No description available.

No description available.

No description available.

Thesis (M.SC. (Aquaculture)) --University of Limpopo, 2011 / The present MSc dissertation emanates from seasonal surveys conducted by the fish parasitological group of the Department of Biodiversity and Aquaculture Research Unit of the University of Limpopo, Turfloop Campus. The first part of the present study was aimed at investigating the metazoan parasites of three cyprinids occurring in the Nwanedi-Luphephe Dams. The main purpose of it was to determine temporal changes in the intensity of infestation in terms of prevalence, mean intensity and abundance of parasite species parasitizing the cyprinids studied over a two year period. Ecological parameters including species host-specificity, seasonality, and gender preference and host size versus species intensity are discussed for each parasite. Altogether 152 specimens were examined for parasites and a total of 2 432 metazoan parasites of ten species were recorded. At the sampling site, all three hosts co-occurred, however, a substantial proportion of Barbus radiatus was collected from the perennial stream feeding one of the twindams. Fish were sampled by means of gill nets and electrofishing or seine netting in accordance with the habitat conditions. Hosts were killed and organs investigated for metazoan parasites. After collection of parasites, standard methods for processing individual parasites were followed. The results obtained revealed the following groups of parasites; monogeneans (ectoparasites) included Dactylogyrus spinicirrus, D. afrolongicornis afrolongicornis, D. afrolongicornis alberti, Afrodiplozoon polycotyleus, Gyrodactylus sp., and Dogielius sp. (all recorded from the gills); Crustacea, Dolops ranarum was found from the mouth cavity, gills and skin of Labeobarbus marequensis. Of these, only two specialists, both monogeneans, were found on Barbus trimaculatus namely, D. afrolongicornis afrolongicornis and D. afrolongicornis alberti. Based on morphology of the haptoral hard parts, these two species were almost similar to each other than to D. spinicirrus. The appreciable difference between D. afrolongicornis afrolongicornis and D. afrolongicornis alberti was mainly in the shape of the marginal bar. Both D. spinicirrus and A. polycotyleus were widely distributed and recorded on the gills of all hosts during all seasons. Both species were recorded for the first time on B. radiatus. Also, D. spinicirrus was recorded for the first time on the gills of B. trimaculatus. Based on comparison with the original material, the species could be identified to species level. These analyses provided sufficient evidence for restoration of Afrodiplozoon polycotyleus as a valid taxon. The existence of two species, Gyrodactylus sp. and Dogielius sp. were recorded for the first time on B. radiatus in South Africa, and this possibly represents new species. The endoparasites included the following groups: digeneans- Diplostomulum metacercariae from the eyes of Lb. marequensis, Ornithodiplostomum sp. and black spot (grubs) were recorded from B. trimaculatus. The latter was also recorded in the muscle of B. radiatus. Unidentified digenean cysts were recovered from the gills and in the body cavity of both Lb. marequensis and B. trimaculatus; nematodes were represented by Contracaecum larvae in the body cavity of both Lb. marequensis and B. trimaculatus; cestodes were represented by gryporynchid larvae from the intestine of B. radiatus. The general high prevalence and intensities of ectoparasites recorded is an indication that the Nwanedi-Luphephe Dams has a biotic mechanism which might have enabled it to sustain the growth rate of ectoparasite intra-population. There was no correlation between either fish length or condition factor and the number of parasites. The study indicated that the abundance of monogeneans is partly influenced by season and that of endoparasites was principally governed by the presence of intermediate hosts and definitive hosts. The second part of this dissertation dealt with the health status of Lb. marequensis. Fish health was assessed using condition-related indices including condition factor and a modified Health Assessment Index (HAI) and the associated Parasite Index (PI). The HAI was performed to determine and examine any macroscopic abnormalities regarding external features and internal organs. The purpose of combining the two indices was to use the infestation of the metazoan parasites found on and/or in Lb. marequensis to determine whether or not the environment they live in was healthy. Both indices together with the condition factor provided relatively simple and rapid indications of how well fish were coping in their environment. The HAI score varied amongst the four sampling seasons. The highest individual mean value was 63 in winter, followed by a score of 50 in autumn, while the lowest were 42 and 33 in summer and spring respectively. To authenticate the HAI and PI data, certain water quality variables were measured and are discussed in detail in this dissertation. The Nwanedi-Luphephe Dams are generally believed to have good water quality. This was supported in this study; conditions assessed in fish using the aforementioned indices did not differ greatly between seasons, nor did the conditions deviate appreciably from normality. The HAI values were low overall which signifies a healthy fish profile for the system. The present investigation showed the existence of differences in the occurrence of individual parasite to be linked to water temperature changes. Thus, seasonal changes do influence parasite developmental stages to a certain degree. Tested heavy and trace metals were within the permissible limits as provided by the Department of Water Affairs and Tourism (DWAF, 1996).

