FCRC Annual Report 2007-2008
|
CENTERS OF EXCELLENCE Cellulosic Biofuels Pilot Plant Annual Accountability Measures Report July 2007 – June 2008 |
|
| 1. Competitive Grants Applied For and Received: 13 faculty members submitted a total of 42 grant proposals amounting to $18,551,378 for this period (Appendix 1a). A total of 33 grants have been awarded to 12 faculty members,, with the amount of $29,305,884 (Appendix 1b). | |
| 2. Total Research Expenditures: A total of $ $ 3,572,181was spent for research, $1,744,873 coming from Federal grants,$1,299,353 from State, $319,348 Universities, $104,453 from Industry and $104,154 from Others (Indirect Costs) (Appendix 2a). The budget status for the Center of Excellence Biofuels Demo Plant which is included in the above summary is in Appendix 2b. | |
| 3. Publications in Refereed Journals From Center Research: 49 papers were published in peer-reviewed journals and 11 papers are accepted for publication and in press. Appendix 3. | |
| 4. Professional Presentations Made on Center Research: 6 faculty members 3 Post-Docs, 1 Biol. Sci, and 2 graduate students presented research results in 49 meetings. Appendix 4. | |
| 5. Invention Disclosures Filed and Issued - n/a | |
|
6. Technologies Licensed and Revenues Received –
US Patent 7,323,551: Cloning and sequencing of pyruvate decarboxylase (PDC) genes from bacteria and uses therefor. Maupin-Furlow, JA, LA Talarico, RK Chandra and LO Ingram (2008) Invention Disclosure: UF # 12873. Engineering bacteria for fermentative hydrogen production at high yield. Do, PM, KT Shanmugam, LO Ingram, A Angerhofer, I Hrdy and L Bardonova (2008) |
|
|
Collaboration Effectiveness |
|
| 7. Collaborations with Other Postsecondary Institutions - 5 faculty members are currently involved with 9 post-secondary institutions. Appendix 5. | |
| 8. Collaborations with K-12 Education Systems/Schools: n/a | |
| 9. Collaborations with Private Industry: Six faculty members are recipients of grants or submitted grant proposals to 8 private industries. Appendix 6 | |
| 10. Students Supported with Center Funds: 9 undergrad, 14 grad students and 17 post-docs with a combined 28 FTE were supported by Center Funds (Appendix 7). | |
| 11. Students Graduated - n/a | |
| 12. Job Placements of Graduates Upon Leaving the Center – n/a | |
|
Economic Development Effectiveness |
|
|
13. Business Start-Ups in Florida - BioEnergy International (4 local employees thus far); expansion of Verenium (now over a dozen local employees; formerly Celunol), and assignment of a full time VP for Business Development in Florida by Verenium. Note that Celunol, based solely on UF technology for ethanol, merged with Diversa to form Verenium. |
|
| 14. Jobs Created and Jobs Saved in Florida – at least 20 | |
| 15. Specialized Industry Training and Education - n/a | |
| 16. Dollars Acquired from Venture Capitalists and Other Investments – n/a | |
|
Outreach Activities |
|
| 17. Activities related to public awareness on research results – Information booths were set-up where posters and banners showed UF expertise and research on alternative energy, and brochures and handouts were given out at the Florida State Fair (Tampa, FL), Waste to Fuel Meeting (Orlando, FL), the University Florida Foundation Annual Stakeholders’ Meeting (Gainesville, FL), and at the Bioenergy Awareness Days (BEAD II; US National Arboretum, Wash DC). Information on current research are also displayed and maintained at the lobby of the Department of Microbiology and Cell Science, and in the center website http://fcrc.ifas.ufl.edu. | |
|
FCRC Faculty Members and Associates |
|
| We have 21 faculty and associate members coming from: other Florida universities (1), industry (2), and the rest from 5 departments within UF. Appendix 8 | |
Appendix1a. Grants Submitted 2007-2008
| Faculty | Source and Project Title |
Date Submitted |
Amount |
| F Altpeter;
Co-PI – Sollenberger Co-PI - Gallo M., Preston J., Vermerris W
Co-PI: Gallo M., Preston J., Moudgil B. |
USDA CSREES: Developing
Non-invasive Genotypes of the Biofuel and Forage Crop Napiergrass.
USDA-RD / DOE: Genetic Engineering of Sugarcane for Increased Fermentable Sugar Yield from Hemicellulosic Biomass CPBR: Total funding including industry co-funding $430,000, 8/01/2008 - 7/31/2010). Development of a Chloroplast Transformation Protocol for Energycane |
2007
2007
2007 |
$120,000
$866,576
$ 145,000 |
| V de Crecy-Lagard | NIH: Investigations of a new prokaryotic GTP cyclohydrolase I enzyme. |
6.2008 |
$291,000 |
| C Gonzalez | UF Research Office (Internal): Disrupting virulence of Pseudomonas aureginosa by redirecting intracellular pools of Acyl-CoA. |
1.7.2008 |
|
| WB Gurley | CPBR: Zinc finger-based regulation of plant gene expression |
6.22.2007 |
$359,441 |
| FBRC - USF (CBD): A strategy for elimination of human-contaminated raw produce from the food supply |
7.13.2007 |
$193,125 1 yr |
|
| Dow AgroSciences: Evaluation of zinc finger-based proteins (ZFPs) to regulate transcription inplants (early start) |
9.10. 2007 |
$34,018 1 yr |
|
| Pasco County (FLDEP): Feasibility Study / Hydrolysis Test Program for Biomass-to-Ethanol Facility at Pasco County Resource Recovery Facility |
10.18.2007 |
$105,000 |
|
