curriculum vitae james gregory ferry may 16, 2014 …€¦ · biochemistry & molecular biology,...

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CURRICULUM VITAE

James Gregory Ferry

May 16, 2014

BACKGROUND

Address: Department of Biochemistry & Molecular Biology, Pennsylvania State University,

University Park, PA, 16802-4500. Voice: 814/863-5721. Electronic: [email protected]

Education: Postdoctoral training in biochemistry at the University of Georgia (1974-76). Ph.D.

in microbiology/biochemistry from the University of Illinois (1974). B.S. in agronomy/soil

microbiology from the University of Georgia (1968).

Interests: Physiology, biochemistry, and molecular biology of procaryotic anaerobes.

Employment: Stanley Person Professor of Molecular Biology (1997-present), Department of

Biochemistry & Molecular Biology, Penn State University • Distinguished Visiting Scientist

(2010), Synthetic Genomics Inc. • Professor of Microbiology (1995-1996), Department of

Biochemistry & Molecular Biology, Penn State University • Assistant (1976-81) Associate

(1981-86) and Full (1986-95) Professor of Microbiology, Department of Anaerobic

Microbiology, Virginia Polytechnic Institute and State University • Resident Faculty (Summer,

1984), Marine Biological Laboratory, Woods Hole, MA • Visiting Instructor (Summers,

1976-78), Marine Biological Laboratory, Woods Hole, MA • Research Associate (1974-76),

Department of Biochemistry, University of Georgia • Research Assistant (1971-74), Department

of Microbiology, University of Illinois.

Honors: M. P. Bryant Memorial Award (2011) • American Society for Microbiology – Graduate

Teaching Award (2001) • Elected Fellow of the American Academy of Microbiology (1992) •

NATO Visiting Professorship (1985) • NIH Postdoctoral Fellowship, University of Georgia

(1974-76) • USPH Traineeship in Microbiology, University of Illinois (1972-74) • NDEA

Fellowship, University of Illinois (1969-70) • George D. Scarseth Scholarship Award, University

of Illinois (1970) • A. L. Lang Fellowship Award, University of Illinois (1970).

PROFESSIONAL

Service: Co-chair, National Academy of Sciences Committee on Astrobiology and Planetary

Sciences (2012-present) • Co-chair, National Academy of Sciences Committee on the Origin

and Evolution of Life (2009 - 2011) • Member, Editorial board, Journal of Bacteriology (2007-

present) • Editorial Board, Annals of Microbiology (2000 – present) • Director, Center for

Microbial Structural Biology, Pennsylvania State University (1996 - present) • Member of the

International Committee on Systematic Bacteriology - Subcommittee on the Taxonomy of

Methanogenic Bacteria (1986-present) • Member, American Society for Microbiology, Graduate

Microbiology Teaching Award Selection Committee (2003-6 and 2009-13) • Member, American

Society for Microbiology (1976-present) • Editor, Journal of Bacteriology (1992-2002) •

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Member, American Society for Microbiology, Committee on Graduate Education (2003-6) •

Member, NASA Mars Sample Workshop (2000) • Member, (Ad Hoc), Microbial Physiology and

Genetics Study Section, National Institutes of Health (2000) • Member, National Science

Foundation Graduate Fellowship Evaluation Panel (1993-96) • Member, Workshop on the

Changing Environment for Biological Sciences in our Nation's Colleges and Universities (1996)

• Member, National Science Foundation, Young Investigator Awards Evaluation Panel (1994) •

Chair, American Society for Microbiology, Division K (1993-94) • Member, Department of

Energy, Subsurface Microbiology Program Grant Proposal Study Section (1993) • Chair-Elect,

American Society for Microbiology, Division K (1992-93) • Co-chair, International Symposium

on Topics in Microbial Diversity, Metabolism, and Physiology (1992) • Member, Editorial

board, Journal of Bacteriology (1987-91) • Member, editorial board, Applied and Environmental

Microbiology (1983-91) • Member, American Academy of Microbiology colloquium on

Scientific Foundations of Bioremediation: Current Status and Future Needs (1991) • Member,

Department of Energy-Biological Energy Research Program, Grant Proposal Study Section

(1982,86,90) • Member, National Institutes of Health-Special Grant Proposal Study Section,

Human Genome and Model Organisms Project (1989) • Member, National Institutes of

Health-Special Grant Proposal Study Section (1988) • Member, Department of Energy,

Advanced Research and Technology Development program review panel (1987) • Member,

Solar Energy Research Institute and United States Department of Energy, Grant Proposal

Review Panel (1987) • Member, Council of Gordon Research Conferences (1987) • Chairman,

Gordon Research Conference, Biochemistry and Molecular Genetics of Methanogenesis (1987) •

Member, Office of Naval Research-Program in Molecular Biology Grant Proposal Study Section

(1985) • Member, National Institutes of Health - Microbial Physiology and Genetics ad hoc

Grant Proposal Study Section (1984,85) • Resident faculty at the Marine Biological Laboratory,

Woods Hole, MA (Summer, 1984) • Visiting instructor at the Marine Biological Laboratory,

Woods Hole, MA (Summers, 1976-78).

Invited seminars: Shandong University (2014). • University of Hyderabad (2013) • Indian

Institute of Science, Bangalore (2013) • King Abdullah University of Science and Technology,

Saudi Arabia (2013) • 2nd

Annual Carbonic Anhydrase Satellite Meeting, Naples (2013) •

University of Oklahoma (2012) • Canadian Institute for Advanced Research, Toronto (2012) •

Department of Energy 3rd

Biennial Physical Biosciences Research Meeting (2012) • Nebraska

Redox Biology Center 10th

Annual Symposium (2012) • 9th International Carbonic Anhydrase

Conference, Antalya, Turkey (2012) • FEBS Satellite Carbonic Anhydrase Meeting,

Montecatini, Italy (2011) • International Congress on Gastrointestinal Function, Chicago (2011)

• King Abdullah University of Science and Technology, Saudi Arabia (2011) • University of

Illinois-Chicago (2011) • International Conference on Extremophiles, Athens, GA (2011) • 40th

Anniversary: Carbonic Anhydrase, Tallberg, Sweden (2011) • Thermal Biology Institute,

