Published scientific output

Workpackage A: Simple Plant Chassis, Tools and Gene Delivery

Frangedakis F, Guzman-Chavez F, Rebmann M, Markel K, Yu Y, Perraki A, Tse SW, Liu Y, Rever J, Sauret-Gueto S, Goffinet B, Schneider H and Haseloff J (2020). Comparative analysis of early divergent land plants and construction of DNA tools for hyper-expression in Marchantia chloroplasts. BioRxiv 2020.11.27.401802 https://doi.org/10.1101/2020.11.27.401802

Sauret-Güeto S, Frangedakis E, Silvestri L, Rebmann M, Tomaselli M, Markel K, Delmans M, West A, Patron NJ, Haseloff J. (2020). Systematic tools for reprogramming plant gene expression in a simple model, Marchantia polymorpha. ACS Synth. Biol. 9, 4, 864–882 https://doi.org/10.1021/acssynbio.9b00511

Aguilar-Cruz A, Grimanelli D, Haseloff J, Arteaga-Vázquez MA. (2019) DNA methylation in Marchantia. New Phytologist, 223: 575-581

Pollak B, Cerda A, Delmans M, Álamos S, Moyano T, West A, Gutiérrez RA, Patron NJ, Federici F, Haseloff J (2018) Loop Assembly: a simple and open system for recursive fabrication of DNA circuits. New Phytol. 222(1):628-640. doi: 10.1111/nph.15625.

Kahl L, Molloy J, Patron N, Matthewman C, Haseloff J, Grewal D, Johnson R, Endy D. (2018) Opening options for material transfer. Nat Biotechnol. 36(10):923-927. doi: 10.1038/nbt.4263.

Boehm CR, Pollak B, Purswani N, Patron N, and Haseloff J (2017). Synthetic Botany. Cold Spring Harb Perspect Biol. 9(7). pii: a023887. doi: 10.1101/cshperspect.a023887.

Bowman JL, Kohchi T, Yamato KT, Jenkins J, Shu S, Ishizaki K, Yamaoka S, Nishihama R, Nakamura Y, Berger F, Adam C, Aki SS, Althoff F, Araki T, Arteaga-Vazquez MA, Balasubrmanian S, Barry K, Bauer D, Boehm CR, Briginshaw L, Caballero-Perez J, Catarino B, Chen F, Chiyoda S, Chovatia M, Davies KM, Delmans M, Demura T, Dierschke T, Dolan L, Dorantes-Acosta AE, Eklund DM, Florent SN, Flores-Sandoval E, Fujiyama A, Fukuzawa H, Galik B, Grimanelli D, Grimwood J, Grossniklaus U, Hamada T, Haseloff J, Hetherington AJ, Higo A, Hirakawa Y, Hundley HN, Ikeda Y, Inoue K, Inoue SI, Ishida S, Jia Q, Kakita M, Kanazawa T, Kawai Y, Kawashima T, Kennedy M, Kinose K, Kinoshita T, Kohara Y, Koide E, Komatsu K, Kopischke S, Kubo M, Kyozuka J, Lagercrantz U, Lin SS, Lindquist E, Lipzen AM, Lu CW, De Luna E, Martienssen RA, Minamino N, Mizutani M, Mizutani M, Mochizuki N, Monte I, Mosher R, Nagasaki H, Nakagami H, Naramoto S, Nishitani K, Ohtani M, Okamoto T, Okumura M, Phillips J, Pollak B, Reinders A, Rövekamp M, Sano R, Sawa S, Schmid MW, Shirakawa M, Solano R, Spunde A, Suetsugu N, Sugano S, Sugiyama A, Sun R, Suzuki Y, Takenaka M, Takezawa D, Tomogane H, Tsuzuki M, Ueda T, Umeda M, Ward JM, Watanabe Y, Yazaki K, Yokoyama R, Yoshitake Y, Yotsui I, Zachgo S, Schmutz J (2017). Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome. Cell 171(2):287-304.e15. doi: 10.1016/j.cell.2017.09.030

Boehm CR, Ueda M, Nishimura Y, Shikanai T, Haseloff J (2016). A Cyan Fluorescent Reporter Expressed from the Chloroplast Genome of Marchantia polymorpha. Plant Cell Physiol. 57(2):291-9. doi: 10.1093/pcp/pcv160.

Bowman JL, Araki T, Arteaga-Vazquez MA, Berger F, Dolan L, Haseloff J, Ishizaki K, Kyozuka J, Lin SS, Nagasaki H, Nakagami H, Nakajima K, Nakamura Y, OhashiIto K, Sawa S, Shimamura M, Solano R, Tsukaya H, Ueda T, Watanabe Y, Yamato KT, Zachgo S, Kohchi T (2016). The Naming of Names: Guidelines for Gene Nomenclature in Marchantia. Plant Cell Physiol. 57(2):257-61. doi: 10.1093/pcp/pcv193.

Workpackage B: Gene Assembly and Open Registries

Srivastava V, Amanna R, Rowden SJL, Sengupta S, Madhu S, Howe CJ, Wangikar PP (2021) Adaptive laboratory evolution of the fast-growing cyanobacterium Synechococcus elongatus PCC 11801 for improved solvent tolerance. Journal of Bioscience and Bioengineering. doi:10.1016/j.jbiosc.2020.11.012 PMID: 33610455

Grant PK, Szep G, Patange O, Halatek J, Coppard V, Csikász-Nagy A, Haseloff J, Locke JCW, Dalchau N & Phillips A. (2020). Interpretation of morphogen gradients by a synthetic bistable circuit. Nature Communications 11: 5545 https://doi.org/10.1038/s41467-020-19098-w

Dorrell R, Nisbet E, Barbrook A, Rowden S, Howe C. (2019) Integrated genomic and transcriptomic analysis of the peridinin dinoflagellate Amphidinium carterae plastid. Protist 170(4) 358-373 https://doi.org/10.1016/j.protis.2019.06.001

Wey LT, Bombelli P, Chen X, Lawrence JM, Rabideau CM, Rowden SJL, Zhang JZ & Howe CJ. (2019) The Development of Biophotovoltaic Systems for Power Generation and Biological Analysis. ChemElectroChem. 6(21):5375-5386. doi: 10.1002/celc.201900997.

Vasudevan R, Gale GAR, Schiavon AA, Puzorjov A, Malin J, Gillespie MD, Vavitsas K, Zulkower V, Wang B, Howe CJ, Lea-Smith DJ, McCormick AJ. CyanoGate: A Modular Cloning Suite for Engineering Cyanobacteria Based on the Plant MoClo Syntax. Plant Physiol. 2019 May;180(1):39-55. doi: 10.1104/pp.18.01401. Epub 2019 Feb 28.

Martins BMC, Tooke AK, Thomas P, Locke JCW, (2018). Cell size control driven by the circadian clock and environment in cyanobacteria. Proc Natl Acad Sci U S A. 115(48):E11415-E11424. doi: 10.1073/pnas.1811309115.

Kahl L, Molloy J, Patron N, Matthewman C, Haseloff J, Grewal D, Johnson R, Endy D. (2018) Opening options for material transfer. Nat Biotechnol. 36(10):923-927. doi: 10.1038/nbt.4263.

Vazquez-Vilar M, Orzaez D, and Patron, N (2018) DNA Assembly Standards: Setting the Low-Level Programing Code for Plant Biotechnology. Plant Sci. 273:33-41. doi: 10.1016/j.plantsci.2018.02.024.

Rowden S, Bombelli P and Howe C (2018) Design and study of bio-electrochemical system for biotechnological applications and metabolic investigation in Photosynthesis. Methods Mol Biol. 1770:335-346. doi: 10.1007/978-1-4939-7786-4_20.

Bateson P, Fleet JEH, Riseley AS, Janeva E, Marcella AS, Farinea C, Kuptsova M, Conde Pueyo N, Howe CJ, Bombelli P, Parker BM (2018). Electrochemical Characterisation of Bio-Bottle-Voltaic (BBV) Systems Operated with Algae and Built with Recycled Materials. Biology (Basel) 7(2). pii: E26. doi: 10.3390/biology7020026.

