This thesis presents genetic studies of atopic dermatitis (AD) and IgA deficiency in dogs. AD is a chronic inflammatory and pruritic skin disorder caused by allergic reactions against environmental allergens. Both genetic and environmental factors are involved in the development of Canine AD (CAD) and human AD. In Paper I, we performed genome-wide association studies (GWAS) and identified a locus on chromosome 27 significantly associated with CAD in German shepherd dogs (GSDs). The locus contains several genes and fine-mapping indicated strongest association close to the candidate gene PKP2. In Paper II, we performed additional fine-mapping and identified four highly associated SNPs located in regions with transcriptional regulatory potential in epithelial and immune cells. The risk alleles were associated with increased transcriptional activity and the effect on expression was cell-type dependent. These data indicate that multiple cell-type specific enhancers regulate the expression of PKP2, and/or the neighboring genes YARS2, DNM1L and FGD4, and predispose GSDs to CAD. IgA deficiency is the most common primary immune deficiency disorder in both humans and dogs, characterized by a higher risk of recurrent mucosal tract infections, allergic and other immune-mediated diseases. In Paper III, we performed the widest screening (to date) of serum IgA levels in dog breeds (Ndogs=1267, Nbreeds=22) and defined eight breeds as predisposed to low IgA levels. In Paper IV, we performed GWAS in four of the breeds defined as prone to low IgA levels. We used a novel percentile groups-approach to establish breed-specific cut-offs to perform analyses in a close to continuous manner. In total, 35 genomic loci were suggestively associated (p<0.0005) to IgA levels, and three genomic regions (including the genes KIRREL3 and SERPINA9) were genome-wide significantly associated with IgA levels in GSDs. A ~20kb long haplotype on chromosome 28, significantly associated to IgA levels in Shar-Pei dogs, was positioned within the first intron of the gene SLIT1 overlapping with a possible dog domestication sweep. This thesis suggests novel candidate genes involved in two immune-mediated disorders in the dog. Hopefully, these results will become an important resource for the genetic research of the corresponding human diseases.

Objective.Humans differ substantially with respect to susceptibility to human immunodeficiency virus type 1 (HIV-1) infection and disease progression. This heterogeneity is attributed to the interplay between the environment, viral diversity, immune response and host genetics. This study focused on host genetics. We studied the association of single nucleotide polymorphisms (SNPs) in peptidyl prolyl isomerase A (PPIA), transportin 3 (TNPO3) and PC4 or SFRS1 interacting protein 1 (PSIP1) genes with HIV-1 infection and disease progression. These genes code for Cyclophilin A (CypA), Transportin-SR2 (TRN-SR2) and Lens epithelium derived growth factor/p75 (LEDGF/p75) proteins respectively, which are all validated HIV replication cofactors in vitro. Methods. One SNP A1650G in the PPIA gene was genotyped in 168 HIV-1 negative and 47 acutely infected individuals using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). 6 intronic and 2 exonic haplotype tagging (ht) SNPs (rs13242262; rs2305325; rs11768572; rs1154330; rs35060568; rs8043; rs6957529; rs10229001) in the TNPO3 gene, 4 intronic ht SNPs (rs2277191, rs1033056, rs12339417 and rs10283923) and 1 exonic SNP (rs61744944, Q472L) in the PSIP1 gene were genotyped in 195 HIV-1 negative and 52 acutely infected individuals using TaqMan assays. The rs1154330, rs2277191, rs12339417 and rs61744944 were further genotyped in 403 chronically infected individuals. CypA and LEDGF/p75 messenger RNA (mRNA) expression levels in peripheral blood mononuclear cells (PBMCs) were quantified by real-time reverse transcriptase polymerase chain reaction (RT-PCR). The impact of the Q472L mutation on the interaction of LEDGF/p75 with HIV-1 integrase (IN) was measured by AlphaScreen. Results. The minor allele (G) of SNP A1650G (1650G) in the promoter region of PPIA was significantly associated with higher viral load (p<0.01), lower CD4+ T cell counts (p<0.01) and showed a possible association with rapid CD4+ T cell decline (p=0.05). The 1650G was further associated with higher CypA expression post HIV-1 infection. The minor allele (G) of rs1154330 in the intron region of TNPO3 was associated with faster HIV-1 acquisition (p<0.01), lower CD4+ T cell counts, higher viral load during primary infection (p<0.05) and rapid CD4+ T cells decline (p<0.01). The minor allele (A) of rs2277191 (rs2277191A) in the intron region of PSIP1 was more frequent among seropositives (p=0.06). Among individuals followed longitudinally, rs2277191A was associated with higher likelihood of HIV-1 acquisition (p=0.08) and rapid CD4+T cell decline (p=0.04) in the recently infected (primary infection) cohort. In contrast, the minor allele (C) of rs12339417 (rs12339417C) also in the intron region of PSIP1 was associated with higher CD4+ T cell counts during primary infection. The rs12339417C was also associated with slower rate of CD4+ T cell decline (p=0.02) and lower mRNA levels of LEDGF/p75 (p<0.01). Seroconverters had higher preinfection mRNA levels of LEDGF/p75 compared to nonseroconverters (p<0.01) and these levels decreased after HIV-1 infection (p=0.02). The Q472L mutation showed approximately 2-fold decrease in the association constant (Kd), suggesting stronger binding to HIV-1 integrase. Our findings demonstrate, for the first time, that genetic polymorphisms in the TNPO3 and PSIP1 genes may be associated with susceptibility to HIV-1 infection and the disease progression. These data provide in vivo evidence that TRN-SR2 and LEDGF/p75 are important host cofactors for HIV-1 replication. This is also the first study to show the association of genetic polymorphisms in the PPIA gene with disease outcome in a population (South African) with high burden of HIV-1 infection. Conclusions. Genetic variation in HIV-1 replication cofactors may be associated with disease outcome in a South African population. These data strongly support the role of these HIV replication cofactors in disease pathogenesis in vivo and suggest that these factors are possible targets for therapeutic interventions. However, these data will need to be replicated in larger cohorts to confirm the effect of these genetic variants. Further studies on how to target these factors in antiviral strategies are needed. / Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2011.

