The identification of homologous protein sequences, using standard alignment-based techniques is difficult when amino acid identity is ≤30% (Remote Homology). Selection acts upon the amino acid sequence because each amino acid has unique physicochemical properties. Therefore, rather than utilizing the symbolic amino acid sequence, it is possible to use the sequence of physicochemical properties in vector form to compare protein sequences. Doing so allows for comparisons to reach beyond the 30% identity threshold. Herein, we validate our physicochemical comparison methods by reliably revealing known remotely homologous relationships, we present how our physicochemical methods can be used to expose seemingly elusive relationships among betacoronaviruses and show that they are also amenable to large-scale classification of domain sequences currently unannotated or improperly annotated in many popular protein domain databases.

Human-dominated landscapes often have habitat loss and fragmentation. These characteristics described at the landscape scale, called landscape elements, influence species diversity and distribution. These landscape elements include such descriptions as the amount of habitat in the landscape and the degree of fragmentation of the habitat. "Optimization of landscape pattern" studies which landscape elements will maximize species diversity and/or distribution. Some general conclusions have emerged from this research. For example, for some bird species the size of the habitat patch in which a species nests has been found to be more important than landscape variables. However, preliminary research suggested that landscape elements such as the matrix are important urban areas. My study addressed this problem by asking: which elements of the landscape are most important for predicting avian species richness and abundance in the Greater Toronto Area? A literature review revealed a number of variables that have been found to influence bird species diversity within a landscape: area of habitat in which the species nests, amount of habitat within the landscape, degree of fragmentation, vegetation characteristics of the habitat patch, and area within the landscape deemed urban in municipal land-use designations (amount of urbanization). From this literature, I formulated four hypotheses describing the most important variables for avian diversity: (1) the area of the habitat patch is most important, (2) only variables describing the habitat patch itself are important, (3) the area of the habitat patch is important, but landscape variables should also be considered and (4) urbanization is most important. These hypotheses were considered competing explanations of bird species diversity at the landscape scale. <br /><br /> A database of breeding bird data and landscape information, in a geographic information system platform, was used to investigate the comparative strength of the competing hypotheses for the Greater Toronto Area. A mathematical expression with a Poisson model format was created to represent each hypothesis. The model selection technique based on Kullback-Leibler information using the Akaike Information Criterion was deemed most appropriate for the comparison of the models. Four separate Poisson model competitions were completed using two habitat types and two response variables: species richness and total abundance. In three of the four competitions, the best model included the habitat area and the amount of urbanization in the landscape. In the forth competition, this model was considered as strong as another model which included habitat area, amount of habitat in the landscape and degree of fragmentation. The results from the model competition support the hypothesis that habitat area is important, but landscape variables must also be considered to explain avian richness and total abundance. It appears that maintaining native bird biodiversity in the Greater Toronto Area should focus on preserving and possibly increasing habitat area and decreasing adjacent urbanization. Exploration of the best model in the forest analysis with the richness response variable found that a 10% increase in habitat area cause approximately a 10% increase in species richness, and a 10% increase in urban area caused approximately a 20% decrease in species richness. Consequently, current natural heritage planning in Ontario should consider urban development as an important negative effect on native birds.

