Tag Archives: Plant Science

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.

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.]

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.]

Seeing the Forest and the Trees: Research on Plant Science Teaching and Learning

CBE Life Sci Educ The September issue of CBE—Life Sciences Education is a Special Focus edition on plant science education:

Plant Behavior. CBE Life Sci Educ September 2, 2014 13:363-368; doi:10.1187/cbe.14-06-0100
Plants are a huge and diverse group of organisms ranging from microscopic marine phytoplankton to enormous terrestrial trees. Stunning, and yet some of us take plants for granted. In this plant issue of LSE, WWW.Life Sciences Education focuses on a botanical topic that most people, even biologists, do not think about—plant behavior.

Book Review: Plant Biology for Young Children. CBE Life Sci Educ September 2, 2014 13:369-370; doi:10.1187/cbe.14-06-0093
My Life as a Plant is an activity book targeted toward helping young children see the importance, relevance, and beauty of plants in our daily lives. The book succeeds at introducing children to plant biology in a fun, inquiry-based, and appropriately challenging way.

Understanding Early Elementary Children’s Conceptual Knowledge of Plant Structure and Function through Drawings. CBE Life Sci Educ September 2, 2014 13:375-386; doi:10.1187/cbe.13-12-0230
We present the results of an early elementary study (K–1) that used children’s drawings to examine children’s understanding of plant structure and function.

Effects of a Research-Infused Botanical Curriculum on Undergraduates’ Content Knowledge, STEM Competencies, and Attitudes toward Plant Sciences. CBE Life Sci Educ September 2, 2014 13:387-396; doi:10.1187/cbe.13-12-0231
This research-infused botanical curriculum increased students’ knowledge and awareness of plant science topics, improved their scientific writing, and enhanced their statistical knowledge.

Connections between Student Explanations and Arguments from Evidence about Plant Growth. CBE Life Sci Educ September 2, 2014 13:397-409; doi:10.1187/cbe.14-02-0028
In an analysis of 22 middle and high school student interviews, we found that many students reinterpret the hypotheses and results of standard investigations of plant growth to match their own understandings. Students may benefit from instructional strategies that scaffold their explanations and inquiry about how plants grow.

Beyond Punnett Squares: Student Word Association and Explanations of Phenotypic Variation through an Integrative Quantitative Genetics Unit Investigating Anthocyanin Inheritance and Expression in Brassica rapa Fast Plants. CBE Life Sci Educ September 2, 2014 13:410-424; doi:10.1187/cbe.13-12-0232
This study explores shifts in student word association and explanations of phenotypic variation through an integrative quantitative genetics unit using Brassica rapa Fast Plants.

Optimizing Learning of Scientific Category Knowledge in the Classroom: The Case of Plant Identification. CBE Life Sci Educ September 2, 2014 13:425-436; doi:10.1187/cbe.13-11-0224
The software program Visual Learning—Plant Identification offers a solution to problems in category learning, such as plant identification. It uses well-established learning principles, including development of perceptual expertise in an active-learning format, spacing of practice, interleaving of examples, and testing effects to train conceptual learning.

Attention “Blinks” Differently for Plants and Animals. CBE Life Sci Educ September 2, 2014 13:437-443; doi:10.1187/cbe.14-05-0080
We use an established paradigm in visual cognition, the “attentional blink,” to demonstrate that our attention is captured more slowly by plants than by animals. This suggests fundamental differences in how the visual system processes plants, which may contribute to plant blindness considered broadly.

 

An explosive mix: C4, C3, C2 and CCM

Image: Ninghui Shi/Wikimedia Commons.

Image: Ninghui Shi/Wikimedia Commons.