Includes list of publications arising from the thesis. / Bibliography: leaves 327-341. / 341, [15] leaves : ill. (some col.) ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / Examines the effect of adverse storage on the immunogenicity of pertussis, diphtheria and tetanus vaccines, the protective efficacy of pertussis vaccines and the effect of premature birth on antibody response to routine childhood immunisations. / Thesis (Ph.D.)--University of Adelaide, Dept. of Paediatrics, 2002?

Thesis (Ph. D.)--Institute of Immunology and Allergy Research, Westmead Millennium Institute, Westmead Hospital, University of Sydney, 2003. / Bibliography: leaves 177-222.

Thesis (Ph. D.)--Northeastern University, 2008. / Title from title page (viewed March 3, 2009). Graduate School of Arts and Sciences, Dept. of Biology. Includes bibliographical references (p. 172-190).

Thesis (Ph. D.)--University of Sydney, 2003. / Title from title screen (viewed Apr. 28, 2008). Submitted in fulfilment of the requirements for the degree of Doctor of Philosophy to the Institute of Immunology and Allergy Research, Westmead Millennium Institute, Westmead Hospital. Includes bibliography. Also available in print form.

Thesis (Ph. D.)--University of Wisconsin--Madison, 1995. / Typescript. eContent provider-neutral record in process. Description based on print version record. Includes bibliographical references (leaves 287-330).

