Correspondence analyses showing the distribution of spiders on the fogged trees.

<p>Spider communities on deciduous trees and conifers are clearly separated exhibiting a larger similarity within than between groups (A). For both deciduous (B) and coniferous (C) trees, tree-species-specific patterns were identified. No such pattern was found for the oak trees.</p

Guild distribution.

<p>Box-plots showing characteristic types of distributions of guilds on different tree species. Abbreviation: Space-web weavers = Spa, tangle weavers = Tan, orb-web weavers = Orb, ambushers = Amb, stalkers = Sta, foliage runners = Fol. Guild composition was uniform on most trees (<i>Quercus</i>, <i>Carpinus</i>, <i>Betula</i> and <i>Picea</i>), while <i>Alnus</i> and <i>Pinus</i> were dominated by tangle and orb-web weavers.</p

Diversity of spider communities.

<p>Diversity of spider communities collected by insecticidal knock down from deciduous and coniferous trees in Poland. Rarefaction values (RAF) computed on standardized individual numbers (ind) allow direct comparison suggesting large differences in species diversity among tree species (Qr = <i>Q. robur</i>, Cb = <i>C. betulus</i>, Ag = <i>A. glutinosa</i>, Bp = <i>B. pendula</i>, Pt = <i>P. tremula</i>, Pa = <i>P. abies</i>, Ps = <i>P. sylvestris</i>).</p

Beta diversity of spider communities.

<p>Comparison of spider communities per tree species on the beta diversity level. The density distribution of Morisita-Horn values of 1000 permutations of ten randomly chosen trees visualizes differences in community composition independent of sample size. Beta diversity was largest on oak, followed by spruce and alder trees.</p

Analysis of global DNA methylation changes in primary human fibroblasts in the early phase following X-ray irradiation

<div><p>Epigenetic alterations may contribute to the generation of cancer cells in a multi-step process of tumorigenesis following irradiation of normal body cells. Primary human fibroblasts with intact cell cycle checkpoints were used as a model to test whether X-ray irradiation with 2 and 4 Gray induces direct epigenetic effects (within the first cell cycle) in the exposed cells. ELISA-based fluorometric assays were consistent with slightly reduced global DNA methylation and hydroxymethylation, however the observed between-group differences were usually not significant. Similarly, bisulfite pyrosequencing of interspersed LINE-1 repeats and centromeric α-satellite DNA did not detect significant methylation differences between irradiated and non-irradiated cultures. Methylation of interspersed ALU repeats appeared to be slightly increased (one percentage point; p = 0.01) at 6 h after irradiation with 4 Gy. Single-cell analysis showed comparable variations in repeat methylation among individual cells in both irradiated and control cultures. Radiation-induced changes in global repeat methylation, if any, were much smaller than methylation variation between different fibroblast strains. Interestingly, α-satellite DNA methylation positively correlated with gestational age. Finally, 450K methylation arrays mainly targeting genes and CpG islands were used for global DNA methylation analysis. There were no detectable methylation differences in genic (promoter, 5' UTR, first exon, gene body, 3' UTR) and intergenic regions between irradiated and control fibroblast cultures. Although we cannot exclude minor effects, i.e. on individual CpG sites, collectively our data suggest that global DNA methylation remains rather stable in irradiated normal body cells in the early phase of DNA damage response.</p></div

DNA methylation of repetitive elements in irradiated versus non-irradiated fibroblast cultures.

<p>Global methylation of interspersed ALU and LINE-1 repeats, and α-satellite DNA was determined by bisulfite pyrosequencing in primary human fibroblasts at 6 and 24 h after irradiation with 2 and 4 Gray, respectively. For each time point and dose, the number of analyzed cultures is given in parenthesis. Results are presented as mean (of different cultures) over means (triplicate measurements) ± standard error. Asterisk denotes a significant (p < 0.05) between-group difference.</p

Additional file 4: Table S3. of Epigenetic signatures of gestational diabetes mellitus on cord blood methylation

Multivariate analyses (adjusting for maternal BMI, gestational age, and fetal sex): CpG methylation of candidate genes in GDM versus control FCB samples. (DOC 68 kb

Global DNA methylation and hydroxymethylation in irradiated versus non-irradiated fibroblast cultures.

<p>Global 5-mC and 5-hmC levels were measured by ELISA-based assays in primary human fibroblasts at 6 and 24 h after X-ray irradiation with 2 and 4 Gy, respectively. For each time point and dose, the number of analyzed cultures is given in parenthesis. Results are presented as mean (of different cultures) over means (triplicate measurements) ± standard error. Asterisk denotes a significant (p < 0.05) between-group difference.</p

Global DNA methylation in genic and intergenic regions of irradiated versus non-irradiated fibroblast cultures.

<p>DNA methylation was assessed with Illumina 450K arrays in primary human fibroblasts at 1–24 h after irradiation with 2 Gy (upper panel) and at 6–72 h after 4 Gy (lower panel). The bars represent the average methylation of all analyzed CpGs that have been annotated to a particular category (promoter, 5' UTR, first exon, gene body, 3' UTR, intergenic). TSS200 is the region from transcription start site (TSS) to -200 bp, TSS1500 from -200 bp to -1,500 bp upstream of TSS. Data are presented as means over means.</p

Box plots showing the distribution of repeat DNA methylation in single cells.

<p>DNA methylation of interspersed ALU and LINE-1 repeats, and α-satellite DNA was determined by bisulfite pyrosequencing in individual fibroblasts from two independent cultures at 24 h after irradiation with 2 Gy and 4 Gy, respectively. For each culture, time point, and dose, the number of analyzed cells is given in parenthesis. The median is represented by a horizontal line. The bottom of the box indicates the 25^th percentile, the top the 75^th percentile. Outliers are shown as circles and extreme outliers as stars.</p