The role of MYCN-mediated transcriptional repression in neuronal physiopathology

MYC is a transcription factor that can activate transcription of several targets by direct binding to their promoters at specific DNA sequences (E-box). Recent findings have also shown that it can exert its biological role by repressing transcription of other set of genes. C-MYC can mediate repression on its target genes through interaction with factors bound to promoter regions but not through direct recognition of typical E-Boxes. In this thesis, we investigated whether MYCN can also repress gene transcription and how this is mechanistically achieved. Moreover, expression of TRKA, P75NTR and ABCC3 is attenuated in aggressive MYCN-amplified tumors, suggesting a causal link between elevated MYCN activity and transcriptional repression of these three genes. We found that MYCN is physically associated with gene promoters in vivo in proximity of the transcriptional start sites and this association requires interactions with SP1 and/or MIZ-1. Furthermore, we show that this interaction could interfere with SP1 and MIZ-1 activation functions by recruiting co-repressors such as DNMT3a or HDACs. Studies in vitro suggest that MYCN interacts through distinct domains with SP1, MIZ-1 and HDAC1 supporting the idea that MYCN may form different complexes by interacting with different proteins. Re-expression of endogenous TRKA and P75NTR with exposure to the TSA sensitizes neuroblastoma to NGF-mediated apoptosis, whereas ectopic expression of ABCC3 decreases cell motility without interfering with growth. Finally, using shRNA whole genome library, we dissected the P75NTR repression trying to identify novel factors inside and/or outside MYCN complex for future therapeutic approaches. Overall, our results support a model in which MYCN can repress gene transcription by direct interaction with SP1 and/or MIZ-1, and provide further lines of evidence on the importance of transcriptional repression induced by Myc in tumor biology.

Il critico teatrale come operatore di scrittura scenica. La critica teatrale italiana tra pratica organizzativa e utilizzo dei nuovi media nel Nuovo Teatro e in alcune esperienze dal 2003 ad oggi

La crisi del “teatro come servizio pubblico” degli Stabili, Piccolo Teatro in testa, si manifesta allo stadio di insoddisfazione interna già alla fine degli anni Cinquanta. Se dal punto di vista della pratica scenica, la prima faglia di rottura è pressoché unanimemente ricondotta alla comparsa delle primissime messe in scena –discusse, irritanti e provocatorie- di Carmelo Bene e Quartucci (1959-60) più difficile è individuare il corrispettivo di un critico-intellettuale apportatore di una altrettanto deflagrante rottura. I nomi di Arbasino e di Flaiano sono, in questo caso, i primi che vengono alla mente, ma, seppure portatori di una critica sensibile al “teatro ufficiale”, così come viene ribattezzato dopo il Convegno di Ivrea (1967) il modello attuato dagli Stabili, essi non possono, a ben vedere, essere considerati i veri promotori di una modalità differente di fare critica che, a partire da quel Convegno, si accompagnerà stabilmente alla ricerca scenica del Nuovo Teatro. Ma in cosa consiste, allora, questa nuova “operatività” critica? Si tratta principalmente di una modalità capace di operare alle soglie della scrittura, abbracciando una progressiva, ma costante fuoriuscita dalla redazione di cronache teatrali, per ripensare radicalmente la propria attività in nuovi spazi operativi quali le riviste e l’editoria di settore, un rapporto sempre più stretto con i mass-media quali radio e televisione e la pratica organizzativa di momenti spettacolari e teorici al contempo -festival, convegni, rassegne e premi- per una forma di partecipazione poi identificata come “sporcarsi le mani”. La seconda parte della tesi è una raccolta documentaria sull’oggi. A partire dal Manifesto dei Critici Impuri redatto nel 2003 a Prato da un gruppo di critici dell'ultima generazione, la tesi utilizza quella dichiarazione come punto di partenza per creare un piccolo archivio sull’oggi raccogliendo le elaborazioni di alcune delle esperienze più significative di questi dieci anni. Ricca appendice di materiali.

La scuola di Gundēšābūr. La conoscenza del corpo umano (anatomia e fisiologia) e la trasmissione delle teorie medico-scientifiche nel mondo sasanide e post-sasanide.

