Dalla città alla casa, dalla casa alla città: la mutevole ricerca di un Piano per il ben-essere urbano

La ricerca si propone di definire le linee guida per la stesura di un Piano che si occupi di qualità della vita e di benessere. Il richiamo alla qualità e al benessere è positivamente innovativo, in quanto impone agli organi decisionali di sintonizzarsi con la soggettività attiva dei cittadini e, contemporaneamente, rende evidente la necessità di un approccio più ampio e trasversale al tema della città e di una più stretta relazione dei tecnici/esperti con i responsabili degli organismi politicoamministrativi. La ricerca vuole indagare i limiti dell’urbanistica moderna di fronte alla complessità di bisogni e di nuove necessità espresse dalle popolazioni urbane contemporanee. La domanda dei servizi è notevolmente cambiata rispetto a quella degli anni Sessanta, oltre che sul piano quantitativo anche e soprattutto sul piano qualitativo, a causa degli intervenuti cambiamenti sociali che hanno trasformato la città moderna non solo dal punto di vista strutturale ma anche dal punto di vista culturale: l’intermittenza della cittadinanza, per cui le città sono sempre più vissute e godute da cittadini del mondo (turisti e/o visitatori, temporaneamente presenti) e da cittadini diffusi (suburbani, provinciali, metropolitani); la radicale trasformazione della struttura familiare, per cui la famiglia-tipo costituita da una coppia con figli, solido riferimento per l’economia e la politica, è oggi minoritaria; l’irregolarità e flessibilità dei calendari, delle agende e dei ritmi di vita della popolazione attiva; la mobilità sociale, per cui gli individui hanno traiettorie di vita e pratiche quotidiane meno determinate dalle loro origini sociali di quanto avveniva nel passato; l’elevazione del livello di istruzione e quindi l’incremento della domanda di cultura; la crescita della popolazione anziana e la forte individualizzazione sociale hanno generato una domanda di città espressa dalla gente estremamente variegata ed eterogenea, frammentata e volatile, e per alcuni aspetti assolutamente nuova. Accanto a vecchie e consolidate richieste – la città efficiente, funzionale, produttiva, accessibile a tutti – sorgono nuove domande, ideali e bisogni che hanno come oggetto la bellezza, la varietà, la fruibilità, la sicurezza, la capacità di stupire e divertire, la sostenibilità, la ricerca di nuove identità, domande che esprimono il desiderio di vivere e di godere la città, di stare bene in città, domande che non possono essere più soddisfatte attraverso un’idea di welfare semplicemente basata sull’istruzione, la sanità, il sistema pensionistico e l’assistenza sociale. La città moderna ovvero l’idea moderna della città, organizzata solo sui concetti di ordine, regolarità, pulizia, uguaglianza e buon governo, è stata consegnata alla storia passata trasformandosi ora in qualcosa di assai diverso che facciamo fatica a rappresentare, a descrivere, a raccontare. La città contemporanea può essere rappresentata in molteplici modi, sia dal punto di vista urbanistico che dal punto di vista sociale: nella letteratura recente è evidente la difficoltà di definire e di racchiudere entro limiti certi l’oggetto “città” e la mancanza di un convincimento forte nell’interpretazione delle trasformazioni politiche, economiche e sociali che hanno investito la società e il mondo nel secolo scorso. La città contemporanea, al di là degli ambiti amministrativi, delle espansioni territoriali e degli assetti urbanistici, delle infrastrutture, della tecnologia, del funzionalismo e dei mercati globali, è anche luogo delle relazioni umane, rappresentazione dei rapporti tra gli individui e dello spazio urbano in cui queste relazioni si muovono. La città è sia concentrazione fisica di persone e di edifici, ma anche varietà di usi e di gruppi, densità di rapporti sociali; è il luogo in cui avvengono i processi di coesione o di esclusione sociale, luogo delle norme culturali che regolano i comportamenti, dell’identità che si esprime materialmente e simbolicamente nello spazio pubblico della vita cittadina. Per studiare la città contemporanea è necessario utilizzare un approccio nuovo, fatto di contaminazioni e saperi trasversali forniti da altre discipline, come la sociologia e le scienze umane, che pure contribuiscono a costruire