Category Archives: News

Sponsor a genome…?

Image: Kurt Stüber/Wikimedia Commons.

Image: Kurt Stüber/Wikimedia Commons.

Crowdsourcing – ‘the practice of obtaining needed services, ideas, or content by soliciting contributions from a large group of people, and especially from an online community, rather than from traditional employees or suppliers’ –was the name of the game a few years ago. And in a biological context it was famously exploited to investigate protein folding using the program/‘game’ FoldIt. And so skillful have participants in this exercise become that their combined talents are now being exploited to design completely new proteins, such as new catalysts for photosynthesis.

Helping plant science we also now have crowdfunding, ‘the collection of finance from backers — the “crowd” — to fund an initiative and which usually occurs on Internet platforms’. And an intriguing example of this phenomenon is the call for funds to help sequence the genome of Azolla filiculoides by a team based at Professor Kathleen Pryer’s Seed-Free Vascular Plants laboratory at Duke University (Durham, North Carolina, USA), in collaboration with Professor Paul Wolf at Utah State University (USA). The funding opportunity is hosted by the appropriately named ‘Experiment’, a ‘platform for enabling new scientific discoveries’. Although you might expect universities to be funding the research, that has become increasingly difficult to secure and might not always be forthcoming, especially in cases of ‘risky’ projects. That’s where organisations such as Experiment, which exists to help secure funding that will allow new ideas to get off the ground, especially ‘the innovative and high-risk ideas with the biggest impact’, come into their own. Acting primarily as a shop window, Experiment advertise projects to would-be sponsors – who in true egalitarian style can be anybody, true citizen science in action – and only charge a fee for their services when the project becomes fully funded. And at 8% of the funding total secured that fee is much lower than normal university overhead charges, which take large shares of research funding provided by more traditional sources such as government-funded research organisations!

Anyway, back to the Azolla project. The modest sum of US$15 000 is sought to generate a draft sequence of the genomes of Azolla and its symbiotic N-fixing bacteria, with a view to understanding the two-way, inter-kingdom language that codes for the molecular machinery underlying this symbiotic partnership, and possibly tailor it to suit our needs. Why? Azolla is a ‘superorganism’, consisting of not just the fern but also a diverse array of symbiotic bacteria. It is this unique microbiota that converts nitrogen into organic forms and makes Azolla a perfect bio-fertilizer. In a world where we are ever more concerned about pollution by increasing use of synthetic fertilisers to increase crop yields to meet an increasing demand for food by a growing human population, you might think that this is the sort of project that should be funded by tax dollars extracted from the populace by governments, rather than expecting their already-taxed citizenry to dig into their own pockets effectively twice over. But it always pays to look at the fine print: ‘Genomic sequencing of this unique Azolla–Nostoc system would cost well under $1 million’. Whilst $15k is well under $1 million, I suspect the final figure required will be much closer to $1 million than $15k, which I guess is what’s hinted at behind the text ‘as a start, the funding of $15 000 will get us reasonably good quality genomes [P. Cuttings’ emphasis] for the Azolla superorganism that can jumpstart various exciting research programs’ in the project’s ‘budget overview’. Maybe more traditional sources of funding will pick up the remaining US$985 000 if the project’s potential is demonstrated on the shoestring budget? If only because, although approximately US$1 million is considerably more than the $15 000 sought, that’s ‘far less than the $8 billion each year that US farmers pay for nitrogen fertilizer’ – much of which finds its way into rivers and streams, damaging delicate water systems. This small step toward potentially helping crops to use less synthetic nitrogen could benefit farmers’ bottom lines, the environment and the prices we pay for food’. Hear, hear! And as I write this on 9th June 2014 there are 32 days left to pledge and add to the then-current total of US$1625. Good luck securing the rest of the funding!

 

[What we haven’t got space to go into here – but which also emphasises another unique characteristic of Azolla – is the role it played in global cooling in the Arctic Azolla Event of 50 million years ago. A famously fascinating fern, indeed! – Ed.]

Clear way ahead for leaf research

Image: Benjamin Blonder/Cleared Leaf Image Database.

Image: Benjamin Blonder/Cleared Leaf Image Database.

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 physiologyecology 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.

M people and the ‘B’ word…

Image: Wikimedia Commons.

Image: Wikimedia Commons.

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 blogvideo-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.]

