Friday Film: 3D Arabidopsis flower

Categories: teaching resources
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Published on: September 28, 2012

David Livingston from the USDA Agricultural Research Service made a beautiful video of the construction of an Arabidopsis flower using 248 sections of an Arabidopsis flower that was paraffin-embedded and sectioned at 20 microns. It includes images of the internal structure of the flower. The method he used is published in Livingston et al., 2010.

Friday film: Botany consultant on Avatar

Categories: teaching resources
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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:


Gene and protein names and symbols

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Published on: September 20, 2012

Scientific writing is a minefield of possible mistakes and embarrassments. Even after you’ve managed the nearly impossible task of writing, in the passive voice and past tense, twenty pages of science which your PI (if you’re a student or post-doc) and collaborators have OK’d after multiple rounds of staring at red, green, and blue track-changes, there is still the awful task of checking the formatting of species, genera, gene and protein names. Unless one of the authors is a journal editor, in which case you may have got to that stage much earlier. And although you get used to that uninspiring writing style early on, the protocol for referring to genes and proteins can feel like a constant battle, as it differs between species, and sometimes between journals too.

Well, GARNet can’t help much with the actual writing of your papers or thesis. If you want some help or inspiration with that, try this article on scientific writing on ScienceCareers which is both helpful and funny, and these exercises. We have put this list of plant species and generally accepted ways of writing gene and protein names and symbols however – enjoy!


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 the tomato genome

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Published on: August 31, 2012

In May, a consortium of researchers from 14 nations finally finished sequencing and annotating the tomato genome. They started in 2003 without the benefit of next generation sequencing (NGS), but in 2008 when there was no end in sight, the consortium took up three methods of NGS: Illumina, SOLiD, and 454. Four years later, the project was complete.

Annotation of the tomato genome is still ongoing, but much of the annotated genome can be found at the Sol Genomics Network.

What else can next generation sequencing do? The next GARNet workshop, Tools and Technologies to Advance Plant Research, is a day dedicated to exploring the opportunites presented by NGS. Speakers will speak on a range of ways they have used NGS, including chromatin mapping, RNA sequencing, and generation of new Arabidopsis mutant lines.

Teaching Resources

Tomato: Decoded video from Science 360

Solanaceae school activities from the Sol Genomics network

Teaching resources from the University of Leicester including two ‘sequencing’ activities for 14-16s

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…)

Orange sweet potato champions biofortified foods in Africa

Two Ugandan children dig in to a plate of orange sweet potato (Credit: HarvestPlus)

According to a study published in the Journal of Nutrition this month, eating orange sweet potato reduces the prevelance of vitamin A deficiency in children in Uganda and Mozambique. Vitamin A is critical for the development of good vision as it is an essential component of rhodopsin, a pigment in photoreceptor cells in the eye. Consequently in poor communities in Africa and south-east Asia, where diets poor in vitamin A are widespread, vitamin A deficiency is the leading cause of preventable blindness. Healthy levels of vitamin A are also necessary for normal organ formation and maintenance. Orange-fleshed sweet potato varieties contain more than 50-fold more β-carotene, which is converted to vitamin A after ingestion, than the yellow or white varieties commonly eaten in African countries.

The study monitored the effects of the Orange Sweet Potato (OSP) project, which was funded by the Bill and Melinda Gates foundation and coordinated by HarvestPlus. The conclusions predict a promising future for the use of biofortified foods bred for increased nutritional value. It was the first large-scale study of its kind, involving 24 000 households from Uganda and Mozambique. Nutritionists and farmers educated communities on the health benefits of orange sweet potato and on growing, storing, and commercialising orange sweet potato crops. Local women were also given recipes and information about hygiene practices. (more…)

Synthetic enzyme reduces lignin content

Public domain image. Source: Glazer, A. W., and Nikaido, H. (1995). Microbial Biotechnology: fundamentals of applied microbiology. San Francisco: W. H. Freeman, p. 340. ISBN 0-71672608-4

Highlighted article: Kewwi Zhang, Mohammad-Wadud Bhuiya, Jorge Rencoret Pazo, Yuchen Miao, Hoon Kim, John Ralph, and Chang-Jun Liu (2012) An Engineered Monolignol 4-O-Methyltransferase Depresses Lignin Biosynthesis and Confers Novel Metabolic Capability in Arabidopsis. Plant Cell Preview.

Zhang et al. reduce lignin content by introducing an artificial enzyme to the cell wall biosynthesis pathway. This is the first time synthetic biology has been used to change cell wall structure, which is usually modified by changing the expression of endogenous enzymes or introducing a protein from another organism. In fact at the moment, synthetic biology is not a common method of manipulating any plant pathway.

Relevant background

public domain image, courtesy of Chino

Lignin is one of three components of secondary cell walls. It is the part which makes extracting sugar from the cell wall, for example for second generation biofuel production, difficult.

Lignin is made up of three monolignols: coniferyl, sinapyl, and p-coumaryl.

They are synthesised in the cytosol and transported to the cell wall. At the cell wall, the monolignols are oxidised, causing their phenol group to become radicalised. The phenoxy radicals polymerise to form the lignin macromolecule.

The Liu lab had the idea of preventing monolignol oxidation by methylation of the phenol group so that the phenoxy radicals were prevented from forming. Their first attempt was to synthesise a selection of monolignol 4-O-methyltransferases (MOMTs). The artificial MOMTS were fusions of two naturally occurring enzymes: lignin biosynthesis pathway methyltransferase COMT, which does not have any 4-O-methyltransferase activity; and fairy fan enzyme isoeugenol O-methyltransferase, which catalyzes 4-O-methylation of isoeugenol and eugenol, but doesn’t affect monolignols. Although several of these artificial enzymes were able to 4-O-methylate monolignols as expected in vitro, they had no activity in vivo.


Zhang et al. used MOMT3, a promising enzyme from their earlier work, as a starting point. (more…)

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