Jacqueline Vanni Shanks
Department of Chemical & Biological Engineering
Iowa State University
January, 2012
Table of Contents
Education: .................................................................................................................................................................... 1
Professional Experience: ............................................................................................................................................. 1
Honorary and Professional Societies: ........................................................................................................................ 1
Special Appointments or Awards:.............................................................................................................................. 2
Research Activities: ..................................................................................................................................................... 2 Research Interests .......................................................................................................................................................... 2 Current Funding ............................................................................................................................................................. 2 Past Funding .................................................................................................................................................................. 3 Thesis Research Directed .............................................................................................................................................. 6
Teaching Experience: .................................................................................................................................................. 7 Iowa State University .................................................................................................................................................... 7 Rice University .............................................................................................................................................................. 7 Caltech ........................................................................................................................................................................... 8
University Service: ....................................................................................................................................................... 8 Iowa State University .................................................................................................................................................... 8 Rice University .............................................................................................................................................................. 8
Professional Service: .................................................................................................................................................... 9 Editorial and Advisory Board Memberships ................................................................................................................. 9 National Committees, Workshops ................................................................................................................................. 9 Workshops ................................................................................................................................................................... 10 Offices ......................................................................................................................................................................... 10 Organizer of Symposia ................................................................................................................................................ 10 Chair of Sessions ......................................................................................................................................................... 10 Reviewer ...................................................................................................................................................................... 10
Community Service: .................................................................................................................................................. 11
Research Publications: .............................................................................................................................................. 11
Books: ......................................................................................................................................................................... 18
Book Chapters: .......................................................................................................................................................... 18
Technical Reports: ..................................................................................................................................................... 19
Technical Software: ................................................................................................................................................... 19
Educational Publications: ......................................................................................................................................... 19
Textbooks: .................................................................................................................................................................. 19
Textbook Web Site: ................................................................................................................................................... 19
Educational Software: ............................................................................................................................................... 19
Lecturer of Continuing-Education Courses: ........................................................................................................... 19
Technical Presentations at Conferences-Abstracts: ............................................................................................... 20
Invited Lectures at Universities, Companies, and Conferences: ........................................................................... 31
Postdoctoral Research Fellows Supervised: ............................................................................................................ 33
Graduate Students Supervised: ................................................................................................................................ 33
Undergrad Research Students Supervised: ............................................................................................................. 33
Undergrad “Labbie” Students Supervised, Iowa State University: ...................................................................... 38
Undergrad Education (Computation) Students Supervised (with S.H. Davis), Rice University: ....................... 38
High School Research Students Supervised: ........................................................................................................... 38
1
JACQUELINE VANNI SHANKS
Curriculum Vitae
Date of Birth: May 10, 1961
Citizenship: United States
Place of Birth: Des Moines, IA
Position: Manley R. Hoppe Professor in Chemical and Biological Engineering
Education:
B.S., Iowa State University, Chemical Engineering 1983
Ph.D., California Institute of Technology, Chemical Engineering 1989
Ph.D. Advisor: James E. Bailey
Professional Experience:
1981-1982 Teaching Assistant, Iowa State University
1982 Process Engineer, Pillsbury, Minneapolis, MN
1982-1983 Undergraduate Research, Iowa State University
1983 Process Engineer, General Electric Corporation, Mount Vernon, IN
1985 SURF Student Advisor, California Institute of Technology
1985 Teaching Assistant, California Institute of Technology
1984-1988 Research Assistant, California Institute of Technology
1988-1993 Assistant Professor in Chemical Engineering, Rice University
1993-1999 Associate Professor in Chemical Engineering, Rice University
1997-1999 Associate Professor in Bioengineering, Rice University
1999 Professor in Bioengineering, Rice University
July 1, 1999-2005 Professor in Chemical Engineering, Iowa State University
July 1, 2001- Adjunct Professor in Bioengineering, Rice University
July 1, 2005-2009 Professor in Chemical & Biological Engineering, Iowa State University
Sept. 1, 2008- 2010 Thrust 2 Co-Leader, NSF Center for Biorenewable Chemicals (CBiRC),
Iowa State University
July 1, 2009- Manley R. Hoppe Professor in Chemical & Biological Engineering, Iowa
State University
Sept. 1, 2010- Thrust 2 Leader, NSF Center for Biorenewable Chemicals (CBiRC), Iowa
State University
Honorary and Professional Societies:
American Chemical Society (ACS)
American Institute of Chemical Engineers (AIChE)
American Institute of Medical and Biological Engineering, Fellow
Houston Society for Engineering in Medicine and Biology (HSEMB)
Steering Committee 1991-1995
Omega Chi Epsilon
Sigma Xi
Society for In Vitro Biology (SIVB)
Society of Women Engineers (SWE)
Tau Beta Pi
2
Special Appointments or Awards:
State of Iowa Scholarship 1979-1980
Atlantic Richfield Scholarship 1980-1981
3M Scholarship 1981-1982
Senior Design Award 1983
Senior Research Fellowship 1982-1983
Farmland Industries Scholarship 1982-1983
Graduation with Distinction, Iowa State University 1983
Weyerhauser Company Foundation Predoctoral Fellowship 1983-1984
Amoco Outstanding Young Faculty in Engineering Award 1991
Rice Nomination Presidential Faculty Fellow 1991
Outstanding Faculty Associate, Rice University 1991 and 1992
Rice Nomination Camille-Dreyfus Teacher Scholar 1992
Outstanding Faculty Associate, Wiess College 1992
Herschel Rich Invention Award 1992
NSF Young Investigator Award 1992-1997
Professional Progress in Engineering Award, Iowa State University 1994
American Institute of Medical and Biological Engineering, Fellow 2000
Associate Editor, Biotechnology Progress 2002-2003
Van Lanen Award, Division of Biochemical Technology, ACS 2004
ISU University Foundation Award for Outstanding Achievement in Research 2005
Women of Innovation Award for Research Innovation and Leadership,
by the Technology Association of Iowa 2008
AIChE Food, Pharmaceutical and Bioengineering Division, Area 15c Plenary Award 2010
Research Activities:
Research Interests
Metabolic engineering of biorenewable chemicals.
Metabolic engineering of plant secondary metabolites.
NMR spectroscopic techniques for characterization of cellular metabolism.
Analytical methods for analysis of metabolic pathways.
Enhancement of bioprocess productivity from manipulation of cellular metabolism via changes in
genetic composition or environment.
Current Funding
Principal Investigator, “Evaluate and Identify Metabolic Control Points Determining Assimilate
Partitioning in Developing Seed,” Pioneer Hi-Bred International, $300,000 (11/01/07–10/31/12).
Thrust 2 Leader [Shanks, B, P.I.,] “ERC: Center for Biorenewable Chemicals,” National Science
Foundation, $16,250,000 (08/01/08–07/31/13).
Principal Investigator [with Nikolau, B. (Co-P.I.) and Bobik, T. from ISU; Wolfe, G. (Co-P.I.) from
California State University, Chico; Nadathur, G. (co-PI) from University of Puerto Rico], “ EFRI-
HyBi: Bioengineering a System for the Direct Production of Biological Hydrocarbons for
Biofuels,” NSF, $2,059,528,” (9/1/09 – 8/31/13).
Co-Principal Investigator, [with Vigil, D. (PI)]. “Energy Efficient Cultivation of Microalgae and
Simultaneous Separation of Products using a Novel Taylor Vortex Reactor-Separator” Conoco
Phillips Company. $131,601 (1/1/2011 – 12/31/2012).
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Past Funding
Principal Investigator [with Gibson, S. (Co-P.I.) from Univ. of Minnesota and San, K. Y. (Co-P.I.)
from Rice University], “Collaborative Research: Molecular Genetic and Metabolic Analyses to
Characterize Terpenoid Indole Alkaloid Pathways,” NSF, $174,624 (ISU portion) (9/1/07-8/31/09).
Principal Investigator, “Metabolic Flux Analysis in Plants,” Pioneer Hi-Bred International,
$349,188 (05/01/06-04/31/10).
Principal Investigator [with Dickerson, J. (Co-P.I)], "Understanding oil/protein partitioning in
developing soybean embryos: Linking transcript data and metabolic fluxes," Plant Sciences
Institute, $50,000 (7/1/06-6/31/09).
Participant [with Narashimhan, P.I.], “REU Site in Biological Materials and Processes (BioMaP),”
National Science Foundation, $370,639, (02/01/2006-01/31/2009).
Co-Principal Investigator [Andreotti, P.I., with nine others] “Graduate Research Training Program
in the area of Molecular Biophysics,” Roy J. Carver Charitable Trust, $494,436 (11/06 – 10/09).
Co-Principal Investigator [with Gonzalez, R. (P.I.) and San, K. Y. (Co-P.I.) from Rice University],
“Collaborative Research: Metabolic Engineering of E. coli Sugar-Utilization Regulatory Systems
for the Consumption of Plant Biomass Sugars,” Interagency Program in Metabolic Engineering
[NSF (Rice-ISU), U.S. Dept. of Agriculture (ISU), U.S. Dept. of Energy (ISU), Environmental
Protection Agency (Rice)] $569,872 (ISU Portion) (8/15/03-8/31/07).
Co-Principal Investigator [Hong, P.I., with Andreotti, Pruski, Schmidt-Rohr] “Acquisition of a 600
MHz Spectrometer for Biomolecular and Materials Research,” NSF, DBI-0421374, $957,600
(07/04-06/07)
Principal Investigator [with Oliver, D. (Co-P.I)], “Genetic and Biochemical Basis for the
Transformation of Energetic Materials (RDX, TNT, DNTs) by Plants,” SERDP, $828,419
(09/01/02-09/26/06).
Principal Investigator “Integrating molecular, physiological, and agronomic approaches to meet IP
soybean markets of the near future,” ISU Agronomy Foundation, $52,250 (4/1/04-08/31/06). [Part
of larger project with Westgate, M., Batchelor, W., and Nikolau, B.]
Principal Investigator [with Gibson, S. (Co-P.I.) and San, K. Y. (Co-P.I.) from Rice University],
“Collaborative Research: Metabolic Engineering of Hairy Roots for Alkaloid Production,” NSF,
$241,947 (ISU portion) for the period August 15, 2002-July 31, 2006.
Co-Principal Investigator [with Glatz, C. E. (PI), Mallapragada, S. K. (co-PI), Reilly, P. J., Huba,
M. (co-PI)], “Chemicals from Biorenewables,” NSF CRCD Program, $418,000, with ISU match up
to $540,000 (03/01-02/06).
Principal Investigator “Managing Stress Tolerance and Seed Composition of Glyphosate-Resistant
Soybeans,” Iowa Soybean Board, $46,022 (2/1/03-6/31/04). [Part of larger project with
Westgate, M.]
4
Participant [with Brown, R. (PI ) et. al.], “Multi-Disciplinary Education and Training in Biobased
Products: Graduate Major in Bioresource Engineering,” DOE, $375,000, 7/01-6/04.
Principal Investigator [with Spalding, M. (Co-P.I.) and Westgate, M. (Co-P.I.)], “Development of
NMR Tools for Metabolic Flux Maps of Soybean Seeds,” Plant Science Institute, $50,000 for the
period July 15, 2001-June 31, 2003.
Principal Investigator [with Gibson, S. (Co-P.I.) and San, K. Y. (Co-P.I.) from Rice University],
“Quantifying and Directing Metabolite Flux: Application in Tryptophan Overproduction and Indole
Alkaloid Accumulation in Plant Tissues,” NSF, $197,000 (ISU portion), $ 280,000 (Rice portion)
for the period August 15, 2000-July 31, 2003.
Co-Principal Investigator [with Westgate, M. E. (PI), Hurburgh, C. (co-PI), Nikolau, B (co-PI),
Wurtele, E. (co-PI)] “An Integrated Research Program to Improve the Composition and Value of
Iowa Soybeans,” Iowa Soybean Promotion Board, $124,592 (9/01-8/02).
Participant [with Nikolau, B (PI), and 16 others], “Metabolomics Research Laboratory,” Keck
Foundation, $1,000,000, (7/31/01). {ISU Match 1.3 million}.
Principal Investigator: “Plant Metabolic Engineering Research,” ISU Biotechnology Council,
$150,000 for the period July 1, 1999-June 30, 2002.
Principal Investigator: “Plant Metabolic Engineering Research,” Iowa State University Center for
Crop Utilization Research, $35,000 for the period July 1, 1999-June 30, 2002.
Co-Principal Investigator [with Oliver, D. (P.I.)], “Genetics of 2,4,6-Trinitrotoluene (TNT)
Metabolism by Plants,” SPRIG, ISU, $15,000, January 1, 2001-December 31, 2001.
Principal Investigator: “Plant Metabolic Engineering Research,” Cargill, $25,000 for the period
July 1, 1999-June 30, 2001.
Co-Principal Investigator [with Hughes, J. (P.I.), Bennett, C. (Co-P.I.), Rudolph, F. (Co-P.I.)],
“A Coupled Evaluation of Biotransformation Pathways and Toxicity Reduction for Explosives in
Remediation Systems or the Natural Environments,” Defense Special Weapons Agency, U.S. Dept.
of Defense, $1,981,480 for the period September 30, 1997-October 1, 1999.
Principal Investigator, “Young Investigator Award,” NSF BCS-9257938, $322,750 (includes
$5,250 from private donors) for the period November 1, 1992-January 31, 1999.
Principal Investigator, “Phytoremediation of TNT,” TX Advanced Technology Program 003604-
045, $148,157 for the period January 1, 1996-August 31, 1998.
Principal Investigator, “Young Investigator Award Matching,” Procter and Gamble Company,
$22,500 for the period March 1, 1993-February 28, 1997.
Principal Investigator, “NMR Studies of Elicitation-Mechanism and Metabolic Effects,” Welch
Foundation C-1197, $94,000 for the period June 1, 1993-May 31, 1996.
Principal Investigator (with San, K. Y.), “HPLC Photodiode Array and System Upgrade,” NSF
BES-9411928, $27,278 for the period August 1, 1994-July 31, 1996.
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Co-Principal Investigator [with Hughes, J. (P.I.)], “In situ Biochemical Remediation of
Trinitrotoluene-Contaminated Soils: Integrated Laboratory and Field Studies: Biochemical
Transformations and Pathways,” EPA Hazardous Substance Research Centers Program, $225,000
for the period February 1, 1994-September 30, 1995.
Principal Investigator, “NMR Studies of Biochemical Mechanism of Elicitation-Metabolic
Responses,” Welch Foundation Grant C-1197, $90,000 for the period June 1, 1990-May 31, 1993.
Principal Investigator, “Probing Cellular Processes for Productivity Enhancement in Hairy Root
Cultures of C. roseus,” NSF Grant BCS-9009992, $72,800 for the period July 1, 1990-February 28,
1993.
Co-Principal Investigator [with Mikos, A. (P.I.), Zygourakis, K. (co-P.I.)], “Gel Permeation
Chromatography,” NSF Grant BCS 9213197, $26,567 for the period August 1992-July 1993.
