Research Interests

The research in our lab focuses on systems biology. Our work is highly interdisciplinary, involving engineering, molecular biology and biophysics, to better understand the effect various pathways have on cellular behavior. We work with several different microbes, primarily filamentous fungi, using proteomic analysis to carry out functional genomic studies and a sophisticated set of analytical tools to assess cellular morphology and material properties.
Currently, we’re studying autophagy. This important pathway recycles large proteins and even whole organelles. We think engineering it may lead to increased productivity in  bioprocesses. To understand how to alter the pathway, we make targeted gene deletions and use sophisticated tools to assess the resulting cellular phenotypes.	Pollack et al. 2009
Proteomic Analysis helps us understand how genetic or environmental changes effect cells at the molecular level. This is a two dimensional gel used to separate proteins which are then identified using a mass spectrometer.
Digital Image Analysis allows us to quantify  cellular level changes observed using both optical and fluorescent microscopy.	Pollack et al. 2009
Atomic Force Microsocopy (AFM) allows us to visualize the unaltered surface of living cells at very high resolution.  We have also developed a method for using AFM to measure cell wall material properties as a function of position.	Zhao et al. 2005.

Selected Publications

J.R. Garcia, H.J. Cha, G.G. Rao, M.R. Marten, W.E. Bentley, “Microbial nar-GFP cell sensors reveal oxygen limitations in highly agitated and aerated laboratory-scale fermentors,”  Microbial Cell Factories, 8:6 (2009).
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J.K. Pollack, S.D. Harris, and M.R. Marten, “Autophagy in Filamentous Fungi,” Fungal Genetics and Biology, 46:1–8 (2009).  
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M.P. Zustiak, J.K. Pollack, M.R. Marten and M.J. Betenbaugh, “Feast or famine: autophagy control and engineering in eukaryotic cell culture,” Current Opinion in Biotechnology, 19:518–526, 2008.
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J.K. Pollack, Z.J. Li, and M.R. Marten, “Fungal mycelia show lag time before re-growth on endogenous carbon,” Bioengineering and Biotechnology, in print (2008).
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Y. Kim, M.P. Nandakumar, M.R. Marten, “The current state of proteome profiling in the filamentous fungal genus Aspergillus.  Briefings in Functional Genomics and Proteomics, in print (2007).
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Y. Kim, M.P. Nandakumar, M.R. Marten, “Proteomics of filamentous fungi,” Trends in Biotechnology, 25:395-400, (2007).
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Y. Kim, M.P. Nandakumar, M.R. Marten, “Proteome map of Aspergillus nidulans during osmoadaptation,” Fungal Genetics & Biology,  44:886-895, (2007).
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Nandakumar, M.P., Cheung, A.  & Marten, M.R. “Proteomic analysis of extracellular proteins from E. coli W3110,” Journal of Proteome Research, 5:1155-1161, (2006).
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Potra, F.A., Liu, X., Seillier-Moiseiwitsch, F., Roy, A., Hang, Y., Marten, M.R., Raman, B. & Whisnant, C., Protein Image Alignment via Piecewise Affine, Journal of Computational Biology, 13: 614–630 (2006).
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Vallejos, J.R., Kostov, Y., Marten, M.R., and Rao, G., Confocal optical system: a novel noninvasive sensor to study mixing. Biotechnology Progress, 21:1531-1536 (2005).
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Vallejos, J.R., Kostov, Y., Ram, A., French, J.A., Marten, M.R., and Rao, G., Optical Analysis of Liquid Mixing in a Microbioreactor. Biotechnol. Bioeng., 93:906-911 (2005).
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Raman, B.; Nandakumar, M.P.; Muthuvijayan, V.; Marten, M.R. Proteome Analysis to Assess Physiological Changes in Escherichia Coli Grown under Glucose-Limited Fed-Batch Conditions. Biotechnol Bioeng, 92: 384-92 (2005).
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Nandakumar R, Nandakumar M.P., Marten M.R. and Ross, J.M, “Proteome analysis of cell wall associated proteins from Staphylococcus aureus: lysis and sample preparation protocols,” J. Proteome Research, 21(1):292-9, (2005).
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Zhao, L., Schaefer, D., and Marten, M.R., Assessment of Elasticity and Topography of Aspergillus nidulans Spores via Atomic Force Microscopy. Applied and Environmental Microbiology, 71:955 (2005).
[abstract] [full text]

