BSPP News Summer 2002 - Online Edition

The Newsletter of the British Society for Plant Pathology
Number 42, Summer 2002

DRASTIC: a Database Resource for Analysis of 
Signal Transduction In Cells
 

Readers of Molecular Plant Pathology will have seen our paper: Lyon GD, Newton AC, Marshall B, 2002. The need for a standard nomenclature for gene classification and a generic, automated tool to assist in hypothesis formulation in cell signalling. Molecular Plant Pathology 3, 103-9. The web site referred to in this paper is now on-line at http://www.drastic.org.uk

The site contains information on the molecular response of plants to infection by plant pathogens and an important database of genes up- or down-regulated in response to infection, treatment with chemicals that modify resistance, and various abiotic stresses. The link to the searchable database is one of the quick links on the right hand side (see picture of web page below). The information in the database is derived from published information but this is the first occasion that expression data of this type has been brought together in a searchable format. The site contains information that is focused on host-pathogen interactions, but covers a wide range of plants, and is expanding daily.

We are attempting to put as much relevant information into the database as possible, but this may take a while owing to the large amounts of data published. The site will never be complete, as the current gene regulation database - and others which will be added - will be continuously updated from newly published (public domain) data. However, if you know of any key papers that we have missed, please let us know so that we can add the information. The more complete the database, the more useful it will be to everybody.

In the longer term, our objective is to build a user-friendly, intuitive graphical interface for investigating gene regulation data. This will be based on a much-enhanced version of the current database together with novel graphical tools. These are being developed with colleagues at the University of Abertay, where development of state-of-the-art interactive graphics for computer games results in many innovative solutions which can be exploited. 

The project developed in response to the problem of making sense of the huge quantities of gene expression data being generated. Despite these data, it is disappointing that the scientific community has not devised a cell signalling model integrating and visualising these data. This is due, at least partially, to a lack of common systems of nomenclature. Also the sheer size and complexity of the task has probably inhibited any individual from bringing the knowledge together into a unified structure. There are clearly many aspects of cell biology that are similar, even between plants and animals, that could facilitate development of a generic model. Therefore, we have also attempted to generate discussion on a gene-coding or nucleotide classification system which is 'user-friendly', facilitates the construction of signal transduction models and enables rapid identification of orthologs of genes from different organisms. This information is crucial for integration with an intuitive graphical interface so we have attempted, perhaps naively, to tackle this issue too. Whilst there are some international projects that address the problem of assigning unique numbers to genes, none suggest a nucleotide classification system that provides biological information about, for example, function and cellular location, that is transparent within the code. Our Molecular Plant Pathology paper discusses these issues and identifies the need for a more formal, semi-automated approach to modeling signal transduction utilising the strengths of the proposed classification approach. By way of illustration, an example of a possible nucleotide function code is suggested to demonstrate more clearly the benefits of such a system, and this can also be found on the web site.

Figure - Nuclear events associated with disease resistance-related plant responses (pdf, 84kb)

We hope you will regularly access and use the resources of this web site and send us information for the database. Your comments for improvements will be most helpful. 

Adrian Newton, Gary Lyon, Bruce Marshall
E-mail: gary@drastic.org.uk  or  adrian@drastic.org.uk
Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, Scotland


People and Places

Institute of Arable Crops Research

As the re-development plan continues apace, more news of staff changes. Kim Hammond-Kosack joined the Plant-Pathogen Interactions Division at IACR-Rothamsted in April. Kim, who was previously the leader of Monsanto's global molecular disease control programme, will be leading a new research programme on wheat pathogenesis. The emphasis of the programme will be to use molecular and functional genomics tools to identify (1) the common core of fungal pathogenicity genes required by cereal specialising non-biotrophic fungi to cause disease and, (2) the key plant genes orchestrating defence responses to multiple cereal pathogens.

A major emphasis of the wheat pathogenesis programme is the cereal stem base disease complex and Fusarium ear blight. Fusarium is a global problem for cereal production and cannot currently be adequately controlled by fungicides or resistant cultivars. Fusarium ear blight infections can have profound effects on wheat grain quality and food safety, due to the production of mycotoxins. The new programme will also include ongoing work on Mycosphaerella graminicola and cereal viruses transmitted by soilborne fungi. 

