Experimental design methodologies for the identification of Michaelis-Menten type kinetics

The main objective of this work was to investigate the application of experimental design techniques for the identification of Michaelis-Menten kinetic parameters. More specifically, this study attempts to elucidate the relative advantages/disadvantages of employing complex experimental design techniques in relation to equidistant sampling when applied to different reactor operation modes. All studies were supported by simulation data of a generic enzymatic process that obeys to the Michaelis-Menten kinetic equation. Different aspects were investigated, such as the influence of the reactor operation mode (batch, fed-batch with pulse wise feeding and fed-batch with continuous feeding) and the experimental design optimality criteria on the effectiveness of kinetic parameters identification. The following experimental design optimality criteria were investigated: 1) minimization of the sum of the diagonal of the Fisher information matrix (FIM) inverse (A-criterion), 2) maximization of the determinant of the FIM (D-criterion), 3) maximization of the smallest eigenvalue of the FIM (E-criterion) and 4) minimization of the quotient between the largest and the smallest eigenvalue (modified E-criterion). The comparison and assessment of the different methodologies was made on the basis of the Cramér-Rao lower bounds (CRLB) error in respect to the parameters vmax and Km of the Michaelis-Menten kinetic equation. In what concerns the reactor operation mode, it was concluded that fed-batch (pulses) is better than batch operation for parameter identification. When the former operation mode is adopted, the vmax CRLB error is lowered by 18.6 % while the Km CRLB error is lowered by 26.4 % when compared to the batch operation mode. Regarding the optimality criteria, the best method was the A-criterion, with an average vmax CRLB of 6.34 % and 5.27 %, for batch and fed-batch (pulses), respectively, while presenting a Km’s CRLB of 25.1 % and 18.1 %, for batch and fed-batch (pulses), respectively. As a general conclusion of the present study, it can be stated that experimental design is justified if the starting parameters CRLB errors are inferior to 19.5 % (vmax) and 45% (Km), for batch processes, and inferior to 42 % and to 50% for fed-batch (pulses) process. Otherwise equidistant sampling is a more rational decision. This conclusion clearly supports that, for fed-batch operation, the use of experimental design is likely to largely improve the identification of Michaelis-Menten kinetic parameters.

Transport mechanism in ionic liquid membranes and the study of thiomersal biodegradation

The initial goal of this work was the development of a supported liquid membrane (SLM) bioreactor for the remediation of vaccine production effluents contaminated with a highly toxic organomercurial – thiomersal. Therefore, two main aspects were focused on: 1) the development of a stable supported liquid membrane – using room temperature ionic liquids (RTILs) – for the selective transport of thiomersal from the wastewater to a biological compartment, 2) study of the biodegradation kinetics of thiomersal to metallic mercury by a Pseudomonas putida strain. The first part of the work focused on the evaluation of the physicochemical properties of ionic liquids and on the SLMs’ operational stability. The results obtained showed that, although it is possible to obtain a SLM with a high stability, water possesses nonnegligible solubility in the RTILs studied. The formation of water clusters inside the hydrophobic ionic liquid was identified and found to regulate the transport of water and small ions. In practical terms, this meant that, although it was possible to transport thiomersal from the vaccine effluent to the biological compartment, complete isolation of the microbial culture could not be guaranteed and the membrane might ultimately be permeable to other species present in the aqueous vaccine wastewater. It was therefore decided not to operate the initially targeted integrated system but, instead, the biological system by itself. Additionally, attention was given to the development of a thorough understanding of the transport mechanisms involved in the solubilisation and transport of water through supported liquid membranes with RTILs as well as to the evaluation of the effect of water uptake by the SLM in the transport mechanisms of water-soluble solutes and its effect on SLM performance. The results obtained highlighted the determinant role played by water – solubilised inside the ionic liquids – on the transport mechanism. It became clear that the transport mechanism of water and water-soluble solutes through SLMs with [CnMIM][PF6] RTILs was regulated by the dynamics of water clusters inside the RTIL, rather than by molecular diffusion through the bulk of the ionic liquid. Although the stability tests vi performed showed that there were no significant losses of organic phase from the membrane pores, the formation of water clusters inside the ionic liquid, which constitute new, non-selective environments for solute transport, leads to a clear deterioration of SLM performance and selectivity. Nevertheless, electrical impedance spectroscopy characterisation of the SLMs showed that the formation of water clusters did not seem to have a detrimental effect on the SLMs’ electrical characteristics and highlighted the potential of using this type of membranes in electrochemical applications with low resistance requirements. The second part of the work studied the kinetics of thiomersal degradation by a pure culture of P. putida spi3 strain, in batch culture and using a synthe tic wastewater. A continuous ly stirred tank reactor fed with the synthetic wastewater was also operated and the bioreactor’s performance and robustness, when exposed to thiomersal shock loads, were evaluated. Finally, a bioreactor for the biological treatment of a real va ccine production effluent was set up and operated at different dilution rates. Thus it was possible to treat a real thiomersal-contaminated effluent, lowering the outlet mercury concentration to values below the European limit for mercury effluent discharges.

