The Proximity Ligation Assay (PLA) is a relatively new method which utilizes the strength of both immunoassays and DNA detection. PLA has the capacity of high multiplexing due to the high specificity achieved with both dual protein-binding and dual primer binding during detection with Real-Time PCR. We developed a multiplexed PLA protocol that can measure 28 biomarkers in human EDTA plasma. The method was tested on 46 individuals diagnosed with colorectal cancer and 48 age matched healthy controls. The results are very promising as we re-discover the most well-known biomarkers for colorectal cancer and also find some potential new markers (significance tested with students T-test with p<0.05). Further improvements of the protocol are needed to decrease the variation.

As antibiotic resistant bacterial strains are becoming more prevalent in healthcare settings, it is necessary to find alternative methods of detecting and treating these infections. One of the antibiotic resistant strains of interest is the carbapenem-resistant Enterobacteriaceae (CRE). CREs have the ability to evade some of the most potent antibiotics currently in use and employ carbapenemases to negate the effect of antibiotics. The three most common carbapenemase genes, found in carbapenem-resistant Enterobacteriaceae along with a gene found only in Escherichia coli were chosen to create a qPCR assay for rapid detection of resistant infections. The carbapenemase genes are KPC, VIM and NDM and the E. coli gene is uidA, a β-glucuronidase gene. Consensus sequences were obtained from each of the genes to account for the many variants of each gene. We were able to triplex the assay and test it against a library for twenty isolates varying by which gene they contain. Additional research has been conducted on the library of carbapenem-resistant Enterobacteriaceae using bacteriophages or phage. The Phage Hunters class isolated and identified twenty phage that infect K. pneumoniae. Out of the twenty phage, seven phage were able to effectively infect carbapenem-resistant K. pneumoniae.

Conventional methods of body fluid identification use labor-intensive, technologically diverse techniques that are performed in a series, not parallel, manner and are costly in terms of time and sample. Furthermore, for some frequently encountered body fluids, such as saliva or vaginal secretions, no confirmatory technique exists. Terminally differentiated cells, such as blood lymphocytes or epithelial cells lining the oral cavity, have a unique pattern of gene expression, which is evinced by the presence and relative abundance of specific mRNA species. If the type and abundance of mRNAs can be determined in a stain or tissue sample recovered at the crime scene, it would be possible to definitively identify the tissue or body fluid in question. Advantages of an mRNA-based approach, compared to conventional biochemical analysis, include greater specificity, simultaneous and semi-automated analysis though a common assay format, improved timeliness, decreased sample consumption and compatibility with DNA extraction methodologies. In this report, we demonstrate that RNA is stable in biological stains and can be recovered in sufficient quantity and quality for analysis using reverse transcriptasepolymerase chain reaction assay (RT-PCR). We have identified sets of candidate tissuespecific genes for body fluids and tissues of forensic interest, namely blood, saliva, semen, vaginal secretions, menstrual blood, urine, skin, muscle, adipose, and brain. We also report the identification of a new housekeeping gene for use in mRNA based assays. Select body fluid-specific genes have been incorporated into multiplex PCR and real-time PCR assays. These assays allow for the positive identification of blood, saliva, semen,vaginal secretions, and/or menstrual blood in a stain. The final task of this work was the molecular characterization of mRNA degradation patterns in biological stains, which not only has fundamental importance in possibly revealing mRNA degradation pathways in dried biological stains, but may ultimately lead to better assay design strategies for mRNA markers for forensic use. An mRNA-based approach described in this report could allow the facile identification of the tissue components present in a body fluid stain and could conceivably supplant the battery of serological and biochemical tests currently employed in the forensic serology laboratory.

Overweight (BMI 25–29) or obese (BMI over 30) pregnant women have an increased risk of complications during pregnancy and childbirth that can harm both women and their children.Due to increased risk for several complications such as of giving birth to large children, malformations or still births, the children have higher risk of obesity, blood pressure diseases and diabetes in childhood and later in life compared with children of normal weight. Various factors affect nutrient supply to the fetus such as activity of transport proteins, maternal and fetal blood flow to and from the placenta and placental metabolism. X-box-binding protein1 (XBP-1) is an important transcription factor that is part of the endoplasmic reticulum (ER)and facilitates the breakdown of misfolded proteins and gives ER good quality control over proteins. The purpose of this work was to study the XBP-1 protein in the placenta and see if the cells are stressed in women with obesity and compare levels of this protein with women who are normal weight. Placental expression of XBP-1 was analyzed by use of two different methods western blot including 36 women in three different groups, 12 women who were normal weight, 12 women who were obese and 12 women who were overweight. The second method was real- time polymerase chain reaction (RT- PCR) including 20 women in two different groups, 10 women who were normal weight and 10 women who were obese. The result showed that there was no protein detected in the placenta but there were bands in positive control. XBP-1 mRNA expression did not differ between study groups but there was a tendency towards a significant correlation mRNA and birth weight of the children. This indicate that it may a correlation between them, but our results should be confirmed with larger studies.