Questo lavoro traccia un quadro della diffusione e trasmissione delle conoscenze riguardanti l’anatomia e la fisiologia del corpo umano nel mondo iranico in età sasanide (III-VII sec. d.C.). La tesi analizza il ruolo delle scuole di medicina in territorio iranico, come quelle sorte a Nisibi e Gundēšābūr, delle figure dei re sasanidi interessati alla filosofia e alla scienza greca, e dei centri di studio teologico e medico che, ad opera dei cristiani siro-orientali, si fecero promotori della conoscenza medico-scientifica greca in terra d’Iran.

Phenotypic and molecular characterization of ethylene biosynthesis in apples

Ethylene plays an important role in apple fruit development. Its biosynthesis is catalyzed by two enzymes ACS and ACO. The first is considered to catalyzes the rate-limiting step of ethylene production and in apple two different alleles (MdACS1-1 and MdACS1-2) of this gene have been identified. The presence in the promoter region of MdACS1-2 allele of a SINE insertion is considered to be responsible for a low transcription level and a pronounced reduction in ethylene production in apple cultivar homozygous for this allele. However, the specific expression of each MdACS1 allele has never been reported as well as any in vivo analysis of its 5’-flanking region. With the present study we addressed these issues by developing a set of qPCR allele specific primers for MdACS1 and by a functional characterization of the MdACS1 promoters by transient expression analysis. qPCR analysis on different apple tissues and stages of development demonstrated that MdACS1-2 allele is never express and that MdACS1-1 allele is ripening-related and expresses predominantly but not exclusively in apple fruit. To test MdACS1 promoter in fruit the only protocol available in literature for transient transformation of apple fruit was evaluated and optimized. Twenty chimeric promoter::reporter constructs were generated and analyzed by Agrobacterium-transient transformation. The in vivo analysis allowed to identify an enhancer-like region of 261 bp in MdACS1 promoter and a region of 57 bp in MdACS1-2 responsible, also if not alone, in the inactivation of the MdACS1-2 allele. Through the assessment of ethylene production in a segregating progeny derived from the cross between Fuji and Mondial Gala (homozygous for MdACS1-2 allele) we demonstrated that at least two other genes may be involved in apple ethylene production. An hypothesis that could explain the difference between Fuji and Mondial Gala have been proposed.

Transcriptional responses of the Helicobacter pylori cag pathogenicity island

The severity of Helicobacter pylori infections largely depends on the genetic diversity of the infecting strain, and particularly on the presence of the cag pathogenicity island (cag-PAI). This virulence locus encodes a type-IV secretion system able to translocate in the host cell at least the cag-encoded toxin CagA and peptidoglycan fragments, that together are responsible for the pathogenic phenotype in the host. Little is known about the bacterial regulators that underlie the coordinated expression of cag gene products, needed to assemble a functional secretion system apparatus. To fill this gap, a comprehensive analysis of the transcriptional regulation of the cag-PAI operons was undertaken. To pursue this goal, a robust tool for the analysis of gene expression in H. pylori was first implemented. A bioluminescent reporter system based on the P. luminescens luxCDABE operon was constructed and validated by comparisons with transcriptional analyses, then it was systematically used for the comprehensive study and mapping of the cag promoters. The identification of bona fide cag promoters had permitted to pinpoint the set of cag transcriptional units of the PAI. The responses of these cag transcriptional units to metabolic stress signals were analyzed in detail, and integrated with transcription studies in deletion mutants of important H. pylori virulence regulators and protein-DNA interaction analyses to map the binding sites of the regulators. Finally, a small regulatory RNA cncR1 encoded by the cag-PAI was identified, and the 5’- and 3’-ends of the molecule were mapped by primer extension analyses, northern blot and studies with lux reporter constructs. To identify regulatory effects exerted by cncR1 on the H. pylori gene expression, the cncR1 knock out strain was derived and compared to the parental wild type strain by a macroarray approach. Results suggest a negative effect exerted by cncR1 on the regulome of the alternative sigma54 factor.

