Caratterizzazione genomica di virus influenzali suini in Italia mediante next generation sequencing

I sottotipi H1N1, H1N2 e H3N2 di influenza A virus sono largamente diffusi nella popolazione suina di tutto il mondo. Nel presente lavoro è stato sviluppato un protocollo di sequenziamento di c.d. nuova generazione, su piattaforma Ion Torrent PGM, idoneo per l’analisi di tutti i virus influenzali suini (SIV). Per valutare l’evoluzione molecolare dei SIV italiani, sono stati sequenziati ed analizzati mediante analisi genomica e filogenetica un totale di sessantadue ceppi di SIV appartenenti ai sottotipi H1N1, H1N2 e H3N2, isolati in Italia dal 1998 al 2014. Sono stati evidenziati in sei campioni due fenomeni di riassortimento: tutti i SIV H1N2 esaminati presentavano una neuraminidasi di derivazione umana, diversa da quella dei SIV H1N2 circolanti in Europa, inoltre l’emoagglutinina (HA) di due isolati H1N2 era originata dal riassortimento con un SIV H1N1 avian-like. L’analisi molecolare dell’HA ha permesso di rivelare un’inserzione di due amminoacidi in quattro SIV H1N1 pandemici e una delezione di due aminoacidi in quattro SIV H1N2, entrambe a livello del sito di legame con il recettore cellulare. E’ stata inoltre evidenziata un’elevata omologia di un SIV H1N1 con ceppi europei isolati negli anni ’80, suggerendo la possibile origine vaccinale di questo virus. E’ stato possibile, in aggiunta, applicare il nuovo protocollo sviluppato per sequenziare un virus influenzale aviare altamente patogeno trasmesso all’uomo, direttamente da campione biologico. La diversità genetica nei SIV esaminati in questo studio conferma l’importanza di un continuo monitoraggio della costellazione genomica dei virus influenzali nella popolazione suina.

Struttura filogenetica della comunità batterica associata ad Ostreopsis cf. Ovata in colture batch e dinamiche di crescita

Negli ultimi 10 anni i blooms attribuibili alla dinoflagellata bentonica Ostreopsis cf. ovata sono aumentati in termini di frequenza ed intensità lungo le coste del Mediterraneo, avendo ripercussioni negative sulla salute umana e forti impatti sulle comunità marine bentoniche, ciò a seguito della produzione di potenti tossine (composti palitossina-simili) da parte della microalga. Tra i fattori ecologici che innescano o regolano le dinamiche dei bloom tossici le interazioni tra microalghe e batteri sono in misura sempre maggiore oggetto di ricerca. In questo studio è stata analizzata la struttura filogenetica della comunità batterica associata ad O. cf. ovata in colture batch e valutate le dinamiche successionali della stessa in relazione alle differenti fasi di crescita della microalga (oltre che in relazione alle dinamiche di abbondanza virale). Lo studio filogenetico è stato effettuato tramite l’ausilio di metodiche molecolari di sequenziamento di next generation (Ion Torrent). Le abbondanze dei batteri e delle particelle virali sono state determinate tramite microscopia ad epifluorescenza; l’abbondanza cellulare algale è stata stimata tramite metodo Uthermohl. Il contributo della frazione batterica ad elevata attività respiratoria è stato determinato tramite doppia colorazione con coloranti DAPI e CTC. Dai dati emersi si evince che la comunità batterica attraversa due fasi di crescita distinte, una più marcata e concomitante con la fase esponenziale di O. cf. ovata, l'altra quando la microalga è in fase media stazionaria. Per quanto concerne la composizione filogenetica della comunità sono stati rilevati 12 phyla, 17 classi e 150 generi, sebbene i dati ottenuti abbiano rilevato una forte dominanza del phylum Proteobacteria con la classe Alphaproteobacteria, seguita dal phylum Bacteroidetes con la classe Sphingobacteria. Variazioni nella struttura filogenetica della comunità batterica, a livello di generi, tra le diverse fasi di crescita della microalga ha permesso di evidenziare ed ipotizzare particolari interazioni di tipo mutualistico e di tipo competitivo.