| US EnviroFuels (FLDEP): Process and design for a commercial sugar-to-etanol integrated biorefinery: Validation and optimization for sweet sorghum. |
10.18.2007 |
$500,000 |
|
| FL Board of Governors: Consortium on Super Center on Energy |
12.3.2007 |
$4.375M out of $40M |
|
| USDA CSREES: National Needs Fellowships – Biomass systems engineering fellowship |
5.8.2008 |
0 |
|
| FHTCC – BioEnergy LLC Sponsored Research: Biocatalysts for the conversion of carbohydrates to value-added biochemicals. |
4.1.2008 |
$250,000 |
|
| Verenium Corp: Bioethanol sponsored research |
10.1.2007 |
$250,000 |
|
| NO Keyhani | FCPRAC: Development of Asian citrus psyllid, Diaphorina citri, tissue culture cell lines and their use for cultivation of Liberibacter asiaticus and high-throughput antimicrobial testing. |
7.10 |
$125,720 2 yrs |
| G Lorca & C Gonzalez | DOD DTRA: Neutralization of Francisella and Coxiella pathogenicity determinants by FDA approved drugs. |
8.17 |
$1,500,000 |
| NIH: Identification of new Lactobacillus regulators responsive to FD-approved drugs |
6.16.2007 3.16.2008 |
100,000 resubmit |
|
| DOE DE-FG02-05ER15650 Competitive renewal: Identification of Proteasome Substrates of the Haloarchaeon |
8.29 |
$380,169 |
|
| DOE EB Program: Proteasomes and post-translational modification of Haloferax volcanii |
7.31 |
$380,168 |
|
| WLNicholson
Co-PI |
NASA: Biotoxicity of Mars Soils: Compatibility of Terrestrial Microorganisms to Simulated Conditions of Special Regions on Mars |
8.7 |
$280,856 |
| NASA GSRP: Grad Fellowship for Amy Perkins |
2.15.2008 |
$30,000 |
|
| NASA Office of Lunar Advanced Science and Exploration Research: Survival of microorganisms from an analog human space habitat under simulated lunar and Martian conditions. |
9. 20 |
$546,374 |
|
| NASA Office of Lunar Advanced Science and Exploration Research: Survival, growth, and evolution of terrestial bacteria in martian environments |
9. 20 |
$468,374 3yrs |
|
| USDA DOE Direct conversion of hemicellulose to biobased products |
7. 11 white paper |
0 |
|
| USDA-DOE–Genetic Engineering of Sugarcane for Increased Fermentable Sugar Yield from Hemicellulosic Biomass |
11/16, 2007 |
$229,308 |
|
| USDA – Bacterial Systems for processing hemicellulose to biobased prioducts ( Biobased products and bioenergy production research) |
10/1/2008-9/30/2011 |
$1,131,938 |
|
| NIH – Biofilm formation and dispersal mechanisms R01 GM066794-05A1 |
4.1.2008-3.31.2009 |
43,950 |
|
| CPBR - Development of a chloroplast transformation protocol for energycane. |
6/2008 |
45,000 |
|
| USDA-CSREES-NRI: Functional genomics of the termite gut |
06/2008 |
$738,000 |
|
| FL Energy Systems Consortium (FESC) Whitepaper: Digestion of cellulosic biomass by recombinant termite lignocellulases |
11/2007 |
$475,276 |
|
| DOE – Joint Genome Institute: A proposal to sequence the genome of the termite R. flavipes (invited full proposal) |
01/2008 |
$0.00 |
|
| Florida DEP – Renewable Energy Program: Digestion of cellulosic biomass by recombinant termite lignocellulases |
10/2007 |
$442,350 |
|
| DOE Golden DEFG3604GO14019:
Engineering thermotolerant biocatalysts for biomass conversion.
(Supplemental Funding) |
10.15.2007 |
$400,619 |
|
| USDA-DOE: Developing biocatalysts for fermentation of biomass sugars to butanol as an alternate fuel source |
11.16.2007 |
$900,000 |
|
| DOT (UNIV OF TENNESSEE): Evaluation of reduced lignin softwood and hardwoods for improved conversion to bioethanol. |
10.1.2007 |
$42,750 |
|
| FCPRAC: ReducingLliberibacter in the plant by inoculation with an antibiotic producing Rhizobium strain |
7.10 |
$35,000 |
|
| NASA Office of Lunar Advanced Science and Exploration Research: Survival of microorganisms from an analog human space habitat under simulated lunar and Martian conditions. |
9. 20 |
(546,374) |
|
| NSF MO: Collaborative Research: How are archaeal diversity, abundance, and function regulated in agroecosystems? |
10. 8.2007 |
$1,500,000 |
|
| NIH NICHD (UF Medicine): Intestinal microecology inflammatory,markers and necrotizing enterocolitis. |
11/16/2007 |
$463,139 |
|
| NSF: Individual Presidential Award for Excellence Science, Mathematics and Engineering Mentoring: Howard M Johnson |
3.4.2008 |
$10,000 |
|
| Juvenile Diabetes Foundation: Correlatino of humat gut microbiota with the onset of type 1 diabetes. |
5.1.2008 9.1.2008-8.31.2011 |
$674,853 |
|
|
13 |
|||
| TOTAL # FACULTY |
42 |
||
| TOTAL NUMBER OF GRANTS SUBMITTED |
$18,551,378 |
||
Appendix 1b. Grants Awarded 2007-2008
| AWARDED |
|||
| Start/ End Dates |
Amount |
||
| USDA-CSREES: Developing Non-invasive Genotypes of the Biofuel and Forage Crop Napiergrass. | 10/01/2008 - 9/30/2010 |
$120,000 |
|
| USDA-RD / DOE: Genetic Engineering of Sugarcane for Increased Fermentable Sugar Yield from Hemicellulosic Biomass | 7/01/2008 - 6/30/2011 |
$866,576 |
|
| CPBR: Development of a Chloroplast Transformation Protocol for Energycane. Industry co-funding | 8/01/2008 - 7/31/2010 |
$145,000 $285,000 |
|
| Total Altpeter | |||
| DOE SE-PS02-07ER07-14: Phylogenomics-guided validation of function for conserved unknown genes | 9/1/2007 8/31/2010 |
500,000.00 |
|
| EVOLUGATE: Characterization of microorganisms obtained by experimental evolution | 1.2.2008 7.1.2008 |
11,002.50 |
|
