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At least 91 records · Page 5Linked to original sources
PubMed2006

Implications for molecular mechanisms of glycoprotein hormone receptors using a new sequence-structure-function analysis resource.

Comparison between wild-type and mutated glycoprotein hormone receptors (GPHRs), TSH receptor, FSH receptor, and LH-chorionic gonadotropin receptor is established to identify determinants involved in molecular activation mechanism. The basic aims of the current work are 1) the discrimination of receptor phenotypes according to the differences between activity states they represent, 2) the assignment of classified phenotypes to three-dimensional structural positions to reveal 3) functional-structural hot spots and 4) interrelations between determinants that are responsible for corresponding activity states. Because it is hard to survey the vast amount of pathogenic and site-directed mutations at GPHRs and to improve an almost isolated consideration of individual point mutations, we present a system for systematic and diversified sequence-structure-function analysis (http://www.fmp-berlin.de/ssfa). To combine all mutagenesis data into one set, we converted the functional data into unified scaled values. This at least enables their comparison in a rough classification manner. In this study we describe the compiled data set and a wide spectrum of functions for user-driven searches and classification of receptor functionalities such as cell surface expression, maximum of hormone binding capability, and basal as well as hormone-induced Galphas/Galphaq mediated cAMP/inositol phosphate accumulation. Complementary to known databases, our data set and bioinformatics tools allow functional and biochemical specificities to be linked with spatial features to reveal concealed structure-function relationships by a semiquantitative analysis. A comprehensive discrimination of specificities of pathogenic mutations and in vitro mutant phenotypes and their relation to signaling mechanisms of GPHRs demonstrates the utility of sequence-structure-function analysis. Moreover, new interrelations of determinants important for selective G protein-mediated activation of GPHRs are resumed.

Animals↗
PubMed2003

Sputnik: a database platform for comparative plant genomics.

Two million plant ESTs, from 20 different plant species, and totalling more than one 1000 Mbp of DNA sequence, represents a formidable transcriptomic resource. Sputnik uses the potential of this sequence resource to fill some of the information gap in the un-sequenced plant genomes and to serve as the foundation for in silicio comparative plant genomics. The complexity of the individual EST collections has been reduced using optimised EST clustering techniques. Annotation of cluster sequences is performed by exploiting and transferring information from the comprehensive knowledgebase already produced for the completed model plant genome (Arabidopsis thaliana) and by performing additional state of-the-art sequence analyses relevant to today's plant biologist. Functional predictions, comparative analyses and associative annotations for 500 000 plant EST derived peptides make Sputnik (http://mips.gsf.de/proj/sputnik/) a valid platform for contemporary plant genomics.

Databases, Nucleic Acid↗
PubMed1996

The construction of Arabidopsis expressed sequence tag assemblies. A new resource to facilitate gene identification.

The generation of large numbers of partial cDNA sequences, or expressed sequence tags (ESTs), has provided a method with which to sample a large number of genes from an organism. More than 25,000 Arabidopsis thaliana ESTs have been deposited in public databases, producing the largest collection of ESTs for any plant species. We describe here the application of a method of reducing redundancy and increasing information content in this collection by grouping overlapping ESTs representing the same gene into a "contig" or assembly. The increased information content of these assemblies allows more putative identifications to be assigned based on the results of similarity searches with nucleotide and protein databases. The results of this analysis indicate that sequence information is available for approximately 12,600 nonoverlapping ESTs from Arabidopsis. Comparison of the assemblies with 953 Arabidopsis coding sequences indicates that up to 57% of all Arabidopsis genes are represented by an EST. Clustering analysis of these sequences suggests that between 300 and 700 gene families are represented by between 700 and 2000 sequences in the EST database. A database of the assembled sequences, their putative identifications, and cellular roles is available through the World Wide Web.

Arabidopsis↗
PubMed1988

Complete amino acid sequence of rat liver 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase.

