RHdb: the radiation hybrid database

Since July 1995, the European Bioinformatics Institute (EBI) has maintained RHdb (http://www.ebi.ac.uk/RHdb ), a public database for radiation hybrid data. Radiation hybrid mapping is an important technique for determining high resolution maps. RHdb is also served by CORBA servers. The EBI is an Outstation of the European Molecular Biology Laboratory (EMBL).     

RHdb: the Radiation Hybrid database

Since July 1995, the European Bioinformatics Institute (EBI) has maintained RHdb (http://www.ebi.ac.uk/RHdb), a public database for radiation hybrid data. Radiation hybrid mapping is an important technique for determining high resolution maps. RHdb is also served by CORBA servers. The EBI is an Outstation of the European Molecular Biology Laboratory (EMBL).     

The radiation hybrid database.

Since July 1995, the European Bioinformatics Institute (EBI) has maintained the Radiation Hybrid database (RHdb; http://www.ebi.ac. uk/RHdb ), a public database for radiation hybrid data. Radiation hybrid mapping is an important technique for determining high resolution maps. Recently, CORBA access has been added to RHdb. The EBI is an Outstation of the European Molecular Biology Laboratory (EMBL).     

The Radiation Hybrid Database.

Since July 1995, the European Bioinformatics Institute (EBI) has maintained RHdb (http://www.ebi.ac.uk/RHdb/RHdb.html ), a public database for radiation hybrid data. Radiation hybrid mapping is an important technique for determining high resolution maps. Recently, CORBA access has been added to Rhdb. The EBI is an Outstation of the European Molecular Biology Laboratory (EMBL).     

The European Bioinformatics Institute (EBI) databases.

The European Bioinformatics Institute (EBI) maintains and distributes the EMBL Nucleotide Sequence database, Europe's primary nucleotide sequence data resource. The EBI also maintains and distributes the SWISS-PROT Protein Sequence database, in collaboration with Amos Bairoch of the University of Geneva. Over fifty additional specialist molecular biology databases, as well as software and documentation of interest to molecular biologists are available. The EBI network services include database searching and sequence similarity searching facilities.     

The European Bioinformatics Institute (EBI) databases.

This paper describes the databases and services of the European Bioinformatics Institute (EBI). In collaboration with DDBJ and GenBank/NCBI, the EBI maintains and distributes the EMBL Nucleotide Sequence Database, Europe's primary nucleotide sequence data resource. The EBI also maintains and distributes the SWISS-PROT Protein Sequence Database, in collaboration with Amos Bairoch of the University of Geneva. Over thirty additional specialist molecular biology databases, as well as software and documentation of interest to molecular biologists, are also available. The EBI network services include database searching, entry retrieval, and sequence similarity searching facilities.     

Equine dinucleotide repeat loci COR081–COR100

The nucleotide sequences data reported in this paper were submitted to the EMBL library at the European Bioinformatics Institute (EBI).     

The EBI SRS server-new features

MOTIVATION: Here we report on recent developments at the EBI SRS server (http://srs.ebi.ac.uk). SRS has become an integration system for both data retrieval and sequence analysis applications. The EBI SRS server is a primary gateway to major databases in the field of molecular biology produced and supported at EBI as well as European public access point to the MEDLINE database provided by US National Library of Medicine (NLM). It is a reference server for latest developments in data and application integration. The new additions include: concept of virtual databases, integration of XML databases like the Integrated Resource of Protein Domains and Functional Sites (InterPro), Gene Ontology (GO), MEDLINE, Metabolic pathways, etc., user friendly data representation in 'Nice views', SRSQuickSearch bookmarklets. AVAILABILITY: SRS6 is a licensed product of LION Bioscience AG freely available for academics. The EBI SRS server (http://srs.ebi.ac.uk) is a free central resource for molecular biology data as well as a reference server for the latest developments in data integration.     

