Introduction
Tropical Plant Pathology (TPP) is the study of plant diseases, their causes, and the interactions with the environment. The primary thrust in the program focuses on agricultural crops of economic importance; however, opportunities exist for discovery research in natural ecosystems and the laboratory. The field consists of several sub-disciplines including phytomycology, plant virology, bacteriology, nematology, epidemiology, crop protection, and molecular biology of host-pathogen interactions.
This handbook sets forth the basic policies, requirements and procedures for graduate students pursuing degrees in Tropical Plant Pathology for the Master of Science and the Doctor of Philosophy. One should read this very carefully so that one is clear about their responsibilities as a student and the responsibilities of the program to the student. For any questions about the information presented here, please contact Dr. Brent Sipes, Graduate Chair. The earlier matters of concern are clarify, the less likely it is to create problems later. We wish all students great success in pursuing their educational goals and hope that this handbook provides students with a tool to meet those goals.
Program Goals
The Tropical Plant Pathology Graduate Program has three goals for students. The faculty expect students to communicate effectively, to be competent and knowledgeable biologists, and to conduct research in plant pathology. The student learning outcomes associated with theses goals are:
- TPP students communicate effectively
- TPP students will write and defend a thesis of original phytopathological research.
- TPP students will present the findings of their research in oral and/or poster formats at scientific forums.
- TPP students will publish the results of their research in peer-reviewed journals.
- TPP students will assist others in learning the science of plant pathology.
- TPP students are competent and knowledgeable biologists
- TPP students will have a basic understanding of molecular biology and genetics.
- TPP students will demonstrate a general knowledge of the four major pathogen groups.
- TPP students will possess understanding of plant disease epidemiology.
- TPP students will have strong knowledge of their specialized field of study.
- TPP students conduct research in plant pathology
- TPP students will propose and formulate research hypothesis and objectives to address relevant plant pathological questions.
- TPP students will conduct research using appropriate designs and methods.
Program History
Early plant disease research predates the formation of the college and was conducted by notable plant pathologists, like Nathan Cobb at the Hawaii Sugar Planters Association and others at the Agricultural Experiment Station. In 1915 plant pathology was one of the five divisions of the college and by 1936 it was a department.
In August 1941 plant pathology became one of the first casualties of World War II when its senior faculty member, Keith Paris, uncertain about the fate of Hawaii wrote, “The more I read of conditions the more I wonder if I want to go back to work in Honolulu. The latest idea in the minds of the authorities seems to be a carrier slipping thru on a suicide mission, the bombing of the oil tanks and general disablement of Pearl Harbor”. Paris stayed on the mainland and the remaining department members, Kauo Kikuta and Minoru Matsuura, were transferred to the department of Vegetable Crops and the Kamuela experiment station. The department was reactivated in 1945 with the hiring of Walter Hendrix and James Lyle.
Over the next 15 years plant pathology played an important role in the development of agriculture in Hawaii. Joined by Mamoru Ishii, Oliver Holtzman, and Minoru Aragaki, the department conducted research and extension activities focused on controlling diseases of fruit, ornamental and vegetable crops. With the use of short term contracts, they benefitted from the services of distinguished plant pathologists like Benjamin Chitwood, William Feder, Yuichi Honda, James Hunter, Harry Murakishi, Chris Hayward, and Allen Sher.
With the boom in educational resources between 1960 and 1970, the department tripled to 13 faculty—developing a strong program in fungal pathogens, nematology, virology, bacteriology, epidemiology, and host-pathogen interactions. Under the leadership of Ivan Buddenhagen, the department moved toward an international perspective with projects throughout tropical Asia and Africa. Buddenhagen founded the first plant disease clinic in Pacific region and staffed it with an experienced diagnostician, Albert Martinez. In 1973, the department took a daring first step by hiring Anne Alvarez as the first female extension plant pathologist in the US. Wen-Hsiung Ko (a Fellow of the American Phytopathological Society) pioneered seminal research into the sexual reproduction of oomycetes. Eduardo Trujillo discovered unique ways to control invasive weeds exploiting fungal pathogens which were released into Hawaii’s forests and grazing lands. Walter Apt and Kenneth Rohrbach came to the department with the closing of the Pineapple Research Institute bringing expertise on nematode and fungal diseases of pineapple. Don Schmitt (a Fellow of the Society of Nematologists) spearheaded the use of resistant rootstock for control of a devastating nematode disease of Kona coffee. Suresh Patil, produced students like Marty Dickman and Robert Birch (an Outstanding CTAHR Alumnus), who now lead major research programs in Texas and Australia.
Instruction has been integral to the mission of plant pathology. A MS degree was offered in 1962 and the PhD in 1971. The 120 students awarded graduate degrees in plant pathology have gone on to successful careers in academia, state and federal agencies, and private industry in Hawai‘i, the U.S. mainland, Asia, Australia, Europe and Africa.