Montana State University (2010) • National Academy of Sciences Committee on the Origin and

Evolution of Life (2010) • Canadian Institute for Advanced Research Astrobiology Workshop,

University of Toronto (2010) • National Astrobiology Institute Workshop, Montana State

University (2010) • Gordon Research Conference on Archaea (2009) • 8th

International

Conference on the Carbonic Anhydrases • University of Southern California (2009) • Virginia

Tech (2008) • Clemson University (2008) • LUCA Technologies (2007) • Synthetic Genomics

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(2007) • 11th Evolutionary Biology Meeting (2007) • University of Georgia (2007) • University

of California, Berkeley (2007) • 7th International Conference on the Carbonic Anhydrases

(2006) • International Conference on Extremophiles (2006) • Gordon Conference on Molecular

Basis of One-Carbon Metabolism (2006) • American Society for Microbiology (2006) •

University of Florida (2006) • North Carolina State University (2006) • Institut Pasteur, Paris

(2006) • National Workshop on Astrobiology, Capri, Italy (2005) • Italian National Research

Council, Institute of Protein Biochemistry, Naples (2005) • University of Naples, Department of

Biological Chemistry (2005) • University of Florence (2005) • International symposium on

Archaea, the First Generation, Germany (2005) • Gordon Research Conference on Archaea:

Ecology, Metabolism and Molecular Biology (2005) • International symposium on Syntrophic

Microbiology, UCLA (2005) • University of Queensland, Brisbane (2005) • University of New

South Wales, Sydney (2005) • National Academies Workshop on the Limits of Organic Life in

Planetary Systems (2004) • Gordon Research Conference on Molecular Basis of Microbial One-

Carbon Metabolism (2004) • American Chemical Society Annual Meeting (2004) • Macquarie

University, Sydney (2004) • 5th International Conference on Extremophiles (2004) • Australian

Society for Microbiology (2004) • University of Maryland (2004) • 6th International Conference

on the Carbonic Anhydrases, Bratislava, Slovakia (2003) • Northeastern University (2003) •

Gordon Research Conference on Archaea: Ecology, Metabolism, & Molecular Biology (2003) •

University of Bologna (2002) • Rutgers University (2002) • Gordon Research Conference on

Environmental Bioinorganic Chemistry (2002) • Gordon Research Conference on the Molecular

Basis of One-Carbon Metabolism (2002) • 4th International Congress on Extremophiles, Naples

(2002) • Stanford University (2001) • Utah State University (2001) • Cornell University (2001) •

University of New South Wales (2001) • Georgia Institute of Technology (2000) • National

Institutes of Health (2000) • University of Georgia - Power of Anaerobes Conference (2000) •

University of Wisconsin-LaCrosse - Symposium on Industrial and Fermentation Microbiology

(2000) • University of Washington - Conference on Carbonic Anhydrase (2000) • Gordon

Research Conference (1999) • Keystone Symposium (1999) • Duke University (1999) • Wake

Forest University (1999) • Purdue University (1999) • University of California, Santa Barbara

(1999) • University of Delaware (1999) • Italian Society for Molecular Biology and Biophysics

(1998) • Gordon Research Conference (1998) • University of Maryland (1998) • University of

Georgia (1998) • Royston C. Clowes Memorial Lecture, University of Texas-Dallas (1998) •

University of Texas-Dallas (1998) • Texas A&M University (1998) • Northern Illinois

University (1997) • University of Florida (1997) • University of Minnesota (1997) • University

of Georgia (1996) • Gordon Research Conference (1996) • Max-Planck Institüt für Biochemie,

Martinsreid (1996) • Phillips University, Marburg (1996) • Penn State Lectures on the Frontiers

of Science (1996) • Hershey Medical Center, Penn State University (1996) • American Society

for Microbiology Annual Meeting (1996) • University of Washington (1996) • Utah State

University (1996) • University of Utah (1996) • Bridgewater College (1996) • Clemson

Technical Center (1996) • Fourth International Conference on the Carbonic Anhydrases, Oxford

University (1995) • Microbial Physiology Summer Course, Ohio State University (1995) •

Ludwig Maximilians Universität (1995) • Eighth International Symposium on Microbial Growth

on C1 Compounds, California Institute of Technology (1995) • Symposium on Topics in Rumen

Microbiology, the Environmental Applications of Microorganisms and Biodiversity, University

of Illinois (1995) • University of Massachusetts (1995) • Stanford University (1994) • University

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of California, Los Angeles (1994) • DuPont Central Research and Development (1994) •

American Society for Microbiology Annual Meeting (1994) • University of Maryland (1994) •

American Society for Microbiology Annual Meeting (1993) • University of Wisconsin (1993) •

Gordon Research Conference on Molecular Aspects of Methanogenesis (1993) • University of

Georgia (1992) • University of Nebraska (1992) • International Conference on Bioinorganic and

Biotechnological Aspects of Environmental Chemistry, University of Florence (1992) • Seventh

International Symposium on Microbial Growth on C-1 Compounds, University of Warwick

(1992) • International Symposium on Topics in Microbial Diversity, Metabolism and

Physiology, University of Illinois (1992) • American Society for Microbiology Annual Meeting

(1992) • Medical College of Virginia (1992) • University of Iowa (1992) • The Sixteenth

International Congress on Microbial Ecology and Disease, Virginia Tech (1991) • American

Society for Microbiology Annual Meeting (1991) • The Pennsylvania State University (1991) •

FASEB Summer Research Conference on Folic Acid, Vitamin B-12, and One-Carbon

Metabolism (1990) • Gordon Research Conference on Molecular Aspects of Methanogenesis

(1990) • American Society for Microbiology, 90th Annual Meeting (1990) • Cornell University

(1990) • IGT International Symposium on Gas, Oil, Coal, and Environmental Biotechnology

(1989) • Shimizu Institute of Technology, Tokyo (1989) • University of Regensburg (1989) •

University of Ulm (1989) • Sixth International Symposium on Microbial Growth on C-1

Compounds, University of Göttingen (1989) • University of California, Los Angeles (1989) •

University of Oklahoma (1989) • Swiss Federal Institute, Zurich (1988) • University of Bologna

