O vírus da hepatite C (HCV) é uma importante causa de doença hepática crônica e de complicações associadas, tais como cirrose e hepatocarcinoma (HCC). Fatores virais e do hospedeiro são conhecidos preditores da terapia antiviral. Fatores do hospedeiro preditores da resposta viral sustentada (RVS) foram descobertos por estudos de associação genômica ampla (GWAS), correspondendo a polimorfismos de nucleotídeo único (SNPs) nos genes IFNL3 e IFNL4 (rs8099917, rs12979860 e rs368234815). O objetivo do presente trabalho foi verificar as frequências genotípicas dos SNPs rs8099917, rs12979860 e rs368234815 e avaliar a associação entre estes SNPs e a evolução clínica e a resposta ao tratamento da infecção pelo HCV tendo em conta a ancestralidade genética da população estudada. Neste estudo, foi observada a associação dos três polimorfismos tanto com o desfecho clínico quanto com a resposta ao tratamento com interferon peguilado (PEG-IFN) e ribavirina (RBV). Os polimorfismos rs12979860 e rs368234815 foram associados com aumento da sensibilidade (respectivamente 97,7%, IC 95% 87,2-100, e 93,3%, IC 95% 81,3-98,3) e com um maior valor preditivo de uma resposta positiva ao tratamento. Na análise multivariada ajustada por sexo, idade e ancestralidade genética, o haplótipo G/T/?G foi relacionado com a não-resposta ao tratamento (OR = 21,09, IC 95% 5,33-83,51; p < 0,001) e com uma chance maior de desenvolver infecção crônica (OR = 5,46, IC 95% 2,06-14,46; p=0,001), quando comparado com haplótipo T/C/TT. Estes resultados podem ajudar a ajustar políticas de tratamento para a infecção por HCV em populações com tais características genéticas, assim como nos permitem conhecer o perfil genético da nossa população em relação a esses polimorfismos / Hepatitis C virus (HCV) infection is a major cause of chronic liver disease and associated complications such as liver cirrhosis and hepatocellular carcinoma (HCC). Viral and host factors are known to be predictors for anti-viral therapy. Host factors predictors of sustained viral response (SVR) were discovered by Genome-Wide Association Studies (GWAS), including single nucleotide polymorphisms (SNPs) near or on genes IFNL3 and IFNL4 (rs8099917, rs12979860 and rs368234815). The aim of the present work was verify the genotype frequencies of SNPs rs8099917, rs12979860 and rs368234815, and evaluate the association between these SNPs and HCV infection outcome taking into account the genetic ancestry of the population. In this study, there was an association of the three polymorphisms with both clinical outcome and response to treatment with pegylated interferon (PEG-IFN) and ribavirin (RBV). The polymorphisms rs12979860 and rs368234815 showed increased sensitivity (97.7%, 95% CI 87.2-100, and 93.3%, 95% CI 81.3-98.3 respectively) and greater predictive value of a positive response to treatment. In multivariable analysis adjusted by gender, age and genetic ancestry, the haplotype G/T/?G was related to non-response to treatment (OR = 21.09, 95% CI 5.33-83.51; p < 0.001) and to a higher chance to develop chronic infection (OR = 5.46, 95% CI 2.06-14.46; p=0.001) when compared to haplotype T/C/TT. These findings may help to adjust our treatment policies for HCV infection in populations with such genetic characteristics, as well as allowing us to get to know the genetic profile of our population for these polymorphisms

Thesis (Ph. D.)--Uniformed Services University of the Health Sciences, 2005. / Typescript (photocopy).

Indiana University-Purdue University Indianapolis (IUPUI) / Bone growth can be impaired due to disease, such as osteoporosis. Currently, intermittent parathyroid hormone (PTH) treatment is the only approved therapy in the United States for anabolic bone growth in osteoporosis patients. The anabolic effects of PTH treatment are due, at least in part, to modulation of the Wnt/β-catenin pathway. Activation of the Wnt/ β-catenin pathway using a small molecule inhibitor of GSK3β was previously shown to increase markers of bone formation in vitro. Our study utilized a zebrafish model system to study Wnt activated fin regeneration and bone growth. Wnt signaling is the first genetically identified step in fin regeneration, and bony rays are the main structure in zebrafish fins. Thus, zebrafish fin regeneration may be a useful model to study Wnt signaling mediated bone growth. Fin regeneration experiments were conducted using various concentrations of a GSK3β inhibitor compound, LSN 2105786, for different treatment periods and regenerative outgrowth was measured at 4 and 7 days post amputation. Experiments revealed continuous low concentration (4-5 nM) treatment to be most effective at increasing regeneration. Higher concentrations inhibited fin growth, perhaps by excessive stimulation of differentiation programs. In situ hybridization experiments were performed to examine effects of GSK3β inhibitor on Wnt responsive gene expression. Experiments showed temporal and spatial changes on individual gene markers following GSK3β inhibitor treatment. Additionally, confocal microscopy and immunofluorescence labeling data indicated that the Wnt signaling intracellular signal transducer, β-catenin, accumulates throughout GSK3β inhibitor treated tissues. Finally, experiments revealed increased cell proliferation in fin regenerates following LSN 2105786 treatment. Together, these data indicate that bone growth in zebrafish fin regeneration is improved by activating Wnt signaling. Zebrafish Wnt signaling experiments provide a good model to study bone growth and bone repair mechanisms, and may provide an efficient drug discovery platform.

