Education

• Postdoctoral Associate, University of Florida
• Ph.D., California Inst. of Technology, 2004
• B.S., Chemical Engineering, Ohio University, 1997

Professional Experience

• Assistant Professor, Chemical Engineering, Pennsylvania State University, 2004 – 2010
• Associate Professor, Chemical Engineering, Pennsylvania State University, 2010
• Associate Professor, Chemical & Biomolecular Engineering, University of Houston, 2011 – present

Courses

• CHEE 2331, Chemical Processes (Fall Semester)

Research Interests

Nature provides a vast collection of biological systems which have evolved mechanisms to achieve catalysis, regulation, molecular recognition, and energy utilization with incredible efficiency. Our ability to successfully re-design and harness such systems is integral to realizing a future of cost-effective "green" chemistry, renewable fuels and chemicals, bioremediation, and "next-generation" therapeutics.

Research in the Cirino laboratory interfaces Chemical Engineering with the biological sciences, with emphases in biomolecular engineering, metabolic engineering, and biocatalysis.  Recent research efforts are summarized in the poster presentations below (right click to view larger images).  By applying biological design principles at the molecular level (e.g., engineer proteins) as well as the systems level (e.g., engineer metabolic pathways and gene regulation) we are creating novel microbial strains with improved biocatalytic efficiency (e.g. increased supply of NADPH to transformations of interest), and we are designing novel biosensors by customizing regulatory proteins, with broad applications in synthetic biology and biocatalyst development.

Metabolic Engineering

Metabolic engineering is defined as the improvement of cellular activities by manipulation of enzymatic, transport, and regulatory functions of the cell with the use of recombinant DNA technology. Current research in our lab is aimed at modifying microbial metabolism to carry out new or improved bioconversions for the production of various secondary metabolites. This typically requires expression of foreign genes in an amenable microbial host (e.g. E. coli).  Several stages of genetic optimization are then required to improve efficiency and productivity.  As strategies to improve strain performance parameters are developed and tested, we gain new insights into microbial metabolism and physiology, further informing the design process.

In one example, we engineer the metabolism of E. coli to create biocatalytic strains which maximize yields on reducing equivalents in the form of NADPH, derived from renewable biomass sugars. This reducing power is subsequently channeled away from aerobic respiration and into driving reactions of interest, such as the reduction of xylose to xylitol (a sweetener and synthetic building block molecule).

In other examples, we are improving flux of precursors metabolites (e.g. acetyl-CoA and malonyl-CoA) toward the synthesis  of secondary metabolites (natural products such as polyketides and isoprenoids) by genetically modified bacteria.  This is largely accomplished via a "directed evolution" strategy in which large numbers of genetic variants are created and screened for improved properties.  This in turn requires high throughput screening of target compounds, which we achieve by creating customized molecular reporters derived from natural regulatory proteins.

Protein Engineering/Molecular Recognition

We are using combinatorial (evolutionary) as well as rational (structure-based) protein design techniques to engineer transcriptional regulatory proteins to serve as customized biosensors. These proteins are being designed to recognize specific non-native molecules of interest ("effectors") and report their presence and concentration by regulating expression of a reporter gene.  Such endogenous biosensors serve as powerful tools in synthetic biology and facilitate subsequent protein engineering and metabolic engineering efforts in our lab and others.

Additional projects include engineering oxygenase enzymes to accommodate new or improved activities, and implementing our custom-designed regulatory proteins in high-throughput screening of novel enzyme and microbial biocatalysts (see above).  All research projects draw from a broad base of knowledge and experimental techniques spanning many disciplines, the common goal being that we use biology to solve problems pertinent to the expanding field of Chemical Engineering.

Computation and modeling contribute to many areas of our research by reducing experimental variables and guiding experimental efforts. Likewise, experimental results can provide information leading to improved biological models. This complementary exchange of information is realized through collaborations with Dr. Costas Maranas at Penn State University.

We gratefully acknowledge the National Science Foundation for numerous grants to support these research projects.

Research Group

Cirino lab members

Post-doctoral associate

• Dr. Joseph Gredell

Graduate Students

• Christopher Frei
• Ye Li
• Mizan Rahman
• Bala Ramesh (primary advisor is Dr. Navin Varadarajan)

Former lab members:

Postdocs

• Dr. Shuang-Yan Tang (now Professor at Kunming University of Science and Technology)
• Dr. Hui Li

Graduate Students

• Dr. Olubolaji Akinterinwa (PhD 2010): currently at Procter & Gamble
• Dr. Jonathan Chin (PhD 2010): currently at Algenol Biofuels
• Dr. Reza Khankal (PhD 2010): currently at Glycos Biotechnology
• Dr. Hossein Fazelinia (Ph.D.  2009 co-advised by C.Maranas)
• Lexan Lhu (M.S.; employed at Joule Biotechnologies, MA)
• Christopher Frei (M.S. 2010): now a Ph.D. student in Cirino lab
• Francesca Luziatelli (visiting student from U of Tuscia, Italy)

Lois Eppihimer (lab manager)

PSU Honors College Undergrad Researchers

• Caroline Monroe
• Anthony Tascone
• Renae Patch
• Garrett Tobin

Other Undergraduate Researchers

• Oliver Chou (U Colorado Boulder)
• Kyle Schutter (Brown University)
• Nicholas Linn (NC State)
• Berook T. Alemayehu (U Maryland: Baltimore County)
• Audrey Leung (University of Iowa)
• Jeremy Sargent (Penn State)
• J. Lane Weaver (Penn State)
• Jon P. Badalamenti (Penn State)
• Lucien E Weiss (Penn State)
• Julie Sawlsville (Penn State)
• Geoff Geise (Penn State)
• Doug Haag (Penn State)
• Megan Rex (Penn State)
• Chris Cottle (Penn State)
• Panagiotis A Papadopoulos (Penn State)
• Matthew Zapadka (Penn State)
• Samhita Banavar (PA Governor’s school for high school students)

Work-Study Students

• Ryan Noraas
• Tiffany Veet
• Khai Van
• John Ajak

Awards and Honors

• 2006 N.S.F. CAREER Award Recipient
• Associate Editor: BMC Biotechnology
• Editorial Board Member: Biotechnology Letters, Biotechnology Journal, Journal of Biological Engineering
• Guest Editor, “Applications of Synthetic Biology in Microbial Biotechnology”, Journal of Biomedicine and Biotechnology (2009)
• ACS BIOT 2012 Program Chair
• SIM Biocatalysis program co-chair, 2010 - 2012

Professional Activities

• Councilor, Institute of Biological Engineering (IBE), 2006-2010
• Faculty Advisor, Penn State iGEM Undergrad Research (Synthetic Biology) 2006 - 2009
• Instructor, Fundamentals of Bioseparation Techniques, Penn State Biotechnology Training Program (2004 - 2010)