Weeding the Gems - Page 62 of 67 - the GARNet community blog

The cost of glucosinolate biosynthesis

Categories: Summary for non-specialists, systems biology, teaching resources

Tags: glucosinolates, New Phytologist, plant defence, systems biology

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Published on: October 2, 2012

Highighted article: Michaël Bekaert, Patrick P. Edger, Corey M. Hudson, J.Chris Pires, Gavin C. Conant (2012) Metabolic and evolutionary costs of herbivory defense: systems biology of glucosinolate synthesis. New Phytologist 196:596–605.

Research published in a current New Phytologist paper uses a systems biology approach to demonstrate the metabolic and evolutionary costs of producing glucosinolates for defence. Bekart et al. used AraGEM (Oliveira Dal’Molin et al., 2010) as a starting point. They collected data on Arabidopsis glucosinolate genes by scouring published papers and downloading their expression patterns from AtGenExpress. This information was integrated into the basic dataset from AraGEM. The complete list of genes involved in glucosinolate reactions, including references, is in Supplementary Table S1 of the paper.

The team performed flux balance analysis on the integrated database to estimate metabolic and energy flux through reactions in the system both with glucosinolate biosynthesis activity and with none. They found that glucosinolate biosynthesis affected flux incidentally through 241 reactions in addition to the 196 reactions which are only active when glucosinolates are being produced.

The main finding of the research is the heavy cost of glucosinolate biosynthesis. Sulphur import dramatically increased when glucosinolates were being synthesised, and demand for water, carbon dioxide, ammonia, and photons increased too. Despite the increase in substrate import, biomass synthesis fell by around 15% during glucosinolate production. This cost is reflected in other studies demonstrating that the evolutionary competitive edge glucosinolates give to plants is a disadvantage when there are no predators around (Mauricio, 1997), and reduces the number of seeds and flowers produced per plant compared to non-producers (Stowe and Marquis, 2011). (more…)

Friday Film: 3D Arabidopsis flower

by Charis Cook

Categories: teaching resources

Tags: Friday film

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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.

Working with Natural Antisense Transcripts

by Charis Cook

Categories: methods, resource, Summary for non-specialists, systems biology

Tags: methods, resource

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Published on: September 27, 2012

In January of this year Nucleic Acids Research published a paper describing a database of plant natural antisense transcripts (NATs), PlantNATsDB (Chen, Yuan et al., 2012). It contains around 2 million NATs from 69 plant species, and has a simple viewer showing the two loci involved in each NAT, any overlap, the NAT type, and an option for more detail. It is also possible for search for NATs for specific loci. It is important to note however that the database was last updated a year ago, in September 2011.

This month’s Plant Methods also features a NATs tool, a protocol for NAT identification in plant tissue (Collani and Baraccia, 2012). It is a simple PCR based method, and relies on prior knowledge of the existence of a NAT, as specific primers are needed. Used in association with PlantNATsDB, this is a useful technique. (more…)

NIAB Innovation Farm GM workshop 2: Public Good Programme?

by Charis Cook

Categories: biofortified foods, synthetic biology, Workshops

Tags: biofortified foods, NIAB, synthetic biology, workshops

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Published on: September 25, 2012

Cows and maize, a major GM cattle feed.

For responses to last week’s news story about the GM maize feeding trial that appeared to cause tumours in rats, GARNet suggests: New Scientist, the Science Media Centre, UKPSF, or for a rather more biting commentary, Forbes.

As discussed in the previous post, GM plant products are commonly used worldwide for food and for animal feedstock. But strict European regulations mean growing a GM crop and bringing its product to market is very difficult in Europe. Any progress toward GM products on the European market, especially under a public good programme, is dependent on a relaxation of EU regulations for GM. The consensus view from the NIAB Innovation farm workshop GM: Is it time for a public good programme? was that if GM was treated as another breeding method, and GM crops were subject to the same regulations as conventionally bred plant varieties, industry would be far more likely to invest in GMOs.

Anti-GM feeling in the general public has reduced recently, but governments still implement anti-GM legislation. This in itself makes a government-supported public good programme unlikely in a European country. A public good programme would also have to overcome several technical and legal barriers. A framework would be needed to allow open access to technology and outputs, therefore a unique intellectual property arrangement would have to be implemented. A wide stakeholder steering group, independent of any one institution, to deal with these and other issues would be essential. Several people wondered what exactly a public good programme would look like – there is a successful public GMO programme in China, but it depends almost entirely on government funding and a similar financial commitment from the UK government is unlikely, at least in the near future. (more…)

Friday film: Botany consultant on Avatar

by Charis Cook

Categories: teaching resources

Tags: Friday film, 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: http://www.youtube.com/watch?v=J-l9fuumJ8w

Gene and protein names and symbols

by Charis Cook

Categories: resource, teaching resources

Tags: science writing

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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!

(more…)

NIAB Innovation Farm GM workshop 1: Background to GM discussions

by Charis Cook

Categories: biofortified foods, Workshops

Tags: biofortified foods, NIAB, synthetic biology, workshops

Comments: 1 Comment

Published on: September 18, 2012

On 12^th September, I attended a workshop at NIAB Innovation Farm entitled ‘GM – Is it time for a public good programme?’ There were some very good points made throughout the day, and instead of a chronological account of the presentations, two blog posts on the workshop will outline the main themes that came out of the discussions. The programme is on the Innovation Farm website.

The CEO and Director of NIAB TAG, Tina Barsby, kicked off proceedings by outlining the definition of public good: a ‘good’ that is non-excludable and non-rivalrous, and therefore not produced primarily for profit. Making it clear that the workshop was to be very much focussed on the UK and Europe, Barsby argued that as a market for GM products has failed to materialise, it is time for a non-profit, public good programme, perhaps supported by the government. However throughout the day, it became clear that a commercial market for GM cannot yet be written off.

Barsby went on to describe why GM technology in agriculture is necessary. Farmers battling crop diseases and world leaders trying to ensure a reliable food supply both have the same problem – crop productivity is too low for the demands placed upon it. GM is one of the solutions to this problem, and while in Europe transgenic crops are not farmed, genetic modification is universally used in conventional breeding; from mutagenesis to marker assisted selection. Genetic engineering has the potential to make crops resistant to disease, contain increased nutrition, and withstand extreme weather conditions. (more…)

Traditional varieties are key to modern rice farming

by Charis Cook

Categories: biofortified foods, Summary for non-specialists, teaching resources

Tags: agriculture, biofortified foods, plant nutrients, rice, summary for non-specialists, teaching resources

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Published on: September 13, 2012

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…)

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