TNF/p38α/polycomb signaling to Pax7 locus in satellite cells links inflammation to the epigenetic control of muscle regeneration

How regeneration cues are converted into the epigenetic information that controls gene expression in adult stem cells is currently unknown. We identified an inflammation-activated signaling in muscle stem (satellite) cells, by which the polycomb repressive complex 2 (PRC2) represses Pax7 expression during muscle regeneration. TNF-activated p38α kinase promotes the interaction between YY1 and PRC2, via threonine 372 phosphorylation of EZH2, the enzymatic subunit of the complex, leading to the formation of repressive chromatin on Pax7 promoter. TNF-α antibodies stimulate satellite cell proliferation in regenerating muscles of dystrophic or normal mice. Genetic knockdown or pharmacological inhibition of the enzymatic components of the p38/PRC2 signaling--p38α and EZH2--invariably promote Pax7 expression and expansion of satellite cells that retain their differentiation potential upon signaling resumption. Genetic knockdown of Pax7 impaired satellite cell proliferation in response to p38 inhibition, thereby establishing the biological link between p38/PRC2 signaling to Pax7 and satellite cell decision to proliferate or differentiate.     

A New Statistic to Evaluate Imputation Reliability

Background

As the amount of data from genome wide association studies grows dramatically, many interesting scientific questions require imputation to combine or expand datasets. However, there are two situations for which imputation has been problematic: (1) polymorphisms with low minor allele frequency (MAF), and (2) datasets where subjects are genotyped on different platforms. Traditional measures of imputation cannot effectively address these problems.

Methodology/Principal Findings

We introduce a new statistic, the imputation quality score (IQS). In order to differentiate between well-imputed and poorly-imputed single nucleotide polymorphisms (SNPs), IQS adjusts the concordance between imputed and genotyped SNPs for chance. We first evaluated IQS in relation to minor allele frequency. Using a sample of subjects genotyped on the Illumina 1 M array, we extracted those SNPs that were also on the Illumina 550 K array and imputed them to the full set of the 1 M SNPs. As expected, the average IQS value drops dramatically with a decrease in minor allele frequency, indicating that IQS appropriately adjusts for minor allele frequency. We then evaluated whether IQS can filter poorly-imputed SNPs in situations where cases and controls are genotyped on different platforms. Randomly dividing the data into “cases” and “controls”, we extracted the Illumina 550 K SNPs from the cases and imputed the remaining Illumina 1 M SNPs. The initial Q-Q plot for the test of association between cases and controls was grossly distorted (λ = 1.15) and had 4016 false positives, reflecting imputation error. After filtering out SNPs with IQS<0.9, the Q-Q plot was acceptable and there were no longer false positives. We then evaluated the robustness of IQS computed independently on the two halves of the data. In both European Americans and African Americans the correlation was >0.99 demonstrating that a database of IQS values from common imputations could be used as an effective filter to combine data genotyped on different platforms.

Conclusions/Significance

IQS effectively differentiates well-imputed and poorly-imputed SNPs. It is particularly useful for SNPs with low minor allele frequency and when datasets are genotyped on different platforms.     

Phenylurea herbicides induce cytogenetic effects in Chinese hamster cell lines

The intensive use of herbicides over the last few decades has caused a general increase of environmental pollution. It is thus very important to evaluate the possible genotoxic properties of these chemical compounds as well as identifying their mode of action. Phenylurea herbicides are selective agents widely used for the control of infestant plants. Of these herbicides, which are widely used in agriculture, we analysed four of the less intensively studied molecules. More precisely, we investigated the genotoxic effects of fenuron, chlorotoluron, diuron, and difenoxuron by analyses of chromosomal aberrations (CAs) and sister chromatid exchange (SCE) in exposed mammalian cells. We used the Chinese hamster ovary (CHO) and epithelial liver (CHEL) cell lines, endowed with the absence or the presence, respectively, of an enzymatic system to activate pro-mutagenic compounds. Our results show that all herbicides tested induce, at high concentrations, an increasing number of CAs in non-metabolising CHO cells. Instead, in the exposed CHEL cell line, the four herbicides induced CAs also at the lowest dose-level. In the CHEL cells, a statistically significant increase of SCE was also observed. The phenylurea herbicides showed direct genotoxic activity, but the cytogenetic effects were greatly enhanced after metabolic conversion. These data, together with other information on phenylurea herbicides, are of great interest from the environmental point of view, and for human health. In fact, intensive use of herbicides contaminates soil, surface water, groundwater and agricultural products, and thus should be taken in particular consideration not only for those initiatives to specifically protect exposed workers, but also to safeguard the health of consumers of agricultural products.     

