Polymerase chain reaction-based method for the identification of Leishmania (Viannia) braziliensis and Leishmania (Viannia) guyanensis in mucosal tissues conserved in paraffin

ABSTRACTINTRODUCTION: In the Americas, mucosal leishmaniasis is primarily associated with infection by Leishmania (Viannia) braziliensis. However, Leishmania (Viannia) guyanensis is another important cause of this disease in the Brazilian Amazon. In this study, we aimed at detecting Leishmaniadeoxyribonucleic acid (DNA) within paraffin-embedded fragments of mucosal tissues, and characterizing the infecting parasite species.METHODS: We evaluated samples collected from 114 patients treated at a reference center in the Brazilian Amazon by polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) analyses.RESULTS: Direct examination of biopsy imprints detected parasites in 10 of the 114 samples, while evaluation of hematoxylin and eosin-stained slides detected amastigotes in an additional 17 samples. Meanwhile, 31/114 samples (27.2%) were positive for Leishmania spp. kinetoplast deoxyribonucleic acid (kDNA) by PCR analysis. Of these, 17 (54.8%) yielded amplification of the mini-exon PCR target, thereby allowing for PCR-RFLP-based identification. Six of the samples were identified as L. (V.) braziliensis, while the remaining 11 were identified as L. (V.) guyanensis.CONCLUSIONS: The results of this study demonstrate the feasibility of applying molecular techniques for the diagnosis of human parasites within paraffin-embedded tissues. Moreover, our findings confirm that L. (V.) guyanensisis a relevant causative agent of mucosal leishmaniasis in the Brazilian Amazon.

Implementation of membrane processes for improvement of the detection of food contaminants

The EM3E Master is an Education Programme supported by the European Commission, the European Membrane Society (EMS), the European Membrane House (EMH), and a large international network of industrial companies, research centres and universities (http://www.em3e.eu)

Sol-gel entrapped biosystems: enzyme(s) and whole cells

In this work two different procedures to utilize the sol-gel technology were applied to immobilize/encapsulate enzymes and living cells. CO2 has reached levels in the atmosphere that make it a pollutant. New methods to utilize this gas to obtain products of added value can be very important, both from an environmentally point of view and from an economic standpoint. The first goal of this work was to study the first reaction of a sequential, three-step, enzymatic process that carries out the conversion of CO2 to methanol. Of the three oxidoreductases involved, our focus was on formate dehydrogenase (FateDH) that converts CO2 to formate. This reaction requires the presence of the cofactor β-nicotinamide adenine dinucleotide in reduced form (NADH). The cofactor is expensive and unstable. Our experiments were directed towards generating NADH from its oxidized form (NAD+), using glutamate dehydrogenase (GDH). The formation of NADH from NAD+ in aqueous medium was studied with both free and sol-gel entrapped GDH. This reaction was then followed by the conversion of CO2 to formate, catalysed by free or sol-gel entrapped FateDH. The quantification of NADH/NAD+ was made using UV/Vis spectroscopy. Our results showed that it was possible to couple the GDH-catalyzed generation of the cofactor NADH with the FateDH-catalyzed conversion of CO2, as confirmed by the detection of formate in the medium, using High Performance Liquid Chromatography (HPLC). The immobilization of living cells can be advantageous from the standpoint of ease of recovery, reutilization and physical separation from the medium. Also dead cells may not always exhibit enzymatic activities found with living cells. In this work cell encapsulation was performed using Escherichia coli bacteria. To reduce toxicity for living organisms, the sol-gel method was different than for enzymes, and involved the use of aqueous-based precursors. Initial encapsulation experiments and viability tests were carried out with E. coli K12. Our results showed that sol-gel entrapment of the cells was achieved, and that cell viability could be increased with additives, namely betaine that led to greater viability improvement and was selected for further studies. For an approach to “in-cell” Nuclear Magnetic Resonance (NMR) experiments, the expression of the protein ctCBM11 was performed in E. coli BL21. It was possible to obtain an NMR signal from the entrapped cells, a considerable proportion of which remained alive after the NMR experiments. However, it was not possible to obtain a distinctive NMR signal from the target protein to distinguish it from the other proteins in the cell.

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.

