Made available in DSpace on 2015-09-25T12:21:26Z (GMT). No. of bitstreams: 1 PDF - Vandre Guevara Lyra Batista.pdf: 915279 bytes, checksum: db4c1c0fb945a68ca720e9082f021bfc (MD5) Previous issue date: 2012-08-22 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / The use of public database, generated from genome projects, such as NCBI, CottonDB, SUCEST FORESTs, among others, is of great importance for molecular studies, especially those related to gene expression, since, in possession of sequences deposited, it is possible to isolate new genes or prospect and know their role in various ontogenetic stages. In plants, a stage of great demand for knowledge is related to reproduction. Currently, several studies with Arabidopsis thaliana involving identification and characterization of genes associated with reproductive organs, especially the bud phenology, has enabled major advances in our understanding of functions and can correlate them with other species. For plant species possessing large commodities such as cotton, these results are relevant, considering that several studies developed with this aim culture studies that enhance the expression quantitative trait dependent physiology of reproduction. In this study, we investigated the temporal and spatial expression of genes that are expressed in cotton bud by semiquantitative RT-PCR and qPCR. We selected four genes with a history of expression in floral buds (cottonbud7, cottonbud8, and cottonbud9 cottonbud10) and used for primer design. Tissue samples of flower buds (2-8 mm, 10-12 mm and 14-20 mm), leaves, stems and roots were collected and used for total RNA extraction and cDNA synthesis. The results of gene expression analyzes showed expression of selected genes in all tissues investigated, though genes cottonbud7 cottonbud10 and showed a stable expression in all phases investigated bud. It was observed further that the cottonbud10 showed a slightly higher expression in floral bud, when compared to other genes. The analysis of gene expression via cottonbud10 qPCR corroborate the results obtained with the RT-PCR. The results obtained in this study provide information about genes to promising research projects involving the improvement program for cotton. / A utilização de banco de dados públicos, gerados a partir de projetos genoma, como o NCBI, CottonDB, SUCEST, FORESTs, entre outros, é de grande relevância para estudos moleculares, especialmente aos relacionados a expressão gênica, uma vez que, de posse das sequências depositadas, é possível prospectar ou isolar novos genes e conhecer sua função em várias fases ontogenéticas. Em plantas, uma das fases de grande demanda de conhecimento é a relacionada com a reprodução. Atualmente, vários estudos com Arabidopsis thaliana envolvendo identificação e caracterização de genes associados aos órgãos reprodutores, especialmente a fenologia do botão floral, tem possibilitado grandes avanços no conhecimento de funções, podendo correlacioná-las em outras espécies. Para espécies vegetais detentoras de grandes commodities, como algodão, tais resultados são relevantes, considerando que várias pesquisas desenvolvidas com essa cultura visam estudos que potencializem a expressão de características quantitativas dependentes da fisiologia de reprodução. Neste trabalho, investigou-se a expressão temporal e espacial de genes que se expressam em botão floral de algodoeiro por meio de RTPCR semiquantitativa e qPCR. Foram selecionados quatro genes com histórico prévio de expressão em botão floral (cottonbud7, cottonbud8, cottonbud9 e cottonbud10) e utilizados para desenho de primers. Amostras de tecidos de botões florais (2-8 mm; 10-12 mm e 14-20 mm), folhas, hastes e raízes foram coletadas e utilizadas para a extração de RNA total e síntese de cDNA. Os resultados das análises de expressão gênica mostraram expressão dos genes selecionados em todos os tecidos investigados, contudo os genes cottonbud7 e cottonbud10 apresentaram estabilidade da expressão em todas as fases investigadas do botão floral. Pôde-se observar ainda, que o cottonbud10 apresentou nível de expressão levemente superior em botão floral, quando comparado aos demais genes. As análises de expressão do gene cottonbud10 via qPCR corroboram com os resultados obtidos com o RT-PCR. Os resultados obtidos neste trabalho, fornecem informações sobre genes promissores para trabalhos de pesquisa envolvendo o programa de melhoramento do algodão.

This study focused on isolating important wood decay fungi from two field sites located in Harrison County, MS, and Oktibbeha County, MS. Southern Yellow Pine samples of various types and treatments including: Cu8, CuOm, ACQ, PCP, proprietary organic biocide, and un-treated were collected, and fungal isolates were cultured. DNA was extracted from isolated fungal cultures and amplified by polymerase chain reaction (PCR). The internal transcribe spacer (ITS) region was sequenced, and fungal cultures were identified by comparison to sequences on GenBank using BLAST. A total of 68 fungal isolates were recovered and successfully identified from 196 samples. Thirteen basidiomycete isolates were identified, with Veluticeps fimbriata occurring most frequently. The white-rot ascomycete, Daldinia fissa was also common. Two sequence-specific oligonucleotide probes (SSOP) were designed using Lasergene® PrimerSelect software. Unsuccessful attempts were made to attach poly (dT) tails to the probes in order to cross link the probes to nylon membranes.

