A key solution to the devastating effects of viral pathogens is to understand how they gain a foothold in the host cells and against other competing pathogens. The overarching goals of my research program are to:

1. elucidate how +ssRNA plant viruses parasitize the host translation apparatus to synthesize their proteins. Indeed viruses must co-opt host translation apparatus to synthesize their own proteins. Consequently, they have evolved unique strategies to outcompete host mRNAs for these limiting machineries. Many deviates from the canonical cap-dependent translation process by relying on various translation elements. The ability of viral RNA sequences to drive powerful protein expression opens opportunities for biotechnology in this era of plant pharmaceutical farming.
2. dissect how these viruses avoid or subvert host defenses; of specific interest are the various mechanisms of resistance against Potato Virus Y (PVY), which remains a major threat for potato production. The defense strategies include loss or mutation of essential host eukaryotic translation initiation factors eIF4E that can’t longer be physically recruited by PVY, and the strain-specific Ny_tbr gene, popular in commercial varieties of potatoes but only efficient against PVY ^O and not the necrotic strains that are dominating the crop fields.
3. explore how viruses interact with other common pathogens, undermining the ecological role of viruses as potential drivers of evolution of disease epidemics and severity by positively and/or negatively regulating fungal pathogenicity.

• Pl Path/Botany 123 Plants, Parasites, and People
  • Intro Video
• Pl Path/Botany/Entom 505 Plant-Microbe Interactions: Molecular and Ecological Aspects
• ENVIR ST 402/NUT SC 421 Global Field Experience: UW Food systems and Environments in Northern Japan.
• Inter-Ag 175: WISE Seminar
• Inter-Ag 155: First year CALS seminar “Issues in Agriculture, Environment and Life Science”

1. Hussain, S., Ishii, M., Takeshita, J., Rakotondrafara, A. M., Murray, C., Masayuki, T., Kanuka, H., Aiuchi, D. (2026) Behavioral change of Anopheles stephensi (Diptera: Culicidae) by infection of entomopathogenic fungus Beauveria pseudobassiana (Hypocreales: Cordycipitaceae). Applied Entomology and Zoology. https://doi.org/10.1007/s13355-026-00953-z
2. Shu P., Wu C-F, Lawrence A.J., Feng C., Knopke-Mooney O., Kiani Y., Chowdury R., Lasky D., Groves C., Smith D., Marzano, S-Y, Rakotondrafara A.M. (2025) Sclerotinia sclerotiorum growth is suppressed by mycoviral encoded protein-induced hypovirulence.  PLOS Pathogens. https://doi.org/10.1371/journal.ppat.1013813
3. Gutierrez P., Fuller J., Stroschein S., VanDenTop A., Halterman D., Rakotondrafara A.M. (2025). Potato virus Y restricts Alternaria solani growth during co-infection. Molecular Plant Microbe Interactio. DOI: 10.1094/MPMI-03-25-0026-R
4. Stroschein S.M., Grunwald D.J., Rioux R., Rakotondrafara A.M. (2025). Prevalence and severity of Iris severe mosaic virus in Wisconsin iris production. Crop protection. Vol 193. https://doi.org/10.1016/j.cropro.2025.107196
5. Alex B., Zhang Z., Lasky D., Garcia-Ruiz H., Halterman D., Rakotondrafara A.M. (2024). Potato Ny_tbr senses multiple potyviral HCPro effectors through recognition of a single phosphorylatable amino acid residue. Molecular Plant Pathology. 25(11):e70027. doi: 10.1111/mpp.70027.
6. Hussain R., Kanuak, H. Rakotondrafara AM. Tani, M., Aiuchi D (2024) Pathogenicity and sublethal activity of orally administrated entomopathogenic fungi against adult mosquitoes species, Aedes aegypto (Diptera: Cilicidae) and Anopheles stephensi (Diptera: Culicidae). Journal of Invertebrate Pathology 207:108233. doi: 10.1016/j.jip.2024.108233.