A Proteína de Ligação à Manose (MBL) é um membro da família das colectinas humanas que atua como molécula de defesa e desempenha um papel importante na imunidade inata. A MBL se liga a carboidratos na superfície de microorganismos, desencadeando a opsonização e fagocitose. Essa ligação também resulta na ativação do sistema complemento. Já foi descrito que a MBL reconhece e se liga a proteína gp120 do Vírus da Imunodeficiência Humana-1 (HIV-1), mas o papel dessa molécula na infecção pelo HIV-1 ainda não está claro. Vários polimorfismos no gene MBL2 foram descritos como capazes de alterar a conformação da proteína, levando a baixos níveis séricos de MBL, e susceptibilidade aumentada a infecções. Entre eles, duas variantes na região promotora (-550 H/L e -221 X/Y), e três variantes no éxon 1, Arg52Cys, Gly54Asp e Gly57Glu (coletivamente chamadas de alelo 0, enquanto a combinação dos três alelos selvagens é chamada de A) foram analisadas no presente trabalho. Nosso objetivo foi investigar o papel da MBL na infecção pelo HIV-1, através da análise dos polimorfismos localizados nas regiões promotora e do éxon 1 do gene MBL2. Nós investigamos a prevalência dos alelos variantes em 410 pacientes infectados pelo HIV-1 do Hospital de Clínicas de Porto Alegre e 345 indivíduos não infectados. Todos os indivíduos são da região Sul do Brasil. As variantes localizadas na região promotora foram genotipadas usando a técnica PCR-SSP e as variantes do éxon 1 foram analisadas por PCR em tempo real, usando um ensaio de temperatura de melting e confirmação por PCR-RFLP. As freqüências genotípicas e alélicas foram comparadas entre os dois grupos analisados, indivíduos positivos para HIV-1 e controles, usando o teste de qui-quadrado. As análises foram realizadas subdividindo os indivíduos de acordo com a origem étnica. Entre os indivíduos Euro-descendentes, uma maior freqüência do genótipo LX/LX foi observada entre pacientes, quando comparada com controles (p<0,001). As análises haplotípicas também demonstraram uma maior freqüência dos haplótipos associados com baixos níveis de MBL entre os pacientes infectados pelo HIV-1 (p=0,0001). Entre os indivíduos Afro-descendentes, as freqüências dos genótipos LY/LY e HY/HY foram maiores entre os pacientes, quando comparadas com os controles (p=0,009 e p=0,02). Nosso trabalho encontrou uma maior freqüência dos genótipos associados com baixos níveis de MBL entre os pacientes Euro-descendentes, sugerindo um papel potencial para a MBL na susceptibilidade à infecção pelo HIV-1 entre indivíduos Eurodescendentes. / Mannose-binding lectin (MBL) is a member of the collectin protein family that acts as a defence molecule and plays an important role in innate immune responses. MBL binds to carbohydrates on the surface of microorganisms, leading to opsonisation and phagocytosis. This binding also results in activation of the complement system. It was already described that MBL recognizes and binds to gp120 protein of human immunodeficiency virus-1 (HIV-1), but the role of such molecule on HIV infection is still debated. Several MBL2 gene polymorphisms were described as capable of disrupting the MBL protein resulting in low serum levels and increased susceptibility to infections. Among them, two variants in the promoter region (-550 H/L and -221 X/Y) and three variants in exon 1, Arg52Cys, Gly54Asp and Gly57Glu (that are collectively called allele 0, while the combination of the three wild-type alleles is called A), were analyzed in the present work. Our aim was to investigate the role of MBL on HIV-1 infected subjects through the analysis of the polymorphisms located in the MBL2 promoter and exon 1 regions. We investigated the prevalence of the variant alleles in 410 HIV-1 infected patients from the Hospital de Clínicas de Porto Alegre (HCPA), and in 345 uninfected individuals. All individuals are from Southern Brazil. The variants from the promoter were genotyped using PCRSSP and the variants from the exon 1 were analyzed by Real-time PCR using a melting temperature assay and were confirmed by PCR-RFLP. Polymorphisms genotype and allele frequencies in the two groups analyzed, namely HIV-1 positive subjects and controls, were compared using Chi-square-test. The analyses were performed subdividing the individuals according to their ethnic origin. Among Euro-derived individuals a higher frequency of the LX/LX genotype in patients was observed when compared to controls (p<0.001). The haplotypic analysis also showed a higher frequency of the haplotypes associated with lower MBL levels among HIV-1 infected patients (p=0.0001). Among Afro-derived individuals the frequencies of LY/LY and HY/HY genotypes were higher in patients when compared to controls (p=0.009 and p=0.02). An increased frequency of genotypes associated with low MBL levels was observed among Euro-derived patients, suggesting a potential role for MBL in the susceptibility to HIV-1 infection in Euro-derived individuals.