No description available.

All animals have evolved mechanisms to recognise and eliminate nonself in order to defend against invading pathogens and to prevent chimerism, the fusion between genetically distinct conspecifics. Like other metazoans, sponges are known to rely on sophisticated systems to maintain their self-integrity. As poriferans are also considered one of the most ancient extant metazoan phyla, they represent a critical comparative model for understanding the early evolution of immunity and self/nonself recognition in animals. The Toll-like receptor (TLR) signalling cascade plays a crucial role in immunity, and recent findings in the sponge Suberites domuncula suggest that its origin could predate eumetazoan cladogenesis. My genome and expressed sequence tag (EST) screens of the demosponge Amphimedon queenslandica detected homologues to most components of this pathway, supporting the notion that a primordial TLR signalling cascade emerged at the dawn of the Metazoa. The sponge also encodes a couple of putative TLR-related proteins (AmqIgTIRs) that consist of at least one extracellular immunoglobulin (Ig) and an intracellular Toll/Interleukin-1 receptor/resistance (TIR) domain. The presence of other unconventional TLRs in S. domuncula and in cnidarian representatives, implies that an ancestral TLR probably existed in the last common ancestor of all living metazoans, and independent duplication and divergence events led to the variety of forms observed in animals. Among the putative transcription factors present in Amphimedon, which are known to be activated by the TLR signalling cascade in other eumetazoans, I detected a single member of the Rel/nuclear factor-kappaB (NF-κB) family, AmqNF-κB, which is also the only Rel homology domain (RHD)-containing gene present in the sponge. This gene encodes a protein that is equipped with both a RHD and ankyrin (ANK) repeats, suggesting that the ancestral metazoan NF-κB was configured identically to contemporary vertebrate and sponge forms, and that the truncated NF-κB found in Nematostella vectensis resulted from the secondary loss of ANK. Aside from immunity, the Toll and TLR pathways contribute to a variety of biological processes in bilaterians, however their functions have only been investigated in detail in a limited number of metazoan model organisms. While studies have tested the immune role of various sponge genes, including components of the TLR cascade, no research has yet established whether they are also involved in development. Therefore, I investigated the expression of some of the immunity-related genes I isolated in Amphimedon in a developmental and immune context to shed light on the potential ancestral function(s) of the proteins they encode. Using in situ hybridisation, I demonstrate that AmqIgTIR2, AmqMyD88, AmqTollip, AmqPellino and AmqNF-ĸB are expressed during A. queenslandica early development. In contrast, the spatial and temporal expression of AmqIgTIR1 suggests it might encode a receptor that is specifically involved in the detection of metamorphic cues in larvae. A real-time quantitative PCR (qPCR) study performed on a pool of adult sponge cDNAs indicates that the expression levels of AmqIgTIR1, AmqIgTIR2, AmqMyD88 and AmqTollip are significantly affected by a nine-hour incubation in 50 µg/ml of lipopolysaccharide (LPS), and to a lesser extent by 105 colony forming units (cfu)/ml of live Vibrio harveyi. The gene expression of AmqIgTIR1 and AmqIgTIR2 suggests that they may encode proteins with antagonistic immunological functions. While AmqPellino and AmqNF-ĸB do not appear to be affected by LPS and Vibrio exposure, it is possible that these genes do not participate in the early immune response of poriferans. Together, my data indicate that the sponge genes surveyed might encode proteins that perform developmental, sensory and immunological functions, suggesting their roles could have also been multifaceted in the last common ancestor to all living metazoans. As is observed in other invertebrates, poriferans display an ontogenic shift in allorecognition; genetically different individuals can fuse during early development but, in most instances, not as adults. However, there is a limited understanding of the cellular organisation of sponge chimeras and the onset of poriferan allorecognition response. By following the fates of fluorescently