Databases (collections of information that are organised ‘so that it can easily be accessed, managed, and updated’) are everywhere these days and, as repositories of data that can be explored by interested parties – and maybe new connections made and insights revealed – they are an extremely useful resource for science. Indeed, access to large data sets is so important to modern-day scientific endeavour that a new journal has recently been established to publish the outcome of such studies. Scientific Data is an open-access, online-only publication for descriptions of scientifically valuable datasets that exists to help you publish, discover and reuse research data and will ‘complement and promote public data repositories’. And in the tradition of science belonging to us all, the journal’s primary article type, the ‘Data Descriptor’, is designed to make your data more discoverable, interpretable and reusable. However, for such journals to achieve their noble and philanthropic aims, the necessary databases of ‘stuff’ need to exist – or be created. One such facility whose birth caught my eye(!) recently was the ClearedLeavesDB, an online database of cleared plant leaf images – its existence and purpose has been highlighted by Abhiram Das et al., who developed it. Leaf vein networks (LVNs) are important to both the structure and function of leaves and there is a growing body of work linking LVN structure to the physiology, ecology and evolution of land plants. Recognising the importance of LVNs, the team developed this digital archive that enables online viewing, sharing and disseminating of collections of images of cleared leaves (which usually have the LVNs enhanced) held by both institutions and individual researchers. We applaud this initiative and trust that its objectives – to facilitate research advances in the study of leaf structure and function, to preserve and archive cleared leaf data in an electronic, accessible format, and to promote the exchange of new data and ideas for the plant biology community – are met.
No, this is not an item about M People, an ‘English house music band which formed in 1990 and achieved success throughout most of the 1990s’, nor about using profane language… Anyway, how would any of that be relevant to a straitlaced, sober, serious botanical news round-up that is the hallmark of a P. Cuttings item? It is about the phenomenon (I don’t think that’s too strong a word) known as ‘Dr M’. If you’ve not encountered this gentleman, then you should – we can probably all learn a little from him in our eternal quest to big-up botany and help to enthuse the next generation of plant biologists (or, at least, attempt to engender plant appreciation into the citizens of tomorrow). Dr M is the moniker of Dr Jonathan Mitchley, botanist and plant ecologist who goes WILD about teaching plant identification at the University of Reading (UK), and also acts as an ecological consultant with RSK Ltd. Looking like one imagines the Peter Pan of phytology should look like, his grinning visage beams botanical radiance upon all who chance upon his various web-based antics. His enthusiasm for all things verdant seems boundless and is evident in his varied offerings, such as his blog, video-based plant ID quizzes and his YouTube-tastic Poaceae song. Maybe all of his outputs may not be to everyone’s taste, but they’re worth a look – you are highly likely to find something you can ‘borrow’ to enhance your own teaching of botany. In any event it’s really uplifting to see Dr M and ‘his people’ having so much botanical fun! As Dr M himself is wont to say, ‘Rock on, Botanists!!!’ Indeed (!).
[The true diehards amongst you might like to consider the extended-play, blooper-enhanced version of the Poaceae song on YouTube. Right, now what is the collective noun for a group of botanists? Answers, on a postcard-sized sheet of herbarium paper, please to… And in breaking news – well it was when this piece was penned – Dr M is now Associate Professor of Field Botany at the University of Reading – Ed.]
It just had to happen, but we didn’t know it would take nearly 150 years to come to fruition. And fruition is an apt word because the creation of a new botanical journal has recently been announced by the publishers behind Nature, the world’s premier general science journal. Imaginatively entitled Nature Plants, this new organ is due to be officially published in January 2015 but already has interweb presence with a blog and can be ‘followed’ on such social media as Facebook and Twitter. Its aim is to provide a fully rounded picture of the most accomplished and significant advances in the plant sciences, and will cover ‘all aspects of plants be it their evolution, development or metabolism, their interactions with the environment, or their societal significance’. Furthermore, along with original research, Nature Plants will also deliver ‘Commentaries, Reviews, News and Views’ from across the full range of disciplines concerned with the plant sciences (i.e. a bit like the Annals of Botany…). However, with topics covered in the journal including (deep breath) ‘agronomy, genomics, biochemistry, metabolism, biofuels, metabolomics, biophysics, molecular biology, cell biology, photosynthesis, defence physiology, development, plant–microbe interactions, disease resistance, proteomics ecology, secondary metabolism, economics, sociology, evolution, symbiosis, food security, systems biology, forestry and water use’, I do hope they leave something for other – more established – botanical journals, such as the Annals of Botany!
