The viroid and viroid-like RNA database.

This is an online database to facilitate research on viroid, viroid-like RNAs and human hepatitis delta virus (vHDV) by presenting a large number of sequences and related data in a comprehensive and user-friendly format (e.g. position of their self-catalytic domains, open reading frame of the vHDV, prediction of the most stable secondary structures, etc.). Most of these RNA species share a common proposed replication pattern known as a DNA-independent rolling circle mechanism. Together, these species form the 'brotherhood' of the smallest known auto-replicable RNAs. This online database is available on the World Wide Web at http://www.callisto.si.usherb.ca/jpperra     

SubViral RNA: a database of the smallest known auto-replicable RNA species

We describe here the establishment of an online database containing a large number of sequences and related data on viroids, viroid-like RNAs and human hepatitis delta virus (vHDV) in a customizable and user-friendly format. This database is available on the World Wide Web at http://penelope.med.usherb.ca/subviral.     

Compilation and analysis of viroid and viroid-like RNA sequences.

We have created a catalogue comprising all viroid and viroid-like RNA sequences which to our knowledge have been either published or were available from on-line sequence libraries as of October 1, 1995. In the development of this catalogue nomenclature ambiguities were removed, the likely ancestral sequence of most species was determined and the most stable secondary structures of these sequences were predicted using the MulFold package. Only viroids of PSTVd-type possessed a rod-like secondary structure, while most other viroids adopted branched secondary structures. Several viroids have predicted secondary structures that include either a Y or cruciform structure reminiscent of the tRNA-like end of virus genomes at an extremity. However, it remains unknown whether or not these predicted structures are adopted in solution, and if they serve a particular function in vivo. Additional information such as the position of the self-catalytic domains are included in the catalogue. An analysis of the data compilated in the catalogue is included. The catalogue will be available on the world wide web (http://www.callistro.si.usherb.ca/jpperra), on computer disk and in printed form. It should provide an excellent reference point for further studies.     

Update of MmtDB: a Metazoa mitochondrial DNA variants database.

The present paper describes the improvements in MmtDB, a specialised database designed to collect Metazoa mitochondrial DNA variants. Priority in the data collection has been given to Metazoa for which a large amount of variants is available, e.g., for humans. Starting from the sequences available in the Nucleotide Sequence Databases, the redundant sequences have been removed and new sequences from other sources have been added. Value-added information is associated to each variant sequence, e.g., analysed region, experimental method, tissue and cell lines, population data, sex, age, family code and information about the variation events (nucleotide position, involved gene, restriction site gain or loss). Cross-references are introduced to the EMBL Data Library, as well as an internal cross-referencing among MmtDB entries according to tissual, heteroplasmic, familiar and aplotypical correlation. Furthermore MmtDB has a new section, AMmtDB: Aligned Metazoan mitochondrial biosequences. MmtDB can be accessed through the World Wide Web at URL http://WWW.ba.cnr.it/[symbol: see text]areamt08/MmtDBWWW.htm     

A phylogenetic delimitation of the "Sphagnum subsecundum complex" (Sphagnaceae, Bryophyta)

A seemingly obvious but sometimes overlooked premise of any evolutionary analysis is delineating the group of taxa under study. This is especially problematic in some bryophyte groups because of morphological simplicity and convergence. This research applies information from nucleotide sequences for eight plastid and nuclear loci to delineate a group of northern hemisphere peat moss species, the so-called Sphagnum subsecundum complex, which includes species known to be gametophytically haploid or diploid (i.e., sporophytically diploid-tetraploid). Despite the fact that S. subsecundum and several species in the complex have been attributed disjunct ranges that include all major continents, phylogenetic analyses suggest that the group is actually restricted to Europe and eastern North America. Plants from western North America, from California to Alaska, which are morphologically similar to species of the S. subsecundum complex in eastern N. America and Europe, actually belong to a different deep clade within Sphagnum section Subsecunda. One species often considered part of the S. subsecundum complex, S. contortum, likely has a reticulate history involving species in the two deepest clades within section Subsecunda. Nucleotide sequences have a strong geographic structure across the section Subsecunda, but shallow tip clades suggest repeated long-distance dispersal in the section as well.     

广东南岭国家级自然保护区大东山昆虫名录(Ⅱ)

报道广东南岭国家级自然保护区大东山管理站所辖林区同翅目和半翅目等二目昆虫名录,计有41科179属247种,其中半翅目的叉头薄蝽Brachymna bificeps Chen为本研究发现的新种.     

