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Progress Report
The Florida Center for Renewable
Chemicals and Fuels (FCRC)
July
2004- June 2005
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CONTACT INFORMATION
Dr. Lonnie
O. Ingram
Director |
ingram@ufl.edu
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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 |
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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 |
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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
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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.
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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)
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Microbiology |
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Conferences, Seminars, and Workshops
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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.
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Table. 1. Conferences, Workshops, and Meetings Attended by
Faculty Members and Students
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Conference/Seminar/
Workshop |
Date and Place
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Attendees/Poster
Presenters/Speakers
* - graduate student;
**- post-doc
***- undergrad student |
Topic
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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. |
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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. |
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RNA
Editing – Gordon Conference |
Jan
23-27, 2005
Ventura, CA |
V. de
Crecy-Lagard |
Finding
missing genes by comparative genomics: tRNA modification goldmine. |
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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 |
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Patent
Hearing |
Jan
29-Feb 3, 2005 Munich, Germany |
LO
Ingram |
Patent
hearing concerning a challenge to UF patent on ethanol production
from biomass. |
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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. |
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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. |
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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. |
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CPBR
2005 Symposium |
March
2-3, 2005 Washington DC. |
James
F. Preston |
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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. .
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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. |
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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. |
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World
Congress on Industrial Bioprocessing and Biotechnology |
April
20-22, 2005
Orlando, FL. |
LO
Ingram |
Microorganisms for the Production of Renewable Fuels and Chemicals |
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National Academy of Sciences Annual Meeting |
April
30-May 4, 2005
Washington, DC. |
LO
Ingram |
Attendee as member. |
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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. |
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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 |
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ME
Rasche |
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Y. Kim* |
Alternative fermentation pathway in
Escherichia coli. |
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Wright,
A. J. * and J. A. Maupin-Furlow |
Molecular characterization of Haloferax volcanii 20S
proteasomes reveals an intramolecular mechanism of
b-protein
processing. |
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Gil, M.
A. *and J. A. Maupin-Furlow. |
Co-transcription of proteasome and tRNA modification genes of the
haloarchaeon Haloferax volcanii. |
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Reuter, C. J. *
and J. A. Maupin-Furlow |
Molecular characterization of the proteasome-activating nucleotidase
subtypes of the haloarchaeon Haloferax.
volcanii.
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Kirkland, P. A. * and J. A. Maupin-Furlow |
of
native proteasomal substrates of Haloferax volcanii using a
degadomic approach. |
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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. |
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Kirkland, P. A. * and J. A. Maupin-Furlow. |
Proteomics and the halophilic archaea. |
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Gil,
M. A. * and J. A. Maupin-Furlow |
Connect
the dots: organization of proteasomal operons of the haloarchaeon
Haloferax volcanii. |
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14th
Conversation |
Albany, NY
June
14-18, 2005 |
Valerie
de Crecy-Lagard |
Finding
missing genes by comparative genomics: the tRNA modification
goldmine. |
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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. |
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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. |
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Wright, A. J. * and J. A. Maupin-Furlow |
Molecular characterization of Haloferax volcanii 20S
proteasomes reveals an intramolecular mechanism of
b-protein
processing. |
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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. |
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Reuter,
C. J. * and J. A. Maupin-Furlow. |
Analysis of substrate recognition by Pan/20S Proteasome isoforms in
the haloarchaeon Haloferax volcanii. |
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Kirkland, A. P. * and J. A. Maupin-Furlow |
Development of green fluorescent protein-based expression vectors to
identify regulated promoters of Haloferax
volcanii. |
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Wright,
A. J. * and J. A. Maupin-Furlow. |
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Mutational analysis of the Thr active site of the beta-protein in
20S proteasomes reveals beta-protein processing via an
intramolecular mechanism. |
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Service
Faculty members have been actively involved in several academic service
activities. They include:
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Faculty Member |
Type of Service |
Institution/Society |
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Fellow |
American Academy of Microbiology, 1998-present |
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Society of Industrial Microbiology and Biotechnology, 2001-present |
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Member |
U.S.
National Academy of Sciences, 2001-present |
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Editorial Board |
Biotechnology Letters 1996-present |
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Metabolic Engineering 1998-present |
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Member, Grant Review Panel |
DOE,
USDA, Interagency Metabolic Engineering Initiative |
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Grant Proposal Reviewer |
NSF,
NIH, DOE, USDA, several state programs, Canada, Australia, Hong
Kong, Consortium for Plant Biotechnology Research |
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Editorial Board Member |
Archaea,
2001 – present.
Frontiers
in Bioscience, 2000 – present. |
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Review Panel Member
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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. |
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Review Referee |
National Science
Foundation, 1996 – present.
U.S. Department of Energy,
1996 – present. |
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Review Team Leader |
USDA NRCS, Site Visit of
Biomass R&D Initiative Project, April 2005. |
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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 |
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Awards Committee Member |
Southeastern Branch American Society for Microbiology 2004 – 2005. |
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Editorial board Member
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Journal Bacteriology |
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Reviewer
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Nature New Biology, Applied and Environmental Microbiology,
Journal of Bacteriology, Journal of Experimental Microbiology,
Carbohydrate Research, Peptides and Proteins Lett. |
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Graduate Coordinator |
Microbiology and Cell Science Department. 2003-2004 |
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Graduate Coordinator |
Microbiology and Cell Science Department 2004-present |
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Grant
Proposal Review Panel |
NSF,
Metabolic Biochemistry October 2002-2005; DOE Basic Energy
Sciences and NABIR 2005 |
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Ad
hoc grant proposal reviewer |
NSF;
1999-2005; DOE Basic Energy Biosciences, 2005 |
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Ad
hoc reviewer for journals |
Journal of bacteriology, 2005 |
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GRE
Panel |
Biochemistry, Molecular Biology and Cell Biology 2004-2006 |
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Policy Committee, SE Branch, ASM |
2002-2006 |
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Awards
The following students received travel awards in support of
their attendance and presentations at scientific meetings:
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Name |
Award/Sponsor |
Date/Place |
Conference |
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Reuter, Christopher J
Wright, Amy |
Extremophile Student Travel
Award |
2004
Cambridge, MD
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5th International
Conference on Extremophiles |
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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
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| 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 |
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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 |
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*Visiting Fulbright Scholar, Instituto
de Investigaciones Biológicas, Facultad de Ciencias
Exactas y Naturales, Universidad Nacional de Mar del Plata, Argentina).
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Patents and Publications
Patents
Approved Patent 2005
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Patent
Number
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Date
Approved
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Country |
Authors |
Title |
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6,849,434 B2 |
02/01/2005 |
U.S.A |
Lonnie O. Ingram,
Maria Barbosa-Alleyne |
Ethanol Production by
Recombinant Hosts |
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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 |
| |
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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 |
| |
|
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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 |
| |
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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
|
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|
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
|
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