Stuart MacFarlane
Current research interests
- Plant viruses are widespread in the natural environment and exhibit enormous variation in their structure and composition. Agricultural crops are under constant attack from viruses making an understanding of virus biology a necessity for devising new, more effective approaches to prevent virus disease in plants.
-
Current work includes a range of studies of viruses of raspberry, an important crop in Scotland in terms of both economics and nutritional health. Viruses are a major cause of disease in raspberry and other woody perennial crops and over time their disease impact increases as the plants become infected with mixtures of different viruses. We have characterised a number of viruses that are known to exist in the UK raspberry crop but are not well understood, (Black raspberry necrosis virus (BRNV), Raspberry leaf mottle virus (RLMV) and Raspberry vein chlorosis virus (RVCV)), to develop molecular diagnostics to be used in The James Hutton Institute High Health Certification Scheme. We also have generated an infectious clone system to aid research into Raspberry bushy dwarf virus (RBDV), a virus of great importance to the raspberry industry because of its involvement in crumbly fruit disease.
Recently we discovered a new, negative-strand RNA virus that is transmitted by eriophyid mites and is responsible for the emerging problem of leaf blotch disorder in many raspberry plantations. This new virus, Raspberry leaf blotch virus (RLBV), belongs to a newly identified group of plant viruses that cause disease in a wide variety of important crops. The molecular structure of these plant viruses shows that they are related to an important group of human and animal-infecting viruses, the bunyaviruses, and further study of RLBV may reveal parallels between the infection processes of these different viruses.
- New work has been started to study the resistance reactions of different potato cultivars to aphid-transmitted viruses, such as PVY, and to the nematode-transmitted virus, TRV, which causes spraing in potato tubers.
Past research
- In recent years I have researched the mechanism of action of the P19 protein of Tomato bushy stunt virus (TBSV). This is a pathogenicity protein that has a role in suppression of RNA silencing, symptom production in plants, and long- and short-distance movement of the virus within the plant. We have discovered an interaction between P19 and members of the ALY family of plant proteins.
- Other aspects of my research have included fundamental studies, primarily on Tobacco rattle virus (TRV), an important pathogen of potatoes in Scotland, Europe and North America, and Pea early-browning virus (PEBV), to understand the mechanism of transmission of these viruses by nematodes, a process that is central to the diseases they cause in the field.
- More recently it has been realised that plant viruses can be developed into tools that have great potential for functional genomic analysis of plants. I have engineered TRV, and the related viruses PEBV and Pepper ringspot virus (PepRSV), to be useful as vectors for gene expression and gene silencing in a variety of plant species.
Bibliography
- Spechenkova, N.; Samarskaya, V; Kalinina, N.; Zavriev, S.; MacFarlane, S.; Love, A.; Taliansky, M. (2023) Plant Poly(ADP-Ribose) Polymerase 1 Is a Potential Mediator of Cross-Talk between the Cajal Body Protein Coilin and Salicylic Acid-Mediated Antiviral Defence, Viruses, 15(6), Art. 1282
- Incarbone, M.; Bradamante, G.; Wegschneider, T.; Rozhon, W.; Nguyen, V.; Gutzat, R.; Mérai, Z.; Lendl, T.; MacFarlane, S.; Nodine, M.; Mittelsten Scheid, O. (2023) Salicylic acid and RNA interference mediate antiviral immunity of plant stem cells, Proceedings of the National Academy of Sciences USA, 120(42), Art. E2302069120
- Cowan, G.; MacFarlane, S.; Torrance, L. (2023) A new simple and effective method for PLRV infection to screen for virus resistance in potato, Journal of Virological Methods, 315, Art. 114691
- Wang, Y.; Durairaj, J.; G. Suárez Duran, H.; van Velzen, R.; Liao, C.; Flokova, K.; Chojnacka, A.; MacFarlane, S.; Eric Schranz, M.; H. Medema, M.; van Dijk, A.; Dong, L.; Bouwmeester, H.J. (2022) The tomato cytochrome P450 CYP712G1 catalyses the double oxidation of orobanchol en route to the rhizosphere signalling strigolactone, solanacol, New Phytologist, 235(5), 1884-1899
- Miao, R.; Ye, Z.; MacFarlane, S.; Li, Y.; Mao, Q.; Tian, Y.; Deng, Z.; Sun, Z.; Yang, J.; Li, J.; Yan, F.; Chen, J.; Yu, C. (2022) The P3N-PIPO Protein Encoded by Wheat Yellow Mosaic Virus Is a Pathogenicity Determinant and Promotes Its Pathogenicity through Interaction with NbRLK6 in Nicotiana benthamiana, Viruses, 14(10), Art. 2171
- Yu, C.; Miao, R.; Ye, Z.; MacFarlane, S.; Lu, Y.; Li, J.; Yang, J.; Yan, F.; Dai, L.; Chen, J. (2021) Transcriptional Slippage of a Bymovirus P3N-PIPO Gene Expressed from a PVX Vector in Nicotiana benthamiana, Viruses, 13(7), Article No. 1247
- Jiang, L.L.; Lu, Y.W.; Zheng, X.Y.; Yang, X.; Chen, Y.; Zhang, T.H.; Zhao, X.; Wang, S.; Zhao, X.; Song, X.J.; Zhang, X.X.; Peng, J.J.; Zheng, H.Y.; Lin, L.; MacFarlane, S.; Liu, Y.L.; Chen, J.P.; Yan, F. (2021) The plant protein NbP3IP directs degradation of Rice stripe virus p3 silencing suppressor protein to limit virus infection through interaction with the autophagy-related protein NbATG8., New Phytologist, 229(2), 1036-1051
- MacFarlane, S.A. (2021) Tobraviruses (Virgaviridae), In: Bamfor, D.H. & Zuckerman, M. (eds.). Encyclopedia of Virology, Volume 3. Cambridge, MA: Academic Press, 4th ed., pp 743-748.
