August 1, 2009

Center for Applied Microbiology-Annual Report July 1, 2008-June 30, 2009

To: Dr. Chin Yang From: Dr. Susan Anagnost, Dr. James Nakas, Dr. Christopher Nomura, Dr. Chun Wang, Dr. Christopher Whipps Re: Annual Report, Center for Applied Microbiology, July 1, 2008-June 30, 2009 Cc: Dr. Neil Ringler (Dean of Research), Dr. Bruce Bongarten (Provost), Dr. Donald Leopold (Chairperson, EFB), Ms. Brenda Greenfield (Director, ESF Foundation) The Center for Applied Microbiology was established in 2004 through a generous donation by Dr. Chin Yang and has now completed the fifth full year of operation. Following is a summary of research-related activities, supported in part by funds allocated from the Center for Applied Microbiology, during the period July 1, 2008-June 30, 2009. Research Activities During this Report Period I. Dr. Susan Anagnost Publications (refereed)

Rosenbaum P.F., Crawford J.A., Anagnost S.E., Wang C.J.K., Hunt A., Anbar R.D., Hargrave T.M., Hall G.E., Liu C.C., and Abraham J.L. 2009. Indoor airborne fungi and wheeze in the first year of life among a cohort of infants at risk for asthma. Journal of Exposure Science and Environmental Epidemiology. In press. Newhouse, A., Zhou, S., DaRin, M. and S. Anagnost. Macroarray Detection and Identification of Bioaerosol Fungi from Mixed Samples. Submitted to Applied and Environmental Microbiology.

Research Presentations/Posters Anagnost, Susan E.

Crawford, J., Rosenbaum, P., Anagnost, S., Hunt, A. and J. Abraham. 2009. Home conditions and indoor airborne fungal levels in a cohort of infants at risk for asthma. Proceedings and Poster presentation, Healthy Buildings 2009, Syracuse, New York, September 2009. Submitted April 2009. Manchester, K., Han, Y., Anagnost, S.E., Luk, Y.and D. Ren. Control of wood decay fungi by brominated furanones. Abstract, Annual Meeting of the American Institute for Chemical Engineers. AIChE 2008 Annual Meeting, Philadelphia, PA November 16-21, 2008.

Newhouse, A. and S.E. Anagnost. 2008. Membrane-based DNA technique to simultaneously detect opportunistic, pathogenic and wood-decay fungi in buildings. Syracuse CoE Symposium, Center of Excellence in Environmental and Energy Systems, Syracuse, New York. September 29-30.

Darin, Matthew P., Anagnost, Susan E., Newhouse, Andrew E., and Richard K. Dickinson. 2008. A New Analytical Technique for the Detection and Identification of Fungal Bioaerosols in Buildings. Poster presentation at the Mycological Society of America 2008 Annual Meeting, Pennsylvania State University, State College, PA, August 10-13, 2008.

Sponsored Research Projects for the period July 1, 2008-June 30, 2009: Susan Anagnost

Susan E. Anagnost and Matthew Darin. Application and demonstration of macroarray analytical techniques for the detection of fungal bioaerosols in buildings. Subcontract to Matthew Darin, Bluepoint Environmental Services, NYIEQ, Syracuse Center of Excellence TAD project award, U.S. Environmental Protection Agency. January 1 to Dec. 31, 2008. (Actual start date June 2008) $41,000. A no-cost extension was approved extending the grant to April 30 2009.

Susan E. Anagnost, C.J.K. Wang, and Shuang Zhou. Membrane-based DNA technique to simultaneously detect opportunistic, pathogenic and wood-decay fungi in buildings. Syracuse Center of Excellence CARTI project award, U.S. Environmental Protection Agency Award No: X-83232501-0. May 1 2007-April 30 2008. A no-cost extension was approved April 2008 extending the grant to April 30 2009. $100,000.

Submitted: Anagnost, Susan E., and Crovella, Paul L. Balanced Ventilation for Point Source Control in High Performance Homes. New York State Energy Research and Development Authority. $ 79,589.

II. Dr. James Nakas RESEARCH COMPLETED OR UNDERWAY

A. Departmental Research (unsupported, boot-legged; title - % time spent) Involved in a project using Jerusalem artichokes as a source of fermentable carbon for production of ethanol. Collaborating with a local farmer, Mr. Charles Garber, who supplies the starting material. Publications

A. Papers Published

Gitsov, I., J. Hamzik,J. Ryan, A. Simonyan, J. P. Nakas, S. Omori,A. Krastanov, T. Cohen, and S.W. Tanenbaum. 2008. Enzymatic nanoreactors for environmentally benign biotransformations.1. Formation and catalytic activity of supramolecular complexes of laccase and linear-dendritic block copolymers. Biomacromolecules 9: 804-811.

Stoutenburg, R.M., J.A. Perrotta, T.E. Amidon, and J.P. Nakas. 2008. Ethanol production from a

membrane purified hemicellulosic hydrolysate derived from sugar maple by Pichia stipitis, NRRL Y-7124. BioResources 3: 1349-1358.

Zhu, Chengjun, C.T. Nomura, J.A. Perrotta, A.J. Stipanovic, and J.P. Nakas. 2009. Production and

characterization of poly-3-hydroxybutyrate from biodiesel-glycerol by Burkholderia cepacia ATCC 17759. Biotechnol. Prog. (submitted).

B. Patents Nakas, J.P., S.W. Tanenbaum, and T. Keenan. 2008. Bioconversion of xylan and levulinic acid to

biodegradable thermoplastics. European patent issued Nov. 5, 2008. Eur. Pat. No. EP 1585821. US and Canadian patents still pending.