tagged cells derived from genetically distinct Amphimedon larvae that are fused together at metamorphosis, I establish that there is a rapid ontogenic shift in the sponge allogeneic response about two weeks after the initiation of metamorphosis. Moreover, the molecular basis of the poriferan allorecognition system is possibly involved in creating differential cell affinities, which underlie the construction of the sponge body plan. Compatible with this scenario is the observation that cells from postlarvae that are allowed to develop for two weeks before contact do not fuse, and form a distinct boundary between genotypes. The molecules responsible for sponge cell reaggregation, the aggregation factors (AFs), have been proposed to drive the allorecognition response in poriferans. Notably, the Amphimedon genome encodes six putative AFs, of which five occur in a cluster. These findings indicate that the polymorphic variation observed in other poriferan AFs is probably the result of allelic variations of multiple genes belonging to the same family.

Discernir as relações evolutivas entre os grandes grupos animais tem representado um formidável desafio para a Ciência. Os filos animais possuem arquiteturas corporais bastante distintas e por isso difíceis de serem comparadas. Ao mesmo tempo, seu registro fóssil converge aproximadamente para um mesmo intervalo na escala geológica, dificultando uma reconstrução filogenética com caracteres morfológicos. A disponibilidade de dados moleculares sobre os organismos abriu, contudo, novas possibilidades na filogenia animal. Esta dissertação buscou explorar essas possibilidades inferindo uma filogenia com métodos de distância e máxima verossimilhança, a partir de todos os genomas mitocondriais, completamente seqüenciados até o momento. No entanto, apenas alguns grandes agrupamentos como Diploblastica, Bilateria, Deuterostomia e Protostomia foram recuperados com forte suporte estatístico, além de pequenos agrupamentos de animais de mesma ordem ou família, indicando que os efeitos da rápida radiação no Cambriano se estenderam também ao registro molecular. Os resultados também indicam a necessidade de buscar modelos de evolução mais aderentes a este cenário. Deuterostomia, por exemplo, só foi recuperado monofileticamente assumindo-se a distribuição gama para variabilidade entre-sítios, ao custo, entretanto, da perda de definição nos ramos menores. Nematóides e Platelmintos, por sua vez, revelam um possível viés no skew (desvio) do conteúdo GC e AT de seus genes mitocondriais, que não é adequadamente mapeado por modelos de substituição reversíveis. Os indícios são de que a resolução da filogenia animal depende ainda de uma melhor compreensão da evolução molecular em escala genômica. / Inferring the evolutive relations between the animal phyla has been a formidable challenge to Science. The animal phyla represent quite distinct baupläne (body architectures) and are, therefore, difficult to compare. At the same time, their fossil record converges mostly to the same period on the geological scale. The recent availability of molecular data has, however, inaugurated a new front in animal phylogeny. The present work explores this opportunity by inferring a phylogeny with distance and maximum likelihood methods, employing all animal mitochondrial genomes ever sequenced. The results present only a few bigger groups with strong statistical support, like Diploblastica, Bilasteria, Protostomia and Deutorostomia, and many smaller groups of animals belonging to the same order or family. These results seems to confirm that the phyla radiated in such a short time interval that the phylogenetic signal did not hold out to produce a satisfactory resolution of the animal tree to date. Some limits may have yet to be tested, through models of evolution more fit to this scenario. For example was only recovered with the use of gamma distances for site-to-site substitution rate variability, at the expense of compressing the smaller branches throughout the tree. Nematodes and Platyhelminthes reveal a bias in GC and AT skew that cannot be adequately mapped by any reversible substitution pattern. Nevertheless, even if corrections are found for these issues, it is well possible that the hope of a better resolution in the animal tree will lie further on, by a better understanding of the evolutive process in a genomic scale.

