Barry Flinn

Educational Background

Ph.D. Botany
University of British Columbia 1992

M.Sc. Biology
Queens University at Kingston 1986

B.Sc. Biology (Honours)
Queens University at Kingston 1982

Profile

I have been carrying out tissue culture, transformation, molecular biology, biochemistry, and functional genomics since my Ph.D. studies at the University of British Columbia, and subsequent post-doctoral training at the University of Georgia (1992-1994) and the University of Ottawa (1994-1996).

I have extensive biotechnology experience in applied biology research environments. While a Staff Scientist and eventual Project Leader at Genesis Research and Development Corporation (1996-2000: Auckland, New Zealand), I oversaw large-scale gene and promoter candidate discovery and screening efforts from the largest forestry gene database at that time. Some of this work was carried out in collaboration with Arborgen LLC, and also involved Westvaco and International Paper. Following this, I served as Research Director for Solanum Genomics International Inc. (2000-2005: Fredericton, NB, Canada), as well as the Co-Lead Investigator for the Genome Canada-funded Canadian Potato Genome Project. My potato efforts were primarily focused on the generation of gene and microarray expression profiling data to identify genes associated with potato development, as well as resistance and susceptibility to Late Blight, and helping in the development of activation-tagged mutant potato lines.

Most recently (2005-2015), I served as the Founding Director of the Institute (later Center) for Sustainable and Renewable Resources at the Virginia Tech-affiliated Institute for Advanced Learning and Research (IALR - Danville, VA), and as an Adjunct Professor in 1) Horticulture and 2) Forest Resources and Environmental Conservation at Virginia Tech. The overall focus of the IALR was on applied research for economic development in southern Virginia. While at the IALR, I helped create a research institute targeting basic research with commercialization potential in: 1) high value horticulture and forestry crop development, 2) bio-based products, and 3) molecular breeding for biomass and bioenergy crops.

My efforts have resulted in over 40 publications, several US and international patents, as well as a start-up business spin-off. I also have significant experience mentoring high school, undergraduate and graduate students, as well as extensive outreach experience with the public. I am interested in using my interests in basic and applied science to aid in knowledge generation, and the translation from discovery to commercialization and economic development.

Research Interests

Over a 9 year period (1996-2005), I was heavily engaged in both conifer and potato genomics efforts, carrying out gene discovery, gene expression profiling and gene function testing targeting an understanding of the regulation of embryogenesis, and the modulation of key developmental traits of commercial interest, much of this in applied commercial biotechnology research settings.

While at the Institute for Advanced Learning and Research (2005-2015) and as an Adjunct Professor at Virginia Tech, I continued my research efforts on plant development, targeting various experimental systems:
• conifers (somatic embryogenesis control in pine and fir species, developmental gene expression during embryogenesis, extracellular protease involvement in pine embryogenesis)
• potato (mutant screening for genes regulating trait development, epigenetic changes during potato development in response to beneficial endophytic microbes),
• Arabidopsis (molecular biology and biochemistry of extracellular matrix metalloproteinases)
• monocot bioenergy crops (propagation, mutation breeding and endophyte-mediated performance enhancement with switchgrass, Miscanthus and Arundo)

My most current research efforts focused on the biochemistry, functionality and biotechnological applications of specific proteins (plant extracellular matrix metalloproteinases and StBTB/POZ1 – a BTB/POZ-domain protein associated with various potato developmental phenotypes), as well as on the use of, and molecular mechanisms by which beneficial bacterial endophytes enhance plant development and performance.

At Clemson, my primary role is focused on administrative management of the Kresovich lab's DOE ARPA-E TERRA project. In addition, I am developing research efforts focused on: 1) Tissue culture and transformation systems for use in sorghum functional genomics, and 2) Endophyte-mediated sorghum performance enhancement.

Publications

Lara-Chavez A, Lowman S, Kim-Dura S, Tang Y, Zhang J, Udvardi M, Nowak J, Flinn B, Mei C. 2015. Global gene expression profiling of two switchgrass cultivars following inoculation with Burkholderia phytofirmans strain PsJN. J Exp Bot 66:4337-4350.

Aulakh SS, Veilleux RE, Tang G, Flinn BS. 2015. Characterization of a potato activation tagged mutant, nikku, and its partial revertant. Planta 241:1481-1495.

Lowman JS, Lara-Chavez A, Kim-Dura S, Flinn B, Nowak J, Mei C. 2015. Switchgrass field performance on two soils as affected by bacterization of seedlings with Burkholderia phytofirmans strain PsJN. BioEnergy Research 8:440-449.

Aulakh SS, Veilleux RE, Dickerman AW, Tang G, Flinn BS. 2014. Characterization and RNA-seq analysis of underperformer, an activation-tagged potato mutant. Plant Mol Biol 84:635-658.

Da K, Farish-Williford H, Flinn B. 2013. Acclimatization of micropropagated Icelandic Poppy ‘Temptress’ plantlets. Acta Hort 988:93-98.

Pantazis CJ, Fisk S, Mills K, Flinn BS, Shulaev V, Veilleux RE, Dan Y. 2013. Development of an efficient transformation method by Agrobacterium tumefaciens and high throughput spray assay to identify transgenic plants for woodland strawberry (Fragaria vesca) using NPTII selection. Plant Cell Rep 32:329-337.

