Backreef and beach carbonate sediments of the Red Sea,Saudi Arabia: impacts of reef geometry and currents on sediment composition

Three sites in the Red Sea were investigated to assess the variability of composition in Holocene sediments of the backreef environment within 0–2 m of water depth. This is important because composition of the sediment is commonly used to estimate water depth in ancient carbonate rocks. The site located at the King Abdullah Economic City (Saudi Arabia) contains a fringing reef with the reef tract located very close to the beach at the north end, flaring to the south to produce a narrower backreef area compared to the other two sites. This geometry produces a north to south current with a velocity of up to 15 cm s^?1, particularly during high onshore winds. The sediments contain predominantly non-skeletal grains, including peloids, coated grains, ooids, and grapestones that form on the bottom. The percentage of coralgal grains in the sediment was significantly lower than at the other two sites studied. Om Al Misk Island and Shoaiba have a much lower-velocity current within the backreef zone and contain predominantly coralgal sediments from the beach to the landward edge of the reef tract. The two locations containing the predominantly coralgal microfacies were statistically similar, but the King Abdullah Economic City site was statistically different despite having a similar water depth profile. Slight differences in reef configuration, including reef orientation and distance from the shore, can produce considerable differences in sediment thickness and composition within the backreef environment, which should induce caution in the interpretation of water depth in ancient carbonate rocks using composition.

     

Importance of vpr for infection of rhesus monkeys with simian immunodeficiency virus.

The importance of the vpr gene for simian immunodeficiency virus (SIV) replication, persistence, and disease progression was examined by using the infectious pathogenic molecular clone called SIVmac239. The ATG start codon of the vpr gene was converted to TTG by site-specific mutagenesis. The constructed Vpr- mutant virus is identical with the parental SIVmac239/nef-stop virus with the exception of this one nucleotide. These viruses replicated with similar kinetics and to similar extents in rhesus monkey lymphocyte cultures and in the human CEMX174 cell line. Five rhesus monkeys were inoculated with the Vpr- variant of SIVmac239/nef-stop, and two monkeys received SIVmac239/nef-stop as controls. Both controls showed reversion of the TAA stop signal in nef by 2 weeks postinfection, as has been observed previously. Reversion of the TAA stop codon in nef also occurred in the five monkeys that received the Vpr- variant, but reversion was delayed on average to about 4 weeks. Thus, the mutation in vpr appeared to delay the rapidity with which reversion occurred in the nef gene. Reversion of the TTG sequence in vpr to ATG was observed in three of the five test animals. Reversion in vpr was first observed in these three animals 4 to 8 weeks postinfection. No vpr revertants were found over the entire 66 weeks of observation in the other two test animals that received the vpr mutant. Antibodies to vpr developed in those three animals in which reversion of vpr was documented, but antibodies to vpr were not observed in the two animals in which reversion of vpr was not detected. Antibody responses to gag and to whole virus antigens were of similar strength in all seven animals. Both control animals and two of the test animals in which vpr reverted maintained high virus loads and developed progressive disease. Low virus burden and no disease have been observed in the two animals in which vpr did not revert and in the one animal in which vpr reversion was first detected only at 8 weeks. The reversion of vpr in three of the five test animals indicates that there is significant selective pressure for functional forms of vpr in vivo. Furthermore, the results suggest that both vpr and nef are important for maximal SIV replication and persistence in vivo and for disease progression.     

Sustaining Control of Schistosomiasis Mansoni in Western C?te d’Ivoire: Results from a SCORE Study,One Year after Initial Praziquantel Administration

Background

The Schistosomiasis Consortium for Operational Research and Evaluation (SCORE) has launched several large-scale trials to determine the best strategies for gaining and sustaining control of schistosomiasis and transitioning toward elimination. In Côte d’Ivoire, a 5-year cluster-randomized trial is being implemented in 75 schools to sustain the control of schistosomiasis mansoni. We report Schistosoma mansoni infection levels in children one year after the initial school-based treatment (SBT) with praziquantel and compare with baseline results to determine the effect of the intervention.

Methodology

The baseline cross-sectional survey was conducted in late 2011/early 2012 and the first follow-up in May 2013. Three consecutive stool samples were collected from 9- to 12-year-old children in 75 schools at baseline and 50 schools at follow-up. Stool samples were subjected to duplicate Kato-Katz thick smears. Directly observed treatment (DOT) coverage of the SBT was assessed and the prevalence and intensity of S. mansoni infection compared between baseline and follow-up.