The EMBL Nucleotide Sequence Database: major new developments

The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl/) incorporates, organizes and distributes nucleotide sequences from all available public sources. The database is located and maintained at the European Bioinformatics Institute (EBI) near Cambridge, UK. In an international collaboration with DDBJ (Japan) and GenBank (USA), data are exchanged amongst the collaborating databases on a daily basis to achieve optimal synchronization. Webin is the preferred web-based submission system for individual submitters, while automatic procedures allow incorporation of sequence data from large-scale genome sequencing centres and from the European Patent Office (EPO). Database releases are produced quarterly. Network services allow free access to the most up-to-date data collection via FTP, Email and World Wide Web interfaces. EBI's Sequence Retrieval System (SRS) integrates and links the main nucleotide and protein databases plus many other specialized molecular biology databases. For sequence similarity searching, a variety of tools (e.g. Fasta, BLAST) are available which allow external users to compare their own sequences against the latest data in the EMBL Nucleotide Sequence Database and SWISS-PROT. All resources can be accessed via the EBI home page at http://www.ebi.ac.uk.     

The EMBL Nucleotide Sequence Database.

The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl.html) constitutes Europe's primary nucleotide sequence resource. Main sources for DNA and RNA sequences are direct submissions from individual researchers, genome sequencing projects and patent applications. While automatic procedures allow incorporation of sequence data from large-scale genome sequencing centres and from the European Patent Office (EPO), the preferred submission tool for individual submitters is Webin (WWW). Through all stages, dataflow is monitored by EBI biologists communicating with the sequencing groups. In collaboration with DDBJ and GenBank the database is produced, maintained and distributed at the European Bioinformatics Institute (EBI). Database releases are produced quarterly and are distributed on CD-ROM. Network services allow access to the most up-to-date data collection via Internet and World Wide Web interface. EBI's Sequence Retrieval System (SRS) is a Network Browser for Databanks in Molecular Biology, integrating and linking the main nucleotide and protein databases, plus many specialised databases. For sequence similarity searching a variety of tools (e.g. Blitz, Fasta, Blast etc) are available for external users to compare their own sequences against the most currently available data in the EMBL Nucleotide Sequence Database and SWISS-PROT.     

The EMBL Nucleotide Sequence Database

The EMBL Nucleotide Sequence Database (aka EMBL-Bank; http://www.ebi.ac.uk/embl/) incorporates, organises and distributes nucleotide sequences from all available public sources. EMBL-Bank is located and maintained at the European Bioinformatics Institute (EBI) near Cambridge, UK. In an international collaboration with DDBJ (Japan) and GenBank (USA), data are exchanged amongst the collaborating databases on a daily basis. Major contributors to the EMBL database are individual scientists and genome project groups. Webin is the preferred web-based submission system for individual submitters, whilst automatic procedures allow incorporation of sequence data from large-scale genome sequencing centres and from the European Patent Office (EPO). Database releases are produced quarterly. Network services allow free access to the most up-to-date data collection via FTP, email and World Wide Web interfaces. EBI’s Sequence Retrieval System (SRS), a network browser for databanks in molecular biology, integrates and links the main nucleotide and protein databases plus many other specialized databases. For sequence similarity searching, a variety of tools (e.g. Blitz, Fasta, BLAST) are available which allow external users to compare their own sequences against the latest data in the EMBL Nucleotide Sequence Database and SWISS-PROT. All resources can be accessed via the EBI home page at http://www.ebi.ac.uk.     

Effect of Holstein-Friesian genetic group on peripartum and early lactation haematological and acute phase proteins profiles, health and fertility

Pasture-based Holstein-Friesian cows from three genetic groups differing in the Irish 'Economic Breeding Index' (EBI) value and genetic background, namely North-American (NA) national average EBI genetic merit (LOW-NA, n = 42), North-American high EBI genetic merit (HIGH-NA, n = 42) and New Zealand (NZ) high EBI genetic merit (HIGH-NZ, n = 42), were studied. These genetic groups have been selected in different environments: pasture for NZ and confinement for NA. The objective was to determine the effect of genetic group on haematological and acute phase proteins profiles (white blood cell (WBC) counts, red blood cell (RBC) counts, acute phase proteins: serum amyloid A (SAA) and haptoglobin), health (rectal temperature (RT), clinical mastitis (CM) and somatic cell score), calving performance (stillbirth, calving assistance) and post-partum reproductive parameters (endometritis and ovarian cyclicity). Blood sampling and data recording took place 3 weeks pre-calving up to 7 weeks post-calving. Linear mixed models, logistic regression and generalised estimating equations were used for data analysis. HIGH-NZ animals had the highest (P < 0.05) RBC mean corpuscular volume (50.0 fl), exhibited a different WBC distribution pattern (P < 0.05) and had the lowest (P < 0.05) mean RT (38.4°C) for the first 10 days post-calving. These findings suggest enhanced reticulocyte turnover, peripartum response mechanisms and thermoregulation in the HIGH-NZ compared to the other two genetic groups. LOW-NA animals had the highest SAA peak throughout the peripartum period (55.12 mg/l, P < 0.05) and a tendency for higher somatic cell scores (P < 0.10) in early lactation. The HIGH-NA animals had the lowest incidence of udder quarter milk sample bacteria at calving, suggesting better udder health when commencing lactation. No differences were detected between genetic groups in calving performance, post-partum reproductive parameters or CM in the first 42 days post-calving. These results suggest that while inherited peripartum adaptation strategies have been developed by the different genetic groups selected in different environments (pasture = NZ v. confinement = NA), such differences have minimal impact on peripartum clinical health.     

