Understanding the two-component sensing System of virulent bacteria

Report for the scientific sojourn carried out at the l’ Institute for Computational Molecular Science of the Temple University, United States, from 2010 to 2012. Two-component systems (TCS) are used by pathogenic bacteria to sense the environment within a host and activate mechanisms related to virulence and antimicrobial resistance. A prototypical example is the PhoQ/PhoP system, which is the major regulator of virulence in Salmonella. Hence, PhoQ is an attractive target for the design of new antibiotics against foodborne diseases. Inhibition of the PhoQ-mediated bacterial virulence does not result in growth inhibition, presenting less selective pressure for the generation of antibiotic resistance. Moreover, PhoQ is a histidine kinase (HK) and it is absent in animals. Nevertheless, the design of satisfactory HK inhibitors has been proven to be a challenge. To compete with the intracellular ATP concentrations, the affinity of a HK inhibidor must be in the micromolar-nanomolar range, whereas the current lead compounds have at best millimolar affinities. Moreover, the drug selectivity depends on the conformation of a highly variable loop, referred to as the “ATP-lid, which is difficult to study by X-Ray crystallography due to its flexibility. I have investigated the binding of different HK inhibitors to PhoQ. In particular, all-atom molecular dynamics simulations have been combined with enhanced sampling techniques in order to provide structural and dynamic information of the conformation of the ATP-lid. Transient interactions between these drugs and the ATP-lid have been identified and the free energy of the different binding modes has been estimated. The results obtained pinpoint the importance of protein flexibility in the HK-inhibitor binding, and constitute a first step in developing more potent and selective drugs. The computational resources of the hosting institution as well as the experience of the members of the group in drug binding and free energy methods have been crucial to carry out this work.

Evolutionary history and its relevance in understanding and conserving southern African biodiversity