Public Service Presentations Invited by Cayuga-Onondaga BOCES as a participant on a panel discussion on sustainability, Friday, April 3, 2009, Auburn, New York, attendance approximately 50.

V. Public Service A. Funded Service (include consulting activities)

Member, Institutional Biosafety Committee, Bristol-Myers Squibb Corp.

B. 1. Grant-supported Research The following list of current and pending is provided by the Office Of Research Programs ograms Programs: Currently, two graduate students, Wenyang Pan and Chengjun Zhu are supported b grMr. Zhu is supported by

V. PUBLIC SERVICE A. Funded Service (include consulting activities) Member, Institutional Biosafety Committee, Bristol-Myers Squibb Co., Syracuse, New York

B. Unfunded Service to Governmental Agencies, Public Interest Groups, etc.

1) On the advisory committee for the central New York Biotechnology Research Center (CNYBRC) soon to be located at the Kennedy Square complex on Fayette Street.

2) Invited member of panel discussion group on sustainability for Cayuga-Onondaga BOCES, April 3, 2009, Auburn, New York, attendance 50 (approx.) VI. PROFESSIONAL DEVELOPMENT A. Professional Honors and Awards (for teaching, research, outreach, etc.)

European patent issued Nov.5, 2008 on “Biodegradable Thermoplastics from Xylan and Levulinic Acid, Eur. Pat. No. EP 1585821. US and Canadian patents still pending.

B. 1. Activities in Professional Organizations (offices held, service as chairman, member,

participant or consultant) Institutional Biosafety Committee—Bristol-Myers Squibb Corp.

2. Professional Society Membership American Society for Microbiology 3. Other Professional Activities

a. Editorial activity

Journal (s) Responsibility

Other (books, symposia, etc.)

b. Reviewer

Journal(s)

Occasional reviewer for the journal “BioResources” No. of manuscripts 1 C. Further Education/Re-training Undertaken, Leaves, Workshops, etc.

Closer collaboration with Tessy Plastics, Albany Molecular Research Institute, and Welch Allyn to further develop and refine our purification of polyhydroxyalkanoates (PHAs) for industrial purposes.

VII. ADMINISTRATIVE AND SERVICE RESPONSIBILITIES (include committee participation) A. Department-level

1) Member: Promotion and Tenure Committee 2) Member: Search Committee for Cellular and Molecular Biologist Result: George Bachand was hired 3) Still teaching English as a Second Language (to ESF international students) as a member of Literacy Volunteers of Greater Syracuse

B. College-level

1) Member: Radiation Safety Committee 2) Member: Advisory Committee: CNY Biotechnology Research Center 3) Member: Institutional Biosafety Committee: Bristol Myers-Squibb Corp. 4) Chairperson: Institutional Biosafety Committee (ESF) 5) Director, Center for Applied Microbiology

VIII SUMMARY OF SIGNIFICANT ACTIVITIES AND ACCOMPLISHMENTS DURING THIS REPORTING PERIOD, ESPECIALLY THOSE MOST NOTEWORTHY AND RELATIVE TO THE COLLEGE’S AND DEPARTMENT’S MISSION.

1) Students: During the past year I have taken on two new graduate students who have been part of my group since May, 2008 (Rosanna Stoutenburg), and Sept., 2008 (Chris Addona). Both have now reached a point where they are fully functional in the laboratory, and indeed, would be fully functional in any microbiology laboratory. They have received good training and taken to it well. I have also had one undergraduate student (Joseph Gredder) working in the laboratory since Sept. 2008 and he has also become fully competent and would never embarrass ESF by his performance in any respected microbiology laboratory. My two other graduate students (Chengjun Zhu and Wenyang Pan) continue to do outstanding work and will do well after ESF. Joe Perrotta (Research

Technical Specialist) has been with me for a number of years and provides invaluable service in assisting in the training of all my graduate students as well as undergraduates.

I still continue to teach English as a Second Language to international students at ESF and routinely have 4 to 6 students each semester. We generally meet once a week and focus on pronunciation, vocabulary, current events, etc., etc.

2) Department/College: During the past year, my contributions to the department/college

have probably been most noteworthy in the areas of service as exemplified by a) Searching for a new cellular/molecular biologist which resulted in the hiring of

George Bachand b) Work on the Promotion and Tenure Committee c) Participation in many many meetings of the CNY Biotechnology Research Center

as part of the advisory committee. A site (former Kennedy complex, Fayette Street) has been identified, purchased, site remediation and demolition work begun, and numerous discussions have taken place with architects who have now designed the building and construction layout. Completion is scheduled for 2011.

d) Participation in the certificate program in Bioprocess Engineering with four students (all from BMS) who are conducting research in my laboratory on hydrogen production and the results will be presented at a graduation ceremony/reception later this summer.

3) Self: This past year has been particularly gratifying to me as I feel that a few milestones

have been met which had been churning away for, in some cases, extended periods of time.

a) Probably the most significant accomplishment was being issued a(n) European patent for our work on biodegradable polymers from wood-based feedstocks. The patent was issued on Nov. 5, 2008 and can be viewed at the European Patent Office web site under EP 1585821. This describes our work on the bioconversion of the hemicellulosic component of wood to biodegradable thermoplastics using a bacterial fermentation. I believe patents have been issued on only three other occasions in the 30 years I have been in EFB (the three being Teale, Powell, and Smart/Abrahamson/Volk).The US and Canadian patent applications for our work are still pending.

b) I was very pleased this past year to receive some significant funding (~$500k) for our biodegradable polymer work from a consortium involving Tessy Plastics, Welch Allyn, Blue Highway (a spin-off of WA), ESF, and NYSERDA. For the past few years I have tried to pull together a group effort whereupon we at ESF would produce the raw polymer for delivery to Tessy Plastics who would then fabricate the polymer into disposable medical products. This has now been accomplished using the pilot plant fermenter (400L) and the production of kilogram quantities of PHA which were subsequently processed by injection molding by Tessy Plastics into ear tips for use with an otoscope. Welch Allyn, which distributes the product worldwide, will now evaluate the PHA product for various quality assurance criteria compared to the normal polypropylene-derived product. The photo below shows a comparison between the usual polypropylene-derived product (black) and the PHA-derived product (brown).

