TABLE OF CONTENTS
 

                              Table of Contents ……………………………………………………….   1

                        Introduction ……………………………………………………………..   2

                              Faculty Members and Staff …………………………………...……..   2

                        Research Scientists and Post-Docs ……………………………...…..   3

                        Graduate Research Trainees …………………...…………………….   3

                              Conferences, Seminars, Workshops …………………………………….   4-7       

                        Service …………....……………………………………………………..   8-9

                              Awards ………………………………………………………………..  10

                        Patents ……………….. ………………………………………………  11-14

                              Approved ……………………………………………...…..  11

                              Pending US Patents ………………………………………..  11-12

                              Pending International Patents ……………………………...  12-13

                              Invention Disclosures ………….…………………………..  14

                        Publications …………………………………………………….…...  14-18

                                      In Press ………………………………………………...….  14

                                      Published     Chapter Review ……………………………… 14-15

                                      Journals ……………………………………...................…. 15-18

                         On-Going Research ……………………………………………………...  19-22

                              Acknowledgments ……………………………………………………….  23

                        Contact Information …………………………………………………….   24         

 

 

 

 

 

 

Introduction

 

            The Florida Center for Renewable Chemicals and Fuels (FCRC) was established five years ago in response to the country’s need for fuels and chemicals from renewable resources instead of petroleum which is largely imported.  FCRC provides a venue for research and graduate training in the multidisciplinary areas in the production of chemicals and fuels from biomass, and the improvement of biomass as a biorefinery feedstock.       

            Research and graduate training 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.

           

  Faculty and Staff

 The Center has 10 in-house faculty members, 2 from other departments and colleges, and 1 from the University of North Florida. A total of 11 post-docs and 10 technical assistants presently devote 100% of their time to research, the areas of which are also shown below.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Adjunct Faculty:     David Beall, University of North Florida

 

 

 

 

 

 

 

 

 

Gary Peter, Assoc Professor, School of Forest Research &. Conservation

 Shouguang Jin, Assoc Professor, UF College of Medicine

 

Research Scientists and Post-Doctoral Associates:

 

Name	Degree/Position	Mentor/Lab
Bohannon-Grabar	Post-Doc	Dr. Lonnie O. Ingram
Eun Min Cho	Post-Doc	Dr. Nemat Keyhani
Virginia Chow	Post-Doc	Dr. James F. Preston, III
Eva Czarnecka-Verner	Research Faculty	Dr. William B. Gurley
Basma El-Yacoubi	Post-Doc	Dr. Valerie De Crecy-Lagard
Kevin O’Grady	Post-Doc	Dr. William B. Gurley
Guang Nong	Post-Doc	Dr. James F. Preston, III
Xueli Zhang	Post-Doc	Dr. Lonnie O. Ingram
Guanyin Zhou	Post-doc	Dr. Julie Maupin-Furlow

 

 

Graduate Trainees:

Conferences, Seminars, and Workshops

 

n-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. Starting Spring of 2006, graduate and laboratory seminars were opened for participation to the whole department.

 

