This study focused on the management of the red sea urchin Loxechinus albus fishery in Chile. The main objective was to design, construct, implement and assess a computer-based simulation model to analyse the biological effects, socio-economic consequences and spatial dynamics resulting from coastal management plans applied to this resource under the system of AMEBR. This was accomplished by using systems dynamics (SD) and geographical information systems (GIS) modelling, in a process of model development, run, optimisation, sensitivity analysis and risk management, and a series of field-based activities carried out at the cove of Quintay. The GIS model developed for allocating sea urchins restocking sites offered a flexible, cost-effective, user-friendly and descriptive technique for support decision-making on management of this species and other benthic resources. Final site selection for restocking was based on the identification, quantification and selection of higher suitability¦availability combinations (site categories). This map showed 16 different suitability¦availability combinations or site categories, ranging from 4¦100 to 8¦100 (suitability points¦availability %). These had an average of 6.44¦69.37 (covering an area of 82.5 Ha overall equivalent to 81.21% of the study area. This site classification demonstrated high heterogeneity between options, and revealed the full variety of alternatives for decision-making. More importantly, the generally high suitability indexes as well as available area emphasised the prospects for restocking sea urchins in this study area. Over and above of the quantitative outcomes obtained from running the GISRM (suitable and available restocking sites) and the BSESM (alternative strategic management plans), the case study-based analysis made it possible to disclose the wider issues related to the red sea urchin coastal management. These results demonstrated the biological inefficiency of traditional size/seasonal restriction-based approach (macro-scenario 1) for sustainable management of the target species. More importantly, final outcomes strongly suggested that a combination of adaptive restocking-based enhancement activities and flexible exploitation constituted a highly attractive approach (macro-scenario 3) for stock management of this fishery in terms of harvestable stock and related incomes. However from the economic analysis, stocking was also found to be economically unfeasible, being a rather cost intensive exercise negatively affected by high natural mortality rates. A single-variable optimisation analysis demonstrated that a higher survival rate is needed to generate sufficient profits to cover major restocking costs and a positive payment, or a cost reduction is essential to make up for the loss. On top to these practical constraints, based on the distinctive modest economic situation prevailing for most Chilean coves and hence their limited capacity to pay for stocking material, unless adequate and constant funding is available to support artisanal associations, they are very unlikely to develop mass release programmes. Given the economic (i.e.: high operating costs) and technical (i.e.: low survival rates) limitations conditioning stocking-based management cost-effectiveness and applicability, wide implementation of mass releases as a major approach for management of the red sea urchin fishery is very unlikely to take place in Chile. This study presents a methodology and offers a tool to design, evaluate and optimise coastal management plans for the red sea urchin in a dynamic, interactive, systematic, integrated and flexible way. The optional strategic management plans proposed on this study may not be applied equally to any AMEBR, as they are the outputs arising from a single cove-specific analysis. Still, the complete methodological framework and analysis procedures developed may be applied to run the BSESM and optimise management of a red sea urchin fishery at any other AMEBR case of study.

The thesis is focused on anatomy and implementation of dissections of 4 selected model invertebrates in school practice. The selected model species include swan mussel (Anodonta cygnea), stick insect (Medauroidea extradentata), cockchafer (Melolontha melolontha) and sea urchin (Echinus esculentus). In case of the cockchafer, the text is based on this model species, but the supporting photographs of dissection are taken from the tropical cetoniid beetle Pachnoda, which has very similar internal anatomy with the cockchafer. For all selected animals, I describe external and internal morphology as well as recommended methods of obtaining the material, proper killing of specimens, and dissection techniques. The text is supplemented with original digital macrophotographs. The thesis includes also an overview of primary and secondary school textbooks with focus on anatomy of the selected animals. The text is supplemented by a glossary of morphological terminology used in this thesis. Attached is a photographic atlas of dissections, which is a combination of this master thesis and my bachelor thesis (defended in 2010), in which I dealt with five model invertebrates in the same way. This is Ascaris suum, Lumbricus terrestris, Helix pomatia, Procambarus aff. fallax and Archimandrita tesselata. The complete...