A Proteína de Ligação à Manose (MBL) é um membro da família das colectinas humanas que atua como molécula de defesa e desempenha um papel importante na imunidade inata. A MBL se liga a carboidratos na superfície de microorganismos, desencadeando a opsonização e fagocitose. Essa ligação também resulta na ativação do sistema complemento. Já foi descrito que a MBL reconhece e se liga a proteína gp120 do Vírus da Imunodeficiência Humana-1 (HIV-1), mas o papel dessa molécula na infecção pelo HIV-1 ainda não está claro. Vários polimorfismos no gene MBL2 foram descritos como capazes de alterar a conformação da proteína, levando a baixos níveis séricos de MBL, e susceptibilidade aumentada a infecções. Entre eles, duas variantes na região promotora (-550 H/L e -221 X/Y), e três variantes no éxon 1, Arg52Cys, Gly54Asp e Gly57Glu (coletivamente chamadas de alelo 0, enquanto a combinação dos três alelos selvagens é chamada de A) foram analisadas no presente trabalho. Nosso objetivo foi investigar o papel da MBL na infecção pelo HIV-1, através da análise dos polimorfismos localizados nas regiões promotora e do éxon 1 do gene MBL2. Nós investigamos a prevalência dos alelos variantes em 410 pacientes infectados pelo HIV-1 do Hospital de Clínicas de Porto Alegre e 345 indivíduos não infectados. Todos os indivíduos são da região Sul do Brasil. As variantes localizadas na região promotora foram genotipadas usando a técnica PCR-SSP e as variantes do éxon 1 foram analisadas por PCR em tempo real, usando um ensaio de temperatura de melting e confirmação por PCR-RFLP. As freqüências genotípicas e alélicas foram comparadas entre os dois grupos analisados, indivíduos positivos para HIV-1 e controles, usando o teste de qui-quadrado. As análises foram realizadas subdividindo os indivíduos de acordo com a origem étnica. Entre os indivíduos Euro-descendentes, uma maior freqüência do genótipo LX/LX foi observada entre pacientes, quando comparada com controles (p<0,001). As análises haplotípicas também demonstraram uma maior freqüência dos haplótipos associados com baixos níveis de MBL entre os pacientes infectados pelo HIV-1 (p=0,0001). Entre os indivíduos Afro-descendentes, as freqüências dos genótipos LY/LY e HY/HY foram maiores entre os pacientes, quando comparadas com os controles (p=0,009 e p=0,02). Nosso trabalho encontrou uma maior freqüência dos genótipos associados com baixos níveis de MBL entre os pacientes Euro-descendentes, sugerindo um papel potencial para a MBL na susceptibilidade à infecção pelo HIV-1 entre indivíduos Eurodescendentes. / Mannose-binding lectin (MBL) is a member of the collectin protein family that acts as a defence molecule and plays an important role in innate immune responses. MBL binds to carbohydrates on the surface of microorganisms, leading to opsonisation and phagocytosis. This binding also results in activation of the complement system. It was already described that MBL recognizes and binds to gp120 protein of human immunodeficiency virus-1 (HIV-1), but the role of such molecule on HIV infection is still debated. Several MBL2 gene polymorphisms were described as capable of disrupting the MBL protein resulting in low serum levels and increased susceptibility to infections. Among them, two variants in the promoter region (-550 H/L and -221 X/Y) and three variants in exon 1, Arg52Cys, Gly54Asp and Gly57Glu (that are collectively called allele 0, while the combination of the three wild-type alleles is called A), were analyzed in the present work. Our aim was to investigate the role of MBL on HIV-1 infected subjects through the analysis of the polymorphisms located in the MBL2 promoter and exon 1 regions. We investigated the prevalence of the variant alleles in 410 HIV-1 infected patients from the Hospital de Clínicas de Porto Alegre (HCPA), and in 345 uninfected individuals. All individuals are from Southern Brazil. The variants from the promoter were genotyped using PCRSSP and the variants from the exon 1 were analyzed by Real-time PCR using a melting temperature assay and were confirmed by PCR-RFLP. Polymorphisms genotype and allele frequencies in the two groups analyzed, namely HIV-1 positive subjects and controls, were compared using Chi-square-test. The analyses were performed subdividing the individuals according to their ethnic origin. Among Euro-derived individuals a higher frequency of the LX/LX genotype in patients was observed when compared to controls (p<0.001). The haplotypic analysis also showed a higher frequency of the haplotypes associated with lower MBL levels among HIV-1 infected patients (p=0.0001). Among Afro-derived individuals the frequencies of LY/LY and HY/HY genotypes were higher in patients when compared to controls (p=0.009 and p=0.02). An increased frequency of genotypes associated with low MBL levels was observed among Euro-derived patients, suggesting a potential role for MBL in the susceptibility to HIV-1 infection in Euro-derived individuals.