[Have others heard that the original Nature – in keeping with its soon-to-be somewhat impoverished science coverage – is being retitled Nature Cosmology, Palaentology and Non-botany? Whilst we wish this new venture well, it will be interesting to see if anybody publishes in the new journal because, and despite the undoubted cachet and kudos associated with the word Nature in the article’s citation, it won’t have an Impact Factor (IF) for a few years. Now, who wants to risk having publications on their CV in journals with no IF with potential damage to promotion prospects and career advancement (not that IFs should be used for such purposes – see e.g. EASE statement on inappropriate use of Impact Factors? Just saying. – Ed.]
The ‘alpha’ category is widely regarded as the best of its kind; think of alpha (males) in the context of animal behaviour and Aldous Huxley’s Brave New World, an α+ grade on your exams or the sports cars from Alfa Romeo. But omega – right at the other end of the Greek alphabet – is also merit-worthy, especially when it’s omega fatty acids (FAs), which are polyunsaturated FAs needed for human metabolism. However, since they cannot be made de novo by the human body – and are therefore considered ‘essential’ – it is necessary to acquire them in the diet.
Two of the three essential omega FAs needed for human metabolism – Eicosapentaenoic acid (EPA) and Docosahexaenoic acid (DHA) – are derived from marine sources, such as fish. The third – alpha-Linolenic acid (ALA – which, despite its name, is still an omega fatty acid!) comes from plant products and is used in the body to produce EPA, which in turn is used to generate DHA. One way of getting your essential omegas is to consume milk produced by cows that have grazed on fresh grass/red clover, whose milk has been shown to increase in ALA as a result. But if you are milk-averse or lactose intolerant this won’t work for you. Another dietary strategy is to eat fish. However, with concerns about dwindling fish stocks, and recognising that fish themselves actually get their omegas from the algae that they have ingested, a more imaginative – and plant-based – avenue is being promoted.
Using a GMO (genetically modified organism) Noemi Ruiz-Lopez et al. have successfully demonstrated high-level accumulation of fish-oil omega-3 long-chain polyunsaturated fatty acids in a transgenic (which includes at least one gene from an alga…) oilseed crop plant. Using heterologous genes (i.e. genes from organisms different to the host crop species) the Rothamsted Research (Harpenden, UK) -based team have developed Camelina sativa (like arabidopsis, a member of the Brassicaceae) whose seeds accumulate up to 12 % EPA and 14 % DHA (which levels are equivalent to those in fish oils). On the back of expectations that this could represent a sustainable, terrestrial source of these fatty acids, Rothamsted Research has applied to Defra (the UK government’s Department for Environment, Food and Rural Affairs) ‘to conduct a field trial of Camelina plants that have been genetically modified to produce omega-3 oils that may provide health, environmental and societal benefits’. Interestingly, one of the enzymes in the 5-gene cassette used to genetically manipulate EPA levels in the plant is derived from Phytophthora infestans – the potato blight-causing oomycete (definitely NOT a fungus) which infamously caused so much devastation to the potato crop of Europe in the 19th century. Maybe this is an opportunity for that notorious plant pest to do some good for a change! And something to ponder as you fry your naturally omega FA-enriched fish in GM-enhanced camelina oil…? Regardless, let us hope that false flax (an alternative common name for the plant) does not give false hope but, rather, provides ‘gold-of-pleasure’ (another of its common names). And that this 21st century fish oil project has more to offer than the 19th century’s over-promising, under-delivering pedlars of ‘snake oil’! Here’s a video showcasing the work at the 2014 UKPSF meeting.
