Impact of human activities on stonefly (Insecta,Plecoptera) ecological metrics in the Hron River (Slovakia)

A total of 57 stonefly species have been recorded in the Hron River. The natural gradient (slope and stream width) and pollution gradient of the river were defined using CCA based on physical, chemical and stonefly data. Stonefly metrics (abundance, richness/diversity, sensitivy/tolerance and functional metrics) were used to estimate the quality of the Hron River and the degree of proximity to its natural state. Similar results were obtained using two different methods. The first method was based on the homogeneity of variance and the interquartile range of different groups of stretches of the Hron River and the second was based on deviations from the expected values of biological metrics in a given stretch of the river. These values continuously decreased with increasing distance from the spring area, with the exception of the saprobic index, which increased in a downstream direction, and the stonefly average score, which did not change significantly along the whole river flow. The Stonefly Average Score (SAS) metric is universal for a variety of habitats such as the Hron River upstream and downstream, and is a reliable indicator of water quality and the natural course of a stream.     

The adult diet of <Emphasis Type="Italic">Xanthoperla apicalis</Emphasis> and <Emphasis Type="Italic">Siphonoperla torrentium</Emphasis> (Plecoptera,Chloroperlidae) in the Danube basin (Slovakia)

The gut contents of adult Xanthoperla apicalis and Siphonoperla torrentium were analysed. X. apicalis females eat mainly pollen, while males feed principally on detritus and pollen. Adults of S. torrentium, regardless of sex, eat mainly pollen. The presence of animal remains (claws and leg and antennae segments of Arthropoda) in the gut of several individuals of both species was observed and discussed.     

Allelic mapping bias in RNA-sequencing is not a major confounder in eQTL studies

Background

RNA sequencing (RNA-seq) is the current gold-standard method to quantify gene expression for expression quantitative trait locus (eQTL) studies. However, a potential caveat in these studies is that RNA-seq reads carrying the non-reference allele of variant loci can have lower probability to map correctly to the reference genome, which could bias gene quantifications and cause false positive eQTL associations. In this study, we analyze the effect of this allelic mapping bias in eQTL discovery.

Results

We simulate RNA-seq read mapping over 9.5 M common SNPs and indels, with 15.6% of variants showing biased mapping rate for reference versus non-reference reads. However, removing potentially biased RNA-seq reads from an eQTL dataset of 185 individuals has a very small effect on gene and exon quantifications and eQTL discovery. We detect only a handful of likely false positive eQTLs, and overall eQTL SNPs show no significant enrichment for high mapping bias.

Conclusion

Our results suggest that RNA-seq quantifications are generally robust against allelic mapping bias, and that this does not have a severe effect on eQTL discovery. Nevertheless, we provide our catalog of putatively biased loci to allow better controlling for mapping bias to obtain more accurate results in future RNA-seq studies.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0467-2) contains supplementary material, which is available to authorized users.     

A directional strategy for monitoring Cre-mediated recombination at the cellular level in the mouse

Functional redundancies, compensatory mechanisms, and lethal phenotypes often prevent the full analysis of gene functions through generation of germline null mutations in the mouse. The use of site-specific recombinases, such as Cre, which catalyzes recombination between loxP sites, has allowed the engineering of mice harboring targeted somatic mutations, which are both temporally controlled and cell-type restricted. Many Cre-expressing mouse lines exist, but only a few transgenic lines are available that harbor a reporter gene whose expression is dependent on a Cre-mediated event. Moreover, their use to monitor gene ablation at the level of individual cells is often limited, as in some tissues the reporter gene may be silenced, be affected by position-effect variegation, or reside in a chromatin configuration inaccessible for recombination. Thus, one cannot validly extrapolate from the expression of a reporter transgene to an identical ablation pattern for the conditional allele of a given gene. By combining the ability of Cre recombinase to invert or excise a DNA fragment, depending on the orientation of the flanking loxP sites, and the availability of both wild-type (WT) and mutant loxP sites, we designed a Cre-dependent genetic switch (FLEx switch) through which the expression of a given gene is turned off, while the expression of another one is concomitantly turned on. We demonstrate the efficiency and reliability of this switch to readily detect, in the mouse, at the single cell level, Cre-mediated gene ablation. We discuss how this strategy can be used to generate genetic modifications in a conditional manner.     

Benthic macroinvertebrates along the Czech part of the Labe and lower section of the Vltava rivers from 1996–2005, with a particular focus on rare and alien species

In the Czech part of the Labe River and the lower part of the Vltava River, we examined if the benthic macroinvertebrate composition changed from 1996 to 2005 due to expected improvements in water quality resulting from socioeconomic changes in the Czech Republic since the 1990s. Special attention was given to rare and alien species. The four biological metrics used (Number of taxa, BMWP, Number of sensitive taxa, and Number of EPT taxa) demonstrated that there was indeed an improvement in water quality as well as a slight improvement of the Labe microhabitats during the investigated period. An increasing Number of taxa over time was observed at most sites. Two main concurrent ecological processes are recently in progress in the Labe: a recovery of native species and an expansion of alien species, some of which are considered invasive. The caddisfly Setodes punctatus and the beetle Pomatinus substriatus, considered as regionally extinct in the Czech Republic until 2005, were rediscovered during our investigations. Findings of the crustacean Hemimysis anomala (invasive) and the chironomids Stenochironomus sp. and Lipiniella sp. were the first records of these taxa in the Czech Republic.     

