HIV-1 has claimed the lives of millions of people globally and continues to spread despite development of highly active antiretroviral therapy. In 2013, 2.1 million new infections occurred and over 35 million people were living with HIV-1 infection. A prophylactic HIV-1 vaccine that can prevent infection or reduce viremia and subsequent transmission will always be an important part of the solution to bring this epidemic under control. In this thesis, the first HIV-1 vaccine candidate to focus on conserved regions of the virus (HIVconsv) was assessed in a phase I clinical trial conducted in healthy HIV-1/2 negative volunteers in Oxford. The HIVconsv T-cell immunogen was delivered using three leading vaccine modalities (DNA (D), modified vaccinia virus Ankara (M) and chimpanzee adenovirus serotype 63 (C)), in several novel heterologous prime-boost regimens. The frequency of T cells elicited through HIVconsv vaccination in the CM and DDDCM regimens surpassed that of previous HIV-1 cell-mediated vaccines. A large proportion of these T cells produced multiple cytokines and proliferated in response to recall peptides. The breadth of T-cell responses were also greater than the non-efficacious STEP study vaccine, with an average of 10 T-cell epitopes per vaccine recipient recognised across CM and DDDCM regimens. In vitro HIV-1 control mediated by CD8⁺ T cells was demonstrated for all vaccinees receiving the CM regimen, mainly against clade A (U455) and clade B (IIIB) isolates. Two vaccinees, demonstrated superior control of 6/8 and 7/8 viruses from the panel. The CM regimen induced significantly higher magnitudes of viral inhibition compared to the DDDCM or DDDMC regimens, with this regimen showing potential to overcome the disadvantage for subjects of carrying non-protective HLA alleles. Investigation of T-cell specificities revealed that the frequencies of T cells specific for conserved Gag but more so Pol regions significantly correlated with in vitro virus control. Direct examination of peptide expanded T-cell lines showed that all Pol pool- and limited Gag pool-specific cell lines reduced HIV-1 replication in vitro. In most individuals, targeting multiple HIV-1 epitopes concomitantly resulted in higher levels of virus inhibition than targeting a single viral epitope and two T-cell specificities showed enhanced control of HIV-1; the first within Pol (TAFTIPSI) and second from Gag (TERQANFL). These data support further development of the conserved region strategy for T-cell vaccines against HIV-1.

Thesis advisor: Jeffrey H. Chuang / Gene regulation is perhaps least understood among vertebrate species, where cell differentiation, tissue-types and body-plans indicate a complexity in need of careful coordination to achieve such hierarchical design. Recent studies reveal the intricacy of vertebrate gene regulation through diverse events including transcriptional regulatory histone modifications and non-coding DNA [1-5]. Almost 98% of the human genome is noncoding DNA, much of which may be actively involved in regulating healthy and disease-state gene expression and environmental response [6]. Conserved noncoding elements (CNEs) are sequences of noncoding DNA that are known to regulate gene expression [7-9]. The CNEs identified thus far are a small percentage of the total noncoding DNA in the human genome, and many identified CNEs still lack experimental characterization [10]. Thus, there is a need for functional characterization and streamlined identification of CNEs in order to more fully annotate vertebrate genomes and understand gene expression. The work in this thesis identified over 6000 CNEs and experimentally characterized over 150 CNEs conserved between zebrafish and human (> 60% DNA sequence conservation), using the experimental model Danio rerio (zebrafish). Functional, tissue and time-specific CNEs were identified through analysis of conservation, accelerated evolution, distance, GC content, motifs, transcription factors and gene function. In addition, a searchable database and website was created to host data and facilitate collaborative research between experimental and computational labs. While non-coding DNA is an important area of discovery for gene regulation, protein-coding DNA also has the potential to contain non-coding transcriptional information. DNA is typically conceptualized as either noncoding or protein coding. An underlying assumption to this framework assumes that the function of noncoding DNA is "regulatory" and coding DNA is "protein coding." Consequently, the potential for DNA to harbor both types of information in one sequence has been minimally researched. For the second-half of this thesis, I identified and experimentally tested 31 conserved coding exons ( > 60% zebrafish and human DNA sequence conservation) in zebrafish. To improve annotation of live embryonic expression, a novel voice-recognition expression analysis system was developed that allows quick comparison and annotation of embryonic expression at the microscope. In addition, a website and webtool to calculate significant expression was created as a resource for experimental research on anatomical analysis in whole organisms. The experimental results show that a large number of protein-coding DNA sequences can act as non-coding enhancers. This knowledge may impact methods to identify noncoding signals and, further, the scientific conceptualizations of coding and noncoding DNA in the genome. / Thesis (PhD) — Boston College, 2011. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Biology.

