Use of real-time PCR to evaluate two DNA extraction methods from food

The DNA extraction is a critical step in Genetically Modified Organisms analysis based on real-time PCR. In this study, the CTAB and DNeasy methods provided good quality and quantity of DNA from the texturized soy protein, infant formula, and soy milk samples. Concerning the Certified Reference Material consisting of 5% Roundup Ready® soybean, neither method yielded DNA of good quality. However, the dilution test applied in the CTAB extracts showed no interference of inhibitory substances. The PCR efficiencies of lectin target amplification were not statistically different, and the coefficients of correlation (R²) demonstrated high degree of correlation between the copy numbers and the threshold cycle (Ct) values. ANOVA showed suitable adjustment of the regression and absence of significant linear deviations. The efficiencies of the p35S amplification were not statistically different, and all R² values using DNeasy extracts were above 0.98 with no significant linear deviations. Two out of three R² values using CTAB extracts were lower than 0.98, corresponding to lower degree of correlation, and the lack-of-fit test showed significant linear deviation in one run. The comparative analysis of the Ct values for the p35S and lectin targets demonstrated no statistical significant differences between the analytical curves of each target.

Extraction of DNA from honey and its amplification by PCR for botanical identification

The physiochemical and biological properties of honey are directly associated to its floral origin. Some current commonly used methods for identification of botanical origin of honey involve palynological analysis, chromatographic methods, or direct observation of the bee behavior. However, these methods can be less sensitive and time consuming. DNA-based methods have become popular due to their simplicity, quickness, and reliability. The main objective of this research is to introduce a protocol for the extraction of DNA from honey and demonstrate that the molecular analysis of the extracted DNA can be used for its botanical identification. The original CTAB-based protocol for the extraction of DNA from plants was modified and used in the DNA extraction from honey. DNA extraction was carried out from different honey samples with similar results in each replication. The extracted DNA was amplified by PCR using plant specific primers, confirming that the DNA extracted using the modified protocol is of plant origin and has good quality for analysis of PCR products and that it can be used for botanical identification of honey.

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.

The Elucidation of the involvement of endonuclease DNase y in reducing DNA transfection efficiency in mammalian cells

Gene therapy is predicated upon efficient gene transfer. While viral vectors are the method of choice for transformation efficiency, the immunogenicity and safety concerns remain problematic. Non-viral vectors, on the other hand, have shown high degrees of safety and are mostly non-immunogenic in nature. However, non-viral vectors usually suffer from low levels oftransformation efficiency and transgene expression. Thus, increasing transformation efficiency ofnon-viral vectors, in particular by calcium phosphate co-precipitation technique, is a way of generating a suitable vector for gene therapy and is the aim of this study. It is a long known fact that different cell lines have different transfection efficiencies regardless oftransfection methodology (Lin et a!., 1994). Using commonly available cell lines Madine-Darby Bovine Kidney (MDBK), HeLa and Human Embryonic Kidney (HEK-293), we have shown a decreasing trend ofDNase activity based on a plasmid digestion assay. From densitometry studies, as much as a 40% reduction in DNase activity was observed when comparing HEK-293 (least active) to MDBK (most active). Using various biochemical assays, it was determined that DNase y, in particular, was expressed more highly in MDBK cells than both HeLa and HEK-293. Upon cloning of the bovine DNase y gene, we utilized the sequence information to construct antisense expressing plasmids via both traditional antisense RNA (pASDGneoM) and siRNA (psiRNA-S4, psiRNA-S11 and psiRNA-S16). For the construction ofpASDGneoM, the 3' end of the DNase y was inserted in opposite orientation under a cytomegalovirus (CMV) promoter such that the expression ofRNA complementary to the DNase 2 ymRNA occurred. For siRNA plasmids, the sequence was screened to yield optimal short sequences for siRNA inhibition. The silencing ofbovine DNase y led to an increase in transfection efficiency based on traditional calcium phosphate co-precipitation technique; stable clones of siRNA-producing MDBK cell lines (psiRNA-S4 Bland psiRNA-S4 B4) both demol).strated 4-fold increases in transfection efficiency. Furthermore, serial transfection of antisense DNase y plasmid pASDGneoM and reporter pCMV-~ showed a maximum of 8-fold increase in transfection efficiency when the two separate transfections were carried out 4 hours apart (i.e. transfection ofpASDGneoM, separated by four hours, then transfection ofpCMV-~). Together, these results demonstrate the involvement ofDNase y in reducing transfection efficiency, at least by traditional calcium phosphate technique.

