Whole Genome Sequencing of Field Isolates Reveals a Common Duplication of the Duffy Binding Protein Gene in Malagasy Plasmodium vivax Strains

Background

Plasmodium vivax is the most prevalent human malaria parasite, causing serious public health problems in malaria-endemic countries. Until recently the Duffy-negative blood group phenotype was considered to confer resistance to vivax malaria for most African ethnicities. We and others have reported that P. vivax strains in African countries from Madagascar to Mauritania display capacity to cause clinical vivax malaria in Duffy-negative people. New insights must now explain Duffy-independent P. vivax invasion of human erythrocytes.

Methods/Principal Findings

Through recent whole genome sequencing we obtained ≥70× coverage of the P. vivax genome from five field-isolates, resulting in ≥93% of the Sal I reference sequenced at coverage greater than 20×. Combined with sequences from one additional Malagasy field isolate and from five monkey-adapted strains, we describe here identification of DNA sequence rearrangements in the P. vivax genome, including discovery of a duplication of the P. vivax Duffy binding protein (PvDBP) gene. A survey of Malagasy patients infected with P. vivax showed that the PvDBP duplication was present in numerous locations in Madagascar and found in over 50% of infected patients evaluated. Extended geographic surveys showed that the PvDBP duplication was detected frequently in vivax patients living in East Africa and in some residents of non-African P. vivax-endemic countries. Additionally, the PvDBP duplication was observed in travelers seeking treatment of vivax malaria upon returning home. PvDBP duplication prevalence was highest in west-central Madagascar sites where the highest frequencies of P. vivax-infected, Duffy-negative people were reported.

Conclusions/Significance

The highly conserved nature of the sequence involved in the PvDBP duplication suggests that it has occurred in a recent evolutionary time frame. These data suggest that PvDBP, a merozoite surface protein involved in red cell adhesion is rapidly evolving, possibly in response to constraints imposed by erythrocyte Duffy negativity in some human populations.     

Evidence of Habitat Structuring Aedes albopictus Populations in Réunion Island

Arbovirus vector dynamics and spread are influenced by climatic, environmental and geographic factors. Major Chikungunya and Dengue fever outbreaks occurring the last 10 years have coincided with the expansion of the mosquito vector Aedes albopictus to nearly all the continents. We characterized the ecological (larval development sites, population dynamics, insemination and daily survival rates) and genetic (diversity, gene flow, population structure) features of two Aedes albopictus populations from distinct environments (rural and urban) on Réunion Island, in the South-West Indian Ocean. Microsatellite analysis suggests population sub-structuring Ae. albopictus populations. Two genetic clusters were identified that were significantly linked to natural versus urban habitats with a mixed population in both areas. Ae. albopictus individuals prefer urban areas for mating and immature development, where hosts and containers that serve as larval development sites are readily available and support high population densities, whereas natural environments appear to serve as reservoirs for the mosquito.     

A typical browser, the roe deer, may consume substantial quantities of grasses in open landscapes

In open landscapes, grass leaves provide an abundant resource for ruminants, with potentially high nutritional value. However, their extensive digestion requires a long fermentation time, achieved through large rumen and the stratification of the rumen content. Due to anatomical and physiological differences, ruminants differ in their ability to process grass leaves. Particularly, the small roe deer, with its viscous saliva and unstratified rumen content, is generally classified as a strict browser. We hypothesised that roe deer may be able to use grass leaves in some circumstances, notably when the availability of other resources declines and when the quality of grass leaves is high. We expected that (1) grass leave consumption should be higher in open landscapes than in forest habitat because grasses are more widely available and more nutritious in open landscapes and (2) grass leave consumption should increase in winter when the availability of other resources declines. We assessed grass consumption by microscopic analysis of roe deer faecal pellets collected monthly both in forest habitat and in the surrounding open landscape. We found that both the occurrence and the proportion of grass leaves in the faeces were higher in the open landscape (predicted mean proportion 0.31) than in the forest (predicted mean proportion 0.05). In addition, the proportion of grass leaves in the faeces was higher in winter and lower in spring in both forest and open landscape. We suggest that roe deer are able to use grass leaves with unusually high nutritional quality in winter in this mild climate area. This involves a certain level of digestive plasticity to efficiently digest high quality grasses and may confer nutritional benefit to individuals feeding in an open landscape.     

