Environmental factors, clipping and fire: effects on cerrado (Brazilian savanna) native and invasive grasses

The Brazilian Cerrado houses a hugely diverse biota and is considered a conservation hotspot. One of the greatest threats to the integrity of this ecosystem is introduced African grasses, which can competitively exclude native grasses and cause changes in the microclimate and other disturbances. The Cerrado is a mosaic vegetation that provides different combinations, both spatially and temporally, of conditions that can become natural stressors to the herbaceous vegetation (water, nutrient and light availability). These mosaics are reflected in differences in relationships among native and invasive species, affecting competition and creating situations (place/season) that are more, or less, susceptible to invasion. The present study aimed to identify the different biological responses of native (Aristida recurvata, Aristida setifolia, Axonopus barbigerus, Echinolaena inflexa, Gymnopogon spicatus, Paspalum gardnerianum, Paspalum stellatum, Schizachyrium microstachyum, Schizachyrium sanguineum) and invasive (Melinis minutiflora and Andropogon gayanus) grasses to variations in natural stressors and to disturbance (fire and clipping), in order to understand changes in ecosystem functioning and competition processes between the grasses, and to understand invasion dynamics in this ecosystem. The presence of invasive species proved to affect the ecosystem functioning by increasing soil feeding activity. These differences were no longer observed in the dry season or when fires were frequent, showing that water availability and fire are more detrimental to soil feeding activity than is the vegetation. Laboratory experiments showed that both drought and flood simulated scenarios damaged both species, although the invasive species performed better under all watering conditions and responded better to fertilization. Underlying mechanisms such as the efficiency of photosynthesis and antioxidant mechanisms helped to explain this behavior. The invasive species grew faster and showed less cellular damage and a healthier photosystem, reflected in higher assimilation rates under stress. These differences between the native and invasive species were reduced with clipping, especially in dry soil with no fertilization, where the native species recovered better in relation to the pre-clipping levels. Flooding was as stressful as drought, but the invasive species can bypass this issue by growing an extensive root system, especially in the better-drained soils. Fire is more detrimental than clipping, with a slower recovery, while post-fire temperatures affect the germination of both invasive and native seeds and may be an important factor influencing the persistence of a diverse biota. This approach will finally contribute to the choice of the appropriate management techniques to preserve the Cerrado’s biodiversity.

Surface reactivity enhancement of silica-based glass-ceramic scaffolds

A paradigm shift is taking place from using transplanting tissue and synthetic implants to a tissue engineering approach that aims to regenerate damaged tissues by combining cells from the body with highly porous scaffold biomaterials, which act as templates, guiding the growth of new tissue. The central focus of this thesis was to produce porous glass and glass-ceramic scaffolds that exhibits a bioactive and biocompatible behaviour with specific surface reactivity in synthetic physiological fluids and cell-scaffold interactions, enhanced by composition and thermal treatments applied. Understanding the sintering behaviour and the interaction between the densification and crystallization processes of glass powders was essential for assessing the ideal sintering conditions for obtaining a glass scaffolds for tissue engineering applications. Our main goal was to carry out a comprehensive study of the bioactive glass sintering, identifying the powder size and sintering variables effect, for future design of sintered glass scaffolds with competent microstructures. The developed scaffolds prepared by the salt sintering method using a 3CaO.P2O5 - SiO2 - MgO glass system, with additions of Na2O with a salt, NaCl, exhibit high porosity, interconnectivity, pore size distribution and mechanical strength suitable for bone repair applications. The replacement of 6 % MgO by Na2O in the glass network allowed to tailor the dissolution rate and bioactivity of the glass scaffolds. Regarding the biological assessment, the incorporation of sodium to the composition resulted in an inibition cell response for small periods. Nevertheless it was demonstrated that for 21 days the cells response recovered and are similar for both glass compositions. The in vitro behaviour of the glass scaffolds was tested by introducing scaffolds to simulated body fluid for 21 days. Energy-dispersive Xray spectroscopy and SEM analyses proved the existence of CaP crystals for both compositions. Crystallization forming whitlockite was observed to affect the dissolution behaviour in simulated body fluid. By performing different heat treatments, it was possible to control the bioactivity and biocompatability of the glass scaffolds by means of a controlled crystallization. To recover and tune the bioactivity of the glass-ceramic with 82 % crystalline phase, different methods have been applied including functionalization using 3- aminopropyl-triethoxysilane (APTES). The glass ceramic modified surface exhibited an accelerated crystalline hydroxyapatite layer formation upon immersion in SBF after 21 days while the as prepared glass-ceramic had no detected formation of calcium phosphate up to 5 months. A sufficient mechanical support for bone tissue regeneration that biodegrade later at a tailorable rate was achievable with the glass–ceramic scaffold. Considering the biological assessment, scaffolds demonstrated an inductive effect on the proliferation of cells. The cells showed a normal morphology and high growth rate when compared to standard culture plates. This study opens up new possibilities for using 3CaO.P2O5–SiO2–MgO glass to manufacture various structures, while tailoring their bioactivity by controlling the content of the crystalline phase. Additionally, the in vitro behaviour of these structures suggests the high potential of these materials to be used in the field of tissue regeneration.

