Friday Film: 3D Arabidopsis flower

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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

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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?

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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

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!


NIAB Innovation Farm GM workshop 1: Background to GM discussions

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Published on: September 18, 2012

On 12th 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

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…)

High-throughput, cheap, reliable DNA extraction method

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Published on: September 11, 2012

Highlighted article: Zhanguo Xin and Junping Chen (2012) A high throughput DNA extraction method with high yield and quality. Plant Methods 2012, 8:26 doi:10.1186/1746-4811-8-26

Judging by the fact that it was accessed 1400 times in less than a month, the DNA extraction method described by Xin and Chen in last month’s Plant Methods must be worth a look.

Having had a look, I can tell you it seems to be an invaluable method for cheap, reliable high-throughput DNA extraction. It works on seeds and leaves from a number of plants, and according to the abstract, one person can manage 192 extractions in a working day. Using the price estimation in the paper, this would cost about £13 in total for consumables.

The protocol is clear and easy to follow, setting out exactly what reagents, consumables and equipment you will need so there will be no panicked begging of microtitr plates from a friend halfway through the extraction. As well as standard lab equipment which should be accessible to most researchers, you will need MagAttract Suspension G. MagAttract provides  the simple, efficient clean up step, while the rest of the protocol is based on a traditional CTAB extraction method.

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