Progress in pollen research

Time lapse video of Arabisopsis pollen grains germinating and growing pollen tubes. Credit: .

As an officer for GARNet, the Arabidopsis research network, I am happy to share the news that we can now add pollen germination to the long list of things for which our Arabidopsis can be called a model plant. The research is published in New Phytologist, and is currently in early view.

The importance of studying pollen for plant reproduction research is obvious, but it is also an excellent and widely used system for studying cell growth and development. Some plants, such as tobacco, have pollen that can be germinated on cue, and monitored in all sorts of ways as through germination, cell development, and pollen tube growth. Unfortunately brassicas, including Arabidopsis thaliana, do not have such amenable pollen.

A team of researchers from Oxford have developed a method that yields fast, reliable germination of A.thaliana pollen. The pollen tubes that grow are long and morphologically normal.

The method uses a cellulose-based membrane covering an agarose pad, all set up on a glass microscope slide. In the authors’ view, this protocol was more successful than other attempts because the environment surrounding the pollen mimics the stigma – so not only does this paper present a method of studying Arabidopsis pollen, but it provides novel information about the environmental cues required for pollen germination. The method was optimized for temperature and pH as well as the ratios of reagents used to make the materials.

Although this paper was about Arabidopsis and marks an important development for Arabidopsis researchers working on pollen and cell growth, it is also significant for Brassica researchers. The Brassica family contains many commercially important crops, and this method can surely be adapted to serve research into cabbage, oilseed rape, or other Brassica species.

Highlighted article: M. J. Rodriguez-Enriquez, S. Mehdi, H. G. Dickinson and R. T. Grant-Downton (2012) A novel method for efficient in vitro germination and tube growth of Arabidopsis thaliana pollen. New Phytologist (Early View) doi: 10.1111/nph.12037

GARNet workshop in Tweets

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Published on: November 29, 2012

The GARNet Tools and Technologies to Advance Plant Research workshop took place on Monday this week. It was my first attempt at live-tweeting, so I failed to take any meaningful notes for a proper blog post about it. However, you can see the abstract book here and the speakers’ slides will be online soon. In the meantime, I made a Storify of tweets from the workshop – who needs notes when you have Twitter? Thanks to @plantscience, @LiverpoolPlants, and @NeilHall_uk who all tweeted on the day and whose tweets are in the Storify.

On academic fraud

Categories: Open Access
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Published on: November 23, 2012

Mind-blowing, outrageous criminal fraud is rare in scientific research, but fraudulent practices such as turning a blind eye to contradictory data or failing to report anomalies are commonplace in laboratories worldwide. The building tide of retractions and the growing need to see all data, including anomalies and negative results, for big data experiments has brought these activities into the limelight, and preventing fraud in research has become an important issue for modern science.

Medical trials are frequently brought up in discussions about scientific fraud. It is easy to see why they are publicised, as inaccurate trials can cause thousands of people to have unnecessary or even harmful treatment. But fraud occurs in all science, and in non-medical research there are less emotive, but still serious, consequences of fraudulent activity.

I may be naïve, but I think in plant science and other areas, where the stakes are not as high as in medical research, most scientists do not deliberately reject data and only publish the minority of results that fit a favourite hypothesis. They do actively bury projects that just don’t go anywhere, as evidenced by many frustrated PhD students with a thesis full of negative results but no publications. As Ed Yong put it in the SpotOn London session ‘Fixing the Fraud,’ negative results are becoming an endangered species.

Causing someone to unwittingly replicate doomed experiments because you did not publish your perceived failed experiment may lead to wasted time and effort, but I would hesitate to call it fraud. An excellent example is described by Jim Caryl in his SciLogs blog The Gene Gym. Jim recently published his finding that a class of tetracyclin resistant genes identified in 1996 was actually a plasmid replication gene, and did not confer any kind of antibiotic resistance. The original authors did not set out to deceive, and scientists who used the gene in their research must have had negative results, which they did not publish. 