Kim S, Lowman S, Hou G, Nowak J, Flinn B, Mei C. 2012. Growth promotion and colonization of switchgrass (Panicum virgatum) cv. Alamo by bacterial endophyte Burkholderia phytofirmans strain PsJN. Biotechnol Biofuels 5:37.

Lara-Chavez A, Egertsdotter U, Flinn BS. 2012. Comparison of gene expression markers during zygotic and somatic embryogenesis in pine. In Vitro Cell Dev Biol-Plant 48:341-354.

Da K, Nowak J, Flinn B. 2012. Potato cytosine methylation and gene expression changes induced by a beneficial bacterial endophyte, Burkholderia phytofirmans strain PsJN. Plant Physiol Biochem 50:24-34.

Veilleux RE, Oosumi T, Wadl PA, Baxter AJ, Holt SH, Ruiz-Rojas JJ, Pattison J, Flinn B, Dan Y, Nessler C, Shulaev V. 2011. Insertional mutagenesis in the diploid strawberry (Fragaria vesca). Acta Hort 941:49-54.

Lara-Chavez A, Flinn BS, Egertsdotter U. 2011. Initiation of somatic embryogenesis from immature zygotic embryos of Oocarpa pine (Pinus oocarpa). Tree Physiol 31:539-554.

Shulaev V, Sargent DJ, Crowhurst RN, Mockler TC, Folkerts O, Delcher AL, Jaiswal P, Mockaitis K, Liston A, Mane SP, Burns P, Davis TM, Slovin JP, Bassil N, Hellens RP, Evans C, Harkins T, Kodira C, Desany B, Crasta OR, Jensen RV, Allan AC, Michael TP, Setubal JC, Celton JM, Rees DJ, Williams KP, Holt SH, Ruiz Rojas JJ, Chatterjee M, Liu B, Silva H, Meisel L, Adato A, Filichkin SA, Troggio M, Viola R, Ashman TL, Wang H, Dharmawardhana P, Elser J, Raja R, Priest HD, Bryant DW Jr, Fox SE, Givan SA, Wilhelm LJ, Naithani S, Christoffels A, Salama DY, Carter J, Lopez Girona E, Zdepski A, Wang W, Kerstetter RA, Schwab W, Korban SS, Davik J, Monfort A, Denoyes-Rothan B, Arus P, Mittler R, Flinn B, Aharoni A, Bennetzen JL, Salzberg SL, Dickerman AW, Velasco R, Borodovsky M, Veilleux RE, Folta KM. 2011. The genome of woodland strawberry (Frageria vesca). Nat Genet 43:109-118.

Mei C, Flinn BS. 2010. The use of beneficial microbial endophytes for plant biomass and stress tolerance improvement. Recent Pat Biotechnol 4:81-95.

Ratnaparkhe SM, Egertsdotter EMU, Flinn BS. 2009. Identification and characterization of a matrix metalloproteinase (Pta1-MMP) expressed during Loblolly pine (Pinus taeda) seed development, germination completion and early seedling establishment. Planta 230:339-354.

Flinn B. 2008. Plant extracellular matrix metalloproteinases. Funct Plant Biol 35:1183-1193.

Kloosterman B, De Koeyer D, Griffiths R, Flinn B, Steuernagel B, Scholz U, Sonnewald S, Sonnewald U, Bryan GJ, Prat S, Bánfalvi Z, Hammond JP, Geigenberger P, Nielsen KL, Visser RG, Bachem CW. 2008. Genes driving potato tuber initiation and growth: identification based on transcriptional changes using the POCI array. Funct Integr Genomics 8:329-340.

Li X-Q, Griffiths R, De Koeyer D, Rothwell C, Gustafson V, Regan S, Flinn B. 2008. Functional genomic resources for potato. Can J Plant Sci 88:573-581.

Book Chapters:

Mei C, Lara-Chavez A, Lowman S, Flinn B. 2013. The use of endophytes and mycorrhizae in switchgrass biomass production. In Compendium of Bioenergy Plants: Switchgrass (H. Luo and Y. Wu, eds.). CRC Press, Boca Raton, pp. 67-108.

Wilson SR, Flinn B. 2011. Bionanotechnology applications in plants and agriculture. In Bionanotechnology II: Global Prospects (D. E. Reisner, ed.) CRC Press, Boca Raton, pp. 519-535.

Patents:

Vascular-preferred promoters II.
Inventors: Phillips, Jonathan; Puthigae, Sathish; Yao, JiaLong; Flinn, Barry; Forster, Richard S.; Eagleton, Clare.
Assignee: Arborgen LLC
Patent issued: US8389806 03-15-2013

Vascular-preferred promoters I.
Inventors: Phillips, Jonathan; Puthigae, Sathish; Yao, JiaLong; Flinn, Barry; Forster, Richard S.; Eagleton, Clare.
Assignee: Arborgen LLC
Patent issued: US7442786 10-28-2008

Compositions affecting programmed cell death and their use in the modification of forestry
plant development.
Inventors: Flinn, Barry; Lashem, Annette.
Assignee: Genesis Research and Development Corp. Ltd.
Patent issued: US6451604 09-17-2002

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