New Insights into Asian Prunus Viruses in the Light of NGS-Based Full Genome Sequencing

Double stranded RNAs were purified from five Prunus sources of Asian origin and submitted to 454 pyrosequencing after a random, whole genome amplification. Four complete genomes of Asian prunus virus 1 (APV1), APV2 and APV3 were reconstructed from the sequencing reads, as well as four additional, near-complete genome sequences. Phylogenetic analyses confirmed the close relationships of these three viruses and the taxonomical position previously proposed for APV1, the only APV so far completely sequenced. The genetic distances in the respective polymerase and coat protein genes as well as their gene products suggest that APV2 should be considered as a distinct viral species in the genus Foveavirus, even if the amino acid identity levels in the polymerase are very close to the species demarcation criteria for the family Betaflexiviridae. However, the situation is more complex for APV1 and APV3, for which opposite conclusions are obtained depending on the gene (polymerase or coat protein) analyzed. Phylogenetic and recombination analyses suggest that recombination events may have been involved in the evolution of APV. Moreover, genome comparisons show that the unusually long 3’ non-coding region (3'' NCR) is highly variable and a hot spot for indel polymorphisms. In particular, two APV3 variants differing only in their 3’ NCR were identified in a single Prunus source, with 3'' NCRs of 214–312 nt, a size similar to that observed in other foveaviruses, but 567–850 nt smaller than in other APV3 isolates. Overall, this study provides critical genome information of these viruses, frequently associated with Prunus materials, even though their precise role as pathogens remains to be elucidated.     

Biostratigraphie d’après les foraminifères et paléoenvironnements des séries post-Éocène du sondage ASHTART 28, golfe de Gabès (Tunisie)

The Cenozoic sequence of Ashtart 28 well drilled in the Gulf of Gabes (Tunisia) is the subject of a biostratigraphical study. The samples recovered in cuttings from 390 m and downwards allowed to recognize, above the Late Eocene sediments, a sedimentary series, lithologically diversified, nearly 1600 m thick. Marine Pliocene deposits, generally attesting a low bathymetry, lie unconformably above the Messinian (Oued Bel Khedim formation), which shows the usual features of the Mediterranean confinement. The underlying Messinian pre-evaporitic platform series (Melqart formation), that is over 250 m thick, is typical of a perireefal environment. The sediments assigned to the Tortonian (Somâa Sands formation) are continental and occur unconformably above the approximately 500-metres-thick Middle Miocene strata (Saouaf, Mahmoud, Aïn Grab and Salammbô pars formations). The marine Lower Miocene and Oligocene sediments (Salammbô pars and Ketatna formations), that are more than 300 m thick, lie in continuity under the Middle Miocene. The infralittoral Chattian sequence has especially supplied a diversified assemblage of larger foraminifera recovered in other west-mediterranean basins. Datings were obtained based on planktonic and larger benthic foraminifera (Miogypsinidae, Nummulitidae, Lepidocyclinidae) and by correlations obtained by means of well loggings and lithostratigraphy. Benthic foraminifera, mainly listed for the Miocene and Oligocene, are studied from a systematic, stratigraphic and paleogeographic point of view. The paleoenvironments of deposits are defined for each considered stratigraphic interval. Comparisons are sketched with other drillings of the Gulf of Gabes. Thanks to the numerous data obtained by this detailed study, the Ashtart drilling can serve as a reference for the Tertiary sequence of this part of the Mediterranean domain.     

Dramatic efficacy improvement of a DC-based vaccine against AML by CD25 T cell depletion allowing the induction of a long-lasting T cell response

Dendritic cell (DC)-based vaccination is a promising approach to enhance anti-tumor immunity that could be considered for acute myeloid leukemia (AML) patients with high-risk of relapse. Our purpose was to study the efficiency and to optimize the immunogenicity of a DC-based vaccine in a preclinical AML murine model. In this report, C57BL6 mice were vaccinated with DC pulsed with peptides eluted (EP) from the syngeneic C1498 myelomonocytic leukemic cell line in a prophylactic setting. In this model, a natural antileukemic immunity mediated by NK cells was observed in the control unloaded DC-vaccinated group. On the other hand, we showed that the cytotoxic antileukemic immune response induced by vaccination with eluted peptides pulsed-DC (DC/EP), in vitro and in vivo, was mainly mediated by CD4⁺ T cells. Treatment with anti-CD25 antibody to deplete CD4⁺ CD25⁺ regulatory T cells before DC-vaccination dramatically improved the antileukemic immune response induced by immunization, and allowed the development of long-lasting immune responses that were tumor protective after a re-challenge with leukemic cells. Our results suggest that this approach could be successful against weakly immunogenic tumors such as AML, and could be translated in human.     

