Projects

Our citizen science projects constitute an evolving list of research topics that provide opportunities not just for generating real data, but are well-suited for hands-on genetics and genomics education. In the past, we have barcoded fish caught by the lawaiʻa aboard Hōkūleʻa and Hikianalia during the Mālama Honua worldwide voyage, tested Red Hill remediation discharge in Hālawa Stream, and even sequenced an antibiotic-producing microbe isolated from the loʻi kalo at Kawainui. We are always interfacing with our network to identify questions of interest - please contact us if you have an idea you would like to explore with our mobile sequencing lab.

Current Projects

GMO Papaya (introductory)

What proportion of our non-commercial papayas are GM?

Techniques: DNA extraction, PCR, gel electrophoresis

Keywords: GMO, agriculture, environmental health, food sovereignty

Fungi Barcoding (IntRODUCTORY)

Developing a robust database of ITS barcodes for fungi in Hawaiʻi.

Techniques: DNA extraction, PCR, gel electrophoresis, amplicon sequencing, basic bioinformatics

Keywords: Fungi, barcoding, phylogeny, ecology, plant-fungal associations

Lava Cave Microbial Biodiversity (Intermediate)

Sequencing and analyzing the genomes of potentially novel microbial species hidden within Hawaiʻi Island lava caves.

Techniques: DNA extraction, whole-genome sequencing, bioinformatics

Keywords: Microbial biodiversity, early Earth, astrobiology, extremophile biology, quorum sensing, bioprospecting

Nontuberculous mycobacteria (Intermediate)

Uncovering the sources and strains of NTM lung pathogens in our environment through sequencing.

Techniques: Whole-genome sequencing, bioinformatics

Keywords: Lung disease, public health, phylogeny, genome annotation, antibiotic resistance

Microbiomes (Intermediate)

Characterizing the microbial communities inside environment substrates or on or within organisms.

Techniques: DNA extraction, PCR, gel electrophoresis, MinION sequencing, bioinformatics

Keywords: Soil, water, nutrient cycling, metagenomics, bioindicators

Stream Environmental DNA (Advanced)

Pairing eDNA sequencing with field capture surveys to detect rare native species in our island streams.

Techniques: DNA extraction, PCR, gel electrophoresis, sequencing library prep, MinION sequencing, bioinformatics

Keywords: Stream biodiversity, eDNA, invasive ecology, native ʻoʻopu, species richness, rarefaction

Multi-School Collaborations

Endangered Bird Conservation Genomics

In partnership with Kealakehe High School, Hawaiʻi Preparatory Academy and conservation geneticists at the San Diego Zoo Wildlife Alliance, local students have been sequencing and analyzing the genomes of endangered native birds, including the palila and the nēnē.

Past Projects

COVID Variant Trackers (Advanced)

Sequencing real SARS-CoV-2 samples to determine which variants were circulating throughout the islands during the pandemic.

Techniques: Viral genome sequencing, bioinformatics

Keywords: COVID, variant assignment, biogeographical reconstruction, vaccine ethics