Plant research goes EPIC

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Published on: October 25, 2013
A DNA molecule that is methylated on both strands on the center cytosine. DNA methylation plays an important role for epigenetic gene regulation in development

Early last week I attended the EPIC (Epigenomics of Plants International Consortium) one day symposium on Mapping the Epigenomes of Plants and Animals at the John Innes Centre. Epigenomics is an exciting branch of biology, with active, cutting-edge research ongoing in plants, animals and microbes alike.

The EPIC Planning Committee aim to crack and control the ‘second code’ of biology (they overview the field and their plans in a 2012 open access Plant Cell paper). A major step toward this ambitious goal is the CoGe Epigenomics Browser, a web-based comparative genomics system that provides access to 20,000 genomes from 15,000 organisms, and users can take advantage of over 30 tools for the analysis, comparison, and visualisation of genomic data from the scale of whole genomes to individual nucleotides. The creators of CoGe, Eric Lyons and Brian Gregory, have worked with iPlant to build a secure and versatile user-data management system, and like iPlant CoGe has a Wiki with extensive tutorials and support pages.

The biggest session at the Symposium was on DNA methylation. Gavin Kelsey, Mary Gehring and Rob Martienssen, who is speaking at GARNet 2014, spoke about the mechanisms of parental imprinting and their impact, which can continue for generations – and I have to say, at this point I wondered how many lab conflicts and frustration-inducing experimental problems are caused by our current lack of understanding about epigenomic effects!

Julie Ahringer and Doris Wagner spoke about their research digging down into the physical properties of epigenomic features and the mechanisms of chromatin regulation. Oliver Stegle and Claude Becker are both working on understanding how genome, transcriptome, epigenome and environment interact to produce a phenotype. Xiaofeng Cao is applying this approach to controlling agricultural traits in rice.

There were a few non-plant science speakers, including Eric Miska who presented his research on piRNAs, which he has shown are vital for maintaining fertility over generations and are also involved in sperm production. Interestingly Blake Meyers has identified phasiRNAs in maize, small RNAs that are involved in sperm production and he suggested they may have convergently evolved to fulfil a similar role as piRNAs.

Image credit: Christoph Boch via Wikimedia Commons. “Details: The picture shows the crystal structure of a short DNA helix with sequence “accgcCGgcgcc”, which is methylated on both strands at the center cytosine.”

 

Minding the scientific skeleton in the closet

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Published on: October 22, 2013

Two weeks ago, Pamela Roland from UC Davis retracted a Science paper originally published in 2009. She gave her perspective on the events leading to the retraction in a Scientific American blog post. Here a post-doc in her lab gives his side of the story, emphasising the importance of teamwork, honesty, and willingness to speak up at every level of the academic hierarchy.

Benjamin Schwessinger obtained his PhD at The Sainsbury Laboratory, under GARNet Advisory Committee member Cyril Zipfel. He joined Pamela Roland’s UC Davis group in 2011. This post is an edited version of DO mind the scientific skeletons in the closet, originally published on the blog he co-hosts with Ksenia Krasileva, a postdoctoral fellow in Jorge Dubcovskey’s lab.

 

Yet another Science paper retracted today. Nothing much new unfortunately – except that for me and my colleagues this was not just another example of non-reproducible work. We planned our research projects around it. So here are my thoughts about this, and just in time for Halloween.

There has been much talk about the problem of reproducibility of data and the rise in retractions. The discourse is mostly centered around the perpetrators and the negative impact this sloppy or knowingly flawed science has on the industry and the perception of scientific endeavor in society: Who did this awful study? What reviewer did not catch this missing control, the sloppy stats? Why don’t they admit their mistake? What’s wrong with peer-review? Well, much is wrong with the industry, and many people have great ideas about how to tackle some of these issues.

What is usually missed from the discussion is the impact such dubious science can have on young, early career scientists. What do you do if you come to a famous (or not so famous) lab, you get a project, which is based on fantastic data and high impact publications, but you cannot reproduce it? How do you approach this issue? What does it mean for you and your career if your project goes to shreds because it’s based on bad data? Do you get another chance? Will you be forever associated with this flawed data and your reputation damaged? Will you get so disillusioned with science to the point that you leave academia? Do you try to fix the problem or silently move on? Do you tell the boss and explain your situation? Or is it you? Can you just not get it to work? Can it really be that this is all wrong? Why cannot I reproduce this data? And the questions go on and on … I think everyone can appreciate the complexity of the issue. Many people I talked to had their own experience to share.

