Weeding the Gems - Page 60 of 67 - the GARNet community blog

Systems of plant defence

by Charis Cook

Categories: plant pathogens, systems biology

Tags: plant pathogens, systems biology

Comments: 2 Comments

Published on: November 8, 2012

Arabidopsis leaf cells, stained to visualise the cell wall and Botrytis cinerea mycelia

Today’s highlighted paper demonstrates the scale of the pathogen response in greater detail than has been published previously. Windram et al. (2012) profiled gene expression in Arabidopsis thaliana leaves every two hours after infection with Botrytis cinerea, until the fungus was truly established 48 hours after infection.

On the whole, until now research into the pathogen response has been at the pathway-level. Many details are known about the plant pathogen response, for example it is possible to identify loci responsible for resistance, as highlighted on this blog last week, and the intricacies of the oxidative burst are being discovered. When we understand these kinds of details, it is possible to make aphid-repellant crops, and harness the TALE tools used by Xanthomonas spp. to make disease resistant rice. On the other hand, they are just details – a close-up, zoomed in fraction of the whole, and broadly speaking it is luck if a piece of research provides anything of commercial worth.

A systems biology approach allows us to see the whole picture rather than the details of a close-up. From the data in Windram et al., we now know that a third of the Arabidopsis genome is differentially expressed in leaves infected with Botrytis compared to mock-inoculated controls. This represents a huge chunk of defence-related pathways, not previously studied, which could be affected by any attempts to improve pathogen resistance in plants.

This experiment was a timecourse, which allowed the team to record the timings of defence response pathways to two-hour time slots, like ethylene synthesis at 14 hours and response to jasmonic acid at 16 hours post-infection. Additionally, it showed that pathways including translation, photosynthesis, and protein phosphorylation were all down-regulated, and the order and timing in which they occurred. The ability to assign each process a time is important for modelling and predicting regulatory mechanisms. (more…)

Phytotracker

by Charis Cook

Categories: methods, resource

Tags: Plant Methods, resource

Comments: No Comments

Published on: November 6, 2012

Fig. 4 from Nieuwland et al. (2012), showing the Phytotracker labels

If you have ever been frustrated by a less than clearly labeled seed stock, not knowing what the green and yellow dots mean, how long its been in that drawer, or which generation it is, GARNet Chair Jim Murray’s lab in Cardiff have worked out a system that will help.

Phytotracker is a system that organizes your seeds for you. Of course it depends on people recording the tray number and parent lines in the database, and correctly labeling the seed stocks and plasmids in the lab. However, once you’ve done that, you can forget about it because Phytotracker does the remembering for you – everything from which plasmid was used for the transformation to when to harvest the seeds.

The system is well explained in the paper, which was published in Plant Methods in October. If you want to try the system out, you’ll need Filemaker Pro (version 8 or later), or for a fully networked solution Filemaker Pro Advanced (version 8 or later: currently Filemaker Pro is version 12). Your University may already have a site licence! You’ll also need printers in your growth rooms and labs to print labels for the trays, plants, and seed stocks. Commitment from everyone in your group is essential – this system would fall apart if you have a regenade group member who insists on labeling with autoclave tape and a Sharpie. It has been successfully used in Cardiff for five years though, so it looks like a system that is worth committing to.

Highlighted article: Jeroen Nieuwland, Emily Sornay, Angela Marchbank, Barend HJ de Graaf, James AH Murray (2012) Phytotracker, an information management system for easy recording and tracking of plants, seeds and plasmids. Plant Methods 8:43

Download Phytotracker here: http://sourceforge.net/projects/phytotracker/

Arabidopsis basics

by Charis Cook

Categories: teaching resources

Tags: Arabidopsis, Friday film, GARNet

Comments: 1 Comment

Published on: November 2, 2012

We added a new page to this blog to show how basic Arabidopsis research works. This is for anyone who is on the periphery of plant molecular biology but doesn’t work directly on Arabidopsis thaliana – teachers, undergraduates, environmental scientists … whoever.

To go with the new page, here is a time-lapse video of growing Arabidopsis thaliana plants. Although it is a little out-of focus at the beginning, I chose it to show you because it shows how frustrating Arabidopsis research can be! At around 1.20, the plant on the left starts to bolt, which is when the stem begins to grow. It grows so quickly after all those days of watching the rosette leaves get bigger. The plant on the right, which has the same size rosette, doesn’t start to bolt until about 1.34 – it probably won’t catch up with the first plant until they both have siliques that are drying out. Developmental stage is important in a lot of experiments, so it is often necessary to grow far more plants than you expect to use so that you have a good selection of plants at the same growth stage when you start the experiment.