7. Jaramillo Mesa H. and Rakotondrafara A.M. (2023). All eggs in one basket: how potyvirus infection is controlled at a single cap-independent translation event. Seminars in Cell and Development Biology. S1084-9521(22)00379-2. doi: 10.1016/j.semcdb.2022.12.011
8. Grunwald D.J., Stroschein S.M., Grinstead S., Mollow D., Rioux R., Rakotondrafara A.M. (2023). Targeting the highly conserved 3’untranslated region of Iris severe mosaic virus for sensitive monitoring of the disease prevalence in iris production. Plant Disease https://doi.org/10.1094/PDIS-04-23-0631-RE
9. Jaramillo Mesa H., Fischer E., Rakotondrafara A.M. (2022) Multiple cis-acting polypyrimidine tract elements regulate a cooperative mechanism for Triticum mosaic virus internal ribosome entry site activity. Frontiers in Plant Science. 13:864832. doi: 10.3389/fpls.2022.864832.
10. Munthali C. Kinoshita R., Onishi K. Rakotondrafara A.M., Mikami K. Koike M. Tani M., Palta J. Aiuchi D. (2022) A Model Nutrition Control System in Potato Tissue Culture and its Influence on Plant Elemental Composition. Plants: 11 , 2718. https://doi.org/10.3390/plants11202718
11. Combest, M., Moroz, N., Tanaka, K., Rogan, C.J., Anderson, JC, Thura, L., Rakotondrafara, A.M. and Goyer, A. (2021), StPIP1, a predicted PAMP-induced peptide in potato, elicits plant defenses and is associated with disease symptom severity in a compatible interaction. Journal of Experimental botany. 72(12):4472-4488.
12. Moyo D., Ishikura S., Rakotondrafara A, Clayton M., Kinoshita R., Tani M.,  Koike M., Aiuchi D. (2021) Behavioral change of Bemisia tabaci (Gennadius) and Trialeurodes vaporariorum (Westwood) (Hemiptera: Aleyrodidae) infected by Lecanicillium muscarium (Hypocreales: Cordycipitaceae). Applied Entomology and Zoology. https://doi.org/10.1007/s13355-021-00738-6
13. Aiuchi D., Moyo D., Ishikura S., Tani M., Kinoshita R., Rakotondrafara A.M., Koike M. (2020) Virulence of Lecanicillium spp. (Hypocreales cordycipitacea) hybrid strains against various biological stages of the greenhouse whitefly, Trialeurodes vaporariorum (Hemiptera: aleyroidae). Biocontrol Science and Technology 30:9, 1006-1017. doi.org/10.1080/09583157.2020.1771281
14. Gutierrez Sanchez P.A., Babujee L., Jaramillo-Mesa J., Gannon M, Halterman D., Jahn M., Jiang J., Rakotondrafara A.M. (2020). The overexpression of a resistant eIF4E allele controls Potato virus Y at the transcriptome level. BCM genomics 2(1):18.doi:10.1186/s12864-019-6423-5
15. Chowdury R., Lasky D., Karki. H., Zhang Z., Goyer A., Haltermann D., and Rakotondrafara A.M. (2020). Suppression of callose deposition contributes to strain-specificity of the Ny mediated resistance against Potato virus Y. Phytopathology 110(1):1640173. doi.org/10.1094/PHYTO-07-19-0229-FI
16. Kraft J., Peterson M., Ki Cho S., Wang Z., Hui A., Rakotondrafara A.M., Miller C., Miller WA. (2019) The 3’ untranslated region of a plant viral RNA directs efficient cap-independent translation in plant and mammalian systems. Pathogens. 8(1). doi: 3390/pathogens8010028.
17. Jaramillo Mesa , Gannon M., Holshbach E., Zhang J., Roberts R., Buettner M., and Rakotondrafara A.M. (2019). Triticum mosaic virus IRES relies on a picornavirus-like YX-AUG motif to designate the preferred translation initiation site and to likely target the 18S rRNA. Journal of Virology. 93 (5):1-18.
18. Babujee L., Witherell R. A., Mikami K., Aiuchi D., Charkowski A.O. and Rakotondrafara A.M. (2019). Optimization of an isothermal recombinase polymerase amplification method for real-time detection of Potato virus Y in potato and single aphids. Journal of Virological Methods 267:16-21.
