The tmRNA database (tmRDB).

This first release of the tmRNA database (tmRDB) contains 19 tmRNA sequences, a tmRNA sequence alignment with emphasis of base pairs that are supported by comparative sequence analysis, and a tabulation of tmRNA-encoded tag peptides. The tmRNADB also offers an RNA secondary structure diagram of the Escherichia coli tmRNA, as well as PDB-formatted coordinates for three-dimensional modeling. The data are available on the World Wide Web at http://www.uthct. edu/tmRDB/tmRDB.html     

The tmRNA database (tmRDB).

As of September, 1998, a total of 43 sequences are contained within the tmRNA database (tmRDB). The tmRNA sequences are arranged alphabetically and ordered phylogenetically. The alignment of the tmRNAs emphasizes the basepairs that are supported by comparative sequence analysis and establishes minimal secondary structures for the known tmRNAs. A corresponding alignment of the predicted tmRNA-encoded tag peptides is presented. The tmRDB also offers a small number of RNA secondary structure diagrams and PDB-formatted three-dimensional models generated with the program ERNA-3D. The data are available freely at the URL http://psyche.uthct.edu/dbs/tmRDB/tmRDB.++ +html     

The guide RNA database (3.0).

The RNA editing process within the mitochondria of kinetoplastid organisms is controlled by small, trans -acting RNA molecules referred to as guide RNAs. The guide RNA database is a compilation of published guide RNA sequences, currently containing 254 entries from 11 different organisms. Additional information includes RNA secondary and tertiary structure models, information on the gene localisation, literature citations and other relevant facts. The database can be accessed through the World Wide Web (WWW) at http://www.biochem.mpg.de/ goeringe/     

The signal recognition particle database (SRPDB).

The SRPDB (signal recognition particle database) provides aligned SRP RNA and protein sequences, annotated and phylogenetically ordered. This release includes 82 SRP RNAs (including 22 bacterial and 9 archaeal homologs) and a total of 20 protein sequences representing SRP9, SRP14, SRP19, SRP54, SRP68, and SRP72. The offerings also include representative RNA secondary structure diagrams.     

The signal recognition particle database (SRPDB).

The SRPDB (signal recognition particle database) provides annotated SRP RNA sequences from Eucaryotes and Archaea, phylogenetically ordered and aligned with their bacterial equivalents. We also make available representative RNA secondary structure diagrams, where each base pair is proven by comparative sequence analysis. New to this release are 17 SRP RNA sequences (a total of 64 sequences) and alignments of proteins SRP19 and SRP54 with their RNA binding sites.     

宁夏水稻品种微卫星标记数据库的建立

本研究以47份经甄别鉴定的宁夏水稻品种(系)为试验材料,筛选出28对较均匀分布于12条染色体、条带清晰稳定、多态性丰富的SSR标记构建了宁夏水稻微卫星标记数据库。共检测到144个等位基因,标记间差异性位点数3~10个,平均5.14个;平均Nei's遗传多样性指数为0.6187。28个位点上参试材料间均有差异。只在1个位点上存在差异的是宁粳28号和宁粳23号,宁粳23和宁粳35号;其余品种差异性位点均在2个或2个以上,占参试材料的93.6%。28对引物中筛选出10对核心引物,各材料间至少有1对引物存在差异,能够把参试品种(系)一一区分开来。利用这10对引物,在相同的迁移位置上以1、0标记扩增片段的有无,构建了宁夏水稻DNA指纹图谱。     

Update of the Human MitBASE database.

Human MitBASE is a database collecting human mtDNA variants. This database is part of a greater mitochondrial genome database (MitBASE) funded within the EU Biotech Program. The present paper reports the recent improvements in data structure, data quality and data quantity. As far as the database structure is concerned it is now fully designed and implemented. Based on the previously described structure some changes have been made to optimise both data input and data quality. Cross-references with other bio-databases (EMBL, OMIM, MEDLINE) have been implemented. Human MitBASE data can be queried with the MitBASE Simple Query System (http://www.ebi.ac.uk/htbin/Mitbase/mit base.pl) and with SRS at the EBI under the 'Mutation' section (http://srs.ebi.ac.uk/srs5/). At present the HumanMitBASE node contains approximately 5000 variants related to studies investigating population polymorphisms and pathologies.     

Thermodynamic database for protein-nucleic acid interactions (ProNIT).

