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Topic: Metabolomics in C. elegans (Read 569 times) previous topic - next topic

  • cr517
  • [*]
Metabolomics in C. elegans
Hi,
I am starting a project in metabolomics in C. elegans. Does anybody know if they are any guidelines for the experiment? In particular, I would be curious to know how people synchronise their worm populations.
Best,
C.
  • University of Cambridge

  • biswapriya
  • [*]
Re: Metabolomics in C. elegans
Reply #1
Hello,

The best person I know who perform extensive C. elegans + metabolomics" research are Professor Arthur Edison, who was at University of Florida, and now UGA, : http://edison.ccrc.uga.edu/?page_id=356 , and his colleagues Fatma Kaplan: https://biology.ufl.edu/fkaplan/ and Greg Stupp/ Dr. Chris Beecher et al. who published: Isotopic Ratio Outlier Analysis Global Metabolomics of Caenorhabditis elegans : http://pubs.acs.org/doi/abs/10.1021/ac4025413 . But all this NMR-metabolomics.

They would be the best to consult anything on worm metabolomics! :)

Thanks,
Biswa Misra

  • cr517
  • [*]
Re: Metabolomics in C. elegans
Reply #2
Thanks. I should have mentioned we are going to use mass spectrometry. Do you have any links to that as well?
Best.
C.
  • University of Cambridge

  • michael.witting
  • [*]
Re: Metabolomics in C. elegans
Reply #3
Hi,

I'm working since some year on C. elegans metabolomics.
We syncronise our worms with standard protocols used by the C. elegans community, also termed bleaching.
Cultivation is performed according to standard protocols using Nematode Growth Medium and E. coli OP50 as food source.

What do you plan?

Please find below a few references from my work:
https://www.ncbi.nlm.nih.gov/pubmed/26903948
https://www.ncbi.nlm.nih.gov/pubmed/26072113
https://www.ncbi.nlm.nih.gov/pubmed/25544008
https://www.ncbi.nlm.nih.gov/pubmed/25428456
https://www.ncbi.nlm.nih.gov/pubmed/25074420

Best regards,

Michael
  • Helmholtz Zentrum München, Research Unit Analytical BioGeoChemistry

  • cr517
  • [*]
Re: Metabolomics in C. elegans
Reply #4
Dear Michael,
Thank you so much for the references. I am going to have a look at them. I am aware of the bleaching technique. But do you let them reach the arrested L1 stage overnight or directly seed the bleached eggs on a plate? Seeding arrested L1's would be well synchronised but the starvation would confound the 'natural' physiological state. I also grow them on OP50. I would like to analyse the effect of different bacterial diets on the phenotype of C. elegans. So, I would like to compare populations of worms at the same developmental stage in order to minimise the effect of development on the metabolome of C. elegans. Bleaching is easy but given that I want to kill the worms at the young gravid adult stage, they would have time to desynchronise. The alternative is to pick hundreds of worms in a plate for 1 hour and let them lay eggs at the same early stage and then unpick the adult worms. But that would be an aweful lot of work given that I would like to analyse many different bacterial strains. This picking strategy of synchronisation might also not be the best because it would also take time to pick so many worms and that would cause desynchronisation.
  • Last Edit: February 24, 2017, 09:30:09 AM by cr517
  • University of Cambridge

  • michael.witting
  • [*]
Re: Metabolomics in C. elegans
Reply #5
Well,  that's the trick that you arrest L1s and by this they syncronise. I usually seed the arrested L1s to the plates.
If you want to study adults that not a problem, because worms have enough time to "recover" from this state.
But if you are planning to study L1s you might have a problem, then picking is the way forward, but that takes a long time and is a real pain to obtain sufficient material (depends on the type of analysis you are planning).

By the way, if you are from Cambridge, this might be interesting for you:

http://www.babraham.ac.uk/genie-workshop

I'm one of the organizers and if you are interested we can discuss one-on-one there  ;)
  • Helmholtz Zentrum München, Research Unit Analytical BioGeoChemistry

Re: Metabolomics in C. elegans
Reply #6
Be careful with comparing different bacterial feeding strains for the same experiment:
https://www.ncbi.nlm.nih.gov/pubmed/20400348
  • Murdoch University

  • michael.witting
  • [*]
Re: Metabolomics in C. elegans
Reply #7
Hi all.

for people interested in C. elegans metabolomics:
We have started the WormJam "initative", which will curate metabolites, metabolic pathways etc present in the worm and collect everything in a consesus metabolic model. If you are interested in joining have a look into our google group:

https://groups.google.com/forum/#!forum/wormjam

Best regards,

Michael
  • Helmholtz Zentrum München, Research Unit Analytical BioGeoChemistry