Some injection molding problems remain but we continue to focus on manipulating the polymer composition to achieve better separation from the mold after cooling.

c)The production of kilogram quantities of polymer was, in part, achieved due to a collaboration with Albany Molecular Research Institute (AMRI) who provided some critical downstream purification expertise which allowed us to switch solvents from chloroform to dichloromethane and subsequent precipitation in methanol which greatly improved product yield and purity. We look forward to future collaborations with AMRI with the hope that we can offer them something in return for their very generous support. d) Regarding c (above), two methods of regulation are now available to us for producing an even better PHA product. First, we can manipulate the composition by

varying the carbon source which allows the production of a range of polymers from a rather stiff product to a fairly elastic and flexible material. Secondly, growth on glycerol ( a byproduct of biodiesel production) results in PHAs of varying size as the glycerol serves to “end-cap” the polymer, i.e. no additional subunits will be added after glycerol is inserted. Therefore, careful addition of glycerol will produce polymers of different chain lengths which will exhibit different physical-chemical characteristics. It is anticipated that one or both of these measures will result in a better product for use in injection molding applications. e) A few billion pounds of cheese whey are generated within New York State each year. Most cheese producing facilities either pay to dispose of this high BOD “waste” material or will treat it on site using normal wastewater treatment procedures. However, the presence of lactose at a concentration of 4-5% allows fermentation of this byproduct into value-added products. Our goal is to use cheese whey as a feedstock for eventual fermentation to PHAs which could be accomplished at the cheese-making facility. We have been collaborating with Dr. John Fieschko on all aspects of this work. Laboratory experiments have established the feasibility of this process and we are now in the pilot plant phase and have scaled-up the process to 200L. f) The most recent publication listed (under IV) with Dr. Nomura will be the sixth member of the Chemistry Department with whom I have published papers. I am not exactly sure this is an “accomplishment” in the intended sense but it sure has been fun working with them. They’re just so damn good!

IX. A. FUTURE PLANS, AMBITIONS, AND POTENTIAL CONTRIBUTIONS FOR THE PROGRAM IN ENVIRONMENTAL AND FOREST BIOLOGY B. PROJECTED ACTIVITIES FOR NEXT YEAR

1. Summer 2009

a. Course(s) to be offered: No courses offered during the summer

b. Proposed research activity: All research activity will be focused on PHA

production from renewable resources (wood, biodiesel glycerol, and cheese whey)

2. Fall Semester 2009

a. Course(s) to be offered: Microbiology (w/ Castello) and Latin for Scientists

b. Proposed research activity: All research activity will be focused on PHA production from renewable resources (wood, biodiesel glycerol, and cheese whey).

c. University, Professional society, and public service: Promotion and Tenure Committee (EFB), CNY Biotechnology Research Center (advisory committee), Institutional Biosafety Committee (EFB and Bristol-Myers Squibb), English as a second language

3. Spring Semester 2010

a. Course(s) to be offered: Microbial Ecology and Microbiol. Dis. Fish/Wldlife

b. Proposed research activity: Same as in fall.

c. University, professional society, and public service: Same as in fall. III. Dr. Christopher Nomura

Research continues to be a strong. For 2008-2009, we have 4 papers

that have been published, 1 in press, and another submitted. There are several other manuscripts in preparation as well. Research from my group has also been

presented at international, national, and local conferences. I have received several invitations to speak at international conferences and colleges and

universities worldwide. 13 grant proposals were submitted during this time period. 2 (MDA, NYSERDA) were funded, 1 is recommended for funding (NSF) which was a resubmission of a grant that was declined in the first half of this cycle, and 8 were declined. The NSF proposal resubmission was the latest to be funded (the original budget was cut and the proposal was modified to address the concerns of the reviewers) and will allow me to hire a postdoctoral fellow and a graduate student over the next 3 years. Some money from the CAM funds will be used as summer support for students in my group.

Other: As a faculty member for the ESF SCIENCE Corps, I have given talks on biodegradable plastics and liquid nitrogen use. These seminars were well received, and remain popular. I was able to use the relationships developed as a participant with this group to formulate a simple experiment for the kids and to write a strong section for broader impacts for my NSF proposal. In addition, I was interviewed by 360 Magazine, Nikkei (Japanese Wall Street Journal) and Nature Biotechnology on bioplastics production. One of the largest media splashes this year was our involvement with the Butter to Biodiesel project at the NY State Fair. We received a large amount of positive publicity from this project. And I was involved with several interviews for radio and television regarding this topic. Although time consuming, I believe the impact has been great. I was also involved with a presentation and tour for Japanese Environmental Scientists through the US Department of Stateʼs Bureau of Educational and Cultural Affairs and International Center of Syracuse. Graduate students Ms. Qin Wang, a third year graduate student in my lab, passed her candidacy exam for the Ph.D. program in SB3/Chemistry. She was also the recipient of a Jahn Chemistry Emeritus Award (Szwarc). Mr. Ryan Tappel, a first year graduate student, was the recipient of an Outstanding TA award from the Faculty of Chemistry. Undergraduate students Ms. Leticia Izquierdo is participating in Northeast Alliance for Graduate Education and the Professoriate (NEAGEP) at the University of Maine (11-week summer program). Mr. Joeseph Gredder is participating in a summer REU program at the University of Florida. Mr. Alex Mottern will be doing summer research in my laboratory. Mr. Ben Murphy will be continuing work started in spring semester in the laboratory.

