Identifying mutations in Arabidopsis – a faster, cheaper method


Highlighted paper: Liu, McCormack and Sheen (2012) Targeted parallel sequencing of large genonmic regions for identifying mutations in Arabidopsis. Plant Methods 8:12

Kun-hsiang Liu, Matthew McCormack and Jen Sheen from Harvard have developed a PCR-based method of identifying mutations in Arabidopsis. It is cheaper and easier than traditional methods of identifying mutations, using bench-top PCR and a new user-friendly method of bioinformatics analysis using web-based resource Galaxy. Liu et al. estimate that using their method to identify a mutation mapped to a 550kb genomic region will cost roughly US$500, a fraction of the usual ten thousand dollar cost of currently used methods of mutant identification.

Liu et al. tested the new method of identifying mutations by searching for new nitrogen response genes. They generated an Arabidopsis thaliana line in which LUCIFERASE was driven by the promoter for nitrogen response marker NIR. Using EMS-mutagenesis, the team made 25 000 mutant NIR:LUC lines and identified seedlings that were nitrate insensitive (nis) or showed nitrate constitutive response (ncr).

When the lines were made, the phenotypes were identified and a second generation was grown. Three second generation lines – ncr1, nis1 and nis2 – were selected for further investigation.

Liu et al. used their novel TPSeq method to locate the mutations causing the ncr1, nis1 and nis2 phenotypes. (more…)

The week in links

Categories: funding, UKPSF
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Published on: July 27, 2012

At GARNet this week…

– Ruth is heading to the 6th EPSO / 18th FESPB joint Conference in Feiburg and will be keeping us updated on Twitter – you can see her ICAR tweets on Storify.

– GARNet was privy to some UK PlantSci2013 planning and it looks like it will be a great week with exciting speakers from diverse areas of the plant science community. It will be in Dundee in April.

– Workshop talks from the Making Data Accessible to All Workshop hosted by GARNet at Egenis earlier in the month are now online.

– As well as the EU FP7 funding that was launched this month, the EU have earmarked €683 million for life science research in 2013. Go to UKPSF news to find out more.

– The UKPSF are looking for case studies on the impact of UK plant science – do you have any?

– Anne Osterrieder’s guest post on iridescence inadvertently coincided with a Guardian article about growing orchids that use iridescence to mimic insects in your garden.

– We want to encourage you to add yourself to Find a Scientist, the searchable database of plant scientists that lets users search for researchers by research interest, name or institution.

– If you want something to distract you from the weather, try out the Extinct! game on the BBSRC website. I’m afraid to say my outlook as a wild plant was pretty bleak.

Structural colour

Comments: 2 Comments
Published on: July 25, 2012

Guest poster Anne Osterrieder discusses iridescence, caused by ‘structural colour’. This article was originally posted on the Annals of Botany blog as My favourite colour is structural colour on July 11th, 2012.

Hibiscus trionum

What do peacocks, CDs and certain plants have in common? They all have multi-coloured parts – feathers, surfaces or petals – which change their hue depending on the angle you look at them. This physical phenomenon in which an ordered repeating surface structure rather than a pigment gives an object its colour is called iridescence.

Iridescence has evolved multiple times in plants and occurs in a lot of land plant families, from angiosperms to algae and ferns. It can impact on how insects and animals see plants. Dr Heather Whitney, a plant scientist from Bristol University, was awarded the President’s Medal of the Society of Experimental Biology (SEB) last week for her novel and interdisciplinary work. Heather studies how plant surfaces become iridescent and how iridescence influences plant-animal interactions. (more…)

FP7 2013 for Plant Scientists

Categories: funding, Uncategorized
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Published on: July 24, 2012
Credit: Page Schneider, Miroslav Sárička, Studio Tachtig via stock.xchng

At the Launch of the FP7 2013 Work Programmes for the KBBE and ENV themes, presentations were given by members of European Commission teams who developed the calls.

Timothy Hall presented an outline of the planned funding allocation of Theme 2: Food, Agriculture and Fisheries, and Biotechnology. The overall scope is ‘Bio-resource efficiency’, with an emphasis on the integration of basic and applied research, and transfer of knowledge to impact and innovation. They aim to fund broader, interdisciplinary topics that cover topics from more than one activity.

There are three activities in this theme, and the topics most obviously relevant to GARNet community are highlighted below:

2.1 Sustainable production, management of biological resources from land, forest and aquatic environments.

  • Crop breeding and management: Legumes (€5Mx2) and small grain cereals (€5Mx2).
  • Plant health: IPM in fruit crops (€6Mx1) and biocontrol in agriculture and forestry (€9x1M)
  • Agro-meterological crop modelling (€2Mx1).
  • Outreach, translation, impact of results: €6x1M projects to get funding to get product market-ready.

2.2 ‘Fork to farm’: Food, health and well-being

  • This activity is worth checking if you work on improving water-efficiency in plants or increasing Vitamin D levels.

2.3 Biotechnology and biochemistry for sustainable non-food products and processes.

  • Plant high value products (€20M for several projects).
  • Emerging trends in biotechnology with the view to maintain biotechnology at the front line of innovation (€9Mx1).

Alison Imrie gave a presentation outlining Theme 6: Environment (Including Climate Change). In this theme, the emphasis is on the prediction of global changes, as well as tools and technologies for monitoring, prevention and mitigation of, and adaptation to environmental pressures and risks.

The activities are: (more…)

FP7 2013 Funding Programme Launched

Categories: funding
Comments: 2 Comments
Published on: July 23, 2012
money
Credit: Miroslav Sárička

On Friday 7 July I went to the launch of the FP7 2013 Work Programmes for the Food, Agriculture and Fisheries, and Biotechnology (KBBE) and Environment (including climate change) (ENV) themes call in London.

