Modeling and optimization of extracellular polysaccharides production by Enterobacter A47

Polysaccharides are gaining increasing attention as potential environmental friendly and sustainable building blocks in many fields of the (bio)chemical industry. The microbial production of polysaccharides is envisioned as a promising path, since higher biomass growth rates are possible and therefore higher productivities may be achieved compared to vegetable or animal polysaccharides sources. This Ph.D. thesis focuses on the modeling and optimization of a particular microbial polysaccharide, namely the production of extracellular polysaccharides (EPS) by the bacterial strain Enterobacter A47. Enterobacter A47 was found to be a metabolically versatile organism in terms of its adaptability to complex media, notably capable of achieving high growth rates in media containing glycerol byproduct from the biodiesel industry. However, the industrial implementation of this production process is still hampered due to a largely unoptimized process. Kinetic rates from the bioreactor operation are heavily dependent on operational parameters such as temperature, pH, stirring and aeration rate. The increase of culture broth viscosity is a common feature of this culture and has a major impact on the overall performance. This fact complicates the mathematical modeling of the process, limiting the possibility to understand, control and optimize productivity. In order to tackle this difficulty, data-driven mathematical methodologies such as Artificial Neural Networks can be employed to incorporate additional process data to complement the known mathematical description of the fermentation kinetics. In this Ph.D. thesis, we have adopted such an hybrid modeling framework that enabled the incorporation of temperature, pH and viscosity effects on the fermentation kinetics in order to improve the dynamical modeling and optimization of the process. A model-based optimization method was implemented that enabled to design bioreactor optimal control strategies in the sense of EPS productivity maximization. It is also critical to understand EPS synthesis at the level of the bacterial metabolism, since the production of EPS is a tightly regulated process. Methods of pathway analysis provide a means to unravel the fundamental pathways and their controls in bioprocesses. In the present Ph.D. thesis, a novel methodology called Principal Elementary Mode Analysis (PEMA) was developed and implemented that enabled to identify which cellular fluxes are activated under different conditions of temperature and pH. It is shown that differences in these two parameters affect the chemical composition of EPS, hence they are critical for the regulation of the product synthesis. In future studies, the knowledge provided by PEMA could foster the development of metabolically meaningful control strategies that target the EPS sugar content and oder product quality parameters.

Chitosan-based magnetic nanoparticles for osteosarcoma theranostic

Cancer is a well-known disease with a significant impact in society not only due to its incidence, more evident in more developed countries, but also due to the expenses related to medical treat-ments. Cancer research is considered an increasingly logical science with great potential for the development of new treatment options. Advances in nanomedicine have resulted in rapid devel-opment of nanomaterials with considerable potential in cancer diagnostics and treatment. The combination of diagnosis and treatment in a single nano-platform is named theranostic. In this PhD thesis a theranostic system for osteosarcoma was proposed, composed by a magnetic core, a polymeric coating, and a chemotherapeutic drug. The presence of a specific targeting agent, in this case a monoclonal antibody, provides high specificity to the proposed theranostic system. For the core of the proposed theranostic system, stable aqueous suspensions of superparamagnetic iron oxide nanoparticles with an average diameter of 9 nm were produced. Chitosan-based poly-meric nanoparticles with a hydrodynamic diameter around 150 nm were successfully produced. Incorporation of iron oxide nanoparticles into the polymeric ones increased their hydrodynamic diameter to at least 250 nm. A monoclonal antibody specific for a transmembranar protein (car-bonic anhydrase IX) present in solid tumors was developed by hybridoma technology. Functional hybridomas producing the desired monoclonal antibodies were obtained. The proposed theranostic system functionality was evaluated in separated parts of its components. Uncoated and coated iron oxide nanoparticles with chitosan-based polymers generated heat under the application of an external alternating magnetic field. Uncoated iron oxide nanoparticles sta-bilized with oleic acid were able to enhance contrast in magnetic resonance imaging. Drug deliv-ery studies were conducted in chitosan-based polymeric nanoparticles without and with the in-corporation of iron oxide nanoparticles, demonstrating to be an effective drug delivery platform for doxorubicin. The theranostic system proposed in this PhD thesis is very promising for cancer theranostic, demonstrating to be applicable in solid tumors such as osteosarcoma.

