Prediction of drug targets in human pathogens

The identification of new and druggable targets in bacteria is a critical endeavour in pharmaceutical research of novel antibiotics to fight infectious agents. The rapid emergence of resistant bacteria makes today's antibiotics more and more ineffective, consequently increasing the need for new pharmacological targets and novel classes of antibacterial drugs. A new model that combines the singular value decomposition technique with biological filters comprised of a set of protein properties associated with bacterial drug targets and similarity to protein-coding essential genes of E. coli has been developed to predict potential drug targets in the Enterobacteriaceae family [1]. This model identified 99 potential target proteins amongst the studied bacterial family, exhibiting eight different functions that suggest that the disruption of the activities of these proteins is critical for cells. Out of these candidates, one was selected for target confirmation. To find target modulators, receptor-based pharmacophore hypotheses were built and used in the screening of a virtual library of compounds. Postscreening filters were based on physicochemical and topological similarity to known Gram-negative antibiotics and applied to the retrieved compounds. Screening hits passing all filters were docked into the proteins catalytic groove and 15 of the most promising compounds were purchased from their chemical vendors to be experimentally tested in vitro. To the best of our knowledge, this is the first attempt to rationalize the search of compounds to probe the relevance of this candidate as a new pharmacological target.

Effects of light and temperature on isoprene emission at different leaf developmental stages of eschweilera coriacea in central Amazon

Isoprene emission from plants accounts for about one third of annual global volatile organic compound emissions. The largest source of isoprene for the global atmosphere is the Amazon Basin. This study aimed to identify and quantify the isoprene emission and photosynthesis at different levels of light intensity and leaf temperature, in three phenological phases (young mature leaf, old mature leaf and senescent leaf) of Eschweilera coriacea (Matamatá verdadeira), the species with the widest distribution in the central Amazon. In situ photosynthesis and isoprene emission measurements showed that young mature leaf had the highest rates at all light intensities and leaf temperatures. Additionally, it was observed that isoprene emission capacity (Es) changed considerably over different leaf ages. This suggests that aging leads to a reduction of both leaf photosynthetic activity and isoprene production and emission. The algorithm of Guenther et al. (1999) provided good fits to the data when incident light was varied, however differences among E S of all leaf ages influenced on quantic yield predicted by model. When leaf temperature was varied, algorithm prediction was not satisfactory for temperature higher than ~40 °C; this could be because our data did not show isoprene temperature optimum up to 45 °C. Our results are consistent with the hypothesis of the isoprene functional role in protecting plants from high temperatures and highlight the need to include leaf phenology effects in isoprene emission models.

Politically driven cycles in fiscal policy: in depth analysis of the functional components of government expenditures

NIPE - WP 02/2016

The Data Mining applied for the prediction of highway roughness due to overloaded trucks

Currently, the quality of the Indonesian national road network is inadequate due to several constraints, including overcapacity and overloaded trucks. The high deterioration rate of the road infrastructure in developing countries along with major budgetary restrictions and high growth in traffic have led to an emerging need for improving the performance of the highway maintenance system. However, the high number of intervening factors and their complex effects require advanced tools to successfully solve this problem. The high learning capabilities of Data Mining (DM) are a powerful solution to this problem. In the past, these tools have been successfully applied to solve complex and multi-dimensional problems in various scientific fields. Therefore, it is expected that DM can be used to analyze the large amount of data regarding the pavement and traffic, identify the relationship between variables, and provide information regarding the prediction of the data. In this paper, we present a new approach to predict the International Roughness Index (IRI) of pavement based on DM techniques. DM was used to analyze the initial IRI data, including age, Equivalent Single Axle Load (ESAL), crack, potholes, rutting, and long cracks. This model was developed and verified using data from an Integrated Indonesia Road Management System (IIRMS) that was measured with the National Association of Australian State Road Authorities (NAASRA) roughness meter. The results of the proposed approach are compared with the IIRMS analytical model adapted to the IRI, and the advantages of the new approach are highlighted. We show that the novel data-driven model is able to learn (with high accuracy) the complex relationships between the IRI and the contributing factors of overloaded trucks

Fluorescence-based approaches towards the assessment of structural and functional alterations in lysosomes and vacuoles induced by lactoferrin and acetic acid

Dissertação de mestrado em Biofísica e Bionanossistemas

Unnatural amino acids as functional building blocks for fluorophore-labelled peptides

