Submitted by MONALLY CONCEIÇÃO COSTA DE AQUINO null (monallyaquino@yahoo.com.br) on 2018-03-07T16:42:09Z No. of bitstreams: 1 Tese 28_02_18.pdf: 668105 bytes, checksum: 3162eceaf16141ce03dfad0ffdb157e4 (MD5) / Approved for entry into archive by Isabel Pereira de Matos null (isabel@fmva.unesp.br) on 2018-03-08T14:08:56Z (GMT) No. of bitstreams: 1 aquino_mcc_dr_araca_int.pdf: 668105 bytes, checksum: 3162eceaf16141ce03dfad0ffdb157e4 (MD5) / Made available in DSpace on 2018-03-08T14:08:56Z (GMT). No. of bitstreams: 1 aquino_mcc_dr_araca_int.pdf: 668105 bytes, checksum: 3162eceaf16141ce03dfad0ffdb157e4 (MD5) Previous issue date: 2018-02-28 / Outra / Giardia duodenalis é um protozoário flagelado que coloniza o trato intestinal de hospedeiros vertebrados. A caracterização molecular de G. duodenalis revolucionou a compreensão da taxonomia, diversidade genética e epidemiologia da giardíase em seres humanos e animais. Em nosso estudo, realizamos a caracterização molecular de G. duodenalis em bezerros bubalinos do Estado de São Paulo, Brasil. Assim, foram colhidas 183 amostras fecais de animais da raça Murrah, com até seis meses de idade. Estas amostras foram examinadas por meio da reação em cadeia pela polimerase tipo para amplificação da subunidade menor do gene do RNA ribossômico, todas as amostras positivas por esse gene, foram caracterizadas para amplificação parcial dos genes beta-giardina, glutamato desidrogenase e triosefosfato isomerase. G. duodenalis foi verificada em 6,56% das amostras fecais e por meio da análise das sequências, verificou-se 100% de similaridade genética com “assemblage” E. Esta foi a primeira detecção de G. duodenalis “assemblage” E em bezerros bubalinos no Brasil. / Giardia duodenalis is a flagellated protozoan that colonizes the intestinal tract of vertebrate hosts. A molecular characterization of G. duodenalis revolutionized an understanding of the taxonomy, genetic diversity and epidemiology of giardiasis in humans and animals. In our stud, we performed the molecularly characterization of Giardia duodenalis in buffalo calves from State of São Paulo, Brazil. Then, 183 fecal samples of Murrah buffaloes were collected up to six months of age. These samples were examined by nested polymerase chain reaction for parcial amplification of the small subunit of the ribosomal RNA gene. All G. duodenalis-positive samples were characterized by beta-giardin, glutamate dehydrogenase and triosephosphate isomerase genes. G. duodenalis was detected in 6,56% of the faecal samples, and sequence analysis showed 100% genetic similarity with assemblage E. This was the first detection of G. duodenalis assemblage E in buffalo calves in Brazil.