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  

Attendees/Poster Presenters/Speakers * - graduate student; **- post-doc ***- undergrad student	Conference/Seminar/ Workshop	Date and Place	Topic
V. de CrecyLagard	Beilstein Workshop	March 19-23 2006 Rudesheim/Rhein Germany	Experimental Standard Conditions on Enzyme charcterizations
	ASM General conference	May 21-25 2006 Orlando Florida
	FASEB conference Nucleic Acids -	June 10-15 Vermont
Samuel R. Farrah    Johnny Davis*    George Lukasik***	Florida Branch ASM	March 31, 2006 Cocoa  Beach, FL
	106th General Meeting of the American Society for Microbiology	May 21-25, 2006  Orlando, FL
W.B. Gurley	Plant Molecular and Cellular Biology Annual Workshop	May 12-13, 2006. Jacksonville, FL
LO Ingram                                     L O Ingram	NAS US DOE Advisory Group Meeting	July 5-6, 2005 Gaithersburg, MD	Future Research Efforts  in Biosciences
	BCI Meeting	July 6-7, 2005 Boston, MA	Goals and projects to be performed under the BCI-UFRFI Sponsored Research Agreement
	Gordon Research Conference on Applied and Environmental Microbiology	July 24-29, 2005 New  London,  CT	Redesigning E. coli for Renewable Chemicals and Fuels
	12th European Congress on Biotechnology	August 21-24, 2005 Copenhagen, Denmark
	CERES	Nov 8, 2005 LA, CA	Metabolic advances in engineering
	CALTECH	Nov. 9, 2005 Pasadena, CA	Engineering microbial metabolism: fuels and chemicals from lignocellulose.
	DOE Biomass Energy Workshop	December 7-8, 2005 Rockville, MD	Working Group 3 - Conversion
	Meeting with Rep. Grimsley:	Feb. 7-8, 2006 Tallahassee, FL	Accelerating the development of renewable fuels in florida by building an ethanol plant or pilot plant that uses inedible ag and forest residues and MSW waste as a feedstock.
	UF FAES	Feb. 16, 2006 Balm, FL	Biomass Plant Facility - Ethanol
	Amyris Biotecnologies First SAB Meeting	Feb. 22-24, 2006 San Francisco, CA	Consultations and Seminar:  Ethanol from Bomass
	UF –Lecture	March 7, 2006	Fueling Florida’s Future with Ethanol from Biomass.
	AAM-ASM Colloqium	March 9-11, 2006 San Francisco, CA	Committee Meeting and Seminars
	John gray fund for Excellence in Forest Resources and conservation	March 28, 2006; UF	Convener: Research Needs in Biomass and Bioenergy.
	Ist annual JGI Users Meeting	March 29-April 1, 2006 Walnut Creek, CA
	Bio-Energy Network Meeting	April 18, 2006 Ben Hill Griffin Stadium, UF	Commercial Fuel ethanol from lignocellulose.
	2006 Florida Citrus Growers Institute	April 26, 2006 Lake Wales, FL	Speaker: Biofuels in Florida	In-State		Speaker: Biofuels in Florida
	Meeting with CONOCO	May 5, 2006 Houston, TX	Consultancy; seminar		Industry: Biomass to ethanol.
	Florida Crystal Sugar	May 9, 2006 Okeelanta, FL	Consultancy, seminar		Industry – ethanol plant
	Lykes Brothers	May 10, 2006 MCS, UF	Consultancy, seminar		Industry
	UF Energy Working Group	May 15, 2006 UF Grinter Hall	Meeting		UF Energy Expertise
	ASM 106th General Meeting Jonathan Moore* Elliott Miller* Xueli Zhang**	May 23, 2006 Orlando, FL	Microbial Production of Energy		Microbial Production of Energy
	Meeting with BP	June 8-9, 2006 Chicago, IL	Consultancy		Biomass to ethanol
	Meeting with Congressman Putnam	June 13, 2006 Washington, DC	Florida: Biomass to Ethanol		Biomass to ethanol
N. O. Kayhani
JA Maupin- Furlow	Annual Meeting - Branch of the American Society for Microbiology	October 27 – 29, 2005:	Organized and convened session on Extremophiles.
JF Preston, III
ME Rasche	2006 Gordon Conference on the Molecular Basis of Microbial One-Carbon Metabolism,	August 6-11, 2007, Magdalen College, Oxford, England	Discussion Leader for Session on “Methanogenesis”.  Elected to be Vice Chair of Gordon Conference for 2008 and Chair for 2010.
KT Shanmugam
E.W. Triplett	Legume Genomics Meeting	April 12, 2006 Brisbane, Australia
	Genomics of Nitrogen-Fixing Organisms	July 22, 2006 Aarhus, Denmark
	Nitrogen Fixation with Non-Legumes	July 26, 2006 Aarhus, Denmark
	The Bean-Lotus Genomic Interface	July 26, 2006 Aarhus, Denmark
	ASM Annual Meeting	May 21-25, 2006 Orlando, FL

 

