Genomic characterization of adenovirus serotype 7 isolated in Brazil from acute respiratory disease patients during the period from 1980 to 1991

Forty isolates of adenovirus type 7 were analized by restriction enzyme digestion with BamHI, SmaI, EcoRI and HindIII. These isolates were obtained from acute respiratory disease patients during the years 1980 to 1991. Only two genomic types were found: Ad7b and Ad7e, with Ad7b (87.5%) being more frequent than Ad7e (12.5%). The genomic type Ad7e appeared in the years 1980, 1981 and 1983. Ad7b appeared in 1982 and it was the only genomic type found from 1984 to 1991. Both genomic types were responsible for lower (LRTI) and upper (URTI) respiratory tract infection, but the proportion LRTI/URTI is higher for Ad7b (25/6) than for Ad7e (1/4).

New Strategies on Molecular Biology Applied to Microbial Systematics

Systematics is the study of diversity of the organisms and their relationships comprising classification, nomenclature and identification. The term classification or taxonomy means the arrangement of the organisms in groups (rate) and the nomenclature is the attribution of correct international scientific names to organisms and identification is the inclusion of unknown strains in groups derived from classification. Therefore, classification for a stable nomenclature and a perfect identification are required previously. The beginning of the new bacterial systematics era can be remembered by the introduction and application of new taxonomic concepts and techniques, from the 50’s and 60’s. Important progress were achieved using numerical taxonomy and molecular taxonomy. Molecular taxonomy, brought into effect after the emergence of the Molecular Biology resources, provided knowledge that comprises systematics of bacteria, in which occurs great evolutionary interest, or where is observed the necessity of eliminating any environmental interference. When you study the composition and disposition of nucleotides in certain portions of the genetic material, you study searching their genome, much less susceptible to environmental alterations than proteins, codified based on it. In the molecular taxonomy, you can research both DNA and RNA, and the main techniques that have been used in the systematics comprise the build of restriction maps, DNA-DNA hybridization, DNA-RNA hybridization, sequencing of DNA sequencing of sub-units 16S and 23S of rRNA, RAPD, RFLP, PFGE etc. Techniques such as base sequencing, though they are extremely sensible and greatly precise, are relatively onerous and impracticable to the great majority of the bacterial taxonomy laboratories. Several specialized techniques have been applied to taxonomic studies of microorganisms. In the last years, these have included preliminary electrophoretic analysis of soluble proteins and isoenzymes, and subsequently determination of deoxyribonucleic acid base composition and assessment of base sequence homology by means of DNA-RNA hybrid experiments beside others. These various techniques, as expected, have generally indicated a lack of taxonomic information in microbial systematics. There are numberless techniques and methodologies that make bacteria identification and classification study possible, part of them described here, allowing establish different degrees of subspecific and interspecific similarity through phenetic-genetic polymorphism analysis. However, was pointed out the necessity of using more than one technique for better establish similarity degrees within microorganisms. Obtaining data resulting from application of a sole technique isolatedly may not provide significant information from Bacterial Systematics viewpoint

Meningococcal Disease Caused by Neisseria meningitidis Serogroup B Serotype 4 in São Paulo, Brazil, 1990 to 1996

A large epidemic of serogroup B meningococcal disease (MD), has been occurring in greater São Paulo, Brazil, since 1988.21 A Cuban-produced vaccine, based on outer-membrane-protein (OMP) from serogroup B: serotype 4: serosubtype P1.15 (B:4:P1.15) Neisseria meningitidis, was given to about 2.4 million children aged from 3 months to 6 years during 1989 and 1990. The administration of vaccine had little or no measurable effects on this outbreak. In order to detect clonal changes that could explain the continued increase in the incidence of disease after the vaccination, we serotyped isolates recovered between 1990 and 1996 from 834 patients with systemic disease. Strains B:4:P1.15, which was detected in the area as early as 1977, has been the most prevalent phenotype since 1988. These strains are still prevalent in the area and were responsible for about 68% of 834 serogroup B cases in the last 7 years. We analyzed 438 (52%) of these strains by restriction fragment length polymorphism (RFLPs) of rRNA genes (ribotyping). The most frequent pattern obtained was referred to as Rb1 (68%). We concluded that the same clone of B:4:P1.15-Rb1 strains was the most prevalent strain and responsible for the continued increase of incidence of serogroup B MD cases in greater São Paulo during the last 7 years in spite of the vaccination trial.

Genetic diversity of arginine catabolic mobile element in Staphylococcus epidermidis

PLos One, 4(11): ARTe7722

Alternativas Processuais e Valorização de Correntes da Refinaria de Matosinhos.