(1988) • Twenty seventh Plenary Meeting of the International Committee on Space Research,

Helsinki (1988) • Marine Biological Laboratory, Woods Hole (1988) • Michigan State

University (April, 1988) • University of Nijmegan (1987) • Technical University of Delft (1987)

• Cornell University (1987) • Gordon Research Conference on Applied and Environmental

Microbiology (1987) • Gordon Research Conference on Molecular Aspects of Methanogenesis

(1987) • Purdue University (1987) • Mobil Oil Corporation, Central Research Laboratory,

Princeton (1987) • Symposium on the Biotechnology of Anaerobic Digestors, North Carolina

State University (1986) • Fifth International Symposium on Microbial Growth on C-1

Compounds, University of Groningen (1986) • Stanford University (1986) • University of

California, San Francisco (1986) • University of Florida (1986) • Salk Institute Biological

Associates, San Diego (1986) • University of California, Los Angeles (1986) • Ohio State

University (1985) • Hydrogen Transfer Workshop, Woods Hole (1985) • Archaebacteria

Workshop, Max Planck Institute for Biochemistry, Munich (1985) • Celenese Chemical

Company (1985) • University of California, Davis (1984) • Gordon Research Conference on

Biochemistry of Methanogenesis (1984) • Genetics Institute (1984) • Michigan State University

(1984) • University of California, Los Angeles (1984) • Massachusetts Institute of Technology

(1983) • University of Pisa (1983) • University of Bologna (1983) • University of Georgia (1983)

• Cornell University (1982) • Corn Products Company, Chicago (1981) • Argonne National

Laboratory (1981) • University of California, Berkeley (1980) • Catholic University (1980) •

National Bureau of Standards, Washington (1980) • University of South Carolina (1979) • Office

of Naval Research, Washington (1978) • Stanford University (1977) • Clemson University

(1977) • Woods Hole Oceanographic Institution (1976) • Purdue University (1976) • CNRS

Marseille, France (1975) • University of Minnesota (1974).

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TEACHING

Graduate courses taught (Virginia Polytechnic Institute and State University):

"Comparative Metabolism of Anaerobic Bacteria" (AL 5160); 1977-94; the mean student

evaluation for 1977-94 was 3.6/4.0. • "Graduate Seminar" (AL 5101); 1977, 82, 84, 86, 87, and

1989.

Graduate courses taught (Penn State University): "Molecular Biology of Procaryotic

Anaerobes" (BMB 497B), 1996-01; “Astrobiology” (GEOSC 497C), 2001; "Microbial

Diversity" (MICRB 413), 2001; "Biochemistry and Molecular Biology of Anaerobic

Procaryotes" (MICRB 497B), 2004., "Microbiology I" (BMMB 598C), 2006-2008.

Undergraduate courses taught (Penn State University): "Freshman Seminar" (PSU16), 2011-

12.

Past undergraduate thesis students: Ms. Theresa Koehler • Mr. Christopher Bradburn • Mr.

Sean O’Hearn.

Past M.S. students: Mr. David J. Aceti • Ms. Carole A. Dellinger • Ms. Carole J. McIntyre • Mr.

Christopher Peer • Mr. Kevin Hill

Past Ph.D. students (post position): Dr. Stephen F. Baron (Postdoctoral Associate, Virginia

Commonwealth University Medical College) • Dr. Andrew P. Clements (Postdoctoral Associate,

National Institutes of Health) • Dr. John D. Haddock (Postdoctoral Associate, University of

Iowa) • Dr. Peter E. Jablonski (Postdoctoral Associate, University of Idaho) • Dr. Matthew T.

Latimer (Postdoctoral Associate, NCI, Fredrick, MD) • Dr. Harold D. May (Postdoctoral

Associate, USDA Albany, CA) • Dr. Neil L. Schauer (Postdoctoral Associate, University of

Georgia) • Dr. Kevin R. Sowers (Postdoctoral Associate, University of California, Los Angeles)

• Dr. Katherine C. Terlesky (NSF Postdoctoral Fellow, Ohio State University) • Dr. Birgit E.

Alber (Postdoctoral Associate, Frieburg University, Germany; Assistant Professor, Ohio State

University) • Dr. Ubolsree Learksakulpanich (Research Scientist, National Science and

Technology Development Agency, Thailand) • Dr. Tong Zhao • Dr. Rebecca Miles

(DesignWrite, Inc.) • Dr. Birtha Borup (Maxigen, Inc.) • Dr. Prabha Iyer (Postdoctoral

Associate, Pennsylvania State University; Scientist, J. Craig Venter Institute) • Dr. Francisco

Cruz (Postdoctoral Associate, Emory University) • Dr. Sarah Lawrence (Postdoctoral Associate,

Fox Chase Cancer Center) • Dr. Sabrina Zimmerman (Postdoctoral Associate, Scripps Research

Institute, La Jolla) Dr. Eric Patridge (Postdoctoral Associate, Yale University) • Dr. Mingyu

Wang (Assistant Professor, Shandong University • Dr. Matthew Reichlen (Postdoctoral

Associate, University of Colorado).

Past Postdoctoral students (post position): Dr. Darren R. Abbanat (Research Scientist,

American Cyanamid Company) • Dr. Derrick R. Lovley (Research Scientist, USGS, VA) • Dr.

Leon L. Lundie, Jr. (Assistant Professor, New Mexico State University) • Dr. Michael J.K.

Nelson (Research Scientist, ECOVA) • Dr. Pramathesh S. Patel (Research Scientist, Squibb

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Laboratories) • Dr. Rolf Schauder (Assistant Professor, J.W. Goethe Universität, Germany) • Dr.

W. Bruce White (Senior Research Associate, USDA, Ames, Iowa) • Dr. Madeline Rasche

(Assistant Professor, University of Florida) • Dr. Julie Maupin-Furlow (Assistant Professor,

University of Florida) • Dr. Kavita Singh-Wissmann (Research Scientist, Monsanto). • Dr.

