Guidelines and Policies of the Graduate Studies Program for Microbiology and Immunology (Blue Book)

Updated September 19, 2024

The Graduate Affairs Committee will review the academic progress of each student at the conclusion of the Fall and Spring Semesters. For students whose course grades do not meet the required standards, the Committee will recommend a course of action, concerning the continued status of the student, to the Director of the Microbiology and Immunology Graduate Studies Program. Unsatisfactory research performance will be determined by the respective Ph.D. Thesis Advisory Committee and a recommendation by the Advisory Committee will be reviewed by the Graduate Affairs Committee for a course of action to the Director of the Microbiology and Immunology Graduate Studies Program concerning the continued status of the student. All recommendations will take into account any extenuating circumstances that may have adversely affected the student’s performance.

The Department of Microbiology and Immunology uses only courses that evaluate students based on a letter grade for the calculation of Grade Point Averages. Supervised teaching, laboratory research, and thesis guidance grades are excluded. An unsatisfactory grade is a grade less than “B” for a required course and less than “B-” for an elective course.

The Department of Microbiology and Immunology is a collegial and professional environment. It is therefore expected that you will conduct yourself in a professional manner for all aspects of your training. This includes not only the conduct of your experiments, but also conduct during lab meetings, meetings with your mentor and committee, seminars, at conferences, informal interactions with others in the department, etc. A cornerstone of professional conduct is respect for your fellow colleagues. This means being mindful and considerate of others around you, including in the shared cubicle and lab spaces. It also means being respectful of others time, including being prepared in advance for all experiments requiring training or assistance from others, sending your committee meeting report on time, and being present and on time for all engagements such as planned experiments, seminars, lunches, etc. Note that it is your responsibility to stay up to date on rules and regulations of the lab that you join, including all biosafety training. 

Upon entering the Department of Microbiology and Immunology, students must generate an Individual Development Plan (IDP) using the online application. This application will walk the student through the process of IDP construction. Completion of the plan and a face-to-face meeting with the mentor to discuss the plan should occur after the student passes the preliminary qualifying exam and prior to their first committee meeting. In subsequent years, IDPs must be updated at the time of completion of the annual review at the end of the spring semester. The review form includes a check-box to indicate IDP update and mentor discussion.

The University at Buffalo and its Graduate School encourage the prompt consultative resolution of grievances of graduate students as they arise and to provide orderly procedures for the formal consideration and resolution of complaints that cannot be resolved through consultation.  The Academic Grievance Policy can be found on the Graduate School website.

Grievance Definitions and Limits

Definition. A grievance shall include, but is not restricted to, a complaint by a graduate student:

that he or she has been subjected to a violation, misinterpretation or inequitable application of any of the regulations of the university, the Graduate School, a college or school or department or program; or

that he or she has been treated unfairly or inequitably by reason of any act or    condition that is contrary to established policy or practice governing or affecting graduate students at the University at Buffalo.

Time limit. A grievance must be filed within one calendar year from the date of the alleged offense. The department chair (or program director where there is no chair oversight), college or school dean or the dean of the Graduate School may extend this time limit upon demonstration of good cause.

1. There is no financial support provided by the Department or the School of Medicine and Biomedical Sciences.  Therefore, for direct entry into the Microbiology and Immunology Program, students must have a professor in the Department willing to financially support the student for the duration of their doctoral program and M.S. students must provide their own financial support. 
2. For direct entry into the department for Ph.D. students, a letter from the prospective mentor indicating availability of 3 years of funds is required in order for the Department to sign a backstop agreement. 

1. The mentor will provide a letter to the departmental Chair indicating that the funds are available to support a directly admitted student for 3 years and, upon approval by the Chair, will sign a backstop agreement with the Department.
2. The mentor will also provide the Director of Graduate studies and the Graduate Affairs Committee a document that includes the applicant’s transcripts and prior experience. 
3. The student must apply to the program by completing the relevant on-line PPBS application form and submission of all required official documents. These documents include: (i) official transcripts, (ii) three (3) letters of recommendation, and, for international students, (iii) an official TOEFL score report.

1. There are no set deadlines for direct admit applications. But, students and mentors should be aware of class start dates, and to plan their application submissions accordingly to provide sufficient time for their application to be processed (about a month) and for registering for classes.
2. Direct admit students can enroll into the Ph.D. program either in the Spring or Fall semesters. The timeline should be discussed with the mentor, keeping in mind the timeline between admission and completing the prerequisites for taking the qualifying exam. To participate in the Qualifying Examination, students must have earned passing grades in two of the four core courses listed in the Graduate Curriculum, have successfully completed the Critical Analysis course (MIC 610)(offered every Fall), and be in good academic standing (see Academic Status Policies).

1. Satisfactory progress. Students who achieve a 3.00 Grade Point Average (GPA) or above and have not received an unsatisfactory grade in any course will be considered in good academic standing.
2. Academic probation. This status will be ascribed to students who have earned a GPA of 2.50 to 2.99 and have not received an individual course grade less than "C". Students who have a GPA above 3.0, but have received an unsatisfactory grade, will also be placed on probation until the unsatisfactory grade is remediated.
3. Unsatisfactory status. A GPA of less than 2.50 or a course grade less than "C" is unsatisfactory and will result in academic probation and possible suspension of the student's stipend and tuition scholarship for the next semester. It is the responsibility of the student to inform the Graduate Studies Office promptly of any special circumstances that have adversely affected his/her academic performance.