Field and laboratory studies were used to elucidate the factors affecting temporal and spatial variations of species abundance and structure of macroalgal assemblage and environmental variables between fish farming (FFA) and non-fish farming (NFFA) areas in Hsiao-Lu-Chiao island, a coral island in southwestern Taiwan. Four experiments have been approached: 1. field surveys of macroalgal assemblage structure on 5-m and 10-m depth at 3 sampling sites at FFA (FFA1, FFA2 and FFA3) and 1 sampling site at NFFA from September 2004, January 2005 and April 2005; 2.the relationship between abiotic (monthly maximum air temperature, monthly minimum air temperature, monthly mean air temperature, monthly cumulative precipitation, monthly cumulative irradiance, seawater temperature, light extinction coefficient, water motion, and nutrient (NO3-, NO2-, NH4+, SRP, DON, and DOP) and biotic (seaurchin density) factors and spatio-temporal variations in macroalgal structures analyzed by non-parametric multivariate model; 3. Factors affecting macroalgal abundance and structure: (1). Comparison of growth temperature ranges in different species to field temperature fluctuation; (2).Comparison of growth irradiance ranges in different species to field irradiance fluctuation; 4.Herbivore pressure: (1). Spatio-temporal variations of sea urchin abundance and structure of assemblage; (2). Gut contents and food preference of sea urchin experiment; (3). Herbivore exclusion experiment. Macroalgal %cover, biomass, species richness, diversity (H¡¦) and evenness (J¡¦) showed temporal and spatial variations, low values in January 2005 and also low values in the 5 m- and 10 m-depth areas of FFA1 and the 10 m-depth areas of FFA2. The data of k-dominance curve, hierarchical cluster and ANOSIM tests indicate that macroalgal assemblage is different between 4 sampling sites, between 2 depths and between 3 seasons. Ceratodictyon spongiosum is the most important species that separates September and January assemblages from April assemblage and separates the FFA1 and FFA2 assemblages from the FFA3 and NFFA assemblages. BVSTEP analysis shows that nutrients (NO3-, DON, DOP), temperature, monthly cumulative precipitation, and sea urchin density are the factors corresponding to variations of macroalgal assemblages, this correlation is more significant for 5 m-depth assemblage. Fish farming area FFA1and FFA2 assemblage are affect by sea urchin density, temperature and DON. Sea urchin influnces macroalgal abundance and assemblage structure in FFA1 and FFA2. Macroalgal %cover in 5 m-depth area shows a reversal relationship with sea urchin density; however, this relationship is not observed for 10 m-depth area. FFA1 and FFA2 are belong to high grazing pressure sites as indicated by high sea urchin density and exclusion experiment. Sea urchin gut contents and feeding preference test show that sea urchin has strong food selectivity with Hypnea charoides and Gracilaria coronopifolia as the most preferred species. Herbivore exclusion experiment shows that Hypnea charoides and Gracilaria coronopifolia are the species recruited in the cages. Ceratodictyon spongiosum had high biomass in FFA1 and FFA2 in January, which was ¡¥low DOP/high DON¡¦. The coindicence of temporal variations in FFA3 assemblage structure with a change from ¡¦Halimeda opuntia and Boodlea compostia¡¦ ¡÷ ¡¦Amphiroa fragilissima, Corallina phhulifera and Galaxaura oblongata¡¦ ¡÷¡¦Halimeda opuntia and Boodlea compostia¡¦ with low nitrogen/ high phosphorous¡¦ ¡÷¡¦ high nitrogen/ low phosphorous¡¦ ¡÷ ¡¦low nitrogen/ high phosphorous¡¦ suggest a role of ¡¦low nitrogen (NO3-)/high phosphorous (DOP)¡¦ for FFA3 structure modification. NFFA assemblage is controlled by temperature and monthly cumulative precipitation. Monthly cumulative precipitation in September was higher than January and April, in which Boodlea compostia and Gracilaria coronopifolia were dominant algae in September. The temperature growth responses of algae using the continuous-flow outdoor laboratory tank culture system fit their seasonal growth, reflecting the temperature-dependent manner of seasonal variations in abundance. It could be concluded from the present investigation that the structure of benthic macroalgal assemblage in Hsiao-Lu-Chiao island in southwestern Taiwan is affected by predicted natural and pulse disturbances. Temperature fluctuations involve in overall temporal variations in structure. Sea urchin herbivory and nutrient as pulse nutrient modulate the structure in fish farming area while monthly cumulative precipitation is associated with algal structure in non-fish farming area.

