Category Archives: Plant Cuttings

A positive plethora of plant papers!

Image: Ryan Kitko/Wikimedia Commons.

Image: Ryan Kitko/Wikimedia Commons.

Unusually for this column (why give the ‘competition’ a free bit of publicity, after all?), I here wish to promote The Scientist magazine. As a general science news item site it occasionally features plant-related items, but it has surpassed itself with its 1st January 2014 collection. Not only does it feature a wonderful image of the fruit of the lotus plant on its cover, but it also contains four big plant articles(!).

By way of introducing that compilation, Mary Aberlin observes in her editorial that, ‘the panoply of fictional plants offers a large and varied dose of the weird and wonderful. But there’s no need to resort to fiction to find truly unusual plant characteristics’… so, read on! Accordingly, the selection comprises an item by Abby Olena that considers halotropism, a newly identified tropism in roots. This showcases a study by Carlos Galvan-Ampudia et al. that demonstrates active growth of roots of several plant species away from sites of high salt content, and which is not gravitropism. This work begs the question of how many other tropisms might still await discovery in that understudied plant organ.

In ‘Green gold’ Tracy Vence reports on the discovery of gold bioaccumulation in eucalyptus leaves, which was covered on this very blog not so long ago. Megan Scudellari’s article begins by posing the question, ‘What do cells, genes, mutations, transposons, RNA silencing, and DNA recombination have in common?’: the answer – but, of course! – is that all were first discovered in plants; she then considers how plant DNA is challenging preconceptions about the evolution of life (including our own species). And Dan Cossins considers the question of whether plants ‘talk’ to each other. Reviewing a wide-ranging body of work, the conclusion is that plants do communicate and interact with each other, both above and below ground, in surprisingly subtle and sophisticated ways. And by way of demonstrating how the time is right for certain ideas, Kat McGowan has an item in Quanta Magazine on ‘The secret language of plants’.  Almost inevitably these sorts of articles raise the spectre of how intelligent plants are, and that issue is given a good airing in Michael Pollan’s New Yorker article. What a great botanical start to the New Year (which traditionally starts on 10th April…)!

[Visit YouTube for a documentary on plant intelligence, and also if you want to know what plants talk about  – Ed.]

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Caught in the act…

Image: Marie Majaura/Wikimedia Commons.

Image: Marie Majaura/Wikimedia Commons.

Examples abound of ancient life forms trapped in suspended inanimation within amber (fossilised tree resin) and which give us clues about ancient – maybe even extinct – biota and their ecology (e.g. ‘The past is bright, the past is … amber’). A revelation concerning amber-encased plant material suggests that current sexual reproduction in angiosperms may have remained little changed in over 100 million years.

This insight comes from a new, albeit extinct, species named Micropetasos burmensis and work by George Poinar et al. with amber deposits from the mid-Cretaceous in Burma (Republic of the Union of Myanmar). Although given a binomial (with a formal description in English, as now permitted) and clearly a flowering plant, the team ‘prefer to leave the question of its exact familial relationships open at this time’. However, arguably the most interesting aspect of this discovery is the sight of pollen tubes growing out of two grains of pollen and penetrating the flower’s stigma (the receptive part of the female reproductive system). This precedes fertilisation of the egg, which would have begun the process of seed formation, had this act of plant coitus not been interrupted.

Curiously, this is not mentioned explicitly in the journal article, but was only discerned in the press release promoting it). Was that statement too outrageous or speculative for inclusion in the journal article? Surely not; legitimate commentary such as this ought to be encouraged, and only serves to make the discovery even more interesting. Come on, lads, don’t hide your light under a bush(-el)

[OK, you can relax, I’ve saved you the trouble of finding that story about 165-million-year-old fossil insects caught during copulation. Text – and pictures – at the Smithsonian’s website. – Ed.]

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Science: for the sheer fun of it!

Image: Robert Hooke, 1665. Micrographia. Jo. Martyn and Ja. Allestry, London.

Image: Robert Hooke, 1665. Micrographia. Jo. Martyn and Ja. Allestry, London.

