Monthly Archives: May 2012

The clue’s in the title (but is it?)

Image: Petr Heřman/Wikimedia Commons.

Image: Petr Heřman/Wikimedia Commons.

With no disrespect intended to the authors – Takashi Yaeno et al. – who, at first glance, is able to tell me what the article entitled, ‘Phosphatidylinositol monophosphate-binding interface in the oomycete RXLR effector AVR3a is required for its stability in host cells to modulate plant immunity’  is about? I know, I struggled with it, too. And if it wasn’t for the user-friendlier text of such science-news-disseminating sites as PhysOrg.Com – which more-informatively summarises that paper thus, ‘Phytophthora infestans [sadly, that scientific name not italicised], the causal agent of late blight, has evolved to overcome fungicides and major resistance genes that have been bred into commercial potato cultivars. In order to dampen the immune response of its host, P. infestans secretes molecules called disease effectors at the site of infection’ – this eminently newsworthy piece of science would have completely passed me by. OK, I suppose the clue in the title is the term ‘oomycete’, which often – and rightly so on this occasion – rings alarm bells in my mind because I associate it with Phytophthora infestans (an organism that once-upon-a-time was numbered amongst the fungi), which causes a devastating disease of potatoes, potato late blight. Which disease historically – and infamously – caused tremendous suffering in Ireland and is oft-cited as the cause of one of the world’s most famous diasporas that saw hundreds of thousand of Irishmen, -women and -children emigrating to North America in the mid-19th Century.

And the point of this item is to highlight the debate about the importance of the title to a scientific article. Well, there really isn’t any debate – titles are important, as aired in a blog by ‘graduate student bryologist’ Jessica Budke. Musing on the merits of humorous or otherwise titles, Budke cited some intriguing studies that examined these testy titular topics. Hamid Jamali and Mahsa Nikzad in their straightforwardly entitled, ‘Article title type and its relation with the number of downloads and citations’ analysed more than 2000 articles from PLoS journals (Public Library of Science). They concluded that, ‘articles with question titles tended to be downloaded more but cited less than the others. Articles with longer titles were downloaded slightly less than the articles with shorter titles. Titles with colon tended to be longer and receive fewer downloads and citations. As expected, number of downloads and citations were positively correlated’. Also cited by Budke, Itay Sagi and Eldad Yechiam’s equally non-sensationalistically entitled paper, ‘Amusing titles in scientific journals and article citation’ examined articles in Psychological Bulletin and the Psychological Review. They found that, ‘articles with highly amusing titles… received fewer citations’. Interestingly, a responder to Budke’s blog highlighted the case of Tom Rees who has become increasingly irked by titles featuring colons. Hmmm, one of the worst cases of colonic irritation I’ve come across… And, to some extent contradictorily, Thomas Jacques and Neil Sebire – who analysed medical journals – found that, ‘The number of citations was positively correlated with the length of the title, the presence of a colon in the title and the presence of an acronym’.

What can we deduce from the foregoing? You cannot necessarily predict what a good title will be, but that medical types like colons (well, they would, wouldn’t they?). So, Titles: All a bit too hit-and-miss? Maybe, but let’s conclude with some sage words of advice from SciDev.Net, ‘A title should be the fewest possible words that accurately describe the content of the paper’. And – in that vein – one is pleased to report that a subsequent paper from ‘the group of Sophien Kamoun at The Sainsbury Lab’ that began this item has a much-more-obvious-what-it’s-about title in a follow-up article by Tolga Bozkurt et al.: ‘Phytophthora infestans effector AVRblb2 prevents secretion of a plant immune protease at the haustorial interface’. But let’s be honest, though: the main interest in PNAS vol. 108, issue No. 35 – which contained the ‘Yaeno et al. oomycete paper’ – was the fungus-related lager yeast item by Diego Libkind et al.  soberly entitled – but maybe coming to a colon near you…soon?  – ‘Microbe domestication and the identification of the wild genetic stock of lager-brewing yeast’. Which tells how, ‘in the 15th century, when Europeans first began moving people and goods across the Atlantic, a microscopic stowaway somehow made its way to the caves and monasteries of Bavaria’. Cheers!

[Given that – taken together – their titles break every known rule, I intend keeping a very close eye on the citation/download rates of my own Plant Cuttings’ items!] [So do I(!) – Ed.]

Floral traits mediate the pollination role of bees

Floral traits mediate the pollination role of bees

Floral traits mediate the pollination role of bees

Pollen-collecting bees are the most important pollinators globally, but are also the most common pollen thieves and can significantly reduce plant reproduction. Hargreaves et al. investigate whether floral characteristics mediate the roles played by bees – ranging from avid pollen thieves to the plant’s only pollinators – for ten species of Aloe. Pollen theft is promoted by nectar inaccessibility and strong dichogamy, which discourages visits to female-phase flowers. Furthermore, displays of many flowers facilitate deposition of mostly incompatible self-pollen. Thus species-specific floral and inflorescence characteristics govern the efficiency of pollen-collecting bees as pollinators of aloes.

