Senior Research Associate
After completing my degrees at the Universities of Liverpool and Birmingham I left the UK in 1995 in search of good food and warm weather. Since then my work has taken me to Madrid (Spain), Santiago (Chile), Heidelberg (Germany) and Venice (Italy) on topics related to a range plant pathogens affecting a variety cultivated crops both at fundamental and applied levels. My primary research interests focus mainly on virus discovery, molecular diagnostics, virus RNA structure and function, virus evolution and nanobiotechnology. I also have established experience in transgenics, biosafety, microscopy, virus movement, and bioinformatics. I’ve been here at Cornell since 2010.
I have five current research activities, all related to studying viruses:
Diagnostics - improvements in the sensitivity, breadth and user-friendliness of molecular marker detection using established and novel techniques such as: LAMP, HTS, RPA, Arrays, qPCR, RCA, etc.
As detection methods become more sensitive, our ability to identify and monitor viruses in the environment becomes ever more refined allowing us to better implement pre-emptive measures to control the outbreak of a disease. In deciding which diagnostic technique to use there is often a trade-off between high-sensitivity and breadth on the one hand and cost and speed of detection on the other. Deciding which method to use and when is part of the challenge.
Virus Discovery - molecular and biological characterization of novel viruses.
Once a novel virus (or part of it) has been identified we can view its nucleic acids or proteins either as simple biomarkers for detection, or we can begin studying the biology of the virus in order to better understand how it is able to infect (and sometimes damage) its host. This can involve obtaining the nucleic acid information of one virus isolate or multiple isolates to get an impression of the genetic variation within the population or using a range of laboratory techniques to shed light on the mechanisms of virus infection.
Evolution - understanding the processes and mechanisms involved virus adaptation both experimentally and computationally.
Once we have compiled a snapshot of the genetic variation within a virus population, we can use multiple computational tools to test broader global hypotheses using sequential data from public databases. This process is reiterative, allowing us to test and retest microevolutionary ideas in vivo. RNA viruses, in particular, are excellent models to explore the adaptability of genetic material.
RNA structure - determining the structure and role of viral genomic RNA in the infection process.
RNA is a multifunctional biological molecule. RNA viruses have to use it both to encode their genome and as a messenger RNA. Evolutionary constraints on genome size mean that these viruses use their RNA for multiple functions - a “code within a code”. Our interest centers on understanding the structural component of viral RNA and how it functions to interact and co-opt host factors into replicating its own genetic material.
Nanotechnology - exploiting the plasticity of virus encapsidation in the development of viral nanoparticles.
Viruses have evolved over millions of years to produce the “perfect” biological capsule. We exploit this property into developing nano virus-like particles (devoid of genetic material) for use in imaging and drug-delivery systems.
Outreach and Extension Focus
Before Cornell, I was regularly involved in outreach activities with the general public, special interest groups, growers and schools on the subject of biotechnology and biosafety (Veneto, Italy).
At Cornell, my interest in outreach is focused on exploring the link between farming communities across continents and how academia can be used as a hub to facilitate interactions and the exchange of ideas between these communities.
I have a bit of a soft-spot for a "learning-by-doing" approach to teaching. My aim is to guide students to better understand how molecular biological theory and practice are connected and how they can be applied both in the long- and short-term to solve real-world problems.
PLSCI-4300-4301-4302 - Molecular Diagnostics.
A five-credit practical and theoretical course on molecular diagnostic techniques employed today by researchers and the critical role they play in monitoring and controlling the spread of disease. Includes a two-week winterbreak field trip to the vineyards of Chile.
This course has three integrated components:
PLSCI 4300 - Applications in Molecular Diagnostics (Fall)
PLSCI 4301 - Surveying for Disease in Chilean Vineyards (Winter)
PLSCI 4302 - Molecular Diagnostics: From Lab to Viñedo (Spring)
All students either take, in parallel to PLSCI 4300, a Spanish language course (1 credit) for beginners (SPAN 1501) or intermediate to advanced levels (SPAN 3020).
BIOG-2990: Introduction to Research Methods in Biology (1-4 credits)
PLSCI-2990: Introduction to Research Methods in Plant Science (1-4 credits)
BIOG-4990: Independent Undergraduate Research in Biology (1-4 credits)
PLSCI-4990: Independent Undergraduate Research in Biology (1-4 credits)
I also participate in PLPPM 3010: Biology and Management of Plant Diseases, by presenting on the Virology and Diagnostics Lab component.