A doença pulmonar obstrutiva crónica e o exercício: impacto da doença no declínio funcional e importância do treino de exercício nos benefícios para a saúde

RESUMO: A reabilitação respiratória (RR) é uma intervenção abrangente e interdisciplinar dirigida aos doentes respiratórios crónicos e inclui o treino de exercício, programas de educação e de modificação comportamental, entre outros, desenhados individualmente para melhorar o desempenho físico e psicossocial e promover a adesão a longo prazo a comportamentos promotores de saúde. A doença pulmonar obstrutiva crónica (DPOC) é uma doença comum, afetando cerca de 210 milhões de pessoas em todo o mundo, com elevada mortalidade e com custos económicos significativos decorrentes do agravamento progressivo da doença, das hospitalizações e de reinternamentos frequentes. Apesar do crescente conhecimento da DPOC e do papel da RR nos benefícios para a saúde, existem aspetos ainda não esclarecidos que têm impacto na prática clínica e de investigação e nas decisões das autoridades de saúde. A primeira parte desta tese focou a DPOC e o seu impacto negativo e incluiu: o estudo da prevalência da DPOC em Portugal; os fatores clínicos e funcionais que se associam à mortalidade em doentes com DPOC avançada; a morbilidade, impacto funcional e risco dos doentes se tornarem dependentes para as atividades diárias e a influência da inflamação sistémica. A prevalência estimada da DPOC de 14,2% indica que esta é uma doença comum em Portugal e alerta para a necessidade de uma maior sensibilização da população, dos profissionais de saúde e autoridades de saúde com vista a um diagnóstico precoce e à alocação dos recursos terapêuticos adequados. A elevada taxa de mortalidade em doentes com DPOC avançada - 36,6% em 3 anos - associou-se a insuficiência respiratória, a elevado número de exacerbações, ao cancro do pulmão e a reduzida capacidade funcional para a marcha, salientando a importância da referenciação precoce para RR, a identificação e o tratamento das comorbilidades e a prevenção das exacerbações. A aplicação de um questionário que avaliou as atividades da vida diária básicas e instrumentais, permitiu identificar um marcador clínico do risco de dependência, complementando as avaliações funcionais e associando-se a outros marcadores de mau prognóstico, como as exacerbações. Em doentes com DPOC, com FEV1 médio de 46,76% (desvio padrão: 20,90%), 67% da categoria D do GOLD, verificou-se uma associação positiva entre a expressão de genes inflamatórios avaliada pela reação em cadeia da polimerase (ARN mensageiro de IFNg, IL1b, IL6, IL8, TNFa, TGFb1, iNOS) e o índice de massa corporal em repouso, acentuando-se após o exercício. Este estudo aponta a inflamação como o potencial elo de ligação entre a obesidade e a inflamação sistémica em doentes com DPOC. A segunda parte da tese focou a RR, nomeadamente os seus efeitos em doentes das categorias GOLD A, B, C e D; o impacto das comorbilidades nos resultados da RR e os resultados de diferentes intensidades de treino aeróbio. Após o programa de RR, verificaram-se melhorias significativas na capacidade de exercício funcional e de endurance e no estado geral de saúde dos doentes de todas as categorias GOLD. Esta classificação não distingue os doentes que melhor poderão beneficiar desta intervenção, indicando que devem ser referenciados para RR, os doentes sintomáticos ou com repercussão na qualidade de vida, independentemente da categoria da DPOC a que pertençam. A prevalência das comorbilidades no grupo de doentes com DPOC que é referenciado para RR, é elevada, sendo as mais frequentes, as cardiovasculares, as respiratórias e as psicológicas. Apesar de poderem diminuir o impacto da RR, os resultados desta foram semelhantes independentemente do número de comorbilidades. A identificação e o tratamento sistemáticos das comorbilidades conferem maior segurança clínica a esta intervenção terapêutica a qual, por apresentar bons resultados, não deve limitar a referenciação dos doentes. Com o programa de RR, verificou-se melhoria significativa em todos os resultados centrados no doente para ambas as intensidades de treino aeróbio, a 60% e a 80% da potência aeróbica máxima (Wmax), com melhoria do estado geral de saúde, nos sintomas e na capacidade para o exercício, o que questiona a indicação sistemática de elevadas intensidades de treino em doentes com DPOC para a obtenção de benefícios a curto prazo. Na terceira e última parte da tese foi estudado o papel da atividade física na DPOC, focando os fatores que influenciam a atividade física diária; a evolução da capacidade funcional e o estado de saúde 2 anos após um programa de RR e o papel da telemonitorização na quantificação e monitorização da atividade física. Confirmámos que os doentes com DPOC são marcadamente sedentários e os fatores que se associaram ao sedentarismo nestes doentes foram a dispneia e a distância percorrida na prova de marcha de seis minutos. Este estudo sublinha a importância do controlo sintomático, nomeadamente da dispneia, bem como, mais uma vez, o potencial papel da reabilitação respiratória no aumento da capacidade funcional para o exercício e na aquisição de hábitos de vida fisicamente ativa. Verificámos que, apesar de os doentes com DPOC apresentarem benefícios clinicamente significativos na capacidade funcional para o exercício e no estado geral de saúde com o programa de RR, apenas os que se mantêm ativos, podem, no final dos dois anos de seguimento, manter os efeitos benéficos desse programa. O sistema de telemonitorização que combina a oximetria e a quantificação da atividade física provou ser clinicamente útil na avaliação da necessidade de oxigenoterapia de longa duração (OLD) e na aferição do débito de oxigénio em repouso, no esforço e no sono, podendo contribuir para uma melhor adequação da prescrição da OLD. A monitorização dos níveis de atividade física regular é um importante instrumento de avaliação dos programas de RR e o seu uso potencial na telereabilitação permitirá prolongar a eficácia dos programas e reduzir os custos associados aos cuidados de saúde.