Group Members

	Postdoctoral Fellows
	Ph.D. Students
	Masters Students
	Staff
	Former Group Members

Postdoctoral Fellows
	CARLOS J. PAREDES B.Sc. Industrial Chemistry, Universitat Autónoma de Barcelona, Spain (U.A.B.) M.Sc. Biotechnology, U.A.B. Ph.D. Chemistry (Biotechnology program), U.A.B.
[email] website	ADVISOR: E. T. Papoutsakis RESEARCH PROJECT: DNA arrays, pattern recognition and extraction of useful biological information.
	DNA array technologies provide rapid and cost-effective methods of identifying gene expression patterns and genetic variations, and performing the equivalent of thousands of individual Northern hybridization experiments in approximately two days of time. Such an enormous amount of biological information requires methods to isolate the relevant information from the raw data which are typically corrupted by background activities. Methods are also necessary to relate such information with the genetic, metabolic and regulatory information available for each experimental system. My research is aimed at the design, implementation and development of such kind of methods including clustering algorithms, classifiers, identifying DNA motifs, etc.
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Ph.D. Students
	KEITH ALSAKER Graduate Student B.Ch.E., University of Minnesota-Twin Cities
[email]	ADVISOR: E. T. Papoutsakis RESEARCH PROJECT: Metabolic engineering and analysis of solvent tolerance using DNA microarrays
	We use principles of genetics and metabolic engineering to understand how solvent-producing clostridia respond to and can overcome their toxic products (such as solvents and carboxylic acids). More specifically, I am interested in studying over-expression of specialized proteins (such as molecular pumps) that might affect tolerance and in examining quorum-sensing genes that may regulate sporulation and responses to cell density and starvation. In order to identify such genes I use DNA-array based transcriptional analysis to examine solventogenic clostridia cells under a variety of stresses.

	PANI APOSTOLIDIS Graduate Student Dipl. Eng. in Chemical Engineering, Aristotle University
[email]	ADVISOR: E. T. Papoutsakis & W. M. Miller RESEARCH PROJECT: Stem-cell bioengineering

	JACOB R. BORDEN Graduate Student M.B.A., Springhill College M.S., Auburn University B.S., Rose-Hulman Institute of Technology
[email]	ADVISOR: E. T. Papoutsakis RESEARCH PROJECT: Gene Trait Mapping Using DNA Microarrays
	Using DNA microarrays and genetic libraries, it is possible to explore and explain the genetic basis for specific desirable phenotypes. More specifically, Clostridium acetobutylicum produces and shows tolerance to the solvents butanol and acetone. Using fragmented chromosomal DNA, genetic libraries can be created and inserted into C. acetobutylicum to supplement naturally occurring chromosomal genes. Library-containing bacteria are then selected for their ability to grow in butanol containing media. Finally, library DNA from selected cells are gathered and hybridized on a full-genome microarray to ascertain which gene fragment(s) bring about the desired solvent-tolerant phenotype.
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	CHI CHEN IBiS Graduate Student B.S. Life Sciences, Fudan University, P.R. China
[email]	ADVISOR: E. T. Papoutsakis & W. M. Miller RESEARCH PROJECT: Transcriptional analysis of stem-cell differentiation along the megakaryocytic lineage.
	Megakaryocytes, the precursors of platelets, mature and release platelets at sites with higher levels of oxygen tension than that within the bone marrow hematopoietic compartment. I am investigating the regulatory roles of oxygen tension (pO₂) in megakaryocytic differentiation, maturation and apoptosis. Cutting-edge techniques such as cDNA microarray analysis as well as well-established methods such as flow cytometry, and Western analysis and immunofluorescence microscopy are used to elucidate these issues.

	PETER FUHRKEN Graduate Student B.S. Chemical Engineering, Iowa State University
[email]	ADVISOR: E. T. Papoutsakis & W. M. Miller RESEARCH PROJECT: Models of hematopoietic stem cell expansion & differentiation
	Ex vivo culture of hematopoietic stem and progenitor cells has been proposed as a means to generate mature megakaryocytes (MKs, platelet precursor cells) and platelets for use in transplant therapies. While some of the culture conditions which effect in vitro megakaryopoiesis have been elucidated, the underlying transcriptional program governing commitment and differentiation remains poorly understood. I am using global gene expression analysis (specifically DNA microarrays), coupled with traditional cell and molecular biology assays, such as flow cytometry, to develop a clearer picture of this process at the transcriptional level. To do this, the differentiation and maturation process is perturbed by altering culture conditions and the transcriptional data is used to explain the resulting complex phenotypes. Ultimately, we hope to leverage this new knowledge to design improved MK-generating culture systems.