This study reports on the use of the Didactic Unit (DU): Exploring the GenBank with high school students, which involved 20 school hours with a group of 06 volunteer students from the 2nd year of high school at the Military School of Santa Maria - CMSM/RS, during the 2nd semester of 2009. The aforementioned Didactic Unit was developed in the afternoon, whereas the regular school classes took place in the morning period. The DU was structured according to the Three Pedagogic Moments (3PM) proposed by Delizoicov and Angotti (1994), that is: Initial Problematization (IP), Knowledge Organization (KO) and Knowledge Application (KA). The DU included theoretical and practical classes on proteins and protein synthesis and monitored access to the NCBI (National Center Biotechnology Information), using the links OMIM and Entrez Gene. The aim of this DU was to identify whether students achieved better understanding of the relation DNA-RNAprotein, using the NCBI tools aforementioned. In order to evaluate the students performance, conceptual maps based on the score table proposed by Novak and Gowin (1996) were used, as well as individual interviews and analysis of the tests given to the students. The reference conceptual map had 52 points; two students scored 41 and one student scored 26 points, respectively. In the quantitative and the qualitative analyses, it was possible to identify a significant improvement in the conceptual relations of these students about the protein synthesis. The data suggests that the access to the GenBank, which was used as a didactic strategy in the Unit, afforded this improvement. In the students interviews, difficulties concerning the fluency in English were mentioned, which were overcome by using online translators, associated to the English classes that the students have in the Military School. Also, students evaluated positively the opportunity for learning to use new technologies. In the post-test, it was verified an improvement in the scores related to protein and protein synthesis. Finally, it can be inferred that for the small group of students who participated in this study, the experience was of a great value. / Este estudo relata a aplicação da Unidade Didática (UD): Explorando o GenBank com alunos do ensino médio, a qual envolveu 20 horas/aula com um grupo de 06 alunos voluntários do 2º ano do ensino médio do Colégio Militar de Santa Maria - CMSM/RS, durante o 2º semestre de 2009. A referida UD foi desenvolvida no contraturno das atividades escolares dos alunos envolvidos na pesquisa. A UD foi estruturada segundo os Três Momentos Pedagógicos propostos por Delizoicov e Angotti (1994), a saber: Problematização Inicial (PI), Organização do Conhecimento (OC) e Aplicação do conhecimento (AC). A UD constava de aulas teóricas e práticas sobre proteínas e síntese de proteínas e acesso orientado ao NCBI (National Center Biotechnology Information), utilizando os links OMIM e Entrez Gene. A finalidade desta UD era identificar se os alunos compreendiam melhor a relação DNA-RNA-proteína, utilizando as ferramentas do NCBI já citadas anteriormente. Para avaliar esse entendimento dos alunos utilizamos mapas conceituais baseados na tabela de pontuação proposta por Novak e Gowin (1996), assim como entrevistas individuais e análise de testes aplicados aos mesmos. O mapa conceitual de referência tinha 52 pontos; 02 alunos obtiveram 41 e um aluno 26 pontos. Na análise quantitativa e na qualitativa foi possível identificar um avanço significativo nas relações conceituais desses alunos sobre síntese de proteínas. Os dados sugerem que o acesso ao GenBank, utilizado como estratégia didática dentro da UD, possibilitou este avanço. Identificam-se nas entrevistas com os alunos, dificuldades em relação ao domínio da língua inglesa, que foram superadas com o uso dos tradutores online aliado às aulas proporcionadas pelo colégio. Ainda, avaliaram positivamente a possibilidade de conhecerem novas tecnologias. Nos pósteste foi evidenciado um progresso nos escores de acertos sobre os assuntos proteínas e síntese de proteínas. Finalmente, pode-se inferir que, para este pequeno grupo que vivenciou esta experiência, a mesma se revestiu de significado.

