Systems Biology Brings Life Sciences Closer: —Report on the China-UK Systems Biology Workshop 2005

Chen, Ming

In the morning session of the second day, Xueping Zhou (Zhejiang University) introduced a modified viral satellite DNA, DNAβ, which suppresses gene expression in plants. He converted DNAβ into a gene silencing vector (DNAmβ) by replacing its C1 ORF with a multiple cloning site. The satellite DNA vector-based form of virus-induced gene silencing (VIGS) promised to be applicable to other begomovirus/DNAβ systems, which are recently reported to occur in several dicotyledonous crop species, thereby providing a powerful approach to gene discovery and the analysis of gene function in these economically important plants. Glenn McConkey (University of Leeds) presented a talk on metabolic networks and points of disruption for chemotherapy. He focused on comparative genomic analyses of the topology of metabolic networks predicted from sequenced genomes for the description of metabolic pathways and gene identification. The application to protozoan parasites including malaria parasites and agricultural parasites has identified novel pathways and enzymes. Fucheng Lin (Zhejiang University) described functional genomics of the appressorium formation of rice blast fungus Magnaporthe grisea. He discussed the molecular mechanisms of pathogenesis of M. grisea through pathogenic gene cloning and functional analyses (targeted gene replacement, GFP fusion, ultrastructure analyses, etc.) based on mutagenesis strategies (such as promoter trapping and temperature mutants library construction, functional genomics analyses, and molecular genetics). He also developed a good protocol to purify total RNA and proteins of appressoria regarding with these stages. Leo Caves (University of York, UK) outlined platforms for systems biology, covering (1) Data Science: exploratory data analysis and visualisation of high-dimensional data, and (2) Distributed Computing, the GRID, and e-Science: distributed system architectures for biocomputing. Ming Chen (Zhejiang University) presented computational approaches to systematically analyse biopathways. A web-based metabolic information retrieval system was developed to predict metabolic pathways from their rudimentary elements. A computer modeling and simulation technique based on the Petri net methodology was exploited to view the dynamics of biopathways. Comparative analysis of metabolic and signaling pathways was also addressed.