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.
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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
- 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), pp. 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) Integrated proteomics and transcriptomics analyses reveal the transcriptional slippage of P3N-PIPO in a bymovirus., Viruses, 13, 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, 1036-1051.
- MacFarlane, S. A. (2021) Tobraviruses (Virgaviridae), In: Bamfor, D. H. & Zuckerman, M. (eds) Encyclopedia of Virology, 4th Edition. USA: Academic Press, 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, Article No. 197837.
- O'Callaghan, F.E.; Neilson, R.; MacFarlane, S.A.; Dupuy, L.X. (2020) Dynamic biospeckle analysis, a new tool for the fast screening of plant nematicide selectivity., Plant Methods, 15, Article No. 155.
- 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.
- 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, 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, Chapter 4, pp41-61.
- 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.
- 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.; Andreev, D.E.; Taliansky, M.E.; MacFarlane, S.E.; Solovyev, A.G.; Morozov, S.Y. (2013) Single amino acid substitution in the tobacco mosaic virus ORF6 protein suppresses formation of complex with eEF1A and cooperative nucleic acids binding in vitro., Doklady Biochemistry and Biophysics, 448, 1-4.
- 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.
- Yu, C.L.; Karlin, D.G.; Lu, Y.W.; Wright, K.; Chen, J.P.; MacFarlane, S. (2013) Experimental and bioinformatic evidence that raspberry leaf blotch emaravirus P4 is a movement protein of the 30K superfamily., Journal of General Virology, 94, 2117-2128.
- Martin, R.R.; MacFarlane, S.; Sabanadzovic, S.; Quito, D.; Poudel, B.; Tzanetakis, I.E. (2013) Viruses and virus diseases of Rubus., Plant Disease, 97, 168-182.
- McGavin, W.J.; Mitchell, C.; Cock, P.J.A.; Wright, K.M.; MacFarlane, S.A. (2012) Raspberry leaf blotch virus, a putative new member of the genus Emaravirus, encodes a novel genomic RNA., Journal of General Virology, 93, 430-437.
- McMenemy, L.S.; Hartley, S.E.; MacFarlane, S.A.; Karley, A.J.; Shepherd, T.; Johnson, S.N. (2012) Raspberry viruses manipulate the behaviour of their insect vectors., Entomologia Experimentalis et Applicata, 144, 56-68.
- Ashfaq, M.; McGavin, W.J.; MacFarlane, S.A. (2011) RNA2 of TRV SYM breaks the rules for tobravirus genome structure., Virus Research, 160, 435-438.
- Dolan, A.; MacFarlane, S.A.; McGavin, W.J.; Brennan, R.M.; McNicol, J.W. (2011) Blackcurrant reversion virus: validation of an improved diagnostic test, accelerating testing in breeding and certification of blackcurrants., Journal of Berry Research, 1, 201-208.
- 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), pp. 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) Integrated proteomics and transcriptomics analyses reveal the transcriptional slippage of P3N-PIPO in a bymovirus., Viruses, 13, 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, 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, Article No. 197837.
- O'Callaghan, F.E.; Neilson, R.; MacFarlane, S.A.; Dupuy, L.X. (2020) Dynamic biospeckle analysis, a new tool for the fast screening of plant nematicide selectivity., Plant Methods, 15, Article No. 155.
- 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.
- 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, 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.; Andreev, D.E.; Taliansky, M.E.; MacFarlane, S.E.; Solovyev, A.G.; Morozov, S.Y. (2013) Single amino acid substitution in the tobacco mosaic virus ORF6 protein suppresses formation of complex with eEF1A and cooperative nucleic acids binding in vitro., Doklady Biochemistry and Biophysics, 448, 1-4.
- 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.
- Yu, C.L.; Karlin, D.G.; Lu, Y.W.; Wright, K.; Chen, J.P.; MacFarlane, S. (2013) Experimental and bioinformatic evidence that raspberry leaf blotch emaravirus P4 is a movement protein of the 30K superfamily., Journal of General Virology, 94, 2117-2128.
- Martin, R.R.; MacFarlane, S.; Sabanadzovic, S.; Quito, D.; Poudel, B.; Tzanetakis, I.E. (2013) Viruses and virus diseases of Rubus., Plant Disease, 97, 168-182.
- McGavin, W.J.; Mitchell, C.; Cock, P.J.A.; Wright, K.M.; MacFarlane, S.A. (2012) Raspberry leaf blotch virus, a putative new member of the genus Emaravirus, encodes a novel genomic RNA., Journal of General Virology, 93, 430-437.
- McMenemy, L.S.; Hartley, S.E.; MacFarlane, S.A.; Karley, A.J.; Shepherd, T.; Johnson, S.N. (2012) Raspberry viruses manipulate the behaviour of their insect vectors., Entomologia Experimentalis et Applicata, 144, 56-68.
- Ashfaq, M.; McGavin, W.J.; MacFarlane, S.A. (2011) RNA2 of TRV SYM breaks the rules for tobravirus genome structure., Virus Research, 160, 435-438.
- Dolan, A.; MacFarlane, S.A.; McGavin, W.J.; Brennan, R.M.; McNicol, J.W. (2011) Blackcurrant reversion virus: validation of an improved diagnostic test, accelerating testing in breeding and certification of blackcurrants., Journal of Berry Research, 1, 201-208.
- McGavin, W.J.; Cock, P.J.A.; MacFarlane, S.A. (2011) Partial sequence and RT-PCR diagnostic test for the plant rhabdovirus Raspberry vein chlorosis virus., Plant Pathology, 60, 462-467.
- McGavin, W.J. ; McMenemy, L.S.; MacFarlane, S.A. (2010) The complete sequence of a UK strain of Black raspberry necrosis virus., Archives of Virology, 155, 1897-1899.
- MacFarlane, S.A. (2010) Tobraviruses - plant pathogens and tools for biotechnology (Review)., Molecular Plant Pathology, 11, 577-583.
- McGavin, W.J.; MacFarlane, S.A. (2010) Sequence similarities between Raspberry leaf mottle virus, Raspberry leaf spot virus and the closterovirus Raspberry mottle virus., Annals of Applied Biology, 156, 439-448.
- MacFarlane, S.A.; McGavin, W.J. (2009) Genome activation by Raspberry bushy dwarf virus coat protein., Journal of General Virology, 90, 747-753.
- 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, 4th Edition. USA: Academic Press, 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, Chapter 4, pp41-61.
- 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.