The majority of the vertebrate genome sequence is not coding for proteins. In recent years, the evolution of this noncoding fraction of the genome has gained interest. These studies have been greatly facilitated by the availability of full genome sequences. The aim of this thesis is to study evolution of the noncoding vertebrate genome through bioinformatic analysis of large-scale genomic datasets. In a first analysis we addressed the use of conservation of sequence between highly diverged genomes to infer function. We provided evidence for a turnover of the patterns of negative selection. Hence, measures of constraint based on comparisons of diverged genomes might underestimate the functional proportion of the genome. In the following analyses we focused on length variation as found in small-scale insertion and deletion (indel) polymorphisms and microsatellites. For indels in chicken, replication slippage is a likely mutation mechanism, as a large proportion of the indels are parts of tandem-duplicates. Using a set of microsatellite polymorphisms in chicken, where we avoid ascertainment bias, we showed that polymorphism is positively correlated with microsatellite length and AT-content. Furthermore, interruptions in the microsatellite sequence decrease the levels of polymorphism. We also analysed the association between microsatellite polymorphism and recombination in the human genome. Here we found increased levels of microsatellite polymorphism in human recombination hotspots and also similar increases in the frequencies of single nucleotide polymorphisms (SNPs) and indels. This points towards natural selection shaping the levels of variation. Alternatively, recombination is mutagenic for all three kinds of polymorphisms. Finally, I present the program ILAPlot. It is a tool for visualisation, exploration and data extraction based on BLAST. Our combined results highlight the intricate connections between evolutionary phenomena. It also emphasises the importance of length variability in genome evolution, as well as the gradual difference between indels and microsatellites.

Thesis (Ph. D.)--University of Oklahoma. / Bibliography: leaves 120-130.

Conceptualizations of actual biological patterns as preserved in the fossil record must accommodate the results of biotic and abiotic drivers of faunal dynamics. However, those conceptualizations also may reflect cognitive biases resulting from foundational philosophical stances. Whether fossils are conceptualized as the remains of biological entities or as geological objects will affect both taxonomic identifications and secondary inferences derived from those identifications. In addition, operational research bias centered on relativistic views of ‘importance’ of particular components (i.e., taxonomic or skeletal region) of the assemblage results in preferential documentation of some taxa and marginalization of others. I explored the consequences of those specific cognitive and operational biases through examination of Triassic and Eocene faunal assemblages in western North America. For the Triassic I focused on taxonomic and systematic treatments of Paleorhinus, a group of phytosaurs important for the establishment of biochronologic correlations. Specimen-level reexamination of Paleorhinus supported a restricted usage of Paleorhinus as a clade, dissolved a biochronologic connection between terrestrial and marine deposits, and indicated a prior compression of the early part of the Late Triassic as a result of previous conceptualizations of species. I reexamined the Otis Chalk tetrapod assemblage in light of new specimens and modern phylogenetic frameworks. My examination supported a restricted usage of the Otischalkian for biochronologic correlation of the Late Triassic, and emphasized the importance of apomorphic character-based specimen examinations in conjunction with detailed lithostratigraphy prior to the development of biochronologic schema. For the Eocene I focused on undocumented terrestrial reptiles from the late Uintan fauna of West Texas. Specifically I discovered new taxa and new geographic occurrences of amphisbaenians and caimanine crocodylians. The amphisbaenians represent the southernmost record of the clade in the North American Paleogene, and, when combined with other amphisbaenian records, document that the clade responded to late Paleogene climatic changes in ways different from the inferred mammalian response. The new taxon of caimanine crocodylian represents a new geographic and temporal record of that clade. That new record indicates that the biogeographic range of extant caimans represents a climate-driven restriction from a formerly more expansive range, and suggests that the previous geographic and temporal gap in paleodistribution data is related to sampling biases and is not a solely a biological phenomenon. These data indicate that reliable characterization of vertebrate faunal dynamics requires open acknowledgment and appropriate documentation of cognitive and operational biases that affect interpretations of paleontological data. / text

