Publications

A full list of Karen’s publications can be found on her NCBI Bibliography.
A full list of Somen’s publications can be found on his NCBI Bibliography.

*  indicates post-doc, ** indicates graduate student, *** indicates undergraduate student, ¥ indicates international collaborator, † indicates industry collaborator, ¡ indicates government/national laboratory collaborator, § co-first authors

Pre-prints

  • Matthew J. McNulty**, Yongao (Mary) Xiong** and Kevin Yates**, Kalimuthu Karuppanan*, Jacob M. Hilzinger*, Aaron J. Berliner**, Jesse Delzio***, Adam P. Arkin, Nancy E. Lane, Somen Nandi, and Karen A. McDonald (2020). Molecular Pharming to Support Human Life on the Moon, Mars, and Beyond, (In review: Critical Review in Biotechnology) published in Preprints as a preprint
    DOI: 10.20944/preprints202009.0086.v1.

2020

  • Kantharakorn Macharoen**, Min Du***, Seongwon Jung***, Karen McDonald, and Somen Nandi (2020d) Production of Recombinant Butyrylcholinesterase from Transgenic Rice Cell Suspension Cultures in a pilot scale bioreactor Preprint DOI: 10.22541/au.159863166.62966107 (In press Biotechnology and Bioengineering)
  • Kantharakorn Macharoen**, Karen A. McDonaldand Somen Nandi (2020c). A Method to Simplify Bioreactor Processing for Recombinant Protein Production in Rice Cell Suspension Cultures. MethodsX. In press. https://doi.org/10.1016/j.mex.2020.101139
  • Jasmin M. Corbin**§, Matthew J. McNulty**§, Kantharakorn Macharoen**, Karen A. McDonald, and Somen Nandi (2020). Techno‐economic Analysis of Semicontinuous Bioreactor Production of Biopharmaceuticals in Transgenic Rice Cell Suspension Cultures. Biotechnology and Bioengineering.
    DOI: 10.1002/bit.27475

    • Also featured as section cover in Biotechnology and Bioengineering, Oct, 2020, Vol 117 (10) Technoeconomic analysis of semicontinuous bioreactor production of biopharmaceuticals in transgenic rice cell suspension cultures. (DOI https://doi.org/10.1002/bit.27061.
  • Karen A. McDonald and R. Barry Holtz† (2020). From Farm to Finger Prick – A Perspective on How Plants Can Help in the Fight Against COVID-19. Frontiers in Bioengineering and Biotechnology 03 July 2020. DOI: 10.3389/fbioe.2020.00782.
  • Austen Bernardi**, Yihan Huang**, Bradley Harris***, Yongao Xiong**, Somen Nandi, Karen A. McDonald, and Roland Faller (2020). Development and Simulation of Fully Glycosylated Molecular Models of ACE2-Fc Fusion Proteins and Their Interaction with the SARS-CoV-2 Spike Protein Binding Domain. PLoS ONE, 15(8): e0237295.
    DOI: 10.1371/journal.pone.0237295. eCollection 2020 PMID: 32756606.

    • Associated dataset submission: Faller, Roland, Bernardi, Austen, Huang, Yihan, Harris, Bradley, Xiong, Yongao, Nandi, Somen, & McDonald, Karen. (2020). 0 ns and 75 ns configurations of glycosylated ACE2-FC and its interaction with SARS-CoV-2 binding domains [Data set]. doi: 10.25338/B82G9B.
  • Kantharakorn Macharoen**, Qiongyu Li**, Veronica A. Márquez-Escobar*, Jasmine M. Corbin**, Carlito B. Lebrilla, Somen Nandi and Karen A. McDonald (2020b). Effects of Kifunensine on Production and N-glycosylation Modification of Butyrylcholinesterase in a Transgenic Rice Cell Culture Bioreactor. International Journal of Molecular Sciences, 21:6896.
    DOI: 10.3390/ijms21186896.
  • Kantharakorn Macharoen**, Karen A. McDonald, and Somen Nandi (2020a). Simplified Bioreactor Processes for Recombinant Butyrylcholinesterase Production in Transgenic Rice Cell Suspension Cultures. Biochemical Engineering Journal.
    DOI: 10.1016/j.bej.2020.107751.
  • Daniel Tusé, Somen Nandi, Karen A. McDonald, Johannes F. Buyel¥ (2020). The Emergency Response Capacity of Plant-based Biopharmaceutical Manufacturing – What It Is and What It Could Be. Frontiers in Plant Science, October 2020, Vol 11, Article 594019.
    DOI: 10.3389/fpls.2020.594019

