abstract: This project covers the transcription of Three Suites for Cello, opp. 72, 80, and 87, by Benjamin Britten, for guitar. These suites were chosen because of the influence of Bach, which is seen in the texture of the pieces, and because they can be played on guitar with very few changes. Music for unaccompanied cello has a history of being transcribed for guitar, including the Bach cello suites, and is a means for guitarists to expand the repertoire. In addition to documenting the changes made in adapting these pieces for guitar, a brief biographical sketch of the composer and descriptions of each movement are included. Also explained are articulation symbols and terminologies that are uncommon in music written for the guitar, and suggestions on how to perform the multitude of ornaments Britten has written in the score. / Dissertation/Thesis / D.M.A. Music 2012

Vischeria and Eustigmatos are closely related genera occurring in terrestrial habitats. These genera were distinguished by the differences in the features of the cell wall (projections and ridges of different form, smooth surface respectively). Up to date three species of the genus Eustigmatos and twelve species of the genus Vischeria have been described, but nine of the Vischeria species have been rarely, if ever, observed since the original description. This work is focused on evaluating molecular variability, diversity, and taxonomy of the Vischeria/Eustigmatos complex. Ninety seven strains, obtained from public algal collections or newly isolated from localities from all over the world, were studied, including the type strains of two Eustigmatos species and three Vischeria species. Phylogenetic analyses of the ITS2 rDNA and rbcL sequences showed that these genera are not genetically separated. The five types strains each represented a separate evolutionary lineage. Some of the additional lineages included strains morphologically corresponding to the species Eustigmatos magnus. Some of the newly isolated strains are according to the markers examined genetically indistinguishable from known strains from public algal collections. However, some of them are new lineages. Only one of the phylogenetic...

Babesia odocoilei is an intraerythrocytic apicomplexan parasite which infects cervidae, sometimes causing babesiosis. It is vectored by the tick Ixodes scapularis and is distributed throughout the southeastern United States. The geographic and host range continue to extend as new incidence of infection is detected. A genomic DNA region spanning the internal transcribed spacer 1 (ITS1), 5.8S rRNA gene, and ITS2 of ribosomal RNA (rRNA) from 18 B. odocoilei isolates (speciation confirmed by small subunit rRNA analysis) was amplified using the polymerase chain reaction, cloned and sequenced. The isolates originated from 6 different cervidae or bovidae hosts in various U.S. geographic areas. Included in the analysis was a previously described reindeer B. odocoilei-like isolate, RD61, which showed only 99.0% identity in SSU rRNA analysis to B. odocoilei. Percent identity pairwise comparisons among the samples were calculated for both the full ITS1-5.8S-ITS2 and individual genomic regions. Identity values for all comparisons ranged from 90% to 100%, with the exception of RD61, which showed no higher than 88% identity for all gene regions. An analysis of fixed differences identified in the ITS1 and ITS2 gene regions of all clones revealed 21 fixed differences in ITS1, and only 11 in ITS2. Most isolates were found to have 2 overall patterns of fixed differences, although some had 1 or 3. Phylogenetic analysis of all sequences for the entire ITS1-5.8S-ITS2 gene region placed most isolates into 2 distinct groups corresponding to those observed in the analysis of fixed differences. This suggested the presence of at least 2 rRNA transcription units in B. odocoilei. ITS analysis failed to demonstrate host or geographic differences that might serve to pinpoint the source of outbreaks of B. odocoilei in farmed and managed host animals. This failure might result from genetic recombination of ITS genomic regions during the tick vector stage. Lack of conspecificity between the RD61 isolate and B. odocoilei was supported by this study; however, more data are needed to clarify the taxonomic status of this B. odocoilei-like isolate.

Background: Hepatitis E (HEV) is a small, non-enveloped virus that belongs to the viral genus Hepevirus. HEV is a positive sense single-stranded RNA virus and there is insufficient information regarding its replication. This is mainly because the virus has low capacity to grow in normally used cell cultures. Many specific strand assay detection studies have been done in order to understand more about HEV replication. Unfortunately, these assays have the disadvantage of giving false positive results. Aim: The aim of this project was to improve the positive strand assay to increase specificity and eliminate false positivity which is due to high sensitivity of the polymerase chain reaction (PCR). False positivity occurs as remains of transfected material in the cell are amplified. Method: The samples used in this project were swine samples from Sweden and a human sample (plasmid clone of genotype 1) from India. Negative samples, extracted positive samples and transcribed RNA positive sense samples were used. The methods applied were cDNA synthesis, exonuclease I and RNase treatments, DNA purification kits followed by first and nested PCR. Result: The results of this study indicated great improvement of the detection assay especially for the transcribed RNA samples. Best results were obtained at a final concentration of 1.5mM MgCl2 in the mastermix.  Conclusion: Changing the concentration of MgCl2 appeared to have a great effect on PCR specificity. Improving detection assays is very essential as they can be applied in the research field and in public health centers either for diagnosis or tracking disease outbreaks.

