Sicilian Protected Areas Among Tourist Exploitation and Environmental Guardianship

This report pursues the objective to define the connection that ties exploitation of the environment quality in the protected areas and the opportunities of economic and tourist development. Sicilian protected areas involve a territory full of an extraordinary variety and concentration of historical, artistic and environmental resources, so that they represent one of the main tourist attractions of the Island. Unfortunately, the Sicilian protected areas system shows serious backwardnesses, so that the prevailing image is one of wide zones in state of abandonment and degrade. It needs to start a process of investments and programmes in order to realize an integration between both the basical aims of environmental safeguard and the promotion of sustainable touristic and economic activities. The report presents a brief description of protected areas’ features, as long as considering protected territories as an instrument of local economic and social development. The second part of the paper is focused on the main features of the Sicilian protected areas system, in order to highlight the matters concerning the tourist-recreational exploitation of the protected territories in a sustainable viewpoint.

A Strategically Located Arg/Lys Residue Promotes Correct Base Paring During Nucleic Acid Biosynthesis in Polymerases

Polymerases (Pols) synthesize the double-stranded nucleic acids in the Watson-Crick (W-C) conformation, which is critical for DNA and RNA functioning. Yet, the molecular basis to catalyze the W-C base pairing during Pol-mediated nucleic acids biosynthesis remains unclear. Here, through bioinformatics analyses on a large data set of Pol/DNA structures, we first describe the conserved presence of one positively charged residue (Lys or Arg), which is similarly located near the enzymatic two-metal active site, always interacting directly with the incoming substrate (d)NTP. Incidentally, we noted that some Pol/DNA structures showing the alternative Hoogsteen base pairing were often solved with this specific residue either mutated, displaced, or missing. We then used quantum and classical simulations coupled to free-energy calculations to illustrate how, in human DNA Pol-η, the conserved Arg61 favors W-C base pairing through defined interactions with the incoming nucleotide. Taken together, these structural observations and computational results suggest a structural framework in which this specific residue is critical for stabilizing the incoming (d)NTP nucleotide and base pairing during Pol-mediated nucleic acid biosynthesis. These results may benefit enzyme engineering for nucleic acid processing and encourage new drug discovery strategies to modulate Pols function

A Self-Activated Mechanism for Nucleic Acid Polymerization Catalyzed by DNA/RNA Polymerases

The enzymatic polymerization of DNA and RNA is the basis for genetic inheritance for all living organisms. It is catalyzed by the DNA/RNA polymerase (Pol) superfamily. Here, bioinformatics analysis reveals that the incoming nucleotide substrate always forms an H-bond between its 3′-OH and β-phosphate moieties upon formation of the Michaelis complex. This previously unrecognized H-bond implies a novel self-activated mechanism (SAM), which synergistically connects the in situ nucleophile formation with subsequent nucleotide addition and, importantly, nucleic acid translocation. Thus, SAM allows an elegant and efficient closed-loop sequence of chemical and physical steps for Pol catalysis. This is markedly different from previous mechanistic hypotheses. Our proposed mechanism is corroborated via ab initio QM/MM simulations on a specific Pol, the human DNA polymerase-η, an enzyme involved in repairing damaged DNA. The structural conservation of DNA and RNA Pols supports the possible extension of SAM to Pol enzymes from the three domains of life

Multiscale Simulations to Dissect Enzymatic Processing of Nucleic Acids

Nucleic acid polymerization is a key process for genetic inheritance in all living cells. This is performed by a set of DNA/RNA polymerases (Pols) that are effective drug targets in nove therapies. However, DNA damages represent an obstacle for the replication machinery. Here, the role of trans-lesion synthesis polymerases, like DNA Polymerase-η (Pol-η), stand out. Pol-η bypasses ultraviolet-induced basing its function on a highly flexible and conserved R61 and on a transient third ion resolved at the catalytic site in post-reactive state. Nevertheless, how these element assist damaged-DNA replication is still poorly understood. We unravel a highly cooperative mechanism for DNA repair performed by human Pol-η that, via specific R61 conformations, assists the recruitment of the (nucleotide-triphosphate) dNTP in pre-reactive state and ehnances pyrophosphate leaving in post-reactive state. Moreover, bioinformatics analysis revealed that the dNTP always forms an intramolecular H-bond upon formation of the Michaelis-Menten complex. This previously unrecognized H-bond implies a novel self-activated mechanism (SAM), which synergistically connects the in situ nucleophile formation with subsequent nucleotide addition and nucleic acid translocation. Thus, SAM allows an elegant closed-loop sequence of chemical and physical steps for Pols catalysis. Our proposed mechanism is corroborated via ab initio QM/MM simulations on Pol-η. The structural conservation of DNA/RNA Pols supports the extension of SAM to all Pols. Finally, we identified key amino-acids and cations optimally placed nearby the active site of two-metal-ion enzymes and ribozymes such as group-II intron. Such elements interact with the reactants and orient the substrates into the active site, being therefore indispensable for catalysis. Our analysis suggests an unprecedented extension of the two-metal-ion architecture in DNA and RNA polymerases, nucleases and ribozymes. In spite of different biopolymer scaffolds, size and biological function, these enzymes have surprisingly preserved previously-unrecognized positively-charged elements at conserved structural positions to aid DNA and RNA processing