The Human Papillomavirus (HPV) is a virus of the Papillomaviridae family and its genome consists of DNA. It is the main cause of viral sexual transmission. Cervical cancer or uterine colon cancer is the second most common occurrence among women worldwide. Recent studies have proven that some types of HPV are mainly responsible for the development of this type of cancer. In accordance to its oncogenic activity this viral group was divided in low and high risk types. Brazil does not have a representative amount of data related to the prevalence of HPV infection. The incidence data of the virus is obtained through the analysis of carriers of the invasive carcinoma of uterine colon, cervical intraepithelial neoplasias, and others types of infections associated. Molecular assays have been showing throughout the years an excellent sensitivity and specificity in the detection of the HPV s DNA. Nowadays, in situ hybridization techniques are being used as method of choice for the detection of the viral DNA. In many studies, the Polymerase Chain Reaction (PCR) with the application of the primers MY09 and MY11 have shown efficiency in viral tracking, consequently, the development of molecular diagnostics allow monitoring of the disease, decreasing mortality rates caused by cancer of the cervix. The DNA sequencing is an efficient methodology used for the molecular characterization of the viral types, which allows the accomplishment of the alignment for similarity of the sequences obtained through others that were already identified and deposited in the GenBank. The current study s purpose was to identify the different types of HPV and the presence of co-infections through PCR and sequencing of a hyper-variable region of the L1 gene. The studied sample consisted of 515 female volunteers, which 111 (21.55%) presented the incidence of the HPV DNA. Within the acquired specimens, 50% were considered high oncogenic risk (the major incidence was types 16 and 58) and 7.21% had multiple infection. The determination of the base sequencing of the L1 gene is essential to the identification of the viral type. However, the sequencing of the complete gene and both DNA chains become financially unviable for the majority of the specialized laboratories. A practical approach applied in this study was to determine the sequencing of a specific region of the L1 gene with 450pb, where the identification of the HPV became possible by following this methodology. The techniques used showed the necessity of the application of a more sensible and specific viral diagnosis, which contributes to the viral infection control and to the reduction of the mortality rate caused by cervical cancer. / Fundação de Amparo a Pesquisa do Estado de Alagoas / O Papilomavírus Humano (HPV) é um vírus da família Papillomaviridae e possui o seu genoma constituído de DNA. É o causador da transmissão sexual viral de maior frequência. O câncer cervical ou câncer de colo de útero possui a segunda maior ocorrência nas mulheres de todo o mundo. Estudos recentes têm comprovado que alguns tipos de HPV são os principais responsáveis pelo desenvolvimento deste tipo de câncer. De acordo com a sua atividade na carninogênese esse grupo viral foi dividido em tipos de baixo e de alto risco oncogênico. O Brasil ainda não possui uma quantidade representativa de dados relacionados à prevalência de infecção por HPV, os dados de incidência do vírus são obtidos através da análise de portadores de carcinoma invasivo de colo uterino, neoplasias intraepiteliais cervicais e outros tipos de infecções associadas. Ensaios moleculares vêm mostrando ao longo dos anos uma alta sensibilidade e especificidade na detecção do DNA do HPV. Atualmente são utilizadas técnicas de hibridização como método de escolha para a detecção do DNA viral. Em muitos estudos a Reação em Cadeia da Polimerase (PCR) com a aplicação dos primers MY09 e MY11 demonstrou eficiência no rastreamento viral, consequentemente, o desenvolvimento desse diagnóstico molecular possibilitaria o monitoramento da doença, diminuindo as taxas de mortalidade causada pelo câncer de colo do útero. O sequenciamento de DNA é uma metodologia eficiente para a caracterização molecular dos tipos virais, permitindo a realização do alinhamento por similaridade das sequencias obtidas com outras já identificadas e depositadas no GenBank. O presente trabalho teve como propósito identificar os diferentes tipos de HPV e a presença de co-infecções, através de PCR e sequenciamento de uma região hipervariável do gene L1. A amostra estudada foi composta de 515 voluntárias das quais 111 (21,55%) apresentaram a presença do DNA do HPV. Entre os espécimes encontrados 50% são considerados de alto risco oncogênico (maior incidência dos tipos 16 e 58) e 7,21% possuíam infecção múltipla. A determinação das sequencias de base do gene L1 é fundamental para a identificação do tipo viral. Entretanto o sequenciamento do gene completo e em ambos os sentidos da cadeia de DNA se tornam inviáveis financeiramente para a maioria dos laboratórios especializados. Uma abordagem prática aplicada no estudo foi determinar a sequencia de uma região específica do gene L1 contendo 450pb, sendo possível a identificação do HPV seguindo essa metodologia. As técnicas utilizadas mostraram a necessidade da aplicação de um diagnóstico viral mais sensível e específico, contribuindo para o controle da infecção viral e para a diminuição da incidência e da mortalidade causadas pelo câncer cervical.