The complete amino acid sequence of 6-phospho-fructo-2-kinase/fructose-2,6-bisphosphatase from rat liver was determined by direct analysis of the S-carboxamidomethyl protein. A complete set of nonoverlapping peptides was produced by cleavage with a combination of cyanogen bromide and specific proteolytic enzymes. The active enzyme is a dimer of two identical polypeptide chains composed of 470 amino acids each. The NH2-terminal amino acid residue of the polypeptide chain was shown to be N-acetylserine by fast atom bombardment mass spectrometry of the purified N-terminal tetradecapeptide isolated after cleavage of the intact S-carboxamidomethylated protein with lysyl endoproteinase (Achromobacter protease I). Alignment of the set of unique peptides was accomplished by the analysis of selected overlapping peptides generated by proteolytic cleavage of the intact protein and the larger purified cyanogen bromide peptides with trypsin, Staphylococcus aureus V8 protease, and lysyl endoproteinase. Four nonoverlapping peptides were aligned by comparison with the amino acid sequence predicted from a partial cDNA clone encoding amino acid positions 166-470 of 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase (Colosia, A.D., Lively, M., El-Maghrabi, M. R., and Pilkis, S. J. (1987) Biochem. Biophys. Res. Commun. 143, 1092-1098). The nucleotide sequence of the cDNA corroborated the peptide sequence determined by direct methods. A search of the Protein Identification Resource protein sequence database revealed that the overall amino acid sequence appears to be unique since no obviously homologous sequences were identified. However, a 100-residue segment of 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase (residues 250-349), including the active site histidine residue of the bisphosphatase domain, was found to be homologous to the active site regions of yeast phosphoglycerate mutase and human bisphosphoglycerate mutase.

Amino Acid Sequence↗
PubMed1999

Resource partition history and evolutionary specialization of subunits in complex systems.

Specialization for part of the resources available is a common adaptation leading to diversification in biological systems. In complex ecological communities, the history of diversification of parts of a system correlates with the structure of the system in present times. Abundances and sequences of resource partition of species expected by a sequential broken stick model are compared with observed abundances of species and their sequences of evolutionary divergence. Where resources are abundant, first resource partitions correspond to most ancient speciations, and last to recent speciations. The inverse is true when resources are scarce, agreeing with the occupation of extreme habitats by recent species. Diverging species seem to specialize by dividing the niche of common ancestors. Similar trends exist inside genera as well as between families, suggesting similar patterns in diversification and specialization at other levels of biological organization, such as evolution of functional complexes of macromolecules and organs embryogenesis.

Animals↗
PubMed2005

RARGE: a large-scale database of RIKEN Arabidopsis resources ranging from transcriptome to phenome.

The RIKEN Arabidopsis Genome Encyclopedia (RARGE) database houses information on biological resources ranging from transcriptome to phenome, including RIKEN Arabidopsis full-length (RAFL) complementary DNAs (cDNAs), their promoter regions, Dissociation (Ds) transposon-tagged lines and expression data from microarray experiments. RARGE provides tools for searching by resource code, sequence homology or keyword, and rapid access to detailed information on the resources. We have isolated 245 946 RAFL cDNA clones and collected 11 933 transposon-tagged lines, which are available from the RIKEN Bioresource Center and are stored in RARGE. The RARGE web interface can be accessed at http://rarge.gsc.riken.jp/. Additionally, we report 90 000 new RAFL cDNA clones here.

Arabidopsis↗
PubMed2004

EyeSite: a semi-automated database of protein families in the eye.

The EyeSite is a web-based database of protein families for proteins that function in the eye and their homologous sequences. The resource clusters proteins at different levels of homology in order to facilitate functional annotation of sequences and modelling of proteins from structural homologues. Eye proteins are organized into the tissue types in which they function and are clustered into homologous families using a novel protocol employing the TribeMCL algorithm. Homologous families are further subdivided into sequence clusters for which multiple sequence alignments are generated. Structural annotations from the CATH domain database are provided for nearly 90% of the sequences, and protein family annotations from the Pfam database for approximately 86%. Homology models have also been generated where appropriate. The EyeSite is stored in a relational database and is extensively linked to other online bioinformatics resources to help relate allelic variants, annotations and clinical details to the derived data in the database. The EyeSite is available for online search, sequence information and model retrieval at http://eyesite.cryst.bbk.ac.uk/.

Amino Acid Sequence↗
PubMed1994

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.

Amino Acid Sequence↗
PubMed1996

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.

Amino Acid Sequence↗
PubMed2007

Generating unigene collections of expressed sequence tag sequences for use in mass spectrometry identification.

Expressed sequence tag sequences remain the largest resource of DNA sequence for most organisms despite recent advances in genome sequencing. These sequences are short, fragmented versions of the expressed genes. By DNA sequence assembly, the fragments can be assembled into contiguous DNA sequences that are better suited for protein identification by mass spectrometry.

Cluster Analysis↗
PubMed1999

The Genome Sequence DataBase: towards an integrated functional genomics resource.

