Regional and local patterns of genetic variation and structure in yellow‐necked mice ‐ the roles of geographic distance,population abundance,and winter severity

The goal of this study, conducted in seven large woodlands and three areas with small woodlots in northeastern Poland in 2004–2008, was to infer genetic structure in yellow‐necked mouse Apodemus flavicollis population and to evaluate the roles of environmental and population ecology variables in shaping the spatial pattern of genetic variation using 768 samples genotyped at 13 microsatellite loci. Genetic variation was very high in all studied regions. The primal genetic subdivision was observed between the northern and the southern parts of the study area, which harbored two major clusters and the intermediate area of highly admixed individuals. The probability of assignment of individual mice to the northern cluster increased significantly with lower temperatures of January and July and declined in regions with higher proportion of deciduous and mixed forests. Despite the detected structure, genetic differentiation among regions was very low. Fine‐scale structure was shaped by the population density, whereas higher level structure was mainly shaped by geographic distance. Genetic similarity indices were highly influenced by mouse abundance (which positively correlated with the share of deciduous forests in the studied regions) and exhibited the greatest change between 0 and 1 km in the forests, 0 and 5 km in small woodlots. Isolation by distance pattern, calculated among regions, was highly significant but such relationship between genetic and geographic distance was much weaker, and held the linearity at very fine scale (~1.5 km), when analyses were conducted at individual level.     

Performance of Scanning Near-Field Optical Microscope Probes with Single Groove and Various Metal Coatings

We investigate the performance of a simple corrugated aperture scanning near-field optical microscope (SNOM) probe with various cladding metals. The probes have only one corrugation, however, they offer increased transmission over both uncorrugated probes and those with many grooves. Enhancement of light throughput results from excitation of surface plasmons at the corrugation at the core–cladding interface. We show how the choice of metal influences radiation properties of grooved probes.     

(13)C CP MAS NMR and crystal structure of methyl glycopyranosides

The X-ray diffraction analysis, (13)C CP MAS NMR spectra and powder X-ray diffraction patterns were obtained for selected methyl glycosides: alpha- and beta-d-lyxopyranosides (1, 2), alpha- and beta-l-arabinopyranosides (3, 4), alpha- and beta-d-xylopyranosides (5, 6) and beta-d-ribopyranoside (7) and the results were confirmed by GIAO DFT calculations of shielding constants. In X-ray diffraction analysis of 1 and 2, a characteristic shortening and lengthening of selected bonds was observed in molecules of 1 due to anomeric effect and, in crystal lattice of 1 and 2, hydrogen bonds of different patterns were present. Also, an additional intramolecular hydrogen bond with the participation of ring oxygen atom was observed in 1. The observed differences in chemical shifts between solid state and solution come from conformational effects and formation of various intermolecular hydrogen bonds. The changes in chemical shifts originating from intermolecular hydrogen bonds were smaller in magnitude than conformational effects. Furthermore, the powder X-ray diffraction (PXRD) performed for 4, 5 and 7 revealed that 7 existed as a mixture of two polymorphs, and one of them probably consisted of two non-equivalent molecules.     

Genetic parameters for milk urea concentration and milk traits in Polish Holstein-Friesian cows

Milk urea concentration (MU) used by dairy producers for management purposes can be affected by selection for milk traits. To assess this problem, genetic parameters for MU in Polish Holstein-Friesian cattle were estimated for the first three lactations. The genetic correlation of MU with milk production traits, lactose percentage, fat to protein ratio (FPR) and somatic cell score (SCS) were computed with two 5-trait random regression test-day models, separately for each lactation. Data used for estimation (159,044 daily observations) came from 50 randomly sampled herds. (Co)variance components were estimated with the Bayesian Gibbs sampling method. The coefficient of variation for MU in all three parities was high (40–41 %). Average daily heritabilities of MU were 0.22 for the first parity and 0.21 for the second and third lactations. Average genetic correlations for different days in milk in the first three lactations between MU and other traits varied. They were small and negative for protein percentage (from ?0.24 to ?0.11) and for SCS (from ?0.14 to ?0.09). The weakest genetic correlation between MU and fat percentage, and between MU and lactose percentage were observed (from ?0.10 to 0.10). Negative average genetic correlation with the fat to protein ratio was observed only in the first lactation (?0.14). Genetic correlations with yield traits were positive and ranged from low to moderate for protein (from 0.09 to 0.33), fat (from 0.16 to 0.35) and milk yield (from 0.20 to 0.42). These results suggest that the selection on yield traits and SCS tends to increase MU slightly.     

Werner syndrome protein works as a dimer for unwinding and replication fork regression

The determination of the oligomeric state of functional enzymes is essential for the mechanistic understanding of their catalytic activities. RecQ helicases have diverse biochemical activities, but it is still unclear how their activities are related to their oligomeric states. We use single-molecule multi-color fluorescence imaging to determine the oligomeric states of Werner syndrome protein (WRN) during its unwinding and replication fork regression activities. We reveal that WRN binds to a forked DNA as a dimer, and unwinds it without any change of its oligomeric state. In contrast, WRN binds to a replication fork as a tetramer, and is dimerized during activation of replication fork regression. By selectively inhibiting the helicase activity of WRN on specific strands, we reveal how the active dimers of WRN distinctly use the energy of ATP hydrolysis for repetitive unwinding and replication fork regression.     

