RBO Lab Meeting

Posted on October 25, 2011 by Cath@VWXYNot?
  • Our lab manager mentioned that some journals are starting to ask for certification to prove that the cell lines described in submitted manuscripts have tested negative for mycoplasma contamination during the course of the study (for the uninitiated, mycoplasma are bacteria that can seriously interfere with the interpretation of any data generated from cultured cells, which they manage to infect with great frequency and, seemingly, glee). No certificates, no publication. I think this is an excellent idea; however, I’ve written, edited or been otherwise involved with the submission of dozens of manuscripts of this kind, and I’ve never heard of such a practice, which I also would have expected to show up on at least one of the blogs I read. Was this just a ploy to make procrastinators hand over their cells for testing (said lab manager has been asking for weeks for people to prepare and assemble their cells), or should I really be buying shares in mycoplasma testing companies?
  • The meeting also included a presentation by a grad student who’s been with us for a while, but is just starting a new side project. The student spent the first two thirds or so of their short talk describing their efforts to optimise the various sample preparation steps… and the remaining time describing a hypothetical dataset that reflects the results they might reasonably expect to see once the assay’s running. This included a description of how the data would be generated, measured, normalised, and analysed. I’ve never seen anyone do this before, but I think it’s actually a fantastic idea for someone who’s just starting a new project; the feedback you get on your planned analysis could help you optimise the assay and choose the best controls before you even start, for example, and you’ll probably get better feedback when showing a mock analysis using actual numbers, rather than describing your plans in more abstract terms. Thoughts?
  • Video clips in talks are great. So are robots. Showing video clips of robots doing awesome stuff will make every bona fide geek in the room go “COOOOOOL!!!!” simultaneously.
  • “Regardless of the total number of slides to be presented, lab meetings will expand to fill every last minute of the time allotted to them”. Discuss.

About Cath@VWXYNot?

"one of the sillier science bloggers [...] I thought I should give a warning to the more staid members of the community." - Bob O'Hara, December 2010
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25 Responses to RBO Lab Meeting

  1. ricardipus says:
    October 26, 2011 at 1:25 am

    I think the analysis, interpretation and presentation of simulated data already has a name: computational biology.

  2. chall says:
    October 26, 2011 at 3:14 am

    Mycoplasma sucks. And it’s so messing up assays. And there are pretty easy kits to buy (one PCR and one luminescence come to mind). Of course, they aren’t too cheap….

    I haven’t heard about it being routine for a journal to ask for a mycoplasma test though. Only that good lab practice would be to check the frozen stock once, and if you notice the cells behaving oddly? I mean, you should clean the hood and clean room and not have any mycoplasma there…. duh ^^ *stating obvious things*

  3. rpg says:
    October 26, 2011 at 9:37 am

    You don’t need a kit for mycoplasma testing. Ask me nicely and I should be able to tell you the primers and conditions required for PCR amplification.

    (And, if you’re into it, DAPI staining works quite well too.)

    • chall says:
      October 26, 2011 at 2:13 pm

      🙂 I should’ve separated the PCR from the kit…. alas….

      Where I am now we have to use the kit (FDA approved) since… well, it is FDA approved ^^ Industry.

      • Cath@VWXYNot? says:
        October 26, 2011 at 5:01 pm

        If the rumours are true, I wonder if a journal would accept a home-brew mycoplasma test? I don’t see why not, if all the right controls are in place. Perhaps every paper will start including a mycoplasma test PCR & gel as a compulsory supplemental figure…

        • chall says:
          October 26, 2011 at 7:15 pm

          although, wouldn’t one argue that “in a proper lab the cell cultures should be controled and not being mycoplasma negative” which would make it redundant in a paper?

          (I know, I still believe that people are interested in actually having proper controls and want their data to be proper… ^^)

  4. cromercrox says:
    October 26, 2011 at 1:28 pm

    I’ll show you mycoplasma if you show me yourcoplasma.

  5. Mermaid says:
    October 26, 2011 at 3:03 pm

    “Regardless of the total number of slides to be presented, lab meetings will expand to fill every last minute of the time allotted to them”

    Meetings expand like spray foam insulation.

    Even with one item on the agenda, you have a 99.9% chance of being trapped at least until the scheduled end time. Or perhaps this is just my current impression based on my recent ratio of meetings:real work. Or perhaps I just need more coffee. It might also help with my creativity when coming up with comparisons :).

  6. Steve Caplan says:
    October 26, 2011 at 5:55 pm

    Mycoplasma are an essential part of animal/human cells. Since there is MORE bacterial DNA in a human than human DNA, we need to look at humans (and their cells) as symbiotic organisms–meaning that Mycoplasma are an essential component of human cells and any cell lines lacking them should be treated with suspicion.

  7. Cath@VWXYNot? says:
    October 26, 2011 at 7:19 pm

    I’m currently wondering what percentage of all relevant papers published in the last 50 years would have been accepted if a mycoplasma test was demanded before acceptance, and thinking maybe 30%…

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