HUMAN GENOME VARIATIONS AND EVOLUTION WITH A FOCUS ON THE ANALYSIS OF TRANSPOSABLE ELEMENTS

Genome sequence varies in numerous ways among individuals although the gross architecture is fixed for all humans. Retrotransposons create one of the most abundant structural variants in the human genome and are divided in many families, with certain members in some families, e.g., L1, Alu, SVA, and HERV-K, remaining active for transposition. Along with other types of genomic variants, retrotransponson-derived variants contribute to the whole spectrum of genome variants in humans. With the advancement of sequencing techniques, many human genomes are being sequenced at the individual level, fueling the comparative research on these variants among individuals. In this thesis, the evolution and functional impact of structural variations is examined primarily focusing on retrotransposons in the context of human evolution. The thesis comprises of three different studies on the topics that are presented in three data chapters. First, the recent evolution of all human specific AluYb members, representing the second most active subfamily of Alus, was tracked to identify their source/master copy using a novel approach. All human-specific AluYb elements from the reference genome were extracted, aligned with one another to construct clusters of similar copies and each cluster was analyzed to generate the evolutionary relationship between the members of the cluster. The approach resulted in identification of one major driver copy of all human specific Yb8 and the source copy of the Yb9 lineage. Three new subfamilies within the AluYb family – Yb8a1, Yb10 and Yb11 were also identified, with Yb11 being the youngest and most polymorphic. Second, an attempt to construct a relation between transposable elements (TEs) and tandem repeats (TRs) was made at a genome-wide scale for the first time. Upon sequence comparison, positional cross-checking and other relevant analyses, it was observed that over 20% of all TRs are derived from TEs. This result established the first connection between these two types of repetitive elements, and extends our appreciation for the impact of TEs on genomes. Furthermore, only 6% of these TE-derived TRs follow the already postulated initiation and expansion mechanisms, suggesting that the others are likely to follow a yet-unidentified mechanism. Third, by taking a combination of multiple computational approaches involving all types of genetic variations published so far including transposable elements, the first whole genome sequence of the most recent common ancestor of all modern human populations that diverged into different populations around 125,000-100,000 years ago was constructed. The study shows that the current reference genome sequence is 8.89 million base pairs larger than our common ancestor’s genome, contributed by a whole spectrum of genetic mechanisms. The use of this ancestral reference genome to facilitate the analysis of personal genomes was demonstrated using an example genome and more insightful recent evolutionary analyses involving the Neanderthal genome. The three data chapters presented in this thesis conclude that the tandem repeats and transposable elements are not two entirely distinctly isolated elements as over 20% TRs are actually derived from TEs. Certain subfamilies of TEs themselves are still evolving with the generation of newer subfamilies. The evolutionary analyses of all TEs along with other genomic variants helped to construct the genome sequence of the most recent common ancestor to all modern human populations which provides a better alternative to human reference genome and can be a useful resource for the study of personal genomics, population genetics, human and primate evolution.

Petrography and geochemistry of the McArthur Township area, Ontario /

The McArthur Township area in the Archean Abitibi Belt of northeast Ontario contains northwesterly trending volcanic rocks which are located on a limb of a large syncline. The axial trace of the syncline passes through the adjacent Douglas Township. The Archean volcanic rocks and associated sedimentary rocks are intruded and deformed by two large plutons and a few smaller hypabyssal intrusions. A petrographic and geochemical study of the Precambrian rocks exposed 1n the study area was undertaken in order to investigate the metamorphic grade and geochemical characteristics of the rocks. All the samples were studied with the microscope and analysis of 20 major and trace elements were determined on a selection of the less altered specimens by x-ray fluorescence. Three different periods of igneous activity have occurred in the study area. The first two periods were dominated by volcanic extrusive rocks accompanied by gabbroic sills. The third cycle is the diapiric intrusion of the granitic plutons and subsequent metamorphism of the older rocks to the low to medium grade. Two periods of sedimentation are also recognized in the study area which occurred after the first and second cycle of volcanism. Chemically, the lavas are subdivided into three main associations: (1) The komatiitic association is characterized by high MgO, high Ni, low Ti02 and a low FeO*/(FeO* + MgO) ratio. They occupy the base of each volcanic cycle and some of the flows exhibit spinifex textures. (2) The tholeiitic association displays distinct iron and titanium enrichment trends in the intermediate membersor -i r (3) The calc-alkaline association contains low FeO* and TI02 and high Ni contents relative to modern calc-alkaline types. They are formed at the end of each cycle of volcanism and overlie the tholeiitic flows. All three associations of the first volcanic cycle are exposed in the study area, while the second cycle is represented by a komatiltic sequence. The volcanic rocks were possibly formed by multiple partial melting of the Archean mantle to produce parental magmas under various P - T conditions.