Short Pulse equation derived by Schafer and Wayne is a nonlinear partial differential equation that describes ultra short laser propagation in a dispersive optical medium such as optical fibers. Some properties of this equation e.g. traveling wave solution and its soliton structure and some of its conserved quantities were investigated. Conserved quantities were obtained by mass conservation law, lax pair method and transformation between Sine-Gordon and short pulse equation. As a result, loop soliton characteristic and six conserved quantities were found.

In this thesis, conformal transformations in d and two dimensions and the results of conformal symmetry in classical and quantum field theories are reviewed. After investigating the conformal group and its algebra, various aspects of conformal invariance in field theories, like conserved charges, correlation functions and the Ward identities are discussed. The central charge and the Virasoro algebra are briefly touched upon.

An investigation into structures of bi-integrable and tri-integrable couplings is undertaken. Our study is based on semi-direct sums of matrix Lie algebras. By introducing new classes of matrix loop Lie algebras, we form new Lax pairs and generate several new bi-integrable and tri-integrable couplings of soliton hierarchies through zero curvature equations. Moreover, we discuss properties of the resulting bi-integrable couplings, including infinitely many commuting symmetries and conserved densities. Their Hamiltonian structures are furnished by applying the variational identities associated with the presented matrix loop Lie algebras. The goal of this dissertation is to demonstrate the efficiency of our approach and discover rich structures of bi-integrable and tri-integrable couplings by manipulating matrix Lie algebras.

