Análise da pureza genética e discriminação de cultivares de vinca (Catharanthus roseus (L.) G.Don) usando "random amplified polymorphic DNA" em DNA extraído de sementes e folhas

A técnica "Random Amplified Polymorphic DNA" (RAPD) surgiu como uma ferramenta útil para testar a pureza genética e a discriminação de cultivares em muitas espécies. É uma técnica simples, rápida, relativamente de baixo custo e permite o uso de DNA extraído de sementes secas, o que é muito importante em um programa de análise de sementes. O uso desta tecnologia no teste da pureza genética pode ser muito interessante para algumas espécies, como a vinca (Catharanthus roseus (L.) G.Don), pois pouco se conhece a respeito da seqüência de seu DNA. É interessante, também, pelo fato de existir grande número de "primers" comercialmente disponíveis, que podem ser prontamente utilizados para gerar dados. Essa técnica pode ser mais facilmente utilizada para gerar padrões de bandas polimórficas suficientes para discriminar genótipos diferentes. Todavia, no presente estudo, os padrões RAPD de bandas obtidas de amostras de DNA extraído de sementes de vinca em "bulk" foram não-consistentes, o mesmo ocorrendo com o uso de DNA extraído de sementes individuais de um mesmo cultivar, o que evidencia que a técnica não é aplicável para testar a pureza genética e a discriminação de cultivares de vinca. Entretanto, os padrões de bandas RAPD gerados a partir de DNA extraído de tecido foliar de plântulas foram mais reproduzíveis e poderiam ser considerados na caracterização de cultivares.

Rekombinanttitekniikalla tuotettujen vasta-aineiden käyttö immunodiagnostiikassa ; rekombinantti-DNA-tekniikalla tuotetun Fab-fragmentin käyttö sydänperäisen troponiini I:n immunomäärityksessä

Rekombinanttivasta-aineet ovat synteettisesti valmistettuja vasta-aineita, jolloin niiden tuottamiseen ei tarvita eläintä. Rekombinantti-DNA-tekniikalla pystytään valmistamaan eri vasta-aineluokkia tai pelkästään niiden fragmentteja lähes mitä tahansa antigeeniä vastaan. Vasta-aineita voidaan etsiä eri antigeenejä vastaan ilmentämällä niitä esimerkiksi bakteriofagien tai solujen pinnalla, ja niiden sitomiskykyä kohteeseensa voidaan parantaa erilaisten mutaatioiden avulla. Rekombinanttivasta-aineita voidaan hyödyntää laajasti erilaisissa immunodiagnostisissa menetelmissä lääketieteessä, ympäristö- sekä elintarviketutkimuksissa. Tänä päivänä rekombinanttivasta-aineita käytetään myös terapiahoidossa. Immunomääritysten ongelmana voivat olla erilaiset häiriötekijät, jotka saattavat aiheuttaa väärän positiivisen tai negatiivisen tuloksen. Rekombinanttivasta-aineilla, erityisesti vasta-ainefragmenteilla voidaan vähentää määritysten häiriötä ja parantaa tulosten luotettavuutta. Rekombinanttivasta-aineiden hyötyjä ovat myös niiden nopea tuottaminen, helppo muokkaaminen sekä monipuolisuus erilaisia antigeenejä vastaan. Tutkimuksen kokeellisen työn tarkoitus oli kehittää uudelle rekombinantti-DNA-teknii-kalla tuotetulle osittain humanisoidulle Fab-fragmentille troponiini I -immunomääritys. Sydänperäinen troponiini I on sydäninfarktille spesifinen merkkiaine, jota voidaan mitata verestä. Työssä käytettävässä immunomäärityksessä sitojavasta-aineina käytettiin kahta biotinyloitua vasta-ainetta, joista toinen oli hiiren monoklonaalinen vasta-aine ja toinen oli kimeerinen Fab-fragmentti. Määrityksen leimana käytettiin uutta Fab-fragmenttia, joka kiinnitettiin kovalenttisesti europiumkelaatteja sisältävään nanopartikkeliin. Työssä pystyttiin kehittämään uudelle Fab-fragmentille partikkelipäällystysmenetelmä ja sitä hyödyntävä cTnI-immunomääritys. Määrityksen korkeaa taustaa saatiin merkittävästi vähennettyä käyttämällä määrityksessä polyetyleeniglykolilinkkeriä, joka esti leimavasta-aineen epäspesifistä sitoutumista. Immunomäärityksen herkkyyden parantamiseksi optimointeja tarvitaan lisää, mutta määritykselle on mahdollista kuitenkin saavuttaa tulevaisuudessa herkkä immunomääritys, jonka alttius häiriötekijöille on pieni.

