Dr. Lonnie O. Ingram Director	ingram@ufl.edu	Tel: (352) 392-8176 Fax: (352) 846-0969
Dr. Keelnatham T. Shanmugam Associate Director	shan@ufl.edu	Tel: (352) 392-2490 Fax: (352) 392-5922
Dr. Sheilachu P. Gomez Assistant Director	spgomez@ufl.edu	Tel/Fax: (352) 392-00237
Florida Center for Renewable Chemicals and Fuels (FCRC) University of Florida, Institute of Food and Agricultural Sciences Department of Microbiology and Cell Science Bldg. 981 Museum Road, PO Box 110700 Gainesville, FL 32611-0700 http://fcrc.ifas.ufl.edu

TABLE OF CONTENTS

Contact Information

Table of Contents

Introduction

Faculty Members

Conferences, Seminars, Workshops

Service

Awards

Graduate Research Assistantships

Post-Docs and Research Faculty Support

Patents :

Approved ; Pending; US Patents; Pending International Patents; Invention Disclosures

Publications:

In Press; Published Chapter Review; Journals

On-Going Research

Acknowledgments

Introduction

The Florida Center for Renewable Chemicals and Fuels (FCRC) is mandated to provide a focus in the area of multidisciplinary education and research in the production of chemicals and fuels from biomass, and the improvement of biomass as a biorefinery feedstock.

Graduate training and support are provided by investigator-driven competitive research grants and industrial sponsored research agreements. Specific areas of research are guided by the objectives of sponsoring agencies and companies as defined in the awards. Tuition support is provided for up to 4 years by the Dean of the College of Agriculture and Life Sciences.

Research programs are currently conducted by our member faculties in the following areas: Microbial Metabolic Engineering, Microbial Biochemistry and Physiology, Hydrogen Research, Methanogenic and Halophilic Archaea Proteosomes, Bacterial Pathogenesis, Molecular Biology of Metanogens, Environmental Microbiology, Comparative Bacterial Genomics, and Plant- Endophytic Bacterial Interactions.

Faculty Members

The Center has 10 in-house faculty members, 2 from other departments and colleges, and 1 adjunct member.

Valerie de Crecy-Lagard
(Assistant Professor) Comparative genomics, bacterial genetics, experimental evolution, genetic code.

Samuel Farrah
(Professor) Adsorption of microorganisms to solids; modification of solids to increase adsorption or inactivation of microorganisms

William B. Gurley
(Professor) Functional analysis of heat shock transcription factors

Shouguang Jin (Associate Professor)
   Dept of Molecular Genetics and
   Microbiology, College of Medicine Molecular pathogenesis of Pseudomonas aeruginosa; Agrobacterium mediated transformation

Nemat O. Keyhani
(Assistant Professor) Bacterial pathogenesis; toxin production and modes of action; carbohydrate metabolism; signal transduction and applications for marine natural products

Lonnie O. Ingram
(Distinguished Professor) Metabolic engineering of bacteria for fuel ethanol and bio-chemical production

Julie Maupin-Furlow
(Associate Professor) Genetics and biochemistry of ATP-dependent proteolysis

Gary Peter (Associate Professor)
   School of Forest Resources &
   Conservation Forest genomics and cell biology.

James Preston
(Professor) Microbial genetics and biochemistry

Madeline Rasche
(Associate Professor) Biochemistry of methanogenesis; protein structure and function

K. T. Shanmugam
(Professor) Metabolic engineering for fuel and chemicals; regulation of metabolic pathways.

Eric W. Triplett
(Professor) Biology of the interaction between plants and endophytic bacteria

David Beall
(Adjunct Faculty)
Microbiology

Conferences, Seminars, and Workshops

In-house seminars were regularly conducted during the Fall and Spring Semesters. Research progress reports by graduate students, post-docs, staff members, and research faculty members were presented for discussion and comments. Twenty five to thirty people attended these weekly seminars.

Faculty members, post-docs, and their students attended various national and international conferences and seminars to present research results and to interact with other researchers from other academic institutions and industries. The Table in the following pages shows the conference participation, seminar or workshop, place and date, and topics presented by FCRC associated researchers.

