Escherichia coli isoladas de infecções do trato urinário (ITU) são conhecidas como E. coli uropatogênicas (UPEC). Dentre as E. coli diarreiogênicas, o patótipo denominado E. coli enteroagregativa (EAEC) é definido pela produção do padrão de adesão agregativa em células epiteliais cultivadas. Estudos recentes mostraram que algumas cepas de UPEC albergam propriedades de virulência de EAEC, indicando que cepas de EAEC podem causar ITU. Assim sendo, o objetivo deste estudo foi analisar as relações filogenéticas entre cepas de EAEC que apresentam marcadores genéticos de E. coli extraintestinais (ExPEC) e cepas de UPEC com e sem marcadores genéticos de EAEC. Para tal, foram selecionadas 92 EAEC, 8 UPEC com e 10 sem marcadores de EAEC. As 92 EAEC foram analisadas quanto à presença dos genes considerados como marcadores de cepas de ExPEC (papA/papC, sfa/foc, afa/dra, iutA, kpsMT II), detectando 30 (32,6%) cepas com esse perfil. Estas 30 cepas foram selecionadas para análises de filogrupos e multilocus sequence type (MLST) junto às cepas de UPEC. Foi observado que 17 (54,4%) cepas de EAEC e 3 (16,6%) de UPEC pertenceram ao filogrupo A, 2 (6,45%) EAEC e 1 (5,5%) UPEC ao filogrupo B1, 3 (9,68%) EAEC e 8 (44,4%) UPEC ao filogrupo B2, 6 (19,35%) EAEC e 2 (11,1%) UPEC ao filogrupo D, 1 (3,2%) EAEC e 4 (22,2%) UPEC ao filogrupo E, 1 (3,2%) EAEC ao filogrupo F e 1 EAEC (3,2%) não pôde ser classificada de acordo com esta metodologia. Comparando os dois grupos de UPEC notou-se que dentre as cepas com marcadores de EAEC 3 (37,5%) pertenceram ao filogrupo E, 2 (25%) aos filogrupos A e D e 1 (12,5%) ao filogrupo B1. Dentre as cepas sem marcadores de EAEC 1 (10%) pertenceu ao filogrupo A, 1 (10%) ao filogrupo E e 8 (80%) ao filogrupo B2. As análises de MLST através do sequenciamento dos genes recA, fumC, icd, mdh, purA, adk e gyrB permitiram determinar 42 sequence types (ST) distintos, dos quais 22 foram descritos neste estudo. Os mais comuns foram o ST 10 (5 cepas) e ST 95 e ST 746 (ambos com 2 cepas cada). A árvore filogenética gerada confirmou esses dados, mostrando o grupamento das cepas de EAEC com marcadores de ExPEC com as cepas de UPEC com marcadores de EAEC. Em resumo, o presente estudo mostrou que um subgrupo de cepas de EAEC está inserido nos mesmos grupos filogenéticos de cepas de UPEC com marcadores de EAEC apresentando, portanto, correlação filogenética. Houve diferenças de distribuição filogenética entre cepas de UPEC com e sem marcador de EAEC. Concui-se que cepas de EAEC podem apresentar potencial uropatogênico, tanto no curso de uma infecção diarreica, quanto em carreadores assintomáticos. / Escherichia coli isolated from urinary tract infections (UTI) are known as uropathogenic E. coli (UPEC). Among the diarrheagenic E. coli, the enteroaggregative E. coli (EAEC) pathotype is defined by the production of the aggregative adherence on cultured epithelial cells. Recent studies have shown that some UPEC strains harbor virulence properties of EAEC, indicating that EAEC strains can cause UTI. Therefore, the aim of this study was to analyze the phylogenetic relationships among EAEC strains that have genetic markers of extraintestinal E. coli (ExPEC) and UPEC strains, with and without genetic markers of EAEC. For that reason, we selected 92 EAEC, 8 UPEC with and 10 without EAEC markers. The 92 EAEC were analyzed for the presence of genes considered as markers for ExPEC strains (papA/papC, sfa/foc, afa/dra, iutA, kpsMT II), detecting 30 (32.6%) strains with that profile. These 30 strains were selected for phylogroup and multilocus sequence type (MLST) analysis with the UPEC strains. It was observed that 17 (54.4%) EAEC and 3 (16.6%) UPEC belonged to the phylogroup A, 2 (6.45%) EAEC and 1 (5.5%) UPEC to the phylogroup B1, 3 (9.68%) EAEC and 8 (44.4%) UPEC to the phylogroup B2, 6 (19.35%) EAEC and 2 (11.1%) UPEC to the phylogroup D, 1 (3.2%) EAEC and 4 (22.2%) UPEC to the phylogroup E, 1 (3.2%) EAEC to the phylogroup F and 1 (3.2%) EAEC could not be classified according to this methodology. Comparing the two groups of UPEC it was observed that among the UPEC strains with EAEC markers, 3 (37.5%) belonged to the phylogroup E, 2 (25%) to the phylogroups A and D and 1 (12.5%) to the phylogroup B1. Among the UPEC strains without EAEC markers, 1 (10%) belonged to the phylogroup A, 1 (10%) to the phylogroup E and 8 (80%) to the phylogroup B2. The MLST analysis by sequencing of recA, fumC, icd, mdh, purA, adk and gyrB genes allowed to determine 42 distinct sequence types (ST), of whom, 22 were described in this study. The most common were ST 10 (5 strains), and ST 95 and ST 746 (both with two strains each). The phylogenetic tree generated confirmed that data, showing the clustering of EAEC strains (harboring ExPEC markers) with the UPEC strains (harboring EAEC markers). In summary, the current study showed that a subgroup of EAEC strains are clustered in the same phylogenetic groups of UPEC strains with EAEC markers and, thus, present phylogenetic correlation. Also, there were differences in phylogenetic distribution among UPEC strains with and without EAEC markers. In conclusion, EAEC strains may have uropathogenic potential, either in the course of a diarrheal infection or in asymptomatic carriers.