Principal Investigator (with Gustin, M.), “Refractive Index Detector for the HPLC,” National
Institute of Health (NIH) Small Instrumentation Grant (administered by Rice), $6,415,
September 1, 1992.
Co-Principal Investigator (with McIntire, L. V., et al.), “Ultra Low Temperature Freezer,” NIH
Small Instrumentation Grant (administered by Rice), $5,294, September 1, 1992.
Principal Investigator, “MAC Computer for Development of the ChE Programs and Modules,” Rice
University Undergraduate Teaching Committee and the Brown Foundation, $7,838, June 1992.
Principal Investigator, “Herschel Rich Invention Award,” Rice Engineering Alumni Association
Award, $1,000, April 23, 1992.
Principal Investigator (with King, G. C.), “NMRi Software for the Rice University 500 MHz NMR
Center,” New Methods Research Inc. Grant, $35,000 for the period October 1, 1990-November 1,
1991.
Co-Principal Investigator [with Mikos, A. (P.I.), Zygourakis, K. (Co-P.I.)], “UV/VIS System,” NIH
Biomedical Research Support Grant (administered by Rice), $3,100, September 1, 1992.
Principal Investigator, “Outstanding Young Faculty in Engineering,” Amoco Foundation Grant,
$1,750, June 27, 1991.
Co-Principal Investigator [with King, G. C. (P.I.), et al.], “Purchase of a 500 MHz NMR System,”
NIH Grant RR05759-01, $400,000 for the period May 1990-May 1991.
Co-Principal Investigator (with McIntire, L.V., et al.), “Flow Cytometer for Biochemical
Engineering Research,” NSF Grant EET-89-6775, $89,400 for the period July 1989-July 1990.
Principal Investigator, “Microcomputer Grant,” Rice University Grant, $2,500 for the period
August 1988-July 1989.
Principal Investigator, “Faculty Research Grant,” Rice University Grant, $977 for the period
August 1988-July 1989.
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Thesis Research Directed
Doctoral Theses:
Hei-Chan Lee (Principal-Advisor: Glacken, M. W.), “Metabolic Characterization of T Cell
Lymphoblastoid, Jurkat, in the Presence of Respiration Inhibitors in a Continuous Reactor” (1992).
Chih-Huang Ho, “Metabolic Studies of Catharanthus roseus Hairy Root Cultures by 31
P and 13
C
Nuclear Magnetic Resonance Spectroscopy” (1994).
Rajiv Bhadra, “Establishment, Cultivation, and Optimization of Hairy Roots of Catharanthus
roseus for the Synthesis of Indole Alkaloids” (1995).
Sundeep Vani, “Bioreactor Design for Scaleup of Catharanthus roseus Hairy Root Cultures for
Production of Indole Alkaloids” (1996).
Brenda Mann, “In vivo 31
P and 13
C Nuclear Magnetic Resonance Spectroscopy to Study Cellular
Metabolism” (1997).
Sushil Rijhwani, “Stress as a Means to Enhance Secondary Metabolite Productivity and to Probe
Metabolic Pathways” (1997).
John Morgan, “Analysis of Metabolic Flux of Secondary Metabolite Pathways of Catharanthus
roseus Hairy Root Cultures” (1999).
Erik Hughes (Principal-Advisor: San, K.Y.) “Metabolic Engineering of Catharanthus roseus Hairy
Roots Using an Inducible Promoter System” (2003).
Ganesh Sriram, “Flux Analysis in Central Carbon Metabolism in Plants: 13
C NMR Experiments and
Analysis” (2004).
Murali Subramanian. “TNT Phytotransformation in Native and Genetically Modified Species:
Significance of Aromatic Hydroxlamines in the Metabolic Pathway” (2004).
Vidya Iyer. “13
C Metabolic Flux Analysis of Soybean Central Carbon Metabolism: Response to
Temperature and Genotype Effects” (2006).
Guy Sander. “Quantitative Analysis of Metabolic Pathways in Catharanthus roseus Hairy
Roots Metabolically Engineered for Terpenoid Indole Alkaloid Overproduction” (2009).
Master Theses:
Marie Dominique Fernet, “High Resolution NMR Studies of Metabolism in Wild-Type and High
Osmolarity Mutants of S. cerevisiae” (1992).
John Lauritzen, “Catharanthus roseus as a Model System for the Study of the Phytoremediation of
TNT” (1998).
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Vidya Iyer, “Metabolic Fluxes in Developing Soybean Embryos Grown at Varying Temperatures,
Quantified by Biosynthetically Directed Fractional 13-C Labeling Experiments” (2003).
Sarah Rollo, “Phytotransformation of Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX): A Study of
the Biochemical Pathway in Arabidopsis thaliana” (2005).
Madhuresh Choudhury, “Metabolic Engineering of Escherichia coli for the Efficient Utilization of
Plant Sugar Mixtures,” (2008).
Marvin Mercado, “Standard Operating Procedures for Flux Analysis in Escherichia coli,” Oral
Defense (2009) .
Yanfen Fu, “Metabolic Flux Analysis of Escherichia coli MG1655 Under Octanoic Acid
Stress,” (2011).
Teaching Experience:
Iowa State University
Primary:
ChE 210 (U) “Material and Energy Balances” Fall 1999, 2000, 2002, 2007; Spring 2010
Use of basic mathematical concepts, physical laws, stoichiometry, and thermodynamic
properties of matter to obtain material and energy balances for steady state and
unsteady state systems
ChE 325 (U) “Chemical Engineering Lab I” Spring 2000
Friction factor and viscosity lab modules
ChE 381 (U) “Thermodynamics” Spring 2001, 2003, 2008; Fall 2006; Spring 2008, 2009
ChE 406 (U) “Environmental Chemodynamics” Fall 2004, 2005, 2008, 2009,2011
ChE 415/515 (U/G) “Biochemical Engineering” Spring 2005, 2006, 2007
ChE 525X (U/G,N) “Metabolic Engineering” Spring 2002
ChE 525L (U/G,N) “Metabolic Engineering Laboratory” Spring 2002
Engr 101 (U) “Seminar for Freshmen in Chemical Engineering” Fall 2000-2003
Rice University
Primary:
Bioe 698 (G) “Graduate Seminar” Fall 1998
Ceng 301 (U) “Chemical Engineering Fundamentals” Fall 1988-1994; 1996-1998
Use of basic mathematical concepts, physical laws, stoichiometry, and thermodynamic
properties of matter to obtain material and energy balances for steady state and
unsteady state systems.
Bioe 562; Ceng 562 (G, N) Spring 1989; 1991; 1994; 1997
“NMR Applications in Engineering” (Formerly Ceng 720; 582)
Survey of the basic principles and applications of nuclear magnetic resonance
spectroscopy to bioengineering and chemical engineering problems, using material
from the current literature. Includes in vivo NMR, imaging, NMR microscopy,
2-dimensional methods, solid state.
Ceng 662 (G) “Graduate Seminar” Spring 1990, 1995
Nsci 102 (U) “Natural Science” Spring 1992
Guest Lecturer:
Bioe 551 “Introduction to Bioengineering” Phytocatalysis
Bios 425 “Plant Molecular Biology” Metabolic Engineering in Plants
8
Bios 482 “NMR Spectroscopy” In Vivo NMR; Enzyme Kinetics in vivo
Hons 470 “Rice University Scholars Program” Effective Oral Presentations
Caltech
Ch. E. 163 (G) “Biochemical Engineering” (with Prof. James E. Bailey) 1985
U=Undergraduate; G=Graduate; N=New Course not Previously Given
University Service:
Iowa State University
University:
Engineering Curriculum Committee 2002-2005
Engineering Representative, Radiation Safety Committee 2004-2011
Faculty Senate Women and Minorities Committee 2000-2001
College of Engineering Cluster Champion (Bio) 2008-2009
Dean of Engineering Search Committee 2008-2009
University (General):
Engineering Representative, Biotechnology Council 2008-2011
Engineering Representative, Plant Sciences Institute Council 2003-2008
Plant Sciences Institute Graduate Fellowship Committee 2004-2007
Faculty Search Committee, Dept. of Food Science and Nutrition 1999-2002
Chemical Engineering:
Faculty mentor, Dr. Laura Jarboe 2008- present
Promotion and Tenure Committee, Chair 2006-2010
Safety Committee 2005-2008
Chair Search Committee 2004-2005
Post Tenure Review 2003-2006
Faculty mentor, Dr. Ramon Gonzalez 2002-2005
Governance Committee, Chair 2004-2005
Governance Committee 2002-2005
Curriculum Committee, Chair 2001-2004
Scholarship Committee 1999-2003
Faculty Search Committee, Chair 2000-2002
Faculty Search Committee 1999-2000, 2002-2003, 2007-2008, 2011-2012
Undergrad Recruiting & Minority Student Enhancement 1999-2001, 2005-2007
Internet Committee 1999-2001
Rice University
University Standing Committees:
Committee on Affirmative Action 1989-1993
University Council 1990
Faculty Council 1990
Marshalls Committee 1996-1998
Rice Athletic Committee 1996-1999
Chair, Rice Athletic Committee 1998-1999
University (General):
Wiess College Faculty Associate 1989-1995
Academic Blue Chip Recruiter for Admissions 1989-1999
9
Faculty Club Board of Directors 1991-1995
Nanotechnology Task Force 1993-1994
Provost Search Committee 1993-1994
Nanotechnology Committee 1994-1996
Sid Rich College Faculty Associate 1998-1999
Rice Women’s Conference Planning Committee 1998-1999
Engineering and Sciences:
Chair of SWE Panel and Open Forum on Women in Engineering, Rice 1990
Dean’s Committee on a new course in Technology 1991
Tau Beta Pi Advisor 1994-1996
Clare Booth Luce Fellowship Committee and Mentor 1994-1996
Co-Chair (w/Joe Hughes) Engineering Ad hoc Committee on Dept. Structure 1997
Natural Science Curriculum Committee 1998-1999
Bioengineering:
Curriculum Development Committee 1993-1998
Undergraduate Committee 1996-1999
Faculty Search Committee 1997-1999
Chair, Undergraduate Committee 1998-1999
Chemical Engineering:
Undergraduate Committee 1988-1999
Library Representative 1989-1991
Graduate Student Symposium 1990 and 1991, 1995
Strategic Plan Committee 1996
Faculty Search Committee 1997-1998
Professional Service:
Editorial and Advisory Board Memberships
Guest Editor, Biochemical Engineering, Current Opinion in Biotechnology 2000
Associate Editor, Biotechnology Progress 2002-2003
Guest Editor, Metabolic Engineering 2002
Editorial Advisory Board, Biotechnology Progress 2000-present
Scientific Advisory Committee, Metabolic Engineering VI Conference 2005-2006
Advisory Board, NSF project: Educational Materials to Enhance CHE Curricula with 2007-2009
Biological Applications, San Jose State University and University of Arkansas
Editorial Advisory Board, Current Opinion in Biotechnology 2010-present
Advisory Board, DOE, The Office of Biological and Environmental Research (BER) 2011-present
Advisory Committee (BERAC)
National Committees, Workshops
National Research Council Committee on Biobased Industrial Products 1994-1999
National Academy of Engineering Workshop, “Academic Engineering February 1994
Research in a Changing World”
USDA Cooperative State Research, Education, and Extension February 4-8, 2001
Service (CSREES) Review Team, Agricultural and Biological
Engineering Department, Purdue University
Metabolic Engineering, Young investigator award, subcommittee member 2002, 2004
ACS, BIOT Division, various award committees, subcommittee member 2003-present
10
AIChE, FP&BE Award Committee, subcommittee member 2007
Search Committee for Editor of Biotechnology Progress 2009-2010
NSF Math and Physical Science (MPS) Energy Workshop (invited speaker) March, 2010
Arlington, VA 22230.
Workshops
Plasma Workshop, National Center for Genome Resources, Santa Fe, NM May 1999
Zia Symposium and Workshop on Computer Modeling of Plant January 2000
Metabolism, Las Cruces, NM
Division Officer Training Conference, ACS, Clearwater Beach, FL January 2000
Malaysian-MIT Biotechnology Partnership Program Workshop, May 2000
Bioreactor Processes for Plant Cell Cultures, Cambridge, MA
“Coaching Strong Women in the Art of Strategic Persuasion” November 2001
Workshop sponsored by the Committee on the Advancement of
Women Chemists, ACS, Reno, NV
“Using Assessment Effectively” workshop sponsored by Fall 2001
Dr. Mary Huba, ISU Center for Teaching Excellence, Ames, IA
Offices
Steering Committee of the HSEMB 1991-1995
ACS Alternate Councilor, BIOT Division 1995-1997
ACS Newsletter Editor, BIOT Division 1998-2000
ACS Chair-Elect, BIOT Division 2000
ACS Chair, BIOT Division 2001
ACS Past-Chair, BIOT Division 2002
Organizer of Symposia
Organizer of Biotechnology Symposia of HSEMB 1991-1995
Chair of Sessions
Chair of Biotechnology Sessions of HSEMB 1990-1992, 1994, 1997
AIChE, Chair of Plant Tissue Culture Sessions 1993, 1994, 2003
ACS, Chair of Plant Tissue Culture Sessions 1996
ACS, Chair of Biocatalysis/Bioremediation Session 1998
ACS, Chair of Plant Transgenic/Engineering Session 1999
Metabolic Engineering Conference, Chair of Plant Met. Engineering 2002
ACS, Chair of Plant Transgenic/Engineering Session 2003
Natural Products Conference, Chair of Cell Environment Optimization 2006
Natural Products Conference, Chair of Plant Cell Culture Session 2008
Metabolic Engineering Conference, Chair of Nutrition and Agriculture Session 2008
Reviewer
Research Proposals and Panels:
Australian Research Council, Large Research Grants Program
Interagency Panel on Metabolic Engineering proposals
NSF
NIH
NSF Panel on Emerging Frontiers in Research and Innovation; Engr.
NSF Panel on Career Awards; Biotech. and Bioeng.
NSF Panel on Quantitative Systems Biology; Biotech. and Bioeng.
NSF Panel on SBIR proposals; Biotech. and Bioeng.
NSF Panel on Engineering Equipment proposals; Biotech. and Bioeng.
11
NSF Panel on Research Initiation proposals; Biotech. and Bioeng.
