August 2012 - Weeding the Gems

NGS and the tomato genome

Categories: methods, teaching resources, Workshops

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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

Method: New and improved multiplex PCR

by Charis Cook

Categories: methods, Summary for non-specialists

Tags: methods, PCR, Plant Methods, summary for non-specialists

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Published on: August 30, 2012

Highlighted article: Daxing Wen and Chuqing Zhang (2012) Universal Multiplex PCR: a novel method of simultaneous amplification of multiple DNA fragments. Plant Methods 8:32 (Online preview) doi: 10.1186/1746-4811-8-32

Background

Multiplex PCR allows amplification of multiple targets in a single PCR experiment. It is possible to amplify several sections of a single template, or to amplify different templates using a number of primer sets. If there are multiple primers in a reaction, it can be difficult optimise the PCR reaction to maximise the efficiency of every primer, and it is likely that some cross-hybridisation and mis-priming will occur.

Figure 3B from Wen and Zhange (2012). A comparison of multiplex PCR (Lanes 1-4) and universal multiplex PCR (lanes 5-8), using the same primers with universal adaptors. The band intensity from traditional PCR is very variable, but it is consistently strong when the universal adaptors are used.

Image credit: BioMed Central

The Method

Wen and Zhang from Shandong Agricultural University have devised a way around the inconveniences of multiplex PCR to develop a universal multiplex PCR method. ‘Universal adaptors’ are linked to specific primers, making the annealing temperature of the adaptor-primer structures 70°C. (more…)

Links for Women in Science (and family men too)

by Charis Cook

Categories: funding, resource, Women in Science

Tags: Athena Charter, funding, grants, Women in Science

Comments: 1 Comment

Published on: August 28, 2012

Some institutions which support women in science and family-friendly working practices

At the University where I did my PhD, male PIs far outnumbered female PIs in the School of Biological Sciences. The Head of School and all the Heads of Departments were male. The faculty lists of other universities show a similar story – and this is in life sciences, the science subject most dominated by girls at A-level. Gender balance among fellows of Royal Society is even more skewed, perhaps reflecting the wider scope of the Society, at 5% female.

These unbalanced ratios are not seen at school, university or even at post-doc level, so there is a time early in academic careers when more women than men leave academic research. The UK Resource Centre for Women in SET and the Royal Society of Chemistry commissioned a report to find out why. The report concluded that the lack of women in many areas of academia can seem isolating and off-putting; and an academic career demands a working life dictated by experiments and deadlines, with no room for part-time work or career breaks. The report also notes that both men and women are put off by the difficulties of life in academia, but more men than women are happy to make the sacrifices.

There are organisations and individuals calling for change, and providing support for female researchers at all stages of their careers. I have collected them below – feel free to get in touch if you know of any others.

Please note that many of these funds are available to men who require flexible working times and support for dependants. Most of them are not open now, but call for proposals annually or bi-annually. (more…)

Coming up soon

by Charis Cook

Categories: resource, UKPSF, Workshops

Tags: conferences, events, resources, UKPSF, workshops

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Published on: August 27, 2012

These are just a few of the events listed on the UKPSF Events Calender.

Register now for the GARNet New Technologies to Advance Plant Research workshop: http://www2.warwick.ac.uk/fac/sci/lifesci/news/newtech

Warwick Crop Centre are holding an Open Afternoon on 19^th September. Visitors will be able to view the facilities, including field and glasshouse trials, and learn about the research and training opportunities.

Also on 19^th September, EBI are holding a training course for PhD students and post-docs to train them to use the new PhytoPath resource.

The BBSRC funded Wheat Improvement Strategic Programme are running a course on wheat genetics at the John Innes Centre on 19-22 November 2012. There are only 10 places available but it will be a good introduction to cereals research and crop breeding for undergraduates, postgraduates or junior breeders. Apply here until 1 October.

There will be an international meeting on Imaging in Cell Biology in Windsor Great Park on 14-17 October. There are free places for graduate students and post-docs.

The International Symposium on Plant Photobiology will be held in Edinburgh in June 2013. To mark the launch of the event, a special launch price is available until 2 September – book early to get the good rate!

And something else…

Help GARNet assess the use of new Arabidopsis lines by doing a very short survey on MAGIC lines.

New open access resource for plant pest and disease management, detailed on PlantSci.

PLoS ONE have put together an impressive collection of all their synthetic biology papers.

NGS and root endophyte assembly cues

by Charis Cook

Categories: Summary for non-specialists, teaching resources, Workshops

Tags: endophyte, microbiology, plant-microbe interactions, teaching resources

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Published on: August 24, 2012

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

Background

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

by Charis Cook

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

Tags: agriculture, biofortified foods, Gates Foundation, nutrition, synthetic biology, vitamin A

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Published on: August 22, 2012

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…)

Resource: Dataset of Arabidopsis genes with a loss-of-function mutant phenotype

by Charis Cook

Categories: methods, resource, Summary for non-specialists

Tags: gene, methods, phenotype, resources

Comments: No Comments

Published on: August 21, 2012

Highlighted article: J. Lloyd and D. Meinke (2012) A Comprehensive Dataset of Genes with a Loss-of-Function Mutant Phenotype in Arabidopsis thaliana. Plant Physiology, January 2012 pp.111.192393.

In plant science, many published papers involve at least one loss-of-function mutant. A huge number of mutant Arabidopsis lines exist in labs all around the world, detailed in as many journal articles. Now however the genotype and phenotype information for loss-of-function Arabidopsis mutants is stored one place: a dataset assembled by Johnny Lloyd and David Meinke of Oklahoma State University.

Lloyd and Meinke painstakingly went through TAIR, their own database SeedGenes.org, and PubMed to find 2400 Arabidopsis thaliana genes with a loss-of-function mutant phenotype. Out of necessity, the database excludes the effects of under- or over- expression of genes.

The phenotypic effects of gene knock-outs were classified into four groups: essential, morphological, cellular-biochemical, and conditional. The groups were divided into classes reflecting the developmental stage or organ where the phenotype manifests itself, and further divided into subsets which specify the characteristic affected by the phenotype, for example ‘pigmentation’, ‘gamerophyte defective’, and ‘stomata, trichomes’.

The dataset is found in the supplementary data of the paper. Supplemental Table 2 is the complete dataset. On tab 1 the dataset is sorted by locus number and includes 19 columns of information on the gene and the mutant phenotype. This information encompasses the classification of the phenotype, a description of the phenotype, and a reference to the lab in which the research was carried out. (more…)

Tools and Technologies to Advance Plant Research

by Charis Cook

Categories: methods, Workshops

Tags: GARNet, GARNet workshop, next generation sequencing

Comments: 1 Comment

Published on: August 17, 2012

Next generation sequencing is now this-generation – it is the go-to method of analysis in much of molecular biology. GARNet is running a free Genetics Society Arabidopsis Sectional Interest Group workshop on the varied applications of next generation sequencing, including identifying novel mutations, RNA sequencing and chromatin mapping, to introduce researchers new to NGS to this new technology and how it can advance plant research.

For more information, including the programme and registration form, go to:

http://www2.warwick.ac.uk/fac/sci/lifesci/news/newtech/

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