Comunicação oral convidada - IL4

Highly functional and biodegradable nanofibrous scaffolds combined with stem cells for bone and cartilage tissue engineering

Among the various possible embodiements of Advanced Therapies and in particular of Tissue Engineering the use of temporary scaffolds to regenerate tissue defects is one of the key issues. The scaffolds should be specifically designed to create environments that promote tissue development and not merely to support the maintenance of communities of cells. To achieve that goal, highly functional scaffolds may combine specific morphologies and surface chemistry with the local release of bioactive agents. Many biomaterials have been proposed to produce scaffolds aiming the regeneration of a wealth of human tissues. We have a particular interest in developing systems based in nanofibrous biodegradable polymers1,2. Those demanding applications require a combination of mechanical properties, processability, cell-friendly surfaces and tunable biodegradability that need to be tailored for the specific application envisioned. Those biomaterials are usually processed by different routes into devices with wide range of morphologies such as biodegradable fibers and meshes, films or particles and adaptable to different biomedical applications. In our approach, we combine the temporary scaffolds populated with therapeutically relevant communities of cells to generate a hybrid implant. For that we have explored different sources of adult and also embryonic stem cells. We are exploring the use of adult MSCs3, namely obtained from the bone marrow for the development autologous-based therapies. We also develop strategies based in extra-embryonic tissues, such as amniotic fluid (AF) and the perivascular region of the umbilical cord4 (Whartonâ s Jelly, WJ). Those tissues offer many advantages over both embryonic and other adult stem cell sourcess. These tissues are frequently discarded at parturition and its extracorporeal nature facilitates tissue donation by the patients. The comparatively large volume of tissue and ease of physical manipulation facilitates the isolation of larger numbers of stem cells. The fetal stem cells appear to have more pronounced immunomodulatory properties than adult MSCs. This allogeneic escape mechanism may be of therapeutic value, because the transplantation of readily available allogeneic human MSCs would be preferable as opposed to the required expansion stage (involving both time and logistic effort) of autologous cells. Topics to be covered: This talk will review our latest developments of nanostructured-based biomaterials and scaffolds in combination with stem cells for bone and cartilage tissue engineering.

Evolution of the functional properties of titanium–silver thin films for biomedical applications: Influence of in-vacuum annealing

In this work, the thermal stability of TiAgx thin films, deposited by magnetron sputtering, was evaluated, envisaging their application in biomedical devices, namely as electrodes for biosignal acquisition. Based on the composition and microstructural characterization, a set of four representative TiAgx thin films was selected in order to infer whether they are thermally stable in terms of functional properties. In order to achieve this purpose, the structural and morphological evolution of the films with annealing temperature was correlated with their electrical, mechanical and thermal properties. Two distinct zones were identified and two samples from each zone were extensively analysed. In the first zone (zone I), Ti was the main component (Ti-rich zone) while in the second, zone II, the Ag content was more significant. The selected samples were annealed in vacuum at four different temperatures up to 500 oC. For the samples produced within zone I, small microstructural changes were observed due to the recrystallization of the Ti structure and grain size increment. Also, no significant changes were observed with annealing temperature regarding the f l ’ functional properties, being thermally stable up to 500 oC. For higher Ag contents (zone II) the energy supplied by thermal treatments was sufficient to activate the crystallization of Ti-Ag intermetallic phases. A strong increase of the grain size of these phases was also reported. The structural and morphological organization proved to be determinant for the physical responses of the TiAgx system. The hardness and Y g’s modulus were significantly improved with the formation of the intermetallic phases. The silver addition and annealing treatments also played an important role in the electrical conductivity of the films, which was once again improved by the formation of Ti-Ag phases. The thermal diffusivity of the films was practically unchanged with the heat-treatment. This set of results shows that this intermetallic-like thin film system has good thermal stability up to high temperatures (as high as 500 oC), which in case of the highest Ag content zone is particularly evident for electrical and mechanical properties, showing an important improvement. Hardness increases about three times, while resistivity values become half of those from the lowest Ag contents zone. These set of characteristics are consistent with the targeted applications, namely in terms of biomedical sensing devices.