Stronger Short-Term Effects of Mowing Than Extreme Summer Weather on a Subalpine Grassland

Mowing is known to favor plant diversity and influence ecosystem functioning in semi-natural grasslands. This effect could be influenced by climate variability, especially in regions with harsh climate, such as subalpine zones. In particular, short-term extreme weather fluctuations may induce rapid plant responses, affecting in turn the response to mowing. We tested the effects of concomitant summer weather manipulation and mowing on a subalpine grassland in the Central French Alps for two consecutive years. We addressed two questions: (1) How is a subalpine grassland affected by extreme summer weather? (2) Does extreme summer weather alter mowing effects on the grassland plant diversity and functioning? We used a multi-level, integrative approach assessing the responses of six abundant plant species, as well as effects on plant community structure, biomass production, and litter decomposition rates. Extreme summer weather was simulated by increasing summer temperature by 1.1°C, and decreasing summer rainfall by 80%—resulting in a 30% decrease in total annual precipitation. In addition, a heat-wave event was simulated during the first year of the experiment. This weather manipulation was combined with a late-summer mowing treatment (mown vs. unmown). Extreme summer weather mainly increased leaf senescence and decreased plant vegetative growth. Leaf litter decomposition was slowed, but only for species characterized by the fastest rates of litter decomposition. Mowing increased plant diversity by restricting the dominant grass species, thereby favoring subordinates. In the short term, this subalpine grassland was rather resistant to extreme summer weather, whereas mowing cessation remained the main factor affecting its biodiversity.     

Action of retinol on viable cell recovery and clonogenic potential of HTC cells after in vitro hyperthermia]

The aim of this study was to investigate if the association of both hyperthermic and Retinol treatment of HTC hepatoma cells could be useful in antitumor therapy. Treatment with 5 microM Retinol was carried out before or after hyperthermia (42 degrees C or 44 degrees C, one hour; in the latter case it was performed in cells already thermo-selected. We took into consideration two parameters, i.e. the number of the collected vital cells (evaluated by the trypan blue-exclusion test) and the clonal efficiency of these cells (calculated as number of colonies obtained from 250 cells cultured for 5 days). Thermal treatment alone caused a decrease of the number of the collected vital cells and of their clonal efficiency only in the cell cultures incubated at 44 degrees C. Instead the control thermo-selected cells, both at 42 degrees C and at 44 degrees C, showed both decreased clonal efficiency and yield of the vital cells. Compared with the control cultures treated with 0.1% Ethanol, used as vitamin A solvent, only cell cultures treated with Retinol before hyperthermia showed a decreased number of collected viable cells, nevertheless their clonal efficiency was unchanged.     

Multisequence comparisons in protein coding genes. Search for functional constraints

A very powerful method for detecting functional constraints operative in biological macromolecules is presented. This method entails performing a base permanence analysis of protein coding genes at each codon position simultaneously in different species. It calculates the degree of permanence of subregions of the gene by dividing it into segments, c codons long, counting how many sites remain unchanged in each segment among all species compared. By comparing the base permanence among several sequences with the expectations based on a stochastic evolutionary process, gene regions showing different degrees of conservation can be selected. This means that wherever the permanence deviates significantly from the expected value generated by the simulation, the corresponding regions are considered "constrained" or "hypervariable". The constrained regions are of two types: alpha and beta. The alpha regions result from constraints at the amino acid level, whereas the beta regions are those probably involved in "control" processing. The method has been applied to mitochondrial genes coding for subunit 6 of the ATPase and subunit 1 of the cytochrome oxidase in four mammalian species: human, rat, mouse, and cow. In the two mitochondrial genes a few regions that are highly conserved in all codon positions have been identified. Among these regions a sequence, common to both genes, that is complementary to a strongly conserved region of 12S rRNA has been found. This method can also be of great help in studying molecular evolution mechanisms.     

