Monthly Archives: January 2013

Phytonumeracy

Image: Franz Eugen Köhler, Köhler's Medizinal-Pflanzen. Gera-Untermhaus, 1897.

Image: Franz Eugen Köhler, Köhler’s Medizinal-Pflanzen. Gera-Untermhaus, 1897.

Echoing a plea from Ron Milo and Robert Last that computational methods [which is sort of ‘math(s)’…] should be used to gain deeper understanding of the fundamental principles that govern regulation of metabolic pathways in plants, here’s advance notice of The Sixth Mathematics in the Plant Sciences Study Group meeting. Taking place from 25–28th March 2013 at the University of Nottingham (UK), this annual workshop ‘gives a handful of plant and crop scientists the opportunity to present a research question to around 40 mathematicians and computer scientists’. At the 4-day number-fest modellers tackle the problems in teams, ‘resulting in a great deal of progress made in a very short time’, which is encouraging. But here’s the real temptation: ‘problems presented at the previous five study groups have led to successful grant proposals, studentships and publications (e.g. Scott Grandison). Plus, problems from any area of plant and crop science are welcomed. AND no prior experience of mathematical modelling is required. Can we, er, count you in? And by way of timely proof that numerical approaches can yield botanical insights, we have Pascal-Antoine Christin et al. investigating ‘anatomical enablers and the evolution of C4 photosynthesis in grasses’. The team examined leaf anatomical characters of the co-called PACMAD clade (which contains members using both C4 and C3 photosynthetic carbon-fixation pathways) and the BEP clade (which contains only C3 members), particularly factors as basic as the size of the bundle sheath (BS) cells and the closeness of BSs. Their modelling indicated that evolution of C4 photosynthesis is favoured when the proportion of BS tissue is higher than 15 % (which results from a combination of short distances between BSs and large BS cells). This particular combination of anatomy is found in the PACMAD clade, which is inferred to explain the clustering of C4 origins in this lineage. And, putting that study into a bigger evo-ecophysiological landscape, we have Howard Griffiths et al.’s review that explores the ‘original function of the BS in C3 lineages, providing an insight for selection pressures leading to the derived C4 pathway’. And if you’ve now got a taste for numbers and various C-fixation pathways, Arren Bar-Even et al. ‘survey carbon fixation pathways through a quantitative lens’.

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Prediction of mixed-species litter decomposition

Prediction of mixed-species litter decomposition

Prediction of mixed-species litter decomposition

The complex dynamics of interacting biological organisms that form ecological systems make predictions of processes difficult and often imprecise. In this context, Tardif and Shipley  explore the acceptability of the biomass-ratio hypothesis, operationalized as community-weighted means, and a new hypothesis (idiosyncratic annulment) for predicting the decomposition of multispecies litter mixtures. They find deviations from expectation but an average bias of approximately zero and a decreasing variability with increasing species richness (SR). They conclude that, since SR increases with increasing spatial scale, the spatial scale will be a determinant in the prediction of ecosystems processes, such as litter decomposition rates.

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Current research in sweet potato…

Image: Wikimedia Commons.

Image: Wikimedia Commons.

Although some way removed from the manic antics of an ambitious medic named Dr Frankenstein (the sort of Creationist who gives ‘Intelligent Design’ a bad name…) attempting to revivify a corpse with electric shocks, Kazunori Hironaka et al. have increased the levels of purported life-supporting polyphenols in sweet potato by 60% using an electric current.

Polyphenols have been much-promoted because of their potential health benefits, particularly as anti-oxidants, so any method that increases their abundance in a foodstuff is of interest. But sweet potato (Ipomoea batatas) isn’t just any foodstuff; it has been ranked highest in nutritional value against a wide range of vegetables, and even proclaimed as the ‘uber tuber’. More than 95% of the global crop grows in developing countries (where it is the fifth most-important food), and where malnutrition is a serious problem; by many measures, sweet potato is ‘big potatoes’. Hence, there is considerable interest in a way that can further increase the sweet potato’s role in relieving hunger and improving nutrition and health.

The electrical treatment apparently does not affect the vegetable’s flavour, and is inexpensive and simple enough to be used on small farms or in food distribution centres. Hironaka is the same researcher who 2 years ago announced an increase in antioxidant levels in ‘normal’ potato (Solanum tuberosum) using ultrasound (and electric current). Truly, shocking!

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The role of ROS in soybean seed germination

The role of ROS in soybean seed germination

The role of ROS in soybean seed germination

Reactive oxygen species (ROS), such as hydrogen peroxide (H2O2), can promote seed germination in a number of species but their role in soybean has not been fully determined. Ishibashi et al. use the anti-oxidant N-acetylcysteine to counteract the effects of ROS in germinating seeds of soybean, Glcine max, and study endogenous ethylene content, the number and area of cells in the root tip, and the expression of genes related to ethylene biosynthesis. They find that H2O2 promotes germination and N-acetylcysteine suppresses it, and this latter effect is associated with suppressed expression of genes related to ethylene biosynthesis. They conclude that ROS produced in the embryonic axis after imbibition induces the production of endogenous ethylene, which promotes cell elongation in the root tip.