Composti perfluorurati: Valutazione degli effetti biologici e molecolari in modelli cellulari

L’acido perfluorottanoico (PFOA) e l’acido perfluoronanoico (PFNA) sono composti perfluorurati (PFCs) comunemente utilizzati nell’industria, negli ultimi 60 anni, per diverse applicazioni. A causa della loro resistenza alla degradazione, questi composti sono in grado di accumularsi nell’ambiente e negli organismi viventi, da cui possono essere assunti in particolare attraverso la dieta. Le esistenti evidenze sugli effetti dell’esposizione negli animali, tra cui la potenziale cancerogenicità, hanno accresciuto l’interesse sui possibili rischi per la salute nell’uomo. Recenti studi sull’uomo indicano che i PFC sono presenti nel siero, con livelli molto alti soprattutto nei lavoratori cronicamente esposti, e sono associati positivamente al cancro al seno e alla prostata. Inoltre, sono state riportate proprietà estrogen-like e variazioni nei livelli di metilazione sui promotori di alcuni geni. L’esposizione in utero è stata associata positivamente a ipometilazione globale del DNA nel siero cordonale. L’obiettivo di questo studio è stato quello di indagare gli effetti dell’esposizione a questi perfluorurati su linee cellulari tumorali e primarie umane (MOLM-13, RPMI, HEPG2, MCF7,WBC, HMEC e MCF12A), appartenenti a diversi tessuti target, utilizzando un ampio range di concentrazioni (3.12 nM - 500 μM). In particolare, si è valutato: la vitalità, il ciclo cellulare, l’espressione genica, la metilazione globale del DNA e la metilazione gene specifica. Dai risultati è emerso come entrambi i perfluorurati abbiano effetti biologici: PFOA presenta un effetto prevalente citostatico, PFNA prevalentemente citotossico. L’effetto è, però, prevalente sulle linee cellulari primarie di epitelio mammario (HMEC, MCF12A), anche a concentrazioni riscontrate in lavoratori cronicamente esposti (≥31,25 µM). Dall’analisi su queste cellule primarie, non risultano variazioni significative della metilazione globale del DNA alle concentrazioni di 15,6 e 31,25 µM. Emergono invece variazioni sui geni marcatori del cancro al seno, del ciclo cellulare, dell’apoptosi, del pathway di PPAR-α e degli estrogeni, ad una concentrazione di 31,25 µM di entrambi i PFCs.

Involvement of the opioid system and BDNF in neuroplastic alterations occurring in neuropathic pain conditions

Chronic pain affects one in five adults, reducing quality of life and increasing risk of developing co-morbidities such as depression. Neuropathic pain results by lesions to the nervous system that alter its structure and function leading to spontaneous pain and amplified responses to noxious and innocuous stimuli. The Opioid System is probably the most important system involved in control of nociceptive transmission. Dynorphin and nociceptin systems have been suggested key mediators of some neuropathic pain aspects. An important role also for BDNF has been recently suggested since its involvement in the peripheral and central sensitization phenomena is known. We studied neuroplastic alterations occurring in chronic pain in mice subjected to the chronic constriction injury (CCI). We investigated gene expression alterations of both BDNF and Opioid System at spinal level at different intervals of time. A transient upregulation of pBDNF and pDYN was observed in spinal cord, while increasing upregulation of ppN/OFQ was found in the DRGs of injured mice. Development of neuropathic behavioral signs has been observed in ICR/CD-1 and BDNF+/+ mice, subjected to CCI. A different development of these signs was observed in BDNF+/-. We also studied gene expression changes of investigated systems in different brain areas fourteen days after surgery. We found pBDNF, pDYN, pKOP, ppN/OFQ and pNOP gene expression alterations in several areas of CCI mice. In the same brain regions we also determined bioactive nociceptin peptide levels, and elevated N/OFQ levels were observed in the amygdala area. Histone modifications studies have been performed in BDNF and DYN gene promoters of CCI animal spinal cord showing selected alterations in pDYN gene promoter. In addition, a preliminary characterization of the innovative NOP-EGFP mice was performed. Overall, our results could be useful to understand which and how neuropeptidergic systems are involved in neuroplastic mechanism occurring in neuropathic pain.