Submitted by Luciana Ferreira (lucgeral@gmail.com) on 2015-03-04T15:47:31Z No. of bitstreams: 2 Dissertação - Laís Carneiro Naziasene Lima - 2014.pdf: 3242345 bytes, checksum: d0ace95b026350f2bf41251459258252 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2015-03-05T10:40:24Z (GMT) No. of bitstreams: 2 Dissertação - Laís Carneiro Naziasene Lima - 2014.pdf: 3242345 bytes, checksum: d0ace95b026350f2bf41251459258252 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Made available in DSpace on 2015-03-05T10:40:24Z (GMT). No. of bitstreams: 2 Dissertação - Laís Carneiro Naziasene Lima - 2014.pdf: 3242345 bytes, checksum: d0ace95b026350f2bf41251459258252 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Previous issue date: 2014-05-08 / Fundação de Amparo à Pesquisa do Estado de Goiás - FAPEG / The increase in the number of fungal infections by Candida species, as a result of the significant increase of immunocompromised patients emphasizes the importance of studies associated to this genre. The resistance of these strains to antifungal drugs is observe in specific isolates, as well as infections associated with biofilm formation (BF). The aim of this study was to compare the susceptibility profile of sessile and planktonic cells of different Candida isolates, differentiating species by multiplex qPCR and scanning electron microscopy. The sample consisted of 10 C. albicans, 10 C. parapsilosis and 1 C. tropicalis. The genetic material was extracted by phenolchloroform extraction of the sample C. tropicalis, ATCC 28367 (C. albicans) and ATCC 22019 (C. parapsilosis) for use in a species-specific multiplex qPCR assay with analysis of differences in the curve fusion. Microdilution plate test and reduction of the tetrazolium salt for 21 isolates were performed for the susceptibility of sessile and free cells, respectively. The evaluation of the ultrastructure of the biofilm was performed on strips of polyurethane with visualization by scanning electron microscopy. The amplified products from C. albicans obtained three melting peaks with values of 75,2 °C, 76,8 °C and 79,8 °C, while C. tropicalis and C. parapsilosis showed one peak with values 73,5 °C and 78,5 °C, respectively. The identification test showed to be reliable for the identification of the most common species in the study. All of Candida yeasts were able to form biofilm with own organization of each specie. The in vitro susceptibility test of planktonic cells demonstrated that amphotericin B and caspofungin showed better activity compared to fluconazole and voriconazole who obtained 19% of resistant strains, all C. albicans. In assessing of the CIMs50% and CIMs80% of sessile cells, we observed an increase of at least 60 times the values of planktonic cells. It was observed a high percentage of BF that demonstrates the need for diagnosis and combat against this biomass formed by Candida species. The BF is a virulence factor determinant for decrease of susceptibility to antifungal agents thus compromising antifungal therapy. / O aumento no número de infecções fúngicas por espécies de Candida, como resultado do expressivo aumento de pacientes imunocomprometidos destaca a importância de estudos relacionados a esse gênero. A resistência destas leveduras aos fármacos antifúngicos é observada em isolados específicos, assim como em infecções associadas com a formação de biofilme (FB). O objetivo deste estudo foi comparar o perfil de suscetibilidade in vitro de células sésseis e planctônicas de diferentes isolados de Candida, diferenciando as espécies por qPCR multiplex e microscopia eletrônica de varredura. A amostra foi composta de 10 C. albicans, 10 C. parapsilosis e 1 C. tropicalis. O material genético foi extraído pelo método de extração fenol-clorofórmio da amostra de C. tropicalis, ATCC 28367 (C. albicans) e ATCC 22019 (C. parapsilosis) para utilização no ensaio espécie-específico qPCR multiplex com avaliação das diferenças na curva de fusão. Foram realizados teste de microdiluição em placa e redução do sal tetrazólio para 21 isolados a fim de determinar a suscetibilidade de células livres e sésseis, respectivamente. A avaliação da ultraestrutura do biofilme foi realizada em tiras de poliuretano com visualização por microscopia eletrônica de varredura. Os produtos amplificados de C. albicans, obtiveram três picos de fusão com valores de 75,2°C, 76,8°C e 79,8°C, enquanto C. parapsilosis e C. tropicalis mostraram um pico de valores 73,5°C e 78,5°C, respectivamente. O teste de identificação apresentou-se confiável para a identificação das espécies mais comuns no estudo. Todas as leveduras de Candida foram capazes de formar biofilme com organização própria de cada espécie. O teste de suscetibilidade in vitro das células planctônicas demonstrou que anfotericina B e caspofungina apresentaram melhor atividade em comparação com o fluconazol e voriconazol que obtiveram 19% das amostras resistentes, sendo todas C. albicans. Na avaliação da CIMs50% e CIMs80% das células sésseis, observou-se um aumento de pelo menos 60 vezes dos valores das células planctônicas. Foi observada porcentagem elevada de FB que demonstra a necessidade do diagnóstico e combate à essa biomassa formada pelas espécies de Candida, pois é um fator de virulência determinante para a diminuição da suscetibilidade aos antifúngicos comprometendo assim a terapêutica antifúngica.