Layer-by-layer technique to developing functional nanolaminate films with antifungal activity

The layer-by-layer (LbL) deposition method was used to build up alternating layers (five) of different polyelectrolyte solutions (alginate, zein-carvacrol nanocapsules, chitosan and chitosan-carvacrol emulsions) on an aminolysed/charged polyethylene terephthalate (A/C PET) film. These nanolaminated films were characterised by contact angle measurements and through the determination of water vapour (WVTR) and oxygen (O2TR) transmission rates. The effect of active nanolaminated films against the Alternaria sp. and Rhizopus stolonifer was also evaluated. This procedure allowed developing optically transparent nanolaminated films with tuneable water vapour and gas properties and antifungal activity. The water and oxygen transmission rate values for the multilayer films were lower than those previously reported for the neat alginate or chitosan films. The presence of carvacrol and zein nanocapsules significantly decreased the water transmission rate (up to 40 %) of the nanolaminated films. However, the O2TR behaved differently and was only improved (up to 45 %) when carvacrol was encapsulated, i.e. nanolaminated films prepared by alternating alginate with nanocapsules of zein-carvacrol layers showed better oxygen barrier properties than those prepared as an emulsion of chitosan and carvacrol. These films containing zein-carvacrol nanocapsules also showed the highest antifungal activity (30 %), which did not significantly differ from those obtained with the highest amount of carvacrol, probably due to the controlled release of the active agent (carvacrol) from the zein-carvacrol nanocapsules. Thus, this work shows that nanolaminated films prepared with alternating layers of alginate and zein-carvacrol nanocapsules can be considered to improve the shelf-life of foodstuffs.

Longitudinal evaluation, acceptability and long-term retention of knowledge on a horizontally integrated organic and functional systems course

Undergraduate medical education is moving from traditional disciplinary basic science courses into more integrated curricula. Integration models based on organ systems originated in the 1950s, but few longitudinal studies have evaluated their effectiveness. This article outlines the development and implementation of the Organic and Functional Systems (OFS) courses at the University of Minho in Portugal, using evidence collected over 10 years. It describes the organization of content, student academic performance and acceptability of the courses, the evaluation of preparedness for future courses and the retention of knowledge on basic sciences. Students consistently rated the OFS courses highly. Physician tutors in subsequent clinical attachments considered that students were appropriately prepared. Performance in the International Foundations of Medicine examination of a self-selected sample of students revealed similar performances in basic science items after the last OFS course and 4 years later, at the moment of graduation. In conclusion, the organizational and pedagogical approaches of the OFS courses achieve high acceptability by students and result in positive outcomes in terms of preparedness for subsequent training and long-term retention of basic science knowledge.

Development of computational and experimental methods for biomass composition and evaluation of its impact in genome-scale models prediction

The use of genome-scale metabolic models has been rapidly increasing in fields such as metabolic engineering. An important part of a metabolic model is the biomass equation since this reaction will ultimately determine the predictive capacity of the model in terms of essentiality and flux distributions. Thus, in order to obtain a reliable metabolic model the biomass precursors and their coefficients must be as precise as possible. Ideally, determination of the biomass composition would be performed experimentally, but when no experimental data are available this is established by approximation to closely related organisms. Computational methods however, can extract some information from the genome such as amino acid and nucleotide compositions. The main objectives of this study were to compare the biomass composition of several organisms and to evaluate how biomass precursor coefficients affected the predictability of several genome-scale metabolic models by comparing predictions with experimental data in literature. For that, the biomass macromolecular composition was experimentally determined and the amino acid composition was both experimentally and computationally estimated for several organisms. Sensitivity analysis studies were also performed with the Escherichia coli iAF1260 metabolic model concerning specific growth rates and flux distributions. The results obtained suggest that the macromolecular composition is conserved among related organisms. Contrasting, experimental data for amino acid composition seem to have no similarities for related organisms. It was also observed that the impact of macromolecular composition on specific growth rates and flux distributions is larger than the impact of amino acid composition, even when data from closely related organisms are used.

Detection of functional changes of the fetal heart in the first trimester of gestation

The authors consider the possibility of using color Doppler of the ductus venosus and the measurement of nuchal translucency as a screening test for alterations in fetal cardiac functions in the first trimester of gestation. Review of the literature suggests that the combination of the ultrasonographic measurement of nuchal translucency and Doppler at 10 and 14 weeks of gestation can be effective in detecting certain cardiac abnormalities. This conclusion, however, is preliminary and needs to be further investigated.

