Tag Archives: Plant Science

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.


[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.]

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.]

Why Botany is Important #epso2014

Society of Biology calls for investment in plant science This week guest author Charlie Haynes is AoB Blog’s roving reporter at the EPSO/FESPB plant biology Europe conference. This post is his pre-conference manifesto.


On the first day of the EPSO/FESPB plant biology Europe conference it’s worth considering why botany is important.

Like many others whilst studying GCSE and A Level biology I found the botanical themed part of the syllabus dull and uninteresting. I arrived at university to find myself surrounded by those with similar experiences in their schools. Not one person I met during my first year of Biological Sciences at Leicester said they wanted to be a professional botanist. Luckily I turned up to all of my lectures and found myself interested and maybe even enjoying some of the botany and ecology modules that I was initially less than thrilled about taking. But there are serious emerging issues in plant science and ecology that need more talent.

  • A burgeoning world population needs ever greater crop yields as people become increasingly affluent and demand a higher quality and quantity of food produce.
  • Climate change is increasing the incidence of severe weather conditions such as droughts and heavy rains. Some climate models show that with a temperature rise of 2 degrees Celsius by 2050 will lower wheat yields by an average of 50%.
  • Despite large scale agricultural enterprises, an estimated 50% of world food production is from small small farmers. Many of these are subsistence farmers. The average Vietnamese farm is approximately 340 times smaller than the average US farm. New innovative strategies need to help these farmers use this space effectively.
  • Disease can still strike harvests dead in their tracks destroying livelihoods and causing skyrocketing food prices.
  • With more individuals demanding a western style lifestyle, the need for fresh water is also climbing. A potato has a water footprint of 25 litres. A hamburger has a water footprint of an estimated 2400 litres. But we live on a planet where only 2.5% of all water is fresh water and much of this is trapped at the polar ice caps. Developing plants capable of reducing their water footprint is vital in some chronically dry regions.
  • Nutritional deficits and diseases account for millions of deaths and over 2 billion are malnourished. Not only does the total number of calories produced need to increase, but there also needs to be an increase in global dietary variance and quality.

Have I missed anything else blindingly obviously that screams a need for plant science in the 21st century?

If so please let me know in the comments below, I would love to hear from you!


Planting the seeds

Dandelion Plant growth and development is a foundation concept in the science curriculum. Focus on plant characteristics and life cycles in early grades is particularly important because some evidence suggests that as children develop, their ability to notice plants, their assumptions about the importance of plants, and their interest in plants deteriorates. The conceptual understanding students develop about plants in the elementary grades therefore serves as a foundation for later science learning.

Work is needed to understand how elementary students can be supported to formulate scientific explanations, particularly about topics such as seed structure and function where students exhibit a variety of alternate conceptions. A new paper examines explanation-construction within the context of a long-term investigation about plants in three third-grade classrooms and asks the following research questions:

  1. How do third-grade students formulate written scientific explanations about seed structure and function?
  2. In what ways and why do third-grade teachers provide instructional support for students’ formulation of scientific explanations about seed structure and function?


Scientific Practices in Elementary Classrooms: Third-Grade Students’ Scientific Explanations for Seed Structure and Function. Science Education, 14 May 2014 doi: 10.1002/sce.21121
Abstract: Elementary science standards emphasize that students should develop conceptual understanding of the characteristics and life cycles of plants, yet few studies have focused on early learners’ reasoning about seed structure and function. The purpose of this study is twofold: to (a) examine third-grade students’ formulation of explanations about seed structure and function within the context of a commercially published science unit and (b) examine their teachers’ ideas about and instructional practices to support students’ formulation of scientific explanations. Data, collected around a long-term plant investigation, included classroom observations, teacher interviews, and students’ written artifacts. Study findings suggest a link between the teachers’ ideas about scientific explanations, their instructional scaffolding, and students’ written explanations. Teachers who emphasized a single “correct explanation” rarely supported their students’ explanation-construction, either through discourse or writing. However, one teacher emphasized the importance of each student generating his/her own explanation and more frequently supported students to do so in the classroom. The evidentiary basis of her students’ written explanations was found to be much stronger than those from students in the other two classrooms. Overall, these findings indicate that teachers’ conceptions about scientific explanations are crucial to their instructional practices, which may in turn impact students’ explanation-construction.


