BSPP News Autumn 2002 - Online EditionThe Newsletter of the British Society for Plant Pathology
Number 43, Autumn 2002
A Week in the Life of a Once and Future Plant Pathologist
A brief explanation: Bob O'Hara did a PhD with James Brown at the John Innes Centre where he distinguished himself by (a) writing an excellent thesis on the population genetics of cereal powdery mildew and (b) cycling to work in a T-shirt whatever the weather in Norwich - fog, sleet, hail or snow. As global warming quickened, Bob, along with other subarctic creatures, migrated ever further north, first to Risø National Laboratory, Denmark, where he continued to work on mildew, then to the renowned Metapopulation Research Group at the University of Helsinki, Finland. After several years of messing around with insects and suchlike, he's come back to plant pathogens (which apparently have metapopulations too).
Spent the morning at home - doing the ironing, and then playing with the output of some data analysis - putting the statistics into tables. This is the tedious end of statistical analysis - having done the analysis, I have to summarise the results so that they can be understood by a biologist.
Go into my office in the centre of the city. It is on the site of the building where the Finnish declaration of independence from Russia was signed. Nowadays, the site is occupied by mathematicians and an Alko store (you can guess what is sold at Alko). What this says about the development of the Finnish state I am not sure, although the fact that both pursuits seem to lead to a state of incoherence cannot be without significance.
I spend the afternoon trying to understand what my computer code is doing. I have a time series of spore production by a wood rotting fungus (Phlebia centrifuga, seeing as you ask), and am trying to correlate this to a bunch of meteorological variables. This is part of a project on biodiversity in old growth forests, involving the Finnish Meteorological Institute and a former Finnish basketball player. I thought it was going to be a simple problem, but the data decided not to co-operate and so I have to write a programme to analyse the data - the standard packages break down in despair when I try to use them. Now the problem is different - unless I find the bug, I will break down in despair instead.
Another morning at home, reviewing a paper and doing some ironing. The paper represents the only piece of plant pathology done this week. It is interesting, but (as always) there are some problems, and it could do with some bits being re-thought. Like the decision to make it over 50 pages long. My suspicion is that I will end up recommending that it be accepted, but that another submission should be encouraged. I feel this is a measure of my advancement in science. The first few papers I received to review were passed on to me by my supervisor, Dr. J<censored by the editor>, presumably because they were so bad that they were best dealt with by a lowly oik who would not be able to complain. I then moved up to papers which were still ripe for rejection, but needed a bit of work to see what was wrong. I have yet to gain acceptance as a scientist, by which I mean that I will actually recommend that a paper be accepted.
Talk about the data I was dealing with on Monday morning to Juha, the guy in charge of it. The discussion goes smoothly - there are still a couple of things that need to be done, but the analysis is basically there. This is good news - it means that I get my name on another paper without the stress of writing the thing (this is replaced by the stress of having to correct the language. I live in a nation whose first language does not have such words as "the", "on", "by" etc. If it comes to that, they only grudgingly accept the existence of a word for "yes"). After this I enact a plan to start the downfall of Finnish culture - I lend a friend a tape of the Goon Show.
Get up, and alternate between reviewing the paper, and doing the ironing. In the end, I find myself in a quandary. Once the paper has been revised, I think it will be a very nice piece of work, and suitable for a bigger journal than the one it was sent to. Of course, I cannot write "The authors should revised the paper, and then send it to a better journal than this" in my comments, it might not be appreciated by the editors.
Into my office in town, and back to the programme. Aaagh! I do get an email to tell me from my friend with the Goon show tape complaining that he was laughing so much that he would miss the next gag. Another one corrupted!
Go out to do some fieldwork, so no ironing. I am acting as a slave for Johan, my South African friend who works on carabid beetles (they are black, but the really exciting ones have red legs. Yes, I do mean the beetles). We have to go to our field site, Tvärminne biological station, which is about 100 km southwest of Helsinki. Quite a few of the carabid species found on the small islands in the archipelago off the coast of Finland are flightless, which has been making us wonder how they get there. About 60 years ago the son of the man who founded Tvärminne did some experiments which consisted of putting some carabids in buckets of Baltic water and seeing how long they survived. He discovered that it took several days to die (this man later became the rector of the university. I will draw no connection between these two incidents). We decided to catch some of these swimming beetles by putting traps on some of the many small rocks that jut out of the sea, but do not have any vegetation on them (i.e. which cannot support a population). This means driving out to a small rock in a boat, me leaping out with the line, and then holding the boat whilst Johan places the traps in cracks in the rock. Normal pitfall traps are too wide to fit in the cracks, so I came up with the idea of making bags out of thick polythene, with wire around the neck to keep them open. These had to be sealed somehow, which I did by heat. Hence the ironing.