Stephen Altschul on BLAST, BRCA1 and the Wild Duck

by Guest Blogger

Categories: guest blogger

Tags: guest blogger, interview

Comments: No Comments

Published on: November 1, 2012

Guest post by Sandra Smieszek

The creator of the basic local alignment search tool (BLAST) and an eminent bioinformatics forerunner and literati does not call for much introduction. Stephen Altschul (pictured right) graduated summa cum laude from Harvard University, and has a Ph.D. from MIT, both in mathematics. What BLAST can do for us is something we all know yet the quintessence is in how it originated, and even more interestingly, the man behind the scenes. It is certainly my great pleasure to introduce Stephen Altschul, who will provide us not solely with the story of his algorithms, but additionally of the power-law explosion of bioinformatics over the past decade.

SS BLAST was published in Journal of Molecular Biology in 1990. Since that time it has been cited over 43,568 times. How does that feel?

Certainly accomplished, it was designed to be faster than FASTA at finding very strong similarities. It was something of a surprise that it performed as well as it did at finding weak similarities as well.

SS What influences directed you to your specific area of research? Who influenced your scientific thinking early in your career, and how?

Having graduated, I spent a lot of time reading about potential applied mathematical problems in biology. Among the inspirational books I read was a textbook entitled Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison by Sankoff and Kruskal. I read The Double Helix by James Watson. I travelled a lot to conferences, yet speaking of individuals that had particular impact, David J. Lipman, the present director of NCBI, was my great inspiration. That is a route I took from mathematics per se to the world of bioinformatics.

SS What scientific discovery over the past couple of years had a major impact upon you?

The most exciting discovery I was involved with as it unfolded was certainly the characterisation of BRCA1 in early 1990s. It was a perfect example of applying sequence alignment tools for significant discovery of functional motifs of BRCA1. I want to credit Peer Bork along with Eugene Koonin. We mapped out the functional motifs. BRCA1 was partitioned into globular and not globular domains. We have noticed a similarity between the designated 53BP1 that has been identified by its ability to bind p53. The other hits included KIAA0170 and RAD9. The probability exceeded 87% that a pattern as strong as the previously noted ‘granin motif’ would be shared by a random sequence as long as BRCA1 and the then-extant motif database, thus lending no statistical support to the relevance of this motif. Now the C-terminus of BRCA1 is known to contain two 95-residue BRCT domains, which are also found in many other proteins involved in DNA repair and cell cycle regulation. The crystal structure was later defined. It is not solely the story of characterization of one of the most important tumor suppressor genes in cancer, but additionally the story of how well-applied statistics can shed light on true positive interesting domains in this example.

SS What was the most difficult stage in your career?

I guess right after graduation getting applied problems was the most difficult stage, but it did not last long. I ended up working in a ‘lucky field’ – one that has grown rapidly over the past decade. (more…)

The genetics of broad-spectrum resistance

by Charis Cook

Categories: plant pathogens, Summary for non-specialists, teaching resources

Tags: Arabidopsis, New Phytologist, plant pathogens, summary for non-specialists, teaching resources

Comments: 1 Comment

Published on: October 30, 2012

Downy mildew infection of Arabidopsis thaliana seedlings

Highlighted article: Dmitry Lapin, Rhonda C. Meyer, Hideki Takahashi, Ulrike Bechtold, Guido Van den Ackerveken (2012) Broad-spectrum resistance of Arabidopsis C24 to downy mildew is mediated by different combinations of isolate-specific loci. New Phytologist DOI: 10.1111/j.1469-8137.2012.04344.x

It is a mark of how effective plant immune systems are that most bacteria, fungi, and viruses do not affect plants at all either because plant tissues are not suitable for them to live in, or they are fended off. Of course there are pathogens that are compatible with plants – and within species that share compatibility, there are pockets of resistance. Some sub-groups are resistant to specific pathogen isolates, and this is caused by dominant resistant genes. A much broader, more complicated, and less common form of resistance occurs when a particular accession is resistant to a whole pathogen species, or several species. This is broad-spectrum resistance, and it can be caused by a simple dominant gene or multiple genes. Natural broad-spectrum resistance is not simple to transfer from its origin to a commercial crop because it can come from a complex set of genes which are not necessarily all dominant. (more…)

Varying degrees of open access

by Charis Cook

Categories: Open Access

Tags: Friday film, publishing

Comments: No Comments

Published on: October 26, 2012

One of the things that this summer’s GARNet workshop, Making Data Accessible to All, made Ruth and I think about was the varying degrees of open access allowed by publishers. All journals accommodate open access, as some funding bodies now demand all research undertaken with their funds be published open access. This service is not free, so it will usually only be used when the funding body demands it. If open access is something you feel strongly about, PLOS have a useful ‘Open Access Spectrum,’ which can be used to judge journals on an open access grid. This may be useful in thinking about where to publish your work.

