:: Microbiology Graduate Student Handbook ::updated September 2011 Introduction The Microbiology Graduate Program is designed to provide students with opportunities to acquire the knowledge and skills needed to embark on careers as independent microbiologists. Features of the program include instruction on various aspects of microbiology, oral and written communication, laboratory techniques, teaching and research skills and professional working practices. A major feature of the program is the production of a doctoral dissertation or a master’s thesis that satisfies the University’s and Department’s criteria. The University’s regulations summarize these as follows: “The dissertation [or thesis] in its completed form will be judged largely upon the ability of the candidate to review and make critical use of the literature; to formulate a problem, plan a method of attack and work systematically towards a solution; to summarize the material or data, and draw conclusions based thereon. Scholastic attainment in writing and presenting the results of the study will be crucial. The goal of the dissertation [or thesis] is to make a contribution to knowledge. It should be of publishable quality.” This Graduate Student Handbook describes the policies, requirements and guidelines for the Graduate Program in Microbiology and has been formally agreed upon by the faculty of the Department. This handbook constitutes a contract between the student and the faculty when the student enters the Graduate Program (acceptance of offer), and that handbook edition applies for the duration of the Graduate Students tenure at the Department. The Microbiology Graduate Program operates within the University’s regulations as described in the Graduate School Bulletin and the Graduate Student Handbook. These publications are issued by the Graduate School and the Graduate Dean’s Office, respectively, and students are expected to be familiar with relevant regulations. The Department’s Graduate Program Director (GPD) is also available for consultation concerning any aspect of the program. Faculty Advisor and Mandatory Laboratory Rotations Regular first semester student positions start with a Teaching Assistantship. For those positions rotations are mandatory for the first two full semesters. A listing of currently offered rotation projects is provided to all students prior to the semester, and includes both research themes and associated techniques for each rotation. A rotation project lasts for one semester. A third rotation is optional. Rotations are taken for credit, and will be evaluated as pass/fail. During the rotations the Guidance Committee offers advise to students on which courses to take. At the time of first registration, a member of the faculty is assigned as rotation advisor for each student by the GPD after a discussion with the students. Rotations provide first-semester students exposure to the different research groups to determine favored areas of research and compatibility with advisor and research group. We encourage students to consider rotating through 2 or 3 laboratories before deciding who their PhD advisor will be. Rotation students should join a lab by the end of their final rotation and are encouraged to seek a lab with research funding support. The advisor must be a member of the Department of Microbiology, although adjunct professors may serve as advisors. Adjunct professors are not guaranteed TA support by the Department of Microbiology. Should the student change dissertation advisor, the new advisor becomes the faculty advisor for the student, and a new research program is begun. Laboratory and Fire Safety Training Laboratory and Fire Safety Training is required for faculty, staff, and students, graduates and undergraduates, post-doctorates and visiting scholars before initial assignment to a laboratory. This requirement can be satisfied by attending a two-hour seminar. This seminar includes one hour of Laboratory Safety Training, one-half hour of Hazardous Waste and one-half hour of Fire Safety Training. Environmental Health and Safety (EH&S) will schedule at least one session monthly. Check the upcoming seminars on the EH&S homepage at http://www.ehs.umass.edu for the times and locations. Fire and safety training has to be updated annually in an online session provided by EH&S. Financial Support and Conditions of Employment Students are normally admitted to the Microbiology Graduate Program only if they have financial support as approved by the Department. For most students, this support takes the form of an assistantship provided by the Department, and in general we support all students on an assistantship. Initially such support is in the form of a teaching assistantship, then later in the program students are typically supported on research assistantships provided by faculty research grants or contracts. Some students are supported by external sources, such as government scholarships, foundation stipends, or by assistantships from other University-based sources outside the Department. The selection of research assistant appointments, terms of contract, and other details of such appointments fall entirely within the purview of the faculty member who is the principal investigator on the grant, subject to Department and University regulations. Graduate students appointed as teaching or research assistants may not, in general, accept concurrent employment elsewhere. Exceptions must be approved by both the GPD