Hi,
We are studying how neural signals guide behavior. Using calcium imaging, we found ADL neurons responded to a chemical stimulus.
Based on this result, can we say the chemical stimulus might induce differential gene expression in ADL neurons? If not, what else should we do to lead to such assumption?
IMHO, you really can’t make that claim until you show some genes changing in expression in response to your stimulus. You could say it, but it would be completely speculative and if in a paper would have to clearly state that this was speculative and list other possibilities (ie. regulate the release of a neurotransmitter without changing gene expression). If you have candidate genes to test, you could try to use promoter:FP reporters, or single molecule FISH to demonstrate a change in expression. If the chemical stimulus could act in multiple cell types, you could consider microarrays or RNA-seq on whole animal mRNA isolates to get candidate differentially regulated genes. More elegant would be to do RNA-seq on ADL -/+ stimulus (ie. isolate the cells, or do some sort of cell-specific mRNA labeling like TU-tagging).
As an aside, I feel that most interventions will cause some genes to change in expression. There’s a lot of noise in gene expression and the challenge will be for you to find genes that change in expression in response to your chemical stimulus that are responsible for your changes in behaviour (assuming that this is the cause of any phenotype observed).
Monday, 6am: weather fair…mood, well… Jordan has graciously provided a helpful outline on how one might conduct a research project designed to study the effects of a certain chemical on a particular neurone.
I find your question a little worrying; 1) for you and 2) for your lab head if you are not he/she. I mean, with all due respect, if one sets out on the great ocean of gene expression - behaviour exploration then one might be expected to pack a few things for the voyage? If you want to study the effect of a chemical stimulus on a specific neurone then one normally thinks a little further than the first experiment. One might decide to do some preliminary experiments to rule out particular pathways using available mutants / RNAi / chemical inhibitors etc etc.
Also, fundamental questions like does the chemical stimulus relate to a behavioural change, is it dose-dependent, is it stage dependent etc need answering. There appears to be a cart but no sign of a horse here.
as Irving Goffman (at least) once said, ‘give me a nickel’s worth of your best Java’…I need it.