Cheryl Ingram-Smith (Research Associate, Clemson University) • Dr. Robert Barber (Assistant

Professor, University of Wisconsin-Parkside) • Dr. Kerry Smith (Assistant Professor, Clemson

University, 2001) • Dr. Brian Tripp (Assistant Professor, Western Michigan University, 2001) •

Dr. Richard Ding (Senior Research Associate, University of Massachusetts) • Dr. Andrea Gorrell

(Assistant Professor, University of Northern British Columbia) • Dr. Qingbo Li (Assistant

Professor, University of Illinois, Chicago) • Dr. Daniel Lessner (Assistant Professor, University

of Arkansas) • Dr. Ricardo Jasso-Chavez (University of Mexico) • Dr. Iris Porat. • Dr. Suharti

Suharti (Assistant Professor, University of Malang, Indonesia) • Dr. Venkata Vepachedu

(Research Associate, Penn State University) • Dr. Adepu Kiran Kumar (Group Leader, Codon

Biosciences).

Current postdoctoral students (Ph.D.-granting institution): Dr. Siva Sai Kumar (Central

Food Technological Research Institute, Mysore, India).

Current graduate students (Ph.D.): Mohammed Almishwat (joint with Prof. Murakami).

RESEARCH

Past funding: The Upjohn Company, Methanogenic Inhibitors, $19,000 (1979-81). • The

Upjohn Company, Biosynthesis of Coenzyme F420, $13,640 (1981-82). • Pratt Animal Nutrition

Progra?m, Identification of Potential Feedstuff Additives Highly Specific for the Inhibition of

Waste Gas Production in Ruminants, $34,421 (1979-81). • Pratt Animal Nutrition Program,

Mechanism of Methane Inhibition in the Rumen by Monensin, $35,200 (1982-84). • National

Science Foundation, Hydrogenase- and Hydrogenase-Linked Electron Transport in

Methanogenic Bacteria, $63,326 (co-investigator), (1979-81). • National Science Foundation,

Hydrogenase- and Formate Dehydrogenase-Linked Electron Transport in Methanogenic

Bacteria, $80,000 (1981-84). • Syracuse Research Corporation, Evaluation of Glycolic Acid as

a Substrate for Methanogenesis, $24,930 (1981-82). • Gas Research Institute, Microbiological

Studies Towards Optimization of Methane From Plant Biomass, $126,919 (co-investigator)

(1979-82). • Gas Research Institute, Microbiological and Chemical Studies on the Anaerobic

Conversion of Coal-Derived Compounds to Methane, $143,544 (1982-84). • Gas Research

Institute, Microbiological and Biochemical Studies Towards Optimization of Substrate

Utilization by Methanogenic Bacteria, $408,385 (1982-85). • Genetics Institute, Genetics of

Methanogenic Bacteria, $50,260 (1984-86). • Dynatech, Biochemical Studies on Ring Fission

by Anaerobic Bacteria, $50,000 (1985-1987). • Gas Research Institute, Enzymological and

Genetic Studies of One-Carbon Reactions in the Pathway of Acetate Utilization by

Methanogenic Bacteria, $519,831 (1986-88). • National Science Foundation, Hydrogenase-

and Formate Dehydrogenase-Linked Electron Transport in Methanogenic Bacteria, $183,000

(1984-88). • Department of Energy, Enzymological Studies of One-Carbon Reactions in the

Pathway of Acetate Utilization by Methanogenic Bacteria, $208,998 (1986-1989). • Virginia

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Center for Innovative Technology, Biotechnology Institute, Characterization of the Formate

Dehydrogenase Operon from Methanobacterium formicicum, $39,847 (1989-91). • Virginia

Center for Innovative Technology, Biobased Materials Center, Enzymology of the Anaerobic

Detoxification of Phenolic Compounds, $45,000. (1989-92). • Gas Research Institute,

Molecular Biology of One-Carbon Metabolism in Anaerobic Bacteria, $345,000 (1989-92). •

Department of Energy, Enzymological Studies of One-Carbon Reactions in the Pathway of

Acetate Utilization by Methanogenic Bacteria, $459,000 (1990-95). • Office of Naval Research,

Enzymological and Molecular Genetic Studies to Determine the Potential for Marine

Methanogenic Microorganisms to Detoxify Chlorinated Hydrocarbons, $414,702 (1991-95). •

National Science Foundation, Biochemistry and Molecular Genetics of Formate Utilization in

Methanogenic Bacteria, $185,000 (1992-95). • National Institutes of Health, Molecular Biology

of Acetate Conversion to Methane, $403,145 (1992-95). • Department of Energy, Enzymology

of the Pathway for Acetate Conversion to Methane in Methanosarcina thermophila, $355,000

(1995-98). • E.I. DuPont de Nemours and Company, Microbial Purification of Dimethylamine,

$55,000 (1998-99). • Department of Energy, Conference on Microbial Structural Biology:

Novel Enzymes from Diverse Microbes, $4,000 (1997-98). • National Science Foundation,

Proteasomes in the Methanogenic Archaea, $255,000 (1996-99), principal investigator. •

National Institutes of Health, Procaryotic Carbonic Anhydrases, $921,217 (1996-2000),

principal investigator. • National Institutes of Health Fellowship to Dr. Robert Barber,

Regulation and Selectivity of Proteolysis in Archaea, $64,336 (1998-2000), sponsor. •

Department of Energy, Enzymology of the Pathway for Acetate Conversion to Methane in

Methanosarcina thermophila, $324,000 (1998-2001), principal investigator. • National Science

Foundation Research Training Grant, Structure/Function of Novel Enzymes from Diverse

Microbes, $1,646,355 ($310,000 proportion) (1996-2004), co-principal investigator. • National

Institutes of Health Individual Award for Mr. Frank Cruz, Biochemistry of a Novel Iron-Sulfur

Flavoprotein, $66,000 (2000-2003), sponsor. National Aeronautics and Space Administration

Penn State Astrobiology Research Center, $4,633,319 ($150,000 proportion) (1998-2003), co-

principal investigator. • National Institutes of Health, Enzymology of Acetotrophic

Methanogenesis Supplement Frank Cruz, $37,843 (2003-2004), P.I. • Department of Energy,

Enzymology of the Pathway for Acetate Conversion to Methane in Methanosarcina thermophila,