Interactions of G-quadruplex binders and Topoisomerase I inhibitors in cancer cells

Top1-DNA cleavage complexes (Top1ccs) trigger an accumulation of antisense RNAPII transcripts specifically at active divergent CpG-island promoters in a replication independent and Top1 dependent manner, leading to transcription-dependent genome instability and altered transcription regulation. Using different cancer cell lines of colon and osteo origins, we show that they display different sensitivity to CPT and G4 binder that is independent from Top1 level. To look at the interactions between Top1 and G4, we show that co-treatment with G4 binders potentiate the cell cytotoxicity of CPT regardless of the treatment sequences. Potentiation is indicated by a reduced inhibition concentration (IC50) with a more profound cytotoxicity in CPT-resistant cell lines, HCT15 and U2OS, hence, indicating an interaction between Top1inhibitor and G4 binders. Moreover, computational analysis confirmed the present of G4 motifs in genes with CPT-induced antisense transcription. G4 motifs are present mostly 5000 bp upstream from transcription start site and notably lower in genes. Comparisons between genes with no antisense transcription and genes with antisense transcription show that G4 motifs in this region are notably lower in the genes with antisense transcripts. Since CPT increases negative supercoils at promoters of intermediate activity, the formation of G4 is also increased in CPT-treated cells. Suprisingly, formation of G4 is regulated in parallel to the transient stabilization of R-loops, indicating a role in response to CPT-induced stress. G4 formation is highly elevated in Pyridostatin treated cells, which previous study shows increased formation of γH2Ax foci. This effect is also seen in the CPT-resistant cell lines, HCT15, indicating that the formation is a general event in response to CPT. We also show that R-loop formation is greatly increased in Pyridostatin treated cells. In order to study the role of R-loops and G4 structures in Top1cc-dependant repair pathway, we inhibited tyrosyl-phosphodiestrase 1 (TDP-1) using a TDP-1 inhibitor.

Natural compounds Camptothecin and Triptolide: highly specific enzyme inhibitors and tools to dissect transcriptional functions

With this work I elucidated new and unexpected mechanisms of two strong and highly specific transcription inhibitors: Triptolide and Campthotecin. Triptolide (TPL) is a diterpene epoxide derived from the Chinese plant Trypterigium Wilfoordii Hook F. TPL inhibits the ATPase activity of XPB, a subunit of the general transcription factor TFIIH. In this thesis I found that degradation of Rbp1 (the largest subunit of RNA Polymerase II) caused by TPL treatments, is preceded by an hyperphosphorylation event at serine 5 of the carboxy-terminal domain (CTD) of Rbp1. This event is concomitant with a block of RNA Polymerase II at promoters of active genes. The enzyme responsible for Ser5 hyperphosphorylation event is CDK7. Notably, CDK7 downregulation rescued both Ser5 hyperphosphorylation and Rbp1 degradation triggered by TPL. Camptothecin (CPT), derived from the plant Camptotheca acuminata, specifically inhibits topoisomerase 1 (Top1). We first found that CPT induced antisense transcription at divergent CpG islands promoter. Interestingly, by immunofluorescence experiments, CPT was found to induce a burst of R loop structures (DNA/RNA hybrids) at nucleoli and mitochondria. We then decided to investigate the role of Top1 in R loop homeostasis through a short interfering RNA approach (RNAi). Using DNA/RNA immunoprecipitation techniques coupled to NGS I found that Top1 depletion induces an increase of R loops at a genome-wide level. We found that such increase occurs on the entire gene body. At a subset of loci R loops resulted particularly stressed after Top1 depletion: some of these genes showed the formation of new R loops structures, whereas other loci showed a reduction of R loops. Interestingly we found that new peaks usually appear at tandem or divergent genes in the entire gene body, while losses of R loop peaks seems to be a feature specific of 3’ end regions of convergent genes.

Regulatory networks of Neisseria meningitidis and their implications for pathogenesis

