Thesis (Ph. D.)--University of Wisconsin, 1964. / Typescript. Vita. eContent provider-neutral record in process. Description based on print version record. Bibliography: leaves 76-82.

Thesis (Ph. D.)--University of Wisconsin--Madison, 1933. / Typescript. eContent provider-neutral record in process. Description based on print version record. Includes bibliographical references (leaves 22-24).

Universiẗat, Diss.--Kaiserslautern, 1999.

Inducible defenses alter the strength of interaction in food webs. Theoretical models that incorporate their effects are therefore critical for predicting community dynamics and stability. I examined ecological effects of an inducible morphological defense in a microbial model. I first investigated the effect of genotype. number of predators, and previous exposure to predators on the speed and maximum level of defense for eight clones in three species of the ciliate Euplotes. The effectiveness of defense depends on both of these aspects of defense induction: therefore these traits should evolve in concert. The speed and maximum level of induction varied among genotypes, showing that there is genetic variance for these traits and the potential for evolutionary change under selection. Higher predator densities led to more rapid induction and higher maximum levels of defense. but previous exposure to predators had no detectable effect on either of these traits. I then used a model selection approach to determine the shape of the functional response of clones that differed in their level of defense, and to estimate and compare the model parameters attack rate and handling time. Defense decreased the attack rate of Euploes on Chlorella vulgar-is algae in one highly defended clone, but did not affect the functional response in two less defended clones. My results demonstrate that Euploes ciliates can precisely and rapidly adjust their morphological defense to the magnitude of predation risk in a way that varies among genotypes. This variation will lead to diversity in prey vulnerability to predators under natural conditions and translates to genetically-based differences in the foraging impact on resources of Euplotes. These estimates of ecological effects of induced defense in this system allow their inclusion in the development and testing of dynamic models. This in turn will inform our understanding of the influence of induced defenses and related trait-mediated indirect effects on community dynamics and stability.

Thesis (Ph. D.)--Ludwig-Maximilians-Universität München, 2003. / Title from PDF title page (viewed on May 13, 2006). Vita. Includes bibliographical references (p. 136-146).

Thesis (Ph.D.)--University of Alabama at Birmingham, 2007. / Title from PDF title page (viewed on Sept. 16, 2009). Includes bibliographical references.

Ciliates are model organisms for studying programmed genome rearrangement because each cell houses two distinct genomes. During postzygotic development, the somatic genome rearranges from a copy of the germline genome via extensive genome remodeling, including DNA elimination, religation and sometimes translocation or inversion of genomic regions. Previous studies of this process were restricted to a few model ciliates including Tetrahymena thermophila, Paramecium tetraurelia and Oxytricha trifallax. Oxytricha diverged from Tetrahymena and Paramecium over one billion years ago, and it possesses a massively fragmented and scrambled germline genome. My thesis compares Oxytricha to more closely related ciliates to address the evolutionary origin of genome complexity. Chapter 1 provides a general introduction to genome architecture, comparison of well-studied ciliate genomes and challenges of studying genome rearrangement in non-model ciliates. Chapter 2 describes a computational pipeline, SIGAR (Split-read Inference of Genome Architecture and Rearrangements), which infers genome rearrangement features without a germline genome assembly. We validated the pipeline using a published Oxytricha dataset, and also applied it to six diverse ciliate species including Ichthyophthirius multifiliis, a fish pathogen. This pipeline enables pilot surveys or exploration of chromosomal rearrangement in ciliates with limited germline DNA access, thereby providing new insights into the evolution of DNA rearrangement. Chapter 3 presents a comparative genomic study of three ciliate species including Oxytricha trifallax, Tetmemena sp. and Euplotes woodruffi. Collaborating with my colleagues, I assembled and annotated germline genomes in Tetmemena and E. woodruffi, as well as E. woodruffi’s somatic genome. We identified scrambled genes in all three species, especially the earlier-diverged E. woodruffi, though at a lower level (7.3% of gene loci) compared to Oxytricha (15.6%) and Tetmemena (13.6%). E. woodruffi may therefore represent an intermediate between the nonscrambled ancestral genome and more massively scrambled genomes as can be seen in Oxytricha and Tetmemena. We also found that scrambled genes tend to have more paralogs or have partial MDS duplications, suggesting that local duplications might play a role in the evolutionary origin of scrambled genes. Chapter 4 reports a new genetic code identified in a basal spirotrich ciliate, Licnophora macfarlandi. Ciliates have been a hot spot for the evolution of alternative genetic codes. All variant genetic codes in ciliates reassign canonical stop codons to amino acids, and in most cases the UAA and UAG are reassigned to the same amino acid, or are both used as stop codons. The codon usage analysis in Licnophora revealed an unprecedented genetic code that translates the UAA to glutamic acid and the UAG to glutamine. We also detected candidate tRNAs from the somatic genome which can recognize the UAA and UAG. Chapter 5 describes possible future directions to understand the genome complexity of ciliates.