Evolução, ato ou efeito de evoluir, sequência de transformações, desenvolvimento progressivo. Se tudo à nossa volta se transforma, a indústria tem de acompanhar esse sistema evolutivo, tornando assim imprescindível alterar ou melhorar processos de produção quando estes não se enquadram com a realidade, ou porque o mercado se altera, ou porque as necessidades mudam, ou por simplesmente ser mais rentável. Sendo a Galp Energia uma empresa que se encontra sempre na vanguarda da evolução tecnológica, encontra no Departamento de Engenharia Química do Instituto Superior de Engenharia do Porto um aliado na procura do melhor modo de valorizar os seus produtos. A Refinaria de Matosinhos tem atualmente duas correntes de gasolina leve e uma de refinado que apresentam grande potencialidade de valorização. Parte destas correntes incorporam atualmente a pool de nafta química da refinaria que é vendida à Repsol Polímeros. O desafio que é proposto baseia-se em valorizar essas correntes através da sua isomerização aumentando o seu RON podendo então ter como fim a pool de gasolinas. Tirando partido da tecnologia disponível para este efeito são apresentados quatro cenários de possíveis soluções. Sendo os dois primeiros excluídos por violarem restrições impostas, o terceiro e quarto cenários foram analisados de um ponto de vista económico. O terceiro cenário conduz a gasolina leve da Fábrica de Aromáticos para a pool de gasolinas sem qualquer tratamento e a gasolina leve da Fábrica de Combustíveis continua a integrar a pool de nafta química. O refinado da Fábrica de Aromáticos será enviado para um splitter, sendo a corrente de topo destinada à pool de nafta química e a corrente de fundo enviada a um reator de isomerização, Isomalk-4SM, passando previamente por uma torre de argila de forma a assegurar que a restrição em teor de olefinas no reator não é violada. O efluente, com RON maior, integrará igualmente a pool de gasolinas. No quarto cenário a corrente de refinado da Fábrica de Aromáticos não sofre qualquer tratamento, continuando a alimentar a unidade de solventes, a gasolina leve da Fábrica de Aromáticos irá diretamente para a pool de gasolinas e a gasolina leve da Fábrica de Combustíveis passará pelo Isomalk-2SM para aumentar o índice de octanos garantido assim ter condições de integrar a pool de gasolinas. Dissertação de Mestrado em Engenharia Química Isomerização de Gasolina Leve O terceiro cenário apresenta um aumento de 4 576 773 € anuais nas receitas e o quarto alcança 11 333 982 € anuais. O investimento inicial total do terceiro cenário é de 28 821 608 € quando o quarto cenário carece de um investimento inicial de apenas 18 028 349 €. Quanto aos custos associados à implementação da unidade estes demonstram-se elevados, o terceiro cenário apresenta um custo de 23 133 429 € enquanto o do quarto cenário é de 13 998 797 €. O quarto cenário apresenta-se assim como a solução mais rentável para o objetivo desta dissertação.

Constraint-based modeling of minimum set covering: application to species differentation

Work presented in the context of the European Master in Computational Logics, as partial requisit for the graduation as Master in Computational Logics

Biological and genetic characteristics of uropathogenic Escherichia coli strains

The aim of the present study was to determine biological characteristics such as expression of fimbriae, Congo red binding, production of hemolysin and aerobactin, adhesion to HeLa and uroepithelial cells and invasion of HeLa cells by Escherichia coli isolates obtained from patients showing clinical signs of urinary tract infection (UTI). Also, the presence of genes (apa, afa, spa) for fimbria expression and cytotoxic necrotizing factors (CNF1, CNF2) was assayed using specific primers in PCR. The data obtained were compared with the clonal relationships obtained by analysis of multilocus enzyme electrophoresis (MLEE), restriction fragment length polymorphism (RFLP) of the rDNA (ribotyping) and enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR). All isolates but one presented a combination of at least two of the characteristics studied, a fact suggesting the presence of pathogenicity islands (PAIs). Diffuse adherence type to HeLa cells was observed to occur in most of the strains, but adhesion to uroepithelial cells seems to be a more reliable test to verify pathogenicity. Although four strains seemed to be able to invade HeLa cells when assayed by light microscopy, electron microscopy studies demonstrated that these strains were not invasive. MLEE, RFLP and ERIC-PCR were able to group the isolates differently into main clusters that were not correlated with the presence of pathogenic traits.