Principal Findings

The S. mansoni prevalence in the 75 schools surveyed at baseline was 22.1% (95% confidence interval (CI): 19.5–24.4%). The DOT coverage was 84.2%. In the 50 schools surveyed at baseline and one year after treatment, the overall prevalence of S. mansoni infection decreased significantly from 19.7% (95% CI: 18.5–20.8%) to 12.8% (95% CI: 11.9–13.8%), while the arithmetic mean S. mansoni eggs per gram of stool (EPG) among infected children slightly increased from 92.2 EPG (95% CI: 79.2–105.3 EPG) to 109.3 EPG (95% CI: 82.7–135.9 EPG). In two of the 50 schools, the prevalence increased significantly, despite a DOT coverage of >75%.

Conclusions/Significance

One year after the initial SBT, the S. mansoni prevalence had decreased. Despite this positive trend, an increase was observed in some schools. Moreover, the infection intensity among S. mansoni-infected children was slightly higher at the 1-year follow-up compared to the baseline situation. Our results emphasize the heterogeneity of transmission dynamics and provide a benchmark for the future yearly follow-up surveys of this multi-year SCORE intervention study.     

Nonreplicating Vaccinia Virus Vectors Expressing the H5 Influenza Virus Hemagglutinin Produced in Modified Vero Cells Induce Robust Protection

The timely development of safe and effective vaccines against avian influenza virus of the H5N1 subtype will be of the utmost importance in the event of a pandemic. Our aim was first to develop a safe live vaccine which induces both humoral and cell-mediated immune responses against human H5N1 influenza viruses and second, since the supply of embryonated eggs for traditional influenza vaccine production may be endangered in a pandemic, an egg-independent production procedure based on a permanent cell line. In the present article, the generation of a complementing Vero cell line suitable for the production of safe poxviral vaccines is described. This cell line was used to produce a replication-deficient vaccinia virus vector H5N1 live vaccine, dVV-HA5, expressing the hemagglutinin of a virulent clade 1 H5N1 strain. This experimental vaccine was compared with a formalin-inactivated whole-virus vaccine based on the same clade and with different replicating poxvirus-vectored vaccines. Mice were immunized to assess protective immunity after high-dose challenge with the highly virulent A/Vietnam/1203/2004(H5N1) strain. A single dose of the defective live vaccine induced complete protection from lethal homologous virus challenge and also full cross-protection against clade 0 and 2 challenge viruses. Neutralizing antibody levels were comparable to those induced by the inactivated vaccine. Unlike the whole-virus vaccine, the dVV-HA5 vaccine induced substantial amounts of gamma interferon-secreting CD8 T cells. Thus, the nonreplicating recombinant vaccinia virus vectors are promising vaccine candidates that induce a broad immune response and can be produced in an egg-independent and adjuvant-independent manner in a proven vector system.Avian H5N1 influenza viruses, currently circulating mainly in southeast Asia, are likely to cause the next influenza pandemic (18, 26, 37). The supply of embryonated eggs for traditional influenza vaccine production may be endangered in this case. Efforts to produce inactivated H5N1 vaccines in permanent cells have resulted in large-scale manufacturing, for instance, in Vero cells (21). This approach, based either on fermentation of H5N1 wild-type (wt) viruses (21) or on viruses attenuated by reverse genetics (9, 31), is the most straightforward strategy for egg-independent, rapid vaccine production.A further approach that may result in more widely available, egg-independent H5 vaccines is the use of recombinant viral vectors expressing protective antigens. Promising protection results were obtained so far with adenovirus-based vectors in mouse models (13, 14). Adenovirus vectors are usually produced in permanent complementing cell lines (11) and have been widely used in clinical trials. Cancellation of a recent trial involving human immunodeficiency virus adenovirus vectors due to suspected enhancement of disease, however, may complicate the future use of these vectors (41). Poxvirus vectors, including recombinant modified vaccinia virus Ankara (MVA) (1, 43), constitute a further class of vectors that have been used to express H5N1 influenza virus antigens (5, 22, 44, 46). Usually, however, the large-scale production of MVA is carried out in primary chicken cells, since these are the most efficient production substrates and are also accepted by regulators. In a pandemic, this production platform may not be available because permanent nontumorigenic avian cell lines are currently not available for production.In this study, we used a permanent cell line, modified Vero cells, to produce nonreplicating vaccinia virus vectors expressing the H5 hemagglutinin (HA), the major influenza virus protective antigen. The defective vaccinia virus (dVV) vectors are safe due to their lack of replication capacity in normal hosts, while they share the superior immunizing properties of poxviral live vaccines (15, 33). Previously, a permanent cell line based on rabbit kidney cells was engineered to express the essential vaccinia virus D4R gene encoding the enzyme uracil-DNA-glycosylase. This cell line allowed the construction of replication-deficient vaccinia virus vectors (15). In this work, a complementing system based on Vero cells was established and used to produce the defective vaccinia virus vector dVV-HA5. The vector was used to immunize mice and was compared to an inactivated whole-virus (whv) vaccine and to replicating control viruses. The dVV-HA5 candidate vaccine induced neutralizing antibodies and full protection, similar to results with an inactivated whv vaccine. Further, it is important to ensure that the immune responses generated by a pandemic influenza vaccine give long-lived, broad, cross-clade protection. While antibody responses to influenza virus provide protective immunity, T-cell responses are also thought to play an important role in clearance of and recovery from infections. Thus, a vaccine which can produce both effective humoral and T-cell responses would be advantageous. A vaccinia virus vector-based pandemic influenza vaccine has the potential to provide this advantage.     