Production of 3-hydroxy-γ-decalactone, the precursor of two decenolides with flavouring properties, by the yeast Yarrowia lipolytica

3-Hydroxy-γ-decalactone is the precursor of dec-2 and dec-3-en-4-olides which are valuable aroma compounds not yet produced. To promote the accumulation of this lactone, the yeast Yarrowia lipolytica was placed in different environmental conditions aiming at altering β-oxidation fluxes. The concentration of substrate, pH, aeration and dissolved oxygen level were modified. We observed an important accumulation at low aeration (0.40 molar yields) and, to a lesser extent, at lower pH (0.15). As oxygen played a key-role, we evaluated its effect at fixed dissolved oxygen and at the pH which was the most favourable to the biotransformation (pH 4.5). At 5% and 30% dissolved oxygen, yields reached 0.50. β-Oxidation fluxes are very dependent on the presence of oxygen and conditions of accumulation of 3-hydroxy-γ-decalactone with very high yields were identified. These results are an important step in the production of the two decenolides. Moreover, they show the high dependence of β-oxidation fluxes on environmental conditions and relate these conditions to the accumulation of intermediates, results that are of interest to all the processes using yeast on lipids or alkanes.     

Tsukamurella tyrosinosolvens - An unusual case report of bacteremic pneumonia after lung transplantation

Intravesical administration of Bacillus Calmette-Guérin is used as a treatment method in superficial bladder cancer. While it is generally well tolerated, serious side effects may develop. Granulomatous hepatitis cases have been previously reported; however, only one case with tuberculous peritonitis exists in the current literature. We hereby present two cases, one of which is the second tubercular peritonitis case following Bacillus Calmette-Guérin treatment to be reported, and the other a case with granulomatous hepatitis. Complete cure was achieved in both cases with specific therapy. In the patient who developed peritonitis, intravesical Bacillus Calmette-Guérin therapy was recommenced after antituberculosis treatment, and completed without further complications.     

Allelic Diversity among Helicobacter pylori Outer Membrane Protein Genes homB and homA Generated by Recombination

Recombination is one of the main mechanisms contributing to Helicobacter pylori genomic variability. homB and homA are paralogous genes coding for H. pylori outer membrane proteins (OMPs). Both genes display allelic variation yielded by polymorphisms of the genes'' middle regions, with six different alleles. This study used bioinformatic and statistical analyses to evaluate whether the allelic diversity of homB and homA is generated by recombination. A detailed molecular analysis of the most prevalent homB allelic variant was also performed to establish its molecular profile. The two most prevalent homB and homA allelic variants resulted from interallelic homologous recombination between the rarest allelic variants of each gene, with a crossover point localized in the middle of the genes, containing the allelic region. Molecular analysis of the most prevalent homB allele revealed a geographic partition among Western and East Asian strains, more noticeable for the 5′ and 3′ homB regions than for the middle allelic regions. In conclusion, the diversity of the 5′ and 3′ homB regions reflect the strains'' geographical origin, and variants likely occur via the accumulation of single nucleotide polymorphisms. On the other hand, homologous recombination seems to play an important role in the diversification of the highly polymorphic homB and homA allele-defining regions, where the most prevalent alleles worldwide result from genomic exchange between the rarest variants of each gene, suggesting that the resulting combinations confer biological advantages to H. pylori. This phenomenon illustrates an evolutionary scenario in which recombination appears to be associated with ecological success.The Gram-negative bacterium Helicobacter pylori colonizes the stomachs of more than half of the world''s population, and this infection is associated with diverse gastroduodenal diseases (6, 16, 27). The risk of developing severe gastric diseases is influenced by H. pylori strain-dependent factors, among which are several outer membrane proteins (OMPs) that have been identified as virulence factors such as the babA/babB, hopZ, hopQ, sabA, oipA, and homB proteins (8, 17, 24, 28, 31, 48).The homB gene and its highly similar (90% similarity at the nucleotide level) paralogous gene, homA, are members of the H. pylori OMP gene family (2). Both genes can be present in the H. pylori genome at two conserved loci, as a single copy or as two copies (homA/homA, homB/homB, homA/homB, or homB/homA) (28, 29). The homB gene has been proposed as a H. pylori virulence candidate, since its presence was correlated with severe gastroduodenal disease (19, 30) and with corpus inflammation and atrophy, as demonstrated by pathological analyses (19). Moreover, a putative role as an adhesin was suggested for the corresponding protein HomB, since homB knockout mutant strains showed significantly reduced binding (28). HomB was also shown to be antigenic and implicated in the in vitro activation of interleukin-8 secretion (28).In contrast, the homA gene has been correlated with nonulcer gastritis (28, 30), and histological analyses did not show any association between the presence of the homA gene and inflammation or atrophy (19). The corresponding protein was also shown to be antigenic in humans (29).Similar to other H. pylori OMP-encoding genes, such as babA/babB, hopM/hopN and hopQ (8, 20, 32), homB and homA genes display allelic variation which, in this case, was shown to occur in 300-bp regions localized in the middle of these genes, with homB displaying greater allelic diversity than homA (29). This highly polymorphic region, spanning from approximately 750 to 1,050 bp in homB (≈2,007 bp) and from 720 to 980 bp in homA (≈1,980 bp), was identified by the analysis of the similarity plot of each gene (29). Based on these plots, three segments were thus defined for those genes, where segments 1, 2, and 3 correspond to the regions preceding, matching, and following the allelic zone, respectively (see Fig. ​Fig.2C)2C) (29). Moreover, detailed sequence analyses, at nucleotide and amino acid levels, of homB and homA segment 2 were also performed, revealing the existence of six distinct and well-conserved allelic variants denominated AI to AVI. Five distinct alleles were observed for homB (AI, AII, AIII, AV, and AVI), while three allelic variants were observed for the homA gene (AII, AIII, and AIV). The variants AI, AV, and AVI were exclusively observed in homB, whereas AIV was present only in homA. Each gene displayed a predominant worldwide allelic variant (AI and AII for homB and homA, respectively), which was present in up to 80% of the clinical strains (29).Open in a separate windowFIG. 2.(A, B) Nucleotide sequences of crossovers for Helicobacter pylori homB (A) and homA (B) genes. Numbers represent positions relative to the start codon of homB or homA, dots represent positions where nucleotides match between the recombinant and the parental sequences, and hyphens represent deletions. Crossover regions are highlighted in gray, bordered by two informative sites (in boldface), obtained from SimPlot/bootscan analyses. Between the informative sites, the recombinant allele displays no specific similarity with any of the parental alleles. (C) Localization of the crossover regions within the allelic regions for homB and homA.H. pylori displays one of the highest levels of genomic variability known among bacteria, and the high frequency of recombination is one of the main mechanisms contributing to that diversity (11, 39-41). Intragenomic recombination involving some of the OMP paralogous genes was also known to take place during infection, probably reflecting the selective pressure for adhesion, which may differ across different hosts as well as within an individual over time (5, 20, 38).Accordingly, the present study aimed to identify recombination phenomena that may have occurred within and between homB and homA allelic variants, which may underlie the genetic diversity and generation of alleles. Furthermore, considering that homB presents a worldwide dispersion (homA is rarely found among East Asian strains) and that the AI allele is the predominant homB variant worldwide (29), a detailed molecular analysis of this allele was performed in order to establish its molecular profile.     

