Collaborations and training in integrative biology

The prevalence of first systems and then synthetic biology in BBSRC and wider UK research funding calls, the establishment of The Genome Analysis Centre (TGAC), the fact that the term ‘big data’ is mentioned in nearly every meeting of any type about the biological sciences … all these point to the irreversible integration of mathematics into biology.

This blog post is for two groups of people: plant scientists who feel they lack the expertise to confidently maneuver in the world of integrative biology; and theoreticians either interested in plant science, or who would rather not have to spend quite as much time dealing with the mathematical problems of the plant scientists in their professional or non-professional circles. (more…)

Starting your interdisciplinary journey

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Published on: May 14, 2013

This is a guest post by Susie Lydon, Outreach Officer at the University of Nottingham

Plant science is becoming increasingly interdisciplinary, and for early career researchers, gaining experience in working across the traditional subject boundaries can be very useful. A common problem is that many of the training opportunities in relevant areas of maths and computer science assume a level of background knowledge which many biologists do not have (or do not feel confident about).

The Centre for Plant Integrative Biology at the University of Nottingham has been running ‘summer schools’ (which actually take place in early September!) for six years now which aim to bridge the gap for interdisciplinary ‘beginners’.

Mathematical Modelling for Biologists is a four-day residential course which provides an introduction to biological modelling. The course comprises integrated lectures and computer practical classes, and the background knowledge assumed is ‘rusty A-level maths’ or equivalent. Participants learn from examples taken from gene regulation, biochemical reactions, population dynamics, and epidemiology.

Image Analysis for Biologists is a three-day residential course running for the second time in September 2013. The aims of this course are to allow participants gain an understanding of image analysis approaches commonly used in the biological sciences, and confidence in applying them. Like the modelling course, it comprises integrated lectures and practicals using relevant software. Many of the examples are drawn from CPIB’s work in plant image analysis, but the course is open to biologists from any discipline.

For more information about these courses, and to apply to attend in September 2013, visit the CPIB events page, or contact CPIB’s Outreach Officer, Dr Susie Lydon.

Image credits: Centre for Plant Integrative Biology

How do jasmonates control plant development?

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Published on: March 5, 2013

Jasmonates mediate responses to plant biotic- and abiotic-stress and influence plant development as well as secondary metabolism (for a recent review, see Avanci et al. 2010, GMR 9:484; Acosta and Farmer 2010, Arabidopsis Book PMC3244945. Today’s highlighted paper, at the moment in advanced view from Plant Physiology, sheds new light on the elusive mechanism behind the jasmonate inhibitory effect on plant organ development and growth, which has traditionally taken a back seat to its involvement in the stress response.

The authors used a range of traditional and systems-based methods to uncover the mechanism of growth inhibition by jasmonates (JA). First of all, they looked at the cell size and cell number in the first true leaves of Arabidopsis mutants altered in JA synthesis and perception, aos and coi1 respectively, in the presence and absence of methyl jasmonate (MeJA) treatment. Both cell size and cell number were reduced after treatment with MeJA in aos1 and the Col gl1 wildtype. This effect was minimal in coi-1, demonstrating the importance of COI1 in JA-mediated cell growth inhibition. Importantly, using flow cytometry they also showed that MeJA delays the switch from the mitotic cell cycle to the endoreduplication cycle, again in a COI1-dependent manner, as well as inhibiting mitotic cycle itself.

MeJA treated Arabidopsis seedlings. From left to right: col gl1, aos1, coi1

To work out the mechanism for JA’s effect on cell size, number, and ploidy, Noir, Bömer et al. performed novel global transcriptional profiling to identify the molecular players whose expression is regulated during leaf development by jasmonate via COI1. Senior author on the paper Alessandra Devoto from Royal Holloway, University of London explained, (more…)

An Introduction to Synthetic Biology for Plant Researchers

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Published on: February 20, 2013

 

Synthetic biology is a fast-growing research area both in the UK and further afield and UK policy makers and funders are taking it very seriously. In November last year, George Osborne announced a £20 million investment for Synthetic Biology and as a result Synthetic Biology is one of the few research areas in the BBSRC portfolio to receive an increase in funding. This is in addition to the numerous schemes that are already supporting Synthetic Biology (including BBSRC, EPSRC and TSB). 

To make sure that UK plant researchers can make the most of these funding opportunities, GARNet is hosting a meeting to introduce the concept of Synthetic Biology and the many and varied applications of Synthetic Biology at the molecular, cell and whole plant level.

Like Systems Biology before it, Synthetic Biology can be viewed as both a tool and a scientific approach for understanding and furthering basic science and as a means of developing commercially important plant products. Synthetic Biology in plants is under-researched, but has enormous potential and it is time for UK scientists of all disciplines to explore it.

So to make sure you understand what Synthetic Biology is and how you might apply to your research area, make sure you register for An Introduction to Opportunities in Plant Synthetic Biology. For more information go to: http://www2.warwick.ac.uk/fac/sci/lifesci/news/synbio. Please note that registration fee covers the cost of accommodation and meals during the meeting

To help us promote the meeting, please print out this poster and put it up in your department. Please also forward this email to anyone from other departments you think will be interested.


New Methods and Resources (I)

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Published on: February 5, 2013

On this blog, I highlight a new method or resource pretty regularly. I used to work in what I think is a fairly normal UK plant science lab, so I try to comment on aspects I would have found useful to know about, for example if the method requires a machine not every lab has, or if it is unclear about anything. However, there are many, probably excellent, new open software and techniques which I don’t highlight on the blog because I am completely unfamiliar with their background.