| UF Research Offiice: "Genomic Analysis of Vibrio vulnificus: Understanding and Preventing Human Disease by Understanding Lifestyle in Mammals, Oysters, and Biofilms" | 5.1.2008 |
9,213.00 |
|
| Total – de Crecy |
600,216.50 |
||
| Jamie S. Foster | UCF (NASA POST-DOC): Microbial Mats, solar radiation, and genetic response | 8.1.2007 7.31.2008 |
25,000.00 |
| Total Foster |
25,000.00 |
||
| WB Gurley | CPBR(+ Dow Agrosciences and ArborGen) - Zinc finger-based regulation of plant gene expression | 3.1.2008 1.31.2010 |
359,441.00 |
| FBRC - USF (CBD): A strategy for elimination of human-contaminated raw produce from the food supply | 5.1.2008 4.30.2009 |
193,125.00 |
|
| Fl Dept of AG & Consumer Ser: Developing promoters that will prevent expression of foreign genes in fruit | 9.30.2008 9.29.2009 |
50,000.00 |
|
| UF Foundation |
71,000.00 |
||
| Total Gurley |
.00 |
||
| LO Ingram | |||
| Co-PI, Forest Res & Conserv | SUNGRANT: Evaluation of Reduced Lignin Softwood and Hardwoods for Improved Conversion to Bioethanol | 10.1.2007 9.30.2008 |
49,950.00 |
| Verenium: Verenium Sponsored Research | 8.21.2007 2.28.2008 |
250,000.00 |
|
| BioEnergy LLC: Production of organic acids, polymers, and sugar-based specialty chenicals | 04.1.2007 03.31.2010 |
1,000,000.00 |
|
| FL State Legislature: Cellulosic Ethanol Research Pilot Plant |
20,000,000.00 |
||
| FHTCC: Bioenergy sponsored research on biomass conversion to organic acids: Biocatlysts for the conversion of carbohydrates to biochemicals | 6.1.2007 5.31.2008 |
100,000.00 |
|
| DOE-CDP Congressionally Directed Programs: Florida Renwable Energy program | 5.1.2008 4.30.2009 |
738,000.00 |
|
| HATCH: IFAS Energy Projects |
500,000.00 |
||
| Total Ingram |
.00 |
||
| NO Keyhani | NSF REU Site: Fueling a microbiology research training network from the University of Florida. (transfer from Rasche) | 3.1.2007 2.28.2010 |
242,363.00 |
| Total Keyhani |
242,363.00 |
||
| JA Maupin-Furlow | DOE JGI: Sequencing the genome of the alkaliphilic haloarcheaon Natrialba magadii ATCC4309, Community Sequencing Program, Department of Energy, JGI CSP 788459 | 16.05.2007 present |
No $ compensation |
| DOE Biosciences, DE-FG02-05ER15650: Proteasomes and Post-translational Modification of Haloferax volcanii Proteins | 7.15.2008 7.14.2010 |
380,169.00 |
|
| Total Maupin-Furlow |
380,169.00 |
||
| WL Nicholson Co-PI: Schuerger |
NASA GSRP: NNX07AO60H - Grad Fellowship for Amy Perkins | 7.23.2007 7.22.2008 |
30,000.00 |
| NASA Astrobiology: NNH06ZDA001N-EXOB: Astrobiology: Exobiology and Evolutionary Biology - Survival, growth, and evolution of terrestrial bacteria in martian environments. | 7.1.2008 6.30.2011 |
468,374.00 |
|
| Co-PI with Schuerger | NASA: Biotoxicity of Mars Soils: Compatibility of Terrestrial Microorganisms to Simulated Conditions of Special Regions on Mars | 6.1.2008 5.30.2011 |
89,389.00 |
| Co-PI with Schuerger | NASA Lunar Advanced Science and Exploriation Research (LASER) Program): Survival of microorganisms recovered from an analog human space and exposed to simulated lunar conditions. | 6.1.2008 5.31.2012.2011 |
546,847.00 |
| Total Nicholson |
1,134,610.00 |
||
| JF Preston | |||
| Ingram, Shan | |||
| Altpeter- PI | USDA-DOE–Genetic Engineering of Sugarcane for Increased Fermentable Sugar Yield from Hemicellulosic Biomass | Awarded |
In Process |
| Romeo - PI | NIH – Biofilm formation and dispersal mechanisms R01 GM066794-05A1 | 4.1.2008 3.31.2009 |
43,950.00 |
| Peter - PI | DOT(Univ of Tennessee: Evaluation of reduced lignin softwood and hardwoods for improved conversion to bioethanol. | 10.1.2007 9.30.2008 |
42,750.00 |
| Total Preston |
.00 |
||
| M Scharf | CPBR - Consortium for Plant Biotechnology Research /DOE: Genomic dissection of cellulose utilization in termites | 2008 |
$120,000 |
| Total Scharf |
$120,000 |
||
| KT Shanmugam | DOE Golden DEFG3604GO14019:
Engineering thermotolerant biocatalysts for biomass conversion.
(Supplemental Funding) |
10.15.2007 |
400,619.00 |
| Peter - PI | DOT (UNIV OF TENNESSEE): Evaluation of reduced lignin softwood and hardwoods for improved conversion to bioethanol. | 10.1.2007 9.30.2008 |
42,750.00 |
| Total Shan |
443,369.00 |
||
| EW Triplett | NSF: Integrating genomics through the undergraduate microbiology curriculum | 1.1.2008 12.31.2009 |
155,365.00 |
| With Co-PI Drew | FCPRAC: ReducingLliberibacter in the plant by inoculation with an antibiotic producing Rhizobium strain |
35,000.00 |
|
| Co-PI: Univ Colorado, Oregon State Univ | NSF MO: Collaborative Research: How are archaeal diversity, abundance, and function regulated in agroecosystems? | Awarded |
1,500,000.00 |
| Total Triplett |
.00 |
||
| NUMBER OF RECIPIENT FACULTY 12 | |||
|
TOTAL AMOUNT AWARDED $29,305,884 |
|||
Appendix 2. FCRC Summary of Expenses July 2007 - June 2008
| SOURCE OF FUNDING |
|||||
| FACULTY |
Federal |
State |
Industry/Private |
University |
Other (IDC) |
| De Crecy |
88,058.20 |
11,009.01 |
74,595.47 |
||
|
313,765.61 |
|||||
|
19,149.10 |
|||||
| Foster |
1,628.83 |
||||
| Gurley |
30,918.35 |
14,516.64 |
|||
|
37.50 |
|||||
| Ingram |
71,808.67 |
10,4154 |
186,796.58 |
104,153.87 |
|
|
291,027.61 |
451,348.13 |
35,140.92 |
|||
|
667,672.00 |
|||||
| Maupin |
76,939.59 |
||||
|
100,465.64 |
|||||
| Nicholson |
25,709.14 |