NSF and EPA Panel on Sustainable Technology
U.S. Department of Agriculture
U.S. Department of Energy
U.S. Department of Energy, site-visit reviewer for JBEI center renewal
Manuscripts:
AIChE Journal
Biotechnology and Bioengineering
Biotechnology Progress
Chemosphere Environmental Science and Technology
Enzyme and Microbial Technology
International Journal of Phytoremediation
JACS
Journal of Biological Chemistry
Journal of Biotechnology
Journal of Experimental Botany
Mathematical Biosciences
Metabolic Engineering
Plant Physiology
Phytochemistry
Phytochemistry Reviews
Tissue Engineering
Trends in Biotechnology
Community Service:
Memorial Drive Presbyterian Church Sunday School Teacher, Older 2s 1995-1996
Memorial Drive Presbyterian Church Sunday School Teacher, Older 2s 1998-1999
MDPC Little Yellow School House Science Lecture, Volunteer 1997-1998
Bunker Hill Elementary Volunteer 1998-1999
Westview School for Special Needs, Volunteer 1998-1999
Collegiate Presbyterian Church, Christian Education, early youth 2000-2002
Collegiate Presbyterian Church, Christian Education, youth 2002-2008
Collegiate Presbyterian Church, Design Committee 2003-2004
Collegiate Presbyterian Church, University Ministry Committee 2004-2005, 2008
Sawyer Elementary Volunteer 2000-2007
"A Noble Tale of Plant Chemotherapy Drugs", Talk to Golden K Kiwanis,
Ames, IA August 7, 2008
Research Publications:
h-index: 20
Number of Citations (Thomson ISI) shown in [square brackets] for selected publications as of
January, 2012
1. Galazzo, J. L., Shanks, J. V. and Bailey, J. E., “Comparison of Suspended and Immobilized Yeast
Metabolism Using 31
P Nuclear Magnetic Resonance Spectroscopy,” Biotechnology Techniques, 1, 1-
6 (1987).
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2. Bailey, J. E., Axe, D. D., Doran, P. M., Galazzo, J. L., Reardon, K. F., Seressiotis, A. and Shanks, J.
V., “Redirection of Cellular Metabolism: Analysis and Synthesis,” Ann. N. Y. Acad. Sci., 506, 1-23
(1987).
3. Bailey, J. E., Khosla, C., and Shanks, J. V., “Enhancement of Cell Growth Characteristics Using
Genetic Engineering,” Proceedings 8th International Biotechnology Symposium, in Paris, 424-432
(1988).
4. Shanks, J. V. and Bailey, J. E., “Estimation of Intracellular Sugar Phosphate Concentrations in
Saccharomyces cerevisiae Using 31
P Nuclear Magnetic Resonance Spectroscopy,” Biotechnol.
Bioeng., 32, 1138-1152 (1988).
5. Shanks, J. V. and Bailey, J. E., “Elucidation of the Cytoplasmic and Vacuolar Components in the
Intracellular Inorganic Phosphate Region in the 31
P NMR Spectrum of Yeast,” Biotechnol. Bioeng.,
35, 1102-1110 (1990).
6. Bailey, J. E., Birnbaum, S., Galazzo, J. L., Khosla, C. and Shanks, J. V., “Strategies and Challenges
in Metabolic Engineering,” Ann. N. Y. Acad. Sci., 589, 1-15 (1990).
7. Galazzo, J. L., Shanks, J. V. and Bailey, J. E., “Comparison of Intracellular Sugar-Phosphate Levels
from 31
P Nuclear Magnetic Resonance Spectroscopy of Intact Cells and Cell-Free Extracts,”
Biotechnol. Bioeng., 35, 1164-1168 (1990).
8. Shanks, J. V. and Bailey, J .E., “Comparison of Wild-Type and Reg1 Mutant Saccharomyces
cerevisiae Metabolic Levels During Glucose and Galactose Metabolism Using 31
P NMR
Spectroscopy,” Biotechnol. Bioeng., 35, 395-407 (1990).
9. Bhadra, R., Ho, C.-H., Rosi, S. and Shanks, J. V., “Establishment and Cultivation of Hairy Root
Lines of Catharanthus roseus ,” In Vitro Cell. Dev. Biol., 26, 69A (1990).
10. Bailey, J. E. and Shanks, J. V., “31
P and 13
C NMR Studies of Recombinant Saccharomyces
cerevisiae with Altered Glucose Phosphorylation Activities,” Bioprocess Engineering, 6, 273-284
(1991). (Error in order of authors in final print; should be Shanks and Bailey).
11. Bhadra, R., Ho, C.-H., and Shanks, J. V., “Growth Characteristics of Hairy Root Lines of
Catharanthus roseus,” In Vitro Cell. Dev. Biol., 27, 109A (1991).
12. Ho, C.-H. and Shanks, J. V., “Effects of Initial Medium pH on Growth and Metabolism of Hairy
Root Cultures of Catharanthus roseus-A Study with 31
P and 13
C NMR Spectroscopy,” Biotechnol.
Lett., 14, 959-964 (1992).
13. Bhadra, R., Vani, S. and Shanks, J. V., “Production of Indole Alkaloids by Selected Hairy Root
Lines of Catharanthus roseus,” Biotechnol. Bioeng., 41, 581-592 (1993).
14. Fernet, M.-D., Melvin, B., Gustin, M. and Shanks, J. V., “13
C NMR Spectroscopy Studies of
Glucose Metabolism in Osmolarity Mutants of Saccharomyces cerevisiae,” Enzyme and Microbial
Technology, 16, 207-215 (1994).
15. Bhadra, R. and Shanks, J. V., “Statistical Design of the Effect of Inoculum Conditions on Growth of
Hairy Root Cultures of Catharanthus roseus,” Biotechnology Techniques, 9, 681-686 (1995).
13
16. Melvin, B. K. and Shanks, J. V., “Influence of Aeration on Cytoplasmic pH of Yeast in an NMR
Airlift Reactor,” Biotechnology Progress, 12, 257-265 (1996).
17. Lauritzen, J., Hughes, J. and Shanks, J. V., “Phytoremediation of TNT: C. roseus Hairy Roots as a
Model System,” Proceedings of the Fifth World Congress of Chemical Engineering, 3, 795-800
(1996).
18. Hughes, J. B., Shanks, J., Vanderford, M., Lauritzen, J. and Bhadra, R., “Transformation of TNT by
Aquatic Plants and Plant Tissue Cultures,” Environmental Sci. and Tech., 31, 266-271 (1997).
19. Vanderford, M., Shanks, J. V. and Hughes, J. B., “Phytotransformation of Trinitrotoluene (TNT) and
Distribution of Metabolic Products in Myriophyllum aquaticum,” Biotechnology Letters, 19, 277-280
(1997).
29. Bhadra, R. and Shanks, J. V., “Transient Studies of Nutrient Uptake, Growth, and Indole Alkaloid
Accumulation in Heterotrophic Cultures of Hairy Roots of Catharanthus roseus” Biotechnology and
Bioengineering, 55, 527-534 (1997).
21. Shanks, J. V., Bhadra, R., Morgan, J., Rijhwani, S. K., and Vani, S., “Quantification of Metabolites
in the Indole Alkaloid Pathways of Catharanthus roseus: Implications for Metabolic Engineering,”
Biotechnology and Bioengineering, 58, 333-338 (1998).
22. Rijhwani, S. K. and Shanks, J. V., “Effect of Subculture Cycle on Growth and Indole Alkaloid
Biosynthesis by Catharanthus roseus Hairy Root Cultures,” Enzyme and Microbial Technology, 22,
606-611 (1998).
23. Rijhwani, S. K. and Shanks, J. V., “Effect of Elicitor Dosage and Exposure Time on Biosynthesis of
Indole Alkaloids by Catharanthus roseus Hairy Root Cultures,” Biotechnology Progress, 14, 442-
449 (1998).
24. Bhadra, R., Morgan, J. and Shanks, J. V., “Transient Studies of Light-adapted Cultures of Hairy
Roots of Catharanthus roseus: Growth and Indole Alkaloid Accumulation,” Biotechnology and
Bioengineering, 60, 670-678 (1998).
25. Bhadra, R., Wayment, D., Hughes, J. and Shanks, J. V., “Biochemical Pathways of 2,4,6-TNT
Abatement by Phytoremediation,” AIChE Symposium Series, Topical Conference on Pollution
Prevention and Environmental Reduction, Miami Beach, FL, (1998).
26. Morgan, J. and Shanks, J. V., “Inhibitor Studies of Tabersonine Metabolism in Catharanthus roseus
Hairy Roots,” Phytochemistry, 51, 61-68 (1999).
27. Rijhwani, S. K., Ho, C.-H. and Shanks, J. V., “In vivo 31
P and Multilabel 13
C NMR Measurements
for Evaluation of Plant Metabolic Pathways” Metabolic Engineering, 1, 12-25 (1999).
28. Bhadra, R., Wayment, D., Hughes, J. and Shanks, J. V., “Confirmation of Conjugation Processes
during TNT Metabolism by Axenic Plant Roots,” Environmental Sci. and Tech., 33, 446-452 (1999).
30. Bhadra, R., Wayment, D., Hughes, J. and Shanks, J. V., “Conjugate Formation During the
Metabolism of 2,4,6-Trinitrotoluene in Plant Roots,” in A. Leeson and B. C. Alleman (Eds.),
Phytoremediation and Innovation Strategies for Specialized Remedial Applications, Vol. 5(6),
pp. 21-125, Batelle Press, Columbus, OH (1999).
14
31. Shanks, J. V., Morgan, J., “Plant Hairy Root Culture,” Current Opinion in Biotechnology, 10, 151-
155 (1999).
32. Bhadra, R., Wayment, D., Hughes, J. and Shanks, J. V., “Characterization of Oxidation Products of
TNT Metabolism in Aquatic Phytoremediation Systems of Myriophyllum aquaticum,”
Environmental Sci. and Tech., 33, 3354-3361 (1999).
33. Wayment, D. G., Bhadra, R., Lauritzen, J., Hughes, J. and Shanks, J. V., “A Transient Study of
Formation of Conjugates During TNT Metabolism by Plant Tissues,” International Journal of
Phytoremediation, 1(3), 227-239 (1999).
34. Morgan, J. A., Barney, C. S., Penn, A.H. and Shanks, J. V., “The Effect of Buffered Media on
Growth and Alkaloid Productivity of C. roseus Hairy Root Cultures,” Applied Microbiology and
Biotechnology, 53, 262-265 (2000).
35. Bhadra, R., Spanggord, R. J., Wayment, D., Hughes, J. and Shanks, J. V., “Oxidative Metabolism of
2,4,6- Trinitrotoluene in Aquatic Phytoremediation Systems of Myriophyllum aquaticum,” Wetlands
Remediation Int. Conf., 127-132 (2000).
36. Morgan, J. and Shanks, J. V., “Determination of metabolic rate-limitations by precursor feeding in
Catharanthus roseus hairy root cultures,” Journal of Biotechnology, 79, 137-145 (2000).
37. Shanks, J. V. and Stephanopoulos, G. “Biochemical Engineering: Bridging the Gap between Gene
and Product,” Current Opinion in Biotechnology, 11, 169-170 (2000).
38. Shanks, J. V. “In Situ NMR Systems,” Current Issues in Molecular Biology, 3, 15-26 (2001).
39. Bhadra, R., Wayment, D. G., Williams, R. K., Barman, S. N., Stone, M. B., Hughes, J. B., and
Shanks, J. V., “Studies on plant-mediated fate of the explosives RDX and HMX,” Chemosphere,
44/5, 1259-1264 (2001).
40. Sriram, G. and Shanks, J. V., “A mathematical model for carbon bond labeling NMR experiments:
Analytical solutions and sensitivity analysis for the effect of reaction reversibilities on estimated
fluxes.” Proc. 31st Annual Biochemical Engineering Symposium, Manhattan, KS, September 08,
2001, 45–54.
41. Hughes, E. and Shanks, J. V., “Metabolic Engineering of Plants for Alkaloid Production,” Metabolic
Engineering, 4, 41-48 (2002).
42. Hansen, A. and Shanks, J. V., “Plant Metabolic Engineering-Entering the S Curve,” Metabolic
Engineering, 4, 1-2 (2002).
43. Morgan, J. and Shanks, J. V., “Quantification of Metabolic Flux in Plant Secondary Metabolism by a
Biogenetic Organizational Approach,” Metabolic Engineering, 4, 257-262 (2002).
44. Hughes, E. Hong, S.-B., Shanks, J. V., San K.-Y., and Gibson, S. I. “Characterization of an
Inducible Promoter System in Catharanthus roseus Hairy Roots,” Biotechnology Progress, 18,
1183-1186 (2002).
15
45. Iyer, V. V., Sriram, G., Fulton, D. B., Westgate, M. E., Spalding, M. H., and Shanks, J. V.,
“Development of NMR tools to obtain metabolic flux maps for soybean seeds.” Proc. 32nd Annual
Biochemical Engineering Symposium, Ames, IA, October 5 (2002) 83-89.
46. O. González-Rivera, Sriram, G., and Shanks, J. V., “Determination of the biomass composition of
Catharanthus roseus hairy roots.” Proc. 32nd Annual Biochemical Engineering Symposium, Ames,
IA, October 5, (2002) 65-70.
47. Hong, S. B., Hughes, E. K., Shanks, J. V., San, K. Y., and Gibson, S. “Role of the Non-Mevalonate
Pathway in Indole Alkaloid Production by Catharanthus roseus Hairy Roots,” Biotechnology
Progress, 19, 1105-1108 (2003).
48. Shanks, J. V., Oliver, D. J., Moon H., Rollo, S., and Subramanian, M., “Genetic and Biochemical
Basis for the Transformation of Energetic Materials (RDX, TNT, DNTs) by Plants,” Proceedings of
the American Institute of Chemical Engineers Annual Meeting, San Francisco, CA, November 16-21
(2003). Paper62d.
49. Moon, H., Subramanian, M., Rollo, S., Oliver, D. J., Shanks, J. V., and Moon, Hangsik, “Use of
Arabidopsis as a Model System for Genetic and Biochemical Studies of TNT Transformation in
Plants,” Proceedings of the First Conference on Sustainable Range Management, B. Alleman and
S. Downes (Eds), New Orleans, LA, January 5-8 (2004), Paper C3-04.
50. Sriram, G. and Shanks, J. V., “Improvements in Metabolic Flux Analysis using Carbon Bond
Labeling Experiments: Bondomer Balancing and Boolean Function Mapping,” Metabol. Eng, 6,
116-132 (2004).
51. Hughes, E., Hong, S.-B., Shanks, J. V., San, K.-Y., and Gibson, S. I. “Expression of a Feedback-
Resistant Anthranilate Synthase in Catharanthus roseus Hairy Roots Provides Evidence for Tight
Regulation of Terpenoid Indole Alkaloid Levels,” Biotechnol. Bioeng., 86, 718-727 (2004).
52. Hughes, E. H., Hong, S.-B., Gibson, S. I., Shanks, J. V., and San, K.-Y., “Metabolic Engineering of
the Indole Pathway in Catharanthus roseus Hairy Roots and Increased Accumulation of Tryptamine
and Serpentine,” Metabolic Engineering, 6, 268-276 (2004).
53. Sriram, G., Fulton, D. B., Iyer, V. V., Peterson, J. M., Zhou, R., Westgate, M. E., Spalding, M. H.,
and Shanks, J. V., “Quantification of Compartmented Metabolic Fluxes in Developing Soybean
(Glycine max) Embryos by Employing Biosynthetically Directed Fractional 13
C Labeling, 2-D
[13
C, 1H] NMR and Comprehensive Isotopomer Balancing,” Plant Physiol. 136, 3043-3057 (2004).