1. Satisfactory progress. A GPA of 3.00 or above with no unsatisfactory grades is considered satisfactory for the semester. A Cumulative Grade Point Average (CGPA) of 3.00 or above with remediation of all unsatisfactory grades in required courses is necessary for unqualified status in the program.
2. Academic probation. Any student who has a CGPA between 2.50 and 2.99 and has received no unsatisfactory grades will be placed on probation. In order to advance into the second year there must be evidence of academic progress, i.e., higher GPA in the Spring Semester than the Fall Semester. Students with an unsatisfactory grade in a required departmental course will be placed on probation (regardless of CGPA) until that unsatisfactory grade is remediated. Academic probation will also affect the ability of the student to enter a laboratory on a permanent basis.
3. Unsatisfactory status. Students with CGPA less than 2.50 at the end of their first year will be dismissed from the Microbiology and Immunology Graduate Studies Program unless there are well documented and compelling extenuating circumstances.

A. For the duration of their doctoral program, students are expected to attain and maintain a minimum CGPA of 3.00 and to remediate unsatisfactory grades in courses required by the Department of Microbiology and Immunology. Unsatisfactory research performance as determined by the respective Ph.D. Thesis Advisory Committee and documented on the Committee Report form with specific recommendations for remediation, will result in a “U” grade and academic probation by the Department of Microbiology and Immunology. Failure to satisfy the terms of the probation will lead to dismissal from the program.

B. Students with less than a 3.00 CGPA at the end of their third semester will not be permitted to take the qualifying examination for admission to Ph.D. candidacy and may be dismissed from the program. Students who have completed all of the required courses and are in good standing (satisfactory progress) at the start of the fourth semester will be expected to take the Preliminary Qualifying Examination for admission to Ph.D. candidacy. Any student wishing to defer the examination to a later time must petition for the exception.

C. Prior to the fifth semester of residence (Fall Semester of year 3), each student is to arrange with his/her thesis advisor for the appointment of a Ph.D. Thesis Advisory Committee (refer to guidelines for Ph.D. Committee). The proposed Ph.D. Thesis Guidance Committee should be submitted to the Graduate Affairs Committee for approval. The student should convene the first meeting within six months following successful completion of the Qualifying Examination and hold a minimum of one meeting in each subsequent semester (within 6 month intervals). Students in violation of this policy will not be considered in good standing in the Graduate Studies Program and will not be permitted to register for courses or research credits in the subsequent semester until the committee has met.

D. The ability of a student to enter a laboratory for thesis research is a requirement for further advancement in the program.

Students must petition for entry into the Microbiology and Immunology Department. At the time of application, the student’s record will be considered in total. Any grades less than a “B” [3.0] in a Department required course, a grade of “B-” or below in any course, or a Grade Point Average (GPA) of less than 3.0 are not acceptable. In cases where a student with any of these three conditions is accepted into the department, the student will be placed on academic probation to allow the condition to be corrected/remediated, usually for a period of one semester. Failure to achieve satisfactory status within the prescribed time is grounds for dismissal from the program.

An unsatisfactory grade is a grade less than “B” for a required course and less than “B-” for any elective course.

1. Satisfactory progress. Students who achieve a 3.0 GPA or above and have received satisfactory grades will be considered in good academic standing.
2. Academic probation. This status will be ascribed to students who have a GPA of 2.50 to 2.99 and have not received any unsatisfactory grades. Students who have received a GPA greater than 3.0 but have received any unsatisfactory grades, will also be placed on probation until the deficient grade is remediated.
3. Unsatisfactory status. A GPA of less than 2.5 or a course grade less than a “C” grade is unsatisfactory and will result in academic probation and possible suspension of the student’s tuition scholarship for the next semester. It is the student’s responsibility to inform the Graduate Director or Graduate Studies Office of any special circumstances that may have adversely affected their academic performance.

1. Students who have completed all of the required courses and are in good standing (satisfactory progress) at the start of the second semester in the MIC program will be expected to take the Preliminary Qualifying Examination for admission to Ph.D. candidacy. Any student wishing to defer the examination to a later time must petition for the exception. Students on academic probation or in unsatisfactory status will not be permitted to take the Preliminary Qualifying Examination for admission to Ph.D. candidacy.
2. Students with a CGPA less than 2.5 will be dismissed from the program unless there are well documented and compelling extenuating circumstances.
3. The ability of a student to enter a laboratory for thesis research is a requirement for further advancement in the program.
4. Following completion of their second semester in the MIC program each student in Good academic standing is to arrange with their thesis advisor for the selection of a Ph.D. Thesis Advisory Committee. A Selection of Committee form should be submitted to the Graduate Studies Office for approval of the committee composition by the Microbiology and Immunology Graduate Affairs Committee. The student should convene the first Thesis Advisory Committee meeting within six months of successful completion of the Preliminary Qualifying Examination and hold a minimum of one meeting in each subsequent semester (within six month intervals). Students in violation of this policy will not be considered in good standing in the Graduate Studies Program and will not be permitted to register for courses or research credits in the subsequent semester until the committee has met.

Students are expected to maintain a CGPA of 3.0 and to remediate any unsatisfactory grades. Failure to do so will result in dismissal from the program. Unsatisfactory research performance as determined by the respective Ph.D. Thesis Advisory Committee and documented on the Committee Report form with specific recommendations for remediation, will result in a “U” grade and academic probation. Failure to satisfy the terms of the probation will lead to dismissal from the program.

All Master’s students are admitted into a coursework program; additional project and thesis options are voluntary and require one prior semester of Introduction to MS Research (MIC 596) as well as approval of the participating faculty advisor (both project or thesis) and the program director (thesis track only).

1. Course-based option (default): After completion of the required coursework, students must successfully pass a comprehensive examination to fulfill the M.S. degree requirements. Students wishing to pursue the additional project or thesis options, must find a faculty advisor willing to provide project guidance or research supervision.
   
   Comprehensive Exam
   
   Student has until the grading deadline to select which core courses count as required. Student then has up to two weeks to take the Comprehensive exam (though both the selection of the required courses and the completion of the Comprehensive exam can happen quicker). A grade of B or better is required for passing of the Comprehensive exam.
   
