Improvement of a photoautotrophic chassis robustness for synthetic biology applications

Cyanobacteria are photoautotrophic microorganisms with great potential for the biotechnological industry due to their low nutrient requirements, photosynthetic capacities and metabolic plasticity. In biotechnology, the energy sector is one of the main targets for their utilization, especially to produce the so called third generation biofuels, which are regarded as one of the best replacements for petroleum-based fuels. Although, several issues could be solved, others arise from the use of cyanobacteria, namely the need for high amounts of freshwater and contamination/predation by other microorganisms that affect cultivation efficiencies. The cultivation of cyanobacteria in seawater could solve this issue, since it has a very stable and rich chemical composition. Among cyanobacteria, the model microorganism Synechocystis sp. PCC 6803 is one of the most studied with its genome fully sequenced and genomic, transcriptomic and proteomic data available to better predict its phenotypic behaviors/characteristics. Despite suitable for genetic engineering and implementation as a microbial cell factory, Synechocystis’ growth rate is negatively affected by increasing salinity levels. Therefore, it is important to improve. To achieve this, several strategies involving the constitutive overexpression of the native genes encoding the proteins involved in the production of the compatible solute glucosylglycerol were implemented, following synthetic biology principles. A preliminary transcription analysis of selected mutants revealed that the assembled synthetic devices are functional at the transcriptional level. However, under different salinities, the mutants did not show improved robustness to salinity in terms of growth, compared with the wild-type. Nevertheless, some mutants carrying synthetic devices appear to have a better physiological response under seawater’s NaCl concentration than in 0% (w/v) NaCl.

Exchange rate pressure in Angola

The objective of this work is to develop an operational tool to analyze exchange rate pressure in the context of Angola. The Angolan economy exhibits a number of relevant characteristics: a closed financial account, a partially controlled current account, a highly dollarized economy and exports (oil) price determined in World markets. These features have a direct effect on the demand of foreign currency and motivate their inclusion in the specification of a model for Angola. The model provides the rational for a measure of an exchange market rate pressure (EMP) index that contains exports changes, imports changes, the foreign interest rate and inflation and the change in foreign reserves corrected for a measure dollarization. The empirical performance new measure is comparable (slightly better) to the performance of the EMP indexes obtained in Eichengreen Rose and Wyplosz (1994) and Klassen and Jager (2011).

Growth rate of a terra firme rain forest in Brazilian Amazonia over an eight-year period in response to logging

This paper deals with growth rates of trees > 5cm dbh over an eight-year period from 257 species at the Tapajós National Forest. The discussion is centred on the behaviour of the forest after logging. Permanent sample plots were established in 1981 and measured at the first time. The area was logged in 1982. Measurements after logging occurred in 1983, 1987 and 1989. Considering all species together, diameter increment was similar for both intensities of logging until five years after logging. Light-demanding species showed significantly higher growth rates than shade-tolerant species in the logged forest, with greater increment in the heavier treatment intensity. Commercial species also had higher growth rates in the heavier logged area, although those were significantly different only in the period from one to five years after logging. In the undisturbed forest, growth rates increased with increasing dbh size. At species level, growth rate varied between and within treatments, as well as between trees within species, depending mainly on degree of canopy opening. The logging favoured the growth of commercial species, chiefly the light-demanders. Therefore, if the same growth conditions continue being given, for example by silvicultural treatments, to those species of commercial interest, the forest would reach a stock available for harvesting around year 30 after logging. However, the high variation in increment rates indicates that an eight-year period is not sufficient to allow predictions on cutting cycles or polycyclic management systems for the study forest.

Exploring chemical conversions in metabolic networks by tracing atoms transitions

Dissertação de mestrado em Bioinformática

Modeling microbes: New methods for integrated metabolic and regulatory network reconstruction

PhD Thesis in Bioengineering

High strain rate constitutive modeling forhistorical structures subjected to blast loading

Doctoral Thesis Civil Engineering

Empathy and heart rate variability: a need and a mechanism of emotion regulation

Dissertação de mestrado integrado em Psicologia

End-of-day dryness, corneal sensitivity and blink rate in contact lens wearers

Purpose: To study the relationship among the variables intensity ofthe end-of-day (EOD) dryness, corneal sensitivity and blink rate in soft contact lens (CL) wearers. Methods: Thirty-eight soft CL wearers (25 women and 13 men; mean age 27.1 ± 7.2 years) were enrolled. EOD dryness was assessed using a scale of 0–5 (0, none to 5, very intense). Mechanical and thermal (heat and cold) sensitivity were measured using a Belmonte’s gas esthesiometer. The blink rate was recorded using a video camera while subjects were wearing a hydrogel CL and watching a film for 90 min in a controlled environmental chamber. Results: A significant inverse correlation was found between EOD dryness and mechanical sensitivity (r: −0.39; p = 0.02); however, there were no significant correlations between EOD dryness and thermal sensitivity. A significant (r: 0.56; p < 0.001) correlation also was observed between EOD dryness and blink rate, but no correlations were found between blink rate and mechanical or thermal sensitivity. Conclusions: CL wearers with higher corneal sensitivity to mechanical stimulation reported more EOD dryness with habitual CL wear. Moreover, subjects reporting more EOD dryness had an increased blink rates during wear of a standard CL type. The increased blink rate could act to improve the ocular surface environment and relieve symptoms