Alumni Mr. Greg Boyd will be an assistant scientist with the SEA Ocean Science and Sailing Program. Mr. Matt Martino has turned an internship he did last summer into a full-time position at Metabolix, Inc. Ms. Erica Hansen is currently working as a lab technician in Dr. Frederick Altʼs lab at the Immune Disease Institute, Harvard University. Ms. Hoa Nguyen is enrolled in Pharmacy school at Texas Southern University. Ms. Jackie Mueller is enrolled in a doctoral program at University of Hawaii. Mr. David Sgroi is employed as a lab technician. Ms. Jingnan Lu was the recipient of the SUNY Chancellor Award and Faculty of Chemistry Award. She is enrolled in a doctoral program at M.I.T. Mr. Alex Mueller graduated as the top senior in the Department of Chemistry, receiving the Sondheimer Award and is enrolling into the graduate program in Chemistry at SUNY-ESF. Grant Supported Research Current USDA-CSREES/McIntire-Stennis Program Role of nitrogen limitation in polyhydroxyalkanoate production by pseudomonads PI: C.T. Nomura Total Award: $50,911 Award Period Covered: 10/01/07 – 9/30/08 NYSERDA Production of value-added biodegradable plastics from NY State low-value biodiesel process-glycerin PI: C.T. Nomura Co-PI: J. Nakas Total Award: $74,983 Award Period Covered: 07/25/07 – 6/31/10 US Department of Energy Hot water extraction of hardwood chips and utilization of the residual chips and wood

PI: T. Amidon Co-PIs: J. Nakas, B. Ramarao, G. Scott, R. Franics, S. Liu, and C.T. Nomura Total Award: $500,000 Nomura share: $23,000 Award Period Covered: 10/01/07 – 10/31/08 Metropolitan Development Association Manufacture and use of biodegradable polymers in medical applications PI: J. Fieschko Co-PIs: C.T. Nomura, J. Nakas. Total Award: $75,000 Nomura share: $5,238 Award Period Covered: 03/01/08 – 02/28/09 US Department of Energy Hot water extraction of hardwood chips and utilization of the residual chips and wood II PI: T. Amidon Co-PIs: J. Nakas, B. Ramarao, G. Scott, R. Franics, S. Liu, and C.T. Nomura Total Award: $738,000 Nomura share: $35,559 Award Period Covered: 10/01/08 – 10/31/09 NYSERDA PON 1195/Blue Highway LLC Biodegradable Plastics from Renewable Sources for Manufacturing Medical Products in Central New York PI: A. J. Di Rienzo Co-PIs: D. Dana, A. Drauter, J. Nakas , C.T. Nomura, J. Fieschko Total Award: $350,000 Nomura share: ~$100,000 Award Period Covered: 01/01/09 – 12/31/11 Papers published (2008 to present): Zhu, C., Nomura, C.T., Perrota, J., Stipanovic, A.J., and J.P. Nakas. (2009).

Production and characterization of poly-3-hydroxybutyrate from Burkholderia cepacia ATCC17759. Biotechnol Prog (submitted).

Lu, J., Tappel, R.C., and C.T. Nomura. (2009). Biosynthesis of

poly(hydroxyalkanoates). Polym Rev. (in press). Matsumoto, K., Murata, T., Nagao, R., Nomura, C.T., Arai, S., Arai, Y., Takase,

K., Nakashita, H., Taguchi, S., and H. Shimada (2009). Production of short-chain-length/medium-chain-length polyhydroxyalkanoate (PHA)

copolymer in the plastid of Arabidopsis thaliana using an engineered 3-ketoacyl-acyl carrier protein synthase III. Biomacromolecules. 10(4), 686-690.

Spiese, C. E., Kieber, D.J., Nomura, C.T., and R. P. Keane. (2009). Reduction

of dimethyl sulfoxide by marine phytoplankton. Limnol Oceanog. 54(2), 560-570.

Lee, W.-H., Loo, C.-Y., Nomura, C.T., and K. Sudesh. (2008). Biosynthesis of

polyhydroxyalkanoate copolymers from mixtures of plant oils and hydroxyvalerate precursors. Biores Technol. 99(15), 6844-6851.

Nomura, C.T., Tanaka, T., Eguen, T.E., Appah, A.S., Matsumoto, K., Taguchi,

S., Ortiz, C.L., and Y. Doi. (2008). FabG mediates monomer supply for short-chain-length-medium-chain-length polyhydroxyalkanoate (SCL-MCL PHA) copolymer production from both related and non-related carbon sources in Escherichia coli LS5218. Biotechnol Prog. 24(2), 342-351.

Abstracts and presentations at local, national, and international meetings (2008 – present): Nomura, C.T. (2009). Production of biodegradable plastics from biodiesel

process waste glycerol. University of Scranton. February 18. Scranton, PA, USA.

Nicholson, D. and C.T. Nomura. (2009). Use of biodiesel waste glycerol in the

bacterial production of polyhydroxyalkanoate (PHA) biodegradable plastic. Fueling the School. Pennsylvaniaʼs First Intercollegiate Biodiesel Conference. Dickinson College. April 3-4. Carlisle, PA, USA.