PEPS Facilities
The Department of Plant and environmental Protection Sciences is housed predominately in Gilmore Hall and St. John Building on the Manoa campus. Most plant pathology staff are found on the third floor of St. John Plant Science Building. The department also has space in the Pope Environmental Laboratory and at the Magoon Greenhouse Facilities, as well as sites off campus and on neighbor islands. If you require special rooms for seminars, conferences or audio/visual presentations, rooms may be reserved to meet these needs.
Harold St. John Plant Sciences Building Laboratories
Plant Pathology occupies nearly 900 m2 of floor space in St. John. The facilities include eight laboratories, a teaching laboratory, general-use media preparation and incubator rooms, a departmental library, the departmental office, and graduate student offices. Laboratories are equipped for research in bacteriology, mycology, nematology, virology, and extension plant pathology. There are several walk-in ‘cold rooms’ located in the rooms 306. If you require the use of these cold rooms please make arrangements with your advisor.
General-use laboratories (shared by all members of the department) are located in rooms 306, 308 and 311. Room 311 contains two autoclaves, sterile distilled water, an ice machine, a microwave, a drying oven, and a -80oC freezer. Use of the autoclaves is signing up on the sheet located on the table in front of the machines. Please follow directions for the use of the equipment in the room. You must be trained and authorized before using the autoclaves. Incubators are housed in room 306. Incubators are maintained at various temperatures. If you need to use an incubator please see the faculty member who uses the machine and get their permission before placing material in the chamber or altering the temperature. The laboratory in 308 contains equipment which you may use with permission of the appropriate faculty member.
The departmental office is located in rooms 305 and 307. Departmental supplies, the photocopier, facsimile machine, and mailboxes are found in room 305.
Greenhouses
The Department has greenhouse space available at four locations: Pope Environmental Laboratory, Magoon Greenhouse Facilities, the Gilmore roof top, and Whitmore Experimental Station. Greenhouse space is allocated to faculty members and graduate students may obtain greenhouse bench space through their advisors. Mr. Steve Yoshida is our greenhouse technician and provides basic care of plant material and maintenance of the physical facilities in Pope and Magoon. Mr. Gareth Nagai provides limited plant care at the Whitmore greenhouse.
Pope Environmental Laboratory
- 7 bays
- 170 m2 bench space
Pope Environmental Laboratory greenhouses are located adjacent to Sherman Lab, on the mauka side of St. John. These greenhouses are of the standard glasshouse construction type. The Pope headhouse is for the storage of pots and media, for washing and cleaning pots/samples, and for general preparation of experimental treatments. Sterile soil or potting mixtures must be prepared by individual research projects. All experimental supplies are purchased by individual research projects (e.g., fertilizer, stakes, etc.). Pest control is the responsibility of individual research projects.
Magoon Greenhouses
- 7 bays
- 2 bays open shade
- 250 m2 bench space
The Magoon greenhouses are of the standard glasshouse construction type. At Magoon, there is no general work area for preparing experiments (e.g., potting, labeling stakes, etc.). Therefore, prep work must be done on individual benches. Similarly, storage of pots and media must be in Pope Lab head house area of in the storage shed located at Magoon. Greenhouse maintenance and supply procedures are the same as for the Pope greenhouses.
Non-Department Resources
The university has many resources outside of the Department of Plant and Environmental Protection Sciences. Ones that we frequently use are listed below.
CTAHR Computer Lab Large Format Printing
The college computer lab offers poster printing. You prepare your poster on your computer and save it in a Adobe Photoshop (.psd), Adobe Acrobat (.pdf), Microsoft PowerPoint (.ppt) or Image (.jpg, .tiff) file. You take this file to the computer lab in the Ag Sciences building and have it printed out. The lab only supports PC’s; not Mac’s.
Greenwood Molecular Biology Facility
The Greenwood Molecular Biology Facility is a primary research infrastructure operated by the Biotechnology Program of the Pacific Biosciences Research Center. The Facility serves the biomedical and molecular biology research and educational programs of the University and its associated institutions. The Facility is structured to address the needs of researchers for services in genomics, proteomics and bioinformatics. These currently include DNA sequencing, GeneScan/Genotyping, real-time PCR analysis, oligonucleotide synthesis and purification, GeneChip/DNA microarray analysis, custom microarray analysis, peptide and protein sequencing, GCG genetic analysis and database access, and molecular modeling. The Core Facility provides technical support for research.
Biological Electron Microscope Facility
The BEMF is a multi-user/service facility that provides researchers with state-of-the-art instrumentation, training and services for high-resolution scanning electron microscopy, conventional and energy-filtering transmission electron microscopy, optical, fluorescence, and laser scanning confocal microscopy, and image analysis on a recharge basis. The BEMF has a full line of instrumentation for conventional and energy filtering transmission electron microscopy, high resolution field emission scanning electron microscopy with X-Ray microanalysis, brightfield and fluorescence light microscopy and laser scanning confocal microscopy, and laser microdissection with non-contact capture, plus laser optical trapping.
Chemistry Stockroom
The Department of Chemistry is home to two well-supplied stockrooms, containing an array of materials necessary for graduate research. Prior to purchasing supplies an account must be established. Most laboratories in the department have these accounts.