2019

  • McNulty MJ**, Gleba Y¥, Tusé D, Hahn‐Löbmann S¥, Giritch A¥, Nandi S, McDonald KA. (2019) Techno‐economic analysis of a plant‐based platform for manufacturing antimicrobial proteins for food safety. Biotechnol. Prog.
    DOI: 10.1002/btpr.2896
  • Xiong, Y.**, Karuppanan, K.*, Bernardi, A.*, Li, Q.*, Kommineni, V., Dandekar, A.M., Lebrilla, C.B., Faller, R., McDonald, K.A., and Nandi, S. (2019) Effects of N-Glycosylation on the Structure, Function, and Stability of a Plant-Made Fc-Fusion Anthrax Decoy Protein. Frontiers in Plant Science, 10, 768.
    DOI: 10.3389/fpls.2019.00768
  • Kommineni, V †, Markert, M.*, Ren, Z.**, Palle, S. †, Carrillo, B.*, Deng, J., Tejeda, A.**, Nandi, S.; McDonald, K.A., Marcel, S. and Holtz, B. (2019) In Vivo Glycan Engineering via the Mannosidase I Inhibitor (Kifunensine) Improves Efficacy of Rituximab Manufactured in Nicotiana benthamiana Plants. International Journal for Molecular Sciences, 20(1), 194.
    DOI: 10.3390/ijms20010194 
  • Alkanaimsh, S.*, Corbin, J.M.*, Kailemia, M.J.**, Karuppanan, K.**, Rodriguez, R.L., Lebrilla, K.B., McDonald, K.A. and Nandi, S. (2019). Purification and site-specific N-glycosylation analysis of human recombinant butyrylcholinesterase from Nicotiana benthamianaBiochemical Engineering Journal 142: 58–67.
    DOI: org/10.1016/j.bej.2018.11.004

2018

  • Alam, A.***, Jiang, L.***, Kittleson, G. A.***, Steadman, K. D.***, Nandi, S., Fuqua, J. L., Palmer, K.E., Tusé D.† , and McDonald, K. A. (2018). Technoeconomic Modeling of Plant-Based Griffithsin Manufacturing. Frontiers in Bioengineering and Biotechnology, 6, 102.
    DOI: 10.3389/fbioe.2018.00102
  • Huang, Ting-Kuo**, Falk, Bryce W., Dandekar,  Abhaya M., McDonald, Karen A. (2018). Enhancement of Recombinant Protein Production in Transgenic Nicotiana benthamiana Plant Cell Suspension Cultures with Co-Cultivation of Agrobacterium Containing Silencing Suppressors. International Journal of Molecular Sciences. 2018; 19(6):1561.
    DOI: 10.3390/ijms19061561.
  • Sukenik, Sara C.**, Karuppanan, Kalimuthu*, Li, Qiongyu**, Lebrilla, Carlito B., Nandi, Somen, and McDonald, Karen A. (2018). Transient Recombinant Protein Production in Glycoengineered Nicotiana benthamiana Cell Suspension Culture. International Journal of Molecular Sciences, 19(4): 1205.
    DOI: 10.3390/ijms19041205.
  • Silberstein, David Z.**, Karuppanan Kalimuthu*, Aung, Hnin Hnin, Chen, Ching-Hsein, Cross, Carroll E., McDonald,  Karen A. (2018) An Oxidation-Resistant, Recombinant Alpha-1 Antitrypsin Produced in Nicotiana benthamiana. Free Radical Biology and Medicine 120: 303-310.
    DOI: 10.1016/j.freeradbiomed.2018.03.015.
  • Xiong, Yongao**, Li, Qiongyu**, Kailemia, Muchena J.*, Lebrilla, Carlito B., Nandi, Somen and McDonald, KarenA. (2018). Glycoform Modification of Secreted Recombinant Glycoproteins through Kifunensine Addition during Transient Vacuum Agroinfiltration. International Journal of Molecular Sciences19(3): 890.
  • Corbin, Jasmine M.**, Kailemia, Muchena J.*, Cadieux, C. Linn, AlkanaimshSalem**, Karuppanan, Kalimuthu*, Rodriguez, Raymond L., Lebrilla, Carlito B., Cerasoli, Douglas M., McDonald, Karen A. and Nandi, Somen (2018). Purification, Characterization, and N-glycosylation of Recombinant Butyrylcholinesterase from Transgenic Rice Cell Suspension Cultures. Biotechnology and Bioengineering, 115(5), 1301-1310.
    DOI: 10.1002/bit.26557.