Bohn, J. and C.T. Nomura (2009). Current biodiesel production program at ESF.

Fueling the School-Pennsylvaniaʼs First Intercollegiate Biodiesel Conference. April 3-4. Dickinson College, Carlisle, PA, USA.

Lu, J. and C.T. Nomura (2009). Utilization of biodegradable polymers for

removal of polycyclic aromatic hydrocarbons from aqueous solution. Spotlight on Research and Outreach. April 13. Syracuse, NY, USA.

Mueller, A.P. and C.T. Nomura (2009). Glycerol metabolism enhancement.

Spotlight on Research and Outreach. April 13. Syracuse, NY, USA. Murphy, B.M. and C.T. Nomura. (2009). Production of polyhydroxyalkanoates

in transformed Escherichia coli using glycerol. Spotlight on Research and Outreach. April 13. Syracuse, NY, USA.

Sgroi, D.J., Zhu, C., Driscoll, M.J., Nomura, C.T., and J.P. Nakas. Cross-linking and degradation of polyhydroxyalkanoates (PHAs) using a low energy electron beam. Spotlight on Research and Outreach. April 13. Syracuse, NY, USA.

Tappel, R.C., Lu, J., Mueller, J.M., Hansen, E.R., Takase, K., Matsumoto, K.,

Taguchi, S. and C.T. Nomura (2009). Biocatalysts for biodegradable plastics production. Advances in Bioprocessing . March 22-23. Syracuse, NY, USA.

Lu, J. and C.T. Nomura (2009). Utilization of biodegradable polymers for

removal of polycyclic aromatic hydrocarbons. Advances in Bioprocessing. March 22-23. Syracuse, NY, USA.

Mueller, A.P. and C.T. Nomura (2009). Glycerol metabolism enhancement.

Advances in Bioprocessing. March 22-23. Syracuse, NY, USA. Wang, Q. and C.T. Nomura (2009). Monitoring differences in gene expression

levels of Pseudomonas putida KT2440 grown on different carbon sources. Advances in Bioprocessing. March 22-23. Syracuse, NY, USA.

Nomura, C.T. (2008). Protein and metabolic pathway engineering for the

production of polyhydroxyalkanoates. International Symposium on Biological Polyesters (ISBP). Auckland, NZ.

Wang, Q. and C.T. Nomura (2008). Monitoring differences in gene expression

levels of Pseudomonas putida KT2440 grown on different carbon sources. International Symposium on Polymers and the Environment: Emerging Technology and Science. Nashua, NH, USA.

Martino, M.R., Boyd, G.D., Wang, Q., Tappel, R., and C.T. Nomura. (2008).

Coupling biofuel and bioplastic production. International Symposium on Polymers and the Environment: Emerging Technology and Science. Nashua, NH, USA.

Mueller, J.A., Hansen, E.R., Matsumoto, K., Taguchi, K., and C.T. Nomura.

(2008). Biocatalysts for biodegradable plastics production. ACS NERM 2008. Burlington, VT, USA.

Nicholson, D., Stipanovic, A., Nomura, C., and T. Bluhm. (2008). Progress in

Biodegradable poly-3-hydroxyalkanoate (PHA) polymer production: cost reduction investigations. The 236th ACS National Meeting, Philadelphia, PA, USA.

C.T. Nomura. (2008). Bacterial production of polyhydroxyalkanoates from biodiesel process waste glycerol. 2008 World Congress on Industrial Biotechnology and Bioprocessing. April 27-30. Chicago, IL, USA.

Leong, C.R., Jo, S.J., Kitagawa, K., Wang, Q., Matsumoto, K., Nomura, C.T.,

and S. Taguchi. (2008). Production of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) by Corynebacterium glutamicum. Seibutsu-kougakkai. Hokkaido, Japan.

Invited presentations: Nicholson, D. and C.T. Nomura. (2009). Use of biodiesel waste glycerol in the

bacterial production of polyhydroxyalkanoate (PHA) biodegradable plastic. Fueling the School. Pennsylvaniaʼs First Intercollegiate Biodiesel Conference. Dickinson College. April 3-4. Carlisle, PA, USA.

Bohn, J. and C.T. Nomura (2009). Current biodiesel production program at ESF.

Fueling the School-Pennsylvaniaʼs First Intercollegiate Biodiesel Conference. April 3-4. Dickinson College, Carlisle, PA, USA.

Nomura, C.T. (2009). Production of biodegradable plastics from biodiesel

process waste glycerol. University of Scranton. February 18. Scranton, PA, USA.

Nomura, C.T. (2008). Protein and metabolic pathway engineering for the

production of polyhydroxyalkanoates. International Symposium on Biological Polyesters (ISBP). Auckland, NZ.

Nomura, C.T. (2008). Sustainable Concepts in Practice: Biofuels to Bioplastics.

2008 SUNY-ESF Alumni and Family Weekend. SUNY-ESF. September 27. Syracuse, NY, USA.

Affiliations

American Chemical Society ACS-Biotechnology Division ACS-Syracuse American Society for Microbiology

Cellulose Research Institute – SUNY-ESF Michael M. Szwarzc Polymer Research Institute – SUNY-ESF Center for Applied Microbiology – SUNY-ESF

ESF SCIENCE Corps – SUNY-ESF

Ad Hoc Reviewer and Referee Activities Journal of Chemical Technology and Biotechnology

Biochemistry Journal of Biobased Materials and Bioenergy Journal of Polymers and the Environment The Journal of Biomolecular Screening Archives of Microbiology Biomacromolecules Applied and Environmental Microbiology

Journal of Biotechnology Polymer Degradation and Stability FEMS Microbiology Letters International Journal of Biological Macromolecules

Malaysian Journal of Microbiology Canadian Journal of Chemistry ESF Seed Proposals USDA CSREES McIntire-Stennis Proposals USDA CSREES SBIR Proposals

IV. DR. Chun Wang

The New York State Biodiversity Research Institute, Albany, NY- C.J.K. Wang, Wood-inhabiting Microfungi (molds) of New York, $30,643, May 1, 2007 to December 30, 2008.