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
		Society of Industrial Microbiology and Biotechnology, 2001-present
	Member	U.S. National Academy of Sciences, 2001-present
	Editorial Board	Biotechnology Letters 1996-present
		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.
Madeline E. Rasche	Graduate Coordinator	Microbiology and Cell Science Department 2005 - 2006
	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
Kirkland, P. A.* and J. A. Maupin-Furlow.	SEB ASM Student Travel Award	St. Petersburg, FL. 2005.	Ann. Mtg. SE Branch Amer. Soc. Microbiol.
Reuter, C. J.* and J. A. Maupin-Furlow.	SEB ASM Student Travel Award	St..Petersburg, FL. 2005	Ann. Mtg. SE Branch Amer. Soc. Microbiol.
Humbard, M. A.*, Zuobi-Hasona, K.**, and J. A. Maupin-Furlow.  .	SEB ASM Student Travel Award	St..Petersburg, FL. 2005	Ann. Mtg. SE Branch Amer. Soc. Microbiol
Elliot Miller (Poster Presentation)	Grad Student Council Travel Award		ASM General Meeting
Jonathan Moore	IFAS $200 Travel Grant

 

 *Grad Student** Post-Doc

Patents and Publications

 

Patents

New Approved Patents:

 

Patent Number	Date Approved	Country	Authors	Title
7,026,152 B2	04/11/06	U.S.A	Lonnie O. Ingram,  Shengde Zhou	Method and compositions fir simultaneous saccharification and fermentation

 

 

 

 Pending US Patents (19):

 

Application Number	Date Submitted	Authors	Title
60/796,652	05/01/06	KT Shanmugam, LO Ingram, Y Kim,	Ethanol production in non-recombinant hosts
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-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
09/885,294	06/19/01	Lonnie O. Ingram, Stuart Underwood	Methods for Improving Cell Growth and Alcohol Production During Fermentation.
60/288,699	05/04/01	Lonnie O. Ingram, Chanda Raj Krishan, Julie A. Maupin-Furlow	Pyruvate Decarboxylase: A Key Enzyme for the Oxidative Metabolism of Lactic Acid by Acetobacter pasteurianus
60/288,698	05/04/01	Lonnie O. Ingram, Chandra Raj Krishan, Julie A. Maupin-Furlow	Acetobacter Patstuerianus Pyruvate Decarboxylase: Biochemical, Genetic, and Physiological Properties
60/288,671	05/04/01	Lonnie O. Ingram, Lee Ann Talarico, Julie A. Maupin--Furlow	Cloning, Expression, and Characterization of Pyruvate Decarboxylase fro the Acod Tolerant, Anaerobic Gram-Positive Bacteriun Sarcinia ventriculi Goodsir
60/288,638	05/04/01	Lee Ann Talarico, Lonnie O. Ingram, Julie A. Maupin-Furlow	High-level Production of Active  Sarcina ventriculi Pyruvate Decarboxylase in Recombinant Bacillus megaterium
60/288,622	05/04/01	Chandra Raj Krishan, Lonnie O. Ingram, Julie A. Maupin-Furlow	Biochemical and Biophysical characterization of Pyruvate Decarboxylase from the Acetic Acid Bacterium Acetobacter pastuerianus
UF 11469	03/02/05	K.T. Shanmugam, Lonnie O. Ingram, Milind Paetel, Mark Ou, Roberta Harbucker	Production of Chemicals from Lignocellulose, Biomass or Sugars.
UF 11804	09/19/05	Patrick Cirino, Lonnie O. Ingram	Materials and Methods for Efficient Production of Xylitol
UF  11819	08/10/05	Shengde Zhou, Lonnie O. Ingram, K.T Shanmugam, Lorraine Yomano	Materials and Methods for Efficient Lactic Acid production
UF  12023	11/08/05	LO Ingram, KT Shanmugam, S Zhou, TB Causey, LP Yomano, TB Grabar	Materials and Methods for Improved Production of Organic Compounds.

