Thesis (Ph.D.)--University of California, Berkeley, 2007. / (UMI)AAI3275354. Source: Dissertation Abstracts International, Volume: 68-08, Section: B, page: 4969. Adviser: N. Louise Glass.

Thesis (Ph.D.)--University of California, San Francisco, 2009. / Source: Dissertation Abstracts International, Volume: 71-02, Section: B, page: . Adviser: Brian L. Black.

Thesis (Ph.D.)--Indiana University, Dept. of Biology, 2009. / Title from PDF t.p. (viewed on Jul 20, 2010). Source: Dissertation Abstracts International, Volume: 70-12, Section: B, page: 7374. Adviser: Scott D. Michaels.

Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 2009. / Source: Dissertation Abstracts International, Volume: 70-06, Section: B, page: 3318. Adviser: Lawrence B. Schook. Includes bibliographical references (leaves 75-90) Available on microfilm from Pro Quest Information and Learning.

Thesis (PH.D.)--Syracuse University, 2003. / "Publication number AAT 3099727."

<p> Evolution&mdash;the great tinkerer&mdash;has produced the astounding diversity of form within and between existing species. It is a fundamental goal of evolutionary biology to understand the origin of such diversity. What types of genes underlie evolved changes in morphology? Are certain types of mutations (notably changes within regulatory regions) more likely to be used to produce adaptive changes in form? When distinct populations evolve similar morphological changes, are the underlying genetic bases changes to the same genes, the same genetic pathways, or largely independent? Are changes in form modular, or are their concerted changes to multiple developmentally similar organs? The ever cheapening cost of sequencing, coupled the availability of high-quality reference genomes, allows high-throughput approaches to identifying the loci of evolution. The emergence of a robust genome engineering system, CRISPR/Cas9, allows for efficient and direct testing of a gene's phenotype. Combining both of these techniques with a model system with naturally evolved phenotypic variation, the threespine stickleback, allows for systems-level answers to the many evolutionary questions. </p><p> Chapter one outlines the field of evolutionary developmental biology. It proposes two alternative viewpoints for thinking about the evolution of form. The first is the view of the `Modern Synthesis', linking Mendelian inheritance with Darwinian natural selection, which explains evolution as the change in allele frequencies over time. The second views evolution through the lens of deep homology, focusing on changes to developmental programs over time, even across related organs within the same animal. It then introduces key concepts within evolutionary and developmental biology, including <i> cis</i>-regulation of gene expression, and gene regulatory networks. It then provides examples of evolution reusing similar gene regulatory networks, including <i>Hox</i> genes, <i>Pax6</i> dependent eye initiation, and ectodermal placode development. Teeth use highly conserved signaling pathways, during both their initiation and replacement. Threespine sticklebacks <i>Gasterosteus aculeatus</i> have repeatedly adapted following a shift from marine to freshwater environments, with many independently derived populations sharing common morphological traits, including a gain in tooth number. The following chapters investigate this gain in tooth number in multiple distinct populations of sticklebacks. </p><p> Chapter two describes the discovery and mapping of a spontaneous stickleback albino mutation, named <i>casper</i>. <i>casper</i> is a sex-linked recessive mutation that results in oculocutaneous albinism, defective swim bladders, and blood clotting defects. Bulked segregant mapping of <i> casper</i> mutants revealed a strong genetic signal on chromosome 19, the stickleback X chromosome, proximal to the gene <i>Hps5</i>. <i> casper</i> mutants had a unique insertion of a G in the 6^th exon on <i>Hps5</i>. As mutants in the human orthologue of <i> Hps5</i> resulted in similar albino and blood clotting phenotypes, <i> Hps5</i> is a strong candidate underlying the <i>casper</i> phenotype. Further supporting this model, genome editing of <i>Hps5</i> phenocopied <i>casper</i>. Lastly, we show that <i>casper</i> is an excellent tool for visualizing the activity of fluorescent transgenes at late developmental stages due to the near-translucent nature of the mutant animals. </p><p> Chapter three details the fine mapping of a quantitative trail locus (QTL) on chromosome 21 controlling increases in tooth number in a Canadian freshwater stickleback population. Recombinant mapping reduced the QTL-containing region to an 884kb window. Repeated QTL mapping experiments showed the presence of this QTL on multiple, but not all, wild derived chromosomes from the Canadian population. Comparative genome sequencing revealed the perfect correlation with genetic data of ten variants, spanning 4.4kb, all within the 4<i> th</i> intron of the gene <i>Bmp6</i>. Transgenic analysis of this intronic region uncovered its role as a robust tooth enhancer. TALEN induced mutations in <i>Bmp6</i> revealed required roles for the gene in stickleback tooth development. Finally, comparative RNA-seq between <i> Bmp6</i> wild-type and mutant dental tissue showed a loss of mouse hair stem cell genes in <i>Bmp6</i> mutant fish teeth, suggesting deep homology of the regeneration of these two organs. </p><p> Chapter four investigates the evolved changes in gene expression that accompany evolved increases in tooth number in two distinct freshwater populations. Independently derived stickleback populations from California and Canada have both evolved increases in tooth number, and previous work suggested that these populations used distinct genetic changes during their shared morphological changes. RNA-seq analysis of dental tissue from both freshwater populations compared to marine revealed a gain in critical regulators of tooth development in both freshwater populations. These evolved changes in gene expression can be partitioned in <i>cis</i> changes (mutations within regulatory elements of a gene) and trans changes (changes to the overall regulatory environment) using phased RNA-seq data from marine-freshwater F1 hybrids. Many genes show evidence for stabilizing selection of expression levels, with <i>cis </i> and <i>trans</i> changes in opposing directions (Abstract shortened by ProQuest.). </p><p>