and the dissertation advisor prior to acceptance of any other type of employment. Concurrent employment is strongly discouraged by the Department, and students should note that there are University regulations governing the number of hours that a student may work (see the University’s Graduate Student Handbook online: www.umass.edu/gradschool/handbook/). Students appointed as teaching or research assistants are governed by the conditions of the agreement between the University and the Graduate Employee Organization (GEO). Teaching assistant appointments include the January intersession period. Details of public holidays, personal leave, and vacation entitlement can be found in the Graduate Appointment Policies and Procedures document issued by the Graduate School. All students are required to have an OIT Email account, even if they already have an account created with our Department. The OIT account has to be activated to enable registration via SPIRE, however students may forward all email messages from the OIT account to an account that they use regularly. The OIT account allows the Graduate School to send official email notices to all students. Qualifications for Teaching Assistantships
The GPD and Department Head are responsible for assigning teaching assistantships to specific courses. Consideration will be given to the special needs of the instructor and qualifications of the student when appropriate. Master’s Program A minimum of 30 graduate credits and completion of a graduate research project are required for a master’s degree. Twenty-one credits must be in the student’s major field and a minimum of one-half of the total required credits must be on a letter-graded basis. Any portion of the remaining credits may be graded satisfactory subject to prior approval by the department. All graduate students are required to register for the Graduate Seminar course. Credits transferred from another institution cannot be used to satisfy the University’s requirement for graded credits nor the 600-800 course level requirement. Graduate courses which have been applied toward any baccalaureate or advanced degree may not be used for fulfilling requirements for any other master’s degree at the University. Student’s must fill out the Master’s Degree Eligibility Form and obtain the appropriate signatures prior to receiving the degree. Forms can be obtained from the Microbiology main office or from the Graduate School website (www.umass.edu/gradschool/Students_graduation_eligibility_forms.htm). Students must check with the Graduate School for deadline dates. Graduate students who write a thesis cannot count more than 10 thesis credits (MICROBIO 699) toward the Master’s degree. The number of Independent Study credits is limited to 6 for the duration of the Master’s program. Excluding thesis credits, graduate students must earn an additional 6 credits in the 600-800 course level range. Graduate students who do not write a Master’s thesis (e.g., 5th year Master’s students) must earn a minimum of 12 credits in the 600-800 course level range. All students are required to undergo a general examination on their research topic. The examination will be conducted by the student’s advisor and two additional members of the Department. Thesis option students must form a thesis committee that shall consist of one or more members of the Graduate Faculty recommended by the GPD and/or Department Head. All members should have at least adjunct status within the department. A thesis committee has been officially constituted when the Graduate Dean sends formal notification of its formation to all members, the GPD and the student. A thesis option master’s candidate must prepare a suitable thesis outline to be approved and signed on the cover sheet by each member of the approved thesis committee and the GPD or Department Head. The signed copy of the thesis outline is forwarded to the Graduate Records Office for inclusion in the candidate’s file at least 4 months prior to the date that the thesis defense is scheduled. The thesis must be typed in the format prescribed by the Graduate School. The thesis must be approved and signed by all members of the thesis committee and the Department Head. The electronic submission of a Master’s Thesis is available but voluntary. For complete information on Graduate School requirements for preparing and submitting the thesis by paper or electronically, refer to the Graduate School website: http://www.umass.edu/gradschool/thesis/TDindex.html. Ph.D. Program Enrollment A student must take at least 9 credits per semester in order to maintain full-time status (see list of graduate-level Microbiology courses in Appendix 1). In their first two years, students will typically take two instructional courses with an emphasis on qualification courses (see below). All graduate students are required to register for the Graduate Seminar course and give one presentation to the Department each academic year starting in the second year and excluding the year of the final defense. The remaining credits are filled with Independent Study. This latter course typically ranges between 3 and 5 credits per semester and is arranged between the student and their research advisor for that semester. Registration for Independent Study requires the signature of the advisor on a Course Override Form available in the main office. Students are strongly encouraged to enroll in a Journal Club course each semester after their first year.
