New Methods and Resources (II)

Categories: methods
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Published on: February 12, 2013

As promised, here’s part two of my selection of recently published plant methods and resources.

Nisar et al. (2012; Plant Methods 8:50) present a method for easy inflorescence stem grafting in Arabidopsis. I can’t vouch for its ease, but the typical clear Plant Methods format provides plenty of description and comprehensive materials and methods section as well as a step-by-step guide to their customised wedge-cleft grafting technique. The authors even provide a table of technical tricks for each step in the protocol.

Abraham and Elbaum (2012; New Phyt. 197:1012-9) present a method of quantifying microfibril angle in secondary cell walls. The method is technical enough only to be of interest to researchers who need to know the angle of secondary cell wall microfibrils – this is not a look-see ‘Friday afternoon experiment,’ as my old supervisor used to say. To get a full picture, scanning electron microscopy, small-angle X-ray scattering, raman microspectroscopy should all be used in addition to the new technique, which is based on customised polarized light microscopy and LC-PolScope, an imaging software.

Cui et al. (2013; Plant Phys. 161: 36-47) demonstrate that the Tnt1 retrotransposon is a powerful tool for functional genomes in soybean. 62% of insertions from Agrobacterium-mediated transformations using a Tnt1 vector were into annotated genes, indicating the Tnt1 element preferentially inserts into protein-coding regions.  Multiple insertions occurred per transformation, and the transposons did not jump under normal growth conditions. The authors obtained the Tnt1 transposon from plasmid pHLV4909, which contains the entire sequence, and cloned it into the binary vector pZY101 for the transformations.

An argument for plant science funding

Categories: Friday Film, funding
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Published on: February 8, 2013

Today’s Friday Film is a sort of video blog from the Carnegie Institution. I’m not sure why it’s narrated by a computer instead of a person … but it is a concise summary of this June 2012 article in The Scientist by Tom Brutnell and Wolf B. Frommer, in which the authors argue for $100 billion funding for plant science in the US over a 10 year period.

Source: CarnegieInstitution’s Youtube channel.

On Crowdsourcing

Categories: funding
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Published on: February 7, 2013

On Monday the BBSRC launched a ‘Crowdsourcing’ call, the first of its kind in the UK. Up to £2M is available to support a number of crowdsourcing projects. The intention to submit deadline is 5 March, and the full proposal needs to be in by 9 April. 

Crowdsourcing has principally been used for mapping phenomena across large areas, like the ash dieback app launched in the UK last year, or using as many willing volunteers as possible to do something that would take a single researcher and his computer more than their lifetime to complete, from working out potential protein structures with Foldit to searching for aliens with SETI. I searched the web for examples of crowdsourcing, and most of the projects are built on one of these two themes. Despite this, the list I made of the crowdsourced projects I found demonstrates the scope and power of crowdsourcing. Barely any on the list are plant science, but all involve general concepts applicable to many disciplines. Think about if there’s anywhere in your research crowdsourcing could be of assistance. If you have an idea for a crowdsourcing project but didn’t know where to start to set it up, this is an excellent opportunity to kick-start it. (more…)

New Methods and Resources (I)

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Published on: February 5, 2013

On this blog, I highlight a new method or resource pretty regularly. I used to work in what I think is a fairly normal UK plant science lab, so I try to comment on aspects I would have found useful to know about, for example if the method requires a machine not every lab has, or if it is unclear about anything. However, there are many, probably excellent, new open software and techniques which I don’t highlight on the blog because I am completely unfamiliar with their background.

For today, here’s the first part of a round-up of plant methods and resources published over the last few months. If you have used them, feel free to let me know how they worked in the comments, or through email or Twitter. And if you would like to review a method or resource for this blog, please get in touch!

iRootHair is a free, online, curated, expandable database of root hair genomics. Kwasniewski et al. (2013; Plant Phys. 161:28-35) built the database, which currently includes information about 153 root-hair related genes. The majority of the genes are from Arabidopsis, but maize, rice, tomato, and barley genes are also included. There is a page showing figures of various root phenotypes, which users can click through to see the genes associated with a specific phenotype; and a similar one for root processes like tip growth. (more…)

Why are there no pop hits about Arabidopsis?

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Published on: February 1, 2013

Ginny from Science and Plants for Schools pointed this video out to me recently. It’s a fun but entirely accurate love song to everyone’s favourite weed, genetic treasure trove (thanks Malcolm for that great little phrase!) Arabidopsis thaliana. Listen out to the shout out for TAIR!

This video was made by Professor Karmadillo. You can find him on YouTube, on his website, and on Twitter at @singingscience.

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