The TREE of plant science education

Aurora Levesley is the Project Officer for the Gatsby Plant Science TREE. The TREE grew out of the Gatsby Plant Science Summer Schools as a means of sharing the valuable resources produced for and during the Schools. Here she discusses the value of the TREE’s online lectures, which are the subject of a current New Phytologist paper. 

David Beerling at the Gatsby Plant Science Summer School
David Beerling gives a lecture at the Gatsby Plant Science Summer School. This is one of many lectures that have been edited for interactive online delivery and shared on the Plant Science TREE.

The Plant Science TREE is a free online central repository of plant science educational resources. More than 90 research academics and publishers have contributed over 2000 resources, including online research lectures, research-led lecture slides, practicals, video clips and other resources on topical plant science. It was developed by the University of Leeds with funding from the Gatsby Charitable Foundation, and is currently used by scientists, educators and students from over 320 institutes worldwide.

Many students enter biological sciences courses with little interest in or knowledge of plants, and engaging students with plant science early in their studies is arguably an important step in reversing the decline in uptake of this vulnerable yet strategically important subject linked to food security and other globally important issues. Prof Alison Baker of the Centre for Plant Sciences at the University of Leeds, says of the TREE: “The aim is to put a tool in the hands of educators that will engage students in plant science and research, especially where expertise is becoming limited.”

Our recent study, published in New Phytologist, showed the online research lectures that form a large part of the TREE successfully engage undergraduates with plant science (Levesley et al 2014, New Phytologist Early View).

In this study, undergraduates from four UK universities were provided with links to online research lectures as part of their course. The lectures, filmed at the Gatsby Plant Science summer schools, were given by research leaders but pitched at a level to engage undergraduates and provided a first-hand insight into how discoveries are made and science is carried out.

Not only were the online lectures successful in engaging students with plant science and research in general, but students were unanimous in the opinion that they were a good way to learn about a subject. Interestingly the study also showed that the online viewing experience was comparable to watching the research lectures live.

These online undergraduate research lectures are freely available through the Plant Science TREE. Our study shows they represent a valuable plant science education tool to help lecturers and teachers introduce cutting-edge research examples that address globally relevant applied initiatives – as well as curiosity-driven research – to their students. As such they have the potential to change student attitudes to plant science, engage students in research and are able to reach a large and wide global student audience.

The full reference for the Plant Science TREE paper is: Levesley A, Paxton S, Collins R, Baker A and Knight CD. “Engaging students with plant science: the Plant Science TREE”, New Phytologist, published online ahead of print in June 2014.


Molecular Plant Pathology’s Top Ten

Keeping with last week’s plant pathology theme, I thought I’d highlight a paper that came out in the spring in case any plant pathologists missed it. This may also help people in other fields of plant science out there who might need to hold their own in a pathology-based conversation occasionally. In April 2012, Molecular Plant Pathology published ‘The top 10 fungal pathogens in molecular plant pathology,’ as voted for by 495 readers of the journal.

Quesadillas made with corn infected with Ustilago maydis, which is called huitacoche.

The pathogens chosen are:

  1. Magnaporthe oryzae, the cause of rice blast disease.
  2. Botrytis cinerea, also known as grey mold – probably the cause of the mold on the strawberries in the back of the fridge that you bought when they were offer.
  3. Puccinia spp., the cause of an unpleasant range of rust diseases that occur on wheat.
  4. Fusarium graminearum, a cereal pathogen commonly known variously as head blight, ear blight, or, delightfully, head scab. Infected grain can be poisonous.
  5. Fusarium oxysporum, a ubiquitous soil-borne pathogen that can infect many species, including important fruit species, and humans.
  6. Blumeria graminis, powdery mildew, which infects wheat and barley.
  7. Mycosphaerella graminicola is also called Septoria tritici and causes blotch disease in wheat.
  8. Colletotrichum spp. can infect a large range of crops, and latent infections can destroy stores of fruits post-harvest.
  9. Ustilago maydis, or corn smut, is actually cultured on corn cobs by farmers in Mexico, where the infected corn is called huitacoche and is a common recipe ingredient.
  10. Melampsora lini, or flax rust, the classic model plant pathogen.

