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.

Special Issue on Plant Cell Walls – Free Online

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Although plants and many algae (e.g. the Phaeophyceae, brown, and Rhodophyceae, red) are only very distantly related they are united in their possession of carbohydrate-rich cell walls, which are of integral importance being involved in many physiological processes. Furthermore, wall components have applications within food, fuel, pharmaceuticals, fibres (e.g. for textiles and paper) and building materials and have long been an active topic of research. As the major deposit of photosynthetically fixed carbon, and therefore energy investment, cell walls are of undisputed importance to the organisms that possess them, the photosynthetic eukaryotes (plants and algae). The complexities of cell wall components along with their interactions with the biotic and abiotic environment are becoming increasingly revealed.

00 image for blog 2borderThe importance of plant and algal cell walls and their individual components to the function and survival of the organism, and for a number of industrial applications, are illustrated by the breadth of topics covered in a newly published Special Issue of Annals of Botany, containing 27 papers concentrating on various plants and algae, developmental stages, organs, cell wall components, and techniques. The papers are organized into topics under the general headings of (1) cell wall biosynthesis and remodelling, (2) cell wall diversity, and (3) application of new technologies to cell walls, and the Special Issue is available as FREE ACCESS online until 14 December.

00 image for blog 3borderIn their preface the Editors of this Special Issue, Zoë Popper, Marie-Christine Ralet and David Domozych, consider future directions within plant cell wall research. Expansion of the industrial uses of cell walls and potentially novel uses of cell wall components are both avenues likely to direct future research activities. Fundamentally, it is the continued progression from characterization (structure, metabolism, properties and localization) of individual cell wall components through to defining their roles in almost every aspect of plant and algal physiology that will present many of the major challenges in future cell wall research.

Accumulation of ferruginol in heartwood-forming xylem

Accumulation of ferruginol in heartwood-forming xylem

Accumulation of ferruginol in heartwood-forming xylem

Heartwood formation is a unique phenomenon of tree species but the mechanisms by which the substances involved accumulate are unclear. Kuroda et al. use time-of-flight secondary ion mass spectrometry (TOF-SIMS) in conjunction with quantitative analyses to study the distribution of ferruginol in a 30-year tree of Cryptomeria japonica (Taxodiaceae). They find that accumulation begins in the middle of the intermediate wood, initially in the earlywood near the annual ring boundary, then throughout the entire earlywood, and finally across to the whole annual ring in the heartwood. They conclude that the heterogeneous timing of ferruginol accumulation could be related to the distribution of ray parenchyma cells and/or water in the heartwood-forming xylem.

Cambial reactivation and formation of earlywood vessels in oak

Cambial reactivation and formation of earlywood vessels in oak

Cambial reactivation and formation of earlywood vessels in oak

The continuous formation of earlywood vessels is crucial for the growth of ring-porous hardwoods. Kudo et al. study Quercus serrate seedlings and find that a combination of localized heating and disbudding of dormant stems results in earlier cambial reactivation and differentiation of first vessel elements than in non-heated seedlings. A few narrow vessel elements are formed during heating after disbudding, while many large earlywood vessel elements are formed in heated seedlings with buds. The results suggest that elevated temperature is a direct trigger for differentiation of first vessel elements, and that whilst bud growth is not essential for differentiation of first vessel elements, it might be important for the continuous formation of wide vessel elements.

Heterozygosity–fitness correlations in pedunculate oak

Heterozygosity–fitness correlations in pedunculate oak

Heterozygosity–fitness correlations in pedunculate oak

Increased homozygosity caused by population fragmentation can directly affect individual plant fitness through the expression of deleterious alleles, and drought stress induced by climate change may exacerbate these effects. Vranckx et al. investigate various transpiration and growth traits of seedlings of pedunculate oak, Quercus robur, correlate them with their multilocus heterozygosity (MLH), and then study the effects of drought stress on these relationships. They find significant heterozygosity–fitness correlations for most fitness traits, and high atmospheric stress increases the strength of these correlations for the transpiration variables. They conclude that that ongoing climate change may strengthen the negative fitness responses to low MLH, highlighting the need to maximize individual multilocus heterozygosity in forest tree breeding programs.

Lathyrus diversity and crop improvement (Invited Review)

<i>Lathyrus</i> diversity and crop improvement (Invited Review)

Lathyrus diversity and crop improvement (Invited Review)

The Lathyrus genus (Fabaceae) includes 160 species, some of which have economic importance as food, fodder and ornamental crops (mainly L. sativus, L. cicera and L. odoratus, respectively) and are cultivated in over 1.5 million ha worldwide. Vaz Patto and Rubiales review the current status and future prospects of Lathyrus diversity conservation and characterization, highlighting their use in L. sativus and L. cicera breeding. They conclude that efforts for improvement of these species should concentrate on the development of publicly available joint core collections, and on high-resolution genotyping. This should result in more efficient and faster breeding approaches, which are especially needed for these neglected, under-utilized Lathyrus species.

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.]

Nitrate uptake modelling in plants: root activity

Nitrate uptake modelling in plants: root activity

Nitrate uptake modelling in plants: root activity qNitrate uptake modelling in plants: root activity

Using a thermodynamic flow–force interpretation of nitrate uptake isotherms, Malagoli and Le Deunff  develop a functional– structural model to predict N uptake in winter oilseed rape, Brassica napus. The structural component of the model, the active root biomass, is derived from a combination of root mapping in the field, the relationship between specific root length and external nitrate concentration, and the assignment of an absorption capacity related to integrated root system age. They find that model simulations are well matched to measured data for N uptake under field conditions at three different levels of fertilizer application. Model ouputs indicate that the topsoil layers contain about 80 % of the total root system and account for 90–95 % of N taken up at harvest.

Nitrate uptake modelling in plants: functional components

Nitrate uptake modelling in plants: functional components

Nitrate uptake modelling in plants: functional components

Difficulties in linking the various regulations of nitrate transport acting at different levels of time and on different spatial scales have hindered the development of models for nitrogen uptake. Le Deunff and Malagoli  substitute the more usual enzyme–substrate interpretation for a flow–force approach of nitrogen uptake isotherms and combine it with experimentally determined regulation in order to model nitrate in winter oilseed rape, Brassica napus. This approach avoids the use of unique nitrate uptake reference kinetics and allows root plasticity in response to environmental and in planta factors to be taken into account. Furthermore, it allows the regulation of nitrate uptake by roots to be scaled up relatively easily in time from hours to months.