Delmans M, Pollak B, and Haseloff J, (2017). MarpoDB: An open registry for Marchantia polymorpha genetic parts. Plant Cell Physiol. 58(1):e5. doi: 10.1093/pcp/pcw201.

Martins BM, Das AK, Antunes L, Locke JC (2016). Frequency doubling in the cyanobacterial circadian clock. Mol Syst Biol. 12(12):896. doi: 10.15252/msb.20167087.

Patron N. (2016). DNA Assembly for Plant Biology. Current Protocols in Plant Biology 1:604-616 https://doi.org/10.1002/cppb.20038

Patron NJ (2016) Synthetic Plants. Synthetic Biology Handbook. Ed: Darren Nesbeth. CRC Press. ISBN 978146656847

Patron NJ (2016). Blueprints for Green Biotechnology: Development and Application of Standards for Plant Synthetic Biology. Biochem Soc Trans. 44(3):702-8. doi: 10.1042/BST20160044.

Patron NJ (2016). Synthetic Biology and Gene Cloning. Encyclopedia of Applied Plant Sciences 2nd Edition. Editor-in-Chiefs: Brian Thomas Denis and J Murphy Brian G Murray. Academic Press. eBook ISBN: 9780123948083 Hardcover ISBN: 9780123948076

Patron NJ, Orzaez D, Marillonnet S, Warzecha H, Matthewman C, Youles M, Raitskin O, Leveau A, Farré G, Rogers C, Smith A, Hibberd J, Webb AA, Locke J, Schornack S, Ajioka J, Baulcombe DC, Zipfel C, Kamoun S, Jones JD, Kuhn H, Robatzek S, Van Esse HP, Sanders D, Oldroyd G, Martin C, Field R, O'Connor S, Fox S, Wulff B, Miller B, Breakspear A, Radhakrishnan G, Delaux PM, Loqué D, Granell A, Tissier A, Shih P, Brutnell TP, Quick WP, Rischer H, Fraser PD, Aharoni A, Raines C, South PF, Ané JM, Hamberger BR, Langdale J, Stougaard J, Bouwmeester H, Udvardi M, Murray JA, Ntoukakis V, Schäfer P, Denby K, Edwards KJ, Osbourn A, Haseloff J. (2015). Standards for plant synthetic biology: a common syntax for exchange of DNA parts. New Phytologist 208(1):13-9. doi: 10.1111/nph.13532.

Rutten V, Munabi A, Riche F, Lewy G, Wilson H, Pipan M, Bhate S, Nghiem T-A, Kaufhold W, Haseloff J, Rubert A, González A, Quijano A, Llopis I, Gavaldá J, Estellés L, Vásquez M, Orzáez D, Deal C, Gray J, Spiegel M, Monsey S, Middlemiss A, Day J, Patron NJ (2015) A Standard Type IIS Syntax for Plants. RFC #106 (http://hdl.handle.net/1721.1/96069)

Workpackage C: New mechanisms for regulation of gene expression

Mehrshahi P., Nguyen G.T.D.T., Gorchs Rovira A., Sayer A., Llavero-Pasquina M., Huei Sin M.L., Medcalf E.J., Mendoza-Ochoa G.I., Scaife M.A., and Smith A.G. (2020) Development of Novel Riboswitches for Synthetic Biology in the Green Alga Chlamydomonas. ACS Synth. Biol. 9 (6) 1406–1417. doi: 10.1021/acssynbio.0c00082

Andriotis VME, Smith AM (2019) The plastidial pentose phosphate pathway is essential for postglobular embryo development in Arabidopsis. PNAS 116 (30) 15297-15306; DOI: 10.1073/pnas.1908556116

Rovira, A.G. and Smith, A.G. (2019), PPR proteins – orchestrators of organelle RNA metabolism. Physiol Plantarum 166: 451-459. https://doi.org/10.1111/ppl.12950

Chung, B.Y.-W., Valli, A., Deery, M.J., Navarro, F.J., Brown, K., Hnatova, S., Howard, J., Molnar, A., and Baulcombe, D.C. (2019). Distinct roles of Argonaute in the green alga Chlamydomonas reveal evolutionary conserved mode of miRNA-mediated gene expression. Sci. Rep. 9: 1–12. doi: 10.1038/s41598-019-47415-x

Navarro FJ and Baulcombe D. (2019) miRNA-mediated regulation of synthetic gene circuits in the green alga Chlamydomonas reinhardtii. ACS Synth Biol. 8(2):358-370. doi: 10.1021/acssynbio.8b00393.

Crozet P, Navarro FJ, Willmund F, Mehrshahi P, Bakowski K, Lauersen KJ, Pérez-Pérez ME, Auroy P, Gorchs Rovira A, Sauret-Gueto S, Niemeyer J, Spaniol B, Theis J, Trösch R, Westrich LD, Vavitsas K, Baier T, Hübner W, de Carpentier F, Cassarini M, Danon A, Henri J, Marchand CH, de Mia M, Sarkissian K, Baulcombe DC, Peltier G, Crespo JL, Kruse O, Jensen PE, Schroda M, Smith AG, Lemaire SD (2018) Birth of a Photosynthetic Chassis: A MoClo Toolkit Enabling Synthetic Biology in the Microalga Chlamydomonas reinhardtii. ACS Synth Biol. 7(9):2074-2086. doi: 10.1021/acssynbio.8b00251.

Brodie J, Chan CX, De Clerck O, Cock JM, Coelho SM, Gachon C, Grossman AR, Mock T, Raven JA, Smith AG, Yoon HS, Bhattacharya D (2017). The Algal Revolution. Trends Plant Sci. 22(8):726-738. doi: 10.1016/j.tplants.2017.05.005.

Moses T, Mehrshahi P, Smith AG, Goossens A (2017) Synthetic biology approaches for the production of plant metabolites in unicellular organisms. J Exp Bot, 68: 4057-4074. doi: 10.1093/jxb/erx119

Nguyen GTDT, Scaife MA, Helliwell KE, Smith AG (2016) Role of riboswitches in gene regulation and their potential for algal biotechnology. J Phycol. 52(3):320-8. doi: 10.1111/jpy.12416.

Scaife MA, Smith AG (2016) Towards developing algal synthetic biology. Biochem Soc Trans. 44(3):716-22. doi: 10.1042/BST20160061.

Scaife MA, Nguyen GTDT, Rico J, Lambert D, Helliwell KE, Smith AG (2015) Establishing Chlamydomonas reinhardtii as an industrial biotechnology host. Plant J. 82(3):532-46. doi: 10.1111/tpj.12781.

Workpackage D: Genome Engineering

Hayta S, Smedley MA, Clarke M, Forner M, Harwood WA (2021) An Efficient Agrobacterium-Mediated Transformation Protocol for Hexaploid and Tetraploid Wheat. Curr Protoc. 1(3):e58. https://doi.org/10.1002/cpz1.58.

Smedley MA, Hayta S, Clarke M, Harwood WA (2021) CRISPR-Cas9 Based Genome Editing in Wheat. Curr Protoc. 1(3):e65. https://doi.org/10.1002/cpz1.65.

Debernardi JM, Tricoli DM, Ercoli MF, Hayta S, Ronald P, Palatnik JF, Dubcovsky J (2020). A GRF-GIF chimeric protein improves the regeneration efficiency of transgenic plants. Nature Biotechnology 38: 1274–1279 https://doi.org/10.1038/s41587-020-0703-0

Patron, N. J. (2020) Beyond natural: synthetic expansions of botanical form and function. New Phytologist 2: 295-310 https://doi.org/10.1111/nph.16562

Nimmo IC, Barbrook AC, Lassadi I, Chen JE, Geisler K, Smith AG, Aranda M, Purton S, Waller RF, Nisbet RER, Howe CJ (2019) Genetic transformation of the dinoflagellate chloroplast. eLife. 2019; 8: e45292. doi: 10.7554/eLife.45292

Raitskin O, Schudoma C, West A, Patron NJ. (2019) Comparison of efficiency and specificity of CRISPR-associated (Cas) nucleases in plants: An expanded toolkit for precision genome engineering. PLoS One. 14(2):e0211598. doi: 10.1371/journal.pone.0211598.