Spotlight on macronutrients (Part 2): Nitrogen, in a bit of a fix…

Image: Wikimedia Commons.

Image: Wikimedia Commons.

In this and my next few posts we conclude our look at essential plant macronutrients that started in some previous articles, and this time concentrate on the last four of the nine elements – C, H, O, P, K, N, S, Ca and Mg – in that category (and try to bring a Cuttings-esque twist to that quartet).


Nitrogen, in a bit of a fix…

Nitrogen (N) is a major component of many compounds in plants, e.g. it is present in all amino acids, which are the building blocks of proteins – and hence cell membranesenzymes and nutritionally important storage or reserve proteins; and it is an important constituent of nucleotides, which are major components of nucleic acids, such as RNA (ribonucleic acid) and DNA (deoxyribonucleic acid), and of the ‘energy molecule’ ATP (adenosine triphosphate). As a major component of plants, N is needed in relatively large amounts – which is why it is termed a macronutrient. Fortunate then, you might think, that plants are virtually surrounded by an unlimited amount of nitrogen in the atmosphere,  which consists of approx. 78% of this gaseous element in the form of dinitrogen, N2. Sadly, in that state plants cannot use it; it must be converted to forms that they can use, such as the ammonium (NH4+, from ammonia – NH3) and nitrate (NO3) ions.


Whilst plants cannot themselves convert N2 into NH3, many groups of plants – e.g. famously, the legumes – have teamed up with bacteria that can undertake that chemical reaction in the process known as nitrogen fixation. Some of that fixed nitrogen is used by the plant that hosts the mutualistic microbe, as a sort of rent for the home that the plant provides for the bacteria within root-sited nodules.


Unfortunately, many more plants are not blessed with this in-built nitrogen-fixing partnership and are reliant on appropriate forms of fixed nitrogen from the environment, e.g. NO3. Since N is frequently in short supply in the soil, it is often referred to as a limiting nutrient – an essential nutrient whose amount limits overall plant growth and development. In agricultural settings this deficiency is usually remedied by the addition of chemical fertilisers, often containing phosphorus (P) and potassium (K) in addition to the N. Whilst desired increases in crop growth/yield are obtained by this human intervention, not all of that added nitrogen – and frequently phosphorus, too – is taken up by the crop; substantial amounts of N and P end up in freshwater systems where they can cause highly undesirable problems such as eutrophication. Not only is that damaging to the environment, it is costly – ‘Nitrogen fertilizer costs US farmers approximately US$8 billion each year…’.

Wouldn’t it be great if non-legumes could be persuaded to develop N-fixing bacterial partnerships? Yes, and work by Yan Liang et al. (Science 341: 1384–1387, 2013) encourages that view. The team from The Plant Molecular Biology and Biotechnology Research Center (South Korea) and University of Missouri (USA) have demonstrated that non-legumes – in this instance good old Arabidopsis thaliana, Zea mays (‘corn’) and Solanum lycopersicum (tomato) – do have the ability to respond to the rhizobial lipo-chitin Nod factors that are released by the would-be symbiotic rhizobial bacteria, and which are signal molecules that trigger nodulation in legumes. Although we are still some time away from nodulating N-fixing non-legume crops such as maize and tomato, this discovery does at least show that the rhizobia are recognized as ‘friendly bacteria’ – the plants just have to be trained to let them accept invasion of their tissues by the microbe, and build the nodule, etc, etc…


[Although there are generally recognised to be 17 essential plant nutrientscobalt (Co) is additionally required by the bacteria of the N-fixing nodules,  so indirectly Co is an 18th essential nutrient in those cases – Ed.]