   Remediation of Comprehensive Exam
   
   Student will be allowed to take the section(s) one additional time to remediate inadequacies (a grade less than a B). Student is advised to spend one additional semester in the program (and must be registered for at least 1 credit hour) to prepare for the exam.     
                          
   
2. Project option: After successful participation in MIC 596 in the first spring semester, and with mentoring by a faculty advisor, students may perform work on an applied or theoretical project (MIC 597) with or without a research component. The project must conclude with a written report and a possible presentation to the department. A comprehensive examination will not be required of students selecting this option.
3. Thesis option: To be considered for this option, 1-3 credits of Introduction to MS Research (MIC 596) performed during the spring or summer of the first year must be taken with a faculty member in the department of Microbiology and Immunology. After the first spring semester, but no later than at the conclusion of the first summer, students may then enter into the second year (two semester) thesis-track, which requires:

• mutual agreement between student and advisor, and approval by the program director.
• formation of an advisory committee before the end of drop/add of the second fall semester (minimum of two graduate faculty members from the department).
• an element of original research, with a minimum of additional 6 credits taken in Guided MS Thesis (MIC598), 3 credits each per fall and spring semester of year 2.
• preparation of a formal written thesis that fulfills departmental and Graduate School requirements.
• a successful public defense.
• and submission of the final, approved thesis document to the Graduate School.
• a comprehensive examination will not be required of students selecting this option.

1. Students who finish an academic year with less than a 2.5 CGPA may be dismissed from the program.
2. If CGPA is 2.5-2.99 a student will be placed on academic probation. They will have one year to raise their CGPA to 3.0. Failure to do so will be grounds for dismissal.
3. If during academic probation a student receives a grade of “C” or less the student may be dismissed from the program.

1. If a student receives a grade of “C” or less they will be required to repeat the course at the next academic opportunity.
2. If a student receives a grade of “B-” in any required course, the student is required to meet with their academic advisor to discuss course options for the remediation of the “B-”. The student must earn a grade of “B” or better to consider the course successfully remediated.

 30 total credits minimum.

AND

In consultation with the program director, students may also take electives in other departments not listed above.

AND

72 total credits minimum.

AND

AND

* Courses from this list may also be taken from this list as Elective Advanced Topics.
**If a student has successfully passed BCH503 (Biochemistry) and either BMS 501 (Cell Biology) or BMS 502 (Genetics) or MIC 501 (Microbial Biology and Biotech) with grades of B or better as a student in one of the College’s Master’s Programs, they will be excused from being required to take BMS 515/516.  Additional courses may be considered to fulfill the BMS 515/516 requirement through a petition by the student to the Graduate Affairs Committee.

AND

Elective Courses*

* Students are required to take four semesters total of Advanced topic courses. The prerequisites to take a 600 level MIC Advanced Topic course include relevant 500 level core courses.

* Not all Advanced Topic courses are offered every year.

* MIC599 may be taken as an advanced topic course only if registered for 2 credit hours (see below for details).

Students may register for the same MIC Advanced Topic course twice, but are encouraged to take Advanced Topic courses outside their area of interest.  This includes courses offered by other departments in the JSMBS and the University that would help a student complete their thesis research as well as prepare them for careers after graduation.  Approval of the Department’s Graduate Affairs Committee is necessary for registration for a non-MIC course to fulfill an advanced topic course requirement.

Three additional Advance Topic electives (2 cr) and sufficient research credits to give a minimum total of 72 credits. Students must sign up for at least one research credit for every semester in attendance. Direct admission students who matriculate with advanced credits may be able to design a curriculum after consultation with their mentor and advisory committee and after approval by the Graduate Affairs Committee.

72 total credits minimum.

AND

*Courses from this list may also be taken from this list as Elective Advanced Topics

AND

AND

AND

Elective Courses*

* Students are required to take four semesters total of Advanced topic courses. The prerequisites to take a 600 level MIC Advanced Topic course include relevant 500 level core courses.

* Not all Advanced Topic courses are offered every year.

* MIC599 may be taken as an advanced topic course only if registered for 2 credit hours (see below for details).

* Students may register for the same MIC Advanced Topic course twice, but are encouraged to take Advanced Topic courses outside their area of interest.  This includes courses offered by other departments in the Jacobs School and the university that would help a student complete their thesis research as well as prepare them for careers after graduation.  Approval of the Department’s Graduate Affairs Committee is necessary for registration for a non-MIC course to fulfil an advanced topic course requirement. 

Two additional Advanced Topic electives (2 cr) and sufficient research credits to give a minimum total of 72 credits. Students must sign up for at least one research credit for every semester in attendance.

72 total credits minimum, 36 credits in the Ph.D. phase.

AND

AND

Two of the following elective Advanced Topics courses:

The Qualifying Examination in Microbiology and Immunology should test graduate students in ways relevant to their future career paths. It should avoid simple assessment of a student's ability to learn and store facts but should assure that development has progressed beyond the levels sufficient for good performance in course work.  Given that the Department has decided to specify a "Core Curriculum" for graduate students in Microbiology and Immunology, we expect that successful completion of this "Core" gives the student an appropriate depth and breadth of background knowledge on which to base problem-solving activities. Consequently, the format of the Qualifying Examination described below involves the conception and writing of a research proposal, followed by its oral presentation and defense.  This proposed research must contain a substantial component relating to one or more of the general areas of Microbiology and Immunology (Bacteriology, Virology, Parasitology, Mycology, and Immunology).