- Yang, X.; Tian, Y.; Zhao, X.: Jiang, L.; Chen, Y.; Hu, S.; MacFarlane, S.; Chen, J.; Lu, Y.; Yan, F. (2020) NbALY916 is involved in Potato virus X P25-triggered cell death in Nicotiana benthamiana., Molecular Plant Pathology, 21, 1495-1501.
- Jones, S.; Cowan, G.; MacFarlane, S.; Mukoye, B.; Mangeri, B.C.; Were, H.; Torrance, L. (2020) RNA sequence analysis of diseased groundnut (Arachis hypogaea) reveals the full genome of groundnut rosette assistor virus (GRAV), Virus Research, 277, art.197837
- Torrance, L.; Cowan, G.H.; McLean, K.; MacFarlane, S.; Al-Abedy, A.N.; Armstrong, M.; Lim, T.Y.; Hein, I.; Bryan, G.J. (2020) Natural resistance to potato virus Y in solanum tuberosum group Phureja., Theoretical and Applied Genetics, 133, 967-980.
- Yang, X.; Lu, Y.W.; Wang, F.; Chen, Y.; Tian, Y.Z.; Jiang, L.L.; Pemg, J.J.; Zheng, H.Y.; Lin, L.; Yan, C.Q.; Taliansky, M.; MacFarlane, S.; Wu, Y.H.; Chen, J.P.; Yan, F. (2020) Involvement of the chloroplast gene ferredoxin 1 in multiple responses of Nicotiana benthamiana to Potato virus X infection., Journal of Experimental Botany, 71, 2142-2156.
- O'Callaghan, F.E.; Neilson, R.; MacFarlane, S.A.; Dupuy, L.X. (2019) Dynamic biospeckle analysis, a new tool for the fast screening of plant nematicide selectivity., Plant Methods, 15, Article No. 155.
- Shaw, J.; Yu, C.L.; Makhotenko, A.V.; Makarova, S.S.; Love, A.J.; Kalinina, N.O.; MacFarlane, S.; Chen, J.P.; Taliansky, M.E. (2019) Interaction of a plant virus protein with the signature Cajal body protein coilin facilitates salicylic acid-mediated plant defence responses., New Phytologist, 224, 439-453.
- Jones, S.; McGavin, W.; MacFarlane, S (2019) The complete sequences of two divergent variants of the rhabdovirus raspberry vein chlorosis virus and the design of improved primers for virus detection, Virus Research, 265, 162-165
- Baizan-Edge, A.; Cock, P.; MacFarlane, S.; McGavin, W.; Torrance, L.; Jones, S. (2019) Kodoja: A workflow for virus detection in plants using k-mer analysis of RNA-sequencing data, Journal of General Virology, 100(3), 533-542
- Zhang, T.; Zhao, X.; Jiang, L.; Yang, X.; Chen, Y.; Song, X.; Lu, Y.; Peng, J.; Zheng, H.; Wu, Y.; MacFarlane, S.; Chen, J.; Yan, F. (2018) p15 encoded by Garlic virus X is a pathogenicity factor and RNA silencing suppressor., Journal of General Virology, 99, 1515-1521.
- O'Callaghan, F.E.; Braga, R.A.; Neilson, R.; MacFarlane, S.A.; Dupuy, L.X. (2018) New live screening of plant-nematode interactions in the rhizosphere., Scientific Reports, 8, Article No. 1440.
- Karley, A.J.; Graham, J.; Mitchell, C.; Williams, C.; Mitchell, D.; Jennings, N.; Dolan, A.; McFarlane, S.; Prashar, A.; Begg, G.; Birch, A.N.E. (2018) IPM tools for pest and disease management in raspberry plantations., Crop Protection in Northern Britain 2018: The Dundee Conference, Environmental Management and Crop Production, Apex City Quay Hotel, Dundee, 27-28 February 2018. Conference Proceedings, pp55-58.
- Dolan, A.; MacFarlane, S.; Jennings, S.N. (2018) Pathogens in raspberry and other Rubus spp, In: Graham, J. & Brennan, R. (eds.) Raspberry: Breeding, Challenges and Advances. Springer International Publishing, Cham, 41-61.
- Adams, M.J.; Adkins, S.; Bragard, C.; Gilmer, D.; Li, D.W.; MacFarlane, S.A.; Wong, S.M.; Melcher, U.; Ratti, C.; Ryu, K.H. (2017) ICTV Virus taxonomy profile: Virgaviridae., Journal of General Virology, 98, 1999-2000.
