Reverse genetic studies of Benyvirus - Polymyxa betae molecular interaction: Role of the RNA4-encoded protein in virus transmission

Beet necrotic yellow vein virus (BNYVV), the leading infectious agent that affects sugar beet, is included within viruses transmitted through the soil from plasmodiophorid as Polymyxa betae. BNYVV is the causal agent of Rhizomania, which induces abnormal rootlet proliferation and is widespread in the sugar beet growing areas in Europe, Asia and America; for review see (Peltier et al., 2008). In this latter continent, Beet soil-borne mosaic virus (BSBMV) has been identified (Lee et al., 2001) and belongs to the benyvirus genus together with BNYVV, both vectored by P. betae. BSBMV is widely distributed only in the United States and it has not been reported yet in others countries. It was first identified in Texas as a sugar beet virus morphologically similar but serologically distinct to BNYVV. Subsequent sequence analysis of BSBMV RNAs evidenced similar genomic organization to that of BNYVV but sufficient molecular differences to distinct BSBMV and BNYVV in two different species (Rush et al., 2003). Benyviruses field isolates usually consist of four RNA species but some BNYVV isolates contain a fifth RNA. RNAs -1 contains a single long ORF encoding polypeptide that shares amino acid homology with known viral RNA-dependent RNA polymerases (RdRp) and helicases. RNAs -2 contains six ORFs: capsid protein (CP), one readthrough protein, triple gene block proteins (TGB) that are required for cell-to-cell virus movement and the sixth 14 kDa ORF is a post-translation gene silencing suppressor. RNAs -3 is involved on disease symptoms and is essential for virus systemic movement. BSBMV RNA-3 can be trans-replicated, trans-encapsidated by the BNYVV helper strain (RNA-1 and -2) (Ratti et al., 2009). BNYVV RNA-4 encoded one 31 kDa protein and is essential for vector interactions and virus transmission by P. betae (Rahim et al., 2007). BNYVV RNA-5 encoded 26 kDa protein that improve virus infections and accumulation in the hosts. We are interest on BSBMV effect on Rhizomania studies using powerful tools as full-length infectious cDNA clones. B-type full-length infectious cDNA clones are available (Quillet et al., 1989) as well as A/P-type RNA-3, -4 and -5 from BNYVV (unpublished). A-type BNYVV full-length clones are also available, but RNA-1 cDNA clone still need to be modified. During the PhD program, we start production of BSBMV full-length cDNA clones and we investigate molecular interactions between plant and Benyviruses exploiting biological, epidemiological and molecular similarities/divergences between BSBMV and BNYVV. During my PhD researchrs we obtained full length infectious cDNA clones of BSBMV RNA-1 and -2 and we demonstrate that they transcripts are replicated and packaged in planta and able to substitute BNYVV RNA-1 or RNA-2 in a chimeric viral progeny (BSBMV RNA-1 + BNYVV RNA-2 or BNYVV RNA-1 + BSBMV RNA-2). During BSBMV full-length cDNA clones production, unexpected 1,730 nts long form of BSBMV RNA-4 has been detected from sugar beet roots grown on BSBMV infected soil. Sequence analysis of the new BSBMV RNA-4 form revealed high identity (~100%) with published version of BSBMV RNA-4 sequence (NC_003508) between nucleotides 1-608 and 1,138-1,730, however the new form shows 528 additionally nucleotides between positions 608-1,138 (FJ424610). Two putative ORFs has been identified, the first one (nucleotides 383 to 1,234), encode a protein with predicted mass of 32 kDa (p32) and the second one (nucleotides 885 to 1,244) express an expected product of 13 kDa (p13). As for BSBMV RNA-3 (Ratti et al., 2009), full-length BSBMV RNA-4 cDNA clone permitted to obtain infectious transcripts that BNYVV viral machinery (Stras12) is able to replicate and to encapsidate in planta. Moreover, we demonstrated that BSBMV RNA-4 can substitute BNYVV RNA-4 for an efficient transmission through the vector P. betae in Beta vulgaris plants, demonstrating a very high correlation between BNYVV and BSBMV. At the same time, using BNYVV helper strain, we studied BSBMV RNA-4’s protein expression in planta. We associated a local necrotic lesions phenotype to the p32 protein expression onto mechanically inoculated C. quinoa. Flag or GFP-tagged sequences of p32 and p13 have been expressed in viral context, using Rep3 replicons, based on BNYVV RNA-3. Western blot analyses of local lesions contents, using FLAG-specific antibody, revealed a high molecular weight protein, which suggest either a strong interaction of BSBMV RNA4’s protein with host protein(s) or post translational modifications. GFP-fusion sequences permitted the subcellular localization of BSBMV RNA4’s proteins. Moreover we demonstrated the absence of self-activation domains on p32 by yeast two hybrid system approaches. We also confirmed that p32 protein is essential for virus transmission by P. betae using BNYVV helper strain and BNYVV RNA-3 and we investigated its role by the use of different deleted forms of p32 protein. Serial mechanical inoculation of wild-type BSBMV on C. quinoa plants were performed every 7 days. Deleted form of BSBMV RNA-4 (1298 bp) appeared after 14 passages and its sequence analysis shows deletion of 433 nucleotides between positions 611 and 1044 of RNA-4 new form. We demonstrated that this deleted form can’t support transmission by P. betae using BNYVV helper strain and BNYVV RNA-3, moreover we confirmed our hypothesis that BSBMV RNA-4 described by Lee et al. (2001) is a deleted form. Interesting after 21 passages we identifed one chimeric form of BSBMV RNA-4 and BSBMV RNA-3 (1146 bp). Two putative ORFs has been identified on its sequence, the first one (nucleotides 383 to 562), encode a protein with predicted mass of 7 kDa (p7), corresponding to the N-terminal of p32 protein encoded by BSBMV RNA-4; the second one (nucleotides 562 to 789) express an expected product of 9 kDa (p9) corresponding to the C-terminal of p29 encoded by BSBMV RNA-3. Results obtained by our research in this topic opened new research lines that our laboratories will develop in a closely future. In particular BSBMV p32 and its mutated forms will be used to identify factors, as host or vector protein(s), involved in the virus transmission through P. betae. The new results could allow selection or production of sugar beet plants able to prevent virus transmission then able to reduce viral inoculum in the soil.

