Cell Culture and Fermentation
Optimization Lab
Refereed Journal Publications
These articles may be found online at Pubmed or located using the links below.
  1. Brodsky, A.N., Caldwell, M., Bao, S.E. , and Harcum, S.W.Glycosylation-related genes in NS0 cells are insensitive to moderately elevated ammonium concentrations, Journal of Biotechnology.187: 78–86 (2014).doi:10.1016/j.jbiotec.2014.07.018. 25062658
  2. Harcum, S.W. How to reconnect United States’ academic and industrial researchers to better utilize CHO 'omics in bioprocessing, Pharmaceutical Bioprocessing. 2(5): 383- 388. Oct. (2014). doi: 10.4155/PBP.14.43
  3. Baig, F., Fernando, L.P., Salazar, M.A., Powell, R.R., Bruce, T.F., Harcum, S.W. Dynamic Transcriptional Response of Escherichia coli to Inclusion Body Formation, Biotechnology and Bioengineering.  111: 980-999 (2014). doi: 10.1002/bit.25169. 24338599
  4. Gowtham, Y.K., Miller, K.P., Hodge, D.B., Henson, J.M., Harcum, S.W. A novel two-stage fermentation process for bioethanol production using Saccharomyces pastorianus, Biotechnology Progress. 30: 300-310 (2014). doi: 10.1002/btpr.1850. 24376155
  5. Salazar, M.A., Fernando, L.P., Baig, F., Harcum, S.W. The effects of protein solubility on the RNA Integrity Number (RIN) for recombinant Escherichia coliBiochemical Engineering Journal. 79: 129-135 (2013). doi: 10.1016/j.bej.2013.07.011. 24151430
  6. Brodsky, A.N., Zhang, J., Visconti, R.P., and Harcum, S.W. Expansion of mesenchymal stem cells in atmospheric carbon dioxide, 
    Biotechnology Progress29(5): 1298–1306 (2013). doi: 10.1002/btpr.1782. 23894049
  7. Brodsky, A. N., Caldwell, M., and Harcum, S. W. Glycosylation and post-translational modification gene expression analysis by DNA microarrays for cultured mammalian cells, Methods 56: 408-412 (2012) (INVITED). 22033470
  8. Wuest, D. M.,. Harcum, S. W, and Kelvin H. Lee, K. H. Genomics in Mammalian Cell Culture Bioprocessing, , Advances in Biotechnology 30: 629-638 (2012). (INVITED). 22079893
  9. Miller, K. P., Gowtham, Y. K., Henson, J. M., and Harcum, S. W.  Xylose isomerase improves growth and ethanol production rates from biomass sugars for both Saccharomyces pastorianus and Saccharomyces cerevisiae, Biotechnology Progress (online). doi/10.1002/btpr.1535. 22866331
  10. Haddadin, F. T., Kurtz, H. and Harcum, S. W. Serine Hydroxamate and the Transcriptome of High Cell Density Recombinant Escherichia coli MG1655, Applied Biochemistry and Biotechnology, 157: 124-139 (2009). 18612598
  11. Sharma, S. S., Campbell, J. W., Frisch, D., Blattner, F. R., and Harcum, S. W. Expression of two recombinant chloramphenicol acetyltransferase variants recombinant in highly reduced genome Escherichia coli strains, Biotechnology and Bioengineering, 98: 1056-1070 (2007). 17497738
  12. Chen, P., and Harcum, S. W. Identification of genes sensitive to ammonium in CHO cell cultures using a differential display, Applied Biochemistry and Biotechnology, 141: 349–360 (2007). 18025561
  13. Sharma, S. S., Blattner, F. R., and Harcum, S. W., Robustness of multiple-deletion E. coli strain under bioprocess conditions, Metabolic Engineering 9: 133-141 (2007).