Analysis of coprolites from the extinct mountain goat Myotragus balearicus

Humans colonized the Balearic Islands 5-4 ka ago. They arrived in a uniquely adapted ecosystem with the Balearic mountain goat Myotragus balearicus (Bovidae, Antilopinae, Caprini) as the only large mammal. This mammal went extinct rapidly after human arrival. Several hypotheses have been proposed to explain the extinction of M. balearicus. For the present study ancient DNA analysis (Sanger sequencing, Roche-454, Ion Torrent), and pollen and macrofossil analyses were performed on preserved coprolites from M. balearicus, providing information on its diet and paleo-environment. The information retrieved shows that M. balearicus was heavily dependent on the Balearic box species Buxus balearica during at least part of the year, and that it was most probably a browser. Hindcast ecological niche modelling of B. balearica shows that local distribution of this plant species was affected by climate changes. This suggests that the extinction of M. balearicus can be related to the decline and regional extinction of a plant species that formed a major component of its diet. The vegetation change is thought to be caused by increased aridity occurring throughout the Mediterranean. Previous hypotheses relating the extinction of M. balearicus directly to the arrival of humans on the islands must therefore be adjusted. (C) 2013 University of Washington. Published by Elsevier Inn All rights reserved.

Evolution of genome sequencing techniques

The quality and the speed for genome sequencing has advanced at the same time that technology boundaries are stretched. This advancement has been divided so far in three generations. The first-generation methods enabled sequencing of clonal DNA populations. The second-generation massively increased throughput by parallelizing many reactions while the third-generation methods allow direct sequencing of single DNA molecules. The first techniques to sequence DNA were not developed until the mid-1970s, when two distinct sequencing methods were developed almost simultaneously, one by Alan Maxam and Walter Gilbert, and the other one by Frederick Sanger. The first one is a chemical method to cleave DNA at specific points and the second one uses ddNTPs, which synthesizes a copy from the DNA chain template. Nevertheless, both methods generate fragments of varying lengths that are further electrophoresed. Moreover, it is important to say that until the 1990s, the sequencing of DNA was relatively expensive and it was seen as a long process. Besides, using radiolabeled nucleotides also compounded the problem through safety concerns and prevented the automation. Some advancements within the first generation include the replacement of radioactive labels by fluorescent labeled ddNTPs and cycle sequencing with thermostable DNA polymerase, which allows automation and signal amplification, making the process cheaper, safer and faster. Another method is Pyrosequencing, which is based on the “sequencing by synthesis” principle. It differs from Sanger sequencing, in that it relies on the detection of pyrophosphate release on nucleotide incorporation. By the end of the last millennia, parallelization of this method started the Next Generation Sequencing (NGS) with 454 as the first of many methods that can process multiple samples, calling it the 2º generation sequencing. Here electrophoresis was completely eliminated. One of the methods that is sometimes used is SOLiD, based on sequencing by ligation of fluorescently dye-labeled di-base probes which competes to ligate to the sequencing primer. Specificity of the di-base probe is achieved by interrogating every 1st and 2nd base in each ligation reaction. The widely used Solexa/Illumina method uses modified dNTPs containing so called “reversible terminators” which blocks further polymerization. The terminator also contains a fluorescent label, which can be detected by a camera. Now, the previous step towards the third generation was in charge of Ion Torrent, who developed a technique that is based in a method of “sequencing-by-synthesis”. Its main feature is the detection of hydrogen ions that are released during base incorporation. Likewise, the third generation takes into account nanotechnology advancements for the processing of unique DNA molecules to a real time synthesis sequencing system like PacBio; and finally, the NANOPORE, projected since 1995, also uses Nano-sensors forming channels obtained from bacteria that conducts the sample to a sensor that allows the detection of each nucleotide residue in the DNA strand. The advancements in terms of technology that we have nowadays have been so quick, that it makes wonder: ¿How do we imagine the next generation?

Complete genome of a dengue virus serotype 4 strain from Amazonas, Brazil

Dengue virus (DENV) infections represent a significant concern for public health worldwide, being considered as the most prevalent arthropod-borne virus regarding the number of reported cases. In this study, we report the complete genome sequencing of a DENV serotype 4 isolate, genotype II, obtained in the city of Manaus, directly from the serum sample, applying Ion Torrent sequencing technology. The use of a massive sequencing technology allowed the detection of two variable sites, one in the coding region for the viral envelope protein and the other in the nonstructural 1 coding region within viral populations.

Kinetics of photocatalytic reduction of NO by CO with Pd2+-Ion-Substituted Nano-TiO2

The objective of the present study is to develop the reaction mechanism and kinetics of photoreduction of NO by CO. For this purpose, the reactions were conducted in the presence of Pd-ion-substituted nano-TiO2, Ti1-xPdxO2-delta, which was synthesized via a solution combustion method. The photocatalytic activity was investigated with unsubstituted TiO2, 1% Pd/TiO2(imp), and Ti1-xPdxO2-delta (where x = 0.05-0.3). No appreciable NO conversion was observed over unsubstituted TiO2, although, despite competitive adsorption of NO and CO on the Pd2+ sites, there was a significant reduction of NO over Ti1-xPdxO2-delta. The kinetic model showed that the enhanced catalytic activity is due to the NO photodissociation at the oxide-ion vacancy.