Cell functional enviromics: applications to Pichia pastoris

The present PhD thesis develops the cell functional enviromics (CFE) method to investigate the relationship between environment and cellular physiology. CFE may be defined as the envirome-wide cellular function reconstruction through the collection and systems-level analysis of dynamic envirome data. Throughout the thesis, CFE is illustrated by two main applications to cultures of a constitutive P. pastoris X33 strain expressing a scFv antibody fragment. The first application addresses the challenge of culture media development. A dataset was built from 26 shake flask experiments, with variations in trace elements concentrations and basal medium dilution based on the standard BSM+PTM1. Protein yield showed high sensitivity to culture medium variations, while biomass was essentially determined by BSM dilution. High scFv yield was associated with high overall metabolic fluxes through central carbon pathways concomitantly with a relative shift of carbon flux from biosynthetic towards energy-generating pathways. CFE identified three cellular functions (growth, energy generation and by-product formation) that together described 98.8% of the variance in observed fluxes. Analyses of how medium factors relate to identified cellular functions showed iron and manganese at concentrations close to PTM1 inhibit overall metabolic activity. The second application addresses bioreactor operation. Pilot 50 L fed-batch cultivations, followed by 1H-NMR exometabolite profiling, allowed the acquisition of data for 21 environmental factors over time. CFE identified five major metabolic pathway groups that are frequently activated by the environment. The resulting functional enviromics map may serve as template for future optimization of media composition and feeding strategies for Pichia pastoris. The present PhD thesis is a step forward towards establishing the foundations of CFE that is still at its infancy. The methods developed herein are a contribution for changing the culture media and process development paradigm towards a holistic and systematic discipline in the future.

Polyhydroxyalkanoates production by photosynthetic mixed cultures

Polyhydroxyalkanoates (PHAs) are natural biologically synthesized polymers that have been the subject of much interest in the last decades due to their biodegradability. Thus far, its microbial production is associated with high operational costs, which increases PHA prices and limits its marketability. To address this situation, this thesis’ work proposes the utilization of photosynthetic mixed cultures (PMC) as a new PHA production system that may lead to a reduction in operational costs. In fact, the operational strategies developed in this work led to the selection of PHA accumulating PMCs that, unlike the traditional mixed microbial cultures, do not require aeration, thus permitting savings in this significant operational cost. In particular, the first PHA accumulating PMC tested in this work was selected under non-aerated illuminated conditions in a feast and famine regime, being obtained a consortium of bacteria and algae, where photosynthetic bacteria accumulated PHA during the feast phase and consumed it for growth during the famine phase, using the oxygen produced by algae. In this symbiotic system, a maximum PHA content of 20% cell dry weight (cdw) was reached, proving for the first time, the capacity of a PMC to accumulate PHA. During adaptation to dark/light alternating conditions, the culture decreased its algae content but maintained its viability, achieving a PHA content of 30% cdw. Also, the PMC was found to be able to utilize different volatile fatty acids for PHA production, accumulating up to 20% cdw of a PHA co-polymer composed of 3-hydroxybutyrate (3HB) and 3-hydroxyvalerate (HV) monomers. Finally, a new selective approach for the enrichment of PMCs in PHA accumulating bacteria was tested. Instead of imposing a feast and famine regime, a permanent feast regime was used, thus selecting a PMC that was capable of simultaneously growing and accumulating PHA, being attained a maximum PHA content of 60% cdw, the highest value reported for a PMC thus far. The results presented in this thesis prospect the utilization of cheap, VFA-rich fermented wastes as substrates for PHA production, which combined with this new photosynthetic technology opens up the possibility for direct sunlight illumination, leading to a more cost-effective and environmentally sustainable PHA production process.

Dynamics of serotonergic neurons revealed by fiber photometry

This work was developed in the context of the MIT Portugal Program, area of Bioengineering Systems, in collaboration with the Champalimaud Research Programme, Champalimaud Center for the Unknown, Lisbon, Portugal. The project entitled Dynamics of serotonergic neurons revealed by fiber photometry was carried out at Instituto Gulbenkian de Ciência, Oeiras, Portugal and at the Champalimaud Research Programme, Champalimaud Center for the Unknown, Lisbon, Portugal