||||
|
43,998.45 |
|||||
|
2,673.62 |
|||||
| Preston |
43,180.27 |
46,942.11 |
23,267.27 |
||
|
4,961.01 |
|||||
| Rasche/Keyhani |
33,592.51 |
19,093.78 |
4,853.98 |
||
|
77,313.15 |
13,185.21 |
||||
| Shanmugam |
322,485.48 |
||||
| Triplett |
129,510.36 |
10,785.00 |
1,688.61 |
||
|
70,028.83 |
2,196.62 |
18,362.95 |
|||
|
207.36 |
|||||
|
34,959.32 |
|||||
| TOTAL | |||||
| TOTAL EXPENSES $ 3,572,180.75 | |||||
Appendix 2b
Budget Status for Center of Excellence BioFuels Demo Plant
2007-2008
1. Sponsor: Florida Board of Governors
Award:
$2,250,000.00|
Budget Item |
Amount Allocated |
Expenses |
Balance |
| BioFuels Plant |
1,000,000 |
667,672.00 |
332,328.00 |
| Equipment |
1,000,000 |
409,565.21 |
590,434.79 |
| Operating Expenses |
250,000 |
134,583.33 |
115,416.67 |
| TOTALS |
$2,250,000 |
$ |
$ |
2. Sponsor: IFAS Senior Vice President for Research (USDA CSREES)
Award: January 2007 = $200,000 June 2008 = $300.000
|
Budget Item |
Amount Allocated |
Expenses
|
Balance
|
| BioFuels Plant |
200,000 |
200,000 |
0.00 |
| Operating Expenses |
300,000 |
291,027.61 |
8,972.39 |
|
TOTALS |
$500,000 |
$491,027.61 |
$8,972.39 |
3. Budget Summary
|
Sponsor |
Amount |
Expenses
|
Balance
|
|
Florida Board of Governors
|
$2,250,000 |
$ |
$ |
| IFAS Senior Vice President for Research (USDA CSREES) |
$500,000 |
$491,027.61 |
$8,972.39 |
| TOTALS |
$2,750,000 |
Appendix 3. Publications: In Press* Published* Patents/Invention Disclosures*
In Press
Shively, J. M., G. C. Cannon, S. HeinHorst, J. A. Fuerst, D. A. Bryant, E. Gantt, J. A. Maupin-Furlow, D. Sch
űler, F. Pfeifer, R. Docampo, C. Dahl, J. Preiss, A. Steinbűchel, B. A. Federici. 2009. Intracellular structures of Prokaryotes: Inclusions, compartments and assemblages. Encyclopedia of Microbiology. Elsevier Press, St. Louis, Mo.Kirkland, P. A.1, M. A. Humbard1, C. J. Daniels and J. A. Maupin-Furlow. 2008. Shotgun proteomics of the haloarchaeon Haloferax volcanii. J. Proteome Res. (on line – in press).
Yomano, L.P., S.W. York, S. Zhou, K.T. Shanmugam, and L.O. Ingram. 2008. Re-engineering Escherichia coli strain KO11 for ethanol production from xylose in mineral salts medium. Metabolic Engineering (submitted for publication).
Jarboe, L.R., K.T. Shanmugam, L.O. Ingram. Ethanol Encyclopedia of Microbiology (3rd Ed) Ed. D. Majumder-Russell. Elsevier, 2008 (in press).
Perkins, A.E., A.C. Schuerger, and W.L. Nicholson. 2008. Isolation and characterization of rpoB mutations causing rifampicin resistance in Bacillus subtilis spores exposed to simulated Mars surface conditions. Astrobiology, in press.
X.B. Li, D.A. Huber, G.L. Powell, T.L. White, G.F. Peter (2008). Breeding for Improved Growth and Juvenile Corewood Stiffness in Slash Pine. Canadian J. For. Research. In Press
L.R. Schimleck, J.A. Tyson, P.D. Jones, G.F. Peter, R.F. Daniels, A. Clark, (2008). Investigation of the number of spectra per radial strip and number of radial strips per plantation required for robust Pinus taeda L. wood property calibrations. J. Near Infrared Spectroscopy. In press.
Chow, V., G. Nong, J. F. Preston. 2008. Structure, function and regulation of the aldouronate-utilization gene cluster from Paenibacillus sp. JDR-2. J. Bacteriol. in press.
Scharf, M.E. and Tartar, A. 2008. Insect digestomes as sources for novel lignocellulases. Biofuels, Bioproducts and Biorefining. In Press.
Jantama, K., X. Zhang, J.C. Moore, K.T. Shanmugam, S.A. Svoronos, and L.O. Ingram. 2008. Eliminating side products and increasing succinate yields in engineered strains of Escherichia coli C. Biotechnol Bioeng. August, 2008 preprint; online
Tartar, A., Zhou, X., Boucias, D.G. and Scharf, M.E. (2008) Digestome analysis reveals evidence of collaborative digestion and lignin degradation in the termite R. flavipes. Proc Nat Acad Sci USA (submitted for publication).
Published
2008
Naponelli V., Noiriel A., Ziemak M. J., Beverley S. M., Lye L. F., Plume A. M,, Botella J. R, , Loizeau K., Ravanel S., Rébeillé F., de Crécy-Lagard V., and A. D. Hanson. (2008). Phylogenomic and functional analysis of pterin-4a-carbinolamine dehydratase family (COG2154) proteins in plants and microorganisms. Plant Physiol. 146:1515-27.
Brown, G., A.Singer, M. Proudfoot, S.Tatiana, Y.Kim, C. Chang, I.Dementieva, E. Kuznetsova, C. Gonzalez, A. Joachimiak, A. Savchenko, A.Yakunin. 2008. Functional and structural characterization of four glutaminases from Escherichia coli and Bacillus subtilis. Biochemistry 47:5724:5735.
Peterson J.D., and L.O.Ingram. 2008. Anaerobic respiration in engineered Escherichia coli with an internal electron acceptor to produce fuel ethanol. Ann. N.Y. Acad. Sci. 1125: 363-372.
Miller, E.N., L.O. Ingram. 2008. Sucrose and overexpression of trehalose biosynthetic genes (otsBA) increase dessication tolerance of recombinant Escherichia coli. Biotechnol Lett. 30: 503-508.
Kim, Y., L. O. Ingram and K. T. Shanmugam. 2008. Dihydrolipoamide dehydrogenase mutation alters the NADH sensitivity of pyruvate dehydrogenase complex of Escherichia coli K-12. J. Bacteriol. 190:3851-3858.
Kirkland, P. A., M. A. Gil, I. M. Karadzic, and J. A. Maupin-Furlow. 2008. Genetic and proteomic analyses of a proteasome-activating nucleotidase A mutant of the haloarchaeon Haloferax volcanii. J. Bacteriol. 190:193-205.