- He, Y.; Zhang, H.; Sun, Z.; Li, J.; Hong, G.; Zhu, Q.; Zhou, X.; MacFarlane, S.; Yan, F.; Chen, J. (2017) Jasmonic acid-mediated defense suppresses brassinosteroid-mediated susceptibility to Rice black streaked dwarf virus infection in rice., New Phytologist, 214, 388-399.
- Jones, S.; Baizan-Edge, A.; MacFarlane, S.; Torrance, L. (2017) Viral diagnostics in plants using next generation sequencing: computational analysis in practice., Frontiers in Plant Science, 8, Article No. 1770.
- Sahi, G.; Hedley, P.P.; Morris, J.; Loake, G.J.; MacFarlane, S.A. (2016) Molecular and biochemical examination of spraing disease in potato tuber in response to Tobacco rattle virus infection., Molecular Plant-Microbe Interactions (MPMI), 29, 822-828.
- Lu, Y.W.; Yin, M.Y.; Wang, X.D.; Chen, B.H.; Yang, X.; Peng, J.J.; Zheng, H.Y.; Zhao, J.P.; Lin, L.; Yu, C.L.; MacFarlane, S.; He, J.Q.; Liu, Y.; Chen, J.P.; Dai, L.Y.; Yan, F. (2016) The unfolded protein response and programmed cell death are induced by expression of garlic virus X p11 in Nicotiana benthamiana., Journal of General Virology, 97, 1462-1468.
- McGavin, W.; MacFarlane, S.A. (2016) The complete nucleotide sequence of Pelargonium leaf curl virus., Archives of Virology, 161, 1415-1417.
- Hunter, L.J.R.; Brockington, S.F.; Murphy, A.M.; Pate, A.E.; Gruden, K.; MacFarlane, S.A.; Palukaitis, P.; Carr, J.P. (2016) RNA-dependent RNA polymerase 1 in potato (Solanum tuberosum) and its relationship to other plant RNA-dependent RNA polymerases., Scientific Reports, 6, Article No. 23082.
- MacFarlane, S.A.; Zasada, I.A.; Lemaire, O.; Demangeat, G. (2016) Nematode-borne plant viruses., In: Brown, J.K. (ed.). Vector-Mediated Transmission of Plant Pathogens. American Phytopathological Society Press, St. Paul, MN., 365-378.
- Lu, Y.W.; McGavin, W.; Cock, P.J.A.; Schnettler, E.; Yan, F.; Chen, J.P.; MacFarlane, S.A. (2015) Newly identified RNAs of raspberry leaf blotch virus encoding a related group of proteins., Journal of General Virology, 96, 3432-3439.
- MacFarlane, S.; McGavin, W.; Tzanetakis, I. (2015) Virus-testing by PCR and RT-PCR amplification in berry fruit., In: Lacomme, C. (ed.). Plant Pathology: Techniques and Protocols. (Methods in Molecular Biology, 1302) Springer, New York, 227-248.
- Spechenkova, N.; Samarskaya, V; Kalinina, N.; Zavriev, S.; MacFarlane, S.; Love, A.; Taliansky, M. (2023) Plant Poly(ADP-Ribose) Polymerase 1 Is a Potential Mediator of Cross-Talk between the Cajal Body Protein Coilin and Salicylic Acid-Mediated Antiviral Defence, Viruses, 15(6), Art. 1282
- Incarbone, M.; Bradamante, G.; Wegschneider, T.; Rozhon, W.; Nguyen, V.; Gutzat, R.; Mérai, Z.; Lendl, T.; MacFarlane, S.; Nodine, M.; Mittelsten Scheid, O. (2023) Salicylic acid and RNA interference mediate antiviral immunity of plant stem cells, Proceedings of the National Academy of Sciences USA, 120(42), Art. E2302069120
- Cowan, G.; MacFarlane, S.; Torrance, L. (2023) A new simple and effective method for PLRV infection to screen for virus resistance in potato, Journal of Virological Methods, 315, Art. 114691
- Wang, Y.; Durairaj, J.; G. Suárez Duran, H.; van Velzen, R.; Liao, C.; Flokova, K.; Chojnacka, A.; MacFarlane, S.; Eric Schranz, M.; H. Medema, M.; van Dijk, A.; Dong, L.; Bouwmeester, H.J. (2022) The tomato cytochrome P450 CYP712G1 catalyses the double oxidation of orobanchol en route to the rhizosphere signalling strigolactone, solanacol, New Phytologist, 235(5), 1884-1899
- Miao, R.; Ye, Z.; MacFarlane, S.; Li, Y.; Mao, Q.; Tian, Y.; Deng, Z.; Sun, Z.; Yang, J.; Li, J.; Yan, F.; Chen, J.; Yu, C. (2022) The P3N-PIPO Protein Encoded by Wheat Yellow Mosaic Virus Is a Pathogenicity Determinant and Promotes Its Pathogenicity through Interaction with NbRLK6 in Nicotiana benthamiana, Viruses, 14(10), Art. 2171
- Yu, C.; Miao, R.; Ye, Z.; MacFarlane, S.; Lu, Y.; Li, J.; Yang, J.; Yan, F.; Dai, L.; Chen, J. (2021) Transcriptional Slippage of a Bymovirus P3N-PIPO Gene Expressed from a PVX Vector in Nicotiana benthamiana, Viruses, 13(7), Article No. 1247
- Jiang, L.L.; Lu, Y.W.; Zheng, X.Y.; Yang, X.; Chen, Y.; Zhang, T.H.; Zhao, X.; Wang, S.; Zhao, X.; Song, X.J.; Zhang, X.X.; Peng, J.J.; Zheng, H.Y.; Lin, L.; MacFarlane, S.; Liu, Y.L.; Chen, J.P.; Yan, F. (2021) The plant protein NbP3IP directs degradation of Rice stripe virus p3 silencing suppressor protein to limit virus infection through interaction with the autophagy-related protein NbATG8., New Phytologist, 229(2), 1036-1051
- Yang, X.; Tian, Y.; Zhao, X.: Jiang, L.; Chen, Y.; Hu, S.; MacFarlane, S.; Chen, J.; Lu, Y.; Yan, F. (2020) NbALY916 is involved in Potato virus X P25-triggered cell death in Nicotiana benthamiana., Molecular Plant Pathology, 21, 1495-1501.