** Note that audited and dropped courses cannot be included in status calculations.
Students enrolled in the Ph.D. program are considered doctoral students. Candidacy is recommended for doctoral students by the Department upon satisfactory completion of both, coursework and passing the Preliminary Examination. After the Preliminary Examination students enrolled in the Ph.D. program are considered doctoral candidates, and thus eligible to receive the degree of Ph.D. Qualification in Three Core Areas In order to proceed onto the doctoral program, each graduate student must qualify in three core areas within the Microbiology program. These core areas include the following (Note: some core areas have more than one course): Courses in these areas are offered every 1-2 years so students should plan accordingly. Students are expected to qualify in their three core course areas by the end of the Spring Semester of their second year, although exceptions can be made if the student receives permission from the GPD or the Department Head. Requirements for qualification vary with the instructors, but all courses in which a student qualifies count towards the three cores areas. Certain highly intensive laboratory course can count as a core area fulfilment, however the decision rests with the instructor. Certain courses outside the Department can also be taken, however only upon agreement with the respective faculty members within the Department of Microbiology and the GPD. Guidance Committee Within the first semester the students are offered an informal and brief guidance meeting with the Department Guidance Committee. This committee consists of the GPD, the Department Head, and two experienced faculty members. About one week prior to this meeting new graduate students will provide the GPD with a one page sheet indicating background, interests, research and other plans, and course choices. Preliminary Comprehensive Examination The Graduate School requires the successful completion of the Preliminary Comprehensive Examination (i.e., the prelim exam) prior to continuation onto the Doctoral Program. Each Department establishes its own criteria for the examination. In Microbiology, the exam is usually given in the Spring of the student’s second academic year. Each student must successfully demonstrate the following in order to proceed in the Ph.D. program:
The exam will be administered by a committee composed of three Microbiology faculty members. Adjunct faculty members cannot be a committee member for this exam. The committee members will be selected by the student, their advisor, and the GPD or the Department Head. The student’s advisor may not serve on their committee but may attend the exam as an observer. The three committee members generally represent the research interests and expertise of the student and the areas of microbiology in which they choose to be examined. Each committee will select a chairperson from among its three members who will write a brief summary of the exam and the findings of the committee for the GPD. The exam has both written and oral components. The written portion culminates into a research proposal that is accomplished in stages so that the student’s committee can monitor the progress of the student. Students are encouraged to discuss the outline of their proposal with their committee prior to its submission. It is left up to the individual committee members to decide how much review of the proposal they are willing to provide prior to the examination. After completion of the proposal, the committee will determine whether the student is prepared for the oral portion of the exam. The oral exam is conducted by the committee members and will focus on, but not be limited to, the three areas of microbiology chosen by the student. If a student has already qualified in two core areas, but has to postpone qualification in the third core area to the following Spring semester due to scheduling conflicts, the preliminary examination can be held prior to completion of the third core qualification with the consent of all three committee members and the GPD. Description of the Examination Process The written portion of the examination will consist of a research proposal that meets the following criteria:
a) One page summary of proposed project that is non-technical, introduces the topic and states the major objectives, how they will be accomplished and the relevance of the results to the field. Students should consult the NSF/NIH (www.nsf.gov/pubsys/ods/getpub.cfm?gpg; www.niaid.nih.gov/ncn/grants/default.htm) Proposal Guidelines for more details and meet with their committee members prior to writing their proposal to discuss their topic and immediately following the completion of their proposal. Preliminary results from laboratory research may be used in the proposal to demonstrate the technical capabilities of the student. Students have to submit their proposal to their committee two weeks prior to their anticipated oral examination, but it is highly recommended that the graduate student engages in proposal related discussions with committee members prior to this date. Findings of the Committee At the conclusion of the oral exam, the committee will make one of the following recommendations:
If the student is given the option of re-examination, then they will have one more opportunity to satisfactorily complete the examination as recommended by the committee. This must be done within six months from the date of their first exam unless granted permission by their committee. If the student does not pass the exam on their second attempt, then they will have until the end of that academic semester or up to six months to complete work within the Department. This will be decided upon by the student, their advisor, the GPD and the Department Head. If the comprehensive exam is the last item prior to candidacy, the candidacy form will suffice to alert the Graduate School that the student has passed the exam. Doctoral Dissertation Committee and Prospectus Upon successful completion of the Preliminary Comprehensive Examination, the Doctoral Dissertation Committee is appointed by the Graduate Dean upon nomination and recommendation by the GPD or Department Head. The Committee is composed of at least four graduate faculty members: the chairperson – a member of the Department, two additional members from the Department of Microbiology, and one member from “outside” the candidate’s department or program, who is a faculty member from UMass or Five Colleges and has Graduate Faculty Status. Adjunct faculty members in the Department of Microbiology can serve as the chair of the dissertation committee. The committee has been officially constituted when the Graduate Dean sends formal notification of its formation to each committee member, the GPD, and to the graduate candidate. Members of the Dissertation Committee must agree to not only assist in the supervision of the dissertation project, but also conduct the Final Oral Examination. Selection of the committee is a matter of “academic judgment” which should be made by the GPD, the Department Head and/or the advisor, and approved by the Graduate Dean. Candidates should be reminded that most of the faculty are on nine-month contracts and should not necessarily assume that committee members will be available during the summer months. While not recommended, it is acceptable to have a Dissertation committee member participate via video conference. After successful completion of the preliminary examination, Graduate students become Dissertation Candidates. Candidates are required to meet with their Dissertation Committee at least once within a 12 months period. It is highly recommended that the candidate prepares the first committee meeting with the dissertation committee shortly after the preliminary examination, i.e. within less than a 12 month period (we recommend after six month). In the meeting with the dissertation committee the candidate is encouraged to outline his or her dissertation progress, and show a timetable of ongoing and future work needed to complete the dissertation. The purpose of the committee in these meetings is to provide guidance and feedback on the Candidate’s research and department requirements (i.e. publication requirement, residency requirement) towards the completion of his or her dissertation (see Appendix 2 for additonal advise). Failure to hold the annual Dissertation Committee meeting might jeopardize the travel support provided to candidates by the Department. Once a year, usually following the committee meeting, the main advisor of the graduate candidate has to prepare a brief Annual Graduate Student Progress Report. This report is signed by the graduate student, and submitted to the GPD. After passing the Preliminary Comprehensive Examination, the graduate degree candidate must prepare a dissertation prospectus describing the research to be conducted, analyzed, and presented in the dissertation. The cover sheet must be signed by each member of the Dissertation Committee to indicate approval of the topic and its plan of execution. The GPD or Department Head signs and forwards the prospectus to the Graduate Records office. A copy of the signed cover sheet must be submitted to the Department of Microbiology Office. The Graduate School requires that this copy must be received at least 7 months prior to the Final Oral Examination. However, the Department of Microbiology strongly encourages candidates to complete their prospectus by the end of their third year. Description of the Prospectus Process The Prospectus process has both written and oral components. The written portion will follow the format of a NIH or NSF proposal. The page limit should be discussed in agreement with all members of the Dissertation Committee. The candidates should also contact individual committee members about what additional items they request for the Prospectus.
It is essential that the proposed research will be performed primarily by the candidate. The Prospectus should be reviewed by and discussed with the candidate’s advisor prior to submission to the Dissertation Committee. The Prospectus should be distributed to the candidate’s committee at least 2 weeks prior to their anticipated meeting. The Prospectus is a formal summary of existing and proposed research, and not an examination. It is either approved or not approved by the Dissertation Committee. The result of the Prospectus Defense is forwarded to the Graduate Records Office directly following the approval by the Dissertation Committee. Residency Requirement A doctoral candidate, a student who successfully passed the preliminary comprehensive exam, must fulfill the Residency Requirement. The Graduate School's residency requirement is fulfilled by taking two consecutive semesters of Full-time enrollment of MICROBIO 899—Ph.D. Dissertation (nine credits per semester) in residence at the University. The residency year must be either in a Fall/Spring or Spring/Fall sequence. During this year, the student must spend some part of each week physically on campus. Doctoral students enrolled in recognized off-campus programs may satisfy this regulation at their off-campus site. The Doctoral Residency Requirement is based on the expectation that degree recipients should at some point have a significant interaction with members of the Graduate Faculty of their Program. Graduate candidates are not required to register for the Graduate Seminar course during the residency year. Publication Requirement The Department of Microbiology requires that the candidate has at least one first-authored manuscript published or ‘in press’ in a professional peer-reviewed journal from their dissertation research prior to the scheduling of the candidate’s Final Oral Examination. Authorship decisions will follow the criteria for autorship credit of the International Committee of Medical Journal Editors. To be included in the list of authors a contributor’s involvement must meet the following three conditions: (a) Concept and design, or analysis and interpretation of data, (b) Drafting or critical revision for important intellectual content, (c) Final approval of the version to be published. Final Oral Examination The oral examination will be in two parts: a seminar presenting the dissertation research results to the campus