Structural integrity of the PCI domain of eIF3a/TIF32 is required for mRNA recruitment to the 43S pre-initiation complexes

Transfer of genetic information from genes into proteins is mediated by messenger RNA (mRNA) that must be first recruited to ribosomal pre-initiation complexes (PICs) by a mechanism that is still poorly understood. Recent studies showed that besides eIF4F and poly(A)-binding protein, eIF3 also plays a critical role in this process, yet the molecular mechanism of its action is unknown. We showed previously that the PCI domain of the eIF3c/NIP1 subunit of yeast eIF3 is involved in RNA binding. To assess the role of the second PCI domain of eIF3 present in eIF3a/TIF32, we performed its mutational analysis and identified a 10-Ala-substitution (Box37) that severely reduces amounts of model mRNA in the 43–48S PICs in vivo as the major, if not the only, detectable defect. Crystal structure analysis of the a/TIF32-PCI domain at 2.65-Å resolution showed that it is required for integrity of the eIF3 core and, similarly to the c/NIP1-PCI, is capable of RNA binding. The putative RNA-binding surface defined by positively charged areas contains two Box37 residues, R363 and K364. Their substitutions with alanines severely impair the mRNA recruitment step in vivo suggesting that a/TIF32-PCI represents one of the key domains ensuring stable and efficient mRNA delivery to the PICs.     

RNAdigest: A Web-Based Tool for the Analysis and Prediction of Structure - Specific RNAse Digestion Results

Despite recent developments in analyzing RNA secondary structures, relatively few RNA structures have been determined. To date, many investigators have relied on the traditional method of using structure-specific RNAse enzymes to probe RNA secondary structures. However, if these data were combined with novel computational approaches, investigators would have an informative and valuable tool for RNA structural analysis. To this end, we created the web server “RNAdigest.” RNAdigest uses mfold RNA structural models in order to predict the results of RNAse digestion experiments. Furthermore, RNAdigest also utilizes both RNA sequence and the experimental digestion patterns to formulate the constraints for predicting secondary structures of the RNA. Thus, RNAdigest allows for the structural interpretation of RNAse digestion experiments. Overall, RNAdigest simplifies RNAse digestion result analyses while allowing for the identification of unique fragments. These unique fragments can then be used for testing predicted mfold structures and for designing structural-specific DNA/RNA probes.     

Effect of Incubation on Bacterial Communities of Eggshells in a Temperate Bird,the Eurasian Magpie (Pica pica)

Inhibitory effect of incubation on microbial growth has extensively been studied in wild bird populations using culture-based methods and conflicting results exist on whether incubation selectively affects the growth of microbes on the egg surface. In this study, we employed culture-independent methods, quantitative PCR and 16S rRNA gene pyrosequencing, to elucidate the effect of incubation on the bacterial abundance and bacterial community composition on the eggshells of the Eurasian Magpie (Pica pica). We found that total bacterial abundance increased and diversity decreased on incubated eggs while there were no changes on non-incubated eggs. Interestingly, Gram-positive Bacillus, which include mostly harmless species, became dominant and genus Pseudomonas, which include opportunistic avian egg pathogens, were significantly reduced after incubation. These results suggest that avian incubation in temperate regions may promote the growth of harmless (or benevolent) bacteria and suppress the growth of pathogenic bacterial taxa and consequently reduce the diversity of microbes on the egg surface. We hypothesize that this may occur due to difference in sensitivity to dehydration on the egg surface among microbes, combined with the introduction of Bacillus from bird feathers and due to the presence of antibiotics that certain bacteria produce.     

Selection on dispersal in isolated butterfly metapopulations

In most metapopulation models dispersal is assumed to be a fixed species-specific trait, but in reality dispersal abilities are highly sensitive to various selective pressures. Strict isolation of a metapopulation, which precludes any influx of immigrants (and their genes) from outside and makes it impossible for emigrants to reach other localities with suitable habitat, thus reducing fitness benefits of long-distance dispersal to zero, may be expected to impose strong selection against dispersal. We tested the above prediction by comparing dispersal parameters derived with the Virtual Migration model for isolated and non-isolated metapopulations of two species of large blue Maculinea (= Phengaris) butterflies, surveyed with intensive mark-recapture. Mortality during dispersal was found to be twice (in M. teleius) to five times higher (in M. arion) in isolated metapopulations. Isolation also resulted in significantly reduced dispersal distances in isolated metapopulations, with the effect being particularly strong in M. arion females. Apart from its evolutionary and ecological consequences, dispersal depression in isolated butterfly metapopulations implied by our results has serious conservation implications. It provides a clear argument against using parameter values obtained in a different environmental setting in modelling applications, e.g., Population Viability Analyses or environmental impact assessment. Furthermore, it underlines the importance of establishing well-connected networks of suitable habitats prior to species release in areas where reintroductions are planned.     

