SPPS Newsletter December 2006

Index of Issue IV 2006

The SPPS PhD conference is set for Haslev Højskole south of Copenhagen. From www.huh.as

The 5th biannual SPPS PhD conference has been scheduled for January 24-27 2008 and will take place at Haslev Højskole 60 km south of Copenhagen. An organizing committee has been established with 7 PhD students from Department of Plant Biology and Department of Agricultural Sciences at KVL and Department of Molecular Biology at University of Copenhagen. One of the organizers is Anne Steenbæk who was secretary of SPPS until October this year when Cherry Nielsen took over.

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Renew or sign up now. Graphic by Gorm Palmgren.

It is time to renew your membership for 2007 – or to sign up if you are not already a member. Renew right here or go to our Members section to learn more about the benefits of joining SPPS and see how you can signup online.

SPPS membership fee is only DKK 200 (US$ 35) or DKK 1100 (US$ 195) including a full years subscription to our international journal Physiologi Plantarum. For this low prize you get a lot:

  • Free bimonthly SPPS newsletter
  • Discounts on registration fees to SPPS Congresses
  • Possibilities of obtaining travel grants
  • No page charges for Physiologia Plantarum
  • An electronic membership directory

Renew or sign up right now here!

Transcriptomics, proteomics and metabolomics reveal biological function. From Goodacre (2005) J Exp Bot 56: 245.

Omics has become the new mantra in molecular research. With the publication of the complete Arabidopsis genome in 2000 and the human genome in 2001 the beginning of the new millennium was rightfully dubbed the genomic era. However, realizing that genomic data alone do not equal information the huge amount of data from these and several other genome projects called for an immediate need to extract useful information from it.

Whereas genomics had revealed the static sequences of genes and proteins, focus was now shifted to their dynamic functions and interactions. Consequently, a new field of molecular biology emerged where novel technologies were exploited in order to understand the complex, biological function of the genome. Under the common name functional genomics, three main aspects of ‘-omics’ are now widely used for this quest: transcriptomics, proteomics and metabolomics.

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Professor Jan K. Schjørring, President of SPPS, his experiences and impressions on omics technologies. Photo courtesy of SPPS.

1. Omics requires expertise and expensive equipment – is it worth the investment?
Of course – it is the only way to obtain the holistic data that are required for understanding the complex processes in living organisms.

2. Will omics drain resources from other important research areas?
Not necessarily – omics is an essential tool in systems biology and thus important also for research in e.g. plant-environment interactions, crop physiology and plant breeding.

3. Should omics ideally be performed in national/regional centres, or should every institution have their own facilities?
To ensure method development, flexibility and timely processing every institution should have dedicated new technologies provided these can be placed in active research environments where they constitute an integrated part of front-line research projects. When the tasks become more routine based, like e.g. high-throughput genome sequencing or micro-array transcriptome analysis they can be centralized/commercialized.

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Atle Bones hosted the annual NARC meeting in Trondheim. Photo by Gorm Palmgren.

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).

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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 here: Casado-Diaz et al (December 2006) Physiologia Plantarum 128: 633-650

Japanese researchers have taken a proteomics approach to study osmotic stress in rice. Proteins were extracted from basal leaves of seedlings treated with mannitol and separated using 2D PAGE. Of 327 detected proteins, the steady state level of 12 increased in a time and concentration dependent manner, whereas it decreased for 3 proteins. Proteins that accumulated during osmotic stress were found to be present even before stress induction in an osmotic-tolerant cultivar.

Source: Zang & Komatsu (13 December 2006) Phytochemistry, in press

Genes involved in salt stress have been intensively studied, but relatively little is known about how they affect the plants biochemical make up. To investigate this, Japanese and Korean researchers performed metabolic profiling of Arabidopsis cell cultures grown in 100 nM NaCl. Eight samples were taken within 72 hours after beginning of salt-stress and each of them were profiled for small polar, primary metabolites using GC/MS and LC/MS. The results showed that the most pronounced short term effects were induction of the methylation cycle as well as lignin and glycinebetaine biosynthesis, whereas long term effects were co-induction of glycolysis and sucrose metabolism.

Source: Kim et al (21 November 2006) J Exp Bot doi:10.1093/jxb/erl216