Here is what’s frightening:  sloppy science and misconduct, I thought, is something you read about in journals and not something I would experience myself. This would never affect me or close friends in other labs, who are all great scientists in my eyes. I was wrong. (more…)

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…)

AHDB Crop Research Conference: Knowing your enemy

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Published on: October 9, 2013

GARNet Research and Engagement Officer Lisa Martin reports on the AHDB Crop Research Conference.

On 25 September, I hopped on the train down to London to attend the Agriculture and Horticulture Development Board (AHDB)’s Crop Research Conference. This event set out to bring together researchers and the agricultural industry “to take the latest research out of the laboratory and into the field”. The theme for the day was “Knowing your enemy – the future of crop protection” and speakers were divided into three categories.

In ‘Advances in Genomics’ we heard from Lin Field from Rothamsted Research, who spoke about her work in insect genomics. Paul Birch from the James Hutton Institute also provided insights into Phytophthera pathogenomics and disease resistance, while Rick Mumford from the Food and Environment Research Agency (FERA) spoke on the subject of advances in plant diagnostics.

In particular, Dr Mumford highlighted the recent development of Loop-mediated isothermal AMPlification (LAMP) technology; a rapid, field-based diagnostic method of DNA amplification that has the ability to produce conclusive test results in as little as 10–15 minutes, and provides improvements over traditional PCR methods. He also spoke about how next generation sequencing (NGS) is being used to identify new plant viruses, especially a recent breakthrough in identifying a novel virus responsible for internal carrot browning.

On to ‘Population and Evolutionary Biology’. In this section, John Lucas from Rothamsted Research gave an update on the evolution of fungicide resistance, while Paul Nicholson from the John Innes Centre spoke on the subject of wheat resistance to Fusarium head blight. Rothamsted’s Stephen Parnell also gave a very interesting talk on how mathematical modelling can help predict the spread of pests and diseases through early warning surveillance.

Also in this section was a presentation by Paul Neve from the University of Warwick’s Crop Centre, which was on the subject of herbicide resistance in weeds. Dr Neve explained that low rate herbicide application allows for the selection of hereditary resistance traits in weeds, and once that resistance is endemic, it can have devastating effects. To this end, Dr Neve’s work mostly focuses on understanding the evolutionary processes that lead to resistance, as this, he believes, is the key to combating the outcomes of resistance.

L-R: Allan Downie, Jurriaan Ton, Alison Karley and panel Chair Keith Norman from Velcourt Ltd. Photo by Lisa Martin.

Lastly, after lunch, it was time for some ‘Lessons from Ecology’ and here presentations were given by Alison Karley, an agroecologist from the James Hutton Institute who works on optimising biocontrol; Jurriaan Ton from the University of Sheffield who brought us up to speed with recent advances in understanding and manipulating plant immunity; and finally Allan Downie from the John Innes Centre and co-ordinator of the Nornex consortium of scientists working on Ash Dieback disease.

A champion of open access, Professor Downie declared that “open access data will revolutionise science” and highlighted the ways in which crowdsourcing and citizen science are being used to understand Ash Dieback. These methods include the Facebook game Fraxinus that has allowed members of the public to help increase understanding of the Hymenoscyphus pseudoalbidus (a.k.a. Chalara fraxinea) genome, and the open access website OpenAshDieback, to which scientists are being encouraged to contribute data analysis and knowledge in the hope of, ultimately, limiting the impact of Ash Dieback.

To end on a high note over wine and canapés, the Science Minister David Willetts had been invited to present awards to the winners of a PhD student poster competition. The deserving winner was Rachel Goddard from John Innes Centre whose work on finding alternative semi-dwarfing genes that confer yield benefits to crop plants without compromising plant immunity caught the judges’ eyes. Congratulations, Rachel!

I live-tweeted throughout the conference, so please check out @GARNetweets for more insights, or search Twitter for #AHDBconf. You can also find the poster and speaker abstracts, and the speaker presentations, on the HGCA website here, and photos of the event are here.

Celebrating Basic Plant Science: Siobhan Braybrook

The first in our series of Celebrating Basic Plant Science articles comes from Siobhan Braybrook, a Career Development Fellow at the Sainsbury Laboratory at the University of Cambridge. She explains her work on plant development and discusses why she thinks basic plant science is value for money. 

In parts of India people have built ‘living bridges’ with traditional methods. Could developmental biology build the living bridges of the future?

