Residue and soil dissipation kinetics of chloroacetanilide herbicides on rice (Oryzae sativa L.) and assessing the impact on soil microbial parameters and enzyme activity.

The present investigation determines the persistence of herbicides like butachlor and pretilachlor in Indian soil, and their impact on soil biological properties including microbial biomass carbon (MBC), total microbial population numbers, and enzyme activities. Butachlor was degraded faster in autumn rice soil (t1/2 of 10-13 days) than in winter rice soil (half-life of 16-18 days). The t1/2 of pretilachlor in winter rice was 12-16 days. Regardless of the seasons under cultivation, no pesticide residue was detected in rice at harvest. Herbicides induced an initial decline (0-14th days after application) in MBC (averages of 332.7-478.4 g g-1 dry soil in autumn rice and 299.6-444.3 g g-1 dry soil in winter rice), microbial populations (averages of 6.4 cfu g-1 in autumn rice and 4.6 cfu g-1 in winter rice), and phosphatase (averages of 242.6-269.3 µg p-nitrophenol g-1 dry soil h-1 in autumn rice and 188.2-212.2 µg p-nitrophenol g-1 dry soil h-1 in winter rice). The application of herbicides favored dehydrogenase (averages of 123.1-156.7 g TPF g-1 dry soil in autumn and 126.7-151.1 g TPF g-1 dry soil in winter) and urease activities (averages of 279.0-340.4 g NH4 g-1 soil 2 h-1 in autumn and 226.7-296.5 g NH4 g-1 soil 2 h-1 in winter) in rice soil at 0-14th DAA. The study suggests that applications of butachlor and pretilachlor at the rates of 1000 g ha-1 and 750 g ha-1, respectively, to control the weeds in the transplanted rice fields do not have any negative impact on the harvested rice and associated soil environment.

ArrayExpress update--trends in database growth and links to data analysis tools.

The ArrayExpress Archive of Functional Genomics Data (http://www.ebi.ac.uk/arrayexpress) is one of three international functional genomics public data repositories, alongside the Gene Expression Omnibus at NCBI and the DDBJ Omics Archive, supporting peer-reviewed publications. It accepts data generated by sequencing or array-based technologies and currently contains data from almost a million assays, from over 30 000 experiments. The proportion of sequencing-based submissions has grown significantly over the last 2 years and has reached, in 2012, 15% of all new data. All data are available from ArrayExpress in MAGE-TAB format, which allows robust linking to data analysis and visualization tools, including Bioconductor and GenomeSpace. Additionally, R objects, for microarray data, and binary alignment format files, for sequencing data, have been generated for a significant proportion of ArrayExpress data.

ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments.

The ArrayExpress Archive (http://www.ebi.ac.uk/arrayexpress) is one of the three international public repositories of functional genomics data supporting publications. It includes data generated by sequencing or array-based technologies. Data are submitted by users and imported directly from the NCBI Gene Expression Omnibus. The ArrayExpress Archive is closely integrated with the Gene Expression Atlas and the sequence databases at the European Bioinformatics Institute. Advanced queries provided via ontology enabled interfaces include queries based on technology and sample attributes such as disease, cell types and anatomy.

ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression.

ArrayExpress http://www.ebi.ac.uk/arrayexpress consists of three components: the ArrayExpress Repository--a public archive of functional genomics experiments and supporting data, the ArrayExpress Warehouse--a database of gene expression profiles and other bio-measurements and the ArrayExpress Atlas--a new summary database and meta-analytical tool of ranked gene expression across multiple experiments and different biological conditions. The Repository contains data from over 6000 experiments comprising approximately 200,000 assays, and the database doubles in size every 15 months. The majority of the data are array based, but other data types are included, most recently-ultra high-throughput sequencing transcriptomics and epigenetic data. The Warehouse and Atlas allow users to query for differentially expressed genes by gene names and properties, experimental conditions and sample properties, or a combination of both. In this update, we describe the ArrayExpress developments over the last two years.

The ArrayExpress gene expression database: a software engineering and implementation perspective.

MOTIVATION: The lack of microarray data management systems and databases is still one of the major problems faced by many life sciences laboratories. While developing the public repository for microarray data ArrayExpress we had to find novel solutions to many non-trivial software engineering problems. Our experience will be both relevant and useful for most bioinformaticians involved in developing information systems for a wide range of high-throughput technologies. RESULTS: ArrayExpress has been online since February 2002, growing exponentially to well over 10,000 hybridizations (as of September 2004). It has been demonstrated that our chosen design and implementation works for databases aimed at storage, access and sharing of high-throughput data. AVAILABILITY: The ArrayExpress database is available at http://www.ebi.ac.uk/arrayexpress/. The software is open source. CONTACT: ugis@ebi.ac.uk.

Plant-based microarray data at the European Bioinformatics Institute. Introducing AtMIAMExpress, a submission tool for Arabidopsis gene expression data to ArrayExpress.

ArrayExpress is a public microarray repository founded on the Minimum Information About a Microarray Experiment (MIAME) principles that stores MIAME-compliant gene expression data. Plant-based data sets represent approximately one-quarter of the experiments in ArrayExpress. The majority are based on Arabidopsis (Arabidopsis thaliana); however, there are other data sets based on Triticum aestivum, Hordeum vulgare, and Populus subsp. AtMIAMExpress is an open-source Web-based software application for the submission of Arabidopsis-based microarray data to ArrayExpress. AtMIAMExpress exports data in MAGE-ML format for upload to any MAGE-ML-compliant application, such as J-Express and ArrayExpress. It was designed as a tool for users with minimal bioinformatics expertise, has comprehensive help and user support, and represents a simple solution to meeting the MIAME guidelines for the Arabidopsis community. Plant data are queryable both in ArrayExpress and in the Data Warehouse databases, which support queries based on gene-centric and sample-centric annotation. The AtMIAMExpress submission tool is available at http://www.ebi.ac.uk/at-miamexpress/. The software is open source and is available from http://sourceforge.net/projects/miamexpress/. For information, contact miamexpress@ebi.ac.uk.