Tuncel A, Corbin KR, Ahn‐Jarvis J, Harris S, Hawkins E, Smedley MA, Harwood W, Warren FJ, Patron NJ, Smith AM (2019) Cas9-mediated mutagenesis of potato starch branching enzymes generates a range of tuber starch phenotypes. Plant Biotechnol J. 17(12):2259-2271. doi: 10.1111/pbi.13137.

Salzman AE (2017) Controlling Relative Gene Expression Using Orthologous Regulatory Elements: Exploring Future Prospects of Tuneable Control for the Manufacture of Natural Products. Masters thesis. University of East Anglia.

Volpi e Silva N and Patron N (2017) CRISPR-based Tools for Plant Genome Engineering. Emerging Topics in Life Sciences doi: 10.1042/ETLS20170011

Raitskin O, Patron NJ, (2016). Multigene Engineering with RNA guided Cas9 Nuclease. Current Opinion in Biotechnology 37; 69-75 https://doi.org/10.1016/j.copbio.2015.11.008

Belhaj K, Chaparro-Garcia A, Kamoun S, Patron NJ, Nekrasov V (2015). Editing plant genomes with CRISPR/Cas9. Curr Opin Biotechnol. 32:76-84. doi: 10.1016/j.copbio.2014.11.007.

Lawrenson T, Shorinola O, Stacey N, Liu C, Østergaard L, Patron NJ, Uauy C, Harwood, W (2015). Induction of targeted, heritable mutations in barley and Brassica oleracea using RNA guided Cas9 nuclease. Genome Biol. 16:258. doi: 10.1186/s13059-015-0826-7.

Workpackage E: Digital tools

Ho PY, Martins BMC, Amir A. (2020) A Mechanistic Model of the Regulation of Division Timing by the Circadian Clock in Cyanobacteria. Biophysical Journal. Volume 118, Issue 12, Pages 2905-2913, https://doi.org/10.1016/j.bpj.2020.04.038.

Boehm CR, Grant PK, Haseloff J. (2018). Programmed hierarchical patterning of bacterial populations. Nat Commun. 9(1):776. doi: 10.1038/s41467-018-03069-3.

Delmans M, Haseloff J, (2018). µCube: A Framework for 3D Printable Optomechanics. Journal of Open Hardware, 2. 10.5334/joh.8.

Kan A, Del Valle I, Rudge T, Federici F, Haseloff J. (2018). Intercellular adhesion promotes clonal mixing in growing bacterial populations. J R Soc Interface. 15(146). pii: 20180406. doi: 10.1098/rsif.2018.0406.

Delmans M, Pollak B, and Haseloff J., (2017). MarpoDB: An open registry for Marchantia polymorpha genetic parts. Plant Cell Physiol. 58(1):e5. doi: 10.1093/pcp/pcw201.

Nuñez IN, Matute TF, Del Valle ID, Kan A, Choksi A, Endy D, Haseloff J, Rudge TJ, Federici F (2017). Artificial Symmetry-Breaking for Morphogenetic Engineering Bacterial Colonies. ACS Synth Biol. 6(2):256-265. doi: 10.1021/acssynbio.6b00149.

Grant PK, Dalchau N, Brown JR, Federici F, Rudge TJ, Yordanov B, Patange O, Phillips A, Haseloff J (2016). Orthogonal intercellular signaling for programmed spatial behavior. Mol Syst Biol. 12(1):849. doi: 10.15252/msb.20156590.

Martins BM, Das AK, Antunes L, Locke JC (2016). Frequency doubling in the cyanobacterial circadian clock. Mol Syst Biol. 12(12):896. doi: 10.15252/msb.20167087.

Rudge T, Brown J, Federici F, Dalchau N, Phillips A, Ajioka J, & Haseloff J (2016). Characterization of intrinsic properties of promoters. ACS Synth Biol. 5(1):89-98. doi: 10.1021/acssynbio.5b00116.

Workpackage F: Modules for engineering photosynthesis and leaf metabolism

Müller LM, Mombaerts L, Pankin A, Davis SJ, Webb AAR, Goncalves J, von Korff M (2020) Differential Effects of Day/Night Cues and the Circadian Clock on the Barley Transcriptome. Plant Physiol. Jun; 183(2): 765–779. doi: 10.1104/pp.19.01411

Dickinson, P., Kneřová, J., Szecówka, M., Stevenson, S.R., Burgess, S.J., Mulvey, H., Bågman, A-M., Gaudinier, A., Brady, S.M., Hibberd, J.M. (2020). A bipartite transcription factor module controlling expression in the bundle sheath of Arabidopsis thaliana. Nature Plants 6:1468–1479 https://doi.org/10.1038/s41477-020-00805-w

Burgess, S.J. Reyna-Llorens, I., Stevenson, S.R., Singh, P., Jaeger, K., Hibberd, J.M. (2019) Genome-wide transcription factor binding in leaves from C3 and C4 grasses. The Plant Cell 31(10):2297-2314. doi: 10.1105/tpc.19.00078.

Borba AR, Serra TS, Górska A, Gouveia P, Cordeiro AM, Reyna-Llorens I, Kneřová J, Barros PM, Abreu IA, Oliveira MM, Hibberd JM, Saibo NJM (2018). Synergistic binding of bHLH transcription factors to the promoter of the maize NADP-ME gene used in C4 photosynthesis is based on an ancient code found in the ancestral C3 state. Mol Biol Evol. 35(7):1690-1705. doi: 10.1093/molbev/msy060.

Kneřová, J., Dickinson, P.J., Szecówka, M., Burgess, S.J. Mulvey, M., Bågman, A-M., Gaudinier, A., Brady, S.M. and Hibberd, J.M. (2018) A single cis-element that controls cell-type specific expression in Arabidopsis. BioRxiv doi: https://doi.org/10.1101/380188.

Reyna-Llorens I, Burgess SJ, Reeves G, Singh P, Stevenson SR, Williams BP, Stanley S, Hibberd JM (2018). Ancient duons may underpin spatial patterning of gene expression in C4 leaves. Proc Natl Acad Sci U S A. 115(8):1931-1936. doi: 10.1073/pnas.1720576115.

Burgess, S.J., Reyna-Llorens, I., Jaeger, K., Hibberd, J.M. (2017). A transcription factor binding atlas for photosynthesis in cereals identifies a key role for coding sequence in the regulation of gene expression. BioRxiv pre-print doi: https://doi.org/10.1101/165787

Kümpers BM, Burgess SJ, Reyna-Llorens I, Smith-Unna R, Boursnell C, Hibberd JM (2017). Shared characteristics underpinning C4 leaf maturation derived from analysis of multiple C3 and C4 species of Flaveria. J Exp Bot. 68(2):177-189. doi: 10.1093/jxb/erw488.

Reyna-Llorens I, Hibberd JM (2017). Recruitment of pre-existing networks during the evolution of C4 photosynthesis. Philos Trans R Soc Lond B Biol Sci. 372(1730). pii: 20160386. doi: 10.1098/rstb.2016.0386.

Aubry S, Aresheva O, Reyna-Llorens I, Smith-Unna RD, Hibberd JM, Genty B (2016). A Specific Transcriptome Signature for Guard Cells from the C4 Plant Gynandropsis gynandra. Plant Physiol. 170(3):1345-57. doi: 10.1104/pp.15.01203.

Hibberd JM, Furbank RT (2016). In retrospect: Fifty years of C4 photosynthesis. Nature 538(7624):177-179. doi: 10.1038/538177b.

Hibberd JM, Furbank RT (2016). Wheat genomics: Seeds of C4 photosynthesis. Nat Plants. 2(11):16172. doi: 10.1038/nplants.2016.172.

