Metabolic and morphogenetic engineering of Bacillus subtilis: biotechnology for industry

Dissertation presented to obtain the Ph.D. degree in “Biology” at the Institute of Chemical and Biological Technology of the New University of Lisbon

Biochemical and spectroscopic characterization of the membrane-bound nitrate reductase from Marinobacter hydrocarbonoclasticus 617

J Biol Inorg Chem (2008) 13:1321–1333 DOI 10.1007/s00775-008-0416-1

Functional characterization and directed engineering of redox proteins for a rational improvement of Bioelectrochemical systems

In recent years, new methods of clean and environmentally friendly energy production have been the focus of intense research efforts. Microbial fuel cells (MFCs) are devices that utilize naturally occurring microorganisms that feed on organic matter, like waste water, while producing electrical energy. The natural habitats of bacteria thriving in microbial fuel cells are usually marine and freshwater sediments. These microorganisms are called dissimilatory metal reducing bacteria (DMRB), but in addition to metals like iron and manganese, they can use organic compounds like DMSO or TMAO, radionuclides and electrodes as terminal electron acceptors in their metabolic pathways.(...)

Practices and trends of telework in the Portuguese industry: the results of surveys in the textile, metal and software sectors

The aim of the TeleRisk Project on labour relations and professional risks within the context of teleworking in Portugal – supported by IDICT – Institute for Development and Inspection of Working Conditions (Ministry of Labour), is to study the practices and forms of teleworking in the manufacturing sectors in Portugal. The project chose also the software industry as a reference sector, even though it does not intend to exclude from the study any other sector of activity or the so-called “hybrid” forms of work. However, the latter must have some of the characteristics of telework. The project thus takes into account the so-called “traditional” sectors of activity, namely textile and machinery and metal engineering (machinery and equipment), not usually associated to this type of work. However, telework could include, in the so-called “traditional” sectors, other variations that are not found in technologically based sectors. One of the evaluation methods for the dynamics associated to telework consisted in carrying out surveys by means of questionnaires, aimed at employers in the sectors analysed. This paper presents some of the results of those surveys. It is important to mention that, being a preliminary analysis, it means that it does not pretend to have exhausted all the issues in the survey, but has meant that it shows the bigger tendencies, in terms of teleworking practices, of the Portuguese industry.

Automatic sleep apnea detection and sleep classification using the ECG and the SpO2 signals

Dissertation for a Masters Degree in Computer and Electronic Engineering

Hexose and pentose transport inascomycetousyeasts: an overview

FEMS Yeast Research, Vol. 9, nº 4

Characterization of the abn2(yxiA) encoding a Bacillus subtilis GH43 arabinanase, Abn2, and its role in arabino-polysaccharides degradation.

Journal of Bacteriology (Junho 2008) 4272-4280

Model morphisms (MoMo) to enable language independent information models and interoperable business networks

MSc. Dissertation presented at Faculdade de Ciências e Tecnologia of Universidade Nova de Lisboa to obtain the Master degree in Electrical and Computer Engineering

Software languages engineering: experimental evaluation

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

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

The inhibitory activity of synthetic compounds and ions against transporters of multi-drug resistant bacteria

RESUMO: Sessenta e três derivados de hidantoína foram utilizados para avaliar possíveis efeitos de modulação na actividade das bombas de efluxo (BE) na Salmonella NCTC 13349 utilizando um método fluorimétrico semi-automático. Nenhum dos compostos apresentaram actividade anti-bacteriana até concentrações de 240 mg/L. Entre todos os compostos, SZ-7 demonstrou possuir propriedades de modulação de effluxo na presença de glucose. Para testar esta actividade, estirpes de Salmonella resistentes à ciprofloxacina, induzidas a elevados níveis de resistência com sobre-expressão de BE, foram expostas ao SZ-7. Este derivado afectou a susceptibilidade das estirpes à ciprofloxacina. Uma vez que os 63 compostos estudados apresentaram pouco efeito inibitório /cumulativo, apesar de serem conhecidos pelos seus efeitos moduladores de BE-dependentes de iões em eucariotas, foi questionado o papel dos iões na regulação de BE bacterianas, que poderão influenciar a eficácia de novos compostos. Para este estudo, utilizamos a Escherichia coli AG100 como modelo, devido ao extenso conhecimento no que respeita a estrutura e actividade das BE. Devido à importância de iões de cálcio (Ca2+) nos canais de transporte membranar e na actividade de ATPases, a sua actividade na modulação do efluxo foi investigada. De resultados anteriormente obtidos concluiu-se que a pH 5 o efluxo é independente de energia metabólica; contudo, a pH 8 é absolutamente dependente, sendo que o Ca2+ é indispensável para manter a actividade das ATPases bacterianas. A acumulação/effluxo de EtBr pela E. coli AG100 foi determinada na presença/ausência de Ca2+, clorpromazina (inibidor de ligação de Ca2+ a proteínas), e ácido etilenodiamino tetra-acético (quelante de Ca2+). Acumulação/effluxo aumentou a pH 8, contudo o Ca2+ reverte estes efeitos evidenciando a sua importância no funcionamento das BE bacterianas. Em resumo este trabalho colocou em evidência que muitos aspectos bioquímicos e bioenergéticos devem ser tomados em consideração no estudo da resistência bacteriana mediada por BE.------- ABSTRACT: Sixty-three hydantoin derivatives were evaluated for their modulating effects on efflux pump (EP) activity of Salmonella NCTC 13349 utilizing a semi-automatic fluorometric method. None of the compounds presented antibacterial activities at concentrations as high as 240 mg/L. Among all compounds, SZ-7 showed possible efflux modulating activity in the presence of glucose, indicative of a potential EP inhibitor. To verify its potential effects, ciprofloxacin-resistant Salmonella strains, induced to high level resistance with over-expressing EPs, were exposed to SZ-7. This derivative affected the susceptibility of the ciprofloxacin-resistant strains. Since the 63 compounds studied had very low inhibitory/accumulative effects, even though their known for being efficient in modulating ion-driven eukaryotic EPs, we questioned whether ions had a leading role in regulating bacterial EPs, influencing the effectiveness of new compounds. For this study we used Escherichia coli AG100 as a model, due to the extensive knowledge on its EPs structure and activity. Owing the importance of calcium ions (Ca2+) for membrane transport channels and activity of ATPases, the role of Ca2+ was investigated. From previous results we concluded that at pH 5 efflux is independent of metabolic energy; however, at pH 8 it is entirely dependent of metabolic energy and the Ca2+ ions are essential to maintain the activity of bacterial ATPases. Accumulation and efflux of ethidium bromide (EtBr) by E. coli AG100 was determined in the presence and absence of Ca2+, chlorpromazine (inhibitor of Ca2+-binding to proteins), and ethylenediaminetetraacetic acid (Ca2+ chelator). Accumulation of EtBr increased at pH 8; however Ca2+ reversed these effects providing information as to the importance of this ion in the regulation of bacterial EP systems. Overall this work puts in evidence that many biochemical and bioenergetic aspects related to the strains physiology need to be taken into consideration in bacterial drug resistance mediated by EPs.