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Evolution of genome size in Carex

Evolution of genome size in <i>Carex</i>

Evolution of genome size in Carex

Knowledge of evolution of genome size in species with holocentric chromosomes is limited. Lipnerová et al. study genome size and base composition in the holocentric genus Carex (Cyperaceae) in relation to chromosome number. They find that genomes are relatively small and very GC-poor compared with other angiosperms, with genome size positively correlated with GC content and negatively correlated with chromosome number. They identify seven polyploid and two potentially polyploid species in Carex subgenus Carex, and determine that this subgenus exhibits larger genome sizes and a higher rate of genome size evolution compared to subgenus Vignea. They conclude that evolution of genomes and karyotypes in the Carex genus is promoted by frequent chromosomal fissions/fusions, rare polyploidy, and common repetitive DNA proliferation/removal.

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Nanoparticles may compromise crops

Image: Priester et al. 2012, PNAS.

Image: Priester et al. 2012, PNAS.

Advances (ever an optimistic notion!) in technology take many forms and may have unanticipated consequences. Take, for example, the emerging discipline of nanotechnology, which works with structures that are intermediate between isolated atoms and bulk materials – in the range of 1–100 nm, and which often display physical attributes substantially different from those displayed by either atoms or bulk materials (e.g. Zhong Wang). Not surprisingly, therefore, concerns have been expressed about the effects that manufactured nanomaterials (MNMs) may have on human health or other biota if they ‘escape’ into the environment.

John Priester et al.  examined the response of a major crop – soybean – to farm soil amended with two ‘high-production’ metal oxide MNMs, nano-CeO2 and nano-ZnO. Amongst other findings, they show that plant growth and yield diminished with nano-CeO2, and nitrogen fixation was shut down at high nano-CeO2 concentration. As the authors chillingly – but calmly – conclude, ‘these findings forewarn of agriculturally associated human and environmental risks from the accelerating use of MNMs’. You have been warned!

However, and not that I’m cynical or anything like that, I’m a little exercised by the fact that the manuscript was received for review on 1st April (2012). I don’t know about the rest of the world, but there is a tradition in the UK of playing what are euphemistically termed ‘pranks’ – ‘practical jokes’ and the like – on April Fool’s Day, 1st April. But those antics are only permitted up until 12 noon on that date. So, I’m hoping that the paper was received during the afternoon of that day. Plus, having been published in such an august organ as PNAS some months after that date, I’m guessing that this is a genuine piece of science. Further reassurance comes from the fact that it has subsequently elicited a letter that challenges the study’s conclusions. Co-authored by Rothamsted Research’s Professor Steve McGrath (UK PI for a transatlantic consortium set up to investigate the environmental and human health implications of nanotechnology), that epistle needs to be taken seriously. And it has been, in the robust rebuttal by way of reply thereto by the original paper’s authors. Consequently, we should be rightly concerned about those nanomaterials (or not, per Lombi et al.…).

[One of the most famous April Fool’s Day hoaxes in the UK – and which is coincidentally botanical! – was the BBC’s news item in 1957 that purported to show the ‘harvesting’ of spaghetti in Switzerland. And it has even been voted ‘the top April Fools prank in history’ – Ed.]

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How does a plant get a taste for meat?

A tasty looking pork steak

Sticky Pork Steak with Soy and Ginger Sauce. Photo: avlxyz/Flickr

One of the reasons carnivorous plants are so popular has to be their weirdness. They turn a lot of assumptions about plants upside down. But how does a plant become carnivorous? I can see how an animal might stumble on a new snack, but a cabbage isn’t going to feel pecking one morning and decide it might nibble on a butterfly.

A paper by Nishi et al, in this month’s Annals of Botany has an answer. In the case of Paepalanthus bromelioides it’s protocarnivorous thanks to some help from its friends.

Paepalanthus bromelioides is a bromeliad that lives in south-east Brazil. It looks like it could be carnivorous. Its leaves reflect UV light. Its central tank is acidic. The leaves have a slippery wax that causes insects to lose their footing. There’d be good reason for it to be carnivorous too. Its habitat is well-lit but nutrient poor. It’s thought that carnivorous plants are looking for snacks to supplement their diet, and if there are few nutrients then the benefits of trapping insects outweigh the costs. But Paepalanthus bromelioides doesn’t trap insects. Also the plant doesn’t make any proteolytic enzymes. These are the enzymes that break down proteins for digestion. Anything that breaks down is due to activity by bacteria living in the rosette of the plant.

Paepalanthus bromelioides sat on a termite mound

Paepalanthus bromelioides. Photo by Nishi et al.

Nishi et al. looked closer at the plant. It is surrounded by predators. Spiders patrol the leaves looking for insects sheltering among them. The plant itself tends to sit on termite mounds were there is an insect factory converting detritus into nutrients. Instead of being a failed carnivore, is the plant working cultivating these creatures to aid its digestion?