$385,000 (2001-2004), P.I. • National Institutes of Health, Enzymology of Acetotrophic

Methanogenesis, $749,242 (2000-2004), P.I.. • Advanced Resources International,

Methanogenic Conversion of Carbon Dioxide into Methane, $100,000, (2005-2006), P.I.. •

Maren Foundation, Understanding the Role of -Class Carbonic Anhydrases in

Nature, $25,000, (2006-2007). • Air Force Office of Sponsored Research,

Structural and Functional Mechanisms of Adaptations of Ado-Met and WrbA in Extremophilic

Organisms, $89,000, (2007) • National Science Foundation, Methanosarcina genomics,

$1,389,771 (2002-2008), P.I. • NASA National Astrobiology Institute, Evolution of a Habitable

Planet - Oxygen and Anaerobes, $294,663 (2003-2008), Co-P.I. • NIH National Research

Council Fellowship, Oxygen Adaptation of the Archaeon Methanosarcina thermophila $98,000

(2005-2008), sponsor for Dr. Dan Lessner. • Department of Energy, New Perspectives on

Acetate and One-Carbon Metabolism in the Methanoarchaea, $360,000, (2005-2008), P.I.. •

Maren Foundation, Proton Transfer in Cam, the Archetype of the Gamma Class of Carbonic

Anhydrases, $12,700, (2007-2008). • Pennsylvania State University, Microbiological

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Conversion of Coal to Methane, $150,000, (2006 - 2008) • Air Force Office of Sponsored

Research, Structural, thermodynamic and functional mechanisms of adaptations WrbA and

AdoMetDC proteins in extremophilic organisms, $ 78,165, (2007-2008). Air Force Office of

Sponsored Research, Structural and Functional Mechanisms of Adaptations of WrbA in

Extremophilic Organisms, $216,000, (2008-2009) • National Science Foundation, Biochemistry

and Physiology of the Rnf Complex From the Archaeon Methanosarcina Acetivorans, $ 461,370,

(2008-2011) • Department of Energy, The Oxidative Stress Response in Methanoarchaea, $

119,072, (2008-2011) • National Science Foundation, Acquisition of Waters Acquity-Synapt G2

LC-MS to enable Metabolomics Research at Penn State, $369,550 (2011-2012) • National

Aeronautics and Space Agency, Signatures of Life from Earth and Beyond, $189,035 (2009-

2014)

Current funding: Department of Energy, New Perspectives on Acetate and One-Carbon

Metabolism in the Methanoarchaea: Carbonic Anhydrase, $450,000 (2011-2014). • Department

of Energy ARPA-e, Engineering a Methane-To-Acetate Pathway for Producing Liquid Biofuels,

$3,000,000 (2014-2016).

Patents: Jablonski, P. E., and J. G. Ferry. 1995. Use of carbon monoxide dehydrogenase for

bioremediation of toxic compounds. United States Patent No. 5,466,600.

PUBLICATIONS

Books:

1. Ferry, J. G. (ed.) 1993. Methanogenesis. Chapman and Hall, New York.

2. Ljungdahl, L. G., M. W. Adams, L. L. Barton, J. G. Ferry, and M. K. Johnson (ed.) 2003.

Biochemistry and Physiology of Anaerobic Bacteria. Springer-Verlag, New York.

Journal and review articles:

(* Denotes students)

1. Ferry, J. G., P. H. Smith, and R. S. Wolfe. 1974. Methanospirillum, a new genus of

methanogenic bacteria, and characterization of Methanospirillum hungatii

sp. nov. International Journal of Systematic Bacteriology. 24:465-469.

2. Ferry, J. G., D. W. Sherod, H. D. Peck, Jr., and L. G. Ljungdahl. 1976. Levels of

formyltetrahydrofolate synthetase and methylenetetrahydrofolate dehydrogenase in

methanogenic bacteria, p.151-155. In H.G. Schlegel, G. Gottschalk, and N. Pfenning (ed.),

Symposium on microbial production and utilization of Gases (H2, CH4, CO). E. Goltze K. G.,

Gottingen.

3. Ferry, J. G., and R. S. Wolfe. 1976. Anaerobic degradation of benzoate to methane by a

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microbial consortium. Archives for Microbiology. 107:33-40.

4. Ferry, J.G., and R.S. Wolfe. 1977. Nutritional and biochemical characterization of

Methanospirillum hungatii. Applied and Environmental Microbiology. 34:371-376.

5. *Schauer, N. L., and J. G. Ferry. 1980. Metabolism of formate in Methanobacterium

formicicum. Journal of Bacteriology. 142:800-807.

6. *Schauer, N. L., and J. G. Ferry. 1982. Properties of formate dehydrogenase in

Methanobacterium formicicum. Journal of Bacteriology. 150:1-7.

7. *Schauer, N. L., *D. P. Brown, and J. G. Ferry. 1982. Kinetics of formate metabolism in

Methanobacterium formicicum and Methanospirillum hungatei. Applied and Environmental

Microbiology. 44:549-554.

8. Barber, M. J., L. M. Siegel, *N. L. Schauer, *H. D. May, and J. G. Ferry. 1983. Formate

dehydrogenase from Methanobacterium formicicum: electron paramagnetic resonance

spectroscopy of the molybdenum and iron-sulfur centers. Journal of Biological Chemistry.

258:10839-10845.

9. *Schauer, N. L., and J. G. Ferry. 1983. FAD requirement for the reduction of coenzyme F420

by formate dehydrogenase from Methanobacterium formicicum. Journal of Bacteriology.

155:467-472.

10. *Sowers, K. R., and J. G. Ferry. 1983. Isolation and characterization of a methylotrophic

marine methanogen, Methanococcoides methylutens gen. nov., sp. nov. Applied and

Environmental Microbiology. 45:684-690.

11. Ferry, J. G., and *K. R. Sowers. 1983. Principles of the microbial conversion of biomass to

methane, p. 91-110. In F. Zucconi, M. de Bertoldi, and S. Coppola (ed.), International

symposium on biological reclamation of urban wastes, Naples.

12. *Dellinger, C. A., and J. G. Ferry. 1984. Effect of monensin on growth and methanogenesis

of Methanobacterium formicicum. Applied and Environmental Microbiology. 48:680-682.

