Analysis of symmetries in models of multi-strain infections

In mathematical studies of the dynamics of multi-strain diseases caused by antigenically diverse pathogens, there is a substantial interest in analytical insights. Using the example of a generic model of multi-strain diseases with cross-immunity between strains, we show that a significant understanding of the stability of steady states and possible dynamical behaviours can be achieved when the symmetry of interactions between strains is taken into account. Techniques of equivariant bifurcation theory allow one to identify the type of possible symmetry-breaking Hopf bifurcation, as well as to classify different periodic solutions in terms of their spatial and temporal symmetries. The approach is also illustrated on other models of multi-strain diseases, where the same methodology provides a systematic understanding of bifurcation scenarios and periodic behaviours. The results of the analysis are quite generic, and have wider implications for understanding the dynamics of a large class of models of multi-strain diseases.     

Mouthparts in Leptotrombidium larvae (Acariformes: Trombiculidae)

Mouthparts of Leptotrombidium larvae (Acariformes: Trombiculidae), potential vectors of tsutsugamushi disease agents, were studied in detail using light microscopy, scanning electron microscopy, and transmission electron microscopy. The mouthparts incorporated within the pseudotagma gnathosoma are composed of the infracapitulum ventrally and the chelicerae dorsally. The ventral wall of the infracapitulum is formed by a wide mentum posteriorly and a narrowed malapophysis anteriorly. The malapophysis firmly envelops the distal cheliceral portions by its lateral walls. The lateral lips of the malapophysis are flexible structures hiding the cheliceral blades in inactive condition and turning back forming a type of temporary sucker closely applied to the host skin during feeding. The roof of the infracapitulum is formed by a weakly sclerotized labrum anteriorly and a cervix with the capitular apodemes extending posteriorly. The labral muscles are lacking. The capitular apodemes serve as origin for pharyngeal dilators running to the dorsal wall of the pharynx fused with the bottom of the infracapitulum. The basal cheliceral segments are separated from each other besides the very posterior portions where they are movably joined by the inner walls. The sigmoid pieces serve for insertion of the cheliceral elevators originating at the posterior portions of the basal segments. The movable digits reveal the solid basal sclerite and the cheliceral blade curved upward with a tricuspid cap on its tip. Dendrites of nerve cells run along the digits to their tips. The ganglia are placed within the basal segments just behind the movable digits. The chelicerae also reveal well developed flexible fixed digits overhanging the basal portions of the blades. The gnathosoma possesses several sets of extrinsic muscles originating at the scutum and at the soft cuticle behind it. Laterally, the gnathosoma bears five‐segmented palps with a trifurcate palpal claw. J. Morphol. 277:424–444, 2016. © 2016 Wiley Periodicals, Inc.     

Migration timing and distance from shore of southbound eastern Pacific gray whales (Eschrichtius robustus) off Ensenada,Baja California,Mexico

Eastern Pacific gray whales were monitored off Ensenada, Mexico, during the southbound migration. The objectives were to determine southbound migration timing and width of the migration corridor during three seasons (2003–2006). Migration timing was determined by fitting a generalized additive model to the shore counts for each season and estimating the 10, 50, and 90 percentiles of the fitted curves. To estimate abundance from shore‐based counts, a probability density function for the shore based distances was estimated by a product of a gamma distribution fit to the boat survey distance data for 2006/2007 and a half‐normal detection function using combined data of the three seasons. The parameters of the gamma distribution were corrected to account for less boat survey effort carried out 20–40 km than 0–20 km from shore. The onset of the migration off Ensenada was in late December/early January and ended around 13 February. The median date was 23–26 January for the first and third season and a week early for the second season. Boat surveys indicated a wide (20 km) migration corridor but most gray whales traveled within 9.9 km from shore. The estimated total number of whales during watch hours was 2,298 (95% CI = 1,536–4,447).     