Advanced Studies in Genomics, Proteomics and Bioinformatics (ASGPB) DNA Sequencing Service
ASGPB is committed to specifically support high-throughput projects such as genome-wide analyses and will assist with the preparation of relevant grant applications. In addition, ASGPB will provide assistance with sequence assembly and bioinformatic analysis of sequencing projects. ASGPB offers the following services:
- Construction and validation of random-sheared DNA fragment libraries.
- High-throughput, automated template preparation using Eppendorff kits or the overnight high-throughput template preparation via the Rolling Circle Amplification (RCA) method.
- Assembly and processing of DNA sequencing reactions in 96-well microtiter plate format.
Departmental Services
Our department, college and university have many services which are available for your official business. These include secretarial services, a photocopier, state vehicles, telephones, office supplies, computers, audio-visual aids, and mail services. You must limit your use of these services to activities which are directly related to your research project. Any abuse of these services is a serious offense and could result in being expelled from the university.
Keys
You will need keys to enter most buildings after hours and on weekends. Most students will be assigned keys to open St. John, St. John 300, and the laboratory in which they work. These and other needed keys may be obtained through the secretary in St. John 307.
Email and Mail
Your UH Username is your electronic key to gaining access to the university's online services like email, Internet access, registration for classes, and various other services. You may request your UH Username online from the UH Account Management page by clicking on the "Get a UH Username!" link. Your account should be ready within six minutes. Most services, such as MyUH, will be available to you once your account is created. Your UH Email Account (@hawaii.edu) will be available for use after fifteen 15 minutes. You will need to provide the following information to apply for an account:
After you have completed the form, use the Continue button to submit your request. The online request system will check the Account Management database for your full legal name and the information above. If your information is found within the Account Management database, you will be asked to create a password for your UH Username. You need to select two questions and furnish the answers for these two questions. In the future, these two questions will allow you to reset your password online.
Upon arrival in the department, you will be assigned a mailbox, located in St. John 305, where your post office mail and announcements are placed. Names are arranged alphabetically in groups of faculty, staff, and students. Campus and U.S. mail will be delivered here. Campus mail is to be used for business correspondence within campus. Place your business mail in the office box marked metered mail for it to be marked with postage. Clearly mark any special instructions on the envelop to avoid having the mail return because of insufficient postage. The staff will be glad to explain the mail system.
Secretarial Services
The departmental secretary is available to type official documents which are required by the department. Official documents include but are not limited to reports and publications. When making a request to the secretary, please have it in their box(es) soon enough to allow it to be completed in a timely fashion. Students are responsible for typing or processing their thesis/dissertation.
Photocopier
The photocopier is available for student use but is limited to activates related to your thesis research. You are not allowed to copy books or to copy personal documents. Please avoid violation of copyright laws by using the photocopy machine.
State Vehicles
Cars, trucks, and vans may be leased from the University Transportation Services. These vehicles may be used for research. Permission to lease a vehicle is obtained through your academic advisor. Vehicle reservations are made by calling the Transportation Services (68875). Please reserve a vehicle as far in advance as possible; numbers of rental vehicles available are limited and may de difficult to reserve at times. Vehicles available for leasing include sedans, pick-up trucks, utility vehicles, and vans.
Telephones
Telephones are available for research and academic use. Calls within campus may be placed by dialing the last five digits of the phone number, i.e. 6-xxxx. Local calls (those off-campus but on Oahu) may be placed by dialing 9 + the 8 digit number. Long distance calls, calls to neighbor islands, and calls to the U.S. mainland or international destinations, may be placed only from telephones which are authorized for long distance calls. Permission for student long distance calls may be obtained from your academic advisor.
Facsimile Machine
A facsimile machine is available to send and receive messages. Our FAX number is 956-2832. Calls are recorded in the log book located next to the FAX machine, and should be charged to a Department account. Therefore, students should obtain advisor’s permission before using the FAX machine. Local facsimiles do not require an account number, only approval form your academic advisor.
Office Supplies
General office supplies are available for research related activities. Writing tablets, pencils, pens, and folders, etc. are located in cabinets in St. John 305. Please see the secretary if you are unable to locate the supplies.
Audio Visual Aids
Audio/visual aids are available for academic and research use. St. John 302 and St. John 307 are equipted with a computer, projection, and internet connection. Cameras and microphones allow for video conferencing if needed.
Purchasing
Students must order all research related supplies through your advisor/laboratory. Each laboratory has a system for purchasing supplies and these can differ from laboratory to laboratory. We use P-cards, purchase orders, and reimbursements for supplies. Have your advisor explain the ordering system in your laboratory as soon as you arrive and begin work.
Computing Services
The University of Hawaii Information Technology Services (ITS) provides services across the broad range of computing and communications technologies that support learning, teaching, research, public services and administration. Information technology support is available to faculty, staff and students of the UH system.