54. Rollo, S., Moon, H., Subramanian, M., Oliver, D. J., and Shanks, J. V., “Toxicity of RDX on
Germination of Arabidopsis thaliana,” Proceedings of the 33rd Annual Biochemical Engineering
Symposium, Lincoln, NE, April (2004).
55. Rollo, S., Moon, H., Subramanian, M., Oliver, D. J., and Shanks, J. V., “Phytoremediation of RDX:
Using Arabidopsis thaliana to Determine the Genetics and Biochemistry of the Transformation
Pathway,” Proceedings of the American Institute of Chemical Engineers Annual Meeting, Austin,
TX, November (2004), Paper 285e.
56. Shanks, J. V., “Phytochemical engineering: Combining Chemical Reaction Engineering with Plant
Science,” AIChE Journal 51, 2-7, (2005).
16
57. Peebles, C.A.M., Hong, S.-B., Gibson, S. I., Shanks, J. V., and San, K.-Y., “The Transient Effects
of Over-expressing Anthranilate Synthase α and β subunits in Catharanthus roseus Hairy Roots,”
Biotech. Progress, 21, 1572-1576, (2005).
58. Hong, S.-B., Peebles, C.A.M., Shanks, J. V., San, K.-Y., and Gibson, S. I., “Expression of the
Arabidopsis feedback-insensitive Anthranilate Synthase Induced by Holoenzyme and Tryptophan
Decarboxylase Genes in Catharanthus roseus Hairy Roots,” J. Biotech., 122, 28-38, (2006).
59. Hong, S.-B., Peebles, C.A.M., Shanks, J. V., San, K.-Y., and Gibson, S. I., “Terpenoid Indole
Alkaloid Production by Catharanthus roseus Hairy Roots Induced by Agrobacterium tumefaciens
Harboring rol ABC Genes,” Biotech. Bioeng., 93, 386-390, (2006).
60. Peebles, C. A.M., Hong, S.-B., Gibson, S. I., Shanks, J. V., and San, K.-Y., “Effects of Terpenoid
Precursor Feeding on Catharanthus roseus Hairy Roots Over-expressing the alpha or the alpha and
beta Subunits of Anthranilate Synthase,” Biotech. Bioeng., 93, 534-540, (2006).
61. Subramanian, M., Oliver, D. J. and Shanks, J. V. “TNT Phytotransformation Pathway
Characteristics in Arabidopsis: Role of Aromatic Hydroxylamines,” Biotech. Progress, 22, 208-216,
(2006).
62. Glatz, C. E., Gonzalez, R., Huba, M., Mallapragada, S. K., Narasimhan, B., Reilly, P. J., Saunders,
K., and Shanks, J. V. “Problem-Based Learning Biotechnology Courses in Chemical Engineering,”
Biotechnology Progress, 22, 173-178 (2006).
63. Yoon, J. M., Oliver, D. J., Shanks, J. V., “Phytotransformation of 2,4-Dinitrotoluene in Arabidopsis
thaliana: Toxicity, Fate, and Gene Expression Studies in vitro”, Biotechnology Progress, 22, 1524 -
1531 (2006).
64. Sriram, G., González-Rivera, O. and Shanks, J. V. “Determination of Biomass Composition of
Catharanthus roseus Hairy Roots for Metabolic Flux Analysis,” Biotechnology Progress, 22, 1659
- 1663 (2006).
65. Yoon, J. M., Oliver, D. J., Shanks, J. V., “Phytotransformation and Phytoremediation of 2,6-
Dinitrotoluene using a Model Plant, Arabidopsis thaliana”, Chemosphere, 68,1050–1057 (2007).
66. Hannink, N. K., Subramanian M., Rosser, S. J., Basran A., Murray, J. A. H., Shanks, J. V. and
Bruce, N. C. “Enhanced Transformation of TNT by Tobacco Plants Expressing a Bacterial
Nitroreductase,” International Journal of Phytoremediation, 9, 385-401 (2007).
67. Sriram, G., Fulton, D. B. and Shanks, J. V. “Flux Quantification in Central Carbon Metabolism of
Catharanthus roseus Hairy Roots by 13
C Labeling and Comprehensive Bondomer Balancing”,
Phytochemistry, 68, 2243-2257 (2007).
68. Sriram, G., Iyer, V. V., Fulton, D. B., and Shanks, J. V. “Identification of Hexose Hydrolysis
Products in Metabolic Flux Analytes: A Case Study of Levulinic acid in Plant Protein
Hydrolysate”, Metabolic Engineering, 9, 442-451 (2007).
69. Peebles, C.A.M., Gibson, S. I., Shanks, J. V., and San, K.-Y., “Characterization of an Ethanol
Inducible Promoter System in Catharanthus roseus Hairy Roots,” Biotechnology Progress, 23,
1258 -1260 (2007).
17
70. Peebles, C.A.M., Gibson, S. I., Shanks, J. V., and San, K.-Y., “A Study on the Long-Term
Maintenance of a Transgenic Catharanthus roseus Hairy Root Line,” Biotechnology Progress, 23,
1517 -1518, (2007).
71. Iyer, V.V., Sriram, G., Fulton, D. B., Zhou, R., Westgate, M.E., and Shanks, J.V., “Metabolic Flux
Maps Comparing the Effect of Temperature on Protein and Oil Biosynthesis in Developing
Soybean Cotyledons” Plant Cell and Environment, 31 (4), 506–517 (2008).
72. Sander, G.W., Gibson, S.I., San, K.Y., and Shanks, J.V., "Metabolic Engineering of Catharanthus
roseus Hairy Roots for Terpenoid Indole Alkaloid Production under Light and Dark Conditions",
Proceedings of the 37th Annual Biochemical Engineering Symposium, 37, 39 - (2008).
73. Binder, B.Y.K., Peebles, C.A.M., Shanks, J.V., and K.-Y. San, “The Effects of UV-B Stress on the
Production of Terpenoid Indole Alkaloids in Catharanthus roseus Hairy Roots,” Biotechnol. Prog.
25, 861–865 (2009).
74. Peebles, C.A.M., E.H. Hughes, J.V. Shanks, and K.-Y. San, “Transcriptional response of the
terpenoid indole alkaloid pathway to the overexpression of ORCA3 along with jasmonic acid
elicitation of Catharanthus roseus hairy roots over time,” Metabolic Engineering, Metab. Eng., 11,
76-86 (2009).
75. Peebles, C.A.M., Sander, G.W., Li, M., Gibson, S.I., Shanks, J.V. and K.-Y. San, “Long term
maintenance of a transgenic Catharanthus roseus hairy root line expressing feedback-insensitive
anthranilate synthase holoenzyme,” Biotechnology and Bioengineering, 102, 1521 - (2009).
76. Peebles, C.A.M., Shanks, J.V., and K.-Y. San, “The role of the octadecanoid pathway in the
production of terpenoid indole alkaloids in Catharanthus roseus hairy roots under normal and UV-
B stress conditions,” Biotechnol. Bioeng. 103, 1248-1254 (2009).
77. Murarka, A., Clomburg, J. M., Moran, S., Shanks, J. V. and R. Gonzalez. “Metabolic Analysis of
Wild-Type Escherichia coli and a Pyruvate Dehydrogenase Complex (PDHC)-deficient derivative
reveals the Role of PDHC in the Fermentative Metabolism of Glucose,” J. Biological
Chemistry,285, 31548-31558 (2010).
78. Peebles, C.A.M., Sander, G. W., Hughes, E. H., Peacock, R., J.V. Shanks, and K.-Y. San, “The
Expression of 1-deoxy-D-xylulose Synthase and Geraniol 10-hydroxylase or Anthranilate Synthase
Increases Terpenoid Indole Alkaloid Accumulation in Catharanthus roseus Hairy Roots,”
Metabolic Engineering 13, 234-240 (2011). http://dx.doi.org/10.1016/j.ymben.2010.11.005
79. Li, M., Peebles, C.A.M., J.V. Shanks, and K.-Y. San, “Effect of Nitric Oxide on Growth and
Terpenoid Indole Alkaloid Production in Catharanthus roseus Hairy Root Cultures,” Biotechnology
Progress 27, 625-630 (2011).
80. Choudhary, M.K., Yoon, J.M., Gonzalez, R. and J.V. Shanks, “Re-examination of metabolic fluxes
in Escherichia coli during anaerobic fermentation of glucose using 13
C labeling experiments and 2-
dimensional nuclear magnetic resonance (NMR) spectroscopy,” Biotechnology and Bioprocess
Engineering 16, 419-437 (2011). DOI: 10.1007/s12257-010-0449-5
81. Iyer, V.V., Ling, L. Studham, M., Westgate, M.E., Wurtele, E.S. and Shanks, J.V. “Metabolic
Flux and Transcriptional Profiling of Soybean Isolines with Varying Protein Production,”
Submitted to Biochemical Journal, 2011.
18
Books:
Committee on Biobased Industrial Products, “Biobased Industrial Products,” National Research
Council, National Academy Press, August 1999.
Book Foreword:
Foreword by J. V. Shanks. p. v-vi, Plant Metabolic Networks, J. Schwender, Ed. Springer Plant
Sciences, 2009, pp. 409
Book Chapters:
1. Shanks, J. V. and Bhadra, R., “Characteristics of Selected Hairy Root Lines of Catharanthus
roseus,” pp. 51-63 in Hairy Roots, P.M. Doran, Ed., Harwood Academic Publishers, Chur,
Switzerland, ©1997, pp. 237.
2. Morgan, J., Rijhwani, S. K., and Shanks, J. V., “Metabolic Engineering for the Production of Plant
Secondary Metabolites,” pp. 325-352 in Metabolic Engineering, S. Y. Lee and E. T. Papoutsakis,
Eds., Marcel Dekker, ©1999.
3. Rijhwani, S. K., Bhadra, R., Ho, C.-H., Morgan, J., Vani, S., and Shanks, J. V., “Quantification of
Metabolic Fluxes for Metabolic Engineering of Plant Products,” pp 45-60 in Plant Cell and Tissue
Culture for the Production of Food Ingredients, T. J. Fu, G. Singh, and W. R. Curtis, Eds., Plenum
Publishing Corporation, New York, NY, ©1999.
4. Shanks, J. V., “In situ NMR Systems,” in NMR in Microbiology: Theory and Applications, J.-N.
Barbotin and J.-C. Portais, Eds., Horizon Scientific Press, Wymondham, UK. ©2000.
5. Burken, J. G., Shanks, J. V., and Thompson, P. L., “Phytoremediation and Plant Metabolism of
Explosives and Nitroaromatic Compounds,” in Biodegradation of Nitroaromatic Compounds and
Explosives, J. Spain, J. Hughes, and H. Knackmuss, Eds., CRC Press, ©2000.
6. Subramanian, M. and Shanks, J. V., “Role of Plants in Transformation of Explosives” pp. 389-408
in Phytoremediation: Degradation and Control of Contaminants, S. McCutcheon and J.L. Schnoor,
Eds., Wiley and Sons, Inc., ©2003.
7. Yoon, J.M., Oliver, D.J. and Shanks, J. V. “Plant Transformation Pathways of Energetic Materials
(RDX, TNT, DNTs). pp. 103-116 in, Agricultural Biotechnology: Beyond Food and Energy to
Health and the Environment, National Agricultural Biotechnology Council Report 17, A.
Eaglesham, R. Bessin, R. Trigiano, R. W. T. Hardy, Eds. National Agricultural Biotechnology
Council, Ithaca, New York, ©2005.
8. Iyer, V. V., Sriram, G. and Shanks, J. V. “Metabolic Flux Maps of Central Carbon Metabolism in
Plants: Isotope Labeling Analysis.” pp 125-144 In Concepts in Plant Metabolomics, B. J. Nikolau
and E. S. Wurtele, Eds. Springer Publishers. April 2007.
9. Sriram G., Shanks J.V. “Application of Isotopomer Data and Mathematical Modeling in Flux
Quantification.” In: Mathematical Modeling in Nutrition and Health Sciences Hanigan M.D.,
Novotny J.A., Marstaller C.L., Eds., Virginia Tech press, Blacksburg, VA. ©2007.
10. Brown M., Shanks J.V. “Linear Hydrocarbon Producing Pathways in Plants, Algae and Microbes.”
pp 1-12 In: Sustainable Bioenergy and Bioproducts , Gopalakrishnan, K., van Leeuwen J.H.,
Brown R.L., Eds., Springer-Verlag, © 2012, DOI: 10.1007/978-1-4471-2324-8.
19
11. Truong, Q., Yoon, J.M., and Shanks, J. V. “Isotopomer Measurement Techniques in Metabolic
Flux Analysis: NMR” In, Plant Metabolism: Methods and Protocols. Methods in Molecular
Biology. Sriram, G. Eds. Humana Press, In press.
Technical Reports:
1. Hughes, J. and Shanks, J. V., “Biochemical Transformations and Pathways From Phytoremediation
of TNT-Contaminated Soils,” Research Brief #11, Hazardous Substance Research Center/South &
Southwest, 1996.
2. Shanks, J. V., “Phytoremediation of TNT: C. roseus Hairy Roots as a Model System,” Course
Notebook, IBC Conference on Phytoremediation, Washington, DC, May 1996.
3. Shanks, J. V., Oliver, D.J., Moon, H. Subramanian, M., Yoon, J.M., Rollo, S. “Genetic and
Biochemical Basis for the Transformation of Energetic Materials (RDX, TNT, DNTs) by Plants,”
SERDP Final Report, Washington, D.C., April 2007.
Technical Software:
NMR2Flux, ISURF 3399, Iowa State University, Sriram, G. and Shanks, J. V., © 2005.
Educational Publications:
1. Davis, S. H. and Shanks, J. V., “Computer Tools For Chemical Engineering Courses at Rice
University,” ASEE Annual Conference Proceedings, Vol. II, 1459-1463 (1991).
2. Davis, S. H. and Shanks, J. V., “Computer Modules for Chemical Engineering Flowsheet
Simulation,” Annual Meeting, AIChE, Software Presentation, AIChE Manuscript, pp. 24 (1991).
3. Davis, S. H. and Shanks, J. V., “Simulation Programs Used in Chemical Engineering at Rice
University,” ASEE Annual Conference Proceedings, Vol. II, 1034-1037 (1992).
4. Glatz, C. E., Gonzalez, R., Huba, M., Mallapragada, S. K., Narasimhan, B., Reilly, P. J., Saunders,
K., and Shanks, J. V. “Problem-Based Learning Biotechnology Courses in Chemical Engineering,”
Biotechnology Progress, 22, 173-178 (2006).
Textbooks:
Davis, S. H. and Shanks, J. V., Chemical Engineering Fundamentals, Rice University, ©1989,
©1990, ©1991, ©1992, ©1993, ©1994, pp. 231.
Textbook Web Site:
Davis, S. H. and Shanks, J. V., Chemical Engineering Fundamentals, Rice University. 1996, 1997,
1998 http://www.owlnet.rice.edu/~ceng301/
Educational Software:
Macintosh Simulation Programs, Chemical Engineering Dept., Rice University, Davis, S. H. and
Shanks, J. V., © 1991, © 1992.