13. *Lovley, D. R., R. C. Greening, and J. G. Ferry. 1984. Rapidly growing rumen

methanogenic organism that synthesizes coenzyme M and has a high affinity for formate.

Applied and Environmental Microbiology. 48:81-87.

14. *Lovley, D. R., R. H. White, and J. G. Ferry. 1984. Identification of methyl coenzyme M as

an intermediate in methanogenesis from acetate in Methanosarcina spp. Journal of Bacteriology.

160:521-525.

15. *Nelson, M. J. K., and J. G. Ferry. 1984. Carbon monoxide-dependent methyl coenzyme M

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methylreductase in acetotrophic Methanosarcina spp. Journal of Bacteriology. 160:526-532.

16. *Nelson, M. J. K., *D. P. Brown, and J. G. Ferry. 1984. FAD requirement for the reduction

of coenzyme F420 by hydrogenase from Methanobacterium formicicum. Biochemical and

Biophysical Research Communications. 120:775-781.

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31. Barber, M. J., *H. D. May, and J. G. Ferry. 1986. Inactivation of formate dehydrogenase

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33. *Terlesky, K. C., M. J. Barber, *D. J. Aceti, and J. G. Ferry. 1987. EPR properties of the

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36. *Terlesky, K. C., and J. G. Ferry. 1988. Ferredoxin requirement for electron transport from

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41. *Patel, P. S., and J. G. Ferry. 1988. Characterization of the upstream region of the formate

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43. *Haddock, J. D., and J. G. Ferry. 1989. Purification and characterization of phloroglucinol

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45. *Baron, S. F., and J. G. Ferry. 1989. Purification and properties of the membrane-associated

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46. *Baron, S. F., and J. G. Ferry. 1989. Reconstitution and properties of a coenzyme F420-

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47. *Lundie, Jr. L. L., and J. G. Ferry. 1989. Activation of acetate by Methanosarcina

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64. *Jablonski, P. E., and J. G. Ferry. 1992. Reductive dechlorination of trichloroethylene by

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65. *Jablonski, P. E., W.-P. Lu, S. W. Ragsdale and J. G. Ferry. 1993. Characterization of the

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66. *Haddock, J. D., and J. G. Ferry. 1993. Initial steps in the anaerobic degradation of 3,4,5-

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97. *Singh-Wissmann, K., *C. Ingram-Smith, *R. D. Miles, and J. G. Ferry. 1998.

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98. *Maupin-Furlow, J. A., H. C. Aldrich, and J. G. Ferry. 1998. Biochemical characterization

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99. Becker, D. F., *U. Leartsakulpanich, K. K. Surerus, J. G. Ferry, and S. W. Ragsdale. 1998.

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102. *Alber, B. E., C. M. Colangelo, J. Dong, C. M. V. Stålhandske, T. T. Baird, C. Tu, C. A.

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111. *Leartsakulpanich, U., M. L. Antonkine, and J. G. Ferry. 2000. Site-specific mutational

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analyses reveal multiple homologs of genes encoding enzymes of the methanol:coenzyme M

methyltransferase system that are differentially expressed in methanol- and acetate-grown

Methanosarcina thermophila FEMS Microbiology Letters. 215:127-132.

131. Tu, C., R. S. Rowlett, *B. C. Tripp, J. G. Ferry, and D. N. Silverman. 2002. Chemical

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132. Ferry, J. G. 2003. One-carbon metabolism in methanogenic anaerobes, p. 143-156. In L. G.

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133. *Iyer, P. P., *S. H. Lawrence, H. P. Yennawar, and J. G. Ferry. 2003. Expression,

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134. *Ding, Y.-H. R., and J. G. Ferry. 2004. Flavin mononucleotide-binding flavoprotein family

in the domain Archaea. Journal of Bacteriology. 186:90-97.

135. *Tripp, B. C., *C. B. Bell III, *F. Cruz, C. Krebs, and J. G. Ferry. 2004. A role for iron in

an ancient carbonic anhydrase. Journal of Biological Chemistry. 279:6683-6687.

136. *Iyer, P. P., *S. H. Lawrence, K. B. Luther, K. R. Rajashankar, H. P. Yennawar, J. G.

Ferry, and H. Schindelin. 2004. Crystal Structure of phosphotransacetylase from the

methanogenic archaeon Methanosarcina thermophila. Structure. 12:559-567.

137. Innocenti, A., *S. Zimmerman, J. G. Ferry, A. Scozzafava, and C. T. Supuran. 2004.

Carbonic anhydrase inhibitors. Inhibition of the zinc and cobalt γ-class enzyme from the

archaeon Methanosarcina thermophila with anions. Bio-organic and Medicinal Chemistry

Letters. 14:3327-3331.

138. Innocenti, A., *S. Zimmerman, J. G. Ferry, A. Scozzafava, and C. T. Supuran. 2004.

Carbonic anhydrase inhibitors. Inhibition of the beta-class enzyme from the methanoarchaeon

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Chemistry Letters. 14:4563-4567.

139. *Zimmerman, S., A. Innocenti, A. Casini, J. G. Ferry, A. Scozzafava, and C. T. Supuran.

2004. Carbonic anhydrase inhibitors. Inhibition of the prokaryotic beta and gamma-class

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enzymes from Archaea with sulfonamides. Bioorganic and Medicinal Chemistry Letters.

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140. Parisi, G., M. Perales, M. S. Fornasari, A. Colaneri, N. González-Schain, D. Gómez-Casati,

*S. Zimmermann, A. Brennicke, A. Araya, J. G. Ferry, J. Echave, and E. Zabaleta. 2004. Gamma

carbonic anhydrases in plant mitochondria. Plant Molecular Biology. 55:193-207.

141. *Li, Q., L. Li, T. Rejtar, B. L. Karger, and J. G. Ferry. 2005. Proteome of Methanosarcina

acetivorans. Part I: an expanded view of the biology of the cell. Journal of Proteome Research.

4:112-128.

142. *Li, Q., L. Li, T. Rejtar, B. L. Karger, and J. G. Ferry. 2005. Proteome of Methanosarcina

acetivorans. Part II: comparison of protein levels in acetate- and methanol-grown cells. Journal

of Proteome Research. 4:129-135.