DNA polymerase activity in trophoblast giant cells in the mouse /

In the developing mouse embryo, the diploid trophectoderm is known to undergo a diploid to giant cell transformation. These cells arise by a process of endoreduplication, characterized by replication of the entire genome without subsequent mitosis or cell division, leading to polyploidy and the formation of giant nuclei. Studies of 13.5 day rat trophoblast derived from the parietal yolk sac have indicated a relatively low rate of DNA polymerase a activity, the noinnal eukaryotic replicase, in comparison to that of DNA polymerase g. These results have suggested that endoreduplication in trophoblast giant cells may not employ the normal replicase enzyme, DNA polymerase a. In order to determine whether a 'switch' from DNA polymerase to DNA polymerase is a necessary concomitant of the diploid to giant cell transformation, two distinct populations of trophoblast giant cells, the primary giant cell derived from the mural trophectoderm and the secondary giant cell derived from the polar trophoectoderm were used. These two populations of trophoblast giant cells can be obtained from the tissue outgrowths of 3.5da blastocysts and the extraembryonic ectoderm (EX) and ectoplacental cone (EPC) of 7.5 day embryos respectively. Tissue outgrowths were treated with aphidicolin, a specific reversible inhibitor of eukaryotic DNA polymerase a, on various days after explantation. The effect of aphidicolin treatment was assessed both qualitatively, using autoradiography and quantitatively by scintillation counting and Feulgen staining. 3 DNA synthesis was measured in control and treated cultures after a Hthymidine pulse. Scintillation counts of the embryo proper revealed that DNA synthesis was consistently inhibited by greater than 907. in the presence of aphidicolin. Inhibition of DNA synthesis in the EX and EPC varied between 81-957. and 82-987. respectively, indicating that most DNA synthesis was mediated by DNA polymerase a, but that a small but significant amount of residual synthesis was indicated. A qualitative approach was then applied to determine whether the apparent residual DNA synthesis was restricted to a subpopulation of giant cells or whether all giant cells displayed a low level of DNA synthesis. Autoradiographs of the ICM of blastocysts and the embryo proper of 7.5da embryos, which acted as diploid control population, was completely inhibited regardless of duration in explant culture. In contrast, primary trophoblast giant cells derived from blastocysts and secondary giant cells derived from the EX and EPC were observed to possess some heavily labelled cells after aphidicolin treatment. These results suggest that although DNA polymerase a is the primary replicating enzyme responsible for endoreduplication in mouse trophoblast giant cells, some nonactivity is also observed. A DNA polymerase assay employing tissue lysates of outgrown 7.5da embryo, EX and EPC tissues was used to attempt to confirm the presence of higher nonactivity in tissues possessing trophoblast giant cells. Employing a series of inhibitors of DNA polymerases, it would appear that DNA polymerase a is the major polymerase active in all tissues of the 7.5da mouse embryo. The nature of the putative residual DNA synthetic activity could not be unequivically determined in this study. Therefore, these results suggest that both primary and secondary trophoblast giant cells possess and use DNA polymerase a in endoreduplicative DNA synthesis. It would appear that the high levels of DNA polymerase g activity reported in trophoblast tissue derived from the 13.5 da rat yolk sac was not a general feature of all endoreduplication.

Significance of DNA base excision repair in the maintenance of mitochondrial function in Saccharomyces cerevisiae /

Mitochondria have an important role in cell metabolism, being the major site of ATP production via oxidative phosphorylation (OXPHOS). Accumulation of mtDNA mutations have been linked to the development of respiratory dysfunction, apoptosis, and aging. Base excision repair (BER) is the major and the only certain repair pathway existing in mitochondria that is in responsible for removing and repairing various base modifications as well as abasic sites (AP sites). In this research, Saccharomyces cerevisiae (S. cerevisiae) BER gene knockout strains, including 3 single DNA glycosylase gene knockout strains and Ap endonuclease (Apn 1 p) knockout strain were used to examine the importance of this DNA repair pathway to the maintenance of respiratory function. Here, I show that individual DNA glycosylases are nonessential in maintenance of normal function in yeast mitochondria, corroborating with previous research in mammalian experimental models. The yeast strain lacking Apn 1 p activity exhibits respiratory deficits, including inefficient and significantly low intracellular ATP level, which maybe due to partial uncoupling of OXPHOS. Growth of this yeast strain on respiratory medium is inhibited, but no evidence was found for increased ROS level in Apn 1 p mitochondria. This strain also shows an increased cell size, and this observation combined with an uncoupled OXPHOS may indicate a premature aging in the Apnlp knockout strain, but more evidence is needed to support this hypothesis. However, the BER is necessary for maintenance of mitochondrial function in respiring S.cerevisiae.

Factors affecting DNA uptake by mammalian cells

The ability to introduce DNA and express custom DNA sequences in bacteria opened the door for improvements in a large number of fields including agriculture, pharmacology, medicine, nutrition, etc. The ability to introduce foreign DNA sequences into mammalian cells in an efficient manner would have a large impact on therapeutic applications especially gene therapy. The methods in use today suffer from low efficiencies and sometimes toxicity. In this work a number of factors were evaluated for their effect onONA uptake efficiency. The factors studied included exposure to sublethal concentration of hydrogen peroxide which have been show to lead to destabilisation ofthe lysosomes. These exposures have proven to be very toxic to cells when combined with either the calcium phosphate or the lipofectAMINE® transfection methods. Another factor evaluated was exposure to Electro-Magnetic Fields (EMF). This was fuelled by the fact that EMF have been shown to mediate a number of effects on cell structure and/or physiology. EMF exposure by itself was not sufficient to induce the cells to pick up the DNA, therefore its effect on calcium phosphate and lipofectAMINE® was tested. Although some positive results were obtained, the variability of these results exceeded by far any observed enhancements which discouraged any further work on EMF. Also tested was the possible effect the presence of the cytomegalovirus (CMV) sequence might have on DNA uptake (based on previous results in this lab). It was found that the presence ofCMV in the DNA sequence does not enhance uptake or slow down degradation of the internalised DNA. The final factor tested was the effect of basic amino acids on transfection efficiency. It was found that arginine can enhance DNA uptake by about 170% v/ith calcium phosphate and about 200% with LipofectAMINE®. A model was proposed to explain the effect of arginine as well as the lack of effect from other amino acids.