Tiron as a spin-trap for superoxide radicals produced by the respiratory chain of submitochondrial particles

Tiron can be used as a spin-trap for O2 radicals generated by the respiratory chain of submitochondrial particles (SMP). Using this sensitive method, it was shown that the O2 (radical) production by the succinate-oxidizing SMP can be reduced by antimycin or 4-nonyl-2-hydroxyquinoline-N-oxide, the effects of both antibiotics being abolished and prevented by cyanide. It is suggested tht the O2 radicals are produced due to autooxidation of ubisemiquinone which is formed as an intermediate upon one-electron oxidation of CoQH2 by cytochrome c1. The effects of antimycin, 2-nonyl-4-hydroxyquinoline-N-oxide and cyanide on the O2 (radical) generation correlate with the effects of these inhibitors on a steady-state concentration of ubisemiquinone predicted by the Mitchell's Q-cycle hypothesis.     

Role of pyruvate kinase in non-specific changes of carbon photosynthetic metabolism, caused by the photophosphorylation inhibition]

The decrease in the level of NADP reduction in chloroplasts under injections of cofactors of pseudocyclic FMN photophosphorylation (vitamin K3 and methylviologen) into pea, tomato and cucumber leaves resulted in the decrease of 14CO2 autotrophic accumulation rate and in the change of distribution of assimilated carbon among the assimilation products. The inhibition of synthesis of labelled sugars and the increase of the content of 3-phosphoglyceric and glyceric acids in the labelled low molecular fraction were observed in all the experiments. Similar changes in the distribution of synthesized in Kalvin cycle labelled products, associated with the inhibition of its reduction unit, were observed under the effect of photophosphorylation uncoupling agents. However, the decrease of ATP/NADP ratio in chloroplasts resulted in the simultaneous increase of fixed 14CO2 incorporation into alanine. The role of pyruvate kinase in "alanine" effect, characteristic of non-specific changes of carbon photosynthetic metabolism, is discussed on the basis of the authors' previous data on the effect of phosphorylation on glycolysis reactions and on the basis of results of ADP introduction into leaf cuts.     

Variation in eggshell traits between geographically distant populations of pied flycatchers Ficedula hypoleuca

The expression and impact of maternal effects may vary greatly between populations and environments. However, little is known about large‐scale geographical patterns of variation in maternal deposition to eggs. In birds, as in other oviparous animals, the outermost maternal component of an egg is the shell, which protects the embryo, provides essential mineral resources and allows its interaction with the environment in the form of gas exchange. In this study, we explored variation of eggshell traits (mass, thickness, pore density and pigmentation) across 15 pied flycatcher populations at a large geographic scale. We found significant between‐population variation in all eggshell traits, except in pore density, suggesting spatial variation in their adaptive benefits or in the females’ physiological limitations during egg laying. Between‐ population variation in shell structure was not due to geographic location (latitude and longitude) or habitat type. However, eggshells were thicker in populations that experienced higher ambient temperature during egg laying. This could be a result of maternal resource allocation to the shell being constrained under low temperatures or of an adaptation to reduce egg water loss under high temperatures. We also found that eggshell colour intensity was positively associated with biliverdin pigment concentration, shell thickness and pore density. To conclude, our findings reveal large‐ scale between‐population variation of eggshell traits, although we found little environmental dependency in their expression. Our findings call for further studies that explore other environmental factors (e.g. calcium availability and pollution levels) and social factors like sexual selection intensity that may account for differences in shell structure between populations.     

tcR: an R package for T cell receptor repertoire advanced data analysis

Background

The Immunoglobulins (IG) and the T cell receptors (TR) play the key role in antigen recognition during the adaptive immune response. Recent progress in next-generation sequencing technologies has provided an opportunity for the deep T cell receptor repertoire profiling. However, a specialised software is required for the rational analysis of massive data generated by next-generation sequencing.

Results

Here we introduce tcR, a new R package, representing a platform for the advanced analysis of T cell receptor repertoires, which includes diversity measures, shared T cell receptor sequences identification, gene usage statistics computation and other widely used methods. The tool has proven its utility in recent research studies.