Decisions of technology innovation: the role of indicators

This work presents research conducted to understand the role of indicators in decisions of technology innovation. A gap was detected in the literature of innovation and technology assessment about the use and influence of indicators in this type of decision. It was important to address this gap because indicators are often frequent elements of innovation and technology assessment studies. The research was designed to determine the extent of the use and influence of indicators in decisions of technology innovation, to characterize the role of indicators in these decisions, and to understand how indicators are used in these decisions. The latter involved the test of four possible explanatory factors: the type and phase of decision, and the context and process of construction of evidence. Furthermore, it focused on three Portuguese innovation groups: public researchers, business R&D&I leaders and policymakers. The research used a combination of methods to collect quantitative and qualitative information, such as surveys, case studies and social network analysis. This research concluded that the use of indicators is different from their influence in decisions of technology innovation. In fact, there is a high use of indicators in these decisions, but lower and differentiated differences in their influence in each innovation group. This suggests that political-behavioural methods are also involved in the decisions to different degrees. The main social influences in the decisions came mostly from hierarchies, knowledge-based contacts and users. Furthermore, the research established that indicators played mostly symbolic roles in decisions of policymakers and business R&D&I leaders, although their role with researchers was more differentiated. Indicators were also described as helpful instruments to conduct a reasonable interpretation of data and to balance options in innovation and technology assessments studies, in particular when contextualised, described in detail and with discussion upon the options made. Results suggest that there are four main explanatory factors for the role of indicators in these decisions: First, the type of decision appears to be a factor to consider when explaining the role of indicators. In fact, each type of decision had different influences on the way indicators are used, and each type of decision used different types of indicators. Results for policy-making were particularly different from decisions of acquisition and development of products/technology. Second, the phase of the decision can help to understand the role indicators play in these decisions. Results distinguished between two phases detected in all decisions – before and after the decision – as well as two other phases that can be used to complement the decision process and where indicators can be involved. Third, the context of decision is an important factor to consider when explaining the way indicators are taken into consideration in policy decisions. In fact, the role of indicators can be influenced by the particular context of the decision maker, in which all types of evidence can be selected or downplayed. More importantly, the use of persuasive analytical evidence appears to be related with the dispute existent in the policy context. Fourth and last, the process of construction of evidence is a factor to consider when explaining the way indicators are involved in these decisions. In fact, indicators and other evidence were brought to the decision processes according to their availability and capacity to support the different arguments and interests of the actors and stakeholders. In one case, an indicator lost much persuasion strength with the controversies that it went through during the decision process. Therefore, it can be argued that the use of indicators is high but not very influential; their role is mostly symbolic to policymakers and business decisions, but varies among researchers. The role of indicators in these decisions depends on the type and phase of the decision and the context and process of construction of evidence. The latter two are related to the particular context of each decision maker, the existence of elements of dispute and controversies that influence the way indicators are introduced in the decision-making process.

Studies on the eucalyptus leaf disease complex in Portugal

Native from south eastern Australia, Eucalyptus globulus is the main species in eucalypts plantations in Portugal. The most serious foliar disease in eucalypt plantations is linked to Mycosphaerella senso lato, which affects young trees in the juvenile phase foliage causing leaf necrosis. This disease results in reduced growth rate of the host and lower wood volume, thus causing significant productivity losses. The most common name for this disease was Mycosphaerella Leaf Disease that became inappropriate when most of the pathogens on eucalypts were re-distributed into several genera. The term "Eucalyptus Leaf Disease Complex" is now more appropriate. The overall aim of this thesis was to investigate the Eucalyptus Leaf Disease Complex in Portugal, focusing on species diversity, taxonomy and the role played by each species in the disease complex on Eucalyptus globulus. Literature on the Eucalyptus Leaf Disease Complex was reviewed and the species were distributed into several genera. A survey based on symptomatic leaves collected from several Eucalyptus globulus plantations and characterized by morphological and molecular tools provided an overview of species incidence and of the most frequent species in the disease complex. The present work reveals additional species of Mycosphaerella senso lato associated with eucalypt plantations in Portugal. Thus, five new records of Teratosphaeria and phylogenetically related species were added to the Iberian Peninsula, namely, Neodevriesia hilliana, for the first time on Myrtaceae; Quasiteratosphaeria mexicana, Teratosphaericola pseudoafricana, Teratosphaeria pluritubularis and Teratosphaeria lusitanica, a new species. Furthermore, new anamorphic structures were found and two new combinations were made. Regarding other genera, some species were observed for the first time, such as Cladosporium cladosporioides, Fusicladium eucalypti, Mycosphaerella madeirae, in the mainland. In addition to leave diseases, Teratosphaeria gauchensis was found causing a severe stem and trunk canker on Eucalyptus globulus. The aggressiveness of several species was compared to evaluate each species individually in the complex, permitting to distinguish different behaviours, from primary to secondary pathogens. Cladosporium cladosporioides, M. communis and M. lateralis, appeared to be more aggressive than Teratosphaeria nubilosa. In fact, contrary to the prevailing views on this disease complex, Teratosphaeria nubilosa is not the only species responsible for the disease, which clearly involves a complex of species acting together.