Habitat use under predation risk: hunting, roads and human dwellings influence the spatial behaviour of roe deer

Wildlife populations are subjected to increasing pressure linked to human activities, which introduce multiple stressors. Recently, in addition to direct effects, it has been shown that indirect (non-lethal) effects of predation risk are predominant in many populations. Predation risk is often structured in space and time, generating a heterogeneous “landscape of fear” within which animals can minimize risks by modifying their habitat use. Furthermore, for ungulates, resource quality seems to be positively correlated with human-related sources of risk. We studied the trade-off between access to resources of high-quality and risk-taking by contrasting habitat use of roe deer during daytime with that during nighttime for 94 roe deer in a hunted population. Our first hypothesis was that roe deer should avoid human disturbance by modifying their habitat use during daytime compared to nighttime. Our results supported this, as roe deer mainly used open fields during nighttime, but used more forested habitats during daytime, when human disturbance is higher. Moreover, we found that diel patterns in habitat use were influenced by hunting disturbance. Indeed, the roe deer decreased their use of high-crops during daytime, an important source of cover and food, during the hunting season. The proximity of roads and dwellings also affected habitat use, since roe deer used open fields during daytime to a greater extent when the distance to these sources of disturbance was higher. Hence, our results suggest that roe deer resolve the trade-off between the acquisition of high-quality resources and risk avoidance by modifying their habitat use between day and night.     

Brachypodium distachyon as a model plant toward improved biofuel crops: Search for secreted proteins involved in biogenesis and disassembly of cell wall polymers

Polysaccharides make up about 75% of plant cell walls and can be broken down to produce sugar substrates (saccharification) from which a whole range of products can be obtained, including bioethanol. Cell walls also contain 5–10% of proteins, which could be used to tailor them for agroindustrial uses. Here we present cell wall proteomics data of Brachypodium distachyon, a model plant for temperate grasses. Leaves and culms were analyzed during active growth and at mature stage. Altogether, 559 proteins were identified by LC‐MS/MS and bioinformatics, among which 314 have predicted signal peptides. Sixty‐three proteins were shared by two organs at two developmental stages where they could play housekeeping functions. Differences were observed between organs and stages of development, especially at the level of glycoside hydrolases and oxidoreductases. Differences were also found between the known cell wall proteomes of B. distachyon, Oryza sativa, and the Arabidopsis thaliana dicot. Three glycoside hydrolases could be immunolocalized in cell walls using polyclonal antibodies against proteotypic peptides. Organ‐specific expression consistent with proteomics results could be observed as well as cell‐specific localization. Moreover, the high number of proteins of unknown function in B. distachyon cell wall proteomes opens new fields of research for monocot cell walls.     

In Situ Monitoring of the 2D Aggregation Process of Thiol-Coated Gold Nanoparticles Using Interparticle Plasmon Coupling

Near-field plasmon coupling between neighboring gold nanoparticles, measured by polarized optical waveguide lightmode spectroscopy, is employed to study the surface self-assembly of alcanethiol-capped gold nanoparticles during solvent evaporation. The waveguide used is a monomode optical fiber half-coupler. The sample is deposited on the surface of the waveguide and absorption spectra are continuously collected during the solvent evaporation process with a temporal resolution of 0.2 s. The absorption spectra show a progressive red shift of the plasmon peak caused by increasing interparticle near-field coupling. This shift can be used to determine the distance between particles by comparison to theoretical values calculated using the discrete dipoles approximation. The technique is demonstrated for the assembly of 10 nm gold particles capped with thiol ligands of two different lengths. Interestingly, in the case of dodecanethiol-capped particles, the extinction spectrum not only shifts to longer wavelengths, but also changes in shape during the drying process. About half a second before the solvent completely evaporates, the spectrum broadens as a second component appears. This feature is tentatively attributed to the formation of a significant population of particle clusters as a result of incomplete screening of van der Waals attractions by the shorter ligand.     