Temporal dynamics of bird community composition: an analysis of baseline conditions from long-term data

Numerous anthropogenic activities threaten the biodiversity found on earth. Because all ecological communities constantly experience temporal turnover due to natural processes, it is important to distinguish between change due to anthropogenic impact and the underlying natural rate of change. In this study, we used data sets on breeding bird communities that covered at least 20 consecutive years, from a variety of terrestrial ecosystems, to address two main questions. (1) How fast does the composition of bird communities change over time, and can we identify a baseline of natural change that distinguishes primeval systems from systems experiencing varying degrees of human impact? (2) How do patterns of temporal variation in composition vary among bird communities in ecosystems with different anthropogenic impacts? Time lag analysis (TLA) showed a pattern of increasing rate of temporal compositional change from large-scale primeval systems to disturbed and protected systems to distinctly successional systems. TLA slopes of <0.04 were typical for breeding bird communities with natural turnover, while communities subjected to anthropogenic impact were characterised by TLA slopes of >0.04. Most of the temporal variability of breeding bird communities was explained by slow changes occurring over decades, regardless of the intensity of human impact. In most of the time series, medium- and short-wave periodicity was not detected, with the exception of breeding bird communities subjected to periodic pulses (e.g. caterpillar outbreaks causing food resource peaks).     

Dynamics of estrogen-induced oxidative stress

The objective of this study was to assess the dynamics of oxidative damage to cellular macromolecules such as proteins, lipids and DNA under conditions of oxidative stress triggering early stages of estrogen-dependent carcinogenesis. A rodent model of carcinogenesis was used. Syrian hamsters were sacrificed after 1, 3, 5 h and one month from the initial implantation of estradiol. Matching control groups were used. Kidneys as target organs for estradiol-mediated oxidative stress were excised and homogenized for biochemical assays. Subcellular fractions were isolated. Carbonyl groups (as a marker of protein oxidation) and lipid hydroxyperoxides were assessed. DNA was isolated and 8-oxodGuo was assessed. Electron paramagnetic resonance spectroscopy was used to confirm the results for lipid peroxidation. Exposition to estradiol in the rodent model leads to damage of macromolecules of the cell, including proteins and DNA, but not lipids. Proteins appear to be the primary target of the damage but are closely followed by DNA. It has previously been speculated that protein peroxides can increase DNA modifications. This time sequence was observed in our study. Nevertheless, the direct relation between protein and DNA damage still remains unsolved.     

Patterns of predator behaviour and Wood Warbler Phylloscopus sibilatrix nest survival in a primaeval forest

Understanding the foraging behaviour of predators is key to interpreting the role of anti‐predator adaptations of birds in reducing nest losses. Conducting research in primaeval habitats, with a low level of direct human interference, is particularly valuable in the understanding of predator–prey interactions. Using nest cameras, we investigated the identity and behaviour of potential and actual predators appearing at Wood Warbler Phylloscopus sibilatrix nests, and the importance of different predator groups for nest survival, in the primaeval part of Bia?owie?a Forest (Poland). Mammals formed the main predator group (30 of 32 nest depredations), particularly medium‐sized carnivores (24 of 32), which attacked nests more frequently than merely passing by. This contrasted with other species, especially small rodents, which were commonly recorded near nests but rarely attacked them. Most nest attacks (22 of 32) took place at night and nest survival did not depend on nest visibility, indicating a reduced utility of nest concealment in defence against predators using mainly sound or olfaction when hunting. Daily nest survival declined strongly with nest progression (from egg‐laying to fledging of chicks), probably due to increased predator detection of nests containing older and louder chicks, rather than to increasing parental activity at nests during the day. The set of actual nest predators differed from some previous studies in human‐transformed habitats, showing that Wood Warblers may face different threats in modified vs. near‐pristine environments.     

Antioxidants protect the yeast Saccharomyces cerevisiae against hypertonic stress

Yeast (Saccharomyces cerevisiae) mutants lacking CuZnSOD have been reported to be hypersensitive to hypertonic media and to show increased oxidative damage. This study demonstrates that hypertonic medium (containing 0.8?M NaCl) increases the generation of superoxide and other reactive species in yeast cells. Other sequelae of exposure to hypertonic medium include oxidation of cellular low-molecular weight thiols and decrease in total antioxidant capacity of cellular extracts. Δsod1 mutant is more sensitive than a wild-type strain to colony growth inhibition on a hypertonic medium. Anaerobic conditions, ascorbate, glutathione, cysteine and dithiothreitol are able to ameliorate this growth inhibition but a range of other antioxidants does not protect. The protective ability of the antioxidants does not correlate with the rate of their reactions with superoxide but seems to be conditioned by low redox potential for one-electron oxidation of free radicals of the antioxidants. It suggests that repair of low-redox potential targets rather than prevention of their damage by superoxide is important in the antioxidant protection against oxidative stress induced by hypertonic conditions.     

A pivotal role for the multifunctional calcium/calmodulin-dependent protein kinase II in T cells: from activation to unresponsiveness

Stimulation of the TCR leads to an oscillatory release of free calcium that activates members of the calcium/calmodulin-dependent protein kinase II (CaMKII) family. The CaMKII molecules have profound and lasting effects on cellular signaling in several cell types, yet the role of CaMKII in T cells is still poorly characterized. In this report we describe a splice variant of CaMKIIbeta, CaMKIIbeta'e, in mouse T cells. We have determined its function, along with that of CaMKIIgamma, by introducing the active and kinase-dead mutants into activated P14 TCR transgenic T cells using retroviral transduction. Active CaMKII enhanced the proliferation and cytotoxic activity of T cells while reducing their IL-2 production. Furthermore, it induced a profound state of unresponsiveness that could be overcome only by prolonged culture in IL-2. These results indicate that members of the CaMKII family play an important role in regulation of CD8 T cell proliferation, cytotoxic effector function, and the response to restimulation.