As if the task of explaining the details of the ‘normal’ C3 Calvin Cycle of photosynthesis (P/S) to our students isn’t hard enough, we also need to appraise them of C4 P/S  – with its spatial separation of initial CO2 fixation into organic acids in mesophyll cells and its subsequent release and re-fixation via the enzyme Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase)  into the photosynthetic Calvin Cycle proper within bundle sheath cells*. As testing and trying as that is, nature always has to go one ‘better’, and ‘spoil’ things. So, the fin-de-millennial recognition of a variant of this C4 P/S in which initial CO2 fixation into 4-carbon acids and its subsequent release and re-fixation into the Calvin Cycle of C3 P/S takes place within a single cell is kind of unwelcome (no matter how fascinating it is!). Well, anyway, it exists – in such higher plants as Suaeda (Borszczowia) aralocaspica, Bienertia cycloptera, B. sinuspersici and B. kavirense, all in the Chenopodiaceae (now within the Amaranthaceae) – so we need to get over it, and try and understand it. And that’s what Samantha Stutz et al. have been doing. Although these plants perform spatial separation of the two CO2 fixation events within a single mesophyll cell, they do so using two distinct – dimorphic – chloroplasts. Already known is that light is necessary for development of the dimorphic chloroplasts in cotyledons in B. aralocaspica. In the dark they only have a single structural plastid type (which expresses Rubisco): light induces formation of dimorphic chloroplasts from the single plastid pool, and structural polarization leads to the single-cell C4 syndrome. The aim of Stutz et al.’s study was to determine how growth under limited light affects leaf structure, biochemistry and efficiency of the single-cell CO2-concentrating mechanism. Overall, the team found that the fully developed single-cell C4 system in B. sinuspersici is robust when grown under ‘moderate light’. Where might this sort of work be going? Well, whilst it is interesting for its own sake – the pure pursuit of knowledge – it has a more applied dimension too. Central to all of this single-cell photosynthetic biology and biochemistry is the concept of CCM, carbon-concentrating mechanisms, whereby levels of CO2 are increased in the vicinity of Rubisco so that it favours photosynthesis – CO2-fixation – over photorespiration (so-called C2 photosynthesis) which uses O2 as substrate and consequently reduces photosynthetic efficiency. Well, in bids to replicate some of the greater photosynthetic efficiency of C4 plants (largely by virtue of their diverse CCMs…), an attractive notion is to engineer various forms of CCM into C3 crop plants. This approach is exemplified in the work of Mitsue Miyao et al., where they attempted to exploit enzymes of the facultative C4 aquatic plant Hydrilla verticillata (which engages in single-cell C4 P/S) to convert rice from its typical C3 P/S into a single-cell C4 photosynthesiser. Although they didn’t achieve their goal (and it’s good to know that ‘negative’ results can still be published!), their article is an interesting and soul-bearing account of the lessons learned in this work. As we continue our quest for that elusive boost in photosynthetic yield, we’ll no doubt continue to exploit any biochemical variant on the photosynthetic theme that nature displays. Which begs the question: how many more variants exist amongst the 325,000 species of flowering plants (let alone all the algae and other members of the plant kingdom)? Seems like we need more plant anatomists, plant biochemists, plant physiologists – as well as plant taxonomists (see my last post on this blog) – after all!

 

* That’s C4 P/S as opposed to CAM (Crassulacean acid metabolism), which is also a version of C4 P/S but which involves temporal separation of the same two carbon-fixation events in plants such as pineapple, cacti and agave. However, CAM is hardly ever referred to as C4 P/S because the all-powerful Zea Supremacy lobby has commandeered the term for that spatially separated C4 version found in plants such as maize… but don’t get me started on that!

 

[Intriguingly, and in addition to its dimorphic chloroplasts, Suaeda aralocaspica has dimorphic seeds, which exhibit distinct differences in dormancy and germination characteristics. Now, they say that things come in threes, so what’s the third dimorphy about this iconic species…? – Ed.]

A day in the life…

Image: Wikimedia Commons.

Image: Wikimedia Commons.

Well, dissident Russian novelist Alexander Solzhenitsyn did it (with Ivan Denisovich), that Swinging Sixties phenomenon, the mop-topped beat combo that is The Beatles did it with typical inventivenesss and musicality – and probably a ‘little help from their friends’* – and now labs are getting in on the act. Welcome to The Node’s ‘a day in the life of a …’ seriesThe Node was launched in June 2010 by Development, a leading research journal in the field of developmental biology, and its publisher, The Company of Biologists, as a non-commercial information resource and community site for the developmental biology community, and ‘a place to share news about and with the developmental biology [which includes plant and non-plant-based work… – Ed.] community around the world’. Designed to give insights into the working of the labs – and the people – that try to unravel development, it has already showcased Narender Kumar, graduate student, in an arabidopsis lab at Louisiana State University (USA), and Dr James Lloyd in a moss lab at the University of Leeds (UK). I’d like to think that these insights into the more human sides of plant development research might help to inspire the next generation to get involved in plant biology research and rise to the challenges of the 21st century that so often revolve around food and energy security – solutions to both of which conundra will have important botanical dimensions.

* The Rolling Stone magazine voted the Beatles’ A day in the life to be that group’s best song, and the 28th best song of all time.

[And if you’d like to read more about plants in the lab., check out the University of Bristol’s School of Chemistry’s ‘Plants in the Lab’ website, which ‘by bringing beautiful and interesting plants and flowers into the laboratory setting and then explaining what some of the molecules produced naturally mean to chemists, we are hoping to challenge the familiar divide between nature and laboratory’. Talking of Bristol University, who’s our favourite Trollope-loving botanist? Melville Wills Professor of Botany Alistair Hetherington (whose botanical life story is told in Current Biology.) And for the day when you have to leave the lab – maybe to go to another one..? – Natalie Butterfield has the ‘perfect lab leaving list’ for you. – Ed.]