Miocene catfishes (Ariidae,Bagridae) from Lisbon: a Nilotic (or Sudanian) type fauna

Miocene catfishes from Lisbon are dealt with. Two distinct sets of pectoral and dorsal pterygiophores are described. That from the Langhian V-b is referred to Arius sp. probably close to A. heudeloti. Another ser from the uppermost Burdigalian V-a may be ascribed to a bagrid, cf. Chrysichthys sp., identified for the first time in this region. The catfish and Lates association is sctrikingly similar to African, nilotic or sudanian ones as far as freshwaters are concerned. In marine, coastal environments, stenotherm warm-water forms (Polynemids, large barracudas and several sharks) indicate, as a model, faunas like chose from Cape Verde to northern Angola. There is some gradation for brackish waters (fig. 1). Catfishes and Lates probably migrated into the Iberian Peninsule in the lower Miocene. They are unknown after Langhian V-b except for a reappearance of Arius in the middle Tortonian VII-b. Decreasing temperatures and aridity account for local extinction at least in freshwaters. Expansion of these fishes have been made easier owing to the displacement of land masses chat narrowed or closed the marine waterway between Europe and Africa. Salinity tolerance is not necessarily the sole explanation for migration. Catfishes plus Lates associations colonized inland waters from both sides of the Paleomediterranean. Local extinction may have weighed more in the development of modern distribution patterns than migration.

Synthesis, characterization and reactivity of new cobalt, palladium and nickel complexes bearing α-diimines and P, O ligands

This work describes the synthesis and characterization of a series of new α-diimine and P,O, β-keto and acetamide phosphines ligands, and their complexation to Ni(II), Co(II),Co(III) and Pd(II) to obtain a series of new compounds aiming to study their structural characteristics and to test their catalytic activity. All the compounds synthesized were characterized by the usual spectroscopic and spectrometric techniques: Elemental Analysis, MALDI-TOF-MS spectrometry, IR, UV-vis, 1H, 13C and 31P NMR spectroscopies. Some of the paramagnetic compounds were also characterized by EPR. For the majority of the compounds it was possible to solve their solid state structure by single crystal X-ray diffraction. Tests for olefin polymerization were performed in order to determine the catalytic activity of the Co(II) complexes. Chapter I presents a brief introduction to homogenous catalysis, highlighting the reactions catalyzed by the type of compounds described in this thesis, namely olefin polymerization and oligomerization and reactions catalyzed by the complexes bearing α-diimines and P,O type ligands. Chapter II is dedicated to the description of the synthesis of new α-diimines cobalt (II) complexes, of general formula [CoX2(α-diimine)], where X = Cl or I and the α-diimines are bis(aryl)acenaphthenequinonediimine) (Ar-BIAN) and 1,4-diaryl-2,3-dimethyl-1,4-diaza-1,3-butadiene (Ar-DAB). Structures solved by single crystal X-ray diffraction were obtained for all the described complexes. For some of the compounds, X-band EPR measurements were performed on polycrystalline samples, showing a high-spin Co(II) (S = 3/2) ion, in a distorted axial environment. EPR single crystal experiments on two of the compounds allowed us to determine the g tensor orientation in the molecular structure. In Chapter III we continue with the synthesis and characterization of more cobalt (II)complexes bearing α-diimines of general formula [CoX2(α-diimine)], with X = Cl or I and α-diimines are bis(aryl)acenaphthenequinonediimine) (Ar-BIAN) and 1,4-diaryl-2,3-dimethyl- 1,4-diaza-1,3-butadiene (Ar-DAB). The structures of three of the new compounds synthesized were determined by single crystal X-ray diffraction. A NMR paramagnetic characterization of all the compounds described is presented. Ethylene polymerization tests were done to determine the catalytic activity of several of the Co(II) complexes described in Chapter II and III and their results are shown. In Chapter IV a new rigid bidentate ligand, bis(1-naphthylimino)acenaphthene, and its complexes with Zn(II) and Pd(II), were synthesized. Both the ligand and its complexes show syn and anti isomers. Structures of the ligand and the anti isomer of the Pd(II) complex were solved by single crystal X-ray diffraction. All the compounds were characterized by elemental analysis, MALDI-TOF-MS spectrometry, and by IR, UV-vis, 1H, 13C, 1H-1H COSY, 1H-13C HSQC, 1H-13C HSQC-TOCSY and 1H-1H NOESY NMR when necessary. DFT studies showed that both conformers of [PdCl2(BIAN)] are isoenergetics and can be obtain experimentally. However, we can predict that the isomerization process is not available in square-planar complex, but is possible for the free ligand. The molecular geometry is very similar in both isomers, and only different orientations for naphthyl groups can be expected. Chapter V describes the synthesis of new P, O type ligands, β-keto phosphine, R2PCH2C(O)Ph, and acetamide phosphine R2PNHC(O)Me, as well as a series of new cobalt(III) complexes namely [(η5-C5H5)CoI2{Ph2PCH2C(O)Ph}], and [(η5- C5H5)CoI2{Ph2PNHC(O)Me}]. Treating these Co(III) compounds with an excess of Et3N, resulted in complexes η2-phosphinoenolate [(η5-C5H5)CoI{Ph2PCH…C(…O)Ph}] and η2- acetamide phosphine [(η5-C5H5)CoI{Ph2PN…C(…O)Me}]. Nickel (II) complexes were also obtained: cis-[Ni(Ph2PN…C(…O)Me)2] and cis-[Ni((i-Pr)2PN…C(…O)Me)2]. Their geometry and isomerism were discussed. Seven structures of the compounds described in this chapter were determined by single crystal X-ray diffraction. The general conclusions of this work can be found in Chapter VI.

