Insights into molecular and cellular events involved in normal and pathological vertebral development and fusion using zebrafish as model organism

The vertebral column and its units, the vertebrae, are fundamental features, characteristic of all vertebrates. Developmental segregation of the vertebral bodies as articulated units is an intrinsic requirement to guarantee the proper function of the spine. Whenever these units become fused either during development or postsegmentation, movement is affected in a more or less severe manner, depending on the number of vertebrae affected. Nevertheless, fusion may occur as part of regular development and as a physiological requirement, like in the tetrapod sacrum or in fish posterior vertebrae forming the urostyle. In order to meet the main objective of this PhD project, which aimed to better understand the molecular and cellular events underlying vertebral fusion under physiological and pathological conditions, a detailed characterization of the vertebral fusion occurring in zebrafish caudal fin region was conducted. This showed that fusion in the caudal fin region comprised 5 vertebral bodies, from which, only fusion between [PU1++U1] and ural2 [U2+] was still traceable during development. This involved bone deposition around the notochord sheath while fusion within the remaining vertebral bodies occur at the level of the notochord sheath, as during the early establishment of the vertebral bodies. A comparison approach between the caudal fin vertebrae and the remaining vertebral column showed conserved features such as the presence of mineralization related proteins as Osteocalcin were identified throughout the vertebral column, independently on the mineralization patterns. This unexpected presence of Osteocalcin in notochord sheath, here identified as Oc1, suggested that this gene, opposing to Oc2, generally associated with bone formation and mature osteoblast activity, is potentially associated with early mineralization events including chordacentrum formation. Nevertheless, major differences between caudal fin region and anterior vertebral bodies considering arch histology and mineralization patterns, led us to use RA as an inductive factor for vertebral fusion, allowing a direct comparison of equivalent structures under normal and fusion events. This fusion phenotype was associated with notochord sheath ectopic mineralization instead of ectopic perichordal bone formation related with increased osteoblast activity, as suggested in previous reports. Additionally, alterations in ECM content, cell adhesion and blood coagulation were discussed as potentially related with the fusion phenotype. Finally, Matrix gla protein, upregulated upon RA treatment and shown to be associated with chordacentrum mineralization sites in regular development, was further described considering its potential function in vertebral formation and pathological fusion. Therefore with this work we propose zebrafish caudal fin vertebral fusion as a potential model to study both congenital and postsegmentation fusion and we present candidate factors and genes that may be further explored in order to clarify whether we can prevent vertebral fusion.

Higher order model for analysis of magneto-electro-elastic plates

In this paper is presented an higher-order model for static and free vibration analyses of magneto-electro-elastic plates, wich allows the analysis of thin and thick plates, which allows the analysis of thin and thick plates. The finite element model is a single layer triangular plate/shell element with 24 degrees of fredom for the generalized mechanical displacements. Two degrees on freedom are introduced per each element layer, one corresponding to the electrical potential and the other for magnetic potential. Solutions are obtained for different laminations of the magneto-electro-elastic plate, as well as for the purely elastic plate as a special case.

Optimal dynamic control of laminated adaptive structures using a higher order model and a genetic algorithm

This paper deals with a finite element formulation based on the classical laminated plate theory, for active control of thin plate laminated structures with integrated piezoelectric layers, acting as sensors and actuators. The control is initialized through a previous optimization of the core of the laminated structure, in order to minimize the vibration amplitude. Also the optimization of the patches position is performed to maximize the piezoelectric actuator efficiency. The genetic algorithm is used for these purposes. The finite element model is a single layer triangular plate/shell element with 24 degrees of freedom for the generalized displacements, and one electrical potential degree of freedom for each piezoelectric element layer, which can be surface bonded or embedded on the laminate. To achieve a mechanism of active control of the structure dynamic response, a feedback control algorithm is used, coupling the sensor and active piezoelectric layers. To calculate the dynamic response of the laminated structures the Newmark method is considered. The model is applied in the solution of an illustrative case and the results are presented and discussed.

A three-dimensional hydrodynamic model with generic vertical coordinate

A three-dimensional primitive equation model and its application to a tidal estuary is described. The model solves the primitive equations for incompressible fluids with Boussinesq and hydrostatic approximations. The discretization is based on the finite volume method and allows a general vertical coordinate. The computational code is implemented in such a way that different vertical coordinates can be used in different parts of the domain. The model was designed to be able to simulate the flow both in the open ocean and in coastal and estuarine zones and can be coupled in a simple way to ecological models. The model was implemented successfully in several estuarine and coastal areas. Results are show for the Sado estuary in Portugal to illustrate model accuracy and potential. Quantitative validation is based on field data (water levels and velocities) while qualitative verification is based on the analysis of secondary flows.

Finit element model for active control of adaptive laminated structures

A finite element formulation for active vibration control of thin plate laminated structures with integrated piezoelectric layers, acting as sensors and actuators in presented. The finite element model is a nonconforming single layer triangular plate/shell element with 18 degrees of freedom for the generalized displacements and one electrical potential degree of freedom for each piezoelectric element layer, and is based on the kirchhoff classical laminated theory. To achieve a mechanism of active control of the structure dynamic response, a feedback control algorithm is used, coupling the sensor and active piezoelectric layers, and Newmark method is used to calculate yhe dynamic response of the laminated structures. The model is applied in the solution of several illustrative cases, and the results are presented and discussed.

Assessing the effects of pseudo-absences on predictive distribution model performance

Modelling species distributions with presence data from atlases, museum collections and databases is challenging. In this paper, we compare seven procedures to generate pseudoabsence data, which in turn are used to generate GLM-logistic regressed models when reliable absence data are not available. We use pseudo-absences selected randomly or by means of presence-only methods (ENFA and MDE) to model the distribution of a threatened endemic Iberian moth species (Graellsia isabelae). The results show that the pseudo-absence selection method greatly influences the percentage of explained variability, the scores of the accuracy measures and, most importantly, the degree of constraint in the distribution estimated. As we extract pseudo-absences from environmental regions further from the optimum established by presence data, the models generated obtain better accuracy scores, and over-prediction increases. When variables other than environmental ones influence the distribution of the species (i.e., non-equilibrium state) and precise information on absences is non-existent, the random selection of pseudo-absences or their selection from environmental localities similar to those of species presence data generates the most constrained predictive distribution maps, because pseudo-absences can be located within environmentally suitable areas. This study showsthat ifwe do not have reliable absence data, the method of pseudo-absence selection strongly conditions the obtained model, generating different model predictions in the gradient between potential and realized distributions.

Ecologic zonation model of the benthic foraminifera and thecamoebians of Guadiana river estuary and application in paleoenvironmental reconstruction

Tese de doutoramento, Ciências do Mar ( Processos de Ecossistemas Marinhos), Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2012