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.     

Interdisciplinary research towards management of non-timber forest resources in lowland rain forests of Sri Lanka

Lowland and mid-elevational rainforests of Sri Lanka harbor a relict, endemic-rich flora which is also rich in timber and non-timber forest resources. These forests supply nearly half the total wood requirements of the country and are dwindling rapidly; management of the forests to conserve the biological richness and maintain environmental services is therefore a difficult proposition. This predicament is further compounded by the dependency of rural people on a range of non-timber forest resources for their subsistence and income. A forestry master plan recently prepared for Sri Lanka has not given adequate recognition to the important role played by non-timber forest resources in rural livelihood. This oversight is primarily due to the lack of quantitative information to justify the role of non-timber forest resources in forestry sector development. Forestry policies that ignore these resources often anger local people, leading the villagers to vent their disapproval through destructive actions such as burning timber plantations. Long-term interdisciplinary research in ecology, reproductive and soil biology, ethnobiology, silviculture, rural sociology and resource economics in progress at Sinharaja attempts to address these questions of sustainable development of forest resources in an integrated mode. While research oriented toward conservation investigates both short- and long-term ecosystem dynamics in natural and modified forest stands, utilization-oriented research probes the impact of increased human disturbance, particularly the impact of rural communities on dwindling forest resources, as well as the effect of forest conservation on rural livelihood. These studies continue to seek alternative methods of forest management which are socially acceptable, economically viable, and ecologically sustainable for multiple uses. These methods will assist in the refinement of current forest policies, forestry planning, and the implementation of new policies and plans in Sri Lanka.     

Environmental influence on calving interval and estimates of its repeatability in the Murrah buffalo in Sri Lanka

Data on 2375 calvings in 726 Murrah buffalo cows were analysed for the period 1968 to 1979 on two state farms (Ridiyagama and Polonnaruwa) in the dry zone of Sri Lanka. The mean ages at first calving were 51.0 (S.D. 8.6) and 52.1 (S.D. 10.5) months, the calving intervals 530.6 (S.D. 168.2) and 538.6 (S.D. 166.7) days, and the repeatabilities of calving intervals 0.36 ± 0.02 and 0.43 ± 0.02 for the two farms, respectively. The calving interval was significantly influenced (P ? 0.01) by the individual cow, year and season of conception, and parity. Conception during January to March led to the shortest calving interval, and during October to December to the longest. The highest percentage of conceptions occurred some 2–5 months after the peak rainfall.     

ArrayExpress: a public database of gene expression data at EBI

ArrayExpress is a public repository for microarray-based gene expression data, resulting from the implementation of the MAGE object model to ensure accurate data structuring and the MIAME standard, which defines the annotation requirements. ArrayExpress accepts data as MAGE-ML files for direct submissions or data from MIAMExpress, the MIAME compliant web-based annotation and submission tool of EBI. A team of curators supports the submission process, providing assistance in data annotation. Data retrieval is performed through a dedicated web interface. Relevant results may be exported to ExpressionProfiler, the EBI based expression analysis tool available online (http://www.ebi.ac.uk/arrayexpress).     

Role of non-timber forest products in the economy of peripheral communities of knuckles national wilderness area of Sri Lanka: A farming systems approach

The Knuckles range of forests has been identified as a unique biological resource in Sri Lanka with much biodiversity. It is also important as a watershed which feeds the Mahaweli reservoir system. Having considered the present hazardous land-use practices such as cardamum production and shifting cultivation, the Knuckles range has been declared a national wilderness area. The Forest Department is in the process of preparing the management plan for the area. There are about 48 villages in the vicinity of the forest. This study attempts to estimate the composition of income in the peripheral communities, ticularly the extraction of non-timber forest products (NTFP) from this range of forests. Data were collected using structured questionnaires from 60 households in three villages in the vicinity of the forest. The rural economy is described using a farming systems approach and the net income contributed by each activity in the farming system was estimated. Results show that nine components of the farming system use resources from the village and the forest, with at least 47 plant species used by the villagers for different purposes. Cardamum production and shifting cultivation contribute significantly to the total income of the household, but the majority of households in the study depend upon forest resources to supply some portion of their income. Nevertheless, the monetary value of the annual income generated by NTFP is much lower than income from either cardamum production or shifting cultivation. If cardamum production and shifting cultivation are to be restricted under the conservation program, there could be additional pressure put on NTFP. Therefore, we suggest a study of the natural regen-eration capacity of selected NTFP; such information should be used in finalizing the management plan in the Knuckles range of forests.     

