A Bridge Crosses the Active-Site Canyon of the Epstein-Barr Virus Nuclease with DNase and RNase Activities

Epstein-Barr virus, a double-stranded DNA (dsDNA) virus, is a major human pathogen from the herpesvirus family. The nuclease is one of the lytic cycle proteins required for successful viral replication. In addition to the previously described endonuclease and exonuclease activities on single-stranded DNA and dsDNA substrates, we observed an RNase activity for Epstein-Barr virus nuclease in the presence of Mn²⁺, giving a possible explanation for its role in host mRNA degradation. Its crystal structure shows a catalytic core of the D-(D/E)XK nuclease superfamily closely related to the exonuclease from bacteriophage lambda with a bridge across the active-site canyon. This bridge may reduce endonuclease activity, ensure processivity or play a role in strand separation of dsDNA substrates. As the DNA strand that is subject to cleavage is likely to make a sharp turn in front of the bridge, endonuclease activity on single-stranded DNA stretches appears to be possible, explaining the cleavage of circular substrates.     

Diphtheria in Lao PDR: Insufficient Coverage or Ineffective Vaccine?

Background

During late 2012 and early 2013 several outbreaks of diphthe-ria were notified in the North of the Lao People’s Democratic Republic. The aim of this study was to determine whether the re-emergence of this vaccine-preventable disease was due to insufficient vaccination coverage or reduction of vaccine effectiveness within the affected regions.

Methods

A serosurvey was conducted in the Huaphan Province on a cluster sampling of 132 children aged 12–59 months. Serum samples, socio-demographic data, nutri-tional status and vaccination history were collected when available. Anti-diphtheria and anti-tetanus IgG antibody levels were measured by ELISA.

Results

Overall, 63.6% of participants had detectable diphtheria antibodies and 71.2% tetanus antibodies. Factors independently associated with non-vaccination against diphtheria were the distance from the health centre (OR: 6.35 [95% CI: 1.4–28.8], p = 0.01), the Lao Theung ethnicity (OR: 12.2 [95% CI:1,74–85, 4], p = 0.01) and the lack of advice on vac-cination given at birth (OR: 9.8 [95% CI: 1.5–63.8], (p = 0.01) while the level of maternal edu-cation was a protective factor (OR: 0.08 [95% CI: 0.008–0.81], p = 0.03). Most respondents claimed financial difficulties as the main reason for non-vaccination. Out of 55 children whose vaccination certificates stated that they were given all 3 doses of diphtheria-containing vaccine, 83.6% had diphtheria antibodies and 92.7% had tetanus antibodies. Furthermore, despite a high prevalence of stunted and underweight children (53% and 25.8%, respectively), the low levels of anti-diphtheria antibodies were not correlated to the nutritional status.

Conclusions

Our data highlight a significant deficit in both the vaccination coverage and diphtheria vaccine effectiveness within the Huaphan Province. Technical defi-ciencies in the methods of storage and distribution of vaccines as well as unreliability of vac-cination cards are discussed. Several hypotheses are advanced to explain such a decline in immunity against diphtheria and recommendations are provided to prevent future outbreaks.     

Effects of heat on the germination of sclerophyllous forest species in the highlands of Madagascar

The effects of fire on germination have been extensively studied in many ecosystems. Several studies have shown that plant species in ecosystems frequently exposed to fire can survive through two main mechanisms: vegetative regeneration (re‐sprouts) and recruitment of new individuals from a fire‐resistant seed bank. In Africa, an increase in temperature can break seed dormancy and stimulate germination of some herbaceous and woody species. In Madagascar, the once widespread highland ecosystems dominated by woody species are now highly fragmented and dominated by anthropic grasslands and fields, with a significantly reduced area occupied by sclerophyllous forests referred to as ‘tapia woodlands’. Six species of this endemic vegetation type were studied: Abrahamia ibityensis (Anacardiaceae), Aphloia theiformis (Aphloiaceae), Carissa edulis (Apocynaceae), Pentachlaena latifolia (Sarcolaenaceae), Uapaca bojeri (Phyllanthaceae) and Vaccinium secundiflorum (Ericaceae). Germination tests were conducted (i) by soaking seeds in water for 24 h (imbibition) or (ii) by exposing the seeds to dry heat. Four different temperatures (40, 60, 80 and 120°C) were applied, and seeds were exposed for 10, 30, 60 and 90 min. To simulate hotter faster‐burning fires, two higher temperatures (100 and 120°C) were also used by exposing seeds to dry heat for 5 min. The results did not reveal any significant effect of 24‐h water imbibition on germination. For most species, germination decreased with increasing temperature of treatment using dry heat. Uapaca bojeri did not germinate under any treatment. Further studies on the biological and ecological characteristics of tapia woodland species in response to fire are needed to help guide conservation, management and restoration activities focusing on this endemic vegetation type.     

Comparison of plant communities on the Ibity and Itremo massifs,Madagascar, with contrasting conservation histories and current status

Background: Deforestation processes and species extinction on islands have made them the focus of substantial efforts to create and strengthen local environmental organisations, establish new protected areas and improve natural resource management. In Madagascar, despite promising new policies, the flora and fauna are under serious threat. More than 80% of the island shows a significant loss of natural plant cover. Current levels of diversity reflect natural disturbance regimes, with fire representing one of the more important factors.

Aims: We compared two new protected areas (Ibity and Itremo) with different environmental and management contexts to identify the roles and impacts of the environmental conditions and the different types of management applied by their respective local communities on vegetation. Both areas have extensive stands of tapia (Uapaca bojeri) woodland.

Methods: Herbaceous vegetation surveys were carried out enumerating 16 1-m² quadrats in each of 10 sites on Ibity and seven on Itremo to characterise plant community composition and structure, complemented by tree and shrub surveys within three 40 × 40 m quadrats at each site.

