A Doença de Alzheimer (DA) é uma desordem neurodegenerativa influenciada por elementos genéticos e ambientais. O diagnóstico é baseado em parâmetros clínicos, mas sua confirmação é post-mortem, após avaliação patológica durante a autópsia. A identificação de biomarcadores baseados em tecido periférico como o sangue permitiria um diagnóstico menos invasivo e mais preciso, como também poderia servir como marcador de predisposição, conversão, progressão e resposta à tratamento. Para atingir tal objetivo, métodos de prospecção em larga escala de perfis de expressão gênica e protéica têm sido extensamente aplicados. O presente estudo se propôs a selecionar e validar potenciais candidatos a biomarcadores na DA, e também, de identificar potenciais biomarcadores pelo desenvolvimento de perfis proteômicos de plaquetas de pacientes. Dados publicados de microarray para DA foram comparados e genes com perfil de expressão similar em pelo menos dois estudos independentes foram selecionados. Foram identificados 4 genes de expressão aumentada em pacientes (HLADRB1, HLAB, CIRBP, S100A4) e 4 genes de expressão diminuída (CALM1, ATP5J2, KIF1B, FLOT1), que posteriormente foram submetidos a validação por PCR em tempo-real em amostras de RNA extraído a partir de leucócitos de sangue periférico de 20 pacientes e 20 controles idosos. Ao mesmo tempo, padronizamos e traçamos o perfil proteômico de pools de proteínas de plaquetas de pacientes do sexo feminino e masculino e seus respectivos controles idosos por Eletroforese Bidimensional (2-D). Dentre os genes analisados por meio de PCR em tempo-real, três (ATP5J2, S100A4 e KIF1B) apresentaram expressão aumentada no grupo DA em relação ao grupo controle (p >0,05). Estes genes podem estar envolvidos na resposta inflamatória periférica e indução da apoptose. A padronização do perfil proteômico por 2-DE foi bem sucedida e um conjunto de 5 proteínas diferencialmente expressas para ambos os gêneros foram obtidas, mas não foi possível a sua identificação por Espectrometria de Massas devido a massa limitada dessas proteínas em cada spot. Por ambas as técnicas foi possível identificar perfis diferentes de expressão gênica e protéica entre pacientes e controles idosos, demonstrando que sangue periférico é uma boa matriz de prospecção de biomarcadores de doenças neurodegenerativas. / Alzheimer\'s disease (AD) is a neurodegenerative disorder influenced by genetic and environmental elements. The diagnosis is based on clinical parameters, but its confirmation needs post-mortem pathologic evaluation at autopsy. The identification of biomarkers based on peripheral tissue would allow a less invasive and more accurate diagnosis, but could also serve as a marker of predisposition, conversion, progression and response to treatment. To achieve this goal, methods of exploring large-scale gene expression profiles and protein have been extensively applied. The present study proposed to select and validate potential candidate genes for biomarkers in AD, and also identify potential biomarkers from proteomic profiles of platelets of these patients. Published microarray data for AD were compared and genes with similar expression profile in at least two independent studies were selected. We identified four up-regulated genes (HLADRB1, HLAB, CIRBP, S100A4) and four down-regulated genes in patients (CALM1, ATP5J2, KIF1B, FLOT1), which were then submitted to validation by real time PCR in RNA samples extracted from peripheral blood leukocytes of 20 patients and 20 elderly controls. At the same time, standardized, and traced the proteomic profile of platelet proteins pools of female patients and male elders and their respective controls by two-dimensional electrophoresis (2-D). Among the genes analyzed by real time PCR three of them (ATP5J2, S100A4 and KIF1B) showed increased expression in the AD group compared to the control group (p> 0.05). These genes may be involved in peripheral inflammatory response and induction of apoptosis. The standardization of proteomic profile by 2-DE has been successful and a set of five differentially expressed proteins in both genders were obtained, but could not be identified by mass spectrometry due to limited mass of these proteins in each spot. For both techniques were able to identify different patterns of gene and protein expression between patients and elderly controls, demonstrating that peripheral blood is a good prospect source of biomarkers for neurodegenerative diseases.

