Protein prosthesis: β‐peptides as reverse‐turn surrogates

The introduction of non‐natural modules could provide unprecedented control over folding/unfolding behavior, conformational stability, and biological function of proteins. Success requires the interrogation of candidate modules in natural contexts. Here, expressed protein ligation is used to replace a reverse turn in bovine pancreatic ribonuclease (RNase A) with a synthetic β‐dipeptide: β²‐homoalanine–β³‐homoalanine. This segment is known to adopt an unnatural reverse‐turn conformation that contains a 10‐membered ring hydrogen bond, but one with a donor–acceptor pattern opposite to that in the 10‐membered rings of natural reverse turns. The RNase A variant has intact enzymatic activity, but unfolds more quickly and has diminished conformational stability relative to native RNase A. These data indicate that hydrogen‐bonding pattern merits careful consideration in the selection of beneficial reverse‐turn surrogates.     

Molecular phylogeography of the viperine snake Natrix maura (Serpentes: Colubridae): Evidence for strong intraspecific differentiation

The molecular phylogeography of the viperine snake, Natrix maura (Linnaeus, 1758), was investigated using complete sequences of the mitochondrial cytochrome b gene and genomic ISSR-PCR fingerprinting. In a total of 120 samples, 44 unique cytochrome b haplotypes were found which defined three major genetic lineages associated with samples from Morocco, Tunisia and Europe, respectively. The same lineages were supported by nuclear data. A possible fourth lineage exists in southern Spain. Genetic distances of cytochrome b sequences between the three main lineages were in the range of 3.9–5.6%, suggesting independent evolution since the early Pliocene. Distinction of the three major lineages at the subspecies or species level is discussed to account taxonomically for the high intraspecific variation in the viperine snake. A more detailed analysis of the European samples based on genetic diversity indices and a network reconstruction suggests a complex Pleistocene history for the viperine snake in Europe. Clear differentiation was found between populations south and north of the central Iberian mountain ranges, suggesting Pleistocene glacial refugia both in the southern and northern Iberian peninsula. In the south, genetic diversity was associated with the main river valleys, whereas northern haplotypes were more broadly distributed, indicating gene flow or postglacial range expansions. Unexpectedly high levels of genetic variation in southeastern France and northwestern Italy would be compatible with the hypothesis of a glacial refugium north of the Pyrenees or in Italy. However, due to the dependence of N. maura on warm climates, the assumption of a northern refugium seems unwarranted. We believe that further sampling in northern Spain is likely to reveal genetically diverse populations which could have served as sources for postglacial recolonization of France and Italy.     

Pigs’ preferences for rooting materials measured in a three-choice maze-test

The aim of this experiment was to investigate pigs’ preferences for rooting materials. Eighteen materials were allocated to six categories each of which consisted of three similar materials based on characteristics such as structure, size of particles, complexity, destructibility and digestibility. Twelve pairs of pigs chose among the three materials of each of the six categories in a balanced design. Within each category each pair was given four instantaneous choices among the three materials in a three-armed maze. ‘No choice’ was scored if the pigs did not enter one of the maze-arms within 90 s. Thus there were four options in each choice situation. The results were analysed using a random utility model incorporating random intercepts to account for the repeated testing of the same animals. The pigs expressed clear preferences within the category EARTH, where compost and peat were preferred to wood-shavings and no choice. In the category CHIP the most probable rank-order was spruce chip, willow chip, fir chip and no choice, while in the category ROUGH the most probable rank-order was maize-silage, grass silage, sugar beets and no choice. However, in these two categories none of the probabilities were sufficiently large to signify a preference for any of the three materials although the probabilities of the ‘no choice’ option were low. The pigs expressed no preferences among any of the four options including ‘no choice’ in the categories TOY (sisal robe, Bite-Rite, wooden beam), HAY (alfalfa hay mixed with straw, seed grass hay, barley straw with under-seed), and STRAW (long straw, chopped straw and straw pellets).     

Follicular dendritic cells emerge from ubiquitous perivascular precursors

The differentiation of follicular dendritic cells (FDC) is essential to the remarkable microanatomic plasticity of lymphoid follicles. Here we show that FDC arise from ubiquitous perivascular precursors (preFDC) expressing platelet-derived growth factor receptor β (PDGFRβ). PDGFRβ-Cre-driven reporter gene recombination resulted in FDC labeling, whereas conditional ablation of PDGFRβ(+)-derived cells abolished FDC, indicating that FDC originate from PDGFRβ(+) cells. Lymphotoxin-α-overexpressing prion protein (PrP)(+) kidneys developed PrP(+) FDC after transplantation into PrP(-) mice, confirming that preFDC exist outside lymphoid organs. Adipose tissue-derived PDGFRβ(+) stromal-vascular cells responded to FDC maturation factors and, when transplanted into lymphotoxin β receptor (LTβR)(-) kidney capsules, differentiated into Mfge8(+)CD21/35(+)FcγRIIβ(+)PrP(+) FDC capable of trapping immune complexes and recruiting B cells. Spleens of lymphocyte-deficient mice contained perivascular PDGFRβ(+) FDC precursors whose expansion required both lymphoid tissue inducer (LTi) cells and lymphotoxin. The ubiquity of preFDC and their strategic location at blood vessels may explain the de novo generation of organized lymphoid tissue at sites of lymphocytic inflammation.     

