Dramatic Potentiation of the Antiviral Activity of HIV Antibodies by Cholesterol Conjugation

The broadly neutralizing antibodies HIV 2F5 and 4E10, which bind to overlapping epitopes in the membrane-proximal external region of the fusion protein gp41, have been proposed to use a two-step mechanism for neutralization; first, they bind and preconcentrate at the viral membrane through their long, hydrophobic CDRH3 loops, and second, they form a high affinity complex with the protein epitope. Accordingly, mutagenesis of the CDRH3 can abolish their neutralizing activity, with no change in the affinity for the peptide epitope. We show here that we can mimic this mechanism by conjugating a cholesterol group outside of the paratope of an antibody. Cholesterol-conjugated antibodies bind to lipid raft domains on the membrane, and because of this enrichment, they show increased antiviral potency. In particular, we find that cholesterol conjugation (i) rescues the antiviral activity of CDRH3-mutated 2F5, (ii) increases the antiviral activity of WT 2F5, (iii) potentiates the non-membrane-binding HIV antibody D5 10–100-fold (depending on the virus strain), and (iv) increases synergy between 2F5 and D5. Conjugation can be made at several positions, including variable and constant domains. Cholesterol conjugation therefore appears to be a general strategy to boost the potency of antiviral antibodies, and, because membrane affinity is engineered outside of the antibody paratope, it can complement affinity maturation strategies.     

Discovery of a SAR11 growth requirement for thiamin's pyrimidine precursor and its distribution in the Sargasso Sea

Vitamin traffic, the production of organic growth factors by some microbial community members and their use by other taxa, is being scrutinized as a potential explanation for the variation and highly connected behavior observed in ocean plankton by community network analysis. Thiamin (vitamin B₁), a cofactor in many essential biochemical reactions that modify carbon–carbon bonds of organic compounds, is distributed in complex patterns at subpicomolar concentrations in the marine surface layer (0–300 m). Sequenced genomes from organisms belonging to the abundant and ubiquitous SAR11 clade of marine chemoheterotrophic bacteria contain genes coding for a complete thiamin biosynthetic pathway, except for thiC, encoding the 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP) synthase, which is required for de novo synthesis of thiamin''s pyrimidine moiety. Here we demonstrate that the SAR11 isolate ‘Candidatus Pelagibacter ubique'', strain HTCC1062, is auxotrophic for the thiamin precursor HMP, and cannot use exogenous thiamin for growth. In culture, strain HTCC1062 required 0.7 zeptomoles per cell (ca. 400 HMP molecules per cell). Measurements of dissolved HMP in the Sargasso Sea surface layer showed that HMP ranged from undetectable (detection limit: 2.4 pM) to 35.7 pM, with maximum concentrations coincident with the deep chlorophyll maximum. In culture, some marine cyanobacteria, microalgae and bacteria exuded HMP, and in the Western Sargasso Sea, HMP profiles changed between the morning and evening, suggesting a dynamic biological flux from producers to consumers.     

Diel movement of smallmouth yellowfish Labeobarbus aeneus in the Vaal River,South Africa

Diel movements of Orange–Vaal smallmouth yellowfish Labeobarbus aeneus (Burchell, 1822) in the Vaal River, South Africa, were determined by externally attaching radio transmitters to 11 adult fish and manually tracking them between March and May 2012. Twenty-four radio telemetry monitoring surveys produced 2 304 diel tracks. At night, yellowfish displayed a preference for slow shallow (<0.3?m s?1, <0.5?m) and fast shallow habitats (>0.3?m s?1, <0.3?m), whereas by day they avoided these habitats, preferring fast deep areas (>0.3?m s?1, >0.3?m). The average total distance of 272?m moved per 24-hour period was three times greater than the diel range, and the average maximum displacement per minute was significantly higher in daytime (4?m) than at night (1.5?m). These findings suggest that L. aeneus is active primarily during the day in fast-flowing, deeper waters, and relatively inactive at night, when it occupies shallower habitats. This behaviour should be further explored to identify causal mechanisms underlying the diel habitat shifts in this species such as water temperature, foraging tactics and/or predator avoidance.     