2017

  • Leth, Ingrid K.** and McDonald Karen A. (2017). Growth Kinetics and Scale-up of Agrobacterium tumefaciensApplied Microbiology and Biotechnology, 101(12):4895-4903.
    DOI: 10.1007/s00253-017-8241-5
  • Leth, Ingrid K.** and McDonald K.A. (2017).  Media Development for Large Scale Agrobacterium tumefaciens Culture.” Biotechnology Progress, 33(5):1218.
    DOI: 10.1002/btpr.2504.
  • Karuppanan, Kalimuthu*, Duhra-Gill, Sifti**, Kailemia, Muchena J.*, Phu, My L., Lebrilla, Carlito B., Dandekar, Abhaya M., Rodriguez, Raymond L., Nandi, Somen and McDonald Karen A. (2017). Expression, Purification, and Biophysical Characterization of a Secreted Anthrax Decoy Fusion Protein in Nicotiana benthamianaInternational Journal of Molecular Sciences, 18(1):89.
    DOI: 10.3390/ijms18010089

2016

  • Nandi S., Kwong A.T.***, Holtz B.R., Erwin R.L., Marcel S., McDonald K.A. (2016). “Techno-economic analysis of a transient plant-based platform for monoclonal antibody production.” mAbs. 8(8):1456-1466.
    DOI: 10.1080/19420862.2016.1227901
  • Nandi, S., Thota, S.*, Nag, A.*, Divyasukhananda, S.¥, P Goswami¥, Aravindakshan, A., Rodriguez, RL., and Mukherjee, B (2016) Computing for rural empowerment: enabled by last-mile telecommunications.  IEEE Communications 54 (6), 102-109.
    DOI: 10.1109/MCOM.2016.7498095
  • Goswami, R.¥, Dasgupta, P.¥, Saha, S., Venkatapuram, P.***, and Nandi, S. (2016). Resource integration in smallholder farms for sustainable livelihoods in developing countries Cogent Food & Agriculture 2(1) 1-15.
    DOI: 10.1080/23311932.2016.1272151
  • Jung S.**, McDonald K.A. (2016). “Improved Transient Production of a Cellulase Enzyme in Detached Sunflower Leaves Using Plant Hormones.” Biotechnology and Bioprocess Engineering. Nov;21(6):726-732.
    DOI: 10.1007/s12257-016-0410-3
  • Alkanaimsh S.**, Karuppanan K.*, Guerrero A.*, Tu A.M., Hashimoto B.**, Hwang M.S.*, Phu M.L., Arzola L.*, Lebrilla C.B., Dandekar A.M., Falk B.W., Nandi S., Rodriguez R.L., McDonald K.A. (2016). “Transient Expression of Tetrameric Recombinant Human Butyrylcholinesterase in Nicotiana benthamiana.” Frontiers in plant science. 7:743.
    DOI: 10.3389/fpls.2016.00743
  • Corbin J.M.**, Hashimoto B.I.**, Karuppanan K.*, Kyser Z.R.***, Wu L.†, Roberts B.A.†, Noe A.R.†, Rodriguez R.L., McDonald K.A., Nandi S. (2016). “Semicontinuous Bioreactor Production of Recombinant Butyrylcholinesterase in Transgenic Rice Cell Suspension Cultures.” Frontiers in plant science. 7:412.
    DOI: 10.3389/fpls.2016.00412

