Computational investigation of the Plasmodium falciparum fatty acid biosynthetic pathway toward the discovery of novel antimalarials

The structural peculiarities of a protein are related to its biological function. In the fatty acid elongation cycle, one small carrier protein shuttles and delivers the acyl intermediates from one enzyme to the other. The carrier has to recognize several enzymatic counterparts, specifically interact with each of them, and finally transiently deliver the carried substrate to the active site. Carry out such a complex game requires the players to be flexible and efficiently adapt their structure to the interacting protein or substrate. In a drug discovery effort, the structure-function relationships of a target system should be taken into account to optimistically interfere with its biological function. In this doctoral work, the essential role of structural plasticity in key steps of fatty acid biosynthesis in Plasmodium falciparum is investigated by means of molecular simulations. The key steps considered include the delivery of acyl substrates and the structural rearrangements of catalytic pockets upon ligand binding. The ground-level bases for carrier/enzyme recognition and interaction are also put forward. The structural features of the target have driven the selection of proper drug discovery tools, which captured the dynamics of biological processes and could allow the rational design of novel inhibitors. The model may be perspectively used for the identification of novel pathway-based antimalarial compounds.

Modelling coupled physical-biogeochemical processes in ice-covered oceans

The last decades have seen a large effort of the scientific community to study and understand the physics of sea ice. We currently have a wide - even though still not exhaustive - knowledge of the sea ice dynamics and thermodynamics and of their temporal and spatial variability. Sea ice biogeochemistry is instead largely unknown. Sea ice algae production may account for up to 25% of overall primary production in ice-covered waters of the Southern Ocean. However, the influence of physical factors, such as the location of ice formation, the role of snow cover and light availability on sea ice primary production is poorly understood. There are only sparse localized observations and little knowledge of the functioning of sea ice biogeochemistry at larger scales. Modelling becomes then an auxiliary tool to help qualifying and quantifying the role of sea ice biogeochemistry in the ocean dynamics. In this thesis, a novel approach is used for the modelling and coupling of sea ice biogeochemistry - and in particular its primary production - to sea ice physics. Previous attempts were based on the coupling of rather complex sea ice physical models to empirical or relatively simple biological or biogeochemical models. The focus is moved here to a more biologically-oriented point of view. A simple, however comprehensive, physical model of the sea ice thermodynamics (ESIM) was developed and coupled to a novel sea ice implementation (BFM-SI) of the Biogeochemical Flux Model (BFM). The BFM is a comprehensive model, largely used and validated in the open ocean environment and in regional seas. The physical model has been developed having in mind the biogeochemical properties of sea ice and the physical inputs required to model sea ice biogeochemistry. The central concept of the coupling is the modelling of the Biologically-Active-Layer (BAL), which is the time-varying fraction of sea ice that is continuously connected to the ocean via brines pockets and channels and it acts as rich habitat for many microorganisms. The physical model provides the key physical properties of the BAL (e.g., brines volume, temperature and salinity), and the BFM-SI simulates the physiological and ecological response of the biological community to the physical enviroment. The new biogeochemical model is also coupled to the pelagic BFM through the exchange of organic and inorganic matter at the boundaries between the two systems . This is done by computing the entrapment of matter and gases when sea ice grows and release to the ocean when sea ice melts to ensure mass conservation. The model was tested in different ice-covered regions of the world ocean to test the generality of the parameterizations. The focus was particularly on the regions of landfast ice, where primary production is generally large. The implementation of the BFM in sea ice and the coupling structure in General Circulation Models will add a new component to the latters (and in general to Earth System Models), which will be able to provide adequate estimate of the role and importance of sea ice biogeochemistry in the global carbon cycle.

La neoangiogenesi nel reimpianto autologo di tessuto ovarico in pazienti a rischio di fallimento ovarico precoce: ottimizzazione dei metodi di crioconservazione di corticle ovarica

Introduzione L’efficacia dei chemio/radioterapici ha aumentato notevolmente l’aspettativa di vita delle pazienti oncologiche, tuttavia, questi trattamenti possono compromettere la funzionalità ovarica. La crioconservazione di tessuto ovarico, con il successivo reimpianto, ha lo scopo di preservare la fertilità delle pazienti a rischio di fallimento ovarico precoce. Scopo dello studio Definire la migliore procedura di crioconservazione e reimpianto in grado di ottenere la neovascolarizzazione del tessuto reimpiantato nel minor tempo possibile al fine di diminuire la perdita follicolare causata dall’ischemia durante la procedura. Materiali e metodi Per ciascuna paziente (3) le biopsie ovariche, sono state prelevate laparoscopicamente e crioconservate secondo il protocollo di congelamento lento/scongelamento rapido. Campioni di corticale ovarica sono stati processati per l’analisi istologica, ultrastrutturale, immuistochimica e confocale per valutare la preservazione morfologiaca del tessuto. Le fettine di corticale ovarica sono state scongelate e reimpiantate ortotopicamente (2), nelle ovaia e in due tasche peritoneali, o eterotopicamente (1), in due tasche create nel sottocute sovrapubico. Risultati Le analisi di microscopia hanno mostrato il mantenimento di una discreta morfologia dello stroma, e dei vasi criopreservati e un lieve ma non significativo danneggiamento dei follicoli scongelati. Tutte le pazienti hanno mostrato la ripresa della funzionalità endocrina rispettivamente dopo 2/4 mesi dal reimpianto. Il color-doppler, inoltre ha rivelato un significativo aumento della vascolarizzazione ovarica rispetto alla quasi totale assenza di vascolarizzazione prima del reimpianto, quando le pazienti mostravano una conclamata menopausa. Conclusioni Lo studio ha confermato la ripresa della vascolarizzazione dell’ovaio in seguito a reimpianto avascolare di fettine di corticale, senza l’impiego di fattori esogeni o meccanici aggiuntivi, in tempi concordanti con i dati della letteratura. I risultati sono incoraggianti e l’avanzare degli studi e della ricerca potranno contribuire allo sviluppo di nuove metodologie di reimpianto che possano avere un successo clinico ed una sicurezza superiori a quelle finora ottenute.