Codon ambiguities as a mechanism to alter the genetic code in Saccharomyces cerevisiae

Although the genetic code is generally viewed as immutable, alterations to its standard form occur in the three domains of life. A remarkable alteration to the standard genetic code occurs in many fungi of the Saccharomycotina CTG clade where the Leucine CUG codon has been reassigned to Serine by a novel transfer RNA (Ser-tRNACAG). The host laboratory made a major breakthrough by reversing this atypical genetic code alteration in the human pathogen Candida albicans using a combination of tRNA engineering, gene recombination and forced evolution. These results raised the hypothesis that synthetic codon ambiguities combined with experimental evolution may release codons from their frozen state. In this thesis we tested this hypothesis using S. cerevisiae as a model system. We generated ambiguity at specific codons in a two-step approach, involving deletion of tRNA genes followed by expression of non-cognate tRNAs that are able to compensate the deleted tRNA. Driven by the notion that rare codons are more susceptible to reassignment than those that are frequently used, we used two deletion strains where there is no cognate tRNA to decode the rare CUC-Leu codon and AGG-Arg codon. We exploited the vulnerability of the latter by engineering mutant tRNAs that misincorporate Ser at these sites. These recombinant strains were evolved over time using experimental evolution. Although there was a strong negative impact on the growth rate of strains expressing mutant tRNAs at high level, such expression at low level had little effect on cell fitness. We found that not only codon ambiguity, but also destabilization of the endogenous tRNA pool has a strong negative impact in growth rate. After evolution, strains expressing the mutant tRNA at high level recovered significantly in several growth parameters, showing that these strains adapt and exhibit higher tolerance to codon ambiguity. A fluorescent reporter system allowing the monitoring of Ser misincorporation showed that serine was indeed incorporated and possibly codon reassignment was achieved. Beside the overall negative consequences of codon ambiguity, we demonstrated that codons that tolerate the loss of their cognate tRNA can also tolerate high Ser misincorporation. This raises the hypothesis that these codons can be reassigned to standard and eventually to new amino acids for the production of proteins with novel properties, contributing to the field of synthetic biology and biotechnology.

Emerging Technologies

This book, written when Walker was Visiting Professor at the Technical University Munich in 2011, describes his research on the effects of digital technology on architectural design and construction, and on the development of ‘digital craft’. The primary example given is The Swarm, a digitally designed and manufactured pavilion, produced with students while Walker was at TU Munich. It now stands outside the Bayerischen Architektenkammer (Bavarian Chamber of Architects) in Munich. Through such research-by-design, Walker asks larger questions: what can designers craft without a master craftsman’s skills, and how can craft skills be recovered through digital fabrication? Another example in the book is the Swoosh Pavilion, one of two public-space-scale architectural pavilion prototypes Walker developed between 2008 and 2009 at the Architectural Association (AA), using applied digital modelling and CNC techniques to investigate methods of teaching and testing digital processes through making. Swoosh (2008) and a second AA pavilion, Driftwood (2009), were discussed by Walker and Martin Self, his co-investigator, in ‘Fractal, bad hair, Swoosh and Driftwood pavilions of Intermediate Unit 2, 2006–2009’, published in the AD reader, Manufacturing the Bespoke (2012), which includes essays by well-known critics and designers such as Mathias Kohler and Michael Stacey. Both AA pavilions were sponsored by FinnForest Merk, Arup, HOK and Building Design Magazine, and were seen by large international audiences in Bedford Square, London during the 2008–9 ‘AA Projects Review’ shows. The book Making Pavilions (Walker and Self, AA Agenda No. 9, Architectural Association Press, 2011) also discusses their work over seven years of teaching at the Architectural Association. At the same time, Walker collaborated on a series of Serpentine pavilions, commissioned annually by the Serpentine Gallery, London, co-designing these experimental structures with internationally renowned architects Daniel Libeskind, Oscar Niemeyer, Toyo Ito and Alvaro Siza.