- Jones, S.; Cowan, G.; MacFarlane, S.; Mukoye, B.; Mangeri, B.C.; Were, H.; Torrance, L. (2020) RNA sequence analysis of diseased groundnut (Arachis hypogaea) reveals the full genome of groundnut rosette assistor virus (GRAV), Virus Research, 277, art.197837
- Torrance, L.; Cowan, G.H.; McLean, K.; MacFarlane, S.; Al-Abedy, A.N.; Armstrong, M.; Lim, T.Y.; Hein, I.; Bryan, G.J. (2020) Natural resistance to potato virus Y in solanum tuberosum group Phureja., Theoretical and Applied Genetics, 133, 967-980.
- Yang, X.; Lu, Y.W.; Wang, F.; Chen, Y.; Tian, Y.Z.; Jiang, L.L.; Pemg, J.J.; Zheng, H.Y.; Lin, L.; Yan, C.Q.; Taliansky, M.; MacFarlane, S.; Wu, Y.H.; Chen, J.P.; Yan, F. (2020) Involvement of the chloroplast gene ferredoxin 1 in multiple responses of Nicotiana benthamiana to Potato virus X infection., Journal of Experimental Botany, 71, 2142-2156.
- O'Callaghan, F.E.; Neilson, R.; MacFarlane, S.A.; Dupuy, L.X. (2019) Dynamic biospeckle analysis, a new tool for the fast screening of plant nematicide selectivity., Plant Methods, 15, Article No. 155.
- Shaw, J.; Yu, C.L.; Makhotenko, A.V.; Makarova, S.S.; Love, A.J.; Kalinina, N.O.; MacFarlane, S.; Chen, J.P.; Taliansky, M.E. (2019) Interaction of a plant virus protein with the signature Cajal body protein coilin facilitates salicylic acid-mediated plant defence responses., New Phytologist, 224, 439-453.
- Jones, S.; McGavin, W.; MacFarlane, S (2019) The complete sequences of two divergent variants of the rhabdovirus raspberry vein chlorosis virus and the design of improved primers for virus detection, Virus Research, 265, 162-165
- Baizan-Edge, A.; Cock, P.; MacFarlane, S.; McGavin, W.; Torrance, L.; Jones, S. (2019) Kodoja: A workflow for virus detection in plants using k-mer analysis of RNA-sequencing data, Journal of General Virology, 100(3), 533-542
- Zhang, T.; Zhao, X.; Jiang, L.; Yang, X.; Chen, Y.; Song, X.; Lu, Y.; Peng, J.; Zheng, H.; Wu, Y.; MacFarlane, S.; Chen, J.; Yan, F. (2018) p15 encoded by Garlic virus X is a pathogenicity factor and RNA silencing suppressor., Journal of General Virology, 99, 1515-1521.
- O'Callaghan, F.E.; Braga, R.A.; Neilson, R.; MacFarlane, S.A.; Dupuy, L.X. (2018) New live screening of plant-nematode interactions in the rhizosphere., Scientific Reports, 8, Article No. 1440.
- Adams, M.J.; Adkins, S.; Bragard, C.; Gilmer, D.; Li, D.W.; MacFarlane, S.A.; Wong, S.M.; Melcher, U.; Ratti, C.; Ryu, K.H. (2017) ICTV Virus taxonomy profile: Virgaviridae., Journal of General Virology, 98, 1999-2000.
- He, Y.; Zhang, H.; Sun, Z.; Li, J.; Hong, G.; Zhu, Q.; Zhou, X.; MacFarlane, S.; Yan, F.; Chen, J. (2017) Jasmonic acid-mediated defense suppresses brassinosteroid-mediated susceptibility to Rice black streaked dwarf virus infection in rice., New Phytologist, 214, 388-399.
