Age-dependent flea (Siphonaptera) parasitism in rodents: a host's life history matters

We studied age-dependent patterns of flea infestation in 7 species of rodents from Slovakia (Apodemus agrarius, A. flavicollis, A. sylvaticus, A. uralensis, Clethrionomys glareolus, Microtus arvalis, and M. subterraneus). We estimated the age of the host from its body mass and expected the host age-dependent pattern of flea abundance, the level of aggregation, and prevalence to be in agreement with theoretical predictions. We expected that the mean abundance and the level of aggregation of fleas would be lowest in hosts of smallest and largest size classes and highest in hosts of medium size classes, whereas pattern of variation of prevalence with host age would be either convex or asymptotic. In general, mean abundance and species richness of fleas increased with an increase in host age, although the pressure of flea parasitism in terms of number of fleas per unit host body surface decreased with host age. We found 2 clear patterns of the change in flea aggregation and prevalence with host age. The first pattern demonstrated a peak of flea aggregation and a trough of flea prevalence in animals of middle age classes (Apodemus species and C. glareolus). The second pattern was an increase of both flea aggregation and flea prevalence with host age (both Microtus species). Consequently, we did not find unequivocal evidence for the main role of either parasite-induced host mortality or acquired resistance in host age-dependent pattern of flea parasitism. Our results suggest that this pattern can be generated by various processes and is strongly affected by natural history parameters of a host species such as dispersal pattern, spatial distribution, and structure of shelters.     

Prenatal Exposure to Maternal Cigarette Smoking and Accumulation of Intra‐abdominal Fat During Adolescence

In industrialized countries, prenatal exposure to maternal cigarette smoking (PEMCS) is the most common environmental insult to the fetus. Here, we tested the hypothesis that PEMCS amplifies accumulation of abdominal fat during the accelerated weight gain occurring in late puberty. This hypothesis was tested in 508 adolescents (12–18 years, 237 exposed prenatally to maternal cigarette smoking) in whom subcutaneous and intra‐abdominal fat were quantified with magnetic resonance imaging (MRI). We found that, in early puberty, exposed and nonexposed adolescents did not differ in MRI‐based measures of adiposity. In late puberty, on the other hand, exposed compared with nonexposed adolescents demonstrated markedly higher quantities of both subcutaneous fat (by 26%, P = 0.004) and intra‐abdominal fat (by 33%, P = 0.001). These group differences remained virtually unchanged after adjusting for sex and potential confounders, including birth weight and breastfeeding. As such, our results suggest that PEMCS may represent a major risk factor for the development of abdominal obesity at the later stages of puberty.     

The reverse cholesterol transport pathway improves understanding of genetic networks for fat deposition and muscle growth in beef cattle

In the present study, thirteen genes involved in the reverse cholesterol transport (RCT) pathway were investigated for their associations with three fat depositions, eight fatty acid compositions and two growth-related phenotypes in a Wagyu x Limousin reference population, including 6 F(1) bulls, 113 F(1) dams, and 246 F(2) progeny. A total of 37 amplicons were used to screen single nucleotide polymorphisms (SNPs) on 6 F(1) bulls. Among 36 SNPs detected in 11 of these 13 genes, 19 were selected for genotyping by the Sequenom assay design on all F(2) progeny. Single-marker analysis revealed seven SNPs in ATP binding cassette A1, apolipoproteins A1, B and E, phospholipid transfer protein and paraoxinase 1 genes significantly associated with nine phenotypes (P<0.05). Previously, we reported genetic networks associated with 19 complex phenotypes based on a total of 138 genetic polymorphisms derived from 71 known functional genes. Therefore, after Bonferroni correction, these significant (adjusted P<0.05) and suggestive (adjusted P<0.10) associations were then used to identify genetic networks related to the RCT pathway. Multiple-marker analysis suggested possible genetic networks involving the RCT pathway for kidney-pelvic-heart fat percentage, rib-eye area, and subcutaneous fat depth phenotypes with markers derived from paraoxinase 1, apolipoproteins A1 and E, respectively. The present study confirmed that genes involved in cholesterol homeostasis are useful targets for investigating obesity in humans as well as for improving meat quality phenotypes in a livestock production.     

Intravenous rutin in rat exacerbates isoprenaline-induced cardiotoxicity likely due to intracellular oxidative stress

Objectives: Rutin, quercetin-3-O-rutinoside, a natural flavonol glycoside, has shown various in vitro benefits with potential use treating human diseases, especially cardiovascular system disorders. Antioxidant properties are assumed to underlie the majority of these benefits. Yet rutin pro-oxidant properties have been reported as well. Our research group has recently shown aggravating effects on isoprenaline (ISO)-induced cardiotoxicity in Wistar:Han rats after 24?hours.