Orientador: Wanderley Dias da Silveira / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-23T07:50:57Z (GMT). No. of bitstreams: 1 Silveira_Flavio_M.pdf: 7271586 bytes, checksum: 61c4ca3b97e4b7443d820cd714394fa8 (MD5) Previous issue date: 2013 / Resumo: O resumo poderá ser visualizado no texto completo da tese digital / Abstract: The abstract is available with the full electronic document / Mestrado / Microbiologia / Mestre em Genética e Biologia Molecular

Three overlapping DNA fragments from the lower operon of Pseudomonas putida TOL plasmid pDK1, covering the xy1IH genes and downstream flanking region, were cloned into pUC19. They include a 2.8 kbp XhoI fragment, a 2.7 kbp PstI fragment and a 2.0 kbp EcoRI-HindIII fragment. They were subjected to DNA sequence analysis. The xy1I (4-oxalocrotonate decarboxylase) and xy1H (4-oxalocrotonate tautomerase) genes were found to possess coding regions of 792 and 189 nucleotides, respectively. A possible transcriptional terminator resembling E. coli rho-independent terminators was identified downstream of the translational stop of xy1H. An additional stem and loop structure was found in the intergenic region between xy1I and xy1H. The individual ORF's of the oxalocrotonate branch (xy1G, xy1I and xy1H) have been cloned into pUC18/19. The expression of the xy1G gene in E. coli was successfully assayed spectrophotometrically.