[For more on the proposed GM trials, there is a dedicated Questions and Answers Section on the Rothamsted Research website. But what we really want to know is whether there is a hidden agenda to use the GM-crop to produce jet fuel for the F-22 raptor supersonic fighter aircraft, which apparently can fly very well using biofuel produced from Camelina… In which case, maybe GM stands for Go Mach – Ed.]
[Update - since this piece was originally penned, not only has the GM trial been approved but it has taken place and the crop harvested. It is anticipated that the results will be published in an open access journal later this year - Ed.]
As well-read botanists, readers of this blog site are probably quite knowledgeable on the subject of epiphytic plants, which are plants – such as mosses, liverworts, ferns, cacti, orchids and bromeliads – that live on the outer surface of other plants. However, most of us are probably less familiar with the concept (and reality…) of endophytic plants, which live within the body of other plants. Or, where we’ve heard of the term it is likely to be more in the context of endophytic fungi or bacteria. Strange as it may seem, endophytes can also be found amongst the angiosperms. And, by way of giving a ‘shout-out’ for those curious plants who’ve adopted this most couch-potato of lifestyles, I’m pleased to advise that a new key (plus consideration of the systematics of this worldwide family, a map, and colour photos of most species’ sexual organs…) to the Apodanthaceae (a family of two genera comprising 10 species) has been published by Sidonie Bellot and Susanne Renner.
Living as endo-parasites permanently inside trees or shrubs of the families Salicaceae or Fabaceae, these plants emerge only to flower and fruit; consequently the Apodanthaceae is among the least-known families of flowering plants. Since the plants do not carry out any photosynthesis of their own, they are completely dependent upon their host for their nutrition (i.e. they are also holoparasitic). Endophytes, curious organisms(!). However, probably more famous is the equally holoparasitic relative of Apodanthes and Pilostyles, Rafflesia. Notwithstanding the smallness of its vegetative body, R. arnoldii has the honour of producing a flower >100 cm in diameter and weighing up to 10 kg. Amongst its other claims to fame – or should that be infamy? – is the smelliness of the flower’s odour, which is reminiscent of rotting flesh and which has earned it the rather ghoulish appellation of ‘corpse flower’. Furthermore, as well as stealing nutriment from its host, Rafflesia has also famously ‘borrowed’ many genes from the vine within which it resides, by the non-reproductive DNA transmission process known as horizontal transfer of genes. So, and although allegedly named in honour of Sir Thomas Stamford Raffles (both the ‘Father of Singapore’ and the ‘Father of the London Zoo’), this curious case of karyo-kleptomania seems more reminiscent of the antics of one A. J. Raffles, ‘gentleman thief’! And there’s even more bizarre genetic antics with the ‘suggestion’ (scientist’s code ‘for highly likely probability’…) that R. lagascae may be devoid of a chloroplast genome. I don’t know – flowering plants devoid of leaves, roots, shoots and some without chloroplast DNA. Are they really plants? Discuss!
Of the plethora of aspects of plant growth and development that the hormone (OK, plant growth regulator…) auxin is implicated in/involved with (e.g. embryo development, leaf formation, phototropism, gravitropism, fruit development, abscission, root initiation and development…), surely one of the most enduring is apical dominance.
Apical dominance is the phenomenon whereby the outgrowth of buds on the side of a shoot is suppressed in favour of growth by the apical bud (hence its name…). Maintenance of this suppression has long been assumed to be due to the production of auxin by the apical bud and its transport down the stem, which effectively keeps the lateral buds in check. Understandably, outgrowth of lateral buds upon removal of the apical bud – and its associated auxin-production and outflow – is a key bit of evidence for the role of auxin in this phenomenon.
Just as you should never (ever…) take anything for granted in science (or anything else), it’s rather satisfying to note that work by Michael Mason et al. – and rather pleasingly from ‘down under’ – has seemingly burst that little bubble of plant physiological certainty. The primarily Australia-based team show that bud outgrowth following apical bud removal takes place >24 hours before changes in auxin content in the adjacent stem, i.e. ‘initiation of bud growth after shoot tip loss cannot be dependent on apical auxin supply’. However, upon removal of the shoot tip, sugars not only accumulate in axillary buds, but do so within a timeframe that correlates with bud release. Rather than auxin being the main lateral-growth suppressant, the team conclude that enhancement in sugar supply is both necessary and sufficient for suppressed buds to be released from apical dominance. Ah, the sweet smell of success? G’day Bruces, Sheilas… and ‘possums’ everywhere!
