<p>The human skin provides us with an excellent protective barrier and possesses a remarkable ability of constant renewal. Basal cell carcinoma is the most common type of skin cancer. The aim of this project was to verify results from an earlier study investigating the molecular differences between basal cell carcinoma (BCC) and basal cells of normal human epidermis. In that study microdissection of cell populations from BCC and basal cells of normal epidermis respectively was performed in five cases of confirmed BCC. Following RNA extraction and amplification, a gene expression analysis was performed using a 46 k human cDNA microarray. Comparison of expression profiles showed a differential expression of approximately 300 genes in BCC. An upregulation of signaling pathways previously known to be of importance in BCC development could be observed, as well as a downregulation of differentiation markers, MHC class II molecules, and proteins active in scavenging of oxygen radicals. We wanted to confirm these findings for a number of selected genes, using real time PCR. The focal point of this project was microdissection of cells from BCC and subsequent isolation of RNA. Microdissection based methods offer a possibility of selecting well defined cell populations for further analysis by using a focused laser beam. Initially tests in order to optimize the method were also performed, concerning the dehydration process and choice of slides used in microdissection. Isolation of RNA may, as we experienced, be associated with problems due to destruction of RNA by degrading enzymes.</p>

No description available.

Submitted by Cássia Santos (cassia.bcufg@gmail.com) on 2017-03-24T12:53:45Z No. of bitstreams: 2 Dissertação - Geisiane Alves Rocha - 2017.pdf: 2262501 bytes, checksum: 07907cdfd4fccd850c41b5d258f6f6a5 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2017-03-24T13:02:10Z (GMT) No. of bitstreams: 2 Dissertação - Geisiane Alves Rocha - 2017.pdf: 2262501 bytes, checksum: 07907cdfd4fccd850c41b5d258f6f6a5 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Made available in DSpace on 2017-03-24T13:02:10Z (GMT). No. of bitstreams: 2 Dissertação - Geisiane Alves Rocha - 2017.pdf: 2262501 bytes, checksum: 07907cdfd4fccd850c41b5d258f6f6a5 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2017-02-20 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / To understand how new viruses arise in agriculture, the interface zones between native systems and cultivated areas become an interesting object of study. The small number of studies focused on the detection of viruses, mainly with RNA genomes, in cerrado tree species in the interface zones is due to the difficulty of extracting quality nucleic acids for the necessary analysis. In the case of DNA viruses, such as begomovirus, to date there have been no reports on tree species in this type of vegetation. Begomovirus are among the main pathogens in different cultures in Brazil. However, in soybeans, one of the main crops in the country, these viruses are not among the most important pathogens for the culture, however, it is of great importance to identify different hosts of these viruses and in which environments they occur to know their diversity. The objective of this study was to detect and identify begomovirus in cerrado native trees and cultivated soybean plants near native vegetation areas, as well as to establish an efficient RNA extraction protocol for cerrado species in order to facilitate future related research with these plants. For begomovirus detection, samples of 30 tree species were collected from two areas of cerrado, in soybean the sampling was carried out in three areas of the Escola de Agronomia da Universidade Federal de Goiás - Regional Goiânia - planted with different cultivars. For all samples, DNA extraction was performed using a modified CTAB method and the detection was done by means of PCR using primers PAL1v1978 and PAR1c496. For the extraction of RNA, four methods were tested for Xylopia aromatica and Piper arboreum: TRIzol® reagent (method 1), TRIzol® reagent with modifications (method 2) and two methods using CTAB buffer (methods 3 and 4) that present differences in buffers composition in each method. The one that presented the best results was tested to obtain purified RNA of five cerrado tree species. Method 4 was chosen because of its best absorbance ratio (A260 / A280) when compared to the other methods. The RT-PCR of the RNA extracted from five species of cerrado areas showed good results after RNA extraction performed by method 4, qualifying this method as appropriate to obtain quality RNA for the molecular analysis of cerrado species. In the detection of begomovirus in 30 tree species of the cerrado, only Cardiopetalum calophyllum was positive. This is the first report of begomovirus in Brazilian cerrado tree species. The presence of two begomovirus species, Sida micrantha mosaic virus (SimMV) and Tomato severe rugose virus (ToSRV), were detected in one of the areas in the soybean sampled in the areas of the Escola de Agronomia. The ToSRV species was not previously reported in soybean and presents great