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
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.
Y. Kim, N. Islam, B.J. Moss, M.P. Nandakumar, M.R. Marten, “Autophagy induced by rapamycin and carbon-starvation have distinct proteome profiles in Aspergillus nidulans,” Biotechnology Bioengineering, 108:2705-2715, (2011). doi: 10.1002/bit.23223.
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).
J.K. Pollack, S.D. Harris, and M.R. Marten, “Autophagy in Filamentous Fungi,” Fungal Genetics and Biology, 46:1ñ8 (2009).
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, 19:518ñ526, 2008.
J. Pollack, Z.J. Li, and M.R. Marten, “Fungal mycelia show lag time before re-growth on endogenous carbon,” Biotechnology and Bioengineering, 100: 458ñ465, 2007.
B.J. Moss, Y. Kim, M. P. Nandakumar, and M.R. Marten, “Quantifying Metabolic Activity of Filamentous Fungi Using a Colorimetric XTT Assay,” Biotechnology Progress, 24:780 - 783, 2008.
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).
Y. Kim, M.P. Nandakumar, M.R. Marten, “Proteomics of filamentous fungi,” Trends in Biotechnology, 25:395-400, (2007).
Y. Kim, M.P. Nandakumar, M.R. Marten, “Proteome map of Aspergillus nidulans during osmoadaptation,” Fungal Genetics & Biology, 44:886-895, (2007).
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).