Submitted by KARLA NASCIMENTO SENA null (karlla_senna@hotmail.com) on 2016-04-29T02:25:07Z No. of bitstreams: 1 mestrado fim.pdf: 2662913 bytes, checksum: 021b82295d8e222cce56cc6707c2651b (MD5) / Approved for entry into archive by Felipe Augusto Arakaki (arakaki@reitoria.unesp.br) on 2016-05-02T13:48:45Z (GMT) No. of bitstreams: 1 sena_kn_me_ilha.pdf: 2662913 bytes, checksum: 021b82295d8e222cce56cc6707c2651b (MD5) / Made available in DSpace on 2016-05-02T13:48:45Z (GMT). No. of bitstreams: 1 sena_kn_me_ilha.pdf: 2662913 bytes, checksum: 021b82295d8e222cce56cc6707c2651b (MD5) Previous issue date: 2016-03-03 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / O solo é considerado, na atualidade, o mais importante reservatório e o mais eficiente estabilizador de carbono orgânico. Por outro lado, a agricultura é considerada a segunda maior emissora de carbono, atrás apenas da emissão gerada por combustíveis fósseis. O carbono orgânico (CO) introduzido nos solos, em sua maior parte via matéria orgânica, tem papel relevante em vários atributos e destacada importância ainda mais em solos arenosos. Dentro deste contexto, o objetivo deste trabalho foi verificar as alterações nos teores e no estoque de CO, a influência deste carbono sobre atributos físicos, químicos e microbiológicos do solo, em áreas de conversão pastagem-eucalipto, de reflorestamento com eucalipto e de cerrado conservado, na região leste do Estado de Mato Grosso do Sul. As coletas de solo foram realizadas nos meses de agosto e setembro de 2014, em campo, nas camadas de 0,0-0,05, 0,05-0,10 e 0,10-0,30 m. Em função do objetivo proposto foram realizadas análises de fertilidade do solo (P, MO, pH, K, Ca, Mg, H+Al, Al, S, B, Cu, Fe, Mn, e Zn), carbono orgânico total e o cálculo do Estoque de Carbono (EstC). Avaliaram-se também os atributos estabilidade de agregados, densidade (Ds), macro e microporosidade, porosidade total (PT), velocidade de infiltração da água no solo, infiltração acumulada de água, resistência mecânica do solo à penetração (RP), carbono da biomassa microbiana (CBM), respiração basal (C-CO2) e quociente metabólico (qCO2) do solo. O delineamento experimental utilizado foi em blocos inteiramente casualizados, composto por 4 blocos, com 9 repetições por bloco, totalizando 36 pontos amostrais por sistema de manejo a ser avaliado. Neste caso foram comparadas, uma área de pastagem degradada (PAST), uma área de conversão pastagem degradada-eucalipto, ocorrida há 2 anos (EU2), uma área de conversão pastagem degradada-reflorestamento com eucalipto (EU15), e uma área sob cerrado conservado (CC), considerada como controle. Ao final observou-se que a conversão do CC em áreas de cultivo comercial acelera o processo de perda do CO e da qualidade física do solo, sendo a pastagem responsável pela maior degradação do solo, apresentando resistência do solo à penetração, em nivel de restrição ao desenvolvimento da vegetação. Nestes solos, por sua textura arenosa, a análise da estabilidade de agregados necessita ser acompanhada de uma avaliação morfológica, pois este tipo de solo pode apresentar grãos de areia isolados com tamanho de macroagregados. Após 15 anos de introdução do eucalipto em área de pastagem, observam-se sinais de recuperação de alguns atributos físicos do solo, como redução na densidade e aumento na porosidade, o que não ocorre para PAST e EU2. O CC apresenta maiores conteúdos de MO, com diferenças significativas em relação aos Sistemas de Manejo (SM) em avaliação, apenas na profundidade de 0,00-0,05m, reforçando a importância da deposição de material vegetal à superfície. O comportamento da fertilidade do solo, entre os sistemas de manejo e CC, foi semelhante quanto ao teor de MO, com redução do teor de nutriente em profundidade, apontando a relação da matéria orgânica com a fertilidade e sua importância em suprir o solo, mostrando que a textura arenosa apresenta reduzida capacidade para retenção de cátions, consequentemente apresenta alto potencial de lixiviação. O estoque de carbono, também, diminui em profundidade em todos sistemas avaliados. No entanto, o CO na profundidade 0,10 a 0,30 m não apresentou influência do uso imputado ao solo, sinalizando desta forma a possibilidade de sua permanência no solo por maiores períodos. Os sistemas de uso do solo avaliados reduziram o CO e o EctC, indicando degradação do solo quando comparado ao CC. O CBM, C-CO2 liberado e qCO2 foram influenciados pelos sistemas de manejo. A liberação de C-CO2, decorrente da atividade microbiana do solo indica o CC e PAST como os SM de melhor desempenho, comprovando a influência da cobertura vegetal, do sistema radicular e da adição de dejetos bovinos sobre a atividade dos microrganismos. O estudo sugere que a integração silvopastoril seja adotada nestas areas de baixa fertilidade para preservar a qualidade dos solos. / The soil is, in nowadays, considered the most important carbon pool and effective carbon stabilizer. On the other hand, the agriculture is considered the second largest carbon emitting, after fossil fuels. This organic carbon (CO) introduced into the soil, mainly via organic matter, has an important role in soil formation and properties, besides detached importance for sandy soil. This study aimed to verify changes in the organic carbon, amounts and storage, the influence of this on some soil physical properties, on areas of conversion pasture-eucalyptus (EU2), pasture-eucalyptus reforestation (EU15) compared to pasture (PAST) and natural vegetation (CC), in the Mato Grosso do Sul State, eastern region. The soil was sampled with four replications, in the depths of 0.0-0.05, 0.05-0.10 and 0.10 - 0.30 m. Due to the proposed objective it was carried out soil fertility analysis ( P, MO, pH, K, Ca, Mg, H+Al, Al, S, B, Cu, Fe, Mn and Zn), total organic carbon, made if the calculation of carbon stock (EstC), it was determined aggregate stability, bulk density (BD), macro and microporosity, total porosity (TP), water infiltration rate in the soil, accumulated water infiltration , mechanical resistance soil penetration (RP) , microbial biomass carbon (MBC), basal respiration (C-CO2) and metabolic quotient (qCO2). The experimental design was a randomized block consisting of 4 blocks, with nine replicates per block, totaling 36 sampling points per management system to be assessed in this case a degraded pasture area (PAST), a grassland conversion of degraded area - eucalipto, which occurred two years before (EU2), a degraded pasture conversion, reforestation area with eucalyptus (EU15), and an area under kept closed (CC) considered as control. At the end it was found that the conversion of DC in commercial farming areas accelerates CO loss process and the physical quality of the soil, with the pasture responsible for the higher degradation, because it presents the soil resistance behavior of the penetration, for example, restrictions on the development of vegetation. These soils, in sandy texture, analysis of aggregate stability needs to be accompanied by a morphological evaluation, as this type of soil can provide sand grains isolated with macroaggregates size. After 15 years of introduction of eucalyptus in pasture area, they observe signs of recovery of some soil physical properties, such as reduction in density and increased porosity, which does not occur to PAST and EU2. The CC had higher OM content, with significant differences from Management Systems (MS) evaluation, only the depth of 0,00-0,05m , reinforcing the importance of the deposition of plant material on the surface . The soil fertility behavior among management systems and the CC, was similar to the OM, with a reduction in depth, confirming the relationship of organic matter with fertility, its importance in supplying the soil and showed that the sandy texture, in fact, has reduced capacity for cation retention, consequently has a high potential for leaching. The carbon stock, as expected, decreased in depth in all systems studied. However CO found in depth from 0,10 to 0,30 m did not influence attributed to the use soil, thereby indicating the possibility of residence of the soil for longer periods of time, into the carbon sequestration field is indeed this period extend for tens or hundreds of years. The land use systems have reduced both the CO and the EctC indicating soil degradation when compared to CC. The CBM, released C-CO2 and qCO2 were influenced by SM. The release of C- CO2, due to the soil microbial activity points to the CC and PAST treatments as better performance of them, proving that management systems, vegetation cover, root system and cattle manure has influenced the activity of microorganisms.

