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Department of Molecular Biosciences and Bioengineering - College of Tropical Agriculture and Human Resources - University of Hawai'i at Manoa

Graduate Program in Molecular Biosciences & Bioengineering (MBBE)

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, biomedical science and bioengineering. Many MBBE graduate students are supervised and supported by cooperating and affiliate graduate faculty from John A. Burns School of Medicine, Cancer Research Center, Pacific Biomedical Research Center, Queens Medical Center, Hawaii Agricultural Research Center, Oceanic Institute, Sea Grant College Program, School of Ocean and Earth Science and Technology, College of Engineering and several departments including Microbiology, Zoology, Human nutrition, Food and Animal Sciences, and Plant and Environmental Protection Sciences.

Graduate Faculty

Cooperating Graduate Faculty

Affiliate Graduate Faculty

Entrance Requirements

Financial Assistance

All students in the MBBE program are currently supported through teaching assistantships, research assistantships or fellowships. In addition, tuition is waived for all assistantships and most fellowships. It is recommended that students interested in research assistantships contact faculty working in their area of interest regarding availability. Additional fellowship support is available from the East-West Center, which offers scholarships to Asian, Pacific and American students for affiliation in one of their programs.

Contact Information

How to Apply

For application form and related information, please write to:

Graduate Division Admission Office 2540 Maile Way, Spalding 354 University of Hawaii Honolulu, Hawaii 96822 Tel: (808) 956-8544 Fax: (808) 956-4257 E-mail : admissions@grad.hawaii.edu

Application material can also be downloaded from the Graduate Division Website: http://www.hawaii.edu/graduate/

For additional information about the Graduate Program in Molecular Biosciences & Bioengineering, please contact:

Dr. Dulal Borthakur Graduate Chair, Molecular Biosciences & 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

General guidelines and requirements for PhD degree in MBBE

General guidelines and requirements for MS Plan-A students in MBBE

General guidelines and requirements for MS Plan-B students in MBBE

List of approved courses for MBBE graduate students

All graduate students are encouraged to take MBBE 401 Molecular Biotechnology or an equivalent course as a prerequisite. The 600-level courses can be selected from the following list of courses. Students can select other courses after obtaining approval from the committee and the Graduate Chair.

Guidelines for preparing a proposal seminar

  1. What is the main idea of your research? Immediately after the title slide, the main idea must be presented in a simple language, so that everyone in the audience can understand what the research is about. Here you describe what the overall goal is and what you want to invent, discover or develop.

  2. Next, you must give a good justification for your research. Why is this research important? Why do you need to invest your time and public funds for this research ?

  3. What is already known? You are not required to provide an extensive review of literature. However, you must tell briefly what is known in this field.

  4. What is not known? After telling briefly what is already known, you have to emphasize what is not known. This should connect you with the specific objectives.

  5. Hypotheses: You may present your hypotheses here or tie them together with specific objectives (below).

  6. Specific objectives: Generally, there should be two or more specific objectives. Three is a good number.

  7. Specific objective 1. Describe how you will accomplish this. Show flow charts if needed. Explain briefly important methods and experiments for this objective.

  8. Specific objective 2. Describe in the same way as for objective 1.

  9. Specific objective 3. Describe as for objectives 1 and 2.

  10. Progress to date: Describe your results so far for each of the objectives. You may not have results for all objectives. You must present convincing results for at least one objective (see below).

  11. If you have a lot of results, show only the most important results. Discuss with your supervisor about your most important results. Other results must be available for presentation, if someone asks.

  12. Explain your results slowly. Make sure that you provide interpretations of your results. Mere presentation of the results will not be enough. You have to explain what these results mean and how they relate to the objectives.

  13. Timetable for completion. Show a timetable for rest of the experiments.

  14. Discussion with your supervisor: It is essential that you show your slides and discuss with your supervisor at least one week prior to your presentation. It is also important to make the presentation before your supervisor and your colleagues in the laboratory. Listen to their criticism and try to improve your presentation. Your research subject may be very complicated and many in the audience may not understand some details or certain slides. However, all scientists and MBBE graduate students who come to attend your presentation must be able to understand the main idea and the important points.