<p> Many adult stem cells are characterized by prolonged quiescence, promoted by cues from their niche. Upon tissue damage, a coordinated transition to the activated state is necessary for successful repair. Non-physiological breaks in quiescence often lead to stem cell depletion and impaired tissue restoration. Here, I identify cadherin-mediated adhesion and signaling between muscle stem cells (satellite cells; SCs) and their myofiber niche as a mechanism that orchestrates the quiescence-to-activation transition. Conditional removal of N-cadherin and M-cadherin in mice leads to a break in SC quiescence with long-term expansion of a regeneration-proficient SC pool. These SCs have an incomplete disruption of the myofiber-SC adhesive junction, and maintain niche residence and cell polarity, yet show properties of SCs in a state of transition from quiescence towards full activation. Among these properties is nuclear localization of b- catenin, which is necessary for this phenotype. These findings are consistent with the conclusion that injury-induced perturbation of niche adhesive junctions is a first step in the quiescence-to-activation transition. </p><p>

<p> Anal squamous cell carcinoma (SCC) which is strongly associated with human papilloma virus (HPV) infection is a rare cancer but its incidence is increasing throughout the world. Even though it represents just 0.4% of all new cancer cases in the US, the mortality rate is estimated at 14%, which is comparable to both breast and prostate cancer mortality rates. To decrease the high rate of mortality and morbidity of anal cancer there is an enormous need for early detection and prevention strategies. Besides understanding the role of HPV infection, we also need to comprehend the basics of genetics and epigenetics involved in anal cancer progression. With both the highest incidence rate and a lower survival rate among African-American men, we are interested in understanding the relationship of HPV, miRNAs and somatic mutations associated with the African-American population in anal cancers. This was accomplished by (1) identifying and determining HPV genotypes associated with anal condylomas, pre-malignant/dysplastic lesions and malignant anal SCC through type specific genotyping, (2) profiling miRNAs in anal SCC based on gender and type of HPV infection to identify novel biomarkers using Nanostring technology, and (3) by identifying oncogenic mutations associated with anal lesions, transformation and progression using novel next generation sequencing methods. Common HPV genotypes associated with our samples included HPV-11, 16, 6, 32, 35, 51, 58, 59, and 68, of which HPV-32, 51, 59 and 68 are not protected by the current FDA approved nonavalent vaccine. Furthermore, 10 of 800 known human miRNAs were significantly dysregulated in SCC samples; these miRNAs (miR-451a, miR-1185-13p, miR-637, miR-4525a-5p, miR-1275, miR-1303, miR-600, miR-892b, miR-297 and miR-944) target tumor suppressor and oncogenes and potentially play an oncomir role in cancer progression. <i>TP53, PIK3CA, PDGFRA, HRAS</i>, and <i> RET</i> were some of the most frequently found somatic mutations in the sample set and it was observed that the accumulation of mutations begin at the condyloma stage. In conclusion, it was determined that three key factors determine the possible progression of anal cancer and can therefore aid in future development of novel targeted therapy approaches: type of HPV infection, epigenetic factors involving miRNAs, and genetic factors such as &lsquo;driver&rsquo; somatic mutations that an individual accumulates over their lifetime.</p><p>