Molybdenum-containing proteins from Sulphate Reducing Bacteria: studying proteins with novel cofactors and revealing new features of old enzymes

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

Type System for the ComponentJ Programming Language

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

Política(s) de saúde no trabalho : um inquérito sociológico às empresas portuguesas

Resumo Política(s) de saúde no trabalho: um inquérito sociológico às empresas portuguesas A literatura portuguesa sobre políticas, programas e actividades de Segurança, Higiene e Saúde no Trabalho (abreviadamente, SH&ST) é ainda escassa. Com este projecto de investigação pretende-se (i) colmatar essa lacuna, (ii) melhorar o conhecimento dos sistemas de gestão da saúde e segurança no trabalho e (iii) contribuir para a protecção e a promoção da saúde dos trabalhadores. Foi construída uma tipologia com cinco grupos principais de políticas, programas e actividades: A (Higiene & Segurança no Trabalho / Melhoria do ambiente físico de trabalho); B (Avaliação de saúde / Vigilância médica / Prestação de cuidados de saúde); C (Prevenção de comportamentos de risco/ Promoção de estilos de vida saudáveis); D (Intervenções a nível organizacional / Melhoria do ambiente psicossocial de trabalho); E (Actividades e programas sociais e de bem-estar). Havia uma lista de mais de 60 actividades possíveis, correspondendo a um índice de realização de 100%. Foi concebido e desenhado, para ser auto-administrado, um questionário sobre Política de Saúde no Local de Trabalho. Foram efectuados dois mailings, e um follow-up telefónico. O trabalho de campo decorreu entre a primavera de 1997 e o verão de 1998. A amostra (n=259) é considerada representativa das duas mil maiores empresas do país. Uma em cada quatro é uma multinacional. A taxa de sindicalização rondava os 30% da população trabalhadora, mas apenas 16% dos respondentes assinalou a existência de representantes dos trabalhadores eleitos para a SH&ST. A hipótese de investigação principal era a de que as empresas com um sistema integrado de gestão da SH&ST seriam também as empresas com um (i) maior número de políticas, programas e actividades de saúde; (ii) maior índice de saúde; (iii) maior índice de realização; e (iv) maior percentagem dos encargos com a SH&ST no total da massa salarial. As actividades de tipo A e B, tradicionalmente associadas à SH&ST, representavam, só por si, mais de 57% do total. Os resultados, correspondentes às respostas da Secção C do questionário, apontam, para (i) a hipervalorização dos exames de medicina do trabalho; e por outro para (ii) o subaproveitamento de um vasto conjunto de actividades (nomeadamente as de tipo D e E), que são correntemente levadas a cabo pelas empresas e que nunca ou raramente são pensadas em termos de protecção e promoção da saúde dos trabalhadores. As actividades e os programas de tipo C (Prevenção de comportamentos de risco/Promoção de estilos de vida saudáveis), ainda eram as menos frequentes entre nós, a seguir aos Programas sociais e de bem-estar (E). É a existência de sistemas de gestão integrados de SH&ST, e não o tamanho da empresa ou outra característica sociodemográfica ou técnico-organizacional, que permite predizer a frequência de políticas de saúde mais activas e mais inovadores. Os três principais motivos ou razões que levam as empresas portuguesas a investir na protecção e promoção da saúde dos seus trabalhadores eram, por ordem de frequência, (i) o absentismo em geral; (ii) a produtividade, qualidade e/ou competitividade, e (iii) a filosofia de gestão ou cultura organizacional. Quanto aos três principais benefícios que são reportados, surge em primeiro lugar (i) a melhoria da saúde dos trabalhadores, seguida da (ii) melhoria do ambiente do ambiente de trabalho e, por fim, (iii) a melhoria da produtividade, qualidade e/ou competitividade.Quanto aos três principais obstáculos que se põem, em geral, ao desenvolvimento das iniciativas de saúde, eles seriam os seguintes, na percepção dos respondentes: (i) a falta de empenho dos trabalhadores; (ii) a falta de tempo; e (iii) os problemas de articulação/ comunicação a nível interno. Por fim, (i) o empenho das estruturas hierárquicas; (ii) a cultura organizacional propícia; e (iii) o sentido de responsabilidade social surgem, destacadamente, como os três principais factores facilitadores do desenvolvimento da política de saúde no trabalho. Tantos estes factores como os obstáculos são de natureza endógena, susceptíveis portanto de controlo por parte dos gestores. Na sua generalidade, os resultados deste trabalho põem em evidência a fraqueza teóricometodológica de grande parte das iniciativas de saúde, realizadas na década de 1990. Muitas delas seriam medidas avulsas, que se inserem na gestão corrente das nossas empresas, e que dificilmente poderão ser tomadas como expressão de uma política de saúde no local de trabalho, (i) definida e assumida pela gestão de topo, (ii) socialmente concertada, (iii) coerente, (iv) baseada na avaliação de necessidades e expectativas de saúde dos trabalhadores, (v) divulgada, conhecida e partilhada por todos, (vi) contingencial, flexível e integrada, e, por fim, (vii) orientada por custos e resultados. Segundo a Declaração do Luxemburgo (1997), a promoção da saúde engloba o esforço conjunto dos empregadores, dos trabalhadores, do Estado e da sociedade civil para melhorar a segurança, a saúde e o bem-estar no trabalho, objectivo isso que pode ser conseguido através da (i) melhoria da organização e das demais condições de trabalho, da (ii) participação efectiva e