Home     Publications           

 Progress Report

  

The Florida Center for Renewable
Chemicals and Fuels (FCRC)

 

July 2001- June 2003

 

University of Florida
Institute of Food and Agricultural Sciences
Microbiology & Cell Science Department
 

 

  

 

 

CONTACT INFORMATION
 



Dr. Lonnie O. Ingram
Director
Bldg. 981 Museum Road, PO Box 110700
Gainesville, Fl 32611-0700
Tel: (352) 392-8176; Fax: (352) 846-0969
 ingram@ufl.edu

  Dr. Keelnathan T. Shanmugam
Associate Director
Bldg. 981 Museum Road, PO Box 110700
Gainesville, Fl 32611-0700
Tel: (352) 392-2490; Fax: (352) 392-5922
 shan@ufl.edu

 Dr. Sheilachu P. Gomez
Assistant Director
Bldg. 981 Museum Road, PO Box 110700
Gainesville, Fl 32611-0700
Tel/Fax: (352) 392-00237
 spgomez@ufl.edu

 

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
 

Introduction

Conferences, Seminars, and Workshops
Service and Awards
Service
 Awards

Research Assistantships

Patents and Publications
Patents
Approved Patents
 US patent applications (16)
 International patent applications (17)

Publications
In Press
 Book Chapter
 Journal Articles
 Other Publications

On-Going Research Projects

Acknowledgments

 

 

 

Introduction
 

The Florida Center for Renewable Chemicals and Fuels (FCRC) was formally established in  2001 for the purpose of providing a focus for the multi-disciplinary education and research in this field. The main goal of FCRC is to contribute to the reduction of the nation’s dependence on imported petroleum through the production of chemicals and fuels from agricultural residues and other biomass.

 The FCRC seeks to discover and implement novel solutions to the conversion of biomass to chemicals and fuels using metabolically engineered bacteria. In addition, the FCRC coordinates bioproducts research by providing a liaison with granting agencies, assisting in the development of competitive grants, and by facilitating graduate education through graduate assistantships, seminar series featuring student and faculty researches. An added component of research on biosensors to detect harmful chemicals in the environment was initiated in the interest of national security.

 Conferences, Seminars, and Workshops

 The Center co-sponsored one regional and one national conference during the past three years. They are the Conference on Interfacing Microbiology and Biotechnology held at the University of Florida, Gainesville, FL on May 17-19, 2001, and the Annual Meeting of the American Society for Microbiology Southeastern Branch, at Gainesville, Florida, on November 7-9, 2002.

Local and in-house seminars presented by faculty members and visiting scientists during the period 2001 to 2003 include the following:   

Faculty Member/Visiting Scientist

Place and Date

Topic

James F. Preston, III

Department of Microbiology and Cell Science, September 3, 2001.

“Pasteuria Spp.: Endospore-Forming Bacterial Parasites Of Cladocerans And Phytopathogenic Nematodes”.

 

Department of Plant Pathology, January 14, 2003.

“Pasteuria Spp.: Endospore-Forming Bacterial Parasites Of Cladocerans And Phytopathogenic Nematodes As Naturally Occurring Biocontrol Agents.”

 In-house seminars are conducted during the Fall and Spring Semesters. Research progress reports by undergraduate, and graduate students, post-docs, staff members, and research faculty members are presented for discussion and suggestions. Twenty five to thirty people regularly attend this weekly seminar.

Faculty members and their students attended conferences and seminars to present research results and to interact with other researchers from other academic and industrial institutions. The Table in the following pages shows the conference, seminar, or workshop, place and date, and topics presented by attendees.

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Table. 1. Conferences, Workshops, and Meetings Attended by Members of the FCRC.

 

Conference/Seminar/
Workshop

 

Date and Place

Attendees/Poster Presenters/Speakers
* - graduate student;
**- post-doc
***- undergrad student
 
Topic

Symposium for the Society of Nematology.

Salt Lake City, 2001

Preston, J.F., D.W. Dickson, J.E. Maruniak, J.A. Brito, L.M. Schmidt, and J.M. Anderson

Pasteuria Spp.: Systematics-Phylogeny Of These Unusual Bacterial Parasites Of Phytopathogenic Nematodes.

Conference on Interfacing Microbiology and Biotechnology

University of Florida, Gainesville, FL May 17-19, 2001.

J.F. Preston, III

 Microbial Strategies For The Depolymerization Of Glucuronoxylan.

Madeline E. Rache

C1 Metabolism And Methanogens

Lonnie O. Ingram and James F. Preston, III

Metabolic Engineering And Regulation

K.T. Shanmugam

Bioinformatics And Global Gene Expression

Julie A. Maupin-Furlow

Nanocompartments Of Prokaryotic Cells

 101st American Society for Microbiology General Meeting

 

Orlando, FL. May 20-24, 2001.

Lonnie O. Ingram 

 

Symposium Speaker: Genetic Engineering For Production Of Industrial Chemicals.

Rebecca M. Harbucker*

Isolation Of A Thermotolerant Acid Resistant Host For The adh And pdc Genes Of Zymomonas mobilis To Enable Cost Effective Production Of Ethanol For Biomass.

ME Rodriguez*

Properties Of The Hemicellulose Fractions Of Lignocellulosic Biomass Affecting Bacterial Ethanol Production.