- Jones, S.; Baizan-Edge, A.; MacFarlane, S.; Torrance, L. (2017) Viral diagnostics in plants using next generation sequencing: computational analysis in practice., Frontiers in Plant Science, 8, Article No. 1770.
- Sahi, G.; Hedley, P.P.; Morris, J.; Loake, G.J.; MacFarlane, S.A. (2016) Molecular and biochemical examination of spraing disease in potato tuber in response to Tobacco rattle virus infection., Molecular Plant-Microbe Interactions (MPMI), 29, 822-828.
- Lu, Y.W.; Yin, M.Y.; Wang, X.D.; Chen, B.H.; Yang, X.; Peng, J.J.; Zheng, H.Y.; Zhao, J.P.; Lin, L.; Yu, C.L.; MacFarlane, S.; He, J.Q.; Liu, Y.; Chen, J.P.; Dai, L.Y.; Yan, F. (2016) The unfolded protein response and programmed cell death are induced by expression of garlic virus X p11 in Nicotiana benthamiana., Journal of General Virology, 97, 1462-1468.
- McGavin, W.; MacFarlane, S.A. (2016) The complete nucleotide sequence of Pelargonium leaf curl virus., Archives of Virology, 161, 1415-1417.
- Hunter, L.J.R.; Brockington, S.F.; Murphy, A.M.; Pate, A.E.; Gruden, K.; MacFarlane, S.A.; Palukaitis, P.; Carr, J.P. (2016) RNA-dependent RNA polymerase 1 in potato (Solanum tuberosum) and its relationship to other plant RNA-dependent RNA polymerases., Scientific Reports, 6, Article No. 23082.
- Lu, Y.W.; McGavin, W.; Cock, P.J.A.; Schnettler, E.; Yan, F.; Chen, J.P.; MacFarlane, S.A. (2015) Newly identified RNAs of raspberry leaf blotch virus encoding a related group of proteins., Journal of General Virology, 96, 3432-3439.
- Scott, S.W.; MacFarlane, S.A.; McGavin, W.J.; Fargette, D. (2014) Cassava Ivorian bacilliform virus is a member of the genus Anulavirus., Archives of Virology, 159, 2791-2793.
- Gushchin,V.A.; Andreev, D.E.; Taliansky, M.; MacFarlane, S.A.; Solovyev, A.G.; Morozov, S.Y. (2013) Replacement of amino acid in the ORF6 protein of tobacco mosaic virus prevents the formation of a complex with eEF1A and the cooperative binding to nucleic acids in vitro., Proceedings of the Russian Academy of Sciences, 448, 1-5.
- Bragard, C.; Caciagli, P.; Lemaire, O.; Lopez-Moya, J.J.; MacFarlane, S.; Peters, D.; Susi, P.; Torrance, L. (2013) Status and prospects of plant virus control through interference with vector transmission., Annual Review of Phytopathology, 51, 177-201.
- Hunter, L.J.R.; Westwood, J.H.; Heath, G.; Macaulay, K.; Smith, A.G.; MacFarlane, S.A.; Palukaitis, P.; Carr, J.P. (2013) Regulation of RNA-dependent RNA polymerase 1 and isochorismate synthase gene expression in arabidopsis., PLoS ONE, 8, Article No. e66530.
- Gushchin, V.A.; Lukhovitskaya, N.I.; Andreev, D.E.; Wright, K.M.; Taliansky, M.E.; Solovyev, A.G.; Morozov, S.; MacFarlane, S.A. (2013) Dynamic localization of two tobamovirus ORF6 proteins involves distinct organellar compartments., Journal of General Virology, 94, 230-240.
- Torrance, L.; Cowan, G.H.; McLean, K.; MacFarlane, S.; Al-Abedy, A.N.; Armstrong, M.; Lim, T.Y.; Hein, I.; Bryan, G.J. (2020) Natural resistance to potato virus Y in solanum tuberosum group Phureja., Theoretical and Applied Genetics, 133, 967-980.
- MacFarlane, S.A. (2021) Tobraviruses (Virgaviridae), In: Bamfor, D.H. & Zuckerman, M. (eds.). Encyclopedia of Virology, Volume 3. Cambridge, MA: Academic Press, 4th ed., pp 743-748.
- Dolan, A.; MacFarlane, S.; Jennings, S.N. (2018) Pathogens in raspberry and other Rubus spp, In: Graham, J. & Brennan, R. (eds.) Raspberry: Breeding, Challenges and Advances. Springer International Publishing, Cham, 41-61.
- MacFarlane, S.A.; Zasada, I.A.; Lemaire, O.; Demangeat, G. (2016) Nematode-borne plant viruses., In: Brown, J.K. (ed.). Vector-Mediated Transmission of Plant Pathogens. American Phytopathological Society Press, St. Paul, MN., 365-378.
- MacFarlane, S.; McGavin, W.; Tzanetakis, I. (2015) Virus-testing by PCR and RT-PCR amplification in berry fruit., In: Lacomme, C. (ed.). Plant Pathology: Techniques and Protocols. (Methods in Molecular Biology, 1302) Springer, New York, 227-248.
- MacFarlane, S.A. (2009) Rubus viruses: Blackberry chlorotic ringspot virus (BCRV)., American Phytopathological Society, Minesota, USA, Volume 2.