Williams, B.P., Burgess, S.J., Reyna-Llorens, I., Knerova, J., Aubry, S., Stanley, S., and Hibberd, J.M. (2016). An Untranslated cis-Element Regulates the Accumulation of Multiple C4 Enzymes in Gynandropsis gynandra Mesophyll Cells. Plant Cell. 28(2):454-65. doi: 10.1105/tpc.15.00570.

Workpackage G: Carbohydrate engineering

Dedola S, Rugen MD, Young RJ, Field RA (2020) Revisiting the Language of Glycoscience: Readers, Writers and Erasers in Carbohydrate Biochemistry. ChemBioChem 2020, 21, 423.

Kuhaudomlarp S, Pergolizzi G, Patron NJ, Henrissat B, Field RA (2019) Unraveling the subtleties of β-(1→3)-glucan phosphorylase specificity in the GH94, GH149 and GH161 glycoside hydrolase families. J Biol Chem. 2019 Apr 19;294(16):6483-6493. doi: 10.1074/jbc.RA119.007712.

Kuhaudomlarp S, Walpole S, Stevenson CEM, Nepogodiev SA, Lawson DM, Angulo J, Field RA (2019). Unravelling the Specificity of Laminaribiose Phosphorylase from Paenibacillus sp. YM-1 towards Donor Substrates Glucose/Mannose 1-Phosphate by Using X-ray Crystallography and Saturation Transfer Difference NMR Spectroscopy. Chembiochem. 20(2):181-192. doi: 10.1002/cbic.201800260.

Temple H, Mortimer JC, Tryfona T, Yu X, Lopez‐Hernandez F, Sorieul M, Anders N, Dupree P (2019) Two members of the DUF579 family are responsible for arabinogalactan methylation in Arabidopsis. Plant Direct. 3(2):e00117. doi: 10.1002/pld3.117.

Wagstaff BA , Rejzek M , Kuhaudomlarp S, Hill L, Mascia I, Nepogodiev SA, Field RA (2019) Discovery of an RmlC/D fusion protein in the microalga Prymnesium parvum and its implications for NDP-β-l-rhamnose biosynthesis in microalgae. J Biol Chem. 294(23):9172-9185. doi: 10.1074/jbc.RA118.006440.

Kuhaudomlarp S, Patron NJ, Henrissat B, Rejzek M, Saalbach G, Field RA (2018). Identification of Euglena gracilis β-1,3-glucan phosphorylase and establishment of a new glycoside hydrolase (GH) family GH149. J Biol Chem. 293(8):2865-2876. doi: 10.1074/jbc.RA117.000936.

Wangpaiboon K, Padungros P, Nakapong S, Charoenwongpaiboon T, Rejzek M, Field RA, Pichyangkura R, (2018). An a-1,6-and a-1,3-linked glucan produced by Leuconostoc citreum ABK-1 alternansucrase with nanoparticle and film-forming properties. Sci Rep. 8(1):8340. doi: 10.1038/s41598-018-26721-w.

Yu L, Lyczakowski JJ, Pereira CS, Kotake T, Yu X, Li A, Mogelsvang S, Skaf MS, and Dupree P. (2018) The Patterned Structure of Galactoglucomannan Suggests It May Bind to Cellulose in Seed Mucilage. Plant Physiol. 178(3): 1011–1026. doi: 10.1104/pp.18.00709

Lyczakowski JJ, Wicher KB, Terrett OM, Faria-Blanc N, Yu X, Brown D, Krogh KBRM, Dupree P, Busse-Wicher M. (2017). Removal of glucuronic acid from xylan is a strategy to improve the conversion of plant biomass to sugars for bioenergy. Biotechnol Biofuels.10:224. doi: 10.1186/s13068-017-0902-1.

O’Neill EC, Kuhaudomlarp S, Rejzek M, Fangel JU, Alagesan K, Kolarich D, Willats WGT, Field RA (2017). Exploring the glycans of Euglena gracilis. Biology (Basel) 6(4). pii: E45. doi: 10.3390/biology6040045.

O'Neill EC, Pergolizzi G, Stevenson CEM, Lawson DM, Nepogodiev SA, Field RA, (2017). Cellodextrin phosphorylase from Ruminiclostridium thermocellum: X-ray crystal structure and substrate specificity analysis. Carbohydr Res. 451:118-132. doi: 10.1016/j.carres.2017.07.005.

Rejzek M, Hill L, Hems ES, Kuhaudomlarp S, Wagstaff BA, Field RA (2017). Profiling of Sugar Nucleotides. Methods Enzymol. 597:209-238. doi: 10.1016/bs.mie.2017.06.005.

O’Neill EC, Saalbach G, Field RA. (2016). Gene Discovery for Synthetic Biology: Exploring the Novel Natural Product Biosynthetic Capacity of Eukaryotic Microalgae. Methods Enzymol. 576:99-120. doi: 10.1016/bs.mie.2016.03.005.

O'Neill EC, Trick M, Hill L, Rejzek M, Dusi RG, Hamilton CJ, Zimba PV, Henrissat B, Field RA. (2015). The transcriptome of Euglena gracilis reveals unexpected metabolic capabilities for carbohydrate and natural product biochemistry. Mol Biosyst. 11(10):2808-20. doi: 10.1039/c5mb00319a.

Workpackage H: Tools for Engineering Plant Natural Products

Houghton, A., Appelhagen, I., & Martin, C. (2021). Natural Blues: Structure Meets Function in Anthocyanins. Plants (Basel, Switzerland), 10(4), 726. https://doi.org/10.3390/plants10040726

Stephenson MJ and Osbourn A (2020). Making drugs out of sunlight and ‘thin air’: An emerging synergy of synthetic biology and natural product chemistry. The Biochemist 42: 34-39. https://doi.org/10.1042/BIO20200044

Nützmann HW, Doerr D, Ramírez-Colmenero A, Sotelo-Fonseca JE, Wegel E, Di Stefano M, Wingett SW, Fraser P, Hurst L, Fernandez-Valverde SL, Osbourn A (2020) Active and repressed biosynthetic gene clusters have spatially distinct chromosome states. PNAS 117 (24) 13800-13809; DOI: 10.1073/pnas.1920474117

Liu Z, Cheema J, Vigouroux M, Hill L, Reed J, Paajanen P, Yant L & Osbourn A. (2020). Formation and diversification of a paradigm biosynthetic gene cluster in plants. Nature Communications 11: 5354. https://doi.org/10.1038/s41467-020-19153-6

Lichman BR, Kamileen MO, Titchiner GR, Saalbach G, Stevenson CEM, Lawson DM, O’Connor SE. (2019) Uncoupled activation and cyclization in catmint reductive terpenoid biosynthesis. Nat Chem Biol. 1; 15(1): 71–79. doi: 10.1038/s41589-018-0185-2

Galdon-Armero J, Arce-Rodriguez ML, Martin C. (2019) A scanning electron microscopy-based screen of leaves of Solanum pennellii (ac. LA716) xSolanum lycopersicum (cv. M82) introgression lines provides a resource for identification of loci involved in epidermal development in tomato. bioRxiv 688077; doi: https://doi.org/10.1101/688077

Hodgson H, De La Pena R, Stephenson MJ, Thimmappa R, Vincent JL, Sattely E, Osbourn A. (2019) Identification of key enzymes responsible for protolimonoid biosynthesis in plants: Opening the door to azadirachtin production. PNAS 116:17096.

Huang A. C., Jiang T., Liu Y. X., Bai Y. C., Reed J., Qu B., Goossens A., Nützmann H. W., Bai Y., Osbourn A. (2019) A specialized metabolic network selectively modulates Arabidopsis root microbiota. Science 364(6440). pii: eaau6389. doi: 10.1126/science.aau6389.

Huang AC, Osbourn A. (2019) Plant terpenes that mediate below-ground interactions: prospects for bioengineering terpenoids for plant protection. Pest Manag Sci. 75(9):2368-2377. doi: 10.1002/ps.5410.

