NEWS FROM
PHYSIOLOGIA PLANTARUM
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Published monthly on behalf of SPPS by Wiley-Blackwell.
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Transcriptomics on spoiled fruit
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Rot in strawberries are often caused by the fungus Colletotrichum acutatum, one of the most important diseases in strawberry production. Only little is known about the molecular biology of the host-pathogen interaction, but now Spanish researchers have used transcriptomics to investigate the genes involved. They generated subtracted cDNA libraries from susceptible and resistant cultivars of strawberry containing only transcripts that were either up- or downregulated after infection with C. acutatum. This revealed a number of defence genes that were activated in the resistant cultivar, and surprisingly the same genes were downregulated in the susceptible cultivar.
Read full article free: Casado-Diaz et al (December 2006) Physiologia Plantarum 128: 633-650
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NEWS IN BRIEF
FROM OTHER JOURNALS
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Proteomics cope with stress
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Source: Zang & Komatsu (13 December 2006) Phytochemistry, in press
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Metabolic profiling over time
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Source: Kim et al (21 November 2006) J Exp Bot doi:10.1093/jxb/erl216
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Scandinavian research institute:
NARC, Norwegian Arabidopsis Research Centre
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Atle Bones hosted the annual NARC meeting in Trondheim. Photo by Gorm Palmgren.
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Norway has committed itself to the new omics technologies. Ten national functional genomics platforms have been established through the Norwegian Research Council's Functional Genomics (FUGE) initiative. The platforms are responsible for developing state-of-the-art technologies within their fields and share this expertise with other scientists so they can perform the most advanced genomic research.
Among them are the Norwegian Arabidopsis Research Centre, NARC, which was established in 2004 for a five year period, and now seems set for five more years after a very positive evaluation by FUGE earlier this year. NARC is headed by Professor Atle Bones from the Norwegian University of Science and Technology in Trondheim and also includes University of Oslo (Professor Reidunn Aalen) and Norwegian University of Life Sciences (Professor Odd-Arne Rognli).
During the annual NARC meeting in Trondheim 30th November 2006, Atle Bones was pleased to note that the centre now serves scientists from 61 research projects with powerful tools of functional genomics. This is up from 41 projects last year and indicates that the centre has encouraged Norwegian scientists to adopt the advanced technologies and take their research to a higher level.
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The high number of posters and speakers at the meeting illustrates the success of NARC. Photo by Gorm Palmgren.
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NARC is operated as a service platform that assists all research projects without prior evaluation. The service is free - except for materials - for scientists from Norway and Sweden and is also offered at a very competitive price for international research groups. In principle, the participating researchers plan the experiments themselves and bring the plant material needed to test their scientific theory. However, NARC often advises on experimental design in order to ensure that proper statistical evaluation can be performed on the results.
In most cases, experts from NARC will also help with interpretation of the complex data acquired during the experiments. This was originally not intended to be part of their services, but experience has shown that it is extremely difficult to evaluate the results if one does not truly understand the potentials and limitations of the techniques.
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DNA micro array analyses are offered at Norwegian University of Science and Technology in Trondheim. Photo by Gorm Palmgren.
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The transcriptional analyses by DNA micro arrays that NARC offers in Trondheim is a good example of such a highly specialized technology where the results must be interpreted from very complex data. Approximately 26,000 Arabidopsis genes represented by short 17-mer oligonucleotides are first positioned on a single glass slide using sophisticated print technology. The scientist can customize the micro arrays by including transgenes or genes from specific mutants and by a double hybridisation technique the expression of each gene can be analyzed.
Two fluorescent probes, red and green, are excited by a laser at different wavelengths, and this is used to compare gene expression between the control and the experimental plant. During 2006, more than 300 samples have been analyzed and many more are expected next year. The micro arrays made at NARC contain 5,000 more genes than those commercially available, and this has prompted international research groups at Max Planck Institute and American universities to have their samples analyzed in Trondheim.
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In situ hybridization and yeast two-hybrid analysis is offered at University of Oslo. Photo by Barbro E. Sæther and Vibeke Alm.
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At the University of Oslo, Reidunn Aalen from the Department of Molecular Biosciences is responsible for the NARC services within in situ hybridization and the yeast two-hybrid system. The first technique is used to determine spatial gene expression patterns in an organ. RNA probes are hybridized directly to thin sections of fixated tissue and visualized by the non-radioactive DIG-labelling system. This technique requires advanced microscopy and imaging equipment which is otherwise not available for most research groups.
The yeast two-hybrid system is also a technique where highly specialized skills and expertise's are needed. The system detects specific protein-protein interactions by causing transformed yeast cells to express a reporter gene when a known bait protein has bound an unknown target protein. In Oslo, they can assist in all the necessary steps including yeast transformation, cDNA library construction, analyses and retesting of positive clones.
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Arabidopsis transformation and green house facilities are offered at Norwegian University of Life Sciences in Oslo. Photo by Ragnhild Nestestog.
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Transformation of Arabidopsis is the main expertise offered by NARC at Norwegian University of Life Sciences in Oslo, where Odd-Arne Rognli is responsible. Scientists bring their own genes of interest and have them inserted into the experimental plant by the 'floral dip method'. Through a collaboration with Nottingham Stock Arabidopsis Centre they can also genotype T-DNA tagged transformants.
In the departments advanced greenhouse facilities, plants can even be grown at very specific conditions. The six growth chambers can be adjusted individually in order to regulate temperature, day-length and humidity as well as both the quality and quantity of light. This enables the researchers to test stress responses, seed vernalization and floral induction among many other possibilities. Special equipment make it possible to handle plants so unintentional crossing can be avoided.
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The NARC meeting was hosted by Norwegian University of Science and Technology. Photo by Gorm Palmgren.
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At the one-day meeting in Trondheim, the broad Norwegian research in Arabidopsis was illustrated by 13 oral presentations and 27 posters. Several projects have been initiated at locations in Norway where there is no tradition of experimental plant molecular biology. This includes the University of Stavanger, University of Tromsø and the breeding company Graminor. It was generally agreed at the meeting, that these institutions could not have carried out functional genomic plant research without the services offered by NARC.
At the end of the session it was decided to mark this expansion by arranging next years meeting in Stavanger where Simon Geir Møller from Department of Mathematics and Natural Sciences will be host.
You can find more information about NARC at the official website.
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