Lecturer of Continuing-Education Courses:
“NMR Spectroscopy” in Advances in Tissue Engineering, Sponsored by Rice University, Houston,
TX, in August for the years 1993, 1994, 1995, 1996, 1997, 1998.
20
Technical Presentations at Conferences-Abstracts:
1. “Application of 31
P NMR Spectroscopy to Fermentation Studies of Recombinant Saccharomyces
cerevisiae,” Annual Meeting, AIChE, New York, NY, November 1987.
2. “Comparison of Wild-Type and Reg1 Mutant Saccharomyces cerevisiae Metabolic Levels and
Rates Using in vivo 31
P NMR,” Annual Meeting, AIChE, Washington, DC, November 1988.
3. “Measurements of Intracellular Levels and pH using 31
P NMR,” Seventh Annual Conference on
Biomedical Research in Houston, Houston, TX, February 1989.
4. “Establishment and Cultivation of Hairy Root Lines of Catharanthus roseus,” Bhadra, R.,
Ho, C.-H., Rosi, S., and Shanks, J. V., Annual Meeting, Tissue Culture Association, In Vitro Cell.
Dev. Biol., 26, 69A (1990).
5. “Establishment and Cultivation of Hairy Root Lines of Catharanthus roseus,” Bhadra, R.,
Ho, C-H., and Shanks, J. V., Annual Meeting, AIChE, Chicago, IL, November 1990.
6. “Identification of Growth and Morphological Characteristics for the Selection of Hairy Root Lines
of C. roseus,” Bhadra, R. and Shanks, J. V., Ninth Annual Conference on Biomedical Engineering
Research in Houston, Houston, TX, February 1991.
7. “Selection and Growth Characteristics of Hairy Root Lines of Catharanthus roseus,” Bhadra, R.
and Shanks, J. V., Spring Meeting of the ACS, Atlanta, GA, April 1991.
8. “Use of NMR in Metabolic Engineering,” Biomedical and Biological Applications of Nuclear
Magnetic Resonance, Galveston-Houston Biological NMR Symposium, Galveston, TX, May 1991.
9. “Growth Characteristics of Hairy Root Lines of Catharanthus roseus,” Bhadra, R., Ho, C.-H., and
Shanks, J. V., Annual Meeting, Tissue Culture Association, In Vitro Cell. Dev. Biol., 27, 109A
(1991).
10. “Nutrient Utilization by Hairy Root Lines of Catharanthus roseus,” Bhadra, R., Vani, S. N., and
Shanks, J. V., Annual Meeting, AIChE, Los Angeles, CA, November 1991.
11. “A Novel Reactor for In Situ Studies of Organ Metabolism,” Ho, C.-H. and Shanks, J. V., Tenth
Annual Conference on Biomedical Engineering Research in Houston, Houston, TX, March 1992.
12. “Alkaloid Yields from Hairy Root Lines of C. roseus,” Vani, S. and Shanks, J. V., Tenth Annual
Conference on Biomedical Engineering Research in Houston, Houston, TX, March 1992.
13. “Alkaloid Production by Hairy Root Lines of Catharanthus roseus,” Bhadra, R., Vani, S., and
Shanks, J. V., Spring Meeting of the ACS, San Francisco, CA, April 1992.
14. “Transgenic Hairy Root Clones for Production of Indole Alkaloids,” Bhadra, R., Ho, C.-H.,
Vani, S. N., and Shanks, J. V., Ninth International Biotechnology Symposium and Exposition,
ACS, Crystal City, VA, August 1992.
15. “31
P and 13
C NMR Spectroscopy for Metabolic Studies of Hairy Roots: A Novel Micro-Reactor,”
Ho, C.-H. and Shanks, J. V., Annual Meeting, AIChE, Miami Beach, FL, November 1992.
21
16. “NMR Spectroscopy Studies of Yeast in an Air-lift Reactor: Comparison of High to Low Cell
Densities,” Rodriguez, M., Mann, B., Fernet, M., and Shanks, J. V., Annual Meeting, AIChE,
Miami Beach, FL, November 1992.
17. “Effects of Initial Medium pH on Hairy Root Metabolism — A Study with 31
P and 13
C NMR
Spectroscopy,” Ho, C.-H. and Shanks, J. V., Annual Meeting, AIChE, Miami Beach, FL,
November 1992.
18. “31
P NMR Studies of Elicitor-Treated Catharanthus roseus Hairy Root Cultures,” Ho, C.-H. and
Shanks, J. V., Eleventh Annual Conference on Biomedical Engineering Research in Houston,
Houston, TX, February 1993.
19. “Effect of Illumination on Hairy Root Cultures of Catharanthus roseus,” Bhadra, R. and Shanks,
J. V., Annual Meeting, AIChE, St. Louis, MO, November 1993.
20. “Growth, Nutrient Utilization and Alkaloid Productivity of C. roseus Hairy Roots in Bioreactors,”
Vani, S. and Shanks, J. V., Annual Meeting, AIChE, St. Louis, MO, November 1993.
21. “NMR Studies of Catharanthus roseus Hairy Root Cultures in Response to Elicitation,”
Ho, C.-H. and Shanks, J. V., Annual Meeting, AIChE, St. Louis, MO, November 1993.
22. “Measurement of Oxygen Uptake Rates and Growth C. roseus Hairy Roots in a Bioreactor,”
Vani, S. and Shanks, J. V., Twelfth Annual Conference on Biomedical Engineering Research in
Houston, Houston, TX, February 1994.
23. “The Response of Hairy Root Cultures of Catharanthus roseus to Illumination” Bhadra, R. and
Shanks, J. V., Twelfth Annual Conference on Biomedical Engineering Research in Houston,
Houston, TX, February 1994.
24. “Reactor Studies of the Effect of CO2 Levels on the Metabolism of Catharanthus roseus Hairy
Roots,” Vani, S. and Shanks, J. V., Annual Meeting, AIChE, San Francisco, CA, November 1994.
25. “Effect of Scaleup on Metabolism of C. roseus Hairy Root Cultures,” Vani, S. and Shanks, J. V.,
Thirteenth Annual Conference on Biomedical Engineering Research in Houston, Houston, TX,
February 1995.
26. “Photoheterotrophic Culture of Hairy Roots of Catharanthus roseus for the Synthesis of Indole
Alkaloids,” Bhadra, R. and Shanks, J. V., Spring Meeting of the ACS, Anaheim, CA, April 1995.
27. “In vivo 13
C NMR Spectroscopy as a Tool to Study Aromatic Hydrocarbon Degradation,”
Melvin, B. K. and Shanks, J. V., Annual Meeting of the AIChE, November 1995.
28. “Elicitation Studies of Catharanthus roseus Hairy Root Cultures,” Rijhwani, S. K. and Shanks,
J. V., Annual Meeting of the AIChE, Miami Beach, FL, November 1995.
29. “Effect of Pectinase on Synthesis of Therapeutically Valuable Secondary Metabolites by
Catharanthus roseus Hairy Root Cultures,” Rijhwani, S. K. and Shanks, J. V., 14th Annual Houston
Conference on Biomedical Engineering Research, Houston, TX, February 1996.
22
30. “Effect of Fungal Wall Components on Indole Alkaloid Synthesis by Catharanthus roseus Hairy
Root Cultures,” Rijhwani, S. K. and Shanks, J. V., National Meeting of the ACS, New Orleans, LA,
March 1996.
31. “An Inhibition ELISA for Measurement of Low Concentrations of Vinblastine, A Plant Secondary
Metabolite,” Budd, S. M. and Shanks, J. V., National Meeting of the ACS, New Orleans, LA,
March 1996.
32. “Phytoremediation of TNT: C. roseus Hairy Roots as a Model System,” Lauritzen, J., Hughes, J.,
and Shanks, J. V., Fifth World Congress of Chemical Engineering, San Diego, CA, July 1996.
33. “Phytoremediation of Explosives,” Hughes, J., Bhadra, R., Lauritzen, J., Vanderford, M., and
Shanks, J. V., Second Annual Symposium on Energy and the Environment, Energy and
Environmental Systems Institute, Rice University, Houston, TX, September 1996.
34. “Quantification of Fluxes in the Indole Alkaloid Pathways of Catharanthus roseus: Implications
for Metabolic Engineering,” Bhadra, R., Budd, S., Ho, C.-H., Morgan, J., Rijhwani, S., Vani, S.,
and Shanks, J. V., Engineering Foundation Conference, Recombinant DNA, Metabolic
Engineering, Danvers, MA, October 1996.
35. “Kinetics and Fate of Transformation of 2,4,6-Trinitrotoluene by Aquatic Plants and Plant Tissue
Cultures,” Bhadra, R., Lauritzen, J., Hughes, J., and Shanks, J. V., Annual Meeting of the AIChE,
Chicago, IL, November 1996.
36. “Metabolism of C. roseus Hairy Root Cultures: A NMR Spectroscopy Based Study,” Rijhwani, S.
and Shanks, J. V., Annual Meeting of the AIChE, Chicago, IL, November 1996.
37. “Metabolic Engineering for the Production of Plant Pharmaceuticals,” Morgan, J., Rijhwani, S.,
Vani, S. and Shanks, J. V., Fifteenth Annual Conference on Biomedical Engineering Research in
Houston, Houston, TX, February 1997.
38. “Effects of Precursor Feeding upon Alkaloid Biosynthesis in Catharanthus roseus Hairy Root
Cultures,” Morgan, J. and Shanks, J. V., National Meeting of the ACS, San Francisco, CA, April
1997.
39. “In situ NMR Spectroscopy as a Technique to Study Elicitation-Induced Metabolic Changes in
Plant Organ Cultures,” Rijhwani, S. and Shanks, J. V., National Meeting of the ACS, San
Francisco, CA, April 1997.
40. “Phytoremediation of Explosives: Hairy Root Cultures as a Model System,” Fourteenth Biennial
Estuarine Research Federation International Conference, Providence, RI, October 1997.
41. “Quantitative Analysis of the Tabersonine Branchpoint in Catharanthus roseus Hairy Root
Cultures,” Morgan, J. and Shanks, J. V., Annual Meeting of the AIChE, San Francisco, CA,
November 1997.
42. “Phytoremediation of 2,4,6-TNT: Plant Transformation Processes,” Bhadra, R., Wayment, D. G.,
Hughes, J., and Shanks, J. V., National Meeting of the ACS, Boston, MA, August 1998.
43. “Strategies to determine Flux Limitations in Indole Alkaloid Pathways of Catharanthus roseus,”
Morgan, J. and Shanks, J. V., National Meeting of the ACS, Boston, MA, August 1998.
23
44. “Quantification of Metabolic Flux in Plant Secondary Metabolism by a Biogenetic Organizational
Approach,” Morgan, J. and Shanks, J. V., Annual Meeting of the AIChE, Miami Beach, FL,
November 1998.
45. “Phytoremediation of HMX and RDX in Hairy Root Cultures of Catharanthus Roseus,” Barman,
S., Williams, R., Bhadra, R., and Shanks, J. V., Annual Meeting of the AIChE, Miami Beach, FL,
November 1998.
46. “Biochemical Pathways of 2,4,6-Trinitrotoluene Abatement by Phytoremediation,” Bhadra, R.,
Wayment, D. G., Hughes, J., and Shanks, J. V., Annual Meeting of the AIChE, Miami Beach, FL,
November 1998.
47. “Fate of RDX and HMX in Phytoremediation Systems,” Williams, R., Stone, M., Barman, S.,
Bhadra, R., Hughes, J., and Shanks, J. V., Annual Meeting of the AIChE, Miami Beach, FL,
November 1998.
48. “Phytoremediation of TNT and the Monoaromatics,” Wayment, D. G., Bhadra, R., Hughes, J., and
Shanks, J. V., National Meeting of the ACS, Anaheim, CA, March 1999.
49. “Conjugate Formation During the Metabolism of 2,4,6-Trinitrotoluene in Plant Roots,” Bhadra, R.,
Wayment, D. G., Hughes, J., and Shanks, J. V., Battelle In Situ Conference for Bioremediation, San
Diego, CA, April 1999.
50. “Plant Metabolism of 2,4,6-Trinitrotoluene and Related Nitroaromatic Compounds,” Second
International Symposium on Biodegradation of Nitroaromatic Compounds and Explosives, Xerox
University, VA, September 1999.
51. “The Characterization of Oxidation Products of TNT Metabolism in Aquatic Phytoremediation
Systems of Myriophyllum aquaticum,” Bhadra, R., Hughes, J. B., Wayment, D., and Shanks, J. V.,
Annual Meeting of the AIChE, Dallas, TX, November 1999.
52. “Indole Alkaloid Production in C. roseus Hairy Roots,” Annual Meeting of the AIChE, Dallas, TX,
November 1999.
53. “Challenges in Engineering Overproduction of Plant Alkaloids,” Engineering Foundation
Conference, Metabolic Engineering III, Colorado Springs, CA, October 2000.
54. “Protein and Nonprotein Nitrogen in C. roseus Hairy Roots,” Hughes, E., San, K. Y., and Shanks, J.
V., Annual Meeting of the AIChE, Los Angeles, CA, November 2000.
55. “Phytoremediation of TNT: Pathway Studies,” Subramanian, M. and Shanks, J. V., Annual Meeting
of the AIChE, Los Angeles, CA, November 2000.
56. “A Strategy for Manipulation of Alkaloid Flux in Catharanthus roseus Hairy Roots,” Hughes, E.,
Hong, S.-B., Gibson, S., San, K.-Y., and Shanks, J. V., Houston Conference on Biomedical
Engineering Research, Houston, TX, February 2001.
57. “A Strategy for Manipulation of Indole Alkaloid Flux in Catharanthus roseus Hairy Roots,” Hong,
S.-B., Hughes, E., Shanks, J. V., San, K.-Y., and Gibson, S., American Society of Plant
Physiologists Annual Meeting, Providence, RI, July 2001.
24
58. “TNT Transformation by Plants: Role of Hydroxylamines,” Subramanian, M. and Shanks, J. V.,
Annual Meeting of the AIChE, Reno, NV, November 2001.
59. “An Inducible Promoter for the Study of Alkaloid Flux in Catharanthus roseus Hairy Roots,”
Hughes, E., Hong, S.-B., Gibson, S., San K. Y., and Shanks, J. V., Annual Meeting of the AIChE,
Los Angeles, CA, November 2001.
60. “A Mathematical Model for Carbon-Bond Labeling Experiments,” Sriram, G. and Shanks J. V.,
Annual Meeting of the AIChE, Reno, NV, November 2001.
61. “Find a Way to Use NMR: Tribute to Jay Bailey,” Annual Meeting of the AIChE, Reno, NV,
November 2001.
62. “Development of a Stoichiometric Model to Describe Primary and Intermediary Metabolism in
Catharanthus roseus Hairy Roots,” Gonzalez-Riviera, O., Denefe, E. L., Sriram, G., and
Shanks, J. V., National Meeting of the ACS, Boston, MA, August 2002.
