Sea Urchin Body Plan Development and Evolution: An Integrative Transcriptomic Approach

My dissertation work integrates comparative transcriptomics and functional analyses to investigate gene expression changes underlying two significant aspects of sea urchin evolution and development: the dramatic developmental changes associated with an ecologically significant shift in life history strategy and the development of the unusual radial body plan of adult sea urchins.

In Chapter 2, I investigate evolutionary changes in gene expression underlying the switch from feeding (planktotrophic) to nonfeeding (lecithotrophic) development in sea urchins. In order to identify these changes, I used Illumina RNA-seq to measure expression dynamics across 7 developmental stages in three sea urchin species: the lecithotroph Heliocidaris erythrogramma, the closely related planktotroph Heliocidaris tuberculata, and an outgroup planktotroph Lytechinus variegatus. My analyses draw on a well-characterized developmental gene regulatory network (GRN) in sea urchins to understand how the ancestral planktotrophic developmental program was altered during the evolution of lecithotrophic development. My results suggest that changes in gene expression profiles occurred more frequently across the transcriptome during the evolution of lecithotrophy than during the persistence of planktotrophy. These changes were even more pronounced within the GRN than across the transcriptome as a whole, and occurred in each network territory (skeletogenic, endomesoderm and ectoderm). I found evidence for both conservation and divergence of regulatory interactions in the network, as well as significant changes in the expression of genes with known roles in larval skeletogenesis, which is dramatically altered in lecithotrophs. I further explored network dynamics between species using coexpression analyses, which allowed me to identify novel players likely involved in sea urchin neurogenesis and endoderm patterning.

In Chapter 3, I investigate developmental changes in gene expression underlying radial body plan development and metamorphosis in H. erythrogramma. Using Illumina RNA-seq, I measured gene expression profiles across larval, metamorphic, and post-metamorphic life cycle phases. My results present a high-resolution view of gene expression dynamics during the complex transition from pre- to post-metamorphic development and suggest that distinct sets of regulatory and effector proteins are used during different life history phases.

Collectively, my investigations provide an important foundation for future, empirical studies to investigate the functional role of gene expression change in the evolution of developmental differences between species and also for the generation of the unusual radial body plan of sea urchins.

Metaphors and metamorphoses: narratives of identity during times of crisis

The narrative of transformative crisis appears in both autobiographical and fictional accounts of individual lives; it typically involves a difficult or traumatic episode and a period of self-questioning out of which a person emerges more able and more emotionally mature than before (Booker, 2005; Erikson, 1968; Tedeschi and Calhoun, 1995). The present study used interviews to elicit 22 narratives about crises experienced between the ages of 25 and 40, and about any developmental transformation and change that surrounded these crises. Analysis revealed a common four-phase process to the crisis episodes, common metaphors and recurrent descriptions of identity metamorphosis, ie. of ‘becoming a new person’. Comparison of these findings with theory on fictional plots shows a clear parallel between the four-phase process of crisis found in the current study and the ‘rebirth’ plot described by Booker (2005). The theoretical significance of these findings and interpretations is discussed.

Ichthyological contributions

Contributions cover notes on the distribution of Zeugopterus norvegicus, a stage in the metamorphosis of Solea, a larval stage of the mackerel, and on growth of young herring in the Thames Estuary.

From plankton to top predators: bottom-up control of a marine food web across four trophic levels

1. Abundant mid-trophic pelagic fish often play a central role in marine ecosystems, both as links between zooplankton and top predators and as important fishery targets. In the North Sea, the lesser sandeel occupies this position, being the main prey of many bird, mammal and fish predators and the target of a major industrial fishery. However, since 2003, sandeel landings have decreased by > 50%, and many sandeel-dependent seabirds experienced breeding failures in 2004. 2. Despite the major economic implications, current understanding of the regulation of key constituents of this ecosystem is poor. Sandeel abundance may be regulated 'bottom-up' by food abundance, often thought to be under climatic control, or 'top-down' by natural or fishery predation. We tested predictions from these two hypotheses by combining unique long-term data sets (1973–2003) on seabird breeding productivity from the Isle of May, SE Scotland, and plankton and fish larvae from the Continuous Plankton Recorder survey. We also tested whether seabird breeding productivity was more tightly linked to sandeel biomass or quality (size) of individual fish. 3. The biomass of larval sandeels increased two- to threefold over the study period and was positively associated with proxies of the abundance of their plankton prey. Breeding productivity of four seabirds bringing multiple prey items to their offspring was positively related to sandeel larval biomass with a 1-year lag, indicating dependence on 1-year-old fish, but in one species bringing individual fish it was strongly associated with the size of adult sandeels. 4. These links are consistent with bottom-up ecosystem regulation and, with evidence from previous studies, indicate how climate-driven changes in plankton communities can affect top predators and potentially human fisheries through the dynamics of key mid-trophic fish. However, the failing recruitment to adult sandeel stocks and the exceptionally low seabird breeding productivity in 2004 were not associated with low sandeel larval biomass in 2003, so other mechanisms (e.g. predation, lack of suitable food after metamorphosis) must have been important in this case. Understanding ecosystem regulation is extremely important for predicting the fate of keystone species, such as sandeels, and their predators.