Zhao, L., Schaefer, D., Xu, H., Modi, S.J., LaCourse, W.R., and Marten, M.R., Elastic properties of the cell wall of Aspergillus nidulans studied with atomic force microscopy (AFM). Biotechnol. Prog., 21:292 (2005).
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Muthuvijayan, V. and Marten, M.R., In silico reconstruction of nutrient-sensing signal transduction pathways in Aspergillus nidulans. In Silico Biol., 4:0050 (2004).
[abstract] [full text]

Bhargava, S., Wenger, K.S., Rane K., Rising V. and Marten M.R., “Effect of cycle time on fungal morphology, broth rheology and recombinant enzyme productivity during pulsed addition of limiting carbon source,” Biotechnology and Bioengineering, 89:524-529 (2005).
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Roy A., Seillier-Moiseiwitsch F., Lee K.R., Hang Y., Marten M.R., Raman B., “Analyzing Two-Dimensional Gel Images.” Chance, 16:13-18 (2003).
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Davidson KM, Sushil S, Eggleton CD, Marten MR, "Using computational fluid dynamics software to estimate circulation time distributions in bioreactors," Biotechnol. Prog. 19:1480-6. (2003).
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Nandakumar MP, Shen J, Raman B, Marten MR., "Solubilization of trichloroacetic acid (TCA) precipitated microbial proteins via naOH for two-dimensional electrophoresis," J Proteome Res. 2:89-93, (2003).
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S. Bhargava, K.S. Wenger, and M.R. Marten, "Pulsed feeding during fed-batch Aspergillus oryzae fermentation leads to improved oxygen mass transfer," Biotechnol. Prog. 19:1091-1094 (2003 ).
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S. Bhargava, K.S. Wenger, and M.R. Marten, "Pulsed addition of limiting carbon during Aspergillus oryzae fermentation leads to improved productivity of a recombinant enzyme," Biotechnology and Bioengineering, 82:111-7 (2003).
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S. Bhargava, M.P. Nandakumar, A. Roy, K.S. Wenger, and M.R. Marten, "Pulsed feeding during fed-batch fungal fermentation leads to reduced viscosity without detrimentally affecting protein expression," Biotechnology and Bioengineering, 81:341-7 (2003).
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M.P. Nandakumar and M.R. Marten, "Comparison of lysis methods and preparation protocols for one- and two-dimensional electrophoresis of Aspergillus oryzae intracellular proteins," Electrophoresis 23:2216-2222 (2002).
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B. Raman, A. Cheung, and M.R. Marten, "Quantitative comparison and evaluation of two commercially available, two dimensional electrophoresis image analysis software packages, Z3 and Melanie," Electrophoresis 23:2194-2202 (2002).
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Z.J. Li, V. Shukla, K.W. Wenger, A.P. Fordyce, A.G. Pedersen, and M.R. Marten “Effects of increased impeller power in a production-scale Aspergillus oryzae fermentation,” Biotechnol.  Prog., 18:437-444 (2002).
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Z.J. Li, S. Bhargava, and M.R. Marten “Measurements of fragmentation rate constant imply that the tensile strength of fungal hyphae can change significantly during growth,” Biotechnol. Lett., 24:1-7 (2002).
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Z.J. Li, V. Shukla, K.W. Wenger, A.P. Fordyce, A.G. Pedersen, and M.R. Marten “Estimation of hyphal tensile strength in production-scale Aspergillus oryzae fungal fermentations,” Biotechnol.  Bioeng., 77:601-613, (2002).
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T. Shanklin, K. Roper,  P.K. Yegneswaran, and M.R. Marten "Selection of Bioprocess Simulation Software", Biotechnol. Bioeng., 72: 483-489, (2001).
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Z.J. Li, V. Shukla, K.W. Wenger, A.P. Fordyce, A.G. Pedersen, and M.R. Marten “Fungal Morphology and Fragmentation behavior in a Fed-Batch Aspergillus oryzae Fermentation at the Production Scale,” Biotechnol.  Bioeng., 70:300-312, (2000).
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M.R. Marten, K.S. Wenger, and S.A. Khan, “Rheology, Mixing Time, and Regime Analysis for a Production-Scale Aspergillus oryzae Fermentation,” Bioreactor and Bioprocess Fluid Dynamics, A.W. Nienow (ed.),  BHRGroup, Cranfield, UK (1997).
[abstract] [full text - pdf]

Collaborations

		Merck & Co., Inc.
Dr. David Schaefer Towson University, Physics Dr. Steven Harris U. Nebraska, Lincoln, Dept. Plant Pathology Dr. Govind Rao: UMBC, Chem & Biochem Engr. Dr. Julia Ross: UMBC, Chem & Biochem Engr

Last Update: November 16, 2009