Plant science, by JoVE!

JoVE 2

Researchers from the University of Warwick published a methodology paper with a twist this week. The paper, published online by the Journal of Visualized Experiments (JoVE), gives step-by-step instructions and video demonstration of a method for purifying a protein and identifying proteins that perform its post-translational modifications.

Authors Sophie Piquerez, Alexi Balmuth, Jan Skenář, Alex JonesJohn Rathjen and Vardis Ntoukakis developed the method in order to characterize the interactions between nucleotide-binding leucine-rich-repeat proteins and the Prf/Pto complex in effector-triggered immunity. In principle the method could be applied to any protein – the protein of interest is epitope-tagged, immunoprecipitated and analysed by MS.

A video journal lends itself to new or improved methodology rather than high impact conclusions. As with a lot of JoVE articles, the scientifically significant results obtained using the protocol have already been published; in this case in Ntoukakis et al. 2013 (PLOS Pathogens, 10.1371/journal.ppat.1003123).

The authors conclude the abstract by saying the paper demonstrates:

  1. Dynamic changes in PTMs such as phosphorylation can be detected by mass spectrometry;
  2. It is important to have sufficient quantities of the protein of interest, and this can compensate for the lack of purity of the immunoprecipitate;
  3. The immunoprecipitation step is essential to get enough protein to do the MS. (more…)

Recently in the GARNet community … (3)

Categories: GARNet, UKPSF
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Published on: February 21, 2014

It’s quietened down in the GARNet office this week and we’ve been catching up on things and preparing for the busy conference season. I’m looking forward to learning how to code with the delegates at our Software Carpentry workshop, and we’re going to Monogram and PlantSci 2014 at Easter too.

We’ve added a new Imaging Resources and Services page to our website. It lists five UK imaging facilities and two suggested resources for new users or students to find out more about biological imaging. The facilities provide a number of services including electron microscopy, in vivo single molecule fluorescence imaging and two-photon microscopy. There are also. Several of the listed facilities have recieved ALERT13 funding for new state-of-the-art equipment which will be available to users through a number of routes.

Nicola Patron, one of the Co-Is on the recently funded OpenPlant Multidisciplinary Synthetic Biology Research Centre, has published a Golden Gate Modular Cloning Toolbox for Plants with Sylvestre Marillonnet, who presented the Golden Gate method at last year’s GARNet conference on plant synthetic biology. The paper (Engler et al., ACS SynBio DOI:10.1021/sb4001504) is free to access, although annoyingly there are hoops to jump through, and the toolbox will be available through Addgene shortly. (edit 14/5/2014: the paper is not free to access)

If you’re a keen writer or interested in science communication, check out this database of science writing competitions. It’s not for plant scientists but it has very useful categories that make it clear whether your country of residence, career, career stage or field of expertise would prevent you entering.

Finally, if you’re a young plant scientist planning on attending PlantSci 2014, don’t forget to submit your abstract to have a chance of being selected to speak – cash prizes are available for the best talks.

Travel grants 2014

Categories: conferences
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Published on: February 18, 2014

It’s that time of year when conference registrations are open and early bird deadlines are coming up fast. If you want to go to one but are unsure about the cost, take a look at the travel grants below. They all have fairly simple application processes and several deadlines throughout the year, but get your applications in within the next few weeks for summer conferences.

Remember, if you’re a student, you can use your training grant to pay for conference fees and travel. Attending and presenting posters or talks at conferences is an important part of a PhD studentship.