A Escherichia coli é uma bactéria que deve ser controlada na indústria alimentar e setor hospitalar. Biosensores magnetoelásticos oferecem a promessa de rápida identificação destes e de outros patógenos prejudiciais. Neste trabalho, tiras amorfas de Metglas 2826MB3 foram cortadas ao tamanho 5 mm x 1 mm, com uma serra de micro corte e, em seguida, foram revestidas com camadas finas de Au e Cr, como foi verificado pela análise de espessuras de filmes Rutherford Backscattering Spectroscopy (RBS). Foram estudadas várias superfícies dos sensores: 1) sensor as-cast, lado roda; 2) sensor as-cast, superfície livre; 3) superfície polida. Uma camada de cistamina (CYS) foi aplicada ao substrato magnetoelástico, formando monocamadas auto organizadas (SAM), seguido de anticorpos, utilizando um protocolo modificado de Hermanson. Foi utilizado a bactéria Escherichia coli ATCC 25922, um anticorpo primário anti E. coli para a formação do bioconjugado e um anticorpo secundário Goat IgG anti-rabbit H&L Alexa Fluor 488 para a microscopia de fluorescência por método imunológico. O crescimento da camada de cistamina foi caracterizado por espectroscopia de infravermelho com transformada de Fourier (FTIR) e microscopia eletrônica de varredura (MEV) para as superfícies. Os biosensores foram expostos a soluções de bactérias e a frequência de ressonância dos sensores foi medida com um analisador de impedância Agilent E5061B até 100 minutos, em 5 biosensores de cada tipo. As reduções na frequência de ressonância, que apresentam a captura de bactérias, foram medidos após a otimização da amplitude do sinal. Para tempos até 40 minutos, a altas taxas de captação foram observadas e, posteriormente, a saturação ocorreu. Os parâmetros associados com uma cinética de captura foram estudados para diferentes superfícies dos sensores. O sensor com uma superfície polida mostrou melhores resultados. Este trabalho mostra que os biosensores magnetoelásticos podem ser úteis para a detecção e quantificação de microrganismos. / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior. / Escherichia coli is a bacteria that must be controlled in the food industry and the hospital sector. Magnetoelastic biosensors offer the promise of rapid identification of these and other harmful pathogens. In this work, strips of amorphous Metglas 2826MB3 were cut to size (5 mm x 1 mm) with a micro-dicing saw and were then coated with thin layers of Cr and Au, as verified by Rutherford backscattering spectroscopy (RBS). Several sensor surfaces were studied: 1) as-cast strip, wheel side; 2) as-cast strip, free surface; 3) thinned and polished surface. A layer of Cystamine (CYS) was applied to the magnetoelastic substrate, forming a self-assembled monolayer (SAM), followed by antibodies, using a modified Hermanson protocol. For our Escherichia coli ATCC 25922, we used both a primary antibody anti E. coli and a secondary antibody Goat anti Rabbit IgG H&L Alexa Fluor 488. The cystamine layer growth was characterized by Fourier transform infrared spectroscopy (FTIR) and scanning electron microscopy (SEM). The biosensors were exposed to solutions of bacteria and the resonant frequency of the sensors was measured with an Agilent E5061B impedance analyzer for times up to 100 minutes. Reductions in the resonant frequency, corresponding to bacteria capture, were measured after optimizing the signal amplitude. For times up to 40 minutes, high capture rates were observed and thereafter saturation occurred. Parameters associated with capture kinetics were studied for different sensor surfaces. The sensor with a polished surface was found the best results. This work shows that magnetoelastic biosensors may be useful for the detection and quantification of microorganisms.

aEPEC é capaz de causar lesão A/E, provocada por proteínas codificadas na região LEE. Foi realizada a análise estrutural e funcional da região LEE de amostras de aEPEC que expressam os padrões ALL, AA e AD, e amostra não aderente (NA). O padrão de adesão característico e capacidade de causar a lesão A/E foram investigados em células epiteliais. As amostras mantiveram o padrão de adesão independentemente da origem da linhagem celular. A lesão A/E foi detectada em algumas linhagens celulares após o contato com as amostras ALL e AD. A presença da região LEE foi detectada intacta e ensaios de PCR em tempo real, microarray e imunodetecção, mostrando a funcionalidade da mesma em todas as amostras. Um plasmídio que expressa a proteína EspFu foi introduzido em todas as 4 amostras, demonstrando não influenciar nos padrões de adesão e nem na capacidade de causar a lesão A/E nas amostras ALL, AA e AD. Mas, a amostra NA expressou o padrão ALL e foi capaz de causar a lesão A/E. Assim, EspFu desempenhou papel na adesão celular além do estabelecimento da lesão A/E in vitro. / aEPEC is capable to cause A/E lesion, triggered by proteins encoded by LEE region. We analyzed structurally and functionally the LEE region of aEPEC strains displaying LAL, AA, DA, and one nonadherent (NA) strain. The adherence characteristics and ability to cause A/E were investigated in epithelial cells. The displayed adherence patterns were independent of the cell line origin. A/E lesion was detected in some cellular lines after contact only with ALL- and AD-strains. LEE region presence was detected intact and real time PCR, microarray and immunodetection, in all samples tested. An EspFu-expressing plasmid was introduced in all strains, demonstrating no influence of this protein neither in the adherence patterns nor in the capacity to cause A/E of the LAL-, AA- and DA-strains. But, NA-strain expressed the LAL pattern and was able to cause A/E. Therefore, EspFu was shown to play a role in cell adhesion in addition to the establishment of the A/E lesion in vitro.