Multisequence comparisons in protein coding genes

A very powerful method for detecting functional constraints operative in biological macromolecules is presented. This method entails performing a base permanence analysis of protein coding genes at each codon position simultaneously in different species. It calculates the degree of permanence of subregions of the gene by dividing it into segments,c codons long, counting how many sites remain unchanged in each segment among all species compared. By comparing the base permanence among several sequences with the expectations based on a stochastic evolutionary process, gene regions showing different degrees of conservation can be selected. This means that wherever the permanence deviates significantly from the expected value generated by the simulation, the corresponding regions are considered “constrained” or “hypervariable”. The constrained regions are of two types: α and β. The α regions result from constraints at the amino acid level, whereas the β regions are those probably involved in “control” processing. The method has been applied to mitochondrial genes coding for subunit 6 of the ATPase and subunit 1 of the cytochrome oxidase in four mammalian species: human, rat, mouse, and cow. In the two mitochondrial genes a few regions that are highly conserved in all codon positions have been identified. Among these regions a sequence, common to both genes, that is complementary to a strongly conserved region of 12S rRNA has been found. This method can also be of great help in studying molecular evolution mechanisms.     

The evolution of the RNase P- and RNase MRP-associated RNAs: Phylogenetic analysis and nucleotide substitution rate

We report a detailed evolutionary study of the RNase P- and RNase MRP- associated RNAs. The analyses were performed on all the available complete sequences of RNase MRP (vertebrates, yeast, plant), nuclear RNase P (vertebrates, yeast), and mitochondrial RNase P (yeast) RNAs. For the first time the phylogenetic distance between these sequences and the nucleotide substitution rates have been quantitatively measured. The analyses were performed by considering the optimal multiple alignments obtained mostly by maximizing similarity between primary sequences. RNase P RNA and MRP RNA display evolutionary dynamics following the molecular clock. Both have similar rates and evolve about one order of magnitude faster than the corresponding small rRNA sequences which have been, so far, the most common gene markers used for phylogeny. However, small rRNAs evolve too slowly to solve close phylogenetic relationships such as those between mammals. The quicker rate of RNase P and MRP RNA allowed us to assess phylogenetic relationships between mammals and other vertebrate species and yeast strains. The phylogenetic data obtained with yeasts perfectly agree with those obtained by functional assays, thus demonstrating the potential offered by this approach for laboratory experiments. Correspondence to: E. Sbisà     

Evolution of T-Cell Receptor Gamma and Delta Constant Region and Other T-Cell-Related Proteins in the Human-Rodent-Artiodactyl Triplet

In this paper we report a detailed comparative and evolutionary analysis of the sequences of constant T-cell receptor (Tcr) Cγδ genes of artiodactyls compared to the homologous sequences of rodents and primates. Because of the frequency and physiological distribution of γδ T-cells in different animals, rodents and humans are defined as ``γδ low' species and ruminants as ``γδ high' species. Such a characteristic seems to be due to an adaptive role of γδ T-cell function. By analyzing the ruminant gene phylogeny of Tcr Cγ we were able to estimate the distance between cattle and sheep at 18 million years ago, a time that is in agreement with other nonmolecular estimates. For Tcr Cγδ genes a peculiar phylogenetic relationship was found, with human and mouse clustering together and leaving artiodactyls apart. By using appropriate outgroups, the same phylogenetic pattern was obtained with other T-cell related sequences: namely, Tcr Cα chain, CD3 γ and δ invariant subunits, Interleukin-2, Interleukin-2 receptor α chain and Interleukin-1β with the exception of Tcr Cβ chain and Interleukin-1α. In contrast, the analysis of all other T-cell nonrelated genes available in primary databases reveals a different tree, where primates and artiodactyls are sister taxa and rodents are apart in accordance with the current view of mammalian phylogeny. These data are relevant to important evolutionary issues. They show how misleading a phylogeny based on a single or on a few homologous genes may be. In addition they demonstrate that genes with correlated functions may evolve in a lineage specific manner probably in relation to environmental conditions.