Choisya ternata est une plante ornementale souvent touchée par la maladie de la pourriture racinaire provoquée par Phytophthora. Cette maladie peut induire de pertes allant jusqu’à 80 %, ce qui implique l’utilisation intensive de produits phytosanitaires. Afin de limiter l’utilisation de ces produits toxiques, une meilleure connaissance des acteurs de la défense des plantes est nécessaire. Pour cela, les objectifs de cette thèse sont I) d’identifier les espèces du genre Phytophthora pathogènes de C. ternata, II) d’étudier des acteurs de défense au niveau racinaire et III) de développer une approche de lutte alternative aux phytosanitaires. L’identification des espèces de Phytophthora par l’amplification et le séquençage de la région ITS, montre la présence de Phytophthora parasitica dans la production de C. ternata en pépinière. Ils mettent aussi en évidence, pour la première fois en France et chez Choisya, la présence de Phytophthora tropicalis. Deux cultivars de C. ternata sont utilisés pour étudier les acteurs de la défense racinaire contre P. parasitica, Aztec pearl (moins sensible à la pourriture racinaire) et Goldfinger (plus sensible). Les arabinogalactane-protéines (AGPs) sont des glycomolécules de la paroi cellulaire qui constitue une barrière physique face aux pathogènes. Des études ont montré le rôle des AGPs dans l’interaction plante-pathogène et plus particulièrement avec les oomycètes. Toutefois, le rôle des AGPs racinaires de Choisya dans l’interaction avec P. parasitica n’est pas étudié. Nos résultats montrent des différences biochimiques au niveau de la composition monosaccharidique des AGPs racinaires d’Aztec pearl en comparaison avec les AGPs de feuilles de ce cultivar et les AGPs de feuilles et de racines de Goldfinger. Contrairement aux autres fractions, ces AGPs n’ont pas augmenté la croissance du mycélium de P. parasitica. Ces résultats suggèrent que l’oomycète n’est pas capable de dégrader cette fraction pour l’utiliser comme une source d’énergie. Pendant l’infection de la plante par P. parasitica, ces AGPs peuvent freiner la pénétration du pathogène, et par conséquent diminuer la sévérité de la maladie. Les plantes ont aussi développé des molécules chimiques nommées métabolites secondaires (MS) capables de les protéger contre leurs agresseurs. Des études ont montré que la partie foliaire de Choisya est riche en MS tels que les alcaloïdes dont plusieurseffets pharmacologiques sont connus. Cependant, leur composition racinaire et leur rôle dans la protection de la plante contre P. parasitica ne sont pas élucidés. Nos résultats montrent que les racines des deux cultivars sont riches en alcaloïdes furoquinoliques. Certains alcaloïdes sont présents en plus grande quantité chez Aztec pearl, mais suite à l’inoculation de zoospores de P. parasitica cette différence n’est plus détectable. De plus, l’extrait contenant les alcaloïdes totaux d’Aztec pearl ont été capables d’inhiber la croissance du mycélium de l’oomycète, contrairement à l’extrait issu de Goldfinger. Ces résultats montrent le rôle potentiel des alcaloïdes furoquinoliques dans la protection de la plante contre cet oomycète. / Choisya ternata is an ornamental plant that suffers from root rot disease due to Phytophthora. This disease can lead to severe production losses (up to 80 %), which require intensive use of phytosanitary products. A better understanding of plants defenses in required in order to reduce the use of these products. Therefore, the objectives of this thesis are I) identifying Phytophthora spp. pathogens of C. ternata, II) studying roots defense actors and III) developing an alternative control approach. Phytophthora spp. identification by ITS region amplification and sequencing highlighted the presence of Phytophthora parasitica on Choisya. Furthermore, Phytophthora tropicalis was identified for the first time in France and on Choisya culture. Two C. ternata cultivars were used to study the plants root defense actors against P. parasitica, Aztec pearl (less susceptible to root rot) and Goldfinger (more susceptible to root rot). Arabinogalactan proteins (AGPs) are glycomolecules of the cell wall which constitutes a physical barrier to pathogens. Studies showed the role of AGPs in the plant-pathogen interaction and more specifically in the case of oomycetes. However, Choisya root AGPs role in the interaction with P. parasitica is not studied. Our results showed biochemical differences in the monosaccharide composition of Aztec pearl root AGPs and the other AGPs fractions (Aztec pearl leaves and Goldfinger roots and leaves). Contrary to other fractions Aztec pearl root AGPs did not increase P. parasitica mycelium growth. These results suggest that oomycete was not able to degrade this fraction and use it as energy source. When P. parasitica infects the plant, these AGPs may be able to slow the infection and reduce disease severity. Plants have also developed chemical molecules known as secondary metabolites (SM) capable of protecting them against attackers. Studies showed that C. ternata leaves are rich with SM as alkaloids that have many pharmacological activities. Nevertheless, roots alkaloids composition