HeatMapper: powerful combined visualization of gene expression profile correlations, genotypes, phenotypes and sample characteristics

Background  

Accurate interpretation of data obtained by unsupervised analysis of large scale expression profiling studies is currently frequently performed by visually combining sample-gene heatmaps and sample characteristics. This method is not optimal for comparing individual samples or groups of samples. Here, we describe an approach to visually integrate the results of unsupervised and supervised cluster analysis using a correlation plot and additional sample metadata.     

Experimental Extinction of Garlic Mustard (Alliaria petiolata) Populations: Implications for Weed Science and Conservation Biology

An assumption of weed science and conservation biology is that small populations are more vulnerable to elimination and extinction than large populations. We tested this with the invasive biennial garlic mustard (Alliaria petiolata). We compared 61 experimental populations from which every flowering plant was removed for 4 years, with 56 control populations. Whereas the majority of the control populations continued to expand in size over the 4 years, experimental populations showed a strong experimental effect, remaining stable in size, declining in size, or going extinct. Small populations were far more vulnerable to extinction than large populations: 43% of small experimental populations (initially fewer than 10 individuals) went extinct, but only 7% of large populations (initially more than 50 individuals). However, some small experimental populations persisted, and in a few cases, larger experimental populations continued to expand even though every flowering individual had been removed. These results and a simple population model suggest the importance of buried seeds in allowing this species to persist despite attempts to eradicate it.     

Immune Challenge and Pre- and Post-copulatory Female Choice in the Cricket Teleogryllus commodus

Life history theory predicts a trade off between the expression of male sexual traits and the immune system. To test for this trade off, male crickets Teleogryllus commodus were injected with bacterial lipopolysaccharides (LPS) to induce an immune response and their subsequent pre- and post-copulatory sexual attractiveness to virgin and non-virgin females was assessed. Pre-copulatory attractiveness was quantified based on the time taken for males to court and mate with a female. Post-copulatory attractiveness was measured as the time that elapsed between mating and a female interrupting sperm transfer by removing the externally attached spermatophore. We found no difference in pre- or post-copulatory attractiveness between LPS and control males. In contrast, virgin females retained spermatophores for almost twice as long as non-virgins, presumably to enhance fertilization and begin egg-laying. Finally, we note that although LPS is a widely used immune elicitor in insects, its effect might be transitory. After 24 h there was no detectable elevation in haemolymph antibacterial activity of LPS injected crickets compared to that of controls.