Studio molecolare dei meccanismi dell'autoincompatibilità gametofitica in pero europeo (Pyrus communis)

Self-incompatibility (SI) systems have evolved in many flowering plants to prevent self-fertilization and thus promote outbreeding. Pear and apple, as many of the species belonging to the Rosaceae, exhibit RNase-mediated gametophytic self-incompatibility, a widespread system carried also by the Solanaceae and Plantaginaceae. Pear orchards must for this reason contain at least two different cultivars that pollenize each other; to guarantee an efficient cross-pollination, they should have overlapping flowering periods and must be genetically compatible. This compatibility is determined by the S-locus, containing at least two genes encoding for a female (pistil) and a male (pollen) determinant. The female determinant in the Rosaceae, Solanaceae and Plantaginaceae system is a stylar glycoprotein with ribonuclease activity (S-RNase), that acts as a specific cytotoxin in incompatible pollen tubes degrading cellular RNAs. Since its identification, the S-RNase gene has been intensively studied and the sequences of a large number of alleles are available in online databases. On the contrary, the male determinant has been only recently identified as a pollen-expressed protein containing a F-box motif, called S-Locus F-box (abbreviated SLF or SFB). Since F-box proteins are best known for their participation to the SCF (Skp1 - Cullin - F-box) E3 ubiquitine ligase enzymatic complex, that is involved in protein degradation through the 26S proteasome pathway, the male determinant is supposed to act mediating the ubiquitination of the S-RNases, targeting them for the degradation in compatible pollen tubes. Attempts to clone SLF/SFB genes in the Pyrinae produced no results until very recently; in apple, the use of genomic libraries allowed the detection of two F-box genes linked to each S haplotype, called SFBB (S-locus F-Box Brothers). In Japanese pear, three SFBB genes linked to each haplotype were cloned from pollen cDNA. The SFBB genes exhibit S haplotype-specific sequence divergence and pollen-specific expression; their multiplicity is a feature whose interpretation is unclear: it has been hypothesized that all of them participate in the S-specific interaction with the RNase, but it is also possible that only one of them is involved in this function. Moreover, even if the S locus male and female determinants are the only responsible for the specificity of the pollen-pistil recognition, many other factors are supposed to play a role in GSI; these are not linked to the S locus and act in a S-haplotype independent manner. They can have a function in regulating the expression of S determinants (group 1 factors), modulating their activity (group 2) or acting downstream, in the accomplishment of the reaction of acceptance or rejection of the pollen tube (group 3). This study was aimed to the elucidation of the molecular mechanism of GSI in European pear (Pyrus communis) as well as in the other Pyrinae; it was divided in two parts, the first focusing on the characterization of male determinants, and the second on factors external to the S locus. The research of S locus F-box genes was primarily aimed to the identification of such genes in European pear, for which sequence data are still not available; moreover, it allowed also to investigate about the S locus structure in the Pyrinae. The analysis was carried out on a pool of varieties of the three species Pyrus communis (European pear), Pyrus pyrifolia (Japanese pear), and Malus × domestica (apple); varieties carrying S haplotypes whose RNases are highly similar were chosen, in order to check whether or not the same level of similarity is maintained also between the male determinants. A total of 82 sequences was obtained, 47 of which represent the first S-locus F-box genes sequenced from European pear. The sequence data strongly support the hypothesis that the S locus structure is conserved among the three species, and presumably among all the Pyrinae; at least five genes have homologs in the analysed S haplotypes, but the number of F-box genes surrounding the S-RNase could be even greater. The high level of sequence divergence and the similarity between alleles linked to highly conserved RNases, suggest a shared ancestral polymorphism also for the F-box genes. The F-box genes identified in European pear were mapped on a segregating population of 91 individuals from the cross 'Abbé Fétel' × 'Max Red Bartlett'. All the genes were placed on the linkage group 17, where the S locus has been placed both in pear and apple maps, and resulted strongly associated to the S-RNase gene. The linkage with the RNase was perfect for some of the F-box genes, while for others very rare single recombination events were identified. The second part of this study was focused on the research of other genes involved in the SI response in pear; it was aimed on one side to the identification of genes differentially expressed in compatible and incompatible crosses, and on the other to the cloning and characterization of the transglutaminase (TGase) gene, whose role may be crucial in pollen rejection. For the identification of differentially expressed genes, controlled pollinations were carried out in four combinations (self pollination, incompatible, half-compatible and fully compatible cross-pollination); expression profiles were compared through cDNA-AFLP. 28 fragments displaying an expression pattern related to compatibility or incompatibility were identified, cloned and sequenced; the sequence analysis allowed to assign a putative annotation to a part of them. The identified genes are involved in very different cellular processes or in defense mechanisms, suggesting a very complex change in gene expression following the pollen/pistil recognition. The pool of genes identified with this technique offers a good basis for further study toward a better understanding of how the SI response is carried out. Among the factors involved in SI response, moreover, an important role may be played by transglutaminase (TGase), an enzyme involved both in post-translational protein modification and in protein cross-linking. The TGase activity detected in pear styles was significantly higher when pollinated in incompatible combinations than in compatible ones, suggesting a role of this enzyme in the abnormal cytoskeletal reorganization observed during pollen rejection reaction. The aim of this part of the work was thus to identify and clone the pear TGase gene; the PCR amplification of fragments of this gene was achieved using primers realized on the alignment between the Arabidopsis TGase gene sequence and several apple EST fragments; the full-length coding sequence of the pear TGase gene was then cloned from cDNA, and provided a precious tool for further study of the in vitro and in vivo action of this enzyme.

