Biomedical subjects

An Zhao

Publications and source records attributed to An Zhao.

5 recordsLinked to original sources

PubMed2006

ATP- and NAD+-dependent DNA ligases share an essential function in the halophilic archaeon Haloferax volcanii.

DNA ligases join the ends of DNA molecules during replication, repair and recombination. ATP-dependent ligases are found predominantly in the eukarya and archaea whereas NAD+-dependent DNA ligases are found only in the eubacteria and in entomopoxviruses. Using the genetically tractable halophile Haloferax volcanii as a model system, we describe the first genetic analysis of archaeal DNA ligase function. We show that the Hfx. volcanii ATP-dependent DNA ligase family member, LigA, is non-essential for cell viability, raising the question of how DNA strands are joined in its absence. We show that Hfx. volcanii also encodes an NAD+-dependent DNA ligase family member, LigN, the first such enzyme to be identified in the archaea, and present phylogenetic analysis indicating that the gene encoding this protein has been acquired by lateral gene transfer (LGT) from eubacteria. As with LigA, we show that LigN is also non-essential for cell viability. Simultaneous inactivation of both proteins is lethal, however, indicating that they now share an essential function. Thus the LigN protein acquired by LGT appears to have been co-opted as a back-up for LigA function, perhaps to provide additional ligase activity under conditions of high genotoxic stress.

Archaeal Proteins↗

PubMed2006

[A quality controllable algorithm for ECG compression based on wavelet transform and ROI coding].

This paper presents an ECG compression algorithm based on wavelet transform and region of interest (ROI) coding. The algorithm has realized near-lossless coding in ROI and quality controllable lossy coding outside of ROI. After mean removal of the original signal, multi-layer orthogonal discrete wavelet transform is performed. Simultaneously,feature extraction is performed on the original signal to find the position of ROI. The coefficients related to the ROI are important coefficients and kept. Otherwise, the energy loss of the transform domain is calculated according to the goal PRDBE (Percentage Root-mean-square Difference with Baseline Eliminated), and then the threshold of the coefficients outside of ROI is determined according to the loss of energy. The important coefficients, which include the coefficients of ROI and the coefficients that are larger than the threshold outside of ROI, are put into a linear quantifier. The map, which records the positions of the important coefficients in the original wavelet coefficients vector, is compressed with a run-length encoder. Huffman coding has been applied to improve the compression ratio. ECG signals taken from the MIT/BIH arrhythmia database are tested, and satisfactory results in terms of clinical information preserving, quality and compress ratio are obtained.

Algorithms↗

PubMed2004

A conformation-constrained peptide library based on insect defensin A.

Here, we reported a conformation-constrained peptide library, that was constructed based on the scaffold of a 29 amino acids peptide derived from insect defensin A. The peptide scaffold was designed utilizing the InsightII molecular modeling software and then displayed on M13 filamentous bacteriophage by fusion with coat protein III. The library was constructed by randomization of seven positions located within the two loops of the peptide scaffold generating approximately 8.3 x 10(8) transformants. Sequences from 14 randomly selected phage clones indicated that the distribution of nucleotides and amino acids paralleled with the expected frequency. Screening against the target proteins: tumor necrosis factor alpha, TNF receptor 1, TNF receptor 2 and monoclonal antibody against BMP-2 showed significant enrichment in all cases. The results presented here show that the reconstructed insect defensin A domain will be a promising non-antibody protein scaffold for the presentation of a phage-displayed constrained peptide library.

Amino Acid Sequence↗

PubMed2003

Identification of anti-TNFalpha peptides with consensus sequence.

Phage displayed peptide library was used to select tumor necrosis factor alpha (TNFalpha) binding peptides. After three sequential rounds of biopanning, some linear TNFalpha-binding peptides were identified from a 12-mer peptide library. A consensus sequence (L/M)HEL(Y/F)(L/M)X(W/Y/F), where X might be variable residue, was deduced from sequences of these peptides. The phages bearing these peptides showed specific binding to immobilized TNFalpha, with over 80% of phages bound being competitively eluted by free TNFalpha. To confirm the binding activity and to explore further functional properties, three peptides with typical structure were selected and expressed as GST-fused protein. These recombinant peptides effectively competed for [125I]TNFalpha binding to TNFR1 in a dose-dependent manner, with IC(50) from 10 to 160 microM. Furthermore, the GST-fused derivatives showed inhibitory effects on TNFalpha-induced cytotoxicity. Taken together, these data demonstrate that the TNFalpha-binding peptides are effective antagonists of TNFalpha and the deduced motif might be useful in development of novel low molecular weight anti-TNFalpha drugs.

Bacteriophages↗

PubMed2003

Identification of mimotopes by screening of a bacterially displayed random peptide library and its use in eliciting an immune response to native HBV-preS.

Bacterially-displayed peptide libraries have been widely used as an alternative to phage-displayed peptide libraries in screening epitopes or mimotopes of antibodies. Using a protective monoclonal antibody (mAb) 3B9 against hepatitis B virus (HBV) preS protein as target, mimotopes were successfully screened from a FliTrx random peptide library. To monitor the enrichment ratios of each round and to isolate higher affinity clones from the library, a modified procedure was performed in which the titer of eluted bacteria from an antibody-coated well (P value) was compared with that from a non-coated well (N value). After sufficient enrichment of the library, bacterial colonies were randomly picked and identified further by the monoclonal bacterial P/N value assay and Western blotting analysis. Immunization of mice with the selected bacterially-displayed mimotopes, including the enriched populations without clone identification, elicited strong specific immune responses against the recombinant preS protein. The present study provides a potentially rapid and effective strategy for the development of engineered live bacterial vaccines without the need for information about the aetiological agents or their antigens.

Animals↗