Tony Gutierrez*

Biotransformation Of Furfural By Ethanologenic Bacteria And Its Effect On Ethanol Production.

Lee Ann Talarico*

Cloning And Characterization Of Pyruvate Decarboxylase From SarcinavVentriculi.

FrankG. Healy*

Development Of Ethanologenic Escherichia coli For The Simultaneous Utilization Of Glucose And Xylose.

Stuart A. Underwood*

Additional Osmoprotectants Are Required For The Efficient Fermentation Of 10% Xylose To Ethanol In Nutrient-Limiting Media

Ramon Gonzalez*

Identification Of Promoters For Programmed Expression Of Recombinant Products Im Escherichia Coli By Transcriptone Analysis.

Steven J. Kaczowka*

Structure And Function Of Proteasomes From A Halophilic Archaeon Halofreax volcanii.

H.L. Wilson*

Purification And Characterization Of The 20S Proteasome And PAN From Methanococcus maripaludis.

Mark S. Ou*

Influence Of The Alpha Subunit On The Proteolytic Activity Of 20S Proteosomes

Kheir Zuobi-Hasona**

Oligosaccharides Containing Glucuronoxylose As Substrates For Selecting Bacteria For Depolymerization Of Hemicellulose.

Shengde Zhou

Fermentation Of Cellulooligosaccharides And Amorphous Cellulose To Ethanol By Cellulolytic Detivatives Of Klebsiella oxytoca.

A.M. Paredes, F. Soyer, H.C. Aldrich, S. Lutke, H Tsuruta, W.Chiu, JM Shively

Three-dimensional structure of Thiobacilllus neapolitanus Carboxysomes as Determined by Cryo-electon Microscopy.

E.M. Sampson, G.D. Haveman, H.C. Aldrich, T.A. Bobik

Effect of  In-Frame pdu Deletions on Polyhedra Body Formation by Salmonella enterica Serovar Typhimurium LT2.

Gordon Research Conference on Archaea: Ecology, Metabolism, and Molecular Biology

2001 Proctor Academy, NH

Steven Kaczowka*

Localization Of The Alpha-1 And Alpha-2 Subunits Of 20S Proteasomes From A Halophilic Archaeon, Haloferax volcanii’

2nd Gordon Conference on Molybdenum and Tungsten Enzymes

Queen’s College, Oxford, England July 1-6, 2001

K.T. Shanmugam

Molybdenum Metabolism.

University of Florida, Dept. of Microbiology and Cell Science

Gainesville, FL, 2001

Julie A. Maupin-Furlow

Energy-dependent Proteolysis in the Archaea.

Gordon Research  Conference, Archaea: Ecology, metabolism, and Microbiology

Andover, NH, 2002

Julie A. Maupin-Furlow

Archael Proteosomes and Proteosome-Activating Nucleotidases.

Brookhaven National Laboratories

Upton, NY, 2001

Julie A. Maupin-Furlow

Proteosomes: Molecular Machines Integral to the Genomes to Life Initiative.

223rd National Meeting of the American Chemical Society.

Orlando, FL April 7-11, 2002.

Preston, J.F., and J.C. Hurlbert

Microbial Strategies For The Depolymerization Of Methylglucuronoxylan.- Payen Award Symposium Honoring Liisa Viikari: Application Of Enzymes To Lignocellulosics.

23rd Symposium on Biotechnology for Fuels and Chemicals

Breckenridge, Colorado May 4-7, 2003

Stuart Underwood*

Optimizing Carbon Partitioning between Biosynthesis and Ethanol Production in Ethanologenic Escherichia coli KO11

James F. Preston, Franz J. St. John and John D. Rice

Selection of Endoxylanases for Depolymerization of Glucuronoxylan from Hemicellulose

 Annual Meeting of the American Society for Microbiology Southeastern Branch

 Gainesville, Florida, on November 7-9, 2002

Lonnie O. Ingram

Engineering E. coli For Renewable Chemicals And Fuels.

K.T. Shanmugam

Whole Genome Expression Analysis Of E. coli Growing Under Aerobic And Anaerobic Condition.

Bryce Causey*

Microbial Platform For The Production Of Oxidized Compounds (Acetate And Pyruvate) From Escherichia coli W3110 ATCC.

Lee Ann Talarico*

Characterization Of Pyruvate Decarboxylase From Sarcina ventriculi.

Franz St. John*

Xylan Utilization By Paenibacillus Sp Secresting a GH10 Xylanase With Significant Homology To GH10 Of Clostridium josui.

Stuart Underwood*

Balancing Carbon Partitioning Between Biosynthesis And Product Formation

Shengde Zhou

Metabolic Engineering Escherichia coli W3110 Fro Production Of Optically Pure D(-) And L(+)-Lactic Acid From Mineral Salts Medium.

Christopher Reuter*

Biochemical Characterization And Subunit Arrangement Of PAN Proteins From Halophilic Archeon Haloferax volcanii.

Steven J. Kaczowka*

Subunit Arrangement Of 20S Proteosomes From Haloferax volanii.

Phoung-Uyen Le***

Thermostability Of Sarcina ventriculi Pyruvate Decarboxylase At Ph 5.5

Brea Duval***

Generation Of Coupled Microtiter Plat Assay For Sarcina ventriculi Pyruvate Decarboxylase.

Cheryl Boice*

Characterization Of Bacteriphages For Use In Adsorption And Transport Studies.