Outcrossing rate of Couratari multiflora (J.Smith) Eyma (Lecythidaceae), a low-density tropical tree species from a central Amazonian rainforest

A multilocus mixed-mating model was used to evaluate the mating system of a population of Couratari multiflora, an emergent tree species found in low densities (1 individual/10 ha) in lowland forests of central Amazonia. We surveyed and observed phenologically 41 trees in an area of 400 ha. From these, only four mother trees were analyzed here because few of them set fruits, which also suffered high predation. No difference was observed between the population multilocus outcrossing rate (t mp = 0.953 ± 0.040) and the average single locus rate (t sp = 0.968 ± 0.132). The four mother trees were highly outcrossed (t m ~ 1). Two out of five loci showed departures from the Hardy-Weinberg Equilibrium (HWE) expectations, and the same results occurred with the mixed-mating model. Besides the low number of trees analyzed, the proportion of loci in HWE suggests random mating in the population. However, the pollen pool was heterogeneous among families, probably due to both the small sample number and the flowering of trees at different times of the flowering season. Reproductive phenology of the population and the results presented here suggest, at least for part of the population, a long-distance pollen movement, around 1,000 m.

Implementation and validation of a strain rate dependent anisotropic continuum model for masonry

A newly developed strain rate dependent anisotropic continuum model is proposed for impact and blast applications in masonry. The present model adopted the usual approach of considering different yield criteria in tension and compression. The analysis of unreinforced block work masonry walls subjected to impact is carried out to validate the capability of the model. Comparison of the numerical predictions and test data revealed good agreement. Next, a parametric study is conducted to evaluate the influence of the tensile strengths along the three orthogonal directions and of the wall thickness on the global behavior of masonry walls.

Dynamic interface model for masonry walls subjected to high strain rate out-of-plane loads

The present study proposes a dynamic constitutive material interface model that includes non-associated flow rule and high strain rate effects, implemented in the finite element code ABAQUS as a user subroutine. First, the model capability is validated with numerical simulations of unreinforced block work masonry walls subjected to low velocity impact. The results obtained are compared with field test data and good agreement is found. Subsequently, a comprehensive parametric analysis is accomplished with different joint tensile strengths and cohesion, and wall thickness to evaluate the effect of the parameter variations on the impact response of masonry walls.

Metabolic profiling and classification of propolis samples from Southern Brazil: an NMR-based platform coupled with machine learning

The chemical composition of propolis is affected by environmental factors and harvest season, making it difficult to standardize its extracts for medicinal usage. By detecting a typical chemical profile associated with propolis from a specific production region or season, certain types of propolis may be used to obtain a specific pharmacological activity. In this study, propolis from three agroecological regions (plain, plateau, and highlands) from southern Brazil, collected over the four seasons of 2010, were investigated through a novel NMR-based metabolomics data analysis workflow. Chemometrics and machine learning algorithms (PLS-DA and RF), including methods to estimate variable importance in classification, were used in this study. The machine learning and feature selection methods permitted construction of models for propolis sample classification with high accuracy (>75%, reaching 90% in the best case), better discriminating samples regarding their collection seasons comparatively to the harvest regions. PLS-DA and RF allowed the identification of biomarkers for sample discrimination, expanding the set of discriminating features and adding relevant information for the identification of the class-determining metabolites. The NMR-based metabolomics analytical platform, coupled to bioinformatic tools, allowed characterization and classification of Brazilian propolis samples regarding the metabolite signature of important compounds, i.e., chemical fingerprint, harvest seasons, and production regions.

The influence of kaolin application on key metabolic pathways associated with grape berry quality: a molecular and biochemical analysis

Dissertação de mestrado em Biologia Molecular, Biotecnologia e Bioempreendedorismo em Plantas

A glycolytic phenotype is associated with prostate cancer progression and aggressiveness: a role for Monocarboxylate Transporters as metabolic targets for therapy.

Metabolic adaptation is considered an emerging hallmark of cancer, whereby cancer cells exhibit high rates of glucose consumption with consequent lactate production. To ensure rapid efflux of lactate, most cancer cells express high levels of monocarboxylate transporters (MCTs), which therefore may constitute suitable therapeutic targets. The impact of MCT inhibition, along with the clinical impact of altered cellular metabolism during prostate cancer (PCa) initiation and progression, has not been described. Using a large cohort of human prostate tissues of different grades, in silico data, in vitro and ex vivo studies, we demonstrate the metabolic heterogeneity of PCa and its clinical relevance. We show an increased glycolytic phenotype in advanced stages of PCa and its correlation with poor prognosis. Finally, we present evidence supporting MCTs as suitable targets in PCa, affecting not only cancer cell proliferation and survival but also the expression of a number of hypoxia-inducible factor target genes associated with poor prognosis. Herein, we suggest that patients with highly glycolytic tumours have poorer outcome, supporting the notion of targeting glycolytic tumour cells in prostate cancer through the use of MCT inhibitors.