Field of Science

Writing the #arseniclife paper

The grad student working on the mass-spectrometry analysis of GFAJ-1 DNA is still making sure his results meet his high standards, but as soon as they are ready he'll send them to me and I'll post them here.  In the meantime, since he and his supervisors have concluded that the DNA contains no arsenic, we've started writing our paper. We're going to submit it to Science as a Brevia.  These are very short peer-reviewed articles (one page, one figure), which we think suits this work very well.

But first we need to replicate our results.  My plan is to generate some detailed growth curves for cultures with various levels of phosphate, with and without 40 mM arsenate.  For this I'll use a BioScreen machine that belongs to a neighbouring lab.  This machine automates collection of optical density data from cultures growing in wells of 100-well plates.  I'll also grow big batches of cells for new DNA preps, using the same media and culture conditions as before.

This should only take a few days, and I hope to have the DNAs ready to send to my collaborators on Monday.

8 comments:

  1. Take caution with measuring growth curves in plate-readers— they often don't shake uniformly enough to make comparisons between strains meaningful... when I was in the van oudenaarden lab most of my work boiled down to taking ODs and measuring growth rates, and we found that the results from plate readers were generally not very robust compared to doing things in small, well-aerated flasks. We found the best way to account for the issue with plate-readers (if you must) is to randomly distribute the replicates for the strains you'd like to compare in the 96-well plate (generally not 100-well as you suggest). This is similar to how spatial biases on microarrays are dealt with.

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  2. The BioScreen uses special 100-well plates, and I'm certainly going to do multiple replicates in randomized wells.

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  3. Hmmm, thanks, good to know! I think some of us use plate readers for bacterial fitness assays... hopefully this doesn't introduce too many artefacts!

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  4. NotAnAstrobiologistJanuary 11, 2012 at 5:11 PM

    Well done Rosie, nice to see this result all but published.

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  5. NotAnAstrobiologistJanuary 11, 2012 at 5:33 PM

    P.S. Consider making a video when you can, so many sites these days are more inclined to share a video over an article.

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  6. These journals usually refuse to publish data opposing their own publications. Given the publicity of #arseniclife, I hope this may be the starting point for a change in policy! Good luck!

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  7. Ironically Science and their reviewers are likely to ask you to do many, many controls to ensure that your negative result is correct. Unfortunately they don't appear to have done that for the original paper.

    It will also be interesting to see if the original paper is retracted once your paper is published. Perhaps they'll just retract part of it, like what happened at first with the CFS baloney.

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