ALEX HARKESS
CAMPUS TREES ARE GIVING STUDENTS MORE THAN A SHADY PLACE TO STUDY The duckweed imaging project gave Harkess’s intern valuable, real-world lab experience, prompting her to pursue a career in plant biology. This is just one example of Harkess’s passion for training the next generation of plant biologists. His passion does not stop at simply mentoring students within his own lab. Harkess and Les Goertzen, PhD, a colleague at Auburn University, are ensuring students across the country can access valuable, hands-on genomics research opportunities, even if their school does not have the capability. They are focusing on an unlikely subject to achieve this goal: iconic campus trees, like the
Duckweeds are jack-of-all-trades plants. They are an excellent plant source of protein for humans and livestock, containing up to 40 percent protein dry mass. Duckweeds are atmospheric and aquatic filters, soaking up heavy met- als and toxins from water and sequestering atmospheric carbon. For more than a decade, duckweed has been used to produce therapeutic proteins, like antibodies. Because of their quick doubling time and the presence of woody materials like lignin and cellulose within duckweed, they are promising sustainable biomass sources for bioenergy and other bioproducts. With the help of a JGI CSP grant, Harkess and several collaborators are laying the groundwork for creating more efficient duckweed varieties with enhanced biofuel traits, such as increased reduction of cellulose or increased starch, as well as duckweeds that can grow larger, faster, and suck up more heavy metals and chemicals. The team is constructing a tree of life that describes the relation- ships between all 37 duckweed species. They hope to understand how useful traits evolved and changed over time, as well as the genes that might influence those traits. Information gained in this project will help unlock the remarkable potential of duckweeds to help combat climate change through carbon storage, carbon cycling, and biofuel production. The ability to easily and quickly phenotype mass quantities of duckweed is critical for validating genome- scale data to understand which gene families and path- ways are involved in duckweed growth and development. However, until recently, no such platforms for monitoring duckweed plants under multiple, simultaneous experi- mental conditions existed. A study published in Plant Direct in July 2022 presents an automated approach for imaging duckweed plants over time. Harkess and Jordan Manchego, a BioTrain* summer intern in his lab, worked with collaborators at the Donald Danforth Plant Science Center to develop the method that serves as a proxy for quantifying accumulated duckweed biomass over time. The protocol combines a macro micro- scope with automated image acquisition capabilities and a computational processing routine for semi-high-through- out phenotyping analysis. This method is transformative for future duckweed studies, paving the way for pheno- typing duckweed from multiple genetic backgrounds and performing a variety of growth assays on a single multi- well plate.
Toomer’s Oaks at Auburn University or the Emancipation Oak at Hampton University.
Their project, called American Campus Tree Genomes (ACTG), was born out of a crowd-funding event at Auburn University. Harkess and Goertzen developed a semester-long curriculum for undergraduate and graduate students at Auburn to assemble, annotate, and publish college campus tree genomes as a cohort. During the pilot semester in 2021, students sequenced Auburn’s beloved Toomer’s Oak tree. The course was a success – all of the students successfully contributed to the release of the Quercus virginiana southern live oak genome, despite 70 percent having never written a manuscript, performed command line bioinformatics, or engaged in plant genomics molecular work, The program minimizes institutional barriers by using the PRAXIS-AI teaching platform, which is entirely browser-based. It also allows teaching and learning to occur in non-traditional settings. As long as students can access the internet, they can do the coursework. Harkess and Goertzen built a framework so that other institutions can easily replicate the experience, from the crowdsource funding to the educational products to the actual science itself. The ACTG program expanded to two partner insti- tutions in 2022: Washington State University students, led by Stephen Ficklin, PhD, are sequencing the WA-38 (Cosmic Crisp™) Apple tree, and University of South Carolina-Aiken students, led by Nathan Hancock, PhD, are sequencing the state tree of South Carolina, Sabal palmetto . Six more schools are already on board for 2023. Harkess hopes to expand the program to reach more than 100 students per year, with an emphasis on including HBCUs and community college students. ■
Live oak
Sabal palmetto
Cosmic Crisp Apple
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