[And if this item has initiated a craving for more sugar-based botanical items, may I recommend Winnie Lin et al.’s Letter investigating nectar secretion and the role of the sugar transporter, aptly named SWEET9? – Ed.]
It has oft been claimed that a picture is worth a thousand words. In the case of certain images in Klementina Kakar et al.’s study entitled ‘CLASP-mediated cortical microtubule organization guides PIN polarization axis’ it seems quite clear that many more than a thousand words have been written about them. Why? The normally genteel world of botanical research has been shaken, stirred and shocked to its very core by a retraction of that paper – which purported to identify the molecular machinery that connects the organisation of microtubules to the regulation of the axis of polarisation of auxin-transporting PIN proteins (which membrane-sited molecules are needed for transport of the plant hormone auxin across plasma membranes and thereby help to maintain polarity of growth and development within the plant). Relating as it does to fundamental aspects of plant growth and development and such phenomena as gravitropism, this is an important finding and understandably published in a very high-impact and influential journal. So what’s gone awry? A retraction is, after all, a very serious state of affairs. Well, and in the words of the same four authors of the original paper, ‘after re-examination of this Letter [this is how Nature articles are formally described], concerns with some of the reported data were raised. It was found that two confocal images were near-identical in panels of Figure 3 and two confocal images were re-used in panels of Figure 4, and that some gel images were inappropriately generated by cutting and pasting of non-adjacent bands. Therefore, we feel that the most responsible action is to retract the paper. We sincerely apologize for any adverse consequences that may have resulted from the paper’s publication’. For more on this, visit the various items at the Retraction Watch* website. Fortunately – for those unaware of this from media reports, etc, but who might otherwise come across the article in their literature searches, the PubMed entry for the original Nature paper does make mention of its subsequent retraction, and provides a link to the retraction notice. Although I don’t know if the paper’s retracted status is indicated on all search engines… However, in the scrabble to find appropriate literature to cite in one’s work, one might overlook that notification. Is this therefore a weakness in the otherwise laudable retraction process/system whereby subsequent readers of those papers may not be aware of their retraction? Maybe we need a form of historical revisionism reminiscent of the rewriting of history in George Orwell’s classic novel Nineteen Eighty-Four to expunge such items from the record totally so that they’re never ever found…? Hmm, what would historians of science make of that? Do let us know!
* Retraction Watch is a blog that reports on retractions of scientific papers. Launched in August 2010 it is produced by science writers Ivan Oransky (executive editor of Reuters Health) and Adam Marcus (managing editor of Anesthesiology News).
[For more on the costs associated with retractions, check out Tracy Vence's commentary at The Scientist. And with such sobering news, if you are concerned that retractions can unduly affect one’s career, Virginia Gewin has some words of comfort. But, if you want more retraction stories, why not check out last year’s ‘Top 10’? – Ed.]
Trees, those magnificent, organic, large – sometimes huge – woody constructions continue to fascinate and inspire all who stop, stand and stare up (and up, and up…) at them. So here’s a selection of tree-based items to maintain – or maybe even initiate? – the phenomenon of arborifascination. But first a question: why did the three-toed sloth come down from the trees?