- MacFarlane, S.A.; Neilson, R. (2009) Testing of transmission of Tobraviruses by nematodes., In: Coico, R., Kowalik, T., Quarles, J.M., Stevenson, B. & Taylor, R.K. (eds.). Current Protocols in Microbiology. John Wiley & Sons, Inc., Chichester, UK, Chapter Suppl 12, 16B.5.1-16B.5.16.
- MacFarlane, S.A. (2008) Tobravirus., In: Mahy, W.J. & Van Regenmortel, M.H.V. (eds.). Encyclopedia of Virology. 3rd edition. Elsevier, Oxford, Chapter 5, 72-76.
- Uhrig, J.F.; MacFarlane, S.A. (2008) Protein-protein interactions in plant virus movement and pathogenicity., In: Nautiyal, C.S. & Dion, P. (eds.). Molecular Mechanisms of Plant and Microbe Coexistence. Springer, Dordrecht, Chapter 15, 319-338.
- MacFarlane, S.A.; Uhrig, J.F. (2008) Yeast two-hybrid assay to identify host-virus interactions., In: Foster, G.D., Johansen, I.E., Hong, Y. & Nagy, P.D. (eds.). Plant Virology Protocols: From viral sequence to protein function. 2nd edition. Humana Press, Totowa, New Jersey, Chapter 44, pp649-672.
- Palukaitis, P.; MacFarlane, S.A. (2006) Viral counter-defense molecules., In: Loebenstein, G. & Carr, J.P. (eds.). Natural Resistance Mechanisms of Plants to Viruses. Springer, Berlin, pp165-185.
- MacFarlane, S.A.; Neilson, R.; Brown, D.J.F. (2002) Nematodes., In: Plumb, R.T. (ed.). Advances in Botanical Research - Plant Virus Vector Interactions. Academic Press, 36, 169-198.
- MacFarlane, S.A.; Neilson, R.; Brown, D.J.F. (2002) Plant Virus Vector Interactions., In: Plumb, R.T. (eds.). Advances in Botanical Research No 36 - Interctions Between Plant Viruses and Their Vectors. Academic Press, London and New York, pp169-198.
- MacFarlane, S.A. (1997) Natural recombination among plant virus genomes: evidence from tobraviruses., In: Mayo, M.A. (ed.). Aspects of ssRNA Virus Genome Organization. Academic Press, pp25-31.
- Dolan, A.; MacFarlane, S.A.; Pitkin, Y.; McGavin, W.J. (2011) Validation of an improved diagnostic test to accelerate the certification of blackcurrant (Ribes nigrum L.) plants for breeding and propagation., Annual Report of the Scottish Crop Research Institute for 2010, pp28-29.
- MacFarlane, S.A.; McGavin, W.J.; Dolan, A. (2008) Discovering new viruses in raspberry crops., Annual Report of the Scottish Crop Research Institute for 2007, pp28-29.
- Kim, S.; Ryabov, E.V.; Gillespie, T.; MacFarlane, S.A.; Haupt, S.; Brown, J.W.S.; Taliansky, M.E. (2007) Nuclear voyage of a plant virus protein., Annual Report of the Scottish Crop Research Institute for 2006, pp22-23.
- Reavy, B.; MacFarlane, S.A. (2001) Cross-kingdom activity of plant virus-encoded silencing suppressors., Annual Report of the Scottish Crop Research Institute for 2000/2001, pp120-123.
- MacFarlane, S.A.; Brown, DJ.F.; Vassilakos, N.; Mooney, A.; Schmitt, C.; Mueller, A.; Prior, D.A.M.; Oparka, K.J. (1998) Molecular biology of the tobravirus genome., Annual Report of the Scottish Crop Research Institute for 1997/98, pp129-131.
- Karley, A.J.; Graham, J.; Mitchell, C.; Williams, C.; Mitchell, D.; Jennings, N.; Dolan, A.; McFarlane, S.; Prashar, A.; Begg, G.; Birch, A.N.E. (2018) IPM tools for pest and disease management in raspberry plantations., Crop Protection in Northern Britain 2018: The Dundee Conference, Environmental Management and Crop Production, Apex City Quay Hotel, Dundee, 27-28 February 2018. Conference Proceedings, pp55-58.
- Taliansky, M.E.; Shaw, J.; Kim, S.; Ryabov, E.; Kalinina, N.O.; MacFarlane, S.A.; Brown, J.W.S. (2011) Involvement of the cell nucleus in plant virus systemic infections., Society for General Microbiology Spring Conference, Harrogate, 11-14 April 2011. Session: Seeing the cell through the Eyes of the Virus.
- McMenemy, L.S.; MacFarlane, S.A.; Hartley, S.E.; Johnson, S.N. (2009) Co-operation between plant enemies - do raspberry viruses attract more aphid vectors., 8th International Symposium on Aphids, Catania, Italy, 8-12 June 2009.
- McMenemy, L.S.; MacFarlane, S.A.; Hartley, S.E.; Johnson, S.E. (2009) Plant mediated interactions with the large raspberry aphid., Ento'09 National Meeting of the Royal Entomological Society, University of Sheffield, 15-17 July 2009.
