Progress Report

The Florida Center for Renewable

Chemicals and Fuels (FCRC)

July 2004- June 2005

 

Text Box: Department of  Microbiology and Cell Science 
          

 

CONTACT INFORMATION

 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.

27th 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 Haloferaxvolcanii. 

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

14th 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.

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

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. 

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

 

5th 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. 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
 

 

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

 

 

 

 

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 (3)

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

 

 

 

Publications

In Press

Gutierrez, T., L.O. Ingram, and J.F. Preston. 2005. Purification and characterization of a furfural reductase (FFR) from Escherichia coli stain LY01: an enzyme important in the detoxification of furfural during ethanol production. J. Biotechnol. In Press.

Rosana E. De Castro, Julie A. Maupin-Furlow, María Inés Giménez, María Karina Herrera Seitz, and Jorge J. Sánchez. 2006. Haloarchaeal proteases and proteolytic systems. FEMS Microbiol. Rev. (in press).

Maupin-Furlow, J. A., M. A. Gil, P. A. Kirkland, M. A. Humbard, C. J. Reuter, and A. J. Wright. 2006. Proteasomes and other nanocompartmentalized proteases. J. M. Shively (ed.) Springer-Verlag. Microbiology Monographs: Complex Intracellular Structures in Prokaryotes (in press).

Maupin-Furlow, J. A., M. A. Gil, P. A. Kirkland, M. A. Humbard, W. Li, C. J. Reuter, and A. J. Wright. 2005. Archaeal proteasomes and other regulatory proteases. Curr. Opin. Microbiol. 8: (in press).

Patel, M., M. Ou, L.O. Ingram and K.T. Shanmugam. 2005. Simultaneous saccharification and fermentation of crystalline cellulose and sugar cane bagasse hemicellulose hydrolysate to lactate by a thermotolerant acidophilic Bacillus sp. Biotechnol. Prog. (In Press).

Talarico, L. A., M. A. Gil, L. O. Ingram, and J. A. Maupin-Furlow. 2005. Construction and expression of ethanol production operon in gram-positive bacteria. Microbiology (in press).

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. (In Press).

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 (In Press)

Kirkland, P. A., J. Busby, S. Stevens, and J. A. Maupin-Furlow. 2005. Advances in Isoelectric Focusing of Halophilic Proteins. Anal. Biochem. (submitted).

 

Published

     Chapters/Review:

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.

     Journals:

Cirz RT, JK Chin, DR Andres, V. de Crecy-Lagard, WA Craig, and FE Romesberg. 2005. Inhibition of mutation and combating the evolution of antibiotic resistance. PLoS Biol. 2005 Jun;3(6):e176. Epub 2005 May 10.

Van Lanen, SG., JS Reader, MA Swairjo, V de Crecy-Lagard, B Lee, D Iwata-Reuyl. 2005. From cyclohydrolase to oxidoreductase: discovery of nitrile reductase activity in a common fold. Proc Natl Acad Sci U S A. 2005 Mar 22;102(12):4264-9. Epub 2005 Mar 14.

Bacher, JM., V de Crecy-Lagard and PR Schimmel. 2005. Inhibited cell growth and protein functional changes from an editing-defective tRNA synthetase. Proc Natl Acad Sci U S A. 2005 Feb 1;102(5):1697-701. Epub 2005 Jan 12.

Tao, Han, Adnan Hasona, Phi Min Do, L.O. Ingram and K.T. Shanmugam. 2005. Global gene expression analysis revealed an unsuspected deo operon under the control of molybdate sensor, ModE protein, in Escherichia coli. Arch Microbiol. 184:225-233.

Metzgar D., JM Bacher, V Pezo, J Reader, V Doring, P Schimmel, P Marliere, and V. de Credy-Lagard. 3005. Acinetobacter sp. ADP1: an ideal model organism for genetic analysis and genome engineering. Nucleic Acids Res. 2004 Oct 28;32(19):5780-90.

