Arabidopsis basics

Categories: teaching resources
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Published on: November 2, 2012

We added a new page to this blog to show how basic Arabidopsis research works. This is for anyone who is on the periphery of plant molecular biology but doesn’t work directly on Arabidopsis thaliana – teachers, undergraduates, environmental scientists … whoever.

To go with the new page, here is a time-lapse video of growing Arabidopsis thaliana plants. Although it is a little out-of focus at the beginning, I chose it to show you because it shows how frustrating Arabidopsis research can be! At around 1.20, the plant on the left starts to bolt, which is when the stem begins to grow. It grows so quickly after all those days of watching the rosette leaves get bigger. The plant on the right, which has the same size rosette, doesn’t start to bolt until about 1.34 – it probably won’t catch up with the first plant until they both have siliques that are drying out. Developmental stage is important in a lot of experiments, so it is often necessary to grow far more plants than you expect to use so that you have a good selection of plants at the same growth stage when you start the experiment.


Varying degrees of open access

Categories: Open Access
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Published on: October 26, 2012

One of the things that this summer’s GARNet workshop, Making Data Accessible to All, made Ruth and I think about was the varying degrees of open access allowed by publishers. All journals accommodate open access, as some funding bodies now demand all research undertaken with their funds be published open access. This service is not free, so it will usually only be used when the funding body demands it. If open access is something you feel strongly about, PLOS have a useful ‘Open Access Spectrum,’ which can be used to judge journals on an open access grid. This may be useful in thinking about where to publish your work.

Publishing policies vary enormously. Some subscription-only journals allow open access after an embargo period of between six months and two years. Some journals allow authors to put their papers or toll-free links to the article on their personal websites or databases like PubMed Central if they chose to (sometimes immediately, sometimes after a set period of time), and others forbid any publication of their articles anywhere except the official, subscriber-only, journal website. It’s always worth a quick search for your paper if you can’t access it through the publisher – there could be an unofficial (but legal!) version or toll-free link out there somewhere!

There is information about specific plant journals below (feel free to leave a comment if I’ve missed anything out), but since it’s Friday, here is a slightly surreal and extremely one-sided video about academic publishing – thanks to aoholcombe:


From systems biology to digital organism

GARNet needs your help to assess the uptake, influence and future of systems biology in the plant science community. This is the second time GARNet has conducted a survey about systems biology, as in 2006 the BBSRC commissioned GARNet to produce a report on how systems biology could best be approached in UK Arabidopsis research. We believe that report and the various activities that accompanied it helped the Arabidopsis community get its foot on the ‘System Biology Ladder’ – and to win some of the associated grants.

Now, six years later, systems biology is supporting systems biology and the digital organism efforts. We feel it is time to write a follow up report to the 2006 Systems Biology report in order to advise the BBSRC and other funders on the community’s capabilities, current needs, and readiness for future initiatives that build on Systems Biology.

Please help us collect data and information for this report by filling in a questionnaire, which will take about 20 minutes of your time. Please click here to go to the questionnaire. Please contribute your ideas before the 5th November.

Video credit: Pacific Biosciences.

Friday Film: Powerful Plants

Categories: teaching resources
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Published on: October 12, 2012

If you thought that plants were stationary, lazy beings, think again. Bladderworts are water-dwelling carnivorous plants that trap prey by storing elastic energy in the trap body and releasing it by very fast opening and closing of a water-tight trap door. This video was made by Phillippe Marmottant and his research group from Grenoble, who published the mechanism of bladderwort action in their 2011 paper.

Another super fast plant is the dogwood species, Cornus canadensis, whose flowers explode faster than a rifle shot as they disperse their pollen.

While exploding plants and super-suction make for exciting viewing, they happen too fast for the human eye to see without the benefit of slow motion footage. It is possible to show slightly slower plant reflexes to students in schools, though – SAPS have a carnivorous plants information page and worksheets.

Friday Film: Automatic cell counting with ImageJ

Categories: methods, resource
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Published on: October 5, 2012

This is a video tutorial on quantifying cells using ImageJ. ImageJ is a free tool for image processing and analysis in Java. I chose to highlight this tutorial as it is clearly explained and may be of use to many plant scientists, but YouTube is a goldmine of other less professional tutorials on using ImageJ for any number of applications. I was particularly interested in this one on quantifying stained liver tissue, as I used to work on secondary cell walls and it would have been a handy tool for qualitative analysis of my many images of phloroglucinol stained tobacco stem cross-sections.

Created by Keene State College’s Center for Engagement, Learning, and Teaching.

Friday Film: 3D Arabidopsis flower

Categories: teaching resources
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Published on: September 28, 2012

David Livingston from the USDA Agricultural Research Service made a beautiful video of the construction of an Arabidopsis flower using 248 sections of an Arabidopsis flower that was paraffin-embedded and sectioned at 20 microns. It includes images of the internal structure of the flower. The method he used is published in Livingston et al., 2010.

Friday film: Botany consultant on Avatar

Categories: teaching resources
Comments: 1 Comment
Published on: September 21, 2012

Professor Jodie Holt from the University of California UC Riverside was the consultant botanist on Avatar. In this video, she gives a lecture to middle school children on the plants in the film and where the real world inspiration for them came from – she has lots of interesting examples from the film which could easily be translated to plant science teaching, and outreach projects. This is quite a long video, but it is fascinating. The Avatar stuff starts at about 15 minutes in, and Jodie takes questions from the children from 36 minutes onwards.

Credit: UCR College of Natural and Agricultural Sciences

If the video is not working, go to YouTube:


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