Novel small-molecule inhibitors of hepatitis C virus entry block viral spread and promote viral clearance in cell culture

Combinations of direct-acting anti-virals offer the potential to improve the efficacy, tolerability and duration of the current treatment regimen for hepatitis C virus (HCV) infection. Viral entry represents a distinct therapeutic target that has been validated clinically for a number of pathogenic viruses. To discover novel inhibitors of HCV entry, we conducted a high throughput screen of a proprietary small-molecule compound library using HCV pseudoviral particle (HCVpp) technology. We independently discovered and optimized a series of 1,3,5-triazine compounds that are potent, selective and non-cytotoxic inhibitors of HCV entry. Representative compounds fully suppress both cell-free virus and cell-to-cell spread of HCV in vitro. We demonstrate, for the first time, that long term treatment of an HCV cell culture with a potent entry inhibitor promotes sustained viral clearance in vitro. We have confirmed that a single amino acid variant, V719G, in the transmembrane domain of E2 is sufficient to confer resistance to multiple compounds from the triazine series. Resistance studies were extended by evaluating both the fusogenic properties and growth kinetics of drug-induced and natural amino acid variants in the HCVpp and HCV cell culture assays. Our results indicate that amino acid variations at position 719 incur a significant fitness penalty. Introduction of I719 into a genotype 1b envelope sequence did not affect HCV entry; however, the overall level of HCV replication was reduced compared to the parental genotype 1b/2a HCV strain. Consistent with these findings, I719 represents a significant fraction of the naturally occurring genotype 1b sequences. Importantly, I719, the most relevant natural polymorphism, did not significantly alter the susceptibility of HCV to the triazine compounds. The preclinical properties of these triazine compounds support further investigation of entry inhibitors as a potential novel therapy for HCV infection.     

Woody plant communities of isolated Afromontane cloud forests in Taita Hills,Kenya

In the Taita Hills in southern Kenya, remnants of the original Afromontane forest vegetation are restricted to isolated mountain peaks. To assess the level of degradation and the need for forest restoration, we examined how forest plant communities and their indicator species vary between and within remnant patches of cloud forest. We used ordinal abundance data to compare plant communities in eight forest fragments. We also analyzed data on the diversity and abundance of trees in 57 0.1 ha plots to compare tree communities within and between the largest two of these fragments, Ngangao (120 ha) and Mbololo (220 ha). The extant vegetation of the Taita Hills at landscape scale consists of secondary moist montane to intermediate montane forest. There was a high species dissimilarity between fragments (69%). Variation in species composition coincided with an abiotic gradient related to elevation. At plot level, secondary successional species and species of forest edges were most abundant and most frequent. Inferred clusters of plots almost entirely coincided with the two forest fragments. Indicator species associated with forest margins and gaps were more frequent in the smaller of the two forest fragments, while indicators for the larger fragment were more typical for less disturbed moist forest. Abiotic site variability but also different levels of disturbance determine site-specific variants of the montane forest. Conservation efforts should not only focus on maintaining forest quantity (size), but also on forest quality (species composition). Late-successional rainforest species are underrepresented in the woody plant communities of the Taita Hills and assisting restoration of viable populations of cloud forest climax tree species is urgently needed.     

Anti-HIV-1 Activities of 1,3-Dioxolane Guanine and 2,6-Diaminopurine Dioxolane

Abstract

DXG and its prodrug DAPD have been demonstrated to be effective inhibitors of HIV-1 in various cells. The EC₅₀s for DXG were 0.032 μM in CBMCs and 0.05 μM in MT-4 cells, which were generally equipotent as 3TC. 3TC-resistant, but not AZT-resistant, HIV-1 had minimum diminished sensitivity to the compounds. Both DXG and DAPD were non-toxic to cells up to 500 μM.     

Diversity of Bacterial Communities in a Profile of a Winter Wheat Field: Known and Unknown Members

In soils, bacteria are very abundant and diverse. They are involved in various agro-ecosystem processes such as the nitrogen cycle, organic matter degradation, and soil formation. Yet, little is known about the distribution and composition of bacterial communities through the soil profile, particularly in agricultural soils, as most studies have focused only on topsoils or forest and grassland soils. In the present work, we have used bar-coded pyrosequencing analysis of the V3 region of the 16S rRNA gene to analyze bacterial diversity in a profile (depths 10, 25, and 45 cm) of a well-characterized field of winter wheat. Taxonomic assignment was carried out with the Ribosomal Database Project (RDP) Classifier program with three bootstrap scores: a main run at 0.80, a confirmation run at 0.99, and a run at 0 to gain information on the unknown bacteria. Our results show that biomass and bacterial quantity and diversity decreased greatly with depth. Depth also had an impact, in terms of relative sequence abundance, on 81 % of the most represented taxonomic ranks, notably the ranks Proteobacteria, Bacteroidetes, Actinobacteridae, and Acidobacteria. Bacterial community composition differed more strongly between the topsoil (10 and 25 cm) and subsoil (45 cm) than between levels in the topsoil, mainly because of shifts in the carbon, nitrogen, and potassium contents. The subsoil also contained more unknown bacteria, 53.96 % on the average, than did the topsoil, with 42.06 % at 10 cm and 45.59 % at 25 cm. Most of these unknown bacteria seem to belong to Deltaproteobacteria, Actinobacteria, Rhizobiales, and Acidobacteria.     

