We know c elegans hermaphrodites have 302 neurons. In reality, can anyone let me know how to determine neuronal location in a transgenic reporter strain? Is there a neuronal map that we can use as a reference?
Thank you!
I assume you’re familiar with WormAtlas, The Mind of a Worm (available as a PDF or as html), and Chris Grove’s Virtual Worm? Or for that matter the diagrams in the back of Worm I, which I think isn’t available online for free?
Those links should help you with the anatomy. If your question is more about finding reporters to confirm neuron identification - that is, a list naming the specific reporters you can use for each neuron - such a thing might be quite useful, but I don’t know offhand if anyone has compiled one.
I think Hillel is being overgenerous in his interepretation of the subtlety of the original question, but nevertheless, a good starting point for those interested in lighting up specific neurones (and who have done the spade work to find out where they are located anatomically) might be Chelur & Chalfie’s 2007 paper:
http://www.ncbi.nlm.nih.gov/pubmed/17283333
see Table 1 in the Suppl. Info.
That table is pretty awesome. Another way to look around is by using WormBase and going to the individual anatomy term’s page and checking out the association tab for expression pattern.
Thank you all for your answers! I am sorry that I didn’t make myself clear. My question is how to determine the expression neurons by looking at fluorescence images. For example, ocr2::gfp is expressed in head neurons AWA, ADL, ADF, and ASH. I wondered how they knew they are right as the locations for the neurons are very close to each other, like ASH is very close to ASI or ASK.
Well, likely by other co-localization experiments with other markers for those cells, and also by looking manually themselves.
If you know the anatomy well enough, just the position and shape of the nucleus relative to the others around it should in theory be enough - but this level of command of the anatomy is extremely rare. Far more commonly, you will investigate all of the nuclei in the immediate vicinity, and rule out those cells with inconsistent process morphology. The set of diagrams in the back of Worm I is really good for this, because they’re really nicely done and all in one place, but any of the resources in my comment above would work.
This should leave you with one or more candidates, and as Snug says you will then usually test whether your reporter is expressing in the same cell as a reporter previously reported to express specifically in that candidate or one of those candidates. You might also use mutations known to specifically affect that candidate (or a subset of cells including that candidate), and see whether expression of your reporter is affected. Similarly you might look at dye filling, or even ablate your expressing cell and compare the phenotype to the reported effects of ablating particular cells in the area.
It’s also a good idea to keep a bit of an open mind, in the past people have been fooled because they were looking at expression in a glial cell, thought it was a neuron, and tried to identify the cell as being the neuron whose nuclear location and process morphology most closely resembled that of the glial cell.
Thank you both for your input!!!
For me, I am trying to make a reporter strain to determine the expression pattern of one gene in the worm by using it own promoter. This was why I started thinking how to determine the specific locations, such as neurons. I still feel difficult after reading your answers, but thank you very much for your help!
Okay, to simplify Hillel’s/Steve’s/my suggestions, do the following:
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Make your reporter strain, figure out roughly what part region of the animal it is expressed (head, body, tail). Take both DIC and fluorescent images of the whole animal at high magnification.
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Use Worm Atlas, specifically the Cell ID section to try and figure out what neurons your reporter is being expressed in.
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Get reporter strains that have known expression patterns corresponding to the neurons you think your reporter is also expressed in. Cross these markers into your transgenic strain.
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Look for co-localization to confirm your expression pattern. If they don’t co-localize, this strain can still be useful in identifying expression in adjacent/neighbouring cells.
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Publish your robust results
Very good suggestions and summary, Snug! Thank you very much! I will follow them to perform my experiments.
Have a wonderful weekend.
Kim