Role of SP-A gene polymorphism in lung transplantation

Lung transplantation is a widely accepted therapeutic option for end stage lung disease. Clinical outcome is yet challenged by primary graft failure responsible for the majority of the early mortality, by chronic allograft dysfunction and chronic rejection accounting for more than 30% of deaths after the third postoperative year. Pulmonary surfactant proteins (SP) A, B, C and D are one of the first host defense mechanisms the lung can mount. SP-A in particular, produced by the type II pneumocytes, is active in the innate and adaptive immune system being an opsonin, but also regulating the macrophage and lymphocyte response. The main hypothesis for this project is that pulmonary surfactant protein A polymorphism may determine the early and long term lung allograft survival. Of note SP-A biologic activity seems to be genetically determined and SP-A polymorphisms have been associated to various lung disease. The two SP-A genes SP-A1 and SP-A2 have several polymorphisms within the coding region, SP-A1 (6A, 6A2-20), and SP-A2(1A, 1A0-13). The SP-A gene expression is regulated by cAMP, TTF-1 and glucocorticoids. In vitro studies have indicated that SP-A1 and SP-A2 gene variants may have a variable response to glucocorticoids. We proposed to determine if SP-A gene polymorphism predicts primary graft dysfunction and/or chronic lung allograft dysfunction and if SP-A may serve as a biomarker of lung allograft dysfunction. We also proposed to study the interaction between immunosuppressive drugs and SP-A expression and determine whether this is dependent on SP-A polymorphisms. This study will generate novel information improving our understanding of lung allograft dysfunction. It is conceivable that the information will stimulate the interest for a multi centre study to investigate if SP-A polymorphism may be integrated in the donor lung selection criteria and/or to implement post transplant tailored immunosuppression.

A multi-methodological approach for the study of polymorphism in organic pigments and pharmaceuticals

The study of polymorphism has an important role in several fields of materials science, because structural differences lead to different physico-chemical properties of the system. This PhD work was dedicated to the investigation of polymorphism in Indigo, Thioindigo and Quinacridone, as case studies among the organic pigments employed as semiconductors, and in Paracetamol, Phenytoin and Nabumetone, chosen among some commonly used API. The aim of the research was to improve the understanding on the structures of bulk crystals and thin films, adopting Raman spectroscopy as the method of choice, while resorting to other experimental techniques to complement the gathered information. Different crystalline polymorphs, in fact, may be conveniently distinguished by their Raman spectra in the region of the lattice phonons (10-150 cm-1), the frequencies of which, probing the inter-molecular interactions, are very sensitive to even slight modifications in the molecular packing. In particular, we have used Confocal Raman Microscopy, which is a powerful, yet simple, technique for the investigation of crystal polymorphism in organic and inorganic materials, being capable of monitoring physical modifications, chemical transformations and phase inhomogeneities in crystal domains at the micrometre scale. In this way, we have investigated bulk crystals and thin film samples obtained with a variety of crystal growth and deposition techniques. Pure polymorphs and samples with phase mixing were found and fully characterized. Raman spectroscopy was complemented mainly by XRD measurements for bulk crystals and by AFM, GIXD and TEM for thin films. Structures and phonons of the investigated polymorphs were computed by DFT methods, and the comparison between theoretical and experimental results was used to assess the relative stability of the polymorphs and to assist the spectroscopic investigation. The Raman measurements were thus found to be able to clarify ambiguities in the phase assignments which otherwise the other methods were unable to solve.

Spectroscopic investigation on photoreactivity, structure and polymorphism of organic molecular crystals

The study of the spectroscopic phenomena in organic solids, in combination with other techniques, is an effective tool for the understanding of the structural properties of materials based on these compounds. This Ph.D. work was dedicated to the spectroscopic investigation of some relevant processes occurring in organic molecular crystals, with the goal of expanding the knowledge on the relationship between structure, dynamics and photoreactivity of these systems. Vibrational spectroscopy has been the technique of choice, always in combination with X-ray diffraction structural studies and often the support of computational methods. The vibrational study of the molecular solid state reaches its full potential when it includes the low-wavenumber region of the lattice-phonon modes, which probe the weak intermolecular interactions and are the fingerprints of the lattice itself. Microscopy is an invaluable addition in the investigation of processes that take place in the micro-meter scale of the crystal micro-domains. In chemical and phase transitions, as well as in polymorph screening and identification, the combination of Raman microscopy and lattice-phonon detection has provided useful information. Research on the fascinating class of single-crystal-to-single-crystal photoreactions, has shown how the homogeneous mechanism of these transformations can be identified by lattice-phonon microscopy, in agreement with the continuous evolution of their XRD patterns. On describing the behavior of the photodimerization mechanism of vitamin K3, the focus was instead on the influence of its polymorphism in governing the product isomerism. Polymorphism is the additional degree of freedom of molecular functional materials, and by advancing in its control and properties, functionalities can be promoted for useful applications. Its investigation focused on thin-film phases, widely employed in organic electronics. The ambiguities in phase identification often emerging by other experimental methods were successfully solved by vibrational measurements.