 

 

 

Pending International Patents (17):

 

Application Number	Date Submitted	Country	Authors	Title
P 02 01 01630   073450   PCT/US02/15038	05/03/02   05/02/02   04/29/02	Argentina   Thailand   PCT	Julie A. Maupin-Furlow Lee Ann Talarico, Krishnan Chandra Raj, Lonnie O. Ingram	Cloning and Sequencing of Pyruvate Decarboxylase(PDC) Genes from Bacteria and Uses Thereof
P 01 01 03040   066460   PCT/US01/19690           0946576.4-4-2405-US0119690	06/26/01   06/22/01   06/19/01   06/19/01   06/19/01     06/19/01   06/19/01   06/19/01	Argentina   Thailand   PCT   Canada   EPO     China   Korea   Vietnam	Shengde Zhou, Lonnie O. Ingram               Shengde Zhou, Lonnie O. Ingram	Methods and Compositions for Simultaneous Saccharification and Fermentation       Methods and Compositions for Simultaneous Saccharification and Fermentation
066459       PCT/US01/19641	06/22/01       06/19/01	Thailand   Argentina   PCT	Lonnie O. Ingram, Stuart Underwood	Methods for Improving Cell Growth and Alcohol Production During Fermentation.
02106753.2   IN/PCT/01/01804/CHE   W-00100102740	09/13/02   12/21/01     12/11/01	Hongkong   India     Indonesia	Lonnie O. Ingram, Shengde Zhou	Recombinant Hosts suitable for simultaneous Saccharification and Fermentation

 

 

Invention Disclosures (7)

 

UF Number	Date Filed	Title	Authors
UF-11645	July 27, 2004	Enhanced Electrical Contact to Microbes in Microbial fuel Cells	Andrew Rinzler, LO Ingram, JC Moore, KT Shanmugam, Z Wu
UF-11799	Feb 22, 2005	Improved Klebsiella oxytoca For Ethanol Production And E. coli Strains Engineered To Produce Xylitol From Xylose.	Lonnie O. Ingram, Patrick C. Cirino, Brent E. Wood, Lorraine P. Yomano, Sean York
UF-11818	March 2, 2005	Ethanol Production in Minimal Medium	Lonnie O. Ingram, Lorraine  P. Yomano, Sean W. York
UF-11799	September 13, 2005	Improved Klebsiella oxytoca for ethanol production.	Lonnie O. Ingram, Brent E. Wood, Lorraine P. Yomano, Sean W. York
UF- 1031	October 2005	Mutations in Escherichia coli that increase the efficiency of production of chemicals from sugars.	LO Ingram, TB Causey, S Zhou, KT Shanmugam
UF-12010	October 3, 2005	Non-recombinant ethanologenic Escherichia coli mutant for fermentation of lignocellulose.	KT Shanmugam, Lonnie O. Ingram, Youngyun Kim
UF- 12126	October 2005	Strain TG114- Methylglyoxal bypass source of chiral contamination in lactate  produced by recombinant Escherichia coli.	LO Ingram, LP Yomano, TB GrabarKT Shanmugam, S Zhou

 

 

 

Publications

In Press

 

Kirkland, P. A.², C. J. Reuter², and J. A. Maupin-Furlow¹*. 2006. Effect of proteasome inhibitor clasto-lactacystin-β-lactone on the proteome of the haloarchaeon Haloferax volcanii (under review).

 

Miller, E.N. and L.O. Ingram. 2006. Combined effect of betaine and trehalose on osmotic tolerance of Escherichia coli in mineral salts medium. (Accepted)

 

Cirino, P.C., J.W. Chin and L.O. Ingram. 2006. Engineering Washerichia coli for xylitol production from glucose-xylose mixtures. Biotechnology and Bioengineering. (Accepted).

           

Kim, Youngyun, L.O. Ingram, and K.T. Shanmugam. 2006. Fermentation of glucose and xylose            to ethannol by a  non-recombinant ethanologenic Escherichia coli. Appl. Environ.             Microbiol. (In Press).

 

 

Published

 

Chapters/Reviews

 

Maupin-Furlow, J. A.¹*, M. A. Humbard², P. A. Kirkland², W. Li², C. J. Reuter², A. J. Wright², and G. Zhou². 2006.  Proteasomes from structure to function: perspectives from archaea.  Curr. Top. Dev. Biol. 75: 125-169 (front cover photo).