Avaliou-se o efeito isolado e associado de pós de origem vegetal e de genótipos de feijoeiro sobre o comportamento, biologia e danos de Zabrotes subfasciatus (Boh.) e Acanthoscelides obtectus (Say). Inicialmente, foi avaliado o efeito dos pós obtidos de 18 plantas sobre a atratividade e mortalidade dos adultos, e oviposição. A seguir, foi testado o efeito de 12 genótipos de feijoeiro incluindo materiais melhorados contendo arcelina (Arc1, Arc2, Arc3 e Arc4) e sem essa proteína (IAC Carioca Aruã, IAC Carioca Pyatã, IAC Carioca Akytã, IAC Maravilha, IAC Una, IAC Bico de Ouro, Porrillo 70 e Goiano Precoce) sobre a oviposição (com e sem chance de escolha) e biologia dos insetos. Com base nestes resultados, foram selecionados, para cada espécie de inseto, quatro genótipos (três resistentes e um suscetível) e quatro pós vegetais, para os quais foi avaliado o efeito associado sobre a atratividade e mortalidade dos adultos, preferência para oviposição, biologia e danos causados pelos insetos. Concluiu-se que: a) os pós obtidos da parte aérea de Chenopodium ambrosioides (erva-de-santa-maria), f. (forma) 1 e f.2; de folhas de Eucalyptus citriodora (eucalipto cheiroso), de Mentha pulegium (poejo) e de Ruta graveolens (arruda), e de cascas de frutos de Citrus reticulata (laranja cv. Murcote) são repelentes aos adultos das duas pragas; b) os pós obtidos de folhas de Ocimum basilicum (alfavaca) e de O. minimum (manjericão) são repelentes apenas para Z. subfasciatus, enquanto os pós de cascas de frutos de Citrus sinensis (laranja cv. Pêra) e de frutos de Lafoensia glyptocarpa (mirindiba) apresentam efeito repelente apenas em relação a A. obtectus; c) o pó de folhas de L. glyptocarpa apresenta atratividade a Z. subfasciatus; d) os pós de C. ambrosioides (f.2), M. pulegium, O. basilicum e R. graveolens apresentam efeito altamente tóxico aos adultos de Z. subfasciatus, causando 100% de mortalidade e impedindo a oviposição; e) em relação a A. obtectus, há total mortalidade de adultos e ausência de oviposição, com o uso de pós de C. ambrosioides (f.2) e de folhas de Coriandrum sativum (coentro); f) em teste sem chance de escolha, o genótipo Arc3 é menos ovipositado por Z. subfasciatus que 'IAC Carioca Pyatã' e 'IAC Bico de Ouro', enquanto, em relação a A. obtectus os materiais são igualmente preferidos para oviposição; g) os materiais contendo arcelina (Arc1, 2, 3 e 4) apresentam resistência do tipo não-preferência para alimentação e/ou antibiose a Z. subfasciatus, alongando o período de desenvolvimento (ovo-adulto) e reduzindo o peso dos adultos, a longevidade e a fecundidade; h) em relação a A. obtectus, a resistência do tipo não-preferência para alimentação e/ou antibiose só ocorre com o Arc1, genótipo em que há alongamento do período de desenvolvimento e menor peso dos adultos; i) 'Goiano Precoce' é o material mais adequado ao desenvolvimento dos dois insetos; j) com o emprego associado de pós vegetais e genótipos resistentes de feijoeiro, ocorre apenas efeito aditivo (e não sinérgico) das duas técnicas de controle para ambas as espécies de insetos; k) o peso consumido de grãos de feijão por Z. subfasciatus e A. obtectus não é afetado pelos pós inseticidas; esse peso, entretanto, é menor nos genótipos contendo arcelina para os dois insetos. / It was evaluated the isolated and associated effects of powders from different vegetal and bean genotypes on the behaviour, biology and damage of Zabrotes subfasciatus (Boh.) and Acanthoscelides obtectus (Say). Initially, it was evaluated the effect of powders of 18 plants on the attractivity and mortality of the adults, and oviposition. Then, the effect of 12 bean genotypes was tested including materials with arcelin (Arc1, Arc2,Arc3 and Arc4) and without this protein (IAC Carioca Aruã, IAC Carioca Pyatã, IAC Carioca Akytã, IAC Maravilha, IAC Una, IAC Bico de Ouro, Porrillo 70 and Goiano Precoce) on the oviposition (free-choice and no-choice tests) and biology of the insects. Based on these results, four genotypes (three resistant and one susceptible) and four powders were selected for