concreta dos trabalhadores bem como do seu (iii) desenvolvimento pessoal. Abstract Health at work policies: a sociological inquiry into Portuguese corporations Portuguese literature on workplace health policies, programs and activities is still scarce. With this research project the author intends (i) to improve knowledge on the Occupational Health and Safety (shortly thereafter, OSH) management systems and (ii) contribute to the development of health promotion initiatives at a corporate level. Five categories of workplace health initiatives have been identified: (i) Occupational Hygiene and Safety / Improvement of Physical Working Environment (type A programs); (ii) Health Screening, Medical Surveillance and Other Occupational Health Care Provision (type B programs); (iii) Preventing Risk Behaviours / Promoting Healthy Life Styles (type C programs); (iv) Organisational Change / Improvement of Psycho-Social Working Environment (type D programs); and (v) Industrial and Social Welfare (type E programs). A mail questionnaire was sent to the Chief Executive Officer of the 1500 largest Portuguese companies, operating in the primary and secondary sectors (≥ 100 employees) or tertiary sector (≥ 75 employees). Response rate has reached about 20% (259 respondents, representing about 300 companies). Carried out between Spring 1997 and Summer 1998, the fieldwork has encompassed two direct mailings and one phone follow-up. Sample is considered to be representative of the two thousand largest companies. One in four is a multinational. Union membership rate is about 30%, but only 16% has reported the existence of a workers’ health and safety representative. The most frequent workplace health initiatives were those under the traditional scope of the OSH field (type A and B programs) (57% of total) (e.g., Periodical Medical Examinations; Individual Protective Equipment; Assessment of Working Ability). In SMEs (< 250) it was less likely to find out some time-consuming and expensive activities (e.g., Training on OSH knowledge and skills, Improvement of environmental parameters as ventilation, lighting, heating).There were significant differences in SMEs, when compared with the larger ones (≥ 250) concerning type B programs such as Periodical medical examinations, GP consultation, Nursing care, Other medical and non-medical specialities (e.g., psychiatrist, psychologist, ergonomist, physiotherapist, occupational social worker). With regard to type C programs, there were a greater percentage of programs centred on Substance abuse (tobacco, alcohol, and drug) than on Other health risk behaviours. SMEs representatives reported very few prevention- oriented programs in the field of Drug abuse, Nutrition, Physical activity, Off- job accidents, Blood pressure or Weight control. Frequency of type D programs included Training on Human Resources Management, Training on Organisational Behaviour, Total Quality Management, Job Design/Ergonomics, and Workplace rehabilitation. In general, implementation of this type of programs (Organisational Change / Improvement of Psychosocial Working Environment) is not largely driven by health considerations. Concerning Industrial and Social Welfare (Type E programs), the larger employers are in a better position than SMEs to offer to their employees a large spectrum of health resources and facilities (e.g., Restaurant, Canteen, Resting room, Transport, Infra-structures for physical activity, Surgery, Complementary social protection, Support to recreational and cultural activities, Magazine or newsletter, Intranet). Other workplace health promotion programs like Training on Stress Management, Employee Assistance Programs, or Self-help groups are uncommon in the Portuguese worksites. The existence of integrated OSH management systems, not the company size, is the main variable explaining the implementation of more active and innovative workplace health policies in Portugal. The three main prompting factors reported by employers for health protection and promotion initiatives are: (i) Employee absenteeism; (ii) Productivity, quality and/or competitiveness; and (iii) Corporate culture/management philosophy. On the other hand, (i) Improved staff’s health, (ii) Improved working environment and (iii) Improved productivity, quality and/or competitiveness were the three main benefits reported by companies’ representatives, as a result of successful implementation of workplace health initiatives. (i) Lack of staff commitment; (ii) Lack of time; and (iii) Problems of co-operation and communication within company or establishment (iii) are perceived to be the main barriers companies must cope with. Asked about the main facilitating factors, these companies have pointed out the following ones: (i) Top management commitment; (ii) Corporate culture; and (iii) Sense of social responsibility. This sociological research report shows the methodological weaknesses of workplace health initiatives, carried out by Portuguese companies during the last ‘90s. In many cases, these programs and actions were not part of a corporate health strategy and policy, (i) based on the assessment of workers’ health needs and expectancies, (ii) advocated by the employer or the chief executive officer, (ii) planned and implemented with the staff consultation and participation or (iv) evaluated according to a cost-benefit analysis. In short, corporate health policy and action were still rather based on more traditional OSH approaches and should be reoriented towards Workplace Health Promotion (WHP) approach. According to the Luxembourg Declaration of