Despite frequently expressed assumptions to the contrary, science – whether it’s botany or some lesser intellectual pursuit – isn’t always about having an idea and undertaking an experiment to test it. Anyway, that type of investigation can be hard work. Fortunately, there is an alternative approach that basically studies ‘what’s there’ and muses on why that might be (or not…), so-called blue skies research.  Sadly, the latter type of science – which I think is much more fun and interesting – is less likely to get financed than the ‘there’s a definite question that we aim to answer’ type of study, and is generally much less common. Nice then to see that, in conversation with Sarah Williams in the Howard Hughes’ Medical Institute’s Fall 2013 issue of the HHMI BulletinDr Richard Flavell (Sterling Professor of Immunobiology at Yale School of Medicine) promotes the view that observation-driven studies have a place in science. He goes further in saying that, ‘there’s nothing wrong with a lab team doing observational study after observational study. They are still helping advance the science, and likely providing fodder for hypothesis-driven studies to come…’. Now that is my kind of science. I do hope those who fund research are listening to – and heeding – this!

Unfortunately, I suspect the more usual reaction to requests to finance such work from the grant-awarding bodies would be similar to that which prompted this acknowledgement in a scientific paper: ‘I thank the National Science Foundation for regularly rejecting my (honest) grant applications for work on real organisms (cf. Szent-Gyorgyi, 1972)…’ (from Leigh Van Valen’s* paper, ‘A new Evolutionary Law’). But occasionally studies along the lines of ‘let’s just see what turns up’ do appear. Take, for example, Michael Proctor and Margaret Bradshaw’s first in a planned series of papers on scanning electron microscopy (SEM) examination of leaves of British sedges in New Journal of Botany**. Acknowledging that the ability to identify sedges in the field is important to many vegetation studies but recognising that inflorescences are available for only a short period each year, the pair have concentrated on SEM studies of leaf surfaces to assist those identification endeavours. Whilst the duo don’t advocate taking a SEM into the field, they do believe that such SEM studies will be ‘useful in putting leaf characters on a firmer footing, and drawing attention to characters which could be useful for identification with a hand-lens or low power microscope’ (which can be taken into the field…). The images need to be seen to be properly appreciated, but the imaging of epicuticular waxes in, for example, Figure 1f attests to their high quality. Bring on Part 2!

[For those expecting to read about ‘botanist’ Richard Flavell PhD, FRS, CBE, former Director of the John Innes Centre, etc, I’m sorry to ‘disappoint’ – Ed.]

* Leigh van Valen is an American evolutionary biologist probably best known for the Red Queen Hypothesis.

** this is the official organ of the BSBI,  the leading society in Britain and Ireland for the study of plant distribution and taxonomy. The Botanical Society of Britain and Ireland was formerly called the Botanical Society of the British Isles, and represents a name change every bit as slick as that of the WWF (which changed from World Wildlife Fund to World Wide Fund for Nature in 1986), and which also allows it to keep its abbreviation of BSBI (which is an initialism not an acronym) the same. The New Journal of Botany is itself the successor to the BSBI’s Watsonia journal, named in honour of Hewett Cottrell Watson (one of the “most colourful figures in the annals of British botany”) who developed the vice-county system in 1852 that currently divides up the United Kingdom and the Republic of Ireland into 152 geographical units for vegetation recording purposes.]

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What’s in a name..? (The whole world!)

Image: Stuart Edwards/ Wikimedia Commons.

Image: Stuart Edwards/ Wikimedia Commons.

Without wishing to get too wistful and harking back to the ‘olden days’, I fondly remember a geography lesson where I stumbled upon the inselberg (!?). The term inselberg comes from the German words Insel (meaning island) and Berg (‘mountain’) and refers to an ‘isolated hill that stands above well-developed plains and appears not unlike an island rising from the sea’. The fact that such structures are amongst the most iconic features of the natural world – e.g. think of Uluru/Ayers Rock in Australia  – makes for a very powerful association between the word and real-world phenomena. And ever since that moment inselberg has been one of those magical words (for me at least…) that conjures up images of exotic landforms and far-off places (I’m writing these words in Bath, UK, so anywhere beyond England counts as exotic!).