Human-dominated landscapes often have habitat loss and fragmentation. These characteristics described at the landscape scale, called landscape elements, influence species diversity and distribution. These landscape elements include such descriptions as the amount of habitat in the landscape and the degree of fragmentation of the habitat. "Optimization of landscape pattern" studies which landscape elements will maximize species diversity and/or distribution. Some general conclusions have emerged from this research. For example, for some bird species the size of the habitat patch in which a species nests has been found to be more important than landscape variables. However, preliminary research suggested that landscape elements such as the matrix are important urban areas. My study addressed this problem by asking: which elements of the landscape are most important for predicting avian species richness and abundance in the Greater Toronto Area? A literature review revealed a number of variables that have been found to influence bird species diversity within a landscape: area of habitat in which the species nests, amount of habitat within the landscape, degree of fragmentation, vegetation characteristics of the habitat patch, and area within the landscape deemed urban in municipal land-use designations (amount of urbanization). From this literature, I formulated four hypotheses describing the most important variables for avian diversity: (1) the area of the habitat patch is most important, (2) only variables describing the habitat patch itself are important, (3) the area of the habitat patch is important, but landscape variables should also be considered and (4) urbanization is most important. These hypotheses were considered competing explanations of bird species diversity at the landscape scale. <br /><br /> A database of breeding bird data and landscape information, in a geographic information system platform, was used to investigate the comparative strength of the competing hypotheses for the Greater Toronto Area. A mathematical expression with a Poisson model format was created to represent each hypothesis. The model selection technique based on Kullback-Leibler information using the Akaike Information Criterion was deemed most appropriate for the comparison of the models. Four separate Poisson model competitions were completed using two habitat types and two response variables: species richness and total abundance. In three of the four competitions, the best model included the habitat area and the amount of urbanization in the landscape. In the forth competition, this model was considered as strong as another model which included habitat area, amount of habitat in the landscape and degree of fragmentation. The results from the model competition support the hypothesis that habitat area is important, but landscape variables must also be considered to explain avian richness and total abundance. It appears that maintaining native bird biodiversity in the Greater Toronto Area should focus on preserving and possibly increasing habitat area and decreasing adjacent urbanization. Exploration of the best model in the forest analysis with the richness response variable found that a 10% increase in habitat area cause approximately a 10% increase in species richness, and a 10% increase in urban area caused approximately a 20% decrease in species richness. Consequently, current natural heritage planning in Ontario should consider urban development as an important negative effect on native birds.

The interactions of the non steroidal anti-inflammatory drug celecoxib with pure and cholesterol containing distearoyl phosphatidylcholine multilamellar vesicles were studied using Fourier transform infrared spectroscopy, differential scanning calorimetry and turbidity technique at 440 nm. The results reveal that celecoxib exerts opposing effects on membrane order in a concentration dependent manner while cholesterol disorders and orders the membrane in the gel and liquid crystalline phase, respectively. Ternary mixtures of DSPC/Cholesterol/celecoxib behave similar to cholesterol with a small effect of celecoxib. While celecoxib decreases fluidity of the DSPC membranes, cholesterol shows an opposite effect, and in ternary mixtures, a dominant effect of cholesterol is observed. Celecoxib induces opposite effects on the hydration status of the carbonyl groups in the binary system whereas / cholesterol induces hydrogen bonding around this group. An evidence of phase separation has also been observed for all three systems (DSPC/celecoxib, DSPC/Chol, and DSPC/Chol/celecoxib). In addition, a possible location of celecoxib in the interfacial region of the membrane has been proposed. Finally, penetration of celecoxib into the hydrophobic core of the ternary system at high cholesterol concentrations and formation of a new phase has also been suggested. Thus, depending on the concentration used, celecoxib induces significant changes in the biophysical properties of membranes that may aid in understanding its mechanism of action. Furthermore, highly complex interactions take place in ternary membrane systems and further investigations are needed to explore them in detail.