The objectives of the research were 1) to complete the identification of 2500 specimens collected from hardwood and conifer forest in 24 counties in New York from 1965 to 2004, and 2) to compile distribution records for each 250 to 300 species of microfungi and to provide up-to-date inventory of Hyphomycetes in New York. These data will be the basis for a book entitled: Lignicolous Hyphomycetes of New York. An EFB undergraduate Cesar S. Herrera-Osorio was my Work/Study student working up to 8 hours per week during the academic year 2007-2008. He worked full-time on the project after he graduated in May 2008. In July and August 2008, the Center for Applied Microbiology provided the stipend for Cesar. Cesar was enthusiastic about studying the microfungi and learned a great deal from this project. He is starting his Ph.D. program at the University of Maryland and doing his thesis at the National Fungus Collection, USDA, Beltsville, Maryland. The BRI grant supported Dr. Catharine Catranis working on this project from May 15 to August 30, 2008. College Work/Study student Christina Chan worked about 8 hours per week in the summer, 2008, as well as during the academic year 2008-2009. This summer Work/Study student Michael Smith works 20 hours per week. To present the inventory of microfungi of New York, the accurate identification of each fungal species is paramount. Re-examination of every collection was initiated. This includes the confirmation of the species identification, updating changes in nomenclature, documenting additional fungal species from each collection. For a better presentation of the distribution of microfungi of New York, I have decided to use the Geographic Information System (GIS). The maps generated are clear and useful, and an improvement of the research report. The original proposal concerned only microfungi of New York. After re-examining all my collections, I decided to include all my collection data in this report. That means to include collections from the Mycological Society of America forays in Indiana, Massachusetts, Vermont, Oregon; Peck forays in Canada; and the British Mycological Society Foray in Wales, United Kingdom. This report will be useful to national and international mycologists interested in biogeography. The final report will cover more than 250 species. The deadline for the final report to BRI has been extended from March 31, 2009 to the end of this summer. Sample pages of the final report are included.

Wood-Inhabiting Microfungi (Molds) of New York

Final Report NYHER 070401

To

The New York State Biodiversity Research Institute

Submitted by

C.J.K. Wang

Department of Environmental and Forest Biology

State University of New York College of Environmental Science and Forestry

Syracuse, New York 13210 March 31, 2009

Figure 1. Collections of Microfungi from 24 Counties in New York State

ID COUNTY NAME ID COUNTY NAME 1 Albany 13 Hamilton 2 Broome 14 Lewis

3 Cattaraugus 15 Onondaga 4 Cayuga 16 Oswego 5 Chautauqua 17 Rensselaer 6 Chemung 18 Schuyler 7 Columbia 19 St.Lawrence

Alysidium Kunze, 1817, in Kunze & Schmidt, Mykologische Hefte (Leipzig) 1:11. Type species: Alysidium fulvum Kunze & J.C. Schmidt, 1817 Key to species: 1. Conidia: globose, 6.25-10 µm; limoniform, 7.5-12.5 x 5-10 µm. . . A. resinae var. resinae 1. Conidia: globose, 5-6.25 µm; limoniform, 7.5-12.5 x 5 µm... A. resinae var. microsporum Alysidium resinae var. resinae (Fr.) M. B. Ellis var. resinae M. B. Ellis, 1971, Dematiaceous Hyphomycetes. p.90. Alysidium resinae var. microsporum (Fr.) M. B. Ellis var. microsporum B. Sutton, 1973, Mycol. Pap. 132. p.8.

8 Cortland 20 Suffolk 9 Delaware 21 Tompkins 10 Dutches 22 Ulster 11 Essex 23 Warren 12 Franklin 24 Wyoming

Specimen # Species

Coll. Date

Coll. Site County Substrate

10293.1 Alysidium resinae var. microsporum 7/12/1967 brock onon Fraxinus americana

9995.1 Alysidium resinae var. resinae 9/28/1966 pratt onon na

11120.1 Alysidium resinae var. resinae 6/29/1971 all catt Fagus grandifolia

11139.1 Alysidium resinae var. resinae 6/29/1971 all catt Ostrya virginiana

11654.0 Alysidium resinae var. resinae 11/3/1978 green onon hardwood

V. Dr. Christopher Whipps RESEARCH COMPLETED OR UNDERWAY

A. Departmental Research (unsupported, boot-legged; title - % time spent)

Parasitism in Lake Pontchartrain fishes in the post-Katrina era (boot-legged - 5%) Disease threats to European Fish: Genetic characterization of Spaherothecum destruens in sunbleak (final analysis and publication boot-legged – 2%) Infectious disease in returning Atlantic salmon on Pennsylvania watersheds (bootlegged – 3% time)

B. 1. Grant-supported Research (source, subject, amount - total award and current year, award period starting and ending dates; list graduate research assistants supported by each grant)

USDA-CREES/McIntire-Stennis Program (8/15/09 – 9/30/12) - $50,500 Monitoring populations of elusive forest wildlife: a modern approach using noninvasive genetic techniques (Co-investigator with J. Frair) ESF Seed Grant Program. $8,000 (04/01/09-03/31/10 ) PI: Whipps Project Title: Systematics and Biodiversity of the Myxozoa Alaska Department of Fish and Game. $3,500 (08/01/08-04/01/09) Ichthyophonus hoferi in returning Alaskan Chinook salmon