I was reminded of that moment when I chanced upon Kåre Arnstein Lye’s paper entitled ‘Studies in African Cyperaceae 38: Cyperus inselbergensis sp. nov. from inselbergs in Gabon and Cameroun’.  Whilst it may seem surprising to the uninitiated that one can generate 38 papers on cyperaceae, whether in Africa or elsewhere, it was the specific epithet of that particular species that caught my eye. The ‘inselberg sedge’ has been so named because ‘it has a very characteristic ecology as it grows in seasonally wet, shallow soils on or close to inselbergs’. And that got me thinking more generally of the power of plant scientific names to excite the imagination and enhance one’s understanding and appreciation of all sorts of events and phenomena; not just botanical ones. For another example of the meaning of botanical names you could do much worse than revisit my earlier post on ‘You can’t be best at everything…’, where the name of the new – albeit extinct – plant formally named as Potomacapnos apeleutheron has a most intriguing origin.

Translating as ‘freedmen’s poppy of the Potomac’,  that name is rich with history in recognising that the sediments from which the prehistoric plant was unearthed were originally exposed by freed slaves who were forcibly removed from the Freedmen’s Colony of Roanoke Island by Union troops during the American Civil War to dig a ditch in 1864. Wow! And that’s before we consider the significance of poppy and Potomac! Scientific names of plants are therefore a great way to study geography, history, births of nations, or any other aspect of world knowledge come to that! Consequently, Mr P Cuttings formally advocates that all children should be taught botany, with emphasis on proper botanical names (and their etymology). Doing so will not only teach them about plants, but will also greatly enhance their understanding of the world, and truly fit them to be knowledgeable citizens for the future. So, let the plants tell their story! (And – more importantly! – let us listen…)

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Feel the force!

Image: Mariana Ruiz Villarreal/Wikimedia Commons.

Image: Mariana Ruiz Villarreal/Wikimedia Commons.

Plants are remarkably sensitive to their environment, responding by appropriate growth and development to a wide range of environmental stimuli. In the case of gravity, the appropriate response is for stems to grow upwards (‘away from the source of gravity’; negative geotropism), and for roots to grow downwards (‘towards the source of gravity’; positive geotropism – for examples, see reviews by Elison Blancaflor and Patrick Masson  and by Miyo Morita). Although the details of the full pathway involved are still the subject of intense research efforts, a role for gravity-stimulated repositioning of cell-located statoliths (starch-bearing amyloplasts) in the gravity-detection side of things has long been proposed. However, the dynamic – rather than settled – nature of such amyloplasts has cast doubt on their effectiveness to act in this way. Now, elegant work by Masatsugu Toyota et al. has demonstrated that amyloplast displacement is necessary for gravisensing (in arabidopsis shoots). Using a custom-built centrifuge microscope they show that ‘sedimentary movements of amyloplasts under hypergravity conditions are linearly correlated with gravitropic curvature in wild-type stems’. Furthermore, and using a range of gravitropic mutants that do not exhibit a normal response under the Earth’s usual 1 g gravity field,  they demonstrate that their ‘hypergravity-induced amyloplast sedimentation and gravitropic curvature… was identical to that of wild-type plants’. Such work supports the view that arabidopsis shoots do have a gravisensing mechanism that converts the number of gravity-settling amyloplasts into gravitropic signals. And restoration of the gravitropic response by hypergravity in the gravitropic mutants examined indicates that those plants probably also have a functional gravisensing mechanism, albeit one that is not triggered at 1 g. Nice work. But in view of recent upsets (see previous ‘Ouch! That must hurt…’ post), I wonder if it also applies to non-arabidopsis plants…? Still, it is good to have the odd positive story about arabidopsis (I suppose…!).

[For more on the tangled web that is plant gravity-sensing and involvement of the actin cytoskeleton, check out the recent review by Elison Blancaflor  – Ed.]

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You can’t be best at everything…

Image: Wikimedia Commons.

Image: Wikimedia Commons.

There is a widespread belief that everything in/of/from/about America is bigger, better, faster, etc, than anything from elsewhere in the world. That is probably the best example of spin over substance ever foisted on an unsuspecting world, and is a true testament to the power of marketing and public relations.

