Arabidopsis in space

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Published on: December 7, 2012
Figure 3E from the paper, showing the slow growth of spaceflight grown seedlings

Plants are background features in a lot of science fiction as terraformers or oxygen supply. Plants in space sometimes have a lead role, like the tiny, precious seedling in Wall-E or the dead plants in the spaceship greenhouse in Sunshine. In real life, NASA is taking plants seriously as morale-boosters, air filters, and food supplies for astronauts on future long-duration missions.

In 1993 for the first time in history, Hilaire et al. were able to observe plants growing in a completely novel environment, and specifically find out exactly what effect gravity has on plants. A paper published in BMC Plant Biology today continued that research, showing that root growth patterns are not affected by gravity. The paper is open access and you can read it here.

Robert Ferl and his team, all from the University of Florida, analysed Arabidopsis seedlings grown on the International Space Station (ISS) and control seedlings an identical growth chamber in Kennedy Space Center, Florida. Their results demonstrate that Arabidopsis thaliana cultivars WS and Col-0 have phototropic shoots and roots that grow away from the shoot and the light source (negative phototropism), whatever the gravity exerted on them. Neither plants grown on the ISS nor plants grown on earth grew in a straight line directly away from the light source, but those grown in space deviated further from that line. The typical sinusoidal waving of Arabidopsis roots was unaffected by the lack of gravity (above; shown better in other figures in the paper). That gravity has little effect on root development confirmed the results of Millar et al. (2011), who worked on A. thaliana cultivar Landsberg grown in the dark on the ISS.

Despite the confirmation that plant roots grow away from the shoot irrespective of their distance from the Earth’s surface, the paper contains bad news for anyone hoping to escape in a spaceship with plant-based oxygen and food supplies. Plants in grown on the ISS grew more slowly and were smaller than their Earth-bound counterparts (above, Figure 3E in the paper). Some other spaceflight experiments showed similar differences in size, but in other cases the opposite was true. In this case, the authors were able to demonstrate that the small size of the space-grown seedlings was due to limited cell elongation, not a problem with cell division, but could not explain why.

Highlighted article: Anna-Lisa Paul, Claire E. Amalfitano and Robert J. Ferl (2012) Plant growth strategies are remodelled by spaceflight. BMC Plant Biology 12:232.

 

Nanoscale plant cell wall architecture

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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

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.

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