Neisseria meningitidis, the leading cause of bacterial meningitis, can adapt to different host niches during human infection. Both transcriptional and post-transcriptional regulatory networks have been identified as playing a crucial role for bacterial stress responses and virulence. We investigated the N. meningitidis transcriptional landscape both by microarray and by RNA sequencing (RNAseq). Microarray analysis of N. meningitidis grown in the presence or absence of glucose allowed us to identify genes regulated by carbon source availability. In particular, we identified a glucose-responsive hexR-like transcriptional regulator in N. meningitidis. Deletion analysis showed that the hexR gene is accountable for a subset of the glucose-responsive regulation, and in vitro assays with the purified protein showed that HexR binds to the promoters of the central metabolic operons of meningococcus, by targeting a DNA region overlapping putative regulatory sequences. Our results indicate that HexR coordinates the central metabolism of meningococcus in response to the availability of glucose, and N. meningitidis strains lacking the hexR gene are also deficient in establishing successful bacteremia in a mouse model of infection. In parallel, RNAseq analysis of N. meningitidis cultured under standard or iron-limiting in vitro growth conditions allowed us to identify novel small non-coding RNAs (sRNAs) potentially involved in N. meningitidis regulatory networks. Manual curation of the RNAseq data generated a list of 51 sRNAs, 8 of which were validated by Northern blotting. Deletion of selected sRNAs caused attenuation of N. meningitidis infection in a murine model, leading to the identification of the first sRNAs influencing meningococcal bacteraemia. Furthermore, we describe the identification and initial characterization of a novel sRNA unique to meningococcus, closely associated to genes relevant for the intracellular survival of pathogenic Neisseriae. Taken together, our findings could help unravel the regulation of N. meningitidis adaptation to the host environment and its implications for pathogenesis.

Epigenetic role of N-Myc in Neuroblastoma

Childhood neuroblastoma is the most common solid tumour of infancy and highly refractory to therapy. One of the most powerful prognostic indicators for this disease is the N-Myc gene amplification, which occurs in approximately 25% of all neuroblastomas. N-Myc is a member of transcription factors belonging to a subclass of the larger group of proteins sharing Basic-Region/Helix–Loop–Helix/Leucin-Zipper (BR/HLH/LZ) motif. N-Myc oncoproteins may determine activation or repression of several genes thanks to different protein-protein interactions that may modulate its transcriptional regulatory ability and therefore its potential for oncogenicity. Chromatin modifications, including histone methylation, have a crucial role in transcription de-regulation of many cancer-related genes. Here, it was investigated whether N-Myc can functionally and/or physically interact with two different factors involved in methyl histone modification: WDR5 (core member of the MLL/Set1 methyltransferase complex) and the de- methylase LSD1. Co-IP assays have demonstrated the presence of both N-Myc-WDR5 and N-Myc-LSD1 complexes in two neuroblastoma cell lines. Human N-Myc amplified cell lines were used as a model system to investigate on transcription activation and/or repression mechanisms carried out by N-Myc-LSD1 and N-Myc-WDR5 protein complexes. qRT-PCR and immunoblot assays underlined the ability of both complexes to positively (N-Myc-WDR5) and negatively (N-Myc-LSD1) influence transcriptional regulation of crititical neuroblastoma N-Myc-related genes, MDM2, p21 and Clusterin. Ch-IP experiments have revealed the binding of the N-Myc complexes above mentioned to the gene promoters analysed. Finally, pharmacological treatment pointed to abolish N-Myc and LSD1 activity were performed to test cellular alterations, such as cell viability and cell cycle progression. Overall, the results presented in this work suggest that N-Myc can interact with two distinct histone methyl modifiers to positively and negatively affect gene transcription in neuroblastoma.

La curiosità del lettore. Momenti della formazione culturale di Ezio Raimondi

L’elaborato si propone di esaminare le tappe principali della formazione intellettuale di Ezio Raimondi (Lizzano in Belvedere, 22 marzo 1924 – Bologna, 18 marzo 2014). Dopo aver illustrato i riflessi dei maestri (Lorenzo Bianchi, Franco Serra, Roberto Longhi, Carlo Calcaterra) nella produzione critica dello studioso, il nostro lavoro, grazie al materiale archivistico dell’Accademia della Crusca, ha tentato di ricostruire da una parte le dinamiche del dialogo instaurato da Ezio Raimondi con Gianfranco Contini, Giorgio Pasquali e Francesco Pagliai, e dall’altra i criteri ecdotici e filologici fissati nell’edizione critica dei Dialoghi di Torquato Tasso (1958). La lunga consuetudine con uno dei massimi poeti nostri, e con un testo di grande rilievo nella storia della cultura nell’età della Controriforma, offrì al giovane studioso la prospettiva più felice, e insieme un saldo fondamento filologico e storico, all’interesse che era venuto crescendo in lui per il Manierismo. Con il sostegno dei documenti del Fondo Riccardo Ricciardi editore, conservati al Centro Apice di Milano, non è sembrato inopportuno discutere, tramite il carteggio tra Ezio Raimondi e Gianni Antonini, le ‘scelte di canone’ dell’antologia Trattatisti e narratori del Seicento (1960). L’analisi della corrispondenza tra Charles Singleton ed Ezio Raimondi si è rivelata, invece, particolarmente stimolante per avanzare qualche proposta interpretativa sulla critica simbolica, della quale lo studioso fu uno dei maggiori promotori. La tesi si conclude con un’Appendice, in cui compare, per la prima volta, un elenco provvisorio del materiale documentario allegato ai libri del professore, da noi inventariato dopo che l’archivio culturale Ezio Raimondi è stato donato dagli eredi dello studioso alla biblioteca del Dipartimento di Filologia Classica e Italianistica dell’Università di Bologna.

