Daily Archives: 24th of September 2010

Modelling root development with signalling control (PMA Special Issue)

Modelling root development with signalling control
Modelling root development with signalling control

There are two major challenges for using functional–structural modelling to study autoregulation of nodulation: reconstruction of legume root architecture and co-ordination of signalling with developmental processes. To meet these challenges, Han et al. use L-studio software and develop techniques for characterising soybean lateral roots, collecting nodule distribution information, simulating root morphogenesis, and synchronising with long-distance root–shoot signals.

New issue, new look, new offer for bloggers and journalists

Annals of Botany October cover

The October edition of Annals of Botany is now available online. As well as the free Plant Cuttings, there’s also a free review of Plant cell biology. From astronomy to zoology. How do you get astronomy and zoology into plants cells? You’ll have to read the review.

There’s a free short communication Did Drosera evolve long scapes to stop their pollinators from being eaten? which we publicised earlier with the press release Sundews just want to be loved.

There’s a new press release out today, Withering well can improve fertility that goes with Marcescent corollas as functional structures: effects on the fecundity of two insect-pollinated plants by Carlos M. Herrera. The papers in the journal are funded either by subscriptions or through Oxford Open so there’s a limit to how much we can give free access too. This is a pain if you want to write or blog about the paper and want to check that I’ve not gone on some strange flight of fancy writing the press release. That’s no longer a problem.

If you want to write about an Annals of Botany paper and you don’t have access to it then we can send you the paper if you’re a science writer. ‘Writer’ includes bloggers, so if you’re a science blogger email us at ANNALSBOTANY [at] le.ac.uk and we’ll get you a copy. This applies to any paper you’d like to write about, not just ones with press releases. I’m working on the principle that an expert in botany is going to see plenty that I’ve missed as potential blog material.

As for the new look, October is on it’s way. It’s getting a bit late for sunflowers in the northern hemisphere so I’ve changed the site here to an autumn theme. I’m told by someone who can recognise different types of trees from quite a long way away that this type of tree is the Larch.

Everyday gripes of a journal editor, part 53: gene or protein?

You can not be serious – some sentences just don't look right without italics

Confession time: one of the main reasons why I chose to study ecology all those years ago was in order to avoid what, to me, were twin peaks of incomprehensibility – biochemistry and genetics. I liked to be able to see what was going on: a plant’s growth, a leaf’s reaction to drought, or stomatal responses to infection were all fine, but when things got subcellular the fog would descend and my mind would wander. So pity my poor chances of comprehending the molecular biology papers that currently abound in the average journal today; sometimes I even struggle to work out whether the author is talking about a gene or a protein… and therein rests my gripe, because there is no reason at all why I should.

OK, conventions do vary a bit from journal to journal, but at a very basic level it seems generally accepted that a gene name should be given in italic type whilst its protein product is given in normal (‘roman’) type. So increased expression of the FLC gene will produce increased amounts of the FLC protein in the cell, a decrease in expression of the MAF2 gene will result in lower amounts of the MAF2 protein. Of course the distinction isn’t needed when the words ‘gene’ and ‘protein’ are present, but clearly you don’t want to repeat them dozens of times in every paragraph – so just use italics instead (and no need to fumble for the ‘italic font’ button: ‘Control + I’ will do the trick in a fraction of the time). And it’s worth being aware that if you don’t make use of italics in your paper then someone else may do so on your behalf: I don’t know of any high-ranking journal that doesn’t carry out some form of editing on accepted papers, and if you don’t make it clear what is a gene and what is a protein then someone else may make a guess on your behalf – and not necessarily get it right, as illustrated by the following sentence that appeared a few years ago in a paper on Arabidopsis: ‘After very long periods of low temperature, however, MAF2 levels decreased and a marked acceleration of flowering occurred’

Now I’m only an ecologist, but I’m not sure the level of a gene can decrease, can it? But am I just being pedantic? In that example it’s pretty clear what is meant, and in terms of the overall effects the gene and the protein are almost synonymous – expression levels of the MAF2 gene decrease so the level of the MAF2 protein in the cell decreases, so what’s the problem? Not much in that simple example, but what about a more complex system where the gene expression increased but some other factor disrupted subsequent production of the protein causing it to decrease, perhaps with several gene/protein systems interacting – would your reader be able to follow it so easily then?

Molecular biology is complicated stuff, so when it comes to clarity every little helps.