Methods: This study was designed to examine in more detail the reasons for the negative effects of rutin (11.5 and 46?mg/kg, i.v.) after administration of ISO (100?mg/kg, s.c.) in rats within 2?hours of continuous experiment and in the H9c2 cardiomyoblast-derived cell line.

Results: Like our previous findings, rutin did not (11.5 or 46?mg/kg, i.v.) reduce the ISO-induced mortality within 2?hours although the lower dose significantly reduced cardiac troponin T (cTnT) and partly improved the histological findings. In contrast, the higher dose increased the mortality in comparison with solvent (1.26% w/v sodium bicarbonate). This was not caused by any specific haemodynamic disturbances. It appears to be associated with oxidative stress as rutin enhanced intracellular reactive oxygen species formation in vitro and had the tendency to increase it in vivo.

Conclusions: Rutin, likely due to its pro-oxidative effects, can exacerbate catecholamine cardiotoxicity depending on the dose used.     

Species assemblages of ladybirds including the harlequin ladybird <Emphasis Type="Italic">Harmonia axyridis</Emphasis>: a comparison at large spatial scale in urban habitats

We evaluated the status of native ladybird assemblages in the presence of the non-native ladybird Harmonia axyridis Pallas (Coleoptera: Coccinellidae) in three European countries. To achieve this, we assessed the abundance of ladybirds from common host plants in urban areas of Great Britain, Czech Republic and Slovak Republic in 2014. We determined (i) the effects of season, host plant, location, abundance of H. axyridis and aphids on the ladybird species assemblage, (ii) the relationship between ladybird abundance and aphid density, (iii) the relationship between diversity of native ladybird species and the abundance of H. axyridis. There was a non-linear relationship between abundance of ladybirds and abundance of aphids but we found the abundance of other ladybird species was not correlated with H. axyridis. We highlight the value of large-spatial scale studies for revealing patterns in community assemblages and ultimately informing understanding of ecosystem resilience.     

Long-lasting Imprint of Former Glassworks on Vegetation Pattern in an Extremely Species-rich Grassland: A Battle of Species Pools on Mesic Soils

Increasing evidence suggests that past human activities have irreversibly changed soil properties and biodiversity patterns. In the White Carpathian Mts (Central-Eastern Europe), a mosaic of hyper-species-rich and species-rich patches have developed in a regularly mown dry grassland in the area of a glassworks abandoned in the eighteenth century. We tested whether and how anthropogenically changed soils affected the distribution of extraordinary species richness. Using magnetometry we detected former furnaces, workspace, waste deposit and unaffected surrounding grasslands and compared their vegetation and environmental conditions. Archaeological features, especially furnaces and waste deposits, showed a higher pH, higher soil concentrations of exchangeable phosphorus, manganese, lead and calcium, and higher productivity. Surrounding grassland showed higher iron and sodium concentrations in the soil, higher N:P ratio in the biomass and higher species richness. Moisture was uniformly lower in soils on archaeological features, where non-trivially a more ‘mesic’ vegetation in terms of European habitat classification occurred. Plant compositional variation was best explained by water-extractable phosphorus. Because nutrient-richer patches were not moister as common elsewhere, and because species richness was only poorly accounted for by productivity, the occurrence of a species-poor ‘mesic’ vegetation on archaeological features was evidently caused by a long-lasting phosphorus oversupply which favours a comparatively small species pool of rather recently arriving species. On the contrary, surrounding phosphorus-poorer grasslands still contain the ancient species pool whose extraordinary size determines the exceptional species richness of grasslands in the study region. Its maintenance or restoration demands a persistent phosphorus deficiency.     

Linking Above- and Belowground Responses to 16 Years of Fertilization,Mowing, and Removal of the Dominant Species in a Temperate Grassland

Species-rich oligotrophic meadows are affected by a wide range of management interventions that influence their functioning and capacity to deliver ecosystem services, but long-term studies on the above- and belowground adaptations to different management tools are still scarce. We focused on the interactive effects of NPK fertilization, mowing, and removal of the initially dominant species (Molinia caerulea) on plant, soil, and microbial responses in wet oligotrophic grassland in a 16-year full-factorial manipulative experiment. Changes in vegetation composition, soil pH, and nutrient availability were accompanied by altered microbial phospholipid fatty acid (PLFA) composition, whereas treatment effects on soil microbial biomass and carbon (C) mineralization were mainly related to changes in soil organic matter (SOM) content and nutrient availability. Fertilization decreased plant species richness aboveground and lowered SOM storage and microbial activity belowground. Mowing preserved high plant diversity and led to more efficient recycling of N within the grassland, whereas Molinia removal significantly affected only plant community composition. Mowing combined with fertilization maintained high species richness only in the short term. Belowground, mowing reduced N leaching from the fertilized system but did not prevent SOM depletion, soil acidification, and concomitant adverse effects on soil microbes. We conclude that annual mowing is the appropriate type of extensive management for oligotrophic species-rich meadows, but the concomitant nutrient depletion should not be compensated for by regular NPK fertilization due to its adverse effects on soil quality.     