Adaptive survival mechanisms and growth limitations of small-stature herb species across a plant diversity gradient

Several biodiversity experiments have shown positive effects of species richness on aboveground biomass production, but highly variable responses of individual species. The well-known fact that the competitive ability of plant species depends on size differences among species, raises the question of effects of community species richness on small-stature subordinate species. We used experimental grasslands differing in species richness (1-60 species) and functional group richness (one to four functional groups) to study biodiversity effects on biomass production and ecophysiological traits of five small-stature herbs (Bellis perennis, Plantago media, Glechoma hederacea, Ranunculus repens and Veronica chamaedrys). We found that ecophysiological adaptations, known as typical shade-tolerance strategies, played an important role with increasing species richness and in relation to a decrease in transmitted light. Specific leaf area and leaf area ratio increased, while area-based leaf nitrogen decreased with increasing community species richness. Community species richness did not affect daily leaf carbohydrate turnover of V. chamaedrys and P. media indicating that these species maintained efficiency of photosynthesis even in low-light environments. This suggests an important possible mechanism of complementarity in such grasslands, whereby smaller species contribute to a better overall efficiency of light use. Nevertheless, these species rarely contributed a large proportion to community biomass production or achieved higher yields in mixtures than expected from monocultures. It seems likely that the allocation to aboveground plant organs to optimise carbon assimilation limited the investment in belowground organs to acquire nutrients and thus hindered these species from increasing their performance in multi-species mixtures.     

Llama-derived single domain antibodies to build multivalent, superpotent and broadened neutralizing anti-viral molecules

For efficient prevention of viral infections and cross protection, simultaneous targeting of multiple viral epitopes is a powerful strategy. Llama heavy chain antibody fragments (VHH) against the trimeric envelope proteins of Respiratory Syncytial Virus (Fusion protein), Rabies virus (Glycoprotein) and H5N1 Influenza (Hemagglutinin 5) were selected from llama derived immune libraries by phage display. Neutralizing VHH recognizing different epitopes in the receptor binding sites on the spikes with affinities in the low nanomolar range were identified for all the three viruses by viral neutralization assays. By fusion of VHH with variable linker lengths, multimeric constructs were made that improved neutralization potencies up to 4,000-fold for RSV, 1,500-fold for Rabies virus and 75-fold for Influenza H5N1. The potencies of the VHH constructs were similar or better than best performing monoclonal antibodies. The cross protection capacity against different viral strains was also improved for all three viruses, both by multivalent (two or three identical VHH) and biparatopic (two different VHH) constructs. By combining a VHH neutralizing RSV subtype A, but not subtype B with a poorly neutralizing VHH with high affinity for subtype B, a biparatopic construct was made with low nanomolar neutralizing potency against both subtypes. Trivalent anti-H5N1 VHH neutralized both Influenza H5N1 clade1 and 2 in a pseudotype assay and was very potent in neutralizing the NIBRG-14 Influenza H5N1 strain with IC(50) of 9 picomolar. Bivalent and biparatopic constructs against Rabies virus cross neutralized both 10 different Genotype 1 strains and Genotype 5.The results show that multimerization of VHH fragments targeting multiple epitopes on a viral trimeric spike protein is a powerful tool for anti-viral therapy to achieve "best-in-class" and broader neutralization capacity.     

Long‐term effects of plant diversity and composition on plant stoichiometry

Plant elemental composition can indicate resource limitation, and changes in key elemental ratios (e.g. plant C:N ratios) can influence rates including herbivory, nutrient recycling, and pathogen infection. Although plant stoichiometry can influence ecosystem‐level processes, very few studies have addressed whether and how plant C:N stoichiometry changes with plant diversity and composition. Here, using two long‐term experimental manipulations of plant diversity (Jena and Cedar Creek), we test whether plant richness (species and functional groups) or composition (functional group proportions) affects temporal trends and variability of community‐wide C:N stoichiometry. Site fertility determined the initial community‐scale C:N ratio. Communities growing on N‐poor soil (Cedar Creek) began with higher C:N ratios than communities growing on N‐rich soil (Jena). However, site‐level plant C:N ratios converged through time, most rapidly in high diversity plots. In Jena, plant community C:N ratios increased. This temporal trend was stronger with increasing richness. However, temporal variability of C:N decreased as plant richness increased. In contrast, C:N decreased over time at Cedar Creek, most strongly at high species and functional richness, whereas the temporal variability of C:N increased with both measures of diversity at this site. Thus, temporal trends in the mean and variability of C:N were underlain by concordant changes among sites in functional group proportions. In particular, the convergence of community‐scale C:N over time at these very different sites was mainly due to increasing proportions of forbs at both sites, replacing high mean C:N (C4 grasses, Cedar Creek) or low C:N (legumes, Jena) species. Diversity amplified this convergence; although temporal trends differed in sign between the sites, these trends increased in magnitude with increasing species richness. Our results suggest a predictive mechanistic link between trends in plant diversity and functional group composition and trends in the many ecosystem rates that depend on aboveground community C:N. Synthesis We compared the effect of plant diversity on the temporal dynamics of community stoichiometry in two long‐term grassland diversity experiments: the Cedar Creek and Jena Experiments. Changes in community C:N ratios were accelerated by increasing diversity at both sites, but in opposite directions depending on soil fertility. Stoichiometry changes were driven by shifts of functional group composition differing in their elemental compositions, the identity of the functional groups depending on the site. Thus, we highlighted that community turnover constrained the effect of diversity on plant stoichiometry at both sites     

