Premièrement, nous avons analysé 14 génomes publiés de M. abscessus montrant quece taxon comprend au moins cinq taxons différents spécifiés par des caractéristiques microbiologiques d’intérêt médical. Au cours d'un deuxième travail, nous avons développé une technique d’identification et de génotypage de M. abscessus qui a permis de distinguer sans ambiguïté M. massiliense de M. bolletii et M. abscessus.Nous avons ensuite analysé le bactériophage de M. bolletii que nous avons nommé Araucaria. La résolution de sa structure 3D a montré une capside et un connecteur similaires à ceux de plusieurs bactériophages de bactéries à Gram négatif et positif; et une queue hélicoïdale décorée par des pointes radiales. La partie basale (baseplate) du phage Araucaria présente des caractéristiques observées dans les phages se liant à des récepteurs de protéines. Araucaria se lie à son hôte en deux temps, un premier par liaison de la queue aux saccharides de l'hôte puis un deuxième par liaison de la baseplate aux protéines de la paroi cellulaire.Nous avons analysé la présence de séquence de phages dans 48 génomes disponibles de M. abscessus. Notre analyse phylogénétique suggère que les espèces de M. abscessus ont été infectées par différents mycobactériophages et ont une histoire évolutive différente de celle des hôtes mycobactériens et contiennent aussi des protéines acquises par transfert horizontal.Enfin, nous avons séquencé et analysé deux mycobactéries non-tuberculeuses responsables d’infections opportunistes, Mycobacterium simiae et Mycobacterium septicum. / In a first step, we reviewed the published genomes of 14 M. abscessus strains showing that M. abscessus sensu lato comprises of five different taxons specified by particular characteristics of microbiological and medical interests. In a second step, based on sequencing of eight intergenic spaces, we developed a Multispacer Sequence Typing technique (MST) for M. abscessus group sub-species identification and strain genotyping. MST clearly differentiates formerly “M. massiliense” organisms from other M. abscessus subsp. bolletii organisms. We also analyzed a bacteriophage from M. bolletii that we named Araucaria. We resolved Araucaria 3D structure, its capsid and connector share close similarity with several phages from Gram- or Gram+ bacteria. The helical tail decorated by radial spikes, possibly host adhesion devices. Its host adsorption device, at the tail tip, assembles features observed in phages binding to protein receptors. All together, these results suggest that Araucaria may infect its mycobacterial host using a mechanism involving adhesion to cell wall saccharides and protein, a feature that remains to be further explored. We also analysed 48 M. abscessus sequenced genomes for encoding prophages. Our phylogenetic analyses suggested that M. abscessus species were infected by different mycobacteriophages and have a different evolutionary history than the bacterial hosts and some proteins that are acquired by horizontal gene transfer mostly mycobacteriophages’ proteins and hypothetical proteins. Finally, we sequenced and analyzed two non-tuberculosis mycobacterium causing human infections, Mycobacterium simiaie and Mycobacterium septicum.

Made available in DSpace on 2014-07-29T12:05:40Z (GMT). No. of bitstreams: 1 tese katia kopp.pdf: 961457 bytes, checksum: 3756d48b10534109e9caa6f1bb961523 (MD5) Previous issue date: 2009-03-30 / Composition and diversity of anuran amphibians in preserved and disturbed environments in the Cerrado of the State of Goiás, Mid-West Brazil. The Cerrado is the second largest biome of Brazil, with an approximate area of 2 million km², which represents about 23% of the total area of the country. Despite the high conversion of natural areas of the Cerrado in agricultural areas and pastures, comparative studies that address aspects of the composition and diversity of frogs from adjacent areas in different states of conservation are lacking. Thus, this study aimed to address taxonomic richness and community composition of anuran amphibians in twelve water bodies located in preserved areas (inside the National Park of Emas - PNE) and disturbed areas located around the PNE to test whether the structure of frogs communities is different in preserved and disturbed areas and whether species richness is correlated with descriptors of the heterogeneity of habitats. Were recorded 25 species of frogs belonging to nine genera of five