Molecular details of INH-C-10 binding to wt KatG and Its S315T mutant

Isoniazid (INH) is still one of the two most effective antitubercular drugs and is included in all recommended multitherapeutic regimens. Because of the increasing resistance of Mycobacterium tuberculosis to INH, mainly associated with mutations in the katG gene, new INH-based compounds have been proposed to circumvent this problem. In this work, we present a detailed comparative study of the molecular determinants of the interactions between wt KatG or its S315T mutant form and either INH or INH-C10, a new acylated INH derivative. MD simulations were used to explore the conformational space of both proteins, and results indicate that the S315T mutation did not have a significant impact on the average size of the access tunnel in the vicinity of these residues. Our simulations also indicate that the steric hindrance role assigned to Asp137 is transient and that electrostatic changes can be important in understanding the enzyme activity data of mutations in KatG. Additionally, molecular docking studies were used to determine the preferred modes of binding of the two substrates. Upon mutation, the apparently less favored docking solution for reaction became the most abundant, suggesting that S315T mutation favors less optimal binding modes. Moreover, the aliphatic tail in INH-C10 seems to bring the hydrazine group closer to the heme, thus favoring the apparent most reactive binding mode, regardless of the enzyme form. The ITC data is in agreement with our interpretation of the C10 alkyl chain role and helped to rationalize the significantly lower experimental MIC value observed for INH-C10. This compound seems to be able to counterbalance most of the conformational restrictions introduced by the mutation, which are thought to be responsible for the decrease in INH activity in the mutated strain. Therefore, INH-C10 appears to be a very promising lead compound for drug development.

Congruences on monoids of order-preserving or order-reversing transformations on a finite chain

Glasgow Mathematical Journal, nº 47 (2005), pg. 413-424

The value of adenosine deaminase (ADA) determination in the diagnosis of tuberculous ascites

In order to evaluate the role of the determination of adenosine deaminase activity (ADA) in ascitic fluid for the diagnosis of tuberculosis, 44 patients were studied. Based on biochemical, cytological, histopathological and microbiological tests, the patients were divided into 5 groups: G1 - tuberculous ascites (n = 8); G2 - malignant ascites (n = 13); G3 - spontaneous bacterial peritonitis (n = 6); G4 - pancreatic ascites (n = 2); G5 - miscelaneous ascites (n = 15). ADA concentration were significantly higher in G1 (133.50 ± 24.74 U/l) compared to the other groups (G2 = 41.85 ± 52.07 U/l; G3 = 10.63 ± 5.87 U/l; G4 = 18.00 ± 7.07 U/l; G5 = 11.23 ± 7.66 U/l). At a cut-off value of >31 U/l, the sensitivity, specificity and positive and negative preditive values were 100%, 92%, 72% and 100%, respectively. ADA concentrations as high as in tuberculous ascites were only found in two malignant ascites caused by lymphoma. We conclude that ADA determination in ascitic fluid is a useful and reliable screening test for diagnosing tuberculous ascites. Values of ADA higher than 31 U/l indicate more invasive methods to confirm the diagnosis of tuberculosis.

Determinants of frailty: the added value of assessing medication

This study aims to analyze which determinants predict frailty in general and each frailty domain (physical, psychological, and social), considering the integral conceptual model of frailty, and particularly to examine the contribution of medication in this prediction. A cross-sectional study was designed using a non-probabilistic sample of 252 community-dwelling elderly from three Portuguese cities. Frailty and determinants of frailty were assessed with the Tilburg Frailty Indicator. The amount and type of different daily-consumed medication were also examined. Hierarchical regression analysis were conducted. The mean age of the participants was 79.2 years (±7.3), and most of them were women (75.8%), widowed (55.6%) and with a low educational level (0–4 years: 63.9%). In this study, determinants explained 46% of the variance of total frailty, and 39.8, 25.3, and 27.7% of physical, psychological, and social frailty respectively. Age, gender, income, death of a loved one in the past year, lifestyle, satisfaction with living environment and self-reported comorbidity predicted total frailty, while each frailty domain was associated with a different set of determinants. The number of daily-consumed drugs was independently associated with physical frailty, and the consumption of medication for the cardiovascular system and for the blood and blood-forming organs explained part of the variance of total and physical frailty. The adverse effects of polymedication and its direct link with the level of comorbidities could explain the independent contribution of the amount of prescribed drugs to frailty prediction. On the other hand, findings in regard to medication type provide further evidence of the association of frailty with cardiovascular risk. In the present study, a significant part of frailty was predicted, and the different contributions of each determinant to frailty domains highlight the relevance of the integral model of frailty. The added value of a simple assessment of medication was considerable, and it should be taken into account for effective identification of frailty.

Presentations for some monoids of injective partial transformations on a finite chain.