Table. 1. Conferences, Workshops, and Meetings Attended by Faculty Members and Students

Conference/Seminar/ Workshop	Date and Place	Attendees/Poster Presenters/Speakers * - graduate student; - post-doc *- undergrad student	Topic
Annual Meeting of the MultiState Project, S1007	Sept. 28-Oct. 2, 2004 Golden, CO	JA Maupin- Furlow	The Science and Engineering for a Biobased Industry and Economy.
USDA-DOE Metabolic Engineering V Meeting	Sept 19-23, 2004 Lake Tahoe, CA	LO Ingram	Bacterial biocatalysts for fuel production.
UF Colloqium on Energy	November 1, 2004 Gainesville, FL	LO Ingram; JA Maupin-Furlow; KT Shanmugam; JF Preston, III	Microbial Biocatalysts for Renewable Fuels and Chemicals.
RNA Editing – Gordon Conference	Jan 23-27, 2005 Ventura, CA	V. de Crecy-Lagard	Finding missing genes by comparative genomics: tRNA modification goldmine.
National Aeronautics and Space Administration (NASA)	Jan. 27, 2005. Kennedy Space Center, Cape Canaveral, FL.	JA Maupin-Furlow	Proteolysis in the Extreme – Structure and Function of Haloarchaeal Proteasomes
Patent Hearing	Jan 29-Feb 3, 2005 Munich, Germany	LO Ingram	Patent hearing concerning a challenge to UF patent on ethanol production from biomass.
Bioinformatics Workshop	February Gainesville, FL	B Bishop, B Nordin, W Waas, J Reader and V. de Crecy-Lagard	Identification of missing genes by comparative genomics: tRNA modification goldmine.
National Academy of Sciences Class Member Meeting	February 5, 2005 Washington, DC.	LO Ingram	Council Designee to Class Membership Committees for Class VI: Applied Biological, Agricultural, and Environmental Sciences.
International Network in Biofixation of CO2 and Greenhouse Gas Abatement with Microalgae and Photobiological Hydrogen Production Consortium	February 24-26, 2005	KT Shanmugam	Microbial production of hydrogen: Approaches to enhance the yield.
CPBR 2005 Symposium	March 2-3, 2005 Washington DC.	James F. Preston	Utilization of Hemicellulose-Derived Glucuronoxylose for Ethanol Production.
Frontiers in Biocatalysis and Biotransformations. Ann. Mtg. Amer. Chem. Soc.,	March 13 – 17, 2005 San Diego, CA.	JA Maupin-Furlow	Archaeal Proteasomes and Protein Quality Control. .
Northern Illinois University Graduate Symposium	April 7-8, 2005 Dekalb, Illinois	LO Ingram	April 7 –Biorefineries: Replacing Imported Oil with Renewable Fuels and Chemicals from Woody Biomass April 8 – Re-Engineering Microorgamisms as Factories for Renewable Fuels and Chemicals.
National CFAR ROC/IFT Seminars on the Hill	April 11, 2005 Washington, DC.	LO Ingram	*key benefits to the economy of maximizing the extraction of utility from biomass.
World Congress on Industrial Bioprocessing and Biotechnology	April 20-22, 2005 Orlando, FL.	LO Ingram	Microorganisms for the Production of Renewable Fuels and Chemicals
National Academy of Sciences Annual Meeting	April 30-May 4, 2005 Washington, DC.	LO Ingram	Attendee as member.
27^th Symposium on Biotechnology for Fuels and Chemicals	May 1-4, 2005	KT Shanmugam and Y. Kim*	Homo-ethanol fermentation by a novel mutant of Escherichia coli.
American Society for Microbiology Annual Meeting	June 5-9, 2005 Atlanta, GA	LO Ingram- speaker	Putting Microbes to Work: The Role of Microbes in Bioengineering, Bioprocessing, and Bioremediation
		ME Rasche
		Y. Kim*	Alternative fermentation pathway in Escherichia coli.
		Wright, A. J. * and J. A. Maupin-Furlow	Molecular characterization of Haloferax volcanii 20S proteasomes reveals an intramolecular mechanism of b-protein processing.
		Gil, M. A. *and J. A. Maupin-Furlow.	Co-transcription of proteasome and tRNA modification genes of the haloarchaeon Haloferax volcanii.
		Reuter, C. J. * and J. A. Maupin-Furlow	Molecular characterization of the proteasome-activating nucleotidase subtypes of the haloarchaeon Haloferax. volcanii.
		Kirkland, P. A. * and J. A. Maupin-Furlow	of native proteasomal substrates of Haloferax volcanii using a degadomic approach.
Fifth Annual IFAS Graduate Research Symposium	2005 Gainesville, FL	Wright, A. J. * and J. A. Maupin-Furlow.	Assembly and processing of 20S proteasomes in Haloferax volcanii.
		Kirkland, P. A. * and J. A. Maupin-Furlow.	Proteomics and the halophilic archaea.
		Gil, M. A. * and J. A. Maupin-Furlow	Connect the dots: organization of proteasomal operons of the haloarchaeon Haloferax volcanii.
14^th Conversation	Albany, NY June 14-18, 2005	Valerie de Crecy-Lagard	Finding missing genes by comparative genomics: the tRNA modification goldmine.
Ann. Mtg. UF Student Science Training Program	2005 Gainesville, FL	Cuddy, KK*** and JA Maupin-Furlow	Green fluorescent protein reporter to probe Haloferax volcanii promoters.
Florida Bioinformatics Workshop	2005 Gainesville, FL.	Gil, M.A. * and J. A. Maupin-Furlow	Co-transcription of proteasome and tRNA modification genes of the haloarchaeon Haloferax volcanii.
Florida Bioinformatics Workshop	2005 Gainesville, FL.	Wright, A. J. * and J. A. Maupin-Furlow	Molecular characterization of Haloferax volcanii 20S proteasomes reveals an intramolecular mechanism of b-protein processing.
5th International Conference on Extremophiles	2004 Cambridge, MD.	Karadzic, I. M.*, M. A. Gil and J. A. Maupin-Furlow	Physiological characterization of a proteasome-deficient mutant of Haloferax volcanii by a differential proteomic approach.
		Reuter, C. J. * and J. A. Maupin-Furlow.	Analysis of substrate recognition by Pan/20S Proteasome isoforms in the haloarchaeon Haloferax volcanii.
		Kirkland, A. P. * and J. A. Maupin-Furlow	Development of green fluorescent protein-based expression vectors to identify regulated promoters of Haloferax volcanii.
		Wright, A. J. * and J. A. Maupin-Furlow.	. Mutational analysis of the Thr active site of the beta-protein in 20S proteasomes reveals beta-protein processing via an intramolecular mechanism.