Growth and breeding of a primitive stalked barnacle Leucolepas longa (Cirripedia: Scalpellomorpha: Eolepadidae: Neolepadinae) inhabiting a volcanic seamount off Papua New Guinea

A pedunculate barnacle, Leucolepas longa, occurs in densities over 1000 individuals m[minus sign]2 on the summit of a small seamount near New Ireland, Papua New Guinea. Most of the population grows on vesicomyid clams projecting from sulphide-rich sediments, or on their dead shells, but the barnacle also settles on rock and on tubes of a vestimentiferan. Collections of several hundred barnacles allowed comparison of population and reproductive characteristics. The barnacle is a suspension feeder with a lightly-armoured stalk that can grow to 40 cm above the bottom. Growth appears to be rapid and both reproduction and recruitment are continuous. The barnacles brood egg masses within the capitular chamber and 46% of one sample was brooding. Lecithotrophic nauplii released upon retrieval to the surface were cultivated for 45 days. Metamorphosis to Stage IV yielded an actively swimming larva about 1 mm long overall, which still contained lipid reserves, indicating capacity for wide dispersal

The Postmodern Non-city in Miquel de Palol’s "El Jardí del Set Crepuscles"

El Jardí del Set Crepuscles –primera novela del escritor y arquitecto catalán Miquel de Palol– nos brinda la oportunidad de reflexionar acerca de la metamorfosis experimentada por la ciudad occidental a principios de los años setenta del siglo pasado. De acuerdo con autores como Henri Lefebvre, David Harvey, Giandomenico Amendola o Edward Soja, el surgimiento de la ciudad posmoderna en el marco de la transición hacia el modo de acumulación postfordista se presenta acompañado por un debilitamiento del tejido social y de la esfera pública y cívica. El objetivo del presente artículo es ilustrar las estrategias narrativas y retóricas con las que el texto de Miquel de Palol representa, y analiza, dicho fenómeno.

'Neo-Latin Writing in the British Isles'

This chapter seeks to identify cultural and generic trends and authorial methodologies that may serve to unify or to differentiate between the histories of neo-Latin literature in England, Scotland, Wales and Ireland. It considers ways in which Latin served to bridge horizontal spaces (both physical and metaphorical) between four British regions, between neo-Latin writers in Britain and their continental predecessors and peers, and between Latin and the respective vernacular(s). It also examines vertical spaces (both chronological and cultural) between the neo-Latin and the classical Latin text, and between the linear demarcations of ‘early modern’, ‘Augustan’ and ‘Romantic’. An assessment of links between nationhood and the neo-Latin text as evinced by anthologies, antiquarian and quasi-historical writing, is followed by examples of generic continuity and metamorphosis in the British neo-Latin pastoral, ode and epigram. The concluding sections offer two generic case-studies (neo-Latin epic and didactic) both of which, it is argued, engendered the birth of specifically British versions of the mock-heroic and mock-didactic.

Interfacial self-assembly of a bacterial hydrophobin

The majority of bacteria in the natural environment live within the confines of a biofilm. The Gram-positive bacterium Bacillus subtilis forms biofilms that exhibit a characteristic wrinkled morphology and a highly hydrophobic surface. A critical component in generating these properties is the protein BslA, which forms a coat across the surface of the sessile community. We recently reported the structure of BslA, and noted the presence of a large surface-exposed hydrophobic patch. Such surface patches are also observed in the class of surface-active proteins known as hydrophobins, and are thought to mediate their interfacial activity. However, although functionally related to the hydrophobins, BslA shares no sequence nor structural similarity, and here we show that the mechanism of action is also distinct. Specifically, our results suggest that the amino acids making up the large, surface-exposed hydrophobic cap in the crystal structure are shielded in aqueous solution by adopting a random coil conformation, enabling the protein to be soluble and monomeric. At an interface, these cap residues refold, inserting the hydrophobic side chains into the air or oil phase and forming a three-stranded β-sheet. This form then self-assembles into a well-ordered 2D rectangular lattice that stabilizes the interface. By replacing a hydrophobic leucine in the center of the cap with a positively charged lysine, we changed the energetics of adsorption and disrupted the formation of the 2D lattice. This limited structural metamorphosis represents a previously unidentified environmentally responsive mechanism for interfacial stabilization by proteins.

