The fine-scale utilization of forest edges by mammalian mesopredators related to patch size and conservation issues in Central European farmland

The marked negative impact of habitat fragmentation and the edge effect on many populations of bird species is a recent major concern in conservation biology. Here, we focus on the edge effect in different sized forest patches in Central European farmland. In particular, we tested whether the distribution of mammalian mesopredators is related to fragment size and distance to habitat edge, and whether the contribution of these factors is additive or interactive. To assess fine-scale utilization of forest edges, we established transects of four scent stations at different distances from forest edges into the interior (0, 25, 50, 100 m) in 146 forest fragments of variable patch size (3.2–5099.6 ha) from May to June, 2008–2009. This large sample size allowed us to perform detailed analyses separately for all detected species. Our findings confirm that mammalian mesopredators strongly prefer habitat edges and small forest fragments. The probability of occurrence tended to decrease with increasing distance from the edge for all seven carnivore species detected. The carnivores’ occurrence was also negatively correlated with forest fragment area. All detected species tended to prefer small fragments, with the exception of the Eurasian badger (showing the reverse but non-significant pattern) and the red fox (no effect of fragment size). In addition, the non-significant interaction between fragment size and distance to edge suggests that both of these factors contribute independently and additively to mesopredator-mediated effects on biota in a fragmented landscape.     

D-trehalose/D-maltose-binding protein from the hyperthermophilic archaeon Thermococcus litoralis: the binding of trehalose and maltose results in different protein conformational states

In this work, we used fluorescence spectroscopy, molecular dynamics simulation, and Fourier transform infrared spectroscopy for investigating the effect of trehalose binding and maltose binding on the structural properties and the physical parameters of the recombinant D-trehalose/D-maltose binding protein (TMBP) from the hyperthermophilic archaeon Thermococcus litoralis. The binding of the two sugars to TMBP was studied in the temperature range 20 degrees-100 degrees C. The results show that TMBP possesses remarkable temperature stability and its secondary structure does not melt up to 90 degrees C. Although both the secondary structure itself and the sequence of melting events were not significantly affected by the sugar binding, the protein assumes different conformations with different physical properties depending whether maltose or trehalose is bound to the protein. At low and moderate temperatures, TMBP possesses a structure that is highly compact both in the absence and in the presence of two sugars. At about 90 degrees C, the structure of the unliganded TMBP partially relaxes whereas both the TMBP/maltose and the TMBP/trehalose complexes remain in the compact state. In addition, Fourier transform infrared results show that the population of alpha-helices exposed to the solvent was smaller in the absence than in the presence of the two sugars. The spectroscopic results are supported by molecular dynamics simulations. Our data on dynamics and stability of TMBP can contribute to a better understanding of transport-related functions of TMBP and constitute ground for targeted modifications of this protein for potential biotechnological applications.     

The strength of direct selection against female promiscuity is associated with rates of extrapair fertilizations in socially monogamous songbirds

A costs-benefits approach has frequently been used to understand the evolutionary origin and maintenance of promiscuity in animal populations. Recent meta-analyses suggest that direct costs to unfaithful females outweigh indirect benefits from infidelity in socially monogamous songbirds, suggesting that in this taxa, extrapair fertilization (EPF) evolved primarily as a self-interest male tactic. Here we present results of comparative analysis to show that standardized selection gradients acting against female infidelity (direct costs of promiscuity) explain variation in EPF rates at an interspecific level in passerines. This result confirms that costs to females resulting from reduced parental care from cheated males constrain promiscuity in this group. Our data indicate that females exert resistance over EPFs when the costs of infidelity are high and, conversely, that the rate of EPFs increases when selection on females to defend themselves against EPF attempts by males is weak and costs of infidelity are low.     

Conformational diversity of single‐stranded DNA from bacterial repetitive extragenic palindromes: Implications for the DNA recognition elements of transposases

Repetitive extragenic palindrome (REP)—associated tyrosine transposase enzymes (RAYTs) bind REP DNA domains and catalyze their cleavage. Genomic sequence analyses identify potential noncoding REP sequences associated with RAYT‐encoding genes. To probe the conformational space of potential RAYT DNA binding domains, we report here spectroscopic and calorimetric measurements that detect and partially characterize the solution conformational heterogeneity of REP oligonucleotides from six bacterial species. Our data reveal most of these REP oligonucleotides adopt multiple conformations, suggesting that RAYTs confront a landscape of potential DNA substrates in dynamic equilibrium that could be selected, enriched, and/or induced via differential binding. Thus, the transposase‐bound DNA motif may not be the predominant conformation of the isolated REP domain. Intriguingly, for several REPs, the circular dichroism spectra suggest guanine tetraplexes as potential alternative or additional RAYT recognition elements, an observation consistent with these REP domains being highly nonrandom, with tetraplex‐favoring 5′‐G and 3′‐C‐rich segments. In fact, the conformational heterogeneity of REP domains detected and reported here, including the formation of noncanonical DNA secondary structures, may reflect a general feature required for recognition by RAYT transposases. Based on our biophysical data, we propose guanine tetraplexes as an additional DNA recognition element for binding by RAYT transposase enzymes. © 2015 Wiley Periodicals, Inc. Biopolymers 103: 585–596, 2015.     