Results: Floristic richness was higher at Ibity. Populations of U. bojeri were better conserved at Itremo.

Conclusions: While the total exclusion of fire is impracticable, careful management should enable the maintenance of natural conditions and at least lead to a reduction in the impacts on the structure of tapia woodland vegetation.     

Non-negative matrix factorization for learning alignment-specific models of protein evolution

Models of protein evolution currently come in two flavors: generalist and specialist. Generalist models (e.g. PAM, JTT, WAG) adopt a one-size-fits-all approach, where a single model is estimated from a number of different protein alignments. Specialist models (e.g. mtREV, rtREV, HIVbetween) can be estimated when a large quantity of data are available for a single organism or gene, and are intended for use on that organism or gene only. Unsurprisingly, specialist models outperform generalist models, but in most instances there simply are not enough data available to estimate them. We propose a method for estimating alignment-specific models of protein evolution in which the complexity of the model is adapted to suit the richness of the data. Our method uses non-negative matrix factorization (NNMF) to learn a set of basis matrices from a general dataset containing a large number of alignments of different proteins, thus capturing the dimensions of important variation. It then learns a set of weights that are specific to the organism or gene of interest and for which only a smaller dataset is available. Thus the alignment-specific model is obtained as a weighted sum of the basis matrices. Having been constrained to vary along only as many dimensions as the data justify, the model has far fewer parameters than would be required to estimate a specialist model. We show that our NNMF procedure produces models that outperform existing methods on all but one of 50 test alignments. The basis matrices we obtain confirm the expectation that amino acid properties tend to be conserved, and allow us to quantify, on specific alignments, how the strength of conservation varies across different properties. We also apply our new models to phylogeny inference and show that the resulting phylogenies are different from, and have improved likelihood over, those inferred under standard models.     

Randomized soil survey of the distribution of Burkholderia pseudomallei in rice fields in Laos

Melioidosis is a major cause of morbidity and mortality in Southeast Asia, where the causative organism (Burkholderia pseudomallei) is present in the soil. In the Lao People's Democratic Republic (Laos), B. pseudomallei is a significant cause of sepsis around the capital, Vientiane, and has been isolated in soil near the city, adjacent to the Mekong River. We explored whether B. pseudomallei occurs in Lao soil distant from the Mekong River, drawing three axes across northwest, northeast, and southern Laos to create nine sampling areas in six provinces. Within each sampling area, a random rice field site containing a grid of 100 sampling points each 5 m apart was selected. Soil was obtained from a depth of 30 cm and cultured for B. pseudomallei. Four of nine sites (44%) were positive for B. pseudomallei, including all three sites in Saravane Province, southern Laos. The highest isolation frequency was in east Saravane, where 94% of soil samples were B. pseudomallei positive with a geometric mean concentration of 464 CFU/g soil (95% confidence interval, 372 to 579 CFU/g soil; range, 25 to 10,850 CFU/g soil). At one site in northwest Laos (Luangnamtha), only one sample (1%) was positive for B. pseudomallei, at a concentration of 80 CFU/g soil. Therefore, B. pseudomallei occurs in Lao soils beyond the immediate vicinity of the Mekong River, alerting physicians to the likelihood of melioidosis in these areas. Further studies are needed to investigate potential climatic, soil, and biological determinants of this heterogeneity.     

Ankyrin repeat and suppressors of cytokine signaling box protein asb-9 targets creatine kinase B for degradation

The suppressors of cytokine signaling (SOCS) proteins inhibit cytokine action by direct interaction with Janus kinases or activated cytokine receptors. In addition to the N-terminal and Src homology 2 domains that mediate these interactions, SOCS proteins contain a C-terminal SOCS box. DNA data base searches have identified a number of other protein families that possess a SOCS box, of which the ankyrin repeat and SOCS box-containing (Asb) proteins constitute the largest. Although it is known that the SOCS proteins are involved in the negative regulation of cytokine signaling, the biological and biochemical functions of the Asbs are largely undefined. Using a proteomics approach, we demonstrate that creatine kinase B (CKB) interacts with Asb-9 in a specific, SOCS box-independent manner. This interaction increases the polyubiquitylation of CKB and decreases total CKB levels within the cell. The targeting of CKB for degradation by Asb-9 was primarily SOCS box-dependent and suggests that Asb-9 acts as a specific ubiquitin ligase regulating levels of this evolutionarily conserved enzyme.     

Interactions between BRCA2 and RAD51 for promoting homologous recombination in Leishmania infantum

In most organisms, the primary function of homologous recombination (HR) is to allow genome protection by the faithful repair of DNA double-strand breaks. The vital step of HR is the search for sequence homology, mediated by the RAD51 recombinase, which is stimulated further by proteins mediators such as the tumor suppressor BRCA2. The biochemical interplay between RAD51 and BRCA2 is unknown in Leishmania or Trypanosoma. Here we show that the Leishmania infantum BRCA2 protein possesses several critical features important for the regulation of DNA recombination at the genetic and biochemical level. A BRCA2 null mutant, generated by gene disruption, displayed genomic instability and gene-targeting defects. Furthermore, cytological studies show that LiRAD51 can no longer localize to the nucleus in this mutant. The Leishmania RAD51 and BRCA2 interact together and the purified proteins bind single-strand DNA. Remarkably, LiBRCA2 is a recombination mediator that stimulates the invasion of a resected DNA double-strand break in an undamaged template by LiRAD51 to form a D-loop structure. Collectively, our data show that LiBRCA2 and LiRAD51 promote HR at the genetic and biochemical level in L. infantum, the causative agent of visceral leishmaniasis.