Role of 5-aminolevulinic acid in the formation of winter rape resistance to sulfonylurea herbicides

Growing of winter rape (Brassica napus L.) plants for 7–8 days in the presence of a sulfonylurea herbicide Magnum (methsulfuron methyl; 200 and 500 mg/L) exerted an organ-specific influence on the seedlings: suppressed hypocotyl and root growth and increased the accumulation of fresh weight of cotyledonary leaves. Exogenous 5-aminolevulinic acid (ALA; 0.1, 1.0, and 10 mg/L) partially negated the adverse effect of Magnum on the length and fresh weight of roots and hypocotyls and stimulated the development of cotyledons. The herbicide suppressed the activity of ascorbate peroxidase (APX). The addition of ALA to the 200 mg/L herbicide solution caused a steady activation of APX as compared with the effect of herbicide alone. In plants grown on Magnum solutions, the activity of glutathione reductase (GR) rose. Positive effect of exogenous ALA was only observed when 500 mg/L herbicide was used (Magnum-500 type of treatment). In plants grown on the Magnum solution, the content of reduced and oxidized forms of glutathione rose. In contrasty, exogenous ALA reduced the total content of glutathione but in this case the ratio between its reduced and oxidized forms rose. In the presence of the herbicide, the content of anthocyans considerably decreased and upon the addition of exogenous ALA their levels rose. In rape plants treated with Magnum, the ability to generate superoxide anion radical was essentially the same as in control plants; however, the content of hydrogen peroxide (H₂O₂) therein rose. The addition of ALA to the herbicide reduced the ability to generate superoxide anion radical and the level of H₂O₂. The activity of acetolactate synthase remained on the control level when 200 mg/L Magnum was used, decreased in the plants of Magnum-500 treatment, and rose upon the addition of exogenous ALA to this type of treatment. It was concluded that ALA had a positive effect on the development of winter rape resistance to Magnum via stimulation of growth processes, activation of APX and GR, predominant elevation of the content of reduced glutathione and anthocyans, and partial recovery of acetolactate synthase activity, which on the whole caused a decrease in the H₂O₂ level and in the ability of plants to generate superoxide anion radical.     

On Extrapolating Past the Range of Observed Data When Making Statistical Predictions in Ecology

Ecologists are increasingly using statistical models to predict animal abundance and occurrence in unsampled locations. The reliability of such predictions depends on a number of factors, including sample size, how far prediction locations are from the observed data, and similarity of predictive covariates in locations where data are gathered to locations where predictions are desired. In this paper, we propose extending Cook’s notion of an independent variable hull (IVH), developed originally for application with linear regression models, to generalized regression models as a way to help assess the potential reliability of predictions in unsampled areas. Predictions occurring inside the generalized independent variable hull (gIVH) can be regarded as interpolations, while predictions occurring outside the gIVH can be regarded as extrapolations worthy of additional investigation or skepticism. We conduct a simulation study to demonstrate the usefulness of this metric for limiting the scope of spatial inference when conducting model-based abundance estimation from survey counts. In this case, limiting inference to the gIVH substantially reduces bias, especially when survey designs are spatially imbalanced. We also demonstrate the utility of the gIVH in diagnosing problematic extrapolations when estimating the relative abundance of ribbon seals in the Bering Sea as a function of predictive covariates. We suggest that ecologists routinely use diagnostics such as the gIVH to help gauge the reliability of predictions from statistical models (such as generalized linear, generalized additive, and spatio-temporal regression models).     

Genome‐wide analysis of Italian sheep diversity reveals a strong geographic pattern and cryptic relationships between breeds

Italy counts several sheep breeds, arisen over centuries as a consequence of ancient and recent genetic and demographic events. To finely reconstruct genetic structure and relationships between Italian sheep, 496 subjects from 19 breeds were typed at 50K single nucleotide polymorphism loci. A subset of foreign breeds from the Sheep HapMap dataset was also included in the analyses. Genetic distances (as visualized either in a network or in a multidimensional scaling analysis of identical by state distances) closely reflected geographic proximity between breeds, with a clear north–south gradient, likely because of high levels of past gene flow and admixture all along the peninsula. Sardinian breeds diverged more from other breeds, a probable consequence of the combined effect of ancient sporadic introgression of feral mouflon and long‐lasting genetic isolation from continental sheep populations. The study allowed the detection of previously undocumented episodes of recent introgression (Delle Langhe into the endangered Altamurana breed) as well as signatures of known, or claimed, historical introgression (Merino into Sopravissana and Gentile di Puglia; Bergamasca into Fabrianese, Appenninica and, to a lesser extent, Leccese). Arguments that would question, from a genomic point of view, the current breed classification of Bergamasca and Biellese into two separate breeds are presented. Finally, a role for traditional transhumance practices in shaping the genetic makeup of Alpine sheep breeds is proposed. The study represents the first exhaustive analysis of Italian sheep diversity in an European context, and it bridges the gap in the previous HapMap panel between Western Mediterranean and Swiss breeds.