Travestis brasileiras em Portugal : percursos, identidades e ambiguidades

Os séculos XX e XXI corresponderam ao agudizar de processos globalizantes potenciados pelas novas tecnologias, quer no âmbito comunicacional, quer industrial, sublinhando dinâmicas de desruralização e de construção de tecidos urbanos densos onde o anonimato se tornou possível na vivência de experiências, outrora reconduzidas ao silêncio do sujeito socialmente isolado. A diferença, enquanto experiência vivida, tornou-se comunitariamente possível, surgindo grupos que delimitam geograficamente determinadas áreas urbanas a que correspondem afinidades eróticas ou de práticas sexuais, inicialmente de gays e lésbicas. Quebra-se na prática a uni-direccionalidade entre sexo e género, entre sexo e sexualidade, questionando-se esquemas de relações assimétricas e modelos de pensamento enraizados (heterossexualidade, patriarcado, machismo, etc.). Rubin (1975 in Lewin 2006, in Vance, 1984) propõe a existência de dois sistemas diferenciados de sexo e género que tornam plausível, sob o ponto de vista analítico, a não correspondência entre sexo, género e sexualidade. O paradigma máximo desta autonomia sistémica alcança-se na construção de uma identidade travesti. Esta identidade mutante, mutável e instável parece acompanhar um mundo de fluxos intensos e interdependências múltiplas. É na sociedade global que as travestis encontram espaço para a vivência comunitária da sua experiência, constituindo-se como um grupo com práticas transnacionais, marcado pela mobilidade de género e geográfica, primeiramente dentro das fronteiras brasileiras e depois para a Europa. Cidade, prostituição e migração surgem como factores chave da disseminação geográfica e identitária desta comunidade. Este projecto tomado sob uma perspectiva global mantêm ou reinventa relações com a estrutura, que aparentemente as apaga enquanto actores sociais e da qual, aparentemente, se auto-excluem.

A type system for value-dependent information flow analysis

Information systems are widespread and used by anyone with computing devices as well as corporations and governments. It is often the case that security leaks are introduced during the development of an application. Reasons for these security bugs are multiple but among them one can easily identify that it is very hard to define and enforce relevant security policies in modern software. This is because modern applications often rely on container sharing and multi-tenancy where, for instance, data can be stored in the same physical space but is logically mapped into different security compartments or data structures. In turn, these security compartments, to which data is classified into in security policies, can also be dynamic and depend on runtime data. In this thesis we introduce and develop the novel notion of dependent information flow types, and focus on the problem of ensuring data confidentiality in data-centric software. Dependent information flow types fit within the standard framework of dependent type theory, but, unlike usual dependent types, crucially allow the security level of a type, rather than just the structural data type itself, to depend on runtime values. Our dependent function and dependent sum information flow types provide a direct, natural and elegant way to express and enforce fine grained security policies on programs. Namely programs that manipulate structured data types in which the security level of a structure field may depend on values dynamically stored in other fields The main contribution of this work is an efficient analysis that allows programmers to verify, during the development phase, whether programs have information leaks, that is, it verifies whether programs protect the confidentiality of the information they manipulate. As such, we also implemented a prototype typechecker that can be found at http://ctp.di.fct.unl.pt/DIFTprototype/.