No description available.

Garry oak (Quercus garryana Douglas ex. Hook) is a white oak (Quercus sect. Quercus) with a geographic range extending from southwestern BC to south-central California. It is the only native white oak in BC and Washington, and is the northernmost species of the California Floristic Province-Pacific Northwest white oak clade. I used molecular methods to address the following questions: 1) What are the patterns of genetic variation within Garry oak? 2) How do these patterns vary geographically, and how did the spatial distribution of the gene lineages come to occupy its current geographical range? 3) Does Garry oak show evidence of genetic interaction with other white oak species in western North America? 4) Is there morphological or genetic evidence to support the three described varieties of Garry oak? I obtained samples of Garry oak from 117 localities over its geographic range, as well as samples of two other California white oaks (Q. lobata and Q. douglasii) and a Rocky Mountain species (Q. gambelii). Analyses of DNA sequence data from four plastid DNA regions revealed 24 distinct molecular variants (haplotypes) in Garry oak. These show a strong south-to-north decrease in genetic diversity, consistent with post-glacial northward expansion. Haplotypes present in the northern part of the range provide evidence of two separate northward migrations, only one of which reached the northern range limit of Garry oak in BC. I found that Garry oak shared plastid DNA haplotypes with two other white oak species, indicating that it hybridizes with other oaks in the southern part of its range. The nuclear ribosomal ITS phylogeny showed poor resolution, but both cpDNA and nrDNA may indicate that Q. garryana is more closely related to the white oaks of central North America than was previously thought. My findings also suggest that the three currently recognized varieties of Garry oak (var. garryana, breweri and semota) are not well differentiated genetically, but show morphological variation at the regional level. This study shows the phylogeographic patterns within Q. garryana. In addition, it contributes to conservation efforts in Garry oak ecosystems by indicating regions of high genetic diversity in Garry oak, including genetically unique populations that may be especially worthy of preservation. / Graduate

<em>Cladophora</em> is a widespread freshwater filamentous cholorophyte genus and is frequently observed in eutrophic waters where it can produce large nuisance blooms. These blooms can have direct impacts on water intake for power generation, irrigation canals and can be aesthetically unpleasant. Much of the ecological and physiological studies on <em>Cladophora</em> have assumed that the populations of this genus in North America belong to the species <em>Cladophora glomerata</em>. However, this has never been tested despite that it is well documented that identifying freshwater <em>Cladophora</em> to the species level is difficult due morphological variability under different ecological conditions. In addition, the species epithets for freshwater <em>Cladophora</em> are based on European collections and it is not clear if these should be applied to North America. This study examines approximately 40 collections of <em>Cladophora</em> from the Laurentian Great Lakes and 43 from various locations in North America ranging from the Northwest Territories to Puerto Rico. Initially we determined the nucleotide sequences of the internal transcribed spacer (ITS) region of the nuclear ribosomal cistron and observed sequence divergence to be low (0-3%), demonstrating an inability for this marker to resolve species delineation as divergence of this region was low. Amplification of the inter-simple sequence repeat (ISSR) regions were used to analyze microsatellite motif frequency throughout the genome to evaluate the biogeography relationships, including diversity, of freshwater <em>Cladophora</em> sp. five different primers were used on 70 individuals. UPGMA analyses of the presence/absence of bands demonstrate that each of the Great Lake populations separate into groups according to the Lake they were initially sampled from. However, collections from North America are highly variable and do not form well supported biogeographic clades. In addition, these collections appear to be distinct from type cultures of freshwater <em>Cladophora</em> from Europe. Supplementary morphological analysis using suggested taxonomically valid criterion (length and diameter of main axis, ultimate branch, and apical cell) none were able to differentiate Great Lake populations.

<em>Cladophora</em> is a widespread freshwater filamentous cholorophyte genus and is frequently observed in eutrophic waters where it can produce large nuisance blooms. These blooms can have direct impacts on water intake for power generation, irrigation canals and can be aesthetically unpleasant. Much of the ecological and physiological studies on <em>Cladophora</em> have assumed that the populations of this genus in North America belong to the species <em>Cladophora glomerata</em>. However, this has never been tested despite that it is well documented that identifying freshwater <em>Cladophora</em> to the species level is difficult due morphological variability under different ecological conditions. In addition, the species epithets for freshwater <em>Cladophora</em> are based on European collections and it is not clear if these should be applied to North America. This study examines approximately 40 collections of <em>Cladophora</em> from the Laurentian Great Lakes and 43 from various locations in North America ranging from the Northwest Territories to Puerto Rico. Initially we determined the nucleotide sequences of the internal transcribed spacer (ITS) region of the nuclear ribosomal cistron and observed sequence divergence to be low (0-3%), demonstrating an inability for this marker to resolve species delineation as divergence of this region was low. Amplification of the inter-simple sequence repeat (ISSR) regions were used to analyze microsatellite motif frequency throughout the genome to evaluate the biogeography relationships, including diversity, of freshwater <em>Cladophora</em> sp. five different primers were used on 70 individuals. UPGMA analyses of the presence/absence of bands demonstrate that each of the Great Lake populations separate into groups according to the Lake they were initially sampled from. However, collections from North America are highly variable and do not form well supported biogeographic clades. In addition, these collections appear to be distinct from type cultures of freshwater <em>Cladophora</em> from Europe. Supplementary morphological analysis using suggested taxonomically valid criterion (length and diameter of main axis, ultimate branch, and apical cell) none were able to differentiate Great Lake populations.

