Thesis (Ph.D.)--University of Adelaide, Dept. of Environmental Biology, 2000. / Bibliography: leaves 126-144.

Bibliography: leaves 126-144. / 144 leaves : ill., maps ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / Thesis (Ph.D.)--University of Adelaide, Dept. of Environmental Biology, 2000

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Since neonates are often the age-class most susceptible to predation, there should be strong selective pressure on prey for the early development of successful antipredator behaviour. The ability to assess predation risk as early as the embryonic stages may increase an individual’s survival, as it would allow young individuals to be better adapted to current predation risk, since present conditions are often a good short-term indicator of future conditions. I exposed embryonic cuttlefish (Sepia officinalis) to the odour of a predator and tested both the responses of the embryos to this stimulus, and the latent effects of both long (approximately 3 weeks)- and short (a few days)- exposure on the behaviour of newly-hatched juveniles, in particular the efficiency of cryptic behaviour on uniform and sandy substrates. Exposure to novel odours, whether they were predators or non-predators, increased the ventilation rate of embryos. This may be adaptive, because it helps an individual survive first encounters with unknown potential dangers before they have opportunity to collect information about a novel stimulus. Long-term exposure to predator odour increased the camouflage efficiencies of juveniles on uniform substrates. On sandy substrate, the exposure did not affect camouflage, but increased the extent of sand digging behaviour. Juveniles were also larger in size at hatching when exposed to predators compared to those that were not. These results were not seen in individuals with only short-term exposure to predator. Short-term exposure also had no effect on camouflage efficiencies on uniform or sandy substrates, or on sand digging behaviour. The results of my thesis indicate that high predation risk during embryonic development induces behavioural and morphological changes in camouflage expression and body size in cuttlefish hatchlings. The behavioural plasticity may provide survival benefits for newly hatched individuals, but may come at a cost in terms of body size. Such behavioural and morphological plasticity may have an impact on predator-prey dynamics and organization of communities.

La seiche commune Sepia officinalis est un Mollusque Céphalopode présent sur les côtes Normandes. En Baie de Seine, elle représente la troisième espèce visée par les flottilles hauturière et côtière, ce qui en fait une ressource économique importante pour la région. Dans un contexte de protection de la ressource, l’étude et la compréhension des mécanismes liés à la reproduction représentent un objectif majeur. Cette étude est donc focalisée sur les mécanismes régulateurs de la ponte, et en particulier sur les facteurs impliqués dans l’émission des ovocytes. Des recherches antérieures effectuées au laboratoire ont mis en évidence un contrôle multifactoriel du processus de ponte, avec trois niveaux de régulation. (i) Les neuropeptides sont impliqués dans la perception des paramètres environnementaux, (ii) les facteurs ovariens assurent la régulation paracrine du tractus génital, et (iii) les phéromones sexuelles, tout en interférant avec la ponte, sont suspectées de jouer un rôle important dans le comportement des géniteurs associé à la reproduction. Cette thèse met en lumière le rôle de 2 familles de neuropeptides identifiées récemment : les CCAPs et les FLGamides (ou So-orcokinines B). Ces deux familles participent au transport de l’ovocyte et à la sécrétion capsulaire en agissant sur l’activité contractile du complexe oviducte/glande de l’oviducte et des glandes nidamentaires principales. Ces neuropeptides sont par ailleurs suspectés de jouer un rôle dans la biosynthèse des protéines vitellines et des protéines capsulaires. Parallèlement, des phéromones sexuelles sont exprimées par la glande de l’oviducte et sécrétées avec les protéines capsulaires. Des travaux antérieurs ont permis de caractériser des produits d’expression issus de clivages de type prohormone convertase. Dans cette nouvelle étude, un second mode de clivage a été mis en évidence avec l’identification de produits de clivage de masse moléculaire supérieure à 20 kDa. L’un de ces produits, la phéromone beta, a été produit en système recombinant mais son activité biologique sur l’appareil génital mâle et sur l’oviducte n’a pas été démontrée. Quant aux tests comportementaux, ils n’ont pu être exploités du fait d’un nombre d’animaux testés trop restreint. Enfin, une approche transcriptomique comparative et différentielle réalisée à partir de l’organe olfactif mâle et du pavillon de l’oviducte a permis d’identifier un récepteur candidat à la liaison avec les phéromones sexuelles / The common cuttlefish (Sepia officinalis) is a Cephalopod mollusk found on the Normandy coasts. In the Bay of Seine, it is the third species targeted by offshore and coastal fleets, so it is an important economic resource for the whole region. In a context of resource protection, the study and understanding of its reproductive mechanisms is a major objective. This study is therefore focused on the regulatory mechanisms of egg-laying, and in particular on the factors involved in the release of oocytes. Previous research in the laboratory demonstrated multifactorial control of the egg-laying process, with three levels of regulation: (i) neuropeptides involved in the perception of environmental cues, (ii) ovarian factors providing paracrine regulation of the genital tract, and (iii) sexual pheromones, which are implied in egg-laying and are suspected to play a determining role in the reproductive behavior. This thesis highlights the role of two families of recently identified neuropeptides called CCAPs and FLGamides (or So-orcokinins B). These two families participate in oocyte transport and in egg capsule secretion by acting on the contractile activity of the oviduct/oviduct gland complex and of the main nidamental glands. These neuropeptides are also suspected to play a role in the biosynthesis of yolk and capsular proteins. At the same time, sex pheromones are expressed by the oviduct gland and secreted along with capsular proteins. Previous work made it possible to characterize expression products resulting from cleavages of the prohormone convertase type. In this new study, a second mode of cleavage is highlighted, evidenced by the identification of cleavage products with MWs greater than 20 kDa. One of these products, beta pheromone, was produced in a recombinant system but its biological activity on the male reproductive system and on the oviduct was not demonstrated. As for behavioral tests, they were not exploited because the number of animals tested was too small. Finally, a comparative and differential transcriptomic approach of the male olfactory organ and the oviduct pavilion evidenced a candidate receptor expected to bind to sex pheromones

Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Mechanical Engineering; and the Woods Hole Oceanographic Institution), June 2014. / Cataloged from PDF version of thesis. "June 2014." / Includes bibliographical references (pages 103-112). / Evolutionary pressures have led to some astonishing camouflage strategies in the animal kingdom. Cephalopods like cuttlefish and octopus mastered a rather unique skill: they can rapidly adapt the way their skin looks in color, texture and pattern, blending in with their backgrounds. Showing a general resemblance to a visual background is one of the many camouflage strategies used in nature. For animals like cuttlefish that can dynamically change the way they look, we would like to be able to determine which camouflage strategy a given pattern serves. For example, does an inexact match to a particular background mean the animal has physiological limitations to the patterns it can show, or is it employing a different camouflage strategy (e.g., disrupting its outline)? This thesis uses a computational and data-driven approach to quantify camouflage patterns of cuttlefish in terms of color and pattern. First, we assess the color match of cuttlefish to the features in its natural background in the eyes of its predators. Then, we study overall body patterns to discover relationships and limitations between chromatic components. To facilitate repeatability of our work by others, we also explore ways for unbiased data acquisition using consumer cameras and conventional spectrometers, which are optical imaging instruments most commonly used in studies of animal coloration and camouflage. This thesis makes the following contributions: (1) Proposes a methodology for scene-specific color calibration for the use of RGB cameras for accurate and consistent data acquisition. (2) Introduces an equation relating the numerical aperture and diameter of the optical fiber of a spectrometer to measurement distance and angle, quantifying the degree of spectral contamination. (3) Presents the first study assessing the color match of cuttlefish (S. officinalis) to its background using in situ spectrometry. (4) Develops a computational approach to pattern quantification using techniques from computer vision, image processing, statistics and pattern recognition; and introduces Cuttlefish 72x5, the first database of calibrated raw (linear) images of cuttlefish. / by Derya Akkaynak. / Ph. D.

