Effective and ecological half-lives of 90Sr and 137Cs observed in wheat and rice in Japan

Published pre-Fukushima food monitoring data from 1963 to 1995 were used to study the long-term presence of 137Cs and 90Sr in rice and wheat. Effective half-lives (T eff) were calculated for rice (137Cs: 5.6 years; 90Sr: 6.7 years) and wheat (137Cs: 3.5 years; 90Sr: 6.2 years), respectively. In rice, 137Cs exhibits a longer T eff because putrefaction processes will lead to the formation of NH4 + ions that are efficient ion exchangers for mineral-adsorbed cesium ions, hence making it more readily available to the plant. Knowledge on the long-term behavior of radiocesium and radiostrontium will be important for Japanese food-safety campaigns after the Fukushima nuclear accident.

EMMA 2--a MAGE-compliant system for the collaborative analysis and integration of microarray data

Background: Understanding transcriptional regulation by genome-wide microarray studies can contribute to unravel complex relationships between genes. Attempts to standardize the annotation of microarray data include the Minimum Information About a Microarray Experiment (MIAME) recommendations, the MAGE-ML format for data interchange, and the use of controlled vocabularies or ontologies. The existing software systems for microarray data analysis implement the mentioned standards only partially and are often hard to use and extend. Integration of genomic annotation data and other sources of external knowledge using open standards is therefore a key requirement for future integrated analysis systems. Results: The EMMA 2 software has been designed to resolve shortcomings with respect to full MAGE-ML and ontology support and makes use of modern data integration techniques. We present a software system that features comprehensive data analysis functions for spotted arrays, and for the most common synthesized oligo arrays such as Agilent, Affymetrix and NimbleGen. The system is based on the full MAGE object model. Analysis functionality is based on R and Bioconductor packages and can make use of a compute cluster for distributed services. Conclusion: Our model-driven approach for automatically implementing a full MAGE object model provides high flexibility and compatibility. Data integration via SOAP-based web-services is advantageous in a distributed client-server environment as the collaborative analysis of microarray data is gaining more and more relevance in international research consortia. The adequacy of the EMMA 2 software design and implementation has been proven by its application in many distributed functional genomics projects. Its scalability makes the current architecture suited for extensions towards future transcriptomics methods based on high-throughput sequencing approaches which have much higher computational requirements than microarrays.