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Second, we tested the hypothesis that nourishment level relates to caste-related gene expression; specifically that low nourishment is associated with more worker-like gene expression patterns, and high nourishment is associated with more gyne-like expression patterns.
Overall, our data suggest that nourishment level caused a partial shift in gene expression, with low nourishment individuals being more worker-like and high nourishment individuals being more gyne-like.
These results support the notion that nourishment level during development can somewhat bias development into queen or worker caste as adults, but leave room for other factors, and thus underscore the complex and multifactorial nature of caste development.
To further explore these data beyond examining an overlap of gene lists, we performed a combined statistical analysis of data from both the nourishment level and caste contrasts, and the results also indicate some overlap in gene expression patterns across the two studies (see Methods, with complete description of the approach and results in Additional file 2 and Additional file 5).
The High-Throughput Sequencing and Genotyping Unit of the W.M. Keck Center University of Illinoiss at Urbana-Champaign) prepared 16 mRNA Seq libraries (n = 4 per group, high and low nourishment level) derived from two experimental nourishment levels (high and low; this study) and unmanipulated castes (queen- and worker-destined; [ 13]) using the "TruSeq RNAseq Sample Prep kit" (Illumina).
The variability of gene expression amongst biological samples is not completely surprising; our previous work has found high inter-individual variation in gene expression [ 13], effects of lab rearing (JM Jandt, JL Thomson, AC Geffre, AL Toth: Rearing environment may bias social traits: A case study with Polistes wasps, submitted), and variable effects of nourishment level on physiology [ 38].
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First, we explored the transcriptional responses of wasp larvae to high and low nourishment levels during laboratory rearing using RNA-sequencing.
In some sense, across the two studies we have a replicated experiment with respect to nourishment levels, which utilizes both the lab and field setting.
From these raw read counts, we identified differentially expressed transcripts (FDR ≤ 0.05, [ 46]) between nourishment manipulation levels (high and low) using the R (Version 3.0.1) [ 61] statistical package DESeq (Version 1.12.0) [ 62] downloaded from the Bioconductor repository [ 63].
Less hands, less machinery, less packaging equate to higher nourishment at all levels".
Food, in Guadgnino's vision, is not just chow -- it's nourishment on all levels, epiphany, art.
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