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Molecular Biosciences and Bioengineering

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Tropical Plant and Soil Sciences


Molecular Biosciences and Bioengineering

Agricultural Science 218
1955 East-West Road
Honolulu, HI 96822

Tel: (808) 956-8384
Fax: (808) 956-3542
E-mail: kinoshi@wiliki.eng.hawaii.edu, mbbe@ctahr.hawaii.edu
Web: www.ctahr.hawaii.edu/ctahr2001/CTAHRCatalog/mbbe.html


*Graduate Faculty

*H. Ako, PhD (Chair)—aquaculture, environmental biochemistry and biotechnology
*D. Borthakur, PhD (Graduate Chair, Molecular Biosciences and Bioengineering)—plant-microbe interaction, plant biotechnology
*P-Y. Yang, PhD (Graduate Chair, Bioengineering)—bioenvironmental engineering
*D. A. Christopher, PhD—photosynthesis, photosensory signal transduction, gene regulation, genomics
*P. C. Fu, PhD—biochemical engineering, metabolic engineering, functional genomics
*L. D. Gautz, PhD—bioproduction control and automation, electromechanical systems engineering
*A. G. Hashimoto, PhD—bioengineering
*D. M. Jenkins, PhD—biosensors and bioinstrumentation
*C. M. Kinoshita, PhD—process engineering, bioenergy, bioremediation
*M. Kumagai, PhD—gene isolation and expression in bacteria, yeast, and plants
*P. S. Leung, PhD—bioproduction systems analysis, aquaculture and fisheries economics
*Q. X. Li, PhD—environmental biochemistry and biotechnology, bioremediation
*J. H. Moy, PhD—bioprocess engineering, radiation biology
*P. V. Nerurkar, PhD—metabolic disorders and alternative medicine; signaling pathways and biochemical mechanisms
*G. Presting, PhD—bioinformatics
*W. W. Su, PhD—biochemical engineering, biotechnology
*C-S. Tang, PhD—biochemistry of natural products, bioremediation
*J-K. Wang, PhD—bioproduction systems engineering, aquacultural engineering
*H. Y. Yamamoto, PhD—plant biochemistry, photosynthesis

Cooperating Graduate Faculty

*M. J. Antal, PhD—alternate energy, combustion
*C. Boyd, PhD—biochemistry, cell and molecular biology
*M. Cooney, PhD—marine biotechnology
*H. G. de Couet, PhD—molecular biology, invertebrate biology, biotechnology
*M. Dunn, PhD—molecular nutrition
*J. Hu, PhD—plant virology
*Y. S. Kim, PhD—animal biotechnology
*J. Kimura, PhD—biochemistry
*J. Leong, PhD—marine biotechnology
*C. C. K. Liu, PhD—hydrology, environmental systems engineering
*S. Malecha, PhD—shrimp biology and biotechnology
*S. M. Masutani, PhD—thermochemical conversion of biomass, sequestration of carbon dioxide
*W. C. McClatchey, PhD—molecular evolution, conservation biology
*C. Morden, PhD—molecular systems
*C. Ray, PhD—groundwater hydrology, bioremediation
*P. Sun, PhD—molecular biology, shrimp biotechnology
*A. Theriault, PhD—medical technology, signal transduction
*M. C. M. Tsang, PhD—materials handling, processing engineering
*S. Q. Turn, PhD—biological process engineering, bioremediation
*G. Y. Wang, PhD—metabolic engineering
*A. Wieczorek, PhD—population biology
*J. Yang, PhD—animal molecular biology and biotechnology
*J. Yu, PhD—bioengineering, marine bioproduct development

Affiliate Graduate Faculty

*H. Albert, PhD—plant molecular biology and biotechnology
*S. Divakaran, PhD—marine bioproducts
*M. M. Fitch, PhD—micropropagation and genetic transformation of papaya
*J. K. Ladha, PhD—nitrogen fixation, soil nutrition, biofertilizer
*C-S Lee, PhD—aquaculture
*R. Ming, PhD—sugarcane breeding and biotechnology
*P. H. Moore, PhD—sugar cane physiology
*S. Moss, PhD—aquaculture
*L. G. Obaldo, PhD—aquacultural engineering
*G. S. D. Pruder, PhD—aquacultural engineering
*J. Zhu, PhD—plant transformation, biotechnology