De Castro, R. E., D. M. Ruiz, M. I. Giménez, M. X. Silveyra, R. A. Paggi, and J.A. Maupin-Furlow. 2008. Gene cloning and heterologous synthesis of a haloalkaliphilic extracellular protease of Natrialba magadii (Nep). Extremophiles 12:677-687.
Bidle, K. A., P. A. Kirkland1, J. Nannen, and J. Maupin-Furlow. 2008. Proteomic analysis of Haloferax volcanii reveals up-regulation of the transcriptional activator PspA in response to salt stress. Microbiology 154:1436-1443.
Itoh, Y., J.D. Rice, C Goller, A. Pannuri, J. Taylor, J. Meisner, T.J. Beveridge, J.F. Preston, III, and T Romeo. 2008. Roles of pgaABCD genes in synthesis, modification and export of the Escherichia coli biofilm adhesion poly-ß-acectyl-d-glucosamine. J. Bacteriology. 3670-3680.
Schmidt, L., L. Mouton, G. Nong, D. Ebert, and J. F. Preston, III. 2008. Genetic and immunological comparison of the cladoceran parasite Pasteuria ramosa with the nematode parasite Pasteuria penetrans. Appl. & Environ. Microbiol. 74:259-264.
Perkins, A. and W.L. Nicholson. 2008. Uncovering metabolic capabilities of Bacillus subtilis using phenotype profiling of rifampicin-resistant rpoB mutants. J. Bacteriol. 190:807-814.
Scheurger, A., P. F-Cavazos, L.A. Clausen, J.E. Mones, P.H. Smith and W.L. Nicholson. 2008. Slow degradation of ATP in simulated mariona environmnents suggests long residence times for the biosignature molecule on spacecraft surfaces on Mars. Icarus. 194:86-100.
Moeller, R., P. Setlow, G. Horneck, T. Berger, G. Reitz, P. Rettberg, A.J. Doherty, R. Okayasu, and W.L. Nicholson. 2008. Role of the major small, acid-soluble spore proteins, spore-specific and universal DNA repair mechanisms in the resistance of Bacillus subtilis spores to high energy charged (HZE) particle bombardment. J. Bacteriol. 190: 1134-1140.
Fajardo-Cavazos, P., A.C. Schuerger, and W.L. Nicholson. 2008. Persistence of biomarker ATP and ATP-generating capability in bacterial cells and spores contaminating spacecraft materials under Earth and simulated Mars environments. Appl. Environ. Microbiol. 74: 5159-5167.
Gioia, J., S. Yerrapragada, X. Qin, H. Jiang, O.C. Igboeli, D. Muzny, S. Gugan-Rocha, Y. Ding, A. Hawes, W. Liu, L Perez, C. Kovar, H. Dinh, S. Lee, L. Nazareth, P. Blyth, M. Holder, C. Buhay, M.R. Tirumalai, Y. Liu, I. Dasgupta, L. Bokgetache, M. Fujita, F. Karouia, P.E. Moorthy, J. Siefert, A. Uzman, P. Buzumbo, A. Verma, H. Zwiya, B.D. McWilliams, A. Olowu, K.D. Clinkenbeard, D. Newcombe, L. Golebiewski, J.F. Petrosino, S.K. Highlander, W.L. Nicholson, G.E. Fox, K. Venkateswaran, and G.M. Weinstock. 2008. Paradoxical DNA repair and peroxide resistance gene conservation in Bacillus pumilus SAFR-032. PLoS ONE 9: e298 (10 pp.)
Peter G (2008) Southern Pines: A resource for bioenergy. In Vermerris V, ed, Genetic Improvement of Bioenergy Crops. Springer, New York, NY, pp 397-414
Liu X, Lee S-C, Casella G, Peter GF (2008) Assessing agreement of clustering methods with gene expression microarray data. Computational Statistics and Data Analysis 52: 5356-5366
Zhou, X., Wheeler, M.M., Oi, F.M. and Scharf, M.E. 2008. RNA interference in the termite R. flavipes through ingestion of double-stranded RNA. Insect Biochem Mol Bio 38, 805-815
Zhou, X., Wheeler, M.M., Oi, F.M. and Scharf, M.E. 2008. Inhibition of termite cellulases by carbohydrate-based cellulase inhibitors: evidence from in vitro biochemistry and in vivo feeding studies. Pestic Biochem Physiol 90, 31-41
Jantama, K., M.J. Haupt, S.A. Svoronos, X. Zhang, J.C. Moore, K.T. Shanmugam, L.O. Ingram. 2008. Combining metabolic engineering and metabolic evolution to develop nonrecombinant strains of Escherichia coli C that produce succinate and malate. Biotechnol and Bioengineering. 99(5): 1140-1153.
Shanmugan, K.T. and L.O. Ingram. 2008. Engineering biocatalysts for production of commodity chemicals. Journal of Molecular Microbiology and Biotechnology. 15:8-15.
Roesch, L.F., F. A. O. Camargo, F. E. Bento and E.W. Triplett. 2008. Biodiversity of diazotrophic bacteria within the soil, root and stem of field-grown maize. Plant Soil 302:71-104.
Drew, J. and E.W. Triplett. 2008. Whole genome sequencing in the undergraduate classroom: outcomes and lessons from a pilot course. J. of Microbiol and Biol. Education. Pp.3-11.
2007
de Crécy, E., Metzgar, D., Allen, C., Penicaud, M., Lyons, B., Hansen, C. J., and de Crécy-Lagard, V. (2007) Development of a novel continuous culture device for experimental evolution of bacterial populations. Appl Microbiol Biotechnol. 77:489-496
de Crécy-Lagard, V., Marck, C., Brochier-Armanet, C., and Grosjean, H. (2007) Comparative RNomics and Modomics in Mollicutes: Prediction of Gene Function and Evolutionary Implications. IUBMB Life, 1-25
de Crécy-Lagard, V., El Yacoubi, B., de la Garza, R. D., Noiriel, A., and Hanson, A. D. (2007) Comparative genomics of bacterial and plant folate synthesis and salvage: predictions and validations. BMC Genomics 8, 245
de Crécy-Lagard V. (2007). Identification of genes encoding tRNA modification enzymes via comparative genomics. In Methods in Enzymology. (Gott, J., ed.) Academic Press, New-York. Vol. 425, Chapter 7 p. 153-83.
de Crécy-Lagard V., and A. D. Hanson. (2007). Finding novel metabolic genes through plant-prokaryote phylogenomics.Trends Microbiol. Sci. 15:563-70.