Seroepidemiology of Dengue virus in Mayotte, Indian Ocean, 2006

Background

Although Dengue virus (DENV) circulation had been documented in neighbouring South-western Indian Ocean Islands, its presence in Mayotte is poorly characterised. To address this issue, we aimed to assess the seroprevalence of dengue IgG antibodies (DENV-IgG Ab) among the population and to investigate potential associations with individual and household characteristics.

Methods/Principal Findings

In November–December 2006 we conducted a cross-sectional serologic survey in Mayotte among 1,154 inhabitants aged ≥2 years by using a multistage cluster random sampling method. The overall prevalence of DENV-specific IgG antibodies (ELISA) was 22.73% (95% CI, 18.16–27.31). The age-specific seroprevalence increased with age (χ² for trend = 11.86, P<0.0006), and was linked with previous known outbreaks in this region. In multivariate analysis, older age, being born in the Comoros and living in a household with a low socioeconomic index were positively associated with DENV IgG antibody positivity.

Conclusions

These findings document substantial prior exposure of the population of Mayotte to DENV and highlight the risk of severe illness due to the possibility of sequential DENV infections. Further investigations characterizing current DENV circulation patterns and associated serotypes are needed.     

Methylene blue for malaria in Africa: results from a dose-finding study in combination with chloroquine

Background

Atovaquone is part of the antimalarial drug combination atovaquone-proguanil (Malarone^®) and inhibits the cytochrome bc₁ complex of the electron transport chain in Plasmodium spp. Molecular modelling showed that amino acid mutations are clustered around a putative atovaquone-binding site resulting in a reduced binding affinity of atovaquone for plasmodial cytochrome b, thus resulting in drug resistance.

Methods

The prevalence of cytochrome b point mutations possibly conferring atovaquone resistance in Plasmodium falciparum isolates in atovaquone treatment-naïve patient cohorts from Lambaréné, Gabon and from South Western Ethiopia was assessed.

Results

Four/40 (10%) mutant types (four different single polymorphisms, one leading to an amino acid change from M to I in a single case) in Gabonese isolates, but all 141/141 isolates were wild type in Ethiopia were found.

Conclusion

In the absence of drug pressure, spontaneous and possibly resistance-conferring mutations are rare.     

A complement fixing polysaccharide from Biophytum petersianum Klotzsch, a medicinal plant from Mali, West Africa

Biophytum petersianum Klotzsch (syn. Biophytum sensitivum (L.) DC) is a medicinal plant having a traditional use, among others, as a wound healing remedy in Mali and other countries. As a water extract of the aerial parts of the plant is a frequently used preparation, we decided to look for a bioactive polysaccharide in this extract. One of the obtained polysaccharide fractions, BP100 III, isolated from a 100 degrees C water extract from the aerial parts of B. petersianum and having a monosaccharide composition typical for pectic substances, was shown to exhibit potent dose-dependent complement fixating activity. The BP100 III fraction was subjected to degradation by endo-alpha-d-(1-->4)-polygalacturonase, and three fractions were obtained by gel filtration. The highest molecular weight fraction, BP100 III.1, had a more potent activity in the complement test system than the native polymer, while the two lower molecular weight fractions were less active than the native polymer. The major part of BP100 III.1 consists of galacturonic acid and rhamnose, with branches being present on both the rhamnose and galacturonic acid residues. Arabinogalactan type II is also present in the polymer, indicating that BP100 III.1 has a structure typical of the hairy region of pectins. The major part of the two other fractions is a galacturonan, containing a strikingly high number of branch points, some to which xylose is attached. These results indicate that the pectic substance in B. petersianum contains both rhamnogalacturonan and xylogalacturonan regions.     