How do we measure the importance of scientific works? Do we require immediate applications? Do we simply need to know? Both basic and applied science are important and vital for our sociological and scientific progress, but we tend to measure their impact with a very immediate and short ruler, one which is biased towards applied outcomes. Basic science is concerned with knowledge for knowledge’s sake, the desire to know. Applied science is directed towards a specific problem and it’s solution. Here, I propose that is impossible to anticipate the value of a basic scientific work beyond its immediate context, and that attempting to do so might just force us to narrow our field of imagination and innovation.

My group focuses on a basic scientific question- we would like to know how plants grow shapes. Our research definitely falls into the category of basic science as we pursue the answer to this question, not with a specific application in mind, but with a simple desire to know. But that does not mean that we don’t find applied directions during our pursuits.

Plant cells are pretty special to me because they exist in a box; the plant cell wall contains all of the other cell contents, allowing the cell to attain high pressures and also being the regulator of cell shape. We use biology, genetics, biochemistry, and materials science to understand how the cell wall controls cell, organ, and whole plant shape. As an example, we have shown with collaborators in France that new organ formation strictly requires a particular change in the cell wall, altered pectin chemistry. It was surprising that something as simple as pectin, the same thing used to make jellies set, was able to control whole plant shape by limiting new organ growth. These experiments have directed us to look at other growth processes that might be controlled, in part, by pectins in the cell wall.

From a basic science standpoint, our findings were very satisfying- we had found out something new and interesting. But they have also led us down some less familiar paths, into the realm of applied science. Can we take what we have learned about a biological material, the cell wall, and design man-made materials that also have the potential to grow? Could we one day place a small block of material on the ground and have it grow into a house? A car? Alternatively, if we understand how the cell wall controls growth, could we plant a seed that grows into a house frame? A chair? It is unlikely that any company would touch this idea without a very, very, very long pole at this time. It is too speculative, maybe even too crazy. But within the realm of basic science, we can continue to chip away at the possibility- with a freedom that does not require a final product right away, a freedom that allows us to grow our ideas along side our plants.

In closing, it is probably highly simplistic to separate basic and applied science. There is cross talk between the two, research projects that exist in a continuum, and research questions that are entangled. However, there are some very special things about basic science: you don’t need to know exactly where you are going in order to end up somewhere cool; you can explore things for the sake of knowledge which gives a lot of freedom; and sometimes you find out unexpected things that end up having massive applied impacts that you might never have anticipated. It is essential that we create a place for such scientific freedoms, that we don’t assume which pursuits have value before they have been investigated, and that we allow for the possibility of novel discoveries.

You can read Siobhan Braybrook’s research about pectin and new organ formation in Braybrook and Peaucelle 2013, PLoS ONE 8(3): e57813 and Peaucelle et al. 2001, Curr. Biol. 21:1720

Image credit: Screwtape via Flickr

 

Celebrating Basic Plant Science

Comments: 1 Comment
Published on: October 1, 2013

Do you know why the government uses taxpayers’ money to fund scientific research with no obvious application to the real world and definitely no short-term gain? Do you think it is valuable to carry out such research? If you’re a scientist, can you explain why your research is important?

At this year’s annual UK Plant Sciences Federation conference, PlantSci 2013, keynote speaker David Baulcombe made his case for the absolute necessity of ‘basic’ plant science research – science done for the sake of curiosity and understanding, to answer a question just because it’s there. He argues that above and beyond simple curiosity, maintaining a diversity of basic plant science research avenues is critical for paradigm shifts and future innovation, which are impossible to predict and can impact not only plant and agricultural science but medical science too. You can see him present his arguments in the video below, kindly provided by the Journal of Experimental Botany.

During the question and answer session after his talk, Baulcombe suggested that it would be a good idea to have some sort of online celebration of basic plant science. We jumped on this idea, and asked a few UK based scientists researching fundamental questions in plant science to write a blog post explaining their research and why they spend their time and energy on it. The ‘Celebrating Basic Plant Science’ series will start this week, and we’ll publish one story a month until we run out of volunteers. For now they’ll be here on the blog, but eventually we’ll give them a more permanent home on the GARNet website.

If you’re interested in finding out more about a certain area of plant science, please feel free to Tweet us (@weedinggems, @garnetweets) or to leave a comment below. If you want to contribute your own story Celebrating Basic Plant Science, we’d love to hear from you – please email charis@garnetcommunity.org.uk

Video credit: Journal of Experimental Botany. See the other talks from PlantSci 2013 here

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