2. Research Proposals pending (as in B.1., above)

Yukon River Restoration and Enhancement Fund (06/09-06/10) $47,163 Ichthyophonus in Chinook salmon – Continuation of a baseline in Emmonak and Eagle, Alaska and potential links to fecundity (PI:Lara Dehn, University of Alaska Fairbanks, Co-PI: Whipps)

3. Research Proposals declined

US Fish and Wildlife Service. $32,500. (Declined). Quantitative and genetic assessment of Ichthyophonus infection in Yukon River Chinook salmon. (PI: Krista M. Nichols, Purdue University; Co-PIs: Larissa Dehn, Christopher Whipps) Great Lakes Fishery Commission Project. $263,455 (Declined). Assessing the role of invasives in the transmission and maintenance of disease in great lake fish communities. (John M. Farrell, Christopher Whipps, Mark Teece (&Geof Eckerlin) New York SeaGrant. $152,134 (Submitted Aug 4, 2008). Declined. Round Goby Invasion of Coastal Wetland Habitats and Risks Posed to Native Fish Communities. (PI: John Farrell. Co-PIs: Mark Teece and Whipps) Department of Defense $500,000 (pre-proposal Aug, 2008). Declined. Association of Blastocystis infections and Gulf War Syndrome. (PI: Capt. Morris S. Jones, David Grant Medical Center; Co-PI: Whipps).

PUBLICATIONS A. Refereed Publications Gunter N.L., Whipps, C.M., Adlard, R.D. 2009. Ceratomyxa (Myxozoa: Bivalvulida): robust

taxon or genus of convenience? International Journal for Parasitology. In Press. Gozlan, R.E., Whipps, C.M., Andreou, D., Arkush, K.D. 2009. Identification of the cyprinid

rosette-like agent as Sphaerothecum destruens, a multihost fish pathogen. International Journal for Parasitology. In Press.

Jones II, M.S., Whipps, C.M., Ganac, R.D., 1, Hudson, N.R., Boroom, K. 2009. Association of Blastocystis Subtype 3 and 1 with Patients from an Oregon Community Presenting with Chronic Gastrointestinal Illness. Parasitology Research. 104(2), 341-345.

Kent, M.L., Feist, S.W., Harper, C., Hoogstraten-Miller, S., Law, J.M., Sánchez-Morgado, J.M., Tanguay, R.L. Sanders, G.E., Spitsbergen, J.M., Whipps, C.M. 2009. Recommendations for Control of Pathogens and Infectious Diseases in Fish Research Facilities. Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology. 149(2), 240–248.

Ferguson, J.A., Atkinson, S.D., Whipps, C.M., Kent, M.L. 2008. Molecular and morphological analysis of Myxobolus spp. of salmonid fishes with the description of Myxobolus fryeri n. sp. Journal of Parasitology. 94(6), 1322-1334.

Whipps, C.M., Matthews, J.L., Kent, M.L. 2008. Distribution and genetic characterization of Mycobacterium chelonae in laboratory zebrafish (Danio rerio). Diseases of Aquatic Organisms. 82(1), 45-54.

Roberts, J.F., Whipps, C.M., Bartholomew, J.L., Jacobson, E.R., and Schneider, L. 2008. Myxidium scripta n. sp. identified in urinary and biliary tract of Louisiana farmed Red Eared Slider turtles Trachemys scripta elegans. Diseases of Aquatic Organisms. 80(3), 199-209.

Jones II, M.S., Ganac, R.D., Hiser, G., Hudson, N.R., Le, A., Whipps, C.M. 2008. Detection of Blastocystis from stool samples using real-time PCR. Parasitology Research. 103(3), 551-557.

Zhao, Y., Sun, C., Kent, M.L., Deng, J., Whipps, C.M. 2008. Description of a new species of Myxobolus (Myxozoa: Myxobolidae) based on morphological and molecular data. Journal of Parasitology. 94(3), 737-742.

B. Papers Presented at Scientific Meetings Apr 27-30, 2009. 34th Annual Eastern Fish Health Workshop, Lake Placid, NY. The curious case of fish apicomplexa; molecular systematics shed light on this enigmatic group. April 24, 2009. NCRR-NIH Workshop: Detection, Impact and Control of Specific Pathogens in Animal Resource Facilities. Bethesda, MD. Specific Infectious Disease Agents and Their Impact on Research: Mycobacterial Infections in Fish. (Invited speaker) February 20, 2009. The Wildlife Society, New York Chapter Annual Meeting, Syracuse, NY. Status of Wildlife Diseases .(Invited speaker) D. Public Service Presentations (lectures, seminars, etc. to and for the public; give group or occasion, date(s), and attendance) PROFESSIONAL DEVELOPMENT

A. 1. Activities in Professional Organizations

Member – 2009 Henry Baldwin Ward Award Committee, American Society of Parasitologists.