abstract: Accounting for over a third of all emerging and re-emerging infections, viruses represent a major public health threat, which researchers and epidemiologists across the world have been attempting to contain for decades. Recently, genomics-based surveillance of viruses through methods such as virus phylogeography has grown into a popular tool for infectious disease monitoring. When conducting such surveillance studies, researchers need to manually retrieve geographic metadata denoting the location of infected host (LOIH) of viruses from public sequence databases such as GenBank and any publication related to their study. The large volume of semi-structured and unstructured information that must be reviewed for this task, along with the ambiguity of geographic locations, make it especially challenging. Prior work has demonstrated that the majority of GenBank records lack sufficient geographic granularity concerning the LOIH of viruses. As a result, reviewing full-text publications is often necessary for conducting in-depth analysis of virus migration, which can be a very time-consuming process. Moreover, integrating geographic metadata pertaining to the LOIH of viruses from different sources, including different fields in GenBank records as well as full-text publications, and normalizing the integrated metadata to unique identifiers for subsequent analysis, are also challenging tasks, often requiring expert domain knowledge. Therefore, automated information extraction (IE) methods could help significantly accelerate this process, positively impacting public health research. However, very few research studies have attempted the use of IE methods in this domain. This work explores the use of novel knowledge-driven geographic IE heuristics for extracting, integrating, and normalizing the LOIH of viruses based on information available in GenBank and related publications; when evaluated on manually annotated test sets, the methods were found to have a high accuracy and shown to be adequate for addressing this challenging problem. It also presents GeoBoost, a pioneering software system for georeferencing GenBank records, as well as a large-scale database containing over two million virus GenBank records georeferenced using the algorithms introduced here. The methods, database and software developed here could help support diverse public health domains focusing on sequence-informed virus surveillance, thereby enhancing existing platforms for controlling and containing disease outbreaks. / Dissertation/Thesis / Doctoral Dissertation Biomedical Informatics 2019

Landwirtschaftliche Systeme müssen sich immerfort an Druckfaktoren wie Klimawandel und Bevölkerungswachstum anpassen. Hierbei spielt die genetische Vielfalt von Pflanzen eine wichtige Rolle, da diese für die Sicherung der Ernährung und des Einkommens von entscheidender Bedeutung ist. Dennoch wird der wirtschaftliche Wert pflanzengenetischer Ressourcen selten untersucht. Um diese Forschungslücke zu schließen, werden in dieser Arbeit drei Bewertungen vorgestellt, welche die wirtschaftlichen Werte pflanzengenetischer Ressourcen untersuchen. Im Rahmen dieser Dissertation werden zwei verschiedene Agrarsystemen analysiert. Diese unterscheiden sich hinsichtlich des Klimas, der agrarökologischen Bedingungen, der landwirtschaftlichen Praxis, der politischen und ökonomischen Rahmenbedingungen sowie der soziokulturellen Verankerung der Kulturart. Die ersten beiden Analysen befassen sich mit der Züchtung und Produktion von Winterweizen in Deutschland. Charakterisiert sind diese durch ein gemäßigtes Klima und intensive Anbaubedingungen. In diesem System überwiegen moderne Sorten, die in einem formalisierten Züchtungsprozess entstanden sind. Es werden die folgenden Forschungsfragen beantwortet: 1) Was ist der ökonomische Wert, der durch den Austausch von Zuchtmaterial entsteht? und 2) Wie hoch ist der mikroökonomische Wert von Resistenzzüchtung? In der dritten Analyse wird ein weiteres Agrarsystem vorgestellt: Die Andenlandwirtschaft, wo im Hochland unter extensiven Bedingungen eine Vielzahl von Kartoffellandrassen angebaut wird. Dort wird folgende Frage analysiert: 3) Welche Mehrwerte wurden durch die Repatriierung oder Neuverteilung von Kartoffellandrassen erzielt? Diese Analysen zeigen, dass die Verfügbarkeit, der Austausch und die Nutzung von pflanzengenetischen Ressourcen die Agrarproduktion verbessern; es entstehen sowohl sektorale, mikroökonomische als auch ernährungsbezogene und kulturelle Mehrwerte. / Agricultural systems must constantly adapt to pressuring events such as climate change and population growth to maintain and improve production processes in a sustainable manner. Thereby the genetic diversity of plants used in agriculture constitute a strategic asset. Nevertheless, their economic value is often overlooked. To fill this research gap, this thesis presents three assessments that produce more evidence on the economic value of plant genetic resources. Two very distinct agricultural systems are discussed. These differ greatly in terms of climate, agroecological conditions, farming practices, seed systems, political and economic frameworks, and the socio-cultural embeddedness of the crop in question. The first two assessments are concerned with winter wheat (Triticum aestivum) breeding and production in the temperate climate and intensive growing conditions in Germany. Modern cultivars created in a formalized breeding process prevail in this system. The following two research questions are elaborated: 1) What is the economic value of exchanging breeding material? and 2) What is the microeconomic value of resistance breeding? The third assessment presents a different agricultural system: Andean agriculture, where a wide variety of potato landraces (Solanum spp.) are grown extensively in the Peruvian highlands. In this case, the research question I investigated is: 3) What are the benefits of repatriating (i.e., redistributing) potato landraces to Andean farmers? These studies demonstrate that the availability, exchange, and adoption of plant genetic resources, which are well adapted to and culturally embedded in specific agricultural systems, improve the overall quantity and sustainability of agricultural production. These improvements can be translated into sectoral, microeconomic as well as nutritional and cultural benefits.