1. To participate in the Qualifying Examination, students must have taken two of the four core courses listed in the Graduate Curriculum and be in good academic standing (see Academic Status Policies). Students may take a course concurrently with the Qualifying Examination. Students will not advance to candidacy until the core curriculum is completed.
2. Any student who is not considered in good academic standing at the end of their first semester/term in the program may not be permitted to complete the qualifying examination for admission to Ph.D. candidacy. The Graduate Affairs Committee will consider petitions from the graduate student and his/her major professor for continuation of the student in the Graduate Studies Program and for permission to take the examination in their second year in the program. It is incumbent on the Graduate Affairs Committee to review promptly the academic performance of each student at the conclusion of each semester/term and to inform the student and his/her major professor of any unsatisfactory status.
3. The Graduate Affairs Committee will also consider postponement of the examination for students who have experienced unexpected serious illness or family hardship prior to or during the examination period. The student must present the extenuating circumstances to the committee at the earliest possible date.

The Proposal Committee will consist of three UB Graduate Faculty who will have the potential to become the student’s Ph.D. Advisory Committee.  At least two members must have primary appointments in the Department of Microbiology and Immunology and one may be (but does not have to be) from another Department.  The committee is chosen by the major professor in consultation with the Director and Associate Director of Graduate Studies and the Department Chair. In addition, the Associate Director of Graduate Studies, in consultation with the Department Chair, will appoint a Proposal Committee Chair preferably the most senior Department of Microbiology and Immunology faculty member on the committee.

The Proposal Committee chair will make sure the process moves in a timely manner; prepare reports, set meeting dates, lead discussions, etc. 

It is expected that the student will have consulted with the major professor regarding the choice of the proposal topic and crafting of the specific aims prior to the beginning of the process. The major professor will be present for the prospectus presentation and has the option of being present in the oral defense examination. However, since the qualifying examination is a departmental assessment of the student's status, the major professor may NOT help with drafting or revising of the proposal or in preparing the student's seminar.

The research proposal should preferably focus on the proposed research project that the student will be expected to work on for their Ph.D. dissertation. The research proposal process will begin with a Thesis Research Prospectus presentation to the Proposal Committee in the second month of the second semester/term of the first year in the program. In preparation for the presentation the student is expected to provide the committee with a document (maximum of 2 pages) outlining the objective of their thesis research, the gaps in knowledge to be filled, and the Specific Aims of the work they plan to complete directed toward that objective. These Specific Aims are anticipated to form the basis for the Research Proposal. The material outlined in the document will then be presented to the Proposal Committee in a 30 minute oral presentation. In cases where the student is delayed in taking the Qualifying Examination and has already written a committee document, that document may be used as the foundation for the Qualifying Examination proposal with the expectation that it will be independently edited to meet the proposal guidelines. In addition, if a student has written a predoctoral fellowship proposal, that too may similarly be used as the foundation for the Qualifying Examination proposal.

This presentation will be evaluated by the student’s Proposal Committee specifically for its suitability as a starting point for a Research Proposal. The Committee Chair will prepare a summary statement of the Proposal Committee discussion, which will be circulated to the committee for approval. A copy of the approved summary statement will be given to the student and the Graduate Affairs within one week of the presentation.

If deemed necessary by the Committee, within one week of the summary statement being provided to the student, the student will submit a revised Thesis Research Prospectus that includes a one-page introduction with a point-by-point response to the critiques contained in the summary statement. The committee may either approve the Thesis Research Prospectus or request a second Thesis Research Prospectus presentation.

If a student does not present satisfactorily with respect to the proposal criteria for the second time, a meeting between the committee and the DGS, Associate DGS or a representative of the Graduate Affairs Committee will be convened and a remediation plan devised. This plan could include, but is not limited to, dismissal from the program, an immediate re-write with new Specific Aims or postponement of the exam for one year.

Each student will submit a written proposal to his/her Proposal Committee within four weeks of the approval of the Thesis Research Prospectus. The goal of the proposal is to test the student’s ability to develop and rigorously test a hypothesis. Students are encouraged to discuss the scientific approach with other students, postdocs and faculty, but may not confer with their major advisor. In addition, everyone, with the exception the major advisor and collaborators who are faculty, may read and critique the proposal prior to the document being formally submitted to the Committee. 

The proposal will be written in the following format:

Specifications:  Document should have 0.5-inch margins all around and be written in Arial 11-point font. 

Specific Aims (1 page):  Included as previously established in Section C1 (first paragraph), the Specific Aims should be a logical extension of published research from the major professor’s and other labs and should contain a brief but explicit statement of the hypothesis to be tested.

Research Strategy (6-8 pages): Contains two subsections, as detailed below: (1) Background & Significance and (2) Approach.  The Research Strategy page limit includes Figures and Figure legends but excludes the Specific Aims and References.

The Background & Significance section should specifically identify the problem, or gap in knowledge, that the proposal is intended to address, and make a case for how the proposed work will address that problem/gap.  It should critically evaluate the most pertinent existing knowledge related to the project and place the proposed work in the context of the larger field of research.

The Approach section should describe how the Specific Aims can be accomplished. This section need not contain exquisite methodological detail, but the student must be sufficiently conversant with the design and procedures to defend their proposal, discuss their limitations, and to describe probable results and their interpretations (see also below). The student is expected to fully understand the conceptual and experimental basis of the proposed methods.

The Approach section must include reference to Rigor and Reproducibility.  Here, the student should include methods of statistical analysis and numbers of replicates to be used. These points can either be in a stand-alone paragraph or integrated into the experimental design. The Approach section must also include a section on how the results will be interpreted including alternative interpretations should the data not support the hypothesis. Finally, alternative technical approaches should be included in the case that the primary approach might fail.  The student also has an option to include preliminary data that they have generated.  If included, these data should either go as a Preliminary Data section at the beginning of the Approach section or as separate sections at the beginning of each Aim.