Incremental Recomputation of Pig Latin’s Nest and Unnest Operators

This master’s thesis addresses the maintenance of pre-computed structures, which store a frequent or expensive query, for the nested bag data type in the high level work-flow language Pig Latin. This thesis defines a model suitable to accommodate incremental expressions over nested bags on Pig Latin. Afterwards, the partitioned normal form for sets is extended with further restrictions, in order to accommodate the nested bag model, allow the Pig Latin nest and unnest operators revert each other, and create a suitable environment to the incremental computations. Subsequently, the extended operators – extended union and extended difference – are defined for the nested bag data model with the partitioned normal form for bags (PNF Bag) restriction, and semantics for the extended operators are given. Finally, incremental data propagation expressions are proposed for the nest and unnest operators on the data model proposed with the PNF Bag restriction, and the proof of correctness is given.

Molecular typing of dengue virus type 2 in Brazil

Strain typing is a critical tool for molecular epidemiological analysis and can provide important information about the spread of dengue viruses. Here, we performed a molecular characterization of DEN-2 viruses isolated in Brazil during 1990-2000 from geographically and temporally distinct areas in order to investigate the genetic distribution of this serotype circulating in the country. Restriction site-specific polymerase chain reaction (RSS)-PCR presented the same pattern for all 52 Brazilian samples, showing the circulation of just one DEN-2 variant. Phylogenetic analysis using progressive pairwise alignments from 240-nucleotide sequences of the E/NS1 junction in 15 isolates showed that they belong to genotype III (Jamaica genotype).

Analysis of the clonal relationship among clinical isolates of Salmonella enterica serovar Infantis by different typing methods

Salmonella Infantis has been the second most common serovar in Argentina in the last two years, being isolated mostly from paediatric hospitalised patients. In order to determine the clonal relationship among Salmonella Infantis strains, we examined 15 isolates from paediatric patient faeces in Argentina (12 geographically related and 3 geographically non-related) by using antimicrobial susceptibility, plasmid profiling, repetitive extragenic palindromic (REP) PCR, enterobacterial repetitive intergenic consensus (ERIC) PCR, and low-frequency restriction analysis of chromosomal DNA by pulsed field gel electrophoresis (PFGE). Four Spanish strains were included as controls of clonal diversity in molecular techniques. Antibiotype and plasmid profile was not useful as epidemiological tools. PFGE and REP-PCR were able to discriminate between Argentinean and Spanish isolates of Salmonella Infantis allowing to detect genetically related strains in three different cities. This finding indicates that a possible spread of a clone of this serovar in the North-eastern Region of Argentina has taken place in 1998.

Adenoviruses isolated from civilian and military personnel in the city of Rio de Janeiro, Brazil

Adenovirus are important pathogen primarily associated to respiratory infections of children and military personnel, even though it is also associated to cases of conjunctivitis and keratoconjunctivitis. We analyzed respiratory secretion collected from subjects with and without respiratory infection symptoms, being 181 civilians and 221 military subjects. The samples were inoculated in HEp-2 and/or A549 tissue cultures for viral isolation. Samples presenting cytopathogenic effect (CPE) in any tissue culture were tested by a polymerase chain reaction (PCR) assay to confirm adenovirus isolation. The isolates confirmed as adenovirus were further analyzed by restriction endonuclease assay for determination of viral species. Three isolates were identified as specie A (two from civilian and one from military), one isolate from military was identified as specie C, and one isolate from civilian was identified as specie D. For two isolates the specie could not be identified.

Mapping of a Leishmania major gene/locus that confers pentamidine resistance by deletion and insertion of transposable element

Pentamidine (PEN) is an alternative compound to treat antimony-resistant leishmaniasis patients, which cellular target remains unclear. One approach to the identification of prospective targets is to identify genes able to mediate PEN resistance following overexpression. Starting from a genomic library of transfected parasites bearing a multicopy episomal cosmid vector containing wild-type Leishmania major DNA, we isolated one locus capable to render PEN resistance to wild type cells after DNA transfection. In order to map this Leishmania locus, cosmid insert was deleted by two successive sets of partial digestion with restriction enzymes, followed by transfection into wild type cells, overexpression, induction and functional tests in the presence of PEN. To determine the Leishmania gene related to PEN resistance, nucleotide sequencing experiments were done through insertion of the transposon Mariner element of Drosophila melanogaster (mosK) into the deleted insert to work as primer island. Using general molecular techniques, we described here this method that permits a quickly identification of a functional gene facilitating nucleotide sequence experiments from large DNA fragments. Followed experiments revealed the presence of a P-Glycoprotein gene in this locus which role in Leishmania metabolism has now been analyzed.