Guidelines for preparing MS/PhD Defense seminar

      For both proposal and defense seminars, you may assume that people in the audience have at least a BS degree and some background in biological sciences. That does not mean that everyone will be able to understand everything you present. There can be some high-level experiments that can be understood only by people trained in your research area. However, you should make the best efforts to make at least half of your presentation understandable to most people in the MBBE audience. It does not matter whether you are working on bioinformatics, cancer research, bioengineering, plant molecular biology or any other branches of molecular biosciences or bioengineering, you have to make at least 50% of your presentation understandable to most people in the audience. The following are the guidelines for preparing a defense seminar.

  1. Discuss with your supervisor. He/she will help you to make difficult things easy.
  2. As you progress in your research, try to make as many presentations as possible, keeping in mind that you are preparing for your final presentation.
  3. Explain to your friends, parents, colleagues and others, whenever possible, what your work is about.
  4. Do not show too many slides in your final presentation. If you have too many results, you do not have to present all. Present only the most important and most relevant results. Again, discuss with your supervisor about it.
  5. Make a powerpoint presentation in front of your supervisor and your lab colleagues at least 10 days prior to your final presentation. Ask them for criticism and try to improve. If necessary, make another presentation before your supervisor 3-4 days prior to your final presentation.
  6. Title slide and a summary preview: After reading the title, give a well-prepared speech for about 3-5 min describing in simple language what your research is about. Some points that can be addressed here are: how this research started, the most important findings (without details), benefits of these findings, and most importantly how you gained insight, experience, and expertise in research. You have to express your excitements for your work. This is like giving a preview of your presentation in simple words. This will make the audience interested in your presentation. This will also serve as a warm-up for your data presentation.
  7. The problem. Describe the problem that your research addressed in one or more slides.
  8. Justifications for your work: Why did you invest 3-5 years of your life for addressing the above problem ? Why are these time and money investments justified ? (at least one slide).
  9. What was already known when you started? You may show a number of slides to present a brief review of literature. Discuss with your supervisor about specifics. This must be short. The review of literature must not be dull, it must be connected well with the problem.
  10. Overall goal of your research (one slide): State how you addressed the problem.
  11. Specific objectives: Dissect the overall goal into specific doable objectives (one slide).
  12. Objective 1. State the objective 1 and the associated hypothesis (one slide). At this stage do not rush. In about one min, try to give a simplified preview of the methods and experiments you conducted in this objective. You should have a well-prepared 1 min speech here. This will help to maintain attention of the audience on your work.
  13. Experiments in objective 1. Using a number of slides, describe the experiments and results for objective 1. You may show short flowcharts to describe methods. Whenever you present some results with tables or graphs, give enough interpretations. Always try to connect results with the problem.
  14. Objectives 2 and 3. Present in the same way as for objective 1. Do not forget to give a 1 min simplified preview of experiments for each objective before going into details.
  15. At the end, remind the audience about the problem you wanted address and how your results addressed some questions. Here again you need to face the audience and stop depending on your slides. Tell briefly (in about 1 min) the highlights of your work.

Guidelines for preparing dissertation/thesis defense announcement flyer

  1. Take a page in landscape page set-up and divide into two columns. Then fold the paper into half. This will make four half pages (both sides) from a standard A4 size paper. You may use a slightly thick paper.
  2. Write your announcement in the format shown in the attached page. Briefly, in the front page, write your dissertation/thesis title, your name etc. In the second page, write the names of your committee members, your publications and future plan. In the third page, provide an abstract of your dissertation/thesis. You may include manuscripts in preparation also under your publications.
  3. Prepare this at least one week before the presentation, get your major advisor's approval and send three copies to the Graduate Chair.
  4. If you would like Graduate Chair to send these copies to your previous mentors and your biology or chemistry teachers who helped you to come to the MBBE Graduate Program, please provide their addresses.
  5. Print it on color papers. Put on the notice board, send to different people as invitations and distribute copies at the time of presentation. Send copies to all those people whom you acknowledge in your dissertation/thesis.

An example of a two-page proposal

Construction of a molecular cytogenetic map of papaya chromosomes

MS student: Yu Cheng
Advisor: Qingyi Yu

Introduction

      We will significantly advance genomic tools and knowledge for tropical trees, an under-explored node of the angiosperms that is of large and growing importance to US agriculture. Papaya is a promising model for tropical fruit genomics due to its short generation time (9-15 months), compact genome (372 Mb), detailed genetic map, high-quality BAC library, near-completion whole genome shotgun sequences, and close relationship to Arabidopsis. Due to the variation of recombination frequency along different regions of chromosomes, gaps remained in the high-density genetic map of papaya and 12 linkage groups were mapped for the 9 pairs of chromosomes. The linkage group 2 in this map is abnormally large, and we suspect that it represents more than one chromosome. Molecular cytogenetics can assign linkage groups to chromosomes and will be the most effective approach to resolve this issue.