Valorization of bio-alcohols into added value chemicals

The present research work focused on the valorisation and upgrading of bio-ethanol over heterogeneous catalysts in a lab-scale continuous gas-flow system. In the Unibo laboratories, catalytic tests have been carried out in the temperature range 300-600°C by feeding an ethanol/He mixture in the reactor. After choosing the reaction conditions, ion-exchanged hydroxyapatite with transition metals (i.e., Fe, Cu) and alkaline earth metal (i.e., Sr) have been synthesized and tested. The Sr-HAP catalyst led to the formation of a complex reaction mixture the composition of which need further optimization in order to fill the requisite to be used as fuel-blend. Then, some zirconium-oxide based catalysts have been prepared through two different methods, precipitation and hydrothermal, by varying some synthetic parameters (i.e., pH, the nature of the base) and by adding a transition metal as dopant agent (i.e., Ti and Y). The presence of a dopant into the zirconia structure favoured the stabilization of the tetragonal or cubic phase against the monoclinic one. Interestingly, 5%mol Ti-doped zirconia exhibited a different catalytic behaviour yielding diethyl ether as major product at 300°C, while all the others samples produced mainly ethylene. Then, the effect of acid-base properties of sepiolite, using alkali metals (i.e., Na, K, Cs) with different metal loading (i.e., 2, 4, 5, 7, 14 wt%) as promoters, and of the redox properties of sepiolite-supported CuO or NiO, on the catalytic conversion of ethanol into n-butanol has been investigated. Thermal treated sepiolite samples mainly acted as acid catalyst, yielding preferentially the dehydration products of ethanol (ethylene and diethyl ether). Best results in terms of activity (ethanol conversion, 59%) and n-butanol selectivity (30%) where obtained at 400ºC and a contact time, W/F, of 2 g/mL·s over the catalyst consisting of sepiolite calcined at 500ºC modified with 7 wt% of cesium.

Mapping socialist solidarities: SWAPO, the Namibian liberation struggle, and the Global Cold War

This thesis addresses the entanglements between the Namibian liberation struggle and the global Cold War, focusing on the socialist support provided to the South West African People Organization (SWAPO), the liberation movement that fought for the independence of the country from the South African regime. This thesis aims at analyzing three socialist models of solidarity with the SWAPO’s struggle that developed especially from the late 1970s. Combining archival sources and biographical accounts, it examines the politics of solidarity with SWAPO implemented by East Germany, Cuba, and the Italian Communist Party. The interest lies in understanding how solidarity was declined and received by internal promoters and external addressees. Thus, I explore how these three actors constructed their concept of solidarity with SWAPO according to their national and ideological contexts and how this was received by the SWAPO members who experienced it in various ways. Each socialist actor promoted solidarity with SWAPO by using varying narratives, pursuing their own objectives, and employing diverse instruments, thus carrying out different and sometimes competing visions of socialism and solidarity. On its side, SWAPO was able to take advantage from such visions, as each of them could serve its different needs in diverse ways. In providing a general overview of these three solidarity policies, this thesis has the objective of highlighting the internal pluralization of the “socialist solidarity regime” while at the same time contributing to the debate on the extent of SWAPO’s commitment to socialism during the Namibian liberation struggle. It argues that, while pragmatism has always guided SWAPO during the liberation struggle and the post-independence period, and non-alignment has always been its international stance, socialism has to some extent been a model for the revolution in Namibia, to the point that it is still influencing the SWAPO party today.