Abstract : Understanding how biodiversity is distributed is central to any conservation effort and has traditionally been based on niche modeling and the causal relationship between spatial distribution of organisms and their environment. More recently, the study of species' evolutionary history and relatedness has permeated the fields of ecology and conservation and, coupled with spatial predictions, provides useful insights to the origin of current biodiversity patterns, community structuring and potential vulnerability to extinction. This thesis explores several key ecological questions by combining the fields of niche modeling and phylogenetics and using important components of southern African biodiversity. The aims of this thesis are to provide comparisons of biodiversity measures, to assess how climate change will affect evolutionary history loss, to ask whether there is a clear link between evolutionary history and morphology and to investigate the potential role of relatedness in macro-climatic niche structuring. The first part of my thesis provides a fine scale comparison and spatial overlap quantification of species richness and phylogenetic diversity predictions for one of the most diverse plant families in the Cape Floristic Region (CFR), the Proteaceae. In several of the measures used, patterns do not match sufficiently to argue that species relatedness information is implicit in species richness patterns. The second part of my thesis predicts how climate change may affect threat and potential extinction of southern African animal and plant taxa. I compare present and future niche models to assess whether predicted species extinction will result in higher or lower V phylogenetic diversity survival than what would be experienced under random extinction processes. l find that predicted extinction will result in lower phylogenetic diversity survival but that this non-random pattern will be detected only after a substantial proportion of the taxa in each group has been lost. The third part of my thesis explores the relationship between phylogenetic and morphological distance in southern African bats to assess whether long evolutionary histories correspond to equally high levels of morphological variation, as predicted by a neutral model of character evolution. I find no such evidence; on the contrary weak negative trends are detected for this group, as well as in simulations of both neutral and convergent character evolution. Finally, I ask whether spatial and climatic niche occupancy in southern African bats is influenced by evolutionary history or not. I relate divergence time between species pairs to climatic niche and range overlap and find no evidence for clear phylogenetic structuring. I argue that this may be due to particularly high levels of micro-niche partitioning. Résumé : Comprendre la distribution de la biodiversité représente un enjeu majeur pour la conservation de la nature. Les analyses se basent le plus souvent sur la modélisation de la niche écologique à travers l'étude des relations causales entre la distribution spatiale des organismes et leur environnement. Depuis peu, l'étude de l'histoire évolutive des organismes est également utilisée dans les domaines de l'écologie et de la conservation. En combinaison avec la modélisation de la distribution spatiale des organismes, cette nouvelle approche fournit des informations pertinentes pour mieux comprendre l'origine des patterns de biodiversité actuels, de la structuration des communautés et des risques potentiels d'extinction. Cette thèse explore plusieurs grandes questions écologiques, en combinant les domaines de la modélisation de la niche et de la phylogénétique. Elle s'applique aux composants importants de la biodiversité de l'Afrique australe. Les objectifs de cette thèse ont été l) de comparer différentes mesures de la biodiversité, 2) d'évaluer l'impact des changements climatiques à venir sur la perte de diversité phylogénétique, 3) d'analyser le lien potentiel entre diversité phylogénétique et diversité morphologique et 4) d'étudier le rôle potentiel de la phylogénie sur la structuration des niches macro-climatiques des espèces. La première partie de cette thèse fournit une comparaison spatiale, et une quantification du chevauchement, entre des prévisions de richesse spécifique et des prédictions de la diversité phylogénétique pour l'une des familles de plantes les plus riches en espèces de la région floristique du Cap (CFR), les Proteaceae. Il résulte des analyses que plusieurs mesures de diversité phylogénétique montraient des distributions spatiales différentes de la richesse spécifique, habituellement utilisée pour édicter des mesures de conservation. La deuxième partie évalue les effets potentiels des changements climatiques attendus sur les taux d'extinction d'animaux et de plantes de l'Afrique australe. Pour cela, des modèles de distribution d'espèces actuels et futurs ont permis de déterminer si l'extinction des espèces se traduira par une plus grande ou une plus petite perte de diversité phylogénétique en comparaison à un processus d'extinction aléatoire. Les résultats ont effectivement montré que l'extinction des espèces liées aux changements climatiques pourrait entraîner une perte plus grande de diversité phylogénétique. Cependant, cette perte ne serait plus grande que celle liée à un processus d'extinction aléatoire qu'à partir d'une forte perte de taxons dans chaque groupe. La troisième partie de cette thèse explore la relation entre distances phylogénétiques et morphologiques d'espèces de chauves-souris de l'Afrique australe. ll s'agit plus précisément de déterminer si une longue histoire évolutive correspond également à des variations morphologiques plus grandes dans ce groupe. Cette relation est en fait prédite par un modèle neutre d'évolution de caractères. Aucune évidence de cette relation n'a émergé des analyses. Au contraire, des tendances négatives ont été détectées, ce qui représenterait la conséquence d'une évolution convergente entre clades et des niveaux élevés de cloisonnement pour chaque clade. Enfin, la dernière partie présente une étude sur la répartition de la niche climatique des chauves-souris de l'Afrique australe. Dans cette étude je rapporte temps de divergence évolutive (ou deux espèces ont divergé depuis un ancêtre commun) au niveau de chevauchement de leurs niches climatiques. Les résultats n'ont pas pu mettre en évidence de lien entre ces deux paramètres. Les résultats soutiennent plutôt l'idée que cela pourrait être I dû à des niveaux particulièrement élevés de répartition de la niche à échelle fine.

Phosphate and zinc transport and signalling in plants: toward a better understanding of their homeostasis interaction.

Inorganic phosphate (Pi) and zinc (Zn) are two essential nutrients for plant growth. In soils, these two minerals are either present in low amounts or are poorly available to plants. Consequently, worldwide agriculture has become dependent on external sources of Pi and Zn fertilizers to increase crop yields. However, this strategy is neither economically nor ecologically sustainable in the long term, particularly for Pi, which is a non-renewable resource. To date, research has emphasized the analysis of mineral nutrition considering each nutrient individually, and showed that Pi and Zn homeostasis is highly regulated in a complex process. Interestingly, numerous observations point to an unexpected interconnection between the homeostasis of the two nutrients. Nevertheless, despite their fundamental importance, the molecular bases and biological significance of these interactions remain largely unknown. Such interconnections can account for shortcomings of current agronomic models that typically focus on improving the assimilation of individual elements. Here, current knowledge on the regulation of the transport and signalling of Pi and Zn individually is reviewed, and then insights are provided on the recent progress made towards a better understanding of the Zn-Pi homeostasis interaction in plants.

MRI newsletter 8: Georeferenced biological databases - A tool for understanding mountain biodiversity

The Mountain Research Initiative invited Dr Eva Spehn, Director of the Global Mountain Biodiversity Assessment (GMBA), and Dr Antoine Guisan, head of the Spatial Ecology Group at the University of Lausanne, to introduce the reader to their coordinated efforts to advance understanding and prediction of mountain biodiversity. Antoine Guisan's EUROMONT project is one of the many scientific projects that may potentially provide data for the new GMBA initiative for a GIS mountain biodiversity database.