  14. Posfai, G., Plunkett III, G., Feher, T., Frisch, D., Keil, G., Umenhoffer, K., Kolisnychenko, V., Stahl, B., Sharma, S. S., de Arruda, M., Burland, V., Harcum, S. W., Blattner, F. R., Emergent Properties of Reduced-Genome Escherichia coli, Science, 312: 1044-1046 (2006). 16645050
  15. Sharma, S. S., Chong, R., Harcum, S. W. Intein-mediated protein purification of fusion proteins expressed under high-cell-density conditions in E. coli, Journal of Biotechnology. 125: 48-56(2006). 16546284
  16. Harcum, S. W. and Haddadin, F. T., Global transcriptome response to heat-shock and dual heat-shock recombinant protein induction in Escherichia coli, Journal of Industrial Microbiology and Biotechnology. 33: 801-814 (2006). 16680459
  17. Chen, P., and Harcum, S. W. Effects of elevated ammonium on glycosylation gene expression in CHO cells, Metabolic Engineering, 8: 123-132 (2006). 16380282
  18. Sharma, S. S., Chong, R., Harcum, S. W. Simulation of the Large-Scale Production of a Soluble Recombinant Protein Expressed in Escherichia coli Using an Intein-Mediated Purification System, Applied Biochemistry and Biotechnology, 126:93-117(2005). 16118465
  19. Chen, P., and Harcum, S. W. Effects of amino acid additions on ammonium stressed CHO cells, Journal of Biotechnology, 117: 277-286 (2005). 15862358
  20. Clark, J.-R. Griffiths, J. Bailey, K. B.,  Harcum, S. W.Development of Method to Quantify Gene Expression Levels for Glycosylation Pathway Genes in CHO Cell Cultures, Applied Biochemistry and Biotechnology, 125: 159-173 (2005). 15917580
  21. Clark, K. J. R., Bailey, K. M., and Harcum, S. W. Effect of galactose feeding on mRNA expression levels in the glycosylation pathway for CHO expressing recombinant IL-4/13 cytokine trap, Biotechnology and Bioengineering, 90: 568-577 (2005). 15818560
  22. Haddadin, F. T., and Harcum, S. W. Transcriptome profiles for high-cell density recombinant and wild-type Escherichia coli, Biotechnology and Bioengineering, 90: 127-153 (2005). 15742388
  23. Clark, K. J. R., Chaplen, F. W. R., Harcum, S. W. Temperature Effects on Product Quality Related Enzymes in Batch tPA CHO Cells, Biotechnology Progress. 20: 1888-1892 (2004). 15575729
  24. Sharma, S. S., Zhang, A., Wang, H., Harcum, S. W., Chong, S. Study of Protein Splicing and Intein-mediated Peptide Bond Cleavage Under High-Cell-Density Conditions, Biotechnology Progress 19: 1085-1095 (2003). 12790686
  25. Jordan, G. L., and Harcum, S. W. Characterization of Up-regulated Proteases in an Industrial Recombinant Escherichia coli Fermentation, Journal of Industrial Microbiology and Biotechnology 28: 74-80 (2002). 12074055
  26. Harcum, S. W. Structured model to predict intracellular amino acid shortages during recombinant protein overexpression in E. coli, Journal of Biotechnology 93: 189-202 (2002). 11755983
  27. Barragan, M. H., and S. W. Harcum. Bioremediation of Acid Mine Drainage via Selective Removal of Metal Ions, Radioactive Waste Management and Environmental Restoration 22: 205-222 (2000).
  28. Marulanda, A. L. B., and Harcum, S. W. Removal of copper and aluminum from solution by immobilized Cyanidium caldarium, Radioactive Waste Management and Environmental Restoration 22: 223-237 (2000).
  29. Yoo, S. D., and Harcum, S. W.Xanthan Gum Production from Waste Sugar Beet Pulp, Bioresource Technology 70: 105-109 (1999). Abstract
  30. Harcum, S. W., and Bentley, W. E. The Heat-Shock and Stringent Responses have Overlapping Protease Activity in Recombinant Escherichia coli: Implications for Heterologous Protein Yield, Applied Biochemistry and Biotechnology 80: 23-37 (1999). 10394618