Chronic symptoms after vestibular neuritis and the high velocity vestibulo-ocular reflex

Hypothesis: As the anterior and posterior semicircular canals are vital to the regulation of gaze stability, particularly during locomotion or vehicular travel, we tested whether the high velocity vestibulo‐ocular reflex (VOR) of the three ipsilesional semicircular canals elicited by the modified Head Impulse Test would correlate with subjective dizziness or vertigo scores after vestibular neuritis (VN). Background: Recovery following acute VN varies with around half reporting persistent symptoms long after the acute episode. However, an unanswered question is whether chronic symptoms are associated with impairment of the high velocity VOR of the anterior or posterior canals. Methods: Twenty patients who had experienced an acute episode of VN at least three months earlier were included in this study. Participants were assessed with the video head impulse test (vHIT) of all six canals, bithermal caloric irrigation, the Dizziness Handicap Inventory (DHI) and the Vertigo Symptoms Scale short‐form (VSS). Results: Of these 20 patients, 12 felt that they had recovered from the initial episode whereas 8 did not and reported elevated DHI and VSS scores. However, we found no correlation between DHI or VSS scores and the ipsilesional single or combined vHIT gain, vHIT gain asymmetry or caloric paresis. The high velocity VOR was not different between patients who felt they had recovered and patients who felt they had not. Conclusions: Our findings suggest that chronic symptoms of dizziness following VN are not associated with the high velocity VOR of the single or combined ipsilesional horizontal, anterior or posterior semicircular canals.

Zooarqueologia e tafonomia de Castanheiro do Vento

Dissertação mest., Arqueologia, Universidade do Algarve, 2007

A desagregação espacial de dados agrícolas: aplicação de uma abordagem baseada na máxima entropia ao concelho de Castelo de Vide

Dissertação mest., Gestão Sustentável de Espaços Rurais, Universidade do Algarve, 2009

A corpus-based translation study on english-persian verb phrase ellipsis

Dissertação de mest., Natural Language Processing & Human Language Technology, Faculdade de Ciências Humanas e Sociais, Univ. do Algarve, 2011

Combined disaggregation of agricultural land uses, livestock numbers and crops' production: an entropy approach

This paper presents several combined agricultural data disaggregation models in order to recover the farms' land uses, the livestock numbers and main crops' productions. The proposed approach estimates incomplete information at disaggregated level through entropy, using an information prior, and generating information for a combined calculation use of data in the estimation of other variables. The models were applied to the region of Algarve, to some rural pilot areas (Salir-Ameixial-Cachopo and Alcoutim) for livestock data, since this data in some Algarve's inland areas is needed for a European forest fire prevention project, and to the agrarian zones in a more complex framework. The results are promising. They were validated, in cross reference to real data, having proven to be valid and reliable. The total error was small and a considerable level of information heterogeneity was recovered. The total error was about 27,9% for the counties' land uses and 21% for the agrarian zones, and for the livestock it was also acceptable. The level of heterogeneity recovered was always higher than 50%, revealing some improvements regarding previous studies.

An autonomous system for ocean acoustic tomography

Vertical line arrays (VLA) are a widely used apparatus in underwater acoustics with applications in sonar prediction, underwater communications and acoustic tomography, among others. Recent developments in digital electronics and communications allow for off-the-shelf development of VLA systems, with a large number of embedded acoustic and non-acoustic sensors able to fulfill application requirements, as opposed to single or few receiver configurations available until only a few years ago. Very often, the flexibility in water column sampling is achieved by splitting the VLA into modules that can be assembled according to the application. Such systems can be deployed and recovered from small vessels with a shorthanded crew, and make it possible for research labs with reduced budgets and operational means (ships and manpower) to gain control over the whole development process, from data acquisition to post-processing.

Genesis of the brecciated rocks from mid atlantic ridge hydrothermal systems : Lucky Strike (37º50’N) and Menez Gwen (37º50’N)

Tese de doutoramento, Geologia (Metalogenia), Universidade de Lisboa, Faculdade de Ciências, 2014

Lancefield group C and G streptococci in human infection : molecular typing, virulence and antimicrobial susceptibility

Tese de doutoramento, Ciências e Tecnologias da Saúde (Microbiologia), Universidade de Lisboa, Faculdade de Medicina, 2014

Partial volume correction using bimodal contrast agents in PET-MRI

Tese de mestrado integrado em Engenharia Biomédica e Biofísica, apresentada à Universidade de Lisboa, através da Faculdade de Ciências, 2014

O tempo das reformas : o papel da companhia de Jesus no enfrentamento com ideais protestantes na Europa do Sul : uma proposta pedagógica

Relatório da prática de ensino supervisionada, Mestrado em Ensino da História e da Geografia no 3º Ciclo do Ensino Básico e no Ensino Secundário, Universidade de Lisboa, 2014

Finding ‘Good Friday’ An explorative study into the sedimentary structures left from the Good Friday tsunami

Senior thesis written for Oceanography 444