Contrasting Cloud Forest Restoration Potential Between Plantations of Different Exotic Tree Species

The role of exotic tree plantations for biodiversity conservation is contested. Such plantations nevertheless offer various ecosystem service benefits, which include carbon storage and facilitation of indigenous tree species regeneration. To assess forest restoration potential in tropical exotic tree plantations, we assessed native cloud forest tree regeneration in 166 plots in ca. 50‐year‐old plantations of five timber species that are widely used in tropical plantations (Pinus patula, Eucalyptus saligna, Cupressus lusitanica, Grevillea robusta and Acacia mearnsii). Differences in species abundance, diversity and composition were compared among plantations, and between plantations and disturbed and undisturbed indigenous Afromontane cloud forest (southeast Kenya) relicts after controlling for environmental variation between plots (i.e. altitude, distance to indigenous forest, soil depth, slope, aspect) and for environmental and stand structural variation (i.e. dominant tree height and basal area). Regenerating trees were mostly early‐successional species. Indigenous tree species regeneration was significantly higher in Grevillea plantations, where the seedling community also included late‐successional tree species. Regeneration under Eucalyptus was particularly poor. Acacia had a strong invasive nature, reducing its potential role and usefulness in indigenous forest restoration. Our study underlined that exotic tree plantations have differential effects on native tree species regeneration, with high potential for Grevillea plantations and low potential for invasive exotic species.     

Can complementarity in water use help to explain diversity–productivity relationships in experimental grassland plots?

Positive diversity–productivity relationships have repeatedly been found in experimental grassland plots, but mechanistic explanations are still under debate. We tested whether complementarity for the exploitation of the soil water resource helps to explain these relationships. In the dry summer of 2003, evapotranspiration (ET) was assessed at the Swedish BIODEPTH site using two different approaches: snapshot measurements of canopy surface temperature and simulation of time-accumulated ET by means of a soil water balance model. More diverse plots were characterized by lower surface temperatures and higher accumulated ET. Transgressive overyielding tests revealed that ET in polycultures was higher than in the best-performing monocultures, but this pattern was reversed at high degrees of water stress. Our results indicate that a more complete exploitation of soil water by more diverse grassland systems is on the one hand likely to be a driver for their increased biomass production, but on the other hand causes the more diverse communities to be affected earlier by drought. Nevertheless, the results also suggest that productivity may (at least partially) be maintained under dry conditions due to the higher likelihood of including drought-tolerant species in the more diverse communities. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Bioenergy production and sustainable development: science base for policymaking remains limited

The possibility of using bioenergy as a climate change mitigation measure has sparked a discussion of whether and how bioenergy production contributes to sustainable development. We undertook a systematic review of the scientific literature to illuminate this relationship and found a limited scientific basis for policymaking. Our results indicate that knowledge on the sustainable development impacts of bioenergy production is concentrated in a few well‐studied countries, focuses on environmental and economic impacts, and mostly relates to dedicated agricultural biomass plantations. The scope and methodological approaches in studies differ widely and only a small share of the studies sufficiently reports on context and/or baseline conditions, which makes it difficult to get a general understanding of the attribution of impacts. Nevertheless, we identified regional patterns of positive or negative impacts for all categories – environmental, economic, institutional, social and technological. In general, economic and technological impacts were more frequently reported as positive, while social and environmental impacts were more frequently reported as negative (with the exception of impacts on direct substitution of GHG emission from fossil fuel). More focused and transparent research is needed to validate these patterns and develop a strong science underpinning for establishing policies and governance agreements that prevent/mitigate negative and promote positive impacts from bioenergy production.     

Increase of biodiversity in homogeneous Scots pine stands by an ecologically diversified management

Three important parameters of biodiversity in first generation Scots pine (Pinus sylvestris) forests on sandy soils have been evaluated: herbal layer diversity, natural regeneration and stand structure. The study took place in the Belgian Campine region, where the original oak–birch forest, degraded to heathlands in the course of time, were finally replaced by monocultures of Scots pine. These first generation pine forests are characterized by a low biodiversity. In maturing stands of this type, however, a spontaneous increase of biodiversity is noticed. Herbal species richness is very limited in all age classes. Different natural regeneration patterns are found. Referring to stand structure, the lengthening of the rotation favours the ingrowth of several hardwood species. As a consequence, the homogenous Scots pine stands are gradually and spontaneously transformed into heterogeneous mixed stands, featuring a noticeable increase in biodiversity. Selected human interventions may further increase biodiversity. The fundamental management principles are discussed: avoidance of major disturbances, lengthening of the rotation period, use of native tree species and natural regeneration, protection of microbiotopes and permanent monitoring.