Urban food planning, city logistics and sustainability: the role of the wholesale produce market. The cases of Parma and Bologna food hubs.

At global level, the population is increasingly concentrating in the cities. In Europe, around 75% of the population lives in urban areas and, according to the European Environmental Agency (2010), urban population is foreseen to increase up to 80 % by 2020. At the same time, the quality of life in the cities is declining and urban pollution keeps increasing in terms of carbon dioxide (CO2) emissions, waste, noise, and lack of greenery. Many of European cities struggle to cope with social, economic and environmental problems resulting from pressures such as overcrowding or decline, social inequity, health problems related to food security and pollution. Nowadays local authorities try to solve these problems related to the environmental sustainability through various urban logistics measures, which directly and indirectly affect the urban food supply system, thus an integrated approach including freight transport and food provisioning policies issues is needed. This research centres on the urban food transport system and its impact on the city environmental sustainability. The main question that drives the research analysis is "How the urban food distribution system affects the ecological sustainability in modern cities?" The research analyses the city logistics project for food transport implemented in Parma, Italy, by the wholesale produce market. The case study investigates the renewed role of the wholesale market in the urban food supply chain as commercial and logistic operator, referring to the concept of food hub. Then, a preliminary analysis on the urban food transport for the city of Bologna is presented. The research aims at suggesting a methodological framework to estimate the urban food demand, the urban food supply and to assess the urban food transport performance, in order to identify external costs indicators that help policymakers in evaluating the environmental sustainability of different logistics measures