During the Late Pliocene and early Pleistocene, when the paleo-Orinoco delta system transited over the Amacuro Shelf and reached the paleo-shelf-break along the southeastern shoreline of Trinidad. At this time onwards, the shelf-edge delta clinoforms developed further eastward. These deltaic clastic wedges serve as the unique analog in the geological record for an accommodation-driven inner-shelf and shelf-edge delta, developed at an oblique foreland tectonic setting situated at a tropical-equatorial paleogeographic setting. These deposits were influenced by strong Atlantic longshore current, tropical storms, and phytodetrital pulses, and with an exceptionally high sediment accumulation rates. These four aspects make the clastic wedges unique candidates for sedimentological, ichnological, and stratigraphic investigation. The primary objectives of this thesis are to: (a) collect, analyze, and integrate outcrop data on lithofacies, trace fossils, and discontinuity surfaces into a comprehensive depositional and ichnological model for the first growth-fault-guided shelf-marginal pulse of the paleo-Orinoco delta, as recorded in the Mayaro Formation outcrops in southeast Trinidad; and (b) deduce the dominant sedimentary processes during the across shelf transit and their impacts on the benthic infauna as preserved in the Morne L’Enfer Formation outcrops of southwest Trinidad, which are possibly slightly older than the Mayaro Formation. The basal interval of the Morne L’Enfer Formation has specifically been investigated for this purpose, where the deltaic clastic wedges are preserved directly above shelf deposits. The entire Mayaro Formation megasequence is categorized into deposits belonging to twelve different subenvironments based on lithofacies associations and ichnological characteristics. Ichnological evidence indicates that the shelf-edge deltas are one of the most extreme marine environments for benthic metazoans to colonize. However, the combinations and ranking of stress factors affecting the colonizing fauna are diverse and distinct in every individual subenvironment indicating the relative dominances of river-influence, waves, and/or sediment-gravity-flows vis-à-vis slope instability. Due to variations in stress factors, the megasequence also displays dual ichnologic and sedimentologic properties of both the shelf-edge delta lobe(s) and the outer shelf delta lobe(s). A minor transient tidal influence can only be observed in the architectural elements, e.g. elongated interbar embayment and interlobe prodeltaic depocentres, which control topography and enhance tidal effect. Discovery of an unusual monospecific Glossifungites Ichnofacies along an incision surface in the midst of the Mayaro Formation succession enabled a substantial overhaul of the earlier understanding of the formation in terms of its depositional model and stacking pattern. The surface has been re-identified as a canyon/gully cut at the shelf-edge, which possibly acted as a conduit for (a) the mass movements and for (b) the coarse clastic (mostly silt to medium-grained sand) sediment transfer to deep marine settings. The monospecific nature of the Glossifungites Ichnofacies suite indicates that the incision surface was under substantial ecological stresses for the colonizing infauna. The stresses might have arisen from slope instability of the steep canyon/gully walls, mass movements above the incision surface, elevated water turbulence, and lowered salinity from river influx. Five different facies tracts have been identified within the canyon/gully-fill, which crosscuts the shelf-edge delta-front. The facies tracts are dominated by different types of sediment-gravity flow deposits, which are systematically stacked and are almost devoid of trace fossils due to rapid sedimentation rates and slope instability. They are also strikingly different from the surrounding deltaic facies. A high-frequency sequence stratigraphic model involving the influence of growth-fault tectonics on the relative sea-level curve has been invoked to explain the incision of the canyon/gully and its sequential filling processes. On the other hand, the transition from the open shelf to inner-shelf deltaic condition as displayed by the basal members of the Morne L’Enfer Formation is strongly dominated by evidences of river influence with the transient background action of fair-weather waves and storm waves. A peculiar pattern of disappearance of trace fossils produced by irregular sea-urchins highlight that the river influence was quite strong not only at the sediment-water interface but also in the water-column, which affected invertebrate larvae. The initial progradation of the clastic wedge on the shelf was dominated by hyperpycnal flows and waves in contrast to tidal domination in the younger members of the formation.

Anthropogenic carbon dioxide (CO2) emissions are increasing the atmospheric CO2 concentration and the oceans are absorbing around 1/3 them. The CO2 hydrolysis increases the H+ concentration, decreasing the pH, while the proportions of the HCO3- and CO32- ions are also affected. This process already led to a decrease of 0.1 pH units in surface seawater. According to "business-as-usual" models, provided by the Intergovernmental Panel on Climate Change (IPCC), the pH is expected to decrease 0.3-0.5 units by 2100 and 0.7-0.8 by 2300. As a result the surface ocean carbonates chemistry will also change: with increasing pCO2, dissolved inorganic carbon will increase and the equilibrium of the carbonate system will shift to higher CO2 and HCO3– levels, while CO32– concentration will decrease. Surface seawaters will progressively become less saturated towards calcite and aragonite saturation state and some particular polar and cold water regions could even become completely undersaturated within the next 50 years. <p>Responses of marine organisms to environmental hypercapnia, i.e. to an excess of CO2 in the aquatic environment, can be extremely variable and the degree of sensitivity varies between species and life stages. Sea urchins are key stone species in many marine ecosystems. They are considered to be particularly vulnerable to ocean acidification effects not only due to the nature of their skeleton (magnesium calcite) whose solubility is similar or higher than that of aragonite, but also because they lack an efficient ion regulatory machinery, being therefore considered poor acid-base regulators. Populations from polar regions are expected to be at an even higher risk since the carbonate chemical changes in surface ocean waters are happening there at a faster rate. <p>The goal of this work was to study the effects of low seawater pH exposure of different life stages of sea urchins, in order to better understand how species from different environments and/or geographic origins would respond and if there would be scope for possible adaptation and/or acclimatization.