Presently, I supervise the research of visiting scientists, post-docs, graduate and undergraduate students.
- Romero, J. L., Carver, G. D., Johnson, P. A., Perry, K. L., & Thompson, J. R. (2019). A rapid, sensitive and inexpensive method for detection of grapevine red blotch virus without tissue extraction using loop-mediated isothermal amplification. Archives of Virology. 1--5.
- Matic, S., Noris, E., Contin, R., Marian, D., & Thompson, J. R. (2019). Engineering partial resistance to cucumber mosaic virus in tobacco using intrabodies specific for the viral polymerase. Phytochemistry. 162:99-108.
- Vargas-Asencio, J., Liou, H., Perry, K. L., & Thompson, J. R. (2019). Evidence for the splicing of grablovirus transcripts reveals a putative novel open reading frame. Journal of General Virology.
- Verosloff, M., Chappell, J., Perry, K. L., Thompson, J. R., & Lucks, J. B. (2019). PLANT-Dx: A Molecular Diagnostic for Point-of-Use Detection of Plant Pathogens. ACS Synthetic Biology.
- Cieniewicz, E. J., Thompson, J. R., McLane, H., Perry, K. L., Dangl, G., Corbett, Q., Martinson, T., Wise, A., Wallis, A. E., O'Connell, J., & others, (2018). Prevalence and genetic diversity of grabloviruses in free-living Vitis spp. Plant Disease. 102:2308-2316.
- Setiono, F. J., Chatterjee, D., Fuchs, M. F., Perry , K. L., & Thompson, J. R. (2018). The distribution and detection of grapevine red blotch virus in its host depends on time of sampling and tissue type. Plant Disease. 102:2187-2193.
- Webster, C. G., Pichon, E., van Munster, M., Monsion, B., Deshoux, ., Gargani, D., Calevro, F., Jimenez, J., Moreno, A., Krenz, B., Thompson, J. R., Perry , K. L., Fereres, A., Blanc, S., & Uzest, M. (2018). Identification of plant virus receptor candidates in the stylets of their aphid vectors. Journal of Virology. 92:e00432-18.
- Watters, K. E., Choudhary, K., Aviran, S., Lucks, J. B., Perry, K. L., & Thompson, J. R. (2018). Probing of RNA structures in a positive sense RNA virus reveals selection pressures for structural elements. Nucleic Acids Research. 46:2573-2584.
- Perry, K. L., McLane, H., Thompson, J. R., & Fuchs, M. F. (2017). A novel grablovirus from non-cultivated grapevine (Vitis sp.) in North America. Archives of Virology. 163:259-262.
- Thompson, J. R., Dasgupta, I., Fuchs, M., Iwanami, T., Karasev, A. V., Petrzik, K., Sanfacon, H., Tzanetakis, I., van der Vlugt, R., Wetzel, T., & Yoshikawa, N. (2017). ICTV Virus Taxonomy Profile: Secoviridae. Journal of General Virology. 98:529-531.
Presentations and Activities
- Los virus de la vid y cómo encontrarlos: refinamientos a su detección y caracterización. September 2019. Institute of Grapevine and Wine Sciences. Logroño, Spain.
- El reto para los diagnósticos moleculares de vid frente a las cada vez mayores sensibilidades. January 2019. Concha Y Toro. Talca, Chile.
- Of viruses and vices. From a familiar generalist to an emerging specialist. September 2018. International Centre for Genetic Engineering and Biotechnology. Trieste, Italy.
- Using a Cross-Curricular Approach in a Molecular Diagnostics Course to Reach a Broader Student Audience. International Congress of Plant Pathology (ICPP) 2018: Plant Health in A Global Economy. July 2018. International Congress of Plant Pathology (ICPP). Boston, MA United States .
- Biological and chemical probing of RNA structures in a positive sense RNA virus. RNAs in All Shapes, Sizes and Forms: Markers and Regulators of Health and Disease, Cornell Weill Medicine Symposium. December 2017. Weill Cornell Medicine, Cornell University. Ithaca, NY.