Workplace Health Promotion in the European Union (1997), WHP is “a combination of: (i) improving the work organisation and environment; (ii) promoting active participation; (iii) encouraging personal development”.Résumée Politique(s) de santé au travail: une enquête sociologique aux entreprises portugaises Au Portugal on ne sait presque rien des politiques de santé au travail, adoptés par les entreprises. Avec ce projet de recherche, on veut (i) améliorer la connaissance sur les systèmes de gestion de la santé et de la sécurité au travail et, au même temps, (ii) contribuer au développement de la promotion de la santé des travailleurs. Une typologie a été usée pour identifier les politiques, programmes et actions de santé au travail: A. Amélioration des conditions de travail / Sécurité au travail; B. Médecine du travail /Santé au travail; C. Prévention des comportements de risque / Promotion de styles de vie sains; D. Interventions organisationnelles / Amélioration des facteurs psychosociaux au travail; E. Gestion de personnel et bien-être social. Un questionnaire postal a été envoyé au représentant maximum des grandes entreprises portugaises, industrielles (≥ 100 employés) ou des services (≥ 75 employés). Le taux de réponse a été environ 20% (259 répondants, concernant trois centaines d’entreprises et d’établissements). La recherche de champ, conduite du printemps 1997 à l’été 1998, a compris deux enquêtes postales et un follow-up téléphonique. L´échantillon est représentatif de la population des deux miles plus grandes entreprises. Un quart sont des multinationales. Le taux de syndicalisation est d’environ 30%. Toutefois, il y a seulement 16% de lieux de travail avec des représentants du personnel pour la santé et sécurité au travail. Les initiatives de santé au travail les plus communes sont celles concernant le domaine plus traditionnel (types A et B) (57% du total): par exemple, les examens de médecine du travail, l’équipement de protection individuelle, les tests d’aptitude au travail. En ce qui concerne les programmes de type C, les plus fréquents sont le contrôle et la prévention des addictions (tabac, alcool, drogue). Les interventions dans le domaine de du système technique et organisationnelle du travail peuvent comprendre les courses de formation en gestion de ressources humaines ou en psychosociologie des organisations, l’ergonomie, le travail posté ou la gestion de la qualité totale. En général, la protection et la promotion de la santé des travailleurs ne sont pas prises en considération dans l’implémentation des initiatives de type D. Il y a des différences quand on compare les grandes entreprises et les moyennes en matière de politique de gestion du personnel e du bien-être (programmes de type E, y compris l’allocation de ressources humaines ou logistiques comme, par exemple, restaurant, journal d’entreprise, transports, installations et équipements sportifs). D’autres activités de promotion de la santé au travail comme la formation en gestion du stress, les programmes d’ assistance aux employés, ou les groupes de soutien et d’auto-aide sont encore très peu fréquents dans les entreprises portugaises. C’est le système intégré de gestion de la santé et de la sécurité au travail, et non pas la taille de l’entreprise, qui aide à prédire l’existence de politiques actives et innovatrices dans ce domaine. Les trois facteurs principaux qui encouragent les actions de santé (prompting factors, en anglais) sont (i) l’absentéisme (y compris la maladie), (ii) les problèmes liés à la productivité, qualité et/ou la compétitivité, et aussi (iii) la culture de l’entreprise/philosophie de gestion. Du coté des bénéfices, on a obtenu surtout l’amélioration (i) de la santé du personnel, (ii) des conditions de travail, et (iii) de la productivité, qualité et/ou compétitivité.Les facteurs qui facilitent les actions de santé au travail sont (i) l’engagement de la direction, (ii) la culture de l’entreprise, et (iii) le sens de responsabilité sociale. Par contre, les obstacles à surmonter, selon les organisations qui ont répondu au questionnaire, seraient surtout (i) le manque d’engagement des travailleurs et de leur représentants, (ii) le temps insuffisant, et (iii) les problèmes de articulation/communication au niveau interne de l’entreprise/établissement. Ce travail de recherche sociologique montre la faiblesse méthodologique des services et activités de santé et sécurité au travail, mis en place par les entreprises portugaises dans les années de 1990, à la suite des accords de concertation sociale de 1991. Dans beaucoup de cas, (i) ces politiques de santé ne font pas partie encore d’un système intégré de gestion, (ii) il n’a pas d’évaluation des besoins et des expectatives des travailleurs, (iii) c’est très bas ou inexistant le niveau de participation du personnel, (iv) on ne fait pas d’analyse coût-bénéfice. On peut conclure que les politiques de santé au travail sont plus proches de la médecine du travail et de la sécurité au travail que de la promotion de la santé des travailleurs. Selon la Déclaration du Luxembourg sur la Promotion de la Santé au Lieu de Travail dans la Communauté Européenne (1997), celle-ci « comprend toutes les mesures des employeurs, des employés et de la société pour améliorer l'état de santé et le bien être des travailleurs » e « ceci peut être obtenu par la concentration des efforts dans les domaines suivants: (i) amélioration de l'organisation du travail et des conditions de travail ; (ii) promotion d'une participation active des collaborateurs ; (iii) renforcement des compétences personnelles ».