Effect of genetic group and feed system on locomotion score, clinical lameness and hoof disorders of pasture-based Holstein-Friesian cows

The aim of the present study was to determine the effect of the genetic group of the Holstein-Friesian (HF) and pasture-based feeding system (3 × 2 factorial arrangement) on locomotion score (six gait aspects scored from one to five), clinical lameness and hoof disorders within a seasonal calving milk production system. The three genetic groups compared had an average Economic Breeding Index (EBI) value of 40, 70 and 80: representing the Irish national average genetic merit (LOW-NA), high EBI genetic merit of North American ancestry (HIGH-NA) and high EBI genetic merit of New Zealand ancestry (HIGH-NZ), respectively. Two feed systems were compared: a high grass allowance, low-concentrate system typical of spring-calving herds in Ireland (control) and a high-concentrate system. Data from 126 cows collected across a complete lactation period were analysed using generalised estimating equations and survival analysis. Genetic group of HF had a significant effect on locomotion score, clinical lameness and hoof disorders. Higher EBI cows (HIGH-NA and HIGH-NZ) had lower hazard of poor locomotion score in some gait aspects (e.g. spine curvature) and lower odds of clinical lameness in the first 200 days post-calving (Odds ratios 0.08 and 0.24, respectively, relative to the LOW-NA) and some hoof disorders (e.g. traumatic lesions) compared with LOW-NA cows. The high-concentrate feed system showed a higher incidence and severity of digital dermatitis (P < 0.01). Thus, high EBI cows have better locomotion, fewer cases of clinical lameness and less-severe hoof disorders (i.e. digital dermatitis, white line disease and traumatic lesions) than low EBI cows. These findings have important implications for cow welfare and productivity.     

Application of European biomonitoring techniques in China: Are they a useful tool?

This paper focuses on the application of various biomonitoring techniques in China. We report a study in the Pearl River Basin (Guangzhou) based on the application of diatom indices as well as a study on the waterways in Wuhan based on evaluation of toxicity (using phytotoxicity, Daphnia magna and Microtox™ tests) and the Extended Biotic Index (EBI). Regarding the diatom indices, acceptable results were obtained based on comparison of the chemical water quality level and the European and Japanese indices, despite a lack of taxonomic information. The toxicity tests applied to the Wuhan waterways (Yangtze and Han Rivers) produced interesting results and can be considered to represent a useful tool for water pollution control in this area. Application of the EBI in Wuhan produced results that were contradictory to the toxicological analyses, as there were no indications of toxicity, whereas EBI indicated poor water quality. It can be concluded that in principle, certain European biological indicators can be considered to represent feasible tools to be applied in China. However, further studies will have to be carried out to develop bioindices based on Chinese data sets. The use of bioindices based on macroinvertebrates is limited to less polluted and smaller rivers with a lithic river substratum, whereas diatom indices are also applicable under extreme conditions (e.g., under high pollution loads or in large river streams with sandy riverbed sediments through installing artificial substrates).     