- McMenemy, L.S.; Johnson, S.N.; Hartley, S.E.; MacFarlane, S.A. (2008) Cooperation between plant enemies - do raspberry viruses attract more aphid vectors?., British Ecological Society Annual Meeting 2008, Imperial College, London, 3-5 September 2008.
- Kim, S.; MacFarlane, S.A.; Kalinina, N.; Rakitina, D.V.; Ryabov, E.; Gillespie, T.; Haupt, S.; Brown, J.W.S.; Taliansky, M.E. (2007) Interaction between a plant virus-encoded protein and the major nucleolar protein fibrillarin, is required for virus systemic infection., AAB Advances in Virology, University of Greenwich, 11-12 September 2007.
- Taliansky, M.E.; Kim, S.; Ryabov, E.V.; Kalinina, N.; Rakitina, D.V.; Gillespie, T.; MacFarlane, S.A.; Brown, J.W.S. (2006) Involvement of the nucleolus in plant virus systemic infection., EMBO Workshop 'The Nucleolus: New Perspectives'. York, 27-30 March 2006.
- Kim, S.; Ryabov, E.V.; MacFarlane, S.A.; Kalinina, N.O.; Rakitina, D.V.; Gillespie, T.; Brown, J.W.S.; Taliansky, M.E. (2006) Involvement of the nulceolus in Umbravirus long-distance movement., Plasmodesmata 2006, Pitlochry, 30 July - 3 August 2006.
- MacFarlane, S.A.; Robinson, D.J. (2004) Transmission of plant viruses by nematodes., In: Gillespie, S., Smith, G.L. & Osbourn, A. (eds.). SGM Symposium 63, Microbe-Vector Interactions in Vector-Borne Diseases. Cambridge University Press, pp263-285.
- Palukaitis, P.; Canto, T.; MacFarlane, S.A. (2004) Further characterization of the TMV4.8 kDa protein., Abstracts of the 23rd Annual Meeting of the American Society for Virology, Montreal, Quebec, Canada, 10-14 July 2004.
- Birch, P.R.J.; Blok, V.C.; Phillips, M.; Jones, J.T.; Stewart, H.E.; Duncan, J.M.; Bryan, G.J.; Waugh, R.; Lyon, G.D.; MacFarlane, S.A.; Avrova, A.O.; Whisson, S.C.; Toth, I.K. (2003) Current and future research at SCRI on the molecular genetics of the interactions between potato and its major pathogens., Acta Horticulturae, 619, 95-119.
- Palukaitis, P.; Canto, T.; MacFarlane, S.A. (2003) Pathogenicity and localization of the tobacco mosaic virus 4,8 kDa protein., Proceedings of the Korean Society of Plant Pathology, Annual Regular Meeting and Special Scientific Presentations, Dunnae, Korea, 9-11 October 2003.
- Karanastasi, E.; Roberts, I.M.; MacFarlane, S.A.; Brown, D.J.F. (1999) The location of specifically retained tobacco rattle virus particles in the oesophageal tract of the vector., Proceedings of the Zoological Institute, Russian Academy of Sciences,St Petersburg, Russia, 280, 107-108.
- Karanastasi, E.; Roberts, I.M.; MacFarlane, S.A.; Brown, D.J.F. (1998) Staining with safranin: a new approach to handling nematodes., Proceedings of the 21st Congresso Brasileiro de Nematologia, Maringa, Brazil, 55-56.
- O'Callaghan, F.; Dupuy, L.; Neilson, R.; MacFarlane, S. (2015) 3D imaging of root-nematode interactions: transparent soil for visualizing host-pathogen processes., Potato Council Meeting on Biofumigation, Harper Adams University, 9 September 2015.
- MacFarlane, S.; Cowan, G.; Al-Abedy, A.; McLean, K.; Bryan, G.; Torrance, L. (2013) A new source of resistance in potato to Potato virus Y., EMBO Plant Virology Workshop, Green Virsuses, from Gene to Landscape, Hyeres-les-Palmiers, France, 7-11 September 2013.
- Hein, I.; Gilroy, E.; Hornyik, C.; Bryan, G.; Milne, I.; Toth, I.K.; Ducreux, L.; Torrance, L.; Milne, L.; Cock, P.; Pritchard, L.; Sharma, K.; MacFarlane, S.; Zhang, R.; Hedley, P.; Jones, J.; Birch, P.; Taylor, M.; Dale, F.; McNaughton, I.; Wright, J.; Prashar, A.; Blok, V.; Carnegie, P.; Chapman, S. (2013) Utilising the potato genome., Potatoes in Practice 2013, Balruddery Farm, Invergowrie, Dundee, 8 August 2013.
- Torrance, L.; Cowan, G.; McLean, K.; Al Abedy, A.; Macfarlane, S.; Bryan, G. (2012) Novel broad spectrum resistance to potato potyviruses Y, V and A., Proceedings Crop Protection in Northern Britain, Dundee, 28-29 February, 2012.
- Torrance, L.; Cowan, G.; Mclean, K.; Al-Abedy, A.; MacFarlane, S.; Bryan, G. (2012) Novel broad-spectrum resistance to potato potyviruses., Phytopathology, 102, 120.