 

Maupin-Furlow, J. A. ¹*, M. A. Gil², M. A. Humbard², P. A. Kirkland², W. Li², C. J. Reuter², and A. J. Wright². 2006.  Proteasomes and other nanocompartmentalized proteases in archaea.  J. M. Shively (ed.) Springer-Verlag.  Microbiology Monographs:  Complex Intracellular Structures in Prokaryotes pp. 23 – 46.

 

De Castro, R. E.¹*, J. A. Maupin-Furlow, M. I. Giménez, M. K. Herrera Seitz, and J. J. Sánchez. 2006. Haloarchaeal proteases and proteolytic systems. FEMS Microbiol. Rev. 30:17-35.

 

Rasche, M. E., and J. G. Ferry. 2005. Molecular Biology of Methanogens and Archaebacteria, 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. (Review

           

Journals

 

DeCrecy-Lagard:

Overbeek, R.; Begley, T.; Butler, R. M.; Choudhuri, J. V.; Chuang, H. Y.; Cohoon, M.; de Crecy-Lagard, and coll. 2005. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res, 33 : 5691-702.

 

Swairjo, M. A.; Reddy, R. P.; Lee, B.; Van Lanen, S. G.; Brown, A.; de Crécy Lagard, V.; Iwata_Reuyl, D.; Schimmel, P., 200., Crystallization and preliminary X-ray characterization of the nitrile reductase QueF- a queuosine biosynthesis enzyme. Acta Crystallogr D Biol Crystallogr F61, 945-948.

 

Waas, W. F.; de Crécy-Lagard, V.; Schimmel, P., 2005. Discovery of a gene family critical to wyosine base formation in a subset of phenylalanine-specific transfer RNAs. J Biol Chem, 280, (45), 37616-22.

 

Reader J. S., Ordoukhanian P. T., Kim J. G., de Crécy-Lagard V., Hwang I., Farrand S., Schimmel P. 2005. Major biocontrol of plant tumors targets tRNA synthetase. Science. 309:1533.

 

Farrah:

Harwood, V.J., A.D. Levine, T.M. Scott, V. Chivukula, J. Lukasik, S.R. Farrah, and J.B. Rose.  2005.  Validity of the indicator organism paradigm for pathogen reduction in reclaimed water and public health protection.  Appl. Environ. Microbiol. 71:3163-3170.

 

Parveen, S., J. Lukasik, T.M. Scott, M.L. Tamplin, K.M. Portier, S. Sheperd, K. Braun and S.R. Farrah.  2005. Geographical variation in antibiotic resistance profiles of Escherichia coli from swine, poultry, beef and dairy cattle farm water retention ponds in Florida.  J. Appl. Microbiol. 100:50-57.

 

Kim, Yun-mi, S. Farrah and R.H. Baney.  2006.  Silanol 0 a novel class of antimicrobial agent.  Electronic J. of Biotechnology  Vol. 9, No. 2.

 

Gurley:

Sehnke, P. C., Laughner, B. J., Lyerly Linebarger, C. R., Gurley, W. B. and Ferl, R. J. 2005 Identification and characterization of GIP1, an Arabidopsis thaliana protein that enhances the DNA binding affinity and reduces the oligomeric state of G-box binding factors.
Cell Res. 5:567-75.

 

Friedberg1, J. N., Bowley, S. R., Bryan D. McKersie, B. D., Gurley, W. B. and Czarnecka-Verner, E. (2006) Isolation and characterization of class A4 heat shock transcription factor from alfalfa. Plant Sci. 171: 332-344. (NOTE: This was published August, 2006)

 

Ingram:

Grabar, T. B. S. Zhou, K. T. Shanmugam, L. P. Yomano, & L. O. Ingram. 2006. Methylglyoxal Bypass identified as Source of Chiral Contamination in L(+) and D(-) Lactate Fermentations by Recombinant Escherichia coli. Bioytechnology Letters 28:1527-1535.