<p>In a first stage we investigated the effects of ocean acidification on the early stages of an intertidal species from temperate regions, the Atlantic Paracentrotus lividus sea urchin, and of a sub-Antarctic species, Arbacia dufresnei. The fertilization, larval development and larval growth were studied on specimens submitted through different pH experimental treatments. The fertilization rate of P. lividus gametes whose progenitors came from a tide pool with high pH decrease was significantly higher, indicating a possible acclimatization or adaptation of gametes to pH stress. Larval size in both species decreased significantly in low pH treatments. However, smaller A. dufresnei echinoplutei were isometric to those of control treatments, showing that size reduction was most likely due to a slower growth rate. In the pH 7.4 (predicted for 2300) treatment, P. lividus presented significantly more abnormal forms than control ones, but A. dufresnei did not. The latter does not seem to be more vulnerable than temperate species, most likely due to acclimatization/adaptation to lower pH seasonal fluctuations experienced by individuals of this population during spring time.<p>In a second stage, adult physiological responses of P. lividus and A. dufresnei to low pH seawaters were studied. Intertidal field P. lividus specimens can experience pH fluctuations of 0.4 units during low tidal cycles, but their coelomic fluid pH will not change. During experimental exposure to low pH, the coelomic fluid (extracellular) pH of both species decreased after weeks of exposure to low seawater pH. However, it owned a certain buffer capacity (higher than that of seawater) which did not seem to be related to passive skeleton dissolution. In laboratory studies, the feeding rate of P. lividus, the RNA/DNA ratio (proxy for protein synthesis and thus metabolism) of both the gonads and the body wall of the studied species and the carbonic anhydrase activity in the body wall (an enzyme involved in calcification and respiratory processes) of A. dufresnei did not differ according to seawater pH. The same was true for spine regeneration (a proxy for calcification) of both species. This shows that both P. lividus and A. dufresnei are able to cope when exposed to mild hypercapnia (lowest investigated pH 7.4) for a mid-term period of time (weeks). In a different set of experiments, pH effects were tested on P. lividus individuals together with two temperatures (10ºC and 16ºC). The pH decrease of the coelomic fluid did not vary between temperatures, neither did its buffer response. The oxygen uptake rates of P. lividus (as a proxy for global metabolic state of the whole organism) increased in lower pH treatments (7.7 and 7.4) in organisms exposed to lower temperatures (10ºC), showing that this was upregulated and that organisms experienced a higher energetic demand to maintain normal physiological functions. For instance, gonad production (given by the RNA/DNA ratio) was not affected neither by temperature, nor pH.<p>Finally, possible morphological and chemical adaptations of cidaroid (“naked”) spines, which are not covered by epidermis, to low magnesium calcite saturation states were investigated. Deep sea field specimens from the Weddell Sea (Antarctica), Ctenocidaris speciosa were studied. Cidaroid spines have an exterior skeleton layer with a polycrystalline constitution that apparently protects the interior part of the monocrystaline skeleton, the stereom (tridimensional magnesium calcite lattice). The cortex of C. speciosa was by its turn divided into two layers. From these, it presented a thicker inner cortex layer and a lower Mg content in specimens collected below the aragonite saturation horizon. The naked cortex seems able to resist to low calcium carbonate saturation state. We suggest that this could be linked to the important organic matrix that surrounds the crystallites of the cortex.<p>Some echinoid species present adaptive features that enable them to deal with low pH stresses. This seems to be related to the environmental conditions to which populations are submitted to. Therefore, organisms already submitted to pH daily or seasonal fluctuations or living in environments undersaturated in calcium carbonate seem to be able to cope with environmental conditions expected in an acidified ocean. Under the realistic scenario of a decrease of ca. 0.4 units of pH by 2100, sea urchins, and echinoderms in general, appear to be robust for most studied processes. Even thought, this general response can depend on different parameters such as exposure time, pH level tested, the process and the life stage considered, our results show that there is scope for echinoids to cope with ocean acidification.<p> / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

