Functional Genomics and Cell Biology of the Dolphin (Tursiops runcatus): Establishment of Novel Molecular Tools to Study Marine Mammals in Changing Environments

The dolphin (Tursiops truncatus) is a mammal that is adapted to life in a totally aquatic environment. Despite the popularity and even iconic status of the dolphin, our knowledge of its physiology, its unique adaptations and the effects on it of environmental stressors are limited. One approach to improve this limited understanding is the implementation of established cellular and molecular methods to provide sensitive and insightful information for dolphin biology. We initiated our studies with the analysis of wild dolphin peripheral blood leukocytes, which have the potential to be informative of the animal’s global immune status. Transcriptomic profiles from almost 200 individual samples were analyzed using a newly developed species-specific microarray to assess its value as a prognostic and diagnostic tool. Functional genomics analyses were informative of stress-induced gene expression profiles and also of geographical location specific transcriptomic signatures, determined by the interaction of genetic, disease and environmental factors. We have developed quantitative metrics to unambiguously characterize the phenotypic properties of dolphin cells in culture. These quantitative metrics can provide identifiable characteristics and baseline data which will enable identification of changes in the cells due to time in culture. We have also developed a novel protocol to isolate primary cultures from cryopreserved tissue of stranded marine mammals, establishing a tissue (and cell) biorepository, a new approach that can provide a solution to the limited availability of samples. The work presented represents the development and application of tools for the study of the biology, health and physiology of the dolphin, and establishes their relevance for future studies of the impact on the dolphin of environmental infection and stress.

The Architecture of the Persian Period in the Levant

The earliest scholars were not concerned about preparing extensive investigations linking the Persian-period building remains excavated in the entire Levant together. Moreover, the research interests of scholars caused some impediments to the study of this period viz in the last decades; the Achaemenid period has been neglected by the scholars who -in turn- focused on the earlier and later periods for religious reasons. Too, while some regions have been studied abundantly, but it was not the case in other areas, which makes our knowledge is incomplete. From the explanation side, some scholars try to interpret the architectural remains from an ethnic perspective or unsubstantiated personal fancies, so their arguments were utterly lacking any objectivity. This thesis explores what are the Persian architectural and ornamental impacts on the Levantine architecture and the relations between Persian-period sites in Syria-Palestine region. Too, the architectural remains and their contents benefited us to clarify the settlement patterns in the regions being discussed. The author analyzed the ground plans of the buildings and their architectural features and ornamental motifs by conducting a descriptive, analytical, and interpretative study. He also conducted comparisons with similar buildings outside the Levant, especially in Fars to obtain a more comprehensive and systematic study, and then extracting any direct or indirect Persian influences. This has given us a better understanding of the nature of the social, political, and religious life in the entire Levant and the knowledge gap has been bridged to a satisfying extent. This study has demonstrated a few of the Achaemenid impacts, especially on the northern coastline of the Levant.

New computational biology tools for the systematic analysis of the structure and expression of human genes

From the late 1980s, the automation of sequencing techniques and the computer spread gave rise to a flourishing number of new molecular structures and sequences and to proliferation of new databases in which to store them. Here are presented three computational approaches able to analyse the massive amount of publicly avalilable data in order to answer to important biological questions. The first strategy studies the incorrect assignment of the first AUG codon in a messenger RNA (mRNA), due to the incomplete determination of its 5' end sequence. An extension of the mRNA 5' coding region was identified in 477 in human loci, out of all human known mRNAs analysed, using an automated expressed sequence tag (EST)-based approach. Proof-of-concept confirmation was obtained by in vitro cloning and sequencing for GNB2L1, QARS and TDP2 and the consequences for the functional studies are discussed. The second approach analyses the codon bias, the phenomenon in which distinct synonymous codons are used with different frequencies, and, following integration with a gene expression profile, estimates the total number of codons present across all the expressed mRNAs (named here "codonome value") in a given biological condition. Systematic analyses across different pathological and normal human tissues and multiple species shows a surprisingly tight correlation between the codon bias and the codonome bias. The third approach is useful to studies the expression of human autism spectrum disorder (ASD) implicated genes. ASD implicated genes sharing microRNA response elements (MREs) for the same microRNA are co-expressed in brain samples from healthy and ASD affected individuals. The different expression of a recently identified long non coding RNA which have four MREs for the same microRNA could disrupt the equilibrium in this network, but further analyses and experiments are needed.