potential to become an important pathogen for this crop and also for uncultivated plants, since this virus causes great losses in other crops, mainly tomato, and it has been demonstrated that its host range has increased in recent years. / Para se entender como novos vírus surgem na agricultura, as zonas de interface entre os sistemas nativos e as áreas cultivadas tornam-se um interessante objeto de estudo. O pequeno número de estudos focados na detecção de vírus, principalmente de RNA, em espécies arbóreas do cerrado nas zonas de interface é devido à dificuldade de extração de ácidos nucleicos de qualidade para análises necessárias. No caso dos vírus de DNA, como os begomovírus, até o momento não haviam relatos em espécies arbóreas nesse tipo de vegetação. Os begomovírus estão entre os principais patógenos em diferentes culturas no Brasil, entretanto em soja, uma das principais culturas do país, esses vírus não estão entre os patógenos mais importantes para cultura, porém, é de grande importância identificar diferentes hospedeiras desses vírus e em que ambientes ocorrem para conhecer sua diversidade. Assim, o objetivo geral do trabalho foi detectar e identificar begomovírus em espécies arbóreas nativas do cerrado e em plantas de soja cultivadas próximas a áreas de vegetação nativa e também estabelecer protocolo de extração de RNA eficiente para espécies do cerrado com intuito de facilitar pesquisas futuras relacionadas com essas plantas. Para detecção de begomovírus, amostras de 30 espécies arbóreas foram coletadas de duas áreas de cerrado, em soja a amostragem foi realizada em três áreas da Escola de Agronomia da Universidade Federal de Goiás – Regional Goiânia – plantadas com diferentes cultivares. Para todas as amostras foi realizada a extração de DNA através de um método CTAB (Brometo de cetil trimetil amônio) modificado e a detecção foi feita por meio de PCR (Reação em cadeia da polimerase) utilizando os primers PAL1v1978 e PAR1c496. Para extração de RNA foram testados quatro métodos a partir de folhas de Xylopia aromatica e Piper arboreum: reagente TRIzol® (método 1), reagente TRIzol® com modificações (método 2) e dois métodos utilizando tampão CTAB (métodos 3 e 4) que possuem diferenças nos tampões utilizados em cada método. O que apresentou os melhores resultados foi testado para a obtenção de RNA purificado de cinco espécies arbóreas de cerrado. O método 4 foi escolhido devido aos seus melhores resultados na razão de absorbância (A260 / A280) quando comparado aos outros métodos. A RT-PCR do RNA extraído de cinco espécies de áreas de cerrado mostrou bons resultados após a extração de RNA realizada pelo método 4, qualificando este método como apropriado para obtenção de RNA de qualidade para análise molecular de espécies do cerrado. Na detecção de begomovírus em 30 espécies arbóreas do cerrado, apenas Cardiopetalum calophyllum foi positiva. Este é o primeiro relato de begomovírus em espécie arbórea do cerrado brasileiro. Na soja, as plantas sintomáticas amostradas nas áreas da Escola de Agronomia foram positivas, sendo que em uma das áreas foi detectada a presença de duas espécies de begomovírus: Sida micrantha mosaic virus (SimMV) e Tomato severe rugose virus (ToSRV). A espécie ToSRV não foi relatada anteriormente em soja e apresenta grande potencial para se tornar um importante patógeno para essa cultura e também para plantas não cultivadas, já que esse vírus causa grandes perdas em outras culturas, principalmente tomateiro, e tem sido demonstrado que sua gama de hospedeiras tem aumentado nos últimos anos.

The human skin provides us with an excellent protective barrier and possesses a remarkable ability of constant renewal. Basal cell carcinoma is the most common type of skin cancer. The aim of this project was to verify results from an earlier study investigating the molecular differences between basal cell carcinoma (BCC) and basal cells of normal human epidermis. In that study microdissection of cell populations from BCC and basal cells of normal epidermis respectively was performed in five cases of confirmed BCC. Following RNA extraction and amplification, a gene expression analysis was performed using a 46 k human cDNA microarray. Comparison of expression profiles showed a differential expression of approximately 300 genes in BCC. An upregulation of signaling pathways previously known to be of importance in BCC development could be observed, as well as a downregulation of differentiation markers, MHC class II molecules, and proteins active in scavenging of oxygen radicals. We wanted to confirm these findings for a number of selected genes, using real time PCR. The focal point of this project was microdissection of cells from BCC and subsequent isolation of RNA. Microdissection based methods offer a possibility of selecting well defined cell populations for further analysis by using a focused laser beam. Initially tests in order to optimize the method were also performed, concerning the dehydration process and choice of slides used in microdissection. Isolation of RNA may, as we experienced, be associated with problems due to destruction of RNA by degrading enzymes.