A plethora of naturally-produced steroid hormones, or artificial homologues of them, are being introduced into the aquatic and terrestrial environments each year. Two examples of these are the natural oestrogen 17-oestradiol (E2) and the oestrogen receptor antagonist, Bisphenol A (BPA), both of which target the ribonucleoprotein telomerase through upregulation of its telomerase reverse transcriptase component, TERT. The main objectives of this study were firstly to isolate and characterize the actual mRNA sequence for the telomerase catalytic subuninit, Tert, in rainbow trout (Oncorhynchus mykiss) (Walbaum, 1792) and European purple sea urchin (Paracentrotus lividus) (Lamarck, 1816), with the aim of developing qPCR assays for the amplification and quantification of Tert. Further objectives were to use these assays in controlled exposure studies to establish whether and to what extent the aforementioned chemicals regulate Tert transcription and by doing so further understand the mechanism of Telomerase gene expression and the extent to which environmental oestrogen can interfere. The initial step of sequence characterization and assay devlopment was successful in the case of rainbow trout where two possible splice variants of Tert mRNA are identified, omTertShort and omTertLong. Two qPCR assays were developed for the relative quantification of both of these splice variants in rainbow trout samples, the latter of these successfully amplifying its target in test samples. In order to demonstrate in vitro and in vivo modulation of telomerase activity and mRNA expression, early life-stages of rainbow trout and purple sea urchin, as well as rainbow trout hepatocytes, were exposed to a range of concentrations of E2 and BPA. Purple sea urchin embryos were exposed to 200, 20 and 2 ng E2/ml for 28 hours until they had reached the stage of pluteus larvaes. Rainbow trout embryos were exposed to 500, 20 and 0.1 ng E2/ml and 600 and 150 ng BPA/ml for 167 days from immediately after fertilization. Rainbow trout hepatocytes were exposed to 20 and 2 ng E2/ml for 48 hours. The results from this study show that telomerase activity as well as TERT mRNA expression can be significantly modulated by exposure to oestrogens and other oestrogenic chemicals. E2 concentrations as low as 20 ng/ml lead to an increase in telomerase activity early-life stages of purple sea urchin and upregulation in the transcription of Tert mRNA in unhatched rainbow trout embryos. BPA induced similar response (600 ng/ml) in hatched rainbow trout alevins larvae. Very high exposures to E2 (500 ng/ml) do however lead to downregulation of Tert mRNA in hatched alevins larvae. Differential regulatory response can be observed between different tissue types of 167 day old fry, with an upregulatory response observed at 0.1 ng E2/ml in liver and muscle tissues, but not in brain. Similarly, brain tissues were observed expressing significantly less mRNA than liver and muscle samples when exposed to BPA (150 ng/ml). It is evident that the previously observed link between environmental oestrogens and telomerase is also present in the two test species examined; purple sea urchin and rainbow trout.

Nous proposons dans cette thèse de caractériser quantitativement la variabilité à différentes échelles au cours de l'embryogenèse. Pour ce faire, nous utilisons une combinaison de modèles mathématiques et de résultats expérimentaux. Dans la première partie, nous utilisons une petite cohorte d'oursins digitaux pour construire une représentation prototypique du lignage cellulaire, reliant les caractéristiques des cellules individuelles avec les dynamiques à l'échelle de l'embryon tout entier. Ce modèle probabiliste multi-niveau et empirique repose sur les symétries des embryons et sur les identités cellulaires; cela permet d'identifier un niveau de granularité générique pour observer les distributions de caractéristiques cellulaires individuelles. Le prototype est défini comme le barycentre de la cohorte dans la variété statistique correspondante. Parmi plusieurs résultats, nous montrons que la variabilité intra-individuelle est impliquée dans la reproductibilité du développement embryonnaire. Dans la seconde partie, nous considérons les mécanismes sources de variabilité au cours du développement et leurs relations à l'évolution. En nous appuyant sur des résultats expérimentaux montrant une pénétrance incomplète et une expressivité variable de phénotype dans une lignée mutante du poisson zèbre, nous proposons une clarification des différents niveaux de variabilité biologique reposant sur une analogie formelle avec le cadre mathématique de la mécanique quantique. Nous trouvons notamment une analogie formelle entre l'intrication quantique et le schéma Mendélien de transmission héréditaire. Dans la troisième partie, nous étudions l'organisation biologique et ses relations aux trajectoires développementales. En adaptant les outils de la topologie algébrique, nous caractérisons des invariants du réseaux de contacts cellulaires extrait d'images de microscopie confocale d'épithéliums de différentes espèces et de différents fonds génétiques. En particulier, nous montrons l'influence des histoires individuelles sur la distribution spatiales des cellules dans un tissu épithélial. / We propose in this thesis to characterize variability quantitatively at various scales during embryogenesis. We use a combination of mathematical models and experimental results. In the first part, we use a small cohort of digital sea urchin embryos to construct a prototypical representation of the cell lineage, which relates individual cell features with embryo-level dynamics. This multi-level data-driven probabilistic model relies on symmetries of the embryo and known cell types, which provide a generic coarse-grained level of observation for distributions of individual cell features. The prototype is defined as the centroid of the cohort in the corresponding statistical manifold. Among several results, we show that intra-individual variability is involved in the reproducibility of the developmental process. In the second part, we consider the mechanisms sources of variability during development and their relations to evolution. Building on experimental results showing variable phenotypic expression and incomplete penetrance in a zebrafish mutant line, we propose a clarification of the various levels of biological variability using a formal analogy with quantum mechanics mathematical framework. Surprisingly, we find a formal analogy between quantum entanglement and Mendel’s idealized scheme of inheritance. In the third part, we study biological organization and its relations to developmental paths. By adapting the tools of algebraic topology, we compute invariants of the network of cellular contacts extracted from confocal microscopy images of epithelia from different species and genetic backgrounds. In particular, we show the influence of individual histories on the spatial distribution of cells in epithelial tissues.