Crystal Structure of an Aquabirnavirus Particle: Insights into Antigenic Diversity and Virulence Determinism

Infectious pancreatic necrosis virus (IPNV), a pathogen of salmon and trout, imposes a severe toll on the aquaculture and sea farming industries. IPNV belongs to the Aquabirnavirus genus in the Birnaviridae family of bisegmented double-stranded RNA viruses. The virions are nonenveloped with a T=13l icosahedral capsid made by the coat protein VP2, the three-dimensional (3D) organization of which is known in detail for the family prototype, the infectious bursal disease virus (IBDV) of poultry. A salient feature of the birnavirus architecture is the presence of 260 trimeric spikes formed by VP2, projecting radially from the capsid. The spikes carry the principal antigenic sites as well as virulence and cell adaptation determinants. We report here the 3.4-Å resolution crystal structure of a subviral particle (SVP) of IPNV, containing 20 VP2 trimers organized with icosahedral symmetry. We show that, as expected, the SVPs have a very similar organization to the IBDV counterparts, with VP2 exhibiting the same overall 3D fold. However, the spikes are significantly different, displaying a more compact organization with tighter packing about the molecular 3-fold axis. Amino acids controlling virulence and cell culture adaptation cluster differently at the top of the spike, i.e., in a central bowl in IBDV and at the periphery in IPNV. In contrast, the spike base features an exposed groove, conserved across birnavirus genera, which contains an integrin-binding motif. Thus, in addition to revealing the viral antigenic determinants, the structure suggests that birnaviruses interact with different receptors for attachment and for cell internalization during entry.Birnaviruses form a distinct family of double-stranded RNA (dsRNA) viruses infecting vertebrates and invertebrates (18). Aquatic birnaviruses are the most abundant and diverse and are grouped in two separate genera: the Aquabirnavirus genus and the Blosnavirus genus, with infectious pancreatic necrosis virus (IPNV) and blotched snakehead virus (BSNV) (16) as respective type species. A third aquatic birnavirus of unassigned genus, Tellina virus 1, was recently described and found to be phylogenetically distant from the two established genera (40). However, the vast majority of aquatic birnaviruses are antigenically related to IPNV (i.e., belong to the Aquabirnavirus genus), regardless of host species or geographical origin (4, 11, 26, 39). They are implicated as etiological agents of disease in a variety of mollusks and fish species important in aquaculture, causing pathologies such as infectious pancreatic necrosis in salmonids, nephroblastoma and branchionephritis in eels, and gill necrosis in clams (21, 34, 50). Viruses in the Aquabirnavirus genus display considerable antigenic diversity and have substantial differences in biological properties such as host range and optimal replication temperature. These features contrast with the properties of other birnaviruses, in particular those infecting terrestrial species (avibirnaviruses and entomobirnaviruses). Based on reciprocal neutralization tests with polyclonal and monoclonal antibodies, nine cross-reacting serotypes (A1 to A9) have been defined for IPNV and related aquabirnaviruses (26). Serotype A2 (also known as Sp) is the most common serotype found in Europe.Birnavirus particles are nonenveloped, displaying a single-shelled T=13l icosahedral capsid of about 70 nm in diameter, composed of 260 trimers of viral protein 2 (VP2) (5, 15, 42). Internal to the virion are VP3, which forms a ribonucleoprotein complex with the genomic RNA (9, 27, 36), and VP1, the viral RNA-dependent RNA polymerase, which is found both free and covalently attached to the genomic RNA (19). The birnavirus genome consists of two segments of dsRNA. While the smaller segment B has a single open reading frame (ORF) coding for VP1, segment A has two, a large and a small ORF, encoding the polyprotein precursor pVP2-VP4-VP3 and the nonstructural VP5, respectively. VP4 is a protease that cleaves its own N and C termini off the polyprotein, thus also releasing pVP2 (the VP2 precursor) and VP3 within the infected cell (3, 20). Subsequent serial cleavages at the C terminus of pVP2 upon particle assembly yield mature VP2 (amino acids 1 to 442 of the IPNV polyprotein) and three other peptides that remain within the virion (22). The longest of these peptides was shown to destabilize cell membranes, suggesting a role during entry (40). Maturation of the pVP2 precursor during assembly and the presence of VP3 are important for correct morphogenesis of icosahedral, T=13l virus particles.Recombinant expression of mature VP2 alone leads to assembly of small, dodecahedral T=1 subviral particles (SVPs) containing 20 VP2 trimers (10). The crystal structures of the SVPs of infectious bursal disease virus of poultry (IBDV) were reported by several groups (15, 23, 31) as well as the three-dimensional (3D) structure of an intact T=13l IBDV virion (15).Exposed at the virion surface, VP2 displays the humoral antigenic determinants of the virus and is the only viral protein shown to induce protective immunity. Furthermore, VP2 plays a key role during virus entry, being responsible for receptor recognition (8). Key residues controlling virulence and cell culture adaptation of IPNV were thus found to map to VP2 (46).We report here the crystal structure of the IPNV SVP and show that, like its IBDV counterpart, it is composed of 20 VP2 trimers organized with T=1 icosahedral symmetry. IPNV VP2 displays the same fold, and the SVP is organized in the same way, as anticipated from the 43% overall amino acid sequence identity between the VP2s of the two viruses. The molecules differ significantly, however, in the loops of domain P, which forms the projections or spikes. In particular, the 3D structure shows a clustering of variable residues in the outermost loops at the top of domain P. Residues associated with virulence and cell culture adaptation map to the most peripheral of these loops—away from the 3-fold axis at the convex top of VP2. This is in contrast to IBDV, in which virulence determinants map to a central bowl at the top of the VP2 spike. These results provide new insights for understanding the determinism of antigenicity and virulence of Aquabirnavirus strains.     