Bacher, J. M., Waas, W. F., Metzgar, D., de Crécy-Lagard, V., and Schimmel, P. (2007) Genetic code ambiguity confers a selective advantage on Acinetobacter baylyi. J Bacteriol 189:6494-6496
Rhee, M. S., J. W. Kim, Y. Qian, L. O. Ingram and K. T. Shanmugam. 2007. Development of plasmid vector and electroporation condition for gene transfer in sporogenic lactic acid bacterium, Bacillus coagulans. Plasmid 58:13-22.
Gil, M. A., K. E. Sherwood1,, and J. A. Maupin-Furlow. 2007. Transcriptional linkage of Haloferax volcanii proteasomal genes with non-proteasomal gene neighbors including RNase P, MOSC domain and SAM-methyltransferase homologs. Microbiology 153: 3009-3022.
Kirkland, P. A., C. J. Reuter, and J. A. Maupin-Furlow. 2007. Effect of proteasome inhibitor clasto-lactacystin-β-lactone on the proteome of the haloarchaeon Haloferax volcanii. Microbiology 153: 2271-2280.
Moeller, R., E. Stackebrandt, G. Reitz, P. Rettberg, A.J. Doherty, G. Horneck, and W.L. Nicholson. 2007. Role of DNA repair by non-homologous end joining in Bacillus subtilis spore resistance to extreme dryness, mono- and polychromatic UV and ionizing radiation J. Bacteriol. 189: 3306-3311.
Moeller, R., T. Douki, J. Cadet, E. Stackebrandt, W. L. Nicholson, P. Rettberg, G. Reitz, andG. Horneck. 2007. UV-radiation-induced formation of DNA bipyrimidine photoproducts in Bacillus subtilis endospores and their repair during germination. Int. Microbiol. 10: 39-46.
Maughan, H., J. Masel, C.W. Birky, Jr., and W.L. Nicholson. 2007. The roles of mutation accumulation and selection in loss of sporulation in experimental populations of Bacillus subtilis. Genetics 177: 937-948.
Fajardo-Cavazos, P., A.C. Schuerger, and W.L. Nicholson. 2007. Testing interplanetarytransfer of bacteria by natural impact phenomena and human spaceflight activities. Acta Astronautica 60: 534-540.
Peter GF (2007) Developments in Biological Fibre Treatment. Pira International, Surrey, UK, p -89.
Peter G, White D, de la Torre R, Singh R, Newman D (2007) The Value of Forest Biotechnology: A Cost Modeling Study with Loblolly Pine and Kraft Linerboard in the Southeastern USA. International Journal of Biotechnology 9: 415-435.
Azencott HR, Peter GF, Prausnitz MR (2007) Influence of the cell wall on intracellular delivery to algal cells by electroporation and sonication. Ultrasound in Medicine and Biology 33: 1805-1817.
Li X, Shupe T, Hse C, Peter G, Eberhardt T (2007) Anatomical and Chemical Composition Changes with Maturation of the Bamboo Species Phyllostachys pubescens. Journal of Tropical Forestry 19: 6-12.
Li XB, Huber DA, Powell GL, White TL, Peter GF (2007) Breeding for improved growth and juvenile corewood stiffness in slash pine. Canadian Journal of Forest Research-Revue Canadienne De Recherche Forestiere 37: 1886-1893.
Roth BE, Li X, Huber DA, Peter GF (2007) Effects of management intensity, genetics and planting density on wood stiffness in a plantation of juvenile loblolly pine in the southeastern USA. Forest Ecology and Management 246: 155-162.
Vales T, Feng X, Ge L, Xu N, Cairney J, Pullman GS, Peter GF 2007. Improved somatic embryo maturation in loblolly pine by monitoring ABA-responsive gene expression. Plant Cell Rep 26: 133-43.
Nong, G., V. Chow, L.M. Schmidt, D.W. Dickson, J.F. Preston. 2007. Multiple-strand displacement and identification of SNPs as markers of genotypic variation of Pasteuria penetrans biotypes infecting root-knot nematodes. FEMS Microbiol. Ecol. 61:327-336.
Chow, V., Nong, J.F. Preston. 2007. Structure, function and regulation of the aldouronate-utlization gene cluster form paenobacillus sp. JDR-2. J Bacteriol. 189:8863-8870.
Zhou, X., Wheeler, M.M., Scharf, M.E. and Oi, F.M. 2007. Molecular and biochemical markers for monitoring dynamic shifts in cellulolytic protozoa in Reticulitermes flavipes. Insect Biochem Mol Biol 37, 1366-1374.
Zhou, X., Smith, J.A., Koehler, P.G., Oi, F.M., Bennett, G.W. and Scharf, M.E. 2007. Correlation of cellulase gene expression and cellulolytic activity throughout the gut of the termite R. flavipes. GENE 395, 29-39.
Zhang, X., K. Jantama, J. C. Moore, K. T. Shanmugam and L. O. Ingram. 2007. Production of L-alanine by metabolically engineered Escherichia coli. Appl Microbiol Biotechnol. 77:355-366.
Jarboe, L.R., T.B. Grabar, L.P. Yomano, K.T. Shanmugam, L.O. Ingram. 2007. Development of ethanologenic bacteria. Book Chapter. Adv. Biochem Engin/Biotechnol 108: 237-261.
Invention Disclosure:
UF # 12873 Engineering bacteria for fermentative hydrogen production at high yield. Do, PM, KT Shanmugam, LO Ingram, A Angerhofer, I Hrdy and L Bardonova (2008)
Patents:
7,323,551 Cloning and sequencing of pyruvate decarboxylase (PDC) genes from bacteria and uses therefor.