Another bad practice which I suspect is fairly common, to varying extents, is biased analysis of results. While this is definitely fraud, it has been overlooked up until now because of the need for conclusive, statistically significant data for papers. Again, Jim Caryl is an example – he struggled to get his important negative result published. Over the last decade, big data experiments requiring raw datasets have become the norm, and authors are usually obligated by their funders or by publishers to provide all their raw data. Yet frequently, datasets are not added to a suitable open access repository (Piowar, 2011), and a 2009 study showed that the rules governing open data are poorly enforced (Savage and Vickers, 2009).

At the SpotOn London session on Fixing the Fraud, the panelists briefly discussed the causes of fraud, pointing at the usual, and probably completely responsible, culprits: the pressure on researchers to publish in the most respected journal they can manage, and the requirements of journals who publish only positive results that point to significant, clear conclusions. (more…)

A very planty November

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Published on: November 23, 2012

November is turning out to be a busy month for the plant science community, and here is a round-up of what you might have missed and what is still to come.

Coming up

NIAB has been granted over £600 000 to provide a community wheat transformation service. This is an excellent opportunity for Arabidopsis researchers to test the application of their research in a commercial crop – around 25 transformations will be granted to model crop researchers. For more information, go to the NIAB website and see this poster. Applications will open shortly.

This year’s meeting of the Genetics Society Arabidopsis special interest group is organized by GARNet and will take place on Monday in Liverpool, focusing on next generation sequencing applications in plant science research. It’s too late to register, but you can see the abstracts here, and the presentation slides will be online soon after the day. We will be live tweeting from the workshop on #ngsplant.

The European Research Area Network for molecular plant science (ERA-CAPS) launched its first joint call on 19 November. Up to £6M of BBSRC funding is available to support UK researchers in ERA-CAPS consortia. The deadline for application is 15 February 2013.

London-dwelling people with an interest in policy will be interested in a new series of events run by the Society of Biology, Policy Lates. On Thursday there will be a debate at Charles Darwin House on Do we need more scientists in Parliament. It is a free event and is now full, but there is a waiting list. I expect there will be live tweeting under #policylates – so keep your Twitter tuned if you want to be there virtually, if not in person.

Recent goings on

The UK Plant Science Federation had its second annual general meeting on 5th November. I wrote a blog post on it for the UKPSF blog, and news from the meeting was also highlighted on this blog by Alan Jones.

I went to the Society of Biology Autumn Members Meeting, where I found out more about the Degree Accreditation Programme. If you feel that original research in UK undergraduate biology courses is poor, get involved by accrediting courses at your own institution, or signing up as an assessor.

The Higher Education team at the Society of Biology launched an Open Educational Resources website last Friday. All the resources on it are peer reviewed by experts, so they are top quality. You can download resources to use yourself, or submit your own resources so they can be used by other lecturers.

NIAB has been granted over £600 000 to provide a community wheat transformation service. This is an excellent opportunity for Arabidopsis researchers to test the application of their research in a commercial crop – around 25 transformations will be granted to model crop researchers. For more information, go to the NIAB website and see this poster. Applications will open shortly.

Overyielding in species mixtures

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Published on: November 22, 2012

Highlighted article: Gerlinde B. De Deyn, Helen Quirk, Simon Oakley, Nick Ostle, Richard D. Bardgett (2012) Increased Plant Carbon Translocation Linked to Overyielding in Grassland Species Mixtures. PLoS ONE 7(9): e45926. doi:10.1371/journal.pone.0045926

Plant biomass yield is often greater in areas where species richness is high than it is in monocultures. This has implications for agriculture, and also the use of non-farmed land as a carbon sink, as more biomass means more carbon assimilation. However, the relationship between growth and species richness on a plot of land is not constant or clear, so a group in Lancaster investigated it. I think their research threw up more questions than it answered, but the authors found intriguing links between lifetime biomass yield and speed of carbon transport from the leaves to other parts of the plants and found that non-legumes and legumes alike benefit from growing alongside one another.

