Structural pattern matching of nonribosomal peptides

Background  

Nonribosomal peptides (NRPs), bioactive secondary metabolites produced by many microorganisms, show a broad range of important biological activities (e.g. antibiotics, immunosuppressants, antitumor agents). NRPs are mainly composed of amino acids but their primary structure is not always linear and can contain cycles or branchings. Furthermore, there are several hundred different monomers that can be incorporated into NRPs. The NORINE database, the first resource entirely dedicated to NRPs, currently stores more than 700 NRPs annotated with their monomeric peptide structure encoded by undirected labeled graphs. This opens a way to a systematic analysis of structural patterns occurring in NRPs. Such studies can investigate the functional role of some monomeric chains, or analyse NRPs that have been computationally predicted from the synthetase protein sequence. A basic operation in such analyses is the search for a given structural pattern in the database.     

Longitudinal study of primary HIV-1 isolates in drug-naïve individuals reveals the emergence of variants sensitive to anti-HIV-1 monoclonal antibodies

To study how virus evolution affects neutralization sensitivity and to determine changes that occur in and around epitopes, we tested the ability of 13 anti-HIV-1 gp120 (anti-V2, anti-V3, anti-CD4bd and anti-carbohydrate) human monoclonal antibodies (mAbs) to neutralize sequential viruses obtained from five HIV-1 chronically infected drug naïve individuals. Overall, primary viruses collected from patients at first visit were resistant to neutralization by all anti-HIV-1 mAbs with the exception of one virus sensitive to IgG1b12. Four of the five patients'' viruses evolved increased sensitivity to neutralization by anti-V3 mAbs. Virus collected from a patient obtained 31 months later, evolved increased sensitivity to anti-V2, anti-V3, and anti-CD4bd mAbs. Furthermore, the anti-V2 and anti-CD4bd mAbs also exhibited increased neutralization capacities against virus collected from a patient 29 months later. Of the seven anti-V3 mAbs, five showed increased potency to neutralize the evolved virus from a patient collected after 11 months, and three exhibited increased potency against viruses from two patients collected 29 and 36 months later. Anti-V3 mAbs exhibited the most breadth and potency in neutralizing the evolving viruses. Sequence analysis of the envelope regions revealed amino acid conservation within the V3 loop, while most of the changes identified occurred outside the core epitopes and in particular within the C3 region; these may account for increased neutralization sensitivity. These studies demonstrate that in vivo, HIV-1 can evolve increased neutralization sensitivity to mAbs and that the spectrum of neutralization capacities by mAbs can be broader when studied in longitudinal analysis.     

Predicting future coexistence in a North American ant community

Global climate change will remodel ecological communities worldwide. However, as a consequence of biotic interactions, communities may respond to climate change in idiosyncratic ways. This makes predictive models that incorporate biotic interactions necessary. We show how such models can be constructed based on empirical studies in combination with predictions or assumptions regarding the abiotic consequences of climate change. Specifically, we consider a well‐studied ant community in North America. First, we use historical data to parameterize a basic model for species coexistence. Using this model, we determine the importance of various factors, including thermal niches, food discovery rates, and food removal rates, to historical species coexistence. We then extend the model to predict how the community will restructure in response to several climate‐related changes, such as increased temperature, shifts in species phenology, and altered resource availability. Interestingly, our mechanistic model suggests that increased temperature and shifts in species phenology can have contrasting effects. Nevertheless, for almost all scenarios considered, we find that the most subordinate ant species suffers most as a result of climate change. More generally, our analysis shows that community composition can respond to climate warming in nonintuitive ways. For example, in the context of a community, it is not necessarily the most heat‐sensitive species that are most at risk. Our results demonstrate how models that account for niche partitioning and interspecific trade‐offs among species can be used to predict the likely idiosyncratic responses of local communities to climate change.     

Role of TASK2 in the control of apoptotic volume decrease in proximal kidney cells

Apoptotic volume decrease (AVD) is prerequisite to apoptotic events that lead to cell death. In a previous study, we demonstrated in kidney proximal cells that the TASK2 channel was involved in the K+ efflux that occurred during regulatory volume decrease. The aim of the present study was to determine the role of the TASK2 channel in the regulation of AVD and apoptosis phenomenon. For this purpose renal cells were immortalized from primary cultures of proximal convoluted tubules (PCT) from wild type and TASK2 knock-out mice (task2-/-). Apoptosis was induced by staurosporine, cyclosporin A, or tumor necrosis factor alpha. Cell volume, K+ conductance, caspase-3, and intracellular reactive oxygen species (ROS) levels were monitored during AVD. In wild type PCT cells the K+ conductance activated during AVD exhibited characteristics of TASK2 currents. In task2-/- PCT cells, AVD and caspase activation were reduced by 59%. Whole cell recordings indicated that large conductance calcium-activated K+ currents inhibited by iberiotoxin (BK channels) partially compensated for the deletion of TASK2 K+ currents in the task2-/- PCT cells. This result explained the residual AVD measured in these cells. In both cell lines, apoptosis was mediated via intracellular ROS increase. Moreover AVD, K+ conductances, and caspase-3 were strongly impaired by ROS scavenger N-acetylcysteine. In conclusion, the main K+ channels involved in staurosporine, cyclosporin A, and tumor necrosis factor-alpha-induced AVD are TASK2 K+ channels in proximal wild type cells and iberiotoxin-sensitive BK channels in proximal task2-/- cells. Both K+ channels could be activated by ROS production.     