TAXONOMIC STUDIES ON THE GENUS SALVIA L. (LABIATAE) IN CENTRAL ANATOLIA, TURKEY SAFI BAGHERPOUR Ph.D., Department of Biological Sciences Supervisor: Prof. Dr. Musa Dogan June 2010, 203 pages This research study is a revision of the genus Salvia (Labiatae) in Central Anatolia. The author has carried out extensive research studies conducted in a 3 year period starting from June 2005 by collecting specimens from all the localities in Central Anatolia, Turkey. Specimens collected from Turkey by the other researchers and kept either in Turkey or abroad were also examined. The samples were studied using their root, stem and leaf morphology including essential characteristics of flowers. Using this information dendograms were obtained and taxa cut off lines were drawn. The cross sectional preparations of stem and leaf were observed for taxonomical evaluation. Salvia taxa leaf surface, flower organs and seed surface were studied for understanding the diagnostic value of their micro morphological characteristics. Anatomical sections of the specimens were analyzed under light microscope and the data was used for further taxa separations. The Salvia species were further investigated for their pollen characteristics such as surface view and dimensions. Numeric taxonomic methods were used for constructing a natural infrageneric grouping in the genus as far as the species allows. Using software and computer grouping each sample was ranked and placed into specific taxa. First the samples were identified by using the species key given in Turkish Flora. According to the Turkish Flora there were two ways to identify samples. One way based on the stamen features and the other based on the leaves and flowers. For nomenclatural reasons the specimens were cross checked with the existing type specimens known from Turkey and kept in some international herbaria. This thesis is formed by two sections. The first section is comprised of introduction, materials and methods and basic findings. Basic finding are the result of morphological, anatomical, palynological and ecological investigations. In the second section of the thesis, a revision of Salvia in Central Anatolia, Turkey is given. This includes results of numeric studies and infrageneric grouping. Soil types and habitat characteristics were also studied. Soil samples were taken from the various locations and analyzed for their content. The populations were revisited to determine the sustainability and vulnerability of each taxon. IUCN threat categories were determined based on habitat information and species limitations. The phenological data and relevant field observations were all recorded. In Central Anatolia 43 Salvia species were found. Among the specimens collected from the area one taxon was re-discovered after 116 years.

<p> Polymerase Chain Reaction (PCR) was developed for a broad range of purposes. As part of developing a very sensitive Immuno-quantitative PCR (iqPCR) assay, we attempted to reproduce two of the published papers, almost always experienced false-positive amplification. Based on personal communication from one of the authors, we suspected that impure reagents were responsible for the false-positive amplification. However, PCR can amplify a small number of DNA into enormous numbers of copies and the possibility of environmental contamination cannot be excluded. In this paper we show that our primers appeared to amplify residual DNA in the <i>Taq</i> DNA polymerase, and induced false-positive results. This finding is not in the published methods papers for iqPCR.</p>

<p> This study assessed the occurrence and impacts of maternal metal transfer in live-bearing fish. The occurrence was investigated in two different species (<i>Gambusia affinis</i>and <i>Heterandria formosa</i>), while the impacts were studied only in <i>G. affinis.</i> Occurrence and impacts were addressed by exposing gravid females for 10 days to 0.15 &mu;M of copper or cadmium, transferring the fish to clean water, monitoring their reproduction and collecting newborn offspring for further analyses of their health and reproductive success. </p><p> Maternal transfer of copper and cadmium occured in both study species. Metal levels decreased in subsequent broods and in broods born later after a female's exposure. Metal exposure impacted the reproductive success of exposed-females; effects included smaller broods and more broods were aborted broods or contained dead offspring. Many effects remained for second broods developing well after the exposure. </p><p> The maternal metal exposure also impacted the offspring's health. Newborn offspring were smaller at birth, had reduced calcium levels, had a lowered metal tolerance, and had cellular membrane damage. When these offspring grew up, they had an increased rate of malformations, a smaller size at sexual maturity, increased gestation time and fewer broods. In spite of the impacts on life history parameters found in the laboratory, effects on population dynamics were very limited for greenhouse mesocosm populations established with the offspring of exposed females. </p><p> Effects for the essential metal (copper) and the nonessential metal (cadmium) were generally similar. A few effects, like those on body size, were evident for copper but not for cadmium. However, several of the more severe impacts, like the increase in malformations and reductions in the number of broods, were greatest for the offspring of the cadmium-exposed females. </p><p> This is the first report demonstrating negative impacts resulting from a short-term maternal metal exposure in live-bearing fishes. Effects were evident not just for reproduction of exposed-females but also for their offspring's health and reproduction. The latter continued beyond the offspring that were developing during exposure. This study demonstrated that the internal development in live-bearing fish may not spare the developing young from impacts caused by a metal-contaminated environment.</p>