 

Zhou, S., T.B. Grabar, K.T. Shanmugam and L.O. Ingram. 2006. Betaine tripled the volumetric productivity of D(-)-lactate by Escherichia coli strain SZ132 in mineral salts medium. Biotechnology Letters. 28(9): 671-676

 

Zhou, S., K. T. Shanmugam, L. P. Yomano, T. B. Grabar and L. O. Ingram. 2006. Fermentation of 12% (w/v) Glucose to 1.2 m Lactate by Escherichia coli Strain SZ194 using Mineral Salts Medium. Biotechnology Letters. 28(9): 663-670

 

Zhou, S., L.P. Yomano, K.T. Shanmugam, and L.O. Ingram. 2005. Fermentation of 10% (w/v) sugar to D(-)-lactate by engineered Escherichia coli B. Biotechnology Letters. 27: 1891-1896.

 

Wood, B.E., L.P. Yomano, S.W. York, and L.O. Ingram. 2005. Development of industrial-medium-required elimination of the 2,3 butanediol fermentation pathway to maintain ethanol yield in an ethanologenic strain if Klebsiella oxytoca. Biotech. Prog.21: 1366-1372.

 

 

Maupin-Furlow:

Humbard, M. A.², S. Stevens Jr., and J. A. Maupin-Furlow¹*. 2006.  Post-translational modification of the 20S proteasomal proteins of the archaeon Haloferax volcanii.  J. Bacteriol. [Epub ahead of print].

 

Dinitz-Bab, E., H. Shmuely, J. Maupin-Furlow, J. Eichler and B. Shaanan¹*. 2006.  Haloferax volcanii PitA:  An example of functional interaction between the Pfam chlorite dismutase and antibiotic biosynthesis monooxygenase families?  Bioinformatics 22:671-675.

 

Kirkland, P. A.², J. Busby, S. Stevens, and J. A. Maupin-Furlow¹*. 2006.  Trizol-based method for sample preparation and isoelectric focusing of halophilic proteins.  Anal. Biochem. 351: 254–259.

 

Talarico, L.A., M.A. Gil, L.O. Ingram, and J.A. Maupin-Furlow. 2005. Construction and expression of an ethanol production operon in gram-positive bacteria. Microbiology 151: 4023-4031.

 

Preston:

St. John, F. J., J.D. Rice, J. F. Preston. 2006. Characterization of XynC from Bacillus subtilis subspecies subtilis strain 168 and analysis of its role in depolymerization of glucuronoxylan. J. Bacteriol. In  Press

 

St. John, F. J., J.D. Rice, J. F. Preston. 2006. Paenibacillus sp. JDR-2 and XynA₁: a novel system for methylglucuronoxylan utilization. Appl. Environ. Microbiol. 72:1496-1506.

 

Gutierrez, T., L.O. Ingram, J.F. Preston. 2006. Purification and characterization of a furfural reductase (FFR) form Escherichia coli stain LYO1 - An enzyme important in the detoxification of furfural during ethanol production. J. Of Biotechnology. 121(2): 154-164.

 

El-Borai, F.E.,  L.W. Duncan, and J.F. Preston, 2005. Bionomics of a phoretic association between a putative Paenibacillus sp. and the entomopathogenic nematode Steinernema diaprepesi. J Nematol. 35:18-25.

 

Itoh, Y., X. Wang, B.J. Hinnebush, J.F. Preston, and T. Romeo. 2005. Depolymerization of  poly-β-1,6-N-acetyl-D-glucosamine disrupts the integrity of diverse bacterial biofilms. J. Bacteriol. 187:382-387.

 

Rasche:

Hamilton, R., Casasús, A., Rasche, M. Narang, A, Svoronos, S. A.*, and Koopman, B*. 2005.  A structured model for denitrifier diauxic growth.  Biotechnology and Bioengineering, 90:501–508

 

Shanmugam:

Patel, M., M. Ou, R. Harbucker, H.C. Aldrich, M.L. Buszko, L.O. Ingram, and K.T. Shanmugam. 2006. Isolation and charactrerization of acid-tolerant, thermophilic bacterial biocatalysts for effective fermentation of biomass-derived sugars to lactic acid. Appl and Environ. Microbiol. 72(5): 3228-3235.

 

Triplett:

Newton, R.J., A.D. Kent, E.W. Triplett, and K.D. McMahon.  2006.  Microbial community dynamics in a humic lake: differential persistence of common freshwater phylotypes. Environ. Microbiol. 8:956-970. 

