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9. Plasmid linking number change induced by topoisomerase I-mediated DNA damage

Author

Hui Zhang, Pu Duann, Chin Tai Lin, Leroy-Fong Liu, and Mei Sun

Subjects
Time Factors, Ultraviolet Rays, DNA damage, Eukaryotic DNA replication, Simian virus 40, Biology, Topoisomerase-I Inhibitor, Transfection, Cell Line, Fungal Proteins, Plasmid, Yeasts, Genetics, Animals, Humans, Micrococcal Nuclease, Enzyme Inhibitors, DNA clamp, Dose-Response Relationship, Drug, Models, Genetic, DNA, Superhelical, Topoisomerase, Chloroquine, Molecular biology, Chromatin, DNA Topoisomerases, Type I, COS Cells, biology.protein, Nucleic Acid Conformation, DNA supercoil, Camptothecin, Topoisomerase I Inhibitors, DNA Damage, Plasmids, Research Article
Abstract

The state of cellular chromatin in response to DNA damage has been examined by monitoring the change in the linking number of circular episomes. COS cells transfected with an SV40-based vector were treated with camptothecin (CPT), a eukaryotic DNA topoisomerase I (TOP1) poison which induces TOP1-mediated DNA damage. Within minutes, a large increase in the linking number (over 10 linking number) of a small fraction (5-15%) of the episomal DNA was observed. A similar CPT-induced increase in plasmid DNA linking number was observed in Saccharomyces cerevisae expressing human DNA TOP1. In this case, the majority of the plasmid DNA can undergo rapid relaxation. The large increase in the plasmid linking number suggests major chromatin structural reorganization in response to TOP I-mediated DNA damage.

Published
1999

16. Optimal Storage Placement for Tree-Structured Networks with Heterogeneous Channel Costs.

Author

Chiu, Ge-Ming, Yen, Li-Hsing, and Chin, Tai-Lin

Subjects
TREE graphs, HETEROGENEOUS computing, COST analysis, QUERYING (Computer science), ALGORITHMS, SIMULATION methods & models, PEER-to-peer architecture (Computer networks), WIRELESS sensor networks, DATA transmission systems
Abstract

This work considers data query applications in tree-structured networks, where a given set of source nodes generate (or collect) data and forward the data to some halfway storage nodes for satisfying queries that call for data generated by all source nodes. The goal is to determine an optimal set of storage nodes that minimizes overall communication cost. Prior work toward this problem assumed homogeneous channel cost, which may not be the case in many network environments. We generalize the optimal storage problem for a tree-structured network by considering heterogeneous channel costs. The necessary and sufficient conditions for the optimal solution are identified, and an algorithm that incurs a linear time cost is proposed. We have also conducted extensive simulations to validate the algorithm and to evaluate its performance. [ABSTRACT FROM AUTHOR]

Published
2011
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