Gorsjean, H., V de Crecy-Lagard, and GR Bjork. 2005. Aminoacylation of the anticodon stem by a tRNA-synthetase paralog: relic of an ancient code? Trends Biochem Sci. 2004 Oct;29(10):519-22.

Chistoserdova, L.*, Rasche, M.E., and Lidstrom, M.E. 2005. Novel tetrahydromethanopterin biosynthesis genes discovered via mutagenesis in Methylobacterium extorquens AM1. J. Bacteriol. 187: 2508-2512.

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

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(4):501–508, 2005.

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.

Karadzic, I. M. and J. A. Maupin-Furlow. 2005. Improvement of two-dimensional gel electrophoresis proteome maps of the haloarchaeon Haloferax volcanii. Proteomics 5:354-359.

Kaczowka, S. J., C. J. Reuter, L. A. Talarico and J. A. Maupin-Furlow. 2005. Recombinant production of Zymomonas mobilis pyruvate decarboxylase in the haloarchaeon Haloferax volcanii. Archaea 1:327-34.

Purvis J.E., L.P. Yomano, and L.O. Ingram. 2005. Enhanced trehalose productionimproves growth of Echerichia coli under osmotic stress. Appl. Envir. Microbiol. 200571: 3761-3769.

Kima, P.E.*, Rasche, M.E. 2004. Sex determination using the polymerase chain reaction. Biochem. and Molecular Biology Educ. 32:115-119.

Maupin-Furlow, J. A., M. A. Gil, I. M. Karadzic, P. A. Kirkland, and C. J. Reuter. 2004. Proteasomes: perspectives from the archaea [update 2004]. Front Biosci. 9:1743-1758.

Maupin-Furlow, J. A., S. J. Kaczowka, C. J. Reuter, K. Zuobi-Hasona, and M. A. Gil.Reuter, C. J., S. J. Kaczowka and J. A. Maupin-Furlow. 2004. Differential regulation of PanA and PanB proteasome-activating nucleotidase and 20S proteasome proteins of the haloarchaeon Haloferax volcanii. J. Bacteriol. 186:7763-7772.

Reuter, C. J. and J. A. Maupin-Furlow. 2004. Analysis of proteasome-dependent proteolysis in Haloferax volcanii cells using short-lived green fluorescent proteins. Appl Envir. Microbiol. 70:7530-7538.

Rasche, M. E.*, Wyles, S. A., and Rosenzvaig, M. 2004. Characterization of two methanopterin biosynthesis mutants of Methylobacterium extorquens by use of a tetrahydromethanopterin bioassay. J. Bacteriol. 186:1565-1570.

Rasche, M. E.* 2004. Outcomes of a research-driven laboratory and literature course designed to enhance undergraduate contributions to original research. Biochem. and Molecular Biology Educ. 32:101-107.

Self, W.T., A. Hasona and K.T. Shanmugam. 2004. Expression and regulation of a silent operon, hyf, coding for hydrogenase 4 isoenzyme in Escherichia coli. J. Bacteriology. 186:580-58

 

 

On-Going Research Projects

Twenty three (22) grants and contracts with a total awarded amount of $7,936,199 were conducted for the year 2004-2005. Of these, 14 were new grant awards.

Investigator(s) Sponsor Duration Amount Project Title
Valerie de Crecy-Lagard NSF National Science Foundation 08/04/2004- 03/31/2006

 $83,308

 Elimination of canonical amino acids from Escherichia coli.
Samuel R. Farrah Orange County 10/01/2003-09/30/2005

 $59,100

Virus monitoring of effluent from joint facility.
NSF National Science Foundation 09/01/2002-   08/31/2005

$25,000

Surface modification for advancing response processes and environmental protection.
 Lonnie O. Ingram

 

US Department of Energy 09/01/2004– 06/30/2006

$200,000

Genetic improvement of Escherichia coli for fuel ethanol production.
U.S. Department of Agriculture/Coop SRS 09/01/2001– 08/31/2005

$300,000

Engineering bacteria for fuel ethanol production.
U.S. Department of Energy 07/01/1996- 06/30/2005 $1,300,000

Ethanol tolerant biocatalysts for fuel ethanol production./Genetic improvement of Escherichia coli for fuel ethanol production.

