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.

New catalytic processes for the synthesis of adipic acid

The aim of my Ph.D. research was to study the new synthetic ways for the production of adipic acid. Three different pathways were studied: i) oxidation of cyclohexanone with molecular oxygen using Keggin – heteropolycompounds as the catalyst, ii) Baeyer – Villiger oxidation of cyclohexanone with hydrogen peroxide in the presence of two different heterogeneous catalysts, titanium silicalite and silica grafted decatungstate, iii) two step synthesis of adipic acid starting from cyclohexene via 1,2-cyclohexanediol. The first step was catalyzed by H2WO4 in the presence of the phase transfer catalyst, the oxidant was hydrogen peroxide. The second step, oxidation of 1,2 – cyclohexanediol was performed in the presence of oxygen and the heterogeneous catalyst – ruthenium on alumina. The results of my research showed that: i) Oxidation of cyclohexanone with molecular oxygen using Keggin heteropolycompounds is possible, anyway the conversion of ketone is low and the selectivity to adipic acid is lowered by the consecutive reaction to from lower diacids. Moreover it was found out, that there are two mechanisms involved: redox type and radicalic chain-reaction autoxidation. The presence of the different mechanism is influenced by the reaction condition. ii) It is possible to perform thermally activated oxidation of cyclohexanone and obtain non negligible amount of the products (caprolactone and adipic acid). Performing the catalyzed reaction it was demonstrated that the choice of the reaction condition and of the catalyst plays a crucial role in the product selectivity, explaining the discrepancies between the literature and our research. iii) Interesting results can be obtained performing the two step oxidation of cyclohexene via 1,2-cyclohexanediol. In the presence of phase transfer catalyst it is possible to obtain high selectivity to alcohol with stoichiometric amount of oxidant. In the second step of the synthesis, the conversion of alcohol is rather low with modest selectivity to adipic acid

Jasmonates and abscisic acid influence fruit ripening and plant water use: practical, physiological and morphological aspects

The aim of the present thesis was to better understand the physiological role of the phytohormones jasmonates (JAs) and abscisic acid (ABA) during fruit ripening in prospect of a possible field application of JAs and ABA to improve fruit yield and quality. In particular, the effects of exogenous application of these substances at different fruit developmental stages and under different experimental conditions were evaluated. Some aspects of the water relations upon ABA treatment were also analysed. Three fruit species, peach (Prunus persica L. Batsch), golden (Actinidia chinensis) and green kiwifruit (Actinidia deliciosa), and several of their cvs, were used for the trials. Different experimental models were adopted: fruits in planta, detached fruit, detached branches with fruit, girdled branches and micropropagated plants. The work was structured into four sets of experiments as follows: (i) Pre-harvest methyl jasmonate (MJ) application was performed at S3/S4 transition under field conditions in Redhaven peach; ethylene production, ripening index, fruit quality and shelf-life were assessed showing that MJ-treated fruit were firmer and thus less ripe than controls as confirmed by the Index of Absorbance Difference (IAD), but exhibited a shorter shelf-life due to an increase in ethylene production. Moreover, the time course of the expression of ethylene-, auxin- and other ripening-related genes was determined. Ripening-related ACO1 and ACS1 transcript accumulation was inhibited though transiently by MJ, and gene expression of the ethylene receptor ETR2 and of the ethylene-related transcription factor ERF2 was also altered. The time course of the expression of several auxin-related genes was strongly affected by MJ suggesting an increase in auxin biosynthesis, altered auxin conjugation and release as well as perception and transport; the need for a correct ethylene/auxin balance during ripening was confirmed. (ii) Pre- and post-harvest ABA applications were carried out under field conditions in Flaminia and O’Henry peach and Stark Red Gold nectarine fruit; ethylene production, ripening index, fruit quality and shelf-life were assessed. Results show that pre-harvest ABA applications increase fruit size and skin color intensity. Also post-harvest ABA treatments alter ripening-related parameters; in particular, while ethylene production is impaired in ABA-treated fruit soluble solids concentration (SSC) is enhanced. Following field ABA applications stem water potential was modified since ABA-treated peach trees retain more water. (iii) Pre- and post-harvest ABA and PDJ treatments were carried out in both kiwifruit species under field conditions at different fruit developmental stages and in post-harvest. Ripening index, fruit quality, plant transpiration, photosynthesis and stomatal conductance were assessed. Pre-harvest treatments enhance SSC in the two cvs and flesh color development in golden kiwifruit. Post-harvest applications of either ABA or ABA plus PDJ lead to increased SSC. In addition, ABA reduces gas exchanges in A. deliciosa. (iv) Spray, drench and dipping ABA treatments were performed in micropropagated peach plants and in peach and nectarine detached branches; plant water use and transpiration, biomass production and fruit dehydration were determined. In both plants and branches ABA significantly reduces water use and fruit dehydration. No negative effects on biomass production were detected. The present information, mainly arising from plant growth regulator application in a field environment, where plants have to cope with multiple biotic and abiotic stresses, may implement the perspectives for the use of these substances in the control of fruit ripening.