Johnny Davis*

Fate Of Bacterial Indicators And Pathogens In Anaerobically Digested Dairy Wastewater.

Yilei Qian

Isolation Of The Xylosidase Gene (Xynb) Operon From Klebsiella oxytoca.

Liesbeth Schmidt**

Detection Of  Pasteuria penetrans P20 Infected Meloidogyne arenaria Race 1 By Polymerase Chain Reaction (PCR).

Vilas Shukla**

Engineering Escherichia coli For Lactic Acid Production From Sucrose.

Brent Wood*

Reprioritization Of Sugar Utilization Profiles By Overexpression Of A CRP* In Escherichia coli KO11

Annual Meeting of the American Society for Microbiology

Salt Lake City, Utah, 2002

Julie A. Maupin-Furlow

Compartmentalization of Proteolysis Mediated by the Archaeal Proteosome.

G.C. Cannon, S. Heinhorst, H.C. Aldrich, E. Williams, J. Shively

Characterization of Halothiobacillus neapolotanus Carboxysomes Rcombinantly Expressed in E. coli.

E.E. Sampson, G.D. Hveman, H.C. Aldrich, T.A. Bobik

Genetic Analysis of the 1,2-propanediol Degradation by Salmonella enterica serovar Typhimurium LT2.

A. Hasona**, H. Tao

Global Gene Expression Analysis of Escherichia coli Reveals a Role for ModE-Mo in Pyrimidine Metabolism.

R.V. Dumitru, H. Palencia, J.M. Takacs, B. DeMontigny, J. Miner, M. Rasche, S.W. Ragsdale

Novel Enzyme Targeted Strategy to Inhibit Methanogenesis.

S.A. Wiles, M. Rosentzvaig, M.E. Rasche

Dentification of the First Methanopterin Biosynthesis Gene in Methylothropic Bacteria.

J. Strate, R. Harris, I. Uz, A. Ogram, M.E. Rasche, A.S. Lindner

Characterization and Activity Comparisons of Methanothropic-Heterothropic Mixed Cultures Derived From Landfill Environments.

University of Georgia, Department of Microbiology

Athens, GA, 2002

Julie A. Maupin-Furlow

Energy-dependent Proteolysis in the Archaea.

DARPA Biological Input-Output Systems Program, Kick-off Meeting

San Diego, CA, June 14-15, 2002

Arlington, VA, May 27-28, 2003


Lonnie O. Ingram, William B. Gurley, Nemat O. Keyhani, Thomas A. Bobik and Shouguang Jin

Sentinel Plants Utilizing Bacterial Two-Component Systems.

Gordon Conference: Biocatalysis Workshop

Meredith, NH, July 11-12, 2002

 

 

  

 

 Lonnie O. Ingram

 

 

 

 

 

 

 

 

 

 

Symposium  Speaker

Society of Industrial. Microbiology and Biotechnology

Philadelphia, Aug 2002

Symposium Speaker

Bioproducts Advisory Group

Washington, DC., September, 2002

Invited Speaker

Basic Energy Sciences Advisory Committee-Sponsored Workshop

Gaithersburg, MD, October 21-24, 2002

Basic Research Needs To Assure A Secure Energy Future

DOE, DOE, BER Genomes to Life Advisory Group

Washington, DC. October, 2002

Invited Speaker

DOE, Basic Energy Science Advisory Group (Future Challenges)

Washington, DC, November, 2002

Invited Speaker

Cargill, Inc.

St. Paul, MN, November 10-11

Review Cargill’s Biobased Chemicals Research And Development Program.

InterAgency (DARPA, DOE, USDA, NSF, NIH, NIST, ONR) Conference

Arlington, Virginia,

2001, 2002,

January 31, 2003

Metabolic Engineering Working Group

25th Symposium on Biotechnology for Fuels and Chemicals

April, 2003

Symposium Speaker

Annual Meeting of the Amer. Society  for Microbiology

Wash DC. May, 17-19, 2003

Symposium Speaker

Consortium for Plant Biotechnology Symposium

Washington DC February 26-27, 2003.

Maria E. Rodriquez, Alfredo Martinez, Sean W. York, Kheir Zuobi-Hasona, Lonnie O. Ingram, K. T. Shanmugam, and James F. Preston

Properties of the Hemicellulose Fractions of Lignocellulosic Biomass Affecting Ethanol Production

 

James F. Preston, Franz J. St John, John D. Rice, Lonnie O. Ingram, and K. T. Shanmugam

Utilization of Hemicellulose-derived Glucuronoxylose for Ethanol Production

James F. Preston, Franz J. St John, John D. Rice, Lonnie O. Ingram, and K. T. Shanmugam

Bioconversion of Lignocellulosics to Alternative Fuels and Chemicals

25th Symposium on Biotechnology for Fuels and Chemicals

Washington, DC, May 4-7, 2003

K.T. Shanmugam

Second Generation Biocatalysts for Production of Fuels and Chemicals from Biomass

1st Annual Meeting of S1007 – The Science and Engineering for a Biobased Industry and Economy

Washington, DC May 8-9, 2003

K.T. Shanmugam

 

Annual Meeting of the American Society for Microbiology

Washington, DC, May 18-22, 2003

Lonnie O. Ingram

Symposium Speaker: Engineering Escherichia coli For The Production Of Higher Value Fermentation Products.