ITS provides your UH Username. Your UH Username is your electronic key to gaining access to the university's online services such as computer labs, a web mail service, Help Desk, MyUH (access to class registration and transcripts), Laulima (a web-based course site), a personal home page, site licensing and discount agreements, software and hardware information, a Unix shell, and information on wireless access on the campus.
Personal computers are available in most of the departmental laboratories and in the graduate student office (St. John 300) in addition to the personal computers available elsewhere on campus. Various software programs are available on the machines. Rules governing the use of these computers are simple in that we ask you to be considerate of fellow users. If it becomes necessary to limit use on the machines, a time sheet for use may be posted.
Library Services
UH Manoa’s libraries offer resources, services, and expertise to facilitate the inquiry, discovery, and exchange of information. Library collections include over three million volumes together with microform units, digital files, manuscripts and archives, audiovisual materials, maps and aerial photographs, and current journals and serial titles in paper and electronic formats. Most electronic resources to which the Library subscribes are RESTRICTED to University of Hawaii at Manoa students, faculty, and staff to comply with licensing agreements. Many free resources are also available: please refer to the Library Help Page for more information. Many tools are available only in paper format. To locate a specific book, print journal, newspaper or government publication that the Library owns, search the Hawai'i Voyager Library Catalog. Ask a librarian for assistance in identifying additional tools related to your research topic.
Degree Requirements
Master’s Program
The MS degree in tropical plant pathology provides a basic education and understanding of the pathogen groupings. The MS degree program is offered under either Plan A (thesis) or Plan B (non-thesis). A total of 30 credit hours are required for each degree option.
M.S. Plan A (Thesis)
This degree option is focused on research and the development of new knowledge. In addtion to the required course work the student must submit an acceptable thesis. Thesis Research credits are initially taken as PEPS 699 under the direction of your advisor. Upon graduation, the 699 credits are converted into PEPS 700 credits. The student must be registered for at least 1 credit of PEPS 700 during the semester that the thesis is submitted.
Course work required for the MS Plan A are 16 credits in courses approved by the candidate’s committee, including PEPS 605, 606, 615, and 615L, and other courses numbered 600-698, excluding PEPS 660 and 699.
Students are also required to take and participate in seminars. PEPS 660 Seminar in Tropical Plant Pathology is required each semester except when you are enrolled in PEPS 799. A minimum of 2 credits in PEPS 660 is required. You are also required to present a proposal and defense seminar PEPS 799 (1 credit hour each for CR/NC). You register for your advisor’s PEPS 799 section. PEPS 799 credits are not counted towards the 30 credit degree requirement.
Plan of Work
You will develop a semester by semester plan of course work in consultation with our advisor. Your plan should ensure that any deficiencies are addressed, that the minimum requirements are satisfied, and that you have taken interesting and appropriate course work. Generally, you will present your plan of work during your first committee meeting. At the conclusion of this first meeting Form I is submitted.
Thesis Proposal
The M.S. thesis topic should be a narrowly defined project which demonstrates your potential to bring a research idea from concept to completion. The appropriate scope of an M.S. project is approximately that of a refereed journal publication, but the end result does not have to be published to earn the M.S. degree. As part of the mentoring process and to facilitate progress toward the degree, your faculty advisor will take an active role in defining suitable and acceptable projects. Your advisor is likely to review and edit your proposal, perhaps several times, before presentation to your full committee.
You must write and submit an acceptable thesis proposal to his/her Thesis Committee ideally within the first year after admission. The proposal should follow the format outlined below and will serve as a template for the finished thesis. Approval of the thesis topic is official after the proposal seminar is given and Form II is filed.
Outline for Thesis Proposal
A. Title
B. Introduction (the topic and related research)
C. Objectives and Hypothesis
D. Material and Methods (organized by objective)
E. Literature Cited
F. Research Schedule (Dates for reaching project and degree milestones)
Thesis Seminar and Defense
Upon completion of the proposed research, each student will write a thesis. The thesis will be written in a style agreed upon by the student and committee chair. We usually follow a journal format. Examples of accepted theses are found in our library. The drafting and revision of a thesis can be a long and arduous process taking 2-3 months. After the thesis has reached and acceptable level, it will be publically presented and read the student’s committee. The final seminar will be scheduled and announced. The committee should receive the thesis at least 2 weeks before the seminar to provide time for review.
After the seminar is completed, the floor is opened to questioning from all students and faculty. Upon the conclusion of the open questioning period, the committee will conduct a private examination. This examination will cover the thesis and related areas. When the examination has concluded, the student will be asked to leave the room and the committee will discuss the acceptability of the thesis and the thesis defense. The acceptance of the thesis is determined by a majority vote of the committee. The student will be asked to return to the room and informed of the committee’s decision. The judgement of the thesis is officially recognized with the filing of Form III and with the signing of the signature page. The student may be asked to make edits or additions to the thesis before the signature page is signed or Form III is submitted to the Graduate Division.
