Mark Sabol ’19 experienced firsthand the rigors of a college-level academic setting while still in high school. During his senior year of high school in nearby Seneca County, a science program included trips to observe and engage with researchers at Cornell University’s research laboratories three times a week. Sabol was placed in Cornell’s Adam Bogdanove lab, School of Integrative Plant Science, where he impressed his lab supervisor, Sara Carpenter, with a diligence and understanding of the subject matter belying his academic inexperience.
“Sara contacted me when I enrolled at Cornell, and I officially joined the lab in the fall semester of my freshman year,” Sabol says.
Having spent his childhood in a largely rural region in Upstate New York, Sabol naturally developed a keen interest in farming techniques and applied to Cornell as an agricultural science major. Once here, however, he realized his interests lay more specifically in plant pathology, a related field that puts emphasis on analyzing food crops and devising techniques to increase their resistance to diseases.
“Analyzing the pathogens affecting these food crops helps us determine what mechanisms they’re using and how we can alter this process to protect the crops.”
How Pathogens Invade Crops, Causing Disease
At the Bogdanove lab, Sabol analyzes bacteria leaf streak and bacteria leaf blight, two pathogens that regularly damage rice crops throughout the world. The bacteria secrete specific proteins into plant cells known as transcription activator-like effectors (TALEs). TALEs travel to the plant cell nucleus, bind to specific DNA sequences in the plant genome, and increase the levels of expression of nearby genes. Some of these changes in gene expression make the plant susceptible to further invasion by the bacteria and disease development. Identifying the TALEs' target—the genes that are turned up—and how those genes function will help scientists develop new ways to prevent disease.
The exact sequence of DNA to which a TAL effector binds is determined by a region of the protein known as the central repeat region (CRR), which contains a number of tandem repeats. These repeats are most often composed of 34 amino acids, which form the fundamental building blocks of proteins. The twelfth and thirteenth amino acids in each repeat vary and together determine to which nucleotide—the fundamental constituents of DNA—the repeat binds. TALEs evolve to target different DNA sequences in the plant by exchanging blocks of repeats and by changing the amino acids at positions 12 and 13. This modular mechanism of DNA recognition allows researchers to engineer TALEs to bind new DNA sequences simply by assembling repeats with the necessary amino acids into a custom CRR.
Protecting Rice against Pathogens
Sabol is working on one of the primary methods for improving rice resistance to pathogens, using TALEs. The method entails identifying TALE binding sites in the rice genome and consequently breeding naturally occurring sequence variants at the site. Or it could also mean directly changing the DNA sequence at those sites through genome editing—preventing TALEs from binding and activating the susceptibility genes. Sabol explains that the process involves designing and building custom repeats with different amino acids at positions 12 and 13 and using them to make designer TAL effectors (dTALEs).
These dTALEs are then utilized to provide data for TALE binding site prediction programs. Using these programs, plant pathologists can input the amino acid sequences of TAL effectors found in the bacteria and predict potential binding sites in rice. Once tested and confirmed, these predicted sites can then be modified through breeding or genome editing, and the resulting rice lines can be tested for their ability to better withstand bacterial attack.
Although the process seems straightforward, Sabol adds that new challenges constantly emerge as he progresses with his work. For example, he is researching the effect of neighboring genetic sequences on the preferential binding process.
“I have learnt to appreciate the level of sophisticated technology which I get to handle, in terms of both equipment and the specifics of research, on an everyday basis.”
“In certain cases, we have observed that while there is a 90 percent chance that a bacterial protein will bind with the predicted genetic sequence in the crop cell, it may sometimes bind with an entirely different sequence along the cell’s DNA strand. We know that the neighboring genetic sequences have a decisive impact on this process, and we’re currently evaluating how exactly they affect the binding process.”
The Joy of Using Innovative Technology
Sabol’s favorite part of the research process, he states, is the constant engagement with cutting-edge technology and newer, improved methods of analyzing food crops and genetic engineering. “Whenever I find out about a new process or piece of technology which I can use in the lab, I’m eager to see how I can incorporate it into my work and how it can help me improve my research. As someone who did not experience any significant exposure to scientific research before Cornell, I have learnt to appreciate the level of sophisticated technology which I get to handle, in terms of both equipment and the specifics of research, on an everyday basis.”
Although he had initially planned to pursue graduate school upon completing his undergraduate degree, Sabol says he has re-evaluated his decision and now plans to work at a research facility after his senior year. In the longer term, he aims to found an entrepreneurial venture through which he can make a significant positive impact in the food security sector.
“If food security problems are solved, I’m confident that a lot of other issues arising from them, including food-related conflicts and economic imbalances, can be simultaneously dealt with,” he says.