This research represents the first multi-year investigation of the feeding ecology of Gombe’s Cercopithecus populations. The main goal of this study was to identify dietary overlap and distinctiveness among the phenotypes in our study group, a mixed species group of guenons comprised of C. ascanius, C. mitis, and C. ascanius x C. mitis hybrids. Field assistants collected feeding data using ad libitum observations as well as instantaneous scan sampling at 30-minute intervals from July 2014 to December 2018. A total of 63 plant species were identified in our group’s diet. Results indicate that a significant difference exists between the diets of each phenotype. The results also found an unusually high percentage of invertebrate eating (54%) in our group. These findings suggest that invertebrates are an important food resource for the Gombe study group and may help facilitate coexistence in an environment where there are many sympatric primate species. / Includes bibliography. / Thesis (M.S.)--Florida Atlantic University, 2019. / FAU Electronic Theses and Dissertations Collection

Breast cancer arises from a series of acquired mutations that disrupt normal mammary epithelial homeostasis and create multi-potent cancer stem cells that can differentiate into clinically distinct breast cancer subtypes. Despite improved therapies and advances in early detection, breast cancer remains the leading diagnosed cancer in women. A predominant mechanism initiating invasion and migration for a variety of cancers including breast, is epithelial-to-mesenchymal transition (EMT). EMT— a trans-differentiation process through which mammary epithelial cells acquire a more aggressive mesenchymal phenotype—is a regulated process during early mammary gland development and involves many transcription factors involved in cell lineage commitment, proliferation, and growth. Despite accumulating evidence for a broad understanding of EMT regulation, the mechanism(s) by which mammary epithelial cells maintain their phenotype is unknown. Mitotic gene bookmarking, i.e., transcription factor binding to target genes during mitosis for post mitotic regulation, is a key epigenetic mechanism to convey regulatory information for cell proliferation, growth, and identity through successive cell divisions. Many phenotypic transcription factors, including the hematopoietic Runt Related Transcription Factor 1 (RUNX1/AML1), bookmark target genes during mitosis. Despite growing evidence, a role for mitotic gene bookmarking in maintaining mammary epithelial phenotype has not been investigated. RUNX1 has been recently identified to play key roles in breast cancer development and progression. Importantly, RUNX1 stabilizes the normal breast epithelial phenotype and prevents EMT through repression of EMT-initiating pathways. Findings reported in this thesis demonstrate that RUNX1 mitotically bookmarks both RNA Pol I and II transcribed genes involved in proliferation, growth, and mammary epithelial phenotype maintenance. Inhibition of RUNX1 DNA binding by a specific small molecule inhibitor led to phenotypic changes, apoptosis, differences in global protein synthesis, and differential expression of ribosomal RNA as well as protein coding genes and long non-coding RNA genes involved in cellular phenotype. Together these findings reveal a novel epigenetic regulatory role of RUNX1 in normal-like breast epithelial cells and strongly suggest that mitotic bookmarking of target genes by RUNX1 is required to maintain breast epithelial phenotype. Disruption of RUNX1 bookmarking results in initiation of epithelial to mesenchymal transition, an essential first step in the onset of breast cancer.

Introduction: The purpose of this study was to examine phenotypic expression of craniofacial form, shape, and size as it relates to the genotype of an individual. Shape analyses were completed on 3-D images of each subject's craniofacial structure by landmarking 45 points of interest on the cranial base, facial bones, and upper and lower jaws. A candidate gene analysis was undertaken focusing on specific genes in the Hippo Signaling Pathway to examine genotype-phenotype correlations that play a role in craniofacial development. This study is a continuation of a larger project aimed at the identification of candidate genes associated with human dento-skeletal bite problems led by Dr. Lina Moreno-Uribe. Methods: The sample size for our study included 166 individuals who had never been treated orthodontically at the time of records. Each individual was genotyped and a CBCT of the craniofacial complex was captured. Each CBCT image was landmarked by a single observer using 45 points to mark points on the cranial base and facial bones including the maxilla and mandible. General Procrustes superimposition was used to find correlations with phenotype and genotype. Size analysis was completed with average Euclidean Distances and ANOVA analysis. Results: 2 SNP's from the FOX03 gene had significant associations with size. The AA genotyped individuals appeared larger in overall size than AB genotyped individuals. 3 SNP's had statistically significant associations with facial form. The FOX06 SNPs had significant associations with increased anterior-posterior growth of the maxilla. The AJUBA SNP had significant associations with increased overall craniofacial breadth. Conclusion: Genes in the Hippo signaling pathway have specific roles in the development of facial form and size.