Conclusions

tcR is an R package for the advanced analysis of T cell receptor repertoires after primary TR sequences extraction from raw sequencing reads. The stable version can be directly installed from The Comprehensive R Archive Network (http://cran.r-project.org/mirrors.html). The source code and development version are available at tcR GitHub (http://imminfo.github.io/tcr/) along with the full documentation and typical usage examples.     

Whole-genome experimental identification of insertion/deletion polymorphisms of interspersed repeats by a new general approach

A new experimental technique for genome-wide detection of integration sites of polymorphic retroelements (REs) is described. The technique allows one to reveal the absence of a retroelement in an individual genome provided that this retroelement is present in at least one of several other genomes under comparison. Since quite a number of genomes are compared simultaneously, the search for polymorphic REs insertions is very efficient. The technique includes two whole-genome selective PCR amplifications of sequences flanking REs: one for a particular genome and another one for a mixture of ten different genomes. A subsequent subtractive hybridization of the obtained amplicons with DNA of a particular genome as driver results in isolation of polymorphic insertions. The technique was successfully applied for identification of 41 new polymorphic human AluYa5/Ya8 insertions. Among them, 18 individual Alu elements first sequenced in this work were not found in the available human genome databases. This result suggests that significant part of polymorphic REs were not identified during genome sequencing and remain to be detected and characterized. The proposed method does not depend on preliminary knowledge of evolutionary history of retroelements and can be applied for identification of insertion/deletion polymorphic markers in genomes of different species.     

Interrelation between the natural antioxidant content and lipid viscosity in normal organelle membranes

Two systems regulating lipid peroxidation (LP) natural antioxidants and structural organization were studied in the liver mitochondria, microsomes and nuclear membranes, using chemiluminescent and spin labelling techniques. Mitochondrial lipids were most protected against LP and were characterized by the maximum content of effective antioxidants and high viscosity. Nuclear lipids were the least protected against the systems studied and had lower antioxidant efficiency and viscosity. Direct correlation between the content of natural antioxidants and lipid viscosity was established.     

Antiradical activity of retinal lipids under illumination

Antiradical activity (ARA) of lipids from cattle in norm and under strong illumination with and without antioxidants was studied by chemoluminiscence method of initiated ethylbenzol oxidation. Lipids ARA from the retina in norm was established to be sufficiently high-3.0 X 10(6) l/mol. s. alpha-tocopherol was proposed to be the main component influencing lipids ARA. Under strong illumination (15 min:, 0.8 J/s) lipids ARA decreased due to intensification of lipid peroxidation (the content of MDA was increased). The antioxidants (alpha-tocopherol, potassium phenozan, ionol) in 0.1 mM concentrations increased the ARA of lipids in spite of light action. Changes in overall inhibitory activity of natural antioxidants and MDA content was antibat.     

Phenological sensitivity to climate change is higher in resident than in migrant bird populations among European cavity breeders

Many organisms adjust their reproductive phenology in response to climate change, but phenological sensitivity to temperature may vary between species. For example, resident and migratory birds have vastly different annual cycles, which can cause differential temperature sensitivity at the breeding grounds, and may affect competitive dynamics. Currently, however, adjustment to climate change in resident and migratory birds have been studied separately or at relatively small geographical scales with varying time series durations and methodologies. Here, we studied differential effects of temperature on resident and migratory birds using the mean egg laying initiation dates from 10 European nest box schemes between 1991 and 2015 that had data on at least one resident tit species and at least one migratory flycatcher species. We found that both tits and flycatchers advanced laying in response to spring warming, but resident tit populations advanced more strongly in relation to temperature increases than migratory flycatchers. These different temperature responses have already led to a divergence in laying dates between tits and flycatchers of on average 0.94 days per decade over the current study period. Interestingly, this divergence was stronger at lower latitudes where the interval between tit and flycatcher phenology is smaller and winter conditions can be considered more favorable for resident birds. This could indicate that phenological adjustment to climate change by flycatchers is increasingly hampered by competition with resident species. Indeed, we found that tit laying date had an additional effect on flycatcher laying date after controlling for temperature, and this effect was strongest in areas with the shortest interval between both species groups. Combined, our results suggest that the differential effect of climate change on species groups with overlapping breeding ecology affects the phenological interval between them, potentially affecting interspecific interactions.