A proteomic approach toward the selection of proteins with enhanced intrinsic conformational stability

Journal of Proteome Research (2006)5: 2720-2726

International partner selection Indian technical textile market

Due to a combination of a vast agricultural industry and a tremendously growing technical textile industry, Ludvig Svensson identified India as target market for possible expansion through domestic production and supply. However, Svensson needed additional information about the industry structure and key players. Therefore, this project focused on a detailed analysis of the technical textile market and its players by following the international partner selection process. Thereby, five key players were identified as potential partners, as well as the need for additional research to determine alternative entry modes, as the market does not currently seem to be receptive for Svensson products.

Spectroscopic characterization of a novel 2 /[4Fe /4S] ferredoxin isolated from Desulfovibrio desulfuricans ATCC 27774

Inorganica Chimica Acta 356 (2003) 215-221

Periplasmic nitrate reductases: structural and spectroscopic studies

Dissertação apresentada para obtenção do grau de Doutor em Bioquímica, especialidade Bioquímica-Física, pela Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa

Spectroscopic Studies and Characterization of a Novel Electron-Transfer Chain

A novel two-component enzyme system from Escherichia coli involving a flavorubredoxin (FlRd) and its reductase was studied in terms of spectroscopic, redox, and biochemical properties of its constituents. FlRd contains one FMN and one rubredoxin (Rd) center per monomer. To assess the role of the Rd domain, FlRd and a truncated form lacking the Rd domain (FlRd¢Rd), were characterized. FlRd contains 2.9 ( 0.5 iron atoms/subunit, whereas FlRd¢Rd contains 2.1 ( 0.6 iron atoms/subunit. While for FlRd one iron atom corresponds to the Rd center, the other two irons, also present in FlRd¢Rd, are most probably due to a di-iron site. Redox titrations of FlRd using EPR and visible spectroscopies allowed us to determine that the Rd site has a reduction potential of -140 ( 15 mV, whereas the FMN undergoes reduction via a red-semiquinone, at -140 ( 15 mV (Flox/Flsq) and -180 ( 15 mV (Flsq/Flred), at pH 7.6. The Rd site has the lowest potential ever reported for a Rd center, which may be correlated with specific amino acid substitutions close to both cysteine clusters. The gene adjacent to that encoding FlRd was found to code for an FAD-containing protein, (flavo)rubredoxin reductase (FlRd-reductase), which is capable of mediating electron transfer from NADH to DesulfoVibrio gigas Rd as well as to E. coli FlRd. Furthermore, electron donation was found to proceed through the Rd domain of FlRd as the Rd-truncated protein does not react with FlRd-reductase. In vitro, this pathway links NADH oxidation with dioxygen reduction. The possible function of this chain is discussed considering the presence of FlRd homologues in all known genomes of anaerobes and facultative aerobes.

The role of the efflux mechanisms in multidrug resistance in Mycobacterium tuberculosis