l’immagine comunemente percepita della città e del territorio, del paesaggio e dell’ambiente. La rappresentazione del sociale urbano varia in base all’idea di cosa è, in un dato momento storico e in un dato contesto, una situazione di benessere delle persone. L’urbanistica moderna mirava al massimo benessere del singolo e della collettività e a modellarsi sulle “effettive necessità delle persone”: nei vecchi manuali di urbanistica compare come appendice al piano regolatore il “Piano dei servizi”, che comprende i servizi distribuiti sul territorio circostante, una sorta di “piano regolatore sociale”, per evitare quartieri separati per fasce di popolazione o per classi. Nella città contemporanea la globalizzazione, le nuove forme di marginalizzazione e di esclusione, l’avvento della cosiddetta “new economy”, la ridefinizione della base produttiva e del mercato del lavoro urbani sono espressione di una complessità sociale che può essere definita sulla base delle transazioni e gli scambi simbolici piuttosto che sui processi di industrializzazione e di modernizzazione verso cui era orientata la città storica, definita moderna. Tutto ciò costituisce quel complesso di questioni che attualmente viene definito “nuovo welfare”, in contrapposizione a quello essenzialmente basato sull’istruzione, sulla sanità, sul sistema pensionistico e sull’assistenza sociale. La ricerca ha quindi analizzato gli strumenti tradizionali della pianificazione e programmazione territoriale, nella loro dimensione operativa e istituzionale: la destinazione principale di tali strumenti consiste nella classificazione e nella sistemazione dei servizi e dei contenitori urbanistici. E’ chiaro, tuttavia, che per poter rispondere alla molteplice complessità di domande, bisogni e desideri espressi dalla società contemporanea le dotazioni effettive per “fare città” devono necessariamente superare i concetti di “standard” e di “zonizzazione”, che risultano essere troppo rigidi e quindi incapaci di adattarsi all’evoluzione di una domanda crescente di qualità e di servizi e allo stesso tempo inadeguati nella gestione del rapporto tra lo spazio domestico e lo spazio collettivo. In questo senso è rilevante il rapporto tra le tipologie abitative e la morfologia urbana e quindi anche l’ambiente intorno alla casa, che stabilisce il rapporto “dalla casa alla città”, perché è in questa dualità che si definisce il rapporto tra spazi privati e spazi pubblici e si contestualizzano i temi della strada, dei negozi, dei luoghi di incontro, degli accessi. Dopo la convergenza dalla scala urbana alla scala edilizia si passa quindi dalla scala edilizia a quella urbana, dal momento che il criterio del benessere attraversa le diverse scale dello spazio abitabile. Non solo, nei sistemi territoriali in cui si è raggiunto un benessere diffuso ed un alto livello di sviluppo economico è emersa la consapevolezza che il concetto stesso di benessere sia non più legato esclusivamente alla capacità di reddito collettiva e/o individuale: oggi la qualità della vita si misura in termini di qualità ambientale e sociale. Ecco dunque la necessità di uno strumento di conoscenza della città contemporanea, da allegare al Piano, in cui vengano definiti i criteri da osservare nella progettazione dello spazio urbano al fine di determinare la qualità e il benessere dell’ambiente costruito, inteso come benessere generalizzato, nel suo significato di “qualità dello star bene”. E’ evidente che per raggiungere tale livello di qualità e benessere è necessario provvedere al soddisfacimento da una parte degli aspetti macroscopici del funzionamento sociale e del tenore di vita attraverso gli indicatori di reddito, occupazione, povertà, criminalità, abitazione, istruzione, etc.; dall’altra dei bisogni primari, elementari e di base, e di quelli secondari, culturali e quindi mutevoli, trapassando dal welfare state allo star bene o well being personale, alla wellness in senso olistico, tutte espressioni di un desiderio di bellezza mentale e fisica e di un nuovo rapporto del corpo con l’ambiente, quindi manifestazione concreta di un’esigenza di ben-essere individuale e collettivo. Ed è questa esigenza, nuova e difficile, che crea la diffusa sensazione dell’inizio di una nuova stagione urbana, molto più di quanto facciano pensare le stesse modifiche fisiche della città.