each insect species. It was evaluated the associated effect on the attractivity and mortality of the adults, preference for oviposition, biology and damage caused by the insects. It was concluded that: powders of the aerial part from Chenopodium ambrosioides f. (form) 1 and f.2; leaves from Eucalyptus citriodora, from Mentha pulegium and from Ruta graveolens, and rinds of fruits from Citrus reticulata (cv. Murcote) are repellents to the adults of the two pests; b) powders of leaves from Ocimum basilicum and O. minimum are repellent only for Z. subfasciatus, while powders of rinds of fruits from Citrus sinensis (cv. Pêra) and fruits from Lafoensia glyptocarpa shows repellent effect only on A. obtectus; c) powder of leaves from L. glyptocarpa shows attractivity on Z. subfasciatus; d) powders from C. ambrosioides (f.2), M. pulegium, O. basilicum and R. graveolens show high toxicity on adults of Z. subfasciatus, causing 100% mortality and inhibiting the oviposition; e) in relation to A. obtectus, total mortality of adults and no oviposition is observed with the use of powders from C. ambrosioides (f.2) and leaves from Coriandrum sativum; f) in no-choice test, Arc3 was less oviposited by Z. subfasciatus than IAC Carioca Pyatã and IAC Bico de Ouro, while in relation to A. obtectus the materials are equally preferred for oviposition; g) the materials with arcelin (Arc1, 2, 3 and 4) show non-preference resistance for feeding and/or antibiose to the Z. subfasciatus, prolonging the time for insect development (egg-adult) and reducing the adult weight, longevity and fecundity; h) in relation to A. obtectus, non-preference resistance for feeding and/or antibiose only occurs with Arc1, genotype that prolongs the development period and reduces the adult weight; i) Goiano Precoce is the most suitable material for the development of both insects; j) with the association of vegeta powders and resistant bean genotypes, only additive effect (and not syhngistic) is observed with the two control tactics for both insect species; k) the weight of consumed bean grains for Z. subfasciatus and A. obtectus was not affected by insecticide powders; however the weight, however, was lower in the genotypes with arcelin for both insects.

Orientador: Maria Silvia Viccari Gatti / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-11T09:06:47Z (GMT). No. of bitstreams: 1 Martini_IzabelJulien_M.pdf: 1690786 bytes, checksum: ad68ca07a7cffdeef9fcdd571b9ae911 (MD5) Previous issue date: 2007 / Resumo: Gastroenterites e diarréias, doenças comuns em humanos, são responsáveis por altas taxas de morbidade e mortalidade em todo o mundo. Os rotavírus são um dos principais agentes dessas doenças, acometendo principalmente crianças com idade inferior a três anos. Esses vírus pertencem à família Reoviridae, gênero Rotavirus, não envelopados e de simetria icosaédrica. Seu genoma é composto por 11 segmentos de RNA dupla fita que podem separar os rotavírus em sete grupos (RV-A a RV-G), dada a migração desses segmentos em eletroforese em gel de poliacrilamida (EGPA). Os RV-A estão mais frequentemente associados a infecções no homem e em outros animais. Os rotavírus apresentam três camadas protéicas concêntricas, com o capsídeo externo contendo a proteína VP4 e a glicoproteína VP7, indutoras de anticorpos neutralizantes. Variações nas seqüências de nucleotídeos dos segmentos genômicos que codificam para essas proteínas diferenciam os rotavírus em genotipos G (VP7) e [P] (VP4). A distribuição desses genótipos é variável nos diferentes países e a utilização da técnica de semi-nested RT-PCR permite a caracterização dos genotipos circulantes, o que é importante para a definição de estratégias vacinais contra esses vírus. O uso de diferentes vacinas contra a rotavirose vem sendo implementado, inclusive no Brasil. Nesse trabalho o objetivo foi caracterizar os genotipos de rotavírus associados a surtos de diarréia em humanos, ocorridos na cidade de Campinas, SP, Brasil, nos anos de 2003 e 2004. Das 328 amostras de fezes estudadas, 98 foram positivas para rotavírus