Weeding the Gems - Page 57 of 67 - the GARNet community blog

Analysing phenotypes and measuring callose

by Charis Cook

Categories: methods, resource, Summary for non-specialists

Tags: methods, Plant Methods, resources

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Published on: January 9, 2013

Part of Figure 7 from Green et al., showing the an example of Phenophyte output.

At the end of last year, you may have missed two useful publications from Plant Methods which use new free online tools to make your life easier.

Phenophyte can help you measure 2D areas quickly and accurately. It was described in November’s Plant Methods by Green et al., a team mainly from Columbia, USA. Users chose if they want to analyse indivudial images, compare before/after images (as shown in the figure to the left), or analyse a timecourse. They then upload the images – the upload tool allows up to 2GB or 500 images, and sequential uploads are possible if required. The computational results can be previewed before submitting the job. When processing is complete, the user will be emailed a link to the results, which must be downloaded within a week. The manual provides detailed tips on how to take the photographs to upload, and the guidance is standard with the exception of the use of a colour/size checker (for example, this one), and the interface is straightforward and friendly.

Figure 5 from Zhou et al., showing the CalloseMeasurer interface and output.

A more specialized application is CalloseMeasurer, from the Robatzek group at The Sainsbury Laboratory. Zhou et al. describe a piece of software for quantifying callose deposition with enough accuracy to quantify the growth of filamentous pathogens within a plant by recognising the spreading network of callose deposition caused by the pathogen. The paper is heavy on technical detail, but guides readers through using CalloseMeasurer in the ‘Image Processing’ section of the paper. Users must have Acapella software installed, and they simply drag and drop the CalloseMeasurer script into the application window and start using the programme.

How many ways can you measure a plant?

by Ruth Bastow

Categories: GARNet, guest blogger, methods

Tags: phenotyping, Ruth Bastow

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Published on: January 8, 2013

In December, Ruth gave a talk at the Julich Plant Phenotyping Centre – here she explains what’s going on in plant phenotyping at the moment.

Recently I had the opportunity to visit and talk at the Julich Plant Phenotyping Centre in Germany and see the wealth of tools and technologies that the centre has available to measure and analyse plant growth and development in a non invasive manner. By using a range of sensors and computer vision tools for quantifying plant traits the centre aims to help overcome the current bottleneck in effectively linking genotype to phenotype.

As a mere amateur in this field, I used CCD cameras during my Ph.D to monitor circadian rhythms and during my post-docs I just counted leaves to determine flowering time. I was amazed by the depth and breadth of analysis that can now be carried out, and on such a large scale.

For example their purpose built automated Rhizo screen enables researchers to non-invasively obtain quantitative measurements of root architectures of plants grown in soil in 2D as well as evaluating shoot area. Whilst a variety of spectral and optical imaging systems sensitive to a wide range of wavelengths provide a plethora information from chlorophyll fluorescence, water content, lignin and cellulose composition to growth dynamics via leaf area. The centre also has a NMR, MRI and PET setup to visualize the inner structure of plant organs and tissue and transport of substances such as CO2. (Fiorani et al. Imaging plants dynamics in heterogenic environments. Current Opinion in Biotechnology, 23: 227-235).

Julich is just one of a number of phenotyping centres that are being established all over Europe, including the UK centre at Aberystwyth. The major European centres have been linked together in the European Plant Phenotyping Network (EPPN). This network offers access to 23 different plant phenotpying facilities spread across the EU. So if you haven’t experienced the power of phenomics yet this might be one way to dip your toe in phenotyping water!

Interview with Steve Kay: How to think big and forge solutions to complex problems

by Guest Blogger

Categories: guest blogger

Tags: interview

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Published on: January 3, 2013

Guest post by Sandra Smieszek

It is certainly my great pleasure to introduce Professor Steve Kay, holder of the Anna H. Bing Dean’s Chair, Dean of College of Letters, Arts and Sciences, and Professor of Biological Sciences at the University of Southern California Dornsife, leader, educator and innovator. He is a member of the National Academy of Sciences, and a fellow of the American Association for the Advancement of Science. He is is a renowned expert on circadian rhythms. He spent two decades identifying the photoreceptors, genes, and complex networks that make these internal clocks tick.

A transformative force in the field of molecular biology, Kay is a world expert on circadian rhythms. He spent two decades identifying the photoreceptors, genes and complex networks that make these internal clocks tick. He is perhaps best known for using blinking mustard plants and glowing fruit flies to explore the molecular genetic basis of circadian clocks in plants, flies, and mammals.

SS: What influences directed you to your specific area of research? Who influenced your scientific thinking early in your career, and how?

SK: I became interested in biology early in my childhood. It all began on the small island of Jersey, off the coast of Normandy. Many of my family members were fisherman, and I spent a lot of time on commercial boats. This exposure marine life coupled with great teachers and my first glimpse through a microscope set me on my path to becoming a scientist.