Take, for example, the arresting title ‘This Could Be the Oldest Flowering Plant Ever Found in North America’. So prevalent is that view of American supremacy and so conditioned are we to its acceptance that many of us will have read that text and mentally added a comma after the words ‘ever found’ (and the importance of comma placement is legendary).  The news story concerns a re-assessment of fossil plants stored away in the USA’s Smithsonian National Museum of Natural History.  Originally thought to be a fern, reinspection and analysis by USA-based Nathan Jud and Leo Hickey now confirms that the fossil is an angiosperm (a flowering plant) between 125 and 115 million years old (Ma) – the Lower Cretaceous – named Potomacapnos apeleutheron.

While this is amongst the oldest flowering plants found in America, it is not the oldest known on Earth. That honour goes – currently! – to the unnamed bearers of ‘angiosperm-like pollen’ and the described genus Afropollis from Middle Triassic deposits in Switzerland that are 247.2–242.0 Ma, as unearthed by Peter Hochuli and Susanne Feist-Burkhardt. The pollen was studied using confocal laser scanning microscopy (CLSM), exploiting the autofluorescence still present in such ancient organic-walled microfossils. Quite dramatically, this announcement pushes back the origin of flowering plants another 100 Ma into history, which must be rather gratifying for the Swiss–German team. So, whilst national self-belief is a good thing to have (rather like patriotism),  it mustn’t blind us to the fact that other countries may have more legitimate claims to ‘biggest and best’ (and which might stray into nationalism). And anyway, it’s only because of ‘accidents of history, geography and politics’ that scientific discoveries are tied to a particular place and claimed for, and/or by, individual countries. Science – and its discoveries – belongs to us all. There, I’ve said it (and with flowers…).

[As usual, Mr Cuttings has tried to be a little mischievous in this item. But it probably won’t halt the activities of those whose lifelong goal is to seek out the biggest, best, etc, so expect further archaefloral revelations from the good old US of A in due course (and maybe further afield…), as more store-rooms replete with rocky riches are rummaged through, re-examined, and re-assessed! And if a good bit of healthy, old-fashioned competition and rivalry can spur on all those engaged in the process of science to even greater things, then so much the better – for us all! – Ed.]

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More myth-busting!

Image: Taro Taylor/Wikimedia Commons.

Image: Taro Taylor/Wikimedia Commons.

It’s a tribute to the fantasticness of plants – and photosynthesis in particular – that even animals want to be like them. Arguably, none more so than some sea slugs, which for many millennia have eaten seaweeds and integrated their chloroplasts into their bodies (a phenomenon known as kleptoplasty). The assumption that underlies such acquisitive behaviour is that the new owners use those sequestered verdant powerhouses as a fuel source for their own purposes. A lovely idea – and one that will have found its way into the textbooks, and featured in lectures based thereon. But! Gregor Christa et al. have concluded that, while such ‘stolen plastids’ display light-dependent CO2 fixation (i.e. photosynthesis), light is not essential for the studied sea slugs – Elysia timida and Plakobranchus ocellatus – to stave off starvation. Indeed, they conclude that the internalized plastids seem to be a slowly digested food source rather than a source of solar power. In other words, this is an example of plants feeding the planet (again!). However, another bonus of this work is that animals are still just animals and not proxy plants. Which is good, because, to paraphrase one Harold Woolhouse,  if one wants to understand the biology of plants one will ultimately have to work on… plants.

[However, if you wish to study animals that penetrate each other in the head during sex, then that’s where sea slugs really come into their own. But if you want more on photosynthetic animals, check out this article by Sarah Rybak  – Ed.]

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Ouch! That must hurt…

Image: Britton & Brown. 1913. An illustrated flora of the northern United States, Canada and the British Possessions. Charles Scribner’s Sons, New York.

Image: Britton & Brown. 1913. An illustrated flora of the northern United States, Canada and the British Possessions. Charles Scribner’s Sons, New York.

