Immune-mediated competition in rodent malaria is most likely caused by induced changes in innate immune clearance of merozoites

Malarial infections are often genetically diverse, leading to competitive interactions between parasites. A quantitative understanding of the competition between strains is essential to understand a wide range of issues, including the evolution of virulence and drug resistance. In this study, we use dynamical-model based Bayesian inference to investigate the cause of competitive suppression of an avirulent clone of Plasmodium chabaudi (AS) by a virulent clone (AJ) in immuno-deficient and competent mice. We test whether competitive suppression is caused by clone-specific differences in one or more of the following processes: adaptive immune clearance of merozoites and parasitised red blood cells (RBCs), background loss of merozoites and parasitised RBCs, RBC age preference, RBC infection rate, burst size, and within-RBC interference. These processes were parameterised in dynamical mathematical models and fitted to experimental data. We found that just one parameter μ, the ratio of background loss rate of merozoites to invasion rate of mature RBCs, needed to be clone-specific to predict the data. Interestingly, μ was found to be the same for both clones in single-clone infections, but different between the clones in mixed infections. The size of this difference was largest in immuno-competent mice and smallest in immuno-deficient mice. This explains why competitive suppression was alleviated in immuno-deficient mice. We found that competitive suppression acts early in infection, even before the day of peak parasitaemia. These results lead us to argue that the innate immune response clearing merozoites is the most likely, but not necessarily the only, mediator of competitive interactions between virulent and avirulent clones. Moreover, in mixed infections we predict there to be an interaction between the clones and the innate immune response which induces changes in the strength of its clearance of merozoites. What this interaction is unknown, but future refinement of the model, challenged with other datasets, may lead to its discovery

How ownership rights over microorganisms affect infectious disease control and innovation: A root-cause analysis of barriers to data sharing as experienced by key stakeholders.

Genetic information of pathogens is an essential input for infectious disease control, public health and for research. Efficiency in preventing and responding to global outbreaks relies on timely access to such information. Still, ownership barriers stand in the way of timely sharing of genetic data from pathogens, frustrating efficient public health responses and ultimately the potential use of such resources in innovations. Under a One Health approach, stakeholders, their interests and ownership issues are manifold and need to be investigated. We interviewed key actors from governmental and non-governmental bodies to identify overlapping and conflicting interests, and the overall challenges for sharing pathogen data, to provide essential inputs to the further development of political and practical strategies for improved data sharing practices

A single-column model intercomparison of a heavily drizzling stratocumulus-topped boundary layer

This study presents an intercomparison of single-column model simulations of a nocturnal heavily drizzling marine stratocumulus-topped boundary layer. Initial conditions and forcings are based on nocturnal flight observations off the coast of California during the DYCOMS-II field experiment. Differences in turbulent and microphysical parameterizations between models were isolated by slightly idealizing and standardizing the specification of surface and radiative fluxes. For most participating models, the case was run at both typical operational vertical resolution of about 100 m and also at high vertical resolution of about 10 m. As in prior stratocumulus intercomparisons, the simulations quickly develop considerable scatter in liquid water path (LWP) between models. However, the simulated dependence of cloud base drizzle fluxes on LWP in most models is broadly consistent with recent observations. Sensitivity tests with drizzle turned off show that drizzle substantially decreases LWP for many models. The sensitivity of entrainment rate to drizzle is more muted. Simulated LWP and entrainment are also sensitive to the inclusion of cloud droplet sedimentation. Many models underestimate the fraction of drizzle that evaporates below cloud base, which may distort the simulated feedbacks of drizzle on turbulence, entrainment, and LWP

Identification of compounds responsible for the anthelmintic effects of chicory (Cichorium intybus) by molecular networking and bio-guided fractionation

10 páginas, 7 figuras.Increasing resistance towards anthelmintic drugs has necessitated the search for alternative treatments for the control of gastrointestinal nematode parasites. Animals fed on chicory (Cichorium intybus L.), a temperate (pasture) crop, have reduced parasite burdens, hence making C. intybus a potentially useful source for novel anthelmintic compounds or a diet-based preventive/therapeutic option. Here, we utilized in vitro bioassays with the parasitic nematode Ascaris suum and molecular networking techniques with five chicory cultivars to identify putative active compounds. Network analysis predicted sesquiterpene lactones (SL) as the most likely group of anthelmintic compounds. Further bioassay-guided fractionation supported these predictions, and isolation of pure compounds demonstrated that the SL 8-deoxylactucin (8-DOL) is the compound most strongly associated with anti-parasitic activity. Furthermore, we showed that 8-DOL acts in a synergistic combination with other SL to exert the anti-parasitic effects. Finally, we established that chicory-derived extracts also showed activity against two ruminant nematodes (Teladorsagia circumcincta and Cooperia oncophora) in in vitro assays. Collectively, our results confirm the anti-parasitic activity of chicory against a range of nematodes, and pave the way for targeted extraction of active compounds or selective breeding of specific cultivars to optimize its future use in human and veterinary medicine.We are very grateful for the guidance and support by Dr. Thomas Ostenfeld Larsen and Christopher Phippen, Technical University of Denmark, Natural product discovery, and the laboratory assistance of Mette Schjelde, University of Copenhagen. This work was funded by the Danish Council for Independent Research (Grant DFF–6111-00394). Fractionation and purification of compounds were further supported by the Green Development and Demonstration Program (GUDP) (Project No. 34009-17-1220). MPE was supported by CONICYT Chile (FONDE-CYT Postdoctorado #317087

