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SILVEC BIOLOGICS, Inc. is a company founded by Anne Simon and Rafael Simon to develop RNA and peptide therapeutics delivered by viruses for treatment of diseases of trees, vines, grasses and other plants. 

WELCOME TO THE SIMON LAB

We study a recently discovered collection of plant viruses called umbra-like viruses (ULVs).  ULVs are unique in encoding a polymerase and can encode a coat protein, but unlike all other plant viruses, most do not encode movement proteins.  Instead, they use host PHLOEM PROTEIN 2 (PP2) as their movement protein. We study their unique movement properties, their astonishing viral transcriptome in which full-length virus sequesters in roots, and their highly unusual -1 ribosomal frameshifting with 6 local and long distance tertiary interactions, two of which unzip a stable hairpin structure and allow for ribosome passage.  In addition, infection of some ULVs cause secondary infections by bacterial and fungal pathogens to accumulate at 10- to 100s of fold higher levels. We also work on virus-induced silencing (VIGS) vectors, which are known to poorly maintain inserted sequences.  We have found that plus-strand viruses in general have substructures with distinctive thermodynamic properties, and that sequences inserted into virus vectors are maintained and not deleted  if they share the same thermodynamic properties. We are working to develop an app that will convert hairpins or longer sequences into virus-like susbstructures that will be maintained in the virus for extended times.

Check out RNAcanvas for interactive drawing and exploration of nucleic acid structures            SITE          PUBLICATION

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  • Congratulations to Philip Johnson (PhD 2024) Senior Scientist, Silvec

  • Congratulations to Postdoc Chanyong Jang Senior Scientist, Silvec

  • Congratulations to Postdoc Sayata Bera Research Associate University of Maryland

  • Congratulations to Postdoc Mohammed Ilyas Research Scientist USDA-Beltsville

  • Congratulations to Postdoc Roberto Toscano-Morales Professor, Instituto Tecnologico de Campeche

  • Congratulations to Postdoc Elizabeth Carino   Scientific Manager, Simplot Plant Sciences

  • Congratulations to Postdoc Jared May Assistant Professor, University of Missouri Kansas City

  • Congratulations to  My-Tra Le  (PhD 2016)  Research Associate Indiana University

  • Congratulations to Micki Kuhlmann (PhD 2016) Director of Operations, Silvec, Inc.

  • Congratulations to Maitreyi Chattopadhyay (PhD 2015) Biologist, FDA

  • Congratulations to Megan Young (PhD 2015)  Expert Consultant at DRT Strategies, Inc.

  • Congratulations to Xuefeng Yuan (Postdoc 2007-2012)   Professor, Shandong Agricultural University

  • Congratulations to Kerong Shi (Postdoc 2008-2010)   Professor, Shandong Agricultural University

  • Congratulations to Rong Guo (PhD 2011)  Biologist/Device Reviewer, FDA

  • Congratulations to Xiaoping Sun.  (PhD 2006)  Professor, Wuhan University (sadly deceased)

  • Congratulations to Fengli Zhang (PhD 2007)  Senior Microbiologist, Wisconsin State Laboratory of Hygiene

  • Congratulations to Jiuchun Zhang (PhD 2006)   Director, Initiative for Genome Editing and Neurodegeneration, Harvard University

  • Congratulations to Hancheng Guan  (PhD 1999) Research Associate Professor, University of Pennsylvania

  • Congratulations to Jianlong Wang  (PhD 1999)  Professor of Medical Sciences,  Columbia University

  • Congratulations to Peter Nagy  Postdoc (1997-1999)   Professor,  University of Kentucky

  • Congratulations to Jong-Won Oh  (PhD 1997)  Professor of Biotechnology, Yonsei University

  • Congratulations to Qingzhong Kong  (PhD 1997)  Associate Professor Case Western University

  • Congratulations to Xiaohua Li (PhD 1992) Senior Scientist, Wugen​ Biotechnology Company

  • Congratulations to Pamela Cascone Ball (PhD 1992) Patent investigator, Jwip & Patent Services, LLC

Jang, C., Needham, J.M., Johnson, P.Z., Gao, F., and Simon, A.E. 2025. Hairpin inserts in viral genomes are stable when they conform to the thermodynamic properties of viral RNA substructures. J Virol In press.

 

McCann, H, Meade, C.D., Williams, L.D., Petrov, A.S., Johnson, P.Z., Simon, A.E., Hoksza, E. P., Nawrocki, D., Chan, P.P., Lowe, T.M., Ribas, C.B., Sweeney, B.A., Madeira, F., Anyango, S., Appasamy, S.D., Deshpande, M., Varadi, M., Velankar, S., Zirbel, C.L., Naiden, A., Jossinet, F., Petrov, A.I. 2025.  R2DT: A comprehensive platform for visualizing RNA secondary structure.  Nucleic Acids Res  53. https://doi.org/10.1093/nar/gkaf032

 

Simon, A.E., Makinen, K., and Verchot, J.M. 2025. Chapter 81: Plant Viruses. In: Field’s Virology, 8th Edition. Eds David M. Knipe, Peter M. Howley. Wolters Kluwer Health/Lippincott Williams & Wilkins, Philadelphia, USA. (In press)

 