families in the 12 water bodies sampled. Species richness was higher in disturbed than in preserved areas. Diversity and equitability were significantly higher in preserved water bodies (P <0.05) while dominance was higher in disturbed water bodies. An analysis of percentage of similarity (SIMPER) showed that the percentage of dissimilarity between the compared groups was 52.26%. The analysis of similarity (ANOSIM) showed significant results on differentiation between groups (Global R = 0.17, P = 0.04). Species richness was not related to any descriptor of heterogeneity. Geographic distance was related to species composition between sampled water bodies (r = -0.35, p = 0.01). At least two non-exclusive factors may be responsible for patterns of species composition and diversity of frogs found in the environments studied: a) the disturbance caused by human action in the use of natural areas for agriculture and livestock enables greater richness of species in disturbed areas, which is consistent with the hypothesis of intermediate disturbance, b) the migration between adjacent ponds allows the maintenance of communities and patterns of species composition. Thus, although species richness was lower in preserved water bodies, the highest diversity recorded in such habitats demonstrates their importance for the maintenance of community integrity and viable frogs populations / As comunidades de anfíbios anuros, inclusive em regiões tropicais, são influenciadas diretamente pelas condições ambientais, as quais desempenham um papel importante na estruturação e regulação das comunidades. Esse estudo teve como objetivo determinar a diversidade de modos reprodutivos, a temporada de vocalização e testar a correlação das variáveis climáticas com a riqueza, a abundância dos anuros adultos e dos girinos e com a atividade de vocalização dos machos em 12 corpos d&#8223;água localizados no interior e entorno do Parque Nacional das Emas, sudoeste do Estado de Goiás, Brasil. Foram realizadas 16 amostragens entre dezembro de 2005 e março de 2008. Um total de 25 espécies de cinco famílias foram registradas: Bufonidae (1 espécie), Hylidae (9 espécies), Leptodactylidae (8 espécies), Leiuperidae (6 espécies), Microhylidae (1 espécie). Quatro padrões de atividade reprodutiva foram reconhecidos entre as espécies: contínuo, intermediário, prolongado e explosivo. A riqueza de anuros adultos, a abundância e atividade de vocalização dos machos foram positivamente relacionadas com a temperatura do ar, umidade e precipitação. A riqueza de girinos foi positivamente relacionada com a precipitação e com a temperatura da água, mas não houve relação da abundância de girinos com nenhum dos descritores climáticos. Foram registrados seis modos reprodutivos 56% das espécies apresentaram modos reprodutivos aquáticos generalizados, e 44% depositam os ovos em ninhos de espuma. As espécies registradas no presente estudo apresentaram predominância de modos reprodutivos generalizados e padrão reprodutivo tipicamente associado ao período quente e chuvoso, como esperado para regiões tropicais sazonais. Entretanto, a segregação temporal entre grupos de espécies dentro do período chuvoso parece facilitar a coexistência de espécies generalistas típicas de áreas abertas e/ou antrópicas

L'objectif de ce travail était d'étudier les interactions entre une plante à phytoremédiatrice ?, Lantana camara (Verbenaceae), le ver de terre, Pontoscolex corethrurus (Glossoscolecidae) et les microorganismes telluriques d'un sol pollué au plomb. Dans un premier temps, il apparaît que dans les sols contaminés, la présence de ver conduit à un accroissement de la biomasse des parties aériennes et racinaires des plantes ainsi qu'à une augmentation de l'absorption de plomb. La caractérisation physico-chimique des agrégats racinaires a montré que l'activité des vers augmente le taux de matière organique, la capacité d'échange cationique ainsi que l'azote total, le potassium total et disponible. De plus, la présence des vers augmente certaines activités enzymatiques de la rhizosphère. La croissance accrue de L. camara pourrait résulter de ces différentes actions. L'action des vers de terre sur les plantes se ferait via les communautés microbiennes telluriques. Ainsi, la biomasse des microorganismes, bactéries et champignons, des agrégats racinaires augmente en présence de vers. La PCR-DGGE n'a pas permis de mettre en évidence de modifications de la structure taxonomique