Abstract not available

The widespread expression of polypeptide growth factors from the earliest stages of embryonic development through to mature issues in the adult organism suggests an involvement in a reiterated developmental process affecting the underlying cellular growth and differentiation of many tissues. The hair follicle has taken on increased significance with the observation that many genetic mutations in these peptide growth factor genes affect its development. The targeted disruption of genes encoding members of the EpidermalGrowth Factor (EGF) and Fibroblast Growth Factor (FGF) families in the mouse has revealed a functional role for these proteins in the regulation of hair follicle growth. Experimental data and other factors are examined and results given. A second experimental system was used to determine if a functional relationship between certain peptide growth factors was conserved in the Merino sheep. The induction of a catagen-like state in the wool follicle and other epidermal changes associated with EGF treatment may be related to the transciptional induction of these peptide growth factors / Doctor of Philosophy (PhD)

While previous research into the pathogenesis of ischaemic and reperfusion injuries has focussed on the cardiac myocyte, there is increasing evidence for a crucial role for coronary vascular injury in the genesis of the post-ischaemic phenotype [1-3]. Post-ischaemic vascular injury may be manifest as a transient or sustained loss of competent vessels, impairment of vascular regulatory mechanisms, and ultimately as the 'no-reflow' phenomenon (inability to sufficiently reperfuse previously ischaemic tissue despite the removal of the initial obstruction or occlusion). It is now appreciated that the earliest distinguishing feature of various forms of vascular injury (including atherosclerosis and infarction) is 'endothelial dysfunction', which is the marked reduction in endothelial-dependent relaxation due to reduced release or action of endothelial nitric oxide (NO). Importantly, vascular injury may worsen myocardial damage in vivo [4,5], significantly limiting tissue salvage and recovery. The pathogenesis of post-ischaemic vascular injury and endothelial dysfunction is incompletely understood, but has generally been considered to reflect a cardiovascular inflammatory response, neutrophils playing a key role. However, while blood-borne cells and inflammatory elements are undoubtedly involved in the 'progression' of vascular injury [6,7], accumulating evidence indicates that they are not the primary 'instigators' [8]. It should be noted that a wealth of controversial findings exists in the vascular injury literature and mechanisms involved remain unclear. Indeed, multiple mechanisms are likely to contribute to post-ischaemic vascular injury. Adenosine receptors are unique in playing a role in physical regulation of coronary function, and also in attenuating injury during and following ischaemia. While the adenosine receptor system has been extensively investigated in terms of effects on myocardial injury [9,10], little is known regarding potential effects of this receptor system on post-ischaemic coronary vascular injury. This thesis initially attempts to further our understanding of the role of adenosine in normal coronary vascular function, subsequent chapters assess the effect of ischaemia-reperfusion on vascular function, and adenosine receptor modification of vascular dysfunction in the isolated asanguinous mouse heart. Specifically, in Chapter 3 the receptor subtype and mechanisms involved in adenosine-receptor mediated coronary vasodilation were assessed in Langendorff perfused mouse and rat hearts. The study revealed that A2A adenosine receptors (A2AARs) mediate coronary dilation in the mouse vs. A2B adenosine receptors (A2BARs) in rat. Furthermore, responses in mouse involve a sensitive endothelial-dependent (NO-dependent) response and NO-independent (KATP-mediated) dilation. Interestingly, the ATP-sensitive potassium channel component predominates over NO-dependent dilation at moderate to high agonist levels. However, the high-sensitivity NO-dependent response may play an important role under physiological conditions when adenosine concentrations and the level of A2AAR activation are low. In Chapter 4 the mechanisms regulating coronary tone under basal conditions and during reactive hyperaemic responses were assessed in Langendorff perfused mouse hearts. The data support a primary role for KATP channels and NO in mediating sustained elevations in flow, irrespective of occlusion duration (5-40 s). However, KATP channels are of primary importance in mediating initial flow adjustments after brief (5-10 s) occlusions, while KATP (and NO) independent processes are increasingly important with longer (20-40 s) occlusion. Evidence is also presented for compensatory changes in KATP and/or NO mediated dilation when one pathway is blocked, and for a modest role for A2AARs in reactive hyperaemia. In Chapter 5 the impact of ischaemia-reperfusion on coronary function was examined, and the role of A1 adenosine receptor (A1AR) activation by endogenous adenosine in modifying post-ischaemic vascular function was assessed in isolated buffer perfused mouse hearts. The results demonstrate that ischaemia does modify vascular control and signficantly impairs coronary endothelial dilation in a model devoid of blood cells. Additionally, the data indicate that post-ischaemic reflow is significantly determined by A2AAR activation by endogenous adenosine, and that A1AR activation by endogenous adenosine protects against this model of vascular injury. Following from Chapter 5, the potential of A1, A2A and A3AR activation by exogenous and endogenous agonists to modulate post-ischaemic vascular dysfunction was examined in Chapter 6. Furthermore, potential mechanisms involved injury and protection were assessed by comparing effects of adenosine receptors to other 'vasoprotective' interventions, including anti-oxidant treatment, Na+/H+ exchange (NHE) inhibition, endothelin (ET) antagonism, and 2,3-butanedione monoxime (BDM). The data acquired confirm that post-ischaemic endothelial dysfunction is reduced by intrinsic A1AR activation, and also that exogenous A3AR activation potently reduces vascular injury. Protection appears unrelated to inhibition of ET or oxidant stress. However, preliminary data suggest A3AR vasoprotection may share signalling with NHE inhibition. Finally, the data reveal that coronary reflow in isolated buffer perfused hearts is not a critical determinant of cardiac injury, suggesting independent injury processes in post-ischaemic myocardium vs. vasculature. Collectively, these studies show that adenosine has a significant role in regulating coronary vascular tone and reactive hyperaemic responses via NO and KATP dependent mechanisms. Ischaemia-reperfusion modifies vascular control and induces significant endothelial dysfunction in the absence of blood, implicating neutrophil independent injury processes. Endogenous adenosine affords intrinsic vasoprotection via A1AR activation, while adenosinergic therapy via exogenous A3AR activation represents a new strategy for directly protecting against post-ischaemic vascular injury.