Theorizing institutional changes: understanding decentralization and federalization in Brazil, Spain and South Africa

In light of the existing theories about institutional change, this paper seeks to advance a common framework to understand the unfolding of decentralization and federalization in three countries: Brazil, Spain, and South Africa. Although in different continents, these three countries witnessed processes after their respective transitions to democracy that transferred administrative and fiscal authority to their regions (decentralization) and vertically distributed political and institutional capacity (federalization). This paper attempts to explain how institutional changes prompted a shift of power and authority towards regional governments by looking at internal sources of change within the intergovernmental arena in the three countries. This analysis is organized around two propositions: that once countries transit to democracy under all-encompassing constitutions there are high incentives for institutional change, and that under a bargained intergovernmental interaction among political actors subnational political elites are able to advance their interests incrementally. In short, through a common framework this paper will explain the evolving dynamics of intergovernmental dynamics in three countries.

Role of complementary therapies in the understanding of primary healthcare professionals: a systematic review

Objective To identify the understanding of the healthcare professionals in relation to the role of complementary therapies in primary health care. Method Systematic review by way of the following information sources: PubMed, CINAHL, PeriEnf, AMED, EMBASE, Web of Science, Psicoinfo and Psicodoc, using the keyword Primary Health Care alone, and associated with the following keywords: Medicinal Plants, Herbal Medicine, Homeopathy, Traditional Chinese Medicine, Acupuncture, Anthroposophical Medicine. Results Twenty-two studies from 1986 to 2011 were included. We identified three styles of practice: conventional medicine, complementary therapies and integrative medicine. Positioning professional practices within these three styles may facilitate discussion of concepts of health care, enhancing the health care provided as a result. Conclusion The work process in primary care presents difficulties for conducting integrative and holistic health care, but this practice has been introduced over time by professionals who integrate conventional medicine and complementary therapies, concerned with the care and well-being of patients.


Understanding the experiences of caregivers of children with tuberculosis in directly observed therapy

Objective To understand the situations and communications experienced by caregivers of children with tuberculosis (TB) with regard to directly observed therapy (DOT). Method A descriptive exploratory study with a qualitative approach was applied and developed in the ambulatory of Programa Einstein na Comunidade de Paraisópolis (PECP). The data were collected using semi-structured interviews of 13 caregivers of children with TB in DOT. The Collective Subject Discourse (CSD) method was used to analyze the data. Results Seven CSDs were identified and grouped into four categories: "Living in a difficult situation", "Changing the family routine", "Responsibility almost always fall son the mother", and "Adapting to the DOT". Conclusions The difficulties faced by the caregiver of the child at the beginning of DOT significantly changed the familiar routine. The responsibility for its continuity was assigned to the mother, who must adapt to the demands of the treatment and face the situation.

Understanding child neglect in a gender context: a study performed in a Brazilian city

OBJECTIVETo describe the phenomenon of child neglect and understand it in a gender context.METHODRetrospective, quantitative, and exploratory study that analyzed reports of violence by a child and adolescent protection network in a Brazilian city. The theoretical and methodological basis applied was TIPESC (Theory of Nursing Praxical Intervention in Collective Health), with a gender emphasis.RESULTSNeglect of children under the age of ten represents more than half the reports received over all the years studied; more boys than girls suffered neglect and 41.4% of the reports of neglect involved children under than age of three; women were identified as being solely responsible in 67.9%, and as accessories in 17.3% of the incidents reported.CONCLUSIONChild neglect is a complex matter, the gender subordinate status inflicted on these children and their mothers who are responsible for their care underscore the social vulnerability of this group.

Development of premature children: caregivers' understanding according to the Bioecological Theory

Abstract OBJECTIVE Understanding the conceptions of premature children caregivers on child development and associated factors. METHOD An exploratory-descriptive qualitative study of 12 families with children under three years of age. Interviews were submitted to thematic content analysis, systematized into the categories of Bioecological Theory of Human Development: Process, Person, Context and Time, and in the Functional Development category. RESULTS There are concerns about impairment in the current and future development of a Person/child defined as fragile as a result of premature birth (Time dimension), minimized by the scope of observable competencies such as motor skills. The Context, especially family and health services, and Proximal Processes, described as one-way caregiver interactions, are considered determinants of development. Functional Development is considered a natural consequence and result of education. The support network is crucial, supporting or limiting care. CONCLUSION Concerns about the development mobilize caregivers to stimulate the premature child/person and requests family and healthcare assistance.