Structure-function relationships in a glycosyltransferase, a phosphatase and an oxidoreductase

Dissertation presented to obtain the Ph.D degree in Biochemistry

A CMMI-compliant requirements management and development process

Requirements Engineering has been acknowledged an essential discipline for Software Quality. Poorly-defined processes for eliciting, analyzing, specifying and validating requirements can lead to unclear issues or misunderstandings on business needs and project’s scope. These typically result in customers’ non-satisfaction with either the products’ quality or the increase of the project’s budget and duration. Maturity models allow an organization to measure the quality of its processes and improve them according to an evolutionary path based on levels. The Capability Maturity Model Integration (CMMI) addresses the aforementioned Requirements Engineering issues. CMMI defines a set of best practices for process improvement that are divided into several process areas. Requirements Management and Requirements Development are the process areas concerned with Requirements Engineering maturity. Altran Portugal is a consulting company concerned with the quality of its software. In 2012, the Solution Center department has developed and applied successfully a set of processes aligned with CMMI-DEV v1.3, what granted them a Level 2 maturity certification. For 2015, they defined an organizational goal of addressing CMMI-DEV maturity level 3. This MSc dissertation is part of this organization effort. In particular, it is concerned with the required process areas that address the activities of Requirements Engineering. Our main goal is to contribute for the development of Altran’s internal engineering processes to conform to the guidelines of the Requirements Development process area. Throughout this dissertation, we started with an evaluation method based on CMMI and conducted a compliance assessment of Altran’s current processes. This allowed demonstrating their alignment with the CMMI Requirements Management process area and to highlight the improvements needed to conform to the Requirements Development process area. Based on the study of alternative solutions for the gaps found, we proposed a new Requirements Management and Development process that was later validated using three different approaches. The main contribution of this dissertation is the new process developed for Altran Portugal. However, given that studies on these topics are not abundant in the literature, we also expect to contribute with useful evidences to the existing body of knowledge with a survey on CMMI and requirements engineering trends. Most importantly, we hope that the implementation of the proposed processes’ improvements will minimize the risks of mishandled requirements, increasing Altran’s performance and taking them one step further to the desired maturity level.

Numerical prediction of diffusion and electric field-induced iron nanoparticle transport

Zero valent iron nanoparticles (nZVI) are considered very promising for the remediation of contaminated soils and groundwaters. However, an important issue related to their limited mobility remains unsolved. Direct current can be used to enhance the nanoparticles transport, based on the same principles of electrokinetic remediation. In this work, a generalized physicochemical model was developed and solved numerically to describe the nZVI transport through porous media under electric field, and with different electrolytes (with different ionic strengths). The model consists of the Nernst–Planck coupled system of equations, which accounts for the mass balance of ionic species in a fluid medium, when both the diffusion and electromigration of the ions are considered. The diffusion and electrophoretic transport of the negatively charged nZVI particles were also considered in the system. The contribution of electroosmotic flow to the overall mass transport was included in the model for all cases. The nZVI effective mobility values in the porous medium are very low (10−7–10−4 cm2 V−1 s−1), due to the counterbalance between the positive electroosmotic flow and the electrophoretic transport of the negatively charged nanoparticles. The higher the nZVI concentration is in the matrix, the higher the aggregation; therefore, low concentration of nZVI suspensions must be used for successful field application.