Abstract The emergence of multi and extensively drug resistant tuberculosis (MDRTB and XDRTB) has increased the concern of public health authorities around the world. The World Health Organization has defined MDRTB as tuberculosis (TB) caused by organisms resistant to at least isoniazid and rifampicin, the main first-line drugs used in TB therapy, whereas XDRTB refers to TB resistant not only to isoniazid and rifampicin, but also to a fluoroquinolone and to at least one of the three injectable second-line drugs, kanamycin, amikacin and capreomycin. Resistance in Mycobacterium tuberculosis is mainly due to the occurrence of spontaneous mutations and followed by selection of mutants by subsequent treatment. However, some resistant clinical isolates do not present mutations in any genes associated with resistance to a given antibiotic, which suggests that other mechanism(s) are involved in the development of drug resistance, namely the presence of efflux pump systems that extrude the drug to the exterior of the cell, preventing access to its target. Increased efflux activity can occur in response to prolonged exposure to subinhibitory concentrations of anti-TB drugs, a situation that may result from inadequate TB therapy. The inhibition of efflux activity with a non-antibiotic inhibitor may restore activity of an antibiotic subject to efflux and thus provide a way to enhance the activity of current anti-TB drugs. The work described in this thesis foccus on the study of efflux mechanisms in the development of multidrug resistance in M. tuberculosis and how phenotypic resistance, mediated by efflux pumps, correlates with genetic resistance. In order to accomplish this goal, several experimental protocols were developed using biological models such as Escherichia coli, the fast growing mycobacteria Mycobacterium smegmatis, and Mycobacterium avium, before their application to M. tuberculosis. This approach allowed the study of the mechanisms that result in the physiological adaptation of E. coli to subinhibitory concentrations of tetracycline (Chapter II), the development of a fluorometric method that allows the detection and quantification of efflux of ethidium bromide (Chapter III), the characterization of the ethidium bromide transport in M. smegmatis (Chapter IV) and the contribution of efflux activity to macrolide resistance in Mycobacterium avium complex (Chapter V). Finally, the methods developed allowed the study of the role of efflux pumps in M. tuberculosis strains induced to isoniazid resistance (Chapter VI). By this manner, in Chapter II it was possible to observe that the physiological adaptation of E. coli to tetracycline results from an interplay between events at the genetic level and protein folding that decrease permeability of the cell envelope and increase efflux pump activity. Furthermore, Chapter III describes the development of a semi-automated fluorometric method that allowed the correlation of this efflux activity with the transport kinetics of ethidium bromide (a known efflux pump substrate) in E. coli and the identification of efflux inhibitors. Concerning M. smegmatis, we have compared the wild-type M. smegmatis mc2155 with knockout mutants for LfrA and MspA for their ability to transport ethidium bromide. The results presented in Chapter IV showed that MspA, the major porin in M. smegmatis, plays an important role in the entrance of ethidium bromide and antibiotics into the cell and that efflux via the LfrA pump is involved in low-level resistance to these compounds in M. smegmatis. Chapter V describes the study of the contribution of efflux pumps to macrolide resistance in clinical M. avium complex isolates. It was demonstrated that resistance to clarithromycin was significantly reduced in the presence of efflux inhibitors such as thioridazine, chlorpromazine and verapamil. These same inhibitors decreased efflux of ethidium bromide and increased the retention of [14C]-erythromycin in these isolates. Finaly, the methods developed with the experimental models mentioned above allowed the study of the role of efflux pumps on M. tuberculosis strains induced to isoniazid resistance. This is described in Chapter VI of this Thesis, where it is demonstrated that induced resistance to isoniazid does not involve mutations in any of the genes known to be associated with isoniazid resistance, but an efflux system that is sensitive to efflux inhibitors. These inhibitors decreased the efflux of ethidium bromide and also reduced the minimum inhibitory concentration of isoniazid in these strains. Moreover, expression analysis showed overexpression of genes that code for efflux pumps in the induced strains relatively to the non-induced parental strains. In conclusion, the work described in this thesis demonstrates that efflux pumps play an important role in the development of drug resistance, namely in mycobacteria. A strategy to overcome efflux-mediated resistance may consist on the use of compounds that inhibit efflux activity, restoring the activity of antimicrobials that are efflux pump substrates, a useful approach particularly in TB where the most effective treatment regimens are becoming uneffective due to the increase of MDRTB/XDRTB.

Enterococcus and biocides: mechanisms of tolerance and selection for vancomycin resistance

Dissertation presented to obtain a Doctoral degree in Biology, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa.

Investigation of trypanothione synthetase of Leishmania infantum as a potential target for new anti-parasitic drugs