An investigation of geological and geochemical characteristics of late-Quaternay sediments in the Georgian Bay Region, Southern Ontario

Core samples of postglacial sediments and sediment surface samples from Shepherd Lake on the Bruce Peninsula, Harts Lake on the Canadian Shield, and two cores from Georgian Bay (core P-l in the western deep part and core P-7 in the eastern shallow part) have been analyzed for pH, grain size distribution, water content, bulk density, loss on ignition at 4500C and 11000 C, major oxides (Si02 ,A1203,!FeO,MgO,CaO, Na20,K20,Ti02 ,MnO and P205) and trace elements (Ba,Zr,Sr,y,S, Zn,Cu,Ni,Ce and Rb). The sediment in Georgian Bay are generally fine grained (fine silt to very fine silty clay) and the grain size decreases from the Canadian Shield (core p-7) towards the Bruce Peninsula (core P-l) along the assumed direction of sediment transport. This trend coincides with a decrease in sorting coefficient and an increase in roundness. Other physical characteristics, such as water content, bulk density and loss on ignition are positively correlated with the composition of sediments and their compaction, as well as with the energy of the depositional environment. Analyses of sediment surface samples from Shepherd Lake and Harts Lake indicate the influence of bedrock and surficial deposits in the watershed on pH condition that is also influenced by the organic matter content and probably I ! I man's activities. Organic matter content increases significantly in the surface sediment in these small lakes as a result of either natural eutrophication or anthropogenic organic loading. The extremely high organic matter content in Shepherd Lake sediment indicates rapid natural eutrophication in this closed basin and high biological productivity during postglacial time, probably due to high nutrient levels and shallow depth. The chemical composition of the Canadian Shield bedrock is positively correlated with the chemical characteristics of predominantly inorganic lake sediments that were derived from the Shield rocks by glacial abrasion and by postglacial weathering and erosion of both bedrock and surficial deposits. High correlation coefficients were found between organic matter in lake sediments and major oxides (Si02,AI203,.~FeO, MgO,CaO,K20 and MnO) , as well as some trace elements (Ba,Y, S,Zn,Cu,Ni and Rb). The chemical composition of sediments in Harts Lake and core P-7 in Georgian Bay on the Canadian Shield differs from the chemistry of sediments in Shepherd Lake and core P-l in Georgian Bay on the Bruce Peninsula. The difference between cores P-l and P-7 is indicated by values of Si02 , AI203 ,:LFeo,Mgo,CaO,Ba,Zr,Sr,y and S, and also by the organic matter content. This study indicates that the processes of sediment transport, depositional environment, weathering of the rocks and surficial deposits in the watershed, as well as chemical composition of source rocks all affect the chemical characteristics of lake sediments. The stratigraphic changes and variations in lake sediment chemistry with regard to major oxides, trace elements, and organic matter content are probably related to the history of glacial and postglacial lake stages of the Georgian Bay Region and, therefore, the geochemical data can make a useful contribution to a better understanding of the Late-Quaternary history of the Great Lakes.

Elements that contribute to staff nurses' commitment to lifelong professional development

This research explored the elements that contribute to staff nurses' commitment to lifelong professional development. This exploration has been undertaken to provide insights into those factors that motivate individuals to continue their education for professional development and for clinical practice improvement. This study was conducted in an acute care hospital in Southern Ontario, and investigated the thoughts and experiences ofhealth care staffworking within that setting. A qualitative case study was undertaken which involved the collection of interview, document, and class observation data. Two exemplary clinical nurse educators and two motivated, professionally committed staffnurses were interviewed during the study. Teaching document review and observation ofclasses involving the clinical nurse educators were conducted to facilitate triangulation of fmdingswith data sources and strategies. These participants provided rich data that were captured in field notes and coded for conceptual meaning. Emerging from the data were the identification ofthree major elements of influence that contribute to staffnurses' commitment to lifelong professional development. Identified within the three intersecting spheres of influence upon staff nurses' lifelong commitment to professionalleaming were the environment, the clinical nurse educator, and the staff nurse. This research explored the intersecting spheres of influence and the elements within the partnership model ofprofessional education for staff nurses.