63. “Development of a Stoichiometric Model for Metabolic Flux Analysis in Catharanthus roseus
Hairy Roots,” Sriram, G., Gonzalez-Riviera, O., and Shanks, J. V., Annual Meeting of the AIChE,
Indianapolis, IN, November 2002.
64. “Metabolic Engineering of the Indole Pathway in Catharanthus roseus Hairy Roots,” Hughes, E.,
Hong, S.-B., Gibson, S., San, K. Y., and Shanks, J. V., Annual Meeting of the AIChE, Indianapolis,
IN, November 2002.
65. “Metabolic Flux Analysis of Developing Soybean (Glycine max) Embryos using a Carbon-Bond
Labeling Experiment,” Sriram, G., Fulton, D. B., Peterson, J., Westgate, M., Spalding, M., and
Shanks, J. V., Annual Meeting of the AIChE, Indianapolis, IN, November 2002.
66. “Phytoremediation of TNT: Pathway Analysis,” Subramanian, M. and Shanks, J. V., Annual
Meeting of the AIChE, Indianapolis, IN, November 2002.
67. “Phytotransformation of TNT through Hydroxylamine Intermediates-Pathway Confirmation,”
Subramanian, M. and Shanks, J. V., Partners in Environmental Technology Technical Symposium
and Workshop, SERDP, Washington, DC, December 2002.
68. “Metabolic engineering of indole alkaloid pathways in Catharanthus roseus hairy roots,” Hughes,
E., Hong, S.-B., Gibson, S., Shanks, J. V., San, K.-Y., 225th ACS National Meeting, New Orleans,
LA, March 23-27, 2003.
69. “Role of the non-mevalonate pathway in indole alkaloid production by Catharanthus roseus hairy
roots,” Hong, S.-B., Hughes, E. H., Shanks, J. V., San, K.-Y., and Gibson, S. I., 225th ACS National
Meeting, New Orleans,LA, March 23-27, 2003.
70. “Role of the non-mevalonate pathway in indole alkaloid production by Catharanthus roseus hairy
roots,” Hong, S.-B., Hughes, E. H., Shanks, J. V., San, K.-Y., and Gibson, S. I., Twentieth
Conference on Biomedical Engineering Research in Houston, Houston, TX, April 3-4, 2003.
25
71. “Metabolic engineering of indole alkaloid pathways in Catharanthus roseus hairy roots,” Hughes,
E., Hong, S.-B., Gibson, S., Shanks, J., and San, K.-Y., Twentieth Conference on Biomedical
Engineering Research in Houston, Houston, TX, April 3-4, 2003.
72. “Using Rubrics to Facilitate Students’ Development of Problem Solving Skills,” Saunders, K. P.,
Glatz, C. E., Huba, M. E., Griffin, M. H., Mallapragada, S. K., and Shanks, J. V., a Multimedia
presentation at the ASEE Annual Meeting, Nashville, TN, June 24, 2003.
73. “PBL Approach to Bioprocessing Lab,” Glatz, C., Saunders, K., Huba, M., Mallapragada, S.,
Narasimhan, B., Reilly, P., and Shanks, J., a poster presented at the NSF Grantees Conference,
Washington, DC, September 2003.
74. “Development of NMR tools to obtain metabolic flux maps for soybean seeds,” Iyer, V. V., Sriram,
G., Westgate, M. E., and Shanks, J. V., AIChE, Annual Meeting, San Francisco, CA, November 16-
21, 2003.
75. “Metabolic flux analysis of sucrose metabolism into protein, oil and starch in soybean seeds,”
Sriram, G., Iyer, V. V., Zhou, R., Fulton, D. B., Westgate, M. E., Spalding, M. H., and Shanks,
J. V., Annual meeting, American Society of Agronomy, Denver, Co, November 2-6, 2003.
76. “Metabolic engineering of indole alkaloid pathways in Catharanthus roseus hairy roots,” Peebles,
C. A., Hughes, E., Hong, S.-B., Gibson, S., Shanks, J. V., and San, K.-Y., 2003 Annual AIChE
meeting, San Francisco, CA, November 16-21, 2003.
77. “Phytoremediation of RDX: Screening Studies on Arabidopsis thaliana,” Rollo, S., Moon, H.,
Subramanian, M., Oliver, D. J., and Shanks, J. V., Annual Meeting of the AIChE, San Francisco,
CA, November 16-21, 2003.
78. “Genetic and Biochemical Basis for the Transformation of Energetic Materials (RDX, TNT, DNTs)
by Plants,” Shanks, J. V., Oliver, D. J., Moon H., Rollo, S., and Subramanian, M., Annual Meeting
of the AIChE, San Francisco, CA, November 16-21, 2003.
79. “Genetic and Biochemical Basis for Plant Transformation of Energetic Materials,” Subramanian,
M., Moon H, Oliver, D, and Shanks, J. V., Partners in Environmental Technology Technical
Symposium and Workshop, SERDP, Washington, DC, December 2003.
80. “Genetic and Biochemical Basis for the Transformation of Energetic Materials (RDX, TNT, DNTs)
by Plants,” Shanks, J. V, Battelle Conference on Range Management, New Orleans, LA, January 6,
2004.
81. “Plant Metabolic Engineering under Construction,” Fourth Interagency Conference on Metabolic
Engineering, NSF, February 6, 2004.
82. “Metabolic engineering of indole alkaloid pathways in Catharanthus roseus hairy roots,” Peebles,
C. A., Hughes, E., Hong, S.-B., Gibson, S., Shanks, J. V., and San, K.-Y., Twenty First Conference
on Biomedical Engineering Research in Houston, Houston, TX, February 12-13, 2004.
83. “Metabolic engineering of the terpenoid indole alkaloid pathways in Catharanthus roseus hairy
roots: The effects of terpenoid precursor feeding on transgenic AS hairy roots,” Peebles, C. A.,
Hughes, E., Hong, S.-B., Gibson, S., Shanks, J. V., and San, K.-Y., 227th ACS National Meeting,
Anaheim, CA, March 28-April 1, 2004.
26
84. “Toxicity of RDX on Germination of Arabidopsis thaliana,” Rollo, S., Moon, H., Subramanian, M.,
Oliver, D. J., and Shanks, J. V., 33rd
Annual Biochemical Engineering Symposium, Lincoln, NE,
April 2004.
85. “Phytotransformation pathways of the energetic material TNT,” Subramanian M., Moon, H., Rollo,
S., Oliver, D., and Shanks J. V., American Association of Ecological Engineers, Fayetteville, AR,
June 2004.
86. Metabolic Flux Maps of Central Carbon Metabolism in Plants,” Third International Congress on
Plant Metabolomics, Ames, IA, June 3-6, 2004.
87. “Metabolic Flux Analysis of Sucrose Metabolism into Protein, Oil, Starch in Soybean Seeds,”
Iyer, V. V., Sriram, G., Fulton, B., Zhou, R., Westgate, M. E., and Shanks, J. V., Third International
Congress on Plant Metabolomics, Ames, IA, June 3-6, 2004.
88. “Quantification of Metabolic Fluxes in Plants from 2-D NMR Data: Mathematical Framework and
Flux Identifiability,” Sriram, G. and Shanks, J. V., Third International Congress on Plant
Metabolomics, Ames, IA, June 3-6, 2004. Poster Award.
89. “Metabolic Engineering of E. coli Sugar-Utilization Regulatory Systems for the Consumption of
Sugar Mixtures,” Dharmadi, Y., Moon, Y., Shanks, J. V., San, K-Y., and Gonzalez, R., Metabolic
Engineering V: Genome to Product, Lake Tahoe, CA, September 19-23, 2004.
90. “An Integrated Metabolic Engineering Study of Hairy Roots for Alkaloid Production,” Shanks,
J. V., San, K.-Y., Gibson, S. I., Hong, S.-B., Hughes, E., Sriram, G., Peebles, C., and Sander, G.,
Metabolic Engineering Conference, Lake Tahoe, September 19-23, 2004.
91. “Quantification of Metabolic Fluxes in Plants from 2-D NMR Data: Mathematical Framework and
Flux Identifiability,” Sriram, G. and Shanks, J. V., Metabolic Engineering V: Genome to Product,
Lake Tahoe, CA, September 19-23, 2004.
92. “A Genetic Network Driven Metabolic Flux Analysis Scheme,” San, K-Y., Bennett, G. N.,
Levanon, S. S., Cox, S., Percy, B., Shanks, J. V., and Gonzalez, R., Metabolic Engineering V:
Genome to Product, Lake Tahoe, CA, September 19-23, 2004.
93. “Integrating Genetic and Environmental Impacts on Seed Composition using Metabolic Flux
Analysis,” Shanks, J. V, Sriram, G., Iyer, V. V., Zhou, R., Fulton, D. B., Westgate, M. E., Annual
Meeting, American Society of Agronomy, Seattle, WA, November 2-6, 2004.
94. “Application of NMR Flux Maps for Analysis of Metabolically Engineered Plant
Tissues,” Sander, G., Hughes, E., San, Ka-Yiu, Gibson, S. I., and Shanks, J. V., Annual Meeting of
the AIChE, Austin, TX November 7-12, 2004.
95. “A Systems Biology Approach for Metabolic Engineering of Escherichia coli Sugar-Utilization
Regulatory Systems,” Dharmadi, Y., Moon, Y., Shanks, J. V., San, K-Y., and Gonzalez, R., Annual
Meeting of the AIChE, Austin, TX, November 7-12, 2004.
96. “Development of a Genetic Network Driven Model for Sugar-Utilization Regulatory Systems,”
San, K-Y., Gonzalez, R., Shanks, J. V., and Peacock, R., Annual Meeting of the AIChE, Austin,
TX, November 7-12, 2004.
27
97. “Metabolic Engineering of the Terpenoid and Indole Pathways in Catharanthus roseus hairy roots,”
Peebles, C. A., Gibson, S., Shanks, J. V., and San, K-Y., Annual Meeting of the AIChE, Austin,
TX, November 7-12, 2004.
98. “Transient Effect of Overexpressing AS on Terpenoid Indole Alkaloid Production in
Catharanthus roseus Hairy Roots,” Peebles, C. A., Gibson, S, Shanks, J. V., and San, K-Y., Annual
Meeting of the AIChE, Austin, TX, November 7-12, 2004.
99. “Phytoremediation of RDX: Using Arabidopsis thaliana to Determine the Genetics and
Biochemistry of the Transformation Pathway,” Rollo, S., Moon, H., Subramanian, M.,
Oliver, D. J., and Shanks, J. V., Annual Meeting of the AIChE, Austin, TX, November 7-12, 2004.
100. “Genetic and Biochemical Basis for Plant Transformation of Energetic Materials,” Oliver, D.,
Moon, H., Rollo, S., Subramanian, M., Yoon, Y. M., and Shanks, J. V., Partners in Environmental
Technology Technical Symposium and Workshop, SERDP, Washington, DC, December 2004.
101. “Prospects for Metabolic Engineering,” Realizing the Vision: Leading Edge Technologies in
Biological Systems, Cosmos Club, Washington DC, December 14, 2004.
102. “Transient Effect of Overexpressing Asαβ on Terpenoid Indole Alkaloid Production in
Catharanthus Roseus Hairy Roots,” Peebles, C. A., Gibson, S, Shanks, J. V., and San, K-Y.,
Twenty Second Conference on Biomedical Engineering Research in Houston, Houston, TX,
February 10-11, 2005.
103. “Metabolic Engineering of the Terpenoid Indole Alkaloid Pathways in Catharanthus roseus Hairy
Roots: Overexpression of the Terpenoid Branch Genes for Geraniol 10-hydroxylase and 1-deoxy-
D-xylulose 5-phosphate Synthase,” Peacock, R., Peebles, C. A., Gibson, S, Shanks, J. V., and San,
K-Y., ACS National Meeting, San Diego, CA, March 2005.
104. “Metabolic Engineering of the Terpenoid Indole Alkaloid Pathways in Catharanthus roseus Hairy
Roots,” Peebles, C. A., Gibson, S, Shanks, J. V., and San, K-Y., ACS National Meeting, San Diego,
CA, March 2005.
105. “The Effect of Overexpressing ASα and DXS in Catharanthus roseus Hairy Roots on the
Terpenoid Indole Alkaloid Pathway,” Peebles, C. A., Gibson, S, Shanks, J. V., and San, K-Y., ACS
National Meeting, San Diego, CA, March 2005.
106. “Plant Transformation Pathways of Energetic Materials (RDX, TNT, DNTs),” NABC Conference,
Nashville, TN, June, 2005.
107. “ Metabolic Engineering for the Production of Tryptophan and Indole Alkaloids in C. roseus,”
Gordon Research Conference on Plant Metabolic Engineering, Tilton, NH, July 14, 2005.
108. “Phytoremediation of Energetic Materials (DNTs and RDX) Using Arabidopsis thaliana”, Yoon, J.
M., Rollo, S., Oliver, D. J., Shanks, J. V., Annual Meeting of the AIChE, Cincinnati, OH, October
2005.
109. “Characterization of the Ecdysone Agonist-Inducible Promoter and the Ethanol Inducible
Promoter in Catharanthus roseus Hairy Roots,” Peebles, C. A., Gibson, S, Shanks, J. V., and San,
K-Y., Annual Meeting of the AIChE, Cincinnati, OH, October 2005.
28
110. “Development of a Mechanistic Model for Sugar-Utilization Regulatory Systems,” Peacock, R.,
Zhu, J., Shanks, J. V., Gonzalez, R. and K.-Y. San. Annual Meeting of the AIChE, Cincinnati, OH,
October 2005.
111. “Overexpression of the Terpenoid Branch Genes for Geraniol 10-hydroxylase and 1-deoxy-D-
xylulose 5-phosphate Synthase,” Peacock, R., Peebles, C. A., Gibson, S, Shanks, J. V., and San,
K-Y., Annual Meeting of the AIChE, Cincinnati, OH, October 2005.
112. “Phytotoxicity and Uptake of Dinitrotoluenes Using Arabidopsis thaliana”, Yoon J. M., Oliver,
D. J., Shanks, J. V., Partners in Environmental Technology Technical Symposium and Workshop,
SERDP, Washington, DC, November 2005.
113. “Metabolic and Gene Expression Profiling of Terpenoid Indole Alkaloid (TIA) Pathways in
Periwinkle Plants Treated with Methyl Jasmonic Acid and Fungal Elicitor,” Wei, S. and S. I.
Gibson, Plant Biology 2006, Boston, MA, 2006.
114. “Metabolic Engineering of Catharanthus roseus Hairy Roots for Production of Indole Alkaloids,”
Shanks, J. V., C. A. M. Peebles, K.-Y. San, S. I. Gibson, S. Wei, and G. Sander, Natural Products
Discovery and Production: New Challenges; New Opportunities, Sante Fe, NM, 2006.