em EGPA, sendo 96 delas RV-A e duas RV-C. Todas as amostras positivas em EGPA para RV-A e outras 96 amostras negativas nesse teste foram submetidas à genotipagem G (G1 a G6 e G8 a G10) e P (P[4] e P[8]). Com os resultados obtidos concluiu-se que a técnica de seminested RT-PCR foi mais sensível na detecção de rotavírus (73,9%) que a EGPA (50,0%) (?2=67,06, valor-p= 0,000 e Kappa= 0,52).Os genotipos de rotavírus mais freqüentes nas amostras coletadas no ano de 2003 (n=38) foram: G1P[8] (38,4%), G3P[8] (15,4%), G5P[8], G9P[8] (7,8%) e G2P[4] (3,9%). Para as amostras enviadas em 2004 (n=290) os genotipos mais freqüentes foram: G3P[8] (18,7%), G9P[8] (13,9%), G1P[8] (8,4%), G5P[8] (6,0%) e G4P[8] (5,4%). A proporção de identificação do genotipo G1P[8] no ano de 2004 foi significativamente maior no ano de 2004 (Z= 3,07; valor-p=0,002). O genotipo emergente G9 foi identificado em 13,5% (n= 26) das amostras estudadas. Infecções mistas com os genotipos G1 e G2, G1 e G8, G2 e G3, G3 e G5 e G5 e G8 foram identificadas em oito amostras de fezes (4,1%). Nas regiões Sul e Sudoeste de Campinas, consideradas como menos favorecidas socio-economicamente, foi verificada maior variabilidade de genotipos circulantes nos dois anos de análise. Os dados obtidos poderão contribuir para a verificação da eficácia da vacina em uso no Brasil contra a rotavirose / Abstract: Gastroenteritis and diarrhea are a important cause of morbidity and mortality worldwide. Rotavirus is the most important etiologic agent of these disorders in infants and young children. These viruses, which form a genus of the Reoviridae family, are icosahedral, non-enveloped and their genome consists of 11 segments of double stranded RNA. When submitted to electrophoresis in polyacrylamide gels the RNAds of rotaviruses classify these viruses into seven groups (RV¿A to RV-G). Group A rotaviruses have been established as the most common cause of severe infections in human and other animals worldwide. The genome of rotaviruses is surrounded by three concentric protein layers. The outer capsid consists of VP4 and VP7 that carry neutralization and protective antigens and allow classification into P and G genotypes, respectively. The VP7 serotype is designated as G serotype (VP7 is a glycoprotein), whereas the VP4 serotype is designated as [P], from protease-sensitive. Many studies have been showed fluctuations in the distribution of rotavirus G-P combinations in many countries, using the seminested RT-PCR. These data, in relation of the circulation of different rotavirus genotypes, are important to establish rotavirus vaccine programs. Since a universal immunization of infants with rotavirus vaccine was introduced in Brazil, it becomes important to characterize rotavirus genotypes associated with diarrhea in humans from Campinas, SP, Brazil, in the years of 2003 and 2004. From 328 faecal samples, 98 were positive to rotavirus in polyacrylamide gel electrophoresis (PAGE), being 96 of them belonging to group A and two to RV-C. All the positive samples in PAGE for RV-A and another 96 negative samples to this test were submitted to semi-nested RT-PCR for G (G1 to G6 and G8 to G10) and P (P[4] and P[8]) genotypes determination. The results obtained showed that that semi-nested RT-PCR was more sensitive to the detection of rotavirus (73.9%) than the PAGE (50.0%) (?2=67.06, p= 0,000 and Kappa= 0,52). In 2003, in 38 faecal samples analyzed were identified as the genotypes G1P[8] (38.4%), G3P[8] (15.4%), G5P[8] (7.8%), G9P[8] (7.8%) and G2P 4] (3.9%). For the samples sent in 2004 (n=290), the genotypes G3P[8] (18.7%), G9P[8] (13.9%), G1P[8] (8.4%), G5P[8] (6.0%) and G4P[8] (5.4%) were identified. The genotype G1P[8] was identified in a higher proportion in 2004 than in 2003 (Z=3.07; p=0.002). The emergent genotype G9 was detected in 13.5% of the samples studied. Mixed infections, with G1 and G2, G1 and G8, G2 and G3, G3 and G5 and G5 and G8 were identified in eight faecal samples (4.1%). In the regions of South and Southwestern of Campinas, both of them considered as less socio-economically favored, a high variability of genotypes circulating in the two years of the study was verified. With these data will be able to contribute to the verification of the effectiveness of vaccines in use in Brazil against rotaviruses / Mestrado / Microbiologia / Mestre em Genética e Biologia Molecular