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第19262号 / 理博第4117号 / 新制||理||1592(附属図書館) / 32264 / 京都大学大学院理学研究科生物科学専攻 / (主査)准教授 森 哲, 教授 沼田 英治, 教授 曽田 貞滋 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

This doctoral work was developed in the frame of bone tissue engineering, dealing with the fabrication of scaffolds for the regeneration of bones. At this purpose, calcium phosphates derived from natural sources are very interesting because they are more similar to the bone mineral and possess better bioactivity. Indeed, the bone mineral is different from synthetic hydroxyapatite as it is non-stoichiometric, nanosized, it presents a high degree of disorder and contains many additional ions and impurities such as CO32-, Mg2+, Sr2+, Na+, etc. These characteristics can be easily obtained by synthesizing hydroxyapatite from natural sources, such as corals, starfishes, seashells, animal bones, bird eggshells etc. The natural sources used in the present work are three types of biogenic calcium carbonate, i.e. calcium carbonate that is produced by living organisms in the form of aragonite or calcite. Among the different sources, three biogenic calcium carbonates were chosen: cuttlefish (Sepia Officinalis) bones, mussel (Mytilus Galloprovincialis) shells and chicken eggshells. Besides their abundance and availability, they were selected because of their different composition: aragonite in cuttlebones, calcite in eggshells and a mixture of aragonite and calcite in mussel shells. After the first chapter, which is a theoretical introduction, this thesis is divided into other five chapters. Chapter 2 contains a careful characterization of the three biogenic raw materials while Chapter 3 deals with the synthesis of hydroxyapatite starting from these natural sources. The process developed here takes place entirely at nearly room temperature, which allows the organic part of the biological materials to be preserved. This synthesis process is basically a wet mechanosynthesis followed by a mild heat treatment (up to 150°C). The study focuses on the influence of several process parameters on the synthesis efficiency: temperature, milling time, pH and raw material. The temperature used to dry the slurry after the wet ball-milling was found to be the most important parameter, the higher the temperature the faster the conversion of CaCO3 into hydroxyapatite. Moreover, aragonite was found to transform more easily into hydroxyapatite with respect to calcite, and also to follow a different reaction path. The synthesis process described in Chapter 3 allowed to produce different bio-derived powders that were found to be non-stoichiometric, nanosized, carbonated hydroxyapatites, containing also additional ions, especially Mg2+ in the eggshell-derived material and Sr2+ in the cuttlebone-derived one. These powders were then used as a starting point for the studies presented in the next three chapters. Chapter 4 shows a very preliminary evaluation of the interaction with human cells in vitro. First, the as-synthesized powders were consolidated by uniaxial pressing and sintering at temperatures between 900°C and 1100°C and their crystallographic composition was analyzed. Then, after having established the non-cytotoxicity of the sintered pellets, osteoblasts from human osteosarcoma cell line were seeded on the pellets and their behavior after 1, 3 and 5 days of culture was observed by confocal microscopy. In general, all materials promoted good cell adhesion and proliferation, especially the eggshell-derived one. At this point, the bio-derived materials were found to induce a good cellular response but, in order to foster the regeneration of bones, a scaffold must also contain a large amount of interconnected porosity. Among the numerous methods to fabricate porous structures, additive manufacturing is surely very attractive due many advantages, such as the possibility of customizing the shape based on tomography images from the patients, the fact that no mold is needed and the freedom of fully designing the porosity. Indeed, not only the size and the amount of porosity are important, but also the shape of the pores and their position and orientation have a deep effect on the interaction with the cells. Therefore, Chapter 5 and Chapter 6 deal with the fabrication of scaffolds by 3D printing, following two different approaches. In the study presented in Chapter 5, the powders synthesized from cuttlebones, mussel shells and eggshells were used in combination with a thermoplastic polymer (PCL, polycaprolactone) to obtain bioactive composites. Composite materials made of 85 wt% PCL and 15 wt% bio-derived hydroxyapatite were used to fabricate porous scaffolds by extrusion 3D printing. The biological in vitro tests showed that the composite scaffolds possess better bioactivity than the pure PCL ones, especially those containing mussel shell- and cuttlebone-derived powders, which promoted the best cell adhesion, proliferation and metabolic activity of human osteosarcoma cells after 7 days of culture. In addition, the elastic compressive modulus, which was found to be between 177-316 MPa, thus in the range of that of trabecular bone, was found to increase of about ∼50% with the addition of the bio-derived nanopowders. Finally, in Chapter 6, the cuttlebone-derived powder was used to fabricate porous bioceramic scaffolds by binder jetting 3D printing. Due to serious technical issues related to the printing of a nanosized powder, 10 wt% of bio-derived powder was mixed with a glass-ceramic powder with bigger particle size. Moreover, the organic part of the cuttlebone had to be previously eliminated by a heat treatment at 800°C. Thanks to the great freedom of design that is allowed by the binder jetting process, scaffolds with two different pore geometries were fabricated: with pores of uniform size and with a size-gradient. Indeed, natural bone possesses a gradient in porosity from the core to the surface, from porous trabecular bone to dense cortical bone. The sintered scaffolds showed a total porosity of ∼60% for the pure glass-ceramic and ∼70% for the glass-ceramic with 10 wt% of cuttlebone-derived nanoparticles, which most probably slowed down the densification by limiting the contact between the glassy particles. All the bioceramic scaffolds promoted good adhesion and proliferation of human bone marrow-derived mesenchymal stem cells in vitro, without any significant difference between the different samples. However, the scaffolds with the cuttlebone-derived powder and with gradient porosity showed the greatest decrease of metabolic activity after 10 days of culture, which could be accounted as a sign of differentiation of stem cells.

