Cancer is a multi-stage process resulting from accumulation of genetic mutations. Data obtained from assaying a tumor only contains the set of mutations in the tumor and lacks information about their temporal order. Learning the chronological order of the genetic mutations is an important step towards understanding the disease. The probability of introduction of a mutation to a tumor increases if certain mutations that promote it, already happened. Such dependencies induce what we call the monotonicity property in cancer progression. A realistic model of cancer progression should take this property into account. In this thesis, we present two models for cancer progression and algorithms for learning them. In the first model, we propose Progression Networks (PNs), which are a special class of Bayesian networks. In learning PNs the issue of monotonicity is taken into consideration. The problem of learning PNs is reduced to Mixed Integer Linear Programming (MILP), which is a NP-hard problem for which very good heuristics exist. We also developed a program, DiProg, for learning PNs. In the second model, the problem of noise in the biological experiments is addressed by introducing hidden variable. We call this model Hidden variable Oncogenetic Network (HON). In a HON, there are two variables assigned to each node, a hidden variable that represents the progression of cancer to the node and an observable random variable that represents the observation of the mutation corresponding to the node. We devised a structural Expectation Maximization (EM) algorithm for learning HONs. In the M-step of the structural EM algorithm, we need to perform a considerable number of inference tasks. Because exact inference is tractable only on Bayesian networks with bounded treewidth, we also developed an algorithm for learning bounded treewidth Bayesian networks by reducing the problem to a MILP. Our algorithms performed well on synthetic data. We also tested them on cytogenetic data from renal cell carcinoma. The learned progression networks from both algorithms are in agreement with the previously published results. MicroRNAs are short non-coding RNAs that are involved in post transcriptional regulation. A-to-I editing of microRNAs converts adenosine to inosine in the double stranded RNA. We developed a method for determining editing levels in mature microRNAs from the high-throughput RNA sequencing data from the mouse brain. Here, for the first time, we showed that the level of editing increases with development. / <p>QC 20130503</p>

Frequent rearrangements, typically through homologous recombination in plant mitochondrial genomes often result in different upstream and downstream sequences for the same gene among a number of species. Transcription and RNA processing signals are therefore different, even among closely related plants. To evaluate the impact of DNA rearrangements on gene expression I conducted a comparative analysis of the S7 ribosomal protein gene (rps7) among a number of grasses: wheat, rice, maize, barley, rye, brome, Lolium and oats (grasses whose evolutionary divergence times range from about 5 to 60 Mya). Using circularized-RT-PCR to simultaneously map rps7 transcript termini I found that 3’ends for various RNA species are homogeneous, mapping to conserved sequences among plants. 5’ termini are more complex and can be both discrete and heterogeneous for different transcripts, both within and among plants. Genome rearrangements upstream of the rps7 start codon for some but not all species has led to plant-specific signals for both rps7 transcription and RNA processing. Termini for rps7 precursor species in wheat and Lolium are very discrete and likely use different upstream tRNAs as processing signals for end-cleavage. A number of potential stem-loop structures have also been identified at or near 5’ and 3’ termini which may function in maturation of transcript ends or provide transcript stability and protection from degradation by ribonucleases. C-to-U RNA editing of non-coding sequences, a rare event, was observed at multiple sites within the 5’ and 3’UTRs among plants. Some sites may even be developmentally regulated as CR-RT-PCR experiments were conducted using mitochondrial RNA isolated from seedlings and germinating embryos. Taken together, my observations demonstrate the frequency of upstream DNA rearrangements and the variety of signals used for expression of rps7 among grasses, providing new insights into the complexities of mRNA production in plant mitochondria.

Frequent rearrangements, typically through homologous recombination in plant mitochondrial genomes often result in different upstream and downstream sequences for the same gene among a number of species. Transcription and RNA processing signals are therefore different, even among closely related plants. To evaluate the impact of DNA rearrangements on gene expression I conducted a comparative analysis of the S7 ribosomal protein gene (rps7) among a number of grasses: wheat, rice, maize, barley, rye, brome, Lolium and oats (grasses whose evolutionary divergence times range from about 5 to 60 Mya). Using circularized-RT-PCR to simultaneously map rps7 transcript termini I found that 3’ends for various RNA species are homogeneous, mapping to conserved sequences among plants. 5’ termini are more complex and can be both discrete and heterogeneous for different transcripts, both within and among plants. Genome rearrangements upstream of the rps7 start codon for some but not all species has led to plant-specific signals for both rps7 transcription and RNA processing. Termini for rps7 precursor species in wheat and Lolium are very discrete and likely use different upstream tRNAs as processing signals for end-cleavage. A number of potential stem-loop structures have also been identified at or near 5’ and 3’ termini which may function in maturation of transcript ends or provide transcript stability and protection from degradation by ribonucleases. C-to-U RNA editing of non-coding sequences, a rare event, was observed at multiple sites within the 5’ and 3’UTRs among plants. Some sites may even be developmentally regulated as CR-RT-PCR experiments were conducted using mitochondrial RNA isolated from seedlings and germinating embryos. Taken together, my observations demonstrate the frequency of upstream DNA rearrangements and the variety of signals used for expression of rps7 among grasses, providing new insights into the complexities of mRNA production in plant mitochondria.

