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, conducted commercial seafood labelling labs and even sequenced an antibiotic-producing microbe isolated from the loʻi kalo at Kawainui. Future projects include 16S metagenomic amplicon sequencing of environmental samples and human immune repertoire analysis.

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 network.

GMO Papaya and transgenic contamination

Is that papaya tree in your backyard or school garden GMO? How would you know? In this project, students bring in samples from their backyard papaya trees to be screened in class via a sequence of 2-3 lab exercises teaching DNA extraction, polymerase chain reaction (PCR) and gel electrophoresis. Students learn to detect unseen genetic modification with genetic tools while exploring the impacts of transgenic contamination in our cultivated landscapes.

Lava Cave Microbial Genomes

Deep inside the slopes of Kīlauea, a unique community of extremophilic bacteria thrives within the inhospitable crevices of caves formed by once flowing lava. This unseen and often uncharacterized biodiversity may hold new compounds of antibiotic or pharmaceutical interest, or reveal ways in which early life on Earth found purchase in a primordial world. Students use MinION sequencing technology and online bioinformatics tools to assemble and explore the genomes of novel bacteria isolated from these unique Hawaiʻi Island environments.

Mahalo nui to our partners in the Donachie Lab at the University of Hawaiʻi at Mānoa for their support and guidance on this project.

Non-Tuberculous Mycobacterial Lung Pathogens

Non-tuberculous mycobacteria (NTMs) are environmental pathogens which cause pulmonary infections which can resemble tuberculosis. In all the U.S.-occupied regions, Hawaiʻi has the highest per capita prevalence of NTM lung disease. NTMs live in diverse environments, from soils to household water fixtures. Hawaiʻi students have sampled hundreds of surfaces in residential, outdoor and commercial spaces in a citizen science effort to isolate the primary sources of exposure. Using MinION whole genome sequencing and bioinformatics, students can help researchers determine which strains in our environment best match those found within patients’ lungs.

Mahalo nui loa to the Honda Lab at National Jewish Health for their continued partnership in developing these projects with us.

COVID VARIANT TRACKERS

As the COVID pandemic extends into its second year, a number of variants of interest and concern have evolved from the original SARS-CoV-2 virus. As the onset of the delta phase of the pandemic has shown, it is not enough to track the virus by case counts and contact tracing alone - we need to understand at a genetic level what variants are where, and what makes them more or less virulent. In Hawaiʻi, the agency tasked with genomic surveillance of the coronavirus is the State Department of Health (DOH). Using deactivated samples sourced from the DOH testing lab, students now have the opportunity to safely contribute towards the sequencing and analysis of real viruses swabbed from local patients using the MinION. The genomes can then be analyzed alongside publicly available sequences (GISAID) from Hawaiʻi in order to reconstruct the virus’ evolutionary and transmission paths through the islands.

Mahalo nui loa to Dr. Marguerite Butler and Ethan Hill of the Pacific Biodiversity Lab at the University of Hawaiʻi at Mānoa for developing this project with us.