Vilas Shukla**

Production Of Lactic Acid From Sucrose By Metabolic Engineered Escherichia coli.

Yilei Qian

Cloning, Characterization And Functional Expression Of The Klebsiella oxytoca Xyloside Utilization Operon (xynb) In Escherichia coli

Stuart Underwood*

Osmoprotectants Stimulate Growth And Ethanol Production By Ethanologenic Escherichia coli.

Franz St. John*

Xylan Utilizing Paenibacillus sp. Encodes A GH10 Xylanase Containing Triplicate Domains For Cell Surface And Substrate Associations.

Bryce Causey*

Engineering The Metabolism Of Escherichia coli W3110 For Homo-Acetate Production.

Steven Kaczowka*

Recombinant Production Of Zymomonas mobilis Pyruvate Decarboxylase I The Archaeon Haloferax volcanii

Shengde Zhou

Novel Escherichia coli Biocatalysts For The Efficient Production Of L(+) And D(-) Lactic Acids From Hexose And Pentose Sugars In Mineral Salts Medium.

Christopher Reuter*

Proteasome-Activating Nucleotidases From Haloferax volcanii: Subunit Complexity And Activity.

Kheir Zoubi-Hasona**

Growth Dependent Post-Translational Modification Of The Alpha1 Subunit Of Halofrex volcanii 20S.

Matt Bechard*

Overproduction Characterization, And Site-Directed Mutagenesis Of RFAP Synthase From The Methanogen Methanothermobacter thermautrophicus Delta H.

Lee Ann Talarico*

Comparison And Analysis Of Pyruvate Decarboxylase Gene Expression In A Gram-Postive Host.

Milind Patel**

Genetic And Biochemical Characterization Of D-Lactate Dehydrogenase From A Secomd Generation Biocatalyst Producing L-(+) Lactic Acid.

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Service and Awards 

Service

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

 Faculty Member

Type of Service

Insitution/Society

James F. Preston, III

 Editorial Board

Journal of Applied and Environmental Microbiology, 1996-2001.

Lonnie O. Ingram

 

Chairman, Fermentation and Biotechnology Division

American Society for Microbiology (Division O), 2000-2001

Symposium Chairman

Soc. of Indust. Microbiol. and Biotechnol., Recent Advances in Fermentation Technology IV,   October 2001

 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

 

 Conference Organizer

“Interfacing Microbiology and Biotechnology”, Gainesville on May 17-19, 2001.

President, ASM Southeastern Branch

 American Society for Microbiology, 2002

Madeline E. Rasche

Secretary-Treasurer

Julie A. Maupin-Furlow, Madeline E.Rasche, Henry C. Aldrich

Local Planners

 Annual Meeting of the Southeastern Branch at Gainesville, Florida. Nov 6-9, 2002

James F. Preston, III

Awards Committee Member

Lonnie O. Ingram

Evaluator

Research and Development Program of Cargill Central Research Division. Nov 2002

 James F. Preston, III

 

 

 

 

 

 

Refereed Journal Reviewer  

 

Science

Applied and Environmental Microbiology

Journal of Experimental Microbiology

Carbohydrate Research

Physiological and Molecular Plant Pathology

James F. Preston, IIIMadeline E. Rasche, Julie A. Maupin-Furlow

Journal of Bacteriology

Madeline E. Rasche

Archives of Microbiology 

Julie A. Maupin-Furlow

Archaea, 2001 – present.

Molecular Microbiology

Canadian Journal of Microbiology

Archives of Biochemistry and Biophysics

FEBS Letters

James F. Preston, III

Member, Faculty Advisory Committee

Vice-President of IFAS, 2002-2004

James F. Preston, III

Member

University Senate, 2002-2004

 Madeline E. Rasche

Panel Member, Grant Proposal Review Board

National Science Foundation, 2002

Grant Proposal Reviewer

National Science Foundation, 1999-2003

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Awards

 Outstanding graduate students received travel grants to present their research results at regional and national meetings, and awards for best research presentations. Sponsors include:  American Society for Microbiology, Institute of Agricultural and Life Sciences, Gordon Research Conference on Archea, UF Student Government, and   Kikoman Corporation.

Student

Award

Sponsor/Purpose

Steven Kaczowka

ASM Sustaining Member Student Travel Award

101th American Society for Microbiology General Meeting, Orlando, FL. May 20-24, 2001

Gordon Research Conference Travel Award

Gordon Research Conference on Archaea: Ecology, Metabolism, and Molecular Biology 2001 Proctor Academy, NH

Brea Duval

President’s Award for Best Paper Presentation by an Undergraduate Student.

 American Society for Microbiology General Meeting, Southeast Branch, Gainesville, Fl,
Nov 7-9, 2002

 

 Lee Ann Talarico

President’s Award for Best Paper Presentation by a Graduate Student.