19. Treder K., Chołuj J, Zacharzewska , Babujee L., Burzyński A., Rakotondrafara A.M. (2018). Magnetic capture reverse transcription loop-mediated amplification assay to detect and differentiate the N and O Potato virus Y serotypes. Archive of Virology 163. 447-458 doi: 10.1007/s00705-017-3635-3.
20. Rakotondrafara A.M., Byamukama E., Plumb T. Roger (2017). Virus Diseases of Cereals. In: eLS. John Wiley & Sons, Ltd: Chichester. DOI: 10.1002/9780470015902.a0000762.pub3
21. Roberts, L. K. Mayberry, K. S. Browning, A.M. Rakotondrafara (2017). Triticum mosaic virus IRES preferentially binds eIF4G over eIFiso4G with distinct usage in translation. PLOS one. 12(1):e0169602. doi: 10.1371/journal.pone.0169602.
22. Roberts, J. Zhang, N. Mihelich, D. Savino, A.M. Rakotondrafara (2017). Manipulation of oat protoplasts for transient expression assays. Methods in Molecular Biology. Ed. Springer. in “Oats: methods and protocols”. Vol. 1536: Oat, 978-1-4939-6680-6, 334999_1_En, (5)
23. Roberts, Z. Zhang, L. Mayberry,T. Satyanarayana, K. Browning, and A. M. Rakotondrafara. An atypical plant viral translation element found in Triticum mosaic virus (2015) Journal of Virology (89 (24)-12427-12440.).
24. Zhang, R. Roberts, and A. M. Rakotondrafara. The role of the 5’ untranslated region of Potyviridae in translation (2015) Virus research 206:74-81
25. Arcibal, K. Morey Gold, S. Flaherty, J. Jiang, M. Jahn, and A. M. Rakotondrafara. (2015) A mutant eIF4E confers resistance to Potato virus Y strains and is inherited in a dominant manner in the potato varieties Atlantic and Russet Norkotah. American journal of Potato Research. 10.1007/s12230-015-9489-x
26. Smirnova; A.E. Firth; D. Scheidecker; V. Brault; C. Reinbold; A. M. Rakotondrafara; B.Y.-W. Chung; W. A. Miller and V. Ziegler-Graff. (2015) A small non-AUG-initiated ORF in poleroviruses and luteoviruses is required for long-distance movement. PLOS Pathogens 11(5):e1004868
27. M. Rakotondrafara and M.W. Hentze, MW. (2011). An efficient factor-depleted mammalian in vitro translation system. Nature Protocols. 6(5):563-71.
28. V. Pisarev, M.A. Skabkin, V.P. Pisareva, O.V. Skabkina, A.M. Rakotondrafara, M.W. Hentze, C.T. Hellen and T.V. Pestova (2010). The role of ABCE1 in eukaryotic post-termination ribosomal recycling. Molecular Cell. 37:196-210.
29. M. Rakotondrafara and W. Allen Miller (2008). In vitro analysis of translational enhancers. in Methods in Molecular Biology: Plant Virology Protocols Vol: II, Humana Press 451:113-124.
30. M. Rakotondrafara, Jacquelyn Jackson, Elizabeth Pettit Kneller and W. Allen Miller (2007). Preparation of oat protoplasts for electroporation. Current Protocols of Microbiology. 16D.3.1-16D.3.12. John Wiley & Sons Inc.
31. M. Rakotondrafara, C. Polacek, E. Harris and W.A. Miller (2006). Oscillating kissing stem-loop interactions mediate 5’ scanning-dependent translation by a viral 3’ cap-independent translation element. RNA, 12:1893-1906.
32. Shen*, A.M. Rakotondrafara* and W.A. Miller (2006). Trans-regulation of translation by a viral subgenomic RNA. Journal of Virology 80:10045-10054.
33. E. Pettit Kneller, A.M. Rakotondrafara and W. Allen Miller (2006). Cap-independent translation of plant viral RNAs. Virus Research, 119, 63-75.