Leveau A., Reed J., Qiao X., Stephenson M. J., Mugford S. T., Melton R. E., Rant J. C., Vickerstaff R., Langdon T., Osbourn A. (2019) Towards take-all control: a C-21ß oxidase required for acylation of triterpene defence compounds in oat. New Phytologist. 221(3):1544-1555. doi: 10.1111/nph.15456.

Liu Z, Suarez Duran HG, Harnvanichvech Y, Stephenson MJ, Schranz ME, Nelson D, Medema MH, Osbourn A. (2019) Drivers of metabolic diversification: how dynamic genomic neighborhoods generate new biosynthetic pathways in the Brassicaceae. New Phytol. Nov 26. doi: 10.1111/nph.16338.

Orme A., Louveau T., Stephenson M.J., Appelhagen I., Melton R.E., Cheema J., Li Y.,Zhao Q., Zhang L., Fan D., Tian Q., Vickerstaff R.J., Langdon T., Han B., Osbourn A. (2019) A non-canonical vacuolar sugar transferase required for biosynthesis of antimicrobial defense compounds in oat. PNAS 116 (52) 27105-27114 https://doi.org/10.1073/pnas.1914652116

Stephenson M. J., Field R. A., Osbourn A. E. (2019) The protosteryl and dammarenyl cation dichotomy in polycyclic triterpene biosynthesis revisited: has this ‘rule’ finally been broken? Nat Prod Rep. doi: 10.1039/c8np00096d. [Epub ahead of print]

Appelhagen I, Wulff-Vester AK, Wendell M, Hvoslef-Eide AK, Russell J, Oertel A, Martens S, Mock HP, Martin C, Matros A (2018). Colour bio-factories: Towards scale-up production of anthocyanins in plant cell cultures. Metab Eng. 48:218-232. doi: 10.1016/j.ymben.2018.06.004.

Boachon B, Buell CR, Crisovan E, Dudareva N, Garcia N, Godden G, Henry L, Kamileen MO, Kates HR, Kilgore MB, Lichman BR, Mavrodiev EV, Newton L, Rodriguez-Lopez C, O'Connor SE, Soltis D, Soltis P, Vaillancourt B, Wiegert-Rininger K, Zhao D (2018). Phylogenomic Mining of the Mints Reveals Multiple Mechanisms Contributing to the Evolution of Chemical Diversity in Lamiaceae. Mol Plant. 11(8):1084-1096. doi: 10.1016/j.molp.2018.06.002.

Dangl J, Osbourn A, Orzaez D et al. (2018). What is the next frontier in plant engineering? Cell 174(3): 499.

Fu R, Martin C, and Zhang Y (2018). Next Generation Plant Metabolic Engineering, Inspired by an Ancient Chinese Irrigation System. Mol Plant. 11(1):47-57. doi: 10.1016/j.molp.2017.09.002.

Galdon-Armero J, Fullana-Pericas M, Mulet PA, Conesa MA, Martin C, Galmes J. (2018). The ratio of trichomes to stomata is associated with water use efficiency in Solanum lycopersicum (tomato). Plant J. 96(3):607-619. doi: 10.1111/tpj.14055.

Hems ES, Wagstaff BA, Saalbach G, Field RA. (2018). CuAAC click chemistry for the enhanced detection of novel alkyne-based natural product toxins. Chem Commun (Camb). 54(86):12234-12237. doi: 10.1039/c8cc05113e. Erratum in: Chem Commun (Camb). 54(93):13161.

Li Y, Wang H, Zhang Y, Martin C. (2018). Can the world's favorite fruit, tomato, provide an effective biosynthetic chassis for high-value metabolites? Plant Cell Rep. 37(10):1443-1450. doi: 10.1007/s00299-018-2283-8.

Louveau T, Orme A, Pfalzgraf H, Stephenson MJ, Melton R, Saalbach G, Hemmings AM, Leveau A, Rejzek M, Vickerstaff RJ, Langdon T, Field RA, Osbourn A. (2018) Analysis of Two New Arabinosyltransferases Belonging to the Carbohydrate Active Enzyme (CAZY) Glycosyl Transferase Family1 Provides Insights into Disease Resistance and Sugar Donor Specificity. Plant Cell. 30(12):3038-3057. doi: 10.1105/tpc.18.00641.

Martin C (2018) A role for plant science in underpinning the objective of global nutritional security? Ann Bot. 122(4):541-553. doi: 10.1093/aob/mcy118.

Nützmann HW, Scazzocchio C, Osbourn A (2018). Metabolic gene clusters in eukaryotes. Annu Rev Genet. 52:159-183 doi: 10.1146/annurev-genet-120417-031237.

Reed J, Osbourn A (2018). Engineering terpenoid production through transient expression in Nicotiana benthamiana. Plant Cell Rep. 37(10):1431-1441. doi: 10.1007/s00299-018-2296-3.

Soubeyrand E, Johnson T, Latimer S, Block A, Kim J, Colquhoun TA, Butelli E, Martin C, Wilson MA, Basset G (2018). The Peroxidative Cleavage of Kaempferol Contributes to the Biosynthesis of the Benzenoid Moiety of Ubiquinone in Plants. Plant Cell. 30(12):2910-2921. doi: 10.1105/tpc.18.00688.

Stewart C, Patron N, Hanson A, Jez J, (2018). Plant metabolic engineering in the synthetic biology era: plant chassis selection. Plant Cell Rep. 37(10):1357-1358. doi: 10.1007/s00299-018-2342-1.

Wulff-Vester A, Wendell M, Matros A, Appelhagen I, Martin C, Hvoslef-Eide AK (2018) ANTHOcyanin production Platform Using Suspension Cultures in custom-made bioreactors. IN VITRO CELLULAR & DEVELOPMENTAL BIOLOGY-PLANT. 2018: 54, S77-S77

Xu JJ, Fang X, Li CY, Zhao Q, Martin C, Chen XY, Yang L. (2018) Characterization of Arabidopsis thaliana Hydroxyphenylpyruvate Reductases in the Tyrosine Conversion Pathway. Front Plant Sci. 9:1305. doi: 10.3389/fpls.2018.01305.

Xue Z, Tan Z, Huang A, Zhou Y, Sun J, Wang X, Thimmappa RB, Stephenson MJ, Osbourn A, Qi X (2018). Identification of key amino acid residues determining product specificity of 2,3-oxidosqualene cyclase in Oryza species. New Phytol. 218(3):1076-1088. doi: 10.1111/nph.15080.

Stephenson MJ, Reed J, Brouwer B, Osbourn A (2018). Transient Expression in Nicotiana Benthamiana Leaves for Triterpene Production at a Preparative Scale. J Vis Exp. (138). doi: 10.3791/58169.

Boobier S, Osbourn A, Mitchell JBO (2017). Can human experts predict solubility better than computers? J Cheminform. 9(1):63. doi: 10.1186/s13321-017-0250-y.

Kautsar SA, Suarez Duran HG, Blin K, Osbourn A, Medema MH (2017). plantiSMASH: automated identification, annotation and expression analysis of plant biosynthetic gene clusters. Nucleic Acids Res. 45(W1):W55-W63. doi: 10.1093/nar/gkx305.

Kries H, Kellner F, Kamileen MO, O'Connor SE. (2017). Inverted stereocontrol of iridoid synthase in snapdragon. J Biol Chem. 292(35):14659-14667. doi: 10.1074/jbc.M117.800979.

Osbourn A. (2017) Painting with betalains. Nat Plants. 3(11):852-853. doi: 10.1038/s41477-017-0049-x.

Owen C, Patron NJ, Huang A, Osbourn A (2017). Harnessing plant metabolic diversity. Curr Opin Chem Biol. 40:24-30. doi: 10.1016/j.cbpa.2017.04.015.