Service

Faculty members have been actively involved in several academic service activities. They include:

Faculty Member	Type of Service	Institution/Society
Lonnie O. Ingram	Fellow	American Academy of Microbiology, 1998-present
	Fellow	Society of Industrial Microbiology and Biotechnology, 2001-present
	Member	U.S. National Academy of Sciences, 2001-present
	Editorial Board	Biotechnology Letters 1996-present
	Editorial Board	Metabolic Engineering 1998-present
	Member, Grant Review Panel	DOE, USDA, Interagency Metabolic Engineering Initiative
	Grant Proposal Reviewer	NSF, NIH, DOE, USDA, several state programs, Canada, Australia, Hong Kong, Consortium for Plant Biotechnology Research
Julie A. Maupin-Furlow	Editorial Board Member	Archaea, 2001 – present. Frontiers in Bioscience, 2000 – present.
	Review Panel Member	Department of Energy, Genomics:Genomes to Life Program, Genome Scale Analysis of Biochemical Pathways in Microbes and Microbial Communities, May 2005. USDA NRI, Biobased Products and Bioenergy Production Research Program, May 2005.
	Review Referee	National Science Foundation, 1996 – present. U.S. Department of Energy, 1996 – present.
	Review Team Leader	USDA NRCS, Site Visit of Biomass R&D Initiative Project, April 2005.
	Ad Hoc Reviewer	2004 – 2005: Applied Genomics and Proteomics, Biotechnology Progress, Current Microbiology, Extremophiles, FEBS Letters, FEMS Microbiology Letters, Journal of Bacteriology, Microbiology and Molecular Biology Reviews, Molecular Microbiology, Proceedings of the National Academy of Sciences, Protein and Peptide Letters, Proteomics, Structure
	Awards Committee Member	Southeastern Branch American Society for Microbiology 2004 – 2005.
James F. Preston, III	Editorial board Member	Journal Bacteriology
	Reviewer	Nature New Biology, Applied and Environmental Microbiology, Journal of Bacteriology, Journal of Experimental Microbiology, Carbohydrate Research, Peptides and Proteins Lett.
	Graduate Coordinator	Microbiology and Cell Science Department. 2003-2004
Madeline E. Rasche	Graduate Coordinator	Microbiology and Cell Science Department 2004-present
	Grant Proposal Review Panel	NSF, Metabolic Biochemistry October 2002-2005; DOE Basic Energy Sciences and NABIR 2005
	Ad hoc grant proposal reviewer	NSF; 1999-2005; DOE Basic Energy Biosciences, 2005
	Ad hoc reviewer for journals	Journal of bacteriology, 2005
	GRE Panel	Biochemistry, Molecular Biology and Cell Biology 2004-2006
	Policy Committee, SE Branch, ASM	2002-2006

Awards

The following students received travel awards in support of their attendance and presentations at scientific meetings:

Name

Award/Sponsor

Date/Place

Conference

Reuter, Christopher J

Wright, Amy

Extremophile Student Travel Award

2004

Cambridge, MD

5^th International Conference on Extremophiles

Research Assistantships

The Dean of the College of Agricultural and Life Sciences, IFAS, granted matching graduate assistantships and
fellowships to the following students:

Graduate Assistant	Start Date Granted	Degree	Mentor
Franz St. John	2001F	PhD	Dr. James F. Preston, III
Christopher Reuter	2002S	PHD	Dr. Julie A. Maupin-Furlow
Maegorzata Gil	2002SU	PhD	Dr. Julie A. Maupin-Furlow
Kim Youngyun	2002	PhD	Dr. K.T. Shanmugam
Phi Min Do	2003F	PhD	Dr. K. T. Shanmugam
Phillip Kirkland	2003F	MS	Dr. Julie A. Maupin-Furlow
Shannon McQuaig	2003F	MS	Dr. Samuel R. Farrah
Jonathan Moore	2003F	PhD	Dr. Lonnie O. Ingram
Amy Wright	2003F	MS	Dr. Julie A. Maupin-Furlow
Matthew Humbard	2004F	PhD	Dr. Julie A. Maupin-Furlow
Benjamin Sloniker	2004F	PhD	Dr. Madeline E. Rasche
Bi Changhao	2004F	PhD	Dr. James F. Preston, III
Brett Kirkland	2004F	PhD	Dr. Nemat O Keyhani
Elliot Miller	2004F	PhD	Dr. Lonnie O. Ingram
Anderson, Jessica	2005F	PhD	Dr. Eric W. Triplett
Defraia, Christopher	2005F	PhD	Dr. Eric W. Triplett
Millwood, Mary	2005F	PhD	Dr. Madeline E. Rasche
Perez-Gedes, Claudia	2005F	PhD	Dr. Julie A. Maupin-Furlow

Post-Docs and Research Faculty Support

The Center supported the following post-docs and research faculty members:

Name	Degree/Position	Mentor/Lab
Shengde Zhou	Research Faculty	Dr. Lonnie O. Ingram
Bohannon-Grabar	Post-Doc	Dr. Lonnie O. Ingram
Eun Min Cho	Post-Doc	Dr. Nemat Keyhani
Eva Czarnecka-Verner	Research Faculty	Dr. William B. Gurley
Rhee, Mun	Post-Doc	Dr. KT Shanmugam
Kevin O’Grady	Post-Doc	Dr. William B. Gurley
Guang Nong	Post-Doc	Dr. James F. Preston, III
Virginia Chow	Post-Doc	Dr. James F. Preston, III
Ivanka Karadzik	Post-Doc	Dr. Julie A. Maupin-Furlow
Rosana De Castro	Assist. Professor*	Dr. Julie A. Maupin-Furlow

*Visiting Fulbright Scholar, Instituto de Investigaciones Biológicas, Facultad de Ciencias
Exactas y Naturales, Universidad Nacional de Mar del Plata, Argentina).

Patents and Publications

Patents

Approved Patent 2005

Patent
Number

Date
Approved

Country

Authors

Title

6,849,434 B2

02/01/2005

U.S.A
Lonnie O. Ingram,
Maria Barbosa-Alleyne Ethanol Production by Recombinant Hosts

Pending US Patents (18):

Application Number	Date Submitted	Authors	Title
60/620,594	10/20/04	Lonnie O. Ingram, KT Shanmugam, JC Moore, Z Wu	Enhanced electrical contact to microbes in microbial fuel cells.
60/424,372	11/06/02	Lonnie O. Ingram, Thomas B. Causey, Shengde Zhou, K. T. Shanmugam	Materials and Methods for the Efficient Production of Acetate and other Products
10/003,741	11/02/02	Lonnie O. Ingram, Jacob L. Snoep, Nico Arfman	Recombinant Glucose Uptake System
60/418,069	10/11/02	Lonnie O. Ingram, Shengde Zhou, Thomas B. Causey, K . T. Shanmugam	Mutation to Increase Production of Fermentation Products
60/378,143	05/13/02	Adnan Hasona, K. T. Shanmugam, Lonnie O. Ingram	Novel Pseudomonas putida EstZ Esterase Gene and Uses Thereof
10/136,960	04/30/02	Julie A. Maupin-Furlow, Lee Ann Talarico, Krishnan Chandra Raj, Lonnie O. Ingram	Cloning and Sequencing of Pyruvate Decaroxylase (pdc) Genes from Bacteria and Uses Thereof
08/834,900	04/16/02	Lonnie O. Ingram, Lorraine Yomano, Sean York	Development of High-Ethanol Resistant Escherichia coli
10/001,218	11/30/01	Lonnie O. Ingram, Maria Barbosa-Alleyne	Ethanol Production in Gram-Positive Microbes
09/885,297	06/19/01	Shengde Zhou, Lonnie O. Ingram	Methods and Compositions for Simultaneous Saccharification and Fermentation
09/885,294	06/19/01	Lonnie O.

Date and Place

Topic