des communautés bactériennes sous l'influence du Pb et/ou du vers, par contre l'analyse des profils physiologiques par plaques Biolog montre clairement une diversification fonctionnelle bactérienne. Les communautés fongiques voient, elles, leur diversité taxonomique, augmenter sous l'action des vers. La restructuration des populations microbiennes, en présence de vers, des agrégats racinaires élaborés par les plantes en milieu pollué au plomb est l'élément déterminant pour la compréhension de l'impact de P. corethrurus sur la croissance et la phytoremédiation de L. camara. L'association de ces deux organismes aurait donc un potentiel considérable pour le traitement de sites industriels pollués au plomb / The objective of this work was to study the interactions between phytoremediating plant Lantana camara (Verbenaceae), the earthworm Pontoscolex corethrurus (Glossocolecidae) and microorganisms in soil contaminated with lead. Initially, it appears that in the contaminated soil, the presence of earthworm leads to an increase in the biomass of root and aerial parts of plants and increased absorption of lead. The physico-chemical characterization of root-aggregates showed that the activity of earthworms increases the rate of organic matter, cation exchange capacity, total nitrogen, total and available potassium. Moreover, the presence of earthworms increases certain enzymatic activities in the rhizosphere. The increased growth of L. camara could result from these different actions. The action of earthworm on plants would be through terrestrial microbial-communities. Thus, the biomass of microorganisms, bacteria and fungi, of root-aggregates increase in the presence of earthworms. By PCR-DGGE, we were unable to demonstrate differences in taxonomic diversity of the bacteria community but the analysis of physiological profiles with Biolog plates showed that the activities of earthworm enhance the functional diversity of soil bacteria. In other hand, the restructuring of fungal taxonomy has been clearly observed by the activity of earthworm. All changes observed can explain increased growth of plants and improved phytoextraction of heavy metal. Finally, the study underlines the role of the earthworms on the growth and the phytoextraction efficiency of the plants. So, the combination of earthworm P. corethrurus and plant L. camara could be considerable potential for the treatment of industrial sites polluted with lead

<p>Vr&scaron;eno je istraživanje intestinalnih nematoda žutogrlog mi&scaron;a (<em>Apodemus flavicollis&nbsp; </em>Melchior, 1834) uzorkovanog sa 18 lokaliteta na teritoriji Srbije, južno od Save i Dunava, sa ciljem pro&scaron;irenja i upotpunjavanja saznanja o ovoj komponenti parazitofaune glodara u ovom delu Evrope. Fauna nematoda crevnog trakta je analizirana sa vi&scaron;e aspekata: kvantitativnog, aspekta zajednica, biolo&scaron;kog, aspekta biodiverziteta i aspekta polne strukture. Pored toga, ispitan je uticaj odabranih<br />spolja&scaron;njih i unutra&scaron;njih faktora na prevalencu i abundancu parazitske infekcije.</p><p>Zabeleženo je prisustvo devet vrsta intestinalnih nematoda, pri čemu je broj vrsta po lokalitetu varirao od 1 do 7. Ukupna prevalenca infekcije iznosila je 81,6%. Najče&scaron;će vrste u uzorku bile su <em>Heligmosomoides polygyrus </em>i&nbsp;<em> Syphacia stroma</em>, koje su<br />se odlikovale najvi&scaron;im prevalencama i intenzitetima infekcije. Distribucija nematoda unutar domaćina je bila agregirana. Broj vrsta po domaćinu varirao je od 1 do 5, ali su najzastupljenije bile infekcije jednom ili dvema vrstama. Najče&scaron;ća kombinacija<br />vrsta bila je&nbsp;<em> H. polygyrus-S. stroma;</em> međutim, odsustvo podataka iz ranijih istraživanja i adekvatnih polaznih modela sprečava dono&scaron;enje zaključaka o mogućim interakcijama i asocijacijama između vrsta.</p><p>Monoksene nematode su bile brojnije i imale veću prevalencu od heteroksenih nematoda, &scaron;to oslikava&nbsp; razlike u njihovim životnim ciklusima. Među monoksenim nematodama, geohelminti u užem smislu su se odlikovali najvećim prevalencama, a ageohelminti najvećom abundancom, u skladu sa životnim strategijama koje teže ka disperziji ili akumulaciji.