Birds are the most diverse extant group of terrestrial vertebrates, and relationships amongst major extant and extinct avian lineages remain hotly debated. A clade of Aves which has received limited attention is the extinct Zygodactylidae, a species-rich group of perching birds that possess a foot with a retroverted fourth toe, an elongate tarsometatarsus and a large intermetacarpal process in the wing. Specimens currently included within Zygodactylidae previously were thought to be sister taxa to songbirds (Passeriformes) or woodpeckers and allies (Piciformes). Zygodactylids were most abundant during the Eocene in North America and Europe and persisted to the Early Miocene. Five exceptionally preserved fossils from the Early Eocene Green River Formation of Wyoming are described, and provide insights into the interrelationships of zygodactylid taxa and the position of the clade within Aves. In an attempt to resolve systematic relationships within zygodactylids, and the position of the clade within Aves, I conducted two sets of phylogenetic analyses. The first focused on clarifying relationships within Zygodactylidae. Each taxon was evaluated for 37 morphological characters. Resulting strict consensus cladograms yield topologies in which two of the new Green River specimens are positioned in a clade within Zygodactylus, a taxon previously known only from the Early Oligocene and Early Miocene of Europe. The second set of analyses sought to assess which extant avian lineage is most closely allied with Zygodactylidae. Those analyses used a dataset of 135 characters evaluated for 57 species and a supraspecific terminal, Zygodactylidae. Scoring of Zygodactylidae was based on morphological observations from all described taxa within Zygodactylidae. The extant species sample was chosen to evaluate previously proposed hypotheses of relationships between Zygodactylidae and other avian clades and included songbirds, parrots and 43 species from the coraciiform-piciform clade (e.g., woodpeckers, galbulids, rollers and motmots). Outgroup species were iteratively swapped to determine if outgroup choice affected recovered estimates of zygodactylid relationships within Aves. Zygodactylidae is the sister taxon to songbirds in the resultant tree topologies. These results forward our understanding of the relationship between Zygodactylidae and Passeriformes within Aves. / text

Proper embryonic development requires precise genetic regulation of cell growth and differentiation. Organogenesis, the origin and formation of internal organs, must be exquisitely choreographed to ensure correct temporal and spatial patterning of functional organs within the developing organism. The liver is a vital organ responsible for hundreds of essential metabolic functions, but the intricate pathways controlling organ specification, differentiation, and positioning have not been fully elucidated. Uncovering the molecular mechanisms involved in hepatogenesis will enhance our understanding of normal liver development as well as inform the design of therapeutics to combat liver disease. Nuclear receptors are evolutionarily recent signal transducers that occupy a special niche in gene regulation, acting as direct connections between a ligand and its downstream transcriptional target. Nuclear receptor signaling governs many physiological processes, however its impact on liver development is not well understood.

No description available.

There is a need for effective and environmentally sensitive methods of controlling vertebrate pest problems in agriculture and urban environment. Nonlethal natural repellents may meet this need where more traditional methods of control, such as scaring, shooting, and trapping, are either ineffectual or unacceptable. Neem (Azadirachta indica A Juss) extracts: oil, seed and leaf powder and chemicals from cockroach (Blaberus giganteus L.) were tested for their repellent properties. In addition defensive volatiles from B. giganteus were tested in an arena based on choice by smell (cheese or insect volatiles). This arena test used laboratory rats (Rattus norvegicus Berk.); females were more active than males. Both sexes visited the holes with cheese more than holes containing insect's volatiles. However in a feeding test with one choice of food the control did not differ from the treatment. Neem products seem to act as antifeedant on rats: neem seed oil, neem seed powder and neem leaf powder reduced rats feeding respectively at concentration of 15 ml of oil/kg, 15--50 g of seed powder/kg, and 25--50 g of leaf powder/kg of rat chow. Overall neem leaf powder was less effective than seed powder and oil. Neem and insect products may have potential in controlling rats particularly in storage situation, which could lead to an important reduction of post-harvest loss of grains in Sahelian and Asian countries.

Closely packed myosin filaments are an example of a disordered biological array responsible for the contraction of muscle. X-ray fiber diffraction data is used to study these biomolecular assemblies but the inherent disorder in muscle makes interpretation of the diffraction data difficult. Limited knowledge of the precise nature of the myosin lattice disorder and its effects on X-ray diffraction data is currently limiting advances in studies on muscle structure and function. This thesis covers theoretical and computational efforts to incorporate the myosin lattice disorder in X-ray diffraction analysis. An automated image analysis program is developed to rapidly and accurately quantitate the disorder from electron micrographs of muscle cross-sections. The observed disorder is modelled as an antiferromagnetic Ising model and the model verified using Monte Carlo simulations. Theory and methods are developed for efficient calculation of cylindrically averaged X-ray diffraction from two-dimensional lattices that incorporate this disorder.

DNA methylation is an epigenetic modification in which a methyl group is covalently added to the DNA. In vertebrate genomes methylation occurs almost exclusively at cytosines immediately followed by a guanine (CpG dinucleotides). Two important aspects of DNA methylation have inspired several recent scientific investigations including those in this dissertation. First, methylated cytosines are hotspots of point mutation due to a methylation-dependent mutation mechanism, which has caused a deficiency of CpGs in vertebrate genomes. Second, DNA methylation in promoters is linked with transcriptional silencing of the associated genes. This dissertation presents the results of four studies in which I investigated the impacts of DNA methylation on the neutral and functional evolution of vertebrate genomes. The results of the first two studies demonstrate that DNA methylation has profound impacts on both inter- and intra-genomic neutral substitution rate variation. The third and fourth studies demonstrate that DNA methylation has played critical roles in shaping the evolution of vertebrate promoters and gene regulation.

Thesis (Ph. D.)--West Virginia University, 2009. / Title from document title page. Document formatted into pages; contains vi, 96 p. : ill. (some col.). Includes abstract. Includes bibliographical references.