Crystal co-ordination of the barium ion

A systematic study has been made of the crystal co-ordination of the barium ion in various compounds whose structures have been solved. Apart from the more common co-ordination polyhedra which are enumerated in text-books, a number of new polyhedra have been identified, particularly in cases where the co-ordination numbers are unusual, such as ten or eleven. According to the radius-ratio rule of Pauling, a co-ordination number of nine or ten is normally expected for the barium ion. The present investigations, however, reveal that it shows a variety of co-ordinations with ligancies from six up to twelve. Some of the factors that might possibly enter in explaining this wide range of co-ordination numbers are discussed. It appears as though the part played by the Ba2+ ion in deciding the structure is secondary, limiting itself only to occupying vacant spaces provided by other atoms in the crystal.

Ion exchange equilibria between (Mn,Co)O solid solution and (Mn,Co)Cr2O4 and (Mn,Co)Al2O4 spinel solid solutions at 1100oC

The compositions of the (Mn,Co)O solid solution with rock salt structure in equilibrium with (Mn,Co)Cr2O4 and (Mn,Co)Al2O4 spinel solid solutions have been determined by X-ray diffraction measurements at 1100° C and an oxygen partial pressure of 10–10 atm. The ion exchange equilibria are quantitatively analysed, using values for activities in the (Mn,Co)O solid solution available in the literature, in order to obtain activities in the spinel solid solutions. The MnAl2O4-CoAl2O4 solid solution exhibits negative deviations from Raoult's law, consistent with the estimated cation disorder in the solid solution, while the MnCr2O4-CoCr2O4 solid solution shows slightly positive deviations. The difference in the Gibbs free energy of formation of the two pure chromites and aluminates derived from the results of this study are in good agreement with recent results obtained from solid oxide galvanic cells and gas-equilibrium techniques.

Enhanced photoluminescence of Gd2O3:Eu3+ nanophosphors with alkali (M = Li+, Na+, K+) metal ion co-doping

Gd1.95Eu0.4M0.01O3 (M = Li+ Na+ K+) nanophosphors have been synthesized by a low temperature solution combustion (LSC) method. Powder X-ray diffraction pattern (PXRD), scanning electron microscopy (SEM), UV-vis and photoluminescence (PL) measurements were carried out to characterize their structural and luminescent properties. The excitation and emission spectra indicated that the phosphor could be well excited by UV light (243 nm) and emit red light about 612 nm. The effect of alkali co-dopant on PL properties has been examined. The results showed that incorporation of Li+, Na+ and K+ in to Gd2O3:Eu3+ phosphor would lead to a remarkable increase of photoluminescence. The PL intensity of Gd2O3:Eu3+ phosphor was improved evidently by co-doping with Li+ ions whose radius is less than that of Gd3+ and hardly with Na+, K+ whose radius is larger than that of Gd3+. The effect of co-dopants on enhanced luminescence was mainly regarded as the result of a suitable local distortion of crystal field surrounding the Eu3+ activator. These results will play an important role in seeking some more effective co-dopants. (C) 2011 Published by Elsevier B.V.

Activation of Lattice Oxygen of TiO2 by Pd2+ Ion: Correlation of Low-Temperature CO and Hydrocarbon Oxidation with Structure of Ti1-xPdxO2-x (x=0.01-0.03)

Lattice oxygen of TiO2 is activated by the substitution of Pd ion in its lattice. Ti1-xPdxO2-x (x = 0.01-0.03) have been synthesized by solution combustion method crystallizing in anatase TiO2 structure. Pd is in +2 oxidation state and Ti is in +4 oxidation state in the catalyst. Pd is more ionic in TiO2 lattice compared to Pd in PdO. Oxygen storage capacity defined by ``amount of oxygen that is used reversibly to oxidize CO'' is as high as 5100 mu mol/g of Ti0.97Pd0.03O1.97. Oxygen is extracted by CO to CO2 in absence of feed oxygen even at room temperature which is more than 20 times compared to pure TiO2. Rate of CO oxidation is 2.75 mu mol g(-1) s(-1) at 60 degrees C over Ti0.97Pd0.03O1.97 and C2H2 gets oxidized to CO2 and H2O at room temperature. Catalyst is not poisoned on long time operation of the reactor. Such high catalytic activity is due to activated lattice oxygen created by the substitution of Pd ion as seen from first-principles density functional theory (DFT) calculations with 96 atom supercells of Ti32O64, Ti31Pd1O63, Ti30Pd2O62, and Ti29Pd3O61. The compounds crystallize in anatase TiO2 structure with Pd2+ ion in nearly square planar geometry and TiO6 octahedra are distorted by the creation of weakly bound oxygens. Structural analysis of Ti31Pd1O63 which is close to 3% Pd ion substituted TiO2 shows that oxygens associated with both Ti and Pd ions in the lattice show bond valence sum of 1.87, a low value characteristic of weak oxygen in the lattice compared to oxygens with valence 2 and above in the same lattice. Exact positions of activated oxygens have been identified in the lattice from DFT calculations.