Computational analyses on the structure-function relation in ion channels

Ion channels are protein molecules, embedded in the lipid bilayer of the cell membranes. They act as powerful sensing elements switching chemicalphysical stimuli into ion-fluxes. At a glance, ion channels are water-filled pores, which can open and close in response to different stimuli (gating), and one once open select the permeating ion species (selectivity). They play a crucial role in several physiological functions, like nerve transmission, muscular contraction, and secretion. Besides, ion channels can be used in technological applications for different purpose (sensing of organic molecules, DNA sequencing). As a result, there is remarkable interest in understanding the molecular determinants of the channel functioning. Nowadays, both the functional and the structural characteristics of ion channels can be experimentally solved. The purpose of this thesis was to investigate the structure-function relation in ion channels, by computational techniques. Most of the analyses focused on the mechanisms of ion conduction, and the numerical methodologies to compute the channel conductance. The standard techniques for atomistic simulation of complex molecular systems (Molecular Dynamics) cannot be routinely used to calculate ion fluxes in membrane channels, because of the high computational resources needed. The main step forward of the PhD research activity was the development of a computational algorithm for the calculation of ion fluxes in protein channels. The algorithm - based on the electrodiffusion theory - is computational inexpensive, and was used for an extensive analysis on the molecular determinants of the channel conductance. The first record of ion-fluxes through a single protein channel dates back to 1976, and since then measuring the single channel conductance has become a standard experimental procedure. Chapter 1 introduces ion channels, and the experimental techniques used to measure the channel currents. The abundance of functional data (channel currents) does not match with an equal abundance of structural data. The bacterial potassium channel KcsA was the first selective ion channels to be experimentally solved (1998), and after KcsA the structures of four different potassium channels were revealed. These experimental data inspired a new era in ion channel modeling. Once the atomic structures of channels are known, it is possible to define mathematical models based on physical descriptions of the molecular systems. These physically based models can provide an atomic description of ion channel functioning, and predict the effect of structural changes. Chapter 2 introduces the computation methods used throughout the thesis to model ion channels functioning at the atomic level. In Chapter 3 and Chapter 4 the ion conduction through potassium channels is analyzed, by an approach based on the Poisson-Nernst-Planck electrodiffusion theory. In the electrodiffusion theory ion conduction is modeled by the drift-diffusion equations, thus describing the ion distributions by continuum functions. The numerical solver of the Poisson- Nernst-Planck equations was tested in the KcsA potassium channel (Chapter 3), and then used to analyze how the atomic structure of the intracellular vestibule of potassium channels affects the conductance (Chapter 4). As a major result, a correlation between the channel conductance and the potassium concentration in the intracellular vestibule emerged. The atomic structure of the channel modulates the potassium concentration in the vestibule, thus its conductance. This mechanism explains the phenotype of the BK potassium channels, a sub-family of potassium channels with high single channel conductance. The functional role of the intracellular vestibule is also the subject of Chapter 5, where the affinity of the potassium channels hEag1 (involved in tumour-cell proliferation) and hErg (important in the cardiac cycle) for several pharmaceutical drugs was compared. Both experimental measurements and molecular modeling were used in order to identify differences in the blocking mechanism of the two channels, which could be exploited in the synthesis of selective blockers. The experimental data pointed out the different role of residue mutations in the blockage of hEag1 and hErg, and the molecular modeling provided a possible explanation based on different binding sites in the intracellular vestibule. Modeling ion channels at the molecular levels relates the functioning of a channel to its atomic structure (Chapters 3-5), and can also be useful to predict the structure of ion channels (Chapter 6-7). In Chapter 6 the structure of the KcsA potassium channel depleted from potassium ions is analyzed by molecular dynamics simulations. Recently, a surprisingly high osmotic permeability of the KcsA channel was experimentally measured. All the available crystallographic structure of KcsA refers to a channel occupied by potassium ions. To conduct water molecules potassium ions must be expelled from KcsA. The structure of the potassium-depleted KcsA channel and the mechanism of water permeation are still unknown, and have been investigated by numerical simulations. Molecular dynamics of KcsA identified a possible atomic structure of the potassium-depleted KcsA channel, and a mechanism for water permeation. The depletion from potassium ions is an extreme situation for potassium channels, unlikely in physiological conditions. However, the simulation of such an extreme condition could help to identify the structural conformations, so the functional states, accessible to potassium ion channels. The last chapter of the thesis deals with the atomic structure of the !- Hemolysin channel. !-Hemolysin is the major determinant of the Staphylococcus Aureus toxicity, and is also the prototype channel for a possible usage in technological applications. The atomic structure of !- Hemolysin was revealed by X-Ray crystallography, but several experimental evidences suggest the presence of an alternative atomic structure. This alternative structure was predicted, combining experimental measurements of single channel currents and numerical simulations. This thesis is organized in two parts, in the first part an overview on ion channels and on the numerical methods adopted throughout the thesis is provided, while the second part describes the research projects tackled in the course of the PhD programme. The aim of the research activity was to relate the functional characteristics of ion channels to their atomic structure. In presenting the different research projects, the role of numerical simulations to analyze the structure-function relation in ion channels is highlighted.