MOTIVATION: Protein-nucleic acid interactions are fundamental to the regulation of gene expression. In order to elucidate the molecular mechanism of protein-nucleic acid recognition and analyze the gene regulation network, not only structural data but also quantitative binding data are necessary. Although there are structural databases for proteins and nucleic acids, there exists no database for their experimental binding data. Thus, we have developed a Thermodynamic Database for Protein-Nucleic Acid Interactions (ProNIT). RESULTS: We have collected experimentally observed binding data from the literature. ProNIT contains several important thermodynamic data for protein-nucleic acid binding, such as dissociation constant (K(d)), association constant (K(a)), Gibbs free energy change (DeltaG), enthalpy change (DeltaH), heat capacity change (DeltaC(p)), experimental conditions, structural information of proteins, nucleic acids and the complex, and literature information. These data are integrated into a relational database system together with structural and functional information to provide flexible searching facilities by using combinations of various terms and parameters. A www interface allows users to search for data based on various conditions, with different display and sorting options, and to visualize molecular structures and their interactions. AVAILABILITY: ProNIT is freely accessible at the URL http://www.rtc.riken.go.jp/jouhou/pronit/pronit.html.     

Virgil database for rich links (1999 update).

With so many databases available for research in the Human Genome Project, it is crucial to efficiently relate information from different resources. For that purpose, we maintain Virgil, a database of rich links for data browsing, data analysis and database interconnection. Virgil current version contains more than 40 000 rich links from five major databases: SWISS-PROT, GenBank, PDB, GDB and OMIM. Materials described in this paper are available from http://www.infobiogen.fr/services/virgil/     

BTKbase, mutation database for X-linked agammaglobulinemia (XLA).

X-linked agammaglobulinemia (XLA) is an immunodeficiency caused by mutations in the gene coding for Bruton's agammaglobulinemia tyrosine kinase (BTK). A database (BTKbase) of BTK mutations has been compiled and the recent update lists 225 entries from 189 unrelated families showing 148 unique molecular events. Each patient is given a unique patient identity number (PIN). Information is included regarding the phenotype including symptoms. Mutations in all the five domains of BTK have been noticed to cause the disease, the most common event being missense mutations. The mutations appear almost uniformly throughout the molecule and frequently affect CpG sites forming arginine residues. A decreased frequency of missense mutations was found in the TH, SH3 and upper lobe of the kinase domain. The putative structural implications of all the missense mutations are given in the database.     

BTKbase, mutation database for X-linked agammaglobulinemia (XLA).

X-linked agammaglobulinemia (XLA) is an immunodeficiency caused by mutations in the gene coding for Bruton's agammaglobulinemia tyrosine kinase (BTK). A database (BTKbase) of BTK mutations has been compiled and the recent update lists 463 mutation entries from 406 unrelated families showing 303 unique molecular events. In addition to mutations, the database also lists variants or polymorphisms. Each patient is given a unique patient identity number (PIN). Information is included regarding the phenotype including symptoms. Mutations in all the five domains of BTK have been noticed to cause the disease, the most common event being missense mutations. The mutations appear almost uniformly throughout the molecule and frequently affect CpG sites that code for arginine residues. The putative structural implications of all the missense mutations are given in the database. The improved version of the registry having a number of new features is available at http://www. helsinki.fi/science/signal/btkbase.html     

Development and characterization of chloroplast microsatellite markers in Macaranga (Euphorbiaceae).

As part of our study on the phylogeography of the ant-plant genus Macaranga, we have screened for polymorphic regions in the chloroplast genome. Initially, ten universal PCR primer pairs targeted at chloroplast microsatellite loci were applied to a small set of specimens, covering various taxonomic levels from intrafamilial to intraspecific. Eight primer pairs produced PCR fragments that behaved as single and discrete bands on agarose gels. The five most promising candidate pairs were further analysed with an extended set of DNA templates, and PCR products were separated on sequencing gels. The number of size variants per locus varied from two to eight, combining into 17 haplotypes among 29 Macaranga accessions from 10 species. Comparative sequencing demonstrated that microsatellites were responsible for the observed size variation at three of five loci, whereas variation at the other loci was caused by larger insertions and (or) deletions (indels). In addition to poly(A) and poly(T) repeats, which are typically found in chloroplast DNA, we also identified a variable (CT)n repeat, with n = 4 to n = 8. Sequencing revealed three examples of size homoplasy, one of which was caused by a single base substitution that raised the actual number of haplotypes to 18. Relationships between haplotypes were assessed by phenetic analyses of size variants and by constructing a parsimony network based on sequence variation. For both types of analysis, the distribution of haplotypes correlated with geographically circumscribed regions rather than with taxonomic boundaries.     