Impact of drug stock-outs on death and retention to care among HIV-infected patients on combination antiretroviral therapy in Abidjan, Côte d'Ivoire

Background

To evaluate the type and frequency of antiretroviral drug stock-outs, and their impact on death and interruption in care among HIV-infected patients in Abidjan, Côte d''Ivoire.

Methods and Findings

We conducted a cohort study of patients who initiated combination antiretroviral therapy (cART) in three adult HIV clinics between February 1, 2006 and June 1, 2007. Follow-up ended on February 1, 2008. The primary outcome was cART regimen modification, defined as at least one drug substitution, or discontinuation for at least one month due to drug stock-outs at the clinic pharmacy. The secondary outcome for patients who were on cART for at least six months was interruption in care, or death. A Cox regression model with time-dependent variables was used to assess the impact of antiretroviral drug stock-outs on interruption in care or death. Overall, 1,554 adults initiated cART and were followed for a mean of 13.2 months. During this time, 72 patients discontinued treatment and 98 modified their regimen because of drug stock-outs. Stock-outs involved nevirapine and fixed-dose combination zidovudine/lamivudine in 27% and 51% of cases. Of 1,554 patients, 839 (54%) initiated cART with fixed-dose stavudine/lamivudine/nevirapine and did not face stock-outs during the study period. Among the 975 patients who were on cART for at least six months, stock-out-related cART discontinuations increased the risk of interruption in care or death (adjusted hazard ratio [HR], 2.83; 95%CI, 1.25–6.44) but cART modifications did not (adjusted HR, 1.21; 95%CI, 0.46–3.16).

Conclusions

cART stock-outs affected at least 11% of population on treatment. Treatment discontinuations due to stock-outs were frequent and doubled the risk of interruption in care or death. These stock-outs did not involve the most common first-line regimen. As access to cART continues to increase in sub-Saharan Africa, first-line regimens should be standardized to decrease the probability of drug stock-outs.     

The pharyngeal pouches and clefts: Development,evolution, structure and derivatives

The pharyngeal arches form the face and neck of the developing embryo. The pharyngeal tissue is divided into distinct arches by the formation of clefts and pouches in between the arches. These clefts and pouches form at the juxtaposition between the ectoderm and endoderm and develop into a variety of essential structures, such as the ear drum, and glands such as the thymus and parathyroids. How these pouches and clefts between the arches form and what structures they develop into is the subject of this review. Differences in pouch derivatives are described in different animals and the evolution of these structures are investigated. The implications of defects in pouch and cleft development on human health are also discussed.     

Functional central polypurine tract provides downstream protection of the human immunodeficiency virus type 1 genome from editing by APOBEC3G and APOBEC3B

Lentiviruses utilize two polypurine tracts for initiation of plus-strand viral DNA synthesis. We have examined to what extent human immunodeficiency virus type 1 plus-strand initiation at the central polypurine tract (cPPT) could protect the viral genome from DNA editing by APOBEC3G and APOBEC3B. The presence of a functional cPPT, but not of a mutated cPPT, extensively reduced editing by both APOBEC3G and APOBEC3B of sequences downstream, but not upstream, of the cPPT, with significant protection observed as far as 400 bp downstream. Thus, in addition to other potential functions, the cPPT could help protect lentiviruses from editing by cytidine deaminases of the APOBEC family.