- Taliansky, M.; Shaw, J.; Kim, S.H.; Ryabov, E.; Kalinina, N.; MacFarlane, S.; Brown, J.W.S. (2011) The nucleolus and plant virus infections., The XV International Congress of Virology, Sapporo, Japan, 6-16 September 2011.
- MacFarlane, S.; McGavin, W.; Cock, P.J.A.; Mitchell, C.A. (2011) Raspberry leaf and bud mite spreads a newly discovered virus to raspberry crops., East Malling Research/HDC Soft Fruit Day, East Malling, Kent, 23 November 2011.
- Taliansky, M.; Shaw, J.; Kim, S.H.; Ryabov, E.; Kalinina, N.; MacFarlane, S.; Brown, J.W.S. (2011) Role of Cajal bodies in plant virus infections., First International SFB 796 Symposium, Mechanisms of Viral Host Cell Manipulation - From Plants to Humans, Bamberg, Germany 2-4 October 2011.
- MacFarlane, S.; McGavin, W.; Cock, P.J.A.; Mitchell, C. (2011) Identification of raspberry leaf blotch virus (RLBV), a new virus associated with the raspberry leaf and bud mite (Phyllocoptes gracilis) and leaf blotch disorder., 10th International Rubus and Ribes Meeting, Zlatibor, Serbia, 22-26 June 2011.
- Kim, S.; MacFarlane, S.A.; Kalinina, N.O.; Rakitina, D.V.; Ryabov, E.V.; Gillespie, T.; Haupt, S.; Brown, J.W.S.; Taliansky, M.E. (2007) Cajal bodies, the nucleolus and fibrillarin are required for a plant virus systemic infection., 20th Wilhelm Bernhard Workshop, International Conference on the Cell Nucleus. St Andrews, 27-31 August 2007, 19.
- Kim, S.; MacFarlane, S.A.; Kalinina, N.O.; Rakitina, D.V.; Ryabov, E.V.; Gillespie, T.; Haupt, S.; Brown, J.W.S.; Taliansky, M.E.; (2007) Cajal bodies, the nucleolus and fibrillarin are required for a plant virus systemic infection., 6th Symposium on Post-Transcriptional Regulation of Plant Gene Expression, Carry-le-Rouet, France, 10-13 May 2007, 22 (Abstract).
- Taliansky, M.E.; Kim, S.; Ryabov, E.V.; Kalinina, N.; Rakitina, D.V.; Gillespie, T.; MacFarlane, S.A.; Brown, J.W.S. (2006) Involvement of the nucleolus and Cajal bodies in plant virus systemic infection., EMBO workshop on Plant Virology: Suppression and Circumvention of Host Defence by Plant Viruses, Haikko, Finland, 1-5 July 2006, 25.
- Vassilakos, N.; Brown, D.J.F.; MacFarlane, S.A. (2000) Studies of vector transmissibility of tobraviruses using transgenic plants expressing the viral RNA2 non-structural transmission proteins., Abstracts of the XIth International Congress of Virology, Sydney, Australia, 249.
- MacFarlane, S.A.; Brown, E.C. (2000) Is recovery from infection by TRV the result of gene silencing?, Abstracts of the ASV Meeting, Fort Collins, Colorado, 21-25 July 2000, 180.
- MacFarlane, S.A. (2000) The 16K cysteine-rich protein of Tobacco rattle virus PpK20 is required for virus multiplication., Abstracts of the XIth International Congress of Virology, Sydney, Australia, 301.
- Boutsika, K.; Sadowska-Rybak, M.; Blok, V.C.; Phillips, M.S.; MacFarlane, S.A.; Heinze, C.; Willingmann, P.; Petz, C.; Adam, G.; Brown, D.J.F. (2000) PCR molecular diagnostics for virus-vector trichodorid nematodes and their associated tobacco rattle virus., Association of Applied Biologists, Advances in Plant Virology, Dundee, 20-22 September 2000 (Abstract).
- Boutsika, K.; Wendt, K.R.; Blok, V.C.; MacFarlane, S.A.; Brown, D.J.F. (1999) Molecular detection of trichodorid nematodes and tobacco rattle tobravirus., Proceedings of the Zoological Institute, Russian Academy of Sciences, St Petersburg, Russia, 105-106 (Abstract).
- Vellios, E.K.; MacFarlane, S.A.; Brown, D.J.F. (1999) Electron microscopy study of the distribution and particle morphology of pea early-browning tobravirus in plant roots., Abstract of the Association of Applied Biologists Meeting, York.
- Boutsika, K.; Wendt, K.R.; Blok, V.C.; MacFarlane, S.A.; Brown, D.J.F. (1999) Molecular relationships of trichodorid nematode vectors and tobacco rattle tobravirus isolates., Proceedings of the Parasitic Helminths from Genomes to Vaccines II. Edinburgh (Abstract).
- Boutsika, K.; Wendt, K.R.; Blok, V.C.; MacFarlane, S.A.; Brown, DJ.F. (1999) Molecular relationships of Trichodorid nematode vectors and tobacco rattle tobravirus isolates.., AAB Meeting, London (Abstract).