The Kikoman Corporation Student Travel Award

 American Society for Microbiology Annual Meeting, Washington, DC, May 18-22, 2003

Stuart Underwood

ASM Division O Student Travel Award

Bryce Causey

ASM Corporate Accounts Program, Division O Student Travel Grant

Bryce Causey,
Matt Bechard, Stuart Underwood, Franz St. John, Steven Kaczowka, Lee Ann Talarico, Christopher Reuter

 IFAS $200 Travel Grant

Stuart Underwood
Franz St. John 

Student Government Travel Grant

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Research Assistantships

 Dr. Jimmy G. Cheek, Dean of the College of Agricultural and Life Sciences, IFAS, granted four matching graduate assistantships in Fall 2002 and five additional slots this Fall 2003:

Graduate Assistant

Date Granted

 Degree

Mentor

Maegorzata Gil

2002

MS

Dr. Julie A. Maupin-Furlow

Jeremy Purvis

2002

MS

Dr. Lonnie O. Ingram

Franz St. John

2002

MS

Dr. James F. Preston, III

Kim Youngyun

2002

MS

Dr. K.T. Shanmugam

Phi Min Do

2003

MS

Dr. K. T. Shanmugam* 

Phillip Kirkland

2003

MS

Dr. Julie A. Maupin-Furlow*

Shannon McQuaig

2003

MS

Dr. Samuel R. Farrah*

Jonathan Moore

2003

MS

Dr. James F. Preston, III*

Amy Wright

2003

MS

Dr. Madeline Rasche*

* provisional mentors; students go on rotation to different labs before choosing their home lab

 The Center currently supports 7 other graduate students, 10 post-docs, and 4 research faculty members:

Name

Degree/Position

Mentor/Lab

Matthew Bechard

MS

Dr. Madeline Rasche

Bryce Causey

PhD

Dr. Lonnie O. Ingram

Shai Lawit

MS

Dr. William B. Gurley

Steven Kaczowka

MS

Dr. Julie A. Maupin-Furlow

Christophen Reuter

MS

Dr. Julie A. Maupin-Furlow

Lee Ann Talarico

PhD

Dr. Julie A. Maupin-Furlow

Brent Wood

PhD

Dr. Lonnie O. Ingram

Patrick Cirino

Visiting Scientist

Dr. Lonnie O. Ingram

Yilei Qian

Research Faculty

Dr. Lonnie O. Ingram

Shengde Zhou

Research Faculty

Dr. Lonnie O. Ingram

Stuart Underwood

Post-Doc

Dr. Lonnie O. Ingram

Eun Min Cho

Post-Doc

Dr. Nemat Keyhani

Eva Czarnecka-Verner

Research Faculty

Dr. William B. Gurley

Haeng Seorg Lee

Post-Doc

Dr. William B. Gurley

Kevin O’Grady

Post-Doc

Dr. William B. Gurley

Tarek Salem

Post-Doc

Dr. William B. Gurley

Ivanka Karadzic

Post-Doc

Dr. Julie Maupin-Furlow

Guang Nong

Post-Doc

Dr. James F. Preston, III

Liesbeth Schmidt

Post-Doc

Dr. James F. Preston, III

Virginia Chow

Post-Doc

Dr. James F. Preston, III

Tao Han

Research Faculty

Dr. K.T. Shanmugam

Milind Patel

Post-Doc

Dr. K.T. Shanmugam

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Patents and Publications

 Patents 

Approved Patents:
 

Application Number

Date Approved

Country

Authors

Title

ZL92101877.0

01/27/01

China

Lonnie O. Ingram,
David S. Beall,
Gerhard F.H.
Burchardt,
Walter V. Guimaraes,
Kazayosi Ohta,
Brent E. Wood,
K. T. Shanmugam

Ethanol Production by Recombinant Hosts

 

 

6,569,632

 

U.S.

Preston, James F., D.W. Dickson, John D. Rice, J.H. Charnecki, J.M. Brito,  Liesbeth M. Schmidt

Monoclonal Antibody Probe for Detection of Adhesins Associated with Mature Endospores of Pasteuria Spp

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US patent applications (16):

Application Number

Date Submitted

Authors

Title

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

10/027,250

12/21/01

Brent Wood, Lonnie O. Ingram

Improvement of Ethanol Production from Lignocellulose

10/024,456

12/17/01

Lonnie O. Ingram, Sean W. York

Ethanol Production Using a Soy Hydrolysate-based Medium or a Yeast Autolysate-based Medium

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

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

Acetobacter Patstuerianus Pyruvate Decarboxylase: Biochemical, Genetic, and Physiological Properties

60/288,671

05/04/01

Lonnie O. Ingram,
Lee Ann Talarico,
Julie A. Maupin

Cloning, Expression, and Characterization of Pyruvate Decarboxylase fro the Acod Tolerant, Anaerobic Gram-Positive Bacteriun Sarcinia ventriculi9 Goodsir

60/288,638

05/04/01

Lee Ann Talarico, Lonnie O. Ingram,
Julie A. Maupin

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

Biochemical and Biophysical characterization of Pyruvate Decarboxylase from the Acetic Acid Bacterium Acetobacter Pastuerianus

 

International patent applications (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

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Publications

 In Press

 Rasche, M. E., Wyles, S. A., and Rosenzvaig, M.  2004.  Characterization of two methanopterin biosynthesis mutants of Methylobacterium extorquens AM1 using a tetrahydromethanopterin bioassay.  J. Bacteriol. (Accepted with revision)

Caccamo, M. A., Malone, C. S., and Rasche, M. E.  2004.  Biochemical characterization of a dihydromethanopterin reductase involved in tetrahydromethanopterin biosynthesis in Methylobacterium extorquens AM1. J. Bacteriol. (Accepted with revision)

Kima, P.E, Rasche, M.E.  2004.  Sex determination using the polymerase chain reaction.  Biochemistry and Molecular Biology Education (Accepted).