Don’t underestimate the druse

Image: Harry T. Horner.

Image: Harry T. Horner.

Although known from plants for a long time, the function of mineral inclusions – included amongst the so-called ergastic substances of old – remains speculative. Frequently composed of calcium oxalate and rather toxic, it has been speculated that druses may deter would-be herbivores, and/or act as store of calcium – often needed in large amounts as a secondary messenger in many signalling pathways within plants.

Well, another role is suggested by Harry (‘Jack’) Horner in leaves of certain succulent Peperomia species. Horner hypothesises that vacuole-located druse crystals in the palisade mesophyll cells – which are situated below recently discovered ‘skylight-like’ regions in the overlaying hypodermal cell walls – may help to focus light on to the chloroplasts that surround the crystals (see figure above). This arrangement may be an adaptation that permits more efficient photosynthesis in the low-light environment where these plants are found.

You’ll need to read the paper – in June’s Annals of Botany, and which is free access – to appreciate the full story, but this elegant structure–function study dramatically demonstrates how much still awaits our discovery and understanding. Plus, this paper was one of an extremely select few – ‘one in a thousand manuscripts’ – accepted for publication without any changes! So, like his namesake of old, our modern-day Jack Horner has produced a real plum: Read and enjoy.

Tales of tethers and tentacles: golgins in plants

Protein transport through the Golgi apparatus

cc JCB

As plant Golgi bodies move through the cell along the actin cytoskeleton, they face the need to maintain their polarized stack structure whilst receiving, processing and distributing protein cargo destined for secretion. Structural proteins, or Golgi matrix proteins, help to hold cisternae together and tethering factors direct cargo carriers to the correct target membranes. This review focuses on golgins, a protein family containing long coiled-coil regions, summarises their known functions in animal cells and highlights recent findings about plant golgins and their putative roles in the plant secretory pathway.

 

Osterrieder, A. (2012) Tales of tethers and tentacles: golgins in plants. Journal of Microscopy, doi: 10.1111/j.1365-2818.2012.03620.x

QTLs for seed yield under different P supply

QTLs for seed yield under different P supply

QTLs for seed yield under different P supply

Low levels of phosphorous in soils seriously limit seed production of Brassica napus. Ding et al. investigate phenotypic variation of seed yield and yield-related traits in B. napus plants grown with contrasting supplies of P, and identify a total of 74 putative quantitative trait loci (QTLs). The results suggest that different genetic determinants are involved in controlling yield and yield-related traits under normal and low P conditions, and the QTLs detected under reduced P supply may prove useful in marker-assisted selection.

Acidic alpha-galactosidase in tobacco floral nectar

Acidic alpha-galactosidase in tobacco floral nectar

Acidic alpha-galactosidase in tobacco floral nectar

Most floral nectar proteins (nectarins) are reported to function in nectar defence, particularly for insect-pollinated outcrossing species. Zha et al. compare nectarin composition in selfing common tobacco (CT; Nicotiana tobaccum) to outcrossing ornamental tobacco plants and find that the most abundant nectarin in CT nectar is an acidic alpha-galactosidase that has not been detected in the nectar of outcrossing sister species. CT fruits do not develop intact skin with galactose inhibition of a-Gal activity in the nectar. The results indicate that floral nectarins in selfing species maintain their functional significance in reproductive organ development.

Resistance to pathogens under variable temperatures

Resistance to pathogens under variable temperatures

Resistance to pathogens under variable temperatures

The biotic and abiotic environment of interacting hosts and parasites may vary considerably over small spatial and temporal scales. Jorgensen examines the effects of differing temperature and soil nutrient conditions on powdery mildew infection of Arabidopsis thaliana, and finds that there is a strong potential for a heterogeneous environment to change the resistance capacity of A. thaliana genotypes, and hence the direction and magnitude of selection in the presence of the pathogen. Transcription levels of RPW8, a resistance-conferring gene, increase after infection and vary between environments, but there is no tight association between transcription and resistance levels.

Putative phytological pugilism (probably…) [or, One species – two genomes?]

Image: Muhammad Irshad Ansari/Wikimedia Commons.

Image: Muhammad Irshad Ansari/Wikimedia Commons.

In the genteel world of botany, one may be surprised to discover that – occasionally! – disagreements can arise, and that tempers can get just a little heated. Well, in an attempt to expose the darker side to the otherwise seemingly tranquil and sweetness-and-light domain of plant biology – and incidentally to show what the ‘-phyte’ suffix really means! – I offer the following cautionary tale. When a species’ genome – draft or otherwise – is published, you assume that to be definitive. But in the case of pigeon pea (Cajanus cajan – ‘an orphan legume crop of resource-poor farmers’) it seems that this may not be the case.