Data analysis tools and methods for DNA microarray and high-throughput sequencing data

The recent rapid development of biotechnological approaches has enabled the production of large whole genome level biological data sets. In order to handle thesedata sets, reliable and efficient automated tools and methods for data processingand result interpretation are required. Bioinformatics, as the field of studying andprocessing biological data, tries to answer this need by combining methods and approaches across computer science, statistics, mathematics and engineering to studyand process biological data. The need is also increasing for tools that can be used by the biological researchers themselves who may not have a strong statistical or computational background, which requires creating tools and pipelines with intuitive user interfaces, robust analysis workflows and strong emphasis on result reportingand visualization. Within this thesis, several data analysis tools and methods have been developed for analyzing high-throughput biological data sets. These approaches, coveringseveral aspects of high-throughput data analysis, are specifically aimed for gene expression and genotyping data although in principle they are suitable for analyzing other data types as well. Coherent handling of the data across the various data analysis steps is highly important in order to ensure robust and reliable results. Thus,robust data analysis workflows are also described, putting the developed tools andmethods into a wider context. The choice of the correct analysis method may also depend on the properties of the specific data setandthereforeguidelinesforchoosing an optimal method are given. The data analysis tools, methods and workflows developed within this thesis have been applied to several research studies, of which two representative examplesare included in the thesis. The first study focuses on spermatogenesis in murinetestis and the second one examines cell lineage specification in mouse embryonicstem cells.

Desiccation tolerance and DNA integrity in Eugenia pleurantha O. Berg. (myrtaceae) seeds

The aim of this study was to assess the desiccation tolerance and DNA integrity in Eugenia pleurantha seeds dehydrated to different moisture contents (MCs). Seeds extracted from mature fruits were submmited to drying in silica gel and evaluated at every five percentual points of decrease from the initial MC (35.5%, fresh weight basis). The effects of dehydration on seeds were verified through germination tests and DNA integrity assessment. Undried seeds achieved 87% germination, value reduced to 36% after being dried to 9.8% MC. When dried slightly more, to 7.4% MC, seeds were no longer able to germinate, suggesting an intermediate behavior in relation to desiccation tolerance. It was observed DNA degradation in seeds with 7.4% MC, which might have contributed to the loss of seed germination.

Desiccation tolerance and dna integrity in Eugenia pleurantha o. berg. (Myrtaceae) seeds

The aim of this study was to assess the desiccation tolerance and DNA integrity in Eugenia pleurantha seeds dehydrated to different moisture contents (MCs). Seeds extracted from mature fruits were dried in silica gel and evaluated at every five percentual points of decrease from the initial MC (35.5%, fresh weight basis). The effects of dehydration on seeds were verified through germination tests and DNA integrity assessment. Undried seeds achieved 87% germination, value reduced to 36% after being dried to 9.8% MC. When dried slightly more, to 7.4% MC, seeds were no longer able to germinate, suggesting an intermediate behavior in relation to desiccation tolerance. DNA degradation was observed in seeds with 7.4% MC, which might have contributed to the loss of seed germination.