Microstructural and geochemical investigation of North American lower-middle Paleozoic trilobites and recent arthropods

Trilobites ¥tere collected from Ordovician and Devonian formations of Ontario} New York} Ohio} Oklahoma} and Indiana. Diversity was generally low} but 19..?telllS and Ph..~tY>ps ¥tere the most abundant species from the Ordovician and Devonian} respectively. Recent marine arthropods ¥tere collected from the Atlantic shore of the middle Florida Keys} and from the Pacific and lagoonal waters at Cape Beale} B. C. Fresh-water arthropods were collected along the shore of the Severn River in northcentral Ontario. Cuticles ¥tere analyzed for major} minor and trace elements, 180 and 13C isotopes, as ¥tell as examined by scanning electron micr?scope to identify original and diagenetic fabrics. Examination of trilobite cuticles by scanning electron microscope revealed several microstructures consistent with those observed in Recent arthropods. Microstructures} such as setae and tegumental gland duct openings} in like sized Lim/IllS and Isoteline trilobites may indicate common ancestral origins for these organisms, or simply parallel cuticle evolutions. The dendritic microstructure, originally' thought to be a diagenetic indicator, was found in Recent specimens and therefore its presence in trilobites may be suggestive of the delicate nature of diagenesis in trilobites. The absence of other primary microstructures in trilobites may indicate alteration, taxonomic control} or that there is some inherent feature of S EM examination which may' not allow detection of some features} while others are apparently visit·le onl~1 under SH.·1. The region of the cuticle sampled for examination is also a major influence in detecting pristine microstructures, as not all areas of trilobite and Recent arthropod cuticles will have microstructures identifiable in a SEM study. Subtleties in the process of alteration, however} ma~·· leave pristine microstructures in cuticles that are partial~/ silicified or do 10m itized, and degree and type of alteration may vary stratigraphically and longitudinally within a unit. The presence of fused matrices, angular calcite rhombs, and pyrite in the cuticle are thought to be indicative of altered cuticles, although pyritization may not affect the entire cuticle. t-~atural processes in Recent arthropods, such as molting, lead to variations in cuticle chemistries, and are thought to reflect the area of concentration of the elements during calcification. The level of sodium in Recent arthropods was found to be higher than that in trilobites, but highly mobile when sUbjected to the actions of VY'€'athering. Less saline water produced lovy'€'r magnesium and higher calcium values in Recent specimens .. and metal variations in pristine Ordovician trilobite cuticle appears to follow the constraints outlined for Recent arthropods, of regulation due to the chemislry of the surrounding medium. In diagenetic analysis, sodium, strontium and magnesium proved most beneficial in separating altered from least altered trilobites. Using this criterion, specimens from shale show the least amount of geochemical alteration, and have an original mineralogy of 1.7 - 2.4 mole % MgC03 (8000 t(> 9500 ppm magnesium) for both /s>..?/e/11S lJA'i.riff!11S and PseIAit'11J17ites I..itmirpin..itl/~ and 2.8 - 3.3 mole % MgC03 (5000 to 7000 ppm magnesium) for Ph.i{).?PS This is Slightly lower than the mineralogy of Recent marine arthropods (4.43 - 12.1 mole % MgC03), and slightly higher than that of fresh-water crayfish (0.96 - 1.82 mole % MgC03). Geochemically pristine trilobites were also found to possess primary microstructures. Stable isotope values and trends support the assertion that marine-meteoriclburial fluids were responsible for the alteration observed in a number of the trilobite specimens. The results of this stUdy suggest that fossil material has to be evaluated separately along taxonomic and lithological lines to arrive at sensible diagenetic and e nvironmenta I interpretations.

The entrepreneur : elements that affect her journey

rhi~~thes-is described an·exploratory study of-four Canadian Women entrepreneurs that can help educators and entrepreneurs increase their knowledge of the entrepreneurial phenomenon. The use of a metaphor rendered the phenomenon more meaningful. Based on observations, interviews, and archival collections, this research examined whether a combination of four personal elements played a role in the entrepreneurial journey. The principal result was that the personal elements were part of a larger, holistic picture that also included contextual and operational elements. The personal elements were found to he particularly vital to an individual at the beginning ofthe journey, while the contextual elements were more important to the entrepreneur as she continued on the journey. Furthermore, it was discovered that the operational elements were crucial to the entrepreneur's decision to continue the journey or to terminate it.