Orientador: Kátia Luciene Maltoni / Resumo: O solo é considerado, na atualidade, o mais importante reservatório e o mais eficiente estabilizador de carbono orgânico. Por outro lado, a agricultura é considerada a segunda maior emissora de carbono, atrás apenas da emissão gerada por combustíveis fósseis. O carbono orgânico (CO) introduzido nos solos, em sua maior parte via matéria orgânica, tem papel relevante em vários atributos e destacada importância ainda mais em solos arenosos. Dentro deste contexto, o objetivo deste trabalho foi verificar as alterações nos teores e no estoque de CO, a influência deste carbono sobre atributos físicos, químicos e microbiológicos do solo, em áreas de conversão pastagem-eucalipto, de reflorestamento com eucalipto e de cerrado conservado, na região leste do Estado de Mato Grosso do Sul. As coletas de solo foram realizadas nos meses de agosto e setembro de 2014, em campo, nas camadas de 0,0-0,05, 0,05-0,10 e 0,10-0,30 m. Em função do objetivo proposto foram realizadas análises de fertilidade do solo (P, MO, pH, K, Ca, Mg, H+Al, Al, S, B, Cu, Fe, Mn, e Zn), carbono orgânico total e o cálculo do Estoque de Carbono (EstC). Avaliaram-se também os atributos estabilidade de agregados, densidade (Ds), macro e microporosidade, porosidade total (PT), velocidade de infiltração da água no solo, infiltração acumulada de água, resistência mecânica do solo à penetração (RP), carbono da biomassa microbiana (CBM), respiração basal (C-CO2) e quociente metabólico (qCO2) do solo. O delineamento experimenta... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The soil is, in nowadays, considered the most important carbon pool and effective carbon stabilizer. On the other hand, the agriculture is considered the second largest carbon emitting, after fossil fuels. This organic carbon (CO) introduced into the soil, mainly via organic matter, has an important role in soil formation and properties, besides detached importance for sandy soil. This study aimed to verify changes in the organic carbon, amounts and storage, the influence of this on some soil physical properties, on areas of conversion pasture-eucalyptus (EU2), pasture-eucalyptus reforestation (EU15) compared to pasture (PAST) and natural vegetation (CC), in the Mato Grosso do Sul State, eastern region. The soil was sampled with four replications, in the depths of 0.0-0.05, 0.05-0.10 and 0.10 - 0.30 m. Due to the proposed objective it was carried out soil fertility analysis ( P, MO, pH, K, Ca, Mg, H+Al, Al, S, B, Cu, Fe, Mn and Zn), total organic carbon, made if the calculation of carbon stock (EstC), it was determined aggregate stability, bulk density (BD), macro and microporosity, total porosity (TP), water infiltration rate in the soil, accumulated water infiltration , mechanical resistance soil penetration (RP) , microbial biomass carbon (MBC), basal respiration (C-CO2) and metabolic quotient (qCO2). The experimental design was a randomized block consisting of 4 blocks, with nine replicates per block, totaling 36 sampling points per management system to be assessed in thi... (Complete abstract click electronic access below) / Mestre

Inclusion of Indigenous communities and Traditional Ecological Knowledges (TEK) alongside reconciliation efforts feature in numerous plans and policies for nature and biodiversity conservation. But to what extent do these agreements present an honest attempt to equally share power and responsibility between Indigenous peoples and governance agencies in protected area management? In this thesis, I trace how including Indigenous communities and their TEK entered Canada’s policy discourse on nature conservation. I focus on the designation of Indigenous Protected and Conserved Areas (IPCAs), which presents Canada’s latest approach towards including Indigenous peoples in protected area management. Through a study of policy documents, I compare changes in Canadian governance agencies’ proposal of and motivations behind Indigenous peoples’ inclusion with insights from Indigenous communities’ documents related to Edéhzíe Protected Area and Thaidene Nëné Indigenous Protected Area. These documents offer insights into Indigenous stewardship practices, emphasize Indigenous self-governance as well as the role of TEK, Western science, and Indigenous languages in IPCA management. Although I conclude that Edéhzíe Protected Area and Thaidene Nëné Indigenous Protected Area present an honest attempt to equally share power and responsibility in IPCA management, I call on governance agencies to further centre Indigenous peoples’ ideas on stewarding biodiversity-rich places, grant rights to self-determination and self-governance, and restore justice.

No description available.

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第18831号 / 理博第4089号 / 新制||理||1588(附属図書館) / 31782 / 京都大学大学院理学研究科生物科学専攻 / (主査)教授 阿形 清和, 教授 緒方 博之, 教授 高田 彰二 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DFAM