13548805670613-46162052c208770f99e83a586780d16c.txt As the technologies for the realisation of the idea of the Semantic Web have evolved rapidly during past few years, it is possible to use them in variety of applications. As they are designed with the ability to process and analyze semantic information found in the data in mind, they are particularly suitable for the task of enhancing relevance of the document retrieval. In this work, we discuss the possibilities of identifying a suitable subset of the expressing capabilities of the SPARQL querying language and create a component that encapsulates the technical details of its usage. Page 1

This diploma thesis deals with the topic of terminology databases, including the creation of a terminology database that incorporates names of trees in Latin, Italian and Czech language. In the first part lexicography, terminography and terminology, disciplines related to the topic of the thesis, are presented. It includes also the summary of their historical development and introduces some basic notions associated with them, such as term, nomenclature, taxonomy, etc. Basic differences between terminography and lexicography and between terminological dictionaries and databases are briefly presented as well. The practical part describes basic methods and procedures used while creating the terminology database in Microsoft Access 2016. The database is also enclosed with the thesis and contains names of trees in Latin, Czech and Italian and some additional information related to those names.

The present thesis surveys topic of taxonomic diversity and phylogeny of bears (Mammalia, Ursidae) and aspects of its contextual setting under effects of changing conceptual and methodological viewpoints. This problem is studied from several perspectives. The historical perspective is represented by a critical overview of the history of specific and infraspecific classification of bears with special respect to mutual influences of this classification and theoretical concepts of species accepted in particular periods. The perspective of material approach is exemplified by a material-based study of taxonomical and phyletic status of selected Pliocene to Middle Pleistocene ursine taxa. Along with deconstruction of some traditional hypotheses this produced a model explaining species diversification in ursine bears and its discussion in terms of factual relevance of included background concepts. In the pre-evolutionary period the bear species were usually understood broadly, as incipient immanent entities, yet exhibiting obvious certain infraspecific variability. This was established using definitions of varieties (mostly not identifiable with present subspecies or infraspecific taxa) considered as unstable modes of particular species. Although, in the post-Darwinian period, the concept and taxonomic...

Phylogeny of selected genera of geckos in the Mediterranean and adjacent regions Jan Červenka Ph.D. thesis Abstract This Ph.D. thesis is composed of three published articles and one manuscript, and is focused on the phylogenetic relationships of selected species of geckos from the Mediterranean and surrounding areas. The group of geckos of interest shares the common characteristic of an absence of adhesive lamellas on their toes. Historically, it was assumed that these species were closely related. Molecular-phylogenetic approaches were used in order to reveal the phylogenetic relationships within this group, especially using the sequential data from mitochondrial genes. Morphological characteristics commonly used in lizards were studied in connection with the ecology of the group. This thesis provides the first more detailed view of the phylogeny of the studied species. The results show that the genus Cyrtopodion, previously considered as monophyletic, in fact is not monophyletic as the genera Bunopus and Agamura represent its inner groups. Mediodactylus, the subgenus of Cyrtopodion, forms monophylum but is not closely related to the other members of the genus and so was reclassified as the independent genus. The enigmatic and yet so far very poorly studied genus Carinatogecko was discovered to be the...

Cyclopoids are together with Calanoids and Harpacticoids a part of the largest, very diverse group of crustaceans and the most numerous aquatic metazoans of the world. The history of their research goes as far back as to the beginning of 19th century when the first cyclopoid copepods were described. The taxonomy of cyclopoids started to develop gradually since that time, adding new and more detailed methods and morphological characters, as well as a certain degree of taxonomical confusion. In last decades, the molecular-genetic techniques of DNA sequencing have become available offering a new independent tool for taxonomists. This work contains different studies concerning the morphology, taxonomy, ecology, distribution and colonisation of cyclopoid copepods, with the use of molecular tools as a uniting element. Chapter 1 of this thesis summarizes basic knowledge about the taxonomy, morphology and biology of cyclopoid copepods and introduces the following chapters containing four studies presented as single publications. The taxonomy of copepods of the genus Cyclops is based mainly on the morphology which is sometimes ambivalent and some of the most problematic species groups are presented here. Chapter 2 presents our unique results, the first reconstruction of phylogenetic relationships among 15...