Nous proposons dans cette thèse de caractériser quantitativement la variabilité à différentes échelles au cours de l'embryogenèse. Pour ce faire, nous utilisons une combinaison de modèles mathématiques et de résultats expérimentaux. Dans la première partie, nous utilisons une petite cohorte d'oursins digitaux pour construire une représentation prototypique du lignage cellulaire, reliant les caractéristiques des cellules individuelles avec les dynamiques à l'échelle de l'embryon tout entier. Ce modèle probabiliste multi-niveau et empirique repose sur les symétries des embryons et sur les identités cellulaires; cela permet d'identifier un niveau de granularité générique pour observer les distributions de caractéristiques cellulaires individuelles. Le prototype est défini comme le barycentre de la cohorte dans la variété statistique correspondante. Parmi plusieurs résultats, nous montrons que la variabilité intra-individuelle est impliquée dans la reproductibilité du développement embryonnaire. Dans la seconde partie, nous considérons les mécanismes sources de variabilité au cours du développement et leurs relations à l'évolution. En nous appuyant sur des résultats expérimentaux montrant une pénétrance incomplète et une expressivité variable de phénotype dans une lignée mutante du poisson zèbre, nous proposons une clarification des différents niveaux de variabilité biologique reposant sur une analogie formelle avec le cadre mathématique de la mécanique quantique. Nous trouvons notamment une analogie formelle entre l'intrication quantique et le schéma Mendélien de transmission héréditaire. Dans la troisième partie, nous étudions l'organisation biologique et ses relations aux trajectoires développementales. En adaptant les outils de la topologie algébrique, nous caractérisons des invariants du réseaux de contacts cellulaires extrait d'images de microscopie confocale d'épithéliums de différentes espèces et de différents fonds génétiques. En particulier, nous montrons l'influence des histoires individuelles sur la distribution spatiales des cellules dans un tissu épithélial. / We propose in this thesis to characterize variability quantitatively at various scales during embryogenesis. We use a combination of mathematical models and experimental results. In the first part, we use a small cohort of digital sea urchin embryos to construct a prototypical representation of the cell lineage, which relates individual cell features with embryo-level dynamics. This multi-level data-driven probabilistic model relies on symmetries of the embryo and known cell types, which provide a generic coarse-grained level of observation for distributions of individual cell features. The prototype is defined as the centroid of the cohort in the corresponding statistical manifold. Among several results, we show that intra-individual variability is involved in the reproducibility of the developmental process. In the second part, we consider the mechanisms sources of variability during development and their relations to evolution. Building on experimental results showing variable phenotypic expression and incomplete penetrance in a zebrafish mutant line, we propose a clarification of the various levels of biological variability using a formal analogy with quantum mechanics mathematical framework. Surprisingly, we find a formal analogy between quantum entanglement and Mendel’s idealized scheme of inheritance. In the third part, we study biological organization and its relations to developmental paths. By adapting the tools of algebraic topology, we compute invariants of the network of cellular contacts extracted from confocal microscopy images of epithelia from different species and genetic backgrounds. In particular, we show the influence of individual histories on the spatial distribution of cells in epithelial tissues.