Communications in Algebra, 33 (2005), p. 587-604

The cardinal and the idempotent number of various monoids of transformations on a finite chain

Bulletin of the Malaysian Mathematical Sciences Society, 2, 34 (1),(2011), p. 79–85

Detection and identification of dengue virus isolates from Brazil by a simplified reverse transcription - polymerase chain reaction (RT-PCR) method

We show here a simplified RT-PCR for identification of dengue virus types 1 and 2. Five dengue virus strains, isolated from Brazilian patients, and yellow fever vaccine 17DD as a negative control, were used in this study. C6/36 cells were infected and supernatants were collected after 7 days. The RT-PCR, done in a single reaction vessel, was carried out following a 1/10 dilution of virus in distilled water or in a detergent mixture containing Nonidet P40. The 50 µl assay reaction mixture included 50 pmol of specific primers amplifying a 482 base pair sequence for dengue type 1 and 210 base pair sequence for dengue type 2. In other assays, we used dengue virus consensus primers having maximum sequence similarity to the four serotypes, amplifying a 511 base pair sequence. The reaction mixture also contained 0.1 mM of the four deoxynucleoside triphosphates, 7.5 U of reverse transcriptase, 1U of thermostable Taq DNA polymerase. The mixture was incubated for 5 minutes at 37ºC for reverse transcription followed by 30 cycles of two-step PCR amplification (92ºC for 60 seconds, 53ºC for 60 seconds) with slow temperature increment. The PCR products were subjected to 1.7% agarose gel electrophoresis and visualized by UV light after staining with ethidium bromide solution. Low virus titer around 10 3, 6 TCID50/ml was detected by RT-PCR for dengue type 1. Specific DNA amplification was observed with all the Brazilian dengue strains by using dengue virus consensus primers. As compared to other RT-PCRs, this assay is less laborious, done in a shorter time, and has reduced risk of contamination

Differentiation of pathogenic and non-pathogenic leptospires by means of the polymerase chain reaction

A polymerase chain reaction was carried out to detect pathogenic leptospires isolated from animals and humans in Argentina. A double set of primers (G1/G2, B64-I/B64-II), described before, were used to amplify by PCR a DNA fragment from serogroups belonging to Leptospira interrogans but did not allow to detect saprophytic strains isolated from soil and water (L. biflexa). This fact represents an advantage since it makes possible the differentiation of pathogenic from non-pathogenic leptospires in cultures. The sensitivity of this assay has been determined, allowing to detect just only 10 leptospires in the reaction tube. Those sets of primers generated either a 285 bp or 360 bp fragment, depending on the pathogenic strain

Implementação do sistema integrado de gestão da qualidade e de investigação, desenvolvimento e inovação (IDI) na Escola Superior de Tecnologia e Gestão de Felgueiras (ESTGF)

Mestrado em Gestão Integrada da Qualidade, Ambiente e Segurança

Detection of mycoplasmas in urethral swabs from HIV-1 infected patients and control individuals using culture techniques and polymerase chain reaction

The objective of the present study was to determine the prevalence of certain mycoplasma species, i.e., Mycoplasma hominis, Ureaplasma urealyticum and Mycoplasma penetrans, in urethral swabs from HIV-1 infected patients compared to swabs from a control group. Mycoplasmas were detected by routine culture techniques and by the Polymerase Chain Reaction (PCR) technique, using 16SrRNA generic primers of conserved region and Mycoplasma penetrans specific primers. The positivity rates obtained with the two methods were comparable. Nevertheless, PCR was more sensitive, while the culture techniques allowed the quantification of the isolates. The results showed no significant difference (p < 0.05) in positivity rates between the methods used for mycoplasma detection.

Projecto solvência II - Modelação do risco de subscrição numa companhia de seguros não vida

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para obtenção do grau de Mestre em Matemática e Aplicações - Actuariado, Estatística e Investigação Operacional

Lean enterprise resource planning

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para obtenção do grau de Mestre em Engenharia e Gestão Industrial

Models and tools for value systems analysis in collaborative environments

Dissertation to obtain the degree of Doctor in Electrical and Computer Engineering, specialization of Collaborative Networks

Susceptibility of Biomphalaria tenagophila and Biomphalaria straminea to Schistosoma mansoni infection detected by low stringency polymerase chain reaction

In order to determine Schistosoma mansoni infection rates in Biomphalaria tenagophila and B. straminea, low stringency polymerase chain reaction (LS-PCR) technique was used as a complementary method to light exposure technique. LS-PCR has already been standardized in our laboratory to detect the trematode DNA in B. glabrata. Higher S. mansoni infection rates were detected using conventional method and LS-PCR. The parasite DNA profile was detected in both species after 7-day exposure to miracidia, using LS-PCR. This technique enables early detection of schistosomiasis transmission focuses, in endemic areas, before the beginning of cercariae shedding.

Polymerase chain reaction (PCR) for the detection of Salmonella in artificially inoculated chicken meat

The aim of this study was to develop a polymerase chain reaction (PCR) protocol for the detection of Salmonella in artificially contaminated chicken meat. Tests were performed with different dilutions of Salmonella Typhimurium or Salmonella Enteritidis cells (10-7, 10-8 or 10-9 CFU/mL) inoculated in chicken meat samples, in order to establish the limits of detection, incubation times (0, 6, 8 and 24 hours of pre-enrichment in PBW 1%) and three DNA extraction protocols (phenol-chloroform, thermal treatment and thermal treatment and Sephaglass). The assay was able to detect until 10-9 CFU/mL of initial dilution of Salmonella cells inoculated in chicken meat, which allows detection of Salmonella within 48 hours, including 24 hours of pre-enrichment and using the phenol-chloroform DNA extraction protocol. As the results are obtained in a shorter time period than that of microbiological culture, this procedure will be useful in the methodology for detection of Salmonella in chicken.