A type system for access control in an object-oriented language

Trabalho apresentado no âmbito do Mestrado em Engenharia Informática, como requisito parcial para obtenção do grau de Mestre em Engenharia Informática

Type inference for conversation types

Trabalho apresentado no âmbito do Mestrado em Engenharia Informática, como requisito parcial para obtenção do grau de Mestre em Engenharia Informática

Identification of mating type genes in the bipolar basidiomycetous yeast rhodosporidium toruloides: first insight into the MAT Locus structure of the sporidiobolales

Eukaryotic Cell, Vol.7, Nº6

Anaerobic bacteria: an investigation of metabolic important enzymes: a novel type of oxygen reductase and enzymes of the tetrapyrrole biosynthesis

Desulfovibrio desulfuricans was the first species of a sulphatereducing bacterium to be isolated, in 1895. Since that time, many questions were raised in the scientific community regarding the metabolic and ecological aspects of these bacteria. At present, there is still a myriad of open questions remaining to be answered to enlarge our knowledge of the metabolic pathways operative in these bacteria that have implications in the sulfur cycle, in biocorrosion, namely in sewers and in oil and gas systems, and in bioremediation of several toxic metals. The work presented in this dissertation aimed at contributing with new insights of enzymes involved in two different metabolic systems on Desulfovibrio species, namely enzymes that play a role in the response to oxidative stress and that are involved in the haem biosynthetic pathway.(...)

A multitask ATPase serving different ABC-type sugar importers in Bacillus subtilis

Journal of Bacteriology (Out 2010) 5312-5318

Miocene c4tfishes (Ariidae, Bagridae) from Lisbon: a Nilotic (or Sudanian) type fauna

Miocene catfishes from Lisbon are dealt with. Two distinct sets of pectoral and dorsal pterygiophores are described. That from the Langhian V-b is referred to Arius sp. probably close to A. Beudeloti. Another set from the uppermost Burdigalian V-a may be ascribed to a bagtid, cf, Chrysichthys sp., identified for the first time in this region. The catfish and Lates association is strikingly similar to African, nilotic or sudanian ones as far as freshwaters are concerned. In marine, coastal environments, stenotherm warm-water forms (Polynemids, large barracudas and several sharks) indicate, as a model, faunas like those from Cape Verde to northern Angola. There is some gradation for brackish waters (fig. 1). Catfishes and Lates probably migrated into the Iberian Peninsule in the lower Miocene. They are unknown after Langhian V-b except for a reappearance of Arius in the middle Tortonian VII-b. Decreasing temperatures and aridity account for local extinction at least in freshwaters. Expansion of these fishes have been made easier owing to the displacement of land masses that narrowed or closed the marine waterway between Europe and Africa. Salinity tolerance is not necessarily the sole explanation for migration. Catfishes plus Lates associations colonized inland waters from both sides of the Paleomediterranean. Local extinction may have weighed more in the development of modern distribution patterns than migration.

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.