Frequency-domain receiver design for doubly-selective channels

This work is devoted to the broadband wireless transmission techniques, which are serious candidates to be implemented in future broadband wireless and cellular systems, aiming at providing high and reliable data transmission and concomitantly high mobility. In order to cope with doubly-selective channels, receiver structures based on OFDM and SC-FDE block transmission techniques, are proposed, which allow cost-effective implementations, using FFT-based signal processing. The first subject to be addressed is the impact of the number of multipath components, and the diversity order, on the asymptotic performance of OFDM and SC-FDE, in uncoded and for different channel coding schemes. The obtained results show that the number of relevant separable multipath components is a key element that influences the performance of OFDM and SC-FDE schemes. Then, the improved estimation and detection performance of OFDM-based broadcasting systems, is introduced employing SFN (Single Frequency Network) operation. An initial coarse channel is obtained with resort to low-power training sequences estimation, and an iterative receiver with joint detection and channel estimation is presented. The achieved results have shown very good performance, close to that with perfect channel estimation. The next topic is related to SFN systems, devoting special attention to time-distortion effects inherent to these networks. Typically, the SFN broadcast wireless systems employ OFDM schemes to cope with severely time-dispersive channels. However, frequency errors, due to CFO, compromises the orthogonality between subcarriers. As an alternative approach, the possibility of using SC-FDE schemes (characterized by reduced envelope fluctuations and higher robustness to carrier frequency errors) is evaluated, and a technique, employing joint CFO estimation and compensation over the severe time-distortion effects, is proposed. Finally, broadband mobile wireless systems, in which the relative motion between the transmitter and receiver induces Doppler shift which is different or each propagation path, is considered, depending on the angle of incidence of that path in relation to the direction of travel. This represents a severe impairment in wireless digital communications systems, since that multipath propagation combined with the Doppler effects, lead to drastic and unpredictable fluctuations of the envelope of the received signal, severely affecting the detection performance. The channel variations due this effect are very difficult to estimate and compensate. In this work we propose a set of SC-FDE iterative receivers implementing efficient estimation and tracking techniques. The performance results show that the proposed receivers have very good performance, even in the presence of significant Doppler spread between the different groups of multipath components.

A arte ao serviço do império e das colónias: o contributo de alguns programas expositivos e museológicos para o discurso de legitimação territorial

Artigo escrito no âmbito da realização de tese de doutoramento em História da Arte financiado por bolsa FCT (SFRH/BD/63763/2009)

Portugal (1928-1968) : Um Filme de J. Leitão de Barros

Apoio financeiro da FCT e do FSE no âmbito do III Quadro Comunitário de Apoio

‘Wooden Man’? : Masculinities in the Work of J. M. Coetzee (Boyhood, Youth and Summertime)

In seeking to advance the possibility of justice, gender and postcolonial studies have argued for the importance of the study of masculinities, through the acknowledgment that a richer understanding of such gendered formations may provide the basis for recognition of the Other and that, left uncriticised, such formations may be continuously delineated by the reproduction of systems of domination. The current study finds as its object the representations of masculinities in J. M. Coetzee’s Boyhood (1997), Youth (2002) and Summertime (2009). As works of transition in terms of Coetzee’s oeuvre - post-apartheid and post-Disgrace - the trilogy provides an account of the development of a man through several stages of life. While portraying the tensions of different geographical and cultural locations, such as apartheid South Africa and the London of the Sixties, the trilogy articulates the various norms that impact in the formation of gender, particularly of masculinities, through a complex system of power relations. The adherence to such norms is never linear, as the trilogy provides imaginative accounts of the contradictions that assist in the formulation of gender, depicting both the allure and the terror that constitute hegemonic masculinity. Located in the intersection of gender and postcolonial studies, the present study is based on the works by Raewyn Connell on masculinities. Animated by such a critical framework, the main research question of the present study is whether the trilogy advances a notion of masculinity that differs from the traditional rigid model, that is, whether there is resistance to hegemonic masculinity and what the spaces inhabited by the subaltern are. It is suggested that the trilogy presents the reader with instances of resistance to normative formulations of masculinity, by contrasting domination with the possibility of justice, and advancing an understanding of the often fatal consequences of gender norms to one’s sense of being in the world.

Developmental and paleontological insights into skull bone homology and evolution

The Gallus gallus (chicken) embryo is a central model organism in evolutionary developmental biology. Its anatomy and developmental genetics have been extensively studied and many relevant evolutionary implications have been made so far. However, important questions regarding the developmental origin of the chicken skull bones are still unresolved such that no solid homology can be established across organisms. This precludes evolutionary comparisons between this and other avian model systems in which skull anatomy has evolved significantly over the last millions of years.(...)

Investigation of Novel Circuits Involved in Virgin Female Receptivity of Drosophila melanogaster

Courtship is a behavior that allows the display of fitness of one sex to the other and gates possible subsequent mating. This behavior is crucial for reproduction and has strong innate components in all animals. Courtship in Drosophila melanogaster consists of a series of highly stereotyped actions that the male performs towards the female. He sings with vibrations of the wings, touches and licks her abdomen, while she evaluates the information presented to her.(...)