Degrees Offered: BS in bioengineering, MS in bioengineering, MS in molecular biosciences and bioengineering, PhD in molecular biosciences and bioengineering

The Academic Program

The Molecular Biosciences and Bioengineering Department features a multidisciplinary faculty having a broad spectrum of interests in biotechnology, molecular biology, biochemistry, and bioengineering. The department’s strong basic and applied research programs and its active, internationally recognized faculty combine to provide students with exciting learning opportunities. The department houses degree-granting programs in Bioengineering (BS and MS) and in Molecular Biosciences and Bioengineering (MS and PhD).

Bioengineering Program

The mission of the Bioengineering (BE) program is to provide engineering students a unique opportunity to study biological systems from the engineering perspective. The Bioengineering program teaches the importance of the systems approach to problem solving. Undergraduate (BS) and graduate (MS) degrees are offered in Bioengineering.

Undergraduate Study

BS in Bioengineering

The mission of the Bioengineering program is to provide students a unique opportunity to study the fundamentals of engineering and biology and the application of engineering and biology, and the application of engineering to biological systems. Example applications in Bioengineering include processing of biomass for alternative energy uses or added value, bioreactor design for producing high-valued biologically-based products, bioremediation and biological treatment of wastes, and sensors and control engineering for biological systems. Undergraduates complete a comprehensive curriculum including the basic sciences (biology, chemistry and physics), engineering mathematics, core engineering (civil, electrical and mechanical) and fundamental and specialized Bioengineering courses. Students receive integrated training in biology and engineering, culminating in a two-semester engineering design sequence.

To fulfill its mission, the Bioengineering program:

  1. Provides students with the fundamentals of engineering;
  2. Trains students to become engineers with the skills to design, manufacture, test, and/or operate systems in which living organisms or biological products are a significant component; and
  3. Graduates students with the skills to function in modern society as expected of a professional engineer with a baccalaureate degree.

The Bachelor of Science in Bioengineering is the only undergraduate degree offered by the program. Students benefit from small class size and one-on-one interactions with faculty.


  • General Education requirements, including the following:
    • SP 151 or 251 (DA)
    • ECON 120 or ECON 130 or ECON 131 (DS)
    • BIOL 171/171L (DB/DY)
    • CHEM 162/162L (DP/DY)
    • ENG 100 or approved FW course (FW)
    • Two approved courses in Global and Multicultural Perspectives (FG)
    • MATH 241, 242/242L, 243, and 244 (FS)
    • PHYS 170/170L and 272/272L (DP/DY)
    • One Social Science course (DS)
    • One Humanities or Literatures course (DH or DL)
    • One course with focus on Contemporary Ethical Issues (E)
    • One course with focus on Hawaiian, Asian, or Pacific issues (H)
    • One course with focus on Oral Communication (O)
    • Five Writing Intensive courses (W)
    • Hawaiian or Second Language (HSL) is not required for the Bioengineering degree
  • College requirements:
    • NREM 310
  • Basic engineering requirements:
    • EE 160 and 211
    • CEE 270, 271, and 320
    • ME 311
    • Engineering mathematics elective (see adviser)
  • Bioengineering requirements:
    • BIOL 172/172L or MICRO 351/351L
    • Biology elective (see adviser)
    • CHEM 272/272L
    • BE 351/351L, 360, 401, 413, 437, 460, 481, and 482
    • At least two courses from BE 405, 420, 421, 431 or 440

A minimum of 126 credit hours is required for graduation.

Graduate Study

MS in Bioengineering

The research areas in bioengineering open to MS students include management of wastes and wastewater; engineering for cell culture, fermentation, micropropagation, and bioconversion; engineering-intensive horticultural and aquatic biosystems; modeling and optimization of bioresource production and processing systems; water management and irrigation system design; spatial decision support systems for environmental protection and resource development; bioremediation; biological and thermochemical conversion; control, automation and mechanization of biological systems. Graduates of the program have entered careers in industry and public agencies or have undertaken further study in a PhD degree program. Intended candidates for the MS must present a bachelor’s degree from an accredited engineering program or the equivalent.