 

Scupham, A.J. and E.W. Triplett.  2006.  Determination of amino acid residues required for the activity of the anti-rhizobial peptide antibiotic trifolitoxin. J. Appl. Microbiol. 100:500-507. 

 

Lau, H.-T., J. Faryna, and E.W. Triplett.  2006.  Aquitalea magnusonii gen. nov. sp. nov., a novel Gram-negative bacterium isolated from a humic lake. Int. J. Syst. Evol. Microbiol. 56:867-871.

 

Pongslip, N., E.W. Triplett, and M.J. Sadowsky.  2005. Detection of homoserine lactone-like quorum sensing molecules in Bradyrhizobium strains.  Current Microbiol. 51:250-254. 

Iniguez, A.L., Y. Dong., H.D. Carter, B.M.M. Ahmer, J.M. Stone, and E.W. Triplett.  2005. Regulation of enteric endophytic bacterial colonization by plant defenses.  Molecular Plant-Microbe Interactions 18:169-178.

 

 

 

 

 

On-Going Research Projects

 

Twenty four (24) grants and contracts with a total awarded amount of $9,574,250 were conducted for the year 2005-2006. An increase of $1,638,051 grant money was received from 7 are new grant awards.

 

1. Elimination of canonical amino acids from Escherichia coli.

            Investigator:      Valerie de Crecy-Lagard

            Sponsor:           NSF     National Science Foundation

Duration:          08/04/2004 – 03/31/2006

            Amount:           $83,308

 

2. From function to gene: tRNA modification in Archaea.

            Investigator:      Valerie de Crecy-Lagard

            Sponsor:           NSF     National Science Foundation

Duration:          08/01/2005– 07/31/2008

            Amount:           $477,810

 

3. Biosynthesis of hypermodified guanosines.

            Investigator:      Valerie de Crecy-Lagard

            Sponsor:           NIH     National Institutes of Health

Duration:          03/01/2006 – 02/28/2011

            Amount:           $1,275,604

 

4. Virus monitoring of effluent from joint facility

            Investigator:      Samuel R. Farrah

Sponsor:           Orange County

Duration:          10/01/2005-09/30/2006

            Amount:           $29,550

 

5. Surface modification for advancing response processes and environmental protection

            Investigator:      Samuel R. Farrah

            Sponsor:           NSF  National Science Foundation

Duration:          09/01/2002 – 08/31/2005

            Amount:           $25,000

 

6. Genetic improvement of Escherichia coli for fuel ethanol production.

            Investigator:      Lonnie O. Ingram

            Sponsor:           US Department of Energy

Duration:          097/01/2004 – 06/30/2009

            Amount:           $590,000

 

7. Engineering bacteria for fuel ethanol production.
            Investigator:      Lonnie O. Ingram        
            Sponsor:           U.S. Department of Agriculture/Coop SRS
            Duration:          09/01/2001 – 08/31/2005
            Amount:           $300,000

 

8. Sentinel plants utilizing bacterial two-component signaling pathways

            Investigators:    Lonnie O. Ingram,  William.B. Gurley,

Nemat O. Keyhani, Shouguang Jin

            Sponsor:           U.S. Department of Defense, DARPA (*Defense Advanced

Research Projects Agency)

Duration:          06/01/2002 – 03/31/2006
Amount:           $1,088,424

 

9. Acid tolerant biocatalysts
            Investigators:    Lonnie O. Ingram,   K.T. Shanmugam
            Sponsor:           Biotechnology Research and Development Corporation (BRDC)

Duration:          10/01/2003 – 09/30/2006

            Amount:           $400,000

 

10.  Celunol (formerly BCI) Sponsored Ethanol Research

            Investigator: Lonnie O. Ingram

            Sponsor: BCI

            Duration: 03/01/2006-03/01/2007

            Amount: $500,000

 

11. Production of organic acids, polymers, and sugar-based specialty chemicals.

            Investigator: Lonnie O. Ingram

            Sponsor: BioEnergy LLC

            Duration: 04/01/2005-03/31/2007

            Amount: $200,000

 