Reed J, Stephenson MJ, Miettinen K, Brouwer B, Leveau A, Brett P, Goss RJM, Goossens A, O'Connell MA, Osbourn A. (2017). A translational synthetic biology platform for rapid access to gram-scale quantities of novel drug-like molecules. Metab Eng. 42:185-193. doi: 10.1016/j.ymben.2017.06.012.

Scarano A, Butelli E, De Santis S, Cavalcanti E, Hill L, De Angelis M, Giovinazzo G, Chieppa M, Martin C, Santino A. (2017). Combined Dietary Anthocyanins, Flavonols, and Stilbenoids Alleviate Inflammatory Bowel Disease Symptoms in Mice. Front Nutr. 4:75. doi: 10.3389/fnut.2017.00075.

Sherden NH, Lichman B, Caputi L, Zhao D, Kamileen MO, Buell CR, O'Connor SE (2017). Identification of iridoid synthases from Nepeta species: Iridoid cyclization does not determine nepetalactone stereochemistry. Phytochemistry. 145:48-56. doi: 10.1016/j.phytochem.2017.10.004.

Alagna F, Geu-Flores F, Kries H, Panara F, Baldoni L, O'Connor SE, Osbourn A. (2016) Identification and characterization of the iridoid synthase involved in oleuropein biosynthesis in olive (Olea europaea) fruits. J Biol Chem. 291(11):5542-54. doi: 10.1074/jbc.M115.701276.

Medema, MH & Osbourn, A (2016) Computational genomic identification and functional reconstitution of plant natural product biosynthetic pathways. Nat Prod Rep. 33(8):951-62. doi: 10.1039/c6np00035e.

Nguyen TD, Faraldos JA, Vardakou M, Salmon M, O'Maille PE, Ro DK (2016). Discovery of germacrene A synthases in Barnadesia spinosa: The first committed step in sesquiterpene lactone biosynthesis in the basal member of the Asteraceae. Biochem Biophys Res Commun. 479(4):622-627. doi: 10.1016/j.bbrc.2016.09.165.

Nützmann HW, Huang A, Osbourn A (2016). Plant metabolic clusters – from genetics to genomics. New Phytol. 211(3):771-89. doi: 10.1111/nph.13981.

Osbourn A., Morgan J. (2016) Editorial overview: Plant biotechnology. Curr Opin Biotechnol. 37:153-154. doi: 10.1016/j.copbio.2015.12.006.

Salmon M, Thimmappa R, Minto R, Melton R, Hughes R, O'Maille P, Hemmings AM, Osbourn A (2016) A conserved amino acid residue critical for product and substrate specificity in plant triterpene synthases. Proc Natl Acad Sci U S A. 113(30):E4407-14. doi: 10.1073/pnas.1605509113.

Yu N, Nützmann HW, MacDonald JT, Moore B, Field B, Berriri S, Trick M, Rosser SJ, Kumar SV, Freemont PS, Osbourn A (2016). Delineation of metabolic gene clusters in plant genomes by chromatin signatures. Nucleic Acids Res. 44(5):2255-65. doi: 10.1093/nar/gkw100.

Zhao Q, Zhang Y, Wang G, Hill L, Weng JK, Chen XY, Xue H, Martin C (2016). A specialized flavone biosynthetic pathway has evolved in the medicinal plant, Scutellaria baicalensis. Sci Adv. 2(4):e1501780. doi: 10.1126/sciadv.1501780.

Zhou Y, Ma Y, Zeng J, Duan L, Xue X, Wang H, Lin T, Liu Z, Zeng K, Zhong Y, Zhang S, Hu Q, Liu M, Zhang H, Reed J, Moses T, Liu X, Huang P, Qing Z, Liu X, Tu P, Kuang H, Zhang Z, Osbourn A, Ro DK, Shang Y, Huang S. (2016) Convergence and divergence of bitterness biosynthesis and regulation in Cucurbitaceae. Nat Plants. 2:16183. doi: 10.1038/nplants.2016.183.

Boutanaev AM, Moses T, Zi J, Nelson DR, Mugford ST, Peters RJ, Osbourn A (2015). Investigation of terpene diversification across multiple sequenced plant genomes. Proc Natl Acad Sci U S A. 112(1):E81-8. doi: 10.1073/pnas.1419547112.

Medema MH, Kottmann R, Yilmaz P, Cummings M, Biggins JB, Blin K, de Bruijn I, Chooi YH, Claesen J, Coates RC, Cruz-Morales P, Duddela S, Düsterhus S, Edwards DJ, Fewer DP, Garg N, Geiger C, Gomez-Escribano JP, Greule A, Hadjithomas M, Haines AS, Helfrich EJ, Hillwig ML, Ishida K, Jones AC, Jones CS, Jungmann K, Kegler C, Kim HU, Kötter P, Krug D, Masschelein J, Melnik AV, Mantovani SM, Monroe EA, Moore M, Moss N, Nützmann HW, Pan G, Pati A, Petras D, Reen FJ, Rosconi F, Rui Z, Tian Z, Tobias NJ, Tsunematsu Y, Wiemann P, Wyckoff E, Yan X, Yim G, Yu F, Xie Y, Aigle B, Apel AK, Balibar CJ, Balskus EP, Barona-Gómez F, Bechthold A, Bode HB, Borriss R, Brady SF, Brakhage AA, Caffrey P, Cheng YQ, Clardy J, Cox RJ, De Mot R, Donadio S, Donia MS, van der Donk WA, Dorrestein PC, Doyle S, Driessen AJ, Ehling-Schulz M, Entian KD, Fischbach MA, Gerwick L, Gerwick WH, Gross H, Gust B, Hertweck C, Höfte M, Jensen SE, Ju J, Katz L, Kaysser L, Klassen JL, Keller NP, Kormanec J, Kuipers OP, Kuzuyama T, Kyrpides NC, Kwon HJ, Lautru S, Lavigne R, Lee CY, Linquan B, Liu X, Liu W, Luzhetskyy A, Mahmud T, Mast Y, Méndez C, Metsä-Ketelä M, Micklefield J, Mitchell DA, Moore BS, Moreira LM, Müller R, Neilan BA, Nett M, Nielsen J, O'Gara F, Oikawa H, Osbourn A, Osburne MS, Ostash B, Payne SM, Pernodet JL, Petricek M, Piel J, Ploux O, Raaijmakers JM, Salas JA, Schmitt EK, Scott B, Seipke RF, Shen B, Sherman DH, Sivonen K, Smanski MJ, Sosio M, Stegmann E, Süssmuth RD, Tahlan K, Thomas CM, Tang Y, Truman AW, Viaud M, Walton JD, Walsh CT, Weber T, van Wezel GP, Wilkinson B, Willey JM, Wohlleben W, Wright GD, Ziemert N, Zhang C, Zotchev SB, Breitling R, Takano E, Glöckner FO (2015). Minimum Information about a Biosynthetic Gene cluster. Nat Chem Biol. 11(9):625-31. doi: 10.1038/nchembio.1890.

Nützmann HW, Osbourn A (2015) Regulation of metabolic gene clusters in Arabidopsis thaliana. New Phytol. 205(2):503-10. doi: 10.1111/nph.13189.

Tohge T, Zhang Y, Peterek S, Matros A, Rallapalli G, Tandrón YA, Butelli E, Kallam K, Hertkorn N, Mock HP, Martin C, Fernie AR.(2015). Ectopic expression of snapdragon transcription factors facilitates the identification of genes encoding enzymes of anthocyanin decoration in tomato. Plant J. 83(4):686-704. doi: 10.1111/tpj.12920.

Zhang Y, Butelli E, Alseekh S, Tohge T, Rallapalli G, Luo J, Kawar PG, Hill L, Santino A, Fernie AR, Martin C (2015). Multilevel engineering facilitates the production of phenylpropanoid compounds in tomato. Nat Commun. 6:8635. doi: 10.1038/ncomms9635.

Zhang Y, De Stefano R, Robine M, Butelli E, Bulling K, Hill L, Rejzek M, Martin C, Schoonbeek HJ (2015). Different Reactive Oxygen Species Scavenging Properties of Flavonoids Determine Their Abilities to Extend the Shelf Life of Tomato. Plant Physiol. 169(3):1568-83. doi: 10.1104/pp.15.00346.