Schadenfreude (taking pleasure in the misfortunes of others) is not the most attractive of human traits, but it can be so satisfying. And I bet there’s more than a little of that throughout the world occasioned by the discovery that the model plant Arabidopsis thaliana  seems not to be such a good model after all. And the reason for this global wave of ‘arabidisenchantia’ relates to a rather fundamental property of cells known as nonsense-mediated mRNA decay (NMD). NMD is a so-called surveillance pathway that reduces errors in gene expression by eliminating aberrant m(essenger)RNAs that would otherwise encode incomplete polypeptides. Important though this process is for cell survival, it had been assumed that plants used it in a different way to animals because a gene for a key protein – SMG1 (phosphatidylinositol 3-kinase-related kinase)in the pathway had not been identified in Arabidopsis thaliana (afka* ‘the universal plant’), nor in fungi. However, and thanks to iconoclastic (albeit probably unintentionally)  work by James Lloyd and Brendan Davies, we [arabothalocentric plant biologists and those who needs must rely on their abundantly-funded researches - which is pretty much all of the rest of us...] can all sleep more soundly in our beds. They show that SMG1 – the gene that codes for SMG1 – is not animal-specific, but is found ‘in a range of eukaryotes, including all examined green plants [my emphasis] with the exception of A. thaliana’. The misconception about the importance of SMG1 in plants appears to have arisen because the gene was lost from A. thaliana ’s genome 5–10 millions of years ago. Interestingly, SMG1 is found in the genome of the closely related A. lyrata… So, A. thaliana is unique after all(!), though not in quite the way its promoters (pun intended…?) might have liked. But if thale cress has carelessly lost this gene, what else has it lost (but which may have been retained by more typical plants)…? I predict more Arabidopsis applecart-upsetting in the future…
* afka = as formerly known as…

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Temperature: getting it right

Image: Robert A. Rohde/Wikimedia Commons.

Image: Robert A. Rohde/Wikimedia Commons.

Many abiotic variables affect plants, e.g. levels of light, carbon dioxide and water. One of the most important of those non-biotic factors is temperature. Now, given its importance you could be forgiven for assuming that it is recorded accurately and correctly. Unfortunately, that isn’t always the case. Take for instance the temperature of the meristem (symbolised as Tmeristem), which is important in driving plant development. For such a crucial aspect of plant biology studies have largely relied on measuring the temperature of the air surrounding the plant (Tair). Tair is measured because it is assumed to represent the meristem temperature because plants are poikilotherms (organisms whose ‘internal temperature varies considerably … Usually the variation is a consequence of variation in the ambient environmental temperature’). Whilst that assumption may seem reasonable – and it does save the would-be investigator the trouble of penetrating the umpteen layers of developing leaves, etc, that may sheathe the apical meristem, it is nonetheless an assumption. And the veracity of assumptions must be tested, which is what Andreas Savvides et al. did. Guess what they found! That’s right: Tmeristem differed from Tair – ranging between –2.6 and 3.8 °C in tomato, and –4.1 and 3.0 °C in cucumber(!). As the team conclude, ‘for properly linking growth and development of plants to temperature… Tmeristem should be used instead of Tair’.

If you’re now intrigued by detecting temperatures within cells, you might like to explore the nanoscale thermometer developed by G. Kucsko et al. Using ‘quantum manipulation of nitrogen vacancy (NV) colour centres in diamond nanocrystals’ it can detect temperature variations as small as 44 mK(!) and can measure the local thermal environment at length scales as low as 200 nm(!!). Or, if you want a more biological approach, check out the genetically encoded sensor that fuses green fluorescent protein to a thermosensing protein derived from Salmonella, as showcased by Shigeki Kiyonaka et al. Although proof of this particular principle was demonstrated with thermogenesis in the iconic mitochondria of brown adipocytes (and the somewhat less iconic endoplasmic reticulum of myotubes), the team envisage it could be used to investigate this phenomenon in other living cells. Maybe even within the cone cells of tropical cycads that undergo impressive increases in temperature, where Tcone can be markedly greater that Tair. In view of concerns about global temperature changes and effects of temperature on regulation of such economically important processes as flowering, accurate temperature information in planta – and an appreciation of the temperature that plants are actually responding to – is likely to become increasingly important.

[For a useful set of slides summarising Savvides et al.’s work, visit slideshare.net. For a less physics-oriented interpretation of the Nature nanoscale thermometry article try the accompanying ‘News and Views’ item by Konstantin Sokolov – Ed.].