IntroduÃÃo: A beta talassemia à um grupo de distÃrbios, cada um resultando de um defeito genÃtico, na velocidade de sÃntese de uma ou mais cadeias globÃnicas da hemoglobina (Hb). A desproporÃÃo na produÃÃo das cadeias globÃnicas pode resultar em eritropoese ineficaz, produÃÃo insuficiente de Hb, hemÃlise e anemia de grau variado. A beta talassemia à mais frequente nos paÃses banhados pelo mar MediterrÃneo, refletindo a participaÃÃo desses povos na formaÃÃo da populaÃÃo brasileira. As mutaÃÃes predominantes no Brasil sÃo a IVS-I-1, IVS-I-6, IVS-I-110 e o CD 39, as quais estÃo associadas a diversos quadros clÃnicos e sÃo, em sua maioria, regionalmente especÃficas. Objetivo: Caracterizar o perfil clÃnico, hematolÃgico e molecular dos indivÃduos adultos com beta talassemia do Hospital UniversitÃrio Walter CantÃdeo, em acompanhamento no centro de referÃncia de Hematologia e Hemoterapia do estado do Cearà (HEMOCE). Metodologia: Foram analisados 22 indivÃduos portadores de beta talassemia, sendo 7 intermediÃria e 15 menor, de ambos os sexos, no perÃodo de fevereiro de 2008 a setembro de 2009. Os dados clÃnicos e laboratoriais: hemograma, nÃveis de Hb A2 e de Hb F; ferro sÃrico; capacidade total e latente de ligaÃÃo do ferro (CTLFe, CLLFe), ferritina e Ãndice de saturaÃÃo da transferrina (IST), foram obtidos dos prontuÃrios, ao diagnÃstico. Cerca de 5 mL de sangue venoso foi coletado em tubo contendo o anticoagulante EDTA para o estudo molecular. A anÃlise das mutaÃÃes foi realizada por meio da tÃcnica da reaÃÃo em cadeia mediada pela polimerase alelo especÃfico (PCR-AE), onde foram analisadas as seguintes mutaÃÃes: IVS-I-1, IVS-I-6, IVS-I-110 e o CD 39. As anÃlises estatÃsticas foram desenvolvidas no software livre R (versÃo 2.7.0) e o nÃvel de significÃncia estabelecido foi 5%. Resultados: Dos 22 pacientes estudados, 15 eram portadores de β talassemia menor e sete intermediÃria. A idade variou de 18 a 68 anos, com mÃdia de 44,7 anos. 18,2 % do sexo masculino e 81,8% do sexo feminino. As mutaÃÃes foram caracterizadas em 68,2% dos casos, que teve como mais frequente a IVS-I-6, seguida do cÃdon 39. A mutaÃÃo IVS-I-I foi caracterizada em um paciente e a IVS-I-110 nÃo foi encontrada. NÃo houve diferenÃa clÃnica significante entre os parÃmetros hematolÃgicos e bioquÃmicos. Houve discrepÃncia entre o fenÃtipo e o genÃtipo em alguns pacientes, porÃm nÃo houve diferenÃa significativa entre as mutaÃÃes e as manifestaÃÃes clÃnicas. ConclusÃes: Os resultados do presente estudo reforÃam o predomÃnio da mutaÃÃo IVS-I-6 no nordeste do Brasil. Recomendam-se estudos posteriores para investigaÃÃo da co-heranÃa com a α talassemia nesses pacientes para justificar a discrepÃncia entre genÃtipos e fenÃtipos. / Background: Beta thalassemia is a group of disorders, each resulting from a genetic defect in the rate of synthesis of one or more globin chains of hemoglobin (Hb). The imbalance in the production of globin chains can result in ineffective erythropoiesis, insufficient production of hemoglobin, hemolysis and anemia of varying degree. Beta thalassemia is more common in countries bordering the Mediterranean Sea, reflecting the participation of these peoples in the formation of the Brazilian population. The predominant mutations in Brazil are the IVS-I-1, IVS-I-6, IVS-I-110 and CD 39, which are associated with different clinical conditions and are mostly regionally specific. Objective: To characterize the clinical, hematological and molecular adults with beta thalassemia of the University Hospital CantÃdeo Walter and followed at a referral center for Hematology of the state of Cearà (Hemoce). Methods: We analyzed 22 individuals with beta thalassemia, 7 intermediate and 15 minor, in both sexes, from February 2008 to September 