During 1998 the primary focus of the Genome Sequence DataBase (GSDB; http://www.ncgr.org/gsdb ) located at the National Center for Genome Resources (NCGR) has been to improve data quality, improve data collections, and provide new methods and tools to access and analyze data. Data quality has been improved by extensive curation of certain data fields necessary for maintaining data collections and for using certain tools. Data quality has also been increased by improvements to the suite of programs that import data from the International Nucleotide Sequence Database Collaboration (IC). The Sequence Tag Alignment and Consensus Knowledgebase (STACK), a database of human expressed gene sequences developed by the South African National Bioinformatics Institute (SANBI), became available within the last year, allowing public access to this valuable resource of expressed sequences. Data access was improved by the addition of the Sequence Viewer, a platform-independent graphical viewer for GSDB sequence data. This tool has also been integrated with other searching and data retrieval tools. A BLAST homology search service was also made available, allowing researchers to search all of the data, including the unique data, that are available from GSDB. These improvements are designed to make GSDB more accessible to users, extend the rich searching capability already present in GSDB, and to facilitate the transition to an integrated system containing many different types of biological data.

Animals↗
PubMed2005

E-MSD: an integrated data resource for bioinformatics.

The Macromolecular Structure Database (MSD) group (http://www.ebi.ac.uk/msd/) continues to enhance the quality and consistency of macromolecular structure data in the worldwide Protein Data Bank (wwPDB) and to work towards the integration of various bioinformatics data resources. One of the major obstacles to the improved integration of structural databases such as MSD and sequence databases like UniProt is the absence of up to date and well-maintained mapping between corresponding entries. We have worked closely with the UniProt group at the EBI to clean up the taxonomy and sequence cross-reference information in the MSD and UniProt databases. This information is vital for the reliable integration of the sequence family databases such as Pfam and Interpro with the structure-oriented databases of SCOP and CATH. This information has been made available to the eFamily group (http://www.efamily.org.uk/) and now forms the basis of the regular interchange of information between the member databases (MSD, UniProt, Pfam, Interpro, SCOP and CATH). This exchange of annotation information has enriched the structural information in the MSD database with annotation from wider sequence-oriented resources. This work was carried out under the 'Structure Integration with Function, Taxonomy and Sequences (SIFTS)' initiative (http://www.ebi.ac.uk/msd-srv/docs/sifts) in the MSD group.

Amino Acid Sequence↗
PubMed1994

Effects of priority assignment of attentional resources, order of testing, and response sequence on tunnel vision.

The effects of relative priority of attentional resources allocated to simultaneous peripheral and foveal tasks, response sequence to the tasks, and order to testing with two levels of foveal cognitive loading on tunnel vision were studied with 32 Chinese undergraduates. Two levels of foveal condition were used for the foveal task while the peripheral task required a single-target detection. Performance decrement value and a significant interaction of levels x eccentricities indicated that tunnel vision was most prominent when the foveal task was primary. Greater magnitude of tunnel vision was obtained when the more difficult foveal task was tested prior to the no-foveal-load condition. Responding sequence to the tasks was nonsignificant.

Adult↗
PubMed2002

PlasmoDB: the Plasmodium genome resource. An integrated database providing tools for accessing, analyzing and mapping expression and sequence data (both finished and unfinished).

PlasmoDB (http://PlasmoDB.org) is the official database of the Plasmodium falciparum genome sequencing consortium. This resource incorporates finished and draft genome sequence data and annotation emerging from Plasmodium sequencing projects. PlasmoDB currently houses information from five parasite species and provides tools for cross-species comparisons. Sequence information is also integrated with other genomic-scale data emerging from the Plasmodium research community, including gene expression analysis from EST, SAGE and microarray projects. The relational schemas used to build PlasmoDB [Genomics Unified Schema (GUS) and RNA Abundance Database (RAD)] employ a highly structured format to accommodate the diverse data types generated by sequence and expression projects. A variety of tools allow researchers to formulate complex, biologically based queries of the database. A version of the database is also available on CD-ROM (Plasmodium GenePlot), facilitating access to the data in situations where Internet access is difficult (e.g. by malaria researchers working in the field). The goal of PlasmoDB is to enhance utilization of the vast quantities of data emerging from genome-scale projects by the global malaria research community.

Animals↗
PubMed2005

Multiple sequence alignment accuracy and evolutionary distance estimation.

