B-type cytochromes of the DOMON domain superfamily (Novel redox elements of plant plasma membrane)

The aim of the present study is understanding the properties of a new group of redox proteins having in common a DOMON-type domain with characteristics of cytochromes b. The superfamily of proteins containing a DOMON of this type includes a few protein families. With the aim of better characterizing this new protein family, the present work addresses both a CyDOM protein (a cytochrome b561) and a protein only comprised of DOMON(AIR12), both of plant origin. Apoplastic ascorbate can be regenerated from monodehydroascorbate by a trans-plasma membrane redox system which uses cytosolic ascorbate as a reductant and comprises a high potential cytochrome b. We identified the major plasma membrane (PM) ascorbate-reducible b-type cytochrome of bean (Phaseolus vulgaris) and soybean (Glycine max) hypocotyls as orthologs of Arabidopsis auxin-responsive gene air12. The protein, which is glycosylated and glycosylphosphatidylinositol-anchored to the external side of the PM in vivo, was expressed in Pichia pastoris in a recombinant form, lacking the glycosylphosphatidylinositol-modification signal, and purified from the culture medium. Recombinant AIR12 is a soluble protein predicted to fold into a β-sandwich domain and belonging to the DOMON superfamily. It is shown to be a b-type cytochrome with a symmetrical α-band at 561 nm, to be fully reduced by ascorbate and fully oxidized by monodehydroascorbate. Redox potentiometry suggests that AIR12 binds two high-potential hemes (Em,7 +135 and +236 mV). Phylogenetic analyses reveal that the auxin-responsive genes AIR12 constitute a new family of plasma membrane b-type cytochromes specific to flowering plants. Although AIR12 is one of the few redox proteins of the PM characterized to date, the role of AIR12 in trans-PM electron transfer would imply interaction with other partners which are still to be identified. Another part of the present project was aimed at understanding of a soybean protein comprised of a DOMON fused with a well-defined b561 cytochrome domain (CyDOM). Various bioinformatic approaches show this protein to be composed of an N-terminal DOMON followed by b561 domain. The latter contains five transmembrane helices featuring highly conserved histidines, which might bind haem groups. The CyDOM has been cloned and expressed in the yeast Pichia pastoris, and spectroscopic analyses have been accomplished on solubilized yeast membranes. CyDOM clearly reveal the properties of b-type cytochrome. The results highlight the fact that CyDOM is clearly able to lead an electron flux through the plasmamembrane. Voltage clamp experiments demonstrate that Xenopus laevis oocytes transformed with CyDOM of soybean exhibit negative electrical currents in presence of an external electron acceptor. Analogous investigations were carried out with SDR2, a CyDOM of Drosophila melanogaster which shows an electron transport capacity even higher than plant CyDOM. As quoted above, these data reinforce those obtained in plant CyDOM on the one hand, and on the other hand allow to attribute to SDR2-like proteins the properties assigned to CyDOM. Was expressed in Regenerated tobacco roots, transiently transformed with infected a with chimeral construct GFP: CyDOM (by A. rhizogenes infection) reveals a plasmamembrane localization of CyDOM both in epidermal cells of the elongation zone of roots and in root hairs. In conclusion. Although the data presented here await to be expanded and in part clarified, it is safe to say they open a new perspective about the role of this group of proteins. The biological relevance of the functional and physiological implications of DOMON redox domains seems noteworthy, and it can but increase with future advances in research. Beyond the very finding, however interesting in itself, of DOMON domains as extracellular cytochromes, the present study testifies to the fact that cytochrome proteins containing DOMON domains of the type of “CyDOM” can transfer electrons through membranes and may represent the most important redox component of the plasmamembrane as yet discovered.

A novel phase variation mechanism in the meningococcus driven by a ligand-responsive repressor and differential spacing of distal promoter elements

Phase variable expression, mediated by high frequency reversible changes in the length of simple sequence repeats, facilitates adaptation of bacterial populations to changing environments and is frequently important in bacterial virulence. Here we elucidate a novel phase variable mechanism for NadA expression, an adhesin and invasin of Neisseria meningitidis. The NadR repressor protein binds to operators flanking the phase variable tract of the nadA promoter gene and contributes to the differential expression levels of phase variant promoters with different numbers of repeats, likely due to different spacing between operators. It is shown that IHF binds between these operators, and may permit looping of the promoter, allowing interaction of NadR at operators located distally or overlapping the promoter. The 4-hydroxyphenylacetic acid, a metabolite of aromatic amino acid catabolism that is secreted in saliva, induces nadA expression by inhibiting the DNA binding activity of the NadR repressor. When induced, only minor differences are evident between NadR-independent transcription levels of promoter phase variants, which are likely due to differential RNA polymerase contacts leading to altered promoter activity. These results suggest that NadA expression is under both stochastic and tight environmental-sensing regulatory control, and both regulations are mediated by the NadR repressor that and may be induced during colonization of the oropharynx where it plays a major role in the successful adhesion and invasion of the mucosa. Hence, simple sequence repeats in promoter regions may be a strategy used by host-adapted bacterial pathogens to randomly switch between expression states that may nonetheless still be induced by appropriate niche-specific signals.