<p> Cellular DNA is condensed and stored with the help of proteins, especially histones. This mix of DNA and proteins is termed chromatin. Manipulations of chromatin include post-translational modifications (PTMs) of histone proteins, such as the addition of methyl or acetyl groups, and the movement of histones by chromatin remodeling complexes to control how tightly or which regions of DNA are condensed or exposed. These actions can impact gene expression and thus influence the differentiation of tissues during development. I investigated if the enzyme protein arginine methyltransferase 5 (PRMT5), which mono- or symmetrically dimethylates arginine, is acting on histones during early development in Xenopus laevis. I also investigated if Williams syndrome transcription factor (WSTF) occurs within chromatin remodeling complexes during early development in X. laevis. WSTF interacts with the protein ISWI in early embryos, indicating it is part of a chromatin remodeling complex during this period of development. </p>

Hemostasis is a crucial function that prevents blood loss after vascular injury by forming platelet-fibrin clots. Disruptions in this process can cause bleeding or thrombotic disorders like hemophilia, von Willebrand disease, or acquired coagulopathies. Zebrafish (Danio rerio) have become an alternative animal model to study mammalian hemostasis disorders. This study focuses on four bleeding disorders, namely Bernard-Soulier syndrome, hemophilia A, hemophilia B, and parahemophilia. To this end, we utilized gp1ba, fv, and fviii mutants with premature stop codons from the Zebrafish International Resource Center (ZIRC), initially obtained as heterozygote and wild-type embryos. After three months of growth, the adults were genotyped and subsequently bred to homozygosity. Through a series of functional assays, we systematically characterized these mutants, identifying phenotypic parallels to the human conditions, Bernard-Soulier syndrome, parahemophilia, and hemophilia A. Previous research in our laboratory identified hemostatic functions for three f9 genes in zebrafish: f9a, f9b, and f9l. Given the absence of knockout models to support these findings, I developed a zebrafish model for hemophilia B by targeting the f9a gene, which is analogous to the human FIX gene. We disrupted the catalytic domain using CRISPR/Cas9 technology at two sites within exon 8, mirroring a common mutation site found in hemophilia B patients. This 72 bp deletion caused prolonged bleeding times and disrupted intrinsic pathways, as verified by the kPTT (kinetic partial thromboplastin time) assay. Western blot and quantitative RT-PCR analyses also confirmed reduced F9a protein and f9a RNA levels. Also at the larval stage, mutants exhibited an extended time to occlusion following venous caudal laser injuries. We also generated an f9l knockout model (functionally linked to the human FX gene), using CRISPR/Cas9 technology to target exon 8. The resulting knockout model had a complex mutation that showed impaired coagulation, confirmed by the kRVVT (kinetic Russell’s viper venom time) assay. Larval studies revealed incomplete penetrance of prolonged bleeding, suggesting intervention by compensatory mechanisms. Unlike f10 zebrafish, f9l mutants exhibited partial lethality, with some mutants surviving beyond nine months. Downregulating f10 in f9l homozygous embryos using morpholinos resulted in 50% mortality within 24 hours, highlighting a functional relationship between f9l and f10. In summary, this comprehensive study advances our understanding of hemostasis in zebrafish, by contributing significantly to the field by establishing models for Bernard-Soulier syndrome, hemophilia A, parahemophilia, and hemophilia B, and by elucidating the role of f9l. These findings provide a solid foundation for future generations of suppressor mutations and gene therapy, offering a robust platform for exploring gene regulation in coagulation and hemostasis.

The Eastern Sector of the Navajo Land Claim is located in the state of New Mexico, and is comprised of areas located across or adjacent to the Continental Divide. Of the 724 specimens processed in the Laboratory, 346 yield tree-ring dates.