at large followed by a closed session with members of the dissertation committee. All Final Oral Examinations/Dissertation Defenses must be announced in the weekly bulletin of the UMass Website (www.umass.edu/loop) to allow interested graduate faculty and others to attend. The Office of Degree Requirements must receive written notification of the scheduling of a Final Oral Examination at least 4 weeks prior to the date of the defense. An examination cannot be held unless it has been publicly announced. The examination must be held on the Amherst campus. All members of the Dissertation Committee must be present at the defense. Following the public presentation of the dissertation, the candidate will meet in closed session with the members of their committee to answer questions related to the dissertation. Normally both parts of the Final Oral Examination will take place on the same day. The result of the Final Oral Examination is forwarded to the Graduate Records Office directly following the examination. Dissertation All dissertations have to be submitted electronically. While it is no longer a requirement of the Graduate School, the Department of Microbiology requests a hardcopy of the final dissertation. The dissertation must be typed in a prescribed style and format on acid-free paper. The dissertation must be approved and signed by all members of the dissertation committee and the Department Head. The Graduate School is the final and only arbitrator of what is an acceptable dissertation. For complete information on Graduate School requirements for preparing and submitting the thesis by paper or electronically, please refer to the Graduate School website: www.umass.edu/gradschool/thesis/TDindex.html. Remaining in Good Standing within the Program The University and the Department believe that the primary responsibility for successful completion of the degree lies with the candidate. All candidates are expected to advance towards their degree as expeditiously as possible while maintaining academic excellence. They are expected to pursue research-related activities year round. Progress is monitored by the GPD in consultation with the candidate’s advisor and their committee. Graduate candidates who are not making satisfactory or reasonable progress toward the completion of their degree program are subject to termination. The statute of limitation for doctoral candidates is six years for students joining the Graduate Program with a Bachelors degree, and four years for students joining the Graduate Program with a related Masters degree. For new doctoral students starting in Summer 2009 or later, the statute of limitation is set at six years prior to achieving candidacy and five years once candidacy is achieved. Candidacy is recommended upon satisfactory completion of coursework and passing the Preliminary Examination. In the rare event that an extension is necessary, extensions of the statute of limitation will be decided by the GPD and the Department Head, and two-year extensions will be considered upon recommendation submitted to the Graduate School by the GPD. Appendix 1: Graduate-Level Courses in Microbiology MICROBIO 542 Immunology Laboratory (Spring). This laboratory course is designed to help students become familiar with and proficient in the performance of principles and protocols in cellular immunology, immunochemistry and clinical serology. This will be accomplished over the course of the semester by exploring the protein chemistry of antibodies, including antibody isolation using salt precipitation, ion exchange, and molecular sieving column chromatography, spectrophotometry, SDS polyacrylamide gel electrophoresis (PAGE), western blotting, immunoprecipitation, enzyme-linked immunoassay (ELISA), and immunofluorescence staining. The student will also perform classic serological assays including the complement fixation test, passive hemagglutination and immunodiffusion (Ouchterlony technique). Anatomy of the lymphatic system will be explored using a mouse model. Specifically, the student will perform mouse dissection, lymph node examination, and isolation of lymphocytes from the mouse spleen and thymus. Finally, the student will be exposed to cellular immunology, including mammalian histology, identification and enumeration of mouse and human leukocytes, normal and diseased lymphoid tissue, and two-color flow cytometric analysis of lymphocyte subpopulations. 3 credits MICROBIO 590L Parasitology Lab (Spring). Interdisciplinary discovery-based laboratory in which students perform individualized experiments. Students use the genetic tool RNA interference to validate potential new drug targets in the protozoan parasite, Trypanosoma brucei. specific techniques include: database searching, primer design and PCR analyses, DNA andRNA isolation, culturing and transfection of eukaryotic cells, inducible RNA interference, epifluorescence analyses, and drug inhibitor studies. Corequisites: MICROBIO 590S or consent of instructor. 3 credits.
Appendix 2: Guidelines to the Dissertation Committee Meeting A committee meeting should cover the time period from the last committee meeting, and include plans until the next committee meeting. To enable guidance, the candidate is encouraged to start with a presentation that includes an outline of the proposed thesis, followed by a summary of recent work and detailed interpretation of the work (e.g. publication ready graphs and tables), and an outline of future work which include a list of planned manuscripts. The future plans for the next six months of research following the committee meeting should be described in greater detail, and the candidate should present the committee also with a detailed outline of the next manuscript and a timeline for its submission. Helpful Websites: UMass Graduate School UMass Graduate Student Handbook SPIRE UMass Microbiology Graduate Student Group (MGSG) Graduate Employee Organization Writing Helpful Advice Degree Progress ~ Ph.D. Year 1
Year 2
Year 3
Year 4 and beyond (commonly, the PhD program takes 5 to 6 years total)
Degree Progress ~ M.S. ~ Non-Thesis
Degree Progress ~ M.S. ~ Thesis Option
|
||
|
Department
of Microbiology
|
|
||