2009. Clinical data and laboratory tests: blood count, levels of Hb A2 and Hb F, serum iron, total capacity and latent iron binding (CTLFe, CLLFe), ferritin and transferrin saturation index (IST) were obtained from medical records, diagnosis. About 5 mL of venous blood was collected in tubes containing EDTA anticoagulant for molecular study. The analysis of mutations was performed using the technique of chain reaction mediated by allele specific polymerase (PCR-AE), where we analyzed the following mutations: IVS-I-1, IVS-I-6, IVS-I-110 and CD 39. Statistical analysis was carried out in software R (version 2.7.0) and the level of significance was 5%. Results: Of 22 patients studied, 15 were patients with β thalassemia minor and seven intermediate. The age ranged 18-68 years with a mean of 44.7 years. 18.2% male and 81.8% female. The mutations were characterized in 68.2% of cases, which had the most frequent IVS-I-6, followed by the codon 39. The mutation IVS-I-1 was found in one patient and IVS-I-110 was not found. There was no significant clinical differences between the hematological and biochemical parameters. There was a discrepancy between phenotype and genotype in some patients, but no significant difference between mutations and clinical manifestations. Conclusions: The results of this study reinforce the dominance of the mutation IVS-I-6 in northeastern Brazil. Are recommended further studies to investigate the co-inheritance with α-thalassemia in these patients to justify the discrepancy between genotypes and phenotypes.

Orientador: Clarice Weis Arns / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-23T15:29:47Z (GMT). No. of bitstreams: 1 Rosa_GislaineNonino_M.pdf: 911936 bytes, checksum: 7194af83e7f30e4bcab42d6488202031 (MD5) Previous issue date: 2007 / Resumo: A cinomose canina tem sido relatada como uma das mais importantes doenças infecto contagiosas dos canídeos selvagens e domésticos. É causada por um agente viral denominado vírus da cinomose canina (CDV). Os vírus pertencem à família Paramyxoviridae , gênero Morbillivirus. São vírus envelopados, com genoma composto por uma fita simples de RNA, polaridade negativa, não segmentado. Alto grau de variabilidade genética no gene da hemaglutinina ( H) tem sido encontrada entre estirpes virais recentes e vacinais, e estas variações podem estar relacionadas ao aumento da ocorrência global da cinomose. No presente estudo, amostras biológicas de cães com sintomatologia sugestiva da cinomose foram analisadas geneticamente. Para a detecção de um fragmento de 882 pb do gene H do CDV padronizou-se uma RT-PCR que mostrou-se capaz de amplificar o material genético viral em amostras de urina, líquido céfalo-raquidiano, sistema nervoso central (SNC), baço , pulmão , fígado , rins, linfonodos, bexiga e timo. As amostras positivas de acordo com a RT-PCR foram encaminhadas para o sequenciamento e análise filogenética. Os resultados encontrados sugerem que estas amostras assemelham-se geneticamente aos vírus agrupados nas linhagens Européia e Ásia-1. A estirpe vacinal Lederle, utilizada como padrão, foi agrupada junto a linhagem América-1 onde encontram-se todas as estirpes vacinais , também conhecidas como "Old CDVs" . Os achados deste trabalho apontam para a ocorrência de estirpes geneticamente distintas daquelas utilizadas na produção de vacinas e mais estudos são necessários para a avaliação da eficácia das vacinas disponíveis, propiciando um melhor controle da doença / Abstract: Canine distemper has been reported as one of the most important infectious diseases of wild and domestic canids. It is caused by a viral agent called canine distemper virus (CDV). Viruses belonging to the family Paramyxoviridae, genus Morbillivirus. They are enveloped viruses with genome composed of a single strand of RNA, negative polarity, not segmented. High degree of genetic variability in the gene for hemagglutinin (H) has been found between recent viral strains and vaccination strains, and these variations may be related to increased overall occurrence distemper. In this study, biological