<p>These studies are based on the isolation of ë replication defective mutants that had acquired multiple point mutations within ë replication initiation genes O and P in a cryptic prophage (Hayes et al., 1998). Each mutant cell arose after shifting wild type cells with a cI[Ts] cryptic ë prophage deleted for int-kil, and from ren into E. coli, from 30oC to 42oC. Derepression of the trapped cryptic prophage kills the host cells (designated as RK+). Rare colony forming units survive and were designated as RK- mutants. This led to a hypothesis that ë replication-triggered cell stress provokes mutator activity, i.e., increases the frequency of replication errors within the simultaneously replicating chromosome of the host E. coli cells. We tested this hypothesis by asking three questions: (1) Do unselected, untargeted (with no link to ë fragment) auxotrophic mutations appear within the RK- mutant population selected from RK+ culture cells? (2) Is replication initiation from the cryptic ë fragment, or, alternatively, just expression of one or more ë genes required for the appearance of the unselected auxotrophic mutations? (3) Do E. coli functions participate in the appearance of unselected auxotrophic mutations within the RK- mutant population? Our results indicate that auxotrophic mutations unlinked to the ë fragment appeared at high frequency within RK- mutants. RK- auxotrophs arising on rich medium were identified by screening the survivor clones for growth on minimal medium. The appearance of RK- auxotrophic colonies at high frequency (>1 per 100 RK- mutants) leads us to conclude that auxotrophic mutations arise during the independent selection for RK- mutants. Conditions that inhibited ë fragment induction fully suppressed the mutator phenotype. Mutation of host dnaB such that the helicase does not support replication initiation from the induced ë fragment completely suppressed host cell killing, but not the appearance of auxotrophic mutations. We asked if E. coli error-prone polymerases IV and V, or gene functions regulated as part of the host SOS response contributed to the provoked mutator phenotype and observed no close correlation. We demonstrated that the RK+ starting cells did not have a distinct intrinsic mutator activity in several ways, including moving the cryptic ë fragment to different E. coli host cells, blocking ë fragment induction by the addition of a cI+ plasmid to eliminate ë gene expression at high temperatures, and independent assays for spontaneous rifampicin resistance. We found that the induced mutator phenotype associated with the appearance of untargeted auxotrophs was linked to the expression of lambda gene P, and did not require replication initiation from the cryptic ë prophage. We also found that the mutator phenotype of the induced cryptic ë fragment increased the frequency of rifampicin resistant colonies among the RK- mutant population. </p>