The role of the West African Monsoon in the tropical to mid-latitudes climate

The interaction between atmosphere–land–ocean–biosphere systems plays a prominent role on the atmospheric dynamics and on the convective rainfall distribution over the West Africa monsoon area during the boreal summer. In particular, the initialization of convective systems in the Sub – Sahelian region has been directly linked to soil moisture heterogeneities identified as the major triggering, development and propagation of convective systems. The present study aims at investigating African monsoon large scale convective dynamics and rainfall diurnal cycle through an exploration of the hypothesis behind the mechanisms of a monsoon phenomenon as an emergence of a collective dynamics of many propagating convective systems. Such hypothesis is based on the existence of an internal self – regulation mechanism among the various components. To achieve these results a multiple analysis was performed based on remote sensed rainfall dataset, and global and regional modelling data for a period of 5 seasons: 2004 - 2008. Satellite rainfall data and convective occurrence variability were studied for assessing typical spatio – temporal signatures and characteristics with an emphasis to the diurnal cycle footprint. A global model and regional model simulation datasets, specifically developed for this analysis and based on Regional Atmospheric Modelling System – RAMS, have been analysed. Results from numerical model datasets highlight the evidence of a synchronization between the destabilization of the convective boundary layer and rainfall occurrence due to the solar radiation forcing through the latent heat release. This supports the conclusion that the studied interacting systems are associated with a process of mutual adjustment of rhythms. Furthermore, this rainfall internal coherence was studied in relation to the West African Heat Low pressure system, which has a prominent role in the large scale summer variability over the Mediterranean area since it is acting as one of dynamic link between sub tropical and midlatitudes variability.

The role of the NadR regulator during infection and its implication for the coverage of a new Meningococcus B vaccine

Background: Neisseria meningitides represents a major cause of meningitis and sepsis. The meningococcal regulator NadR was previously shown to repress the expression of the Neisserial Adhesin A (NadA) and play a major role in its phase-variation. NadA is a surface exposed protein involved in epithelial cell adhesion and colonization and a major component of 4CMenB, a novel vaccine to prevent meningococcus serogroup B infection. The NadR mediated repression of NadA is attenuated by 4-HPA, a natural molecule released in human saliva. Results: In this thesis we investigated the global role of NadR during meningogoccal infection, identifying through microarray analysis the NadR regulon. Two distinct types of NadR targets were identified, differing in their promoter architectures and 4HPA responsive activities: type I are induced, while type II are co-repressed in response to the same 4HPA signal. We then investigate the mechanism of regulation of NadR by 4-HPA, generating NadR mutants and identifying classes or residues involved in either NadR DNA binding or 4HPA responsive activities. Finally, we studied the impact of NadR mediated repression of NadA on the vaccine coverage of 4CMenB. A selected MenB strains is not killed by sera from immunized infants when the strain is grown in vitro, however, in an in vivo passive protection model, the same sera protected infant rats from bacteremia. Finally, using bioluminescent reporters, nadA expression in the infant rat model was induced in vivo at 3 h post-infection. Conclusions: Our results suggest that NadR coordinates a broad transcriptional response to signals present in the human host, enabling the meningococcus to adapt to the relevant host niche. During infectious disease the effect of the same signal on NadR changes between different targets. In particular NadA expression is induced in vivo, leading to efficient killing of meningococcus by anti-NadA antibodies elicited by the 4CMenB vaccine.

Role of the Transcription Factor Sox2 in the Osteogenic Lineage

The Sox2 transcription factor is modified by sumoylation at the K247 position although the addition of SUMO1 and Pias1 promotes the sumoylation of Sox2 at the additional K123 site. The role of sumoylation on Sox2 biological functions was analyzed by comparing the activity of WT and sumoylation mutants on the transcription of the FGF4 gene in HeLa cells and on the downregulation of the Wnt pathwayvin 293T cells. When SUMO1 and PIAS1 promote the sumoylation of WT Sox2, the transcriptional activity of the FGF4 promoter is inhibited showing that Sox2 sumoylation is necessary for the repression function. However, there is no effect of Sox2 sumoylation on β-Catenin activity. Since we were interested in osteoblast differentiation we set up an inducible system for Sox2 in primary osteoblasts. Following Sox2 doxycycline induction, 158 genes were differentially expressed: 120 up-regulated and 38 down-regulated. We annotated as direct Sox2 targets a number of genes involved in osteoblast biology and we further analyzed 3 of them involved in the BMP pathway. The results show that Sox2 regulates the BMP pathway without affecting SMAD phosphorylation, and that Sox2 sumoylation is not necessary for this function. We also found that genes involved in the Hippo pathway were direct Sox2 targets. As the Hippo pathway is activated by Sox2 and Sox2 interacts with the NF2 promoter, we checked the effect of Sox2 on the expression of NF2. We showed that Sox2 down-regulates the transcriptional activity of the NF2 promoter, allowing the transcription of the YAP/TEAD genes in osteoblasts, thus acting as an upstream regulator of the Hippo pathway. We conclude that Sox2 induction in osteoblasts triggers FGF dependent inhibition of the BMP, Wnt and Hippo pathways.

