Two different <i>Xylella fastidiosa</i> strains circulating in Italy: phylogenetic and evolutionary analyses

<p><i>Xylella fastidiosa</i>, a bacterial species infecting a broad range plants, includes five subspecies, <i>fastidiosa, multiplex, pauca, mulberry and sandyi.</i> In Europe, <i>Xylella</i> was isolated in olive trees in southern Italy (Apulia region) during the year 2013. The aim of the present study was to apply phylogenetic and evolutionary analysis to trace the possible origin and way of the entrance of <i>Xylella fastidiosa</i> in Italy. All the genomes available for <i>Xylella fastidiosa</i> spp were downloaded from NCBI. A phylogeographic analysis was performed using BEAST. <i>X. fastidiosa</i> strains belonging to <i>X. fastidiosa</i> subsp. <i>pauca</i> and subsp. <i>sandyi</i> have been reported to infect olive trees and coffee plants, respectively. The phylogeographic analysis also revealed and confirmed these two different ways of provenience <i>X. fastidiosa</i> subsp. <i>pauca</i> from Costa Rica and <i>X. fastidiosa</i> subsp <i>sandyi</i> from California Phylogeny have been an important tool to validate and support the recent hypothesis for <i>X. fastidiosa pauca</i> provenience.</p

MSP classification dendrogram. Dotted lines position indicates the arbitrary distance levels at 500, 180, 140 and 70 used for strains clustering analysis.

<p>MSP classification dendrogram. Dotted lines position indicates the arbitrary distance levels at 500, 180, 140 and 70 used for strains clustering analysis.</p

Non pneumococcal VGS isolates MALDI-TOF, VITEK II, <i>soda and tuf</i> identification versus <i>rpoB</i> genes sequencing: group concordance.

<p>Non pneumococcal VGS isolates MALDI-TOF, VITEK II, <i>soda and tuf</i> identification versus <i>rpoB</i> genes sequencing: group concordance.</p

VGS isolates phenotypic and identification results.

<p>VGS isolates phenotypic and identification results.</p

Sequences of oligonucleotides used in this study.

<p>Sequences of oligonucleotides used in this study.</p

Phylogenesys and homology modeling in Zika virus epidemic: food for thought

<p>Zika virus (ZIKV) is an emerging Flavivirus that have recently caused an outbreak in Brazil and rapid spread in several countries. In this study, the consequences of ZIKV evolution on protein recognition by the host immune system have been analyzed. Evolutionary analysis was combined with homology modeling and T-B cells epitope predictions. Two separate clades, the African one with the Uganda sequence, as the most probable ancestor, and the second one containing all the most recent sequences from the equatorial belt were identified. Brazilian strains clustered all together and closely related to the French Polynesia isolates. A strong presence of a negatively selected site in the envelope gene (<i>Env</i>) protein was evidenced, suggesting a probable purging of deleterious polymorphisms in functionally important genes. Our results show relative conservancy of ZIKV sequences when envelope and other non-structural proteins (NS3 and NS5) are analyzed by homology modeling. However, some regions within the consensus sequence of NS5 protein and to a lesser extent in the envelope protein, show localized high mutation frequency corresponding to a considerable alteration in protein stability. In terms of viral immune escape, envelope protein is under a higher selective pressure than NS5 and NS3 proteins for HLA class I and II molecules. Moreover, envelope mutations that are not strictly related to T-cell immune responses are mostly located on the surface of the protein in putative B-cell epitopes, suggesting an important contribution of B cells in the immune response as well.</p

Kaplan Meier plot of CMV reactivation according to the type of conditioning chemotherapy regimen (BEAM vs. FEAM vs. MEL).

<p>Kaplan Meier plot of CMV reactivation according to the type of conditioning chemotherapy regimen (BEAM vs. FEAM vs. MEL).</p

CMV DNAemia at reactivation distributed between different IL28B/IFNλ4 genotypes.

<p>CMV DNAemia at reactivation distributed between different IL28B/IFNλ4 genotypes.</p

Pre-transplant viral screening.

<p>Pre-transplant viral screening.</p

Lysosomal Acid Lipase Activity Is Reduced Both in Cryptogenic Cirrhosis and in Cirrhosis of Known Etiology - Fig 1

<p>DBS-determined LAL activity in cryptogenic cirrhotics, cirrhotics of known etiology and healthy subjects (Panel A). Percentages of cirrhotic patients and healthy subjects with normal (≥0.8 nmol/spot/h), mildly reduced (range 0.4–0.8 nmol/spot/h), or severely reduced LAL activity (<0.4 nmol/spot/h) (Panel B).</p