Konstantin Kanyuka, previously based at Long Ashton, transferred to Rothamsted in April and will be working with Mike Adams on cereal viruses. Clive Bock left Rothamsted in May to take up a post as research plant pathologist at the USDA agricultural research service unit at Fort Pierce, Florida, where his major task will be battling citrus canker. 

John Lucas
 

Central Science Laboratory

During November 2001 the work of almost everybody at the laboratory was brought under scrutiny as DEFRA carried out a science audit chaired by Prof. Chris Leaver from the Department of Plant Sciences, University of Oxford.  Plant Health Group had a week in the spotlight with all the consultancy and R&D teams presenting aspects of their work and coping with some very intense questioning.  We have only recently received feedback from the exercise but can report that all of the teams impressed the auditors with their enthusiasm, commitment and dedication to quality.  Of course the audit also made some recommendations and although the entire process was disruptive at the time it will have had a positive benefit in the longer term.

Nigel Hardwick returned to the lab just in time for the audit after spending seven months dealing with the foot and mouth disease outbreak in Yorkshire.  Quite by chance Nigel found himself back in the same office he had occupied during his time at ADAS Leeds.  Since returning to the plant side of pathology Nigel has been on his travels again, attending a meeting in Montreal in March on aspects on international policy on the potential importation of genetically modified organisms.  In addition Nigel attended the launch of the Sárvári Research Trust, held at the University of Wales Bangor, for promoting some Hungarian potato cultivars which are claimed to be highly resistant to potato late blight and virus diseases.

In March, Plant Health Group played host to a small party from the Scientific Research Institute for Plant Protection in Tbilisi, Georgia.  The visit was sponsored by DEFRA Plant Health Division and allowed the Institution head, D. J. Naskidashvili, and research director, Dr Z. Sikharulidze, to spend four days in York at both CSL and Foss House. They were able to gain some idea about our research interests and explore possible areas for consultancy and collaboration.  They were accompanied by an interpreter, Dr N. Tchanisvili, from the Eliava Institute, best known for its pioneering work on bacteriophages. 

An old friend of the Plant Health Group virologists returned recently. Roger Jones was formerly employed at the Harpenden laboratory but now works in the Department of Agriculture for Western Australia.  He gave a talk on epidemiological information required to develop integrated virus disease management strategies, mainly concerned with insect (aphids and thrips) vectors.

Claire Sansford has been kept busy on BSPP business with an exponential growth in submissions to New Disease Reports.  In total during the year 2001 she received just under 60 submissions compared to 24 in the previous year.  A record 21 papers from the online journal were published in the December issue of Plant Pathology.  As part of her risk analysis work Claire attended an EC Rapporteurs meeting in Brussels in October 2001 to discuss a risk analysis submitted by South Africa related to citrus blackspot (Guignardia citricarpa).  To facilitate dissemination of the outputs from the EC Fifth Framework Project "Karnal bunt risks" Claire has accepted an invitation to organise an evening workshop on Karnal bunt at ICPP 2003 as well as one to speak on the link between R&D and risk analysis.

Giles Budge has recently joined CSL from ADAS Arthur Rickwood, where he worked as a horticultural pathologist.  He has now turned his hand to the study of soil-borne viruses and is working within Plant Health Group including a particular responsibility for the controlled environment facilities.

Finally, as an early notification, David Stead will organise the 11th ISPP International Conference on Bacterial Plant Pathogens to be held at CSL in York probably in 2004/5.  It is intended that this will include some workshops on diagnostic methods.  David will be looking for organisational assistance with the conference and welcomes any offers of help (d.stead@csl.gov.uk).

Moray Taylor


Molecular Plant Pathology

As we enter the third year for Molecular Plant Pathology, I am pleased to report that the journal is now well established within the international scientific community. Our reputation for a friendly and rapid review process has attracted praise from all areas. Copy flow to the journal is now at an all time high, whilst still maintaining our high editorial standards, this has resulted in the number of articles increasing from 6 in Vol 3:1 and Vol 3:2, to 9 articles in Vol 3:3 and 12 in Vol 3:4. 

We are pleased to see that MPP papers are being cited regularly in such journals as PNAS, Nature, Plant Cell, The Plant Journal, Plant Molecular Biology, Molecular Microbiology, MPMI, Trends in Plant Science, Gene etc. 

Full Table of Contents may be viewed at the journal website at http://www.blackwell-science.com/mpp along with the highly popular Pathogen Profiles that are free to download.

Gary Foster, Editor-in-Chief