631 consecutive patients admitted in rehabilitation after a musculoskeletal traumatism were included and assessed at admission and at discharge. Pain was measured by VAS (Visual Analogical Scale), bio-psycho-social complexity by Intermed scale, and beliefs by judgement on Lickert scales. Four kinds of beliefs were evaluated: fear of a severe origin of pain, fear of movement, fear of pain and feeling of distress (loss of control). The association between the changes in pain and beliefs during the hospitalization was assessed by linear regressions.Results: After adjustment for gender, age, education and native language, patients with a decrease in pain during rehabilitation have higher probability of decreasing their fears. For the distress feeling, this relationship is weaker among bio-psycho-socially complex patients (odds-ratio 1.22 for each decreasing of 10mm/100 VAS) than among non-complex patients (OR 1.47). Patients with a pain decrease of 30% or more during hospitalization have higher probability of seeing their fears decrease, this relationship being stronger in complex patient for fear of a severe origin of pain.Discussion: The relationships between evolution of pain and beliefs move in the same direction. The higher a patient feels pain, the less they could be able to modify their dysfunctional beliefs. When the pain diminishes of 30% or more, the probability to challenge the beliefs is increased. The prognostic with regard to feeling of distress and fear of a severe origin of pain, is worse among bio-psycho-socially complex patients.

Prenatal presentation and postnatal evolution of a patient with Jansen metaphyseal dysplasia with a novel missense mutation in PTH1R.

Wave-shaped ribs were detected at prenatal ultrasound in a 20(+1) week female fetus. At birth, skeletal radiographs showed marked hypomineralization and suggested hypophosphatasia. However, elevated blood calcium and alkaline phosphatase excluded hypophosphatasia and raised the possibility of Jansen metaphyseal dysplasia. Molecular analysis of the PTH/PTHrP receptor gene (PTH1R) showed heterozygosity for a previously undescribed transversion variant (c.1373T>A), which predicts p.Ile458Lys. In vitro evaluation of wild type and mutant PTH/PTHrP receptors supported the pathogenic role of the p.Ile458Lys substitution, and confirmed the diagnosis of Jansen metaphyseal dysplasia. This disorder may present prenatally with wavy ribs and in the newborn with hypomineralization, and may therefore be confused with hypophosphatasia. The mottled metaphyseal lesions typically associated with this disease appear only in childhood.

Evolution of intraspecific variation : a comparative phylogenetic approach

Understanding the evolution of intraspecific variance is a major research question in evolutionary biology. While its importance to processes operating at individual and population levels is well-documented, much less is known about its role in macroevolutionary patterns. Nevertheless, both experimental and theoretical evidence suggest that the intraspecific variance is susceptible to selection, can transform into interspecific variation and, therefore, is crucial for macroevolutionary processes. The main objectives of this thesis were: (l) to investigate which factors impact evolution of intraspecific variation in Polygonaceae and determine if evolution of intraspecific variation influences species diversification; and (2) to develop a novel comparative phylogenetic method to model evolution of intraspecific variation. Using the buckwheat family, Polygonaceae, as a study system, I demonstrated which life-history and ecological traits are relevant to the evolution of intraspecific variation. I analyzed how differential intraspecific variation drives species diversification patterns. I showed with computer simulations the shortcomings of existing comparative methods with respect to intraspecific variation. I developed a novel comparative model that readily incorporates the intraspecific variance into phylogenetic comparative methods. The obtained results are complimentary, because they affect both empirical and methodological aspects of comparative analysis. Overall, I highlight that intraspecific variation is an important contributor to the macroevolutionary patterns and it should be explicitly considered in the comparative phylogenetic analysis. - En biologie évolutive comprendre l'évolution de la variance intraspécifique est un axe de recherche majeur. Bien que l'importance de cette variation soit bien documentée au niveau individuel et populationnel, on en sait beaucoup moins sur son rôle au niveau macroévolutif. Néanmoins, des preuves expérimentales et théoriques suggèrent que la variance intraspécifique est sensible à la sélection et peut se transformer en variation interspécifique. Par conséquent, elle est cruciale pour mieux comprendre les processus macroévolutifs. Les principaux objectifs de ma thèse étaient : (i) d'enquêter sur les facteurs qui affectent l'évolution de la variation intraspécifique chez les Polygonaceae et de déterminer si l'évolution de cette dernière influence la diversification des espèces, et (2) de développer une nouvelle méthode comparative permettant de modéliser l'évolution de la variation intraspécifique dans un cadre phylogénétique. En utilisant comme système d'étude la famille du sarrasin, les Polygonacées, je démontre que les traits d'histoire de vie sont pertinents pour comprendre l'évolution de la variation intraspécifique. J'ai également analysé l'influence de la variation intraspécifique au niveau de la diversification des espèces. J'ai ensuite démontré avec des données simulées les limites des méthodes comparatives existantes vis à vis de la variation intraspécifique. Finalement, j'ai développé un modèle comparatif qui intègre facilement la variance intraspécifique dans les méthodes comparatives phylogénétiques existantes. Les résultats obtenus lors de ma thèse sont complémentaires car ils abordent aspects empiriques et méthodologiques de l'analyse comparative. En conclusion, je souligne que la variation intraspécifique est un facteur important en macroévolution et qu'elle doit être explicitement considérée lors d'analyses comparatives phylogénétiques.