L’Identification rapide et la classification microbienne précise sont cruciales en microbiologie médicale pour la surveillance de la santé humaine et animale, établir un diagnostic clinique approprié et choisir des mesures thérapeutiques et de contrôle optimales. Cependant, les seuils universels utilisés pour la définition des espèces ne sont pas applicables à de nombreux genres bactériens. C'est notamment le cas des espèces du genre Rickettsia, qui expriment peu de caractéristiques phénotypiques distinctives. Compte tenu de la disponibilité des séquences de près de 100 génomes de Rickettsia, nous avons voulu évaluer une gamme de paramètres taxonomiques basés sur l’analyse des séquences génomiques afin de mettre au point des recommandations pour la classification des isolats au niveau de l’espèce et du genre. En comparant le degré de similarité des séquences de 78 génomes de Rickettsia et 61 génomes de 3 genres étroitement apparentés en utilisant 4 paramètres génomiques, nous avons montré que les outils taxonomiques basés sur les séquences génomiques sont simples à utiliser et rapides, et permettent une classification taxonomique fiable et reproductible des isolats de rickettsies avec des seuils spécifiques. Les résultats obtenus nous ont permis d'élaborer des recommandations pour la classification des isolats de rickettsies au niveau du genre et de l'espèce. À l'aide de la taxono-génomique, nous avons également pu décrire 17 nouvelles espèces bactériennes associées à l'homme. L'utilisation des outils génomiques est donc parfaitement adaptée à la classification taxonomique et peut changer radicalement notre vision de la taxonomie et de l'évolution bactérienne à l'avenir. / Rapid identification and precise microbial classification are crucial in medical microbiology for human and animal health monitoring, appropriate clinical diagnosis and selection of optimal therapeutic and control measures. Indeed, the universal used for the definition of species are not applicable to many bacterial genera. This is particularly true of species of the genus Rickettsia which are strictly intracellular alpha-proteobacteria that express few phenotypic characteristics. Given the availability of genomic sequences of nearly 100 rickettsial genomes, we wanted to evaluate a range of taxonomic parameters based on genomic sequence analysis, to develop guidelines for the classification of Rickettsia isolates at the genus and species levels. By comparing the degree of similarity of the sequences of 78 genomes from Rickettsia species and 61 genomes from 3 closely related genera using several genomic parameters, we have shown that genome-based taxonomic tools are simple to use and fast, and allow for a reliable and reproducible taxonomic classification of isolates within species of the genus Rickettsia, with specific thresholds. The obtained results enabled us to develop guidelines for classifying rickettsial isolates at the genus and species levels. Using taxono-genomics, we have also been able to describe 17 new human-associated bacterial species on the basis of a combination of genomic analysis and phenotypic properties. The use of genomic tools is therefore perfectly adapted to taxonomic classification and can dramatically change our vision of taxonomy and bacterial evolution in the future.

