Potato Potato

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Published on: March 27, 2013

The potato, brought across the Atlantic by explorers like Christopher Columbus and Francis Drake during the 15th and 16th Centuries, changed Europe forever. During the 18th Century the large, low-maintenance potato harvests eventually provided European working classes with a more reliable food source than they had ever enjoyed. Decades later, arsenic blends to protect potato crops were the first artificial pesticides. Today’s highlighted paper, published in Nature in March, tells us that potato would still be the local speciality of Andean villagers, in spite of those early European explorers, if it weren’t for natural and cultivated variation of a CYCLING DOF FACTOR. 

Wild potato is found largely in Bolivia and Peru.  There are roughly 180 wild potato species, all of which originated in the Andes and now spread along the west coast of South and Central America, with a few in the southern most states of the USA – all within 40° of latitude from the equator, but with a clear focus between 10° and 20° south (Hijmans and Spooner 2000). These equatorial origins meant the original potatoes brought to Europe had an inherent dependence on short day lengths, and only formed tubers in short autumn and winter days.

Kloosterman et al. compared a wild potato population with a potato population domesticated in Europe. They started out by defining more clearly the ‘potato plant maturity’ QTL on chromosome 5 (Visker et al. 2003), which is associated with onset of tuberization and plant life cycle. They identified a homologue of the A. thaliana CYCLING DOF FACTOR 1 protein which they named StCDF1, which when complete causes potato plants to be late maturing and unable to tuberize in long days. Potatoes with a truncated StCDF1 allele mature early, growing tubers four weeks after planting in long day conditions. (more…)

Testing heat tolerance in the field

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Published on: March 21, 2013

Global climate change and localised human impact, such as waste disposal or fertilizer use, has and will continue to have an effect on the world’s flora, both natural and agricultural. Predicting this effect can be difficult, but it is important. If land managers and farmers know which species will cope well with change, they will be better able to make a decision about the species which will struggle under certain conditions.

If a species is well-researched, it may be possible to look for QTL associated with resistance to heat, drought, flooding, or other abiotic stresses, but of course this does not predict real-world responses reliably and in any case is not an option in all cases. In the lab or greenhouse under controlled conditions, a simple observation experiment can tell you the effects of various conditions on a plant, but again this is not an indication of in situ viability.

Buchner et al. published a method of determining the heat tolerance of plants in the field in this month’s Plant Methods (vol. 9:7). Heat was the only imposed variable in their protocol, so any environmental factors are included in the experiment. The group, from Othmar Buchner’s group at Innsbruck, made their own Heat Tolerance Testing System (HTTS) from a number of pieces of technical equipment, including the customized exposure chambers seen in the image above (Figure 5B in the paper). (more…)

The many advantages of chloroplasts

Chloroplasts are a major advantage to doing synthetic biology in plants. They produce starch and some amino acids as well as hosting photosynthesis, all fully separated from other cellular functions going on in the rest of the cell. Synthetic biology approaches could turn them into individualised micro-factories inside plant cells, synthesising whatever compound you fancy without poisoning the cell and with almost no risk of any transgenes escaping into other plants.

Stable plastid transformation was first achieved in tobacco in 1990.  Since then, chloroplast transformation has been successful in many plant species – a 2009 review by Huan-Hyan Wang et al. (JGG 36:387) contains a nice table summarizing the methods used in each species. Plastid-based biosynthesis of biopharmaceuticals has been researched for years, but synthetic biology technologies make it possible to consider moving beyond synthesis of antigens and relatively simple molecules (for examples see Daniell et al. 2009, Trends in Plant Sci 14:669) to more complex structures.

In today’s highlighted paper, Nielson et al. successfully built the P450-dependant dhurrin pathway into tobacco chloroplast cells. This in itself does not have a major benefit to science, as dhurrin has no real value, but as a proof of concept this is worthy of note. The three-step biosynthesis of dhurrin from L-tyrosine is normally based on the endoplasmic reticulum, and its rate is limited by low concentrations of NADPH. By building the pathway in a chloroplast, the authors have proven not only the feasibility of chloroplast pathway engineering, but also the potential of using reducing power from photosynthesis to run biosynthesis pathways.

For more information about chloroplast engineering, this 2011 paper reviews chloroplast transformation markers and this paper is another example of pathway engineering in chloroplasts.

More generally, to find out about synthetic biology approaches please register for our Synthetic Biology meeting, which aims to introduce synthetic biology to plant scientists. It is £250 for academics, and includes overnight accommodation and meals – there is a reduced rate for students and post-docs.

Highlighted paper: Agnieszka Zygadlo Nielsen, Bibi Ziersen, Kenneth Jensen, Lærke Münter Lassen, Carl Erik Olsen, Birger Lindberg Møller, and Poul Erik Jensen (2013) Redirecting Photosynthetic Reducing Power toward Bioactive Natural Product Synthesis. ACS Synthetic Biology DOI: 10.1021/sb300128r

Image credit: Martin Bahmann, via Wikimedia Commons.

Demystifying GM

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Published on: March 15, 2013

Geraint Parry of the University of Liverpool stepped up to the challenge of communicating the real science of GM at Ignite Liverpool in February. Ignite is a grassroots movement started in Seattle but now established in many cities all over the world. Ignite events consist of many 5-minute powerpoint presentations given by anyone who wants to contribute one about anything they want to talk about. Such a fast-moving event with a diverse audience is of course a great place to communicate science, and you can see Geraint’s excellent presentation in the video above.

If you want to have a go yourself, Ignite Liverpool is next on in May, and there is also an Ignite London, although I don’t know if they will be running another event.

The video is from the Ignite Liverpool YouTube Channel, where you can see other presentations from the event, including this one on ATP.