Johnson, P.Z., Needham, J.M., Lim, N.K., and Simon, A.E. 2024. Direct nanopore RNA sequencing of umbra-like virus-infected plants reveals long non-coding RNAs, specific cleavage sites, D-RNAs, foldback RNAs, and temporal- and tissue-specific profiles. Nucleic Acids Res Genomics Bioinform 6 https://doi.org/10.1093/nargab/lqae104

 

Ying, X., Bera, S., Liu, J., Toscano-Morales, R., Jang, C., Yang, S., Ho, J., and Simon, A.E.  2024. Umbravirus-like RNA viruses are capable of independent systemic plant infection in the absence of encoded movement proteins.  PLoS Biol 22:e3002600. https://doi.org/10.1371/journal.pbio.3002600

 

PLoS Biology commissioned a Primer on the article and Nature Reviews Microbiology covered the article in their News and Comments section “highlighting exciting advances” 

 

Simon, A.E., Quito-Avila, D.F., and Bera, S. 2024.  Expanding the plant virome: umbra-like viruses use host proteins for movement. Annu Rev Virol  doi: 10.1146/annurev-virology-111821-122718.

 

Mikkelsen, A.A., Gao, F., Carino, E., Simon, A.E.S. -1 Programmed ribosomal frameshifting in Class 2 umbravirus-like RNAs uses multiple long-distance interactions to shift between active and inactive structures and destabilize the frameshift stimulating element.  Nucleic Acids Res gkad744 doi.org/10.1093/nar/gkad744.

 

Uhl, S., Jang, C., Frere, J., Jorday, T., Simon, A.E., and tenOever, B.  2023.  ADAR1 biology can hinder effective antiviral RNA interference.  J Virol 97(4):e0024523

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Johnson, P.Z. and Simon, A.E. 2023.  RNAcanvas: interactive drawing and exploration of nucleic acid structures.  Nucleic Acids Res gkad302.

 

Bera, S., Ilyas, M., Mikklesen, A.A., and Simon, A.E.  2023.  Conserved structure associated with different 3’CITEs is important for translation of umbraviruses.  Viruses 15: 638.  doi: 10.3390/v15030638

 

Simon, Anne E., Mäkinen, K., Li, Y., and Verchot, J.  (2022) Plant Viruses.  In:  Field’s Virology, 7th edition. Ed. Peter Hawley. Lippincott Williams & Wilkins, Publishers.

 

Johnson, P.Z., Reuning, H.M., Bera, S., Gao, F., Du, Z., and Simon. A.E. (2022) Novel 3´ proximal replication elements in umbravirus genomes. Viruses 14, 2615 doi.org/10.3390/v14122615 [Journal cover selection]

 

Reyes-Proaño, E.G.,  Mendoza, A., Margaria, P., Menzel, W., Bera, S., Simon, A.E., Quito-Avila, D.F. 2022.  Two new umbravirus-like associated RNAs (ulaRNAs) discovered in maize and Johnsongrass from Ecuador. Arch Virol 167, 2093-2098 doi: 10.1007/s00705-022-05525-4

 

Liu, J., and Simon, A.E.  2022.  Identification of Novel 5ʹ and 3ʹ Translation Enhancers in Umbravirus-like Coat-Protein-Dependent RNA Replicons.  J Virol 96, e0173621   doi: 10.1128/jvi.01736-21.

 

Johnson, P., Kasprzak, W.K., Shapiro, B.A., and Simon, A.E. 2022.  Structural characterization of a new class of PTE 3’ cap independent translation enhancers.  Nucleic Acids Res 50, 1601-1619.

 

Wang, X.,  Olmedo-Velarde, A., Larrea-Sarmiento, A.,  Simon, A.E., Kong, A., Borth, W.,  Suzuki, J.Y.,  Wall, M.M., Hu, J., and Mellzer, M.  2021. Genome characterization of fig umbra-like virus.  Virus Genes 57, 566–570 doi.org/10.1007/s11262-021-01867-4

 

Kwon, S-J, Bodaghi, S, Gadhave, KR, Tzanetakis, IE, Simon, AE, and Vidalakis, G. 2021. Complete nucleotide sequence, genome organization and comparative genomic analyses of citrus yellow-vein associated virus, an umbravirus-like associated virus-like RNA.  Front Microbiol, in press.

 

Liu, J., Carino, E., Bera, S., Gao, F., May, J.P., and Simon, A.E. 2021. Structural analysis and whole genome mapping of a new class of plant virus subviral RNAs:  umbravirus-Like associated RNAs. Viruses 13, 646; https://doi.org/10.3390/v13040646.

 

May, J.P. and Simon, A.E. 2021. Targeting of viral RNAs by Upf1-mediated RNA decay pathways.  Curr Opin Virol 47, 1-8.

 

Ilyas, M, Du, Z. and Simon, A.E. 2021.  Opium poppy mosaic virus has an Xrn-resistant, translated subgenomic RNA and a BTE 3’ CITE.  J Virol  95 (9): e02109-20 DOI: 10.1128/JVI.02109-20 [SPOTLIGHT selection]

 

May, J.P., Johnson, P.Z., Ilyas, M., Gao, F., and Simon, A.E. 2020. Disruption of nonsense-mediated decay by the multifunctional long-distance movement protein of Pea enation mosaic virus 2.  Mbio 11:e00204-20. https://doi.org/10.1128/mBio

 

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