References (length as needed): References supporting the Research Strategy should be listed with full citations, i.e., Authors, Year, Title, Journal, Vol:Pages.

Within one week of receiving the written proposal, each member of the Proposal Committee will submit a written evaluation to the Committee Chair. The evaluations should point out major problems to be addressed and corrections to be made. Within two days of receiving the written evaluations, the Committee Chair will write a summary of the critiques and circulate the summary and all critiques to the Proposal Committee. Upon approval of the summary by the Committee, the Chair will distribute the summary and all critiques to the student (within the two-day time limit). No grade is assigned at this point.

The Committee may request that the student submit a revised proposal.   If so, two weeks after receiving the Proposal Committee’s evaluation requesting a revision, the student must return a revised version to the Committee. At the discretion of the Committee, one additional page in the Research Strategy section may be allowed, if needed to resolve criticisms from the Committee. The revised proposal must include an additional one-page introduction with point-by-point response to the Proposal Committee’s critiques. The Committee will not return this version to the student. If one or more Committee members feel that the quality of this second draft is unacceptable, he/she can request that the Committee meet to discuss these concerns. If all members of the Committee concur, the student can be given a “Fail” grade for the Research Proposal at that time without an oral defense which constitutes grounds for dismissal from the Ph.D. program.

The oral examination will be scheduled by the Committee chair. The student should expect that the oral examination will take place within one week of either 1) the date of receiving notice that no revision is needed or 2) the date they submit the revised proposal. If a revised proposal was submitted, the student is encouraged to meet individually with Proposal Committee members to discuss the revised version before the oral exam.

The Oral Examination typically begins with a 40–45-minute presentation of the written Proposal in the form of a seminar to the committee, with the major focus on the Approach adopted to address the proposal’s Aims. The Committee Chair and Proposal Committee members will question the student about the proposal: its rationale; choice of experiments and experimental design; exploring possible short-comings of the experimental protocols and possible alternative, negative, or false positive results; and evaluate the student’s knowledge of the general area of the proposal; e.g., if on bacterial replication, how does this compare to eukaryotic replication? The objective of the Oral Examination is not simply to have the student recite orally what has been presented in writing, but to examine the student’s overall grasp of the research area in which the lab works and about which the Proposal is written. The mentor may choose to observe the oral examination as a non-voting member of the committee.

The Proposal Committee will evaluate the oral examination and the written proposal to determine a course of action as follows:

CONDITIONAL PASS – Student will be offered remediation in perceived area(s) of weakness in the examination. This may consist of submission of a short paper or tutorial consultation with a faculty member or other proper activity. Additional coursework may also be recommended. An agreed upon remediation must be communicated to the Graduate Affairs Committee within one week of the exam. 

FAIL – Student will be offered a re-examination in one or in several areas. A re-examination will be scheduled in about one month from this date. Unsatisfactory on the re-examination constitutes grounds for dismissal from the program.

• A. Student will submit to the Associate DGS, a list of 3 UB Graduate faculty members to serve on the Qualifying exam committee. At least 2 members must be Departmental Graduate Faculty.
• Committee Chair will be assigned as the most Senior Departmental Graduate Faculty member on the committee.

• Two page document that provides an overview and basis of the research project and anticipated Specific Aims. (SUBMITTED BY JAN 15)
• Present Prospectus to Proposal Committee (and mentor) in a 30’ oral presentation. (MEETING COMPLETED BY FEB 15).
• Committee will determine whether the student’s Prospectus and presentation are suitable starting points for the Research Proposal.
• Committee Chair will prepare summary statement of their discussion and circulate it amongst the committee for their approval. A copy of the approved summary statement will be given to the student and the Graduate Affairs Committee within one week of the presentation.
• If revisions were requested, the student will have one week to submit a revised Prospectus and also include a 1-page response to Committee Members’ comments. The committee may either approve the Thesis Research Prospectus or request a second Thesis Research Prospectus presentation.

• Within 4 weeks after approval of the Prospectus the Proposal will be due.  See Blue Book for formatting details and whom the student may/may not interact with during preparation of the Proposal.
• Within one week, each committee member will provide his/her comments and evaluations of the document to the Committee Chair. The Chair will then provide these comments to the student. No grade will be assigned at this point.
• Within 2 weeks a revised Proposal will be due and must include a 1-page introduction with a point-by-point response to the Committee’s comments.
• The committee will evaluate the revised Proposal and will have two options:

1. Schedule an oral exam within one week of receipt of the document.  The student will not receive any comments on their Proposal.
2. If one or more committee members feel that the revised Proposal is unacceptable, then a meeting will be scheduled. If all agree, a “Fail” grade can be given that will constitute grounds for dismissal. 

• Begins with a 40-45 minute oral presentation to the department that is followed by a question and answer period.
• Immediately followed by closed session with Proposal Committee.  The mentor can be present if they wish but cannot participate in the test.
• Three outcomes are possible

1. Pass
2. Conditional Pass
3. Fail – student will be offered re-examination that can include written and/or oral examinations.  If reexamination is unsatisfactory then the student will be dismissed 

• Research Prospectus: 2 Pages
• Revised Research Prospectus: Introduction with point-by-point response to the reviewers (1 Page)
• Research Prospectus (2 Pages)       
  
• Research Proposal: Specific Aims (1 Page)
• Research Strategy (8 Pages): Includes Significance (gap in knowledge), Approach, Tables and Figures
• Revised Research Proposal
  • Introduction with point-by-point response to the reviewers (1 Page)
  • Specific Aims (1 Page)
• Research Strategy (8 Pages): Includes Significance (~ ½ Page), Background (1-1½ Pages), Approach, Tables and Figures.
  At the discretion of the examination committee, an additional page may be allowed for a total of 9 pages.