The vibrational spectra and the normal coordinate analysis of thiocarbonye halides /|nby C. R. Subramaniam. -- 260 St. Catharines, Ont. : [s. n.],

The infrared and the Raman spectra of eSelF has been obtained for the first time and has been analysed to give the in-plane normal vibrational frequencies of the molecule, in the ground state. A normal co-ordinate analysis has been carried out for the molecules CSF2, CSClF and eSel 2 using a Urey-Bradley type of potential function and the elements of the [L] matrix elements, the distribution of the potential energy in Urey-Bradley space, and the displacement vector diagrams for the normal modes of vibration for these molecules, have been obtained. The bond for~e constants obtained through the normal co-ordinate analysis, have given some interesting results. The stretching force constant, Kes ' varies markedly with halogen substitution and the force constants KeF and Keel also vary with substitution.

The People's Republic of China and her relations with the countries of the association of Southeast Asian nations : 1969-1975

Phe Ihesis examines the evolution of the -policies of the People fs Jtenublie of China towards J?hail°nd, PTal ysia, Singapore, Iidonesia pad the Philip-pines, organised in the Association of Southeast Asian Nations from 1969 to 1975• 2ze first central point of this study is an *ir sumption that the foreign relations of The People's Tepublic of Chi la Towards Southeast ^sia have been motivated by a dynamic interplay of t^o main factors: (1) Farxist-Leninist ideology and ICao J^e-tung Ph^ught, which dictate to China to behave as a revolutionary Dover vhich must assist the insurgent movements in the area in their strug fle to overthrow the local governments; (2) national interest, vhich demands of China to safeguard the southern flank of her territory bordering on Southerst 'sia through Friendly relations, trade and ot*»er conventional inrtniments of diplomacy. hile the tvo main motive factors are nuTually antagonistic and exclusivet the Chinere leaders are nevertheless at te mi ting to oring them iirco a coherent policy under Mao's theory of tve {hniity of op-nosites," vhich believes that it is -possible to reconcile these co-posing tendencies into a dynamic enuibrium through vhich both opnosites could be promoted at the same time although not to the same extent* la other words, the Chinese leaders conceive the dynamic equilibrium as a continuum between them in a mix in which one or the other orientation predominates in different •periods* Bins we might see China1 s conduct motivated in one period by mostly ideological considerations at the expense of the staire-to-state relations, then ve might see her policy in the middle of the continuum and suf ering from immo bill sine and just muddling through, or finally ?fe might see her emphasising friendly ties at the expense of support of revolutionary movements at the other extreme -point of the spectrum* !fhe mechanism vhich enables Peking to move from one pole to the other of the spectrum is activated by the following elementsJ (1) the result of an internal power struggle within the leadership in Peking between ideologically radical and moderate elements, which enables the victorious faction to initiate nev policies; (2) Peking's assessment of the changing intentions and capabilities of the major powers in the area; (3) internal changes within the countries of the area and the changing attitudes of their governments towards China; (4) changing fortunes of revolutionary movements operating in the area* 'Phe second major point of this study is an assertion that while China's conduct toward Southeast *lsia after her foundation in 1949 was primarily based upon ideological considerations, the beginning of the seventies saw the national interest reasserting itself as the leading motive factor* Thus China talks with her neighbours in Southeast asia in terms of relevance of fllong historical ties," casting herself into the role of a benevolent "older brother11 who is entitled to reopect and deference in exchange for patronage and protection* Hence the traditional echoes of the past are emerging ever stronger and influencing her postures towards the region, while the open support to revolutionary moevments is underplayed at the moment.

