Jack Greger
Jack Greger headshot
Year: 2023
Faculty Advisor: Margaret Frank
Mentor: Wei Wei Chen
Mentor: Sijin Li

Monitoring Mobility: An Integrative Approach into Studying Mobile Elements in Plants

Plants like animals have a vascular system, and plants transport mRNA and peptides very long distances through theirs to communicate. In an ever-shifting environmental landscape from accelerating climate change, understanding plant intercellular communication allows us to provide and modify signals which plants may use to survive in situations they may otherwise not have the time or ability to acclimate to. This work aims to decode existing communication pathways and begin re-coding known responses. Mobile mRNA in grafted plants has been identified in multiple studies and has been shown to move between root and shoot systems over long distances, in a bidirectional manner. Quantity, function, and significance of mobile transcripts have garnered much debate. To overcome issues faced by traditional detection methods, we use a system of differential genome alignment followed by masking of uninformative regions. In our graft type in tomato (Solanum lycopersicum) and eggplant (Solanum melongena) this analysis proves essential with 16 million years divergence and 80% orthology between the two genomes. Focusing on a vascular-mobile signal within an environmental adaptive pathway, the C-TERMINALLY ENCODED PEPTIDEs (CEPs) in Arabidopsis thaliana have been demonstrated to engage in root-shoot-root transportation. We sought to understand the conditions that elicit CEP responses and, consequently, how the crosstalk of pathways influences plant responses on a systemic level. We quantified CEPs’ expression in response to an environmental drought stress, Mannitol, through RT-qPCR analysis of treated shoot and root tissues at varying timescales. Further understanding of how CEP influences plant response builds a foundation of knowledge for which approaches to reprogram inputs and outputs of these pathways can be pursued. In an era when genetic sequencing and phenotyping are quickly producing vast amounts of data, database systems such as Breedbase are becoming increasingly necessary in genomics research. Websites that use the Breedbase ecosystem support a range of tasks related to crop breeding, which enact operations on the database in the form of insertions, updates, and deletions of data. Breedbase users requested that a record of these changes be made available on the website as a reference, for archival purposes and correction of errors. This feature was built by running a PostgreSQL database patch, which creates audit tables and inserts audit data every time a change is made to the database. These data, including the timestamp, type of operation, username of the account that committed the change, and state before and after the change, are displayed in dedicated audit pages and sections on the website. These webpages were designed using HTML and JavaScript/jQuery, and database connections are handled via a controller written in Perl. With the advent of audit tables in Breedbase, users will be able to handle their data more efficiently and securely. This is impactful as Breedbase programs mainly focus on staple crops such as cassava, which are integral to food security and economic prosperity. Deformed wing virus (DWV) is a common RNA virus exacerbated in honey bees (Apis mellifera) by Varroa mites. DWV is at epidemic levels in honey bees and poses a major concern for beekeepers. Additionally, DWV can be transmitted from managed honey bees to wild native bee species via shared floral resources. At high levels, DWV can cause deformed wings and altered foraging behavior. However, even low levels could decrease honey bee foraging and flight distances. The present study investigated the correlation between foraging distance and viral load in honey bees foraging on Common Milkweed (Asclepias syriaca) at varying distances from an apiary. Although neither trend was statistically significant, we found that DWV-positive honey bees tended to be found at greater distances from the apiary, while viral loads tended to decrease. We hope to repeat this experiment with a larger sample size of honey bees and apiaries. Additionally, combining data on DWV with other pathogen tests may provide better insight into factors that influence foraging abilities. Ultimately, understanding the impact of deformed wing virus on honey bee flight distances would enrich our knowledge of behavioral impacts of this virus on honey bees. From a conservation standpoint, it could also help predict where and when apiaries might pose a threat to native bee populations and help guide apiary placement in sensitive habitats.

The BTI REU panned out to be the opportunity I desired with hands-on research and a glimpse at the efforts and techniques that underlie scientific development. While I was able to gain experience with genomic analysis, bioinformatics, and genetic techniques, the interpersonal relationships made during my time here are what stood out to me. Throughout this program I have connected with, been supported by, and learned from every member of the Frank Lab. I have been guided to resources within theirs, BTI’s, and CROPPS’ networks which have kindly received me and offered insights on the path ahead of me as an aspiring researcher. As I look back on this experience, I feel tremendous gratitude for the opportunities given to me, the space made for me to feel confident in research, and the relationships I’ve built with faculty, staff, and notably, the other REU students. The BTI REU program has been such a wonderful, educational, and memorable experience. Coming from a university where opportunities for plant science research are limited, it has been very exciting to join a bustling, vibrant plant research community. I am still honing my academic focus, and working in the Mueller Lab, a bioinformatics research group, has been helpful with learning about how computer science and biology intersect. It was also fascinating to observe how an interdisciplinary lab operates and collaborates with other labs at BTI and with partner institutions. Other aspects of the REU program, such as the weekly seminars and science communication workshops, have been very impactful for me in the way that I think about research. I think this research experience has equipped me with skills and perspectives that will be invaluable as I continue on my academic journey. I am so grateful to my mentors, Adrian Powell and Lukas Mueller, as well as Megan Truesdail and Delanie Sickler, for their efforts in coordinating this internship.