Indiana University-Purdue University Indianapolis (IUPUI) / DNA phenotyping is a rapidly developing area of research in forensic biology. Externally visible characteristics (EVCs) can be determined based on genotype data, specifically from single nucleotide polymorphisms (SNPs). These SNPs are chosen based on their association with genes related to the phenotypic expression of interest, with known examples in eye, hair, and skin color traits. DNA phenotyping has forensic importance when unknown biological samples at a crime scene do not result in a criminal database hit; a phenotype profile of the sample can therefore be used to develop investigational leads. IrisPlex, an eye color prediction assay, has previously shown high prediction rates for blue and brown eye color in a European population. The objective of this work was to evaluate its utility in a North American population. We evaluated the six SNPs included in the IrisPlex assay in an admixed population sample collected from a U.S.A. college campus. We used a quantitative method of eye color classification based on (RGB) color components of digital photographs of the eye taken from each study volunteer and placed in one of three eye color categories: brown, intermediate, and blue. Objective color classification was shown to correlate with basic human visual determination making it a feasible option for use in future prediction assay development. In the original IrisPlex study with the Dutch samples, they correct prediction rates achieved were 91.6% for blue eye color and 87.5% for brown eye color. No intermediate eyes were tested. Using these samples and various models, the maximum prediction accuracies of the IrisPlex system achieved was 93% and 33% correct brown and blue eye color predictions, respectively, and 11% for intermediate eye colors. The differences in prediction accuracies is attributed to the genetic differences in allele frequencies within the sample populations tested. Future developments should include incorporation of additional informative SNPs, specifically related to the intermediate eye color, and we recommend the use of a Bayesian approach as a prediction model as likelihood ratios can be determined for reporting purposes.

Indiana University-Purdue University Indianapolis (IUPUI) / The epigenetic state of any cell is, in part, regulated by the interaction of DNA with nuclear histones. Histone tails can be modified in a number of ways that impact on the availability of DNA to interact with transcriptional complexes, including methylation, acetylation, phosphorylation, ubiquituination, and sumoylation. Histones are acetylated by a large family of enzymes, histone acetyl transferases (HATs), and deacetylated by the histone deacetylases (HDACs). Acetylated histones are generally considered markers of genomic regions that are actively being transcribed, whereas deacetylated and methylated histones are generally markers of regions that are inactive. The goal of the present study was to 1) study the epigenetic state with regard to the presence of euchromatin and heterochromatin in the developing chick and murine retina, 2) study and compare the localization patterns of the classical HDACs in the developing chick and murine retina with respect retinal progenitors and early differentiated cell types 3) to test the hypothesis that overall HDAC activity is required for dividing retinal progenitors to leave the cell cycle and differentiate. Our results showed that the classical HDACs were ubiquitously expressed in the developing chick and murine retinas. Species specific differences as well as stage dependent variations were observed in the localization of the HDACs in the cell types that were studied in the chick and murine retina. Our preliminary results also showed that HDAC inhibition may lead to the inability of the cell types to leave the cell cycle and a subsequent increase in the number of progenitor cells present in the developing chick retina.

Indiana University-Purdue University Indianapolis (IUPUI) / Epigenetic alterations have been shown to control cell type specification and differentiation leading to the changes in chromatin structure and organization of many genes. HDACs have been well documented to play an important role in both neurogenesis and gliogenesis in ganglionic eminence and cortex-derived cultures. However, the role of HDACs in glial cell type specification and differentiation in the optic nerve has not been well described. As a first step towards understanding their role in glial cell type specification, we have examined histone acetylation and methylation levels as well as the expression levels and patterns of the classical HDACs in both murine and chick optic nerve. Analysis of mRNA and protein levels in the developing optic nerve indicated that all 11 members of the classical HDAC family were expressed, with a majority declining in expression as development proceeded. Based on the localization pattern in both chick and murine optic nerve glial cells, we were able to group the classical HDACs: predominantly nuclear, nuclear and cytoplasmic, predominantly cytoplasmic. Nuclear expression of HDACs during different stages of development studied in this project in both murine and chick optic nerve glial cells suggests that HDACs play a role in stage-dependent changes in gene expression that accompany differentiation of astrocytes and oligodendrocytes. Examination of localization pattern of the HDACs is the first step towards identifying the specific HDACs involved directly in specification and differentiation of glia in optic nerve.