115. “Metabolic Flux Maps of Central Carbon Metabolism in Soybean Embryos,” J. V. Shanks,
Molecular and Cellular Biology of the Soybean, 11th Biennial Meeting, Lincoln, NE, August, 2006.
116. “Metabolic Engineering of the Terpenoid and Indole Pathways in Catharanthus roseus Hairy
Roots,” Peebles, C. A. M., S. I. Gibson, J. V. Shanks, and K.-Y. San, American Institute of
Chemical Engineers Annual Meeting, San Francisco, CA, November 2006.
117. “The Transient Effect of Jasmonic Acid Feeding along with Orca3 Overexpression in Catharanthus
roseus Hairy Roots.” Peebles, C. A. M., S. I. Gibson, J. V. Shanks, and K.-Y. San, American
Institute of Chemical Engineers Annual Meeting, San Francisco, CA, November 2006.
118. “Design of Isotope Labeling Experiments for Metabolic Flux Analysis in Escherichia coli under
Anaerobic Condition.” Choudhury, M., Y. Dharmadi, R. Gonzalez, K.-Y. San and J. V. Shanks,
American Institute of Chemical Engineers Annual Meeting, San Francisco, CA, November 2006.
119. “Development of a Mechanistic Model for Sugar-Utilization Regulatory Systems” Zhu, J., R.
Peacock, J. V. Shanks, R. Gonzalez, and K.-Y. San, American Institute of Chemical Engineers
Annual Meeting, San Francisco, CA, November 2006.
120. “Perspectives in Metabolic Flux Mapping,” J.V. Shanks, Joint Genomics: GTL Awardee Workshop
V and Metabolic Engineering 2007 and USDA-DOE Plant Feedstock Genomics for Bioenergy
Awardee Workshop 2007, Bethesda, MD., February 13, 2007.
121. “Metabolic Flux Analysis on Soybean Isolines With Different Seed Compositions,” Vidya V. Iyer,
Matthew E. Studham, Mark E. Westgate, Julie Dickerson, Eve S. Wurtele, Jacqueline V. Shanks.
American Institute of Chemical Engineers Annual Meeting, Salt Lake City, UT, November 2007.
29
122. “Metabolic Engineering of the Terpenoid and Indole Pathways in Catharanthus roseus Hairy
Roots,” Peebles, C.A.M., S. I. Gibson, J. V. Shanks, and K.-Y. San. American Institute of Chemical
Engineers Annual Meeting, Salt Lake City, UT, November 2007.
123. “Exploration of the Role of the Octadecanoid Pathway for Terpenoid Indole Alkaloid Production
in Catharanthus roseus Hairy Roots.” Peebles, C.A.M., J.V. Shanks, and K.-Y. San. American
Institute of Chemical Engineers Annual Meeting, Salt Lake City, UT, November 2007.
124. “The Effect of UVB Light on Terpenoid Indole Alkaloid Production in Catharanthus roseus Hairy
Roots.” Binder, B.Y.K., C.A.M. Peebles, K.-Y. San, American Institute of Chemical Engineers
Annual Meeting, Salt Lake City, UT, November 2007.
125. “Unraveling the Sugar Utilization Regulatory Systems in Escherichia coli,” Dharmadi, Y., J. V.
Shanks, K.-Y. San, and R. Gonzalez. American Institute of Chemical Engineers Annual Meeting,
Salt Lake City, UT, November 2007.
126. “Development of a Mechanistic Model for Sugar-Utilization Regulatory Systems,” Zhu, J., R.
Gonzalez, J. V. Shanks, and K.-Y. San. American Institute of Chemical Engineers Annual Meeting,
Salt Lake City, UT, November 2007.
127. “Toxicity and Transformation of Dinitrotoluenes using Arabidopsis thaliana,” Yoon J. M., Oliver,
D. J., Shanks, J. V., The Society of Environmental Toxicology and Chemistry (SETAC) North
America 28th Annual Meeting, Milwaukee, WI, USA, November 2007.
128. “Transient Effects of Overexpressing Anthranilate Synthase α and β Subunits in Catharanthus
roseus Hairy Roots in Light and Dark Conditions,” Sander, G.W., Gibson, S.I., San, K.Y., and J. V.
Shanks, American Society of Plant Biologists, Midwestern Section Annual Meeting, Ames, IA,
March 2008. Poster Award.
129. “Metabolic Engineering of Catharanthus roseus Hairy Roots for Terpenoid Indole Alkaloid
Production under Light and Dark Conditions,” Sander, G.W., Gibson, S.I., San, K.Y., and J. V.
Shanks, 37th Annual Biochemical Engineering Symposium, Ames, IA, April 2008.
130. “Transient Effects of Overexpressing Anthranilate Synthase α and β Subunits in Catharanthus
roseus Hairy Roots in Light and Dark Conditions,” Sander, G.W., Gibson, S.I., San, K.Y., and J. V.
Shanks, 37th Annual Biochemical Engineering Symposium, Ames, IA, April 2008.
131. “The transient effect of overexpressing ORCA3 plus jasmonic acid feeding in Catharanthus roseus
hairy roots,” Peebles, C. A. M., S. I. Gibson, J. V. Shanks, and K.-Y. San, Natural Products
Discovery and Production II: Celebrating Successes of Traditional and Novel Cultures; New
Opportunities, Whistler, British Columbia, Canada, 2008.
132. “Metabolic Engineering of Catharanthus roseus Hairy Roots for Terpenoid Indole Alkaloid
Production under Light and Dark Conditions,” Sander, G.W., Gibson, S.I., San, K.Y., and J. V.
Shanks, Natural Products Discovery and Production II: Celebrating Successes of Traditional and
Novel Cultures; New Opportunities, Whistler, British Columbia, Canada, 2008.
30
133. “Cathedral roseus –and Other Interesting Tales in Plant Metabolic Engineering,” J. V. Shanks,
Phytochemistry Society of North America Annual Meeting, Pullman, WA June 2008.
134. “Metabolic Flux Analysis on Soybean Isolines With Different Seed Compositions” J. V. Shanks,
Metabolic Engineering VII, Puerto Vallarta, Mexico, September, 2008.
135. “Metabolic Flux Analysis of Maize (Zea mays, GS3 X Gaspe) Cell Suspension Culture by Using 13
C Labeling Experiment and 2-Dimensional Nuclear Magnetic Resonance (NMR) Spectroscopy”
J. M.Yoon, Y.Li, H. Kanani, K. Dhugga, J. Lightner, J. V. Shanks, Metabolic Engineering VII,
Puerto Vallarta, Mexico, September, 2008.
136. “Cathedral roseus –and Other Interesting Tales in Plant Metabolic Engineering,” J. V. Shanks,
Danforth Plant Science Symposium, St Louis, MI, October, 2008.
137. “Effects of Nitric Oxide on Growth and Terpenoid Indole Alkaloid Production In Catharanthus
Roseus Hairy Root Cultures Li, M. , Peebles, C.A.M., J. V. Shanks, and K.-Y. San. American
Institute of Chemical Engineers Annual Meeting, Philadelphia, PA, November 2008.
138. “Systems biology approach to understand seed composition: A convergence of metabolomics,
transcriptomics and metabolic flux data to expand the metabolic and regulatory network of
developing soybean seeds”, Li L, Zhou WX, Zhou WG, Demirkale Y, Ransom N, Shanks J, Iyer V,
Nettleton D, Westgate M, Nikolau B, and Wurtele ES International Conference on Legume
Genomics and Genetics 4, Puerto Vallarta, Mexico. September, 2008.
139. “Systems biology approach to understand seed composition: a convergence of bioinformatics,
metabolomics, transcriptomics and metabolic flux data to expand the metabolic and regulatory
network of developing soybean seeds”, Li L, Zhou WX, Yu XM, Zhou WG, Demirkale Y, Ransom
N, Shanks J, Iyer V, Nettleton D, Westgate M, Nikolau B, and Wurtele ES 18th annual Growth
Factor and Signal Transduction Symposium Ames, Iowa. June, 2009.
140. “Harnessing Plant Biochemistry for Industrial Chemicals - Beyond Fuels?”, J.V. Shanks, Plenary
Speaker, Gordon Research Conference on Plant Metabolic Engineering, Waterville Valley Resort in
the White Mountains of New Hampshire, NH, July, 2009.
141. "Flux Cartography in Oil Seeds - Analysis of Metabolic Roadblocks" J.V. Shanks, Intl. Congress
of Plant Molecular Biology, St. Louis, MI, October 26, 2009.
142. “Effects of Nitric Oxide on Growth, Terpenoid Indole Alkaloid Production and Some of the TIA
Gene Transcripts in Catharanthus Roseus Hairy Root Cultures.” Li, M. , Peebles, C.A.M., J. V.
Shanks, and K.-Y. San. American Institute of Chemical Engineers Annual Meeting, Nashville, TN,
November 11, 2009.
143. “Overexpression of Multiple Terpenoid Indole Alkaloid Genes Increases Alkaloid Accumulation in
Catharanthus Roseus Hairy Root Cultures.” Peebles, C.A.M., J. V. Shanks, and K.-Y. San.
American Institute of Chemical Engineers Annual Meeting, Nashville, TN, November 13, 2009.
144. “Alkaloid Extraction and Purification From Catharanthus Roseus Hairy Root Tissue.” Brown, D.,
G. Sander, and J. V. Shanks. American Institute of Chemical Engineers Annual Meeting, Nashville,
TN, November 9, 2009.
31
145. “Bioengineering a System for the Direct Production of Biological Hydrocarbons for Biofuels,”
American Chemical Society Fall Meeting, Boston, MA, August 2010.
146. “Systems Analysis of the Fermentative Metabolism of Escherichia coli”, R. Gonzalez, A. Murarka,
J. M. Clomburg, S.Moran and J. V. Shanks, American Institute of Chemical Engineers Annual
Meeting, Salt Lake City, Utah, November 2010
147. “The Top 10 Reasons ChE’s Should be Interested in (Living) Plants” J. V. Shanks, American
Institute of Chemical Engineers Annual Meeting, AIChE Food, Pharmaceutical and Bioengineering
Division, Area 15c Plenary, Salt Lake City, Utah, November 2010.
148. "Influence of SHaM Media Carbon-to-Nitrogen Ratios on Soybean Somatic Embryos (cv. Jack)
Growth and Composition", Q. Truong and J. V. Shanks, Plant Metabolic Engineering Gordon
Conference, Waterville Valley, New Hampshire, July 2011.
149. “Bioengineering a System for the Direct Production of Biological Hydrocarbons for Biofuels”, M.
Brown, G. Ding, W. Qin, J. Chmielowski, A. Jose, L. Wallace, S. Hoddick, E. Justiniano, M.
Nelson, G. Nadathur, G. Wolfe, B. Nikolau and J. V. Shanks, American Institute of Chemical
Engineers Annual Meeting, Minneapolis, Minnesota, October 2011.
150. “Metabolic Flux Analysis of Escherichia coli MG1655 Under Octanoic Acid Stress”, Y. Fu,
J.M.Yoon, L. Royce, M. Rodriguez-Moya, R. Gonzalez, L.Jarboe and J. V. Shanks, American
Institute of Chemical Engineers Annual Meeting, Minneapolis, Minnesota, October 2011.
151. “Bioengineering a System for the Direct Production of Biological Hydrocarbons for Biofuels”, M.
Brown, G. Ding, W. Qin, J. Chmielowski, A. Jose, L. Wallace, S. Hoddick, E. Justiniano, M.
Nelson, G. Nadathur, G. Wolfe, B. Nikolau and J. V. Shanks, American Institute of Chemical
Engineers Annual Meeting, Minneapolis, Minnesota, October 2011.
152. “Structural Elucidation of Unknown Alkaloids Present in Catharanthus roseus by Precursor Ion
Fingerprinting”, C.D. Flores, G. W. Sander, M.A. Perera and J. V. Shanks, American Institute of
Chemical Engineers Annual Meeting, Minneapolis, Minnesota, October 2011.
153. “Integrating Biological and Chemical Catalysts to Create a Generalized Framework for Producing
Biorenewable Chemicals”, J.V. Shanks, The 6th Sino-US Joint Conference of Chemical
Engineering, SINOPEC Conference Centre, Beijing, China, Nov. 7-10, 2011.
Invited Lectures at Universities, Companies, and Conferences:
1. “Application of in vivo NMR Spectroscopy to Cellular Metabolism from an Engineering
Perspective,” Molecular Biology and Chemistry Program, University of Massachusetts, Amherst,
MA, November 24, 1987.
2. “Use of in vivo NMR Spectroscopy for Metabolic Engineering Applications,” Chemistry Dept.,
University of TX at Dallas, Dallas, TX, November 29, 1989.
3. “Use of in vivo NMR Spectroscopy for Metabolic Engineering Applications,” Chemical
Engineering Dept., Iowa State University, Ames, IA, March 1, 1990.
4. “Establishment and Cultivation of Hairy Root Lines of Catharanthus roseus,” Chemical
Engineering Dept., University of California Davis, Davis, CA, January 14, 1991.
32
5. “Use of NMR in Metabolic Engineering Applications,” Biochemical Engineering Program, Duke
University, Durham, NC, April 1991.
6. “Use of NMR in Metabolic Engineering,” Biomedical and Biological Applications of Nuclear
Magnetic Resonance, Galveston-Houston Biological NMR Symposium, Galveston, TX, May 1991.
7. “Production of Indole Alkaloids by Hairy Root Cultures of Catharanthus roseus,” Biotechnology
Institute and Plant Physiology Program, Penn State University, State College, PA, October 28,
1992.
8. “Production of Indole Alkaloids by Hairy Root Cultures of Catharanthus roseus,” Procter and
Gamble, Corporate Research Center, Cincinnati, OH, November 17, 1992.
9. “Transgenic Root Cultures of Catharanthus roseus: Metabolism and Alkaloid Synthesis,” NIH
Conference: Research Opportunities in Biomolecular Engineering: The Interface Between
Chemical Engineering and Biology, Washington, DC, December 7, 1992.
10. “Production of Indole Alkaloids by Hairy Root Cultures of Catharanthus roseus,” School of
Chemical Engineering, Purdue University, West Lafayette, IN, September 9, 1993.
11. “Building Bridges for Women in Biomedical Engineering and Sciences,” Panel Discussant, Twelfth
Annual Conference on Biomedical Research in Houston; Houston, TX, February 1994
12. “In Situ NMR Spectroscopy as a Research Tool in Plant Biotechnology,” Procter and Gamble,
Corporate Research Center, Cincinnati, OH, May 17, 1994.
13. “Transgenic Root Cultures as Chemical Factories,” Dept. of Chemical Engineering, University of
Houston, Houston, TX, November 1994.
14. “Opportunities and Challenges in the Use of Plant Cell and Tissue Cultures as Production
Systems,” Bristol-Myers Squibb, Seattle, WA, April 28, 1995.
15. “Phytoremediation of TNT: Hairy Root Cultures as a Model System,” IBC Conference on
Phytoremediation, Washington, DC, May 9, 1996.
