Multispacer sequence typing relapsing fever Borreliae in Africa

Background

In Africa, relapsing fevers are neglected arthropod-borne infections caused by closely related Borrelia species. They cause mild to deadly undifferentiated fever particularly severe in pregnant women. Lack of a tool to genotype these Borrelia organisms limits knowledge regarding their reservoirs and their epidemiology.

Methodology/Principal Findings

Genome sequence analysis of Borrelia crocidurae, Borrelia duttonii and Borrelia recurrentis yielded 5 intergenic spacers scattered between 10 chromosomal genes that were incorporated into a multispacer sequence typing (MST) approach. Sequencing these spacers directly from human blood specimens previously found to be infected by B. recurrentis (30 specimens), B. duttonii (17 specimens) and B. crocidurae (13 specimens) resolved these 60 strains and the 3 type strains into 13 species-specific spacer types in the presence of negative controls. B. crocidurae comprised of 8 spacer types, B. duttonii of 3 spacer types and B. recurrentis of 2 spacer types.

Conclusions/Significance

Phylogenetic analyses of MST data suggested that B. duttonii, B. crocidurae and B. recurrentis are variants of a unique ancestral Borrelia species. MST proved to be a suitable approach for identifying and genotyping relapsing fever borreliae in Africa. It could be applied to both vectors and clinical specimens.     

Malat-1-PRC2-EZH1 interaction supports adaptive oxidative stress dependent epigenome remodeling in skeletal myotubes

PRC2-mediated epigenetic function involves the interaction with long non-coding RNAs (lncRNAs). Although the identity of some of these RNAs has been elucidated in the context of developmental programs, their counterparts in postmitotic adult tissue homeostasis remain uncharacterized. To this aim, we used terminally differentiated postmitotic skeletal muscle cells in which oxidative stress induces the dynamic activation of PRC2-Ezh1 through Embryonic Ectoderm Develpment (EED) shuttling to the nucleus. We identify lncRNA Malat-1 as a necessary partner for PRC2-Ezh1-dependent response to oxidative stress. We show that in this pathway, PRC2-EZH1 dynamic assembly, and in turn stress induced skeletal muscle targeted genes repression, depends specifically on Malat-1. Our study reports about PRC2–RNA interactions in the physiological context of adaptive oxidative stress response and identifies the first lncRNA involved in PRC2-Ezh1 function.Subject terms: Gene silencing, Long non-coding RNAs     

A model for the evolution of crèching behaviour in gulls

A crèche is an aggregation of chicks outside nesting territories, within chicks continue to be fed only by their own parents. Several adaptive functions of crèching have been proposed, the most frequent being a reduction in predator pressure. Using an evolutionary stable strategy approach based on the computation of individuals' fecundity, we examined which regime of aerial and terrestrial predation is likely to favour the evolution and stability of the crèching strategy (CS) in gulls. Our results confirm the hypothesis that habitat instability associated with high levels of terrestrial predation favours the evolution and maintenance of crèching behaviour. Moreover, our results suggest that a low aggressiveness against predators may be a pre-adaptation to a CS. In contrast, the high synchronisation often observed in crèching species does not favour the evolution of a crèching behaviour and is thus probably under selection pressures different from those modelled here.     

U‐CARE: Utilities for performing goodness of fit tests and manipulating CApture–REcapture data

In any statistical analysis, assessing the goodness of fit of a model to the data is crucial to avoid drawing incorrect conclusions. U‐CARE is a computer application that deals with the mandatory first steps of the analyses of capture–recapture data: the preparation of the data set and the assessment of the fit of a general model (Cormack‐Jolly‐Seber and variants for single‐state data; Jolly‐Move and variants for multi‐state data). U‐CARE implements the current state of the art in goodness‐of‐fit testing by incorporating components aimed at detecting the most likely departures from assumptions ( Pradel et al. 2003, 2005 ). It is a free and stand‐alone application for Windows.     

Evolutionary allometry reveals a shift in selection pressure on male horn size

How selection pressures acting within species interact with developmental constraints to shape macro‐evolutionary patterns of species divergence is still poorly understood. In particular, whether or not sexual selection affects evolutionary allometry, the increase in trait size with body size across species, of secondary sexual characters, remains largely unknown. In this context, bovid horn size is an especially relevant trait to study because horns are present in both sexes, but the intensity of sexual selection acting on them is expected to vary both among species and between sexes. Using a unique data set of sex‐specific horn size and body mass including 91 species of bovids, we compared the evolutionary allometry between horn size and body mass between sexes while accounting for both the intensity of sexual selection and phylogenetic relationship among species. We found a nonlinear evolutionary allometry where the allometric slope decreased with increasing species body mass. This pattern, much more pronounced in males than in females, suggests either that horn size is limited by some constraints in the largest bovids or is no longer the direct target of sexual selection in very large species.     