Certainly my mentors pushed me to ‘think big’. Trevor Griffiths who was my Ph.D. supervisor, introduced me to the world of plants. It was during my doctoral studies when I discovered that light regulated the expression of the gene that produced the enzyme for chlorophyll synthesis.

It was Trevor Griffiths who advised me to pursue my research in United States. That is when I started a postdoctoral fellowship at a lab of Nam-Hai Chua who focused on light dependent gene expression in plants. He certainly taught me how to approach more than one thing at a time. It was incredibly exciting to work with him on the first vectors for transgenic plants.

SS: What scientific breakthrough over the past couple of years influenced your research directions and why/how?

SK: My ‘eureka’ moment definitely came during my postdoctoral studies. Light signals change in gene expression patterns, I am thinking here particularly of chlorophyll a/b binding CAB gene. The discovery essentially showed how CAB was regulated by the circadian clock. That was in 1985 and it was the first direct evidence for the role of circadian rhythm exerting its effect at a molecular level. It was astonishing.

(more…)

See you in 2013!

by Charis Cook

Categories: something fun

Tags: No Tags

Comments: No Comments

Published on: December 24, 2012

Plant Science for Christmas

by Charis Cook

Categories: something fun

Tags: Christmas, genomics, plant defence

Comments: 1 Comment

Published on: December 20, 2012

Plants make Christmas, from the wreath on the door to the brussels sprouts on the table. In celebration of plant science and this most planty time of year, here’s some Christmassy plant science for you to enthral (or bore?) your nearest and dearest with next week. Perhaps while some of them are trying to watch the Made in Chelsea Christmas Special…

The Holly and the Ivy: Holly reacts to herbivores by making some leaves prickly while leaving others smooth – a form of heterophylly, where a plant has two or more types of leaf. This story from Science Daily also features ivy – science inspired by S’Cliff Richard himself!

I Saw Mummy Kissing Santa Claus: Mistletoe is already a ‘complementary and alternative’ cancer treatment (see the National Cancer Institute for more information), but a new study indicates it may become the source of a new mainstream anti-cancer drug. Researchers from the University of Adelaide have shown that an extract from mistletoe species Fraxini effectively reduces the viability of colon cancer cells, and is more potent than a chemotherapy drug.

We Three Kings: Frankincense is harvested from Boswellia papyrifera by ‘tapping’ the tree trunk and collecting the resin. Over-harvesting a tree ironically causes resin production to fall or cease as the tree expends resources on healing the wounds caused by tapping, and can even kill the tree as pathogens take advantage of the damage to the trunk. The Annals of Botany blog highlighted a paper published in Annals of Botany about the anatomy of the resin secretory system, and how the knowledge can improve sustainability of frankincense harvesting.

Oh Christmas Tree: If you have a live Christmas tree, it’s likely to be very similar to the conifers that dinosaurs roamed around. A study published in BMC Biology in October (Pavy et al., 2012) showed that the genomes of spruce and pine, which diverged 100 million years ago, have high synteny and co-linearity, suggesting no major genome changes have occurred. Senior author on the paper, Professor Jean Bousquet from Université Laval in Quebec, said, “Conifers appear to have achieved a balance with their environment very early. Still today these plants thrive over much of the globe. In contrast, flowering plants are under intense evolutionary pressure as they battle for survival and reproduction.”

Finally, for non-planty but very funny Christmas-based ‘science’ (inverted commas necessary), check out Dr Molecule’s latest blog post.

Image credit: Holly (ilex aquifolium) by Alfred Borchard; Pine Wood by Hajnalka Ardai Mrs., all via stock.xchng.

New GARNet Advisory Committee Members

by Charis Cook

Categories: GARNet

Tags: No Tags

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Published on: December 19, 2012

I am delighted to welcome Nick Harberd (The University of Oxford), Antony Dodd (The University of Bristol), and David Salt (The University of Aberdeen) to the GARNet Advisory Committee. They will be joining the current committee, who are pictured below. Ian Moore, Juliet Coates (neither are pictured) and Nick Smirnoff will be rotating off the committee to make way for the new committee members. Also not pictured are Sabina Leonelli and Charis Cook.

Plant defence with Katherine Denby

by Charis Cook

Categories: Friday Film, plant pathogens, systems biology, teaching resources, UKPSF

Tags: No Tags

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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!”

Looking inside cells with John Runions

by Charis Cook

Categories: Friday Film

Tags: GARNet, video podcast

Comments: 1 Comment

Published on: December 14, 2012

At April’s UK PlantSci 2012 conference, GARNet made video podcasts of five researchers talking about their work, the challenges facing plant scientists, and the state of UK plant science today. Over the next few weeks I’ll be posting them on the blog.

The first video is of John Runions from Oxford Brookes. He explains how he uses fluorescent proteins and microscopy to visualize processes inside living cells, and discusses the importance of Arabidopsis thaliana research for food security and forestry science – in his words, ‘Arabidopsis has been the paradigm in plant biology research.’

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