For many scientists, the culmination of their work into a written report that is published in a scientific journal is the ultimate achievement. To get to this point requires rigorous research, written skill, above all else, determination.
Rhondene Wint, an alumna of the DOE Joint Genome Institute (JGI)-UC Merced internship program and current PhD student, reached this milestone with a recent publication in Molecular Biology and Evolution. “It’s my first publication and it feels so rewarding,” Wint said.
For Axel Visel, JGI Science Deputy and a co-founder of the internship program, this type of achievement is especially rewarding. Wint is listed as the primary author on this publication and drove the entire project, Visel explained. She continued working virtually with her JGI mentors for nearly three years after her internship. “That level of commitment and collaboration between intern and mentor is what we strive for,” Visel said.
Practical Applications for Fungi
Wint began working on the project that culminated in this publication during her summer internship in 2018. She selected one of the projects posted by JGI fungal researchers, Igor Grigoriev and Asaf Salamov, and together, they embarked on a quest to better understand the factors and mechanics of gene expression in over 400 fungi species.
“Fungi are the masters of adaptation,” Wint explained. The fungal kingdom contains over one million different species and evidence of their ancestors can be found in fossil records dating over a billion years old. It’s an insanely diverse group of organisms that include some delicious additions to a savory meal, while others may be useful in the biofuel and synthetic biology fields.
In a living cell, triplets of nucleotides, or codons, dictate which amino acids are assembled, which then band together to build proteins. What Wint and her mentors discovered in the genomes helped to reinforce Charles Darwin’s “survival of the fittest” theory — the most expressed genes found across each of the fungal species were protein-coding hotspots. “Ensuring that the most expressed genes are also the most efficient at making proteins likely factors into why fungi have been so evolutionary and ecologically successful,” Wint said.
“Fungi play an important role in the earth’s ecosystem,” said Salamov, one of Wint’s mentors and a data scientist at the JGI. Previous studies were conducted on one or few genomes, but Wint’s research expands the understanding of hundreds of fungal genomes covering the entire kingdom of fungi. “The information from this project may also have a practical relevance with helping to synthesize codon-optimized fungal genes for various biotechnological purposes,” he said.
To enable such practical applications, Wint also developed and tested a gene sequence-based predictor of gene expression levels using machine learning tools. “This was very exciting to see how Rhondene not only embraced the research question and applied it to such a large data set, but also went all the way through to convert her biological observations into a practical computational application,” said Grigoriev, Wint’s other mentor and head of the JGI Fungal and Algal Program.
Paying It Forward
Wint, originally from Jamaica and the first member of her family to pursue a career in science, said that her eight weeks spent working with Salamov and Grigoriev at the JGI strongly influenced her perspective about what it means to be a scientist. “To see how team science is done at an advanced and large research institute, it left a mark on me,” she said.
In addition to learning about how to navigate and analyze large genomic datasets during the internship, Wint also began learning about how to write about and present her work. The now nine-week program requires all interns to build presentations that help to explain their work and its impacts at Berkeley Lab and beyond.
Last summer, Wint hosted a virtual four-day data carpentry workshop for the incoming 2021 JGI-UC Merced interns to help familiarize incoming students with basic data science skills and portals used by the JGI to process data. These areas had been previously identified as gaps in the curriculum through intern surveys. The addition was well received by the interns and their mentors, and Wint is slated to lead the workshop again in the 2022 program.
“I’m excited — I’m always glad to pay it forward,” said Wint, now in her final year of PhD research at UC Merced. She plans to continue expanding her understanding of mathematics and bioinformatics. “I love data, and when you love something, you can’t help but share it with others.”
- Publication: Wint R et al. Kingdom-Wide Analysis of Fungal Protein-Coding and tRNA Genes Reveals Conserved Patterns of Adaptive Evolution. Mol Biol Evol. 2022 Feb 3;39(2):msab372.doi: 10.1093/molbev/msab372.
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Byline: Ashleigh Papp