Average nrs of pecks±SEM directed to a familiar, readily available food resource in UL and PL parents, and their respective offspring, as measured in a Foraging test.

<p>Significant differences are indicated: * = p<0.05; ** = p<0.01.</p

Significantly differentially expressed gene transcripts between parents treated with Unpredictable Light or Predictable Light based on microarray analysis.

<p>M-fold value is the log2 of the difference in expression level, and B-value is the log odds ratio of expression levels; the B-value estimates the certainty of DE vs non-certainty of DE. The criterium used for significant expression was that B>0. Positive M-values indicate that the transcript is higher expressed in birds treated with Unpredictable Light.</p

Immune gene transcripts which had among the 2.5% highest absolute M-values in each sex and generation.

<p>The table shows the same values with same criteria as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0006405#pone-0006405-t003" target="_blank">table 3</a> for all transcripts included on the microarray from the two immune related genes Ig light chain, Ig heavy chain. Also included are three MHC-transcripts, which were only top ranked in the parents. If not stated otherwise, all transcripts were down-regulated in parents treated with Unpredictable Light (UL) or offspring of UL parents in relation to parents in Predictable Light or their offspring.</p>*<p>Up-regulated.</p>1<p>Annotation was done using Chicken Discovery System.</p>§<p>NA indicate genes filtered away during analysis as low quality spot on microarray. Filtration is dependent on joint properties on all the arrays in the group, hence could fall out differently in relation to which arrays are included.</p

Food competition at adult age in UL and PL parents and their respective offspring as measured in a Dominance test.

<p>Numbers of pecks in the food are given in means±SEM. Significant differences are indicated: * = p<0.05.</p

Weight measurements of surviving birds.

<p>(A) Growth in UL and PL parents; male UL, n = 4; male PL, n = 7; female UL, n = 11; female PL, n = 8. (B) Body weight in offspring of UL and PL parents. The difference between the offspring groups was significant (p<0.01) based on a repeated measure general linear model with parental treatment and sex as independent factors. There was an interaction between parental treatment and sex (p<0.05) illustrated by the small figure in the female diagram. (C) Growth in offspring of UL and PL parents; males with UL parents n = 10; males with PL parents, n = 9; females with UL parents n = 11; females with PL parents n = 10. All values are given as grams with means±SEM.</p

Infections and GenBank sequences in relation to Norwegian municipalities.

<p>Phylogenetic tree of the Saffold virus genotypes and geographical distribution of sequenced samples. Strains from the current study are colored blue. Sequences are denoted with GenBank accesion number, then the country of origin and year of sampling in parentheses. The tree is rooted by using midpoint rooting Scale bars represent 0.1 nucleotide substitutions per site. Only one sequence per infection episode is presented in the phylogenetic tree as the dominating sequence seemed stable and there were no evident mutations in the VP1 sequence during an infection (results not shown), supporting the assumption that consecutive positive samples were part of the same infectious episode.</p

Saffold virus infection episodes in the case and control children.

<p>The number of infection episodes and total samples, with the percent in parentheses, and the results from the mixed effects logistic regression are given for case and control children at different time periods. IA: islet autoimmunity; OR: Odds Ratio; 95% CI: 95% Confidence Interval.</p><p>Saffold virus infection episodes in the case and control children.</p

Primers and Probes used in the Study.

<p>^a position given when aligning to NCBI Reference Sequence: NC_009448.2</p><p>^b F: forward primer; R: reverse primer; P: Probe.</p><p>^c Minor Groove Binder.</p><p>Primers and Probes used in the Study.</p

Probability of having the first infection with Saffold virus during follow-up.

<p>Probability is calculated as 1 minus the Kaplan-Meier estimate. 2A: All children (solid line), case children (dotted line) and control children (dashed line). 2B: All children (solid line) with 95% confidence interval bands. There is no statistical difference between the case and control children.</p

Figure 2

<p>Correlations between magnitude of differential expression of genes between parents and offspring. Diagrams show M-values for the differential expression (comparing stressed vs control parents, and offspring of stressed vs offspring of control parents) of the 500 most differentially expressed genes (largest log₂ difference caused by stress in parents) in (a) red junglefowl, and (b) White Leghorns. Each point represents one spot on the microarray. Positive M-values indicate upregulation and negative downregulation by stress (or by having stressed parents). The average correlation line is shown in both comparisons.</p