Li3MRuO5 (M = Co, Ni), new lithium-rich layered oxides related to LiCoO2: promising electrochemical performance for possible application as cathode materials in lithium ion batteries

We describe the synthesis and crystal structure of Li3MRuO5 (M = Co and Ni), new rock salt related oxides. Both the oxides crystallize in the layered LiCoO2 (alpha-NaFeO2) structure, as revealed by powder XRD data. Magnetic susceptibility data suggest that the oxidation states of transition metals are Li3Co3+(ls)Ru4+(ls) O-5 (ls = low spin) for the M = Co compound and Li3Ni2+Ru5+O5 for the M = Ni compound. Electrochemical investigations of lithium deintercalation-intercalation behaviour reveal that both Co and Ni phases exhibit attractive specific capacities of ca. 200 mA h g(-1) at an average voltage of 4 V that has been interpreted as due to the oxidation of Co3+ and Ru4+ in Li3CoRuO5 and Ni2+ to Ni4+ in the case of Li3NiRuO5. Thus, a different role of Ru ions is played in the isostructural oxides. Finally, in both cases evidence of irreversible behaviour above 4.2 V is observed and interpreted as formation of high valent ions or alternatively oxidation of oxide ions.

Ridge optical waveguide in an Er3+/Yb3+ co-doped phosphate glass produced by He+ ion implantation combined with Ar+ ion beam etching

This paper reports on the fabrication and characterization of a ridge optical waveguide in an Er3+/Yb3+ co-doped phosphate glass. The He+ ion implantation (at energy of 2.8 MeV) is first applied onto the sample to produce a planar waveguide substrate, and then Ar+ ion beam etching (at energy of 500 eV) is carried out to construct rib stripes on the sample surface that has been deposited by a specially designed photoresist mask. According to a reconstructed refractive index profile of the waveguide cross section, the modal distribution of the waveguide is simulated by applying a computer code based on the beam propagation method, which shows reasonable agreement with the experimentally observed waveguide mode by using the end-face coupling method. Simulation of the incident He ions at 2.8 MeV penetrating into the Er3+/Yb3+ co-doped phosphate glass substrate is also performed to provide helpful information on waveguide formation.

The transition from Eu3+ to Eu2+ in SiO2(Eu) thin films prepared by ion implantation and co-sputtering

Eu ions doped SiO2 thin films, SiO2( Eu), were prepared by co-sputtering of SiO2 and Eu2O3 and Eu ion implantation into thermally grown SiO2 films. The Eu-L-3-edge X-ray absorption near edge structure (XANES) spectra of SiO2(Eu) films show a doublet absorption peak structure with energy difference of 7 eV, which indicates the conversion of Eu3+ to Eu2+ at high annealing temperature in N-2. The strong blue luminescence of SiO2(Eu) films prepared by ions implantation after films annealed above 1100 degreesC confirms the above argument.

Study of ion solvation and ion association in polymer gel electrolyte with polyethylene oxide-co-polypropylene oxide as a plasticizer

Using a molal conductance method, ion solvation and ion association in polytriethylene glycol dimethacrylate (PTREGD)-LiClO4 gel electrolytes with amorphous ethylene oxide-co-propylene oxide (EO-co-PO, <(M)over bar (n)>, = 1750) as the plasticizer were investigated. It was found that the fraction of solute existing as single ions (alpha(i)) and ion pairs (alpha(p)) decreases, while that of triple ions (alpha(t)) increases linearly with increasing salt concentration. The dependence of these fractions on molecular weight of plasticizer was also examined. It was shown that alpha(i) and alpha(t) increase and alpha(p) decreases with increasing molecular weight. The result of temperature dependence of these fractions was very interesting: when the temperature is lower than 55 degrees C, alpha(i) increases while alpha(p) and alpha(t) decrease with increasing temperature; however, when the temperature is higher than 55 degrees C, the reverse is true.