For those that don’t know, the objective of the Framework Programme (FP) EU research funding scheme is to enable Europe as a whole to compete with the huge research centers of the USA, Japan, China and India. The EU has funded research and technological development across Europe through framework programmes since 1984. The current FP7 call is the final annual call of FP7, which has been running since 2007.

FP7 2013 is broken into research ‘themes’. Each theme is sub-categorised into ‘activities,’ which include several ‘topics’. The two themes outlined at the launch day are the themes most likely to be relevant to the GARNet community.

From Timothy Hall’s presentation on the KBBE theme, I got the impression that as a general rule, most topics will fund a few projects of around €6-10 million each. Some topics will only fund one project. In both themes discussed, it was clear that proposals that fit the scope of multiple topics would be given preference.

The call was published on 10 July, and applicants have 6 months to submit a proposal. Proposed projects must involve at least three independent entities from three different member states, or if absolutely necessary, ‘associated’ states (nearly anywhere else in the world – see Who Can Apply). The EU wants to encourage partnerships between research groups and Small and Medium Enterprises (SMEs), and some application for funding within certain activities sets out a minimum participation level for SMEs.

National contact points (NCPs) provide free help at all stages of the FP7 application, from assistance putting together a consortium of parties to providing feedback on the draft proposal. The NCPs are listed at the end of this post.

Every presentation emphasised that FP7 starts with an extremely competitive application process. All the speakers agreed that the best proposals have a good consortium of partners, made up of groups with complementary expertise and with no sleeping partners. The project must fit one, or preferably more than one, topic. It must have realistic impact goals – the FP7 funding is a contract and the expected end product, whatever it is, must be delivered. It is essential to read the call carefully and make sure your proposal ticks all the requirements. And they all almost pleaded with the audience not to wait until the last minute to submit.

I’ll be back tomorrow with a more detailed post about the calls. Finally if you weren’t at the ICAR conference, Ruth Bastow who was there for GARNet has collated her tweets so you can pretend you were there!

National Contact Points:

Catherine Holt and Jane Watkins (Beta Technology) KBBE and ENV NCP betaeurope@betatechnology.co.uk

Ewa Block (Technology Strategy Board) Eco-innovation and Industrial Biotechnology NCP ewa.block@tsb.gov.uk

From bench to bountiful harvest … MASC roadmap summarised in current Plant Cell Paper

Highlighted article: Lavagi I., Estelle M., Weckwerth W., Beynon J., and Bastow R. (2012) From Bench to Bountiful Harvests: A Road Map for the Next Decade of Arabidopsis Research. Plant Cell Advance Online Publication.

The Multinational Arabidopsis Steering Committee (MASC), as you might expect from their title, is an international group of Arabidopsis researchers who steer research in a productive direction. MASC reduces redundancy in research and encourages collaborations.  Over the last 20 years, MASC has neatly guided the Arabidopsis community to achievements in genome sequencing, understanding of plant hormones, development of open access bioinformatics resources and much more. Now MASC has planned a roadmap for the next ten years of Arabidopsis research entitled From Bench to Bountiful Harvest.

The roadmap consists of five broad objectives: (more…)

New TAIR10-compatible CDF files and review of RNA labelling methods

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Published on: July 17, 2012

A current paper in Plant Methods assessed the pros and cons of two RNA labeling methods for AGRONOMICS1 tiling arrays, concluding that random priming is more suitable for organelle transcriptome analysis as it can label non-polyadenylated transcripts effectively. They also generated new TAIR-10 based CDF files, which can be used to re-analyse existing AGRANOMICS1 CEL files. The new CDFs can be accessed here.

First of all, the authors gave an overview of the AGRONOMICS1 tiling array. It contains all the probes from the traditionally used Affymetrix ATH1 array, but has additional probes which mean the AGRONOMICS1 array yields expression data for over 7000 more genes, around a third of the genome. 90% of annotated genes on the TAIR9 database are on the array. Mitochondrial and chloroplast genomes are completely represented, and sRNA, tRNA and miRNA can also be detected. The AGRONOMICS1 array has probes that represent both strands of the entire Arabidopsis genome, allowing epigenetic profiling. The quality is comparable to that of the ATH1 array.

Müller et al. compared the GeneChip© IVT express kit, an oligo-dT based RNA labeling technique, with the GeneChip© whole transcript (WT) Sense Target Labeling Assay which uses random hexamers tagged with T7 promotor sequences. Both kits are from Affymetrix, Santa Carla, CA. (more…)

Views on synthetic plant products at the New Phytologist Synthetic Biology Workshop

The three day 4th New Phytologist Workshop on Synthetic Biology started on Wednesday 6th June, and we waited until after the Thursday afternoon coffee break to hear a presentation on plant synthetic biology. It was obvious that plant synthetic biology is not yet as sophisticated as synthetic chemistry and microbiology, and the reasons were implied in many of the talks. Plants are multi-cellular, have weeks-long life cycles and their products cannot simply be skimmed off or distilled from a vat of cells.

Rob Edwards (University of York) was quick to defend plant synthetic biology when I put this to him, pointing out that plant plastids are a means both of expressing a transgene and storing its possibly toxic product, all without affecting the rest of the cell. Plants can be grown cheaply, particularly if engineered to do so, although extracting the product may be expensive and difficult. On the other hand, synthetic biology may be used to enhance the flavor, fragrance or appearance of a fruit or flower and in that case the plant itself is a high-value product which requires no extraction.

While Rob Edwards’ SPPI-net focuses on synthetic biology for non-food plant products, he stated that genetically improved food crops can have great effects. Golden rice has the potential to help prevent blindness in areas where communities living on rice-based diets suffer from vitamin A deficiency, and soybean containing high omega-3 fatty acids can improve cardiovascular health. (more…)

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