  31. Harcum, S. W. Cleaning up Acid Mine Drainage with Microbes, New Mexico Journal of Science, 37: 108-118 (1997).
  32. Harcum, S. W., and Bentley, W. E. Response Dynamics of 26-, 34-, 39-, 54-, and 80-kDa Proteases in Induced Cultures of Recombinant Escherichia coli, Biotechnology and Bioengineering 42: 675-685 (1993). 18613100
  33. Harcum, S. W., and Bentley, W. E. Protease Detection, Characterization, and Quantification in Recombinant Escherichia coli, Biotechnology Techniques 7: 441-447 (1993). Abstract
  34. Harcum, S. W., Dale, B. E., and Seely, R. J. Renaturation of Recombinant Secretory Leukocyte Protease Inhibitor: Aspects of Disulfide Bond Formation Kinetics, Biotechnology Letters 15: 943-948 (1993). Abstract
  35. Harcum, S. W., Ramírez, D. M., and Bentley, W. E. Optimal Nutrient Feed Policies for Heterologous Protein Production, Applied Biochemistry and Biotechnology 34/35: 161-173 (1992). Abstract
Proceedings
# Graduate Student * Presenter
  1. Matthew Pepper#, Li Wang#, Ajay Padmakumar#, Timothy Burg, Sarah Harcum, Richard E Groff*, A Real-time Adaptive Oxygen Transfer Rate Estimator for Metabolism Tracking in Escherichia coli Cultures. Engineering in Medicine and Biology Society (EMBC), 2014 36th Annual International Conference of the IEEE, 26-30, pp. 6191-6194, Aug. 2014, doi: 10.1109/EMBC.2014.6945043
  2. Matthew E. Pepper#*, Li Wang#, Ajay Padmakumar#, Timothy C. Burg, Sarah W. Harcum, Richard E. Groff, A CMI (Cell metabolic indicator)-based controller for achieving high growth rate Escherichia coli cultures, Engineering in Medicine and Biology Society (EMBC), 2014 36th Annual International Conference of the IEEE, 26-30, pp. 2911-2915, Aug. 2014, doi: 10.1109/EMBC.2014.6944232.
Refereed Book Chapters
  1. Harcum, S. (2008) Purification of protein solutions, In Biologically inspired  textiles, Eds. Ellison, M.S., Abbott, A., Woodhead Publishing, Cambridge.
  2. Harcum, S. W. (2006) Protein Glycosylation, In Cell Culture Technology for Pharmaceutical and Cellular-based Therapies, Eds. S. Ozturk and W. S. Hu, Taylor Francis, New York.
  3. Wood, D., Harcum, S. W., and Belfort, G. (2005) Engineering Applications and Future of Inteins, In Homing Endonucleases and Inteins, Eds. M. Belfort, V. Derbyshire, B. L. Stoddard, D. W. Wood, Springer-Verlag.
  4. Andersen, P. K. and Harcum, S. W. (2001) Chemical Engineering Principles, In Handbook of Water Pollution and Waster Minimization, Ed. A. Ghassemi, Marcel Dekker, New York.
Selected Presentations (out of 77)
# Graduate Student °Undergraduate Student *Presenter
  1. Yogender Kumar Gowtham#, Christopher Saski, Sarah W. Harcum (2016) Utilizing RNA-Seq technique to improve molecular understanding of Chinese hamster ovary (CHO) cell bioprocessing. Cell Culture Engineering Conference XV, May, La Quinta, CA.
  2. Daniel Odenwelder#, Arthur Nathan Brodsky#, Sarah W. Harcum (2016) Investigating the reverse Warburg effect: How high extracellular lactate alters breast cancer metabolism. Cell Culture Engineering Conference XV, May, La Quinta, CA.
  3. Yogender Kumar Gowtham#, Christopher Saski, Sarah W. Harcum (2016) Transcriptome analysis of Chinese hamster ovary (CHO) cell lines under low temperature conditions using RNA-seq 251th ACS National Meeting & Exposition. San Diego, CA, USA.
  4. Daniel Odenwelder#, Arthur Nathan Brodsky#, Sarah W. Harcum (2016) Impact of High Extracellular Lactate on Breast Cancer Metabolism, 251th ACS National Meeting & Exposition. San Diego, CA, USA.
  5. Yogender Kumar Gowtham#, Christopher Saski, Sarah W. Harcum (2015). Understanding the transcriptome responses of Chinese hamster ovary (CHO) cells using RNA-seq. 249th ACS National Meeting & Exposition. Denver, CO, USA.
  6. Daniel Odenwelder#, Sarah W. Harcum (2015). Evaluation of bicarbonate free medium for improved mammalian cell growth and monitoring in controlled bioreactors. 249th ACS National Meeting & Exposition. Denver, CO, USA
  7. Brodsky, AN#, Odenwelder, D#, Harcum, SW. (2014) Lactate's Impact on Breast Cancer Metabolism 2014 AIChE Annual Meeting, Atlanta, November.
  8. Gowtham, YK#, Saski, CS, Harcum, SW. (2014) Serum-Free Medium Adaptation of Chinese Hamster Ovary (CHO) Cell Lines: A Transcriptome Analysis Using RNA-Seq, 2014 AIChE Annual Meeting, Atlanta, November.