Immune reconstitution after autologous hematopoietic stem cell transplantation

Abstract The investigation of the web of relationships between the different elements of the immune system has proven instrumental to better understand this complex biological system. This is particularly true in the case of the interactions between B and T lymphocytes, both during cellular development and at the stage of cellular effectors functions. The understanding of the B–T cells interdependency and the possibility to manipulate this relationship may be directly applicable to situations where immunity is deficient, as is the case of cancer or immune suppression after radio and chemotherapy. The work presented here started with the development of a novel and accurate tool to directly assess the diversity of the cellular repertoire (Chapter III). Contractions of T cell receptor diversity have been related with a deficient immune status. This method uses gene chips platforms where nucleic acids coding for lymphocyte receptors are hybridized and is based on the fact that the frequency of hybridization of nucleic acids to the oligonucleotides on a gene chip varies in direct proportion to diversity. Subsequently, and using this new method and other techniques of cell quantification I examined, in an animal model, the role that polyclonal B cells and immunoglobulin exert upon T cell development in the thymus, specifically on the acquisition of a broader repertoire diversity by the T cell receptors (Chapter IV and V). The hypothesis tested was if the presence of more diverse peptides in the thymus, namely polyclonal immunoglobulin, would induce the generation of more diverse T cells precursors. The results obtained demonstrated that the diversity of the T cell compartment is increased by the presence of polyclonal immunoglobulin. Polyclonal immunoglobulin, and particularly the Fab fragments of the molecule, represent the most diverse self-molecules in the body and its peptides are presented by antigen presenting cells to precursor T cells in the thymus during its development. This probably contributes significantly to the generation of receptor diversity. Furthermore, we also demonstrated that a more diverse repertoire of T lymphocytes is associated with a more effective and robust T cell immune function in vivo, as mice with a more diverse T cell receptors reject minor histocompatiblility discordant skin grafts faster than mice with a shrunken T cell receptor repertoire (Chapter V). We believe that a broader T cell receptor diversity allows a more efficient recognition and rejection of a higher range of external and internal aggressions. In this work it is demonstrated that a reduction of TCR diversity by thymectomy in wild type mice significantly increased survival of H-Y incompatible skin grafts, indicating decrease on T cell function. In addiction reconstitution of T-cell diversity in mice with a decreased T cell repertoire diversity with immunoglobulin Fab fragments, lead to a increase on TCR diversity and to a significantly decreased survival of the skin grafts (Chapter V). These results strongly suggest that increases on T cell repertoire diversity contribute to improvement of T cell function. Our results may have important implications on therapy and immune reconstitution in the context of AIDS, cancer, autoimmunity and post myeloablative treatments. Based on the previous results, we tested the clinical hypothesis that patients with haematological malignancies subjected to stem cell transplantation who recovered a robust immune system would have a better survival compared to patients who did not recover such a robust immune system. This study was undertaken by the examination of the progression and overall survival of 42 patients with mantle cell non-Hodgkin lymphoma receiving autologous hematopoietic stem cell transplantation (Chapter VI). The results obtained show that patients who recovered higher numbers of lymphocytes soon after autologous transplantation had a statistically significantly longer progression free and overall survivals. These results demonstrate the positive impact that a more robust immune system reconstitution after stem cell transplantation may have upon the survival of patients with haematological malignancies. In a similar clinical research framework, this dissertation also includes the study of the impact of recovering normal serum levels of polyclonal immunoglobulin on the survival of patients with another B cell haematological malignancy, multiple myeloma, after autologous stem cell transplantation (Chapter VII). The relapse free survival of the 110 patients with multiple myeloma analysed was associated with their ability to recover normal serum levels of the polyclonal compartment of immunoglobulin. These results suggest again the important effect of polyclonal immunoglobulin for the (re)generation of the immune competence. We also studied the impact of a robust immunity for the response to treatment with the antibody anti CD20, rituximab, in patients with non- Hodgkin’s lymphoma (NHL) (Chapter VIII). Patients with higher absolute counts of CD4+ T lymphocytes respond better (in terms of longer progression free survival) to rituximab compared to patients with lower number of CD4+ T lymphocytes. These observations highlight again the fact that a competent immune system is required for the clinical benefit of rituximab therapy in NHL patients. In conclusion, the work presented in this dissertation demonstrates, for the first time, that diverse B cells and polyclonal immunoglobulin promote T cell diversification in the thymus and improve T lymphocyte function. Also, it shows that in the setting of immune reconstitution, as after autologous stem cell transplantation for mantle cell lymphoma and in the setting of immune therapy for NHL, the absolute lymphocyte counts are an independent factor predicting progression free and overall survival. These results can have an important application in the clinical practice since the majority of the current treatments for cancer are immunosuppressive and implicate a subsequent immune recovery. Also, the effects of a number of antineoplastic treatments, including biological agents, depend on the immune system activity. In this way, studies similar to the ones presented here, where methods to improve the immune reconstitution are examined, may prove to be instrumental for a better understanding of the immune system and to guide more efficient treatment options and the design of future clinical trials. Resumo O estudo da rede de inter-relações entre os diversos elementos do sistema immune tem-se mostrado um instrumento essencial para uma melhor compreensão deste complexo sistema biológico. Tal é particularmente verdade no caso das interacções entre os linfócitos B e T, quer durante o desenvolvimento