Les pycnogonides sont une classe d’arthropodes marins comptant plus de 1 400 espèces, et dont nous connaissons mal la diversité et l’histoire évolutive. Cette thèse pluridisciplinaire sur les pycnogonides tropicaux s’articule autour de quatre axes de recherche : (i) description de neuf fossiles de Solnhofen (Jurassique supérieur), grâce à une nouvelle technique de visualisation des volumes ; (ii) analyses phylogénétiques des gènes CO1 et 18S à partir de 107 taxons ; (iii) séquençage Illumina par shotgun et assemblage de 103 nouveaux génomes mitochondriaux ; et (iv) taxonomie intégrative des pycnogonides de Martinique reposant sur 803 spécimens collectés lors de l’expédition Madibenthos (2016) et 172 séquences CO1. Tous les fossiles de Solnhofen étudiés sont rattachés aux pantopodes, marquant leur affinité avec la faune moderne. Deux espèces nouvelles sont décrites. Avec les fossiles de La Voulte-sur-Rhône, ils montrent que les pantopodes étaient déjà diversifiés dans des eaux profondes et lagunaires du Jurassique, suggérant une importante transition de faune entre Paléozoïque et Mésozoïque. De nombreux réarrangements du génome mitochondrial, impliquant principalement les gènes des ARNt, sont mis en évidence. Certains sont corrélés à des changements dans le biais de composition en bases qui peuvent impacter la reconstruction phylogénétique. Malgré ces problèmes, nous retrouvons la monophylie de toutes les familles excepté les Ascorhynchidae, Callipallenidae et Nymphonidae, et identifions des regroupements interfamiliaux, d’un côté entre Ammotheidae, Pallenopsidae, Endeidae et Phoxichilidiidae, et de l’autre, entre Callipallenidae et Nymphonidae. Un très grand nombre de relations intergénériques et interspécifiques est également révélé. Alors que 20 espèces étaient auparavant connues sur les côtes de Martinique, cette étude a permis de multiplier par quatre la diversité connue de l’île, soit un total de 73 espèces. Ces résultats suggèrent une diversité encore plus importante à l’échelle des Caraïbes, que l’on pensait pourtant bien explorées. / Sea spiders are a class of marine arthropods including more than 1,400 species. Their diversity and evolutionary history are still poorly known. In this thesis, tropical pycnogonids were studied using four approaches: (i) nine fossils from Solnhofen (Upper Jurassic) were examined using a new photographic technic improving visualization of body parts; (ii) for phylogeny, CO1 and 18S genes were analyzed for 107 taxa; (iii) 103 new mitochondrial genomes were assembled after Illumina shotgun sequencing; and (iv) 803 sea spiders collected during the Madibenthos expedition (2016) in Martinique were examined for integrative taxonomy using 172 CO1 sequences.All fossils from Sonhofen are shown to share strong affinities with the modern fauna, as they were identified as belonging to Pantopoda. Two new species are described. Together with fossils from La Voulte-sur-Rhône, these results suggest that Pantopoda were already diversified in shallow and deep Jurassic waters, indicating that an important faunal transition occurred between Palaeozoic and Mesozoic. The mitochondrial genome of sea spiders shows many different gene orders and most of the gene rearrangements involve tRNA genes. Some are correlated with changes in base composition bias, which can be misleading for phylogenetic reconstruction. Despite these problems, all families but Ascorhynchidae, Callipallenidae and Nymphonidae were found to be monophyletic. Furthermore, our analyses provide evidence for several interfamilial relationships (between Ammotheidae, Pallenopsidae, Endeidae and Phoxichilidiidae; and between Callipallenidae and Nymphonidae), and for many intergeneric and interspecific relationships. While only 20 pycnogonid species were previously known from Martinique, the number of species was multiplied by four after our study, i.e. 73. These results suggest that many species still remain to be discovered in the Caribbean Sea, whereas this region was thought to be well-explored regarding sea spiders.

The aim of my thesis is to demonstrate the potential of eXtensible Business Reporting Language in the field of corporate reporting and data exchange. XBRL is still little known in the Czech Republic; that is why the first part of the work focuses primarily on the explanation of the basic principles on which this language is founded. Further, the functionality of applications for working with XBRL will be described, followed by an analysis of the benefits that this language can bring to its users. The thesis also covers various approaches that the reporting companies can use when implementing XBRL and analyzes the areas suitable for the introduction of XBRL in the Czech Republic. The last part of the work describes the practical experience with the creation and subsequent use of XBRL instance documents.

Les éponges Homoscleromorpha constituent l’une des grandes Classes des Porifera. Particulièrement bien distribuées dans les grottes sous-marines. Leur taxonomie et systématique sont particulièrement difficiles, à cause de l’absence fréquente de caractères diagnostiques. A partir d’une approche de taxonomie intégrative, couplant morphologie, cytologie et génétique, le premier objectif de cette thèse était d’améliorer la connaissance de la biodiversité des Homoscleromorpha. Les espèces nouvelles représentent 40% des éponges récoltées au cours de cette étude. Ce document présente 3 nouvelles espèces et 1 nouveau genre récemment publiés. L’ensemble des résultats acquis au cours de cette thèse appelle à une redéfinition des deux familles provocant un premier grand bouleversement de la Systématique de ce groupe.Un deuxième grand objectif de cette thèse était d’apporter des connaissances sur la diversité chimique et microbienne de ce groupe d’éponges. En étudiant un grand nombre de représentants nous avions l’ambition d’apporter des éléments de compréhension du succès écologique des Homoscleromorpha dans les grottes sous-marines. A l’aide d’approches metabolomiques et de metabarcoding, nous avons mis en évidence des patrons de diversité chimique et microbienne en fonction de différentes variables, traduisant pour certains un signal phylogénétique et dans d’autres une influence de l’environnement. Cette partie de la thèse était un pré-requis indispensable pour comprendre les capacités adaptatives des holobiontes Homoscleromorpha à travers l’expression de métabolites et/ou l’acquisition de microorganismes spécialisés, et leur évolution dans un environnement contraignant. / Homoscleromorpha sponges constitute one of the four Classes among Porifera. Their taxonomy and systematics are challenging due to the frequent absence of diagnostic characters. Particularly well distributed in cryptic habitats like submarine caves. Using an integrative approach based on morphology, cytology and genetics, the first objective of this thesis was to improve our knowledge on the biodiversity of Homoscleromorpha in submarine caves. New species represents 40% of the Homoscleromorpha collected. Here we present 3 new species and one genus recently published, 11 other new species being currently under description. Our results strongly support a redefinition of the two families of Homoscleromorpha. Our results represents a first grand overturn in the systematics of this group.A second objective of this thesis was to improve our knowledge on the chemical and microbial diversity of Homoscleromorpha but also its variability according to the environmental conditions. Our analysis provides preliminary data to address the question of the ecological success of Homoscleromorpha in submarine caves. Metabolomics and metabarcoding data defined patterns of chemical and microbial diversity according to different explicative variables like the taxonomy, the geographical origin or the ecology of the studied species. The patterns of diversity were supported by chemical and microbial markers and they explain a phylogenetic classification in few cases and a geographic origin in others. This study brings first insights into the understanding of the adaptive capacities of the Homoscleromorpha holobiont, through the expression of particular metabolites and/or microorganism.