Workpackage I: N2 Fixation

Radhakrishnan GV, Keller J, Rich MK, Vernié T, Mbadinga DLM, Vigneron N, Cottret L, Clemente HS, Libourel C, Cheema J, Linde AM, Eklund DM, Cheng S, Wong GKS, Lagercrantz U, Li FW, Oldroyd GED & Delaux PM. (2020) An ancestral signalling pathway is conserved in intracellular symbioses-forming plant lineages. Nature Plants 6: 280–289 https://doi.org/10.1038/s41477-020-0613-7 (Previously published on BioRxiv: https://www.biorxiv.org/content/10.1101/804591v1.full)

Carella P, Gogleva A, Hoey DJ, Bridgen AJ, Stolze SC, Nakagami H, Schornack S. (2019) Conserved Biochemical Defenses Underpin Host Responses to Oomycete Infection in an Early-Divergent Land Plant Lineage. Current Biology 29(14): 2282-2294.e5 https://doi.org/10.1016/j.cub.2019.05.078

Carella P, Evangelisti E, Schornack S (2018). Sticking to it: phytopathogen effector molecules may converge on evolutionarily conserved host targets in green plants. Curr Opin Plant Biol. 44:175-180. doi: 10.1016/j.pbi.2018.04.019.

Carella P, Gogleva A, Tomaselli M, Alfs C, Schornack S (2018). Phytophthora palmivora establishes tissue-specific intracellular infection structures in the earliest divergent land plant lineage. Proc Natl Acad Sci U S A. 115(16):E3846-E3855. doi: 10.1073/pnas.1717900115.

Carella P, Schornack S (2017). Manipulation of Bryophyte Hosts by Pathogenic and Symbiotic Microbes. Plant Cell Physiol. 59(4):651-660. doi: 10.1093/pcp/pcx182.

Delaux PM, Radhakrishnan G, and Oldroyd G (2015). Tracing the evolutionary path to nitrogen-fixing crops. Curr Opin Plant Biol. 26:95-9. doi: 10.1016/j.pbi.2015.06.003.

Delaux PM, Radhakrishnan G, Jayaraman D, Cheema J, Malbreil M, Volkening J, Sekimoto H, Nishiyama T, Melkonian M, Pokorny L, Rothfels C, Sederoff H, Stevenson D, Surek B, Zhang Y, Sussman M, Dunand C, Morris R, Roux C, Wong G, Oldroyd G, Ane JM (2015). Algal ancestor of land plants was preadapted for symbiosis. Proc Natl Acad Sci U S A. 112(43):13390-5. doi: 10.1073/pnas.1515426112.

Workpackage J: Virus-based systems for bioproduction

Thuenemann EC, Le DHT, Lomonossoff GP, Steinmetz NF (2021) Bluetongue Virus Particles as Nanoreactors for Enzyme Delivery and Cancer Therapy. Mol. Pharmaceutics 18, 3, 1150–1156 https://doi.org/10.1021/acs.molpharmaceut.0c01053

Zahmanova G, Mazalovska M, Takova K, Toneva V, Minkov I, Peyret H, Lomonossoff G (2021) Efficient Production of Chimeric Hepatitis B Virus-Like Particles Bearing an Epitope of Hepatitis E Virus Capsid by Transient Expression in Nicotiana benthamiana. Life (Basel, Switzerland) 11(1) doi: 10.3390/life11010064

Ponndorf D, Meshcheriakova Y, Thuenemann EC, Dobon Alonso A, Overman R, Holton N, Dowall S, Kennedy E, Stocks M, Lomonossoff GP, Peyret H (2021) Plant-made dengue virus-like particles produced by co-expression of structural and non-structural proteins induce a humoral immune response in mice. Plant Biotechnology Journal. doi: 10.1111/pbi.13501

Berardi A, Baldelli Bombelli F, Thuenemann EC, Lomonossoff GP, (2019). Viral nanoparticles can elude protein barriers: exploiting rather than imitating nature. Nanoscale. 11(5):2306-2316. doi: 10.1039/c8nr09067j.

Byrne MJ, Steele JFC, Hesketh EL, Walden M, Thompson R, Lomonossoff GP & Ranson NA. (2019) Combining transient expression and cryo-EM to obtain high resolution structures of luteovirid particles. Structure. https://doi.org/10.1016/j.str.2019.09.010

Hesketh EL, Tiede C, Adamson H, Adams TL, Byrne MJ, Meshcheriakova Y, Kruse I, McPherson MJ, Lomonossoff GP, Tomlinson DC, Ranson NA. (2019) Affimer reagents as tools in diagnosing plant virus diseases. Sci Rep. 2019 May 17;9(1):7524. doi: 10.1038/s41598-019-43945-6. PMID: 31101847

Peyret H, Brown J, Lomonossoff G (2019) Improving plant transient expression through the rational design of synthetic 5’ and 3’ untranslated regions. Plant Methods 15: 108 http://dx.doi.org/10.1186/s13007-019-0494-9

Stephenson MJ, Reed J, Brouwer B, Osbourn A (2018). Transient Expression in Nicotiana Benthamiana Leaves for Triterpene Production at a Preparative Scale. J Vis Exp. (138). doi: 10.3791/58169.

Castells-Graells R, Lomonossoff GP, Saunders K (2018) Production of Mosaic Turnip Crinkle Virus-Like Particles Derived by Coinfiltration of Wild-Type and Modified Forms of Virus Coat Protein in Plants. Methods Mol Biol. 1776:3-17. doi: 10.1007/978-1-4939-7808-3_1.

Thuenemann EC, Lomonossoff GP (2018). Delivering Cargo: Plant-Based Production of Bluetongue Virus Core-Like and Virus-Like Particles Containing Fluorescent Proteins. Methods Mol Biol. 1776:319-334. doi: 10.1007/978-1-4939-7808-3_22.

Wege C, Lomonossoff GP (2018). Virus-Derived Nanoparticles for Advanced Technologies. Methods and Protocols Humana press 1776 671

Brillault L, Jutras PV, Dashti N, Thuenemann EC, Morgan G, Lomonossoff GP, Landsberg MJ, Sainsbury F (2017). Engineering Recombinant Virus-like Nanoparticles from Plants for Cellular Delivery. ACS Nano. 11(4):3476-3484. doi: 10.1021/acsnano.6b07747.

Mardanova ES, Blokhina EA, Tsybalova LM, Peyret H, Lomonossoff GP, Ravin NV. (2017). Efficient Transient Expression of Recombinant Proteins in Plants by the Novel pEff Vector Based on the Genome of Potato Virus X. Front Plant Sci. 8:247. doi: 10.3389/fpls.2017.00247.

Meshcheriakova Y, Durrant A, Hesketh EL, Ranson NA, Lomonossoff GP, (2017). Combining high-resolution cryo-electron microscopy and mutagenesis to develop cowpea mosaic virus for bionanotechnology. Biochem Soc Trans. 45(6):1263-1269. doi: 10.1042/BST20160312.

Saunders K, Lomonossoff GP, (2017). In Planta Synthesis of Designer-Length Tobacco Mosaic Virus-Based Nano-Rods That Can Be Used to Fabricate Nano-Wires. Front Plant Sci. 8:1335. doi: 10.3389/fpls.2017.01335.

Steele JFC, Peyret H, Saunders K, Castells-Graells R, Marsian J, Meshcheriakova Y, Lomonossoff GP. (2017). Synthetic plant virology for nanobiotechnology and nanomedicine. Wiley Interdiscip Rev Nanomed Nanobiotechnol. 9(4). doi: 10.1002/wnan.1447.

Lebedev N, Griva I, Dressick WJ, Phelps J, Johnson JE, Meshcheriakova Y, Lomonossoff GP, Soto CM. (2016). A virus-based nanoplasmonic structure as a surface-enhanced Raman biosensor. Biosens Bioelectron. 77:306-14. doi: 10.1016/j.bios.2015.09.032.