Assessment of functional capacity through oxygen consumption in patients with asymptomatic probable heart disease

PURPOSE: To compare peak exercise oxygen consumption (VO2peak) of healthy individuals with asymptomatic individuals with probable heart disease. METHODS: Ninety-eight men were evaluated. They were divided into two groups: 1) 39 healthy individuals (group N) with an age range of 50±4.6 years; and 2) 59 asymptomatic individuals with signs of atherosclerotic and/or hypertensive heart disease (group C) with an age range of 51.9±10.4 years. In regard to age, height, body surface area, percentage of fat, lean body mass, and daily physical activity, both groups were statistically similar. Environmental conditions during the ergometric test were also controlled. RESULTS: Maximal aerobic power (watts), VO2peak, maximal heart rate, and maximal pulmonary ventilation were lower in group C (p<0.01) than in group N; weight, however, was lower in group N (p=0.031) than in group C. Differences in the respiratory gas exchange index, heart rate at rest, and the maximal double product of the two groups were not statistically significant. CONCLUSION: Signs of probable heart disease, even though asymptomatic, may reduce the functional capacity, perhaps due to the lower maximal cardiac output and/or muscle metabolic changes.

Structural and functional characteristics of rat hearts with and without myocardial infarct. Initial experience with doppler echocardiography

OBJECTIVE: To assess by Doppler echocardiography the structural and functional alterations of rat heart with surgical induced extensive myocardial infarction. METHODS: Five weeks after surgical ligature of the left coronary artery, 38 Wistar-EPM rats of both sexes, 10 of them with extensive infarction, undergone anatomical and functional evaluation by Doppler echocardiography and then euthanized for anatomopathological analysis. RESULTS: Echocardiography was 100% sensible and specific to anatomopathological confirmed extensive miocardial infarction. Extensive infarction lead to dilatation of left ventricle (diastolic diameter: 0.89cm vs.0.64cm; systolic: 0.72cm vs. 0.33cm) and left atrium (0.55cm vs. 0.33cm); thinning of left ventricular anterior wall (systolic: 0.14cm vs. 0.23cm, diastolic: 0.11cm vs. 0.14cm); increased mitral E/ A wave relation (6.45 vs. 1.95). Signals of increased end diastolic ventricle pressure, B point in mitral valve tracing in 62.5% and signs of pulmonary hypertension straightening of pulmonary valve (90%) and notching of pulmonary systolic flow (60%) were observed in animals with extensive infarction. CONCLUSION: Doppler echocardiography has a high sensitivity and specificity for detection of chronic extensive infarction. Extensive infarction caused dilatation of left cardiac chambers and showed in Doppler signals of increased end diastolic left ventricular pressure and pulmonary artery pressure.

Congestive heart failure. Correlation between functional class and systolic and diastolic functions assessed by Doppler echocardiography

OBJECTIVE: To evaluate the influence of systolic or diastolic dysfunction, or both on congestive heart failure functional class. METHODS: Thirty-six consecutive patients with a clinical diagnosis of congestive heart failure with sinus rhythm, who were seen between September and November of 1998 answered an adapted questionnaire about tolerance to physical activity for the determination of NYHA functional class. The patients were studied with transthoracic Doppler echocardiography. Two groups were compared: group 1 (19 patients in functional classes I and II) and group 2 (17 patients in functional classes III and IV). RESULTS: The average ejection fraction was significantly higher in group 1 (44.84%±8.04% vs. 32.59%±11.48% with p=0.0007). The mean ratio of the initial/final maximum diastolic filling velocity (E/A) of the left ventricle was significantly smaller in group 1 (1.07±0.72 vs. 1.98±1.49 with p=0.03). The average maximum systolic pulmonary venous velocity (S) was significantly higher in group 1 (53.53cm/s ± 12.02cm/s vs. 43.41cm/s ± 13.55cm/s with p=0.02). The mean ratio of maximum systolic/diastolic pulmonary venous velocity was significantly higher in group 1 (1.52±0.48 vs. 1.08±0.48 with p=0.01). A predominance of pseudo-normal and restrictive diastolic patterns existed in group 2 (58.83% in group 2 vs. 21.06% in group 1 with p=0.03). CONCLUSION: Both the systolic dysfunction index and the patterns of diastolic dysfunction evaluated by Doppler echocardiography worsened with the evolution of congestive heart failure.