Rasche, M. E.  2003. Outcomes of a research-driven laboratory and literature course designed to enhance undergraduate contributions to original research.  Biochemistry and Molecular Biology Education.

Bobik, T.A., Rasche, M.E.  2003.  Purification and partial characterization of the Pyrococcus horikoshii methylmalonyl-CoA epimerase.  Applied Microbiology and Biotechnology.

Dumitru, R., Palencia., H., Schroeder, S. D., DeMontigny, B., Takacs, J., Rasche, M. E., Miner, J. L., and Ragsdale, S. W.  2003.  Targeting methanopterin biosynthesis to inhibit methanogenesis.  Appl. Environ. Microbiol. 

Kaczowka, S.J. and J.A. Maupin-Furlow. 20003. Archael Ptroteasomes: from structure to function [update 2003]. Front. Biosci.

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 Book Chapter


Preston, J.F., J.C. Hurlbert, J.D. Rice, A. Ragunathan, and F.J. St. John. “Microbial Strategies for the Depolymerization of Glucuronoxylan: Leads to the Biotechnological Applications of Endoxylanases. in “Application of Enzymes to Lignocellulosics”, eds S.D. Mansfield and J. N. Saddler,  ACS Symposium Series No. 855. Ch 12. 2003

 Journal Articles:

Yilei, Qian, L.P. Yomano, J.F. Preston, H.C. Aldrich and L.O. Ingram. 2003. Cloning,  characterization and functional expression of the Klebsiella oxytoca xyloside utilization operon (xynTB) in Escherichia coli. Appl Environ Microbiol. 69(10):5957-67.
 

Schmidt, L. M., J. F. Preston, D. W. Dickson, J. D. Rice, T. W. Hewlett. 2003. Environmental quantification of Pasteuriapenetrans endospores using in situ antigen extraction and immunodetection with a monoclonal antibody. FEMS Microbiol. Ecol. 44:17-26.Z
 

Maupin-Furlow, J.A., S.J. Kaczowka, C.J. Reuter, K. Zuobi-Hasona, and M.A. Gil. 2003.  Archael proteasomes: potential in metabolic engineering. Metab. Engin. 5:151-163.
 

Kaczowka, S.J. and J.A. Maupin-furlow. 2003. Subunit topology of the multiple 20S proteasomes from Haloferax volcanii. J. Bacteriology 185:165-174.
 

Preston, J. F., D. W. Dickson, J. E. Maruniak, G. Nong, J. A. Brito, L. M. Schmidt, and R. M. Giblin-Davis. 2003. Pasteuria spp. : Systematics and phylogeny of these bacterial parasites of phytopathogenic nematodes. Journal of Nematology 35: 198-207
 

Brito, J. A, J. F. Preston, D. W.Dickson, R. M. Giblin-Davis, D. S. Williams, H. C. Aldrich, and J. D. Rice. 2003. Temporal Production and Immunolocalization of an Epitope During Pasteuria penetrans sporogenesis. Journal of Nematology 35(3):
 

Bobik, T. A., and Rasche, M. E.  2003.  HPLC assay for methylmalonyl-CoA epimerase. Anal. Bioanal. Chem. 375:344-349.
 

Uz, I, Rasche, M.E., Townsend, T., Ogram, A. V., and Lindner, A. S.  2003.  Characterization of methanogenic and methanotrophic assemblages in landfill samples.  Proceedings of the Royal Society of London B (Biology Letters Suppl.) 270:S202-S205.
 

Bechard ME, Chhatwal S, Garcia RE, Rasche ME.  2003.  Application of a colorimetric assay to identify putative RFAP synthase genes expressed with activity in Escherichia coli.  Biological Procedures Online 5:69-77.
 

Eckert, Richard B., Henry C. Aldrich, Chris A. Edwards, Bruce A. Cookingham. 2003. Microscopic differentiation of internal corrosion initiation mechanisms in natural gas pipeline systems. Corrosion, San Diego, CA
 

Bogan, Bill W., Wendy R. Sullivan, Kevin J. Kayser, KD Derr, Henry C. Aldrich and J. Robert Paterek. 2003. Alkanindiges illinoisensis gen. nov., sp. nov., an obligately hydrocarbonoclastic, aerobic squalane-degrading bacterium isolated from oilfield soils. Int J Syst Evol Microbiol 53: 1389-1395.
 

Gonzalez, R., H. Tao, J. E. Purvis, S. W. York, K. T. Shanmugam and L. O. Ingram.2003. Gene array-based identification of beneficial changes that contribute to increased ethanol tolerance in ethanologenic Escherichia coli LY01. Biotechnol. Prog. 19:612-623.  
 

Zhou, Shengde, K.T. Shanmugam and L.O. Ingram. 2003. Functional replacement of Escherichia coli D(-)-lactate dehydrogenase (ldhA)  with  L(+) -lactate dehydrogenase (ldhL) from Pediococcus acidilactici. Appl. Environ. Microbiol. 60(4): 2237-2244.  
 
Causey, T. B., S. Zhou, K. T. Shanmugam, and L. O. Ingram. 2003. Engineering the metabolism of Escherichia coli W3110 for the conversion of sugar to redox-neutral and oxidized products: homo-acetate production. Proc. Natl. Acad. Sci. USA. 100:825-832.  
 