2. Professional Society Membership

American Fisheries Society (2001-present) American Society of Parasitologists (2002-present) Wildlife Disease Association (2008-present)

3. Other Professional Activities

a. Reviewer

Journal(s) No. of manuscripts Journal of Eukaryotic Microbiology 2 Journal of Fish Diseases 1 Parasitology 1 International Journal for Parasitology 1 Veterinary Parasitology 2 Molecular Phylogenetics and Evolution 1 Folia Parasitologica 1 Journal of Parasitology 1

Agency No. of proposals

Aquaculture Collaborative Research and Development Program (ACRDP) 1

VII. ADMINISTRATIVE AND SERVICE RESPONSIBILITIES A. Department-level EFB Space Committee (Feb 2008 - present). Chair: John Farrell. EFB Curriculum Committee (Jan-Feb 2008, Aug2008-present). Chair: Dylan Parry. EFB Graduate Program Advisory Committee (Aug 2008-present). Chair: Karin Limburg EFB Cell and Molecular Biology Search (Feb 2009 -present). Chair: Bill Powell B. College-level ESF Committee on Promotion and Tenure Policies and Procedures (Feb 2008 - present). Chair: Don Leopold C. University-wide, including Research Foundation

VIII. SUMMARY OF SIGNIFICANT ACTIVITIES AND ACCOMPLISHMENTS DURING THIS REPORTING PERIOD, ESPECIALLY THOSE MOST NOTEWORTHY AND RELATIVE TO THE COLLEGE’S AND DEPARTMENT’S MISSION.

Overview: Two areas that stand out for me in my most noteworthy accomplishments are my involvement in the departmental curriculum committee’s educational assessment plan and my development of the new introductory General Biology II. In both of these cases, the contributions to ESF/EFB, students, and my own professional development cannot be divided. A primary goal for this annual year was to bring an assessment based teaching pedagogy to Gen Bio II, and this way of thinking was cast into the spotlight when the college required an assessment plan for all of our majors. I found this useful as I contributed to the assessment plans of the majors for which I’m directly involved (AFS & BTC), as well as other majors in my role on the CCAC. I believe this will set the tone for our department and students in the years to come and I am pleased to have been involved from the beginning to end.

Students: In addition to my duties as an undergraduate student advisor, I found myself in the role of an informal advisor for several students enrolled in my classes. From my molecular techniques class for example, I advised 5 students, writing 19 letters of recommendation. One student is now accepted to a graduate program and 3 others have summer internships. In my laboratory, 6 undergraduate students had opportunities to be involved in my research, one of which is now employed in my lab for the summer and another will be taking on an honors thesis in her senior year. I have informally advised 6 graduate students on their projects on topics ranging from infectious disease to molecular biology. Perhaps the achievement for which I am most pleased is EFB103. For a new course offering, I believe it went largely as I had anticipated and based on student reviews was generally well received. I look forward to continuing to improve this foundational course in EFB.

Department: My role in curriculum assessment is perhaps the most notable achievement relating directly to EFB as mentioned above. I also served on the Graduate Program Advisory Committee (GPAC), Space Committee, and most recently the Cell Biologist search committee.

Professional: This year I was invited to speak at 2 conferences; a regional wildlife conference and at the National Institutes of Health. I attended 3 other conferences regionally and nationally. A huge area of professional development for me this year was with my teaching. I was able to implement many of the ideas, technologies, and methodologies I have often thought about, for the first time in 2 full courses. I am pleased with the progress here and will continue to build and adapt these courses. In research, 2 small grants were accepted for funding, both of which will build a foundation of data for larger future proposals on animal disease and wildlife population genetics. IX. A. FUTURE PLANS, AMBITIONS, AND POTENTIAL CONTRIBUTIONS FOR THE PROGRAM IN ENVIRONMENTAL AND FOREST BIOLOGY This summer I will be collecting preliminary data that will be used directly for an NSF proposal to investigate the evolutionary relationships of myxozoan fish parasites. At the same time, I will be gathering critical data on distribution and abundance of other fish parasites in New York, providing a critical baseline for future studies. I plan to have a solid understanding of parasites in NY of economic importance and those that are ecologically compelling as I maintain my involvement in both applied and basic scientific research. I will also be co-teaching a Fish and Wildlife Disease course, which will be offered this fall. This course will likely be of interest to students not only in Wildlife and Fisheries majors, but also preveterinary and premed students in other majors, as well as graduate students. It is intended to provide applied skills in disease

biology and a theoretical background to infectious disease. Finally, I will continue to be involved in the development of EFB curriculum, in both my committee work and in teaching Gen Bio II. B. PROJECTED ACTIVITIES FOR NEXT YEAR

1. Summer 2009

Proposed research activity

Parasite survey of fishes in NY waters with a primary focus on myxozoan parasites as supported by SUNY-ESF Seed grant program. Secondarily, this survey provides baseline data on distribution and abundance of other parasites for future projects.

2. Fall Semester 2009 a. Course(s) to be offered

EFB496/796 – Emerging diseases in Fish and Wildlife EFB797 - Applications in Molecular Research

b. Proposed research activity

Continue parasite survey work as above Phylogenetics and developmental biology of protozoan parasites in fishes. Population genetics of wildlife species in NY

c. University, Professional society, and public service EFB committees as above

3. Spring Semester 2010

a. Course(s) to be offered EFB103 - General Biology II Microbiology Seminar

b. Proposed research activity as above

c. University, professional society, and public service EFB committees as above

Budget/Expenditures for the CAM (July 1, 2008-June 30, 2009) During this time period, the Center for Applied Microbiology received an allocation of $28,600 and after expenditures a balance of $5,763 remained. Listed below are the expenditures for Dr. Schuang Zhou (Dr. Anagnost), Mr. Cesar Herrera-Osorio (Dr. Wang), Mr. Chris Addona and Ms. Rosanna Stoutenburg (Dr. Nakas) as well as expenditures for general laboratory supplies.

I realize the above font is unreadable but it was the only way to get everything on single pages. Just highlight the section you want to view and increase the font size. Should you have any questions or concerns regarding this report please do not hesitate to write or call (315-470-6769). Best Regards, Jim Nakas