One-pot synthesis of pegylated ultrasmall iron-oxide nanoparticles and their in vivo evaluation as magnetic resonance imaging contrast agents

A well-defined copolymer poly(oligo(ethylene glycol) methacrylate-co-methacrylic acid) P(OEGMA-co-MAA) was studied as a novel water-soluble biocompatible coating for superparamagnetic iron oxide nanoparticles. This copolymer was prepared via a two-step procedure: a well-defined precursor poly(oligo(ethylene glycol) methacrylate-co-tert-butyl methacrylate), P(OEGMA-co-tBMA) (M(n) = 17300 g mol(-1); M(w)/M(n) = 1.22), was first synthesized by atom-transfer radical polymerization in the presence of the catalyst system copper(I) chloride/2,2'-bipyridyl and subsequently selectively hydrolyzed in acidic conditions. The resulting P(OEGMA-co-MAA) was directly utilized as a polymeric stabilizer in the nanoparticle synthesis. Four batches of ultrasmall PEGylated magnetite nanoparticles (i.e., with an average diameter below 30 nm) were prepared via aqueous coprecipitation of iron salts in the presence of variable amounts of P(OEGMA-co-MAA). The diameter of the nanoparticles could be easily tuned in the range 10-25 nm by varying the initial copolymer concentration. Moreover, the formed PEGylated ferrofluids exhibited a long-term colloidal stability in physiological buffer and could therefore be studied in vivo by magnetic resonance (MR) imaging. Intravenous injection into rats showed no detectable signal in the liver within the first 2 h. Maximum liver accumulation was found after 6 h, suggesting a prolongated circulation of the nanoparticles in the bloodstream as compared to conventional MR imaging contrast agents.     

Cryptic niche conservatism among evolutionary lineages of an invasive lizard

Aim There is increasing evidence that the quality and breadth of ecological niches vary among individuals, populations, evolutionary lineages and therefore also across the range of a species. Sufficient knowledge about niche divergence among clades might thus be crucial for predicting the invasion potential of species. We tested for the first time whether evolutionary lineages of an invasive species vary in their climate niches and invasive potential. Furthermore, we tested whether lineage‐specific models show a better performance than combined models. Location Europe. Methods We used species distribution models (SDMs) based on climatic information at native and invasive ranges to test for intra‐specific niche divergence among mitochondrial DNA (mtDNA) clades of the invasive wall lizard Podarcis muralis. Using DNA barcoding, we assigned 77 invasive populations in Central Europe to eight geographically distinct evolutionary lineages. Niche similarity among lineages was assessed and the predictive power of a combination of clade‐specific SDMs was compared with a combined SDM using the pooled records of all lineages. Results We recorded eight different invasive mtDNA clades in Central Europe. The analysed clades had rather similar realized niches in their native and invasive ranges, whereas inter‐clade niche differentiation was comparatively strong. However, we found only a weak correlation between geographic origin (i.e. mtDNA clade) and invasive occurrences. Clades with narrow realized niches still became successful invaders far outside their native range, most probably due to broader fundamental niches. The combined model using data for all invasive lineages achieved a much better prediction of the invasive potential. Conclusions Our results indicate that the observed niche differentiation among evolutionary lineages is mainly driven by niche realization and not by differences in the fundamental niches. Such cryptic niche conservatism might hamper the success of clade‐specific niche modelling. Cryptic niche conservatism may in general explain the invasion success of species in areas with apparently unsuitable climate.     

Paleodistributions and comparative molecular phylogeography of leafcutter ants (Atta spp.) provide new insight into the origins of Amazonian diversity

The evolutionary basis for high species diversity in tropical regions of the world remains unresolved. Much research has focused on the biogeography of speciation in the Amazon Basin, which harbors the greatest diversity of terrestrial life. The leading hypotheses on allopatric diversification of Amazonian taxa are the Pleistocene refugia, marine incursion, and riverine barrier hypotheses. Recent advances in the fields of phylogeography and species-distribution modeling permit a modern re-evaluation of these hypotheses. Our approach combines comparative, molecular phylogeographic analyses using mitochondrial DNA sequence data with paleodistribution modeling of species ranges at the last glacial maximum (LGM) to test these hypotheses for three co-distributed species of leafcutter ants (Atta spp.). The cumulative results of all tests reject every prediction of the riverine barrier hypothesis, but are unable to reject several predictions of the Pleistocene refugia and marine incursion hypotheses. Coalescent dating analyses suggest that population structure formed recently (Pleistocene-Pliocene), but are unable to reject the possibility that Miocene events may be responsible for structuring populations in two of the three species examined. The available data therefore suggest that either marine incursions in the Miocene or climate changes during the Pleistocene--or both--have shaped the population structure of the three species examined. Our results also reconceptualize the traditional Pleistocene refugia hypothesis, and offer a novel framework for future research into the area.     

Mutual Information Rate and Bounds for It

The amount of information exchanged per unit of time between two nodes in a dynamical network or between two data sets is a powerful concept for analysing complex systems. This quantity, known as the mutual information rate (MIR), is calculated from the mutual information, which is rigorously defined only for random systems. Moreover, the definition of mutual information is based on probabilities of significant events. This work offers a simple alternative way to calculate the MIR in dynamical (deterministic) networks or between two time series (not fully deterministic), and to calculate its upper and lower bounds without having to calculate probabilities, but rather in terms of well known and well defined quantities in dynamical systems. As possible applications of our bounds, we study the relationship between synchronisation and the exchange of information in a system of two coupled maps and in experimental networks of coupled oscillators.