Joint Genome Institute

Berkeley, California
Company size: 285
Anticipated number of internship positions: 1

Opportunity for remote/virtual internship in 2021: yes

About JGI

The Department of Energy (DOE) Joint Genome Institute (JGI), a national user facility located at Lawrence Berkeley National Laboratory, is committed to advancing genomics in support of DOE missions related to clean energy generation and environmental characterization and cleanup. The JGI provides integrated high-throughput sequencing, DNA synthesis, metabolomics and computational analysis to enable systems- based scientific approaches to these challenges. The JGI supports a diverse and vibrant research community dedicated to advancing science in a collaborative, inclusive work environment.

Internship Project Description

–This description represents a potential internship project and is subject to change.–

(Updated 10/28/2020)

The JGI synthetic biology platform provides thousands of DNA assemblies to its research community per year. User projects range from single gene inserts (<1 kilobase) to biosynthetic gene clusters (BGCs; >60kb), combinatorial libraries (Golden Gate, MoClo) and high variant libraries (sgRNA, promoter screening). The program has three core focus areas: High throughput functional genomics, genomics to structure and function, and plant-microbe interactions mediated by secondary metabolites.

The objective of this computational project is to develop a tool for streamlining the design of saturation mutagenesis. By allowing exploration of protein space, sequence saturation mutagenesis enables a fundamental understanding of function as well as both rational and non-deterministic protein engineering, providing new avenues of research in all three focus areas. Under the mentorship of the platform lead, you will code the necessary tool providing automated oligonucleotide design of a given input DNA sequence for a molecular method already established in the laboratory. Options could include random mutagenesis across the length of the sequence, mutagenesis within specific coordinates of the sequence (e.g. of an active site) or predetermined mutations (e.g. every Ala to Lys).

The JGI actively encourages intern participation in interdisciplinary science discussions through weekly seminar series as well as those sponsored by the Biosciences Area and Berkeley Lab.