Synthesis

The Synthetic Biology lab is divided into a DNA synthesis production group and a synthetic biology applications group.

• The DNA synthesis and assembly group: Our production group operates as user facility that aims to provide access to state-of-the-art DNA synthesis and assembly technologies to the broader community. 
  
  We focus our efforts on integrating database mining and sequence design with scaling the production of large, difficult to synthesize constructs such as those involving biosynthetic clusters, or high complexity combinatorial libraries. 
  
  We have developed and continue to improve automated assembly pipelines bringing in new technologies, in particular through adoption of lab automation enabling ever-higher levels of throughput. We also develop methods for efficient QA/QC based on next-generation sequencing technologies including PacBio and Illumina. 

• The synthetic biology user science group: The applications group is focus on developing methods for converting digital information from sequence databases into biotechnological or environmental applications. 
  
  We are interested in: 

  • characterizing novel enzymatic activities using phylogenomic driven approaches, and

  • understanding the design principles for successfully engineering pathways to function in heterologous hosts, by combining combinatorial synthesis, high-throughput screening methodologies, and statistical frameworks for inferring genotype to phenotype associations.

The focus of this group, in recent years, has been to bring generalizable technologies to bacteria, yeasts and algae previously with little to no genetic tools enabling heterologous expression and functional exploration. 

The developed strains represent an additional phase of user-accessible project types, in which DNA-based molecules can be chromosomally integrated into a taxonomically diverse suite of microbial chassis strains for elevated opportunity for expression.

Software Engineers in the Synthetic Biology Informatics Group develop, deploy, and maintain software that support the JGI’s Synthetic Biology Program. 

Representative software includes:

1. gRNA-SeqRET, an organism-agnostic CRISPR gRNA design tool https://grna.jgi.doe.gov/

2. BOOST, which provides a suite of tools to automate sequence design for assembly by Gibson, Yeast recombination and Golden Gate methods

3. SynTrack and associated tools, which track samples through the JGI’s Synthetic Biology pipeline as well as provide process automation support