My research activity has been supported by the bioinformatic platform of the Fondazione Cariplo NOBEL Project named “Understanding DNA damage checkpoint and repair”. The aim of this platform was to investigate the molecular mechanisms involved in the DNA Damage Response (DDR), through a Systems Biology approach. Among the DDR pathways, the focus of my research was the DNA Damage Tolerance (DDT) pathway called Post-Replication Repair (PRR) using Saccharomyces cerevisiae cells as a model system. This pathway leads to the bypass of UV-induced DNA lesions through a mechanism, which is poorly characterized at molecular level in comparison with the Nucleotide Excision Repair (NER) process, the mechanism leading to the effective repair of UV-induces DNA lesions. The data presented in this thesis led to the production of the first mathematical model of PRR in eukaryotic cells. In the work carried out in this thesis I had the difficult task to manage both in silico and in vivo aspects of a Systems Biology project. Given the complexity of the PRR pathway and the lack of critical experimental data, the attempt to build a mathematical model of PRR was an ambitious aim not free from difficulties. Before this study, the crosstalk between PRR and other DDR pathways were unknown and, indeed, the discrepancy between the in vivo data and the in silico simulations, observed under certain experimental conditions, led to additional experiments that uncovered new unpublished aspects of PRR and others that need to be done. In this way the so called “Circle of Systems Biology” applied to PRR can be considered closed and promising for the future: the limit of the model to particular experimental conditions is leading to a new batch of experiments to do and new hypothesis to test.

BYPASS OF UV-INDUCED DNA LESIONS IN SACCHAROMYCES CEREVISIAE: EXPERIMENTAL ANALYSIS AND "IN SILICO" MODELING / F. Amara ; tutor: P. Plevani, M. Muzi-Falconi, D. Besozzi. - : . UNIVERSITA' DEGLI STUDI DI MILANO, 2012 Nov 29. ((24. ciclo, Anno Accademico 2011. [10.13130/amara-flavio_phd2012-11-29].

BYPASS OF UV-INDUCED DNA LESIONS IN SACCHAROMYCES CEREVISIAE: EXPERIMENTAL ANALYSIS AND "IN SILICO" MODELING.

F. Amara
2012

Abstract

My research activity has been supported by the bioinformatic platform of the Fondazione Cariplo NOBEL Project named “Understanding DNA damage checkpoint and repair”. The aim of this platform was to investigate the molecular mechanisms involved in the DNA Damage Response (DDR), through a Systems Biology approach. Among the DDR pathways, the focus of my research was the DNA Damage Tolerance (DDT) pathway called Post-Replication Repair (PRR) using Saccharomyces cerevisiae cells as a model system. This pathway leads to the bypass of UV-induced DNA lesions through a mechanism, which is poorly characterized at molecular level in comparison with the Nucleotide Excision Repair (NER) process, the mechanism leading to the effective repair of UV-induces DNA lesions. The data presented in this thesis led to the production of the first mathematical model of PRR in eukaryotic cells. In the work carried out in this thesis I had the difficult task to manage both in silico and in vivo aspects of a Systems Biology project. Given the complexity of the PRR pathway and the lack of critical experimental data, the attempt to build a mathematical model of PRR was an ambitious aim not free from difficulties. Before this study, the crosstalk between PRR and other DDR pathways were unknown and, indeed, the discrepancy between the in vivo data and the in silico simulations, observed under certain experimental conditions, led to additional experiments that uncovered new unpublished aspects of PRR and others that need to be done. In this way the so called “Circle of Systems Biology” applied to PRR can be considered closed and promising for the future: the limit of the model to particular experimental conditions is leading to a new batch of experiments to do and new hypothesis to test.
PLEVANI, PAOLO
UV-induced DNA damage ; post-replication repair ; nucleotide excision repair ; ubiquitin ; mathematical modeling
Settore BIO/10 - Biochimica
Settore BIO/11 - Biologia Molecolare
Settore INF/01 - Informatica
BYPASS OF UV-INDUCED DNA LESIONS IN SACCHAROMYCES CEREVISIAE: EXPERIMENTAL ANALYSIS AND "IN SILICO" MODELING / F. Amara ; tutor: P. Plevani, M. Muzi-Falconi, D. Besozzi. - : . UNIVERSITA' DEGLI STUDI DI MILANO, 2012 Nov 29. ((24. ciclo, Anno Accademico 2011. [10.13130/amara-flavio_phd2012-11-29].
Doctoral Thesis
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/2434/214278
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