Influence of land use on the taxonomic and functional diversity of dung beetles (Coleoptera: Scarabaeinae) in the southern Atlantic forest of Argentina

The degradation and replacement of native ecosystems affects both their taxonomic and functional biodiversity. However, native species may find a gradient of habitat suitability in different land uses within a region. The aim of this study was to evaluate the effect of land use on the taxonomic and functional diversity of dung beetle assemblages in the southern Atlantic forest of Argentina. Dung beetles were sampled in both the native forest (control) and different land uses (Pine and Yerba mate plantations and cattle pastures) during the 2014 summer, using pitfall traps baited with human feces and rotten meat. Samplings were taken from 20 different sites, with five replicates of each land use and the native forest (100 pitfall traps in total). A total of 1699 beetles of 27 species were captured. Canthon quinquemaculatus, Canthon conformis and Dichotomius sericeus were the most abundant species. Cattle pastures were the land use most negatively affected in their taxonomic and functional diversity, particularly large paracoprid dung beetles. Pine plantations maintained their taxonomic and functional diversity in relation to the native forest and Yerba mate plantations showed, in general, an intermediate situation. Microclimatic conditions (average temperature and humidity and maximum temperature) were correlated with functional diversity (the proportion of large paracoprid dung beetles decreased with increasing temperature) and are probably good predictors to explain the observed patterns of functional diversity of dung beetles. The development of sustainable production systems that preserve the native biodiversity requires the conservation of key components from the ecological niche of native species, especially microclimatic conditions.     

Autoantibodies enhance agonist action and binding to cardiac muscarinic receptors in chronic Chagas' disease

Chronic Chagasic patient immunoglobulins (CChP-IgGs) recognize an acidic amino acid cluster at the second extracellular loop (el2) of cardiac M(2)-muscarinic acetylcholine receptors (M(2)AChRs). These residues correspond to a common binding site for various allosteric agents. We characterized the nature of the M(2)AChR/CChP-IgG interaction in functional and radioligand binding experiments applying the same mainstream strategies previously used for the characterization of other allosteric agents. Dose-response curves of acetylcholine effect on heart rate were constructed with data from isolated heart experiments in the presence of CChP or normal blood donor (NBD) sera. In these experiments, CChP sera but not NBD sera increased the efficacy of agonist action by augmenting the onset of bradyarrhythmias and inducing a Hill slope of 2.5. This effect was blocked by gallamine, an M(2)AChR allosteric antagonist. Correspondingly, CChP-IgGs increased acetylcholine affinity twofold and showed negative cooperativity for [(3)H]-N-methyl scopolamine ([(3)H]-NMS) in allosterism binding assays. A peptide corresponding to the M(2)AChR-el2 blocked this effect. Furthermore, dissociation assays showed that the effect of gallamine on the [(3)H]-NMS off-rate was reverted by CChP-IgGs. Finally, concentration-effect curves for the allosteric delay of W84 on [(3)H]-NMS dissociation right shifted from an IC(50) of 33 nmol/L to 78 nmol/L, 992 nmol/L, and 1670 nmol/L in the presence of 6.7 x 10(- 8), 1.33 x 10(- 7), and 2.0 x 10(- 7) mol/L of anti-el2 affinity-purified CChP-IgGs. Taken together, these findings confirmed a competitive interplay of these ligands at the common allosteric site and revealed the novel allosteric nature of the interaction of CChP-IgGs at the M(2)AChRs as a positive cooperativity effect on acetylcholine action.     

Assessing the impact of climate variation on survival in vertebrate populations

Abstract The impact of the ongoing rapid climate change on natural systems is a major issue for human societies. An important challenge for ecologists is to identify the climatic factors that drive temporal variation in demographic parameters, and, ultimately, the dynamics of natural populations. The analysis of long-term monitoring data at the individual scale is often the only available approach to estimate reliably demographic parameters of vertebrate populations. We review statistical procedures used in these analyses to study links between climatic factors and survival variation in vertebrate populations. We evaluated the efficiency of various statistical procedures from an analysis of survival in a population of white stork, Ciconia ciconia, a simulation study and a critical review of 78 papers published in the ecological literature. We identified six potential methodological problems: (i) the use of statistical models that are not well-suited to the analysis of long-term monitoring data collected at the individual scale; (ii) low ratios of number of statistical units to number of candidate climatic covariates; (iii) collinearity among candidate climatic covariates; (iv) the use of statistics, to assess statistical support for climatic covariates effects, that deal poorly with unexplained variation in survival; (v) spurious detection of effects due to the co-occurrence of trends in survival and the climatic covariate time series; and (vi) assessment of the magnitude of climatic effects on survival using measures that cannot be compared across case studies. The critical review of the ecological literature revealed that five of these six methodological problems were often poorly tackled. As a consequence we concluded that many of these studies generated hypotheses but only few provided solid evidence for impacts of climatic factors on survival or reliable measures of the magnitude of such impacts. We provide practical advice to solve efficiently most of the methodological problems identified. The only frequent issue that still lacks a straightforward solution was the low ratio of the number of statistical units to the number of candidate climatic covariates. In the perspective of increasing this ratio and therefore of producing more robust analyses of the links between climate and demography, we suggest leads to improve the procedures for designing field protocols and selecting a set of candidate climatic covariates. Finally, we present recent statistical methods with potential interest for assessing the impact of climatic factors on demographic parameters.     

On the dimerization of the primitive tRNAs: implications in the origin of genetic code

RNAs that catalyse their own aminoacylation have been recently selected in vitro. These findings support the notion that the primitive aminoacyl-tRNA synthetases may have been RNAs. In this paper, we propose a structural model for the first aminoacyl-tRNA synthetase consisting of an RNA complex formed between two primitive tRNA molecules through two intermolecular loop-strand interactions, and with implications in the origin of the genetic code.