Computational methods for the analysis of protein structure and function

The vast majority of known proteins have not yet been experimentally characterized and little is known about their function. The design and implementation of computational tools can provide insight into the function of proteins based on their sequence, their structure, their evolutionary history and their association with other proteins. Knowledge of the three-dimensional (3D) structure of a protein can lead to a deep understanding of its mode of action and interaction, but currently the structures of <1% of sequences have been experimentally solved. For this reason, it became urgent to develop new methods that are able to computationally extract relevant information from protein sequence and structure. The starting point of my work has been the study of the properties of contacts between protein residues, since they constrain protein folding and characterize different protein structures. Prediction of residue contacts in proteins is an interesting problem whose solution may be useful in protein folding recognition and de novo design. The prediction of these contacts requires the study of the protein inter-residue distances related to the specific type of amino acid pair that are encoded in the so-called contact map. An interesting new way of analyzing those structures came out when network studies were introduced, with pivotal papers demonstrating that protein contact networks also exhibit small-world behavior. In order to highlight constraints for the prediction of protein contact maps and for applications in the field of protein structure prediction and/or reconstruction from experimentally determined contact maps, I studied to which extent the characteristic path length and clustering coefficient of the protein contacts network are values that reveal characteristic features of protein contact maps. Provided that residue contacts are known for a protein sequence, the major features of its 3D structure could be deduced by combining this knowledge with correctly predicted motifs of secondary structure. In the second part of my work I focused on a particular protein structural motif, the coiled-coil, known to mediate a variety of fundamental biological interactions. Coiled-coils are found in a variety of structural forms and in a wide range of proteins including, for example, small units such as leucine zippers that drive the dimerization of many transcription factors or more complex structures such as the family of viral proteins responsible for virus-host membrane fusion. The coiled-coil structural motif is estimated to account for 5-10% of the protein sequences in the various genomes. Given their biological importance, in my work I introduced a Hidden Markov Model (HMM) that exploits the evolutionary information derived from multiple sequence alignments, to predict coiled-coil regions and to discriminate coiled-coil sequences. The results indicate that the new HMM outperforms all the existing programs and can be adopted for the coiled-coil prediction and for large-scale genome annotation. Genome annotation is a key issue in modern computational biology, being the starting point towards the understanding of the complex processes involved in biological networks. The rapid growth in the number of protein sequences and structures available poses new fundamental problems that still deserve an interpretation. Nevertheless, these data are at the basis of the design of new strategies for tackling problems such as the prediction of protein structure and function. Experimental determination of the functions of all these proteins would be a hugely time-consuming and costly task and, in most instances, has not been carried out. As an example, currently, approximately only 20% of annotated proteins in the Homo sapiens genome have been experimentally characterized. A commonly adopted procedure for annotating protein sequences relies on the "inheritance through homology" based on the notion that similar sequences share similar functions and structures. This procedure consists in the assignment of sequences to a specific group of functionally related sequences which had been grouped through clustering techniques. The clustering procedure is based on suitable similarity rules, since predicting protein structure and function from sequence largely depends on the value of sequence identity. However, additional levels of complexity are due to multi-domain proteins, to proteins that share common domains but that do not necessarily share the same function, to the finding that different combinations of shared domains can lead to different biological roles. In the last part of this study I developed and validate a system that contributes to sequence annotation by taking advantage of a validated transfer through inheritance procedure of the molecular functions and of the structural templates. After a cross-genome comparison with the BLAST program, clusters were built on the basis of two stringent constraints on sequence identity and coverage of the alignment. The adopted measure explicity answers to the problem of multi-domain proteins annotation and allows a fine grain division of the whole set of proteomes used, that ensures cluster homogeneity in terms of sequence length. A high level of coverage of structure templates on the length of protein sequences within clusters ensures that multi-domain proteins when present can be templates for sequences of similar length. This annotation procedure includes the possibility of reliably transferring statistically validated functions and structures to sequences considering information available in the present data bases of molecular functions and structures.