We managed to pick the one day during the summer which is not bright sunshine all the time, but instead is developing thunderstorms off the coast. This makes Johan nervous, but I have been watching the storms, and they are several miles, sorry, kilometres, to the south of us. Then we discover how manoeuvrable they are, suddenly changing direction and charging straight at us. We beat a hasty and wet retreat back to the station, and have tea. Eventually the rain stops, and we can go out again to finish our work. Now, of course, these small exposed rocks are slippery with the water. And I am the one having to leap out onto them first, before steadying the boat so that Johan can step regally onto shore. On one of the rocks, I do see a plant covered with mildew, which is gratifying, but only because I get to mention plant pathology again.
"This is me having a cup of coffee whilst waiting for my internet connection."
Spent the morning running some more analyses from the data I had been dealing with on Monday. And in the afternoon, back to my department, to continue trying to find the bug in the programme. Avoid doing any ironing.
Bob O'Hara, University of Helsinki, Finland
The University of Reading
We continue to have a vibrant pathology research culture. Roland
Fox, Simon Gowen, Michael Shaw, and - with one of his trophic hats on -
Paul Hatcher continue to form the main staff here, making us a strong centre
in whole-organism and population pathology. Sally Barnes and
Emily Rayfield graduated this summer, both with theses on Botrytis cinerea;
Tim Mauchline also graduated with a thesis on Verticillium chlamydosporium,
having worked mostly at IACR Rothamsted; and Prashant Mistra successfully
passed his viva on Fusarium culmorum. Femke van den Berg and
James Fountaine have both started PhDs this year, although both are actually
working mostly at IACR-Rothamsted. Femke is working on theory and
on pathogens of wild grasses; James is working on Rhynchosporium.
David Townley has bravely taken on the challenge of clubroot biology and
control, while Prasad Narra is continuing work on F. culmorum.
Next year, the foundation of the "Biocentre" as a central University resource providing access to the latest "-omic" tools is intended to make possible new collaborations and lines of research. We shall see whether funders are prepared to pay enough to allow molecular tools to fulfil their promise in pathology.
On the undergraduate front we are launching our new "Applied Biology" degree this autumn, and hope that it will build to provide an entry to the many areas of the subject in which Reading is strong. This coincides with a complete reorganisation of the pattern of undergraduate teaching, intended to provide more choice for students, and better individualised learning.
A happy event, but with a hollow feeling after it, was the graduation of the final seven students on the Agricultural Botany degree. Applicant numbers have become so low that it was no longer possible to run the degree; but the excellence of the final students was well up to the level of their many illustrious predecessors. We hope that many biology and applied biology students will realise how fascinating the disciplines encompassed in the subject area are and choose to study them. Realistically, the continuing decline in agricultural and horticultural employment means that we shall have to be very creative in our presentation!
Horticulture Research International
HRI is in the middle of the quinquennial review, which assesses HRI's importance for the horticulture industry and its value for money to the Government. We are hopeful of a positive outcome. HRI has had some organisational changes. The former Plant Pathology and Microbiology department is now grouped under the 'Environmental Microbiology' theme (led by Peter Mills), which consists of the teams 'Host Pathogen Interactions' (Jim Beynon), 'Sustainable Disease Resistance' (Eric Holub), 'Crop Disease Management' (Nicola Spence) and 'Mushroom Research' (Kerry Burton).
HRI has won two new contracts with DEFRA in an open competition on vegetable diseases. The first of the new projects, which will be led by Roy Kennedy, aims to develop a disease management system for the production of healthy transplants in glasshouses by developing techniques to detect downy mildew after it has entered glasshouses as air-borne inoculum through vents. Air-borne inoculum, which enters glasshouses from outside, is thought to be the key source of inoculum infecting transplants. Once the pathogen is detected, infection models will be used to predict whether infections are likely to occur and whether control measures are needed. Vegetable brassicas and lettuce, important horticultural cash crops, are chosen as model crops for developing these disease management systems. The second project, which will be led by John Whipps' group, aims to forecast Sclerotinia disease in field grown lettuce. A predictive model for Sclerotinia disease in lettuce will be developed, based on an understanding of the environmental factors affecting apothecial production and ascospore infection. This will be a significant new step in Sclerotinia control, as periods of high disease risk in lettuce crops will be identified and this will enable rational, economic and effective use of current and future foliar fungicides.