The paper gives a ‘resume’ of each one, written by an expert in that particular species. Is your favourite pathogen missing? What other ‘Top 10’ would be interesting to put together?

Paper: DEAN, R., VAN KAN, J. A. L., PRETORIUS, Z. A., HAMMOND-KOSACK, K. E., DI PIETRO, A., SPANU, P. D., RUDD, J. J., DICKMAN, M., KAHMANN, R., ELLIS, J. and FOSTER, G. D. (2012), The Top 10 fungal pathogens in molecular plant pathology. Molecular Plant Pathology, 13: 414–430. doi: 10.1111/j.1364-3703.2011.00783.x

Teaching resources: This is an exercise easily recreated in a tutorial group or classroom. Groups of students could each make a pitch for their plant pathogen (or crop species, or organelle, etc …) and the whole group would vote for which one deserves the ‘top’ spot.

Image credit: Lesley Téllez, via her blog The Mija Chronicles

The genetics of broad-spectrum resistance

Downy mildew infection of Arabidopsis thaliana seedlings

Highlighted article: Dmitry Lapin, Rhonda C. Meyer, Hideki Takahashi, Ulrike Bechtold, Guido Van den Ackerveken (2012) Broad-spectrum resistance of Arabidopsis C24 to downy mildew is mediated by different combinations of isolate-specific loci. New Phytologist DOI: 10.1111/j.1469-8137.2012.04344.x

It is a mark of how effective plant immune systems are that most bacteria, fungi, and viruses do not affect plants at all either because plant tissues are not suitable for them to live in, or they are fended off. Of course there are pathogens that are compatible with plants – and within species that share compatibility, there are pockets of resistance. Some sub-groups are resistant to specific pathogen isolates, and this is caused by dominant resistant genes. A much broader, more complicated, and less common form of resistance occurs when a particular accession is resistant to a whole pathogen species, or several species. This is broad-spectrum resistance, and it can be caused by a simple dominant gene or multiple genes. Natural broad-spectrum resistance is not simple to transfer from its origin to a commercial crop because it can come from a complex set of genes which are not necessarily all dominant. (more…)

From systems biology to digital organism

GARNet needs your help to assess the uptake, influence and future of systems biology in the plant science community. This is the second time GARNet has conducted a survey about systems biology, as in 2006 the BBSRC commissioned GARNet to produce a report on how systems biology could best be approached in UK Arabidopsis research. We believe that report and the various activities that accompanied it helped the Arabidopsis community get its foot on the ‘System Biology Ladder’ – and to win some of the associated grants.

Now, six years later, systems biology is supporting systems biology and the digital organism efforts. We feel it is time to write a follow up report to the 2006 Systems Biology report in order to advise the BBSRC and other funders on the community’s capabilities, current needs, and readiness for future initiatives that build on Systems Biology.

Please help us collect data and information for this report by filling in a questionnaire, which will take about 20 minutes of your time. Please click here to go to the questionnaire. Please contribute your ideas before the 5th November.

Video credit: Pacific Biosciences.

Friday Film: Powerful Plants

Categories: teaching resources
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Published on: October 12, 2012

If you thought that plants were stationary, lazy beings, think again. Bladderworts are water-dwelling carnivorous plants that trap prey by storing elastic energy in the trap body and releasing it by very fast opening and closing of a water-tight trap door. This video was made by Phillippe Marmottant and his research group from Grenoble, who published the mechanism of bladderwort action in their 2011 paper.

Another super fast plant is the dogwood species, Cornus canadensis, whose flowers explode faster than a rifle shot as they disperse their pollen.