Nature, evolution and characterisation of rhizospheric chemical exudates affecting root herbivores

Similar to aboveground herbivores, root-feeding insects must locate and identify suitable resources. In the darkness of soil, they mainly rely on root chemical exudations and, therefore, have evolved specific behaviours. Because of their impact on crop yield, most of our knowledge in belowground chemical ecology is biased towards soil-dwelling insect pests. Yet the increasing literature on volatile-mediated interactions in the ground underpins the great importance of chemical signalling in this ecosystem and its potential in pest control. Here, we explore the ecology and physiology of these chemically based interactions. An evolutionary approach reveals interesting patterns in the response of insects to particular classes of volatile or water-soluble organic compounds commonly emitted by roots. Food web analyses reasonably support that volatiles are used as long-range cues whereas water-soluble molecules serve in host acceptance/rejection by the insect; however, data are still scarce. As a case study, the chemical ecology of Diabrotica virgifera virgifera is discussed and applications of belowground signalling in pest management are examined. Soil chemical ecology is an expanding field of research and will certainly be a hub of our understanding of soil communities and subsequently of the management of belowground ecosystem services.

The magmatic to hydrothermal evolution of the intrusive Mont Saint-Hilaire Complex: Insights into the late-stage evolution of peralkaline rocks

The Cretaceous Mont Saint-Hilaire complex (Quebec, Canada) comprises three major rock units that were emplaced in the following sequence: (I) gabbros; (II) diorites; (III) diverse partly agpaitic foid syenites. The major element compositions of the rock-forming minerals, age-corrected Nd and oxygen isotope data for mineral separates and trace element data of Fe-Mg silicates from the various lithologies imply a common source for all units. The distribution of the rare earth elements in clinopyroxene from the gabbros indicates an ocean island basalt type composition for the parental magma. Gabbros record temperatures of 1200 to 800 degrees C, variable silica activities between 0 center dot 7 and 0 center dot 3, and f(O2) values between -0 center dot 5 and +0 center dot 7 (log delta FMQ, where FMQ is fayalite-magnetite-quartz). The diorites crystallized under uniform a(SiO2) (a(SiO2) = 0 center dot 4-0 center dot 5) and more reduced f(O2) conditions (log delta FMQ similar to-1) between similar to 1100 and similar to 800 degrees C. Phase equilibria in various foid syenites indicate that silica activities decrease from 0 center dot 6-0 center dot 3 at similar to 1000 degrees C to < 0 center dot 3 at similar to 550 degrees C. Release of an aqueous fluid during the transition to the hydrothermal stage caused a(SiO2) to drop to very low values, which results from reduced SiO(2) solubilities in aqueous fluids compared with silicate melts. During the hydrothermal stage, high water activities stabilized zeolite-group minerals. Fluid inclusions record a complex post-magmatic history, which includes trapping of an aqueous fluid that unmixed from the restitic foid syenitic magma. Cogenetic aqueous and carbonic fluid inclusions reflect heterogeneous trapping of coexisting immiscible external fluids in the latest evolutionary stage. The O and C isotope characteristics of fluid-inclusion hosted CO(2) and late-stage carbonates imply that the surrounding limestones were the source of the external fluids. The mineral-rich syenitic rocks at Mont Saint-Hilaire evolved as follows: first, alkalis, high field strength and large ion lithophile elements were pre-enriched in the (late) magmatic and subsequent hydrothermal stages; second, percolation of external fluids in equilibrium with the carbonate host-rocks and mixing processes with internal fluids as well as fluid-rock interaction governed dissolution of pre-existing minerals, element transport and precipitation of mineral assemblages determined by locally variable parameters. It is this hydrothermal interplay between internal and external fluids that is responsible for the mineral wealth found at Mont Saint-Hilaire.