Transposable elements: structure and dynamic of the autonomous retrotransposon R2 in Arthropoda with non-canonical reproduction

Eukaryotic ribosomal DNA constitutes a multi gene family organized in a cluster called nucleolar organizer region (NOR); this region is composed usually by hundreds to thousands of tandemly repeated units. Ribosomal genes, being repeated sequences, evolve following the typical pattern of concerted evolution. The autonomous retroelement R2 inserts in the ribosomal gene 28S, leading to defective 28S rDNA genes. R2 element, being a retrotransposon, performs its activity in the genome multiplying its copy number through a “copy and paste” mechanism called target primed reverse transcription. It consists in the retrotranscription of the element’s mRNA into DNA, then the DNA is integrated in the target site. Since the retrotranscription can be interrupted, but the integration will be carried out anyway, truncated copies of the element will also be present in the genome. The study of these truncated variants is a tool to examine the activity of the element. R2 phylogeny appears, in general, not consistent with that of its hosts, except some cases (e.g. Drosophila spp. and Reticulitermes spp.); moreover R2 is absent in some species (Fugu rubripes, human, mouse, etc.), while other species have more R2 lineages in their genome (the turtle Mauremys reevesii, the Japanese beetle Popilia japonica, etc). R2 elements here presented are isolated in 4 species of notostracan branchiopods and in two species of stick insects, whose reproductive strategies range from strict gonochorism to unisexuality. From sequencing data emerges that in Triops cancriformis (Spanish gonochoric population), in Lepidurus arcticus (two putatively unisexual populations from Iceland) and in Bacillus rossius (gonochoric population from Capalbio) the R2 elements are complete and encode functional proteins, reflecting the general features of this family of transposable elements. On the other hand, R2 from Italian and Austrian populations of T. cancriformis (respectively unisexual and hermaphroditic), Lepidurus lubbocki (two elements within the same Italian population, gonochoric but with unfunctional males) and Bacillus grandii grandii (gonochoric population from Ponte Manghisi) have sequences that encode incomplete or non-functional proteins in which it is possible to recognize only part of the characteristic domains. In Lepidurus couesii (Italian gonochoric populations) different elements were found as in L. lubbocki, and the sequencing is still in progress. Two hypothesis are given to explain the inconsistency of R2/host phylogeny: vertical inheritance of the element followed by extinction/diversification or horizontal transmission. My data support previous study that state the vertical transmission as the most likely explanation; nevertheless horizontal transfer events can’t be excluded. I also studied the element’s activity in Spanish populations of T. cancriformis, in L. lubbocki, in L. arcticus and in gonochoric and parthenogenetic populations of B. rossius. In gonochoric populations of T. cancriformis and B. rossius I found that each individual has its own private set of truncated variants. The situation is the opposite for the remaining hermaphroditic/parthenogenetic species and populations, all individuals sharing – in the so far analyzed samples - the majority of variants. This situation is very interesting, because it isn’t concordant with the Muller’s ratchet theory that hypothesizes the parthenogenetic populations being either devoided of transposable elements or TEs overloaded. My data suggest a possible epigenetic mechanism that can block the retrotransposon activity, and in this way deleterious mutations don’t accumulate.

Il "caso" Maroncelli. Organizzazione del consenso e vincoli massonici nell'Italia radicale e nella New York della Tammany Hall, 1840-1890