Dissertação para obtenção do Grau de Mestre em Biotecnologia

O controlo da tuberculose em Portugal : uma apreciação crítica epidemiológica gl

RESUMO - Com tanto ruído informativo e peças de informação incompletas e descontextualizadas, relativos ao controlo da tuberculose em Portugal, a chegarem ao cidadão e aos profissionais de saúde, não é fácil que eles disponham do conhecimento necessário ao desempenho dos respectivos papéis nesse controlo. O presente artigo pretende contribuir para um ganho real em conhecimento quanto (1) ao progresso no controlo da tuberculose em Portugal, enquadrado na evolução desse controlo noutras regiões pertinentes, e (2) aos aspectos do conhecimento disponível e da intervenção na população portuguesa que suscitem especial atenção, para melhoria no futuro imediato. Tem como estratégia integrar, e elevar ao nível de conhecimento, a informação disponibilizada nas fontes mais credíveis e pertinentes, valorizada no contexto da validade das mesmas fontes e da coerência dos diversos componentes. Relata o resultado de um exercício independente de apreciação crítica, com uma perspectiva epidemiológica. São observados: a situação actual, sobretudo a relativa aos anos de 2006 e 2007, e o desempenho do Programa Nacional de Controlo da Tuberculose (PNT), ambos relativizados à evolução recente e ao panorama internacional. O exercício de observação e revisão independentes baseia-se numa selecção de informação oficial e segue o mesmo método de abordagem que a O.M.S. faz nos seus relatórios anuais, à semelhança de outros exercícios já antes realizados. O controlo da tuberculose tem prosseguido a sua tímida, mas firme, evolução favorável, aproximando-se do nível já conseguido nos países seus vizinhos da Europa Ocidental. Em 2007, Portugal contribuiu para os 9 milhões de casos novos anuais, estimados no mundo, com 2916 casos notificados. A este número corresponde a taxa de incidência notificada de 25,7 por 100 000 habitantes e uma redução de 14% em relação ao ano anterior. Esta evolução afigura-se animadora, ainda que seja desejável um impacte mais acentuado do PNT, conforme é de esperar considerando o grau de desenvolvimento do País. A taxa de detecção de casos novos estimada é elevada e continua uma das melhores da Europa Ocidental — o que desfavorece artificialmente a imagem notificada do País, relativamente aos países com pior capacidade de detecção. A taxa de sucesso terapêutico melhorou de novo, situando- -se acima da meta de 85% preconizada pela O.M.S, para um bom controlo da tuberculose. Uma das consequências importantes é que se consegue um melhor aproveitamento da detecção habitualmente alcançada. O conhecimento no seu conjunto aponta para que o grau de controlo possa e deva realmente ser melhorado, sendo imperiosa a discriminação positiva das áreas geográficas e dos grupos populacionais em que tende a concentrar-se a emergência de maior número de casos e de resistências aos medicamentos. Deverão assim ser reforçados selectivamente tanto os meios de detecção e de intervenção clínica, como a qualidade da organização local da intervenção, para o cumprimento efectivo da estratégia DOTS. Enquanto programa vertical que atravessa os diversos níveis do sistema de cuidados de saúde, o desempenho do PNT sofre os efeitos das atribulações desses serviços, sobretudo os de cuidados primários, funcionando como uma «situação-marcadora» quanto ao desempenho do sistema de saúde. A evidência é de que é nesta primeira linha de cuidados que se decide o sucesso na detecção e no tratamento dos casos de tuberculose, reflectindo-se também aí o grau de desenvolvimento social e os comportamentos das populações, por sua vez determinantes do risco de doença e do sucesso terapêutico. ------------------- ABSTRACT - It is not easy that both the citizen and health professionals get enabled with the required knowledge, in order do play the corresponding roles in the control of tuberculosis, considering all the information noise and incomplete, out of context information pieces about the subject, that reach them. This paper is envisaging to contribute for a real gain in knowledge, regarding: (1) the progress in tuberculosis control in Portugal, framed by the evolution of such control in other pertinent regions and (2) the available knowledge and intervention aspects in the Portuguese population that require a special attention, for improvement. The article’s strategy is to integrate, and raise to a knowledge level, information provided by the most accredited and pertinent sources, interpreted as a function of the validity context of the same sources and of the coherence of the several components. Two aspects are observed: the current situation, in particular concerning years 2006 and 2007, and the performance of the National Programme for the Tuberculosis Control (PNT), both made relative to the recent evolution and to the international panorama. This independent observation and revision exercise is based on a selection of official information and follows the same approach that the World Health Organization (W.H.O.) uses in its annual reports, like other similar exercises previously undertaken. The control of tuberculosis is evolving in a shy, but firm, fashion, getting closer to the level already attained by the neighbor countries, in Western Europe. Portugal has contributed with 2916 new notified cases, to the 9 million annual cases estimated in the world, in 2007. This number corresponds to an incidence rate, for notified cases, of 25.7 per 100000 population, and to a reduction of 14% in one year. Such evolution seems encouraging, although a greater impact of PNT is desirable, as expected in relation to the degree of the Country development. Estimated new cases detection rate is high and keeps being one of the best in Western Europe — and this artificially disadvantages the notified image of the Country, as compared with other countries having a worst detection capacity. Treatment success rate has improved again and it is above the 85% target proposed by W.H.O., so that a good control of the disease is achieved. One of the important consequences is a better use of the attained detection. Altogether, knowledge suggests that the degree of control can and must be in fact better; and that a positive discrimination of geographic areas and population groups, in which a greater number of new cases and drug resistances tend to concentrate, is mandatory. Therefore, either clinical detection and intervention resources, or the quality of the local intervention organization have to be reinforced, if a total fulfillment of DOTS strategy is to be obtained. As a vertical programme that crosses the several levels of the health care system, PNT performance suffers the effects of services tribulations, mainly primary care, thus acting as a «markersituation » as to this system performance. Evidence shows that it is in this first line of care that success in both detection and treatment of tuberculosis cases is decided; and that this level also reveals the degree of social developmen

Characterization of the activity of nitrous oxide reductase: biochemical, spectroscopic and mimetic approaches

Dissertação apresentada para a obtenção do Grau de Doutor em Química Sustentável pela Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia

Fsp27/CIDEC is a CREB target gene induced during fasting and regulated by fatty acid oxidation rate

Dissertação para obtenção do Grau de Mestre em Biotecnologia

Biogenic amines in wine: gene transcription as a tool for selection of Oenococcus oeni starter strains

Dissertation presented to obtain the Ph.D degree in Biology

Compositional and functional analysis of polycomb target chromatin

Dissertation presented to obtain the Ph.D degree in Molecular Biology

New spectroscopic and electrochemical insights on a class I superoxide reductase: evidence for an intramolecular electron-transfer pathway

Biochem. J. (2011) 438,485–494 doi:10.1042/BJ20110836