Next-Generation Sequencing-Based Mutations Scanning Strategy of the BCR-ABL Kinase Domain in Patients with PhiladelPhia-Chromosome Positive Leukemias Treated with Tyrosine Kinase Inhibitors

In chronic myeloid leukemia and Philadelphia-positive acute lymphoblastic leukemia patients resistant to tyrosine kinase inhibitors (TKIs), BCR-ABL kinase domain mutation status is an essential component of the therapeutic decision algorithm. The recent development of Ultra-Deep Sequencing approach (UDS) has opened the way to a more accurate characterization of the mutant clones surviving TKIs conjugating assay sensitivity and throughput. We decided to set-up and validated an UDS-based for BCR-ABL KD mutation screening in order to i) resolve qualitatively and quantitatively the complexity and the clonal structure of mutated populations surviving TKIs, ii) study the dynamic of expansion of mutated clones in relation to TKIs therapy, iii) assess whether UDS may allow more sensitive detection of emerging clones, harboring critical 2GTKIs-resistant mutations predicting for an impending relapse, earlier than SS. UDS was performed on a Roche GS Junior instrument, according to an amplicon sequencing design and protocol set up and validated in the framework of the IRON-II (Interlaboratory Robustness of Next-Generation Sequencing) International consortium.Samples from CML and Ph+ ALL patients who had developed resistance to one or multiple TKIs and collected at regular time-points during treatment were selected for this study. Our results indicate the technical feasibility, accuracy and robustness of our UDS-based BCR-ABL KD mutation screening approach. UDS was found to provide a more accurate picture of BCR-ABL KD mutation status, both in terms of presence/absence of mutations and in terms of clonal complexity and showed that BCR-ABL KD mutations detected by SS are only the “tip of iceberg”. In addition UDS may reliably pick 2GTKIs-resistant mutations earlier than SS in a significantly greater proportion of patients.The enhanced sensitivity as well as the possibility to identify low level mutations point the UDS-based approach as an ideal alternative to conventional sequencing for BCR-ABL KD mutation screening in TKIs-resistant Ph+ leukemia patients

Climate impact studies of sediment transport on the Adriatic coastal zone

The study of the impact of climate change on the environment has been based, until very recently, on an global approach, whose interest from a local point of view is very limited. This thesis, on the contrary, has treated the study of the impact of climate change in the Adriatic Sea basin following a twofold strategy of regionalization and integration of numerical models in order to reproduce the present and future scenarios of the system through a more and more realistic and solid approach. In particular the focus of the study was on the impact on the physical environment and on the sediment transport in the basin. This latter is a very new and original issue, to our knowledge still uninvestigated. The study case of the coastal area of Montenegro was particularly studied, since it is characterized by an important supply of sediment through the Buna/Bojana river, second most important in the Adriatic basin in terms of flow. To do this, a methodology to introduce the tidal processes in a baroclinic primitive equations Ocean General Circulation Model was applied and tidal processes were successfully reproduced in the Adriatic Sea, analyzing also the impacts they have on the mean general circulation, on salt and heat transport and on mixing and stratification of the water column in the different seasons of the year. The new hydrodynamical model has been further coupled with a wave model and with a river and sea sediment transport model, showing good results in the reproduction of sediment transport processes. Finally this complex coupled platform was integrated in the period 2001-2030 under the A1B scenario of IPCC, and the impact of climate change on the physical system and on sediment transport was preliminarily evaluated.

Export Supply Chain Organization and Food Safety and Quality Standards: a case study of the Moroccan Fruit and Vegetable Sector

Agri-food supply chains extend beyond national boundaries, partially facilitated by a policy environment that encourages more liberal international trade. Rising concentration within the downstream sector has driven a shift towards “buyer-driven” global value chains (GVCs) extending internationally with global sourcing and the emergence of multinational key economic players that compete with increase emphasis on product quality attributes. Agri-food systems are thus increasingly governed by a range of inter-related public and private standards, both of which are becoming a priori mandatory, especially in supply chains for high-value and quality-differentiated agri-food products and tend to strongly affect upstream agricultural practices, firms’ internal organization and strategic behaviour and to shape the food chain organization. Notably, increasing attention has been given to the impact of SPS measures on agri-food trade and notably on developing countries’ export performance. Food and agricultural trade is the vital link in the mutual dependency of the global trade system and developing countries. Hence, developing countries derive a substantial portion of their income from food and agricultural trade. In Morocco, fruit and vegetable (especially fresh) are the primary agricultural export. Because of the labor intensity, this sector (especially citrus and tomato) is particularly important in terms of income and employment generation, especially for the female laborers hired in the farms and packing houses. Hence, the emergence of agricultural and agrifood product safety issues and the subsequent tightening of market requirements have challenged mutual gains due to the lack of technical and financial capacities of most developing countries.