  9. Odenwelder, D#, Brodsky, AN#, Harcum, SW. (2014) Evaluation of Stoichiometric and 13C Metabolic Flux Analysis Methods for Determining Intracellular Fluxes in Mammalian Cells, 2014 AIChE Annual Meeting, Atlanta, November.
  10. Pepper, M.#, L. Wang#, A. Padmakumar#, S. Harcum, R. Groff (2014) Tracking Overflow Metabolism for Efficient Growth By Designing a Kalman Estimator for Acid Production in E. coli, 2014 AIChE Annual Meeting, Atlanta, November.
  11. Sarah W. Harcum*, Richard E. Groff, Arthur Nathan Brodsky#, Matthew E. Pepper#, Timothy C. Burg, Li Wang#, and Ajay Padmakumar# (2014) Bioreactor Control Algorithms and Process Developments for Improved Stem Cell Expansion, Cell Culture Engineering XIV, May 4-9, 2014, Quebec City, Canada.
  12. Gowtham, Y.K.*, Saski, C., Harcum, S.W.* (2014) Transcriptome analysis of Chinese hamster ovary (CHO) cells undergoing serum-free medium adaptation using RNA-Seq, 247th American Chemical Society National Meeting & Exposition, March, Dallas, TX (oral presentation).
  13. Caldwell, T.C., Harcum, S.W.* (2014) Characterization of a novel two-stage fermentation process for ethanol production from lignocellulosic materials, 247th American Chemical Society National Meeting & Exposition, March, Dallas, TX (oral presentation).
  14. Brodsky, A. N. and Harcum, S. W.* (2012) Growth and Differentiation of  Mesenchymal Stem Cells in a Novel Media Under Atmospheric Carbon Dioxide Conditions, Cell Culture Engineering XIII, April, Scottsdale, AZ (poster).
  15. Brodsky, A. N.* and Harcum, S. W. (2012) Development of buffer supporting mesenchymal stem cell growth in atmospheric carbon dioxide, 243rd American Chemical Society National Meeting & Exposition, March, San Diego, CA (oral presentation).
  16. Gowtham, Y. K.*, Miller K. P., Henson, J. M., Harcum, S. W. (2012) Production of ethanol from Saccharomyces pastoranius on biomass sugars using a two-stage fermentation process, 243rd American Chemical Society National Meeting & Exposition, March, San Diego, CA (poster).
  17. Miller K.P. *, Caldwell, T., Henson, J.M., Harcum, S. W.  (2011) Ethanol production from biomass sugars by the yeast Saccharomyces pastorianus, 61st Annual Meeting of the Society for Industrial Microbiology, July, New Orleans.
  18. Gowtham, Y.*, Miller K.P. *, Henson, J.M., Harcum, S. W. (2011) A comparison of production of ethanol from Saccharomyces cerevisiae and Saccharomyces pastoranius on xylose, 61st Annual Meeting of the Society for Industrial Microbiology, New Orleans.
  19. Salazar, M.A.*, and Harcum, S.W. (2008) Finding conditions to untangle the recombinant protein inclusion body mess in Escherichia coli, 236th ACS National Meeting, August, Philadelphia, PA.
  20. Harcum, S. W., and Caldwell, M. L. (2007) Bottlenecks in influenza vaccine production in alternative hosts, Immunobiology of Influenza Virus Infection: Approaches for an Emerging Zoonotic Disease, Athens, GA, August.
  21. Harcum, S. W. (2007) Human Genetics: Leveraging the Resources of Clemson University and the Greenwood Genetic Center, Charleston, SC, Science Advisory Board Meeting of the Institute of Nutraceutical Research, June 22 (INVITED).
  22. Harcum, S. W. (2007) Gene expression changes in E. coli due to fermenter stresses, New England BioLabs, Beverly, MA, April 4 (INVITED).
  23. Harcum, S. W. (2007) Gene expression changes in mammalian cells under bioreactor conditions, Pfizer, St. Louis, MO, April 2 (INVITED).
  24. Harcum, S. W.*; Caldwell, M. F. (2006) Effects of ammonium on glycosylation-related gene expression in NS0 cells, 232th ACS National Meeting, September, San Francisco, CA
  25. Blattner, F. R.*, Campbell, J., Frisch, D., de Arruda, M., Burland, V., Plunkett III, G., Harcum, S., Kim, S.-C., Pósfai, G., (2006) Clean, IS-free E. coli: a Safe, Stable Platform for Production and Delivery of Biopharmaceuticals, ASM Biodefense Annual Meeting; Washington DC, February.
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