Note: Reference Pages do not factor into the Page Limitations at any step in the process.

Passing the preliminary doctoral qualifying examination deems the student qualified to proceed with their thesis research project under the guidance of their Major Professor in conjunction with their Ph.D. Thesis Advisory Committee. This document presents the responsibilities of the student, the Major Professor, and the Advisory Committee in the process leading up to the conclusion of the research project, their responsibilities in preparing and evaluating the dissertation document, as well as evaluating the ensuing oral examination and the public defense.

After the student passes the preliminary doctoral qualifying examination, a Ph.D. Thesis Advisory Committee (henceforth referred to as Advisory Committee) will be proposed. The Advisory Committee consists of the Major Professor, and at least three additional UB Graduate Faculty members (preferentially those who served as committee member for the preliminary doctoral qualifying exam, although this is not a requirement). Two of these individuals must have primary faculty appointments in the Department of Microbiology and Immunology and one may be from another Department at UB. Of the two faculty members with primary appointments in Microbiology and Immunology, one will act as the Chair of the Advisory Committee, and serve to moderate the discussion. The Chair will be determined by seniority and/or Advisory Committee consensus at the first committee meeting. The Advisory Committee members are selected by the Major Professor and student and their names are submitted using the appropriate form available in the Graduate Studies Office to the Graduate Affairs Committee for approval.

The student is expected to have Advisory Committee meetings within 6 month intervals beginning in the Fall Semester after successful completion of the preliminary doctoral qualifying examination. The student must prepare a Committee Meeting Progress Report that contains an updated Specific Aims page clearly indicating any changes to the Specific Aims of the thesis project from the Doctoral Qualifying Examination Document and any new data acquired since the completion of the Doctoral Qualifying Examination.
This document must be distributed to the Advisory Committee at least one week prior to its first meeting for discussion at the meeting. A completed Advisory Committee Meeting Report form must be filed in the Graduate Studies Office within three days of a meeting.

All subsequent meetings of the Advisory Committee should be devoted to a review of the student's progress in research. An updated Committee Meeting Progress Report (as described above) in which it is clearly indicated what progress has been made since the previous meeting must be distributed to the advisory committee at least one week prior to a meeting.

It is incumbent upon the student and the Major Professor to hold these meetings on schedule, report them in writing using the Advisory Committee Meeting Report form, and timely submit the report form to the Department Graduate Studies Office. Students will not be permitted to register for courses or laboratory research if a committee meeting was not held during the previous six months or if documentation of this meeting is not submitted to the Department Graduate Studies Office. If an extension is required, the student should contact the Director of Graduate Studies.

The decision concerning completion of the research project and the material to be included in the dissertation is the responsibility of the entire Advisory Committee. If the Advisory Committee cannot resolve disagreements internally, as indicated by any of its members or the student, the Director of Graduate Studies will appoint an ad hoc committee, which will advise the student and Major Professor in resolving the problem. Once the Advisory Committee has determined that the student should begin preparation of their dissertation:

1. This decision must be documented on the Advisory Committee Meeting Report form, which is submitted to the Department Graduate Studies Office. The student should also notify the Graduate Studies Office within three days of this decision.
2. It is the student's responsibility to be aware of and adhere to all deadlines. The student should schedule a meeting with their Major Professor, Graduate Studies Director, or Graduate Studies Staff Assistant to discuss the current departmental and Graduate School guidelines for preparation of a thesis document and review a timetable for the preparation, review and defense of the dissertation.

The student should prepare the document based on the decision reached by the Advisory Committee at the committee meeting where permission to write was given. The format of the thesis is described in the document entitled "Possible thesis formats.” Preparation of the document should be performed with the assistance of the Major Professor. It should be stressed that the student and Major Professor have the highest level of responsibility for the quality of the Ph.D. dissertation.

The date of the oral examination must be scheduled at least 21 days after the thesis document and the Dissertation Response Form are distributed by the student to the Advisory Committee. This form should be filled out by each Advisory Committee member and brought to the oral examination.

The student is responsible for arranging a tentative oral examination date with the Advisory Committee members. The student should also notify Department Graduate Studies Office of the oral examination date and ask for help with arrangements of a room and audio-visual equipment.

The oral examination will be performed by the Oral Examination Committee, which will consist of the Major Professor and Advisory Committee. The Oral Examination Committee will be chaired by the faculty member who chaired the student’s Advisory committee or a designee approved by the Graduate Affairs Committee.

After the oral examination, the student will be excused. The Oral Examination Committee will evaluate the student’s oral examination and thesis document by voting with a show of hands for “Pass”, "Conditional Pass”, or “Fail”. All members must vote.

PASS - If the final decision is “Pass”, the Dissertation Examination Form is signed by the Major Professor and Advisory Committee, to indicate approval of the written document and passing the oral examination. The form is submitted to the Graduate Studies Office and the student can proceed to arrange the public dissertation defense.

CONDITIONAL PASS - A “Conditional Pass” may be given if members of the Oral Examination Committee decide the oral examination and/or dissertation document is not complete or entirely satisfactory. The specific remediation required should be documented on the Dissertation Examination Form.

Should improvements to the document be required, students are responsible to work with the Major Professor to incorporate into the document all comments/suggestions, changes and typographical errors identified by the Oral Examination Committee, and presented on the Dissertation Response Form, within a time frame approved by the Committee, but no longer than one month. The student must provide the Committee members, who have requested to see the document after revision, with a fully corrected version of the thesis document. Should the oral examination be deemed partially unsatisfactory, a reexamination on the whole dissertation or areas associated with the dissertation topic will be scheduled with the Committee members.

Once the Committee members are satisfied with the student’s performance, the Dissertation Examination Form is signed by the Committee members to indicate approval of the written document and passing the examination. The form is submitted to the Department Graduate Studies Office and the student can then proceed to arrange the public dissertation defense.