Maupin-Furlow, JA, LA Talarico, RK Chandra and LO Ingram (2008)
Appendix 4. Research Presentations | Meetings Attended
|
Presenter |
Topic/Venue |
Place and Date |
| V Chow | Microbial Genomics and
Metagenomics Workshop |
DOE Joint Genome Institute at Walnut Creek, California, May 19-23, 2008 |
| P Do | Engineering Escherichia coli for Fermentative Dihydrogen Production: Potential role of NADH-ferredoxin oxidoreductase from the hydrogenosome of anaerobic protozoa. | Biotechnology for Fuels and Chemicals Meeting. Society for Industrial Microbiology. May 4-7, 2008 |
| S P Gomez | Exhibitor, Florida State Fair | Tampa, FL Feb. 7-18, 2008 |
| UF CALS Career Expo | Gainesville, FL Feb 20, 2008 | |
| Exhibitor, UFF Board Meeting | Gainesville, FL, March 8, 2008 | |
| Waste to Fuel Summit: Exhibitor and Meeting Attendee | Orlando, FL April 6-8, 2008 | |
| BioEnergy Awareness Days (BEAD II) Exhibitor and Meeting Attendee | US National Arboretum, Washington DC, 6-19-22, 2008 | |
| Florida Governor’s Action Team on Energy and Climate Change |
Tallahassee, FL Oct 4-5, 14-16, 28-30, 2007; Jan. 31-Feb 2, 2008; March 16-17, 2008 |
|
| SIM RAFT VII Meeting, Inited Speaker of Cellulosic Ethanol |
St. Petersburg, FL Nov.5-7,2007 |
|
| Meeting with Agriculture Commisioner Bronson; Tour of Okaleenta Mill and pilot plant facility |
West Palm Beach, Jan 7-8,2008 |
|
|
ASM Board of Governor’s Meeting |
Tucson, AZ Jan.11-12, 2008 |
|
|
Verenium Corporation Research Progress and Plans |
San Diego, CA Jan.19-21, 2008 |
|
|
Biofuels in the Americas: Technology, Investment and the Path |
Miami, FL Jan. 23-24, 2008 |
|
|
Meeting with BioEnergy LLC |
Gainesville, FL Feb 5, 2008 |
|
| UFF Board Meeting Invited Speaker |
Gainesville, FL , March 8, 2008 |
|
| 4th National 25x25 Renewable Energy Summit; Speaker on Cellulosic Ethanol |
Omaha, NE March11-13, 2008 |
|
| Speaker at SURA Meeting and Recipient of the 2008 Award |
Newport News, VA April 7-8, 2008 |
|
| Annual Meeting of the National Academy of Sciences |
Washington DC April 27-28, 2008 |
|
| Cellulosic ethanol. International Visitor Corps of Jacksonville, Sustainable Development and Renewable Energy |
Gainesville, FL. 7/2007 |
|
| Florida Governor’s Action Team on Energy and Climate Change |
Tallahassee, FL. 8/2007 |
|
|
Alternative Energy Summit |
Jupiter, FL. 8/2007 |
|
| Cellulosic ethanol. Florida Farm Bureau Annual Meeting |
Bushnell, FL. 9/2007 |
|
| Cellulosic Perspective for the Southeast.AHS CARET Summer Meeting at the University of Kentucky, KY. |
UK, KY 8/2007 |
|
| Biofuels Test Pilot Plant. Conceptual Design and Plans for the Cellulosic Ethanol Research Demonstration Plant |
Cincinnati, OH. 9/2007 |
|
| Lactic acid production using vacterial biocatalysts. Bioenergy Investors Meeting |
Gainesville, FL. 9/2007 |
|
| Proteasomes and Metabolic Engineering. Synthetic Genomics, Inc. | La Jolla, Calif., August 13, 2008. | |
| Archaeal Proteasomes and Post-translational Modification. | Ann. Mtg. Society of Industrial Microbiology. August 12, 2008 | |
| Emerging Roles of Proteasomes in Archaea. Ann. Mtg. Amer. Soc. Microbiol. | Boston, MA. June 3, 2008. | |
| Proteasomes and their Global Impact on Archaeal Cells. Gene Regulation and Genome Function in Archaea. Special Research Symposium. | Frankfurt, Germany. October 2, 2007 [Keynote Speaker]. | |
| Archaeal Proteasomes and Post-Translational Regulation. Session: Post-Translational Regulatory Mechanisms of Archaea. Gordon Research Conference, Archaea: Ecology, Metabolism, and Microbiology. | Andover, NH. August 21, 2007. | |
| Archaea as Models for Analysis of Ubiquitin-independent Proteasome Function. | University of Florida. March 26, 2007 | |
| Proteasomes and their Role in Archaeal Physiology. | Ohio State University. March 8, 2007 | |
| Jonathan Moore | Instituto de Biotechnologia, UNAM : Invited speaker and lecturer on renewable energy | Cuarnavaca, Mexico Oct 13-18, 2007 |
| (INVITED ORAL) "Bacillus subtilis as a platform for production of biofuels", Department of Microbiology & Cell Science Graduate Student Symposium. |
Jacksonville Beach, FL, Aug 18, 2007. |
|
| Rifampicin-resistance mutations
in rpoB causing global shifts in Bacillus subtilis physiology and metabolism |
2nd ASM Conference on Integrating Metabolism and Genomics (IMAGE2)Montreal, Canada, May 3, 2007 |
|
| DNA damage, repair, and evolution in bacteria during interplanetary transport |
Astrobiology Small Payloads Workshop, NASA-Ames, CA, June 19, 2007 |
|
| Interplanetary transport of microorganisms: survival, growth, and adaptation. |
Bioastronomy 2007 Meeting, San Juan, Puerto Rico, July 16-20, 2007 |
|
| Bacillus subtilis as a platform for production of biofuels |
Deptof Microbiology & Cell Science Graduate Student Symposium, Jacksonville Beach, FL, Aug 18, 2007 |
|
| Interplanetary Transport of Microorganisms: Biogeological Considerations |
Japan Geoscience Union Meeting, Chiba, Japan, May 25-30, 2008. |
|
| Bacillus subtilis as a platform for bio-based fuels and chemicals |
UF Citrus Research and Education Center, Lake Alfred, FL, May 2, 2008. |
|
| MS Ou | Thermophilic Bacillus coagulans requires Less Cellulases for Simultaneous Saccharification and Fermentation of Cellulose to Products than Mesophilic Microbial Biocatalysts. |
Biotechnology for Fuels and Chemicals Meeting. Society for Industrial Microbiology. May 4-7, 2008 |