Escherichia coli Enteropatogênicas são um importante patógeno causador de diarréia. As EPEC podem ser classificadas em típica e atípica, baseado na presença do plasmídeo EAF. As amostras de EPEC apresentam em seu genoma uma ilha de patogenicidade denominada região LEE, na qual estão contidos os genes relacionados a formação da lesão (A/E). A regulação gênica da região LEE é multifatorial, sendo o principal regulador o gene ler. Até o momento não existem trabalhos sobre a participação de Hfq em EPEC, assim sendo, o presente estudo analisa o papel de Hfq na regulação dos fatores de virulência de EPEC típica (O127:H6) e atípica (O55:H7). A mutagênese do gene hfq foi obtida através do sistema l Red de recombinação alélica. As amostras mutantes apresentaram uma diminuição na capacidade aderir e formar a lesão A/E. Analise transcricional dos mutantes revelou uma significativa diminuição na transcrição do gene espA e do gene eae. Foi possível evidenciar uma diminuição da motilidade das amostras mutantes. A analise in silico revelou a possibilidade do dobramento natural do mRNA ler, ocultando o sitio de ligação do ribossomo. Aqui demonstramos a necessidade Hfq para a transcrição dos genes responsáveis pela lesão A/E. responsible for the A/E lesion. / Enteropathogenic Escherichia coli are an important pathogen responsible for causing diarrhea. EPEC can be classified as typical and atypical, based on the presence of the EAF plasmid. EPEC strains have in their genome a pathogenicity island known as LEE region, where it harbours genes related to the formation of a lesion A/E. LEE regulation is multifactorial, being the ler gene its main regulator. Until now there are no studies on the role of Hfq in EPEC, thus, the present study analyzes the function of Hfq on the regulation of virulence factors in typical EPEC (O127:H6) and atypical (O55:H7) strains. Hfq gene mutagenesis was obtained utilizing the allelic recombination l Red system. The mutant strains demonstrated a decrease in the capability of mutant strains to adhere and form A/E lesion. Transcriptional analysis showed a decrease on the espA gene and eae gene transcription. It was possible to notice a decrease in motility of the mutant strains. In silico analysis revealed the possibility of a natural folding of ler mRNA, concealing the ribosome binding site. With this study we could demonstrate the need of Hfq for the transcription of genes responsible for the A/E lesion.

Apesar de Escherichia coli O157:H7 ainda ser considerado o principal sorotipo envolvido com surtos de enfermidades veiculadas por alimentos entre as E. coli produtoras de toxina de Shiga (STEC), outros sorogrupos estão ganhando importância, como O26, O45, O103, O111, O121 e O145, que estão sendo denominados de \"Top Six STEC non O157\". As STEC são responsáveis por sintomas que variam de uma simples diarreia até diarreia sanguinolenta, que pode evoluir ainda para síndrome hemolítica urêmica e púrpura trombótica trombocitopênica, podendo ocasionar danos crônicos como falência renal e levar a óbito. Para tanto, apresentam diversos fatores de virulência, entre eles, as toxinas de Shiga (Stx) ou verotoxinas (Vtx). Os veículos destes micro-organismos são diversos alimentos, sendo o principal deles, as carnes moídas. Apesar da importância da carne moída como veículo transmissor de STEC, pouco se conhece sobre a sua presença nesse alimento comercializado na cidade de São Paulo, SP. Sendo assim, o objetivo deste trabalho foi pesquisar a presença de STEC em carne moída comercializada no varejo da cidade de São Paulo e caracterizar tais isolados quanto à presença dos seguintes fatores de virulência: stx1, stx2, eae e ehx. Foram coletadas 248 amostras em diferentes bairros da cidade de São Paulo. Para a detecção de E. coli sorogrupo O157 foi utilizada a metodologia ISO 16654 e para a detecção dos sorogrupos O103, O111, O145 e O26 foi empregada a metodologia descrita pelo Surveillance Group for Diseases and Infections of Animals (NRM 006). Uma amostra de carne moída (0,4%) apresentou o micro-organismo pesquisado. A identificação genotípica e bioquímica caracterizou esse isolado como STEC O157:H7, portador de todos os fatores de virulência pesquisados: stx1, stx2, eae e ehx. Foi constatada, também, a expressão das proteínas stx em células Vero. Esse é o primeiro relato da presença de E. coli O157:H7 produtora de toxina de Shiga em carne moída no Brasil. / Although Escherichia coli O157:H7 is still considered the most important serotype involved in foodborne disease outbreaks among Shiga toxin-producing E. coli (STEC), other serogroups are receiving more attention such as O26, O45, O103, O111, O121 and O145, that are being called the \"Top Six STEC non O157\". STEC are responsible for symptoms ranging from simple diarrhea to bloody diarrhea, which can further evolve to hemolytic uremic syndrome and thrombotic thrombocytopenic purpura, which may cause damage such as chronic renal failure and lead to death. To do so, they have several virulence factors, including the Shiga toxins (Stx) or verotoxins (Vtx). The vehicles of these microorganisms are many foods, most notably, the ground beef. Despite the importance of ground beef as a vehicle for transmitting STEC, little is known about their presence in this kind of food sold in São Paulo, SP. Therefore, the objective of this study was to investigate the presence of STEC in ground beef sold at retail level in Sao Paulo city and characterize the isolates for the presence of the following virulence factors: stx1, stx2, eae and ehx. 248 samples were collected in different districts of Sao Paulo city. For the detection of E. coli O157 serogroup the methodology ISO 16654 was used and for the detection of serogroups O103, O111, O145 and O26 the methodology described by the Surveillance Group for Diseases and Infections of Animals (NRM 006) was used. One sample of ground beef (0.4%) showed the presence of the microorganism studied. The biochemical and genotypical identification characterized this isolate as STEC O157:H7, carrying all of the investigated virulence factors: stx1, stx2, eae and ehx. The expression of stx proteins in Vero cells was also observed. This is the first report on the isolation of E. coli O157:H7 Shiga toxin-producing from ground beef in Brazil.