samples from dogs with symptoms suggestive of distemper were analyzed genetically. For the detection of a 882 base pairs (bp) fragment of the gene of CDV H was standardized a RT-PCR wich proved to be capable of amplifying the viral genetic material in urine, cerebrospinal fluid, central nervous system (CNS), spleen , lungs, liver, kidneys, lymph nodes, bladder and thymus. Positive samples according to RT-PCR were sent for sequencing and phylogenetic analysis. The results suggest that these samples are similar to viruses genetically clustered lineages in European and Asia-1. The Lederle vaccine strain, used as standard, was grouped with Latin-1 lineages which are all vaccine strains, also known as "old CDVs." The findings of this study point to the occurrence of genetically distinct strains from those used in vaccine production and more studies are needed to assess the efficacy of vaccines available, providing better control of the disease / Mestrado / Microbiologia / Mestra em Genética e Biologia Molecular

Class of 2016 Abstract / Objectives: To compare the efficacy of direct acting antiviral agents for the treatment of hepatitis C virus genotype 1. Our primary null hypothesis is there will be no significant difference in efficacy among the treatment regimens for hepatitis C virus, genotype 1. Methods: This meta-analysis study will use published literature identified from Embase and PubMed for phase II or III clinical trials evaluating direct acting antiviral drug regimens to treat adults with hepatitis C virus (HCV) genotype 1 infection. The primary outcome of interest is SVR at 12 weeks after treatment initiation. Data will be analyzed both descriptively as well as using Bayesian mixed treatment comparison methods. After extracting the outcome data from individual studies, the data will be analyzed using Winbugs version 1.4.3. Moreover, a random effects model and indirect/mix-treatment comparison will be used during the analysis. The random effects model accounts for both between-study and within-study variance, and is exempted from normality assumption, possessing a wider credible interval. All pair-wise odds ratios will be generated and treatment regimens will be ranked based on the likelihood of achieving SVR. Results: Overall, combinations containing sofosbuvir and ledipasvir were significantly better than all other treatments except for simeprevir (OR 0.52, 95% CI 0.28-1.00). On the other hand, daclatasvir containing regimens were non-inferior only to simeprevir (OR 0.69, 95% CI 0.35-1.31) and grazoprevir (OR 0.66, 95% CI 0.41-1.04) while being inferior to other treatments. Sofosbuvir with ledipasvir was ranked highest in terms of obtaining a sustained viral response, followed by ABT-450, grazoprevir, simeprevir, and daclatasvir respectively. In previously treated patients, sofosbuvir with ledipasvir again demonstrated the best efficacy with only grazoprevir and ABT-450 being non-inferior (OR 0.64, 95% CI 0.3368-1.212 and OR 0.73 95% CI 0.29-1.88 respectively). Sofosbuvir with ledipasvir was followed by grazoprevir, ABT-450, simeprevir, and daclatasvir containing regimens respectively. Finally, in treatment naïve patients, simeprevir containing regimens were non-inferior to all other treatment groups, including sofosbuvir regimens (OR 1.24, 95% CI 0.28-9.93). With the exception of simeprevir, sofosbuvir with ledipasvir demonstrated superiority over all treatments. Simeprevir regimens and sofosbuvir with ledipasvir regimens were followed by ABT-450. In treatment naive patients daclatasvir was found to be non-inferior to grazoprevir (OR 1.26, 95% CI 0.75-2.10). Treatment naive patients were the only group we analyzed in which daclatasvir was not the least effective regimen, with grazoprevir claiming the last position. Conclusions: Our results reject our null hypothesis that there will be no difference between different treatment regimens in HCV genotype 1 patients. Generally, the combination of sofosbuvir and ledipasvir appears to be the most effective, while daclatasvir appears to be the least.