Les voies de signalisation Wnt jouent un rôle important dans divers processus de l’embryogenèse des métazoaires. Par exemple, les signaux WNT sont requis pour l’établissement de la polarité cellulaire, les mouvements de tissus ou la mise en place de la polarité antéropostérieure. La signalisation Wnt tire son nom des protéines WNTs qui sont des protéines secrétées capables de signaler via leurs récepteurs membranaires FRIZZLED (FZD). Une interaction WNT-FZD peut déclencher au moins trois cascades de signalisation distinctes, selon le contexte cellulaire et les couples WNT-FZD impliqués. Chez l'homme, la dérégulation des voies de signalisation Wnt conduit, au cours du développement, à des maladies congénitales, ou chez l'adulte, à des cancers. La compréhension de la diversité numéraire des wnt et des fonctions biologiques qu’ils exercent représente donc un challenge contemporain qu’il est nécessaire de relever, non seulement au titre de l’acquisition de nouvelles connaissances, mais aussi en vue du développement de nouvelles approches à but de diagnostic ou de thérapie. Lors de ma thèse, je me suis dans un premier temps attaché à décrire les patrons d’expression temporels et spatiaux de l’ensemble des gènes wnt et fzd présents chez l’oursin Paracentrotus lividus. L’oursin, comme l’homme, appartient au phylum des deutérostomiens. De plus, son développement est simple et ses embryons se prêtent à l’expérimentation, du fait de multiples approches disponibles pour ce modèle. Par ailleurs, contrairement au lignage des vertébrés, celui de l’oursin n’a pas subi de duplications complète de génome, exhibant ainsi la même diversité de familles de gènes, mais avec moins de redondance au sein de ces dernières, ce qui facilite leur analyse. Etudier les mécanismes qui régissent l'embryogénèse de l’oursin permet donc d’apporter des informations quant aux mécanismes régissant celle des deuterostomes. Mes résultats mettent en évidence que les ligands wnt et les récepteurs fzd sont exprimés de façon dynamique au cours de l’embryogenèse de P. lividus. Fait intéressant, jusqu’à la gastrulation, les gènes codant les récepteurs FZD, présentent des patrons d’expressions distincts, leur somme couvrant néanmoins la très vaste majorité des territoires embryonnaires. Ainsi, cette étude a permis d’établir un catalogue des compatibilités spatio-temporelles potentielles entre les protéines WNT et FZD durant l’embryogenèse d’un deutérostomien, ainsi que des hypothèses quant aux rôles possibles jouées par ces protéines durant ce processus. Dans un second temps, je me suis intéressé à retracer l’évolution des protéines WNT, et à déterminer s’il existait une fonction intrinsèque ancestrale des WNT qui soit conservée, parmi les métazoaires. Pour cela, j’ai d’une part analysé la composition des répertoires wnt de dix-sept espèces de métazoaires, la séquence primaire des protéines qu’ils encodent, la position relative des wnt au sein de leurs génomes respectifs et, pour certaines espèces, l’environnement génomique des wnt. D’autre part, j’ai contribué à vérifier si trois ligands WNT d’éponge et une séquence ancestrale, calculée à partir d’un échantillon de séquences de métazoaires, étaient capable d’activer les voies de signalisation Wnt lorsqu’exprimées chez trois animaux planulozoaires (cnidaires et bilatériens). Les données obtenues au cours de cette étude ont permis d’établir un modèle de diversification de la famille de gènes wnt chez les métazoaires et ont révélé l’existence de fonctions intrinsèques conservées parmi les ligands WNT. / The Wnt signaling pathways play crucial roles during several processes of metazoan embryogenesis. For instance Wnt signaling is involved in morphogenetic movements as well as cell polarity and anteroposterior polarity establishment. Wnt signaling takes its name from the WNT proteins, which are secreted molecules that signal through their cognate receptors, the FRIZZLED (FZD) proteins. A WNT-FZD interaction may trigger several distinct intracellular signaling cascades, depending on the cellular context and the WNT-FZD couples involved. In humans, a deregulation of WNT signaling during embryonic development or adult life leads to congenital diseases and cancers, respectively. Understanding the great diversity of wnt genes and their biological functions is thus a modern-day challenge, which needs to be addressed, not only to