Protection influence on grassland structure in Widou Thiengoly's grazing areas at Ferlo

This work consisted of analysing the impact of protection on the Widou Thiengoly's grasslands structure. Data were collected from three selected sites by the quadrat point methodology, consisting of reading the herbaceous on a 10 m line. These sites were the 2013 defended plot (site A), the 2009 semi‐protected plot (site B) and the unprotected grazing areas or off plot (site C). The results revealed a floristic composition of 45 species, belonging to 34 genera and 17 botanical families. The number of species identified was 28 in site A, 31 in site B and 29 in site C. Despite a certain similarity noted in the number of species, the herbaceous vegetation was more balanced in 2013 plot than in 2009 plot and in off plot where it tended to be homogeneous. The herbaceous cover in October 2015 was 99.8% in the 2013 plot; 98.8% in the 2009 plot; and 96.8% in the unprotected sites. The vertical stratification of herbaceous cover showed a better development at the intermediate strata (between 20 cm and 50 cm) in all the sites except in off plot where small grasses dominated. In this study, protection improved the specific balance, while semi‐protection had a positive effect on the specific richness and growth of the grasses.     

Cryptococcal Meningitis in Senegal: Epidemiology, Laboratory Findings, Therapeutic and Outcome of Cases Diagnosed from 2004 to 2011

Background

Cryptococcal meningitis is one of the most important opportunistic infection and a major contributor to early mortality. In sub-Saharan Africa, particularly in Senegal, prevalence of cryptococcal meningitis remains high. This study aimed to describe the epidemiology, laboratory profile, therapeutic and outcome of cases diagnosed in Dakar.

Methods

We analyzed the cryptococcosis cases diagnosed at the department of parasitology–mycology in Fann Teaching Hospital in Dakar from 2004 to 2011. The diagnosis was confirmed by culture on Sabouraud’s dextrose agar and/or by India ink preparation and/or by cryptococcal antigen detection. The diagnosis methods were assessed by using culture as reference.

Results

A total of 106 cases of cryptococcal meningitis were diagnosed. The prevalence of cryptococcal meningitis was 7.8 %. The mean age of the patients was 40.17 ± 9.89 years. There were slightly more male (53.8 %) than female (46.2 %) patients; 89.6 % were found to be infected with HIV, and the median CD4+ count was 27/mm³. Approximately 79.5 % of the patients had <100 CD4+ lymphocytes/mm³. India ink staining presented sensitivity at 94.11 % and specificity at 100 %. Sensitivity and specificity of cryptococcal antigen detection in cerebrospinal fluid were, respectively, 96.96 and 15.78 %. The most frequently used antifungal drug was fluconazole (86.7 %), and the mortality rate was 62.2 % (66 deaths).

Conclusion

Early diagnosis is essential to control cryptococcosis, and countries should prioritize widespread and reliable access to rapid diagnostic cryptococcus antigen assays. But it is important to make available conventional methods (India ink and culture) in the maximum of laboratory in regional health facilities.