Deep sequencing coming for three taxa at key phylogenetic nodes

Following his recent visit to Cambridge, Josh Mylne (UWA) will be collaborating with Jill Harrison (Cambridge) and Kingsley Dixon (Perth Botanic Garden) to sequence the transcriptomes of three rare taxa at key phylogenetic nodes.

Kingsley collected the lycophytes Phylloglossum drummondii and Isoetes drummondii and the basal angiosperm representative Trithuria bibracteata from Alison Baird Reserve, Kenwick in Western Australia this week.

Lycophytes from the Alison Baird Reserve.

Isoetes drummondii (A,D), Phylloglossum drummondii (B,E) and Trithuria bibracteata (C,F) collected from the Alison Baird reserve.

Although lycophytes formed the dominant land plant tree flora in coal swamps that existed over 300 million years ago,[1] they are now small herbs forming three distinct relict lineages.[2] Whilst club mosses such as Phylloglossum comprise c. 400 species, spike mosses such as Selaginella comprise c.700 species and quillworts such as Isoetes comprise c. 150 species.

As the evolutionary divergence of these three lineages was ancient, and the taxa sampled are rare, the new sequence data will be useful in comparative and phylogenetic studies that seek to sample densely at the base of the plant tree of life to minimize long branch artefacts.

Phylloglossum also has corms, organs with a unique ‘fuzzy morphology’ and root/shoot-like identity.[3] The new sequence data will be helpful to future evo-devo projects aiming to determine homologies.

In contrast, Trithuria comprises just 12 species and sits at a key evolutionary divergence point higher up the plant tree of life. It is an aquatic angiosperm placed in the family Hydatellaceae, one of three families in the basal angiosperm order Nymphales.[4]

Trithuria differs from other water lilies in that it is tiny with narrow grass-like leaves, and the flowers may not be homologous to other angiosperm flowers, having an ‘inside out’ floral whorl arrangement.[5]

Again, the new sequence data will be useful in future systematic and evo-devo studies.

To access the raw reads or de novo assembled transcriptomes when they become available please contact Josh Mylne at joshua.mylne@uwa.edu.au.

Further reading

  1. Taylor et al. (2009). Palaeobotany: The biology and evolution of fossil plants. Academic Press, Burlington.
  2. Pryer et al. (2001). Horsetails and ferns are a monophyletic group and the closest living relatives to seed plants. Nature 409: 618-622. doi:10.1038/35054555
  3. Bower FO. 1885 On the development and morphology of Phylloglossum drummondii. Philosophical Transactions of the Royal Society of London 176:665–678. doi:10.1098/rstl.1885.0012
  4. Saarela et al. (2007). Hydatellaceae identified as a new branch near the base of the angiosperm phylogenetic tree. Nature 446, 312-315. doi:10.1038/nature05612
  5. Rudall et al. (2009). Nonflowers near the base of extant angiosperms? Spatiotemporal arrangement of organs in reproductive units of Hydatellaceae and its bearing on the origin of the flower. American Journal of Botany 96:67-82. doi:10.3732/ajb.0800027

Crocus, saffron-omics and the highest value crop

Saffron, Crocus sativus and origin label

Saffron, Crocus sativus and a protected origin label

Saffron, the stigma of Crocus sativus, is the highest priced agricultural product (often €/$25 or £15 per gram) and a good example of a profitable crop with sustainability, cultural and social values, and high labour demand. I have been discussing –omics studies of the crop – the DNA, RNA, metabolites and secondary products – at the annual meeting of a European Science Foundation COST programme Saffronomics.

www.Saffronomics.org logo

www.Saffronomics.org logo

The ‘Action’ aims to coordinate research on Saffron-omics for crop improvement, traceability of the product, determination of authenticity, adulteration and origin to provide new insights that will lead a sound Saffron Bio-Economy. Despite the high price, the spice costs only a few pence/cents per portion, and adds enormously to the flavour and colour of many dishes. Biologically, saffron is the species Crocus sativus, as recognized by Linnaeus, and it is a sterile triploid with 2n=3x=24 chromosomes.