---------------------------------------------------------------------------------------------------ABSTRACT: Pulmonary rehabilitation (PR) is a comprehensive interdisciplinary intervention that includes, but is not limited to, exercise training, education, and behavior change, individually designed to improve physical and psychological conditions of people with chronic respiratory disease and to promote long-term adherence to health-enhancing behaviors. Chronic obstructive pulmonary disease (COPD) is a common disease, affecting about 210 million people worldwide, with high mortality and significant health-related costs due to disease progression, hospitalizations and frequent hospital readmissions. Although the increasing knowledge about COPD and benefitial outcomes of PR, some aspects with impact in clinical practice, research and health authorities’ decisions, remain to be clarified. The first part of this thesis focused on COPD and its negative impact, including the study of COPD prevalence in Portugal; clinical and functional factors associated with mortality in advanced COPD patients; morbidity, functional impact and risk of others’ dependance to perform activities of daily living; and the role of systemic inflammation. The evidence of 14.2% estimated COPD prevalence as a common disease in Portugal raises the need of an increasing awareness of population, health care professionals and health authorities towards an earlier diagnosis and apropriate treatment resources allocation. High mortality in patients with advanced COPD – 36.6% in 3 years - was associated with respiratory failure, high frequency of exacerbations, lung cancer and a low functional capacity in walking. This highlightens the importance of an earlier referral to PR, comorbidity identification and treatment, and prevention of exacerbations. A questionnaire evaluated basic and instrumental activities of daily living, and identified a clinical marker of the risk of becoming dependent. This clinical marker complemented other functional evaluations and was associated with prognosis markers such as the number of exacerbations. In COPD patients with a mean FEV1 46.76% (SD 20.90%), 67% belonging to GOLD grade D, we found a positive association between inflammatory gene expression evaluated by polymerase chain reaction (IFNg, IL1b, IL6, IL8, TNFa, TGFb1, iNOS RNA messenger) and body mass index at rest, and a further increase with exercise. This study evidenced obesity as one potential link between COPD and systemic inflammation. The second part of this thesis focused PR, namely its outcomes in patients of GOLD categories A, B, C and D; comorbidities impact in PR outcomes, and the impact of different exercise training intensities in patient related outcomes. xviii With PR intervention, we found significant improvement in functional exercise capacity, endurance exercise capacity and health status in patients of all GOLD categories. This classification did not differentiate which patients would benefit more from PR, hence all symptomatic patients with a negative impact in health status should be referred to PR, regardless of the GOLD category they belong to. There is a high prevalence of comorbidities in COPD patients referred to PR, being cardiovascular, respiratory and psychological, the most prevalent. Although some comorbidities might reduce PR impact, the results were similar regardless of the number of comorbidities. Systematic comorbidities identification and treatment provides safety to PR intervention, and its good results should not preclude patients referral. With PR intervention we found a significant improvement in all patient reported outcomes for exercise training intensities at 60% and 80% maximum work rate (Wmax), namely in health status, symptoms and exercise capacity. These findings challenge the current systematic indication of high exercise training intensities to achieve PR short-term benefits. In the third and last part of the thesis, the role of physical activity in COPD was studied, focusing factors that may influence daily physical activity; the evolution of functional capacity and health status two years after a PR program, and the role of a telemonitoring system in physical activity quantification and monitoring. We confirmed that COPD patients are markedly inactive and factors associated with a sedentary lifestyle are dyspnea and 6 minute walking distance. This study emphasized the importance of symptom control, namely of dyspnea, as well as, once again, the potential role of PR in functional exercise improvement and in integrating physically active habits in daily life. We verified that, although COPD patients improve functional exercise capacity and health status after a PR program, only those who kept physical activity habits were able to maintain those effects after 2 years of follow-up. A telemonitoring system that combines oximetry and physical activity quantification proved to be clinically useful in the evaluation of long-term oxygen therapy (LTOT) indication, as well as in the titration of oxygen levels at rest, exertion, and sleeping, which might contribute to a more adequate LTOT prescription. Monitoring of daily physical activity levels is an important PR evaluation instrument and its potential use in telerehabilitation might allow lengthening programs efficacy, while reducing health-care costs.