While exploding plants and super-suction make for exciting viewing, they happen too fast for the human eye to see without the benefit of slow motion footage. It is possible to show slightly slower plant reflexes to students in schools, though – SAPS have a carnivorous plants information page and worksheets.

Friday film: Botany consultant on Avatar

Categories: teaching resources
Comments: 1 Comment
Published on: September 21, 2012

Professor Jodie Holt from the University of California UC Riverside was the consultant botanist on Avatar. In this video, she gives a lecture to middle school children on the plants in the film and where the real world inspiration for them came from – she has lots of interesting examples from the film which could easily be translated to plant science teaching, and outreach projects. This is quite a long video, but it is fascinating. The Avatar stuff starts at about 15 minutes in, and Jodie takes questions from the children from 36 minutes onwards.

Credit: UCR College of Natural and Agricultural Sciences

If the video is not working, go to YouTube:


Traditional varieties are key to modern rice farming

Analysing root growth and yield of rice plants.

Highlighted article: Rico Gamuyao, Joong Hyoun Chin, Juan Pariasca-Tanaka, Paolo Pesaresi, Sheryl Catausan, Cheryl Dalid, Inez Slamet-Loedin, Evelyn Mae Tecson-Mendoza, Matthias Wissuwa & Sigrid Heuer (2012). The protein kinase Pstol1 from traditional rice confers tolerance of phosphorus deficiency. Nature 488, 535–539 doi:10.1038/nature11346

Over centuries, many local rice varieties have been bred into a few modern varieties which are extensively farmed throughout much of Asia. In regions where soil is poor such as western India and Thailand, rice crops are dependent on rainfall, frequently suffering from floods and draughts, and importantly also require phosphorus fertilizer. Phosphorus is an essential plant nutrient, and as phosphorus fertilizer is made from a finite store of phosphorus rock the current situation in the parts of Asia with poor soil is not sustainable.

A solution to this problem was found in a traditional rice variety, Kasalath. Another traditional rice variety has already supplied modern rice breeders with submergence tolerant gene SUB1, which enables rice plants to survive up to two weeks of flooding. A decade ago, a major quantitative trait locus was identified in Kasalath that conferred tolerance to phosphorus deficient soil. This locus was labelled Pup1, and last year the Heuer group at the International Rice Research Institute defined a core set of Pup1 markers and used them to backcross Pup1 into modern rice varieties, which were grown in their natural environments and all produced significantly more rice in P-deficient conditions than their wildtype counterpart. These Pup1 introgression lines also showed improved root growth under stress. (more…)

NGS and root endophyte assembly cues

Cologne and Sanssouci, close to Golm: what effect do the soils at these two historic locations have on the local plant roots?

Highlighted article: Davide Bulgarelli, Matthias Rott, Klaus Schlaeppi, Emiel Ver Loren van Themaat, Nahal Ahmadinejad, Federica Assenza, Philipp Rauf,  Bruno Huettel, Richard Reinhardt, Elmon Schmelzer, Joerg Peplies, Frank Oliver Gloeckner, Rudolf Amann, Thilo Eickhorst, and Paul Schulze-Lefert (2012) Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota Nature 488:91


Although plant-microbe and plant-soil dynamics are widely studied areas of plant science, up until now there has been no broad picture of plant endophytic systems: which phyla are common endophytes; how the populations form; and what affects them. Endophytes colonise plant tissues, where unlike pathogens they do not cause harm or an immune response, and unlike endosymbionts they do not live inside plant cells or have an obvious mutually beneficial relationship with the plant. A recent review on bacterial endophytes is this one by Reinhold-Hurek and Hurek (2011).

Here, Bulgarelli et al. use an Arabidopsis system to shed light on the specifics of below ground plant-bacteria interactions, and set out a methodology for future investigations into other plants and soil types. This study and another article in the same issue of Nature by Lundberg et al. use next generation sequencing (NGS) to show similar cues for assembly of root endophytes. (more…)

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