and role in plant protection are not studied. Our results showed that roots of the two cultivars are riche with furoquinoline alkaloids. Some these alkaloids were more concentrated in Aztec pearl. But after inoculation with P. parasitica zoospores, the difference was not detectable anymore. Moreover, the total alkaloids extract of Aztec pearl inhibited P. parasitica mycelium growth, unlike the extract of Goldfinger. Another strategy of plants protection is the use of beneficial soil microorganisms that limits pathogens development and stimulate plant defenses. These microorganisms are known as biological control agents (BCA) and are sometimes used in horticulture as an alternative control strategy. In our study, treatments of C. ternata by different BCA were evaluated by a developed real time PCR (qPCR) targeting ypt1 and by symptoms annotation. This evaluation showed that combined treatments by Glomus intraradices with Gliocladium catenulatum and G. intraradices with Trichoderma atroviridae (respectively mycorrhizal fungi and filamentous fungi) offer a better protection against P. parasitica.

Currently, there is a growing interest in the use of probiotic products, and there are many of them in the market. With the growing interest, greater emphasis is placed on the identification of declared probiotic microorganisms. Precise identification of microbial composition is often a difficult task and it requires more advanced methods especially in the field of molecular diagnostics. The diploma thesis was focused on the verification of the presence od declared probiotic microorganisms in probiotic food supplements GS Laktobacily Forte 21, Biopron 9 Premium and Linex® Forte. DNA was isolated from the complex matrices by phenol extraction, commercial kit and magnetic carriers F79/L3-PLL in the quality suitable for PCR. Subsequently, the isolated DNA was amplified by real-time polymerase chain reaction using genus- and species-specific primers. The specific PCR product was subjected to agarose gel electrophoresis, whereas species identification was not always in compliance with the data declared by producers. The next part of the thesis was focused on polymerase chain reaction with high-resolution melting analysis to distinguish bacterial strains belonging to the Lactobacillus group and to identify probiotic microorganisms present in the complex matrices of the probiotic food supplements. Eight primer sets were tested (V1F HRM a V1R-HRM, CHAU-V3F a CHAU-V3R, CHAU-V6F a CHAU-V6R, LAC2 a LAC4, LAC1 a LAC2, P1V1 a P2V1, poxcDNAFw a poxPromRVC, poxcDNAFw a poxPromRVT). Three primer pairs (V1F HRM a V1R-HRM, poxcDNAFw a poxPromRVC, poxcDNAFw a poxPromRVT) were evaluated as the most suitable for distinguishing Lactobacillus bacterial strains.

Hyaluronic acid (HA) is an important substance, which is mostly used in pharmaceutical and cosmetic industry. This substance is commonly found in the human body. HA is one of the factors contributing to virulence of microorganisms. Some bacterial strains produce hyaluronic acid in the form of a mucoid capsule that encapsulates the cell to protect bacteria against the immune system of the host organism. One of the main producers is the bacterial strain Streptococcus equi subsp. zooepidemicus. Contipro a.s. uses the strain CO4A to produce hyaluronic acid in large scale. The production strain was obtained by random mutagenesis by UV light. The aim of the work was to study changes in the genome, which led to a significant increase in hyaluronic acid production, using DNA microarray and real-time PCR (qPCR). The genome of the strain CO4A was sequenced and compared to reference ATCC35246 [1]. The size of the genome is 2,167,251 bp and 83 relevant variants (59 SNV and 34 indels) have been identified. Variants in coding regions were annotated and amino acid sequence changes were determined. In SNV mutations there was a change in the amino acid sequence in 45 cases. The change was identified in every case of indel mutations. The expression level of selected groups of genes was monitored in both strains by the method of DNA microarrays. A cascade of increased expression level of amino sugar metabolism genes leading to the synthesis of UDP-N-acetyl glucosamine was observed in strain CO4A (the increase in expression level of these genes compared to ATCC35246 was on average 28 %). Subsequently, the expression of selected genes was verified by qPCR. There was no significant difference in the expression level of the has operon genes of both strains. The effect of supplementation of the culture medium with N-acetylglucosamine (GlcNAc), which is one of the precursors of HA synthesis, was also studied by qPCR. A positive effect of the supplementation of the culture medium with external GlcNAc in the CO4A strain has been recorded. Also, the supplementation has positive effect on the yield of HA from the medium (increase in yield was on average by 17 %). GlcNAc has been shown to have a positive effect on the yield of HA in ATCC35246 strain as well (increase in yield was 9 % on average), but no significant changes in the expression levels were found in selected groups of genes in ATCC35246.