Plan A

  • Twenty-one (21) course credits and nine (9) thesis research credits.
  • Directed Research (course 699) and Thesis (course 700) cannot be used to satisfy course credit requirements
  • Twelve (12) or more course credits must be at 600 level or above.
  • Twelve (12) or more course credits must be in Bioengineering; of these nine (9) must be earned in courses numbered 600-698.
  • One graduate seminar in Bioengineering or equivalent.
  • Pass a final oral examination administered by a committee of three or more graduate faculty, chaired by the student’s thesis adviser.
  • Enrolled in the graduation semester. If all other course work is completed, one credit of BE 700 must be taken in the graduation semester.

Plan B

  • Twenty-seven (27) course credits and three (3) credits of Directed Research (course 699) on a design or research project.
  • The Directed Research (course 600) cannot be used to satisfy course credit requirements.
  • Eighteen (18) or more course credits must be at 600 level or above.
  • Eighteen (18) or more course credits must be in Bioengineering; of these twelve (12) must be earned in courses numbered 600-698.
  • One graduate seminar in Bioengineering or equivalent.
  • Pass a final oral examination administered by a committee of three or more graduate faculty, chaired by the student’s adviser.
  • Enrolled in the graduation semester. If all other course work is completed, one credit of BE 500 must be taken in the graduation semester.

Contact Information

Dr. P. Y. Yang
Graduate Chair, Bioengineering
University of Hawaii
3050 Maile Way, Gilmore 105
Honolulu, HI 96822
Tel: (808) 956-8459
Fax: (808) 956-9269
E-mail: pingyi@hawaii.edu

BE Courses

Molecular Biosciences and Bioengineering Graduate Program

The Molecular Biosciences and Bioengineering (MBBE) graduate program offers both MS and PhD degrees. The MBBE research and graduate training center around understanding the biochemical, nutritional, and molecular-biological processes that underlie growth, development, photosynthesis, and stress, especially as related to tropical agriculture, aquaculture, plant and environmental biotechnology, and bioengineering.

The university’s tropical locale, the importance of agriculture in the economy of this region, and the strong basic orientation of our faculty combine into unique interdisciplinary research and educational opportunities that range from molecular biology and biochemistry to agricultural biotechnology and bioengineering. The program stresses solid foundation in fundamentals, competence in contemporary methods and significant research contributions to plant biology, environmental biochemistry and tropical agricultural biotechnology.

Entrance Requirements

  • Minimum qualifications for admittance as a regular student are an undergraduate degree from an accredited U.S. college or university or equivalent degree from a recognized foreign institution of higher learning and a GPA of at least 3.0 on a 4.0 scale.
  • All prospective students must submit scores from the GRE General Test. In cases where foreign students encounter difficulty in taking the examination, submission of scores may be delayed with permission from the Graduate Division. Foreign students must also submit TOEFL scores (see Graduate Bulletin for exceptions.)
  • All applicants are expected to have completed courses or equivalents in calculus, physics, chemistry through organic and quantitative analysis, basic biology or botany, genetics, biochemistry, plant physiology, and one additional upper division course in either botanical sciences, cellular or molecular biology. While not a requirement, physical chemistry is highly recommended. Students may be accepted with deficiencies in one or more of these areas, however, deficiencies must be made up during the first year as a graduate student. Such courses may not be used for graduate credit.