The Impact of Different Visual Feedbacks in User Training on Motor Imagery Control in BCI

The challenges of research into brain–computer interfaces (BCI) include significant individual differences in learning pace and in the effective operation of BCI devices. The use of neurofeedback training is a popular method of improving the effectiveness BCI operation. The purpose of the present study was to determine to what extent it is possible to improve the effectiveness of operation of sensorimotor rhythm-based brain–computer interfaces (SMR-BCI) by supplementing user training with elements modifying the characteristics of visual feedback. Four experimental groups had training designed to reinforce BCI control by: visual feedback in the form of dummy faces expressing emotions (Group 1); flashing the principal elements of visual feedback (Group 2) and giving both visual feedbacks in one condition (Group 3). The fourth group participated in training with no modifications (Group 4). Training consisted of a series of trials where the subjects directed a ball into a basket located to the right or left side of the screen. In Group 1 a schematic image a face, placed on the controlled object, showed various emotions, depending on the accuracy of control. In Group 2, the cue and targets were flashed with different frequency (4 Hz) than the remaining elements visible on the monitor. Both modifications were also used simultaneously in Group 3. SMR activity during the task was recorded before and after the training. In Group 3 there was a significant improvement in SMR control, compared to subjects in Group 2 and 4 (control). Differences between subjects in Groups 1, 2 and 4 (control) were insignificant. This means that relatively small changes in the training procedure may significantly impact the effectiveness of BCI control. Analysis of behavioural data acquired from all participants at training showed greater effectiveness in directing the object towards the right side of the screen. Subjects with the greatest improvement in SMR control showed a significantly lower difference in the accuracy of rightward and leftward movement than others.     

Frequency of multiple paternity in Myrmica scabrinodis from southern Poland

In haplodiploid insects that create social systems, more than one male may contribute to the progeny of a single female (polyandry). Little is known about the possible evolutionary benefits of multiple mating or the occurrence of this phenomenon across different species of Hymenoptera. Here we present our observations of polyandry in a Myrmica scabrinodis Nylander population from southern Poland. The estimated proportion of multiply mated queens was 0.71 and the average pedigree‐effective mate number was 1.45.     

Does experimentally simulated presence of a common cuckoo (Cuculus canorus) affect egg rejection and breeding success in the red-backed shrike (Lanius collurio)?

acta ethologica - Providing artificial eggs is a commonly used technique to understand brood parasitism, mainly by the common cuckoo (Cuculus canorus). However, the presence of a cuckoo egg in the...     

Protein Unfolding by Biological Unfoldases: Insights from Modeling

The molecular determinants of the high efficiency of biological machines like unfoldases (e.g., the proteasome) are not well understood. We propose a model to study protein translocation into the chamber of biological unfoldases represented as a funnel. It is argued that translocation is a much faster way of unfolding a protein than end-to-end stretching, especially in a low-force regime, because it allows for a conformational freedom while concentrating local tension on consecutive regions of a protein chain and preventing refolding. This results in a serial unfolding of the protein structures dominated by unzipping. Thus, pulling against the unfoldase pore is an efficient catalyst of the unfolding reaction. We also show that the presence of the funnel makes the tension along the backbone of the substrate protein nonuniform even when the protein gets unfolded. Hence, the stalling force measured by single-molecule force spectroscopy techniques may be smaller than the traction force of the unfoldase motor.     

Distribution pattern of the invasive alien plant Bunias orientalis in Rów Podtatrzański trench,north of the Tatra Mts,Poland

Bunias orientalis is an alien species that has spread greatly in recent decades in Central Europe. This coloniser is particularly well (pre)adapted to anthropogenic disturbances and human-mediated dispersal, allowing it to spread mainly along roads and railways. Here, its distribution and population structure is investigated for the sub-montane region located in the northern foothills of the Tatra Mts. Based on 70 phytosociological samples of invading vegetation, the relationships between B. orientalis cover and species diversity, together with the composition of vegetation, were analysed using regression analysis. Comparison of the current distribution of B. orientalis within the investigated area with published records indicates that the expansion rate of this alien species is not particularly high, despite its increased frequency in anthropogenic habitats and meadows. Meadows invaded by this species revealed that increased B. orientalis cover was accompanied by a significant reduction in the values of the Inverse Simpson diversity index and Pielou’s measure of evenness. Reduced diversity was caused by considerable decrease in cover by species of the Molinio-Arrhenatheretea class. However, for anthropogenic habitats, no statistically significant relationships were found to occur between the abundance of B. orientalis, species diversity and vegetation composition.     

Till evolution do us part: The diversity of symbiotic associations across populations of Philaenus spittlebugs

Symbiotic bacteria have played crucial roles in the evolution of sap-feeding insects and can strongly affect host function. However, their diversity and distribution within species are not well understood; we do not know to what extent environmental factors or associations with other species may affect microbial community profiles. We addressed this question in Philaenus spittlebugs by surveying both insect and bacterial marker gene amplicons across multiple host populations. Host mitochondrial sequence data confirmed morphology-based identification of six species and revealed two divergent clades of Philaenus spumarius. All of them hosted the primary symbiont Sulcia that was almost always accompanied by Sodalis. Interestingly, populations and individuals often differed in the presence of Sodalis sequence variants, suggestive of intra-genome 16S rRNA variant polymorphism combined with rapid genome evolution and/or recent additional infections or replacements of the co-primary symbiont. The prevalence of facultative endosymbionts, including Wolbachia, Rickettsia, and Spiroplasma, varied among populations. Notably, cytochrome I oxidase (COI) amplicon data also showed that nearly a quarter of P. spumarius were infected by parasitoid flies (Verralia aucta). One of the Wolbachia operational taxonomic units (OTUs) was exclusively present in Verralia-parasitized specimens, suggestive of parasitoids as their source and highlighting the utility of host gene amplicon sequencing in microbiome studies.