Project title: Optimalization of the regime of marker's examination of clinically important infections in blood donors Project author: Daniela Dušková, M.D. Project supervisor: prof. Vladimír Tesař, M.D., Dr.Sc., MBA, FASN The aim of this project is to contribute to the discussion about introducing the methods of molecular biology into the routine blood donor testing in the transfusions departments in the Czech Republic. The theoretical part includes a brief history and some turning points in transfusion medicine. The next part within the theoretical section is dedicated to the problems of infectious diseases concerning transfusion and the general examination processes used during the selection of blood donors. The end of the theoretical part concentrates on existing possibilities of markers' examination of clinically important infections in blood donors, including the list of processes performed in the Czech Republic, the European Union and other countries. The practical part describes this study, ie. the routine screening test of blood donors using the CMIA method (a routine method) and using RT-Real Time PCR method (a molecular biology method) for detecting infectious markers (HCV, HBV, HIV). Within this part, the principle of both methods and the process of actual examinations are described in...

No description available.

No description available.

Mit klonspezifischer Polymerasekettenreaktion (PCR) ist ein spezifischer Nachweis kleiner DNA-Mengen möglich. Von 47 MF-Patienten wurden aus Hautproben 50 TCR-gamma- und 7 TCR-beta-Sequenzen sequenziert, von 15 bzw. 5 Patienten gelang die Entwicklung eines N-spezifischen Primers. Um einen Zusammenhang zwischen Frequenz der zirkulierenden klonalen Zellen und klinischem Verlauf zu untersuchen, wurden für 4 Patienten im LightCycler die im Blut zirkulierenden klonalen Rearrangements quantifiziert. Ein Vergleich dieser Daten mit dem klinischen Verlauf ergab bei zwei Patienten eine Tendenz zu einem reziproken Verhältnis, bei einem Patienten im Tumorstadium wurde eine gleichsinnige Entwicklung beider Parameter gesehen. Der Nachweis klonaler Rearrangements in Haut- und Blutproben von SPP-Patienten wäre ein Hinweis auf den Lymphomcharakter dieser Erkrankung. Bei 9 von 14 SPP-Patienten wurde in Blutproben mit Hilfe der für VgammaI-Jgamma1/2 spezifischen Konsensusprimer ein monoklonales Rearrangement gefunden. Für 6 Patienten konnte ein klonspezifischer Primer entwickelt werden. Ein Nachweis der klonalen Sequenz aus dem Blut in der Haut war trotz einer geschachtelten PCR nicht möglich. / By clone specific polymerase chain reaction (pcr) small amounts of DNA can be detected. We discovered 50 tcr gamma and 7 tcr beta sequences from skin probes of 47 patients with mycosis fungoides. From 15 respectively 5 patients n-specific primers were designed. In order to examine if there is a relation between frequency of circulating clonal cells and clinical course, for 4 patients circulating clonal cells were quantified by real time pcr in LightCycler. In two patients we saw a reciproce proportion, in one patient with tumourstage disease rising numbers of circulating clonal cells were seen during worsening of clinical course. Detection of clonal rearrangments in skin and blood probes of patients with small plaque parapsoriasis could be a hint for classifying SPP as a lymphoma. In 6/14 patients we designed a clone-specific primer for circulating clonal rearangments. Despite performing a nested pcr circulating clonal rearrangments could not be detected in skin lesions of these patients.