<p> There are approximately 230,000 new diagnoses of prostate cancer every year in the U.S., making prostate cancer the most diagnosed cancer in men. It is responsible for approximately 30,000 deaths per year, with only lung cancer taking more lives. An important distinction must be made in men with prostate cancer. The majority of men with prostate cancer have a relatively indolent form of the disease, meaning high survival rates (100% survival 5 years after diagnosis) and no invasion of the tumor to other organs. However, approximately 4% of men are diagnosed with an aggressive form of the disease, and for these men, the survival rate is a mere 30% after 5 years. And for many patients, it is clinically difficult to differentiate between the indolent and the aggressive forms of the disease. Therefore, it is imperative to develop new genetic models of prostate cancer, and the mouse is an excellent model organism in which to do so. In 2009, mice were used to discover a new type of stem cell, called a castration-resistant Nkx3.1-?expressing cell in the luminal cell population of the prostate. We have used a mouse model targeting these cells to study the roles of two tumor suppressors, adenomatous polyposis coli (Apc) and Smad4. Apc down-regulates the Wnt signaling pathway, which is a carcinogenic pathway in the prostates of humans and mice. Deletion of Apc in mice causes an increase of Wnt signaling and prostate cells to proliferate but not invade, which represents a relatively indolent, precancerous phenotype. Smad4 is a transcription factor that controls the signaling of two pathways: transforming growth factor &beta; and bone morphogenetic protein signaling. Deletion of Smad4 causes these pathways to shut off. When Apc and Smad4 are deleted simultaneously, mice develop aggressive, invasive prostate cancer. This work suggests that these two tumor suppressors &ndash; and the pathways they control &ndash; are important regulators of prostate cancer, could allow for clinicians to differentiate between indolent and aggressive disease, and should be targeted therapeutically in prostate cancer patients.</p><p>

<p> The word "cancer" rarely stands alone, usually prefaced with its anatomical location: lung cancer, prostate cancer, brain cancer. With the advancement of high-throughput omics approaches, specific oncogenic events are reorganizing the landscape of cancer classification, at once creating commonalities between cancers arising in diverse anatomical locations and dividing organ-centric classifications of cancer into a multitude of subtypes. The term "precision medicine" postulates that these new, data-driven groupings based on molecular characterization are the key to making rational therapeutic choices. </p><p> The majority of this dissertation addresses the disconnect between extensive molecular characterization and poor cancer therapy outcomes for patients with glioblastoma multiforme (GBM). Despite clear evidence that hyperproduction of the ligand for PDGFR (platelet-derived growth factor receptor &alpha;) is sufficient to generate GBM of the proneural subtype, anti-PDGFR&alpha; therapeutics have proven disappointing in clinical trials. Cell adaptation contributes to therapeutic escape. In GBM, proneural tumor cells adopt transcriptional profiles of the mesenchymal subtype. The interconversion between the proneural and mesenchymal transcriptional classes within a tumor population presents both a challenge and an opportunity for therapeutic approaches. The proneural subtype has a proliferation phenotype and presents druggable targets such as PDGFR&alpha;. The mesenchymal subtype presents an invasive phenotype, but the targets are more challenging to drug. The typical screening for combination therapies that synergize to induce cell death is not as advantageous here, where the disease management is expected to include cytostatic drugs that act on two different aspects of the phenotype: proneurally mediated proliferation and mesenchymally mediated invasion. This work examines the applicability of a combination approach against a proneural target, PDGFR&alpha;, and mesenchymal targets in the STAT3 (signal transducer and activator of transcription 3) pathway, in the context of a proneural model of GBM.</p><p> The work is concluded with collection of work applying precision medicine in other disease contexts, most notably canine lymphoma.</p><p>