General Requirements

  • All degree requirements shall be those in effect and published in the Graduate Bulletin as of the date of the initial enrollment in the graduate program. All students shall adhere to policies and procedures as established by the UH, the Graduate Division, and the Department.
  • The Graduate Chair or representative shall temporarily advise new students until a major adviser is selected. Uncommitted students should be fully cognizant of the faculty and their programs before selecting a Graduate Advisory Committee Chair. The Graduate Chair must be informed of the selection. In unusual situations, a student may change a Graduate Advisory Committee Chair but only after consultation with all faculty concerned and approval of the temporary or permanent Graduate Advisory Committee.
  • Upon entering the graduate program, each student shall be assigned a temporary Graduate Advisory Committee appointed by the Graduate Chair. The committee will consist of the Graduate Chair and at least two (2) other members of the MBBE Graduate Faculty. This committee shall advise the student on course selection matters, administer the general examination, insure progression in the program, and advise the student until the permanent Graduate Advisory Committee is established.
  • All students shall take a written diagnostic examination during the first semester of residence. The purpose of this examination is to determine the level of understanding in general botany, cytology, anatomy, morphology, biochemistry, and physiology. The length of the examination shall be a maximum of two hours. The date and place shall be determined by the Graduate Chair. The examination shall be administered by a committee of three members of the MBBE Graduate Faculty. Performance on this examination will be used to determine deficiencies.
  • Each student shall meet with the student’s temporary or permanent Graduate Advisory Committee at least once each semester to access academic and reassert progress and to establish goals for the next semester. It is the student’s responsibility to schedule this meeting and to file the Academic Progress Report with the Graduate Chair.
  • All graduate students are encouraged to take MBBE 401 Molecular Biotechnology or an equivalent course as a prerequisite. In addition, a minimum of three (3) of the following 600-level courses are selected with the approval of the Graduate Advisory Committee and the Graduate Chair.
    • MBBE 620 Plant Biochemistry
    • MBBE 680 Methods in Plant Molecular Biology
    • MBBE 687 Advanced Lab Techniques
    • BE 604 Aquaculture Systems
    • BE 606 Instrumentation and Measurement
    • BE 622 Experimental Methods in Cause-Effect Modeling
    • BE 638 Biosystems Modeling
    • BE 648 Biosystems Simulation
    • BE 660 Bioseparation Processes
    • BE 634 Biological Treatment
    • CHEM 633 Molecular Spectroscopy
    • PEPS 630 Plant Virology
    • PEPS 646 Plant Bacterial Interactions
    • PEPS 681 Pesticide Toxicology
    • BOT 669 Molecular Systematics and Evolution
    • BOT 674 Plant Growth and Developmen
    • CMB 621 Cell Molecular Biology I
    • CMB 622 Cell Molecular Biology II
    • CMB 680 Molecular Genetics
    • MICR 625 Advanced Immunology
    • MICR 632 Advanced Microbial Physiology
    • MICR 671 Advanced Microbial Genetics
    • TPSS 440 Tissue Culture/Transformation
    • TPSS 604 Advanced Soil Microbiology
    • TPSS 614 Cellular Genetics of Crops
    • OCN 653 Methods in Microbiology Oceanography
  • MBBE 610 Seminar: All MBBE graduate students shall register for and present a seminar each semester in residence (excluding summer sessions). This requirement can be met by enrolling in MBBE 610, or other equivalent “presentation type” seminar offered in another department with permission of the Graduate Advisory Committee. Thesis/dissertation proposal seminars or defenses cannot be used to meet this requirement.
  • All MBBE graduate students shall maintain a B average (3.0) to be eligible for advancement within a degree program.

Additional Requirements

All MS students are encouraged to submit a thesis (Plan A). Only under very special circumstances, a student may be advised to pursue a MS degree without a thesis (Plan B), which is considered to be a terminal degree. MS Plan A requires a minimum of 12 credit hours of 600 level courses (excluding directed research), 6 credit hours of 400 or higher level courses, and 9 credit hours of research (MBBE 699). The course requirement for each student will be determined in consultation with the Graduate Advisory Committee and the Graduate Chair.

Contact Information

Dr. Dulal Borthakur
Graduate Chair, Molecular Biosciences and Bioengineering
University of Hawaii
1955 East-West Road, Ag. Sci. 218
Honolulu, HI 96822
Tel: (808) 956-6600
Fax: (808) 956-3542
E-mail: dulal@hawaii.edu

MBBE Courses