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.

The Domon Family of Plant Plasma Membrane B-Type Cytochromes: Heterologous Expression, Biochemical Characterization and Physiological Roles in Vivo

The DOMON domain is a domain widespread in nature, predicted to fold in a β-sandwich structure. In plants, AIR12 is constituted by a single DOMON domain located in the apoplastic space and is GPI-modified for anchoring to the plasma membrane. Arabidopsis thaliana AIR12 has been heterologously expressed as a recombinant protein (recAtAIR12) in Pichia pastoris. Spectrophotometrical analysis of the purified protein showed that recAtAir12 is a cytochrome b. RecAtAIR12 is highly glycosylated, it is reduced by ascorbate, superoxide and naftoquinones, oxidised by monodehydroascorbate and oxygen and insensitive to hydrogen peroxide. The addition of recAtAIR12 to permeabilized plasma membranes containing NADH, FeEDTA and menadione, caused a statistically significant increase in hydroxyl radicals as detected by electron paramagnetic resonance. In these conditions, recAtAIR12 has thus a pro-oxidant role. Interestingly, AIR12 is related to the cytochrome domain of cellobiose dehydrogenase which is involved in lignin degradation, possibly via reactive oxygen species (ROS) production. In Arabidopsis the Air12 promoter is specifically activated at sites where cell separations occur and ROS, including •OH, are involved in cell wall modifications. air12 knock-out plants infected with Botrytis cinerea are more resistant than wild-type and air12 complemented plants. Also during B. cinerea infection, cell wall modifications and ROS are involved. Our results thus suggest that AIR12 could be involved in cell wall modifying reactions by interacting with ROS and ascorbate. CyDOMs are plasma membrane redox proteins of plants that are predicted to contain an apoplastic DOMON fused with a transmembrane cytochrome b561 domain. CyDOMs have never been purified nor characterised. The trans-membrane portion of a soybean CyDOM was expressed in E. coli but purification could not be achieved. The DOMON domain was expressed in P. pastoris and shown to be itself a cytochrome b that could be reduced by ascorbate.

Characterization of the structure and iron uptake mechanisms of the Staphylococcus aureus ferric hydroxamate-binding lipoprotein FhuD2

The Reverse Vaccinology (RV) approach allows using genomic information for the delineation of new protein-based vaccines starting from an in silico analysis. The first powerful example of the application of the RV approach is given by the development of a protein-based vaccine against serogroup B Meningococcus. A similar approach was also used to identify new Staphylococcus aureus vaccine candidates, including the ferric hydroxamate-binding lipoprotein FhuD2. S. aureus is a widespread human pathogen, which employs various different strategies for iron uptake, including: (i) siderophore-mediated iron acquisition using the endogenous siderophores staphyloferrin A and B, (ii) siderophore-mediated iron acquisition using xeno-siderophores (the pathway exploited by FhuD2) and (iii) heme-mediated iron acquisition. In this work the high resolution crystal structure of FhuD2 in the iron (III)-siderophore-bound form was determined. FhuD2 belongs to the Periplasmic Binding Protein family (PBP ) class III, and is principally formed by two globular domains, at the N- and C-termini of the protein, that make up a cleft where ferrichrome-iron (III) is bound. The N- and C-terminal domains, connected by a single long α-helix, present Rossmann-like folds, showing a β-stranded core and an α-helical periphery, which do not undergo extensive structural rearrangement when they interact with the ligand, typical of class III PBP members. The structure shows that ferrichrome-bound iron does not come directly into contact with the protein; rather, the metal ion is fully coordinated by six oxygen donors of the hydroxamate groups of three ornithine residues, which, with the three glycine residues, make up the peptide backbone of ferrichrome. Furthermore, it was found that iron-free ferrichrome is able to subtract iron from transferrin. This study shows for the first time the structure of FhuD2, which was found to bind to siderophores ,and that the protein plays an important role in S. aureus colonization and infection phases.