A Transient and Flexible Cation-π Interaction Promotes Hydrolysis of Nucleic Acids in DNA and RNA Nucleases

Metal-dependent DNA and RNA nucleases are enzymes that cleave nucleic acids with great efficiency and precision. These enzyme-mediated hydrolytic reactions are fundamental for the replication, repair, and storage of genetic information within the cell. Here, extensive classical and quantum-based free-energy molecular simulations show that a cation-π interaction is transiently formed in situ at the metal core of Bacteriophage-λ Exonuclease (Exo-λ), during catalysis. This noncovalent interaction (Lys131-Tyr154) triggers nucleophile activation for nucleotide excision. Then, our simulations also show the oscillatory dynamics and swinging of the newly formed cation-π dyad, whose conformational change may favor proton release from the cationic Lys131 to the bulk solution, thus restoring the precatalytic protonation state in Exo-λ. Altogether, we report on the novel mechanistic character of cation-π interactions for catalysis. Structural and bioinformatic analyses support that flexible orientation and transient formation of mobile cation-π interactions may represent a common catalytic strategy to promote nucleic acid hydrolysis in DNA and RNA nucleases

A Self-Activated Mechanism for Nucleic Acid Polymerization Catalyzed by DNA/RNA Polymerases

The enzymatic polymerization of DNA and RNA is the basis for genetic inheritance for all living organisms. It is catalyzed by the DNA/RNA polymerase (Pol) superfamily. Here, bioinformatics analysis reveals that the incoming nucleotide substrate always forms an H-bond between its 3′-OH and β-phosphate moieties upon formation of the Michaelis complex. This previously unrecognized H-bond implies a novel self-activated mechanism (SAM), which synergistically connects the in situ nucleophile formation with subsequent nucleotide addition and, importantly, nucleic acid translocation. Thus, SAM allows an elegant and efficient closed-loop sequence of chemical and physical steps for Pol catalysis. This is markedly different from previous mechanistic hypotheses. Our proposed mechanism is corroborated via ab initio QM/MM simulations on a specific Pol, the human DNA polymerase-η, an enzyme involved in repairing damaged DNA. The structural conservation of DNA and RNA Pols supports the possible extension of SAM to Pol enzymes from the three domains of life

A synthetic genetic polymer with an uncharged backbone chemistry based on alkyl phosphonate nucleic acids

The physicochemical properties of nucleic acids are dominated by their highly charged phosphodiester backbone chemistry. The polyelectrolyte structure decouples information content (base sequence) from bulk properties such as solubility and has been proposed as a defining trait of all informational polymers. However, this conjecture has not been tested experimentally. Here, we describe the encoded synthesis of a genetic polymer with an uncharged backbone chemistry: alkyl-phosphonate nucleic acids (phNA), in which the canonical, negatively charged phosphodiester is replaced by an uncharged P-alkylphosphonodiester backbone. Using synthetic chemistry and polymerase engineering, we describe the enzymatic, DNA-templated synthesis of P-methyl- and P-ethyl-phNAs, and the directed evolution of specific streptavidin-binding phNA aptamer ligands directly from random-sequence, mixed P-methyl- / P-ethyl-phNA repertoires. Our results establish a first example of the DNA-templated enzymatic synthesis and evolution of an uncharged genetic polymer and provide a foundational methodology for their exploration as a source of novel, functional molecules

The Origins and the Biological Consequences of the Pur/Pyr DNA·RNA Asymmetry

We analyze the physical origin and the chemical and biological consequences of the asymmetry that occurs in DNA·RNA hybrids when the purine/pyrimidine (Pu/Py) ratio is different in the DNA and RNA strands. When the DNA strand of the hybrid is Py rich, the duplex is much more stable, rigid, and A-like than when the DNA strand is Pu rich. The origins of this dramatic asymmetry are double: first, the apparently innocuous substitution dT → rU produces a significant decrease in stacking, and second, backbone distortions are larger for DNA(Pu)·RNA(Py) hybrids than for the mirror RNA(Pu)·DNA(Py) ones. The functional impact of the structural and dynamic asymmetry in the biological activities of hybrids is dramatic and can be used to improve the efficiency of antisense-type strategies on the basis of the degradation of hybrids by RNase H or gene editing using CRISPR-Cas9 technology