The aim of this study was to obtain the molecular marker of Taiwania cryptomerioides Hayata based on DNA sequence data of PCR- sequencing and inter-simple sequence repeat (ISSR), and to evaluate the genetic diversity of populations of Taiwania cryptomerioides Hayata and molecular phylogeny of T. cryptomerioides and Taiwania flousiana Gaussen. The sequence data based on the internal transcribed spacer (ITS) of a total of 108 samples of T. cryptomerioides were determined. Eight different populations of T. cryptomerioides and 12 samples of T. flousiana from Yunnan, China were analyzed. The finding of the study showed that heterogeneity of ITS region within individuals of T. cryptomerioides was high by showing high nucleotide diversity among ITS sequences both in T. cryptomerioides ( £k = 0.18153) and T. flousiana ( £k = 0.19751). The findings fit in Tajima¡¦s D test of neutrality based on DNA sequence variation in the ITS region of T. cryptomerioides and T. flousiana. It is not obvious to incorporate into different population through clustering analysis based on data of the ITS region of T. cryptomerioides and T. flousiana. However, slightly genetic differentiation between T. cryptomerioides and T. flousiana was found, which figured of Fst (Fst = 0.0441~ 0.0856, an average value = 0.0611). On the other hand, the samples were studied by using ISSR markers. Of the 100 primers screened, 4 produced highly reproducible ISSR bands, and 24 discernible DNA fragments were generated with 17 being polymorphic. Based on cluster analysis of molecular data, the cluster is not clear among populations of T. cryptomerioides and T. flousiana. The analysis of AMOVA revealed that the variance component between species of T. cryptomerioides and T. flousiana was 38.54¢H (P < 0.001); however, the variance component within species is 61.46 (P < 0.001). The variation within population of T. cryptomerioides was 84.74¢H (P < 0.001) and the variance between populations is 15.26¢H (P < 0.001), indicating that the genetic diversity of individuals within population was high. The aforementioned data suggest that gene flow among different populations of T. cryptomerioides was high, indicating that the genetic diversity was high among individuals of T. cryptomerioides but was low between populations. Furthermore, it is concluded both species are genetically closer and could be grouped into the same species.

The 5’ external transcribed spacer (5’ ETS) of pre-ribosomal RNA, although highly variable in size and sequence, has been shown to be critical for the initiation of rRNA processing. This study further examined the 5’ ETS in Schizosaccharomyces pombe with respect to structural elements that underlie rRNA maturation. Initially, the 5’ ETS/18S rRNA junction region was examined by mutational analyses to detect cis-acting elements critical to known cleavage sites. The results indicated that sequence/structure in the junction region does not direct or strongly influence cleavage at the 5’ end of 18S rRNA. Systematic mutations also were used to examine the significance of previously suggested putative ribosomal protein binding sites or U3 snoRNA binding sites as well as other stem-loop sequences of regions IV, V and VI in the 5’ ETS. The results indicated that the putative U3 snoRNA binding sites were less critical than previously anticipated but have identified elements in regions IV and V with significant influence on the production of mature ribosomal RNA. In vitro studies of interactions between these elements and the U3 snoRNA or cellular protein also were initiated. The results of electrophoretic mobility shift assays indicated a strong interaction between region IV and the U3 snoRNA, suggesting that region IV probably contributes to the function of an important structure in the nucleolar precursor particle, which together with region V and probably other hairpins, may act to organize a stable processing domain. In contrast to the previous studies, which suggested as many as six intermediate cleavage sites in the 5’ ETS of S. pombe, re-examination of termini using hybridization and ligation-mediated RT-PCR indicated only two major cleavage sites. In general the 5’ ETS sequence mutants did not seem to influence the rRNA processing profile significantly but could dramatically affect the quantity of the product, an observation that provided further evidence of quality control, which helps ensure that only functional RNA is incorporated into mature ribosomes. Taken together the results illustrated that various sequence/structural elements in the 5’ ETS could influence or be critical for the maturation of rRNA. The results also support the possibility that the precursor molecule is first organized into one or more processing domains that direct the actual maturation processes. / This study was supported by the Natural Sciences and Engineering Research Council of Canada.