Larval development of the pedunculate barnacles Octolasmis angulata Aurivillius 1894 and Octolasmis cor Aurivillius 1892 (Cirripedia: Thoracica: Poecilasmatidae) from the gills of the mud crab, Scylla tranquebarica Fabricius, 1798

Detailed studies of larval development of Octolasmis angulata and Octolasmis cor are pivotal in understanding the larval morphological evolution as well as enhancing the functional ecology. Six planktotrophic naupliar stages and one non-feeding cyprid stage are documented in details for the first time for the two species of Octolasmis. Morphologically, the larvae of O. angulata and O. cor are similar in body size, setation patterns on the naupliar appendages, labrum, dorsal setae-pores, frontal horns, cyprid carapace, fronto-lateral gland pores, and lattice organs. Numbers of peculiarities were observed on the gnathobases of the antennae and mandible throughout the naupliar life-cycle. The setation pattern on the naupliar appendages are classified based on the segmentation on the naupliar appendages. The nauplius VI of both species undergoes a conspicuous change before metamorphosis into cyprid stage. The cyprid structures begin to form and modify beneath the naupliar body towards the end of stage VI. This study emphasises the importance of the pedunculate barnacle larval developmental studies not only to comprehend the larval morphological evolution but also to fill in the gaps in understanding the modification of the naupliar structures to adapt into the cyprid life-style.

Embryonic and larval ecology and biochemistry of offshore decapods

Understanding the biology of offshore species is hardened by the difficulties of sampling in the deep-sea environment. Additionally, due to the vastness of the open ocean, knowledge of early life histories of pelagic larvae is still relatively scarce. In decapod species with bentho-pelagic lifestyle, the transition from life in the seafloor to the water column not only is associated with drastic morphological metamorphosis, but also with changes in behavior and feeding ecology. The purpose of the present thesis was to investigate physiological, biochemical and behavioral adaptation occurring during early development of such species. The Norway lobster, Nephrops norvegicus, and the crab Monodaeus couchi were used as a model as these two species are encountered off the NE Atlantic shelf at depth greater than 300 m. Chapter 1 introduces the challenges faced by both adult and larvae inhabiting such remote habitats, including the effect of food availability on development and oceanographic processes on dispersal and recruitment. The thesis follows early life histories, starting with within-brood variability in the fatty acid (FA) profile displayed by developing N. norvegicus embryos. There were no differences in the FA composition of embryos sampled from both sides of the brooding chamber in most females. However, all females exhibited significant differences in the FA profiles of embryos sampled from different pleopods. Potential causes for the variations recorded may be differential female investment during oocyte production or shifts in FA catabolism during the incubation period promoted by embryo’s location within the brooding chamber. Next, feeding rates and digestive enzymes activity of the early stage larvae was investigated in N. norvegicus. Both stages were able to maximize food intake when larvae were scarce and showed increased feeding rate following periods of starvation. Amylase activity indicated that carbohydrates are not the primary energy reserve and that feeding may be required soon after hatching to trigger amylase activity. Protease activity indicated that protein reserves are catabolized under starvation. These results indicate that larvae may maximize prey ingestion in the presence of plankton patches with higher food abundance and minimize the deleterious effects induced by previous periods of intermittent starvation or unsuitable prey densities/types. Additionally, changes in enzymatic activity may allow newly hatched N. norvegicus larvae to metabolize protein reserves to overcome short-term starvation. Vertical migration behavior and the influence of oceanographic properties were studied next. All zoeal stages of M. couchi displayed reverse diel vertical migration. Abundance of early stages was correlated with chlorophyll a levels. An ontogenic shift in vertical distribution explained the results; earlier zoeal stages remain in the food-rich upper water column while later stages migrate to the bottom for settlement. This vertical migration behavior is likely to affect horizontal distribution of larvae. Indeed, global current patterns will result in low inter-annual variations in decapod larvae recruitment, but short term variations such as upwelling events will cause deviation from the expected dispersal pattern. Throughout development, from the embryo to metamorphosis into benthic juvenile, offshore decapods face many challenges. For the developing individual survivorship will depend heavily on food availability but also on the reserves passed on by the mother. Even though vertical migration behavior can allow the larvae to take advantage of depth varying currents for transport, the effect of general circulation pattern will superimpose local current and influence feeding conditions and affect dispersal and recruitment.