143. *Gorrell, A., *S. H. Lawrence, and J. G. Ferry. 2005. Structural and kinetic analyses of

arginine residues in the active site of the acetate kinase from Methanosarcina thermophila

Journal of Biological Chemistry. 280:10731-10742.

144. *Ingram-Smith, C., *A. Gorrell, *S. H. Lawrence, *P. Iyer, *K. Smith, and J. G. Ferry.

2005. Characterization of the acetate binding pocket in the Methanosarcina thermophila acetate

kinase. Journal of Bacteriology. 187:2386-2394.

145. Rasche, M. E., and J. G. Ferry. 2005. Methanogens and the archaebacteria, molecular

biology of, p. 237-261. In R. A. Meyers (ed.), Encyclopedia of Molecular Cell Biology and

Molecular Medicine, 2nd ed, vol. 8. Wiley-VCH Verlag GmbH & Co., Weinheim.

146. *Iyer, P., and J. G. Ferry. 2005. Acetate kinase from Methanosarcina thermophila, a key

enzyme for methanogenesis, p. 239-246. In J. L. Barredo (ed.), Microbial Enzymes and

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147. Moran, J. J., C. H. House, K. H. Freeman, and J. G. Ferry. 2005. Trace methane oxidation

studied in several Euryarchaeota under diverse conditions. Archaea. 1:303-309.

148. Andrade, S. L. A, *F. Cruz, C. L. Drennan, V. Ramakrishnan, D. C. Rees, J. G. Ferry, and

O. Einsle. 2005. Structures of the iron-sulfur flavoproteins from Methanosarcina thermophila

and Archaeoglobus fulgidus. Journal of Bacteriology. 187:3848-3854.

149. *Li, Q., L. Li, T. Rejtar, *D. J. Lessner, B. L. Karger, and J. G. Ferry. 2006. Electron

transport in the pathway of acetate conversion to methane in the marine archaeon

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150. *Lawrence, S. H., K. B. Luther, H. Schindelin, and J. G. Ferry. 2006. Structural and

functional studies suggest a catalytic mechanism for the phosphotransacetylase from

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151. *Lawrence, S. H., and J. G. Ferry. 2006. Steady-state kinetic analysis of

phosphotransacetylase from Methanosarcina thermophila. Journal of Bacteriology. 188:1155-

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152. *Cruz, F., and J. G. Ferry. 2006. Interaction of iron-sulfur flavoprotein with oxygen and

hydrogen peroxide. Biochimica et Biophysica Acta. 1760:858-864.

153. *Patridge, E. V., and J. G. Ferry. 2006. WrbA from Escherichia coli and Archaeoglobus

fulgidus is an NAD(P)H:quinone oxidoreductase. Journal of Bacteriology. 188:3498-3506.

154. Ferry, J. G., and C. H. House. 2006. The stepwise evolution of early life driven by energy

conservation. Molecular Biology and Evolution. 23:1286-1292.

155. *Zimmerman, S. A., and J. G. Ferry. 2006. Proposal for a hydrogen bond network in the

active site of the prototypic gamma-class carbonic anhydrase. Biochemistry. 45:5149-5157.

156. Andreev, V. P., L. Li, T. Rejtar, *Q. Li, J. G. Ferry, and B. L. Karger. 2006. A new

algorithm for 15

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157. *Lessner, D. J., L. Li, *Q. Li, T. Rejtar, V. P. Andreev, *M. Reichlen, *K. Hill, J. J.

Moran, B. L. Karger, and J. G. Ferry. 2006. An unconventional pathway for reduction of CO2 to

methane in CO-grown Methanosarcina acetivorans revealed by proteomics. Proceedings

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158. Ferry, J. G. and K. Kastead*. 2007. Methanogenesis. p. 288-314. In R. Cavicchioli (ed.),

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159. Li, L., Q. Li, L. Rohlin, U. Kim, K. Salmon, T. Rejtar, R. P. Gunsalus, B. L. Karger, and J.

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acetivorans grown with acetate versus methanol. Journal of Proteome Research. 6:759-771.

160. Hausrath, E. M., L. J. Liermann, C. H. House, J. G. Ferry, and S. L. Brantley. 2007. The

effect of methanogen growth on mineral substrates: will Ni markers of methanogen-based

communities be detectable in the rock record? Geobiology 5:49-61.

161. Zimmerman*, S. A., J. G. Ferry, and C. Supuran. 2007. Inhibition of the archaeal beta-class

(Cab) and gamma-class (Cam) carbonic anhydrases. Current Topics in Medicinal Chemistry.

7:901-908.

162. Lessner*, D. J., and J. G. Ferry. 2007. The archaeon Methanosarcina acetivorans contains

a protein disulfide reductase with an iron-sulfur cluster. Journal of Bacteriology 189:7475-7484.

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163. Andrade, S. L. A., E. V. Patridge, J. G. Ferry, and O. Einsle. 2007. Crystal structure of the

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164. Gorrell*, A. and J. G. Ferry. 2007. Investigation of the Methanosarcina thermophila

acetate kinase mechanism by fluorescence quenching. Biochemistry 46:14170-14176.

165. Ferry, J. G. 2008. Acetate-Based Methane Production. p. 155-170. In Wall, J., C. S.

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166. Ferry, J. G. and D. J. Lessner*. 2008. Methanogenesis in Marine Sediments. p. 147-157.

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167. Zimmerman*, S. A. and J. G. Ferry. 2008. The and classes of carbonic anhydrase.

Current Pharmaceutical Design 14: 716-721.

168. Suharti*, S., K. Murakami, S. de Vries, and J. G. Ferry. 2008. Structural and biochemical

characterization of flavoredoxin from the archaeon Methanosarcina acetivorans. Biochemistry

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Carbonic anhydrase activators. Activation of the archaeal -class (Cab) and -class (Cam)

carbonic anhydrases with amino acids and amines. Bioorganic & Medicinal Chemistry Letters

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170. MacAuley, S. R., S. A. Zimmerman*, E. E. Apolinario, C. Evilia, Y. Hou, J. G. Ferry, and

K. R. Sowers. 2009. The archetype -class carbonic anhydrase (Cam) contains iron when

synthesized in vivo. Biochemistry 48:817-819.