Evidence for the evolution of multiple genomes in arbuscular mycorrhizal fungi.

Ancient asexuals directly contradict the evolutionary theories that explain why organisms should evolve a sexual life history. The mutualistic, arbuscular mycorrhizal fungi are thought to have been asexual for approximately 400 million years. In the absence of sex, highly divergent descendants of formerly allelic nucleotide sequences are thought to evolve in a genome. In mycorrhizal fungi, where individual offspring receive hundreds of nuclei from the parent, it has been hypothesized that a population of genetically different nuclei should evolve within one individual. Here we use DNA-DNA fluorescent in situ hybridization to show that genetically different nuclei co-exist in individual arbuscular mycorrhizal fungi. We also show that the population genetics techniques used in other organisms are unsuitable for detecting recombination because the assumptions and underlying processes do not fit the fungal genomic structure shown here. Instead we used a phylogenetic approach to show that the within-individual genetic variation that occurs in arbuscular mycorrhizal fungi probably evolved through accumulation of mutations in an essentially clonal genome, with some infrequent recombination events. We conclude that mycorrhizal fungi have evolved to be multi-genomic.

Ecology and evolution of multigenomic arbuscular mycorrhizal fungi.

Arbuscular mycorrhizal fungi (AMF) form extremely important mutualistic symbioses with most plants. Their role in nutrient acquisition, plant community structure, plant diversity, and ecosystem productivity and function has been demonstrated in recent years. New findings on the genetics and biology of AMF also give us a new picture of how these fungi exist in ecosystems. In this article, I bring together some recent findings that indicate that AMF have evolved to contain multiple genomes, that they connect plants together by a hyphal network, and that these different genomes may potentially move around in this network. These findings show the need for more intensive studies on AMF population biology and genetics in order to understand how they have evolved with plants, to better understand their ecological role, and for applying AMF in environmental management programs and in agriculture. A number of key features of AMF population biology have been identified for future studies and most of these concern the need to understand drift, selection, and genetic exchange in multigenomic organisms, a task that has not previously presented itself to evolutionary biologists.

Genomics of secondary metabolite production by Pseudomonas fluorescens Pf-5

The complete sequence of the 7.07 Mb genome of the biological control agent Pseudomonas fluorescens Pf-5 is now available, providing a new opportunity to advance knowledge of biological control through genomics. P. fluorescens Pf-5 is a rhizosphere bacterium that suppresses seedling emergence diseases and produces a spectrum of antibiotics toxic to plant-pathogenic fungi and oomycetes. In addition to six known secondary metabolites produced by Pf-5, three novel secondary metabolite biosynthesis gene clusters identified in the genome could also contribute to biological control. The genomic sequence provides numerous clues as to mechanisms used by the bacterium to survive in the spermosphere and rhizosphere. These features include broad catabolic and transport capabilities for utilizing seed and root exudates, an expanded collection of efflux systems for defense against environmental stress and microbial competition, and the presence of 45 outer membrane receptors that should allow for the uptake of iron from a wide array of siderophores produced by soil microorganisms. As expected for a bacterium with a large genome that lives in a rapidly changing environment, Pf-5 has an extensive collection of regulatory genes, only some of which have been characterized for their roles in regulation of secondary metabolite production or biological control. Consistent with its commensal lifestyle, Pf-5 appears to lack a number of virulence and pathogenicity factors found in plant pathogen.

