Vector NTI

Abstract: The GenBank sequences of UBGAT (UDP-glucose:flavonoid 7-O-glucosyltransferase) genes and their encoding proteins from Scutellaria baicalensisand Scutellaria laeteviolacea, were predicted and analyzed by some bioinformatics methods and tools such as expasy, vector NTI, National Center for Biotechnology Information (NCBI) etc. The results obtained are as follows: both Sbubgat andSlubgat genes contained complete open reading frame (ORF); the formula of SbUBGAT and SbUBGAT were C2193H3462N590O638S11 and C2263H3562N596O664S13, respectively and both proteins were found in the cytoplasm, without transmembrane topological structure, and were hydrophic proteins related to intermediary metabolism and amino acid synthesis; the secondary structure of UBGATs constitute mainly α-helix and random coil and the tertiary structure were modeling. In brief, this study lay theoretical foundation for metabolic mechanism and genetic regulation researches of flavonoids biosynthesis. Key words: Scutellaria baicalensis, Scutellaria laeteviolacea, flavonoids, bioinformatics, UDP-glucose:flavonoid 7-O-glucosyltransferase.

Abstract: The nucleic acid sequences and amino acid sequences of the key isoprenoid synthase 3-hydroxy-3-methylglutaryl-CoA reductase(hmgr) gene from mulberry,which were registered in GenBank,were analyzed by some bioinformatics tools including Vector NTI Suit 8 and so on.The results showed that the nucleic acid sequences in GenBank is genomic DNA of hmgr,and its gene arranges from 1 to 5 905 bp,including promoter,coding sequence and intron.It can speculate that the HMGR protein lies in Mitochondria,with transmembrane topological structure and plastid transport peptide of 22 amino acid residues,and is a hydrophic protein with HMG-CoA-reductase-classⅠdomain.The secondary structure of HMGR mainly consists of α-helix and random coil and the tertiary structures contains two HMG-CoA binding motifs and two NADP(H) binding motifs.

Abstract: BACKGROUND & OBJECTIVE apr-1 was cloned by improved polymerase chain reaction (PCR)-based subtractive hybridization from all-trans retinoic acid (ATRA)-induced apoptotic leukemia HL-60 cells in 1999. Preliminary results showed that apr-1 might be an apoptosis-related gene (GenBank ID: NM_014061). This study was to explore the background of apr-1 through gene cloning, bioinformatic analysis, and subcellular locating. METHODS The cDNA encoding Apr-1 was amplified by reverse transcription-PCR (RT-PCR), and sequenced. Open reading frame (ORF) of apr-1 was analyzed with ORF finder software. Chromosome locus was defined by genome blast software. Conserved domains of amino acids were analyzed by protein blast software. Align (Cluster W) software in Vector NTI software package was used to analyze homogeneous genes (or proteins), and to draw the Phylogenetic Tree. Subcellular localization of apr-1 was performed. RESULTS apr-1 was mapped to chromosome Xp11.22 with the ORF locating in 1 exon. Two MAGE conserved domains were found in Apr-1. Apr-1 shared homology with MAGE-A1, MAGE-B1, MAGE-C1, MAGE-D1, and Necdin. Phylogenetic analysis showed that Apr-1 was more closely related to MAGE-D1 and Necdin. Gene products of apr-1 were located in the nuclei of eukaryocytes. CONCLUSIONS apr-1 is a member of MAGE family, and might belong to type II MAGE genes.

Abstract: Objective To predict the structural and functional characteristics of cs002d09 EST from Clonorchis sinensis full-length cDNA plasmid library and its prospects of application. Methods Utilizing the analysis tools provided by NCBI(http:www.ncbi.nlm.nih.gov/), ExPaSy (http:www.expasy.org/) and the complicated bioinformatics software packages, such as PcGene, Vector NTI suite 8.0 were used to identify a EST clone (NO. cs002d09) from the C. sinensis full-length cDNA plasmid library and analyze its coding region and the physico-chemical properties and structural and functional characteristics of the deduced protein. Results The EST was predicted as a homologue of cathepsin L1, with 1 458 bp in length and a complete coding region 80-1 191 for 371 amino acids. The protein contained a secretory signal peptide of 18 amino acids residues in the N terminus, with stable physico-chemical property. The protein was composed of two spatially relatively independent domains, inhibitory domain (67-127) in the N segment and active catalytic domain in the C-terminal segment. Contradiction to the conserved C-terminal functional domain with a substrate-binding cleft in which bottom lies three key amino acids Cys177, His318 and Asn328 consisting the catalytic sites, the inhibitory domain covered the substrate cleft and was of much lower homology and contained three linear B cell epitopes. Conclusion C. sinensis cathepsin L1 is homologous with cathepsin L1 from other species and is probably a component of excretory-secretory antigen and maybe a promising candidate for vaccine and immunodiagnosis for clonorchiasis.