Structural investigations into the interaction of hemoglobin and part structures with bacterial endotoxins.

An understanding of details of the interaction mechanisms of bacterial endotoxins (lipopolysaccharide, LPS) with the oxygen transport protein hemoglobin is still lacking, despite its high biological relevance. Here, a biophysical investigation into the endotoxin:hemoglobin interaction is presented which comprises the use of various rough mutant LPS as well as free lipid A; in addition to the complete hemoglobin molecule from fetal sheep extract, also the partial structure alpha-chain and the heme-free sample are studied. The investigations comprise the determination of the gel-to-liquid crystalline phase behaviour of the acyl chains of LPS, the ultrastructure (type of aggregate structure and morphology) of the endotoxins, and the incorporation of the hemoglobins into artificial immune cell membranes and into LPS. Our data suggest a model for the interaction between Hb and LPS in which hemoglobins do not react strongly with the hydrophilic or with the hydrophobic moiety of LPS, but with the complete endotoxin aggregate. Hb is able to incorporate into LPS with the longitudinal direction parallel to the lipid A double-layer. Although this does not lead to a strong disturbance of the LPS acyl chain packing, the change of the curvature leads to a slightly conical molecular shape with a change of the three-dimensional arrangement from unilamellar into cubic LPS aggregates. Our previous results show that cubic LPS structures exhibit strong endotoxic activity. The property of Hb on the physical state of LPS described here may explain the observation of an increase in LPS-mediating endotoxicity due to the action of Hb.

3

The hematopoietic stem cell (HSC) is probably the best characterized somatic stem cell and is still the only one regularly used in clinical practice. Nevertheless, expansion of HSCs in vitro has been surprisingly unsuccessful, limiting their full therapeutic potential. During homeostasis, the vast majority of HSCs are found in the bone marrow (BM) localized to specific microenvironments called stem cell "niches." Over the last few years our knowledge of cellular niche components and the signaling molecules that coordinate the crosstalk between HSCs and niche cells has dramatically increased. Here we review the two main niche types found in the BM: the endosteal and the vascular niches, and provide an overview of the different signaling and cell adhesion molecules that form the HSC-niche synapse. Signals from BM niches not only control HSC dormancy, but also regulate the balance between self-renewal and differentiation. In the future, successful expansion of HSCs for therapeutic use will require three-dimensional reconstruction of a stem cell-niche unit.

Effects of season, sex and body size on the feeding ecology of turtle-headed seasnakes (Emydocephalus annulatus) on IndoPacific inshore coral reefs

In terrestrial snakes, many cases of intraspecific shifts in dietary habits as a function of predator sex and body size are driven by gape-limitation - and hence, are most common in species that feed on relatively large prey, and exhibit a wide body-size range. Our data on seasnakes reveal an alternative mechanism for intraspecific niche partitioning, based on sex-specific seasonal anorexia induced by reproductive activities. Turtle-headed seasnakes (Emydocephalus annulatus) on coral reefs in the New Caledonian Lagoon feed entirely on the eggs of demersal-spawning fishes. DNA sequence data (cytochrome b gene) on eggs that we palpated from stomachs of 37 snakes showed that despite this ontogenetic-stage specialization, the prey come from a taxonomically diverse array of species including damselfish (41% of samples, at least 5 species), blennies (41%, 4 species) and gobies (19%, 5 species). The composition of snake diets shifted seasonally (with damselfish dominating in winter but not summer), presumably reflecting seasonality of fish reproduction. That seasonal shift affects male and female snakes differently, because reproduction is incompatible with foraging. Adult female seasnakes ceased feeding when they became heavily distended with developing embryos in late summer, and males ceased feeding while they were mate-searching in winter. The sex divergence in foraging habits may be amplified by sexual size dimorphism; females grow larger than males, and larger snakes (of both sexes) feed more on damselfish (which often lay their eggs in exposed sites) than on blennies and gobies (whose eggs are hidden within narrow crevices). Specific features of reproductive biology of coral-reef fish (seasonality and nest type) have generated intraspecific niche partitioning in these seasnakes, by mechanisms different from those that apply to terrestrial snakes.