The Microbe browser for comparative genomics.

The Microbe browser is a web server providing comparative microbial genomics data. It offers comprehensive, integrated data from GenBank, RefSeq, UniProt, InterPro, Gene Ontology and the Orthologs Matrix Project (OMA) database, displayed along with gene predictions from five software packages. The Microbe browser is daily updated from the source databases and includes all completely sequenced bacterial and archaeal genomes. The data are displayed in an easy-to-use, interactive website based on Ensembl software. The Microbe browser is available at http://microbe.vital-it.ch/. Programmatic access is available through the OMA application programming interface (API) at http://microbe.vital-it.ch/api.

Evolution in subdivided plant populations: concepts, recent advances and future directions.

SUMMARY: Research into the evolution of subdivided plant populations has long involved the study of phenotypic variation across plant geographic ranges and the genetic details underlying that variation. Genetic polymorphism at different marker loci has also allowed us to infer the long- and short-term histories of gene flow within and among populations, including range expansions and colonization-extinction dynamics. However, the advent of affordable genome-wide sequences for large numbers of individuals is opening up new possibilities for the study of subdivided populations. In this review, we consider what the new tools and technologies may allow us to do. In particular, we encourage researchers to look beyond the description of variation and to use genomic tools to address new hypotheses, or old ones afresh. Because subdivided plant populations are complex structures, we caution researchers away from adopting simplistic interpretations of their data, and to consider the patterns they observe in terms of the population genetic processes that have given rise to them; here, the genealogical framework of the coalescent will continue to be conceptually and analytically useful.

Evolution at Two Levels in Fire Ants: The Relationship between Patterns of Gene Expression and Protein Sequence Evolution.

Variation in protein sequence and gene expression each contribute to phenotypic diversity, and may be subject to similar selective pressures. Eusocial insects are particularly useful for investigating the evolutionary link between protein sequence and condition-dependent patterns of gene expression because gene expression plays a central role in determining differences between eusocial insect sexes and castes. We investigated the relationship between protein coding sequence evolution and gene expression patterns in the fire ants Solenopsis invicta, S. richteri, and their hybrids to gain greater insight into how selection jointly operates on gene expression and coding sequence. We found that genes with high expression variability within castes and sexes were frequently differentially expressed between castes and sexes, as well as between species and hybrids. These results indicate that genes showing high variation in expression in one context also tend to show high variation in expression in other contexts. Our analyses further revealed that variation in both intra- and interspecific gene expression was positively associated with rate of protein sequence evolution in Solenopsis. This suggests that selective constraints on a gene operate both at the level of protein sequence and at the level of gene expression regulation. Overall, our study provides one of the strongest demonstrations that selective constraints mediate both protein sequence evolution and gene expression variability across different biological contexts and timescales.

Evolution de l'incidence des cancers et des polypes colorectaux dans le canton de Vaud entre 1983 et 2007. [Trends in incidence of colorectal cancers and polyps in the Swiss canton of Vaud 1983-2007].

Colorectal cancer is the second most frequent cancer at death and third most common neoplasm in Switzerland, with about 1600 deaths and 4000 new cases per year, respectively. This study describes the recent trends in colorectal polyps and cancers in the canton of Vaud where a rare population-based series on polyps has been available since 1983. The most salient results are the exponential increase in the detection rates of polyps since the late 19805, associated with a doubling in the proportion of right-sided polyps, whereas colorectal cancer incidence remained constant over the last 25 years. The apparent paradox between the strong increase in detection and resection of polyps, largely due to screening activity, and the absence of reduction in colorectal cancer incidence in the Vaud population is discussed.