Inheritance of microsatellite loci in the white sturgeon (Acipenser transmontanus).

Nine tetramer motif (GATA)n microsatellite systems were developed for use in the white sturgeon, Acipenser transmontanus. We report inheritance patterns for these nine systems, which range from one possible disomic system to tetrasomy and octosomy, with some systems containing null alleles. Because of the complex modes of inheritance underlying these systems and the highly duplicated nature of the genome, we propose each allele be scored as its own dominant marker, similar to AFLPs or RAPDs. The utility of this method is validated by the observation that individual alleles within a microsatellite system generally fit the expectation for independent transmission and fit the expected transmission frequency for single copy nuclear markers.     

varver: a database of microsatellite variation in vertebrates

Understanding how genetic variation is maintained within a species is important in ecology, evolution, conservation and population genetics. Tremendous efforts have been made to evaluate the patterns of genetic variation in natural populations of various species. For this purpose, microsatellites have played a major role since the 1990s. Here we describe a comprehensive database, varver (Variation in Vertebrates) that provides complete information regarding microsatellite variation in natural populations of vertebrates. For each species, varver includes basic information of the species, a list of publications reporting the microsatellite variation, and tables of genetic variation within and between populations (heterozygosity and F_ST). The geographic location and rough sampling range are also shown for each sampled population. The database should be useful for researchers interested in not only specific species but also comparing multiple species. We discuss the utility of microsatellite data, particularly for meta‐analyses that involve multiple microsatellite loci from various species. We show that in such analyses, it is extremely important to correct for biases caused by differences in mutation rate, mainly due to repeat unit and number.     

Canine X-linked muscular dystrophy in Japan (CXMDJ).

The purpose of this study was to develop a strain of canine X-linked muscular dystrophy (CXMD), a model of Duchenne muscular dystrophy, in Japan. A female beagle was artificially inseminated with frozen-thawed spermatozoa derived from an affected golden retriever. Subsequently, two carrier female dogs (G1 carriers) and four normal male littermates were produced. Thereafter, the two G1 carriers were mated with beagle sires. As a result, each bitch whelped three times, and out of 54 pups, 17 affected male descendants, and 11 carrier female descendants (G2 carriers) were detected. One G2 carrier was then mated with a beagle sire and 15 pups in two whelpings were produced, including five affected males and four carrier females (G3 carriers). A total of 10 female beagles were artificially inseminated to evaluate the fertility of the frozen-thawed spermatozoa from the two affected dogs. The whelping rates of the two affected dogs were 4/5 and the litter sizes were 5.0 +/- 1.41 and 6.0 +/- 0.82, respectively. These results indicate that a canine X-linked muscular dystrophy colony has been established in Japan. We called them CXMDJ.     

Pleosporales in Japan (3). The genus Massarina

 Twelve species of the genus Massarina collected from Japan are reported in this article. Among them, 4 new species, M. constricta, M. japonica, M. submediana, and M. uniserialis, are described, illustrated, and compared to similar species. Two species, M. scirpina and M. ryukyuensis, are described as new combination, and 4 species, M. arundinariae, M. fluviatilis, M. peerallyi, and M. rubi, are reported from Japan for the first time. One bambusicolous species, Metasphaeria tuberculosa, is considered to be a synonym of Massarina bambusina. Received: December 13, 2002 / Accepted: February 6, 2003 Acknowledgments We are grateful to Dr. Shuhei Tanaka, curator of YAM (Yamaguchi University), for the loan of specimens for this study.     

Inheritance of microsatellite loci in the polyploid lake sturgeon (Acipenser fulvescens).

Inheritance in the expression of amplicons for four microsatellite primer pairs was determined using 10 families created from gametes of wild lake sturgeon (Acipenser fulvescens). Loci Afu34 and Afu68 expressed a maximum of two even-intensity bands per individual and had progeny genotype ratios that fit disomic inheritance (P > 0.05). Some variation exhibited at Afu34 and Afu68 was attributable to a null allele. Genotype expression at both loci also indicated that one female parent had transmitted unreduced gametes. Primer Afu39 amplified products that exhibited four gene doses, where genotype counts fit expected ratios for disomic inheritance (P > 0.05) indicating amplification of products from two disomic loci that share alleles. Meiotic drive was evident at the Afu39 loci based on a test for random segregation (P < 0.05). Only the expression of Afu19 gave evidence of tetrasomic inheritance based on a single progeny potentially produced by a double reduction gamete. No evidence for proposed octoploid inheritance was observed.