CHECKERSPOT

About the start-up

Checkerspot is a biotechnology company specializing in the development of high-value fats and oils through precision fermentation of microalgae. The company’s platform enables the production of tailored lipid profiles designed to meet specific functional and nutritional needs, particularly within the food and nutrition sectors. Under the leadership of CEO John Krzywicki, appointed in March 2025, Checkerspot has refined its focus on developing and out-licensing microalgal strains capable of producing fats and oils that are not easily or sustainably sourced from nature.

The company aims to provide partners with specific solutions to their ingredient needs, emphasizing scalability and reliability. For graduate students interested in biotechnology and its applications in food and nutrition, Checkerspot offers opportunities to engage in cutting-edge research and to contribute to the development of innovative solutions addressing challenges in ingredient sourcing and functionality.

Project Title

GENE DISCOVERY AND STRAIN ENGINEERING FOR STRUCTURING FAT PRODUCTION IN MICROALGAE

Project summary

Checkerspot is seeking an intern to support projects aimed at developing novel structuring fats in microalgae. The role will focus on exploring a specific gene family involved in fatty acid or triacylglyceride (TAG) biosynthesis, leveraging public data and bioinformatics tools to identify promising candidates from plants, fungi, or other microalgae. Selected genes may be deployed into existing production strains for functional testing. Alternatively, or additionally, the intern may help identify inducible regulatory elements through expression profiling under varied fermentation conditions. Depending on the student’s skill set, the role could involve expression construct design, strain engineering, and lipid assay-based validation. Interns will gain exposure to the full design-build-test-learn cycle in a collaborative R&D environment.

RESponsibility

• Query public databases to identify candidate genes (e.g., cDNAs or predicted ORFs) representing putative orthologs within a targeted gene family involved in fatty acid or TAG biosynthesis.

• Mine public RNA-seq datasets and perform de novo transcriptome assemblies to recover full-length transcripts from heterologous organisms.

• Design and assemble expression constructs using established regulatory elements and the newly identified candidate genes, and introduce them into optimized platform strains.

• With support from Checkerspot’s Analytical team, screen transformants for changes in fatty acid or TAG composition.

• Collect biomass samples from fermentations run under varied conditions, extract and quality-check total RNA for submission to a CRO for RNA-seq.

• Analyze resulting RNA-seq data to identify differentially expressed genes and inducible regulatory elements.

• Support functional validation of inducible promoters through construct design and strain engineering.

About the candidate

Pluses

• Pursuing a degree in Molecular Biology, Biochemistry, Microbiology, Synthetic Biology, Bioengineering, Bioinformatics or a related field.

• Experience with gene family analysis and ortholog identification using public databases (e.g., NCBI, Ensembl, Phytozome).

• Proficiency in RNA-seq data analysis including transcriptome assembly and differential expression analysis.

• Basic molecular biology techniques including PCR-based cloning and construct design.

• Strong written and verbal communication skills and ability to work both independently and in a collaborative team environment.

Familiarity with fatty acid or lipid biosynthesis pathways in plants, fungi, or microalgae would be a plus. Students with strong bioinformatics backgrounds who are interested in gaining hands-on wet lab experience in molecular biology are also encouraged to apply.