La flore microbienne est un ensemble de micro-organismes comme les bactéries, archées, eucaryotes inférieurs et virus, jouant un rôle important dans l’équilibre d’un écosystème. Cette flore reste encore mal définie car en 2012, seules ~30% des micro-organismes de la flore intestinale humaine étaient caractérisés, et moins de 50% des micro-organismes de la flore fromagère traditionnelle étaient caractérisés au niveau fonctionnel. Depuis 2006, les séquenceurs à ADN de seconde génération permettent d’analyser directement le contenu génique d’un prélèvement de flore sans contrainte d’isolement ou de culture. Toutefois, les séquences d’ADN générées ne sont pas structurées en génome et sont hautement fragmentées, freinant considérablement l’analyse et l’exploitation de ces données. Dans ce travail, nous avons développé de nouvelles méthodes dites de métagénomiques quantitatives, car elles permettent de regrouper les courtes séquences d’ADN ayant la même abondance au sein de plusieurs échantillons métagénomiques, pouvant provenir d’une même espèce microbienne.Au niveau du microbiote intestinal humain, nous avons structuré un catalogue de 3,9 millions de gènes de la flore intestinale humaine en 741 unités ou « clusters » correspondant à des génomes de bactéries, d’archées et d’eucaryotes, que nous appelons espèces métagénomiques (MGS) et 6640 unités correspondant principalement à des génomes de virus, plasmides et divers ilots génomiques comme des CRISPR, que nous appelons unités métagénomiques (MGU). Cette méthode de structuration a ensuite été utilisée pour faciliter des analyses d’associations de la composition de la flore intestinale avec des maladies humaines comme la maladie de Crohn, l’obésité ou le diabète de type 2. Enfin, au niveau des flores alimentaires, nos méthodes ont été utilisées pour constituer un catalogue de 134 génomes d’espèces bactériennes fromagères et caractériser la flore de surface de fromages traditionnels. Ceci nous a permis de détecter la présence de nouvelles bactéries alimentaires, pouvant enrichir la liste des bactéries à possible intérêt technologique dans les produits laitiers fermentés. / The microbial flora is a micro-organism complex containing for example bacteria, archaea, lower eukaryotes and viruses, which play an important role in ecosystem equilibrium. This flora remains poorly defined as in 2012, only ~30% of the intestinal flora micro-organisms have been characterized, and less than 50% of traditional cheese floras were characterized at the functional level. Since 2006, the second generation of DNA sequencers have allowed the direct analysis of the genetic content from a microbial flora sample without isolation or culture limitation. However, the DNA reads generated are not structured with respect to genomes and also are highly fragmented, slowing down dramatically the exploitation and analysis of these data.In this work, a new methodology based on quantitative metagenomic are described., This allows the clustering of short DNA sequences with the same abundance in multiple metagenomic samples, which should originate from the same microbial species. A 3.9 million gene catalog has been built from the human intestinal tract microbiota and divided into 741 units or clusters corresponding to bacteria, archaea and eukaryote genomes. These have been defined as metagenomic species (MGS) and 6640 units of them corresponds mainly to viral genomes, plasmids and genetic islands like CRISPR, with the sub-name of metagenomic units (MGU). This methodology was then used to facilitate the association analysis of the intestinal flora composition with human diseases such as Crohn’s disease, obesity or type 2 diabetes. Within, the alimentary flora, our methods have also been used to constitute a 134 genomic catalog of cheese bacteria and characterize them from the surface of traditional cheeses. This allowed the detection of new alimentary bacteria, that will enriched the list of bacteria with potential interest for the commercial exploitation of fermented products.