Agricoltura biologica e turismo sostenibile nelle aree protette: una scommessa per lo sviluppo locale. Caso studio - Parco delle Madonie

Allevatori e agricoltori spesso osteggiano parchi e aree naturali, accanendosi contro gli ambientalisti, per paura di vincoli alla loro attività produttiva. Gli ambientalisti ne favoriscono la costituzione ignorando sovente i timori degli agricoltori, perché sono luoghi dove la tutela dell’ambiente trova la sua massima espressione. A volte, fortunatamente, si trovano punti di accordo e interesse comune, perché l’area protetta valorizza non solo quello specifico ambiente, ma anche l’intera comunità rurale in essa presente e quindi anche le sue produzioni agricole ed agroalimentari. I punti di contatto tra le aree protette e l’agricoltura biologica sono molti e forti: l’agricoltura biologica si pone come obiettivo la produzione di alimenti sempre più sani e meno manipolati attraverso tecniche agronomiche appropriate; le aree protette si propongono la conservazione degli ambienti naturali e lo sviluppo delle attività sostenibili fra cui ovviamente anche l’agricoltura. La legge quadro delle aree protette prevede iniziative per la promozione economica e sociale e la possibilità di concedere a mezzo di specifiche convenzioni fra i produttori e l’Ente Parco, l’uso del nome e del logo dell’area protetta a servizi e prodotti locali, anche agricoli ed agroalimentari la cui finalità sia l’agevolazione promozionale di attività tradizionali. L’obiettivo del “marchio di origine” è educativo di sensibilizzazione e di formazione della categoria degli imprenditori agricoli. Le dirette conseguenze sono il mantenimento dell’integrità del suolo, la salubrità degli alimenti e la riqualificazione ecologica del territorio, finalità tipiche anche dell’agricoltura biologica. Riconoscendo questo importante legame tra agriturismo e agricoltura biologica, Aiab (Associazione Italiana di Agricoltura Biologica) ha promosso, a partire dal 1998, la costituzione del Circuito degli Agriturismi Bio- Ecologici a cui possono aderire quelle strutture che abbiano deciso di rispettare i criteri fissati dallo specifico standard Aiab e che abbiano ottenuto la certificazione rilasciata dall’Istituto per la Certificazione Etica e Ambientale (Icea). Gli agriturismi presenti nel circuito offrono l’opportunità di vedere e vivere la campagna nei suoi aspetti più affascinanti e originali, che sono il frutto di un sapiente incrocio di paesaggi naturali e tradizioni locali, ma anche del costante impegno degli agricoltori biologici a salvaguardia dell’ambiente e a protezione della sua diversità. E’ per questo che l’agricoltore biologico si rende disponibile ad accompagnare i propri ospiti in visita alle attività aziendali e, in oltre il 70% dei casi, organizza direttamente,o in collaborazione con associazioni esterne, visite ai parchi naturali presenti nelle vicinanze. Gli agriturismi Bio-Ecologici si contraddistinguono anche per una attenzione particolare alla gestione ambientale delle strutture ricettive attraverso la scelta di soluzioni tecnologiche che consentono di abbattere i consumi di energia e acqua, di razionalizzare la gestione e la raccolta differenziata dei rifiuti. Dai primi risultati di un’indagine condotta dal Dipartimento di Economia dei Sistemi Agro-Forestale dell’Università di Palermo sull’agricoltura delle aree protette in Sicilia, emerge l’ampia diffusione delle aziende agrituristiche-biologiche, in particolare nel comprensorio costituito dai 15 comuni che fanno parte del Parco Naturale Regionale delle Madonie (prov. di Palermo). Molti produttori che operano in questo territorio aderiscono al progetto “Saperi e Sapori”, cioè esibiscono i propri prodotti con il marchio del Parco. Il Parco Naturale Regionale delle Madonie è una delle quattro aree protette siciliane. La sua risorsa principale è l’agricoltura. Poiché la qualità alimentare non ha ragion d’essere se non c’è consapevolezza, il progetto, promosso dal Parco e sostenuto anche dalla Provincia di Palermo, ha messo in campo tutte le risorse disponibili sul territorio, a partire dalla conoscenze e dalle tradizioni familiari madonite e, con l’aiuto di Slow Food, ha avviato un progetto di educazione del gusto e di formazione per gli operatori dell’ospitalità e per i piccoli produttori artigiani madoniti