Lomonossoff GP and D’Aoust MA (2016). Plant-produced biopharmaceuticals: A case of technical developments driving clinical deployment. Science 353(6305):1237-40. doi: 10.1126/science.aaf6638.

Saxena P, Thuenemann EC, Sainsbury F, Lomonossoff GP (2016). Virus-Derived Vectors for the Expression of Multiple Proteins Plants. Methods Mol Biol. 1385:39-54. doi: 10.1007/978-1-4939-3289-4_3.

Peyret H., Lomonossoff G. P. (2015). When plant virology met Agrobacterium: the rise of the deconstructed clones. Plant Biotechnol J. 13(8):1121-35. doi: 10.1111/pbi.12412.

Saunders K, Lomonossoff GP. (2015). The Generation of Turnip Crinkle Virus-Like Particles in Plants by the Transient Expression of Wild-Type and Modified Forms of Its Coat Protein. Front Plant Sci. 6:1138. doi: 10.3389/fpls.2015.01138.

Meshcheriakova YA, Saxena P, Lomonossoff GP (2014). Fine-tuning levels of heterologous gene expression in plants by orthogonal variation of the untranslated regions of a nonreplicating transient expression system. Plant Biotechnol J. 12(6):718-27. doi: 10.1111/pbi.12175.

Sainsbury F, and Lomonossoff GP, (2014). Transient expressions of synthetic biology in plants. Curr Opin Plant Biol. 19:1-7. doi: 10.1016/j.pbi.2014.02.003.

Workpackage K: OpenPlant Fund for interdisciplinary research

Urban L, Holzer A, Baronas JJ, Hall M, Braeuninger-Weimer P, Scherm MJ, Kunz DJ, Perera SN, Martin-Herranz DE, Tipper ET, Salter SJ, Stammnitz MR (2020) Freshwater monitoring by nanopore sequencing. bioRxiv 2020.02.06.936302; doi: https://doi.org/10.1101/2020.02.06.936302

Penfold CA, Gherman I, Sybirna A, Wild DL (2019) Inferring Gene Regulatory Networks from Multiple Datasets. Methods Mol Biol. 1883:251-282. doi: 10.1007/978-1-4939-8882-2_11.

Penfold PA, Sybirna A, Reid JE, Huang Y, Wernisch L, Ghahramani Z, Grant M, Surani MA (2018) Branch-recombinant Gaussian processes for analysis of perturbations in biological time series. Bioinformatics. 1; 34(17): i1005–i1013. doi: 10.1093/bioinformatics/bty603

Ghosh S, Watson A, Gonzalez-Navarro OE, Ramirez-Gonzalez R, Yanes L, Mendoza-Suárez M, Simmonds J, Wells R, Rayner T, Green P, Hafeez A, Hayta S, Melton RE, Steed A, Sarkar A, Carter J, Perkins L, Lord J, Tester M, Osbourn A, Moscou MJ, Nicholson P, Harwood W, Martin C, Domoney C, Uauy C, Hazard B, Wulff BBH, Hickey LT (2018) Speed breeding in growth chambers and glasshouses for crop breeding and model plant research. Nat Protoc. 13(12):2944-2963. doi: 10.1038/s41596-018-0072-z.

Yu Z, Boehm CR, Hibberd JM, Abell C, Haseloff J, Burgess SJ, Reyna-Llorens I. (2018) Droplet-based microfluidic analysis and screening of single plant cells. PLoS One. 13(5):e0196810. doi: 10.1371/journal.pone.0196810.

Scott D and Berry D (2018). Genetic Resources in the age of the Nagoya Protocol and gen/genome synthesis. http://www.stis.ed.ac.uk/__data/assets/pdf_file/0005/247595/Nagoya_workshop_report_web.pdf

Juhas M, Ajioka JW, (2017). T7 RNA polymerase-driven inducible cell lysis for DNA transfer from Escherichia coli to Bacillus subtilis. Microb Biotechnol. 10(6):1797-1808. doi: 10.1111/1751-7915.12843.

Nuñez I, Matute T, Herrera R, Keymer J, Marzullo T, Rudge T, Federici F (2017). Low cost and open source multi-fluorescence imaging system for teaching and research in biology and bioengineering. PLOS One 12(11):e0187163. doi: 10.1371/journal.pone.0187163

Sotta N, Duncan S, Tanaka M, Sato T, Marée AF, Fujiwara T, Grieneisen VA. (2017). Rapid transporter regulation prevents substrate flow traffic jams in boron transport. eLife 6:e27038. DOI: 10.7554/eLife.27038

Duncan S, Olsson TSG, Hartley M, Dean C, Rosa S (2016). A method for detecting single mRNA molecules in Arabidopsis thaliana. Plant Methods. 12:13. doi: 10.1186/s13007-016-0114-x.

Juhas M, Ajioka JW. (2016). Integrative bacterial artificial chromosomes for DNA integration into the Bacillus subtilis chromosome. J Microbiol Methods 125:1-7. doi: 10.1016/j.mimet.2016.03.017.

Juhas M, Ajioka JW. (2016). Lambda Red recombinase-mediated integration of the high molecular weight DNA into the Escherichia coli chromosome. Microb Cell Fact. 15(1):172.

Juhas M, Wong C, Ajioka JW (2016). Combining Genes from Multiple Phages for Improved Cell Lysis and DNA Transfer from Escherichia coli to Bacillus subtilis. PLoS One. 11(10):e0165778. doi: 10.1371/journal.pone.0165778.

Liddicoat, J. and Liddell, K. (2016). Open Innovation with Large Bioresources: Goals, Challenges and Proposals. https://papers.ssrn.com/sol3/papers.cfm?abstract_id=2888871

Workpackage L: OpenPlant Forum: responsible innovation

Osbourn A (2020). Mock Orange. London: SPM Publications. ISBN: 978-1-9162263-2-6

Lee NM, Hodgson HE, Hann C, O’Driscoll M, Stebbings S, Matthewman C, Kent M, Rant J & Osbourn A (2020). The Global Garden project: Imagining plant science. Plants, People, Planet 2: 602-613 https://doi.org/10.1002/ppp3.10133

Kahl L, Molloy J, Patron N, Matthewman C, Haseloff J, Grewal D, Johnson R, Endy D. (2018) Opening options for material transfer. Nat Biotechnol. 36(10):923-927. doi: 10.1038/nbt.4263.

Halewood M, Chiurugwi T, Sackville Hamilton R, Kurtz B, Marden E, Welch E, Michiels F, Mozafari J, Sabran M, Patron N, Kersey P, Bastow R, Dorius S, Dias S, McCouch S, Powell W (2018). Plant genetic resources for food and agriculture: opportunities and challenges emerging from the science and information technology revolution. New Phytol. 217(4):1407-1419. doi: 10.1111/nph.14993.

Wintle BC, Boehm CR, Rhodes C, Molloy JC, Millett P, Adam L, Breitling R, Carlson R, Casagrande R, Dando M, Doubleday R, Drexler E, Edwards B, Ellis T, Evans NG, Hammond R, Haseloff J, Kahl L, Kuiken T, Lichman BR, Matthewman CA, Napier JA, ÓhÉigeartaigh SS, Patron NJ, Perello E, Shapira P, Tait J, Takano E, Sutherland WJ. (2017). A transatlantic perspective on 20 emerging issues in biological engineering. Elife 6.pii: e30247. doi: 10.7554/eLife.30247.

Parry G, Patron NJ, Bastow R, Matthewman C (2016). Meeting review: GARNet/OpenPlant CRISPR-Cas Workshop. Plant Methods 12:6 https://doi.org/10.1186/s13007-016-0104-z

Carmichael RE, Boyce A, Matthewman C, Patron NJ (2015). An introduction to synthetic biology in plant systems: ERASynBio/ OpenPlant summer school for early career researchers, September 2014. New Phytol. 208(1):20-2. doi: 10.1111/nph.13433.