Plant disease resistance with Eric Holub

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Published on: January 11, 2013

Here, Eric Holub from the University of Warwick describes his research on the genetics of disease resistance mechanisms as well as a bit about life in academic research in the UK. He explains the real-world application of his research on the model plant Arabidopsis thaliana by saying, “If the plant can control its own diseases, chemical control will be be much less required.”

This is the third video podcast taken at the UK PlantSci conference in 2012. See the previous ones with John Runions and Katherine Denby here and here. To register for UK PlantSci 2013, go to the website.

 

Analysing phenotypes and measuring callose

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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?

Categories: GARNet, guest blogger, methods
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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

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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…)

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