ANNUAL REPORT: June 1, 2008 – May 31, 2009
(i.e., Summer 2008, AY 2008-2009)
DEPARTMENT OF ENVIRONMENTAL AND FOREST BIOLOGY
SUNY-ESF
NAME: James P. Nakas
I. INSTRUCTIONAL ACTIVITIES
1. Regular Course Offerings
Course No.
SUMMER:
EFB 899/999
FALL
SPRING:
Title
Research
Credit
Hrs.
No.
Students
No. of Lab.
Sections
4
4
-------
EFB 303 (w/ Castello) Microbiology
4
61
3
EFB 301
Latin for Scientists
1
46
-------
EFB 496
EFB 796
EFB 496
Microbial Ecology
Microbial Ecology
Microb. Dis. Fish/Wdlife
2
2
1
11
1
10
--------------------------
2. Non-Scheduled Course Offerings (e.g., 496, 899, 999)
Course No.
Title
EFB 899 (fall)
MS Research
EFB 899 (spring)
MS Research
EFB 999 (fall)
PhD Research
EFB 999 (spring)
PhD Research
EFB 420 (summer)
Internship
Credit
Hrs.
10
12
5
1
3
No.
Students
3
3
2
1
1
3. Continuing Education and Extension (short courses, workshops, etc.)
None
4. Guest Lecture Activities
Course No.
Title
None
No. of Lectures
II. STUDENT ADVISING
A. Number of undergraduates for whom you are the student’s official advisor (10-15) and unofficial advisor (none)
B. Graduate Students: (Name, degree sought, starting date, month & year; if a degree was completed, please give
date and full citation for the thesis or dissertation).
1) Christopher Addona--MS--Sept. 2008
2) Wenyang Pan--PhD--Jan. 2008
3) Rosanna Stoutenburg--MS--June 2008
4) Chengjun Zhu--MS--Sept.2007
5) Andrew Henwood--PhD—Sept. 2005
MAJOR PROFESSOR
Five students under “B”
CO-MAJOR PROFESSOR
None
MEMBER, STEERING COMMITTEE (other than those listed above)
Daniel Nicholson-PhD-Paper and Bioprocess Engineering
CHAIRMAN OR READER ON THESIS EXAMS, ETC.
None
III. 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.
IV.
Publications
A. Refereed Publications
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-3hydroxybutyrate from biodiesel-glycerol by Burkholderia cepacia ATCC 17759. Biotechnol. Prog. (submitted).
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.
B. Non-refereed Publications
None
C. Papers Presented at Scientific Meetings
None
D Public Service Presentations (lectures, seminars, etc. to and for the public; give group or occasion, date(s), and
attendance)
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 (source, subject, amount - total award and current year, award period starting
and ending dates; list graduate research assistants supported by each grant).
The following list of current and pending is provided by the Office Of Research Programs:
Currently, two graduate students, Wenyang Pan and Chengjun Zhu are supported b grMr. Zhu is supported by
2. Research Proposals pending (as in B.1., above)
None
IV. PUBLICATIONS (Full bibliographic citation, i.e., do not use "with Jones," or "Jones, et al."; please list only
publications published, in press, or actually submitted during this reporting period --- do not list manuscripts
in preparation).
A. Refereed Publications
B. Non-refereed Publications
C. Papers Presented at Science Meetings (give title, date, occasion, and location)
D. Public Service Presentations (lectures, seminars, etc. to and for the public; give group or occasion, date(s), and
attendance)
V. PUBLIC SERVICE
A. Funded Service (include consulting activities)
1. Government Agencies (Federal, State, Local):
2. Industrial and Commercial Groups, etc.
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.
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
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”
Agency
No. of manuscripts
1
No. of proposals
Other
c. Participation (workshops, symposia, etc.)
Name of workshop, etc.
Date
Place
None
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.
D. Foreign Travel (Where, When, Purpose)
None
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)
C. University-wide, including Research Foundation
None
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. One paragraph on each of the following would be most helpful:
this past year, what have you done for our students, department/college, and self professionally? NOTE: The
information in this section (along with the supporting specific information elsewhere in this report) should be your
strongest case for being considered for a discretionary raise, which I’ll continue to award based on your contributions to
the department and college this reporting period.
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 YOUR OWN
PROFESSIONAL DEVELOPMENT AND THE ENHANCEMENT OF THE PROGRAM IN
ENVIRONMENTAL AND FOREST BIOLOGY (brief summary)
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)
c. University, professional society, and public service
Minimal (i.e. as needed)
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.