I was interested to note that a draft of the pigeon pea genome had been published by Rajeev Varshney and co-workers (Nature Biotechnology). And reading that the report ‘presents the genome of the first orphan legume crop and the second food legume (after soybean)’, I was happy to leave it at that. However, noting that C. cajan ‘plays a substantial role in the livelihood of resource-poor smallholder farmers in marginal environments’, I was keen to find out more about this crop plant and duly consulted the oracle – aka Wikipedia (I can anticipate/sense your communal shudder as I write/you read those words, but I’m allowed to do this – see ‘Embrace Wikipedia!(?)’). Well, I certainly found more than I was expecting, including this gem, ‘The first draft of pigeon pea genome sequence was done by a group of 31 Indian scientists from the Indian Council of Agricultural Research under the leadership of Nagendra Kumar Singh. The paper is published in one of the Indian journal’ [sic]. I don’t know who contributed to the Wikipedia entry, but I tracked down the article referred to – by Nagendra K. Singh et al. (Journal of Plant Biochemistry and Biotechnology), and entitled, ‘The first draft of the pigeonpea genome sequence’. Interestingly, both papers sequenced pigeon pea variety ‘Asha’, but Singh et al.’s was received by the journal on 2nd July 2011, whereas Varshney et al.’s wasn’t received until… 19th July 2011. (Interestingly, Singh et al.’s paper wasn’t cited by Varshney et al. – but you wouldn’t necessarily expect it to be since both manuscripts were received within a few days of each other…). But, as Varshney et al. opine, ‘This reference genome sequence will facilitate the identification of the genetic basis of agronomically important traits, and accelerate the development of improved pigeonpea varieties that could improve food security in many developing countries’. So, whatever the ins-and-outs or rights-and-wrongs of this incident – and we must surely recognise that this has ‘put the cat amongst the “pigeons”’ – isn’t it good that we have such a great genomic resource for this crop plant (that I suspect many of us had probably not heard much about before)? Surely, we can all agree on that?

Well, maybe not. Ultimately, and regardless of who achieved this feat first, how close are the two published genomes? Are they the same? If not, is one more ‘correct’ than the other? Which one should be used to do further work with this important legume, known as ‘the poor man’s meat’?

[Should you desire to read more about this ‘Controversy over pigeonpea genome’, visit http://agrariancrisis.in/2011/11/09/controversy-over-pigeonpea-genome/ or http://www.jamesandthegiantcorn.com/2011/11/26/bad-blood-on-pigeonpea/ – Ed.]

Bullock Ploughing (plowing) in Ethiopia

 

Leaning bullock plowing in Ethiopia

Learning bullock ploughing in Ethiopia

I added a new skill to my CV last week. Most of the farmland of Ethiopia is ploughed with bullock ploughs (plows). One man and two bullocks can plough a quarter of a hectare, about 0.6 acre, per day. This area is known as a Timad and the area is used as a basis for measurement of yield. The video shows two different ploughing teams, starting with one in very stony soil. Note the calls used to control the bullocks. The second series shows another team: they were moved to a flatter area so that I and other scientists could try our hands at ploughing. It is done with one hand on the wooden plough and one holding (or, in my case, tripping over) the whip. My attempt is shown from 1.50 on the video, much to the amusement of the local children. The cattle knew their job and were easy to turn, but were a bit unsettled by the number of people around them. At the end I manage to knock out the wooden mould-board, and the plough becomes uncontrollable. As always, a ferenji (foreigner) accumulates a score of children around him, no matter how remote the area seems to be. The British horse-ploughs I have used have two handles, making them slightly easier to control (and also nearer sea level: the extra exertion needed at 2664m, 8700 feet altitude, is heard by my breathlessness in the video!), but the Ethiopian plough seemed to be less disturbed by hitting large stones.

Correction: 23/5/12: Timad is the term for the area ploughed by a pair of oxen in one day – when the land is soft. The area has been formalized using 50m ropes.

Post-harvest transcriptional changes in onion

Post-harvest transcriptional changes in onion

Post-harvest transcriptional changes in onion

During the transition from endo- to eco-dormancy and subsequent growth, the bulb of onion (Allium cepa) changes from a sink organ to a source, but the mechanisms controlling these processes are not fully understood. Chope et al. carry out detailed analysis of whole-bulb physiology, biochemistry and transcriptional changes in response to sprouting and provide evidence that the monosaccharide-to-disaccharide ratio and zeatin riboside concentration are important factors in discriminating between sprouting and pre-sprouting bulbs. The results also suggest that commercial curing temperatures could be reduced without detrimental effects.