Peripartal changes of estrone, progesterone and prostaglandin in the water buffalo

The peripheral blood plasma concentration of estrone, progesterone and 15-keto-13, 14-dihydroprostaglandin F2alpha (PGF2alpha metabolite) were determined by radioimmunoassay techniques during the peripartal period in 5 buffalo cows belonging to a river type breed. Estrone levels started to increase from below 200 pg/ml about 15 days prior to parturition, and reached high concentrations (400-750 pg/ml) during the last 5 days of pregnancy. The estrone concentration decreased to baseline levels after delivery. The concentration of progesterone fluctuated between 800 and 2000 pg/ml until 15 days before calving and showed a gradual increase during the last 15 days of pregnancy. The progesterone levels declined abruptly on the day of calving and remained below 100 pg/ml for up to 60 days post-partum. Increased levels of the prostaglandin metabolite were recorded from 15 days prior to parturition with further increases occurring during the last 3 days of pregnancy. PGF2alpha metabolite levels declined gradually after parturition, reaching base line levels 15-20 days after calving.     

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.     

ArrayExpress--a public repository for microarray gene expression data at the EBI

ArrayExpress is a new public database of microarray gene expression data at the EBI, which is a generic gene expression database designed to hold data from all microarray platforms. ArrayExpress uses the annotation standard Minimum Information About a Microarray Experiment (MIAME) and the associated XML data exchange format Microarray Gene Expression Markup Language (MAGE-ML) and it is designed to store well annotated data in a structured way. The ArrayExpress infrastructure consists of the database itself, data submissions in MAGE-ML format or via an online submission tool MIAMExpress, online database query interface, and the Expression Profiler online analysis tool. ArrayExpress accepts three types of submission, arrays, experiments and protocols, each of these is assigned an accession number. Help on data submission and annotation is provided by the curation team. The database can be queried on parameters such as author, laboratory, organism, experiment or array types. With an increasing number of organisations adopting MAGE-ML standard, the volume of submissions to ArrayExpress is increasing rapidly. The database can be accessed at http://www.ebi.ac.uk/arrayexpress.     

A closer look at the spectroscopic properties of possible reaction intermediates in wild-type and mutant (E)-4-hydroxy-3-methylbut-2-enyl diphosphate reductase

(E)-4-Hydroxy-3-methylbut-2-enyl diphosphate reductase (IspH or LytB) catalyzes the terminal step of the MEP/DOXP pathway where it converts (E)-4-hydroxy-3-methylbut-2-enyl diphosphate (HMBPP) into the two products, isopentenyl diphosphate and dimethylallyl diphosphate. The reaction involves the reductive elimination of the C4 hydroxyl group, using a total of two electrons. Here we show that the active form of IspH contains a [4Fe-4S] cluster and not the [3Fe-4S] form. Our studies show that the cluster is the direct electron source for the reaction and that a reaction intermediate is bound directly to the cluster. This active form has been trapped in a state, dubbed FeS(A), that was detected by electron paramagnetic resonance (EPR) spectroscopy when one-electron-reduced IspH was incubated with HMBPP. In addition, three mutants of IspH have been prepared and studied, His42, His124, and Glu126 (Aquifex aeolicus numbering), with particular attention paid to the effects on the cluster properties and possible reaction intermediates. None of the mutants significantly affected the properties of the [4Fe-4S](+) cluster, but different effects were observed when one-electron-reduced forms were incubated with HMBPP. Replacing His42 led to an increased K(M) value and a much lower catalytic efficiency, confirming the role of this residue in substrate binding. Replacing the His124 also resulted in a lower catalytic efficiency. In this case, however, the enzyme showed the loss of the [4Fe-4S](+) EPR signal upon addition of HMBPP without the subsequent formation of the FeS(A) signal. Instead, a radical-type signal was observed in some of the samples, indicating that this residue plays a role in the correct positioning of the substrate. The incorrect orientation in the mutant leads to the formation of substrate-based radicals instead of the cluster-bound intermediate complex FeS(A). Replacing the Glu126 also resulted in a lower catalytic efficiency, with yet a third type of EPR signal being detected upon incubation with HMBPP. (31)P and (2)H ENDOR measurements of the FeS(A) species incubated with regular and (2)H-C4-labeled HMBPP reveal that the substrate binds to the enzyme in the proximity of the active-site cluster with C4 adjacent to the site of linkage between the FeS cluster and HMBPP. Comparison of the spectroscopic properties of this intermediate to those of intermediates detected in (E)-4-hydroxy-3-methylbut-2-enyl diphosphate synthase and ferredoxin:thioredoxin reductase suggests that HMBPP binds to the FeS cluster via its hydroxyl group instead of a side-on binding as previously proposed for the species detected in the inactive Glu126 variant. Consequences for the IspH reaction mechanism are discussed.