Answer: to defecate! Sloths are considered to be amongst the most, well, er, slothful of animals that, anecdotally, spend most of their time in trees, doing ‘not a lot’, apart from eating tree leaves [they are arboreal herbivores, after all; Tree Use No. (TUN) 1]. However, not only is this descent to the ground energy-consuming, it also exposes the sloth to potential predators; so why would they risk it? Work by Jonathan Pauli et al. may have the answer to this otherwise inexplicable behaviour. Three-toed sloths* harbour moths, inorganic nitrogen (N) and algae (e.g. green algae Trichophilus spp.) within their fur. The lipid-rich algae are eaten by the sloths and presumably supplement their diet of leaves. By leaving the tree for defecation, the fur-residing moths are transported to their oviposition (egg-laying) sites in sloth dung, which subsequently facilitates further moth colonisation of sloth fur. Since those moths are ‘portals for nutrients’, levels of inorganic N (potentially from moth excreta) in sloth fur increase, which in turn fuels algal growth. As the researchers conclude, ‘these linked mutualisms between moths, sloths and algae appear to aid the sloth in overcoming a highly constrained lifestyle’. Wow! I will never look at a three-toed sloth in quite the same way again.
Also challenging perceived wisdom is work by Marc Ancrenaz et al. Traditionally, orangutans (the world’s largest arboreal mammal) are assumed to be obligate arborealists, swinging seemingly effortlessly from tree to tree (TUN 2) as they navigate their lofty aerial neighbourhood. However, observations of terrestrial activity by these primates in the wild begs the question, why? Hitherto this activity was considered to be a response to habitat disturbance, but Ancrenaz et al. found no difference in instances of this behaviour in disturbed versus non-disturbed areas. They therefore propose that terrestrial locomotion is part of the Bornean orangutan’s natural behavioural repertoire and may increase their ability to cope with at least smaller-scale forest fragmentation, and to cross moderately open spaces in mosaic landscapes. So, it seems that even orangutans can have a bit too much of the ‘high life’ at times.
Finally, a terrestrial–aquatic organism that’s going up in the world. Reviewing evidence of tree-climbing activity in extant crocodilians (crocodiles and alligators), Vladimir Dinets et al. suggest it is much more widespread than previously considered and ‘might have multiple functions’, e.g. as an alternative site for thermoregulation (TUN 4), or increased detectability of prey (TUN 5). So, there you have it, ‘tons’ of alternative tree uses! Trees, helping to make the world an even more amazing place.
* Two-toed sloths don’t go in for this more energetic activity – and have lower densities of moths, lower N levels and reduced algal biomass in their fur…
Botany is not without its mysteries. And one that’s previously eluded solution for 600 years or so is that of the so-called Voynich manuscript, an illustrated codex (a book made up of a number of sheets) consisting of about 240 pages, hand-written in an unknown writing system. Carbon-dated to the early 15th century, there are nevertheless suggestions that it might not be an ancient language but a hoax. And, despite containing many images of plants and other biological entities, its message and purpose has remained obscure (although an imaginative botanical interpretation is that it might represent a mediaeval plant physiology treatise). However, Stephen Bax, Professor of Applied Linguistics at the University of Bedfordshire (UK) has now claimed to have begun to decipher the manuscript’s text.
Progress is slow, but amongst the first few words to have been revealed are juniper, taurus, coriander, Centaurea, chiron, hellebore, Nigella sativa, kesar and cotton. A confident Bax declared, ‘… my research shows conclusively that the manuscript is not a hoax, as some have claimed, and is probably a treatise on nature, perhaps in a Near Eastern or Asian language’. Clearly, some way to go before we have a final, complete version, and can use it as a set text in plant physiology classes (so don’t throw out Taiz & Zeiger’s Plant Physiology just yet!). But another ancient manuscript whose purpose is more obvious is the Tractatus de Herbis (‘Treatise on Medicinal Plants’), a manual of materia medica [‘a Latin medical term for the body of collected knowledge about the therapeutic properties of any substance used for healing (i.e., medicines)’] compiled during the 15th century. This tome has been reproduced in a limited edition facsimile replica of 987 copies (price available ‘on request’, though I suspect that if you’ve got to ask how much it is, you can’t afford it…). This limited edition is accompanied by a full-colour commentary volume by Alain Touwaide,Research Associate of the Department of Botany at the Smithsonian National Museum of Natural History, USA and Scientific Director of the Institute for the Preservation of Medical Traditions at the Smithsonian in Washington, DC (USA).
[If you want to view the Voynich manuscript – for free! – it is available on-line. Even if the majority of the words are elusive, the images are quite wondrous… For more Voynich images and interpretations – e.g. putative plant identifications – Ellie Velinska’s blog is worth a visit – Ed.]