Zhou, S., T.B. Causey, A. Hasona, K.T. Shanmugam, and L.O. Ingram. 2003. Production of optically pure D-lactic acid in mineral salts medium by metabolically engineered Escherichia coli W3110. Appl. Environ. Microbiol. 69(1):399-407.  

Giblin-Davis, R.M., D. S. Williams, S. Bekal, D. W. Dickson, J. A. Brito, J. O. Becker and J. F. Preston.  2003 'Candidatus Pasteuria usgae' sp. nov., an obligate endoparasite of the phytoparasitic nematode Belonolaimus longicaudatus. Int J Syst Evol Microbiol 53: 197-200.
 

Scott J.W., ME Rasche. 2002.  Purification, overproduction, and partial characterization of beta-RFA-P synthase, a key enzyme in the pathway of methanopterin biosynthesis.  J. Bacteriol. 184:4442-4448.
 

Hurlbert, J.C. and J.F. Preston. 2002. Differences in the solution structures of the parallel Beta-helical pectate lyases as determined by limited proteolysis. Biochimica et  Biophysica Acta. 1599:9-20.  
 

Underwood, S.A.,S. Zhou, T. B. Causey, L.P. Yomano, K.T. Shanmugam, and L.O. Ingram. 2002. Genetic changes to optimize carbon partitioning between ethanol and biosynthesis ethanologenic Escherichia coli. Appl. Environ. Microbiol. 68(12): 6263-6272.  
 

Raj, K.C., L.A. Talarico, L.O. Ingram and J.A. Maupin-Furlow. 2002. Cloning and characterization of the Zymobacter palmae pyruvate decarboxylase (pdc): Comparison of bacterial homologoues. Appl. Environ. Microbiol. 68(6): 2869-2876.   

Gutierrez, T., M.L. Buszko, L.O. Ingram, and J.F. Preston. 2002. Reduction of furfural to furfuryl alcohol by ethanologenic strains of bacteria and its effect on ethanol production from xylose. Appl. Biochem. Biotechnol. 98-100: 327-340.
 

Hasona, A., S.W. York, L.P. Yomano, L.O. Ingram and K.T. Shanmugam. 2002. Decreasing the level of ethyl acetate in ethanologenic fermentation broths of Escherichia coli KO11 by expression of Pseudomonas putida estZ esterase. Appl. Environ. Microbiol. 68(6): 2651-2659.
 

Underwood, S.A., M.L. Buszko, K.T. Shanmugam, and L.O. Ingram. 2002. Flux through citrate synthase limits the growth of ethanologenic Escherichia coli KO11 during xylose fermentation. Appl. Environ. Microbiol. 68: 1071-1081.
 

Gonzalez, R. Han Tao, K.T. Shanmugam, S. W. York, and L. O. Ingram. 2002. Global gene expression differences associated with changes in glycolytic flux and growth rate in Escherichia coli during the fermentation of glucose and xylose. Biotechnol. Prog. 18: 6-20.   
 

Bobik TA, Rasche M. E.  2001.  Identification of the human methylmalonyl-CoA racemase gene based on the analysis of prokaryotic gene arrangements. Implications for decoding the human genome.  J. Biol. Chem. 276:37194-37198.
 

Preston, J.F., D.W. Dickson, J.E. Maruniak, J.A. Brito, L.M. Schmidt, and J.M. Anderson. 2001. Pasteuria spp.: Systematics-phylogeny of these unusual bacterial parasites of phytopathogenic nematodes. Phytopathology. 91:S173.
 

Raj, K. C., L.O. Ingram and J. A. Maupin-Furlow. 2001. Pyruvate decarboxylase: a key enzyme for the oxidative metabolism of lactic acid by Acetobacter pasteurianus. Arch. Microbiol. 176: 443-451.
 

Hurlbert, J.C., and J.F. Preston. 2001. Fuctional characterization of a novel xylanase from corn strains of Erwinia chrysanthemi. J. Bacteriol.183: 2093-2100.
 

Hasona, A., Self, W.T. and K. T. Shanmugam. 2001. Transcriptional regulation of the moe (molybdate transport) operon of Escherichia coli. Arch. Microbiol. 175:178-188.
 

Self, W. T., A. M. Grunden, A. Hasona and K. T. Shanmugam. 2001. Molybdate transport. Res. Microbiol. 152:311-321.
 
Self, W. T., A. Hasona and K. T. Shanmugam. 2001.  N-terminal truncations in the FhlA protein result in formate- and MoeA-independent expression of the hyc operon (formate hydrogenlyase) of Escherichia coli. Microbiology. 147:3093-3104.

Talarico, L. A., L.O. Ingram and J.A. Maupin-Furlow. 2001. Production of Gram-positive Sarcina ventriculi pyruvate decarboxylase in Escherichia coli. Microbiology-SGM 147:2425-2433.
 

Zhou, S. and L. O. Ingram. 2001. Simultaneous saccharification and fermentation of amorphous cellulose to ethanol by recombinant Klebsiella oxytoca SZ21 without supplemental cellulase. Biotechnol. Lett. 23: 1455-1462.
 

Han, T., R. Gonzales, A. Martinez, M. Rodriguez, L.O. Ingram, J.F. Preston, and K.T. Shanmugam. 2001. Engineering a homo-ethanol pathway in Eschericia coli: increased glycolytic flux and levels of expression of glycolytic genes during xylose fermentation. J. Bacteriol. 183: (10): 2979-2988.
 