Description of a new species of bat-associated argasid tick (Acari: Argasidae) from Brazil

A new species of argasid tick (Acari: Argasidae) is described from immature and adult specimens collected from several localities in Brazil. A complete morphological account is provided for all postembryonic life stages, i.e., larva, nymph, female, and male. Ornithodoros cavernicolous n. sp. is the 113(th) in the genus. Morphologically, the new species shares common features, e.g., presence of well-developed cheeks and legs with micromammillate cuticle, with other bat-associated argasid ticks included in the subgenus Alectorobius. In particular, the new species is morphologically related to Ornithodoros azteci Matheson, with which it forms a species group. Phylogenetic analysis based on the 16S rRNA gene sequences supports the placement of the new species within a large clade that includes other New World bat-associated argasids. However, the new species seems to represent an independent lineage within the genus Ornithodoros.     

VIDA: a virus database system for the organization of animal virus genome open reading frames

VIDA is a new virus database that organizes open reading frames (ORFs) from partial and complete genomic sequences from animal viruses. Currently VIDA includes all sequences from GenBank for Herpesviridae, Coronaviridae and Arteriviridae. The ORFs are organized into homologous protein families, which are identified on the basis of sequence similarity relationships. Conserved sequence regions of potential functional importance are identified and can be retrieved as sequence alignments. We use a controlled taxonomical and functional classification for all the proteins and protein families in the database. When available, protein structures that are related to the families have also been included. The database is available for online search and sequence information retrieval at http://www.biochem.ucl.ac.uk/bsm/virus_database/ VIDA.html.     

PANTHER: a browsable database of gene products organized by biological function,using curated protein family and subfamily classification

The PANTHER database was designed for high-throughput analysis of protein sequences. One of the key features is a simplified ontology of protein function, which allows browsing of the database by biological functions. Biologist curators have associated the ontology terms with groups of protein sequences rather than individual sequences. Statistical models (Hidden Markov Models, or HMMs) are built from each of these groups. The advantage of this approach is that new sequences can be automatically classified as they become available. To ensure accurate functional classification, HMMs are constructed not only for families, but also for functionally distinct subfamilies. Multiple sequence alignments and phylogenetic trees, including curator-assigned information, are available for each family. The current version of the PANTHER database includes training sequences from all organisms in the GenBank non-redundant protein database, and the HMMs have been used to classify gene products across the entire genomes of human, and Drosophila melanogaster. The ontology terms and protein families and subfamilies, as well as Drosophila gene c;assifications, can be browsed and searched for free. Due to outstanding contractual obligations, access to human gene classifications and to protein family trees and multiple sequence alignments will temporarily require a nominal registration fee. PANTHER is publicly available on the web at http://panther.celera.com.     

Catoptinae subfam. n., a new subfamily of carpenter-moths (Lepidoptera,Cossidae)

The new subfamily of Cossidae; Catoptinae Yakovlev, subfam. n., well distinguished from other representatives of the family, is described. The new subfamily includes two genera: Catopta Staudinger, 1899 (type genus) and Chiangmaiana Kemal et Koçak, 2006. A catalogue of the subfamily is presented. One new synonym Catopta hyrcanus (Christoph, 1888) = Catopta brandti Bryk, 1947, syn. n., is established. The new subfamily has the following distinguishing features: short valvae; reduced processes of transtilla; vesica with numerous cornuti; pearshaped bursa copulatrix; and very short ductus bursae.     

N-terminal amino acid sequences of acid proteases: acid proteases from Penicillium roqueforti and Rhizopus chinensis and alignment with penicillopepsin and mammalian proteases.

The amino-terminal sequence (33 residues) of the acid protease from Penicillium roqueforti has been determined with an automated sequencer. The amino-terminal sequence of Rhizopus pepsin (published by Sepulveda, P., Jackson, K. W. & Tang, J. (1975) Biochem. Biophys. Res. Commun. 63, 1106-1112) has been extended from 27 residues to 39 residues. Also, it was found that two forms of Rhizopus pepsin differ in position 15, where Rhizopus pepsin I has an isoleucine and Rhizopus pepsin II a valine residue. The new sequences have been aligned with the amino-terminal sequences of penicillopepsin (EC 3.4.23.7), pig pepsin (EC 3.4.23.1), calf chymosin (EC 3.4.23.4), human pepsin (EC 3.4.23.2), human gastricsin (EC 3.4.23.3), and cow pepsin (EC 3.4.23.1). Residues 31-35 (numbering based on pig pepsin, Tang, J., Sepulveda, P., Marciniszyn, Jr., J., Chen, K.S.C., Huang, W.-Y. , Tao, N., Liu, D. & Lanier, P. (1973) Proc. Natl. Acad. Sci. U.S.A. 70, 3437-3739) are identical in all enzymes. This section contains one of the two aspartic acids (Asp-32) implicated in the active site. The similarity of the sequences provides strong evidence for the homology of these acid proteases.     