L’évaluation et la gestion des stocks de poissons ont pour objectif d’atteindre une exploitation durable des ressources fournies par les océans. Si les progrès dans ce domaine sont bien réels pour certains stocks de grande importance commerciale, la situation est différente pour les stocks dits à données limitées. Souvent historiquement moins exploités, ces stocks ne bénéficient pas des mêmes ressources, tant économiques qu’humaines, pour réaliser une évaluation de stock permettant par la suite la mise en place de mesures de gestion. Ce travail s’appuie sur deux cas d’étude, le lieu jaune (Pollachius pollachius) et la seiche (Sepia officinalis), afin d’explorer des méthodologies d’évaluation de stocks adaptées aux situations de données limitées. Après une première partie introductive reprenant le contexte de l’évaluation des stocks et présentant les deux cas d’étude, une revue des méthodes d’évaluation de stocks à données limitées est proposée. Une troisième partie compare les résultats d’un modèle de biomasse à deux stades et d’un modèle multi-annuel de déplétion généralisé appliqués au stock de seiche de Manche. Une version améliorée du modèle de biomasse à deux stades codé en Bayésien est également présentée. Le travail se poursuit avec l’application d’un modèle d’analyse intégrée Stock Synthesis au stock de lieu jaune de mer Celtique. Les résultats sont comparés aux résultats de modèles plus simples nécessitant moins de données. Les résultats du modèle Stock Synthesis s’avèrent sensibles aux hypothèses sur la valeur de mortalité naturelle, dont le calcul dépend des paramètres de croissance du stock. La cinquième partie présente l’acquisition et le traitement de nouvelles données qui pourront permettre une meilleure estimation de l’état du stock de lieu jaune. Un modèle hiérarchique Bayésien est construit, permettant un transfert d’information entre trois stocks et la mise à jour des paramètres biologiques du lieu jaune. Le dernier chapitre conclut ce travail en reprenant les principaux résultats obtenus et en élargissant la discussion sur des perspectives de recherche. / The assessment and the management of fish stocks aim at achieving a sustainable exploitation of the resources provided by the oceans. While progress have been made in this field for some stocks of great commercial importance, the situation is different for the so-called “data limited” stocks. Often historically less exploited, these stocks do not benefit from the same economical resources nor workforce to conduct the stock assessments required to set management measures. This work is based on two case studies, pollack (Pollachius pollachius) and cuttlefish (Sepia officinalis). The aim is to investigate the stock assessment methods adapted to data-limited situations. A first introductive part presents the background of fish stock assessment as well as the two case studies. This first chapter is followed by a review of data-limited stock assessment methods. The third part compare the results of a two-stage biomass model with the results of a multi-annual generalized depletion model applied to the English Channel stock of cuttlefish. An improved version of the Bayesian two-stage biomass model is also presented. In the fourth part, a Stock Synthesis model based on integrated analysis methods is applied to the stock of pollack in the Celtic Seas Ecoregion. The results are compared to the results of simpler models which require less data. The Stock Synthesis model results are sensitive to the assumptions on the natural mortality value, which relies on the growth parameters of the stock. The fifth part presents the collection and analysis of new data which will allow a better estimate of pollack stock status. A Bayesian hierarchical model is constructed, allowing information transfer between three stocks and the update of pollack biological parameters. The last chapter concludes this work by summarizing the main results. The discussion is extended to the research perspectives.