Les duplicacions segmentàries (DSs), o també anomenades duplicons o Low copy Repeats (LCRs), són regions de coma mínim 1 kb amb un alt nivell d'identitat (>90%), que estan presents almenys dues vegades en el genoma. La regió 8p23.1 consta de 6.5 Mb a la part distal del braç curt del cromosoma 8 i està flanquejada per duplicacions segmentàries. Degut a la seva arquitectura genòmica aquesta regió és susceptible a patir reordenaments mediats per recombinació homòloga no al·lèlica entre les DSs, com per exemple la inversió polimòrfica de 8p23.1 [inv(8)(p23)], present en un de cada quatre individus de la població general europea i japonesa, així com d'altres reorganitzacions menys corrents.El treball realitzat en aquesta tesi doctoral pretén aprofundir en la caracterització de la complexa arquitectura genòmica d'aquesta regió. En la nostra primera aproximació a l'estudi de les DSs que flanquegen la regió cromosòmica 8p23.1, es va identificar una nova família gènica específica de primats, la família gènica FAM90A.Així, bona part d'aquesta tesi doctoral està centrada en l'anàlisi de l'origen, formació, evolució i expansió de FAM90A en els homínids. Per altra banda també s'ha analitzant en detall la variabilitat de FAM90A com a variant en número de còpia (CNV) en diferents poblacions humanes.Finalment, s'ha establert la freqüència de la inversió que afecta a 8p23.1 en població espanyola. També s'ha procedit a genotipar diversos individus homozigots per la inversió i s'ha predit l' estatus de la inversió en 150 individus del projecte HapMap i s'ha analitzat l'efecte que té aquesta reorganització sobre els nivells d'expressió dels gens de la regió. / Segmental duplications (SDs), also known as duplicons or Low Copy Repeats (LCRs), are regions of a minimum of 1 kb with a high sequence identity level (>90%), which are present at least two times in the genome. The 8p23.1 region extends 6.5 Mb at the distal part of the short arm of chromosome 8 and it is flanked by segmental duplications. Due to its genomic architecture the region is prone to suffer rearrangements mediated by non-allelic homologous recombination between these SDs, such as the polymorphic inversion of 8p23.1 [inv(8)(p23)], which is present in one out of every four of European and Japanese general population individuals, as well as other less frequent rearrangements.The aim of the work presented in this doctoral thesis is to get insights in the characterization of the genomic architecture of this complex region. Our first approach to study the SDs flanking 8p23.1 region resulted in the identification of a novel gene family which is primate specific, the FAM90A gene family. Thus, this doctoral thesis is mainly focused on the analysis of the origins, formation, evolution and expansion of FAM90A in hominoids. It has also been analyzed in detail the variability of FAM90A as a copy number variant (CNV) in different human populations.Finally, it has been established the frequency of the inversion affecting 8p23.1 region in the Spanish population. Several homozygous inverted individuals have been genotyped and the status for the inversion has been predicted for 150 HapMap individuals, as well as the effect of this rearrangement on the gene expression levels of the genes contained in the region.