Martinez, A., M.E. Rodriguez, M.L. Wells, S.W. York, J.F. Preston, and L.O. Ingram. 2001. Detoxification of dilute acid hydrolysates of lignocellulose with lime. Biotechnol. Prog. 17: 287-293.
 

Zhou, S., F.C. Davis, and L.O. Ingram. 2001. Gene integration and expression,a nd extracellular secretion of Erwinia chrysanthemi endoglucanase CelY (celY) and CelZ (celZ) in ethanologenic Klebsiella oxytoca P2. Appl. Environ. Microbiol. 67 (1): 6-14.
 

      

 

Other Publications:

Website: The Florida Center for Renewable Chemicals and Fuels, 2002.  http://fcrc.ifas.ufl.edu
Brochure: The Florida Center for Renewable Chemicals and Fuels, 2002

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On-Going Research Projects

 

Investigator(s) Sponsor Duration Amount Title
James F. Preston, III.,   Lonnie O. Ingram Consortium for Plant Biotechology Research (CPBR) 07/01/2002 – 06/30/2004 $58,890   Utilization of hemicellulose-derived glucurunoxylose for ethano.l  production.
Julie A. Maupin-Furlow National Institute of Health (NIH)   04/01/2000 – 03/31/2005  $888,840 Physiology of proteosomes in Haloferax volcanii
Madeline E. Rasche National Science Foundation (NSF) 05/01/1999 – 04/30/2004 $493,000 Methanopterin biosynthesis in archaea and methylotropic bacteria 
Samuel R. Farrah National Science Foundation (NSF) 09/15/1994 – 09/30/2003 $174,293 Advanced separation processes
Samuel R. Farrah National Science Foundation (NSF) 09/01/2002 – 08/31/2005 $25,000 Surface modification for advancing response processes and environmental protection
Samuel R. Farrah Orange County, Florida  10/01/2002 – 09/30/2003  $29,550 Virus monitoring of effluent from joint facility

 Lonnie O. Ingram, K.T.Shanmugam, James F. Preston,

Julie A. Maupin-Furlow, Henry C. Aldrich, Marian Buszko, 

Jon Stewart, Nancy D. Denslow, Atul  Narang

U.S. Department of Agriculture/Coop SRS 09/15/2000 – 09/30/2003 $2,000,000 Application of functional genomics to recombinant biocatalysts for fuels and chemicals
Lonnie O. Ingram    U.S. Department of Agriculture/Coop SRS 09/01/2001 – 08/31/2004  $300,000 Engineering bacteria for fuel ethanol production.
James F. Preston,III,  DW Dickson U.S. Department of Agriculture 09/15/2002 – 09/14/2004 $80,813 The genome of Pasteuria penetrans: a blueprint for developiing pasteuria spp. for biocontrol of plant paratistic nematode

Lonnie O. Ingram,  William.B. Gurley, Thomas A. Bobik, Nemat O. Keyhani, Shouguang Jin

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

 

 06/01/2002 – 05/31/2005  $2,361,230 Sentinel plants utilizing bacterial two-component signaling pathways
Lonnie O. Ingram U. S. Department of Energy  Chicago Operations Office  07/01/2001 – 06/30/2003  $150,000 Development and commercialization of new ethanol producing strains
Lonnie O. Ingram 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.
James F. Preston, III,  Lonnie O.  Ingram, K.T. Shanmugam U. S. Department of Energy 09/01/2000 – 08/31/2004 $439,061

Complementation of endoxylanase with  glucoronidase and xylosidase for bacterial production of ethanol from lignocellulosic biomass

K.T. Shanmugam, L.O. Ingram, Julie A. Maupin-Furlow, J. F. Preston, III,  H.C. Aldrich

 U.S. Department of Energy 10/01/2001 – 09/30/2002 $400,000 Thermophilic Gram-positive Biocatalysts for Biomass Conversion to Ethanol.
L.O. Ingram, J.F. Preston, III, H.C. Aldrich, K.T. Shanmugam US Department of Energy, NREL 07/15/1999 – 12/31/2002 $573,938 Second generation ethanologen development
 L.O. Ingram US Department of Agricualture  12/01/2000 – 11/30/2002   $90,00 Improved xylose utilization for ethanol fuel production by ethanologenic Escherichia coli.

 

 

 

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Acknowledgments

 

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

UF/IFAS:          

Dr. Winfred M. Phillips. Vice President for Research

Dr. Michael V. Martin, Vice President for Agriculture and Natural Resources

Dr. Joseph C. Joyce, Executive Associate Vice President for Agriculture and
                                    Natural Resources and Budget Director

Dr. Richard L. Jones, Dean for Research and FAES

Dr. William F. Bown, Associate Dean for Research and FAES

Dr. Jimmy Cheek, Dean for Academic Programs and the   

College of Agriculture and Life Sciences

                                                Department of Microbiology and Cell Science

 

 

Grant Agencies:
 

Biotechnology and Research Development Corporation (BRDC)

Consortium for Plant Biotechnology, Inc. (CPBR)

Defense Advanced Research Project Agency (DARPA/USDD)

National Institutes of Health

National Science Foundation

Orange County, Florida

US Department of Agriculture

US Department of Energy

 
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