171. Doerfert*, S. N., M. Reichlen*, P. Iyer, M. Wang*, and J. G. Ferry. 2009. Isolation and

characterization of Methanolobus zinderi sp. nov., a methylotrophic methanogen isolated from a

deep subsurface coal seam. International Journal of Systematic and Evolutionary Microbiology

59:1064-1069.

172. Ferry, J. G., and C. T. Supuran. 2009. Mechanism and inhibition of the class andclass

carbonic anhydrases, p. 285-300. In C. T. Supuran and J.-Y. Winum (ed.), Design of Zinc-

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173. Zafar, M., F. Tasca, G. Lo, E. Patridge*, J. Ferry, G. Noell. 2009. Tryptophan repressor-

binding proteins from Escherichia coli and Archaeoglobus fulgidus as new catalysts for 1,4-

dihydronicotinamide adenine dinucleotide-dependent amperometric biosensors and biofuel cells.

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174. Ferry, J. G. 2009. Biochemistry of Acetotrophic Methanogenesis, p. 357-367. In Timmis,

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175. Ferry, J. G. 2010. The class of carbonic anhydrase. Biochimica Biophysica Acta

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176. Zimmerman*, S. A., Tomb, J.-F. and J. G. Ferry. 2010. Characterization of CamH from

Methanosarcina thermophila, founding member of a subclass of the class of carbonic

anhydrases. Journal of Bacteriology 192:1353-1360.

177. Reichlen*, M. J., Murakami, K. S. and J. G. Ferry. 2010. Functional analysis of the three

TBP homologs in Methanosarcina acetivorans. Journal of Bacteriology 192:1511-1517.

178. Ferry, J. G. 2010. CO in Methanogenesis. Annals of Microbiology. 60:1-12.

179. Ferry, J.G. 2010. How to Make a Living Exhaling Methane. Annual Reviews of

Microbiology 64:453-473.

180. Lessner*, D. J., L. Lhu, C. S. Wahal*, and J. G. Ferry. 2010. An engineered methanogenic

pathway derived from the domains Bacteria and Archaea. mBio:1:e00243-10.

181. Ferry, J. G. 2010. The Chemical Biology of Methanogenesis. Planetary and Space Science.

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182. Kumar, V. K., J. G. Ferry and C. D. Maranas. 2011. Metabolic reconstruction of the

archaeon methanogen Methanosarcina acetivorans. BMC Systems Biology 5:28.

183. Ferry, J. G. 2011. Acetate kinase and phosphotransacetylase. Methods in Enzymology

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184. Ferry, J. G. 2011. Fundamentals of Methanogenic Pathways that are Key to the

Biomethanation of Complex Biomass. Current Opinion in Biotechnology 22:351-357.

185. *Kumar, A. K., N. H. Yennawar, H. P. Yennawar and J. G. Ferry. 2011. Expression,

purification, crystallization and preliminary X-ray crystallographic analysis of a novel plant-type

FTR-like protein from Methanosarcina acetivorans. Acta Crystallographica Section F 67:775-

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186. *Mingyu Wang, Jean-Francois Tomb and James G. Ferry. 2011. Electron transport in

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187. *Vepachedu, V. R., and J. G. Ferry. 2012. Role of the fused corrinoid/methyl transfer

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188. *Reichlen, M. J, *Vepachedu, V. R., Murakami, K. S. and J. G. Ferry. 2012. MreA

functions in the global regulation of methanogenic pathways in Methanosarcina acetivorans.

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189. *Zimmerman, S. A., Domsic, J. F., Tu, C., Robbins, A. H., McKenna, R., Silverman, D. N.,

and J. G. Ferry. 2013. Role of Trp19 and Tyr200 in catalysis by the γ-class carbonic anhydrase

from Methanosarcina thermophila. Archives of Biochemistry and Biophysics. 529:11-17.

190. Ferry, J. G. 2013. Carbonic anhydrases of anaerobic microbes. Bioorganic and Medicinal

Chemistry. 21:1392-1395.

191. McAnulty, M. J., V. R. Vepachedu*, T. K. Wood, and J. G. Ferry. 2013. Biofuels:

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192. Ferry, J. G. 2013. Zinc and Iron, Gamma and Beta Class, Carbonic Anhydrases of the

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193. *Kumar, R. S., W. Hendrick, J. B. Correll, A. D. Patterson, S. B. Melville, and J. G. Ferry.

2013. Biochemistry and physiology of the class carbonic anhydrase (Cpb) from Clostridium

perfringens strain 13. Journal of Bacteriology. 195:2262-2269.

194. *Jasso-Chavez, R., E. E. Apolinario, K. R. Sowers, and J. G. Ferry. 2013. MrpA functions

in energy conversion during acetate-dependent growth of Methanosarcina acetivorans. Journal

of Bacteriology. 195:3987-3994.

195. Appel, A., J. Bercaw, A. Bocarsly, H. Dobbek, D. DuBois, M. Dupuis, J. Ferry, E. Fujita,

R. Hille, P. Kenis, C. Kerfeld, R. Morris, C. Peden, A. Portis, S. Ragsdale, T. Rauchfuss, J.

Reek, L. Seefeldt, R. Thauer, and G. Waldrop. 2013. Frontiers, opportunities, and challenges in

biochemical and chemical catalysis of CO2 fixation. Chemical Reviews. 113:6621-6658.

196. Ferry, J. G. 2013. Acetate: A Key Intermediate during the Anaerobic Degradation of

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197. Vullo, D., R. S. Sai Kumar*, A. Scozzafava, C. Capasso, J. G. Ferry, and C. T. Supuran.

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198. *Kumar, R. S. S., and J. G. Ferry. 2014. Prokaryotic Carbonic Anhydrases of Earth’s

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199. *Suharti, S., M. Wang*, M., S. de Vries, and J. G. Ferry. 2014. Characterization of the

RnfB and RnfG subunits of the Rnf complex from the archaeon Methanosarcina acetivorans.

PLoS One:in press.

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