M.S. Plan B (Non-Thesis)
This degree option is focused on active learning, experiential course work. Students take a core of 13 credits consisting of PEPS 605, 606, 615, and 615L. As such, 19-22 credits in courses approved by the candidate’s committee are required. Additional credits in courses numbered 600-698, excluding PEPS 660 and 699, are needed. These courses must include at least 6 credits selected from PEPS 616, 630, and 646.
Directed research experience is also required of the students in this option. Candidates need 6 credits,with no more than 9 credits counted towards the degree requirements, in PEPS 699 Directed Research. We encourage students to take their directed research underthe direction of 2-3 different faculty members.
Students are also required to take and participate in seminars. PEPS 660 Seminar in Tropical Plant Pathology is required each semester except your last semester when you enrolled in PEPS 799 (CR/NC) to present a culminating seminar. A minimum of 2 credits in PEPS 660 is required. PEPS 799 credits are not counted towards the 30-credit degree requirement.
The Ph.D. Program
Candidates for the Ph.D. program should have earned an M.S. degree in plant pathology or equivalent degree from a recognized institution. Those students with a B.S. or B.A. may petition for admittance into the Ph.D. program only after enrolling in the M.S. program.
The Ph.D. degree has no minimum course requirement. A candidate’s committee develops a course plan together with the student. However Ph.D. students are require to enroll in:
- PEPS 660 Seminar in Tropical Plant Pathology (1 credit hour) each semester, except when enrolled in PEPS 799
- PEPS 799 (1 credit hour for the Proposal Seminar and 1 credit hour for the Defense Seminar, or 2 credit hours total). This course is taken as CR/NC and under the committee chair’s registration number.
- PEPS 800 Dissertation Research (1 credit hour) during semester of graduation
Candidates must also pass comprehensive and final defense examinations. Additionally, a Ph.D. student must submit a dissertation deemed acceptable by their committee.
Dissertation Seminar and Defense
Upon completion of the proposed research, each student will write a dissertation. The dissertation is written in a style agreed upon by the student and committee chair. We usually follow a journal format. Examples of accepted dissertations are found in our library. The drafting and revision of a dissertation can be a long and arduous process taking 2-3 months. After the dissertation has reached and acceptable level, it will be publicly presented and read the student’s committee. The defense seminar will be scheduled and announced. The committee should receive the dissertation at least 2 weeks before the seminar to provide time for review.
After the defense seminar is completed, the floor is opened to questioning from all students and faculty. Upon the conclusion of the open questioning period, the committee will conduct a private examination. This examination will cover the dissertation and related areas. When the examination has concluded, the student will be asked to leave the room and the committee will discuss the acceptability of the dissertation and defense. The acceptance of the dissertation is determined by a majority vote of the committee. The student will be asked to return to the room and informed of the committee’s decision. The judgment of the dissertation is officially recognized with the filing of Form III and with the signing of the signature page. The student may be asked to make edits or additions to the dissertation before the signature page is signed or Form III is submitted to the Graduate Division.
Academic Performance
As a graduate student, you have a right to periodic evaluation of your academic progress, performance, and professional potential. Your advisor is your primary reviewer, followed by your thesis/dissertation committee, and finally by the Tropical Plant Pathology graduate chair and graduate faculty. You should be in regular conversation with your advisor. Your advisor should be made aware of any academic or research troubles that you may encounter. Your thesis/ dissertation committee should meet at least once a year to review your progress and plans for the coming year.
TPP students are expected to remain in “Acceptable Academic Standing” during their tenure. To be in acceptable standing, students must maintain a minimum 3.0 GPA, participate in seminar, and conduct research working towards their degree. A TPP student is making satisfactory progress toward their degree when they hold timely committee meetings, present their proposal, conduct their research, and defend on the schedule proposed and agreed upon by the student, advisor and committee. You have a right to receive a warning when your academic performance or progress is judged to be unsatisfactory.
As a student you can access your educational records. Your transcripts are viewable from the myuh portal. You can access the records that the Tropical Plant Pathology holds by asking your advisor or the graduate chair.
Academic Integrity
Integrity in research is of the highest importance. It represents a commitment to basic values such as fairness, equity, honesty and respect. Your professional integrity is one of the most precious things you possess. We expect and demand high standards of ethical behavior during your tenure in the department. You should expect and demand the same from us.
The following text is from the University of Hawaii Graduate Division webpage:
The University of Hawai'i at Manoa exists for the pursuit of knowledge through teaching, learning, and research conducted in an atmosphere of physical and intellectual freedom. Members of the UHM academic community are committed to engage in teaching, learning, research, and community service and to assist one another in the creation and maintenance of an environment that supports these activities. Members of the academic community may not violate the rights of one another nor disrupt the basic activities of the institution. Students who are disruptive are subject to a variety of disciplinary actions that may include reprimand, probation, restitution, suspension or expulsion. Continued enrollment at UHM is contingent on appropriate academic conduct. Some graduate students are professionals or professionals-in-training in their respective fields, and as such, are subject to the ethical and conduct standards of their profession. Their continued enrollment at UHM is contingent on appropriate academic conduct as well as professional behavior.