Questa tesi parte da un evento “minore” della storia del XIX secolo per tendere, poi, ad alcuni obiettivi particolari. L’evento è costituito da uno strano funerale postumo, quello di Piero Maroncelli, carbonaro finito alla Spielberg, graziato, poi emigrato in Francia e in America, il cui corpo viene sepolto a New York nell’estate del 1846. Quarant’anni dopo, nel 1886, i resti di Maroncelli vengono esumati e – attraverso una “trafila” particolare, di cui è protagonista la Massoneria, da una sponda all’altra dell’Atlantico – solennemente trasferiti nella città natale di Forlì, dove vengono collocati nel pantheon del cimitero monumentale, inaugurato per l’occasione. Gli eventi celebrativi che si consumano a New York e a Forlì sono molto diversi fra loro, anche se avvengono quasi in contemporanea e sotto regie politiche ispirate dal medesimo radicalismo anticlericale. E’ chiaro che Maroncelli è un simbolo e un pretesto: simbolo di un’italianità transnazionale, composta di un “corpo” in transito, fuori dello spazio nazionale, ma appartenente alla patria (quella grande e quella piccola); pretesto per acquisire e rafforzare legami politici, mercè mobilitazioni di massa in un caso fondate sul festival, sulla festa en plein air, nell’altro sui rituali del cordoglio per i “martiri” dell’indipendenza. L’opportunità di comparare questi due contesti – l’Italia, colta nella sua periferia radicale e la New York della Tammany Hall -, non sulla base di ipotesi astratte, ma nella concretezza di un “caso di studio” reale e simultaneo, consente di riflettere sulla pervasività dell’ideologia democratica nella sua accezione ottocentesca, standardizzata dalla Massoneria, e, d’altro canto, sui riti del consenso, colti nelle rispettive tipicità locali. Un gioco di similitudini e di dissomiglianze, quindi. Circa gli obiettivi particolari – al di là della ricostruzione del “caso” Maroncelli -, ho cercato di sondare alcuni temi, proponendone una ricostruzione in primo luogo storiografica. Da un lato, il tema dell’esilio e del trapianto delle esperienze di vita e di relazione al di fuori del proprio contesto d’origine. Maroncelli utilizza, come strumento di identitario e di accreditamento, il fourierismo; la generazione appena successiva alla sua, grazie alla Giovine Italia, possiede già un codice interno, autoctono, cui fare riferimento; alla metà degli anni Cinquanta, ad esso si affiancherà, con successo crescente, la lettura “diplomatica” di ascendenza sabauda. Dall’altro, ho riflettuto sull’aspetto legato ai funerali politici, al cordoglio pubblico, al trasferimento postumo dei corpi. La letteratura disponibile, al riguardo, è assai ricca, e tale da consentire una precisa classificazione del “caso” Maroncelli all’interno di una tipologia della morte laica, ben delineata nell’Italia dell’Ottocento e del primo Novecento. E poi, ancora, ho preso in esame le dinamiche “festive” e di massa, approfondendo quelle legate al mondo dell’emigrazione italiana a Mew York, così distante nel 1886 dall’élite colta di quarant’anni prima, eppure così centrale per il controllo politico della città. Dinamiche alle quali fa da contrappunto, sul versante forlivese, la visione del mondo radicale e massonico locale, dominato dalla figura di Aurelio Saffi e dal suo tentativo di plasmare un’immagine morale e patriottica della città da lasciare ai posteri. Quasi un’ossessione, per il vecchio triumviro della Repubblica romana (morirà nel 1890), che interviene sulla toponomastica, sull’edilizia cemeteriale, sui pantheon civico, sui “ricordi” patriottici. Ho utilizzato fonti secondarie e di prima mano. Anche sulle prime, quantitativamente assai significative, mi sono misurata con un lavoro di composizione e di lettura comparata prima mai tentato. La giustapposizione di chiavi di lettura apparentemente distanti, ma giustificate dalla natura proteiforme e complicata del nostro “caso”, apre, a mio giudizio, interessanti prospettive di ricerca. Circa le fonti di prima mano, ho attinto ai fondi disponibili su Maroncelli presso la Biblioteca comunale di Forlì, alle raccolte del Grande Oriente d’Italia a Roma, a periodici italoamericani assai rari, sparsi in diverse biblioteche italiane, da Milano a Roma. Mi rendo conto che la quantità dei materiali reperiti, sovente molto eterogenei, avrebbero imposto una lettura delle fonti più accurata di quella che, in questa fase della ricerca, sono riuscita a condurre. E’ vero, però, che le suggestioni già recuperabili ad un’analisi mirata al contenuto principale – le feste, la propaganda, il cordoglio – consentono la tessitura di una narrazione non forzata, nella quale il ricordo della Repubblica romana viaggia da una sponda all’altra dell’Atlantica, insieme ai resti di Maroncelli; nella quale il rituale massonico funge da facilitatore e da “mediatore culturale”; nella quale, infine, il linguaggio patriottico e la koinè democratica trans-nazionale riescono incredibilmente a produrre o a incarnare identità. Per quanto tempo? La risposta, nel caso forlivese, è relativamente facile; in quello della “colonia” italiana di New York, presto alterata nella sua connotazione demografica dalla grande emigrazione transoceanica, le cose appaiono più complesse. E, tuttavia, nel 1911, cinquantesimo dell’Unità, qualcuno, nella grande metropoli americana, si sarebbe ricordato di Maroncelli, sia pure in un contesto e con finalità del tutto diverse rispetto al 1886: segno che qualcosa, sotto traccia, era sopravvissuto.