Warfarin, the most commonly prescribed anticoagulant, is principally metabolized by cytochrome P450 2C9 which functions by inhibiting the Vitamin K epoxide reductase. Genes CYP2C9 and VKORC1 code for these two proteins, respectively. CYP2C9 and VKORC1 exhibit genetic polymorphisms that have been shown to affect warfarin response and favorably facilitate warfarin dosing and improve clinical outcomes. However, none of these studies have involved populations from sub-Saharan Africa where the potential benefit of optimal dosing and reduced complications is greatest. Therefore, the thesis describes a study designed to investigate the role of genetic variations in CYP2C9 and VKORC1 on the time taken to reach a stable therapeutic international normalized ratio (INR) and warfarin dose required to maintain a therapeutic INR. This was a cross-sectional study of patients on warfarin to determine the relationship between genetic polymorphism in CYP2C9 and VKORC1 amongst black and mixed ancestry South Africans and clinical surrogates of warfarin metabolism. Medical records were accessed to determine time to INR and warfarin doses. DNA was extracted from blood samples, and genotyping for polymorphism in CYP2C9 (*2,*3,*8,*11) and VKORC1 (1173C>T, 1639G>A, 3730G>A) was accomplished by PCR-RFLP, Sanger sequencing and iPlex Mass Sequencing. Our results show that the genetic profile of CYP2C9 and VKORC1 differs between Black Africans (BA) and their Mixed Ancestry (MA) counterparts. VKORC1-1639AA genotype was observed at frequencies of 0.11 and 0.01 in the MA and BA, respectively. Time to stable INR was not influenced by CYP2C9 and VKORC1. Furthermore, compared to known genetic polymorphisms in these genes from population out of Africa, both qualitative and quantitative differences were observed. Finally, we found that VKORC1 genetic variation significantly affected the doses of warfarin in MA but had no effect in BA. These results suggest that further research in this area is warranted, and that it will be important to include populations from sub-Saharan Africa in future if the potential to develop personalized algorithms which integrate pharmacogenomics to assist with effective warfarin dosing and prevention of warfarin related complications is to be realized.

Genotype data, consisting large numbers of markers, is used as demographic and association studies to determine genes related to specific traits or diseases. Handling of these datasets usually takes a significant amount of time in its application of population structure inference. Therefore, we suggested applying PCA on genotyped data and then clustering algorithms to specify the individuals to their particular subpopulations. We collected both real and simulated datasets in this study. We studied PCA and selected significant features, then applied five different clustering techniques to obtain better results. Furthermore, we studied three different methods for predicting the optimal number of subpopulations in a collected dataset. The results of four different simulated datasets and two real human genotype datasets show that our approach performs well in the inference of population structure. NbClust is more effective to infer subpopulations in the population. In this study, we showed that centroid-based clustering: such as k-means and PAM, performs better than model-based, spectral, and hierarchical clustering algorithms. This approach also has the benefit of being fast and flexible in the inference of population structure.

Genotype by environment interaction (GxE) is the tendency of the phenotypic performance of two or more plant genotypes in one environment to not be predictive of their relative performance in another environment. To discover the importance of GxE in this region, a large set of USDA and commercial hybrids were tested in the regions of practical significance to sunflower production in order to produce recommendations regarding mega-environments for yield and oil. Rank changes for oil content occurred among hybrids and two common factors accounted for 68.6% of the total GxE variation. Breeding programs testing pre-commercial hybrids in multiple environments for oil content could be beneficial. Yield covariates for lodging, bird damage, and disease were significant but occurred in different locations with variable severity each year making it difficult to divide the growing region into mega-environments for yield.

Gene expression responds to the environment and can also evolve rapidly in response to altered selection regimes. Little is known, however, about the extent to which evolutionary adaptation to a particular type of stress involves changes in the within-generation ('plastic') responses of gene expression to the stress. We used microarrays to quantify gene expression plasticity in response to ethanol in laboratory populations of Drosophila melanogaster differing in their history of ethanol exposure. Two populations ('R' populations) were maintained on regular medium, two ('E') were maintained on medium supplemented with ethanol, and two ('M') were maintained in a mixed regime in which half of the population was reared on one medium type, and half on the other, each generation. After more than 300 generations, embryos from each population were collected and exposed to either ethanol or water as a control, and RNA was extracted from the larvae shortly after hatching. Nearly 2000 transcripts showed significant within-generation responses to ethanol exposure. Evolutionary history also affected gene expression: the E and M populations were largely indistinguishable in expression, but differed significantly in expression from the R populations for over 100 transcripts, the majority of which did not show plastic responses. Notably, in no case was the interaction between selection regime and ethanol exposure significant after controlling for multiple comparisons, indicating that adaptation to ethanol in the E and M populations did not involve substantial changes in gene expression plasticity. The results give evidence that expression plasticity evolves considerably more slowly than mean expression.