| Ethanol Pilot Plant Meeting with Engineers |
Cincinnati, OH April 10-11 , 2008 |
|
| 30th Symposium on Biotechnology for Fuels and Chemicals |
New Orleans, LA May 4-7, 2008 |
|
| James Petterson | 30th Symposium on Biotechnology for Fuels and Chemicals |
New Orleans, LA May 4-7, 2008 |
|
Developing Microbial Biocatalysts for Conversion of Lignocellulosic Biomass to Chemicals and Liquid Fuels. Meeting: Energy Biosciences Strategy for India |
New Delhi, India, September 10, 11, 2007 |
|
| Developing Microbial Biocatalysts for Conversion of Lignocellulosic Biomass to Chemicals and Liquid Fuels |
Coskata, NIU Chicago, IL April 9, 2008 |
|
| Producing cehmicals and fuels for biomass-based biorefinery |
Northern Illinois University, Dekalb, Il April 10, 2008 |
|
| Metabolic engineering of microbial biocatalysts for conversion of lignocellulosic biomass to chemicals and fuels |
Northern Illinois Unviersity, Delkalb, IL, April 11, 2008 |
|
| Xueli Zhang | BIT ist Annual World Congress of IBIO Industrial Biotechnology |
Shanghai, China April.15-18, 2008 |
Appendix 5. Collaborations with Postsecondary Institutions
| Faculty | Description of Collaboration | Classification of Institution |
| De Crecy | Subcontract
to: Portland State University Burnham Institute |
Public and Private, non-Florida Institutions |
| Foster | Subcontract grant recipient from Unviersity of Central Florida | Public Florida Institution |
| Collaborator: Rider Unversity | Non-Florida Institution | |
| Collaborator: Universidad Nacional del Mar Plata, Argentina | International Institution | |
| Collaborator: Tamil Nadu Agricultural Unviersity, Tamil Nadu, India | International Institution | |
| Collaborator: University of Djelfa, Algeria | International Institution | |
| Collaborator: Ohio State Unviersity | Public non-Florida Institution | |
| Preston | Subcontract
grant recipient from: Emory University University of Tennessee |
Non-Florida
Private University Non-Florida Public University |
| Triplett | Grant
collaborator:
Seminole Community College Colorado University Oregon State University |
Florida
Public College Non- Florida Public Institutions |
Appendix 6. Collaborations with Private Industry
| Faculty | Description of Collaboration |
| De Crecy-Lagard | Grant sponsor: Evolugate, LLC. |
| Keyhani | Grant Sponsor: Evolugate, LLC |
| Grant sponsor: BioEnergy International | |
| Grant sponsor: Verenium | |
| Grant proposal submitted to US EnviroFuels, LLC | |
| Grant proposal submitted to Pasco County, FL | |
| Grant Sponsor: Dow Agrosciences | |
| Grant Sponsor: ArborGen Company | |
| Grant sponsor: Consortium for Plant Biotechnology Research (CPBR) | |
| Preston | Grant sponsor: Consortium for Plant Biotechnology Research (CPBR) |
| Triplett | Grant sponsor: Consortium for Plant Biotechnology Research (CPBR) |
Appendix 7.
Headcount and FTE totals for undergraduate, graduate, and post-doctorate students.
|
Number and FTE |
|||||||
| Undergrad | FTE | Grad | FTE | Post-Doc | FTE | ||
| De Crecy |
0 |
0 |
1 |
0.5 |
1 |
1 |
1.5 |
| Ingram |
7 |
1.4 |
4 |
2.0 |
7 |
7 |
9.4 |
| Keyhani |
0 |
0 |
1 |
0.5 |
0 |
0 |
0.5 |
| Maupin-Furlow |
16 |
3.2 |
4 |
2.0 |
2 |
1.5 |
6.7 |
| Nicholson |
0 |
0 |
1 |
0.5 |
1 |
1 |
1.5 |
| Preston |
1 |
0.2 |
1 |
0.5 |
3 |
2.5 |
2.7 |
| Shanmugam |
1 |
0.2 |
2 |
1.0 |
3 |
3 |
4.2 |
| Triplett |
0 |
0 |
1 |
0.5 |
1 |
1 |
1.5 |
| TOTAL | |||||||
|
Undergraduate Students |
Grauduate Students |
Post-docs |
| Alex Vela | Changhao Bi | Virginia Chow |
| Andrea Rosero | Phi Do | Ryan Geddes (visiting Engineer) |
| Adriana Penuela | Erin Collins | Zhihong Fu |
| Brelan Moritz | Claudia Geddes | Greg Haveman |
| Christy (Laura) | Matthew Humbard | Laura Jarboe |
| Markeshia | Kaemwich Jantama | Ismael Nieves |
| Price Dehay | Elliot Miller | Guang Nong |
| Raymond Lu | Jonathan Moore | Kevin O’Grady |
| Sebastian Puig | Santosh Pande | John Owens |
| Amy Perkins | James Peterson | |
| Gabriela Phillips | Mun Rhee | |
| Katherine Sherwood | Luiz Roesch | |
| Yue Su | Liesbeth Schmidt | |
| Heather Tyler | Peter Turner | |
| Basma Yacoubi | ||
| Guanyin Zhou | ||
| Qingzhao Wang |
Appendix 8
FCRC Faculty Members and Associates
| Faculty | Associate | Department | Institution |
| Fredy Altpeter | Agronomy, UF |
| Valerie de Crecy-Lagard | Microbiology and Cell Science, UF |
| John M Davis | Sch of Forest Res & Conservation, UF |
| Claudio F Gonzalez | Microbiology and Cell Science, UF |
| William B Gurley | Microbiology and Cell Science, UF |
| Lonnie O Ingram | Microbiology and Cell Science, UF |
| Raphael Katzen | Consulting Engineer |
| Nemat O Keyhani | Microbiology and Cell Science, UF |
| Matias Kirst | Sch of Forest Res & Conservation, UF |
| Graciela Lorca | Microbiology and Cell Science, UF |
| Gregory Luli | Verenium Corporation |
| Julie A Maupin-Furlow | Microbiology and Cell Science, UF |
| Wayne L Nicholson | Microbiology and Cell Science, UF |
| Gary F. Peter | Sch of Forest Res & Conservation, UF |
| George Philippidis | Applied Research Center (ARC),FIU |
| James F Preston, III | Microbiology and Cell Science, UF |
| Pratap Pullammamappallil | Ag & Biol Engineering, UF |
| Michael E. Scharf | Entomology and Nematology, UF |
| KT Shanmugam | Microbiology and Cell Science, UF |
| Eric Triplett | Microbiology and Cell Science, UF |
| Willem Vermerris | Agronomy, UF |