Title

Associate Professor

Education

Ph.D. Chemical Engineering – Purdue University, 1991
M.S. Chemical Engineering – Purdue University, 1988
B.S. Chemical Engineering – State University of New York at Buffalo, 1986

Professional Interests

The broad goal in my laboratory is to establish a better understanding of the interaction between biological and physical phenomena in microbial systems. We have several collaborative projects which involve bacteria, but our primary focus is on filamentous fungi. Currently, the bulk of our work is centered on developing a more fundamental understanding of fungal autophagy.

Autophagy (literally ‘self-eating’) has recently emerged as an important topic in biology, as it plays a key role in cellular development, aging, numerous human diseases and survival during nutrient limitation. Also called type II programmed cell death, autophagy involves recycling of cellular macromolecules and even whole organelles. Most of the molecular components involved have been identified and are highly conserved in species ranging from yeast to man. While autophagy has been studied in several model organisms, almost no information is available on autophagy in filamentous fungi. This is somewhat surprising, as the impact of filamentous fungi on human activity is enormous. While pathogenic fungi are responsible for numerous deaths and billions of dollars in crop damage each year, fungi used in the bioprocessing industry produce billions of dollars in beneficial products annually.  Notably, in each of these cases, autophagy appears to play a prominent role. Not only is autophagy likely to be a fundamental response to nutrient limitation, we hypothesize that autophagy is also a normal, developmentally related phenomenon in filamentous fungi which occurs in nutrient rich conditions. Thus, autophagy is likely to have a significant impact on most of the fungal processes related to man.

We use a sophisticated set of analytical tools (electron microscopy, digital image analysis, dynamic rheometry, atomic force microscopy) to asses fungal morphology and the physical properties of fungal cell walls. As a tool in our molecular studies (of both fungi and bacteria), we use a functional-genomic technique called proteome analysis. This is a two step process involving the separation and subsequent identification of individual proteins from cell lysate. Protein separation is accomplished via two dimensional polyacrylamide gel electrophoresis and results in a gel with a large number of spots. Each spot represents a different protein. With this technique, a large fraction (ideally all) of the proteins in a cell are visualized simultaneously, and subsequently identified using mass spectrometry. Proteome analysis allows us to study complex biological responses in their entirety, rather than as a multitude of individual components. This approach makes it far easier to uncover complex or obscure relationships between gene products.

Publications

Y. Kim, M.P. Nandakumar, M.R. Marten, “Proteomics of filamentous fungi,” Trends in Biotechnology, 25:395-400, (2007).
[abstract] [pdf]

 Y. Kim, M.P. Nandakumar, M.R. Marten, “Proteome map of Aspergillus nidulans during osmoadaptation,” Fungal Genetics & Biology,  44:886-895, (2007). [abstract] [pdf]

M.P. Nandakumar, A. Cheung,  M.R. Marten, “Proteomic analysis of extracellular proteins from Escherichia coli W3110,” Journal of Proteome Research, 5:1155-1161, (2006).[abstract] [pdf]

J.R. Vallejos, Y. Kostov, A. Ram, J.A. French, M.R. Marten, and G. Rao, “Optical analysis of liquid mixing in a microbioreactor.” Biotechnology and Bioengineering, 93:906-911, (2005).[abstract] [pdf]

B. Raman, M.P.Nandakumar, V. Muthuvijayan, M.R. Marten, “Proteome analysis to assess physiological changes in Escherichia coli grown under glucose-limited fed-batch conditions.” Biotechnology and Bioengineering, 92: 384-92, (2005).[abstract] [pdf]

R. Nandakumar, M.P. Nandakumar, M.R. Marten and J.M. Ross,  “Proteome analysis of membrane and cell wall associated proteins from Staphylococcus aureus,” Journal of Proteome Research, 4:250-257, (2005).[abstract]  [pdf]

L. Zhao, , D. Schaefer, and M.R. Marten, “Assessment of elasticity and topography of Aspergillus nidulans spores via atomic force microscopy.” Applied and Environmental Microbiology, 71:955-960, (2005).[abstract] [pdf]

L. Zhao, D. Schaefer, H. Xu, S.J. Modi, W.R. LaCourse, and M.R. Marten, “Elastic properties of the cell wall of Aspergillus nidulans studied with atomic force microscopy (AFM).” Biotechnology Progress, 21:292-299, (2005).[abstract] [pdf]

V. Muthuvijayan, and M.R. Marten, “In silico reconstruction of nutrient-sensing signal transduction pathways in Aspergillus nidulans.” In Silico Biol., 4:605-31, (2004).[abstract] [pdf]

S. Bhargava, K.S. Wenger, K. Rane, V. Rising and M.R. Marten, “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). [abstract] [pdf]