12. Comparative analysis of in vivo-and in-vitro transcripts.

            Investigator:      Nemat O. Keyhani

            Sponsor:           NSF

            Duration:          10/01/2004-09/30/2006

            Amount:           $173,179

 

13. Physiology of proteosomes in Haloferax volcanii

            Investigator:      Julie A. Maupin-Furlow

            Sponsor:           NIH     National Institute of Health

Duration:          04/01/2005 – 03/31/2009

            Amount:           $1,054,850

 

14. Identification of Proteasome Substrates of Haloferax volcanii

            Investigator:      Julie A. Maupin-Furlow

            Sponsor:           US Department of Energy Biosciences

            Duration:          06/01/2005 – 05/31/2008

            Amount:           $360,000

 

15. The Genome of Pasteuria penetrans: a Blueprint for Developing Pasteuria spp. for the

            Biocontrol of Plant-parasitic Nematodes

            Investigator:      J.F. Preston, P.I.; D.W. Dickson, K.T. Shanmugam, and

                                    R.M. Giblin-Davis, Co-PIs

            Sponsor:           U. S. Department of Agriculture, T-STAR

            Duration:          09/15/2002 – 09/14//2005; 09/01/2004- 08/31/2006

            Amount:           $80,813; $41,598

 

16. Biofilm Formation and Dispersal Mechanisms

            Investigator:      J.F. Preston, P.I; subcontractor

            Sponsor:           Emory University (NIH)

            Duration:          09/19/2003-08/31/2007

            Amount:           $72,750

 

 17. Bacterial Conversion of hemicellulose to ethanol

            Investigator:      J.F. Preston, PI; K.T. Shanmugam and L.O. Ingram, Co-PIs 

            Sponsor:           CPBR

            Duration:          08/01/2004-07/31/2006

            Amount:           $279,946

18. Direct conversion of hemicellulose to ethanol.

            Investigator:      J.F. Preston, III

                                    L.O. Ingram

            Sponsor:           CPBR Consortium for Plant Biotechnology

Duration:          07/01/2006 – 06/30/2008

            Amount:           $140,000

 

19. Methanopterin biosynthesis in archaea and methylotropic bacteria

            Investigator:      Madeline E. Rasche

            Sponsor:           National Science Foundation   

Duration:          12/01/2004-12/31/2008

            Amount:           $608,152

 

20. Engineering thermotolerant biocatlysts for  biomass conversion to products.

            Investigator:      K.T. Shanmugam PI Co-PIs

            Sponsor:           U. S. Department of Energy, Golden Office

            Duration:          04/01/2004-03/31/2007

            Amount:           $956,801

 

21. A microbial observatory of the North Temperate Lakes.

            Investigator:      E.W. Triplett PI

            Sponsor:           NSF

            Duration:          11/01/2003-10/31/2005

            Amount:           $275,567

 

22. Genome sequencing of nitrogen-fixing bacterial endophytes.             

            Investigator:      E.W. Triplett PI

            Sponsor:           TIGR

            Duration:          10/01/2004-09/30/2006

            Amount:           $146,711

 

23. MIP: Analysis of endophytic colonization by K. pneumonieae.

            Investigator:      Eric W. Triplett

            Sponsor:           NSF     National Science Foundation

Duration:          08/01/2005 – 07/31/2009

            Amount:           $335,000

 

24. Analysis of a novel mechanism of plant growth promotion.

            Investigator:      Eric W. Triplett

            Sponsor:           CPBR  Consortium for Plant Biotechnology

Duration:          08/01/2006– 07/31/2008

            Amount:           $160,000

 

                                                                                                                                      

Acknowledgments

 

 

The Center would like to acknowledge all of its supporters and sponsors:

 

UF/IFAS:   

Dr. Jimmy Cheek, Vice President for Agriculture and Natural Resources

  Dr. Mark McLellan, Dean for Research and Director, FAES

  Dr. R. Kirby Barrick, Dean for Academic Programs, College of Agriculture and            Life Sciences

                       Dr. Eric W. Triplett, Chair, Department of Microbiology and Cell Science

 

 

             

                Agency/Industry Sponsors: