【報告摘要】

Bacteria have constant battles with various types of invaders, including viruses. The CRISPR–Cas adaptive immune system is a primary defense system in prokaryotic organisms, providing targeted defense against invading DNAs. CRISPR (clusters of regularly interspaced short palindromic repeats) arrays and cas (CRISPR-associated) genes are the key components of the CRISPR–Cas immune systems: bacteria memorize foreign DNAs by incorporating pieces of the invaders into their own genomes, forming spacers between the repeats, and Cas proteins encoded by cas genes are involved in the different stages of the defense process. We developed a targeted assembly approach that greatly improves the identification of CRISPR arrays from metagenomic sequences. Application of our approach to the Human Microbiome Project (HMP) datasets revealed a great diversity of CRISPR arrays among different body sites, in different individuals, and in single individuals over time, providing the very first global view of bacterial immune systems in human-associated microbial communities. As an application of the CRISPR arrays, we used the spacers to fish out the invaders of human microbiomes, resulting in a diverse collection of invasive mobile genetic elements in human microbiomes, an important resource for further study of the interactions between bacteria and invaders. In this seminar, I will talk about the computational tools that we have developed for the studies of CRISPR–Cas systems and our main findings. I will also briefly introduce other computational tools that we have developed for metagenomics data analysis.

【報告人簡介】

Dr. Yuzhen Ye is an Assistant Professor with the School of Informatics and Computing, Bloomington, Indiana. She was a Research Assistant Professor in the Burnham Institute for Medical Research (2004-2007), and was a post-doctoral associate in the same institution from 2001 to 2004. She received her Ph.D. in Computational Biology from Shanghai Institute of Biochemistry in 2001. Dr. Ye received a National Science Foundation (NSF) CAREER Award in 2009. Her projects are currently supported by the NSF and the NIH of USA.