Pregnancy-associated changes in host permissiveness to metastasis

THESIS SUMMARY : Metastasis is a multistep process involving tumour cell-autonomous features, the host tissue stroma of the primary tumour, the blood or lymphatic system as well as a receptive target organ. Most studies on factors influencing metastasis have concentrated on the characteristics of the disseminating tumour cell and on early steps of metastasis including invasion and angiogenesis. Although these steps are necessary for tumour cells to disseminate, it is the challenges encountered in the later steps of metastasis -survival while in the circulation and engraftment and outgrowth in the target organ -that account for the inefficiency of circulating tumour cells in establishing secondary lesions. Full understanding of the metastatic process therefore requires elucidation of the mechanisms that regulate these late steps, and in particular that determine what makes any given tissue permissive for metastatic tumour growth. To address this issue, we assessed the mechanisms whereby a physiological situation -pregnancy -can alter host permissiveness toward metastasis. We show that pregnant NOD/SCID mice -injected intravenously with tumour cells -develop more metastases than their non-pregnant counterparts irrespective of the tumour cell type. There was no direct effect of pregnancy-related circulating factors on tumour cell proliferation, and subcutaneous tumour growth does not vary between pregnant and nonpregnant animals. However, decreased elimination of tumour cells from the lung microvasculature was observed in pregnant mice, prompting us to assess whether pregnancy-related adaptations in innate immunity could account for this differential clearing. We found that natural killer (NK) cell fractions are decreased in blood and spleen of pregnant mice and that NK cell cytotoxicity is impaired, as reported previously. The use of NK-deficient mice or tumour cell lines resistant to NK killing abrogates the difference in metastasis load between pregnant and virgin mice. CD11 b+ Gr-1+ myeloid-derived suppressor cells (MDSC) have previously been shown to accumulate in tumour-bearing mice and to down-modulate NK activity. Accordingly, we show an increase in MDSC in pregnant mouse blood, spleen, lungs and liver. Depletion of MDSC prior to tumour cell injection decreased metastasis load in pregnant NOD/SCID mice but had no effect on virgin mice. Similarly, adoptive transfer of MDSC extracted from pregnant mice into virgin mice lead to increased metastasis take. In parallel, we investigated whether the lung and liver microenvironments are modified during pregnancy thereby providing a more "permissive soil" for the establishment of metastases. A comparative analysis of microarray data of pregnant mouse lungs and liver with "premetastatic niche" gene expression profiles of these organs shows that similar mechanisms could mediate an increase in lung and liver metastasis in pregnant mice and in mice harbouring an aggressive primary tumour. Several commonly up-regulated genes point towards the recruitment of myeloid cells, consistent with the accumulation of MDSC observed in pregnant mice. MDSC have never been evoked in the context of pregnancy before. Although the role of MDSC in pregnancy requires further investigation we suggest that MDSC accumulation constitutes an important and hitherto unrecognised common denominator of maternal immune tolerance and cancer immune escape. RESUME DE THESE : La métastatisation est un processus en plusieurs étapes qui implique des compétences particulières chez les cellules tumorales, le stroma de la tumeur primaire, les vaisseaux sanguins ou lymphatiques ainsi qu'un organe cible' réceptif. Jusqu'alors, la recherche s'est principalement intéressée aux facteurs qui influencent les étapes précoces de la métastatisation donc aux caractéristiques de la cellule métastatique, et aux processus tels que l'invasion et l'angiogenèse, tandis que peu d'études traitent des étapes tardives tel que la survie dans la circulation sanguine et l'établissement d'une lésion dans l'organe cible. En particulier, l'élucidation des facteurs qui déterminent la permissivité d'un tissu à la greffe de cellules disséminantes est indispensable à la compréhension de ce processus complexe qu'est la métastatisation. Nous proposons ici un modèle de souris récapitulant les étapes tardives de la métastatisation dans un contexte d'une permissivité accrue aux métastases chez la souris gravide, et nous évaluons les mécanismes impliqués. Les souris gestantes développent plus de métastases après l'injection intraveineuse de cellules tumorales, indépendamment du type de tumeur d'origine. Les taux élevés d'hormones et de facteurs de croissance chez la souris gravide n'inflúencent pas la prolifération des cellules tumorales et fa croissance de tumeurs sous-cutanées n'est pas non plus accélérée par la gestation. En revanche, une fois injectées, les cellules tumorales sont éliminées ` moins rapidement des vaisseaux pulmonaires chez la souris gravide que chez les contrôles. Cette observation est compatible avec un effet de la gestation sur l'immunité innée et nous avons mis en évidence une diminution des proportions de cellules NK (natural killer) dans le sang et la rate en particulier, ainsi qu'une cytotoxicité moindre envers des cellules tumorales. En utilisant des souris déficientes en cellules NK ou en injectant des cellules résistantes à l'attaqué par des cellules NK, la différence entre souris gestantes et non-gestantes disparaît. Il a été démontré chez des souris porteuses de tumeurs, que l'accumulation de cellules immunosuppressives de la lignée myélo-monocytaire (ou MDSC pour myeloid-derived suppressor tells) pouvait être responsable d'une inhibition de l'activité de cellules NK. Des nombres augmentés de ces cellules, caractérisées par les marqueurs de surface CD11b et Gr-1, ont été trouvés dans le sang, la rate, les poumons et le foie de souris gravides. Leur rôle dans la métastatisation est démontré par le fait que leur dépletion diminue le nombre de lésions secondaires chez la souris gestante, tandis que leur transfert dans des souris non-gestantes augmente le taux de métastases. L'utilisation de puces à ADN sur les foies et poumons de souris gravides a permis de mettre en évidence des différences d'expression génique proches de celles observées dans l'établissement de niches pré-métastatiques. Ceci suggère que des mécanismes similaires pourraient être responsables d'une permissivité accrue aux métastases chez la souris gravide et chez la souris porteuse d'une tumeur primaire agressive, telle que, en particulier, l'accumulation de cellules immunosuppressives dans les organes cibles. C'est la première fois que l'accumulation de MDSC est évoquée chez la souris gravide et nous proposons ici que celles-ci jouent un rôle dans la tolérance immunitaire envers le foetus et sont responsables de l'échappement de cellules tumorales injectées à la surveillance immunitaire par des cellules NK.

