Problems with models?

Image: José Goulão/Wikimedia Commons.

Image: José Goulão/Wikimedia Commons.

Faced with the breath­tak­ing diversity of liv­ing things, com­prom­ises are made and research effort con­cen­trated in a few selec­ted spe­cies – so-called ‘model organ­isms’ – in the hope that bio­lo­gical dis­cov­er­ies made in those will be more widely applic­able to oth­ers of their kind. Accordingly, we have model anim­als, such as fruit fly and zebra fish, and model plants, such as thale cress and rice. We also have model sys­tems, which enable us to focus atten­tion on par­tic­u­lar pro­cesses or bio­chem­ical path­ways rather than the whole organ­ism. A good example from the plant world is the tobacco cell line known as BY-2. This was estab­lished from a cal­lus induced on a seed­ling of the Nicotiana tabacum cul­tivar BY-2, and is used as model sys­tems for higher plants because of its ‘excep­tion­ally high homo­gen­eity’. If you’ve devoted much of your careers to work with that sys­tem you’ll prob­ably already know that Ales Kovarik et al. have recently pub­lished a paper entitled, ‘A plant cul­ture (BY-2) widely used in molecu­lar and cell stud­ies is genet­ic­ally unstable and highly het­ero­gen­eous’. Apparently, and in keep­ing with other long-term cul­tures, BY-2 exists ‘as a com­munity of cells with dif­fer­ent karyo­types reflec­ted in dif­fer­ent chro­mo­some num­bers, mor­pho­lo­gies and dis­tri­bu­tions of satel­lite repeats’. Unwelcome news, indeed! Fortunately, though, no such issues with Arabidopsis. Eh, what’s that you say, Skippy? There are!!?? Oh dear. Some time ago, Alison Anastasio et al. announced wide­spread mis-identification amongst Arabidopsis acces­sions. Of the 5965 acces­sions they examined, they con­cluded that 286 deserved ‘spe­cial atten­tion’ as being poten­tially mis-identified. The brave amongst you can read the rest of the paper, but it is a scary bit of a ‘news’ for those of us who may blindly accept as tru­isms all ‘thale cress treat­ises’. Well, all may not be lost (so to speak) for BY-2 and ara­bidop­sis users alike. Jeroen Nieuwland et al. have announced ‘Phytotracker’, a labor­at­ory man­age­ment inform­a­tion ‘sys­tem spe­cific­ally to organ­ise and track plas­mids, seeds and grow­ing plants that can be used in mixed plat­form envir­on­ments’. Although it has been developed in an ara­bidop­sis molecu­lar genet­ics envir­on­ment, the authors say it can be read­ily adap­ted for ‘almost any plant labor­at­ory research’ – even BY, too, I suspect.

Nigel Chaffey. ORCID 0000-0002-4231-9082

Nigel is a botanist and full-time academic at Bath Spa University (Bath, near Bristol, UK). As News Editor for the Annals of Botany he contributes the monthly Plant Cuttings column to that august international botanical organ. His main goal is to inform (hopefully, in an educational, and entertaining way...) about plants and plant-people interactions.

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