Bioenergetics of cancer cells in anoxia and role of the miRNAs in melanoma resistance to targeted therapies

Tumours are characterized by a metabolic rewiring that helps transformed cells to survive in harsh conditions. The endogenous inhibitor of the ATP-synthase IF1 is overexpressed in several tumours and it has been proposed to drive metabolic adaptation. In ischemic normal-cells, IF1 acts limiting the ATP consumption by the reverse activity of the ATP-synthase, activated by ΔΨm collapse. Conversely, IF1 role in cancer cells is still unclear. It has been proposed that IF1 favours cancer survival by preventing energy dissipation in low oxygen availability, a frequent condition in solid tumours. Our previous data proved that in cancer cells hypoxia does not abolish ΔΨm, avoiding the ATP-synthase reversal and IF1 activation. In this study, we investigated the bioenergetics of cancer cells in conditions mimicking anoxia to evaluate the possible role of IF1. Data obtained indicate that also in cancer cells the ΔΨm collapse induces the ATP-synthase reversal and its inhibition by IF1. Moreover, we demonstrated that upon uncoupling conditions, IF1 favours cancer cells growth preserving ATP levels and energy charge. We also showed that in these conditions IF1 favours the mitochondrial mass renewal, a mechanism we proposed driving apoptosis-resistance. Cancer adaptability is also associated with the onset of therapy resistance, the major challenge for melanoma treatment. Recent studies demonstrated that miRNAs dysregulation drive melanoma progression and drug-resistance by regulating tumour-suppressor and oncogenes. In this context, we attempted to identify and characterize miRNAs driving resistance to vemurafenib in patient-derived metastatic melanoma cells BRAFV600E-mutated. Our results highlighted that several oncogenic pathways are altered in resistant cells, indicating the complexity of both drug-resistance phenomena and miRNAs action. Profiling analysis identified a group of dysregulated miRNAs conserved in vemurafenib-resistance cells from distinct patients, suggesting that they ubiquitously drive drug-resistance. Functional studies performed with a first miRNA confirmed its pivotal role in resistance towards vemurafenib.

Modulation of cancer energy metabolism: the role of the ATPase inhibitor factor 1 (IF1) in the bioenergetics of cancer cells experiencing oxygen deprivation

IF1, the endogenous inhibitor protein of mitochondrial F1Fo-ATPase, has raised interest in cancer research due to its overexpression in solid tumours compared to normal tissues. Physiologically, IF1 protects cells from energy depletion by limiting the ATP hydrolytic activity of ATP synthase triggered by mitochondrial depolarization caused by oxygen deficiency as it occurs during ischemic episodes. Considering both the physiological function of IF1 and that cancer cells in solid tumour are frequently exposed to oxygen deprivation, we hypothesized that IF1 overexpression represents a strategy that cancer cells develop to protect themselves from energy depletion under conditions of low oxygen availability. To assess this, we assayed the bioenergetic changes in 143B and HCT116 cancer cells with different metabolic features following stable silencing of IF1. Interestingly, we found that in both cell lines exposed to oxygen deprivation conditions the presence of IF1 limits the energy dissipation due to the activation of the ATP hydrolytic activity of ATP synthase. Furthermore, the analyses of cellular growth and viability revealed that the IF1 silencing inhibited proliferation in the highly glycolytic 143B cells, while it induced more than 50% of cellular death in HCT116 OXPHOS-dependent cells, indicating that the energetic advantage conferred by IF1 is essential for cancer cell proliferation or survival depending on the energy metabolism of each cell line. Moreover, under mitochondrial depolarization conditions, both mitophagy and mitochondrial biogenesis markers were found up-regulated in IF1-expressing cells only, thus indicating a continuous renewal and preservation of the mitochondrial mass. Taken together, our results sustain the idea that IF1 overexpression supports cancer cell adaptation to hypoxic or anoxic conditions also favouring the proliferation of re-oxygenated cells by promptly providing functional mitochondria.

The role of the Rocky Mountains in shaping the atmospheric mean state and the response to tropical forcing in idealised simulations.