I progetti di Oswald Mathias Ungers per la città di Treviri. Questioni di composizione architettonica

Abstract This PhD thesis focuses on two projects carried out by Oswald Mathias Ungers in the city of Trier. More specifi cally, this study focuses on the relationship between composition principles, architectural forms, historical context and the nature of the city where these buildings have been built. The works carried out by Ungers in Trier are unique experiences - if taken in this master’s works context - and each one of them refl ects - in its specifi c project and architectural composition theme - the results - in terms of design - of a complex research on the fundamentals of architecture carried out by Ungers in more than fi ve decades of his activity. The theoretical and compositional experiment aspect is one of the main subjects to defi ne these buildings in terms of architecture. This aspect is so crucial that it is possible to consider them as an example of radical and specifi c experiences, referred to a specifi c place and based on a specifi c theoretical corpus. More specifi cally, this study focuses on the design activity carried out by Ungers in this city, mainly between the 80s and 90s and in the fi rst decade of the 21st century. It puts forward an interpretation that does not only defi ne the essential features, elements and questions lying behind these two architectures, but fi rst and foremost analyzes the theoretical, methodological and compositional relationship between Ungers and Trier, his adopted city. An increasingly closer relationship between the architect and his city highlights the wider relationship network established between the place and the projects carried out by Ungers in this city and makes it possible to understand the importance of Trier in the work of this architect, in his education and in his way to see, think and make architecture. The projects analyzed - the Thermen am Forum Museum (1988-1996) and the Kaiserthermen entrance hall (2003-2007) - were analyzed in terms of their architectural composition in an attempt to highlight the poetry of these architectures and to fi nd out their progressive, rational - and therefore transmissible - character. This study is an attempt to assess and unveil the compositional themes characterizing these projects while detecting the compositional principles lying behind the works and verifying the design process through which such principles were translated into architecture. Looking at these works as architectural composition examples makes it possible to clarify Ungers’ hermeneutic relationship established with the city’s history and structure. More specifi cally, the main subject of this thesis is the relationship between the architect, his city and history in the architectural solutions offered by two exemplary case studies, which were both built and placed in the historical city center of Trier and both connected with the ancient core of the city. The Thermen am Forum Museum and the Kaiserthermen entrance hall projects are - though being developed at different times of Ungers’ architectural life and though being extremely different in terms of approach to their context, due to their architectural image - two works that can be compared with the historical heritage of the city and this makes them ideal examples of the relationship between architectural forms, history and environment.

Transposable elements dynamics in taxa with different reproductive strategies or speciation rate

In recent years the advances in genomics allowed to understand the importance of Transposable Elements (TE) in the evolution of eukaryotic genomes. In this thesis I face two aspects of the TE impact on the in the animal kingdom. The first part is a comparison of the dynamics of the TE dynamics in three species of stick-insects of the Genus Bacillus. I produced three random genomic libraries of 200 Kbps for the three parental species of the taxon: a gonochoric population of Bacillus rossius (facultative parthenogenetic), Bacillus grandii (gonochoric) and Bacillus atticus (obligate parthenogenetic). The unisexual taxon Bacillus atticus does not shows dramatic differences in TE total content and activity with respect to Bacillus grandii and Bacillus rossius. This datum does not confirm the trend observed in other animal models in which unisexual taxa tend to repress the activity of TE to escape the extinction by accumulation of harmful mutations. In the second part I tried to add a contribute to the debate initiated in recent years about the possibility that a high TE content is linked to a high rate of speciation. I designed an evolutionary framework to establish the different rate of speciation among two or more taxa, then I compared TE dynamics considering the different rates of speciation. The species dataset comprises: 29 mammals, four birds, two fish and two insects. On the whole the majority of comparisons confirms the expected trend. In particular the amount of species analyzed in Mammalia allowed me to get a statistical support (p<0,05) of the fact that the TE activity of recently mobilized elements is positively related with the rate of speciation.