Conference Season

Categories: Workshops
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Published on: March 14, 2013

We are delighted that the Gatsby Charitable Foundation are kindly funding £500 travel bursaries to help four UK-based PhD students attend the annual International Conference on Arabidopsis Research (ICAR) conference, which this year will be in Sydney, Australia, on 24-28 June 2013.

If you would like to apply for this bursary please fill out the GARNet travel bursary GARNet travel bursary form and return it to me (charis@garnetcommunity.org.uk) by the 14th April. To be eligible, you must be a current PhD student Ph.D at the time of the conference, and have submitted a poster abstract to present at the meeting. You must have permission from your supervisor to attend the conference.

If you want to go to a conference but can’t spare the funds or the time to travel to Australia, there are great meetings going on in the UK too. I made a list of travel grants you can use to go to conferences here.

UK PlantSci 2013: 16–17 April, Dundee, Scotland

UK Brassica Research Community: 9 May, Rothamsted.

An Introduction to Opportunities in Plant Synthetic Biology: 21-22 May, Nottingham, England

International Symposium on Plant Photobiology: 3-6 June, Edinburgh, Scotland.


Other major international plant science conferences this year are:

Plant Immunity Pathways and Translation: 7-12 April 2013, Montana, USA.

31st New Phytologist Symposium (Orchid symbioses: models for evolutionary ecology): 14-16 May, Calabria, Italy.

SEB Annual Main Meeting 2013: 3–6 July, Valencia, Spain

ASPB Plant Biology 2013: 20–24 July, Providence RI, USA

7th EPSO Conference: 1–4 September, Peloponnese, Greece

Plant Genome Evolution: 8-10 September, Amsterdam, The Netherlands.

32nd New Phytologist Symposium (Plant interactions with other organisms): 20-23 November, Buenos Aires, Argentina.

What makes an invasive species?

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Published on: March 12, 2013
B. sylvaticum seeds

Brachypodium sylvaticum is a grass species known as slender false brome, and is native to Europe, Asia, and north Africa. It is a common sight in UK woodlands, and grows all over the country. In the USA though, its tufts don’t mark convenient picnic spots in woodland but are destroyed if seen in a new region because this invasive species has colonised miles of Oregon’s woodland floor. An Oregon-based research team has sequenced the B. sylvaticum transcriptome and hopes to use it as a mode for the evolution of invasive species.

Highlighted paper: Samuel E. Fox, Justin Preece, Jeffrey A. Kimbrel, Gina L. Marchini, Abigail Sage, Ken Youens-Clark, Mitchell B. Cruzan, and Pankaj Jaiswal 2013. Sequencing and De Novo Transcriptome Assembly of Brachypodium sylvaticum (Poaceae). Applications in Plant Sciences 1: 1200011

Slender false broom was widely planted in the in the mid part of the 20th century in an attempt to seed mountain rangelands in Utah, Wyoming, and Idaho. It was also planted in experimental gardens in two Oregon cities. The two attempts to establish the species were independent, but microsatellite analysis suggests the plants originated from the samestock of accessions. At some point in the late 20th century, some of these accessions crossed and the hybrids spread rapidly across Oregon’s forests (Rosenthal et al. 2008, Mol Ecol 17:4657). Today in Oregon this aggressive genotypes have formed thick monocultures that completely cover the forest floor at the expense of native flora, and have spread to California and Washington too. (more…)

Arabidopsis hydroponics video method

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Published on: March 8, 2013

One of the most frustrating things in lab-based research is trying to learn a new method from a paper. In my short time in the lab, I sometimes had to follow a trail of breadcrumbs back through several papers to find details of a single step in a protocol, on one occasion digging around in the library archives for a paper from an out-of-publication journal. Once the various reagents had been rounded up, I’d interpreted the protocol (What kind of ‘mixing’? How slowly is ‘slowly add’?), and had failed to accurately measure a solution that dissolved my pipette tips, all I usually had to show for my pains was a questionable precipitate and a lot of washing up – at least for the first attempt.

Researchers from three Australian research centres had similar problems with hydroponic systems described in the literature. Conn et al. designed their own hydroponic system for Arabidopsis and published it in Plant Methods (2013, 9:4) along with the YouTube video above, demonstrating exactly how the protocol works in practice. Plant Methods is a friendly journal for the intrepid researcher attempting protocols new to their research group. This paper is typical and has a comprehensive list of necessary reagents and equipment, and clear step-by-step guide with critical points highlighted.

If you need to grow Arabidopsis in a controlled environment to look at the physiology of the whole plant and you are unhappy with your current growth facilities, take a look at this paper on DIY hydroponics. It is quite a work intensive set-up (drill-bits are mentioned) but most of the equipment is cheap and easily come by.

Video Credit: Matthew Gilliham, via YouTube.

UK Brassica Research Community

Categories: Brassica
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Published on: March 7, 2013

Brassica crops, which include oilseed rape, cabbage, and brussels sprouts, are major components of the UK arable agriculture and horticulture industries. The close relationship between Brassica and Arabidopsis provides exciting opportunities to translate fundamental science to impact by using it to understand and manipulate crop traits.

If you are interested in finding out more about Brassica research and the UK Brassica research community, come to the annual meeting of the UK Brassica Research Community at Rothamsted on 9 May 2013.

A successful UK brassica industry requires fundamental and applied scientists, breeders, and farmers to work together. The UKBRC provides a hub for them to do so. Everyone can catch up at the annual meetings, but for the rest of the year check out the UKBRC website and join the UKBRC mailing list to get news and find resources.

You can register for the event here, and see talks from previous meetings on the UKBRC website. If you currently work with Brassicas and would like to share your research at the meeting, contact Pierre Carion (pierre.carion@rothamsted.ac.uk) to find out more.

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