Shoko Iwai

Post-doctoral Fellow

(Advisor: James Tiedje and Syed Hashsham)

Developing Comprehensive Molecular Detecting Tools to Better Assess PCB Degradation in the Environment

Polychlorinated biphenyls (PCBs) are one of the common contaminants in soils and sediments. It persists in the environment because of the physiochemical characteristics. One of the most effective methods to remove PCBs is bioremediation. Since biological degradation is reflected by the functional genes for degradation, it is critical to know the comprehensive picture of those genes in the environment to understand the biodegradation. Hence, our aim is to develop new comprehensive molecular tools to detect and characterize functional gene for PCB degradation.

Exploring gene diversity
Biphenyl 2,3-dioxygenase genes are responsible for the initial biodegradation step in the breakdown of PCBs. While there have been many studies about biphenyl 2,3-dioxygenase genes by pure cultures, the information about the diversity of this gene and which ones are active in the environment are scarce. Thus, we designed novel primer set for exploring biphenyl 2,3-dioxygenase gene diversities in the environmental samples. The primer set is used for constructing clone libraries from historically contaminated soils and sediments. We are also trying to use 454 sequencing technology (454 Life Sciences, Branford, CT) for phylosequencing analysis of the environmental dioxygenase genes.

Development of comprehensive molecular detecting tools
An oligonucleotide microarray is being developed based on the biphenyl 2,3-dioxygenase gene diversity. The sensitivity and the specificity of the probes are validated. The microarray is applied to the contaminated soils and sediments. The microarray profiles are used for monitoring and estimation of PCB degradation in the environment. BioTrove platform (BioTrove, Inc., Woburn, MA) is also used for quantitative analysis.

Fig. 1. The scheme of this project.