	LISA GIAMMONA Graduate Student B.S. Chemical Engineering, Illinois Institute of Technology
[email]	ADVISOR: E. T. Papoutsakis & W. M. Miller RESEARCH PROJECT: Apoptotic signaling pathways in megakaryocyte differentiation
	Megakaryopoiesis, which leads to the production of platelets, is a complex process that involves the development of polyploid cells via a modified cell cycle in which several rounds of DNA replication occur without cytokinesis. This process of maturation is further characterized by the induction of apoptosis, which is thought to be correlated to and occur concurrently with platelet formation. My research focuses on gaining a better understanding of the apoptotic signaling pathways involved in Mk maturation. Studies also address the question of whether transient inhibition of apoptosis can lead to a delay in the onset of platelet formation, increasing the number of viable Mk cells in culture. This increased knowledge may aid in the optimization of culture conditions for the ex vivo expansion of megakaryocytes.

	LITING HUANG Graduate Student B.S., Massachusetts Institute of Technology
[email]	ADVISOR: E. T. Papoutsakis & W.M. Miller RESEARCH PROJECT: DNA-array based transcriptional analysis of stem-cell differentiation along the granulocytic lineage.
	Microarray technology is a powerful new technique for examining the transcriptional program of cells on a genomic scale. Expression level profiles of all known human genes can be elucidated on a single array. This technology is specifically being applied to hematopoietic systems to discover genes or groups of genes crucial in the maintenance and differentiation pathway of stem cells along various hematopoietic lineages. My research focus on elucidating the transcriptional program of human hematopoietic stem cells along the granulocytic lineage using DNA arrays.
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	RYAN SILLERS Graduate Student B.S. Chemical Engineering, Michigan State University
[email]	ADVISOR: E. T. Papoutsakis RESEARCH PROJECT: Metabolic engineering of solventogenic clostridia
	Various metabolic engineering methods are used to improve the solvent production and tolerance of Clostridium acetobutylicum. Antisense RNA (asRNA) strategies have down-regulated acetone producing pathways to increase the butanol to acetone selectivity. The asRNA is now being co-expressed with genes responsible for butanol production and increased solvent tolerance. Additionally, earlier expression of solventogenic genes will be investigated using alternate promoter sequences. The effects of these experiments will be measured with traditional molecular biology methods and DNA-microarray technologies.

	BRYAN TRACY Graduate Student B.S. Chemical Engineering, North Carolina State University
[email]	ADVISOR: E. T. Papoutsakis RESEARCH PROJECT: Genomic and genetic approach to impart solvent tolerance in solventogenic clostridia

	MIN WANG IBiS Graduate Student B.S. Life Sciences, University of Science & Technology of China
[email]	ADVISOR: E. T. Papoutsakis RESEARCH PROJECT: DNA-array transcriptional analysis of H₂O₂ induced T-cell apoptosis.
	H₂O₂ is physiologically produced in large amounts as a mediator of innate immunity to invading microbes. However, H₂O₂ and other reactive oxygen species (ROS) can have both beneficial as well as detrimental effects. For instance, ROS produced under chronic inflammatory conditions may severely impair the immune system. I am using DNA- array to investigate the molecular mechanism of oxidative stress induced T-cell apoptosis.
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Masters Students
	MOHAB AL-HINAI Masters in Biotechnology Program (MBP) Student B.S. Biotechnology, Sultan Qaboos University, Oman
[email]	ADVISOR: E. T. Papoutsakis RESEARCH PROJECT: Metabolically Engineering C. acetobutylicum

	JAMES CUENCA Masters in Biotechnology Program (MBP) Student B.A. Biological Sciences (BMBCB) & Philosophy, Northwestern University
[email]	ADVISOR: E. T. Papoutsakis RESEARCH PROJECT: Megakaryopoietic stem cell differentiation - optimization of cell culture conditions and flow cytometric analysis

	EUGENE SOO Masters in Biotechnology Program (MBP) Student B.S. Chemical Engineering, Northwestern University
[email]	ADVISOR: E. T. Papoutsakis & W.M. Miller RESEARCH PROJECT: Hematopoietic stem cells along erythroid and granulocytic lineages
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Staff
	MISA MISONO IMC Masters Program Student B.A. Economics, Political Science; Boston University
	POSITION: Project Coordinator

	IWONA SPATH B.S. Biochemistry, University of Illinois at Chicago
	POSITION: Research Technologist
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