Evaluation of large-Eddy simulations via observations of nocturnal marine stratocumulus

Data from the first research flight (RF01) of the second Dynamics and Chemistry of Marine Stratocumulus (DYCOMS-II) field study are used to evaluate the fidelity with which large-eddy simulations (LESs) can represent the turbulent structure of stratocumulus-topped boundary layers. The initial data and forcings for this case placed it in an interesting part of parameter space, near the boundary where cloud-top mixing is thought to render the cloud layer unstable on the one hand, or tending toward a decoupled structure on the other hand. The basis of this evaluation consists of sixteen 4-h simulations from 10 modeling centers over grids whose vertical spacing was 5 m at the cloud-top interface and whose horizontal spacing was 35 m. Extensive sensitivity studies of both the configuration of the case and the numerical setup also enhanced the analysis. Overall it was found that (i) if efforts are made to reduce spurious mixing at cloud top, either by refining the vertical grid or limiting the effects of the subgrid model in this region, then the observed turbulent and thermodynamic structure of the layer can be reproduced with some fidelity; (ii) the base, or native configuration of most simulations greatly overestimated mixing at cloud top, tending toward a decoupled layer in which cloud liquid water path and turbulent intensities were grossly underestimated; (iii) the sensitivity of the simulations to the representation of mixing at cloud top is, to a certain extent, amplified by particulars of this case. Overall the results suggest that the use of LESs to map out the behavior of the stratocumulus-topped boundary layer in this interesting region of parameter space requires a more compelling representation of processes at cloud top. In the absence of significant leaps in the understanding of subgrid-scale (SGS) physics, such a representation can only be achieved by a significant refinement in resolution—a refinement that, while conceivable given existing resources, is probably still beyond the reach of most centers

Identification of compounds responsible for the anthelmintic effects of chicory (Cichorium intybus) by molecular networking and bio-guided fractionation

[EN] Increasing resistance towards anthelmintic drugs has necessitated the search for alternative treatments for the control of gastrointestinal nematode parasites. Animals fed on chicory (Cichorium intybus L.), a temperate (pasture) crop, have reduced parasite burdens, hence making C. intybus a potentially useful source for novel anthelmintic compounds or a diet-based preventive/therapeutic option. Here, we utilized in vitro bioassays with the parasitic nematode Ascaris suum and molecular networking techniques with five chicory cultivars to identify putative active compounds. Network analysis predicted sesquiterpene lactones (SL) as the most likely group of anthelmintic compounds. Further bioassay-guided fractionation supported these predictions, and isolation of pure compounds demonstrated that the SL 8-deoxylactucin (8-DOL) is the compound most strongly associated with anti-parasitic activity. Furthermore, we showed that 8-DOL acts in a synergistic combination with other SL to exert the anti-parasitic effects. Finally, we established that chicory-derived extracts also showed activity against two ruminant nematodes (Teladorsagia circumcincta and Cooperia oncophora) in in vitro assays. Collectively, our results confirm the anti-parasitic activity of chicory against a range of nematodes, and pave the way for targeted extraction of active compounds or selective breeding of specific cultivars to optimize its future use in human and veterinary medicineSIWe are very grateful for the guidance and support by Dr. Thomas Ostenfeld Larsen and Christopher Phippen, Technical University of Denmark, Natural product discovery, and the laboratory assistance of Mette Schjelde, University of Copenhagen. This work was funded by the Danish Council for Independent Research (Grant DFF–6111-00394). Fractionation and purification of compounds were further supported by the Green Development and Demonstration Program (GUDP) (Project No. 34009-17-1220). MPE was supported by CONICYT Chile (FONDECYT Postdoctorado #3170875

Single‐Column Model Simulations of Subtropical Marine Boundary‐Layer Cloud Transitions Under Weakening Inversions

Results are presented of the GASS/EUCLIPSE single‐column model intercomparison study on the subtropical marine low‐level cloud transition. A central goal is to establish the performance of state‐of‐the‐art boundary‐layer schemes for weather and climate models for this cloud regime, using large‐eddy simulations of the same scenes as a reference. A novelty is that the comparison covers four different cases instead of one, in order to broaden the covered parameter space. Three cases are situated in the North‐Eastern Pacific, while one reflects conditions in the North‐Eastern Atlantic. A set of variables is considered that reflects key aspects of the transition process, making use of simple metrics to establish the model performance. Using this method, some longstanding problems in low‐level cloud representation are identified. Considerable spread exists among models concerning the cloud amount, its vertical structure, and the associated impact on radiative transfer. The sign and amplitude of these biases differ somewhat per case, depending on how far the transition has progressed. After cloud breakup the ensemble median exhibits the well‐known “too few too bright” problem. The boundary‐layer deepening rate and its state of decoupling are both underestimated, while the representation of the thin capping cloud layer appears complicated by a lack of vertical resolution. Encouragingly, some models are successful in representing the full set of variables, in particular, the vertical structure and diurnal cycle of the cloud layer in transition. An intriguing result is that the median of the model ensemble performs best, inspiring a new approach in subgrid parameterization

Plasmodium knowlesi Genome Sequences from Clinical Isolates Reveal Extensive Genomic Dimorphism.