The Brassica Conference held at HRI-Wellesbourne earlier this year and organised by HRI, the Horticulture Development Council and the Brassica Growers Association was a great success, with many growers attending. Roy Kennedy presented some of his work on developing Brassicaspot, a disease forecaster for ringspot (Myco-sphaerella brassicicola) and dark leaf spot (Alternaria spp.), and the development of a detection system for air-borne spores of M. brassici-cola. He further demonstrated how the number of fungicide applications could be substantially reduced by combining information on the presence of air-borne spores with the occurrence of good environmental conditions for disease development.
John Carder and Nicola Spence (HRI) and Rory Hillocks (Natural Resources Institute) participated in a workshop in Uganda in May to review progress in a DFID project on 'Characterisation and epidemiology of root rot diseases caused by Fusarium and Pythium spp. in beans in Uganda' (see photo). Several crop management options and technologies that have some influence on root rot have been identified from the project for promotion to farmers as part of an IPM package for disease management. The project is a collaboration between HRI, NRI, the International Centre for Tropical Agriculture (CIAT) and the Ugandan National Agricultural Research Organisation.
John Carder (fifth from right), Nicola Spence (fourth from right)
and Rory Hillocks (on the right) (NRI) and some of the participants
of the workshop on root rot diseases of beans in Uganda.
HRI's Mushroom Day gave a good insight in the research that is being done on virus X. Virus X has been the cause of much concern to the mushroom industry. A current project at HRI, led by Helen Grogan and funded by the HDC, investigates the epidemiology of the virus disease, how it spreads and infects mushroom crops. A significant finding was that the virus is able to transmit from dust particles of infected compost to healthy mushroom crops.
Niaz Sepahvand successfully defended his PhD thesis entitled 'Characterisation of RPP28, a gene in Arabidopsis thaliana conferring isolate specific resistance to Peronospora parasitica'. His academic supervisor was John Mansfield and his supervisor at HRI was Jim Beynon.
David Harris retired after many years at HRI-East Malling in the Entomology and Plant Pathology Departments. David became known world-wide as an authority on Verticillium and Phytophthora species. He also ran the Plant Clinic successfully for a number of years.
Central Science Laboratory
The Great Yorkshire show is held in July and for three days Nigel Hardwick and Moray Taylor teamed up with four students from Rossett School in Harrogate to support the Active Learning Centre which had the general theme of potatoes. The CSL/Rossett School exhibit concentrated on "Potato Nasties" with some particularly gruesome examples of storage diseases, slug damage and late blight. In addition the students were able to demonstrate the use of on site, pocket sized, potato virus detection kits that the Immunological and Molecular Methods team at CSL have developed in recent years.
Members of plant health group who have been on their travels recently include David Jones who went to Costa Rica in May to speak at a Workshop on Sigatoka leaf spot diseases of banana organised by the International Network for the Improvement of Banana and Plantain. David Stead attended the Annual Meeting of the American Phytopathological Society in Milwaukee, USA. He was invited to give a talk on the use of real time PCR for detection of bacteria. Apart from the Real Time PCR session, other highlights were sessions on Sudden Oak Death and on Bioterrorism Issues. A major issue for the USA with regard to bioterrorism and indeed, biological warfare, is the lack of both a centralised national diagnostic facility such as that at CSL and the validation and harmonisation of diagnostic protocols for key plant pathogens as is currently being developed within the EU.
The first week in August saw Daphne Wright and Rick Mumford attending the First Joint Conference of the International Working Groups on Legume and Vegetable Viruses on "Vegetable and Legume Research for the New Millennium" in Bonn, Germany. Daphne presented a poster on "Survival and disinfection of Pepino mosaic virus (PepMV) on surfaces", co-authored with Tim O'Neill of ADAS and Nicola Spence of Horticulture Research International. Rick presented a paper on "Advances in the diagnosis of vegetable viruses: from on-site detection to micro-arrays", this was co-authored with Anna Blockley, Jonathan Flint, Penny Smith, Kathy Walsh, Ian Barker, Chris Danks and Neil Boonham.
Rick also visited Canada in May, at the invitation of the Canadian Food Inspection Agency (CFIA), as part of an expert panel reviewing the Canadian plum pox virus (PPV) eradication campaign. The role of the panel was to assess progress made by the campaign so far and to make recommendations on any changes necessary to improve the chances of eradicating PPV from orchards in Ontario. A further visit is planned for November this year to review the progress of this survey this season.
Finally, a long serving member of staff, Peter Sellar, team Leader of Plant Disease Diagnosis, retired on 31 July after 34 years at CSL.