Enzymatic hydrolysis and characterization of lignocellulosic biomass exposed to electron beam irradiation

Pretreatment of lignocellulosic biomass has been taken up as a global challenge as it comprises a large renewable source of fermentable sugars. In this study, effect of electron beam irradiation (EBI) on a hybrid grass variety investigated as a biomass pretreatment method. Dry biomass samples after characterization were exposed to EBI doses of 0, 75, 150 and 250kGy. The pretreated biomass samples were enzymatically hydrolyzed using Trichoderma reesei ATCC 26921 cellulase for 144h. The enzyme loadings were 15 and 30FPU/g of biomass. The structural changes and degree of crystallinity of the pretreated biomass were studied by FTIR, XRD and SEM analyses. The lignocellulosic biomass sample showed 12.0% extractives, 36.9% cellulose, 28.4% hemicellulose, 11.9% lignin and 8.6% ash. Significant improvements in the reducing sugar and glucose yields were observed in the hydrolysate of EBI pretreated biomass compared to the control. In 250kGy exposed samples 79% of the final reducing sugar yield was released within 48h of hydrolysis at an enzyme loading rate of 30FPU/g of biomass. The IR crystallinity index calculated from the FTIR data and degree of crystallinity (XRD) decreased in the EBI treated samples. A significant negative correlation was observed between degree of crystallinity and the glucose yield from enzymatic hydrolysis.     

5th HUPO BPP Bioinformatics Meeting at the European Bioinformatics Institute in Hinxton, UK--Setting the analysis frame

The Bioinformatics Committee of the HUPO Brain Proteome Project (HUPO BPP) meets regularly to execute the post-lab analyses of the data produced in the HUPO BPP pilot studies. On July 7, 2005 the members came together for the 5th time at the European Bioinformatics Institute (EBI) in Hinxton, UK, hosted by Rolf Apweiler. As a main result, the parameter set of the semi-automated data re-analysis of MS/MS spectra has been elaborated and the subsequent work steps have been defined.     

Gene prediction: the end of the beginning

A report from the conference entitled Genome Based Gene Structure Determination, Hinxton, UK, 1-2 June, 2000, organised by the European Bioinformatics Institute (EBI).     

Molecular genetic diversity of the French-American grapevine hybrids cultivated in North America.

French-American hybrid grapevines are most popular in eastern and mid-western North America: they are hardy cultivars derived from crosses between the European Vitis vinifera and American wild vines. The aim of this study was to characterize their genetic background using 6 microsatellite (SSR) markers and a set of 33 diagnostic RAPD markers. The latter were reproducible with different PCR thermal cyclers. Two SSR loci were found to be synonymous, VrZAG47 and VVMD27. The DNA profile frequencies estimated for each cultivar were much lower with multi-locus SSR data than that obtained from multi-fragment RAPD data. There was no significant correlation between the multi-locus DNA profile frequencies derived from SSRs and those from RAPDs. Estimates of genetic diversity derived from SSRs were generally higher and the average similarity between cultivars was generally lower than values reported for subgroups of V. vinifera, in accordance with expectations for hybrid cultivars. The phenetic relationships depicted by UPGMA (unweighted pair-group method with arithmetic averaging) and neighbor-joining analyses of microsatellite data were congruent and, to a large extent, in agreement with the known pedigree or history of each cultivar. A major dichotomy was observed between one group where the known genetic background was dominated by the North American Vitis riparia and Vitis labrusca, and another one where the genetic background was dominated by the European V. vinifera. Two Kulhmann varieties thought to be synonymous were found to be different, though closely related.     

Integrative proteomics: structure, function, and interaction report on the 3rd joint meeting of the British Society for Proteome Research and the European Bioinformatics Institute, July 2006

This report summarizes the highlights of the recent British Society for Proteome Research (BSPR) meeting jointly organized with the European Bioinformatics Institute (EBI) which was held at the Wellcome Trust Genome Campus, Hinxton, Cambridge, UK in July 2006. This was the third annual scientific meeting organized by the BSPR and EBI and the theme of this years meeting was Integrative Proteomics: Structure, function and interaction. A wealth of local and overseas speakers were invited to discuss both their own work and specific challenges present in modern day proteomic based experiments.     

The EMBL Nucleotide Sequence Database.

The EMBL Nucleotide Sequence Database is a comprehensive database of DNA and RNA sequences directly submitted from researchers and genome sequencing groups and collected from the scientific literature and patent applications. In collaboration with DDBJ and GenBank the database is produced, maintained and distributed at the European Bioinformatics Institute (EBI) and constitutes Europe's primary nucleotide sequence resource. Database releases are produced quarterly and are distributed on CD-ROM. EBI's network services allow access to the most up-to-date data collection via Internet and World Wide Web interface, providing database searching and sequence similarity facilities plus access to a large number of additional databases.