Summary for non-specialists Archives - Page 3 of 6

Imaging trichomes

by Charis Cook

Categories: methods, resource, Summary for non-specialists

Tags: Arabidopsis, methods, resource, trichomes

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Published on: December 13, 2012

cryo-scanning electron microscope image of a trichome on an Arabidopsis leaf

Even if you don’t work on trichomes, you have definitely experienced them first-hand, as stings on nettles are trichomes that have evolved down a particularly nasty route. Other trichomes pack less of a punch, but they are still important for phytochemical production and herbivore defence.

Arabidopsis trichomes are rather more tame than stinging nettle trichomes, and present an excellent way to study cell differentiation as well as being a target for crop improvement. But although trichomes are easy to see using light microscopy, they are difficult to study. Manually counting them and recording their length and position is tiresome in the extreme, and imaging technologies tend to require specialized skills and software that not all labs can access.

In today’s highlighted paper, Pomeranz et al. present a new method of analysing trichomes consisting of polarizing light microscopy (PLM) and a web-based imaging tool. In fact PLM is an old technique described by Ballard in 1916, and is an excellent way of imaging trichomes because of the highly crystalline cellulose in trichome cell walls which confers polarizing (birefringent) properties. As the authors say, this new technique is a ‘repurposed’ method, and the key to the novel technique is the online resource TRICHOMENET, which allows imaging and easy analysis of trichomes, and can be linked with ImageJ.

It certainly appears that this method would be easy to set up in any lab. Preparing samples for PLM involves methanol or ethanol, lactic acid, and a water bath – the method is in the paper or in Bischoff et al. (2010). PLM itself requires polarizing filters, which can be bought in a kit, for example from Motic, or as individual filters. The image is then uploaded to TRICHOMENET, which guides the user through counting the trichomes. Once the data is recorded, TRICHOMENET can analyse trichome positional data, density, and distances.

Highlighted article: Marcelo Pomeranz, Jeffrey Campbell, Dan Siegal-Gaskins, Jacob Engelmeier, Tyler Wilson, Virginia Fernandez Jelena Brkljacic, and Erich Grotewold (2012) High-resolution computational imaging of leaf hair patterning using polarized light microscopy. The Plant Journal ‘Accepted Article’, doi: 10.1111/tpj.12075

Image credit: Emmanuel Boudet.

Arabidopsis in space

by Charis Cook

Categories: Arabidopsis, Summary for non-specialists

Tags: Arabidopsis

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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

by Charis Cook

Categories: Summary for non-specialists

Tags: cell wall, lignin, Science

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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 …

by Charis Cook

Categories: Summary for non-specialists, systems biology

Tags: wheat

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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.

Progress in pollen research

by Charis Cook

Categories: Friday Film, methods, Summary for non-specialists

Tags: Arabidopsis, Friday film, methods, pollen, summary for non-specialists

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Published on: November 30, 2012

Time lapse video of Arabisopsis pollen grains germinating and growing pollen tubes. Credit: massalvaje.

As an officer for GARNet, the Arabidopsis research network, I am happy to share the news that we can now add pollen germination to the long list of things for which our Arabidopsis can be called a model plant. The research is published in New Phytologist, and is currently in early view.

The importance of studying pollen for plant reproduction research is obvious, but it is also an excellent and widely used system for studying cell growth and development. Some plants, such as tobacco, have pollen that can be germinated on cue, and monitored in all sorts of ways as through germination, cell development, and pollen tube growth. Unfortunately brassicas, including Arabidopsis thaliana, do not have such amenable pollen.

A team of researchers from Oxford have developed a method that yields fast, reliable germination of A.thaliana pollen. The pollen tubes that grow are long and morphologically normal.

The method uses a cellulose-based membrane covering an agarose pad, all set up on a glass microscope slide. In the authors’ view, this protocol was more successful than other attempts because the environment surrounding the pollen mimics the stigma – so not only does this paper present a method of studying Arabidopsis pollen, but it provides novel information about the environmental cues required for pollen germination. The method was optimized for temperature and pH as well as the ratios of reagents used to make the materials.

Although this paper was about Arabidopsis and marks an important development for Arabidopsis researchers working on pollen and cell growth, it is also significant for Brassica researchers. The Brassica family contains many commercially important crops, and this method can surely be adapted to serve research into cabbage, oilseed rape, or other Brassica species.

Highlighted article: M. J. Rodriguez-Enriquez, S. Mehdi, H. G. Dickinson and R. T. Grant-Downton (2012) A novel method for efficient in vitro germination and tube growth of Arabidopsis thaliana pollen. New Phytologist (Early View) doi: 10.1111/nph.12037

Overyielding in species mixtures

by Charis Cook

Categories: Summary for non-specialists, teaching resources

Tags: grassland, legumes

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Published on: November 22, 2012

Highlighted article: Gerlinde B. De Deyn, Helen Quirk, Simon Oakley, Nick Ostle, Richard D. Bardgett (2012) Increased Plant Carbon Translocation Linked to Overyielding in Grassland Species Mixtures. PLoS ONE 7(9): e45926. doi:10.1371/journal.pone.0045926

Plant biomass yield is often greater in areas where species richness is high than it is in monocultures. This has implications for agriculture, and also the use of non-farmed land as a carbon sink, as more biomass means more carbon assimilation. However, the relationship between growth and species richness on a plot of land is not constant or clear, so a group in Lancaster investigated it. I think their research threw up more questions than it answered, but the authors found intriguing links between lifetime biomass yield and speed of carbon transport from the leaves to other parts of the plants and found that non-legumes and legumes alike benefit from growing alongside one another.

Deyn et al. planted seedlings in monocultures or in a mixture and sampled soil and plant matter at 2, 24, and 48 hours, and finally at 8 days, after labeling carbon in the system using a ¹³CO₂pulse (Ostle et al., 2003). They assessed carbon assimilation and carbon/nitrogen ratio. Two years later, all the above-ground vegetation was harvested and weighed to obtain ‘yield’ data. The species used were common grassland species Trifolium repens and Lotus cornicalatus (both leguminous species), Plantgo lanceolata, Anthoxanthum odoratum, Achillea millefolium, and Lolium perenne. (more…)

Molecular Plant Pathology’s Top Ten

by Charis Cook

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

Tags: plant pathogens, teaching resources

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Published on: November 13, 2012

Keeping with last week’s plant pathology theme, I thought I’d highlight a paper that came out in the spring in case any plant pathologists missed it. This may also help people in other fields of plant science out there who might need to hold their own in a pathology-based conversation occasionally. In April 2012, Molecular Plant Pathology published ‘The top 10 fungal pathogens in molecular plant pathology,’ as voted for by 495 readers of the journal.

Quesadillas made with corn infected with Ustilago maydis, which is called huitacoche.

The pathogens chosen are:

Magnaporthe oryzae, the cause of rice blast disease.
Botrytis cinerea, also known as grey mold – probably the cause of the mold on the strawberries in the back of the fridge that you bought when they were offer.
Puccinia spp., the cause of an unpleasant range of rust diseases that occur on wheat.
Fusarium graminearum, a cereal pathogen commonly known variously as head blight, ear blight, or, delightfully, head scab. Infected grain can be poisonous.
Fusarium oxysporum, a ubiquitous soil-borne pathogen that can infect many species, including important fruit species, and humans.
Blumeria graminis, powdery mildew, which infects wheat and barley.
Mycosphaerella graminicola is also called Septoria tritici and causes blotch disease in wheat.
Colletotrichum spp. can infect a large range of crops, and latent infections can destroy stores of fruits post-harvest.
Ustilago maydis, or corn smut, is actually cultured on corn cobs by farmers in Mexico, where the infected corn is called huitacoche and is a common recipe ingredient.
Melampsora lini, or flax rust, the classic model plant pathogen.

The paper gives a ‘resume’ of each one, written by an expert in that particular species. Is your favourite pathogen missing? What other ‘Top 10’ would be interesting to put together?

Paper: DEAN, R., VAN KAN, J. A. L., PRETORIUS, Z. A., HAMMOND-KOSACK, K. E., DI PIETRO, A., SPANU, P. D., RUDD, J. J., DICKMAN, M., KAHMANN, R., ELLIS, J. and FOSTER, G. D. (2012), The Top 10 fungal pathogens in molecular plant pathology. Molecular Plant Pathology, 13: 414–430. doi: 10.1111/j.1364-3703.2011.00783.x

Teaching resources: This is an exercise easily recreated in a tutorial group or classroom. Groups of students could each make a pitch for their plant pathogen (or crop species, or organelle, etc …) and the whole group would vote for which one deserves the ‘top’ spot.

Image credit: Lesley Téllez, via her blog The Mija Chronicles

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…)

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