Long‐term study of root biomass in a biodiversity experiment reveals shifts in diversity effects over time

Biodiversity experiments generally report a positive effect of plant biodiversity on aboveground biomass (overyielding), which typically increases with time. Various studies also found overyielding for belowground plant biomass, but this has never been measured over time. Also, potential underlying mechanisms have remained unclear. Differentiation in rooting patterns among plant species and plant functional groups has been proposed as a main driver of the observed biodiversity effect on belowground biomass, leading to more efficient belowground resource use with increasing diversity, but so far there is little evidence to support this. We analyzed standing root biomass and its distribution over the soil profile, along a 1–16 species richness gradient over eight years in the Jena Experiment in Germany, and compared belowground to aboveground overyielding. In our long‐term dataset, total root biomass increased with increasing species richness but this effect was only apparent after four years. The increasingly positive relationship between species richness and root biomass, explaining 12% of overall variation and up to 28% in the last year of our study, was mainly due to decreasing root biomass at low diversity over time. Functional group composition strongly affected total standing root biomass, explaining 44% of variation, with grasses and legumes having strong overall positive and negative effects, respectively. Functional group richness or interactions between functional group presences did not strongly contribute to overyielding. We found no support for the hypothesis that vertical root differentiation increases with species richness, with functional group richness or composition. Other explanations, such as stronger negative plant–soil feedbacks in low‐diverse plant communities on standing root biomass and vertical distribution should be considered.     

Antigenic drift in H5N1 avian influenza virus in poultry is driven by mutations in major antigenic sites of the hemagglutinin molecule analogous to those for human influenza virus

H5N1 highly pathogenic avian influenza virus has been endemic in poultry in Egypt since 2008, notwithstanding the implementation of mass vaccination and culling of infected birds. Extensive circulation of the virus has resulted in a progressive genetic evolution and an antigenic drift. In poultry, the occurrence of antigenic drift in avian influenza viruses is less well documented and the mechanisms remain to be clarified. To test the hypothesis that H5N1 antigenic drift is driven by mechanisms similar to type A influenza viruses in humans, we generated reassortant viruses, by reverse genetics, that harbored molecular changes identified in genetically divergent viruses circulating in the vaccinated population. Parental and reassortant phenotype viruses were antigenically analyzed by hemagglutination inhibition (HI) test and microneutralization (MN) assay. The results of the study indicate that the antigenic drift of H5N1 in poultry is driven by multiple mutations primarily occurring in major antigenic sites at the receptor binding subdomain, similarly to what has been described for human influenza H1 and H3 subtype viruses.     

Positive interactions between nitrogen-fixing legumes and four different neighbouring species in a biodiversity experiment

The importance of facilitative processes due to the presence of nitrogen-fixing legumes in temperate grasslands is a contentious issue in biodiversity experiments. Despite a multitude of studies of fertilization effects of legumes on associated nonfixers in agricultural systems, we know little about the dynamics in more diverse systems. We hypothesised that the identity of target plant species (phytometers) and the diversity of neighbouring plant species would affect the magnitude of such positive species interactions. We therefore sampled aboveground tissues of phytometers planted into all plots of a grassland biodiversity–ecosystem functioning experiment and analysed their N concentrations, δ¹⁵N values and biomasses. The four phytometer species (Festuca pratensis, Plantago lanceolata, Knautia arvensis and Trifolium pratensis) each belonged to one of the four plant functional groups used in the experiment and allowed the effects of diversity on N dynamics in individual species to be assessed. We found significantly lower δ¹⁵N values and higher N concentrations and N contents (amount of N per plant) in phytometer species growing with legumes, indicating a facilitative role for legumes in these grassland ecosystems. Our data suggest that the main driving force behind these facilitative interactions in plots containing legumes was reduced competition for soil nitrate (“nitrate sparing”), with apparent N transfer playing a secondary role. Interestingly, species richness (and to a lesser extent functional group number) significantly decreased δ¹⁵N values, N concentrations and N content irrespective of any legume effect. Possible mechanisms behind this effect, such as increased N mineralisation and nitrate uptake in more diverse plots, now need further investigation. The magnitude of the positive interactions depended on the identity of the phytometer species. Evidence for increased N uptake in communities containing legumes was found in all three nonlegume phytometer species, with a subsequent strong increase in biomass in the grass F. pratensis across all diversity levels, and a lesser biomass gain in P. lanceolata and K. arvensis. In contrast, the legume phytometer species T. pratense was negatively affected when other legumes were present in their host communities across all diversity levels.     

Gone and forgotten: facilitative effects of intercropping combinations did not carry over to affect barley performance in a follow-up crop rotation

Plant and Soil - The pea seeds (Pisum sativum) hosts a complex microbial community that is exposed to environmental constraints modulated by biotic, abiotic and anthropogenic factors. The aim of...