Active Sequences Collection (ASC) database: a new tool to assign functions to protein sequences

Active Sequences Collection (ASC) is a collection of amino acid sequences, with an unique feature: only short sequences are collected, with a demonstrated biological activity. The current version of ASC consists of three sections: DORRS, a collection of active RGD-containing peptides; TRANSIT, a collection of protein regions active as substrates of transglutaminase enzyme (TGase), and BAC, a collection of short peptides with demonstrated biological activity. Literature references for each entry are reported, as well as cross references to other databases, when available. The current version of ASC includes more than 800 different entries. The main scope of this collection is to offer a new tool to investigate the structural features of protein active sites, additionally to similarity searches against large protein databases or searching for known functional patterns. ASC database is available at the web address http://crisceb.unina2.it/ASC/ which also offers a dedicated query interface to compare user-defined protein sequences with the database, as well as an updating interface to allow contribution of new referenced active sequences.     

MIPS bacterial genomes functional annotation benchmark dataset

MOTIVATION: Any development of new methods for automatic functional annotation of proteins according to their sequences requires high-quality data (as benchmark) as well as tedious preparatory work to generate sequence parameters required as input data for the machine learning methods. Different program settings and incompatible protocols make a comparison of the analyzed methods difficult. RESULTS: The MIPS Bacterial Functional Annotation Benchmark dataset (MIPS-BFAB) is a new, high-quality resource comprising four bacterial genomes manually annotated according to the MIPS functional catalogue (FunCat). These resources include precalculated sequence parameters, such as sequence similarity scores, InterPro domain composition and other parameters that could be used to develop and benchmark methods for functional annotation of bacterial protein sequences. These data are provided in XML format and can be used by scientists who are not necessarily experts in genome annotation. AVAILABILITY: BFAB is available at http://mips.gsf.de/proj/bfab     

The annotation of both human and mouse kinomes in UniProtKB/Swiss-Prot: one small step in manual annotation, one giant leap for full comprehension of genomes

Biomolecule phosphorylation by protein kinases is a fundamental cell signaling process in all living cells. Following the comprehensive cataloguing of the protein kinase complement of the human genome (Manning, G., Whyte, D. B., Martinez, R., Hunter, T., and Sudarsanam, S. (2002) The protein kinase complement of the human genome. Science 298, 1912-1934), this review will detail the state-of-the-art human and mouse kinase proteomes as provided in the UniProtKB/Swiss-Prot protein knowledgebase. The sequences of the 480 classical and up to 24 atypical protein kinases now believed to exist in the human genome and 484 classical and up to 24 atypical kinases within the mouse genome have been reviewed and, where necessary, revised. Extensive annotation has been added to each entry. In an era when a wealth of new databases is emerging on the Internet, UniProtKB/Swiss-Prot makes available to the scientific community the most up-to-date and in-depth annotation of these proteins with access to additional external resources linked from within each entry. Incorrect sequence annotations resulting from errors and artifacts have been eliminated. Each entry will be constantly reviewed and updated as new information becomes available with the orthologous enzymes in related species being annotated in a parallel effort and complete kinomes being completed as sequences become available. This ensures that the mammalian kinomes available from UniProtKB/Swiss-Prot are of a consistently high standard with each separate entry acting both as a valuable information resource and a central portal to a wealth of further detail via extensive cross-referencing.     

Balbiani ring DNA: Sequence comparisons and evolutionary history of a family of hierarchically repetitive protein-coding genes

Summary All known types of Balbiani ring (BR) gene consist of multiple, tandemly arranged, ca. 180 to 300-bp repeat units that can be divided into a constant region and a subrepeat region. The latter region includes short tandem subrepeats (SRs). Comparison of all available BR sequences using computer methods has enabled us (a) to define more precisely the constant and subrepeat regions, (b) to infer the evolutionary relationships among the various types of BR repeats, (c) to derive a consensus approximation of an ancestral sequence from a small segment of which the highly diverse present-day SRs may have originated, and (d) to detect an underlying substructure in the constant region, evident in the consensus but not in the present-day sequences and possibly corresponding to an original 39-bp DNA segment from which the extant, giant BR sequences may have evolved. We discuss the processes of reduplication, diversification, and homogenization within the hierarchically repetitive BR sequences as examples of how a simple DNA element may evolve into a diverse family of large, protein-coding genes.     