京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第22065号 / 工博第4646号 / 新制||工||1724(附属図書館) / 京都大学大学院工学研究科マイクロエンジニアリング専攻 / (主査)教授 井上 康博, 教授 中部 主敬, 教授 横川 隆司 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DFAM

Preventing the spread of blood-borne infectious diseases is vital to improving global health outcomes, particularly for low- and middle-income countries (LMICs). Sensitive and accurate diagnosis of infections is vital to this effort. Nucleic acid amplification tests (NAATs), which amplify pathogen nucleic acids, are gold-standard techniques for detection and quantification of pathogen levels. However, standard NAATs such as polymerase chain reaction (PCR) require expensive equipment for blood sample processing and DNA/RNA amplification, making them challenging to implement in resource-limited areas of LMICs. In this work, I developed two methods to simplify sample processing and amplification to make NAATs more accessible for use at the point of care in resource-limited areas of LMICs. The first method enables instrument-free nucleic acid extraction from whole blood. A room temperature lysis chemistry and a paper-and-plastic sample capture device were developed to isolate, purify, and store pathogen DNA and RNA on a paper capture membrane. Extracted nucleic acids can be eluted and used in standard NAATs or in developmental amplification assays. I demonstrated successful isolation of HIV virion RNA and P. falciparum parasite DNA from whole blood samples over several concentrations with >60% recovery. Extracted RNA remains stable on the capture membrane for two weeks at room temperature and 37°C, alleviating the need for cold storage after sample collection. These results are a promising step toward using this method for simplified sample extraction and storage in low-resource settings in LMICs. The second method I developed is a novel isothermal amplification technique for P. falciparum DNA. Sensitive diagnosis of P. falciparum infection is vital to identify and treat low-density, asymptomatic infections and move closer to eliminating malaria. Highly sensitive PCR assays are difficult to deploy in resource-limited areas of LMICs and existing isothermal methods require complex assay design and are often not sensitive enough to diagnose asymptomatic infections. Here, I developed a novel isothermal technique which amplifies multiple regions of the P. falciparum genome, generating a large amount of DNA for better analytical sensitivity. The assay achieves a lower limit of detection of ~23.4 fg P. falciparum gDNA/µL (~1 parasite/µL) in 30 minutes, similar gold-standard PCR assay while using a fraction of the resources required for PCR. Lastly, I adapted the assay for implementation at the point of care. I showed that the assay directly amplifies P. falciparum parasite DNA captured on paper with the paper-and-plastic device previously developed. I also incorporated visual assay readout with lateral flow strips, eliminating the need for specialized equipment to detect amplified DNA. I explored methods to eliminate cold storage of reagents by stabilizing amplification enzymes at room temperature. The work described in this thesis represents two enhanced methods for point of care detection of blood borne pathogens. By simplifying sample extraction, amplification, and detection, the methods described here make NAATs more accessible to low-resource areas of LMICs. The whole blood nucleic acid extraction device and isothermal assay described in this work can be used together for sensitive diagnosis of P. falciparum malaria. The methods can also be used independently, or in combination with other techniques routinely used in the field. The flexibility built in to these methods enables easier integration into existing workflows in LMICs. / 2021-05-18T00:00:00Z

It has been found in previous studies that there is a correlation between the placenta regulatory genes and the weight gain of the mother, Body Mass Index (BMI) as well as the birthweight of the fetus. When the mother gains weight / is overweight, this will affect the gene expression in the placenta, and in turn this triggers the weight gain of the fetus. The aim of the study was to investigate the correlation between the lipoprotein lipase gene and the mother's BMI, weight gain and the child's birth weight by extracting RNA from the placentas and analysing its quality and concentration. cDNA was generated from RNA using reverse transcription and gene expression was amplified using real-time PCR. The data from real-time PCR was used in the comparative Ct-method to calculate a 2˄(-ΔΔCt)-value which represents the RNA-level of the LPL-gene. Lastly this value was analysed by using the two-statistic methods, Pearson's rank correlation and Spearman's correlation, which showed that the value of the correlation coefficient for all the variables was close to the value of zero. The closer the value is to zero, the weaker the association becomes between the different variables. The correlation was 0.045, 0.112 and 0.044 for the child's birth weight, mother's BMI respective weight gain. The results from this study shows that there is no correlation between LPL and the mother's weight gain, BMI, or the child's birth weight.

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