foster general knowledge, but also to allow the identification of novel therapeutic targets and approaches towards future new medical applications.In the course of my Ph.D., I first aimed at describing the spatial and temporal expression patterns of all wnt and fzd genes present in the sea urchin, Paracentrotus lividus. Like humans, sea urchins belong to the deuterostome phyla. In addition, the early development of the sea urchin is relatively simple and is easy to interfere with, thanks to the experimental approaches available for this model. Moreover, the sea urchin lineage did not undergo whole genome duplications, unlike humans, exhibiting the same diversity of gene families, but with less redundancy within the subfamilies, thereby facilitating functional analyses. Thus, studying the mechanisms that drive sea urchin embryogenesis represent a valuable asset to provide insights into the conserved mechanisms controlling the development of deuterostomes. My results show that wnt and fzd genes are expressed in a dynamic fashion throughout P. lividus embryogenesis. Interestingly, until the gastrulation, the genes encoding FZD receptors are expressed in distinct territories that, taken together, cover almost the entire embryo. Accordingly, this work allowed me to establish a catalog of possible WNT-FZD couples likely to form during the embryogenesis of a deuterostome animal, based on the compatibility of their respective spatiotemporal distribution, and to further provide insights into the potential biological functions of these WNT and FZD proteins during this process. The second goal of my Ph.D. was to reconstruct the evolution of the WNT proteins and to determine whether an ancestral intrinsic function of WNTs is conserved within metazoans. To this end, I analyzed the composition of the wnt repertoires of seventeen metazoan species, the primary sequences of the WNT proteins they encode, the relative positions of the wnts within their respective genomes, and, for selected species, the genomic environment of their wnts. In addition, I investigated whether three sponge WNT ligands and an ancestral WNT sequence, which was calculated from a sample of metazoan WNT sequences, are able to trigger Wnt signaling pathways, when expressed in three planulozoan (cnidarian and bilaterian) species. The data obtained during this study allows me to propose a model for the diversification of wnt genes in metazoans and revealed conserved intrinsic functional capabilities for the WNT ligands.

The Neutral Indel Model is able to predict accurately the distribution of indel events in alignments of neutrally evolving genomic sequence. Here, I apply this model to a diverse range of metazoan species pairs, to a number of ends. First, I apply the Neutral Indel Model to alignments of genome sequences for species within the mammalian clade in order to estimate the quantities of functional DNA shared between species pairs. I demonstrate that as the evolutionary divergence between species pairs increases, estimates of functional sequence drop off dramatically. This pattern is not replicated in extensive simulations of genome sequence alignments, suggesting that functional (and mostly non-coding) sequence is turning over at a rapid rate. I also estimate that between 200 and 300 Mb (6.5-10%) of the human genome is under evolutionary constraint, a considerably higher quantity of sequence than has been estimated by previous whole genome analyses. Second, extending my analyses to consider more diverse metazoan species, I provide estimates for functional bases within organisms’ genomes that appear to mirror our conceptions of organismal complexity. Thirdly, I develop the Neutral Indel Model as a method for assessing genome sequence quality, by quantifying indel errors within alignments of closely related (ds < 0.1) species pairs. Applying this method to six primate genome sequence assemblies, I demonstrate that the frequency of indel error events per base varies up to six-fold. Further to this, I show that second generation sequencing technologies can be used to create high quality genome sequence assemblies and to ameliorate errors in pre-existing assemblies. Finally, I analyse patterns of indel mutations in primate transposable elements and show that indels are not randomly distributed within these sequences due to regularly spaced homo-nucleotide motifs.