The effect of two-dimensional squat elements on the seismic behavior of building structures

This thesis reports a study on the seismic response of two-dimensional squat elements and their effect on the behavior of building structures. Part A is devoted to the study of unreinforced masonry infills, while part B is focused on reinforced concrete sandwich walls. Part A begins with a comprehensive review of modelling techniques and code provisions for infilled frame structures. Then state-of-the practice techniques are applied for a real case to test the ability of actual modeling techniques to reproduce observed behaviors. The first developments towards a seismic-resistant masonry infill system are presented. Preliminary design recommendations for the seismic design of the seismic-resistant masonry infill are finally provided. Part B is focused on the seismic behavior of a specific reinforced concrete sandwich panel system. First, the results of in-plane psuudostatic cyclic tests are described. Refinements to the conventional modified compression field theory are introduced in order to better simulate the monotonic envelope of the cyclic response. The refinements deal with the constitutive model for the shotcrete in tension and the embedded bars. Then the hysteretic response of the panels is studied according to a continuum damage model. Damage state limits are identified. Design recommendations for the seismic design of the studied reinforced concrete sandwich walls are finally provided.

Salinity Effect on Horticultural Crops: Morphological, Physiological, and Biomolecular Elements of Salinity Stress Response

Among abiotic stresses, high salinity stress is the most severe environmental stress. High salinity exerts its negative impact mainly by disrupting the ionic and osmotic equilibrium of the cell. In saline soils, high levels of sodium ions lead to plant growth inhibition and even death. Salt tolerance in plants is a multifarious phenomenon involving a variety of changes at molecular, organelle, cellular, tissue as well as whole plant level. In addition, salt tolerant plants show a range of adaptations not only in morphological or structural features but also in metabolic and physiological processes that enable them to survive under extreme saline environments. The main objectives of my dissertation were understanding the main physiological and biomolecular features of plant responses to salinity in different genotypes of horticultural crops that are belonging to different families Solanaceae (tomato) and Cucurbitaceae (melon) and Brassicaceae (cabbage and radish). Several aspects of crop responses to salinity have been addressed with the final aim of combining elements of functional stress response in plants by using several ways for the assessment of plant stress perception that ranging from destructive measurements (eg. leaf area, relative growth rate, leaf area index, and total plant fresh and dry weight), to physiological determinations (eg. stomatal conductance, leaf gas exchanges, water use efficiency, and leaf water relation), to the determination of metabolite accumulation in plant tissue (eg. Proline and protein) as well as evaluation the role of enzymatic antioxidant capacity assay in scavenging reactive oxygen species that have been generated under salinized condition, and finally assessing the gene induction and up-down regulation upon salinization (eg. SOS pathway).

Ragnar Östberg. Genius loci e memorie urbane. Stockholms Stadshuset-Nämndhuset e villa Geber

La ricerca si propone di analizzare una di quelle stagioni architettoniche controverse e lontane dalle internazionali strade maestre del nascente Neues Bauen: il romanticismo-nazionale svedese riletto attraverso l’esperienza del suo massimo esponente, Ragnar Östberg (1866-1945). L’obiettivo della tesi non è solamente quello di una revisione della critica storiografica, facendo così luce su una di quelle personalità considerate marginali, quanto quello di ricavare dalla lettura comparata di due tra i suoi progetti, fino ad ora mai indagati, quegli elementi che fanno dell’architettura un “fatto urbano” in cui la collettività può riconoscersi e parallelamente un fatto di rappresentazione della stessa. L’arcipelago di Stoccolma e quel processo di “renovatio urbis” a cui fu sottoposta proprio agli albori del XX secolo furono gli scenari in cui presero vita i due progetti: il complesso formato dallo Stockholms Stadshuset e la vicina parte mai realizzata del Nämndhuset, e villa Geber. Condensano due dimensioni che la città immersa nel paesaggio contiene: la natura urbana dell’edificio municipale e quella domestica della villa urbana isolata. La ricerca intesse un itinerario di disvelamento attraverso una matrice duale di lettura: “genius loci” e memorie urbane. I capitoli cercano di dimostrare come i due casi-studio siano espressione di quella pendolarità di ricerca tra lo spirito del luogo e le rimembranze delle forme urbane della tradizione. Questa analisi ci conduce in un viaggio alla ricerca dell’atlante delle “memorie urbane”, raccolte nei viaggi e nella formazione, comprendendo così il mondo analogico di riferimenti culturali con altre architetture europee della tradizione. I due progetti sorgono in opposte aree di espansione di Stoccolma e, pur nella loro diversità di scala, sono chiara espressione di appropriatezza al luogo e di strutture formali analoghe. Stockholm Stadshuset-Nämndhuset e villa Geber esprimono il metodo di Östberg, dove i riferimenti raccolti dall’imagination passive sono tramutati ed assemblati grazie alla imagination active.