ABSTRACT
MOTIVATION: Gene expression array technology has become increasingly widespread among researchers who recognize its numerous promises. At the same time, bench biologists and bioinformaticians have come to appreciate increasingly the importance of establishing a collaborative dialog from the onset of a study and of collecting and exchanging detailed information on the many experimental and computational procedures using a structured mechanism. This is crucial for adequate analyses of this kind of data. RESULTS: The RNA Abundance Database (RAD; http://www.cbil.upenn.edu/RAD) provides a comprehensive MIAME-supportive infrastructure for gene expression data management and makes extensive use of ontologies. Specific details on protocols, biomaterials, study designs, etc. are collected through a user-friendly suite of web annotation forms. Software has been developed to generate MAGE-ML documents to enable easy export of studies stored in RAD to any other database accepting data in this format (e.g. ArrayExpress). RAD is part of a more general Genomics Unified Schema (http://www.gusdb.org), which includes a richly annotated gene index (http://www.allgenes.org), thus providing a platform that integrates genomic and transcriptomic data from multiple organisms. This infrastructure enables a large variety of queries that incorporate visualization and analysis tools and have been tailored to serve the specific needs of projects focusing on particular organisms or biological systems.
Subject(s)
Abstracting and Indexing/methods , Database Management Systems , Databases, Nucleic Acid , Documentation/methods , Gene Expression Profiling/methods , Information Storage and Retrieval/methods , RNA/chemistry , RNA/genetics , Internet , Oligonucleotide Array Sequence Analysis/methods , RNA/classification , RNA/metabolism , Software , User-Computer InterfaceABSTRACT
A 150-kDa cytadhesin-like protein from Mycoplasma gallisepticum has been identified. A previously described 583-bp fragment (J.E. Dohms, L.L. Hnatow, P. Whetzel, R. Morgan and C.L. Keeler, Jr., Avian Dis. 37:380-388, 1993) was used to probe a genomic library of M. gallisepticum DNA. An 8.0-kb SacI fragment was identified, cloned, and partially sequenced. Analysis of the resulting 3,750-bp sequence revealed the presence of a 3,366-nucleotide open reading frame, mgc1. The 1,122-amino-acid protein encoded by this open reading frame, MGC1, has characteristics of a class I membrane protein and has homology with the MgPa cytadhesin of Mycoplasma genitalium (26.3%) and the P1 cytadhesin of Mycoplasma pneumoniae (28.7%). A portion of MGC1 was expressed as a glutathione S-transferase fusion protein and used to produce antiserum in rabbits. The antiserum recognizes a 150-kDa protein from M. gallisepticum. The protein is sensitive to trypsin, confirming that it is surface exposed. Primer extension analysis indicates that the mgc1 RNA starts within an upstream open reading frame, suggesting complex control of its expression. This is the first description of a functional gene from M. gallisepticum showing homology to cytadhesin genes from human mycoplasmas.
Subject(s)
Adhesins, Bacterial/genetics , Genes, Bacterial , Mycoplasma/genetics , Adhesins, Bacterial/immunology , Amino Acid Sequence , Animals , Antibodies, Bacterial/biosynthesis , Base Sequence , Chromosome Mapping , Cloning, Molecular , DNA, Bacterial/genetics , Humans , Molecular Sequence Data , Mycoplasma/immunology , Mycoplasma/isolation & purification , Open Reading Frames , Rabbits , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/immunology , Sequence Homology, Amino AcidABSTRACT
Monoclonal antibodies (MAbs) were used to analyze the relatedness of neutralizing epitopes of infectious bursal disease virus (IBDV) strains. The MAb B69 neutralized the homologous D78 virus but not the MD and Del-A variant strains of IBDV. MAbs 33E8 and R63 neutralized D78 and variant strains MD and Del-A. A cDNA clone consisting of a 1000-base-pair fragment of the VP2 gene from the Del-A IBDV strain was translated using an in vitro system. Six peptides were observed following translation, which represented a full-length product (35.5 kilodaltons) and five truncated products. The translated peptides were radioimmunoprecipitated using MAbs B69, 33E8, and R63. Only MAb R63 immunoprecipitated the in vitro translation products from Del-A. MAbs B69 and 33E8 did not immunoprecipitate the in vitro-translated VP2 peptides. The D78 and Del-A viruses were radiolabeled in vivo using 35S-methionine. Proteins from these viruses were examined by radioimmuno-precipitation with MAbs B69, 33E8, and R63. Although the background made interpretation of the results difficult for MAb B69, this MAb clearly immunoprecipitated VP2 of D78. MAb 33E8 immunoprecipitated the D78 VP3 protein, and R63 immunoprecipitated the VP2 protein. MAb R63 also immunoprecipitated the 35S-methionine-labeled VP2 protein from Del-A. It was concluded that the neutralizing epitope represented by 33E8 was located on VP3 and that the epitope represented by R63 is located on both classic and variant viruses in the region of VP2 that is generally thought to contain sequence variability among IBDV strains.