The Interactomes of Influenza Virus NS1 and NS2 Proteins Identify New Host Factors and Provide Insights for ADAR1 Playing a Supportive Role in Virus Replication

Influenza A NS1 and NS2 proteins are encoded by the RNA segment 8 of the viral genome. NS1 is a multifunctional protein and a virulence factor while NS2 is involved in nuclear export of viral ribonucleoprotein complexes. A yeast two-hybrid screening strategy was used to identify host factors supporting NS1 and NS2 functions. More than 560 interactions between 79 cellular proteins and NS1 and NS2 proteins from 9 different influenza virus strains have been identified. These interacting proteins are potentially involved in each step of the infectious process and their contribution to viral replication was tested by RNA interference. Validation of the relevance of these host cell proteins for the viral replication cycle revealed that 7 of the 79 NS1 and/or NS2-interacting proteins positively or negatively controlled virus replication. One of the main factors targeted by NS1 of all virus strains was double-stranded RNA binding domain protein family. In particular, adenosine deaminase acting on RNA 1 (ADAR1) appeared as a pro-viral host factor whose expression is necessary for optimal viral protein synthesis and replication. Surprisingly, ADAR1 also appeared as a pro-viral host factor for dengue virus replication and directly interacted with the viral NS3 protein. ADAR1 editing activity was enhanced by both viruses through dengue virus NS3 and influenza virus NS1 proteins, suggesting a similar virus-host co-evolution.     

An evaluation of analysis pipelines for DNA methylation profiling using the Illumina HumanMethylation450 BeadChip platform

The proper identification of differentially methylated CpGs is central in most epigenetic studies. The Illumina HumanMethylation450 BeadChip is widely used to quantify DNA methylation; nevertheless, the design of an appropriate analysis pipeline faces severe challenges due to the convolution of biological and technical variability and the presence of a signal bias between Infinium I and II probe design types. Despite recent attempts to investigate how to analyze DNA methylation data with such an array design, it has not been possible to perform a comprehensive comparison between different bioinformatics pipelines due to the lack of appropriate data sets having both large sample size and sufficient number of technical replicates. Here we perform such a comparative analysis, targeting the problems of reducing the technical variability, eliminating the probe design bias and reducing the batch effect by exploiting two unpublished data sets, which included technical replicates and were profiled for DNA methylation either on peripheral blood, monocytes or muscle biopsies. We evaluated the performance of different analysis pipelines and demonstrated that: (1) it is critical to correct for the probe design type, since the amplitude of the measured methylation change depends on the underlying chemistry; (2) the effect of different normalization schemes is mixed, and the most effective method in our hands were quantile normalization and Beta Mixture Quantile dilation (BMIQ); (3) it is beneficial to correct for batch effects. In conclusion, our comparative analysis using a comprehensive data set suggests an efficient pipeline for proper identification of differentially methylated CpGs using the Illumina 450K arrays.     

Determinants of Microdamage in Elderly Human Vertebral Trabecular Bone

Previous studies have shown that microdamage accumulates in bone as a result of physiological loading and occurs naturally in human trabecular bone. The purpose of this study was to determine the factors associated with pre-existing microdamage in human vertebral trabecular bone, namely age, architecture, hardness, mineral and organic matrix. Trabecular bone cores were collected from human L2 vertebrae (n = 53) from donors 54–95 years of age (22 men and 30 women, 1 unknown) and previous cited parameters were evaluated. Collagen cross-link content (PYD, DPD, PEN and % of collagen) was measured on surrounding trabecular bone. We found that determinants of microdamage were mostly the age of donors, architecture, mineral characteristics and mature enzymatic cross-links. Moreover, linear microcracks were mostly associated with the bone matrix characteristics whereas diffuse damage was associated with architecture. We conclude that linear and diffuse types of microdamage seemed to have different determinants, with age being critical for both types.