Bonds away : baseball mythology and the 2007 home run chase

In 2007, Barry Bonds hit his 75 6th home run, breaking Hank Aaron's all-time record for most home runs in a Major League career. While it would be expected that such an accomplishment would induce unending praise and adulationfor the new record-holder, Bonds did not receive the treatment typically reserved for a beloved baseball hero. The purpose of this thesis is to assess media representations of the 2007 home run chase in order to shed light upon the factors which led to the mixed representations which accompanied BOlTds ' assault on Aaron's record. Drawingfrom Roland Barthes ' concept of myth, this thesis proposes that Bonds was portrayed in predominantly negative ways because he was seen as failing to embody the values of baseball's mythology. Using a qualitative content analysis of three major American newspapers, this thesis examines portrayals of Bonds and how he was shown both to represent and oppose elements from baseball's mythology, such as youth, and a distant, agrarian past. Recognizing the ways in which baseball is associated with American life, the media representations of Bonds are also evaluated to discern whether he was portrayed as personifYing a distinctly American set of values. The results indicate that, in media coverage of the 2007 home run chase, Bonds was depicted as a player of many contradictions. Most commonly, Bonds' athletic ability and career achievements were contrasted with unflattering descriptions of his character, including discussions of his alleged use of performance-enhancing substances. However, some coverage portrayed Bonds as embodying baseball myth. The findings contribute to an appreciation of the importance of historical context in examining media representations. This understanding is enhanced by an analysis of a selection of articles on Mark McGwire 's record-breaking season in 1998, and careful consideration of, and comparison to, the context under which Bonds performed in 2007. Findings are also shown to support the contemporary existence of a strong American baseball mythology. That Bonds is both condemned for failing to uphold the mythology and praised for personifYing it suggests that the values seen as inherent to baseball continue to act as an American cultural benchmark.

Aboriginal women in education : Honouring our experiences a vision of access to and success within the university

This thesis explores Aboriginal women's access to and success within universities through an examination of Aboriginal women's educational narratives, along with input from key service providers from both the Aboriginal and non-Aboriginal community. Implemented through the Wildfire Research Method, participants engaged in a consensusbased vision of accessible education that honours the spiritual, emotional, intellectual, and physical elements necessary for the success of Aboriginal women in university. This study positions Aboriginal women as agents of social change by allowing them to define their own needs and offer viable solutions to those needs. Further, it connects service providers from the many disconnected sectors that implicate Aboriginal women's education access. The realities of Aboriginal women are contextualized through historical, sociocultural, and political analyses, revealing the need for a decolonizing educational approach. This fosters a shift away from a deficit model toward a cultural and linguistic assets based approach that emphasizes the need for strong cultural identity formation. Participants revealed academic, cultural, and linguistic barriers and offered clear educational specifications for responsive and culturally relevant programming that will assist Aboriginal women in developing and maintaining strong cultural identities. Findings reveal the need for curriculum that focuses on decolonizing and reclaiming Aboriginal women's identities, and program outcomes that encourage balance between two worldviews-traditional and academic-through the application of cultural traditions to modern contexts, along with programming that responds to the immediate needs of Aboriginal women such as childcare, housing, and funding, and provide an opportunity for universities and educators to engage in responsive and culturally grounded educational approaches.

Transposable Elements Are a Significant Contributor to Tandem Repeats in the Human Genome

Sequence repeats are an important phenomenon in the human genome, playing important roles in genomic alteration often with phenotypic consequences. The two major types of repeat elements in the human genome are tandem repeats (TRs) including microsatellites, minisatellites, and satellites and transposable elements (TEs). So far, very little has been known about the relationship between these two types of repeats. In this study, we identified TRs that are derived from TEs either based on sequence similarity or overlapping genomic positions. We then analyzed the distribution of these TRs among TE families/subfamilies. Our study shows that at least 7,276 TRs or 23% of all minisatellites/satellites is derived from TEs, contributing ∼0.32% of the human genome. TRs seem to be generated more likely from younger/more active TEs, and once initiated they are expanded with time via local duplication of the repeat units. The currently postulated mechanisms for origin of TRs can explain only 6% of all TE-derived TRs, indicating the presence of one or more yet to be identified mechanisms for the initiation of such repeats. Our result suggests that TEs are contributing to genome expansion and alteration not only by transposition but also by generating tandem repeats.

Volume-Synchronized Probability of Informed Trading (VPIN), Market Volatility, and High-Frequency Liquidity

We assess the predictive ability of three VPIN metrics on the basis of two highly volatile market events of China, and examine the association between VPIN and toxic-induced volatility through conditional probability analysis and multiple regression. We examine the dynamic relationship on VPIN and high-frequency liquidity using Vector Auto-Regression models, Granger Causality tests, and impulse response analysis. Our results suggest that Bulk Volume VPIN has the best risk-warning effect among major VPIN metrics. VPIN has a positive association with market volatility induced by toxic information flow. Most importantly, we document a positive feedback effect between VPIN and high-frequency liquidity, where a negative liquidity shock boosts up VPIN, which, in turn, leads to further liquidity drain. Our study provides empirical evidence that reflects an intrinsic game between informed traders and market makers when facing toxic information in the high-frequency trading world.