Avaliação da perda da tolerância à dessecação e da quantidade de dna nuclear em sementes de Peltophorum dubium (spreng.) taubert durante e após a germinação

O presente trabalho teve por objetivo a avaliação da perda da tolerância à dessecação (TD) em sementes de Peltophorum dubium durante e após a germinação. As sementes foram colocadas para germinar e, ao atingirem 1, 3 e 5 mm de raiz primária (68% de umidade), foram desidratadas em sílica gel, até atingirem o grau de umidade inicial (8%), sendo em seguida reidratadas e avaliadas quanto à sobrevivência (retomada do crescimento e formação de plântulas normais). Procedimento semelhante foi adotado para os ensaios realizados durante a embebição, onde foram amostradas 100 sementes divididas em quatro repetições de 25 para cada um dos seguintes tempos de embebição: 12, 24, 48, 60 e 72 horas. Em seguida, foram selecionados diferentes pontos de interesse (12, 48 e 60 horas de embebição e raízes primárias com 1 mm de comprimento) para determinação da quantidade de DNA nuclear, afim de analisar possível correlação entre início do ciclo celular e perda da TD. Com relação ao comportamento de sementes germinadas submetidas à secagem e reidratação, para os três comprimentos de raízes primárias amostradas, não houve sobrevivência. Foi observada queda progressiva na sobrevivência de sementes de Peltophorum dubium relacionada ao tempo de embebição, e posterior secagem e reidratação, sugerindo que a perda da TD desta espécie acontece nos estágios iniciais da germinação, antes da protrusão da radícula. Sementes embebidas por 12 h, 24 h, 48 h, 60 h, 72 h e aquelas germinadas, com 1 mm de comprimento radicular, apresentaram índices iguais a 98%, 93%, 83%, 35%, 17% e 0% de sobrevivência respectivamente. Os estudos relacionados ao conteúdo de DNA nuclear não demonstram correlação entre retomada do ciclo celular e perda da TD.

Construction of bovine adenovirus type 3 E1 and E3, substitution plasmids and the sequencing analysis of DNA pol and pTP /

The relative ease to concentrate and purify adenoviruses, their well characterized mid-sized genome, and the ability to delete non-essential regions from their genome to accommodate foreign gene, made adenoviruses a suitable candidate for the construction of vectors. The use of adenoviral vectors in gene therapy, vaccination, and as a general vector system for expressing foreign genes have been documented for some time. In this study, the objective was to rescue a BAV3 E1 or E3 recombinant vector carrying the kanamycin resistant gene, a dominant selectable marker with useful applications in studying vectored gene expression in mammalian cells. To accomplish the objective of this study, more information about BAV3 DNA sequences was required in order to make the manipulation of the virus genome accessible. Therefore, sequencing of the BAV3 genome from 1 1 .7% to 30.8% was carried out. Analysis of the determined sequences revealed the primary structure of important viral gene products coded by E2 including BAV3 DNA pol and precursor to terminal protein. Comparative analysis of these proteins with their counterparts from human and non human adenoviruses revealed important insights as to the evolutionary lineage of BAV3. In order to insert the kanamycin resistance gene in either E1 or E3, it was necessary to delete BAV3 sequences to accommodate the foreign gene so as not to exceed the limit of the packaging capacity of the virus. To construct a recombinant BAV3 in which a foreign gene was inserted in the deleted E1 region, an E1 shuttle vector was constructed. This involved the deletion from the viral sequences a region between 1.3% to 9% and inserting the kanamycin resistance gene to replace the deletion. The E1 shuttle vector contained the left (0%- 53.9%) segment of the genome and was expected to generate BAV3 recombinants that can be grown and propagated in cells that can complement the missing E1 functions. To construct a similar shuttle vector for E3 deletion, DNA sequences extending from 78.9% to 82.5% (1281 bp) were deleted from within the E3 region that had been cloned into a plasmid vector. The deleted region corresponds to those that have been shown to be non-essential for viral replication in cell culture. The resulting plasmid was used to construct another recombinant plasmid with BAV3 DNA sequences extending from 37.1% to 100% and with a deletion of E3 sequences that were replaced by kanamycin resistance gene. This shuttle plasmid was used in cotransfections with digested viral DNA in an attempt to rescue a recombinant BAV3 carrying the kanamycin resistance gene to replace the deleted E3. In spite of repeated attempts of transfection, El or E3 recombinant BAV3 were not isolated. It seems that other approaches should be applied to make a final conclusion on BAV3 infectivity.