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<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.

Hybridization is an important mechanism in diversification. It often makes taxonomy difficult. Lack of strong supported intrageneric classification in genus Pteris (Pteridaceae) could be caused by natural hybridization. Most hybridization documnted in Pteris was based on limited evidence. This study focuses on Pteris cadieri complex, the taxon with putative hybridization. The species complex displayed significant morphological variation and was associated with hybrid origin. Reproductive biology revealed variation in spore number per sporangium, spore size, spore shape and apogamous reproduction, which imply its hybrid origin. Cytology analysis using chromosome counting and flow cytometry identified diploids, triploids, and tetraploids. CpDNA and nuclear DNA supported that Pteris cadieri complex is hybrid origin: paternal and maternal lineages were inferred and 11 taxa were identified. Furthermore, comparing materials form Hainan and Taiwan, , it is clear that the species complex is composed by taxa arisen from multiple hybridization. Systematic inconsistency existed between chloroplast and nuclear phylogenies in Pteris impled that other taxa might have involved in hybridization events, in addition to the Pteris cadieri complex. Hybridization may be very common in Pteris. To infer intrageneric taxonomy of Pteris, effect of reticulate evolution should never be neglected. Finally, based on morphological and evolutionary traits, the taxonomy of Pteris cadieri complex is revised. There are Pteris cadieri Christ, Pteris dimorpha Copel. var. dimorpha, Pteris dimorpha var. plumbea (Christ) Y.-S. Chao, H.-Y. Liu & W.-L. Chiou, Pteris grevilleana Wall. ex Agardh var. grevilleanan, Pteris grevilleana Wall. ex Agardh var. ornata Alderw., and Pteris hainanensis Ching.

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.

Spacer-filled channels are employed in membrane modules in many industrial applications where feed-flow spacers (employed to separate membrane sheets and create flow channels) tend to enhance mass transport characteristics, possibly mitigating fouling and concentration polarization phenomena. In this work direct numerical simulation was performed for the flow in the spacer-filled channels to obtain a better understanding of fluid flow and mass transfer phenomena in these channels. A solute with a Schmidt number of 1 at Reynolds numbers of 300, 500 and 800 (based on the bulk velocity and spacer diameter) was considered. The effect of spacer location was also studied for three different configurations, spacer at the centre of the channel, at off-centre location, and attached to the wall. Instantaneous velocity fields and flow structures such as separation of boundary layer on the walls and on the cylinder, eddies on the walls, recirculation regions and vortex shedding were investigated. A Fourier analysis was carried out on the time series velocity data. Using this analysis the Strouhal number was calculated and the development of the flow towards a broader turbulent state at higher Reynolds number was captured. Other statistical characteristics such as time-averaged velocities and wall shear rates are obtained and discussed. The average pressure loss which represents the operation cost of membrane modules was calculated for the channels and found to be highest for spacer at the centre of the channel and lowest for spacer attached to the wall. Scalar transport equation is directly solved along with Navier-Stokes equation to get the concentration field. Local Sherwood number is obtained on the walls and the relationship between shear stress, vortex shedding, and mass transfer enhancement was explored. The overall Sherwood number and Stanton number of the channels, which indicate the mass transfer performance of the channels, are obtained. It was observed that as spacer approaches the wall mass transfer rate is decreasing. / Thesis (Master, Mechanical and Materials Engineering) -- Queen's University, 2010-11-30 11:44:07.479

To improve fungal identification using a single DNA sequence, I introduce the Barcode Similarity Group (BSG) defined as a cluster of sequences that share greater than or equal to a threshold amount of genetic similarity with each other. As a test case, I created 393 BSGs from 2463 Cortinarius ITS sequences using a 94% similarity cut-off value in DOTUR. Some BSGs may contain multiple species. The BSG database was used to label environmental sequences, find misidentified or mislabeled sequences, and find potential cryptic species and novel species. Expert taxonomists will be needed to perform detailed morphological and phylogenetic studies to identify the individual species within each BSG. The main advantage of using BSGs is that it clusters together sequences using total genetic relatedness and does not rely on any taxonomy for identification. A website was created where the RDP Classifier is used to classify a query sequence into a BSG.

To improve fungal identification using a single DNA sequence, I introduce the Barcode Similarity Group (BSG) defined as a cluster of sequences that share greater than or equal to a threshold amount of genetic similarity with each other. As a test case, I created 393 BSGs from 2463 Cortinarius ITS sequences using a 94% similarity cut-off value in DOTUR. Some BSGs may contain multiple species. The BSG database was used to label environmental sequences, find misidentified or mislabeled sequences, and find potential cryptic species and novel species. Expert taxonomists will be needed to perform detailed morphological and phylogenetic studies to identify the individual species within each BSG. The main advantage of using BSGs is that it clusters together sequences using total genetic relatedness and does not rely on any taxonomy for identification. A website was created where the RDP Classifier is used to classify a query sequence into a BSG.

Hollow fibre and spiral wound membrane (SWM) modules are the most common commercially available membrane modules. The latter dominate especially for RO, NF and UF and are the focus of this study. The main difficulty these types of modules face is concentration polarisation. In SWM modules, the spacer meshes that keep the membrane leaves apart also help reduce the effects of concentration polarisation. The spacer filaments act as flow obstructions, and thus encourage flow destabilisation and increase mass transfer enhancement. One of the detrimental aspects of the use of spacers is an increase of pressure losses in SWM modules. This study analyses the mechanisms that give rise to mass transfer enhancement in narrow spacer-filled channels, and investigates the relationship between flow destabilisation, energy losses and mass transfer. It shows that the regions of high mass transfer on the membrane surface correlate mainly with those regions where the fluid flow is towards the membrane. Based on the insights gained from this analysis, a series of multi-layer spacer designs are proposed and evaluated. In this thesis, a Computational Fluid Dynamics (CFD) model was used to simulate steady and unsteady flows with mass transfer in two- and three-dimensional narrow channels containing spacers. A solute with a Schmidt number of 600 dissolving from the wall and channel Reynolds numbers up to 1683 were considered. A fully-developed concentration profile boundary condition was utilised in order to reduce the computational costs of the simulations. Time averaging and Fourier analysis were performed to gain insight into the dynamics of the different flow regimes encountered, ranging from steady flow to vortex shedding behind the spacer filaments. The relationships between 3D flow effects, vortical flow, pressure drop and mass transfer enhancement were explored. Greater mass transfer enhancement was found for the 3D geometries modelled, when compared with 2D geometries, due to wall shear perpendicular to the bulk flow and streamwise vortices. Form drag was identified as the main component of energy loss for the flow conditions analysed. Implications for the design of improved spacer meshes, such as extra layers of spacer filaments to direct the bulk flow towards the membrane walls, and filament profiles to reduce form drag are discussed.