Adolescents and School Asthma Knowledge and Attitudes

Introduction: bronchial asthma is a chronic disease that affects a high percentage of adolescents, with a significant restriction of daily activities, and is a cause of school absenteeism. The relationships between adolescents and asthma disease in school were assessed, with a view to improving knowledge about the asthmatic adolescent. Methods: a survey was conducted in the Lisbon metropolitan area, covering urban (Lisbon) and rural (Lourinh˜a ) zones and including 1879 students and 81 teachers from the 7th to 9th high school years. The study groups were asthmatic students, their peers, and teachers. A self-administered questionnaire was applied to collect information. The results were compared with a reference group of 91 asthmatic students attending our Department of Immunoallergy-Hospital Dona Estefânia. Cotinine urinary measurements were made in a sample of asthmatics and a control group. Results: the prevalence of current asthma among students was 10%. Estimates of asthma annual burden among 7th to 9th year students from Lisbon and Lourinh˜a high schools included 4,307 days missed from school, 4,148 medical consultations and a minimum of 351 hospital emergency care and 80 hospital admissions. Exposure to passive smoking was not significantly different between asthmatic students and theirs peers. Cotinine urinary measurements did not discriminate between exposed and non-exposed individuals. Cigarette smoking was almost as common among adolescent asthmatics (5.4%) as it was in non-asthmatic subjects (6.7%). However, 55% of asthmatics mentioned active and passive smoking as an asthma exacerbating factor. Asthmatic students, theirs peers and teachers showed a deficient knowledge about asthma (mean group scores: 17.6; 14.2 and 17.7 of a possible 30), particularly in the areas related to asthma recognition and its management. Asthmatics attending our Allergy Department had the highest scores. All groups showed tolerance in the sense of a positive and understanding attitude toward a person with asthma. However, traditional beliefs about asthma disease (dependence, inferiority...) were confirmed. A positive correlation between knowledge levels and tolerance attitudes was found. Conclusion: in view of the dimension of the asthma problem in adolescence and its social and economic impact, it is justifiable to assess the need for the implementation of asthma education programs in schools in order to improve asthma management by the adolescents and their schools.

Human vaccinia-like virus outbreaks in São Paulo and Goiás States, Brazil: virus detection, isolation and identification

Since October 2001, the Adolfo Lutz Institute has been receiving vesicular fluids and scab specimens of patients from Paraíba Valley region in the São Paulo and Minas Gerais States and from São Patricio Valley, in the Goiás State. Epidemiological data suggested that the outbreaks were caused by Cowpox virus or Vaccinia virus. Most of the patients are dairy milkers that had vesiculo-pustular lesions on the hands, arms, forearms, and some of them, on the face. Virus particles with orthopoxvirus morphology were detected by direct electron microscopy (DEM) in samples of 49 (66.21%) patients of a total of 74 analyzed. Viruses were isolated in Vero cell culture and on chorioallantoic membrane (CAM) of embryonated chicken eggs. Among 21 samples submitted to PCR using primers for hemagglutinin (HA) gene, 19 were positive. Restriction digestion with TaqI resulted in four characteristic Vaccinia virus fragments. HA nucleotide sequences showed 99.9% similarity with Cantagalo virus, described as a strain of Vaccinia virus. The only difference observed was the substitution of one nucleotide in the position 616 leading to change in one amino acid of the protein in the position 206. The phylogenetic analysis showed that the isolates clustered together with Cantagalo virus, other Vaccinia strains and Rabbitpox virus.

Toxoplasma gondii genotyping in a dog co-infected with distemper virus and ehrlichiosis rickettsia

This paper reports a toxoplasmosis, erhlichiosis and distemper co-infection in a dog with an exuberant neuropathological clinical picture. Primary involvement was discussed based on information collected in the analysis of the clinical case, such as neurological impairment, epidemiological data, poor immunoprophylactic scheme of the dog affected and the role of these diseases on immunosuppression. Canine distemper and ehrlichiosis were diagnosed based on epidemiologic data, clinical signs, hematological and cytological evaluation. Toxoplasma gondii was isolated and genetically characterized as Type I using restriction analysis (RFLP) with SAG-2 genes. Immunosuppression features of both dogs and human beings are discussed, as well as implications on animal and public health. This is the first report on toxoplasmosis, ehrlichiosis and distemper co-infection in a dog in Brazil, associated with genotyping determination of the T. gondii strain involved.