Audience for annual meeting

Audience for annual meeting

The programme of our Annual Meeting opened with the genomics sessions – the DNA, RNA, genetics and epigenetics. I don’t usually start reviews with, nor indeed include, my own talk, but here its content sets the scene for other work discussed at the meeting. I talked about the work of Nauf Alsayid, who shows the lack of any clear DNA differences between any accessions of saffron – whether from Kashmir, Greece, Italy, Spain, Holland or Iran. I cited a paper from 1900, itself reporting work back to 1844, where the French botanist Monsieur Paul Chappellier reported “for the Saffron, there is only known a single and unique species; for ages it has not produced a single variety”, writing that he was importing bulbs Naples, Athens, Austria, Spain, Cashmere and China (Chappellier P 1900. Creation of an improved variety of Crocus sativus. J. Royal Horticultural Society XXIV Hybrid Conference Report 275-277 – brilliant download, even available free for Kindle!). Plus ça change, plus c’est la même chose!

Highest quality Saffron from Thiercelin 1809

Highest quality Saffron from Thiercelin 1809

After my talk, Jean Marie Thiercelin, the seventh generation of the major saffron and spice company http://www.thiercelin1809.com told me that his grandfather knew Paul Chappellier, and he commented in the history of saffron production in France: Chappellier knew how to produce 10 to 15kg per ha before the First World War. After the war, saffron production stopped altogether in France, but it has restarted this century, with now some 137 growers on 37 ha but production of only some 5kg per ha.

Continuing with the talks, a DNA-sequence level study of saffron by Gerhardt Menzel with Thomas Schmidt (Dresden) analysed of several Gigabases of genomic survey sequence data, revealing about ten distinct tandemly repeated satellite DNA sequences that could be used to identify chromosomes in saffron by in situ hybridization. The species has a 78% repeat content in the DNA, with about 6% being the rDNA, and many different classes of transposons.

Giovanni Giuliano - High trhougput sequencing of saffron RNA and gene discovery

Giovanni Giuliano – High throughput sequencing of saffron RNA and gene discovery

Giovanni Giliano (with Sarah Frusciante, Italy) demonstrated the carotenoid cleavage dioxygenase from saffron stigmas catlayses the first step in saffron crocin biosynthesis, a clear example of the pathway to the critical secondary product giving saffron its value (http://www.pnas.org/content/111/33/12246.short).


Slivia Fluch - Saffronomics Genomics Working Group Leader

Slivia Fluch – Saffronomics Genomics Working Group Leader

Both Matteo Busconi and Silvia Fluch (Austria) discussed epigenetic differences detected from different saffron collections: important for both understanding the controls on gene expression and for determining the origin of samples. Each producing area seems to have distinct profiles. Caterina Villa (Porto) reported results from use of the plant ‘barcoding’ primers ITS and matK with high resolution DNA melting analysis for saffron authentication, and more detail about the chloroplast genomes was presented from Bahattin Tanyolac and his Turkish colleagues. Although wild species of crocus are of interest from several points of view, only one paper, from Joze Bavcon (Slovenia) discussed these in detail, with a report of the natural hybrid Crocus reticulatus x C. vernus.

Joze Bavcon Crocus of Slovenia Book Cover

Joze Bavcon Crocus of Slovenia Book Cover

The next group of talks discussed the saffron metabolome, the analysis of different constituents of Crocus. Crocus is one of the few species to have its own international standard (ISO3632: http://j.mp/isosaffron ), and both quality and purity are measured (including contamination with stamens and pollen, along with detection of adulteration. Several participants were involved in the formulation of the standard, and Gianluca Paredi reported improvements that need less than the ISO methods needing no less than 23g of stigmas! Natural colours from plants such as Buddliea, Calendula, Curcum, Gardenia, safflower (Carthamus Asteraceae), cochineal (from the insect) and turmeric are widely mixed with saffron.

Chair of the Saffronomics Action Professor Maria Tsimidou

Chair of the Saffronomics Action Professor Maria Tsimidou

The Saffronomics project leader, Maria Tsimidou (Greece), used the three ISO3632 peaks for saffron – colouring strength from crocins absorbing at a peak wavelength of 440nm, aroma from safranal at 330nm, and taste (flavour) from picrocrocin at 257 nm – for examination of quality and authenticity of commercial saffron samples. Of 16 samples, 3 were adulterated, and half of the pure samples were graded in ‘category I’. Another amazing figure quoted was the price of saffron in quantity: of 75 tonnes imported to one county, only 35% is priced at more than $500 per kg. Authentic saffron could not be produced for anywhere approaching $1000/kg (typically $10-$15000/kg), so all this bulk product is fraudulent. Technology sessions in the meeting covered alternative quantification approaches to spectroscopy: Laura Ruth Cagliani in Milan tested  different solvents for extraction for NMR-based metabolomic characterization of authentic saffron distributed within the COST partners as well as the NMR evidence of absence of plant adulteration in those saffron samples.