Non‐breeding range size predicts the magnitude of population trends in trans‐Saharan migratory passerine birds

Understanding why populations of some migratory species show a directional change over time, i.e. increase or decrease, while others do not, remains a challenge for ecological research. One possible explanation is that species with smaller non‐breeding ranges may have more pronounced directional population trends, and their populations are thus more sensitive to the variation in environmental conditions in their non‐breeding quarters. According to the serial residency hypothesis, this sensitivity should lead to higher magnitudes (i.e. absolute values) of population trends for species with smaller non‐breeding ranges, with the direction of trend being either positive or negative depending on the nature of the environmental change. We tested this hypothesis using population trends over 2001–2012 for 36 sub‐Saharan migratory passerine birds breeding in Europe. Namely, we related the magnitude of the species' population trends to the size of their sub‐Saharan non‐breeding grounds, whilst controlling for factors including number of migration routes, non‐breeding habitat niche and wetness, breeding habitat type and life‐history strategy. The magnitude of species' population trends grew with decreasing absolute size of sub‐Saharan non‐breeding ranges, and this result remained significant when non‐breeding range size was expressed relative to the size of the breeding range. After repeating the analysis with the trend direction, the relationship with the non‐breeding range size disappeared, indicating that both population decreases and increases are frequent amongst species with small non‐breeding range sizes. Therefore, species with small non‐breeding ranges are at a higher risk of population decline due to adverse factors such as habitat loss or climatic extremes, but their populations are also more likely to increase when suitable conditions appear. As non‐breeding ranges may originate from stochasticity of non‐breeding site selection in naive birds (‘serial‐residency’ hypothesis), it is crucial to maintain a network of stable and resilient habitats over large areas of birds’ non‐breeding quarters.     

Drivers of plant species composition of ecotonal vegetation in two fishpond management types

Wetlands Ecology and Management - Plants play an important role in fishpond littorals, but little is known about factors influencing their presence and growth patterns. We surveyed vegetation of...     

Differences in Conformational Behavior of ATA and TAT Sequences in Single Strand DNA Trimer

Abstract

The conformational behavior of single strand (ss) TAT and ATA trimers of DNA have been studied by computational chemistry tools including CICADA software interfaced with AMBER molecular mechanics and dynamics. The Single-Coordinate-Driving (SCD) method has been used in conjunction with molecular dynamics simulated annealing. It has been revealed that the conformational flexibility of each sequence differs substantially from the other one. Four common conformational families have been found for both trimers. These are: helical, reverse-stacked (base 3), half-stacked (base 3), reverse-stacked (base 1). However, the energies of conformers representing the families are different for both the studied systems. An additional conformational family, bulged, has been found for ss(ATA), while ss(TAT) has been found also in half-stacked (base 1) conformation. In general, ss(TAT) exhibits a higher number of low energy conformations while ss(ATA) shows one interesting low energy conformational interconversion between reverse-stacked (A3) family and half-stacked (A3) family. The high conformational variability of the trimers has been confirmed by flexibility analysis and by molecular dynamics simulations, which have also shown the conformational stability of single conformational families. It has been concluded that the methodology used is able to provide a very detailed picture of the conformational space of these molecules.     

Quinacrine reactivity with prion proteins and prion-derived peptides

Quinacrine is a drug that is known to heal neuronal cell culture infected with prions, which are the causative agents of neurodegenerative diseases called transmissible spongiform encephalopathies. However, the drug fails when it is applied in vivo. In this work, we analyzed the reason for this failure. The drug was suggested to “covalently” modify the prion protein via an acridinyl exchange reaction. To investigate this hypothesis more closely, the acridine moiety of quinacrine was covalently attached to the thiol groups of cysteines belonging to prion-derived peptides and to the full-length prion protein. The labeled compounds were conveniently monitored by fluorescence and absorption spectroscopy in the ultraviolet and visible spectral regions. The acridine moiety demonstrated characteristic UV–vis spectrum, depending on the substituent at the C-9 position of the acridine ring. These results confirm that quinacrine almost exclusively reacts with the thiol groups present in proteins and peptides. The chemical reaction alters the prion properties and increases the concentration of the acridine moiety in the prion protein.     

Index of names of syntaxa typified in 1994

Following the “Index of new names” (Theurillat & Moravec 1998), the present work collects the names of syntaxa (in the sense of the Code of phytosociological nomenclature,Barkman et al. 1986) above subassociation rank typified in 1994. The list comprises 101 names of syntaxa; three names are added to the Index 1992 (Theurillat & Moravec 1995).