FAIL - If the decision is “Fail”, the Oral Examination Committee will clearly outline the reason(s) for the failure to the student. The Chair for the Oral Examination Committee will document in writing using the Dissertation Examination Form, the reason(s) and will make recommendations to the Graduate Affairs Committee for appropriate action.

Faculty must be given at least one week notice prior to the public dissertation defense date. An electronic copy of the abstract and an unbound hard copy of the dissertation should be provided to the Department Graduate Studies Office. The student should notify the Department Office staff if the student will supply their own refreshments.

A seminar on the research work of approximately 50 minutes duration will be presented to the public. The unbound hard copy of the dissertation should be available at the seminar. The seminar will be followed by an open question/answer period, chaired by the Director of Graduate Studies or designee. Upon completion of the public dissertation defense, the Advisory Committee will vote to determine whether the defense was satisfactory. A majority vote will be sufficient for approval. The Graduate School (Multi-purpose) M-Form will be signed by all members of the Advisory Committee and either the Director of Graduate Studies or Department Chair to conclude the approval of the dissertation. If the decision is “unsatisfactory” the committee can decide on any remedial action in consultation with the Director of Graduate Studies and the Department Chair.

The student should see the Graduate School website for a checklist of Graduate School requirements. Those include an approved Application to Candidacy, the Electronic Thesis and Dissertation (ETD) submission and mandatory cataloging and publishing fee, Doctoral Degree Recipients (on-line) Survey, and the Multipurpose “M” form.

*For specific guidelines on writing the dissertation, see next page.

• Table of Contents
• Abstract
• General Introduction/Literature Survey
• Materials and Methods
• Results
• Discussion
• Summary and Conclusions
• Literature Cited

• Table of Contents
• Abstract
• General Introduction/Literature Survey
• Chapters describing individual studies. These would contain relevant introductory
• information and materials and methods and specific discussion of the work.
• Brief general discussion and summary of the work presented in above chapters.
• Literature Cited
• Appendices as Required

The Literature Cited should contain full references including titles and inclusive pagination.

Collaborative experiments and the roles played by others in generating reagents or data should be clearly delineated in the text of the relevant portion of the thesis.

Data presented in the thesis that represents work accomplished by someone other than the author should be noted on the face page of the chapter. The number of such figures should be limited in scope.

Refer to the Graduate School website for a complete listing of Graduate School guidelines.

General guidelines include:

The thesis requires a Title page using the format given by the Graduate School. Do not number the title page; it is assumed to be Roman numeral page i.

A Copyright page is included only if applicable; it would be given Roman numeral page ii and listed in the Table of Contents.

A Dedication page and/or Acknowledgement page are optional. If given, use Roman numerals and list those pages in the Table of Contents.

Use Roman numerals to paginate the Table of Contents, followed by the list of Tables, list of figures, and list of abbreviations.

An Abstract (maximum 350-400 words) for the overall thesis is required by the Graduate School and should describe both the work done and its general relevance. ABSTRACT must be stated on the top center of the abstract page and use Roman numerals for pagination.

The Introduction page follows the abstract page(s) and begins with Arabic number 1. Use Arabic numerals for pagination of all chapters or main division of the document, including any figure pages and reference pages. If using plastic coated paper for figure pages, the page number may be typed on back of the page at the top right corner.

Additional information and samples to prepare the dissertation and for preparation and submission of the Electronic Thesis/Dissertation can be found at the Graduate School website.

Students who have passed their qualifying exam and decide to leave the Ph.D. program before completing the requirements for their degree can petition for a Master’s degree. In such cases, the student must first meet with the Director of Graduate Studies or the Department Chair where they will discuss this process. In general, three requirements must be met for a student to be granted a Master’s degree. First, they must have satisfactorily completed course work required for a Master’s degree and in most cases this would have been accomplished if the student completed their qualifying exam. Second, a scholarly document/thesis must be prepared and submitted to the Director of Graduate Studies. The preliminary qualifying exam proposal will usually be able to satisfy this requirement. Third, the Director of Graduate Studies will prepare a memorandum of understanding (MOU) detailing activities that must be completed by the student. The MOU will be prepared after consulting with the student, former mentor, and other relevant parties. Typically, the MOU will include details such as reagent and notebook organization, laboratory cleanout, and figure preparation.

Once the student, former mentor, and Director of Graduate Studies sign the MOU, the student will be allowed to become a candidate for a Master’s degree and an Application to Candidacy (ATC) form will be filed with the Graduate College. After the student fulfills the requirements of the MOU, a Degree Conferral form (M form) will be submitted to the Graduate College. In consultation with the Director of Graduate Studies, the student will be required to adhere to University guidelines and deadlines to meet degree conferral dates. If degree conferral cannot be achieved during the current academic term, the student must register for one credit hour for an additional semester to meet the next deadline (fall and spring semesters only).

All requests for a Ph.D. student in the Department of Microbiology and Immunology to fulfill a tutor or teaching position should be forwarded to the Graduate Studies Office for appropriate action by the Graduate Affairs Committee.

Ph.D. students who wish to teach or tutor students in a course outside the Supervised Teaching MIC 599 program as described below must petition the Graduate Affairs Committee for approval. A letter of support from the major advisor must accompany the petition. If the student wishes to obtain registration credit for teaching/tutoring, upon approval by the Graduate Affairs Committee, the student may register for two credit hours of the Supervised Teaching MIC 599 course and the student will be graded according to the MIC 599 policy (see item B. section 2).