Exposições museológicas: a moda por narrativas, experiências e conexões

Este estudo apresenta o universo patrimonial pela perspetiva da acessibilidade pública conferida por instituições museológicas. Consiste em exploração e análise das informações e experiências proporcionadas por museus no âmbito da cultura material indumentária e de moda. O foco desta abordagem são as exposições presenciais e os websites institucionais, com ênfase à acessibilidade aos catálogos de coleções. Pela perspectiva do designer como antropólogo neste estudo – com base em estudos de caso e outros dados coletados – são apresentadas ferramentas comparativas da realidade atual e propostas para a disseminação mais alargada, diversificada e especializada das informações cultura material e imaterial de moda. Duas hipóteses orientaram esta tese: - A noção de que as exposições de artefatos de traje podem ser inovadoras em relação às exposições de outros objetos, já que a roupa vincula-se a movimento, toque, corpo e usabilidade que induz experiências e conexões, sentimentos e identidades em uma relação de metamorfose. - A noção de que o potencial de ensino e difusão de uma cultura de design, com destaque aos contextos de Portugal e Brasil, é um campo relevante à visibilidade pública da indústria da moda nestes países e alavanca para um melhor posicionamento na competitividade global. Pelas propostas específicas e pelo contributo de fornecer informações inéditas a respeito do universo investigado, este estudo abre novas perspectivas para futuras investigações, principalmente nas áreas de museologia, museografia, história e teoria da moda e do design, design de exposição, design de produto, estudos da cultura material, comunicação e antropologia do design.

Validação de uma escala de atitudes de alunos relativamente ao uso de uma plataflrma de ensino ao longo da vida

Dissertação de Mestrado, Ciências da Educação, Área de Especialização de Educação e Formação de Adultos, Faculdade de Ciências Humanas e Sociais, Universidade do Algarve, 2007

Joaquim Rodrigo:a contínua reinvenção da pintura

Tese de doutoramento, História (História da Arte), Universidade de Lisboa, Faculdade de Letras, 2014

Engaged Disengagement: Reframing as Feminist Critique in Vanessa Place’s Tragodía

This essay positions Vanessa Place’s Tragodía (2011) as an instance of reframing as contemporary feminist cultural critique. An enquiry into allegory, hermeneutics, and the performative use of indifference in Place’s conceptual writing generates insights into new narrative conditions produced by Place’s work. Tragodía does not represent trauma but rather generates trauma through a poetic practice that has a bipartite structure: conceptual writing (allegory) and Place’s performances of the narratives. Place’s performance is read in this analysis as an ancillary act of reframing that raises the question of what might be at stake in the performative use of indifference. Understood as a strategy of failure, Place’s performance parallels the lack of mediation in the conceptual act of reframing. Positioned counter to the linguistic deformation of the subjects' speech acts and the erasure of affect that occurs in the legal narratives through the act of interpretation, the refusal to interpret implicit in the act of reframing in Tragodía is an ethical gesture, a paratextual pathway to metamorphosis. In its refusal to interpret, Tragodía creates a site of contextual resistance to the oppression of the subjects’ organic narratives by the institutional language of the law, and offers a new textual field of meaning-making.

Translation to success of surgical innovation.

Contemporary thoracic and cardiovascular surgery uses extensive equipment and devices to enable its performance. As the specialties develop and new frontiers are crossed, the technology needs to advance in a parallel fashion. Strokes of genius or problem-solving brain-storming may generate great ideas, but the metamorphosis of an idea into a physical functioning tool requires a lot more than just a thinking process. A modern surgical device is the end-point of a sophisticated, complicated and potentially treacherous route, which incorporates new skills and knowledge acquisition. Processes including technology transfer, commercialisation, corporate and product development, intellectual property and regulatory routes all play pivotal roles in this voyage. Many good ideas may fall by the wayside for a multitude of reasons as they may not be marketable or may be badly marketed. In this article, we attempt to illuminate the components required in the process of surgical innovation, which we believe must remain in the remit of the modern-day thoracic and cardiovascular surgeon.