It must be recognized that members of the academic community have the same privileges and responsibilities with respect to the law, as do members of the larger society. As a result, members of the UHM campus community must acknowledge that when the interests of the university are violated by a student, the student is accountable to the institution and may also be held responsible to civil authorities. These interests of the university are described in the University of Hawai'i at Manoa Student Conduct Code. Any questions regarding the Student Conduct Code should be addressed to the Dean of Students.
To ensure a safe and healthy working environment for faculty, students and staff, the University of Hawai'i at Manoa sets and enforces rigorous safety standards that meet and exceed local, state and federal law. The Environmental Health and Safety Office (EHSO) at the university sets a multitude of rules and regulations pertaining to common laboratory materials and other research related activities in Hawai‘I, and they may be quite different from those at other institutions. The university has specific programs and requirements for:
a. Radioactive material
b. Biological "commodities" - including micro-organisms, plants, animals, biological toxins, cell or tissue samples, recombinant DNA, etc.
c. Compressed gas (SCUBA) diving
d. Certain chemicals and hazardous materials
e. Disposal of hazardous waste
In addition, there are regulations governing the importation and shipment of these materials or types of equipment into the State and/or university. For more information, please visit the EHSO website.
Students who work in a laboratory setting are required to attend and maintain health and safety training in skill areas that are relevant to their work. The EHSO offers a variety of training programs in laboratory safety, radiation safety, hazardous waste, scientific diving, fire extinguisher use, and shipping of biological commodities. Please contact EHSO to check on class schedules or to arrange for training. Labs and lab members must be certified in compliance with EHSO guidelines at all times.
Ph.D. Comprehensive Examination
The comprehensive examination is an oral examination of the candidate’s comprehension of plant pathology and related fields. Prior to the comprehensive examination, the candidate shall decide on three areas of concentration that will be examined in depth. One of these areas must be an outside discipline (e.g., horticulture, genetics, botany, biochemistry, entomology) relevant to plant pathology. The other two areas may be experimental design/statistics or one of the subdisciplines of plant pathology (e.g., mycology, bacteriology, virology, and nematology). The student may be examined on a wider range of subjects as well.
The purpose of the comprehensive examination is to formally determine candidacy to the Ph.D. degree program in Tropical Plant Pathology at the University of Hawaii at Manoa.
The candidate will be asked to integrate knowledge from the range of courses taken under the objectives of the candidate's degree program. At least one member of the student's Advisory Committee will be appointed by the Graduate Chairman to be responsible for the examination in each area during the comprehensive examination. The candidate is expected to schedule the examination with the Graduate Chairman at least 3 weeks prior to the proposed date. Students are encouraged to discuss the nature and extent of potential questions with the committee members prior to the examination. The examination will be chaired by the Graduate Chairman or her/his representative. All members of the candidate’s Advisory Committee must be present, and other members of the graduate faculty are encouraged to attend and participate in the questioning. Passing the comprehensive examination requires the approval by the majority of the members of the Advisory Committee. In the event that the candidate’s performance is not satisfactory, there are several alternatives:
1. The examination may be repeated at a later date.
2. A written examination may be given, followed by another oral examination.
3. A course may be recommended, followed later by another oral examination.
Failure to pass the comprehensive examination on the second attempt will result in removal of the student from the graduate program in Tropical Plant Pathology.
Defense
The final Master’s or Doctoral defense and examination are the culmination of your graduate education and reflects your accomplishments. Your approved thesis or dissertation that is accepted by the Graduate Division becomes a single-author publication and contributes to the body of knowledge in plant pathology.
In accord with Graduate Division policy, you will present the results of your thesis/dissertation in a seminar open to the community. Your oral examination will follow your seminar and be limited to your committee members and all interested members of the Tropical Plant Pathology graduate faculty. In consultation with your advisor, you will select a date for your seminar and exam when your committee can be present. You will reserve an appropriate room, such as St. John 106, Sherman 103 or Gilmore 310. You will notify the graduate chair so that an announcement can be made to the Tropical Plant Pathology graduate faculty. You will post announcements of your upcoming seminar in the buildings.
M.S. Plan A
The M.S. Plan A candidate is required to make a public presentation of her/his thesis research, after which a general examination is given by the graduate faculty. This examination, or defense, consists of a seminar of approximately 40 minutes after which questions are asked by any member of the audience. After a short break, the candidate will be examined further by her/his academic program committee and any other member of the graduate faculty who wishes to attend.
The thesis committee then makes one of the following decisions based upon this examination:
1. Passed.
2. Failed; take examination again at a later date.
3. Failed; drop program in Plant Pathology.
At this time, Form III is completed and submitted to the Graduate Division. After a final copy of the thesis has been approved by the student's Permanent Committee, the thesis is submitted to the Graduate Division.
M.S. Plan B
The M.S. Plan B candidate is required to make a presentation of her/his directed research. The audience, the advisory committee and any other member of the graduate faculty who wishes to participate may ask questions during this culminating event. A short examination by the committee follows the presentation. The exam focuses on the directed research that the student conducted.