Depuis le début de la période industrielle, les activités humaines ont généré une augmentation importante de la concentration atmosphérique en CO2. Une partie de ce CO2 s’accumule dans l’atmosphère, entraînant une augmentation de l’effet de serre naturel et de la température à la surface du globe. Ce processus est plus connu sous le terme réchauffement climatique ou global. De plus, environ 25 % du CO2 produit sont absorbés par les océans. La dissolution du CO2 dans l’eau de mer, entraîne une augmentation de la concentration en protons et en ions bicarbonates (HCO3-) et une diminution de la concentration en ions carbonates (CO32-). Il en résulte une diminution du pH et du taux de saturation de l’eau de mer vis-à-vis du carbonate de calcium. L’ensemble de ces processus est appelé acidification des océans (AO). Le pH des eaux de surface océaniques a déjà diminué de 0,1 unité depuis le début de l’ère industrielle. Ce phénomène devrait s’intensifier au cours du siècle. Selon les prévisions moyennes d’émissions futures de gaz à effet de serre de l’IPCC, la température moyenne des eaux de surface devrait augmenter de 2 à 4 °C et son pH devrait diminuer de 0,3 à 0,4 unité d’ici 2100.<p>Au cours des deux dernières décennies, de nombreuses études ont mis en évidence l’impact négatif de l’AO sur les organismes marins. Les premières études ont été menées principalement en milieu artificiel et ont mis en évidence des conséquences majeures sur la physiologie des organismes, principalement au niveau individuel. Cependant, les dernières études menées dans le domaine ont souligné l'importance de mettre en place des expériences à long terme, à l'échelle de l'écosystème, et dans des conditions plus proches du milieu naturel. Ce type d’étude permet de prendre en compte les interactions écosystémiques et les processus d’acclimatation afin de mieux prévoir les effets directs mais aussi indirects de la diminution du pH dans les océans. <p>L’existence des récifs coralliens tropicaux dépend de la vitesse de formation du socle récifal qui les façonnent (principalement via la calcification des coraux hermatypiques) qui doit rester supérieure à sa (bio)érosion. D’une part, plusieurs études ont montré que le taux de calcification des coraux hermatypiques diminue lorsque la pCO2 augmente. D’autre part, les oursins sont d’importants bioérodeurs des récifs et contribuent donc à la perte de masse calcaire récifale. Cependant, les oursins empêchent également, par leur broutage, le recouvrement des coraux par les algues favorisées par l’AO. Dès lors l’effet de l’élévation de la pCO2 sur les oursins et leur capacité bioérosive peut être déterminant pour l'avenir des récifs coralliens tropicaux au cours du siècle, particulièrement ceux où la densité de ces bioérodeurs est importante. Une telle prédiction est d’autant plus complexe si l’on prend en compte la possible acclimatation des différents acteurs à long terme.<p>Dès lors, le but du présent travail fut d'évaluer l'effet à long terme de l’élévation de la pCO2 prévue en 2100 sur la physiologie et l’activité érosive d’un oursin clé de certains récifs coralliens, Echinometra mathaei, dans un dispositif artificiel reproduisant l’écosystème corallien.<p>La première étape a été la mise en place un outil expérimental permettant de maintenir à long terme un écosystème de récifs coralliens simplifié en condition contrôle et au pH prévu en 2100 tout en maintenant les autres paramètres physico-chimiques identiques et proches du milieu naturel (y compris dans leurs variations journalières). Le système mis en place est composé de scléractiniaires hermatypiques comme constructeurs de récif, d’oursins (E. mathaei) comme bioérodeurs et brouteurs et un substrat calcaire de récif avec ses communautés d’algues, bactéries, archae, champignons et méiofaune. Les variations journalières de pH et de température reproduisent celles mesurées in situ dans le site de La Saline, Ile de La Réunion, d’où proviennent une partie des organismes. Le pH moyen des aquariums contrôles a été maintenu avec succès à une moyenne de 8,09 ± 0,04, celui des aquariums à pCO2 élevée à 7,63 ± 0,02. L’alcalinité totale du système a pu être maintenue entre 2350 et 2450 µmol.kg-1. <p>L’impact de l’AO prévue en 2100 (pH 7,7) sur la physiologie d’E. mathaei été étudié à court terme (sept semaines). La principale source de nourriture des oursins fut la communauté algale se développant sur le substrat, comme en conditions naturelles. Cette étude a permis de mettre en évidence, à court terme, la capacité de résistance de cet oursin à une AO modérée. En effet, la croissance et le métabolisme ne furent pas affectés significativement. Ces observations ont été associées au maintien de la balance acide-base du fluide extracellulaire, le liquide cœlomique, par accumulation de bicarbonates dans celui-ci.