Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees

Orthologs are genes in different species that evolved from a common ancestral gene by speciation. Currently, with the rapid growth of transcriptome data of various species, more reliable orthology information is prerequisite for further studies. However, detection of orthologs could be erroneous if pairwise distance-based methods, such as reciprocal BLAST searches, are utilized. Thus, as a sub-database of H-InvDB, an integrated database of annotated human genes (http://h-invitational.jp/), we constructed a fully curated database of evolutionary features of human genes, called ‘Evola’. In the process of the ortholog detection, computational analysis based on conserved genome synteny and transcript sequence similarity was followed by manual curation by researchers examining phylogenetic trees. In total, 18 968 human genes have orthologs among 11 vertebrates (chimpanzee, mouse, cow, chicken, zebrafish, etc.), either computationally detected or manually curated orthologs. Evola provides amino acid sequence alignments and phylogenetic trees of orthologs and homologs. In ‘dN/dS view’, natural selection on genes can be analyzed between human and other species. In ‘Locus maps’, all transcript variants and their exon/intron structures can be compared among orthologous gene loci. We expect the Evola to serve as a comprehensive and reliable database to be utilized in comparative analyses for obtaining new knowledge about human genes. Evola is available at http://www.h-invitational.jp/evola/

Regioselective one-pot synthesis of 3,5-diarylpyrazoles

2338-2342The 3,5-diarylpyrazolines and pyrazoles have been easily synthesized in excellent yields by the reaction of 2'-hydroxy­chalcones with hydrazine hydrate. The 2'-hydroxychalcones are converted into flavanones and flavones by simple cyclisation methods and then into pyrazolines and pyrazoles, respectively. Alternatively, one-pot synthesis of pyrazoles has also been achieved by converting 2'-hydroxychalcones into pyrazolines and thereafter their dehydrogenation using I2-DMSO reagent. The regiochemistry of pyrazoles obtained via pyrazolines and from flavones has been compared

Ocorrência generalizada do Lettuce mottle virus em três regiões produtoras de alface comercial do Estado de São Paulo Occurrence of Lettuce mottle virus on three lettuce producing areas from São Paulo State

Os sequivírus são vírus isométricos transmitidos por afídeos. Lettuce mottle virus (LeMoV), um provável sequivirus foi descrito no Brasil em 1982 e causa sintomas de mosaico semelhantes aos observados pelo Lettuce mosaic virus (LMV). Um levantamento para ocorrência do LeMoV nos campos de produção de alface de três diferentes regiões do Estado de São Paulo (Mogi das Cruzes, Campinas e Bauru) foi realizado durante 2002 a 2005. RNA total foi extraído e utilizado na detecção, em RT-PCR, com oligonucleotídeos específicos para o LeMoV. Do total de 1362 amostras, 137 (10,05%) foram positivas para o LeMoV. Infecção mista com o LMV foi verificada em 43 amostras (31,4%). Foi verificada a ocorrência do LeMoV nas três diferentes regiões analisadas, porém sua ocorrência foi baixa nas diferentes épocas do ano.<br>Sequiviruses are isometric aphid-borne plant viruses. Lettuce mottle virus (LeMoV), a putative sequivirus was first described in Brazil on 1982 causing similar mosaic symptoms as Lettuce mosaic virus (LMV). A survey for the occurrence of LeMoV on open field conditions was carried out during 2002 to 2005 on Mogi das Cruzes, Campinas and Bauru in São Paulo state. Total RNA was extracted and used on RT-PCR with specific LeMoV primers. On 1362 samples tested, 137 (10,05%) were positive for LeMoV. Mixed infections with LMV was observed on 43 samples (31,4%). The presence of LeMoV was observed in the three different regions, but with low incidence during the year

The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts

Here we report the new features and improvements in our latest release of the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/), a comprehensive annotation resource for human genes and transcripts. H-InvDB, originally developed as an integrated database of the human transcriptome based on extensive annotation of large sets of full-length cDNA (FLcDNA) clones, now provides annotation for 120 558 human mRNAs extracted from the International Nucleotide Sequence Databases (INSD), in addition to 54 978 human FLcDNAs, in the latest release H-InvDB_4.6. We mapped those human transcripts onto the human genome sequences (NCBI build 36.1) and determined 34 699 human gene clusters, which could define 34 057 (98.1%) protein-coding and 642 (1.9%) non-protein-coding loci; 858 (2.5%) transcribed loci overlapped with predicted pseudogenes. For all these transcripts and genes, we provide comprehensive annotation including gene structures, gene functions, alternative splicing variants, functional non-protein-coding RNAs, functional domains, predicted sub cellular localizations, metabolic pathways, predictions of protein 3D structure, mapping of SNPs and microsatellite repeat motifs, co-localization with orphan diseases, gene expression profiles, orthologous genes, protein–protein interactions (PPI) and annotation for gene families. The current H-InvDB annotation resources consist of two main views: Transcript view and Locus view and eight sub-databases: the DiseaseInfo Viewer, H-ANGEL, the Clustering Viewer, G-integra, the TOPO Viewer, Evola, the PPI view and the Gene family/group