As if the task of explaining the details of the ‘normal’ C3 Calvin Cycle of photosynthesis (P/S) to our students isn’t hard enough, we also need to appraise them of C4 P/S – with its spatial separation of initial CO2 fixation into organic acids in mesophyll cells and its subsequent release and re-fixation via the enzyme Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase) into the photosynthetic Calvin Cycle proper within bundle sheath cells*. As testing and trying as that is, nature always has to go one ‘better’, and ‘spoil’ things. So, the fin-de-millennial recognition of a variant of this C4 P/S in which initial CO2 fixation into 4-carbon acids and its subsequent release and re-fixation into the Calvin Cycle of C3 P/S takes place within a single cell is kind of unwelcome (no matter how fascinating it is!). Well, anyway, it exists – in such higher plants as Suaeda (Borszczowia) aralocaspica, Bienertia cycloptera, B. sinuspersici and B. kavirense, all in the Chenopodiaceae (now within the Amaranthaceae) – so we need to get over it, and try and understand it. And that’s what Samantha Stutz et al. have been doing. Although these plants perform spatial separation of the two CO2 fixation events within a single mesophyll cell, they do so using two distinct – dimorphic – chloroplasts. Already known is that light is necessary for development of the dimorphic chloroplasts in cotyledons in B. aralocaspica. In the dark they only have a single structural plastid type (which expresses Rubisco): light induces formation of dimorphic chloroplasts from the single plastid pool, and structural polarization leads to the single-cell C4 syndrome. The aim of Stutz et al.’s study was to determine how growth under limited light affects leaf structure, biochemistry and efficiency of the single-cell CO2-concentrating mechanism. Overall, the team found that the fully developed single-cell C4 system in B. sinuspersici is robust when grown under ‘moderate light’. Where might this sort of work be going? Well, whilst it is interesting for its own sake – the pure pursuit of knowledge – it has a more applied dimension too. Central to all of this single-cell photosynthetic biology and biochemistry is the concept of CCM, carbon-concentrating mechanisms, whereby levels of CO2 are increased in the vicinity of Rubisco so that it favours photosynthesis – CO2-fixation – over photorespiration (so-called C2 photosynthesis) which uses O2 as substrate and consequently reduces photosynthetic efficiency. Well, in bids to replicate some of the greater photosynthetic efficiency of C4 plants (largely by virtue of their diverse CCMs…), an attractive notion is to engineer various forms of CCM into C3 crop plants. This approach is exemplified in the work of Mitsue Miyao et al., where they attempted to exploit enzymes of the facultative C4 aquatic plant Hydrilla verticillata (which engages in single-cell C4 P/S) to convert rice from its typical C3 P/S into a single-cell C4 photosynthesiser. Although they didn’t achieve their goal (and it’s good to know that ‘negative’ results can still be published!), their article is an interesting and soul-bearing account of the lessons learned in this work. As we continue our quest for that elusive boost in photosynthetic yield, we’ll no doubt continue to exploit any biochemical variant on the photosynthetic theme that nature displays. Which begs the question: how many more variants exist amongst the 325,000 species of flowering plants (let alone all the algae and other members of the plant kingdom)? Seems like we need more plant anatomists, plant biochemists, plant physiologists – as well as plant taxonomists (see my last post on this blog) – after all!
* That’s C4 P/S as opposed to CAM (Crassulacean acid metabolism), which is also a version of C4 P/S but which involves temporal separation of the same two carbon-fixation events in plants such as pineapple, cacti and agave. However, CAM is hardly ever referred to as C4 P/S because the all-powerful Zea Supremacy lobby has commandeered the term for that spatially separated C4 version found in plants such as maize… but don’t get me started on that!
[Intriguingly, and in addition to its dimorphic chloroplasts, Suaeda aralocaspica has dimorphic seeds, which exhibit distinct differences in dormancy and germination characteristics. Now, they say that things come in threes, so what’s the third dimorphy about this iconic species…? – Ed.]