Grafting of adipic anhydride to carbon nanotubes through a Diels-Alder cycloaddition/oxidation cascade reaction

Accepted Manuscript

Comparison of different numerical methods for the solution of the time-fractional reaction-diffusion equation with variable diffusion coefficient

In this work we perform a comparison of two different numerical schemes for the solution of the time-fractional diffusion equation with variable diffusion coefficient and a nonlinear source term. The two methods are the implicit numerical scheme presented in [M.L. Morgado, M. Rebelo, Numerical approximation of distributed order reaction- diffusion equations, Journal of Computational and Applied Mathematics 275 (2015) 216-227] that is adapted to our type of equation, and a colocation method where Chebyshev polynomials are used to reduce the fractional differential equation to a system of ordinary differential equations

Improvement of in silico strain engineering methods in Saccharomyces cerevisiae

PhD thesis in Bioengineering

Narrative innovations predict symptom improvement: Studying innovative moments in narrative therapy of depression

Objective:Innovative moments (IMs) are moments in the therapeutic dialog that constitute exceptions toward the client's problems. These narrative markers of meaning transformation are associated with change in different models of therapy and diverse diagnoses. Our goal is to test if IMs precede symptoms change, or, on the contrary, are a mere consequence of symptomatic 15 change. Method: For this purpose, IMs and symptomatology (Outcome Questionnaire-10.2) were assessed at every session in a sample of 10 cases of narrative therapy for depression. Hierarchical linear modeling was conducted to explore whether (i) IMs in a given session predict patients' symptoms in the following session and/or (ii) symptoms in a given session predict IMs in the next session. Results: Results suggested that IMs are better predictors of symptoms than the reverse. Conclusions: These results are discussed considering the contribution of meanings and narrative processes' changes to symptomatic improvement.

Biotechnological approaches for yield improvement of anticancer alkaloids in the plant Catharanthus roseus

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

Comportamento tribológico de biocompósitos de matriz de titânio

Dissertação de mestrado integrado em Engenharia de Materiais

Validação preliminar de uma versão do Caregiver Reaction Assessment em um contexto de pacientes oncológicos em internação

Objetivo Adaptar para o Brasil uma versão portuguesa do Caregiver Reaction Assessment (CRA) e gerar indicadores preliminares de validade e fidedignidade para sua aplicação em cuidadores de pacientes oncológicos internados. Métodos Participaram voluntariamente 53 cuidadores, que responderam a um questionário sociodemográfico, ao CRA e à Escala de Bem-Estar Psicológico (EBEP). A unidimensionalidade e a homogeneidade dos escores do CRA foram avaliadas por meio de análise de componentes principais e de consistência interna, respectivamente. Correlações de Pearson entre escores do CRA e EBEP foram examinadas e utilizadas como indicadores de validade divergente e de construto. Resultados As cinco escalas que compõem o CRA apresentaram bons níveis de unidimensionalidade e homogeneidade, porém as escalas de impacto nas finanças e impacto na saúde obtiveram alfas insuficientes (< 0,7). O escore total do CRA apresentou alfa elevado (0,886). Correlações entre o CRA e a EBEP produziram coeficientes teoricamente interpretáveis, com magnitudes variando entre nulas e moderadas. Conclusão O CRA apresentou bons indicadores de validade e fidedignidade. Algumas adaptações em relação ao conteúdo de determinados itens se mostram, todavia, necessárias, a fim de serem calibradas ao contexto de pessoas atendidas por serviços subsidiados pelo Sistema Único de Saúde.

Force elements and reaction forces

"Series title: Springerbriefs in applied sciences and technology, ISSN 2191-530X"