Nishi’s team used levels of Nitrogen-15, a slightly heavier than usual isotope of nitrogen, to track where Paepalanthus bromelioides was getting its nitrogen from. They also examined the bacteria in the rosette to see if they were helping break down material into nutrients.

For the termites it was relatively easy to set up a test. Termites were given various samples of cardboard and some had been dosed with more 15N than usual. The idea was that the termites would break down the cardboard, leave the nitrogen in the soil and the plant would take it up. The results were odd.

The plants on termite mound did have more nitrogen, but there was no detected increase in 15N, so it’s not certain that the nitrogen is from the mound. Nishi et all note that there wasn’t a lot of rain and this could have scuppered the test.

For nitrogen coming in from the top, there was a clear signal. Spider faeces is a big contributor to the plant’s nitrogen. There were also contributions from carcasses and larvae. Surprisingly the bacteria made no difference.

What seems to be happening is that the plants are using the spiders as part of their digestive system. Digesting an insect is hard work. Instead the spiders are pre-digesting the insects for the plants. The plants then find what the spiders excrete easier to digest. The rosette is handy for channeling everything that falling toward the centre for collection.

All in all it looks like termites contribute around two-thirds of the nitrogen to a healthy Paepalanthus bromelioides and predators in the rosette another quarter.

This kind of assisted digestion shows how fully carnivorous plants like pitcher plants could have developed a taste for animals. It looks like some unfortunate spiders could effectively be eaten by their own toilets.

Nishi A.H., Vasconcellos-Neto J. & Romero G.Q. (2012). The role of multiple partners in a digestive mutualism with a protocarnivorous plant, Annals of Botany, 111 (1) 143-150. DOI:
Subscription paper, with free access after January 2014.

Photo: Sticky Pork Steak with Soy and Ginger Sauce by avlxyz / Flickr. This image licensed under a Creative Commons by-sa licence.
Photo: Paepalanthus bromelioides © Nishi et al.

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Fire and daily temperatures as germination cues

Fire and daily temperatures as germination cues

Fire and daily temperatures as germination cues

Brief but high soil temperatures caused by fire are followed by a more prolonged shift in the range of daily soil temperatures as a result of the removal of vegetation. Santana et al. use experimental fires and mechanical removal of vegetation to study germination of three fire-adapted Mediterranean species, Ulex parviflorus, Cistus albidus and Rosmarinus officinalis. They find that the mean daily maxima for soil temperature in fire-induced gaps is at least 20 °C higher than in soil under vegetation at the sites studied, and these higher fluctuations in daily temperature are the most significant factor in determining both seedling emergence and the amount of ungerminated seeds remaining in the soil. They conclude that seeding capacity in Mediterranean Basin obligate seeders may have evolved as a response to a wide range of disturbances, and not exclusively to fire.

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This one could run and run (and run…)

Image: Wikimedia Commons.

Image: Wikimedia Commons.

‘What would scientists learn if they could run studies that lasted for hundreds or thousands of years—or more?’. In other words, rather than being forced to look at what nature has produced after hundreds of millions of years of evolution, etc., and to infer what might have happened to produce the extant situation, what experiments could you undertake to get evidence for one interpretation or another? This poser was posed by Davide Castelvecchi in Scientific American and received some interesting suggestions. Although most aren’t sufficiently botanical for this blog, that from Robert Hazen – ‘earth scientist at George Mason University (USA)’, and arguably the scientific American – is. He would like to run a 10 000-year series of experiments aiming to solve nothing short of the mystery of the origin of life on Earth, that pivotal moment(s) that created (yep, evolution of living things needs an initial act of ‘creation’ – spontaneous or otherwise…) what we now call biology (i.e. botany and all those other – lesser – life sciences). In a mimic of self-replicating molecules first assembling on the surface of rocks – the ‘most plausible explanation [of life’s origin]’ – Hazen envisages chemical ‘labs-on-chips’ containing hundreds of microscopic wells, each with different combinations of compounds reacting on a variety of mineral surfaces acting as ‘molecular nurseries’. Although I’m a great believer that funding should last for the lifetime of a project, I doubt that any research grant awarder’s coffers will be this deep. Pity.

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Genetic relationships of section Arachis specie

Genetic relationships of section <i>Arachis</i> species

Genetic relationships of section Arachis species

Section Arachis includes cultivated peanut (A. hypogaea), an allotetraploid, and closely related wild species, most of which are diploids. Moretzsohn et al. use sequences from three single-copy genes and microsatellite markers to investigate evolutionary relationships within the section and find that whilst high intraspecific variability is evident, there is good support for most species and the results are consistent with genome groups defined by cytogenetics. Using a molecular clock, the divergence of the major genome groups is estimated as between 2.3 and 2.9 million years ago, indicating that speciation rates are very high. The phylogenetic analyses show that A. duranensis and A. ipaënsis are the genome donors to A. hypogaea.

 

 

 

 

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