celular, quer ao nível das funções celulares efectoras. A compreensão da interdependência entre linfócitos B e T e a possibilidade de manipular esta relação pode ser directamente aplicável a situações em que a imunidade está deficiente, como é o caso das doenças neoplásicas ou da imunossupressão após radio ou quimioterapia. O trabalho apresentado nesta dissertação iniciou-se com o desenvolvimento de um novo método laboratorial para medir directamente a diversidade do reportório celular (Capítulo III). Reduções da diversidade do reportório dos receptores de células T têm sido relacionadas com um estado de imunodeficiência. O método desenvolvido utiliza “gene chips”, aos quais hibridizam os ácidos nucleicos codificantes das cadeias proteicas dos receptores linfocitários. A diversidade é calculada com base na frequência de hibridização do ácido nucleico da amostra aos oligonucleótidos presentes no “gene chip”. De seguida, e utilizando este novo método e outras técnicas de quantificação celular examinei, num modelo animal, o papel que as células policlonais B e a imunoglobulina exercem sobre o desenvolvimento linfocitário T no timo, especificamente na aquisição de um reportório diverso de receptores T (Capítulos IV e V). Testei, então, a hipótese de que a presença no timo de péptidos mais diversos, como a imunoglobulna policlonal, induzisse a génese de precursores T mais diversos. Demonstrámos que a diversidade do compartimento T é aumentado pela presença de imunoglobulina policlonal. A imunoglobulina policlonal, e particularmente os fragmentos Fab desta molécula, representam as moléculas autólogas mais diversas presentes nos organismos vertebrados. Estes péptidos são apresentados por células apresentadoras de antigénio às células precursoras T no timo, durante o desenvolvimento celular T. Tal, provavelmente, contribui para a génese da diversidade dos receptores. Também demonstrámos que a presença de um reportório mais diverso de linfócitos T se associa a um incremento da função imunológica T in vivo. Uma diversidade de receptores T mais extensa parece permitir um reconhecimento e rejeição mais eficientes de um maior número de agressores internos e externos. Demonstrámos que ratinhos com receptores de células T (RCT) com maior diversidade rejeitam transplantes cutâneos discordantes para antigénios minor de histocompatibilidade mais rapidamente do que ratinhos com um menor reportório T (Capítulo V). Por outro lado, uma redução da diversidade do RCT, causada por timectomia de ratinhos de estirpes selvagens, mostrou aumentar significativamente a sobrevivência de transplantes cutâneos incompatíveis para o antigénio H-Y (antigénio minor de histocompatibilidade), indicando uma diminuição da função linfocitária T. Além disso, a reconstituição da diversidade dos linfócitos T em ratinhos com uma diversidade de reportório T diminuída, induzida pela administração de fragmentos Fab de imunoglobulina, conduz a um aumento da diversidade dos RCT e a uma diminuição significativa da sobrevivência dos enxertos cutâneos (Capítulo V). Estes resultados sugerem que o aumento do reportório de células T contribui para uma melhoria das funções celulares T e poderão ter implicações importantes na terapêutica e reconstitutição imunológica em contexto de SIDA, neoplasias, autoimunidade e após tratamentos mieloablativos. Baseado nos resultados anteriores, decidimos testar a hipótese clínica de que doentes com neoplasias hematológicas sujeitos a transplantação de precursores hematopoiéticos e com recuperação imunológica precoce após transplante teriam uma sobrevivência mais longa do que doentes que não recuperassem tão bem a sua imunidade. Analisámos a sobrevivência global e sobrevivência sem doença de 42 doentes com linfoma não Hodgkin de células do manto sujeitos a transplante autólogo de precursores hematopoiéticos (Capítulo VI). Os resultados obtidos mostraram que os doentes que recuperaram contagens mais elevadas de linfócitos imediatamente após o transplante autólogo, apresentaram uma sobrevivência global e sem progressão mais longa do que doentes que não recuperaram contagens linfocitárias tão precocemente. Estes resultados demonstram o efeito positivo de uma reconstitutição imunológica robusta após transplante de presursores hematopoiéticos, sobre a sobrevivência de doentes com neoplasias hematológicas. Do mesmo modo, estudámos o efeito que a recuperação de níveis séricos normais de imunoglobulina policlonal tem na sobrevivência de doentes com outras neoplasias hematológicas de linfócitos B, como o mieloma múltiplo,após transplante autólogo de precursos hematopoiéticos (Capítulo VII). A sobrevivência livre de doença dos 110 doentes com mieloma múltiplo analizados está associada com a sua capacidade de recuperar níveis séricos normais do compartmento policlonal de imunoglobulina. Estes resultados pioneiros indicam a importância da imunoglobulina policlonal para a génese de competência imunológica. Também estudámos o impacto de um sistema imunitário eficiente sobre a resposta ao tratamento com o anticorpo anti CD20, ituximab, em doentes com linfoma não Hodgkin (LNH) (Capítulo VIII). Os resultados mostram que doentes com valores mais elevados de linfócitos T CD4+ respondem melhor (em termos de maior sobrevida livre de doença) ao rituximab, do que doentes com valores mais baixos. Estas observações ilustram a necessidade de um sistema imunitário competente para o benefício clínico da terapêutica com rituximab em doentes com LNH. Em conclusão, o trabalho apresentado nesta dissertação demonstra que as células B e a imunoglobulina policlonal promovem a diversidade das células T no timo e melhoram a função linfocitária T periférica. Concomitantemente, também demonstrámos que, no contexto de reconstituição imune, por exemplo, após transplante autólogo de precursores hematopoiéticos em doentes com linfomas de células do manto, o número absoluto de linfócitos é uma factor independente da sobrevivência. Os resultados demonstram, também, a importância dos valores de linfocitos T na resposta ao tratamento com rituximab no caso de doentes com LNH. O mesmo princípio se prova pelo facto de que doentes com mieloma múltiplo sujeitos a transplante autólogo de precursores hematopoiéticos que recuperam valores normais séricos de imunoglobulinas policlonais, terem melhores taxas de resposta em comparação com doentes que não recuperam valores normais de imunoglobulinas policlonais. Estes resultados podem ter importantes aplicações na prática clínica dado que a maioria dos tratamentos de doenças neoplásicas implica imunossupressão e, subsequente, recuperação imunológica. Estes estudos podem ser um instrumento fundamental para uma melhor compreensão do sistema imune e guiar uma escolha mais eficiente de opções terapêuticas bem como contribuir para a concepção de futuros estudos clínicos.