2015

  • Jung S.K., McDonald K.A., Dandekar A.M. (2015). “Effect of leaf incubation temperature profiles on Agrobacterium tumefaciens-mediated transient expression.” Biotechnology progress. 31(3):783-90.
    DOI: 10.1002/btpr.2077
  • Dinh, Thu Huong ¥, Jang, Nan Young ¥, McDonald, Karen A., & Won, Keehoon ¥. (2015). Cross-linked aggregation of glutamate decarboxylase to extend its activity range toward alkaline pH. Journal of Chemical Technology & Biotechnology, 90(11), 2100-2105. (JIF: 3.10)
    DOI: 10.1002/jctb.4640
  • Nandi, S. and Khush, G.S. (2015) Strategies to Increase Heterologous Protein Expression in Rice Grains. In: Recent Advancements in Gene Expression and Enabling Technologies in Crop Plants (Azhakanandam, K., Silverstone, A., Daniell, H. and Davey, R.M. eds), pp. 241-262. New York, NY: Springer New York.
    DOI: 10.1007/978-1-4939-2202-4
  • Doyle, M.M.***, Garcia, S.**, Bahati, E.¥, Karamuzi, D.¥, Cullor, J.S. and Nandi, S. (2015) Microbiological analysis of raw milk in Rwanda. African Journal of Food Science and Technology 6, 141-143.
    DOI: 10.4315/0362-028X.JFP-13-230

2014

  • Jung S.K.**, Lindenmuth B.E.**, McDonald K.A., Hwang M.S.*, Bui M.Q., Falk B.W., Uratsu S.L., Phu M.L., Dandekar A.M. (2014). “Agrobacterium tumefaciens mediated transient expression of plant cell wall-degrading enzymes in detached sunflower leaves.” Biotechnology progress. 30(4):905-15.
    DOI: 10.1002/btpr.1888
  • Tusé D.†, Tu T.**, McDonald K.A. (2014). “Manufacturing economics of plant-made biologics: case studies in therapeutic and industrial enzymes.” BioMed research international. 2014:256135.
    DOI: 10.1155/2014/256135
  • Kingsbury N.J.**, McDonald K.A. (2014). “Quantitative evaluation of E1 endoglucanase recovery from tobacco leaves using the vacuum infiltration-centrifugation method.” BioMed research international. 2014:483596.
    DOI: 10.1155/2014/483596
  • Nandi S., McDonald K.A. (2014). “Expression of Recombinant Proteins in Plant Cell Culture.” In Hefferon K. (Ed.), Plant-derived Pharmaceuticals: Principles and Applications for Developing Countries. Boston, MA: CABI.

2013

  • Dinh T.H.¥, Ho N.A.¥, Kang T.J., McDonald K.A., Won K. ¥ (2013). “Salt-free production of γ-aminobutyric acid from glutamate using glutamate decarboxylase separated from Escherichia coli.” Journal of Chemical Technology and Biotechnology. Nov 25;89:1432-1436
    DOI: 10.1002/jctb.4251

2012

  • Hwang M.S.*, Lindenmuth B.E.**, McDonald K.A., Falk B.W. (2012). “Bipartite and tripartite Cucumber mosaic virus-based vectors for producing the Acidothermus cellulolyticus endo-1,4-beta-glucanase and other proteins in non-transgenic plants.” BMC Biotechnol. Sep 21;12(1):66.
    DOI: 10.1186/1472-6750-12-66
  • Huang T.K.**, McDonald K.A. (2012). “Bioreactor systems for in vitro production of foreign proteins using plant cell cultures.” Biotechnol Adv. Mar-Apr;30(2):398-409.
    DOI: 10.1016/j.biotechadv.2011.07.016
  • Kjelstrom J.A., McDonald K.A., Hargadon A., Agatstein W., Arnold M. (2012). “The University of California, Davis, Collaborative Model for Biotechnology Education and Training.” Journal of Commercial Biotechnology. 12(4):87-97.
  • Huang T.**, McDonald K.A. (2012). “Molecular Farming Using Bioreactor-Based Plant Cell Suspension Cultures for Recombinant Protein Production.” In Wang A., Ma S., (Eds.), Molecular Farming in Plants. New York, NY: Springer.
  • McDonald K.A. (2012). “In Planta Production of Cell Wall Degrading Enzymes.” In Kole C., Joshi C.P., Shonnard D., (Eds.), Handbook of Bioenergy Crop Plants. Boca Raton, FL: CRC Press.