16. “Chemical Engineering with (Living) Plants,” Dept. of Chemical Engineering, Michigan State
University, East Lansing, MI, November 1996.
17. “Quantification of Metabolic Fluxes for Metabolic Engineering of Plant Products,” National
Meeting of the ACS, San Francisco, CA, April 1997.
18. “Phytoremediation of Explosives: Hairy Root Cultures as a Model System,” Fourteenth Biennial
Estuarine Research Federation International Conference, Providence, RI, October 1997.
19. “Quantification of Metabolic Fluxes for Metabolic Engineering of Plant Products,” DuPont Central
R&D, Wilmington, DE, January 27, 1998.
20. “Quantification of Metabolic Fluxes for Metabolic Engineering in Plants,” Society of In Vitro
Biology, Las Vegas, NV, June 1, 1998.
33
21. “Phytocatalysis: Applications in Metabolic Engineering and Bioremediation,” Dept. of Chemical
and Biochemical Engineering, University of Iowa, Iowa City, IA, October 22, 1998.
22. “Phytocatalysis: Applications in Metabolic Engineering and Bioremediation,” Biotechnology
Series, University of Minnesota, MN, December 3, 1998.
23. “Phytocatalysis: Applications in Metabolic Engineering and Bioremediation,” Dept. of Chemical
Engineering, Iowa State University, Ames, IA, December 17, 1998.
24. “Phytocatalysis: Applications in Metabolic Engineering and Bioremediation,” Dept. of Plant
Science, Rutgers University, NJ, February 19, 1999.
25. “Plant Metabolism of 2,4,6-Trinitrotoluene and Related Nitroaromatic Compounds,” Second
International Symposium on Biodegradation of Nitroaromatic Compounds and Explosives, Xerox
University, VA, September 8, 1999.
26. “Phytocatalysis: Applications in Metabolic Engineering and Bioremediation,” ACS Lectureship,
Dept. of Chemical Engineering, University of Wisconsin, Madison, WI, November 16, 1999.
27. “Quantification of Metabolic Fluxes for Metabolic Engineering of Plant Secondary Metabolites,”
Dept. of Food Science and Human Nutrition, Iowa State University, Ames, IA, April 5, 2000.
28. “Quantification of Metabolic Fluxes for Metabolic Engineering of Plant Products,” Malaysian MIT
Biotechnology Partnership Program Workshop, Bioreactor Processes for Plant Cell Cultures,
Massachusetts Institute of Technology, Cambridge, MA, May 24, 2000.
29. “Phytocatalysis: Applications in Metabolic Engineering and Bioremediation,” Dept. of Chemical
Engineering, Cornell University, Ithaca, NY, November 20, 2000.
30. “Plant Metabolism of TNT, RDX, and HMX,” Presentation, Defense Threat Reduction Agency,
Vegetative Effects Environmental Sensing Program Planning Meeting, Arlington, VA, October 4,
2001.
31. “Applications of Nuclear Magnetic Resonance (NMR) in Metabolic Engineering,” Cargill-Dow
LLC, Minnetonka, MN, October, 2001“Find a Way to Use NMR: Tribute to Jay Bailey,”
Presentation, Annual Meeting of the AIChE, Reno, NV, November 2001.
33. “Genetic and Biochemical Basis for the Transformation of Energetic Materials (RDX, TNT, DNTs)
by Plants,” SERDP Scientific Advisory Board Meeting, Arlington, VA, March 7, 2002.
34. “Plant Metabolic Engineering: Entering the S Curve,” Dept. of Horticulture and Landscape
Architecture, Purdue University, West Lafayette, IN, March 28, 2002.
35. “Genetic and Biochemical Basis for the Transformation of Energetic Materials (RDX, TNT, DNTs)
by Plants,” Presentation, Eglin Airforce Base Range Meeting, Fort Walton Beach, FL, September 7,
2002.
36. “Evolution of Metabolic Engineering,” Annual Meeting of the AIChE, Indianapolis, IN,
November 2002.
34
37. “What Does Plant Metabolism Have to Do With Chemical Engineering?” Dept. of Chemical
Engineering, University of Virginia, December 5, 2002.
38. “Systems Biology: Pathway Engineering Revisited?” Dept. of Chemical Engineering, Rice
University, January 30, 2003.
39. “Genetic and Biochemical Basis for the Transformation of Energetic Materials (RDX, TNT, DNTs)
by Plants,” SERDP Progress Review, Arlington, VA, March, 2003.
41. “Plant Metabolic Engineering: Entering the S Curve,” Keynote Address, Lehman College, City
University of New York, September 15, 2003.
42. “Genetic and Biochemical Basis for the Transformation of Energetic Materials (RDX, TNT, DNTs)
by Plants,” Battelle Conference on Range Management, New Orleans, LA, January 6, 2004.
43. “Genetic and Biochemical Basis for the Transformation of Energetic Materials (RDX, TNT, DNTs)
by Plants,” Joint Interagency Program on Phytoremediation Research, Principal, Investigators
Meeting, NSF, January 21, 2004.
44. “Plant Metabolic Engineering Under Construction,” Fourth Interagency Conference on Metabolic
Engineering, NSF, February 6, 2004.
45. “Metabolic Flux Maps of Central Carbon Metabolism in Plants,” Third International Congress on
Plant Metabolomics, Ames, IA June 3-6, 2004.
46. “Metabolic Flux Maps of Central Carbon Metabolism in Plants,” Iowa State University and
University of Iowa Joint Bioinformatics Workshop, Ames, IA August 6, 2004.
47. “Plant Metabolic Engineering: Under Construction,” Dept. of Horticulture, Iowa State University,
Ames, IA October, 2004.
48. “Integrating Genetic and Environmental Impacts on Seed Composition using Metabolic Flux
Analysis” Presentation, Annual meeting, American Society of Agronomy, Seattle, WA,
November 2-6, 2004.
49. “Prospects for Metabolic Engineering,” Presentation, Realizing the Vision: Leading Edge
Technologies in Biological Systems, Cosmos Club, Washington, DC, December 14, 2004.
50. “Metabolic Flux Maps of Central Carbon Metabolism in Plants,” Presentation, Pioneer Hi-Bred
International, Inc., Johnston, IA March 22, 2005.
51. “Plant Transformation Pathways of Energetic Materials (RDX, TNT, DNTs),” NABC Conference,
Nashville, TN, June, 2005.
52. “Metabolic Engineering for the Production of Tryptophan and Indole Alkaloids in C. roseus,”
Gordon Research Conference on Plant Metabolic Engineering, Tilton, NH, July 14, 2005.
53. “Flux Maps of Plant Metabolic Networks,” Presentation, Graduate Program in Plant Molecular
Biosciences, Washington State University, Pullman, WA, March 28, 2006.
35
54. “Phytochemical Engineering: Combining Chemical Reaction Engineering with Plant Science,”
Presentation, Department of Chemical Engineering, University of Delaware, DE, April 21, 2006.
55. “Metabolic Flux Maps of Central Carbon Metabolism in Soybean Embryos,” Molecular and
Cellular Biology of the Soybean, 11th Biennial Meeting, Lincoln, NE, August, 2006.
56. “Metabolic Flux Maps of Central Carbon Metabolism in Soybean Embryos,” Molecular and
Cellular Biology of the Soybean, Bioinformatics and Computational Biology Faculty Seminar
Series, Iowa State University, Ames, IA October 20, 2006.
57. “Perspectives in Metabolic Flux Mapping,” Joint Genomics: GTL Awardee Workshop V and
Metabolic Engineering 2007 and USDA-DOE Plant Feedstock Genomics for Bioenergy Awardee
Workshop 2007, Bethesda, MD., February 13, 2007.
58. “Cathedral roseus –and Other Interesting Tales in Plant Metabolic Engineering,” 2007 Plant
Science Symposium on Metabolic Engineering, Lincoln, Nebraska, October 4, 2007.
59. “Cathedral roseus –and Other Interesting Tales in Plant Metabolic Engineering,” Interdepartmental
Plant Physiology Symposium, Iowa State University, Ames, IA October 17, 2007.
60. “Phytochemical Engineering: Combining Chemical Reaction Engineering with Plant Science,”
Presentation, Department of Chemical Engineering, Illinois Institute of Technology, Chicago, IL,
November 28, 2007.
61. “Cathedral roseus –and Other Interesting Tales in Plant Metabolic Engineering,” Phytochemistry
Society of North America Annual Meeting, Pullman, WA June 2008.
62. “Metabolic Flux Analysis on Soybean Isolines With Different Seed Compositions” Metabolic
Engineering VII, Puerto Vallarta, Mexico, September, 2008.
63. “Cathedral roseus –and Other Interesting Tales in Plant Metabolic Engineering,” Danforth Plant
Science Symposium, St Louis, MI, October, 2008.
64. “Phytochemical Engineering: Combining Chemical Reaction Engineering with Plant Science,”
Plant Biology Graduate Program, University of Massachusetts, Amherst, MA, presented November
6th, 2008.
65. “Cathedral roseus –and Other Interesting Tales in Plant Metabolic Engineering,” Center for Plant
Cell Biology, University of California Riverside, Riverside, CA presented December 12th, 2008.
66. “Phytochemical Engineering: Combining Chemical Reaction Engineering with Plant Science,”
Presentation, Department of Chemical Engineering, Washington State University, Pullman, WA
March 30, 2009.
67. “Harnessing Plant Biochemistry for Industrial Chemicals - Beyond Fuels?”, Plenary Speaker,
Gordon Research Conference on Plant Metabolic Engineering, Waterville Valley Resort in the
White Mountains of New Hampshire, NH, July, 2009.
68. "Flux Cartography in Oil Seeds - Analysis of Metabolic Roadblocks" BASF, Raleigh-Durham, NC,
September 18, 2009
36
69. "Flux Cartography in Oil Seeds - Analysis of Metabolic Roadblocks" Intl. Congress of Plant
Molecular Biology, St. Louis, MI, October 26, 2009.
70. “Bioengineering a System for the Direct Production of Biological Hydrocarbons for
Biofuels,” American Chemical Society Fall Meeting, Boston, MA, August 2010.
71. " Metabolic Flux Cartography – On the Road to Sustainable Food, Feed, Fuels and
Chemicals” Presentation, Department of Chemical Engineering, Colorado State University, Fort
Collins, CO, October, 2010.
72. “The Top 10 Reasons ChE’s Should be Interested in (Living) Plants” American Institute of
Chemical Engineers Annual Meeting, AIChE Food, Pharmaceutical and Bioengineering Division,
Area 15c Plenary, Salt Lake City, Utah, November 2010
73. “Metabolic Flux Cartography – On the Road to Sustainable Food, Feed, Fuels and
Chemicals”, Minnesota Biotechnology Institute, University of Minnesota, St Paul, MN, April
2011.
74. “Metabolic Flux Cartography – On the Road to Sustainable Food, Feed, Fuels and Chemicals”
Department of Chemical and Biomolecular Engineering, Ohio State University, Columbus, Ohio,
June 2011.
75. “Integrating Biological and Chemical Catalysts to Create a Generalized Framework for Producing
Biorenewable Chemicals”, The 6th Sino-US Joint Conference of Chemical Engineering, SINOPEC
Conference Centre, Beijing, China, Nov. 7-10, 2011.
Postdoctoral Research Fellows Supervised:
Rajiv Bhadra 1996-1999
Darcey Wayment 1997-1999
Jong Moon Yoon 2004 –2010
Guy Sander 2009 - 2010
Graduate Students Supervised:
Hei-Chan Lee 1991-1992
Rajiv Bhadra 1989-1994
Chih-Huang Ho 1989-1994
Marie-Dominique Fernet 1990-1992
Sundeep Vani 1990-1996
Brenda Mann 1992-1996
Sushil Rijhwani 1992-1997
Steven Budd 1993-1996
John Lauritzen 1993-1998
John Morgan 1994-1999
Matt Ring 2000-2001
Erik Hughes 1998-2003
Murali Subramanian 1998-2004
Ganesh Sriram 1999-2004
37
Sarah Rollo 2002-2005
Vidya Iyer 2001-2006
Guy Sander 2003-2009
Madhuresh Choudhary 2003-2008
Yanfen Fu 2009- 2011
Gwen Truong 2007-present
Marvin Mercado 2008-2010
Ting-wei Tee 2009-present
Mark Brown 2009-present
Erin Boggess, BCB (co-advised by Julie Dickerson) 2009-present
Daniel Flores 2011-2011
Preparing Future Faculty Graduate Students Mentor:
Daniela Faas 2007-2010
Biorenewables Resource Laboratory Graduate Student Mentor:
Basak Cinar 2007
Undergrad Research Students Supervised:
Stephanie Rosi 1989-1990
Tom Robbins 1989
Neil Leatherbury 1990-1991
Kathy Hazelton 1990
Mike Janicke 1991-1992
Manuel M. Rodriguez (NSF Graduate Fellowship) 1992-1993
Brian Hamill 1993
Celeste Campbell 1994
Christine Farrier 1994-1995
Jennifer Lynn Miller 1996
Alex Penn (Whitaker Graduate Fellowship) 1997
Christin Barney 1997
Angélica Rodríguez 1997
Soumendra Barman 1998-1999
Rebekah Williams 1998-1999
Rafaél Verduzco 1998
Jason Simmons 1998-1999
Janet Huang 1999
Michael Wald 2000
Nicole Felkey 2000
Erin Denefe 2001
Omar Gonzalez-Riviera 2001-2005
Melissa Swartz 2001
Amish Dalal 2002
Jennifer Rose 2002
Mason McGrady 2002
Chase Beisel (NSF Graduate Fellowship) 2002-2004
Tanya Phillips 2003
Christine Westgate 2003-2004
Hong-Kee Ng 2004
Jennifer Mayard 2004-2005
Shannon Parker 2005-2005
38
James (Doug) Vandermyde 2006- 2007, 2008 - 2010
Bonnie Grider 2006
Ricardo Guraieb 2006
Joe Charlson 2006
John Tjaden 2007
Genevieve Lozier 2007
John Hollerung 2007
Sonali Patel 2007
Michelle Kozmik 2007
Lee Rudebusch 2007-2010
Meredith Breton 2008
Diane Brown (NSF Graduate Fellowship) 2008-2009
Kaelynn Koch 2009
Ezinne Archinivu 2009
Erin Jun 2010-2011
Sian Yun Wong 2010-2011
Miya Williams 2011-present
Trent Lamar 2011
Undergrad “Labbie” Students Supervised, Iowa State University:
Nate Morris 2000
Undergrad Education (Computation) Students Supervised (with S.H. Davis), Rice University:
Tom Robbins 1989
Jagjit Virk 1990
Luis Moreno 1990
Joseph De Vincentis 1990-1992
Tammy Chan 1992
Duke York 1992
David Jaber 1992-1993
Adrian Pennisson 1992-1993
Marcel Levi 1993
John Pérez 1994
Alex Penn 1996
Andrew Duryea 1997
High School Research Students Supervised:
Rubin Flores 1989
Esmerélda Hinosa 1994
Jason Simmons 1995
Christine Westgate 2003