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The thermohaline circulation (THC) corresponds to the large time- and spatial-scales ocean circulation associated with the transport of heat and salt, and is known to be an important factor controlling the climate variability. The large scales involved in the THC make it difficult to observe, and therefore the synergy of numerical models and climate proxy reconstructions is particularly relevant to study the characteristics of this circulation in the present and past climates. In this doctoral thesis, the THC during the Last Glacial Maximum (LGM) and the Present-Day (PD) is explored using a state-of-the-art Ocean General Circulation Model in its high- and low-resolution regimes. By comparing the LGM model outputs with the paleo-proxy reconstructions, it is shown that the high-resolution simulation improves the representation of the sea surface tem- peratures in the regions where the current structures appear to be complex, i.e., the western boundary currents (Agulhas, Kuroshio, Gulf Stream) and the Antarctic Circumpolar Current, although statistical comparisons with paleo- proxy reconstructions are not significantly improved on a global scale. The THC involves a superposition of processes acting at widely different spatial and temporal scales, from the geostrophic large-scale and slowly-varying flow to the mesoscale turbulent eddies and at even smaller-scale, the mixing generated by the internal wave field. Not all these processes can be properly resolved in numerical models, and thus need to be parameterized. Analyzing the THC in an eddy-permitting numerical model, it was found that the temporal scales required for diagnosing the Southern Ocean circulation should not exceed 1 month and the spatial scales needed to be taken into account must be smaller than 1°. Important changes in the nature and intensity of the THC were observed between the LGM and PD simulations. An estimation of the turnover times (i.e., the time it takes for the water parcel to make and entire loop on the Conveyor Belt) revealed that the LGM THC could be more vigorous than under the PD conditions. As a result, the ocean transports of heat and freshwater, the oceanic uptake of CO2, the ventilation of the deep ocean and the reorganization of the passive and active tracers (e.g., temperature, salinity, greenhouse gases, nutrients) can be altered in these different regimes. / <p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 5: Manuscript. </p>

Previously, we have demonstrated that a DNA helicase-like protein, termed RTEL (regulator of telomere length) is essential for the maintenance of genomic stability. RTEL deficiency induced telomere loss and genomic instability, leading to embryonic lethality. However, the role of RTEL in these biological pathways is largely unknown. To uncover RTEL’s function(s), we applied several approaches to identify the proteins that could interact with RTEL. Proliferating Cell Nuclear Antigen (PCNA), the key regulator of the replication fork, was found to be a strong candidate. In this study, we have demonstrated the interaction between RTEL and PCNA. Further characterization of the interaction between RTEL and PCNA revealed that the interaction is important for maintaining genomic stability. Due to the essential role of PCNA in nucleic acid metabolism as a component of the replication and repair machinery, its interaction with RTEL could be the key to the role of RTEL in the maintenance of genomic stability and mouse development. Along with a bioinformatics approach, we have employed several biochemical approaches to identify the interaction of PCNA with RTEL. Using co-immunoprecipitation, we have demonstrated that RTEL can specifically interact with PCNA. A PCR-based mutagenesis method was used to mutate the PCNA-interacting motif (PIP) in RTEL. Further we have demonstrated that several key amino acids in the PIP motif are responsible for mediating RTEL/PCNA interaction by using co-immunoprecipitation and immunofluorescence studies. Using a gene-targeting approach, we have specifically knocked-in a mutant RTEL with a mutation in PIP motif into mouse genome. Thus we have developed a transgenic mouse model to study the significance of the interaction between RTEL/PCNA in vivo. This study not only validated the interaction of RTEL with PCNA, via the PIP box, but also generated the RTEL PIP mutant alleles for further functional analysis by transgenic approaches. We have employed biochemical and cytogenetic studies to characterize the phenotypes in RtelI1169A/I1169A mouse. This is the first direct genetic approach to address whether PCNA is an important downstream mediator of RTEL’s function in the regulation of genomic integrity