Higher plant origins and the phylogeny of green algae

Summary 5S rRNA sequences from six additional green algae lend strong molecular support for the major outlines of higher plant and green algae phylogeny that have been proposed under varying naming conventions by several authors. In particular, the molecular evidence now available unequivocally supports the existence of at least two well-separated divisions of the Chlorobionta: the Chlorophyta and the Streptophyta (i.e., charophytes) (according to the nomenclature of Bremer). The chlamydomonad 5S rRNAs are, however, sufficiently distinct from both clusters that it may ultimately prove preferable to establish a third taxon for them. In support of these conclusions 5S rRNA sequence data now exist for members of four diverse classes of chlorophytes. These sequences all exhibit considerably more phylogenetic affinity to one another than any of them show toward members of the other cluster, the Streptophyta, or the twoChlamydomonas strains. Among the Charophyceae, new 5S rRNA sequences are provided herein for three genera,Spirogyra, Klebsormidium, andColeochate. All of these sequences and the previously publishedNitella sequence show greater resemblance among themselves and to the higher plants than they do to any of the other green algae examined to date. These results demonstrate that an appropriately named taxon that includes these green algae and the higher plants is strongly justified. The 5S rRNA data lack the resolution needed, however, to unequivocally determine which of several subdivisions of the charophytes is the sister group of the land plants. The evolutionary diversity ofChlamydomonas relative to the other green algae was recognized in earlier 5S rRNA studies but was unanticipated by ultrastructural work. These new data provide further evidence for the relative uniqueness of the chlamydomonads and are discussed further.     

A global molecular phylogeny of 147 periwinkle species (Gastropoda,Littorininae)

Reid, D. G., Dyal, P. & Williams, S.T. (2012) A global molecular phylogeny of 147 periwinkle species (Gastropoda, Littorininae). —Zoologica Scripta, 41, 125–136. Complete species‐level molecular phylogenies have been published for several genera of Littorinidae (e.g. Echinolittorina, Littoraria). Here we add new sequence data from three genes (28S rRNA, 12S rRNA, cytochrome oxidase c subunit I) for single specimens of an additional 24 species, to make a data set of 147 (97%) of the 152 recognized species of the subfamily Littorininae. This three‐gene data set is analysed to produce a phylogenetic hypothesis for the subfamily, which includes the first complete species‐level phylogeny of the genus Peasiella and the first three‐gene phylogeny of all Littorina species. The non‐planktotrophic species of Littorina have previously been classified together (as subgenus Neritrema), implying a single origin of this developmental mode. Tests of this hypothesis with the new data are inconclusive, and resolution is not improved in a tree constructed from five genes (adding previously published sequences of 16S rRNA and cytochrome b). Using available fossils for calibration we generate a BEAST chronogram, which emphasizes that the radiation of Littorina is more recent than that of other littorinine genera. A database is provided, listing all known species of Littorininae, with their distributions, development, ecology and gene sequences, as a tool for future evolutionary studies of this model group.     

Comparison of fungal mitochondrial introns reveals extensive homologies in RNA secondary structure

The complete sequences of nine Saccharomyces cerevisiae mitochondrial introns, six of which carry long open reading frames, have already been published. We have recently determined the sequence of an intron in the large ribosomal mitochondrial RNA of Kluyveromyces thermotolerans (Jacquier et al., in preparation), which we found to be closely related to its S. cerevisiae counterpart. This latter result prompted us to undertake a systematic search for possible homologous elements in the other, available sequences with the help of an original computer program. A previously unsuspected wealth of evolutionarily conserved sequences and secondary structures was thus uncovered. Seven at least of the available sequences may be folded up into elaborate secondary structure models, the cores of which are nearly identical. These models result in bringing together the exon-intron junctions into relatively close spatial proximity and looping out either all or most of the sequences in open reading frame, when present. These results and their possible implications with respect to the mechanism of splicing are discussed in the light of available genetic and biochemical data.     

Phylogeny of Trypanosomatidae and Bodonidae (Kinetoplastida) based on 18S rRNA: evidence for paraphyly of Trypanosoma and six other genera

Phylogenetic analysis of 18S rRNA sequences from the families Trypanosomatidae and Bodonidae (Eugelenozoa: Kinetoplastida) was conducted using a variety of methods. Unlike previous analyses using unrooted trees and/or smaller numbers of sequences, the analysis did not support monophyly of the genus Trypanosoma, which includes the major human parasites T. cruzi (cause of Chagas' disease) and T. brucei (cause of African sleeping sickness). The section Salivaria of the genus Trypanosoma fell outside a cluster that includes the section Stercoraria of the genus Trypanosoma, along with members of the genera Leishmania, Endotrypanum, Leptomonas, Herpetomonas, Phytomonas, Crithidia, and Blastocrithidia. The phylogenetic analysis also indicated that the genera Bodo, Cryptobia, Leptomonas, Herpetomonas, Crithidia, and Blastocrithidia are polyphyletic. The results suggested that parasitism of vertebrates has probably arisen independently a number of times within the Trypanosomatidae.