Ph.D. Defense
Each Ph.D. student will defend her/his dissertation. A defense consists of a seminar on the research, and is open to all members of the University of Hawaii community and an examination regarding the details and content of the dissertation. Any member of the graduate faculty may attend. The candidate’s entire committee must attend the thesis/dissertation defense. Substitutes may be appointed for absent committee members using the procedures set out in the Graduate Division Manual. If the defense is acceptable to the Advisory Committee, Form III is submitted to the Graduate Division. If not acceptable, further research may be required by the committee. Only after the final copy of the dissertation has been submitted and approved by the committee is the dissertation submitted to the Graduate Division.
Graduate Division Forms
Three forms are required by the Graduate Division for the MS Plan A (Thesis) and Ph.D. The forms are:
Master's Plan A Form I - Pre-Candidacy Progress
Master's Plan A Form II - Advance to Candidacy
Master's Plan A Form III - Thesis Evaluation
Master's Plan A Form IV - Thesis Submission
Doctorate Form I - Pre-Candidacy Progress
Doctorate Form II - Advance to Candidacy
Doctorate Form III - Dissertation Evaluation
Doctorate Form IV - Dissertation Submission
All forms are found on the Graduate Division website.
Seminars
Several types of seminars take place in the department. TPP students will encounter special seminars by visitors, topic seminars, proposal seminars, defense seminars, discussion groups, journal clubs, and symposia. Special research seminars are presented from time to time by visiting scientists, faculty, staff, students and other guests.
Topic Seminars
As a student you are required to participate in a Topic Seminar (PEPS 660) held each semester if you are not presenting a proposal seminar, a culminating seminar, or defending your thesis/dissertation. THe plant pathology seminar is held Friday afternoons from 1:30 to 2:20. Topic seminars are in an area of plant pathology apart from you own research. Tropical Plant Pathology faculty rotate as leaders of the topic seminar each semester and specifics thus change.
Proposal Seminars
Proposal seminars are presented by students on their thesis/dissertation research. Proposal seminars are normally given early during your tenure as a graduate student. These seminars provide and opportunity for your fellow students, the staff and faculty to learn about your research. Furthermore, the presentation of your proposal will allow critical evaluation and prevention of missteps in your research. Proposal seminars should be scheduled so that all members of your Advisory Committee will be present. Proposal seminars are taken as a PEPS 799 1-credit-hour (CR/NC). Remember that these seminars do not count towards the M.S. 30 credit requirement.
Defense Seminars and Culminating Seminars
These seminars are given during the last semester of your tenure as a student. The defense and culminating seminars represent a summary of a student’s research project. These seminars allow you to share the knowledge and advancement in science that you have made. These seminars should be scheduled so that all members of your Advisory Committee will be present. These seminars are taken as a PEPS 799 1-credit-hour (CR/NC). Remember that these seminars do not count towards the M.S. 30 credit requirement.
Discussion Groups and Journal Clubs
Discussion groups and Journal Clubs form at the beginning of fall and spring semesters. Students are encouraged to participate in group formation and in discussions. Discussions can informal, brown-bag lunch sessions. Often Journals Clubs or Discussion groups are offered as PEPS 691 special topics. Please ask your advisor.
CTAHR Student Research Symposium
Geographic isolation of the University of Hawaii and high travel expense often prevent CTAHR students from presenting their research at professional scientific conferences outside the state. The purpose of the CTAHR Student Research Symposium is to provide students with the opportunity to present their scholarly work in a friendly, yet professional setting similar to national and international conferences. Through travel grant awards, the Symposium enables graduate students to compete for funding to present their research at a scientific conference outside the state. The program consists of research papers and posters presented by graduate students, and research, review papers, capstone projects, and posters presented by undergraduate students. Whereas participation is not required by TPP graduate students at this time, the faculty support and encourage student participation in the symposium.
Advisory Committee
Initiation and successful completion of graduate studies requires early and continued advice from the Tropical Plant Pathology Graduate Faculty. The most important members of this faculty are your advisor and your committee members. When the student is being supported by a research assistantship, the faculty member supporting the student will usually be the students faculty advisor. In those rare instances when a student is not supported by an assistantship, the Tropical Plant Pathology Graduate Chair will serve as the Interim Advisor for the student.
Your relationship with your faculty advisor/committee chair will often determine the success and flow of your academic experience and training in plant pathology. Your advisor is devoted to mentoring you and to your success in your graduate studies. Your Thesis/Dissertation Advisory Committee shares responsibility for reviewing your progress as a graduate student and in guiding you toward completion of your degree requirements. The Advisory Committee will suggest and approve your plan of work. You must keep your committee informed of your progress throughout your tenure in Tropical Plant Pathology. It is recommended that you schedule a committee meeting once every semester.