Genetic studies of lung disease in Cystic Fibrosis are faced with the challenge of identifying a severity measure that accounts for chronic disease progression and mortality attrition. Further, combining analyses across studies requires common phenotypes that are robust to study design and patient ascertainment. This thesis uses data from the North American Cystic Fibrosis Modifier Consortium (Canadian Consortium for CF Genetic Studies (CGS), Johns Hopkins University Twins and Siblings Study (TSS), and University of North Carolina/Case Western Reserve University Gene Modifier Study (GMS)), to calculate two novel phenotypes using age-specific CF percentile values of FEV1 (Forced Expiratory Volume in 1 second), with adjustment for CF age-specific mortality. The normalized residual, mortality adjusted (NoRMA) was designed for population based samples, while KNoRMA, using Kulich percentiles, is robust to sample ascertainment; both account for the effects of age-related disease progression and mortality attrition. NoRMA was computed for 2122 patients representing the Canadian CF population. KNoRMA was computed for these 2122 patients and also 1137 extreme phenotype patients in the GMS study and 1323 patients from multiple CF sib families in the TSS study. Phenotype was distributed in all three samples in a manner consistent with ascertainment differences, reflecting the lung disease severity of each individual in the underlying population. The new phenotype was highly correlated with the previously recommended mixed model phenotype1; 2, but computationally much easier and suited to studies with limited follow up time. As an example of its use, KNoRMA was used to test the association between locus variants in a previously published candidate gene, Transforming Growth Factor β1(TGFβ1), and lung function in CF, in an attempt to provide insight into discrepant results in the literature. A disease progression and mortality adjusted phenotype reduces the need for stratification or additional covariates, increasing statistical power and avoiding possible interpolation distortions.

Recent advances in DNA sequencing technology have enabled entire genomes to be sequenced quickly and accurately, resulting in an exponential increase in the number of organisms whose genome sequences have been elucidated. While the genome sequence of a given organism represents an important starting point in understanding its physiology, the functions of the protein products of many genes are still unknown; as such, computational methods for studying protein function are becoming increasingly important. In addition, this wealth of genomic information has created an unprecedented opportunity to compare the protein content of different organisms; among other applications, this can enable us to improve taxonomic classifications, to develop more accurate diagnostic tests for identifying particular bacteria, and to better understand protein content relationships in both closely-related and distantly-related organisms.<p> This thesis describes the design, evaluation, and use of a program called Proteome Subtraction and Intersection (PSI) that uses an idea called genome subtraction for discovering protein-phenotype relationships and for characterizing differences in protein content in groups of organisms. PSI takes as input a set of proteomes, as well as a partitioning of that set into a subset of "included" proteomes and a subset of "excluded" proteomes. Using reciprocal BLAST hits, PSI finds orthologous relationships among all the proteins in the proteomes from the original set, and then finds groups of orthologous proteins containing at least one orthologue from each of the proteomes in the "included" subset, and none from any of the proteomes in the "excluded" subset.<p> PSI is first applied to finding protein-phenotype relationships. By identifying proteins that are present in all sequenced isolates of the genus <i>Lactobacillus</i>, but not in the related bacterium <i>Pediococcus pentosaceus</i>, proteins are discovered that are likely to be responsible for the difference in cell shape between the lactobacilli and <i>P. pentosaceus</i>. In addition, proteins are identified that may be responsible for resistance to the antibiotic gatifloxacin in some lactic acid bacteria.<p> This thesis also explores the use of PSI for comparing protein content in groups of organisms. Based on the idea of genome subtraction, a novel metric is proposed for comparing the difference in protein content between two organisms. This metric is then used to create a phylogenetic tree for a large set of bacteria, which to the author's knowledge represents the largest phylogenetic tree created to date using protein content. In addition, PSI is used to find the proteomic cohesiveness of isolates of several bacterial species in order to support or refute their current taxonomic classifications.<p> Overall, PSI is a versatile tool with many interesting applications, and should become more and more valuable as additional genomic information becomes available.

Cells in the body respond to mechanical loads in ways that are crucial to normal and disease physiology. Understanding these processes is difficult due to the complex mechanical environment in vivo. In this research, we have developed several cell-stretching devices capable of subjecting cell cultures to non-uniform stretch distributions in order to investigate pathological responses of vascular smooth muscle cells to physiologic stretches. 10T1/2 cells were cyclically stretched with these devices for 24 hours upon silicone membranes, PDMS tubes, and within 3D PEGDA hydrogels. After stretching, altered cell behaviors were measured, including orientation, proliferation (quantified by BrdU incorporation), and gene expression (quantified by real-time, RT-PCR). Cells demonstrated marked changes in orientation, proliferation, and mRNA expression, which all varied with cellular location in the non-uniform environment. More specifically, increased orientation, increased proliferation, and more dramatically altered mRNA expression were found in regions of high, uniaxial stretch, relative to regions of low, near-equibiaxial stretch. These findings demonstrate the capabilities of graded stretch distributions to produce graded cell responses, indicating potentially localized smooth muscle cell behavior in a diseased artery. The novel devices employed herein will hopefully improve our understanding of these complicated cellular pathways, ultimately allowing for improved treatment or prevention of vascular disease.