A Proteína de Ligação à Manose (MBL) é um membro da família das colectinas humanas que atua como molécula de defesa e desempenha um papel importante na imunidade inata. A MBL se liga a carboidratos na superfície de microorganismos, desencadeando a opsonização e fagocitose. Essa ligação também resulta na ativação do sistema complemento. Já foi descrito que a MBL reconhece e se liga a proteína gp120 do Vírus da Imunodeficiência Humana-1 (HIV-1), mas o papel dessa molécula na infecção pelo HIV-1 ainda não está claro. Vários polimorfismos no gene MBL2 foram descritos como capazes de alterar a conformação da proteína, levando a baixos níveis séricos de MBL, e susceptibilidade aumentada a infecções. Entre eles, duas variantes na região promotora (-550 H/L e -221 X/Y), e três variantes no éxon 1, Arg52Cys, Gly54Asp e Gly57Glu (coletivamente chamadas de alelo 0, enquanto a combinação dos três alelos selvagens é chamada de A) foram analisadas no presente trabalho. Nosso objetivo foi investigar o papel da MBL na infecção pelo HIV-1, através da análise dos polimorfismos localizados nas regiões promotora e do éxon 1 do gene MBL2. Nós investigamos a prevalência dos alelos variantes em 410 pacientes infectados pelo HIV-1 do Hospital de Clínicas de Porto Alegre e 345 indivíduos não infectados. Todos os indivíduos são da região Sul do Brasil. As variantes localizadas na região promotora foram genotipadas usando a técnica PCR-SSP e as variantes do éxon 1 foram analisadas por PCR em tempo real, usando um ensaio de temperatura de melting e confirmação por PCR-RFLP. As freqüências genotípicas e alélicas foram comparadas entre os dois grupos analisados, indivíduos positivos para HIV-1 e controles, usando o teste de qui-quadrado. As análises foram realizadas subdividindo os indivíduos de acordo com a origem étnica. Entre os indivíduos Euro-descendentes, uma maior freqüência do genótipo LX/LX foi observada entre pacientes, quando comparada com controles (p<0,001). As análises haplotípicas também demonstraram uma maior freqüência dos haplótipos associados com baixos níveis de MBL entre os pacientes infectados pelo HIV-1 (p=0,0001). Entre os indivíduos Afro-descendentes, as freqüências dos genótipos LY/LY e HY/HY foram maiores entre os pacientes, quando comparadas com os controles (p=0,009 e p=0,02). Nosso trabalho encontrou uma maior freqüência dos genótipos associados com baixos níveis de MBL entre os pacientes Euro-descendentes, sugerindo um papel potencial para a MBL na susceptibilidade à infecção pelo HIV-1 entre indivíduos Eurodescendentes. / Mannose-binding lectin (MBL) is a member of the collectin protein family that acts as a defence molecule and plays an important role in innate immune responses. MBL binds to carbohydrates on the surface of microorganisms, leading to opsonisation and phagocytosis. This binding also results in activation of the complement system. It was already described that MBL recognizes and binds to gp120 protein of human immunodeficiency virus-1 (HIV-1), but the role of such molecule on HIV infection is still debated. Several MBL2 gene polymorphisms were described as capable of disrupting the MBL protein resulting in low serum levels and increased susceptibility to infections. Among them, two variants in the promoter region (-550 H/L and -221 X/Y) and three variants in exon 1, Arg52Cys, Gly54Asp and Gly57Glu (that are collectively called allele 0, while the combination of the three wild-type alleles is called A), were analyzed in the present work. Our aim was to investigate the role of MBL on HIV-1 infected subjects through the analysis of the polymorphisms located in the MBL2 promoter and exon 1 regions. We investigated the prevalence of the variant alleles in 410 HIV-1 infected patients from the Hospital de Clínicas de Porto Alegre (HCPA), and in 345 uninfected individuals. All individuals are from Southern Brazil. The variants from the promoter were genotyped using PCRSSP and the variants from the exon 1 were analyzed by Real-time PCR using a melting temperature assay and were confirmed by PCR-RFLP. Polymorphisms genotype and allele frequencies in the two groups analyzed, namely HIV-1 positive subjects and controls, were compared using Chi-square-test. The analyses were performed subdividing the individuals according to their ethnic origin. Among Euro-derived individuals a higher frequency of the LX/LX genotype in patients was observed when compared to controls (p<0.001). The haplotypic analysis also showed a higher frequency of the haplotypes associated with lower MBL levels among HIV-1 infected patients (p=0.0001). Among Afro-derived individuals the frequencies of LY/LY and HY/HY genotypes were higher in patients when compared to controls (p=0.009 and p=0.02). An increased frequency of genotypes associated with low MBL levels was observed among Euro-derived patients, suggesting a potential role for MBL in the susceptibility to HIV-1 infection in Euro-derived individuals.