Understanding the natural and forced variability of the atmospheric general circulation and its drivers is one of the grand challenges in climate science. It is of paramount importance to understand to what extent the systematic error of climate models affects the processes driving such variability. This is done by performing a set of simulations (ROCK experiments) with an intermediate complexity atmospheric model (SPEEDY), in which the Rocky Mountains orography is increased or decreased to influence the structure of the North Pacific jet stream. For each of these modified-orography experiments, the climatic response to idealized sea surface temperature anomalies of varying intensity in the El Niño Southern Oscillation (ENSO) region is studied. ROCK experiments are characterized by variations in the Pacific jet stream intensity whose extension encompasses the spread of the systematic error found in Coupled Model Intercomparison Project (CMIP6) models. When forced with ENSO-like idealised anomalies, they exhibit a non-negligible sensitivity in the response pattern over the Pacific North American region, indicating that the model mean state can affect the model response to ENSO. It is found that the classical Rossby wave train response to ENSO is more meridionally oriented when the Pacific jet stream is weaker and more zonally oriented with a stronger jet. Rossby wave linear theory suggests that a stronger jet implies a stronger waveguide, which traps Rossby waves at a lower latitude, favouring a zonal propagation of Rossby waves. The shape of the dynamical response to ENSO affects the ENSO impacts on surface temperature and precipitation over Central and North America. A comparison of the SPEEDY results with CMIP6 models suggests a wider applicability of the results to more resources-demanding climate general circulation models (GCMs), opening up to future works focusing on the relationship between Pacific jet misrepresentation and response to external forcing in fully-fledged GCMs.

The predictive role of the human gut microbiota in covid-19: implications for disease severity and post-covid syndrome

The COVID-19 pandemic, sparked by the SARS-CoV-2 virus, stirred global comparisons to historical pandemics. Initially presenting a high mortality rate, it later stabilized globally at around 0.5-3%. Patients manifest a spectrum of symptoms, necessitating efficient triaging for appropriate treatment strategies, ranging from symptomatic relief to antivirals or monoclonal antibodies. Beyond traditional approaches, emerging research suggests a potential link between COVID-19 severity and alterations in gut microbiota composition, impacting inflammatory responses. However, most studies focus on severe hospitalized cases without standardized criteria for severity. Addressing this gap, the first study in this thesis spans diverse COVID-19 severity levels, utilizing 16S rRNA amplicon sequencing on fecal samples from 315 subjects. The findings highlight significant microbiota differences correlated with severity. Machine learning classifiers, including a multi-layer convoluted neural network, demonstrated the potential of microbiota compositional data to predict patient severity, achieving an 84.2% mean balanced accuracy starting one week post-symptom onset. These preliminary results underscore the gut microbiota's potential as a biomarker in clinical decision-making for COVID-19. The second study delves into mild COVID-19 cases, exploring their implications for ‘long COVID’ or Post-Acute COVID-19 Syndrome (PACS). Employing longitudinal analysis, the study unveils dynamic shifts in microbial composition during the acute phase, akin to severe cases. Innovative techniques, including network approaches and spline-based longitudinal analysis, were deployed to assess microbiota dynamics and potential associations with PACS. The research suggests that even in mild cases, similar mechanisms to hospitalized patients are established regarding changes in intestinal microbiota during the acute phase of the infection. These findings lay the foundation for potential microbiota-targeted therapies to mitigate inflammation, potentially preventing long COVID symptoms in the broader population. In essence, these studies offer valuable insights into the intricate relationships between COVID-19 severity, gut microbiota, and the potential for innovative clinical applications.

The effect of adding features on product attractiveness: the role of product perceived congruity

Technological progress has been enabling companies to add disparate features to their existing products. This research investigates the effect of adding more features on consumers’ evaluation of the product, by examining in particular the role of the congruity of the features added with the base product as a variable the moderates the effect of increasing the number of features. Grounding on schema-congruity theory, I propose that the cognitive elaboration associated with the product congruity of the features added explains consumers’ evaluation as the number of new features increases. In particular, it is shown that consumers perceive a benefit from increasing the number of features only when these features are congruent with the product. The underlying mechanisms that explains this finding predicts that when the number of incongruent features increases the cognitive resources necessary to elaborate such incongruities increase and consumers are not willing to spend such resources. However, I further show that when encouraged to consider the new features thoughtfully, consumers do seem able to infer value from increasing the number of moderately incongruent features. Nonetheless, this finding does not apply for those new features that are extremely incongruent with the product. Further evidence for consumers’ ability to resolve the moderate incongruity associated with adding more features is also shown, by studying the moderating role of temporal construal. I propose that consumers perceive an increase in product evaluation as the number of moderately incongruent features increases when consumers consider purchasing the product in the distant future, whereas such an increase is not predicted for the near future scenario. I verify these effect in three experimental studies. Theoretical and managerial implications, and possible avenues of future research are also suggested.