Moschos Polissiou Saffronomics

Moschos Polissiou Saffronomics

A leading group from Thessaloniki was able to detect adulteration with as little as 15% cochineal. EA Petrakis and Moschos Polissiou demonstrated how FT-IR spectroscopy is promising to quantify small amounts of adulterants in saffron – safflower, Gardenia and tumeric – where diffuse reflectance mode provides rapidity, ease of use and minimal sample preparation. Other important reports discussed aging effects on profile of secondary metabolites (Paraskevi Karastamati Greece) and detection of herbicide residues (Christina Mitsi).

H stable Isotope Map from http://www.earthmagazine.org/article/cold-case-files-forging-forensic-isoscapes

H stable Isotope Map from http://www.earthmagazine.org/article/cold-case-files-forging-forensic-isoscapes

Micha Horacek (Austria) presented new results looking at the ratios of stable isotopes in saffron, a technique increasingly used to determine the origin of all agricultural produce. He showed the impressive map of with the gradient of water (hydrogen and oxygen) isotope ratio from North to South and from East to West in Europe. He also showed the differences in nitrogen stable isotope ratios depending of fertilizer use, and sulphur which depends on the underlying geology. Current work with saffron shows considerable year-to-year variation in the position of accessions from different regions of Europe, but the data is still being collected. Soon Micha will be getting a sample of our own, Leicester-lab-produced, saffron to add to his map!

Our hosts at RIKILT, the Food Safety and Quality Institute, Wageningen University, have much advanced applied science on food quality. An eye-opening talk by John van Duynhoven told us about rehydration of freeze dried blanched carrot with dynamic assessment of water movement in samples with and without blanching, freeze drying at -28 and -150C. Another series of images showed water transport and the impact of pre-cooking of rice, using magnetic resonance imaging MRI as a functional measurement of rice cooking. The final section discussed why crackers don’t crack: vapour transport during shelf life of crackers! Modelling of the nature of water transport links processing & formulation to the structure and on to functional and storage implications.


Fran Azafran - a school book about saffron

Fran Azafran – a school book about saffron

For ESF – COST projects, dissemination and public understanding are important, and participants were treated to a preview of a series of six school books about Fran Azafran and Franny Azafran by Manuel Delgado from Cuenca, Spain. I look forward to seeing these in full, and hopefully to their availability in other languages too.


At the podium

At the podium

Like the best of the projects, I feel that saffron science has moved in the last decade, (including research in the consortia www.crocusbank.org and www.saffronomics.org) with notable fundamental, technical and applied outcomes of our research. We know about its relatives and genome structure, key genes, metabolic processes and the key secondary products, and even understand epigenetic control, corm growth and dormancy. After 4000 years of being sold fake saffron, the fraudsters know now that we can test for saffron purity and quality!

Marta Rodlan (Vice Chair of the Action), Jose Antonio Fernández Perez and Jean Marie Thiercelin: key people in saffronomics

Marta Rodlan (Vice Chair of the Action), Jose Antonio Fernández Perez and Jean Marie Thiercelin: key people in saffronomics

Saffronomics Meeting Book Cover

Saffronomics Meeting Book Cover

New plant journal

Image: Wikimedia Commons.

Image: Wikimedia Commons.

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.]

Something fishy in the veggie patch…

Image: Nada Meeks, www.fineartamerica.com.

Image: Nada Meeks, www.fineartamerica.com.

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.]

Plants, the inside story

Image: Anton Joseph Kerner von Marilaun and Adolf Hansen. Pflanzenleben: Erster Band: Der Bau und die Eigenschaften der Pflanzen. Kurt Stüber, 1913.

Image: Anton Joseph Kerner von Marilaun and Adolf Hansen. Pflanzenleben: Erster Band: Der Bau und die Eigenschaften der Pflanzen. Kurt Stüber, 1913.

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 genesSo, 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!

Sugar versus Auxin: which is dominant?

Image: Wikimedia Commons.

Image: Wikimedia Commons.

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 BrucesSheilas… 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.]

Dodgy photos dog phytology

Image: Wikimedia Commons.

Image: Wikimedia Commons.

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.]