BACKGROUND: Sequence alignment is a common tool in bioinformatics and comparative genomics. It is generally assumed that multiple sequence alignment yields better results than pair wise sequence alignment, but this assumption has rarely been tested, and never with the control provided by simulation analysis. This study used sequence simulation to examine the gain in accuracy of adding a third sequence to a pair wise alignment, particularly concentrating on how the phylogenetic position of the additional sequence relative to the first pair changes the accuracy of the initial pair's alignment as well as their estimated evolutionary distance. RESULTS: The maximal gain in alignment accuracy was found not when the third sequence is directly intermediate between the initial two sequences, but rather when it perfectly subdivides the branch leading from the root of the tree to one of the original sequences (making it half as close to one sequence as the other). Evolutionary distance estimation in the multiple alignment framework, however, is largely unrelated to alignment accuracy and rather is dependent on the position of the third sequence; the closer the branch leading to the third sequence is to the root of the tree, the larger the estimated distance between the first two sequences. CONCLUSION: The bias in distance estimation appears to be a direct result of the standard greedy progressive algorithm used by many multiple alignment methods. These results have implications for choosing new taxa and genomes to sequence when resources are limited.

Algorithms↗
PubMedDate not supplied

Polymerase chain reaction-based detection of dermatophyte DNA with a fungus-specific primer system.

There is significant clinical interest in primers which are specific for fungi and do not hybridize to DNA of other eukaryotes or prokaryotes. Such primers would allow specific amplification of fungal DNA from human tissue samples containing fungi. Fungal identification to the species level could follow by direct sequencing or restriction analysis. Several previously described primer systems cross-react with DNA of plants and animals. We have designed a primer system that amplifies a fragment of the gene coding for the small ribosomal subunit 18S rRNA. Database searches and sequence analyses were performed using the HUSAR (Heidelberg Unix Sequence Analysis Resources) computer system at the German Cancer Research Centre, Heidelberg, Germany. Primers TR1 (5'-GTTTCTAGGACCGCCGTA) and TR2 (5'-CTCAAACTTCCATCGACTTG) bind to sequences which are homologous within the fungi, but differ from corresponding DNA fragments of plants and animals. The amplified fragment is 581 base pairs in length and contains variable, and therefore species-specific, regions. The DNA of Trichophyton rubrum, Trichophyton mentagrophytes, Trichophyton verrucosum, Trichophyton terrestre, Microsporum canis, Microsporum gypseum and Epidermophyton floccosum and of several yeast species was amplified by the primers, but not the DNA from 42 normal human skin samples. Furthermore, other DNA preparations from plants and animals, including those from radish, cabbage, wheat and mouse, did not show amplification reactions.

Arthrodermataceae↗
PubMed2004

Arabidopsis to rice. Applying knowledge from a weed to enhance our understanding of a crop species.

Although Arabidopsis is well established as the premiere model species in plant biology, rice (Oryza sativa) is moving up fast as the second-best model organism. In addition to the availability of large sets of genetic, molecular, and genomic resources, two features make rice attractive as a model species: it represents the taxonomically distinct monocots and is a crop species. Plant structural genomics was pioneered on a genome-scale in Arabidopsis and the lessons learned from these efforts were not lost on rice. Indeed, the sequence and annotation of the rice genome has been greatly accelerated by method improvements made in Arabidopsis. For example, the value of full-length cDNA clones and deep expressed sequence tag resources, obtained in Arabidopsis primarily after release of the complete genome, has been recognized by the rice genomics community. For rice >250,000 expressed sequence tags and 28,000 full-length cDNA sequences are available prior to the completion of the genome sequence. With respect to tools for Arabidopsis functional genomics, deep sequence-tagged lines, inexpensive spotted oligonucleotide arrays, and a near-complete whole genome Affymetrix array are publicly available. The development of similar functional genomics resources for rice is in progress that for the most part has been more streamlined based on lessons learned from Arabidopsis. Genomic resource development has been essential to set the stage for hypothesis-driven research, and Arabidopsis continues to provide paradigms for testing in rice to assess function across taxonomic divisions and in a crop species.

Arabidopsis↗
PubMed1995

Elemental signatures of human diets from the Georgia Bight.

Multielement analysis was performed on bone samples extracted from the femora of 39 adults from three mortuary sites (Johns Mound, Santa Catalina de Guale, and Santa Catalina de Guale de Santa Maria) and time periods (late preagricultural, early contact, and late contact) in the Georgia Bight. This study was used to investigate whether elemental analysis would support or contradict other lines of data regarding diets and dietary change previously generated for the region. The data are in agreement with an earlier interpretation, based on stable isotopes, that dietary maize increases through time but fails to support the idea that marine resources decreased in importance. Rather, it appears that the wild plant food component of the diets decreases as maize increases in importance; throughout the sequence, marine resources comprise a significant portion of the diets.

Bone and Bones↗