Deyn et al. planted seedlings in monocultures or in a mixture and sampled soil and plant matter at 2, 24, and 48 hours, and finally at 8 days, after labeling carbon in the system using a 13CO2 pulse (Ostle et al., 2003). They assessed carbon assimilation and carbon/nitrogen ratio. Two years later, all the above-ground vegetation was harvested and weighed to obtain ‘yield’ data. The species used were common grassland species Trifolium repens and Lotus cornicalatus (both leguminous species), Plantgo lanceolata, Anthoxanthum odoratum, Achillea millefolium, and Lolium perenne. (more…)

Success falling from the air: how BeadaMoss has saved Sphagnum moorland

Categories: guest blogger, UKPSF
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Published on: November 20, 2012
Sphagnum moss

I’m delighted that Dr Alan Jones, who presented this story as part of the ‘Good news from UK plant science’ session at the UKPSF AGM, agreed to write a guest blog post for GARNet.

Degradation of the Pennine moorlands in northern England over the last 100 years has been severe. This rocky windswept spine runs through the centre of what was once the industrial powerhouse of Britain, and these upland areas have been subject to intense pressures from atmospheric pollution, overgrazing and recreational activity. The moorland soils are eroding, which rapidly exposes their carbon-rich peat to the elements and so they begin release carbon dioxide. This is a big issue for the UK because, owing to this sort of land degradation, our upland soils are currently releasing the carbon emissions equivalent to that of Manchester.

Eroded peatland in the Yorkshire Peak District.

At their heart, upland soils are built upon the few tiny plants that can survive harsh conditions, waterlogging and low nutrients. Sphagnum mosses are the building block that achieve this, but unfortunately once the soil has eroded, sphagnum cannot recolonize.

With the assistance of Manchester Metropolitan University and a small UK company – MicroPropagation Services, a product has been developed which promises to revolutionise upland conservation and reverse this degradation. The product is BeadaMosstm – a sphagnum culture formed into small gel beads, which stabilise and nurture these young plants, allowing them to re-establish on degraded peatlands where they would otherwise be unable. Remarkably, these green beads are actually airlifted by helicopter, so large quantities can be dropped to target specific areas of remote moorland, where volunteer workers then complete the final painstaking step of inserting them into the soil. (more…)

Plant science hoax

Categories: Friday Film, something fun
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Published on: November 16, 2012

At SpotOn London 2012, I went to a session discussion the prevention of academic fraud. When I was thinking of a Friday Film for this week, I remembered this amazing Panorama hoax from 1957. True, it’s not exactly academic fraud, but it is a false story about plant science, and people actually believed it! I love the deadpan references to plant breeders, environmental conditions, and a plant pest.

Credit: Alexandra Palace Television Society

SpotOn London 2012 in brief

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Published on: November 15, 2012

This weekend, Ruth and I were in London for SpotOn London 2012 at the Wellcome Trust. There were too many incredible sessions to attend, let alone to cover on this little blog – but all the talks were recorded and you can see them on the SpotOn youtube channel. There will be Storifies aplenty before the end of the week, which I will tweet if they cross my path.

I plan to write at least one ‘proper’ post about the sessions I attended, but for now here are some brief summaries of the topics most discussed in the sessions I attended at SpotOn 2012.

Open data: All the speakers and delegates assumed that everyone else understood and supported open access publishing. What was more interesting was the discussions of other issues in open science – digital licensing, openness in peer review, accessibility of raw data. A longer blog post on this is forthcoming, but I recommend Ross Mounce’s blog, in particular this post on price and ‘openness’ in open access journals, for more information about open science.

Crowd-funding: Around the fringes of publically funded science are small projects supported by funds raised by the researchers. Crowd-funded science is very much in the minority, but in the UK the University of Buckingham has survived for over thirty years without government support, including research programmes. For crowd-funding, excellent marketing and PR are crucial. If you have a public-good, sexy, relatively low-cost research project in your to-do list, and you have a flair for public relations and promotion, it is worth considering. You also need to be able to reward donations in some small way. Check out crowd-funded projects by Matthew Partridge (Cranfield University) and Ethan Perstein (Princeton) to find out more, or donate to their projects. Kickstarter is the best platform to raise your funds.

(more…)

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