Reexamining the Role of Incarceration and Stigma in Criminal Law

One of the ways by which the legal system has responded to different sets of problems is the blurring of the traditional boundaries of criminal law, both procedural and substantive. This study aims to explore under what conditions does this trend lead to the improvement of society's welfare by focusing on two distinguishing sanctions in criminal law, incarceration and social stigma. In analyzing how incarceration affects the incentive to an individual to violate a legal standard, we considered the crucial role of the time constraint. This aspect has not been fully explored in the literature on law and economics, especially with respect to the analysis of the beneficiality of imposing either a fine or a prison term. We observed that that when individuals are heterogeneous with respect to wealth and wage income, and when the level of activity can be considered a normal good, only the middle wage and middle income groups can be adequately deterred by a fixed fines alone regime. The existing literature only considers the case of the very poor, deemed as judgment proof. However, since imprisonment is a socially costly way to deprive individuals of their time, other alternatives may be sought such as the imposition of discriminatory monetary fine, partial incapacitation and other alternative sanctions. According to traditional legal theory, the reason why criminal law is obeyed is not mainly due to the monetary sanctions but to the stigma arising from the community’s moral condemnation that accompanies conviction or merely suspicion. However, it is not sufficiently clear whether social stigma always accompanies a criminal conviction. We addressed this issue by identifying the circumstances wherein a criminal conviction carries an additional social stigma. Our results show that social stigma is seen to accompany a conviction under the following conditions: first, when the law coincides with the society's social norms; and second, when the prohibited act provides information on an unobservable attribute or trait of an individual -- crucial in establishing or maintaining social relationships beyond mere economic relationships. Thus, even if the social planner does not impose the social sanction directly, the impact of social stigma can still be influenced by the probability of conviction and the level of the monetary fine imposed as well as the varying degree of correlation between the legal standard violated and the social traits or attributes of the individual. In this respect, criminal law serves as an institution that facilitates cognitive efficiency in the process of imposing the social sanction to the extent that the rest of society is boundedly rational and use judgment heuristics. Paradoxically, using criminal law in order to invoke stigma for the violation of a legal standard may also serve to undermine its strength. To sum, the results of our analysis reveal that the scope of criminal law is narrow both for the purposes of deterrence and cognitive efficiency. While there are certain conditions where the enforcement of criminal law may lead to an increase in social welfare, particularly with respect to incarceration and stigma, we have also identified the channels through which they could affect behavior. Since such mechanisms can be replicated in less costly ways, society should first try or seek to employ these legal institutions before turning to criminal law as a last resort.

The school environment as a teacher. The role of space and place in enhancing ecological literacy and social competence development in children and young people

Can space and place foster child development, and in particular social competence and ecological literacy? If yes, how can space and place do that? This study shows that the answer to the first question is positive and then tries to explain the way space and place can make a difference. The thesis begins with the review of literature from different disciplines – child development and child psychology, education, environmental psychology, architecture and landscape architecture. Some bridges among such disciplines are created and in some cases the ideas from the different areas of research merge: thus, this is an interdisciplinary study. The interdisciplinary knowledge from these disciplines is translated into a range of design suggestions that can foster the development of social competence and ecological literacy. Using scientific knowledge from different disciplines is a way of introducing forms of evidence into the development of design criteria. However, the definition of design criteria also has to pass through the study of a series of school buildings and un-built projects: case studies can give a positive contribution to the criteria because examples and good practices can help “translating” the theoretical knowledge into design ideas and illustrations. To do that, the different case studies have to be assessed in relation to the various themes that emerged in the literature review. Finally, research by design can be used to help define the illustrated design criteria: based on all the background knowledge that has been built, the role of the architect is to provide a series of different design solutions that can give answers to the different “questions” emerged in the literature review.