This program, course designation MIC 599, is intended to provide instruction in teaching techniques and help students develop skills in the organization, presentation, and discussion of course material for instruction of individuals and small groups. This experience will provide faculty with important information to be included in letters of recommendation for students during later employment searches.

will also serve as a teaching supervisor. Depending upon the course opportunities, the student will share the responsibility of presentation of lectures, participation on examination committees, proctoring of examinations, grading of examination papers, as well as laboratory instruction, organization, and preparation of laboratory materials. Students must attend all briefings and demonstrations conducted by the teaching staff. The courses currently designated for supervised teaching is Microbiology 301 (Microbiology for Allied Health) and MIC 401 (Biomedical Microbiology). Specific instructions are issued annually by the Course Directors of MIC 301 and MIC 401. 

1. A student must first obtain written permission from their faculty mentor as well as the MIC 599 Course Director. The student will then meet with the MIC 599 Course Director to discuss the student's participation and responsibilities in the course. For PhD students, it is strongly suggested that MIC 599 is taken after successful completion of both the qualifying exam and required core coursework.
2. The following courses are recommended for supervised teaching: MIC 301 and MIC 401. Other courses that offer a suitable teaching experience may be used, if approved by the Graduate Affairs Committee. The student should inform the Graduate Program Administrator of preferred courses as early as possible. The student's selection of a course for a teaching experience should be consistent with the opportunities available, but may be subject to negotiation depending on the current needs of the department.
3. A grade (satisfactory/unsatisfactory) for the student's performance shall be determined by the MIC 599 faculty supervisor. The following information will be placed in the student's file: (a) an evaluation completed by the faculty supervisor, (b) an evaluation, submitted on the departmental evaluation form, completed by students taking the course used for supervised teaching.

The Course Director MIC 599 will be a member of the Microbiology and Immunology Department faculty, appointed by the Department Chair, and will be responsible for: 

1. Consulting with various departmental course coordinators to determine numbers and types of teaching opportunities per semester.
2. Identifying faculty supervisors who will assist and assess student performance during the semester. This will include guiding students in developing their lecture material and providing feedback to students on their lecture performances.

If a graduate faculty member leaves UB for an appointment at another institution and the student is within one year to finish their Ph.D. research, the Graduate School will allow the departing faculty member to retain their role as major advisor, providing the department approves of the request. The Graduate School does not recommend allowing this if the student is more than a year away from degree completion, however, the Department will consider a request providing the following criteria are met:

1. The mentor and student informs the Department Chair and Director of Graduate Studies of the need to complete the Ph.D. degree in absentia in a timely fashion, preferably 3 – 6 months prior to departure.
2. The student must have successfully passed the Preliminary Doctoral Qualifying Examination.
3. The student must be in good academic standing in the Department.
4. The student and major advisor sends a written statement to the Graduate Affairs Committee to agree to complete the following conditions and policies:

• Completion of the Seminar Requirement If the student has yet to complete their seminar requirement at UB, substitution of seminar and elective courses within the major advisor’s new academic department will require review of syllabi and approval by the Graduate Affairs Committee.
• Ph.D. Advisory Committee Meetings The first committee meeting must occur on site at the University at Buffalo with all members of the student’s Ph.D. Advisory Committee present.
  Subsequent committee meetings can alternate between teleconferences originating from the major advisor’s academic institution and on site meetings at the University at Buffalo following the six-month interval schedule for all students.
  The student will provide an electronic copy of the committee report to all Ph.D. Advisory Committee members at least one week prior to the committee meeting. For teleconferences, the student will provide a copy of their power point presentation to the MIC Graduate Studies Office and to a designated committee member at least one week prior to the meeting. Teleconference meetings must take place within an office (the student can request help from the Graduate office to arrange a room) equipped with a speaker phone and a computer for viewing the power point presentation in order to allow simultaneous participation.
  The student will provide an electronic copy (or fax) of the Ph.D. Advisory Committee Report form with the major advisor signature to the Graduate office within one week of the Committee meeting. After all Committee members have signed the report form, the Graduate office will provide an electronic copy (or fax) of this document to the student and major advisor. The original signed document will be retained in the MIC Graduate Studies Office.
• Ph.D. Oral Defense The Ph.D. examination will occur on site at the University at Buffalo. The student must provide a hard copy of the thesis to all members of the oral defense committee for review according to the timeline required of on-site students. The Graduate office will circulate the thesis approval sheet already signed by the major advisor to the on-site Committee members and will forward an electronic copy (or FAX) to the student and major advisor. In accordance with Department policy, the student will provide a hard copy of the revised thesis to the Graduate Studies Office and to all Committee members requesting a revised document prior to the final examination.

If a graduate faculty member retires from UB with no intention of assuming a faculty appointment at another institution, that faculty member is eligible to continue to serve as the major advisor or as a committee member for a current student providing approval by the Department Graduate Affairs Committee.

Attendance at departmental sponsored seminars is absolutely required for all Ph.D. students in the Department as an integral component of their doctoral training. For seminars at which students are presenting, completion of the online evaluation survey is a requirement as part of the attendance policy.

Failure to attend a given Departmental Seminar, with the exception of infrequent instances for which the student obtained prior permission of the Graduate Director to be excused or in cases of unforeseen illness or emergency, may be a matter for which the Department's Graduate Affairs Committee will be obligated to take action.

The program provides students an opportunity to meet microbiologists and immunologists from around the world and to hear about current research methods and approaches. As with the curriculum for the department graduate program, the departmental seminar program covers material from all areas of interest in the department.

Students should encourage their mentor to propose individuals for speakers in their areas of interest.

Seminars not scheduled at the regular departmental time and day, designated as Special Seminar must be approved by the Department Chair, Department Director of Graduate Studies, and Department Seminar Committee Chair for attendance to be required for all Ph.D. students in the Department. In this event, students will be notified by e-mail. Although regular Special Seminars are optional attendance, they should be given high priority in the students’ schedule.