Made available in DSpace on 2015-03-04T18:50:50Z (GMT). No. of bitstreams: 1 Dissertacao Marcelo Garcia Jun-2007.pdf: 1765034 bytes, checksum: ccb95f7d696b4361f3d25db96fd2d70a (MD5) Previous issue date: 2007-06-01 / Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior / Inferring the evolutive relations between the animal phyla has been a formidable challenge to Science. The animal phyla represent quite distinct baupläne (body architectures) and are, therefore, difficult to compare. At the same time, their fossil record converges mostly to the same period on the geological scale. The recent availability of molecular data has, however, inaugurated a new front in animal phylogeny. The present work explores this opportunity by inferring a phylogeny with distance and maximum likelihood methods, employing all animal mitochondrial genomes ever sequenced. The results present only a few bigger groups with strong statistical support, like Diploblastica, Bilasteria, Protostomia and Deutorostomia, and many smaller groups of animals belonging to the same order or family. These results seems to confirm that the phyla radiated in such a short time interval that the phylogenetic signal did not hold out to produce a satisfactory resolution of the animal tree to date. Some limits may have yet to be tested, through models of evolution more fit to this scenario. For example was only recovered with the use of gamma distances for site-to-site substitution rate variability, at the expense of compressing the smaller branches throughout the tree. Nematodes and Platyhelminthes reveal a bias in GC and AT skew that cannot be adequately mapped by any reversible substitution pattern. Nevertheless, even if corrections are found for these issues, it is well possible that the hope of a better resolution in the animal tree will lie further on, by a better understanding of the evolutive process in a genomic scale. / Discernir as relações evolutivas entre os grandes grupos animais tem representado um formidável desafio para a Ciência. Os filos animais possuem arquiteturas corporais bastante distintas e por isso difíceis de serem comparadas. Ao mesmo tempo, seu registro fóssil converge aproximadamente para um mesmo intervalo na escala geológica, dificultando uma reconstrução filogenética com caracteres morfológicos. A disponibilidade de dados moleculares sobre os organismos abriu, contudo, novas possibilidades na filogenia animal. Esta dissertação buscou explorar essas possibilidades inferindo uma filogenia com métodos de distância e máxima verossimilhança, a partir de todos os genomas mitocondriais, completamente seqüenciados até o momento. No entanto, apenas alguns grandes agrupamentos como Diploblastica, Bilateria, Deuterostomia e Protostomia foram recuperados com forte suporte estatístico, além de pequenos agrupamentos de animais de mesma ordem ou família, indicando que os efeitos da rápida radiação no Cambriano se estenderam também ao registro molecular. Os resultados também indicam a necessidade de buscar modelos de evolução mais aderentes a este cenário. Deuterostomia, por exemplo, só foi recuperado monofileticamente assumindo-se a distribuição gama para variabilidade entre-sítios, ao custo, entretanto, da perda de definição nos ramos menores. Nematóides e Platelmintos, por sua vez, revelam um possível viés no skew (desvio) do conteúdo GC e AT de seus genes mitocondriais, que não é adequadamente mapeado por modelos de substituição reversíveis. Os indícios são de que a resolução da filogenia animal depende ainda de uma melhor compreensão da evolução molecular em escala genômica.