For today, here’s the first part of a round-up of plant methods and resources published over the last few months. If you have used them, feel free to let me know how they worked in the comments, or through email or Twitter. And if you would like to review a method or resource for this blog, please get in touch!

iRootHair is a free, online, curated, expandable database of root hair genomics. Kwasniewski et al. (2013; Plant Phys. 161:28-35) built the database, which currently includes information about 153 root-hair related genes. The majority of the genes are from Arabidopsis, but maize, rice, tomato, and barley genes are also included. There is a page showing figures of various root phenotypes, which users can click through to see the genes associated with a specific phenotype; and a similar one for root processes like tip growth. (more…)

Plant defence with Katherine Denby

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Published on: December 18, 2012

The second of our video podcasts from PlantSci 2012 is from Katherine Denby, from the University of Warwick. She works on how plants respond to changes in their environment, and in particular in response to pathogens. If you have a slightly cloudy idea of what systems biology is she explains it very well here, including how it can affect future food security. She also explains why she works on Arabidopsis, saying, “It’s just so much quicker to do things in Arabidopsis!”

The wheat genome – the best thing since …

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Published on: December 4, 2012

When Anthony Hall trailed the wheat genome paper (Brenchley et al.; published on Thursday) at last week’s GARNet Tools and Technologies workshop, I knew it was excellent blog fodder. When I sat down to read the paper on Friday though, it seemed like a bad choice for a blog post. This is no restricted-access, wordy paper with obvious aspects to highlight in an accessible way; it is open access and describes the bread wheat genome, comparing it to related species concisely and clearly. However, in many ways this paper is important, even a landmark, because of what is not in it. So instead of highlighting the paper, I will attempt to explain why it was all over plant science social media and science news sites, and why it deserved far more coverage from the general media.

First, the bread wheat (Triticum aestivum) genome was, to steal a phrase from the Annals of Botany blog, the Everest of crop genomes. Sequencing it was difficult due to its enormous size. It is a hexaploid, essentially containing the genomes of three separate grass species. First of all Triticum urartu hybridized with a Sitopsis species to form tetraploid species Triticum dicoccoides, which eventually hybridized with Aegilops tauschii around 8000 years ago (for more information, see WheatBP). Both hybridization events increased the ploidy of the offspring. In 2010, the draft sequence of this huge genome was released, and analysing it must have seemed almost impossible. In the end, the genome took the team just two years to analyse – and that is what is published. It is an amazing achievement, which took a multinational team of scientists many years. The analysis showed that the genome contains 94 – 96 000 genes. The team were able to identify the parent species of many gene families and track their development over time.

Second, this work and other high profile ‘big data’ stories celebrate groundbreaking achievements in biological sciences. Sequencing technologies and analysis techniques have advanced beyond recognition since the human genome was sequenced in 2003. Many sequencing methods were used in the wheat genome project, all of which are either out of date or have been upgraded since – so sequencing more wheat genomes in a project similar to ENCODE or the 1001 Genomes project will take far less time. Similarly the computing power needed to analyse 17 gigabase-pairs of DNA sequence was unheard of in 2000, but 12 years later it is not only here, but improving. The bread wheat genome marks wheat’s entry into the ‘big science’ era.

Third, and most importantly, wheat is one of the most important plants on earth. It makes up 20% of the calories consumed by humans (statistic from Brenchley et al.). When crops fail, it affects everyone. This year saw poor weather in wheat regions across the globe, leading to warnings of unprecedented rises in the price of bread in the UK. Plant scientists are working with agriculturalists to improve crops and reduce the risk of harvest failure, but a 2011 Science paper (Lobell et al., 2011) commented that in some regions, the negative effects of climate change offset the technological advances that should increase crop yields. A fully sequenced and analysed bread wheat genome is a great asset for crop scientists working on developing breeds that may, for example, be able to withstand draughts and floods, and contain higher levels of nutrients.

The wheat genome sequence is not only a triumph for crop scientists. The more information there is out there on wheat ‘omics,’ the easier it is for Arabidopsis researchers to transfer their knowledge to wheat and improve the ‘impact’ of their projects – or find out in advance that for that particular gene or process, cross-over is impossible.

The sequencing of the Arabidopsis thaliana genome was completed in 2000, causing a paradigm shift in plant research. In 2005 Bevan and Walsh published an overview of the progress made in the first five years after the annotated genome was published, including the establishment of large stocks of the gene disruption lines now taken for granted. The sequencing of the wheat genome opens up new avenues of research for crop scientists and I am looking forward to seeing the results in the coming years.

There are instructions on how to download and use the wheat genome sequence at MIPS.

Highlighted paper: Rachel Brenchley, Manuel Spannagl, Matthias Pfeifer, Gary L. A. Barker, Rosalinda D’Amore, Alexandra M. Allen, Neil McKenzie, Melissa Kramer, Arnaud Kerhornou, Dan Bolser, Suzanne Kay, Darren Waite, Martin Trick, Ian Bancroft, Yong Gu, Naxin Huo, Ming-Cheng Luo, Sunish Sehgal, Bikram Gill, Sharyar Kianian, Olin Anderson, Paul Kersey, Jan Dvorak, W. Richard McCombie, Anthony Hall, Klaus F. X. Mayer, Keith J. Edwards, Michael W. Bevan & Neil Hall (2012) Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature 491, 705–710 doi:10.1038/nature11650

Image credits: Great Harvest by MMNoergaar and Challah by ladySorrow, both via stock.xchng.

Systems of plant defence

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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…)

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