Rational confederation of genes and diseases: NGS interpretation via GeneCards,MalaCards and VarElect

Background

A key challenge in the realm of human disease research is next generation sequencing (NGS) interpretation, whereby identified filtered variant-harboring genes are associated with a patient’s disease phenotypes. This necessitates bioinformatics tools linked to comprehensive knowledgebases. The GeneCards suite databases, which include GeneCards (human genes), MalaCards (human diseases) and PathCards (human pathways) together with additional tools, are presented with the focus on MalaCards utility for NGS interpretation as well as for large scale bioinformatic analyses.

Results

VarElect, our NGS interpretation tool, leverages the broad information in the GeneCards suite databases. MalaCards algorithms unify disease-related terms and annotations from 69 sources. Further, MalaCards defines hierarchical relatedness—aliases, disease families, a related diseases network, categories and ontological classifications. GeneCards and MalaCards delineate and share a multi-tiered, scored gene-disease network, with stringency levels, including the definition of elite status—high quality gene-disease pairs, coming from manually curated trustworthy sources, that includes 4500 genes for 8000 diseases. This unique resource is key to NGS interpretation by VarElect. VarElect, a comprehensive search tool that helps infer both direct and indirect links between genes and user-supplied disease/phenotype terms, is robustly strengthened by the information found in MalaCards. The indirect mode benefits from GeneCards’ diverse gene-to-gene relationships, including SuperPaths—integrated biological pathways from 12 information sources. We are currently adding an important information layer in the form of “disease SuperPaths”, generated from the gene-disease matrix by an algorithm similar to that previously employed for biological pathway unification. This allows the discovery of novel gene-disease and disease–disease relationships. The advent of whole genome sequencing necessitates capacities to go beyond protein coding genes. GeneCards is highly useful in this respect, as it also addresses 101,976 non-protein-coding RNA genes. In a more recent development, we are currently adding an inclusive map of regulatory elements and their inferred target genes, generated by integration from 4 resources.

Conclusions

MalaCards provides a rich big-data scaffold for in silico biomedical discovery within the gene-disease universe. VarElect, which depends significantly on both GeneCards and MalaCards power, is a potent tool for supporting the interpretation of wet-lab experiments, notably NGS analyses of disease. The GeneCards suite has thus transcended its 2-decade role in biomedical research, maturing into a key player in clinical investigation.

     

Direct interaction of DNA repair protein tyrosyl DNA phosphodiesterase 1 and the DNA ligase III catalytic domain is regulated by phosphorylation of its flexible N-terminus

Tyrosyl DNA phosphodiesterase 1 (TDP1) and DNA Ligase IIIα (LigIIIα) are key enzymes in single-strand break (SSB) repair. TDP1 removes 3′-tyrosine residues remaining after degradation of DNA topoisomerase (TOP) 1 cleavage complexes trapped by either DNA lesions or TOP1 inhibitors. It is not known how TDP1 is linked to subsequent processing and LigIIIα-catalyzed joining of the SSB. Here we define a direct interaction between the TDP1 catalytic domain and the LigIII DNA-binding domain (DBD) regulated by conformational changes in the unstructured TDP1 N-terminal region induced by phosphorylation and/or alterations in amino acid sequence. Full-length and N-terminally truncated TDP1 are more effective at correcting SSB repair defects in TDP1 null cells compared with full-length TDP1 with amino acid substitutions of an N-terminal serine residue phosphorylated in response to DNA damage. TDP1 forms a stable complex with LigIII_170–755, as well as full-length LigIIIα alone or in complex with the DNA repair scaffold protein XRCC1. Small-angle X-ray scattering and negative stain electron microscopy combined with mapping of the interacting regions identified a TDP1/LigIIIα compact dimer of heterodimers in which the two LigIII catalytic cores are positioned in the center, whereas the two TDP1 molecules are located at the edges of the core complex flanked by highly flexible regions that can interact with other repair proteins and SSBs. As TDP1and LigIIIα together repair adducts caused by TOP1 cancer chemotherapy inhibitors, the defined interaction architecture and regulation of this enzyme complex provide insights into a key repair pathway in nonmalignant and cancer cells.