Plasmodium knowlesi is a newly described zoonosis that causes malaria in the human population that can be severe and fatal. The study of P. knowlesi parasites from human clinical isolates is relatively new and, in order to obtain maximum information from patient sample collections, we explored the possibility of generating P. knowlesi genome sequences from archived clinical isolates. Our patient sample collection consisted of frozen whole blood samples that contained excessive human DNA contamination and, in that form, were not suitable for parasite genome sequencing. We developed a method to reduce the amount of human DNA in the thawed blood samples in preparation for high throughput parasite genome sequencing using Illumina HiSeq and MiSeq sequencing platforms. Seven of fifteen samples processed had sufficiently pure P. knowlesi DNA for whole genome sequencing. The reads were mapped to the P. knowlesi H strain reference genome and an average mapping of 90% was obtained. Genes with low coverage were removed leaving 4623 genes for subsequent analyses. Previously we identified a DNA sequence dimorphism on a small fragment of the P. knowlesi normocyte binding protein xa gene on chromosome 14. We used the genome data to assemble full-length Pknbpxa sequences and discovered that the dimorphism extended along the gene. An in-house algorithm was developed to detect SNP sites co-associating with the dimorphism. More than half of the P. knowlesi genome was dimorphic, involving genes on all chromosomes and suggesting that two distinct types of P. knowlesi infect the human population in Sarawak, Malaysian Borneo. We use P. knowlesi clinical samples to demonstrate that Plasmodium DNA from archived patient samples can produce high quality genome data. We show that analyses, of even small numbers of difficult clinical malaria isolates, can generate comprehensive genomic information that will improve our understanding of malaria parasite diversity and pathobiology

Behavioural evidence for self-medication in bumblebees?

The presence of antimicrobial secondary metabolites in nectar suggests that pollinators, which are threatened globally by emergent disease, may benefit from the consumption of nectars rich in these metabolites. We tested whether nicotine, a nectar secondary metabolite common in Solanaceae and Tilia species, is used by parasitized bumblebees as a source of self-medication , using a series of toxicological, microbiological and behavioural experiments. Caged bees infected with Crithidia bombi had a slight preference for sucrose solution laced with the alkaloid and behavioural tests showed that the parasite infection induced an increased consumption of nicotine during foraging activity, though nicotine had an appetite-reducing effect overall. When ingested, nicotine delayed the progression of a gut infection in bumblebees by a few days, but dietary nicotine did not clear the infection, and after 10 days the parasite load approached that of control bees. Moreover, when pathogens were exposed to the alkaloid prior to host ingestion, the protozoan's viability was not directly affected, suggesting that anti-parasite effects were relatively weak. Nicotine consumption in a single dose did not impose any cost even in starved bees but the alkaloid had detrimental effects on healthy bees if consistently consumed for weeks. These toxic effects disappeared in infected bees, suggesting that detoxification costs might have been counterbalanced by the advantages in slowing the progression of the infection. Nicotine consumption did not affect bee lifespan but the reduction in the parasite load may have other likely unexplored subtle benefits both for individual bees and their colony.  Potential evidence for self-medication is discussed. The contention that secondary metabolites in nectar may be under selection from pollinators, or used by plants to enhance their own reproductive success, remains to be confirmed.D.B. was supported by a Marie Curie Intra European Fellowship within the 7th European Community Framework Programm

Characterization of Within-Host Plasmodium falciparum Diversity Using Next-Generation Sequence Data

Our understanding of the composition of multi-clonal malarial infections and the epidemiological factors which shape their diversity remain poorly understood. Traditionally within-host diversity has been defined in terms of the multiplicity of infection (MOI) derived by PCR-based genotyping. Massively parallel, single molecule sequencing technologies now enable individual read counts to be derived on genome-wide datasets facilitating the development of new statistical approaches to describe within-host diversity. In this class of measures the FWS metric characterizes within-host diversity and its relationship to population level diversity. Utilizing P. falciparum field isolates from patients in West Africa we here explore the relationship between the traditional MOI and FWS approaches. FWS statistics were derived from read count data at 86,158 SNPs in 64 samples sequenced on the Illumina GA platform. MOI estimates were derived by PCR at the msp-1 and -2 loci. Significant correlations were observed between the two measures, particularly with the msp-1 locus (P = 5.92×10−5). The FWS metric should be more robust than the PCR-based approach owing to reduced sensitivity to potential locus-specific artifacts. Furthermore the FWS metric captures information on a range of parameters which influence out-crossing risk including the number of clones (MOI), their relative proportions and genetic divergence. This approach should provide novel insights into the factors which correlate with, and shape within-host diversity