Growth of Escherichia coli A-l under aerobic conditions in an enriched medium with a total amount of 0.2 per cent glucose was biphasic and asparaginase II activity was detected after depletion of ammonia from the growth medium in the second phase of growth. Glucose was exhausted two hours before ammonia and three hours before asparaginase II activity was detected. The concentration of 3',5'-cyclic adenosine monophosphate was found to fluctuate when the dissolved oxygen in the medium reached a low level, when glucose and ammonia were exhausted, and when the cells entered the second stationary phase of growth. Culture tube studies of the growth of E_j_ coli A-l in three per cent nutrient broth with varied concentrations of ammonium chloride and potassium nitrate gave lower specific activity of asparaginase II when this was compared to that seen in three per cent nutrient broth alone. The addition of glucose to the same medium before asparaginase II activity was detected resulted in the production of acid by E. coli A-l with cessation of growth; however, addition after L-asparaginase synthesis had started did not affect the specific activity of the enzyme. The addition of ammonium chloride suppressed L-asparaginase synthesis, but addition after enzyme synthesis started had no affect. These findings suggest that asparaginase II is produced by E. coli A-l in response to low concentrations of ammonia and that exogenously supplied nitrogen compounds may play a major role in the regulation of this enzyme. It is suggested that E. coli A-l produced L-asparaginase in order to obtain ammonia for the synthesis of glutamine from glutamate. The synthesis of glutamine from glutamate is the first step of a highly branched pathway which ultimately leads to the synthesis of many of the important macromolecules of the cell.

In this project, a neural network based system is used to classify the promoter regions found in Escherichia coli DNA sequences. An unsupervised algorithm based on the self-organizing feature map is used to classify the sequences and a dynamic programming algorithm is used too query the trained neural networks. In order to generalize the neural network's weights for display purposes, a back propagation supervised learning algorithm based on the conjugate gradient method is used to map the weights to one of the fifteen combinations of adenine, cytosine, guanine, and thymine (the chemical components of DNA). The results show that this method is able to classify the training sequences into discrete sub-classes which provide a query base for classifying new sequences. This method can be used for any class of sequences and can be extended for use in searching sequence databases. / Thesis / Master of Science (MS)

The carbamoyl region of the active site of aspartate transcarbamoylase from Escherichia coli was probed using an enzyme assay in which the two substrates were varied near their respective K_m 's. The inhibitors tested, some synthesized and some commercially available, were chosen to satisfy the structural requirements for binding to either the dicarboxylate or phosphate region with a substituent capable of extending into the carbamoyl region. However, the dicarboxylate based inhibitors were found to bind in an abnormal manner (unlike L-aspartate or succinate on which they were based). The carbamoyl region was found to contain a positively charged side-chain and preliminary results indicate that tetrahedral groups are not preferred over trigonal moieties. It is suggested that electrostatic stabilization of the negative charge which develops in the transition state may be a major factor in promoting catalysis. The identity of this charged group in the carbamoyl region is postulated to be His134 based on available X-ray diffraction data. The binding subsites of the active site of this enzyme were also found to be oriented in essentially the same plane. These results will greatly aid in the design of future mechanism-based inhibitors to this enzyme that may have therapeutic value (at this time the mammalian enzyme is thought to have a similar catalytic mechanism). / Thesis / Master of Science (MS)