Using universal primer Ty1-copia retrotransposon RT,43 Ty1-copia like retrotransposon RT with high heterogeneity, stop codon mutation and frameshift mutation were amplified by PCR from genomic DNA of Zhejiang Lin'an (C15) and Yunnan Guangnan (A39) of Dendrobium officinale. The length of these sequences varied from 260 to 266 bp, and was rich in AT and consistency ranged from 47.1% to 97.7%. Different c/s-acting regulatory elements induced by low temperature, heat, light, all kinds of plant growth regulating substances and the starting transcription signals, corresponding to CAAT box, TATA box conserved sequences and some other regulatory elements. When being translated into amino acids, ten sequences presented stop codon mutation, five sequences presented frameshift mutation, and thirty-seven sequences presented conserved sequence "SLYGKQ" mutation. Six categories were identified through phylogenic analysis after alignment analyses of their amino acid sequences, and with other plants (eg. Triticum aestivum, Eleocharis quinqueflora) having high homology, which indicated that horizontal transmission of retrotransposon occurred among the plants in the past.
Amino Acid Sequence ; Cloning, Molecular ; Conserved Sequence ; DNA, Plant ; genetics ; Dendrobium ; enzymology ; genetics ; Molecular Sequence Data ; Phylogeny ; RNA-Directed DNA Polymerase ; chemistry ; genetics ; Retroelements ; genetics ; TATA Box ; genetics

Previously, we have established an epsilon library and selected out a series of RNA aptamers with higher affinity to P protein based on the in vitro Systematic Evolution of Ligands by Exponential Enrichment (SELEX) in duck hepatitis B virus (DHBV) system. In order to study the structural elements within the epsilon that is essential for initiating priming of HBV reverse transcriptase (P protein), all selected aptamers were subjected to in vitro priming assay and RNA secondary structure probing. We found that all those aptamers supporting priming had an undamaged bulge, while those lacking of the bulge no more support priming. Our results suggest an undamaged bulge within Depsilon is indispensable for initiating priming of P protein.
Base Sequence ; Hepatitis B Virus, Duck ; chemistry ; enzymology ; genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; RNA, Viral ; chemistry ; genetics ; RNA-Directed DNA Polymerase ; genetics ; metabolism ; Reverse Transcription ; Sequence Alignment ; Viral Proteins ; genetics ; metabolism

To gain information on retrotransposons in the genome of Paragonimus westermani, PCR was carried out with degenerate primers, specific to protease and reverse transcriptase (rt) genes of long-terminal-repeat (LTR) retrotransposons. The PCR products were cloned and sequenced, after which 12 different retrotransposon-related sequences were isolated from the trematode genome. These showed various degrees of identity to the polyprotein of divergent retrotransposon families. A phylogenetic analysis demonstrated that these sequences could be classified into three different families of LTR retrotransposons, namely, Xena, Bel, and Gypsy families. Of these, two mRNA transcripts were detected by reverse transcriptase-PCR, showing that these two elements preserved their mobile activities. The genomic distributions of these two sequences were found to be highly repetitive. These results suggest that there are diverse retrotransposons including the ancient Xena family in the genome of P. westermani, which may have been involved in the evolution of the host genome.
Amino Acid Sequence ; Animals ; Cloning, Molecular ; DNA, Helminth/analysis ; *Evolution, Molecular ; *Genome ; Molecular Sequence Data ; Paragonimus/*genetics ; Phylogeny ; RNA-Directed DNA Polymerase/chemistry/genetics ; Retroelements/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Terminal Repeat Sequences/*genetics

OBJECTIVETo investigate the molecular characteristics of noroviruses detected in Beijing.

METHODSFrom January to March 2007, cases from both outbreaks and sporadic episodes of acute nonbacterial gastroenteritis were investigated in Beijing, and the fecal specimens of the patients were collected. Noroviruses were detected by a reverse transcription polymerase chain reaction (RT-PCR), and then the PCR products were cloned and sequenced.

RESULTSA total of 27 positive cases were identified as caused by noroviruses among the 38 patients with acute viral gastroenteritis, and four PCR products were randomly selected for further studies on sequencing. When comparing to the nucleotide sequences of norovirus reference strains from GenBank, the highest homology was found between the four isolates and the norovirus GII/4 strains. The four strains isolated from Beijing were almost identical to the GII/4 variants that causing epidemics in the Netherlands and in Japan with the homology of 97.8%-98.5% and 95.2%-95.9%, respectively. Phylogenetic analysis revealed that the four isolates were located at the same branch as the norovirus GII/4 variants in Netherlands and Japan.

CONCLUSIONNew norovirus GII/4 variants were found in Beijing, and data from sequence analysis showed that the four isolates and the epidemic strains isolated from both the Netherlands and Japan in 2006 belonged to the same group of norovirus GII/4.

Amino Acid Sequence ; Caliciviridae Infections ; epidemiology ; virology ; China ; epidemiology ; Gastroenteritis ; virology ; Humans ; Molecular Sequence Data ; Norovirus ; enzymology ; Phylogeny ; RNA-Directed DNA Polymerase ; chemistry ; classification ; genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Homology, Amino Acid ; Viral Proteins ; chemistry ; classification ; genetics

BACKGROUND/AIMS: To develop a novel treatment method for hepatitis B virus (HBV) infection, we aimed to make a human monoclonal antibody inhibiting reverse transcriptase (RT) activity of P protein which was important in HBV replication by using phage display technique. Therefore, we analysed the usability of human monoclonal antibody as a protein based gene therapy. METHODS: Reverse transcriptase/polymerase (RT/POL) functional motif of P protein of HBV was cloned in pMAL-c vector and expressed as maltose binding fusion protein form. The RT/POL recombinant protein (pMRT/POL) was purified by amylose resin column. Using human single chain Fv phage antibody library with 1.1x10(10) size, human antibody against pMRT/POL was selected with BIAcore panning. Selected antibody fragments were analyzed for the activity of RT inhibition. Finally, they were analyzed for the affinity with BIAcore and the complementarity determining regions with nucleotide sequencing. RESULTS: pMRT/POL recombinant protein expressed in E. coli showed RT activity, 1microgram of recombinant protein had an activity equivalent to 5 unit of MMLV RT. By BIAcore panning, we could select 3 clones; POL-A5, POL-B8 and POL-B12. Each clone's RT inhibiting activity were 52-82%, affinity against antigen were 8.15x10(-8) M to 1.75x10(-6) M. CONCLUSIONS: Human monoclonal antibodies produced in this study showed low affinity, but efficiently inhibited the activity of RT in vitro. If POL-A5, POL-B8, and POL-B12 can be converted to intracellular antibody form, it can be used for protein-based gene therapy by inhibiting the replication through the neutralization of polymerase protein of HBV.
Antibodies, Monoclonal/biosynthesis/genetics/*pharmacology ; Complementarity Determining Regions/chemistry ; Gene Products, pol/*antagonists & inhibitors/genetics/immunology ; Genetic Vectors ; Hepatitis B virus/enzymology/genetics ; Humans ; Peptide Library ; RNA-Directed DNA Polymerase/genetics/*immunology ; Recombinant Fusion Proteins/biosynthesis/genetics ; Reverse Transcriptase Inhibitors/chemistry/metabolism/*pharmacology