The Arrival of Siberian Ancestry Connecting the Eastern Baltic to Uralic Speakers further East

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The BRCT domain of mammalian Rev1 is involved in regulating DNA translesion synthesis

Rev1 is a deoxycytidyl transferase associated with DNA translesion synthesis (TLS). In addition to its catalytic domain, Rev1 possesses a so-called BRCA1 C-terminal (BRCT) domain. Here, we describe cells and mice containing a targeted deletion of this domain. Rev1^B/B mice are healthy, fertile and display normal somatic hypermutation. Rev1^B/B cells display an elevated spontaneous frequency of intragenic deletions at Hprt. In addition, these cells were sensitized to exogenous DNA damages. Ultraviolet-C (UV-C) light induced a delayed progression through late S and G2 phases of the cell cycle and many chromatid aberrations, specifically in a subset of mutant cells, but not enhanced sister chromatid exchanges (SCE). UV-C-induced mutagenesis was reduced and mutations at thymidine–thymidine dimers were absent in Rev1^B/B cells, the opposite phenotype of UV-C-exposed cells from XP-V patients, lacking TLS polymerase η. This suggests that the enhanced UV-induced mutagenesis in XP-V patients may depend on error-prone Rev1-dependent TLS. Together, these data indicate a regulatory role of the Rev1 BRCT domain in TLS of a limited spectrum of endogenous and exogenous nucleotide damages during a defined phase of the cell cycle.     

Comparative analysis of some aspects of mitochondrial metabolism in differentiated and undifferentiated neuroblastoma cells

The aim of the present study is to clarify some aspects of the mechanisms of regulation of mitochondrial metabolism in neuroblastoma (NB) cells. Experiments were performed on murine Neuro-2a (N2a) cell line, and the same cells differentiated by all-trans-retinoic acid (dN2a) served as in vitro model of normal neurons. Oxygraphy and Metabolic Control Analysis (MCA) were applied to characterize the function of mitochondrial oxidative phosphorylation (OXPHOS) in NB cells. Flux control coefficients (FCCs) for components of the OXPHOS system were determined using titration studies with specific non-competitive inhibitors in the presence of exogenously added ADP. Respiration rates of undifferentiated Neuro-2a cells (uN2a) and the FCC of Complex-II in these cells were found to be considerably lower than those in dN2a cells. Our results show that NB is not an exclusively glycolytic tumor and could produce a considerable part of ATP via OXPHOS. Two important enzymes - hexokinase-2 and adenylate kinase-2 can play a role in the generation of ATP in NB cells. MCA has shown that in uN2a cells the key sites in the regulation of OXPHOS are complexes I, II and IV, whereas in dN2a cells complexes II and IV. Results obtained for the phosphate and adenine nucleotide carriers showed that in dN2a cells these carriers exerted lower control over the OXPHOS than in undifferentiated cells. The sum of FCCs for both types of NB cells was found to exceed significantly that for normal cells suggesting that in these cells the respiratory chain was somehow reorganized or assembled into large supercomplexes.     

Direct measurement of energy fluxes from mitochondria into cytoplasm in permeabilized cardiac cells <Emphasis Type="Italic">in situ:</Emphasis> some evidence for mitochondrial interactosome

The aim of this study was to measure energy fluxes from mitochondria in isolated permeabilized cardiomyocytes. Respiration of permeabilized cardiomyocytes and mitochondrial membrane potential were measured in presence of MgATP, pyruvate kinase – phosphoenolpyruvate and creatine. ATP and phosphocreatine concentrations in medium surrounding cardiomyocytes were determined. While ATP concentration did not change in time, mitochondria effectively produced phosphocreatine (PCr) with PCr/O₂ ratio equal to 5.68 ± 0.14. Addition of heterodimeric tubulin to isolated mitochondria was found to increase apparent Km for exogenous ADP from 11 ± 2 μM to 330 ± 47 μM, but creatine again decreased it to 23 ± 6 μM. These results show directly that under physiological conditions the major energy carrier from mitochondria into cytoplasm is PCr, produced by mitochondrial creatine kinase (MtCK), which functional coupling to adenine nucleotide translocase is enhanced by selective limitation of permeability of mitochondrial outer membrane within supercomplex ATP Synthasome-MtCK-VDAC-tubulin, Mitochondrial Interactosome.