Neutralization Profiles of Primary Human Immunodeficiency Virus Type 1 Isolates in the Context of Coreceptor Usage

Most strains of human immunodeficiency virus type 1 (HIV-1) which have only been carried in vitro in peripheral blood mononuclear cells (primary isolates) can be neutralized by antibodies, but their sensitivity to neutralization varies considerably. To study the parameters that contribute to the differential neutralization sensitivity of primary HIV-1 isolates, we developed a neutralization assay with a panel of genetically engineered cell lines (GHOST cells) that express CD4, one of eight chemokine receptors which function as HIV-1 coreceptors, and a Tat-dependent green fluorescent protein reporter cassette which permits the evaluation and quantitation of HIV-1 infection by flow cytometry. All 21 primary isolates from several clades could grow in the various GHOST cell lines, and their use of one or more coreceptors could easily be defined by flow cytometric analysis. Ten of these primary isolates, three that were CXCR4 (X4)-tropic, three that were CCR5 (R5)-tropic, and four that were dual- or polytropic were chosen for study of their sensitivity to neutralization by human monoclonal and polyclonal antibodies. Viruses from the X4-tropic category of viruses were first tested since they have generally been considered to be particularly neutralization sensitive. It was found that the X4-tropic virus group contained both neutralization-sensitive and neutralization-resistant viruses. Similar results were obtained with R5-tropic viruses and with dual- or polytropic viruses. Within each category of viruses, neutralization sensitivity and resistance could be observed. Therefore, sensitivity to neutralization appears to be the consequence of factors that influence the antibody-virus interaction and its sequelae rather than coreceptor usage. Neutralization of various viruses by the V3-specific monoclonal antibody, 447-52D, was shown to be dependent not only on the presence of the relevant epitope but also on its presentation. An epitope within the envelope of a particular virus is not sufficient to render a virus sensitive to neutralization by an antibody that recognizes that epitope. Moreover, conformation-dependent factors may overcome the need for absolute fidelity in the match between an antibody and its core epitope, permitting sufficient affinity between the viral envelope protein and the antibody to neutralize the virus. The studies indicate that the neutralization sensitivity of HIV-1 primary isolates is a consequence of the complex interaction between virus, antibody, and target cell.     

Elevated CO2 effects on decomposition processes in a grazed grassland

The effects of elevated atmospheric CO₂ (475 μL L^?1) on in situ decomposition of plant litter and animal faecal material were studied over 2 years in a free air CO₂ enrichment (FACE) facility. The pasture was grazed by sheep and contained a mixture of C₃ and C₄ grasses, legumes and forbs. There was no effect of elevated CO₂ on decomposition within plant species but marked differences between species with faster decomposition in dicots; a group that increased in abundance at elevated CO₂. Decomposition of mixed herbage root material occurred at a similar rate to that of leaf litter suggesting that any CO₂‐induced increase in carbon allocation to roots would not reduce rates of decomposition. Sheep faeces resulting from a ‘high‐CO₂ diet’ decomposed significantly slower during summer but not during winter. The overall outcome of these experiments were explored using scenarios that took account of changes in botanical composition, allocation to roots and the presence of herbivores. In the absence of herbivores, elevated CO₂ led to a 15% increase in the rate of mass loss and an 18% increase in the rate of nitrogen (N) release. In the presence of herbivores, these effects were partially removed (11% increase in rate of mass loss and 9% decrease in N release rate) because of the recycling occurring through the animals in the form of faeces.     

A first estimate of sea turtle bycatch in the industrial trawling fishery of Gabon

Gabon hosts nesting grounds for several sea turtle species, including the world’s largest rookery for the leatherback turtle (Dermochelys coriacea), Africa’s largest rookery for the olive ridley turtle (Lepidochelys olivacea) and smaller aggregations of the hawksbill turtle (Eretmochelys imbricata) and green turtle (Chelonia mydas). To assess the level of incidental captures of turtles by the Gabonese trawl fishery, an onboard observer program was conducted in the period 2012–2013. A total of 143 turtles were captured by 15 trawlers during 271 fishing days. The olive ridley turtle was the main species captured (80% of bycaught turtles), with mostly adult-sized individuals. The remaining 20% included green turtles, hawksbill turtles, leatherback turtles and undetermined species. Bycatch per unit of effort (BPUE) of olive ridley turtles varied greatly depending on the period of the year (range of means: 0.261–2.270). Dead and comatose turtles were 6.2 and 24.6% respectively (n = 65). By applying the available fishing effort to two BPUE scenarios (excluding or considering a seasonal peak), the total annual number of captures was estimated as ranging between 1026 (CI 95% 746–1343) and 2581 (CI 95% 1641–3788) olive ridley turtles, with a mortality ranging from 63 (CI 95% 13–135) to 794 (CI 95% 415–1282) turtles per year depending on the scenario and on the fate of comatose turtles. Such a potential mortality may be reason for concern for the local breeding population of olive ridley turtles and recommendations in terms of possible conservation measures and further research are given.