Para obter resultados rápidos e confiáveis que permitam o monitoramento da segurança microbiológica de alimentos, seja pela indústria ou pelos órgãos de fiscalização, diversos métodos alternativos têm sido desenvolvidos para a detecção e quantificação de Salmonella. Os propósitos do estudo foram avaliar a viabilidade de emprego do QIAamp® DNA Stool Mini Kit para extração e purificação de DNA de Salmonella; validar ensaios baseados em PCR-tempo real (PCR-RT) para quantificar o DNA de Salmonella empregando ttr ou tuf e desenvolver um ensaio para quantificar Salmonella baseado na transcriptase reversa-PCR-tempo real (RT-PCR-RT). Para avaliação do QIAamp® DNA Stool Mini Kit empregaram-se fezes coletadas diretamente do reto de animais infectados ou não, sendo estas últimas artificialmente contaminadas e submetidas à extração segundo protocolo do fabricante. As amostras de DNA isoladas foram quantificadas empregando um ensaio Salmonella-específico PCR-RT utilizando como alvo o lócus ttr. O mesmo ensaio foi utilizado para células de Salmonella provenientes de meio de cultura. O ensaio PCR-RT baseado no alvo tuf foi validado empregando-se primeiramente cepas de diferentes sorotipos de Salmonella e de outras Enterobacteriaceae. A seguir sua eficiência foi avaliada para alimentos-modelo (ave e suíno) artificialmente contaminadas com elevada (≈ 6 log UFC/mL) e baixa (≈ 2 log UFC/mL) população de Salmonella Typhimurium DT 104. A validação do método quantitativo de Salmonella por RT-PCR-RT foi realizada primeiramente com células em meio de cultura e posteriormente nos mesmos alimentos-modelo utilizados para PCR-RT. Em ambos os métodos, alíquotas dos alimentos-modelo foram mantidas a 20 ºC e a 8 ºC, sendo examinadas em diferentes tempos pós-inoculação. Como controle empregou-se a enumeração de microrganismos mesófilos totais e de Salmonella por técnicas convencionais. A taxa de recuperação de Salmonella em fezes suínas artificialmente inoculadas, após tratamento com QIAamp® DNA Stool Kit, variou entre 25% a 50%, dependendo da quantidade inicial de células. Empregando o DNA extraído e submetendo-o à PCR-RT para o ttr obteve-se limite de detecção de 2,8 log UFC eq/g de fezes; método que foi menos sensível que o convencional. A quantificação de Salmonella por PCR-RT empregando tuf apresentou limite de detecção menor que 1 log UFC eq. Os resultados obtidos com este método, empregando-se células em meio de cultura ou alimentos-modelo, foram, de maneira geral, ligeiramente inferiores aos do método convencional. A eficiência de amplificação para PCR-RT e tuf foi de 94%. O método RT-PCR-RT apresentou limite de detecção semelhante ao obtido com o ttr (2 log UFC eq) e sua eficiência de amplificação foi de 100%. Observou-se que tuf é expresso na fase logarítmica de multiplicação bacteriana, o que o torna um bom indicador da viabilidade de Salmonella. / In order to get fast and trustworthy results that allow monitoring the microbiological food safety either by industries or governmental agencies, diverse alternative methods have been developed for Salmonella detection and quantification. The purposes of this study were to evaluate the viability of the use of QIAamp® DNA Stool Mini Kit for Salmonella DNA extraction and purification; to validate assays based on real time-PCR (PCR-RT) to quantify Salmonella DNA by using ttr or tuf, and to develop an assay to quantify Salmonella based on reverse transcriptase- PCR-real time (RT-PCR-RT). For QIAamp® DNA Stool Mini Kit evaluation feces taken directly from the rectum of infected or health animals were used, with the former being artificially contaminated. Samples were submitted to DNA extraction, according to manufacturers protocol. The isolated DNA were quantified using a Salmonella-specific PCR-RT targeting the ttr locus. The same assay was used for Salmonella cells originated from culture medium. The PCR-RT assay with tuf as target was first validated employing different Salmonella serovars and other Enterobacteriaceae strains. After, its efficiency was evaluated on food-models (chicken and swine) spiked with high (≈ 6 log CFU/mL) and low (≈ 2 log CFU/mL) Salmonella Typhimurium DT 104 populations. The validation of the quantitative RT-PCR-RT method was first conducted with cells grown in culture medium, and then in the same food-model used for PCR-RT. For both methods aliquots of foodmodels were maintained at 20 ºC and 8 ºC being evaluated at different incubation times. Enumeration of total mesophilic microorganisms and Salmonella based on conventional methods were used as controls. The DNA recovery rate in swine feces artificially inoculated, after QIAamp® DNA Stool Mini Kit treatment, was between 25% to 50% depending the initial amount of cells. Using the extracted DNA and submitting it to PCR-RT for ttr a detection level of 2,8 CFU eq/g of feces was obtained. This method showed lower sensitivity than the conventional. Salmonella quantification by PCR-RT employing tuf showed a detection level lower than 1 log CFU eq. The results obtained with this method and cells suspended in culture medium or in food-model systems were, in general slightly lower that those obtained with the conventional method. The efficiency of amplification for PCR-RT tuf was 94%. Detection limit of RT-PCR-RT was similar to that of ttr (2 log CFU eq) and efficiency of amplification was 100%. tuf was expressed in logarithmic phase of bacteria growth curve showing that it is a good viability indicator for Salmonella.