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Money doesn’t grow on trees… (2) [Or, From cuddly koalas to bird poo…]

Image: David Iliff/Wikimedia Commons (CC-BY-SA 3.0).

Image: David Iliff/Wikimedia Commons (CC-BY-SA 3.0).

OK, I know, this item is the real ‘money doesn’t grow on trees’ story you were expecting. So, I’ll try not to disappoint. Melvyn Lintern et al. provide the first evidence of particulate gold (Au) within natural – i.e. not from laboratory experimentation (and therefore which evidence doesn’t count..?) – specimens of living biological tissue.  The living biological tissue in question is that of the iconic Australian plant species eucalyptus, the gum tree. Apparently, and hitherto, reports of Au from plant samples have led to questions as to whether the Au was within the tissues (and therefore absorbed) or adsorbed onto the external surfaces as a result of aerial contamination. The team consider their discovery to demonstrate active biogeochemical absorption of Au, and it may therefore be used as a sort of bioassay (quite how quantitative this is may require further testing – maybe even experimentation…) to indicate the presence of soil-based Au deposits within the reach of the tree’s roots (the presumed route for uptake of the metal from the soil). The overall effect of this study is a little spoilt by the final sentence of the abstract, which begins, ‘This observation conclusively demonstrates active biogeochemical adsorption of Au…’. Shouldn’t that ante-penultimate word be absorption? Potential use of plants as agents to absorb metals – and other compounds – from soils and waters has been widely touted as a method for cleaning up such environments and comes under the broad category of phytoremediation. However, the fact that some plants may accumulate economically important metals – such as gold – has long been recognised and underlies the practice of geobotanical prospecting, which apparently dates as far back as the 5th century BCE in China. Whilst this study isn’t necessarily proposing use of eucalyptus in a bioindicator capacity, the authors do suggest that the gold therein might be extractable on a commercial basis. For more on this topic, see Sheoran et al.’s articles on ‘phytomining’ in general and of that for gold in particular. Anyway, I think somebody’s missing a trick here. What’s the iconic Australian animal species? The herbivorous koala, which famously has a diet rich in leaves of… eucalyptus. Now, applying the well-known principle of biomagnification – whereby organisms higher up the food chain accumulate materials from what they feed on – if koalas can be persuaded to eat only Au-loaded gum-tree leaves, then maybe their faecal pellets may contain gold, but concentrated to much higher levels than those found within their food source. Just a little nugget (!) of information I’m happy to share. All somebody needs to do is harvest the stuff (but isn’t that why postgrads/postdocs were invented..?). What’s that you say, where there’s muck there’s brass? Indeed! After all, we all know how expensive coffee is when made from the ‘beans’ that have been peristaltically massaged and ‘processed’ by passage through the alimentary tract of the Asian palm civet! And in a more scientifically imaginative  – though similarly scatologically-inclined – ‘muck = brass’ way the veracity in this wise saying is verified by work in Australia’s antipodean neighbour, New Zealand. Exhibit A, the evidence base that is the coprolite (‘fossilized feces’)  recently exploited by Jamie Wood et al. [http://dx.doi.org/10.1073/pnas.1307700110] to discern information about the ecology of four sympatric (species living in the same geographical area) species of moa – flightless herbivorous birds, which became extinct in New Zealand about 600 years ago. Unfortunately, there’s insufficient space for the details of the study here, but it involves identification of vegetation from pollen, aDNA (ancient DNA),  and plant macrofossils within the bird droppings (and therefore inferences about moas’ diet and habitat). This is a great example of that admirable ‘rolling-up-your-shirt-sleeves-and-getting-your-hands-dirty’ dedication to the cause of true science; definitely not merely going through the motions(!). What, after all, is more valuable than brass, or even gold? Knowledge! Well, some sorts of knowledge anyway, because, and rather vaguely, the Antipodean team’s ‘golden gum tree’ article just mentions ‘Eucalyptus trees’; there’s no further taxonomic help to their identity in the Supplementary Information either. So, although the article itself is Open Access, maybe naming the species concerned is too commercially sensitive for general consumption?

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