Unlike mammals, adult salamanders possess an intrinsic ability to regenerate complex organs and tissue types, making them an exciting and useful model to study tissue regeneration. The aims of this thesis are two fold, (1) to develop and characterize a reproducible cardiac regeneration model system in the newt, and (2) to decipher the cellular and molecular underpinnings involved in regeneration. In Paper I of this thesis we developed a novel and reproducible heart regeneration model system in the red-spotted newt and demonstrated for the first time the newt’s ability to regenerate functional myocardial muscle, following resection injury, without scarring. The observed findings coincide with an increase in several developmental cardiac transcription factors, wide-spread cellular proliferation of cardiomyocytes and non-cardiomyocyte populations in the ventricle and reverse-remodeling at later time points during regeneration. Of further interest was the identification of functionally active Islet1+ve and GATA4+ve cardiac precursor cells in regenerating areas. The observation of such cell types further compels the similarity between mammalian cardiac development and newt cardiac regeneration and justifies these animals as suitable model organisms for studying heart regeneration. In Paper II we wanted to decipher the molecular cues possibly driving cardiac regeneration in newts. Here we used qualitative and quantitative methods to delineate the function microRNAs (miRNAs) have in this process. One interesting candidate, miR-128, a known tumor suppressor miRNA and regulator of myogenesis, was found to have a regulatory role in controlling non-cardiomyocyte hyperplasia during newt cardiac regeneration. Of further interest was the discovery of a novel binding site of miR-128 in the 3’UTR of Islet1. We speculate that the natural increase in miR-128 expression levels during cardiac regeneration functions as a fine-tuning mechanism to control cellular proliferation of precursor cells. In Paper III of my thesis we sought to explore if a link exists between RNA editing, a wide-spread post-transcriptional process and regeneration. We observed that A-to-I editing enzymes (ADARs) are present in regenerating newt tissues and the localization of ADAR1 alternates between nuclear and cytoplasmic compartments during regeneration. This activity of ADAR1 during regeneration may be partly responsible for driving the cellular plasticity that is needed during multiple phases of tissue regeneration in the red-spotted newt. / <p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 2: Manuscript.</p>

RNA editing by adenosine deamination is catalyzed by members of an enzyme family known as adenosine deaminases that act on RNA (ADARs). ADARs can change the structure of RNA by changing an AU base-pair to an IU mismatch. This frequently modifies the function of the encoded protein, and an emerging theme associated with A-to-I mRNA editing is that tissues often regulate the ratio of proteins expressed from edited and unedited mRNAs to fine-tune cellular responses and functions. In mammals, pre-mRNA of receptor proteins involved in neurotransmission, including serotonin receptors and glutamate receptors, are edited. Currently, only a limited number of human ADAR substrates are known, whereas indirect evidence suggests a substantial fraction of all pre-mRNAs being affected. To identify RNAs containing inosine residues, this study used a multi step approach; including (1) inosine-specific base cleavage and RNase T1 digestion, (2) purification of polyA-tailed mRNA, (3) RT w/ T7-polydT primer, (4) probe synthesis and microarray analysis. Using this method it is possible to identify novel targets of A to I editing. Approximately 100 genes showed a significant decrease in two arrays. Future analysis of these targets should reveal the biomedical significance of A-to-I editing.

Project Report (M.Pub.) - Simon Fraser University, 2005. / Project Report (Master of Publishing Program) / Simon Fraser University. Also issued in digital format and available on the World Wide Web.

This paper consists of the different components of the introduction to “The Wanderer: a Hypertext Edition” presently housed on the server of the University of Saskatchewan’s Digital Research Centre. All the contents of this paper are available as part of that edition, although in a somewhat different format. This thesis contains two parts: the general introduction concerns the poem’s contents, context, and manuscript circumstance while the editorial introduction argues the rationale for this edition and the particulars of my editorial decisions. The editorial introduction explores how the single extant manuscript witness of “The Wanderer” has been inaccurately represented in transcription as well as the importance of transparency in one’s choices as an editor. The editorial introduction explains how this edition’s principles of transparency and interpretation over authority are based on clear objectives that were made after a survey of scholarly resources freely available on the web that revealed a great need for a freely available critical edition. These principles inform the edition’s rationale and specific editorial choices. The product of such an introduction is an edition that presents its editorial decisions in a transparent manner so that the user can distinguish between aspects of the text present in the document and those introduced by the editor.

No description available.

Frequent rearrangements, typically through homologous recombination in plant mitochondrial genomes often result in different upstream and downstream sequences for the same gene among a number of species. Transcription and RNA processing signals are therefore different, even among closely related plants. To evaluate the impact of DNA rearrangements on gene expression I conducted a comparative analysis of the S7 ribosomal protein gene (rps7) among a number of grasses: wheat, rice, maize, barley, rye, brome, Lolium and oats (grasses whose evolutionary divergence times range from about 5 to 60 Mya). Using circularized-RT-PCR to simultaneously map rps7 transcript termini I found that 3’ends for various RNA species are homogeneous, mapping to conserved sequences among plants. 5’ termini are more complex and can be both discrete and heterogeneous for different transcripts, both within and among plants. Genome rearrangements upstream of the rps7 start codon for some but not all species has led to plant-specific signals for both rps7 transcription and RNA processing. Termini for rps7 precursor species in wheat and Lolium are very discrete and likely use different upstream tRNAs as processing signals for end-cleavage. A number of potential stem-loop structures have also been identified at or near 5’ and 3’ termini which may function in maturation of transcript ends or provide transcript stability and protection from degradation by ribonucleases. C-to-U RNA editing of non-coding sequences, a rare event, was observed at multiple sites within the 5’ and 3’UTRs among plants. Some sites may even be developmentally regulated as CR-RT-PCR experiments were conducted using mitochondrial RNA isolated from seedlings and germinating embryos. Taken together, my observations demonstrate the frequency of upstream DNA rearrangements and the variety of signals used for expression of rps7 among grasses, providing new insights into the complexities of mRNA production in plant mitochondria.

Diss. (sammanfattning) Stockholm : Univ., 2004. / Härtill 4 uppsatser.