<p>Une même expérience a ensuite été réalisée à long terme. La diminution du pH a été induite progressivement durant six mois jusqu'à atteindre un pH moyen de 7,65 qui fut ensuite maintenu à cette valeur pendant sept mois supplémentaires. La capacité de régulation de la balance acide-base du liquide cœlomique et la résistance d’E. mathaei à l’AO a été confirmée à long terme. Tant la croissance que le métabolisme et les propriétés mécaniques du squelette ne furent pas affectés. Cette résistance apparaît liée aux capacités de régulation acide-base d’E. mathaei, un trait apparemment d’origine génétique. Cette résistance pourrait également dépendre de la quantité et de la qualité de la nourriture disponible (calcaire ou non). Il est suggéré que les ions bicarbonates impliqués dans la régulation acide-base proviendraient en partie de la nourriture. <p>Parallèlement à ces mesures physiologiques, l’activité érosive d’E. mathaei a été mesurée. Les résultats indiquent que le taux de bioérosion triple en conditions acidifiées (pH 7,65). Cette augmentation serait liée à l’augmentation de l'activité de broutage des oursins et à la dissolution biologique du substrat, les propriétés mécaniques des dents des oursins et du squelette des coraux ne semblant pas affectés significativement. Nous suggérons que cette activité érosive accrue pourrait avoir un impact sur l'équilibre dynamique entre bioerosion et bioaccrétion des coraux et pourrait déterminer l'avenir des récifs coralliens où E. mathaei est le principal bioérodeur. Il faut toutefois noter que l’activité érosive de cet oursin est liée à une consommation accrue des macro-algues en compétition avec les coraux et algues corallines, favorisant ainsi ces derniers.<p>Les résultats obtenus, associés à ceux provenant de la littérature, indiquent que les changements globaux pourraient provoquer un changement profond des écosystèmes coralliens tropicaux. En effet, l’ensemble des bioérodeurs principaux étudiés jusqu’à présent semblent résistants aux changements climatiques globaux et montrent une augmentation de leur activité érosive. Dans le cas des récifs ayant déjà à l’heure actuelle une faible calcification nette, l’augmentation de la bioérosion pourrait mener à l’érosion nette et à la réduction puis à la disparition du récif. La prédiction du devenir des récifs coralliens tropicaux à l’échelle planétaire doit toutefois prendre en compte de nombreux paramètres :acclimatation, résistance/sensibilité et interactions des différents acteurs des récifs. D’autres études comparables à celles menées dans le présent travail devraient être mises en place afin de tester ces différents facteurs. Les données obtenues pourraient dès lors être utilisées dans la construction d’un modèle mécanistique permettant de mettre en place localement des mesures de conservation du récif, en complément de l’indispensable réduction massive de l’émission de CO2 atmosphérique à l’échelle mondiale.<p><p><p><p><p> / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

Ce travail porte sur l'utilisation et l'exploitation des invertébrés marins (mollusques, crustacés et échinodermes) durant la Protohistoire sur les côtes de la Manche et de l'Atlantique en France. Il repose sur l'inventaire de 197 sites ayant livré ce type de faune. 32 ont fait l'objet d'une étude archéomalacologique, dont 17 dans le cadre de cette thèse. Les résultats obtenus permettent d'aborder des thématiques variées, comme les environnements exploités, l'économie de subsistance (mode alimentaire, spécificité géographique, réseau d'échange), l'artisanat (teinture, parure, matériau de construction, etc.) et les pratiques funéraires et cultuelles (dépôt, repas rituels). L'étude des invertébrés marins contribue ainsi à une meilleure compréhension des systèmes socio-économiques et culturels des communautés littorales et continentales durant la Protohistoire. / This work deals with the use and exploitation of marine invertebrates (molluscs, crustaceans and echinoderms) during the Protohistory on the Channel and Atlantic coasts in France. It relies on the inventory of 197 sites characterized by the presence of this type of fauna. Some archaeomalacological studies have been realized on 32 of these sites, of which 17 during this thesis. The results allow to approach various themes, such as the environments exploited, the subsistence economy (food, geographical variations, exchange network), crafts (dyeing, beads, building material, etc.) and funeral and ritual practices (hoard, ritual meal). The study of the marine invertebrates thus contributes to a better understanding of the socio-economical and cultural systems of the littoral and continental communities during the Protohistory. / Este trabajo se centra en el uso y explotación de los invertebrados marinos (moluscos, crustáceos y equinodermos) durante la Protohistoria en la costa de la Mancha y Atlántica de Francia. La investigación se basa en un inventario de 197 sitios arqueológicos con presencia de restos malacológicos, sobre 32 de ellos se ha realizado un estudio arqueomalacológico, de los cuales 17 se han desarrollado e incluido en el contexto de esta tesis doctoral. Los resultados obtenidos se han orientado a tratar una variedad de cuestiones, como el medioambiente explotado, la economía de subsistencia a partir de diferentes perspectivas (la alimentación, las especificaciones geográfica, o las redes de intercambio), la producción artesanal (tintes, elementos de adorno o material de construcción), o las prácticas funerarias y rituales (elementos de ajuar, comidas rituales). El estudio de los invertebrados marinos contribuye así a una mejor comprensión de los sistemas culturales y socio-económicos de las comunidades costeras y también continentales a lo largo de la Protohistoria.