This much is known…Arabidopsis science-art

Proving that science and art aren’t mutually exclusive, check out this gorgeous animation that has recently been produced by engineer-turned-Fine Art student Andrew Styan.

this much is known from Andrew Styan on Vimeo.

Andrew recently took part in a science-art course, tutored in part by Dr Gordon Simpson, an Arabidopsis researcher who works within Dundee’s Department of Plant Sciences.

Inspired by Dr Simpson’s work, Andrew’s animation This Much is Known represents 25 years of Arabidopsis research and demonstrates how our understanding of this little weed has expanded in such a relatively short time.

Using the Scopus database, he searched for all Arabidopsis papers published in the last 25 years, and the keywords associated with them. Each bubble that appears on the screen represents a different keyword, with the size of the bubble growing as more papers on that topic are published.

I think it’s very clever and very beautiful! Thanks Andrew, and Gordon!

If there are any other budding science-artists out there who have produced some cool work on Arabidopsis or other plant science, we’d love to see it so please email lisa@garnetcommunity.org.uk.

Plant science – making an impact on scientific publishing

Categories: Arabidopsis, resource
Comments: No Comments
Published on: September 5, 2013

This year is proving to be a good year for plant science publications. So far there have been special plant science issues in Science and Genome Biology (and I have it on good authority that there will be plant synthetic biology special issue of another journal coming soon) as well as a landmark birthday for New Phytologist.

Special Issues for Plant Science

The open access journal Genome Biology published their Plant Science Special Issue in June 2013. It was guest edited by Mario Caccamo, acting director and Head of Bioinformatics at The Genome Analysis Centre. He discusses the issue and explains the importance of plant genomics, alongside Dale Sanders and other experts, in this podcast from Biome, BMC’s online magazine. The special issue itself features a whole host of UK researchers, including  Cristobal UauySebastian SchornackAnna Amtmann and Edgar Huitema.

The Science Special Issue, published just last month, unsurprisingly had a much broader focus – Smarter Pest Control. The featured reports take a global look at issues surrounding crop protection from pests, including RNAi-based pesticides, possible health problems caused by traditional pesticides, and tracking the effects of pesticides in wild animal populations.

New Phytologist Celebration

The Lancaster based journal New Phytologist, founded in 1902, is celebrating 200 volumes in October. By my reckoning, it’s the second oldest plant science journal in the world, after Annals of Botany which began life in 1887 as the Journal of Botanical Science (special mention for strictly botany journal, Flora). There is an incredible celebratory Virtual Special Issue of New Phytologist available here, featuring historic articles from throughout the journal’s lifetime including a 1904 critique of the then fashionable field of plant-based ecology from the great man himself, Sir Arthur Tansley.

Arabidopsis UK research roundup

On a related more local note, our new team member Lisa has been searching the literature each week for publications from UK Arabidopsis or other basic plant science researchers. She’s posting the Arabidopsis Research Round-up to the GARNet News pages, so check it out if you want to keep up with new research from your UK colleagues. If you’ve been published and want to make sure we spot your paper (we’re not perfect!), feel free to email Lisa at lisa@garnetcommunity.org.uk to let her know.

Nanoscale plant cell wall architecture

Comments: No Comments
Published on: December 6, 2012

Highlighted article: Shi-You Ding, Yu-San Liu, Yining Zeng, Michael E. Himmel, John O. Baker, Edward A. Bayer (2012) How Does Plant Cell Wall Nanoscale Architecture Correlate with Enzymatic Digestibility? Science 23:1055-1060

cell walls stained with phloroglucinol, which stains lignin (not from paper)

I spent three years trying to uncover the various mysteries of plant cell wall architecture without ever considering using an imaging approach. Admittedly, I was a PhD student in a molecular biology group and the necessary microscopy equipment was not exactly under my nose, but Ding et al. (paper published in November’s issue of Science) make such good use of imaging for cell wall research, I am kicking myself for not being as inventive Shi-You Ding and his group at NREL in Colorado, USA.

The paper describes the use of bright-field microscopy, confocal laser scanning microscopy, two-colour stimulated Raman scattering microscopy, and atomic force microscopy to look at the structure of primary and secondary cell walls. The authors were able to follow degradation by bacterial cellulosomes and fungal cellulases of cell walls that were untreated or stripped of lignin.

As the authors say in the abstract, their main conclusions are in support of existing ideas. It has been reasonably well established that lignin is the main barrier to enzyme digestibility, but in my opinion this is the best evidence so far that this is the case. The second conclusion, the theory that leaving the polymers intact as much as possible during pretreatment because damaged micro- or macro-fibres are less effectively hydrolysed than structurally intact ones, is not demonstrated at all in this paper.

For me, there are two results in particular in this paper that are novel and useful. First of all, the atomic force microscopy images in this paper show that the acid chlorite delignification method is an efficient way of stripping away lignin with minimal polysaccharide damage.

Secondly, there is evidence that fungal cellulases use different mechanisms to bacterial cellulosomes, and act more quickly to hydrolyse de-lignified cell walls under the conditions used. Both pieces of information are valuable to cell wall researchers and biofuel producers, and projects like my PhD will run more smoothly because of them.

Image credit: Charis Cook

Summary for non-specialists: Science paper on epigenetics

Comments: 1 Comment
Published on: June 21, 2012

One of the things I wanted to do on this blog was to highlight recent plant science journal articles, and when I found back-to-back papers on Arabidopsis research in Science I thought they would be a good place to start.

But when I started to read, I realised the obvious – my cell wall biochemistry background will be no help at all when trying to understand other areas of plant science research. But I still want to highlight high-impact articles like this on the blog, so I decided to have a Summary for non-specialists series. Please feel free to comment if I’ve got something horribly wrong, and of course if anyone would like to provide a Summary by a Specialist that would be great!

Highlighted article

Qian et al., June 2012. A Histone Acetyltransferase Regulates Active DNA Demethylation in Arabidopsis. Science 336: 1445-1447

Prior to this research, little was known about the regulation of DNA methylation, or how DNA and histone modifications were related. Here, Qian et al. define a process in which histone modification is an essential part of DNA methylation. This research opens the door to deeper understanding of the regulation and mechanism of DNA modification, and possible manipulation of epigenetic mechanisms.

(more…)

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