Objectives

      The overall goal of the proposed project is to develop papaya as a model system for the identification, characterization, and cloning of agronomically important genes, to elucidate the genome structure and organization of a tropical tree species, and ultimately to apply the obtained knowledge and technology towards improving the quality and productivity of crop species. We have recently constructed a deep coverage BAC library and a high density genetic map, fingerprinted 26,244 BAC clones for physical map construction, and sequenced 66,023 BAC ends as elements necessary for achieving these objectives.

Specific objectives
  1. Assign each linkage group of the papaya high density map to individual chromosomes by in situ hybridization of selected DNA markers mapped to each linkage group.
  2. Define the breakpoint of linkage group 2 and clarify the orders of linkage groups on chromosomes.

Approach

An example of defense seminar announcement flyer

ORAL PUBLIC EXAMINATION
FOR THE DEGREE OF DOCTOR OF PHILOSOPHY

Functions of mid and pyd genes required for mimosine degradation by Rhizobium sp. strain TAL1145

Jonathan David Awaya
2:15 PM
October 13, 2005
Agricultural Science Building, Room 219
Department of Molecular Biosciences and Bioengineering
University of Hawaii at Manoa

COMMITTEE MEMBERS
Dr. Dulal Borthakur (Chair)
Dr. Sean Callahan
Dr. Tung Hoang
Dr. John Hu
Dr. Qing Li

PUBLICATIONS

  1. Awaya JD, Fox PM, Borthakur D (2005) pyd genes of Rhizobium sp. strain TAL1145 are required for degradation of 3-hydroxy-4-pyridone, an aromatic intermediate in mimosine metabolism. J. Bacteriol. 187 (13): 4480-4487.
  2. Awaya J, Fox PM and Borthakur D (2003) Genes encoding a fructose-1,6-bisphosphate aldolase and a fructose-1,6-bisphosphatase are present within the gene cluster for mimosine degradation in Rhizobium sp. strain TAL1145. Plant Soil 257: 11-18.
  3. Awaya J, Walton C and Borthakur D. The pydA-pydB fusion gene produces an active dioxygenase-hydrolase protein in Rhizobium and Escherichia coli that degrades 3-hydroxy-4-pyridone, an intermediate of mimosine metabolism (manuscript in preparation).

FUTURE PLAN

Postdoctoral research at Notre Dame starting on February 1, 2006

ABSTRACT

      Mimosine and 3-hydroxy-4-pyridone (HP) are toxic aromatic compounds produced in tree-legume leucaena (Leucaena leucocephala). These can be degraded by some leucaena-nodulating Rhizobium strains, such as TAL1145. Previously, a cosmid clone, pUHR263, containing the mid and pyd genes for mimosine and HP degradation, was isolated from a clone library of TAL1145. The aim of this project was to identify genes for mimosine and HP degradation in pUHR263 and determine their functions. Mimosine degradation by Rhizobium involves at least two major steps; in the first step mimosine is degraded to HP, which is then converted to pyruvate, formate and ammonia in the second step. Two structural genes, pydA and pydB, encode a meta-cleavage dioxygenase and a hydrolase, respectively. pydA and pydB are required for degradation of HP, and pydC, pydD and pydE encode proteins of an ABC-transport system involved in the uptake of HP by TAL1145. pydA, pydB, pydC, pydD, and pydE are induced by HP, although pydA and pydB show low levels of expression in the absence of HP. pydA and pydB are cotranscribed while pydC, pydD, and pydE are each transcribed from separate promoters. pydR is located upstream of the pyd genes and encodes a transcriptional regulator for the activation of pydA and pydB in the presence of HP. Elucidation of the HP degradation pathway in Rhizobium sp. strain TAL1145 may provide a useful strategy to genetically engineer leucaena and rhizosphere bacteria to disrupt the biosynthesis of mimosine and for bioremediation of aromatic toxins, respectively.

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Awards Received by students
List MS Theses
List of MS Plan-B Research
List of PhD dissertations
Students' Publication