Biomedical subjects

Jijun Tang

Publications and source records attributed to Jijun Tang.

4 recordsLinked to original sources

PubMed2006

In vitro selection of DNA aptamer against abrin toxin and aptamer-based abrin direct detection.

Abrin toxin as the target protein, belongs to class II ribosome-inactivating proteins family, has high toxicity to eukaryotic cells. Here, we firstly report the DNA aptamers, isolated by in vitro selection, recognize abrin toxin with high affinity and specificity, and have the advantage of no cross-reaction with structure-similar protein ricin toxin over antibodies. Then, a highly selective and sensitive aptamer-based abrin assay was established using a molecular light switching reagent [Ru(phen)(2)(dppz)](2+) with a limit of detection of 1 nM and a wide linear range from 1 to 400 nM with the correlation coefficient of 0.993. This assay can be successfully directly performed not only in physiological buffer but also in more complicated biological matrix, such as diluted serum.

Abrin↗

PubMed2006

Adaptive evolution of chloroplast genome structure inferred using a parametric bootstrap approach.

BACKGROUND: Genome rearrangements influence gene order and configuration of gene clusters in all genomes. Most land plant chloroplast DNAs (cpDNAs) share a highly conserved gene content and with notable exceptions, a largely co-linear gene order. Conserved gene orders may reflect a slow intrinsic rate of neutral chromosomal rearrangements, or selective constraint. It is unknown to what extent observed changes in gene order are random or adaptive. We investigate the influence of natural selection on gene order in association with increased rate of chromosomal rearrangement. We use a novel parametric bootstrap approach to test if directional selection is responsible for the clustering of functionally related genes observed in the highly rearranged chloroplast genome of the unicellular green alga Chlamydomonas reinhardtii, relative to ancestral chloroplast genomes. RESULTS: Ancestral gene orders were inferred and then subjected to simulated rearrangement events under the random breakage model with varying ratios of inversions and transpositions. We found that adjacent chloroplast genes in C. reinhardtii were located on the same strand much more frequently than in simulated genomes that were generated under a random rearrangement processes (increased sidedness; p < 0.0001). In addition, functionally related genes were found to be more clustered than those evolved under random rearrangements (p < 0.0001). We report evidence of co-transcription of neighboring genes, which may be responsible for the observed gene clusters in C. reinhardtii cpDNA. CONCLUSION: Simulations and experimental evidence suggest that both selective maintenance and directional selection for gene clusters are determinants of chloroplast gene order.

Adaptation, Physiological↗

PubMed2006

The DNA aptamers that specifically recognize ricin toxin are selected by two in vitro selection methods.

Aptamers which specifically recognize cytotoxin ricin were successfully selected using the two different in vitro selection methods. One selection method was used to isolate aptamers by affinity chromatography. Another selection method, named CE-SELEX, was carried out using CE as a separation approach. The high separation efficiency of CE evidently improved the rate of enrichment and obviously shortened the selection rounds, with near 87.2% binding just after the fourth round of selection. The aptamers A3, C1, and C5, derived from the two selection methods, were found to possess high affinity and specificity for ricin with the Kd values in the low nanomolar range, and did not recognize abrin toxin similar to ricin in the structures and properties, or BSA. Among the aptamers selected, A3 isolated by affinity chromatography shared extensive sequence similarity with C1 and C5 derived from CE-SELEX. They differed by only one base from each other. Their stable secondary structures predicted also had very similar structure motifs, and all folded a long and internal loop-embedded loop stem structure by base pairing. The ELISA and dot-blot analysis also proved that the selected DNA aptamers had the high specificity to ricin toxin.

Aptamers, Nucleotide↗

PubMed2003

Scaling up accurate phylogenetic reconstruction from gene-order data.

MOTIVATION: Phylogenetic reconstruction from gene-order data has attracted increasing attention from both biologists and computer scientists over the last few years. Methods used in reconstruction include distance-based methods (such as neighbor-joining), parsimony methods using sequence-based encodings, Bayesian approaches, and direct optimization. The latter, pioneered by Sankoff and extended by us with the software suite GRAPPA, is the most accurate approach, but cannot handle more than about 15 genomes of limited size (e.g. organelles). RESULTS: We report here on our successful efforts to scale up direct optimization through a two-step approach: the first step decomposes the dataset into smaller pieces and runs the direct optimization (GRAPPA) on the smaller pieces, while the second step builds a tree from the results obtained on the smaller pieces. We used the sophisticated disk-covering method (DCM) pioneered by Warnow and her group, suitably modified to take into account the computational limitations of GRAPPA. We find that DCM-GRAPPA scales gracefully to at least 1000 genomes of a few hundred genes each and retains surprisingly high accuracy throughout the range: in our experiments, the topological error rate rarely exceeded a few percent. Thus, reconstruction based on gene-order data can now be accomplished with high accuracy on datasets of significant size.

Algorithms↗