Publishing policies vary enormously. Some subscription-only journals allow open access after an embargo period of between six months and two years. Some journals allow authors to put their papers or toll-free links to the article on their personal websites or databases like PubMed Central if they chose to (sometimes immediately, sometimes after a set period of time), and others forbid any publication of their articles anywhere except the official, subscriber-only, journal website. It’s always worth a quick search for your paper if you can’t access it through the publisher – there could be an unofficial (but legal!) version or toll-free link out there somewhere!

There is information about specific plant journals below (feel free to leave a comment if I’ve missed anything out), but since it’s Friday, here is a slightly surreal and extremely one-sided video about academic publishing – thanks to aoholcombe:

(more…)

Guest post: Plantwise Knowledge Bank Map

by Guest Blogger

Categories: guest blogger, plant pathogens, resource

Tags: CABI, guest blogger, plant pathogens, resource

Comments: No Comments

Published on: October 25, 2012

Tim Holmes works for CABI, a not-for-profit international organization that improves people’s lives by providing information and applying scientific expertise to solve problems in agriculture and the environment. Plantwise is an initiative, led by CABI, to improve food security and the lives of the rural poor by reducing crop losses. It is for the Plantwise Knowledge Bank, that Tim tackles the challenge of presenting species distribution data to a diverse group of users.

Plantwise is the biggest project that the whole of CABI has ever been engaged in together. It brings together all the strands of our work, from the publishing business, through scientific research, to international development. The Knowledge Bank is my bit of the programme, and something I’m immensely proud of. We’ve been developing a suite of data and information tools over the last few years, and it’s to one of these that I’d like to introduce you now.

The Plantwise Knowledge Bank Map was the first tool concept that we presented back in 2010, and straight away it was our number one priority to make it a reality. The genesis was a crude, but cool looking, Google Earth presentation of CABI’s plant pest distribution data. The globe spun and zoomed impressively, but it wasn’t going to be the useful scientific tool that we were after. For starters you couldn’t see the whole of the Earth’s surface at once; problematic if you wanted to get a Baumgartner’s-Eye view of the worldwide range of a pest! It was problematic too if you wanted to build it into a website that would fling around large datasets AND do so for users with restricted internet bandwidth. So we trialled many different bits of mapping software and settled on something that would display a Google Maps-style projection and would let us do as much of the map production leg-work on our servers. It would be familiar and fast. (more…)

Funding round-up: Winter

by Charis Cook

Categories: funding

Tags: BBSRC, European Commission, funding

Comments: No Comments

Published on: October 23, 2012

Research awards

Gates Foundation Grand Challenges Exploration: Deadline 7 November. £100 000 is available to fund development of an idea that can help solve one of the Gates Foundation’s Grand Challenges. If you have an idea to do with agricultural development or medicinal plants, take a look at this. It is a short application, which requires no prior data – worth a try for a project too risky to pitch to a different funding body!

FP7 KBBE: Deadline 5 February. See previous blog posts (1, 2) on this call.

BBSRC Responsive Mode: Deadline 9 January. The bread and butter of plant science research. Remember to apply to Committee C if your work is to do with ‘genes or development,’ as its remit has changed. There will be a plant scientist sitting on it. Committee B remains the main route for plants and microbes.

BBSRC LINK and BBSRC Industrial Partnership Awards: Deadline 9 January. Funding available for collaboration between a research group and industrial partner, who must fund at least 50% of the total economic cost of the project for a LINK award, or 10% for an IPA.

ERC Synergy Grant: Deadline 10 January. Up to €15 000 000 is available for a project lasting up to six years. Groups of between 2 and 4 PIs and their groups can apply for this huge grant. This is part of the FP7 Ideas Work Programme and proposals must comply with their priorities. According to the Guide for Applicants, ‘The aim is to promote substantial advances in the frontiers of knowledge, and to encourage new productive lines of enquiry … methods and techniques, including unconventional approaches and investigations at the interface between established disciplines.’ (more…)

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