Ping Xu, Ph.D.

Professor

Phone: (804) 827-6264

Fax: (804) 828-0150

         
           
             
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Laboratory Interests:

1. Systems Biology for Essential gene identification Essential genes are indispensable genes for organisms to grow and reproduce progeny under certain environment. A living organism will die before generating progeny without essential gene function. There are three types of EG that depend on the living organism and the surrounding environments includeing absoultely essential genes,  conditional essential genes and development essential genes. Our current genome-wide essential gene identification inindicated that essential genes associated with genetic information processing, cell envelope and energy producing. Based on our finding, we built ePath (https://www.pubapps.vcu.edu/epath/), an essential gene database for >4000 bacterial speceis. 

2. Oral Biofilm and Bacterial interaction  Oral biofilm is important for periodontal diseases in which pioneers provide substrates allowing colonization of subsequent pathogens. Oral bacterial interactions, especially coaggregations between pioneering colonizers (such as mitis group streptococci, MGS) and pathogenic species (such as Porphyromonas gingivalis or Fusobacterium nucleatum), are important for periodontal diseases. A comprehensive S. sanguinis deletion mutant library has been created that including 2048 mutants. We have identified a S. sanguinis two-component system (TCS) gene that is responsible for increased adherence with P. gingivalis and F. nucleatum. We will screen the inclusive set mutants for biofilm genes. Biofilm genes will be studied in network by association of genomics, transcriptomics, metabolomics and proteomics data as we did previously for essential genes identification. The associations of biofilm genes in S. sanguinis will be studied in the gene network using systems biology approach.

 3. Microbiome and Comparative Genomics. We collaborate with other faculties in VCU are studying oral microbial community and human microbiome from clinical patients using next generation sequence technology. Next generation DNA sequencing technologies are applied to study the biological diversity of uncultured microorganisms in human mouth, or microbiome. We are interested in studying the medical microbial diversities in different biology niches.

 4. Antibacterial Drug Development and Antibiotic Resistance. Our current genome-wide essential gene identification provides numerous drug targets for streptococci. We have developed a model to identify essential genes for different bacterial species. Besides S. sanguinis, we have already predicted and confirmed essential genes, using our model, for S. pneumoniae, Streptococcus mutans, Bacillus subtilis and Staphylococcus aureus. These essential genes will become potential targets for antibacterial drug development. Furthermore, as emerging of many antibiotic resistant bacteria recently, the identification of all essential genes in pathogens will provide new strategies to control infective diseases.

Current Funds:

 01DE023078 

 Research Protocols

 Laboratory Safety

 

 Manuscript