&Scaron;enonov indeks diverziteta cele uzoračke populacije iznosio je 1,44 &scaron;to je visoka vrednost u odnosu na one iz drugih delova Evrope. Nije uočena značajna negativna korelacija između udaljenosti lokaliteta i vrednosti Sorensenovog indeksa,ukazujući da je prostorni faktor značajan u strukturiranju zajednica intestinalnih nematoda i na lokalnom nivou. Odnos polova je bio neravnomeran, uglavnom u korist ženki, u skladu sa podacima drugih autora. Ženke su ujedno bile krupnije od mužjaka, saglasno sa ranijim nalazima za parazitske nematode. Nadmorska visina nije uticala na abundancu intestinalnih nematoda. Pol domaćina je uticao na prevalencu dve vrste: prevalenca&nbsp; <em>S. stroma</em>&nbsp; je bila veća kod mužjaka, a prevalenca<em> Trichuris muris</em>&nbsp; kod ženki. Kao značajan faktor uticao je na abundancu samo kod vrste&nbsp;<em> Aonchotheca annulosa</em>; abundanca ove vrste bila je veća kod mužjaka. Rezultati sugeri&scaron;u da je uticaj pola domaćina na nivo parazitske infekcije izuzetno kompleksan fenomen.&nbsp; Prevalenca i abundanca infekcije intestinalnim nematodama je bila veća kod domaćina sa B hromozomima.&nbsp; Lokalitet je bio značajan faktor u variranju abundance nematoda. Uzrast i prisustvo drugih vrsta nematoda su&nbsp; takođe ispoljavali značajan efekat. Povećanje abundance nematoda sa uzrastom&nbsp; se vezuje za dužu izloženost starijih jedinki parazitima. Iako je registrovan uticaj abundance jedne vrste na abundancu druge, on ne predstavlja čvrst dokaz za postojanje interakcija između vrsta.</p> / <p>A study of intestinal nematode parasites was conducted on the yellow-necked mouse (<em>Apodemus flavicollis&nbsp;</em> Melchior, 1834) sampled from 18 sites from Serbia south of the Sava and Danube rivers. The aim of the study was to broaden and enrich the data on this category of rodent parasites in this part of Europe. The nematode fauna of the gastrointestinal tract was analysed from quantitative, community, biological, biodiversity and sex ratio aspects. In addition, selected extrinsic and intrinsic factors were tested for their influence on the prevalence and abundance of infection.</p><p>Nine species of&nbsp; intestinal nematodes were noted, 1 to 7 per site. Total sample prevalence was 81.6%. <em>Heligmosomoides polygyrus</em>&nbsp; and&nbsp; <em>Syphacia stroma</em> were the most common species, with the highest prevalence and intensity values. Nematodes were aggregated within their hosts. Infracommunity richness varied from 1 to 5, but infections with one or two species were most common. The most frequent<br />combination&nbsp; of species was <em>H. polygyrus-S. stroma</em>, but in absence of prior research and adequate null models, conclusions of possible interactions and associations between species could not be drawn.</p><p>Monoxenous nematodes were more abundant and prevalent than heteroxenous species, reflecting the differences in their life cycles. Of the monoxenous nematodes, geohelminths<em> sensu stricto</em> had the highest prevalence values, whereas ageohelminths were most abundant, with respect to their life strategies that favour either dispersal or accumulation. Shannon&rsquo;s diversity index for the total sample was 1.44, a high value compared to those from other European based studies. A significant negative correlation between site distance and Sorensen index values was not found, implying that spatial factors have an important role in structuring intestinal nematode communities on a local scale. Sex ratio was generally female-biased, in agreement with data from other authors. In addition, females were larger than males, congruent with previous findings for parasitic nematodes.</p><p>Elevation did not significantly influence intestinal nematode abundance. Host sex influenced the prevalence of two species: for <em>S. stroma</em> prevalence was higher in males, and for <em>Trichuris muris</em> in females. Influence of host sex on abundance was found only for <em>Aonchotheca annulosa</em>, with abundances of this parasite higher in male mice. The results suggest that the effectof host sex on parasite infection levels is a highly complex phenomenon.&nbsp; Infection prevalence and abundance was higher in hosts that carried B chromosomes. Site was a significant factor in explaining variations in nematode abundance. Hostage and presence of other nematode species&nbsp; also exibited effects.&nbsp; An increase in nematode abundance with host age&nbsp; is explained by prolonged exposure to parasites in older host individuals. Although results indicate that the abundance of one species influences the abundance of another, this is not firm evidence of the existence of species interactions.</p>