  • Company of Biologists travel grants from the Society of Experimental Biology: Deadlines 31 March, 30 June, 30 September, 31 December 2014. Funding to attend a UK (£250) or international (£500) conference. You have to be a member of SEB, or to buy a multi-year membership, to apply.
  • Honor Fell travel award from the British Society for Cell Biology, sponsored by the Company of Biologists: Rolling deadline. Up to £300 for UK meetings and more for international travel is available to students and post-docs.
  • Biochemical Society travel grant: 7 deadlines throughout 2014 – submit as early as possible. Members of the Biochemical Society can apply for a travel grant of up to £750 to attend a meeting.
  • British Society of Plant Pathology travel grants: Deadlines 28 Febrary, 31 May, 31 August, 30 November 2014. Travel funds are available for BSPP members to assist with expenses for conferences, study tours and visits. The amount available varies, but will not be more than half the cost of your trip.
  • Society of Biology travel grants: Students and early career researchers can apply for £500 for overseas travel in connection with biological study, teaching, research, or attending a conference.
  • Genetics Society Conference Grants: Deadlines 1 May, 1 August, 1, November. Up to £750 is available to PhD students and post-docs within two years of their viva to cover travel, accommodation, and registration cost for conferences and meetings. Also, up to £150 is available for travel to Genetics Society meetings.

Why not try and get some funds to attend UK conferences PlantSci 2014 (£200 is up for grabs for the best student/postdoc talks!), SEB 2014 or our very own GARNet 2014?

GEO for plant scientists: Sharing data

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Published on: February 13, 2014

There is currently no microarray service provider in the UK that uploads your plant science microarray data to GEO on your behalf, but publication requires your data to be shared. The most common request from journals is that it is shared on GEO.

GEO has this information page about data submission. While the high-throughput sequence submission guidelines are a still little complicated, microarray experiments have well-established (and enforced!) minimum information requirements and the four main microarray chip providers have customized information pages. An email address is provided for users to email enquiries and ask for help from GEO’s curators.

The Affymetrix page is probably the most useful for UK plant sciences. Spreadsheet-based submission is recommended for Affymetrix deposits, so users should submit an Excel metadata worksheet, CEL files, and processed data for example a Tiling Array. The page gives advice on how to find certain information is given on finding GEO-specific information, and there are template and example spreadsheets.

Once submitted, your dataset becomes a GEO accession and can be identified with a unique accession number. The accession number should be used when you or anyone else references or links to your dataset, which seems like an easy means of tracking its usage within the community.

GEO for plant scientists: How to find Arabidopsis microarray data

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Published on: February 13, 2014

Submission of gene expression data to the Gene Expression Omnibus is now a requirement of publication in most journals, so it is an extremely valuable resource. It is also extremely big, and full of data that isn’t relevant to your question or task at hand – but it is easy to find the right data using the search bar if you follow a few rules. There are example searches on the GEO homepage.

To find data relating to Arabidopsis thaliana, search: (Arabidopsis thaliana[organism])

To find Arabidopsis microarray data, search: (Arabidopsis thaliana[organism]) AND “expression profiling by array”

The easiest way to find other Arabidopsis datasets is to search: (Arabidopsis thaliana[organism]). On the left hand side of the window, there is a ‘Study type’ section. If you click on ‘More…’ a list of study types pops up from which you can select the data type you are looking for (see screen shot below).

You can add any search term you like to the search bar. For example, you could specify author, publication time, types of tissue or stress… or any combination of these. Just keep adding AND in between each term. For example: (Arabidopsis thaliana[organism]) AND “expression profiling by array” AND leaf

GEO provides an informative guide to how to download original records or curated datasets individually or in bulk. You can download data directly from Accession Viewer pages (eg this one) in SOFT, MINiML or TXT formats. Raw data is also available in TAR. You can also do bulk downloads via GEO’s FTP site. All files are compressed using gzip.

It’s also possible to access GEO programmatically in order to, for example, quickly retrieve CEL files from Arabidopsis stress experiments. Again, GEO provide a guide to this, although this is probably something better tackled with some pre-existing knowledge of programming.

GEO post

Photosynthesis for fresh water

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Published on: February 10, 2014

Annegret Honsbein is a post-doc in Anna Amtmann‘s lab at the University of Glasgow. As she explains in this guest post, she is working on an EPSRC project that hopes to harness the power of photosynthesis to desalinate sea water. 

