[Show abstract][Hide abstract] ABSTRACT: Small nucleolar RNAs (snoRNAs) and Cajal body-specific RNAs (scaRNAs) are named for their subcellular localization within nucleoli and Cajal bodies (conserved subnuclear organelles present in the nucleoplasm), respectively. They have been found to play important roles in rRNA, tRNA, snRNAs, and even mRNA modification and processing. All snoRNAs fall in two categories, box C/D snoRNAs and box H/ACA snoRNAs, according to their distinct sequence and secondary structure features. Box C/D snoRNAs and box H/ACA snoRNAs mainly function in guiding 2'-O-ribose methylation and pseudouridilation, respectively. ScaRNAs possess both box C/D snoRNA and box H/ACA snoRNA sequence motif features, but guide snRNA modifications that are transcribed by RNA polymerase II. Here we present a Web-based sno/scaRNA database, called sno/scaRNAbase, to facilitate the sno/scaRNA research in terms of providing a more comprehensive knowledge base. Covering 1979 records derived from 85 organisms for the first time, sno/scaRNAbase is not only dedicated to filling gaps between existing organism-specific sno/scaRNA databases that are focused on different sno/scaRNA aspects, but also provides sno/scaRNA scientists with an opportunity to adopt a unified nomenclature for sno/scaRNAs. Derived from a systematic literature curation and annotation effort, the sno/scaRNAbase provides an easy-to-use gateway to important sno/scaRNA features such as sequence motifs, possible functions, homologues, secondary structures, genomics organization, sno/scaRNA gene's chromosome location, and more. Approximate searches, in addition to accurate and straightforward searches, make the database search more flexible. A BLAST search engine is implemented to enable blast of query sequences against all sno/scaRNAbase sequences. Thus our sno/scaRNAbase serves as a more uniform and friendly platform for sno/scaRNA research. The database is free available at http://gene.fudan.sh.cn/snoRNAbase.nsf.
Preview · Article · Feb 2007 · Nucleic Acids Research
[Show abstract][Hide abstract] ABSTRACT: The availability of data on the pig genome sequence prompted us to characterize the porcine IFN-alpha (PoIFN-alpha) multigene family. Fourteen functional PoIFN-alpha genes and two PoIFN-alpha pseudogenes were detected in the porcine genome. Multiple sequence alignment revealed a C-terminal deletion of eight residues in six subtypes. A phylogenetic tree of the porcine IFN-alpha gene family defined the evolutionary relationship of the various subtypes. In addition, analysis of the evolutionary rate and the effect of positive selection suggested that the C-terminal deletion is a strategy for preservation in the genome. Eight PoIFN-alpha subtypes were isolated from the porcine liver genome and expressed in BHK-21 cells line. We detected the level of transcription by real-time quantitative RT-PCR analysis. The antiviral activities of the products were determined by WISH cells/Vesicular Stomatitis Virus (VSV) and PK 15 cells/Pseudorabies Virus (PRV) respectively. We found the antiviral activities of intact PoIFN-alpha genes are approximately 2-50 times higher than those of the subtypes with C-terminal deletions in WISH cells and 15-55 times higher in PK 15 cells. There was no obvious difference between the subtypes with and without C-terminal deletion on acid susceptibility.
[Show abstract][Hide abstract] ABSTRACT: Rv3487c (lipF), a member of the lipase family of Mycobacterium tuberculosis, is related to virulence of this pathogen. Real-time RT-PCR analysis indicated that Rv3487c was induced at low pH in M. tuberculosis cultured in vitro. The gene of Rv3487c was cloned and expressed as fusion protein in Escherichia coli. After removal of the N-terminal domain of the fusion partner by enterokinase treatment, the effect of pH, temperature, and detergents on the purified enzyme activity and stability was characterized. Rv3487c could efficiently hydrolyze short chain esters. The catalytic triad of Rv3487c consists of residues Ser90, Glu189, and His219 as demonstrated by amino acid sequence alignment, three-dimensional modeling, and site-directed mutagenesis.
No preview · Article · Aug 2005 · Protein Expression and Purification
[Show abstract][Hide abstract] ABSTRACT: Peptide nucleic acids (PNAs) are nucleic acid analogs with the deoxyribose phosphate backbone replaced by pseudo-peptide polymers
to which the nucleobases are linked. The achiral, uncharged and rather flexible properties of the peptide backbone permit
peptide nucleic acids more potential than oligonucleotides in application to antisence and antigenic reagents. The process
of PNA binding to DNA duplex and forming triplex is the first step of PNA interacting with PNA. But there are no PNA.2DNA
triplex crystal data up to date and little has been reported on the structure features and the force of the PNA.2DNA triplex.
In this work, PNA(T).DNA(AT) triplexes are successfully built and the structures and forces to stabilize the triplex alter
optimizations and molecule dynamics are systematically examined, which are expected to aid in the application of PNAs as anticense
and antigene agents.
No preview · Article · Nov 2003 · Chinese Science Bulletin
[Show abstract][Hide abstract] ABSTRACT: Synonymous codon bias has been examined in 78 human genes (19967 codons) and measured by relative synonymous codon usage (RSCU).
Relative frequencies of all kinds of dinucleotides in 2,3 or 3,4 codon positions have been calculated, and codon-anticodon
binding strength has been estimated by the stacking energies of codon-anticodon bases in Watson-Crick pairs. The data show
common features in synonymous codon bias for all codon families in human genes: all C-ending codons, which possess the strongest
codon-anticodon binding energies, are the most favored codons in almost all codon families, and those codons with medium codon-anticodon
binding energies are avoided. Data analysis suggests that besides isochore and genome signature, codon-anticodon binding strength
may be closely related to synonymous codon choice in human genes. The join-effect of these factors on human genes results
in the common features in codon bias.
Keywordscodon bias-synonymous codons-human genes
No preview · Article · Jun 2001 · Chinese Science Bulletin
[Show abstract][Hide abstract] ABSTRACT: Since the first intein (Sce VMA) was found inSaccharomydes cerevisiae ATPases gene in 1990, more and more inteins were identified. It is necessary to analyze the new inteins to understand the
sequence charateristics of inteins. By searching protein and nucleic acid database systematically, 101 inteins were found,
of which 69 inteins contain homing endonuclease motifs. We only analyze the 69 inteins since most inteins are the classic
inteins with homing endonuclease motifs. We found that the distribution of these inteins is particular among species and protein.
By multiple sequence alignment, some new sequence characteristics were found and the motifs described previously were revised.
Keywordsintein distribution-location of intein-sequence charateristics
No preview · Article · May 2001 · Chinese Science Bulletin