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.

Non linear application of an in-house finite elements software

Questa tesi si pone come obiettivo l'analisi delle componenti di sollecitazione statica di un serbatoio, in acciaio API 5L X52, sottoposto a carichi di flessione e pressione interna attraverso il programma agli elementi finiti PLCd4, sviluppato presso l'International Center for Numerical Methods in Engineering (CIMNE - Barcelona). Questo tipo di analisi rientra nel progetto europeo ULCF, il cui traguardo è lo studio della fatica a bassissimo numero di cicli per strutture in acciaio. Prima di osservare la struttura completa del serbatoio è stato studiato il comportamento del materiale per implementare all'interno del programma una nuova tipologia di curva che rappresentasse al meglio l'andamento delle tensioni interne. Attraverso il lavoro di preparazione alla tesi è stato inserito all'interno del programma un algoritmo per la distribuzione delle pressioni superficiali sui corpi 3D, successivamente utilizzato per l'analisi della pressione interna nel serbatoio. Sono state effettuate analisi FEM del serbatoio in diverse configurazioni di carico ove si è cercato di modellare al meglio la struttura portante relativa al caso reale di "full scale test". Dal punto di vista analitico i risultati ottenuti sono soddisfacenti in quanto rispecchiano un corretto comportamento del serbatoio in condizioni di pressioni molto elevate e confermano la bontà del programma nell'analisi computazionale.

Study of the mechanisms of shear transfer in fiber-reinforced concrete elements

matlab functions for the validation of push-off tests results

The construction of TRIGA-TRAP and direct high-precision Penning trap mass measurements on rare-earth elements and americium

Nuclear masses are an important quantity to study nuclear structure since they reflect the sum of all nucleonic interactions. Many experimental possibilities exist to precisely measure masses, out of which the Penning trap is the tool to reach the highest precision. Moreover, absolute mass measurements can be performed using carbon, the atomic-mass standard, as a reference. The new double-Penning trap mass spectrometer TRIGA-TRAP has been installed and commissioned within this thesis work, which is the very first experimental setup of this kind located at a nuclear reactor. New technical developments have been carried out such as a reliable non-resonant laser ablation ion source for the production of carbon cluster ions and are still continued, like a non-destructive ion detection technique for single-ion measurements. Neutron-rich fission products will be available by the reactor that are important for nuclear astrophysics, especially the r-process. Prior to the on-line coupling to the reactor, TRIGA-TRAP already performed off-line mass measurements on stable and long-lived isotopes and will continue this program. The main focus within this thesis was on certain rare-earth nuclides in the well-established region of deformation around N~90. Another field of interest are mass measurements on actinoids to test mass models and to provide direct links to the mass standard. Within this thesis, the mass of 241-Am could be measured directly for the first time.

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).

Hadronic matrix elements in lattice QCD

The lattice formulation of Quantum ChromoDynamics (QCD) has become a reliable tool providing an ab initio calculation of low-energy quantities. Despite numerous successes, systematic uncertainties, such as discretisation effects, finite-size effects, and contaminations from excited states, are inherent in any lattice calculation. Simulations with controlled systematic uncertainties and close to the physical pion mass have become state-of-the-art. We present such a calculation for various hadronic matrix elements using non-perturbatively O(a)-improved Wilson fermions with two dynamical light quark flavours. The main topics covered in this thesis are the axial charge of the nucleon, the electro-magnetic form factors of the nucleon, and the leading hadronic contributions to the anomalous magnetic moment of the muon. Lattice simulations typically tend to underestimate the axial charge of the nucleon by 5 − 10%. We show that including excited state contaminations using the summed operator insertion method leads to agreement with the experimentally determined value. Further studies of systematic uncertainties reveal only small discretisation effects. For the electro-magnetic form factors of the nucleon, we see a similar contamination from excited states as for the axial charge. The electro-magnetic radii, extracted from a dipole fit to the momentum dependence of the form factors, show no indication of finite-size or cutoff effects. If we include excited states using the summed operator insertion method, we achieve better agreement with the radii from phenomenology. The anomalous magnetic moment of the muon can be measured and predicted to very high precision. The theoretical prediction of the anomalous magnetic moment receives contribution from strong, weak, and electro-magnetic interactions, where the hadronic contributions dominate the uncertainties. A persistent 3σ tension between the experimental determination and the theoretical calculation is found, which is considered to be an indication for physics beyond the Standard Model. We present a calculation of the connected part of the hadronic vacuum polarisation using lattice QCD. Partially twisted boundary conditions lead to a significant improvement of the vacuum polarisation in the region of small momentum transfer, which is crucial in the extraction of the hadronic vacuum polarisation.

Interaction between axial force, shear and bending moment in reinforced concrete elements

Il collasso di diverse colonne, caratterizzate da danneggiamenti simili, quali ampie fessure fortemente inclinate ad entrambe le estremità dell’elemento, lo schiacciamento del calcestruzzo e l’instabilità dei ferri longitudinali, ha portato ad interrogarsi riguardo gli effetti dell’interazione tra lo sforzo normale, il taglio ed il momento flettente. Lo studio è iniziato con una ricerca bibliografica che ha evidenziato una sostanziale carenza nella trattazione dell’argomento. Il problema è stato approcciato attraverso una ricerca di formule della scienza delle costruzioni, allo scopo di mettere in relazione lo sforzo assiale, il taglio ed il momento; la ricerca si è principalmente concentrata sulla teoria di Mohr. In un primo momento è stata considerata l’interazione tra solo due componenti di sollecitazione: sforzo assiale e taglio. L’analisi ha condotto alla costruzione di un dominio elastico di taglio e sforzo assiale che, confrontato con il dominio della Modified Compression Field Theory, trovata tramite ricerca bibliografica, ha permesso di concludere che i risultati sono assolutamente paragonabili. L’analisi si è poi orientata verso l’interazione tra sforzo assiale, taglio e momento flettente. Imponendo due criteri di rottura, il raggiungimento della resistenza a trazione ed a compressione del calcestruzzo, inserendo le componenti di sollecitazione tramite le formule di Navier e Jourawsky, sono state definite due formule che mettono in relazione le tre azioni e che, implementate nel software Matlab, hanno permesso la costruzione di un dominio tridimensionale. In questo caso non è stato possibile confrontare i risultati, non avendo la ricerca bibliografica mostrato niente di paragonabile. Lo studio si è poi concentrato sullo sviluppo di una procedura che tenta di analizzare il comportamento di una sezione sottoposta a sforzo normale, taglio e momento: è stato sviluppato un modello a fibre della sezione nel tentativo di condurre un calcolo non lineare, corrispondente ad una sequenza di analisi lineari. La procedura è stata applicata a casi reali di crollo, confermando l’avvenimento dei collassi.