MBI International 07/01/2004-06/30/2005

$50,000

Optimization of AFEX treatments for the conversion of lignocellulosic materials to fuel ethanol.

BCI, Inc. 03/01/2005-02/28/2006

$250,000

 BCI Sponsored Ethanol Research
BioEnergy LLC 04/01/2005-03/31/2007

 $100,000

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

Lonnie O. Ingram,
William.B. Gurley,

Nemat O. Keyhani,
Shouguang Jin

U.S. Department of Defense, DARPA (*Defense Advanced Research Projects Agency)

06/01/2002 – 03/31/2006 $1,088,424 Sentinel plants utilizing bacterial two-component signaling pathways.
Lonnie O. Ingram, K.T. Shanmugam Biotechnology Research and Development Corporation (BRDC) 10/01/2003 – 09/30/2006

$400,000

. Acid tolerant biocatalysts.
Nemat O. Keyhani NSF 10/01/2004-09/30/2006

$173,179

Comparative analysis of in vivo-and in-vitro transcripts.
Julie A. Maupin-Furlow NIH National Institute of Health 04/01/2005 – 03/31/2010 $1,054,850 Physiology of proteosomes in Haloferax volcanii
US Department of Energy Biosciences 06/01/2005 – 05/31/2008

$360,000

dentification of Proteasome Substrates of Haloferax volcanii.

J.F. Preston, P.I.; D.W. Dickson, K.T. Shanmugam, and R.M. Giblin-Davis

 

U. S. Department of Agriculture, T-STAR 09/15/2002 – 09/14//2005

09/01/2004-
08/31/2005

$80,813

 $41,598

The Genome of Pasteuria penetrans: a Blueprint for Developing Pasteuria spp. for the Biocontrol of Plant-parasitic Nematodes

 

J.F. Preston Emory University (NIH) 09/19/2003-08/31/2006 $72,750 Biofilm Formation and Dispersal Mechanisms.
J.F. Preston, PI; K.T. Shanmugam and L.O. Ingram CPBR 08/01/2004-07/31/2006 $279,946 Bacterial Conversion of hemicellulose to ethanol.
Madeline E. Rasche National Science Foundation 12/01/2004-12/31/2008

$608,152

 Methanopterin biosynthesis in archaea and methylotropic bacteria.
K.T. Shanmugam subcontractor to Benemann Associates (U. S. Department of Energy) 07/14/2004-03/31/2005 $30,000 Engineering thermotolerant biocatlysts for biomass conversion to products.
 K.T. Shanmugam U. S. Department of Energy, Golden Office 04/01/2004-03/31/2007 $956,801 Engineering thermotolerant biocatalysts for biomas conversion to fuels and chemicals.
E.W. Triplett  NSF 11/01/2003-10/31/2005 $275,567 A microbial observatory of the North Temperate Lakes.
E.W. Triplett TIGR 10/01/2004-09/30/2006 $146,711 Genome sequencing of nitrogen-fixing bacterial endophytes.

 

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 (then Dean of CALS)
  • Dr. Mark McLellan, Dean for Research and Director, FAES
  • Dr. E. Jane Luzar, Associate Dean for Academic Programs and the College of Agriculture and Life Sciences
  • Dr. Eric W. Triplett, Chair, Department of Microbiology and Cell Science

  • GRANTING AGENCIES:
             
             BCI
             BIOENERGY (Bionol)
             Biotechnology Research and Development
                   Corporation (BRDC)                                   
             Consortium for Plant Biotechnology, Inc. (CPBR)     
             Defense Advanced Research Project Agency
                   (DARPA/USDD)
             MBI International   
             National Institutes of Health
             National Science Foundation
             Orange County, Florida
             US Department of Agriculture
             US Department of Energy