Good genes and good luck: Ammonoid diversity and the end-Permian mass extinction

The end-Permian mass extinction removed more than 80% of marine genera. Ammonoid cephalopods were among the organisms most affected by this crisis. The analysis of a global diversity data set of ammonoid genera covering about 106 million years centered on the Permian-Triassic boundary (PTB) shows that Triassic ammonoids actually reached levels of diversity higher than in the Permian less than 2 million years after the PTB. The data favor a hierarchical rather than logistic model of diversification coupled with a niche incumbency hypothesis. This explosive and nondelayed diversification contrasts with the slow and delayed character of the Triassic biotic recovery as currently illustrated for other, mainly benthic groups such as bivalves and gastropods.

Bioelectrochemical Treatment of Contaminated Groundwater

To remove these pollutants from groundwater, different technologies can be used. Currently, the Environmental Protection Agency (EPA) considers ion exchange, reverse osmosis and reverse electrodialysis to be effective methods for the decrease of their concentrations, below their limit in drinking water. These technologies have some drawbacks, such as low selectivity towards the target pollutant, high energy or chemicals requirements, and the generation of waste brine (pollutants are separated from water, not treated), which require an additional treatment. Bio Electro Chemical Systems (BES) could fill this niche

Generic brands and product differentiation strategies

Generic or own brand products were initially only lesser expensive copies of the branded label alternative, but nowadays, pricing alone is not enough in order to survive in the Fast Moving Consumer Goods (FMCG) or Consumer Packaged Goods (CPG)markets. With this in mind manufacturers of generic brands have adapted to this rapidlygrowing niche by investing in design and marketing during the initial phase in order to be perceived as having a quality product comparable to that of the branded products. In addition, they have gone further ahead with a second phase and resorted to innovativeproduct differentiation strategies and even pure innovation in many cases. These strategies have granted generic brands constantly increasing market shares and a position of equals relative to national brands.Using previous analyses and case studies, this paper will provide conceptual and empirical evidence to explain the surprisingly fast growth and penetration of generic supermarket brands, which in their relatively short lifespan, have grown to rival the historical market leaders, the branded products. According to this analysis, the main conclusion is that the growth in generic brands can be explained not only by price competition, but also by the use of innovative product differentiation strategies.

Diagnostic and identification in situ of fungal pathogens in superficial mycosis

Fungi are divided in 3 groups in the field of medical mycology. The dermatophytes are filamentous fungi able to grow on keratinized tissues from human or animals. They are the main cause of superficial and cutaneous mycoses of the skin and its appendix (hair and nail). The yeasts, or dimorphic fungi, can be responsible of diverse types of infections (superficial to deep mycoses). The moulds include all Non-dermatophyte Filamentous Fungi (NDF). In medical mycology, the most representative moulds are Aspergillus spp., Fusarium spp. and Mucor spp. Diagnosis of mycosis is currently based on direct mycological examination of biological samples, as well as macroscopic and microscopic identification of the infectious fungus in culture assay. However, culture assays were found to remain sterile in roughly 40% of cases otherwise positive by direct mycological examinations. Additionally, results from culture assays are often difficult to interpret as various NDF are sometimes isolated. This thesis work is composed of three projects focusing on the development of new assays for direct in situ identification of fungi from dermatological samples. Part 1. A Polymerase Chain Reaction - Terminal Restriction Fragment Length Polymorphism assay (PCR-TRFLP) targeting the 28S rDNA was developed to identify dermatophytes and NDF in nails with suspected onychomycosis. This method is faster and more efficient than culture. It further enables the distinction of more than one agent in case of mixed infection. A fast and reliable assay for the identification of dermatophytes and NDF in onychomycosis was found to be highly relevant since onychomycosis with Fusarium spp. or other NDF are weakly responsive or unresponsive to standard onychomycosis treatments with oral terbinafine and itraconazole. Part 2. A nested PCR-sequencing assay targeting the 28S rDNA was developed to identify dermatophyte species in skin and hair samples. This method is especially suitable for tinea capitis where dermatophytes identification is critical for subsequently prescribing the adequate treatment. The challenge presented when performing direct PCR fungi identification in skin and hair differs from that seen in onychomycosis as small amount of material is generally collected, few fungal elements are present in the clinical sample and one dermatophyte among a dozen species must be identified. Part 3. Fusarium spp. is currently isolated from nails with a frequency of 15% of that of dermatophytes in the laboratory of Mycology of the CHUV (2005-2012). The aim of this work was to examine if the intensive use of terbinafine and itraconazole could be a cause of the high incidence of Fusarium nail infections. For that purpose, two different methods, specific PCR and TRFLP, were used to detect both Fusarium spp. and Trichophyton spp. in nails of previously treated or untreated patients. TRFLP assay was found to be less sensitive than classical PCR assays specifically detecting Fusarium spp. or Trichophyton spp. Independently of the detection method used, the prevalence of Fusarium spp. appears not to be higher in patients previously treated by oral standard treatment with terbinafine and azoles which are highly effective to fight Trichophyton spp. in nails. In many cases Fusarium sp. was detected in samples of patients not previously subjected to antifungal therapy. Therefore, these treatments do not appear to favor the establishment of Fusarium spp. after elimination of a dermatophyte in nail infection. - En mycologie médicale, les champignons sont classés en 3 groupes. Les dermatophytes sont des champignons filamenteux capables de se développer dans les tissus kératinisés des hommes et des animaux, ils représentent la principale cause des mycoses superficielles et cutanées de la peau et de ses appendices (ongles et cheveux). Les levures, ou champignons dimorphiques, peuvent être responsables de divers types d'infections (superficielles à profondes). Les moisissures incluent tous les champignons filamenteux non-dermatophytes (NDF), les Aspergillus spp., les Fusarium spp. et les Mucor spp. sont les principales espèces rencontrées. Le diagnostic d'une mycose est basé sur un examen mycologique direct des prélèvements biologiques ainsi que sur l'identification macroscopique et microscopique du champignon infectieux isolé en culture. Cependant, dans environ 40% des cas, l'identification de l'agent pathogène est impossible par cette méthode car la culture reste stérile, bien que l'examen direct soit positif. De plus, la croissance de moisissures et/ou autres contaminants peut rendre l'interprétation de l'examen difficile. Ce travail de thèse est composé de trois projets focalisés sur le développement de nouvelles méthodes d'identification des champignons directement à partir d'échantillons dermatologiques. Projet 1. Une méthode de Réaction en chaîne de polymérase couplée à du polymorphisme de longueur des fragments de restriction terminaux (PCR-TRFLP), en ciblant l'ADN ribosomal 28S, a été développée pour l'identification des dermatophytes et moisissures dans les ongles avec suspicion d'onychomycoses. Cette technique s'est avérée plus rapide et plus efficace que la culture, permettant l'identification de plusieurs champignons en même temps. Posséder une méthode d'identification rapide et fiable des dermatophytes et des NDF dans les onychomycoses a été jugée nécessaire du fait que les Fusarium et d'autres NDF sont peu ou pas sensibles aux traitements oraux standards à la terbinafine et à Γ itraconazole. Projet 2. Une PCR nichée couplée au séquençage d'un fragment de l'ADN ribosomal 28S a été développée afin de différencier les dermatophytes dans la peau et les cheveux. Cette méthode est particulièrement adaptée au cas de tinea capitis, où l'identification du dermatophyte est essentielle afin de prescrire le traitement adéquat. Le problème de l'identification du pathogène fongique dans les cheveux et la peau diffère des onychomycoses car de petites quantités sont prélevées chez les patients, peu d'éléments fongiques sont présents et il faut discriminer un dermatophyte parmi une douzaine d'espèces potentielles. Projet 3. Au laboratoire de Mycologie du CHUV, les Fusarium ont été isolé dans les ongles à une fréquence de 15% pour la période 2005-2012. Le but de ce travail était d'examiner si l'utilisation intensive de terbinafine et d'itraconazole pouvait être une des causes de la forte incidence des infections des ongles par Fusarium. A cet effet, deux méthodes ont été utilisées pour détecter à la fois Fusarium spp. et Trichophyton spp., la PCR spécifique et le TRFLP. Indépendamment de la méthode choisie, il en résulte que la prévalence des Fusarium η'apparaît pas liée à un traitement au préalable des patients avec de la terbinafine ou des azoles, thérapies très efficaces contre les Trichophyton spp. dans les ongles. De plus, il existe de nombreux cas où Fusarium était détecté chez des patients non traités.

Integrating species distribution models (SDMs) and phylogeography for two species of Alpine Primula.

The major intention of the present study was to investigate whether an approach combining the use of niche-based palaeodistribution modeling and phylo-geography would support or modify hypotheses about the Quaternary distributional history derived from phylogeographic methods alone. Our study system comprised two closely related species of Alpine Primula. We used species distribution models based on the extant distribution of the species and last glacial maximum (LGM) climate models to predict the distribution of the two species during the LGM. Phylogeographic data were generated using amplified fragment length polymorphisms (AFLPs). In Primula hirsuta, models of past distribution and phylogeographic data are partly congruent and support the hypothesis of widespread nunatak survival in the Central Alps. Species distribution models (SDMs) allowed us to differentiate between alpine regions that harbor potential nunatak areas and regions that have been colonized from other areas. SDMs revealed that diversity is a good indicator for nunataks, while rarity is a good indicator for peripheral relict populations that were not source for the recolonization of the inner Alps. In P. daonensis, palaeo-distribution models and phylogeographic data are incongruent. Besides the uncertainty inherent to this type of modeling approach (e.g., relatively coarse 1-km grain size), disagreement of models and data may partly be caused by shifts of ecological niche in both species. Nevertheless, we demonstrate that the combination of palaeo-distribution modeling with phylogeographical approaches provides a more differentiated picture of the distributional history of species and partly supports (P. hirsuta) and partly modifies (P. daonensis and P. hirsuta) hypotheses of Quaternary distributional history. Some of the refugial area indicated by palaeodistribution models could not have been identified with phylogeographic data.

Estequiometria i metabolòmica d'Alopecurus pratensis i Holcus lanatus en condicions de sequera

La variabilitat de l’estequiometria elemental dels organismes a causa de l’ontogènia i dels canvis en les condicions ambientals està relacionada amb la variabilitat metabolòmica. Això és degut a que els elements operen majoritàriament com a parts de compostos moleculars. Així doncs, la hipòtesi realitzada per Rivas-Ubach et al., (2012), la qual postula que els estudis estequiomètrics i metabolòmics d’un conjunt d’espècies vegetals exposades a condicions ambientals diferents han de mostrar la flexibilitat que posseeix un organisme a l’hora de modular la seva estequiometria i el seu metaboloma per tal de mantenir la forma òptima sota condicions variants, esdevé la base que sustenta l’experiment EVENT II. A partir de l’estudi de les relacions estequiomètriques, -principalment C:N:P- i del metabolisme d’Alopecurus pratensis i Holcus lanatus en situacions simulades de sequera, s’han obtingut resultats que evidencien una clara diferenciació a nivell d’espècie, de part de la planta i de tractament. El metabolisme i l’estequiometria diferencial que presenten ambdues gramínies dóna suport a la hipòtesi del nínxol biogeoquímic. A nivell de parts de la planta, s’observa un clar augment de la relació C:nutrients a la part aèria, mentre que a les arrels, aquesta relació disminueix. La part aèria doncs, necessita més C per invertir en funcions estructurals, mentre que l’elevada concentració de nutrients i metabòlits a les arrels donen indicis de la presència de mecanismes osmòtics per a facilitar l’entrada d’aigua, i de creixement, per a la recerca de noves fonts d’aigua, observant-se una disminució de la relació part aèria:arrels. Un altre factor que demostra aquest creixement radicular són les baixes relacions N:P trobades, fet que dóna suport a la hipòtesi de la velocitat de creixement.

Modelling ecological niches with support vector machines

1. The ecological niche is a fundamental biological concept. Modelling species' niches is central to numerous ecological applications, including predicting species invasions, identifying reservoirs for disease, nature reserve design and forecasting the effects of anthropogenic and natural climate change on species' ranges. 2. A computational analogue of Hutchinson's ecological niche concept (the multidimensional hyperspace of species' environmental requirements) is the support of the distribution of environments in which the species persist. Recently developed machine-learning algorithms can estimate the support of such high-dimensional distributions. We show how support vector machines can be used to map ecological niches using only observations of species presence to train distribution models for 106 species of woody plants and trees in a montane environment using up to nine environmental covariates. 3. We compared the accuracy of three methods that differ in their approaches to reducing model complexity. We tested models with independent observations of both species presence and species absence. We found that the simplest procedure, which uses all available variables and no pre-processing to reduce correlation, was best overall. Ecological niche models based on support vector machines are theoretically superior to models that rely on simulating pseudo-absence data and are comparable in empirical tests. 4. Synthesis and applications. Accurate species distribution models are crucial for effective environmental planning, management and conservation, and for unravelling the role of the environment in human health and welfare. Models based on distribution estimation rather than classification overcome theoretical and practical obstacles that pervade species distribution modelling. In particular, ecological niche models based on machine-learning algorithms for estimating the support of a statistical distribution provide a promising new approach to identifying species' potential distributions and to project changes in these distributions as a result of climate change, land use and landscape alteration.

An improved approach for predicting the distribution of rare and endangered species from occurrence and pseudo-absence data

1. Few examples of habitat-modelling studies of rare and endangered species exist in the literature, although from a conservation perspective predicting their distribution would prove particularly useful. Paucity of data and lack of valid absences are the probable reasons for this shortcoming. Analytic solutions to accommodate the lack of absence include the ecological niche factor analysis (ENFA) and the use of generalized linear models (GLM) with simulated pseudo-absences. 2. In this study we tested a new approach to generating pseudo-absences, based on a preliminary ENFA habitat suitability (HS) map, for the endangered species Eryngium alpinum. This method of generating pseudo-absences was compared with two others: (i) use of a GLM with pseudo-absences generated totally at random, and (ii) use of an ENFA only. 3. The influence of two different spatial resolutions (i.e. grain) was also assessed for tackling the dilemma of quality (grain) vs. quantity (number of occurrences). Each combination of the three above-mentioned methods with the two grains generated a distinct HS map. 4. Four evaluation measures were used for comparing these HS maps: total deviance explained, best kappa, Gini coefficient and minimal predicted area (MPA). The last is a new evaluation criterion proposed in this study. 5. Results showed that (i) GLM models using ENFA-weighted pseudo-absence provide better results, except for the MPA value, and that (ii) quality (spatial resolution and locational accuracy) of the data appears to be more important than quantity (number of occurrences). Furthermore, the proposed MPA value is suggested as a useful measure of model evaluation when used to complement classical statistical measures. 6. Synthesis and applications. We suggest that the use of ENFA-weighted pseudo-absence is a possible way to enhance the quality of GLM-based potential distribution maps and that data quality (i.e. spatial resolution) prevails over quantity (i.e. number of data). Increased accuracy of potential distribution maps could help to define better suitable areas for species protection and reintroduction.

Detection of siderophores in endophytic bacteria Methylobacterium spp. associated with Xylella fastidiosa subsp. pauca

The objective of this work was to study the production of siderophores by endophytic bacteria Methylobacterium spp., which occupy the same ecological niche as Xylella fastidiosa subsp. pauca (Xfp) in citrus plants. The siderophore production of Methylobacterium strains was tested according to chromeazurol agar assay test (CAS), Csáky test (hydroxamate-type) and Arnow test (catechol-type). In addition, the ability of Xfp to use siderophores, in vitro, produced by endophytic bacteria as source of iron, was evaluated. All 37 strains of Methylobacterium spp. tested were CAS-positive for siderophore production. Methylobacterium spp. produced hydroxamate-type, but not catechol-type siderophores. In vitro growth of Xfp was stimulated by the presence of supernatant siderophores of endophytic Methylobacterium mesophilicum.

Signalling pathways in skin homeostasis

SUMMARY The results presented here contribute to a better understanding of the crucial molecular relationships and signalling cues exchanged by several fundamental cell types (epidermal keratinocytes, dermal fibroblasts, immune and endothelial cells) of the skin. Importantly we provide evidence to directly implicate Wnt/ß-catenin signalling as a putative player in different cell types (keratinocytes and neutrophils) in mediation of the cutaneous inflammatory response (Fart A). Finally we highlight the importance of several molecules, specifically expressed in the hair follicle stem cell niche to the morphogenesis and homeostasis of the hair follicle (Part B). PART A Currently the body of work pertaining to Wnt signalling and immune cells largely focuses on Wnt signalling in the development of these cells. The data presented here suggests a novel mechanism in which Wnt signalling appears to modulate immune cell recruitment to the skin. Keratinocytes are major contributors to early inflammatory responses by the release of chemokines which recruit immune cells. The resultant inflammatory response is a dynamic process of sequentially infiltrating immune cells governed by a network of growth factors, chemokines and cytokines. In wild type mice the response is typified by a rapid and substantial infiltration of neutrophils followed at later time points by macrophages and Tcells. The expression of the canonical Wnt pathway activating ligand, Wnt3a, is able to induce a strong neutrophil infiltration in the dermis. This response originates in keratinocytes, as it is abrogated upon keratinocyte-specific ablation of ß-catenin. Notably, this suggests that the crucial cross talk between these resident cells and recruited immune cells is, in part, mediated by Wnt signalling. In corroboration of this role of Wnt-mediated recruitment of neutrophils, expression of the Wnt inhibitory ligand sFRPI during acute inflammation results in a dramatic 'dampening' of immune cell infiltration in particular of neutrophil chemoattraction. Importantly, an intrinsic Wnt signalling pathway is essential for neutrophil chemoattraction in response to inflammatory stimuli. There is a marked reduction of neutrophil infiltration in mice grafted with a ß-catenin deficient bone marrow upon TPA induced cutaneous inflammation. Additionally, neutrophils lacking Wnt/ß-catenin fail to respond to IFNγ, an early inflammatory cue, in vitro. In combination, these data indicate a potent function of Wnt signalling in immune cell recruitment and the modulation of the inflammatory response. PART B Tissue specific stem cells form the cellular base on which tissue homeostasis and repair of adult tissue relies. The maintenance of this stem cell pool is highly dependent on the immediate environment or niche. We have identified three genes, the fibroblast growth factor receptor 1 (FGFR1), serpin protease inhibitor (serpin F1) and the haematopoietic cell phosphatase (Hcph) to be specifically expressed in a small population of stromal cells which are in close contact to bulge stem cells. These specialized stromal cells might represent an essential mesenchymal component of the skin stem cell niche and may regulate stem cell proliferation and differentiation. Multiple FGFR1 isoforms are generated through alternate transcript splicing and are able to interact with both FGFs and cell adhesion molecules. Two predominant forms of the receptor are FGFR1-α and FGFR1-ß. Expression of a dominant negative form of the alpha isoform prevents hair follicle morphogenesis altogether. Given that FGFR1-ß signals principally through the FGF ligands, this data indicates that FGF signalling is dispensable for follicle morphogenesis. Moreover the loss of follicular morphogenesis upon suggests a requirement for signalling via cell adhesion molecule association with the receptor as FGFR1 α has a greater affinity for these molecules. The expression of the second candidate niche gene serpin f1, lead to the complete ablation of hair follicle morphogenesis. The serpin f1 product, pigment-epithelial derived factor (PEDF) has potent anti-angiogenic effects. Immunohistochemical analysis using CD31, a endothelial cell marker, revealed that although these cells are present, they have are disorganised and do not form vessels. Interestingly, endothelial cells have been found to contribute to the neuronal stem cell niche and our results suggest a similar mechanism in the skin. SHP1, the Hcph gene product, is a phosphatase which acts in the haematopoetic system. Motheaten mice carrying spontaneous mutations in the Hcph gene have patchy alopecia in their skin and severe defects in their haematopoietic system. However the haematopoietic rescue of the mouse does not result in normal follicular homeostasis. Additionally, ablation of Hcph in either the dermal or keratinocyte compartments of the skin produces hair follicles with abberant morphologies. This data indicates that although SHP1 is not essential for hair follicle morphogenesis it is required in both epidermal and dermal compartments to maintain follicular morphology. RÉSUMÉ PARTIE A Jusqu'à présent, les travaux dédiés à l'étude de la voie de signalisation Wnt dans le système immunitaire se sont essentiellement concentrés sur son rôle dans le développement des cellules immunitaires. Les données présentées ici suggèrent fortement et de manière nouvelle, l'existence d'un mécanisme par lequel la voie de signalisation Wnt/ß-caténine module le recrutement de cellules immunitaires dans un tissu périphérique, la peau, et ainsi la réponse inflammatoire cutanée. La réponse inflammatoire cutanée est un processus dynamique d'infiltration séquentielle de diverses cellules immunitaires, orchestré par un réseau de facteurs de croissance, chémokines et cytokines. Les kératinocytes sont des contributeurs majeurs à la réponse inflammatoire précoce par la libération de chémokines qui permettent ensuite de recruter les cellules immunitaires. Dans des souris sauvages, la réponse est d'abord caractérisée par une infiltration rapide et substantielle de neutrophiles, suivie par celle des macrophages et des lymphocytes T. L'expression d'un ligand activateur de le voie canonique de signalisation Wnt (après injection infra-dermique de fibroblastes sur-exprimant Wnt-3a) induit une infiltration dermique très marquée de neutrophiles. De plus, la réponse est éliminée en l'absence de ß-caténine spécifiquement dans les kératinocytes, indiquant que ces cellules sont à l'origine de la réponse. De manière remarquable, ceci suggère qu'une signalisation cruciale entre ces cellules résidentes de la peau et les cellules immunitaires recrutées est, au moins en partie, médiée par la voie Wnt. Corroborant ce rôle de la voie Wnt/ß-caténine dans le recrutement des neutrophiles, l'expression d'un ligand inhibiteur de la voie (sFRP1) résulte au cours d'une inflammation aigüe en une réduction spectaculaire de l'infiltration des cellules immunitaires en général, et des neutrophiles en particulier. De manière importante, la voie de signalisation Wnt est intrinsèquement requise pour la chémoattraction des neutrophiles en réponse à un stimulus inflammatoire. En effet, suite à une inflammation cutanée induite par un ester de phorbol (TPA), une réduction notable de l'infiltration des neutrophiles est observée dans des souris préalablement greffées avec de la moelle osseuse constituée de cellules déficientes en ß-caténine. De plus, in vitro, les neutrophiles sans ß-caténine ne répondent pas à une stimulation par l'interféron γ, qui est pourtant un signal inflammatoire établi in vivo. En conclusion, nos données indiquent que la voie de signalisation Wnt/ß-caténine joue une fonction active dans le recrutement des cellules immunitaires vers un organe périphérique, la peau, ainsi que dans la modulation, à plusieurs niveaux, de la réponse inflammatoire cutanée. PARTIE B Les cellules souches tissu-spécifiques forment la base cellulaire sur laquelle repose l'homéostase et la réparation tissulaires chez l'adulte. La maintenance de ce réservoir de cellules souches est hautement dépendante de leur environnement cellulaire immédiat, encore appelé «niche des cellules souches». Dans la peau, ces cellules stromales spécialisées représentent un compartiment mésenchymateux essentiel de la niche des cellules souches en régulant leurs prolifération et différentiation. Nous avons identifié trois gènes, le «récepteur 1 àux facteurs de croissance des fibroblastes » (Fgfr1 ), l' «inhibiteur de protéase à sérine » (serpinf1 ou pedf) et la « phosphatase des cellules hématopoiétiques » (Hcph ou Ptpn6), comme spécifiquement exprimés par une petite population de cellules stromales qui sont étroitement associées aux cellules souches de la peau (localisées au niveau du bombement du follicule pileux). Pour analyser leur fonction dans ce contexte, nous avons utilisé un test de reconstitution complète de peau murine en combinaison à des. transductions géniques basées sur l'utilisation de lentivirus. Ce test repose sur le mélange de deux compartiments cellulaires, épidermique (kératinocytes) et dermique (fibroblastes), greffés sur une zone ouverte de peau du dos d'une souris pour ensemble reconstituer la peau. Des isoformes multiples de FGFR1 sont générées par épissage alternatif de transcrits et sont capables d'interagir à la fois avec les FGFs (facteurs de croissance des fibroblastes) et les molécules d'adhésion cellulaires. Les deux formes prédominantes du récepteur, FGFR1-α et FGFR1-ß, ne différent que par le «domaine ressemblant aux immunoglobulines 1 » (immunoglobulin-like 1 domain), absent de FGFR1-ß. De plus, FGFR1-ß a une affinité plus grande pour les FGFs et plus faible pour les molécules d'adhésion cellulaires telles que la Ncadhérine (connue pour activer FGFR). La sur-expression de l'une ou l'autre des formes n'empêche pas la morphogenèse folliculaire mais conduit à la formation de follicules aberrants. Toutefois, une différence phénotypique majeure est observée lorsqu'une forme «Dominant-Négatif » (DN) est exprimée dans le compartiment dermique. La sur-expression de FGFR1-ß DN conduit en effet à la formation de follicules petits et tronqués, avec des gaines épithéliales et un bulbe élargis ainsi qu'une petite papille dermique. Par contre, l'expression de FGFR1-α DN abolit complètement la morphogenèse folliculaire. Etant donné que la signalisation par FGFR1-ß est principalement dépendante des ligands FGFs, ces données indiquent que la signalisation par ceux-cì est non-nécessaire à la morphogenèse folliculaire. De plus, l'abolition du processus par la sur-expression de FGFR1-a DN suggëre une signalisation nécessaire entre le récepteur FGFR1 et une ou des molécules d'adhésion cellulaire. L'expression de notre second candidat comme gène spécifique de la niche des cellules souches de la peau, serpinf1, prévient la morphogenèse folliculaire. Seules de petites structures ressemblant à des cystes sont observées après reconstitution de la peau. De plus, dans ces transplants, aucune cellule CD34-positive (marqueur des cellules souches) n'est retrouvée associé à ces cystes. Le produit du gène serpin f1, le «facteur dérivé d'épithélium pigmentaire » (PEDF) est un puissant facteur anti-angiogénique. Nous avons donc analysé la vascularisation des transplants par immunohistochirnies utilisant CD31, un marqueur des cellules endothéliales. Nos résultats révèlent que les cellules endothéliales sont bien présentes, mais de manière désorganisée et ne formant pas de vaisseaux. De manière intéressante, les cellules endothéliales contribuent activement à la niche des cellules souches neuronales, et nos résultats suggèrent donc l'existence possible d'un mécanisme similaire dans la peau. SHP1, le produit du gène Hcph, est une phosphatase quì agit dans le système hématopoiétique. Les souris « motheaten »qui portent des mutations spontanées du gène ont une alopécie inégale au niveau de la peau et de sévères troubles du système hématopoiétique. Pour s'assurer que le phénotype observé au niveau de la peau n'est pas une conséquence d'un défaut du système hématopoiétique, nous avons transplanté des souris Hcph -/- avec de la moelle osseuse sauvage afin de restaurer la fonction de SHP 1 dans le système hématopoiétique. Toutefois, le défaut de morphologie folliculaire est maintenu. De plus, l'ablation d'Hcph dans le compartiment dermique ou épidermique d'essais de reconstitution de peau conduit à la production de follicules pileux avec des morphologies aberrantes. Ces données indiquent que SHP1 n'est pas essentiel à la morphogenèse folliculaire mais est toutefois requis à la fois dans les compartiments épidermiques et dermiques pour la maintenance de la forme du follicule.

Impacts of climate change on Swiss biodiversity: An indicator taxa approach

We present a new indicator taxa approach to the prediction of climate change effects on biodiversity at the national level in Switzerland. As indicators, we select a set of the most widely distributed species that account for 95% of geographical variation in sampled species richness of birds, butterflies, and vascular plants. Species data come from a national program designed to monitor spatial and temporal trends in species richness. We examine some opportunities and limitations in using these data. We develop ecological niche models for the species as functions of both climate and land cover variables. We project these models to the future using climate predictions that correspond to two IPCC 3rd assessment scenarios for the development of 'greenhouse' gas emissions. We find that models that are calibrated with Swiss national monitoring data perform well in 10-fold cross-validation, but can fail to capture the hot-dry end of environmental gradients that constrain some species distributions. Models for indicator species in all three higher taxa predict that climate change will result in turnover in species composition even where there is little net change in predicted species richness. Indicator species from high elevations lose most areas of suitable climate even under the relatively mild B2 scenario. We project some areas to increase in the number of species for which climate conditions are suitable early in the current century, but these areas become less suitable for a majority of species by the end of the century. Selection of indicator species based on rank prevalence results in a set of models that predict observed species richness better than a similar set of species selected based on high rank of model AUC values. An indicator species approach based on selected species that are relatively common may facilitate the use of national monitoring data for predicting climate change effects on the distribution of biodiversity.