Water covers more than 70% of Earth’s surface but less than 2% of it is available as freshwater. Many of the driest regions of our planet are close to the sea but irrigating fields with seawater – even if diluted – leads to build-up of salt in the soil to levels toxic to all common food crops. Current desalination technologies, such as membrane-based reverse osmosis, are successfully used in large-scale desalination plants, but they are expensive and energy inefficient.

desalinationOur multi-disciplinary EPSRC-funded project takes a synthetic biology approach to the development of an innovative desalination technology based on biological processes. We are a team of biologists and engineers from the Universities of Glasgow, Sheffield, Newcastle, Robert Gordon University at Aberdeen and Imperial College London, led by Dr. Anna Amtmann from Glasgow University.

Our idea is solar energy-fuelled desalination – with a twist. Instead of using solar panels we intend to let photosynthetic microorganisms desalinate the sea water. Cyanobacteria are ideal candidates, and we are currently working with two strains that are naturally able to adapt to a wide range of salt concentrations from fresh to sea water.

In principle, salt is toxic to all living cells, which is why most living systems have developed means to actively export sodium. In some cyanobacteria species that grow to very high densities, this ability means they actually form a low-salt reservoir within their saline environment.

We intend to use this low-salt reservoir as ion exchanger to extract the salt from the surrounding seawater. We aim to engineer cyanobacteria so we can switch off the endogenous salt export mechanism towards the end of their growth cycle, and activate a synthetic intracellular sodium accumulation unit. This synthetic unit will be assembled from membrane transport proteins evolved by different organisms to import sodium and chloride ions.

Our team’s engineers are developing techniques to manipulate the surface properties of the cyanobacteria and effectively separate the ‘salty’ cells from the desalinated water before they die, preventing release of the accumulated salt back into the ‘fresh’ water.

The final stage of the project will be to build a model version of the actual plant that could house our photosynthesis-driven bio-desalination process.

This work is published in: Jaime M. Amezaga, Anna Amtmann, Catherine A. Biggs, Tom Bond, Catherine J. Gandy, Annegret Honsbein, Esther Karunakaran, Linda Lawton, Mary Ann Madsen, Konstantinos Minas and Michael R. Templeton (2014) Biodesalination: A Case Study for Applications of Photosynthetic Bacteria in Water Treatment. Plant Physiology 164: 1661-1676; doi: http:/​/​dx.​doi.​org/​10.​1104/​pp.​113.​233973.

Image c/o Annegret Honsbein.

Recently in the GARNet community (2) …

Categories: Arabidopsis, something fun
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Published on: February 7, 2014

This week has been another busy one for GARNet.

The meeting report for our May 2013 synthetic biology workshop has been published in the Journal of Experimental Botany. You can download An Introduction to Opportunities in Plant Synthetic Biology for free here.

GARNet Advisory Committee member John Doonan, Director of the National Phenomics Centre at IBERS in Aberystwyth also published a paper this week, as highlighted in Lisa’s weekly Arabidopsis Research Round-up. It’s an excellent paper (Zheng et al.; PNAS 10.1073/pnas.1318460111) – but it’s a shame the press release was almost entirely about wheat!

We’ve been planning another Software Carpentry bootcamp with Liverpool after our Warwick event filled up so quickly. It’s early days but we’ll be sure to keep you informed.

Finally, in response to this blog post by Professor Ian Crute, I wish to make a statement. My thanks to Professor Crute for protecting my identity, but I feel it is time to admit my mistake in order to act as a warning to others who live-tweet events. I feel it is my duty to publically announce that I would never intentionally refer to plant science or Prof Crute as ‘pants’. Indeed I hold both of them in high esteem. My message to Tweeps everywhere is this: Please check your tweets before tapping that ‘TWEET’ button!

As a related aside, Lisa and I have discovered that pant science is actually a real thing! You learn something new every day.

pants

In Photos: UK Plant Sciences Report Launch

Categories: UKPSF
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Published on: February 3, 2014

Thanks to Society of Biology Regional Coordinator David Urry for wielding the Society camera throughout the launch of the UKPSF report ‘UK Plant Science: Current Status and Future Challenges’, and letting me use some photos!

The GARNet website has a news piece on the launch, and tweets about the report are collected here

Not put off by the long, damp queue for the Faraday Lecture, the plant sciences community gathered in the Marble Hall at the Royal Society.

crowd 900

(more…)

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