Marine biodiversity survey in the Northern Red Sea: a large-scale monitoring carried out in collaboration with volunteer divers

Concerns over global change and its effect on coral reef survivorship have highlighted the need for long-term datasets and proxy records, to interpret environmental trends and inform policymakers. Citizen science programs have showed to be a valid method for collecting data, reducing financial and time costs for institutions. This study is based on the elaboration of data collected by recreational divers and its main purpose is to evaluate changes in the state of coral reef biodiversity in the Red Sea over a long term period and validate the volunteer-based monitoring method. Volunteers recreational divers completed a questionnaire after each dive, recording the presence of 72 animal taxa and negative reef conditions. Comparisons were made between records from volunteers and independent records from a marine biologist who performed the same dive at the same time. A total of 500 volunteers were tested in 78 validation trials. Relative values of accuracy, reliability and similarity seem to be comparable to those performed by volunteer divers on precise transects in other projects, or in community-based terrestrial monitoring. 9301 recreational divers participated in the monitoring program, completing 23,059 survey questionnaires in a 5-year period. The volunteer-sightings-based index showed significant differences between the geographical areas. The area of Hurghada is distinguished by a medium-low biodiversity index, heavily damaged by a not controlled anthropic exploitation. Coral reefs along the Ras Mohammed National Park at Sharm el Sheikh, conversely showed high biodiversity index. The detected pattern seems to be correlated with the conservation measures adopted. In our experience and that of other research institutes, citizen science can integrate conventional methods and significantly reduce costs and time. Involving recreational divers we were able to build a large data set, covering a wide geographic area. The main limitation remains the difficulty of obtaining an homogeneous spatial sampling distribution.

The biological basis of autism spectrum disorders: evaluation of oxidative stress and erytrocyte membrane alterations

This case-control study involved a total of 29 autistic children (Au) aged 6 to 12 years, and 28 gender and age-matched typically developing children (TD). We evaluated a high number of peripheral oxidative stress parameters, erythrocyte and lymphocyte membrane functional features and membrane lipid composition of erythrocyte. Erythrocyte TBARS, Peroxiredoxin II, Protein Carbonyl Groups and urinary HEL and isoprostane levels were elevated in AU (confirming an imbalance of the redox status of Au); other oxidative stress markers or associated parameters (urinary 8-oxo-dG, plasma Total antioxidant capacity and plasma carbonyl groups, erythrocyte SOD and catalase activities) were unchanged, whilst peroxiredoxin I showed a trend of elevated levels in red blood cells of Au children. A very significant reduction of both erythrocyte and lymphocyte Na+, K+-ATPase activity (NKA), a reduction of erythrocyte membrane fluidity, a reduction of phospatydyl serine exposition on erythrocyte membranes, an alteration in erythrocyte fatty acid membrane profile (increase in MUFA and in ω6/ω3 ratio due to decrease in EPA and DHA) and a reduction of cholesterol content of erythrocyte membrane were found in Au compared to TD, without change in erythrocyte membrane sialic acid content and in lymphocyte membrane fluidity. Some Au clinical features appear to be correlated with these findings; in particular, hyperactivity score appears to be related with some parameters of the lipidomic profile and membrane fluidity, and ADOS and CARS score are inversely related to peroxiredoxin II levels. Oxidative stress and erythrocyte structural and functional alterations may play a role in the pathogenesis of Autism Spectrum Disorders and could be potentially utilized as peripheral biomarkers.

Pathophysiology of bile acid aspiration in lung transplant recipients

Duodeno-gastroesophageal reflux aspiration is associated with chronic lung allograft dysfunction (CLAD) and aspiration of bile acids (BA), functional molecules in the gastro-intestinal tract with emulsifying properties. While links between reflux aspiration to lung disease have been identified, the relevance of bile acid as molecular ligands and outcome predictors is poorly defined. We sought to determine and quantify the various BA species in airways of the lung transplant recipients to better understand the various effects of aspirated BA that contribute to post-transplantation outcomes and to investigate their molecular effects on airway function and contractility.