Because of its importance, your thesis/dissertation committee should be formed in a timely fashion. Your committee must be formed in accord with Graduate Division Policy. Master committees require a minimum of three faculty—two from the graduate faculty in Tropical Plant Pathology. A Ph.D. committee requires a minimum of five committee members—three must be from within the graduate faculty of Tropical Plant Pathology and at least one of the remaining members from outside the Tropical Plant Pathology faculty. The Graduate Division has a web site to search for qualified members of the Graduate Faculty. The outside member of your committee will read and critique your thesis/dissertation, participate in your oral exam, and may submit an independent report to the graduate dean. The outside member insures fairness in the examination and maintenance of academic standards. You may have more members than the minimum number of committee members but excessive numbers will not be allowed.
You should choose your thesis/dissertation committee members in consultation with your advisor. Your committee should be formed by your second semester of residence in the department. Select faculty that bring expertise to provide you proper guidance. You want your committee to be composed of faculty that will ensure high professional standards. If the need arises, the composition of a constituted committee can be changed by submitting a memorandum to the Graduate Chair justifying the proposed change.
When you and your advisor have decided upon the composition of your thesis/dissertation committee, you will convene the group. Some advisors prefer to have the committee meet before you present your proposal seminar to discuss your plan of work. At this time you may submit a completed Student Progress Form I - Advancement to Candidacy. Other advisors will have you convene your committee, present your proposal seminar, and discuss your plan of work. Upon completion of your proposal seminar you will submit a completed Student Progress Form II - Advancement to Thesis Stage to the Graduate Chair for approval.
In completing the progress forms, remember that Tropical Plant Pathology does not have a qualifying exam or require a first language exam. Your committee will tell you of any deficiencies. We do not use interim advisors, so your advisor’s name will be used.
All members of your Advisory Committee must approve and sign your completed thesis.
In the Ph.D. Program, the Advisory Committee will administer your comprehensive and final examinations. A majority of your committee must approve of your dissertation and the oral defense of your dissertation. A minority member has the right to appeal to the Graduate Division for a final decision.
Theses and Dissertations
The Graduate Division has a style and policy manual which must be followed. However the acceptable style is very broad and most Tropical Plant Pathology students follow a journal article format. You should agree upon a style with your Adviser. All previous plant pathology theses and dissertations can be found in our library and you may use these as guides.
Judgment
The acceptability of the final version of any thesis or dissertation will be decided by majority of the Advisory Committee and officially recognized with the signing of the signature page. There are no minimum or maximum page numbers. Multiple original signature pages should be obtain to submit to the Graduate Division and the department.
Submission
Theses and dissertations are due at the Graduate Records Office by the deadline specified in the Academic Calendar. The Tropical Plant Pathology Graduate Faculty requires a printed copy of your thesis/dissertation on a high quality acid-free or 100% cotton paper. This departmental copy will be bound and placed in the Plant Pathology Library.
Timelines
Ph.D. Candidates
M.S. Plan A Candidates
M.S. Plan B
Graduate Research Assistantship Policies
Our policies are consistent with University policies as described in the Graduate Assistant Overview. We have two types of assistantships in the department research and research/teaching. The research assistantships are grant funded and controlled by individual faculty. The research/teaching assistantships are a funded in part from faculty grants and from college allotted funds. Both types of assistantships come with health insurance and tuition waivers. Neither assistantship accrues vacation leave.
Research assistantships (RA) supports the research activities of a faculty who is the principal investigator of a funded project. Graduate students are hired at 0.5 FTE (a half time appointment). The specific duties of a RA will vary depending on the needs of the project and faculty member. The assigned duties may be directly or tangentially related to the RA’s program of study. At the discretion of the faculty, results from the research project may be incorporated into a thesis or dissertation. The RA can be held to 20 hours work/week for the faculty. Often, and especially when the research will be incorporated into the student’s thesis or dissertation, much more hours given to the research endeavors.
Research/Teaching assistantships (which we usually refer to as TA) come with the responsibility of assisting with the departmental instruction mission. There are generally two TA each semester and each one is responsible for contributing 10 hours/week to the instructional mission. The TA will be assigned to assist with classes being taught. The courses taught change each semester, and vary between undergraduate and graduate level. Faculty instructing each semester will have different needs of the TA and the assistance will be agreed upon each semester. Some faculty desire and some courses require greater TA involvement. However, TA instructional activities should not exceed an average of 10 hours/week over the fall and spring semesters.
RA and TA are advertised in a variety of ways including posting around campus, in professional society newsletters, and on the internet. Upon application, the faculty member offering the assistantship reviews and selects the candidate. Individual faculty determine the criteria for renewal and termination, as well as evaluate performance, of the graduate assistant. Assitantships are offered on an annual basis or for shorter term appointments. Generally, students are eligible for an assistantship until they have graduated or funding has been exhausted.
Professional/Scientific Meetings
TPP graduate students are encouraged to attend professional meetings. Funding for travel to scientific meetings may come from a variety of sources. Grants from may be available form your advisor. The department often has an annual solicitation for travel support. The Graduate Student Organization usually has a call for travel support. Professional societies, such as the American Phytopathological Society, also support student travel to their meetings.