2011

  • Jung S.**, McDonald K.A. (2011). “Visual Gene Developer: a fully programmable bioinformatics software for synthetic gene optimization.” BMC Bioinformatics, 12(1): 340.
    DOI: 10.1186/1471-2105-12-340
  • Arzola L.**, Chen J.***, Rattanaporn K.**, Maclean J.M.†, McDonald K.A. (2011). “Transient Co-Expression of Post-Transcriptional Gene Silencing Suppressors for Increased in Planta Expression of a Recombinant Anthrax Receptor Fusion Protein.” Int. J. Mol. Sci, 12: 4975-4990.
    DOI: 10.3390/ijms12084975
  • Lindenmuth B.E.**, McDonald K.A. (2011). “Production and characterization of Acidothermus cellulolyticus endoglucanase in Pichia pastoris.” Protein Expression and Purification, 77(2): 153-158.
    DOI: 10.1016/j.pep.2011.01.006
  • McDonald K.A. (2011). “Bioreactions and Bioreactor Operation: Heterologous Protein Expression.” In Moo-Young M. (Ed.), Comprehensive Biotechnology. Waltham, MA: Elsevier.

2010

  • Huang T.K.**, Plesha M.A.**, McDonald K.A. (2010). “Semicontinuous Bioreactor Production of a Recombinant Human Therapeutic Protein Using a Chemically Inducible Viral Amplicon Expression System in Transgenic Plant Cell Suspension Cultures.” Biotechnology and Bioengineering, 106(3): 408-421.
    DOI: 10.1002/bit.22713

2009

  • Huang T.K.**, McDonald K.A.  (2009). “Bioreactor Engineering for Recombinant Protein Production in Plant Cell Suspension Cultures.” Biochemical Engineering Journal, 45: 168-184.
    DOI: 10.1016/j.bej.2009.02.008
  • Plesha M.A.**, Huang T.K.**, Dandekar A.M., Falk B.W., McDonald K.A. (2009). “Optimization of the Bioprocessing Conditions for Scale-Up of Transient Production of a Heterologous Protein in Plants Using a Chemically Inducible Viral Amplicon Expression System.” Biotechnology Progress, 25(3): 722-734.
    DOI: 10.1002/btpr.149
  • Huang T.K.**, Plesha M.A.**, Falk B.W., Dandekar A.M., McDonald K.A. (2009). “Bioreactor Strategies for Improving Production Yield and Functionality of a Recombinant Human Protein in Transgenic Tobacco Cell Cultures.” Biotechnology and Bioengineering, 102(2): 508-520.
    DOI: 10.1002/bit.22061

2007

  • Plesha M.A.**, Huang T.K.**, Dandekar A.M., Falk B.W., McDonald K.A. (2007). “High-Level Transient Production of a Heterologous Protein in Plants by Optimizing Induction of a Chemically Inducible Viral Amplicon Expression System” Biotechnology Progress, 23(6): 1277-1285.
    DOI: 10.1021/bp070238s
  • Zapalac E.**, McDonald K.A. (2007). “Economic and Environmental Assessment of the Purification of Alpha-1-Antitrypsin from Transgenic Plant Cell Suspension Cultures.” In Heinzle E., Biwer A. (Eds.), Development of Sustainable Bioprocesses – Modeling and Assessment. (pp. 261-270). Hoboken, NJ: Wiley.