Helicase-like Transcription Factor (HLTF) is a DNA helicase protein which is homologous to SNF/SWI family. It has been demonstrated to be a functional homolog of yeast Rad5, required for the maintenance of genomic stability. Although the physiologic role of HLTF is largely unknown,inactivation of HLTF by promoter hypermethylation has been found in more than 40% human colon cancers. In this study, we have applied mouse transgenic approaches to determine whether loss of HLTF function could be important for colorectal carcinogenesis. HLTF knockout mice were generated by the deletion of first 5 exons of the HLTF gene. The complete loss of HLTF expression in HLTF -/- mice was confirmed by northern blot and real time RT-PCR assays. HLTF -/- mice did not show any developmental defects within a 2-year observation indicating that HLTF is dispensable for mouse development. Furthermore, HLTF -/- mice were free of intestinal or colorectal tumors or other types of tumors, suggesting that loss of HLTF function alone is not sufficient to drive oncogenic transformation in intestinal track and other tissues. To determine whether loss of HLTF function could cooperate with other tumor suppressors in the formation of colorectal cancers, we have bred HLTF knockout mice with the mutant mice for APC (adenomtous polyposis coli) and P53. In HLTF -/-APC Min/+ mice, a significantly increased formation of intestinal adenocarcinoma and colorectal cancers were observed. Although very few HLTF -/-P53 -/- mice developed colorectal cancers, these mice had increased incidence of the formation of metastatic lymphomas. Cytogenetic analysis of colorectal cancer cells derived from HLTF -/-APC Min/+ mice demonstrated a high incidence of gross chromosomal instabilities, including Robertsonian fusions, fragments and aneuploidy. All these genetic alterations were not observed in the intestinal tumor cells from APC Min/+, implicating that loss of HLTF function could induce genomic instability which contributes to intestinal carcinogenesis. To further investigate the role of HLTF in colorectal carcinogenesis, we have also applied a shRNA knockdown approach to down-regulate HLTF expression in human HCT-116 colon cancer cells. HCT-116 cells highly express HLTF and show less chromosomal instability, making these cells as a very useful model to investigate the loss of function of HLTF in human colorectal carcinogenesis. Using Western blot approach, we confirmed that HLTF knockdown HCT-116 cells had less than 5% of HLTF expression as compared to the scramble controls. By inoculating HLTF knockdown HCT-116 cells to Rag1 -/-IL2 -/- immunocompromised mice, we further demonstrated that HLTF knockdown promote tumor growth and invasion. Moreover, spectral karyotyping analysis revealed that HLTF knockdown human colon cancer cells had significantly increased chromosomal instability, including both aneuploidy and chromosomal translocation. Taken together, our work strongly indicates that loss of HLTF function can promote the malignant transformation of intestinal or colonic adenomas to carcinomas by inducing genomic instability. Given the high frequency of epigenetic inactivation by hypermethylation of HLTF in human colon cancers, our studies strongly suggest that this epigenetic alteration could be directly involved in the development of colorectal cancer rather than a consequence of this carcinogenesis.

Modeling and simulation have always been essential steps in innovation, the processesof developing new products. This is especially the case for cyber-physical systems, whichare complex systems of networked physical and computational components. Modelingplays a key role in model-based design. Immersion techniques speed up the modelingprocess by presenting the design more intuitively. This thesis investigates the possibilityof improving support of immersion in Acumen, a free and open source software platformfor modeling and simulation of cyber-physical systems. To be consistent with theopen and free nature of Acumen, we investigate immersion options that would not entailadded cost to users.This thesis shows that it is possible to allow users to interact with an Acumen model, simulateand animate them simultaneously, and synchronize the simulation with real worldtime. The results show that the immersion techniques can be easily used without degradingthe performance of Acumen simulation, and help users understand and developAcumen models. Finally, we show why it is important to build a hardware independent3D visualization for Acumen, namely, that it allows users to use Acumen without acumbersome set-up process.iii

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