INTRODUCTION TO THE DEPARTMENT ORGANIZATION

Current Chair of the Biology Department: Gloster Aaron, gaaron@wesleyan.edu

• Biology Office Staff

  Administrative Assistant ("AA"): Shana Sperry, ssperry@wesleyan.edu

  Your primary contact for departmental administration. The AA maintains departmental files and webpages, coordinates departmental events, communicates information within the department as well as between the department and other offices, assists with preparation of reports and other materials, manages course listings and calendars, and assigns advisors to undergraduate majors, among other things. The AA also works closely with the department chair, who is their immediate supervisor, and frequently with the Accounting Specialist.

  Accounting Specialist: Suzanne Bussolari, sbussolari@wesleyan.edu

  Your primary contact for departmental finance and budget issues. The Accounting Specialist manages the departmental budget, the budgets of individual faculty members, payment of student workers and graduate student stipends, and assists with grant budgets, graduate travel budgeting and paperwork. They work closely with the department chair and the chair of the Biology Finance Committee.

• Facility & Laboratory Staff

  Science Facilities and Property Specialist: Horace Chambers, hfchambers@wesleyan.edu

  Your primary contact for shipping and receiving items. Works with the Facilities office to maintain and upgrade the building and infrastructure in accordance with local, state, and federal codes. Manages maintenance and custodial work in the building, including specialized waste disposal. In the Chemical Stockroom, he assists with the online chemical inventory system and processes and delivers incoming shipments and supplies. He also performs other important tasks within the department as needed: for example, he can be invaluable for timely receipt of deliveries (e.g., temperature regulated reagents) to the building.

  Animal Care Facilities Specialist: Pete Shatos, pshatos@wesleyan.edu

  Ensures department is following all federal and state guidelines for the institutional care and use of animals within Wesleyan. Reports and maintains all records for the USDA covered animals that we house here. He also manages staffing issues and any mechanical issues within the animal care facility. Two part-time animal care staff members (Angela Stachelek and Sera Brown) also keep the animal care facility running.

  Biology Laboratory Coordinator: Joan Duigan, jduignan@wesleyan.edu

  Supports the graduate student TAs who teach Biology Lab 191 and 192. Purchases and maintains equipment used during lab, order supplies and chemicals, and make all the necessary reagents. She is available before the lab to answer any questions or to provide one-on-one training and is available during the lab to answer any technical questions the TAs or the students might have.

  Scientific Imaging Support Specialist: Dr. Rafael Pimenta, rpimenta@wesleyan.edu

  Specializes in utilizing advanced imaging technologies to support and enhance research across various scientific disciplines. His role involves operating and maintaining state-of-the-art equipment, such as the Leica SP8 confocal laser scanning microscope (CLSM) and the HITACHI SU5000 Field Emission - Scanning Electron Microscope (FE-SEM). He collaborates with faculty, researchers, and students at all levels, regardless of their technical expertise, to design, develop, and execute imaging experiments, providing comprehensive support throughout the entire imaging process.

  Manager of Scientific Facilities and Instrumentation: Dr. Camille Keeler, ckeeler01@wesleyan.edu

  Directs repairs and maintenance on essential building functions, manages both hazardous and non-hazardous scientific materials disposal, and shares her insights on site renovations and upgrades. She also trains students on matters of safety and the operation of core scientific equipment such as the NMR and mass spectrometers. Camille repairs shared scientific equipment and provides oversight on the procurement of new instrumentation.

  Scientific Instructional Laboratory Support Specialist: Jessica Cuneo, jcuneo@wesleyan.edu

  Supports the chemistry teaching labs and manages the stockroom, which is utilized by Biology and many other Wesleyan departments. Assists with various maintenance and chemical hygiene tasks in the building.

OVERVIEW OF THE PROGRAM STRUCTURE AND REQUIREMENTS

As a first-year Ph.D. student, you will start your research experience in your first semester. You should choose your first lab rotation prior to starting your first year. However, in rare cases this decision may be made when you arrive on campus and meet with the Pre-Candidacy Committee (PCC), which is the first of three committees that will guide you through your Ph.D. You are encouraged to do at least one lab rotation outside of your thesis lab, although in some cases, with prior agreement between the student, mentor, and PCC, rotations may be waived.

General Requirements

• Coursework Requirements
  1. All Ph.D. students are required to register for at least one course credit each semester that they are enrolled in the university. For every semester enrolled, the student must take BIOL 549/550: Research Tutorial. Until you have achieved final year status, the other courses taken for credit must include:
     1. A journal club course:
        1. BIOL 505/506: Cell and Development
        2. BIOL 507/508: Evolution
        3. BIOL 509/510: Neuroscience
        4. BIOL 547/548: Environmental Biology
        5. MB&B507/508: Molecular Biophysics
        6. MB&B585/586: Molecular Biology
     2. BIOL 557: Advanced Research Seminar 
        
        
  2. Before completing the Ph.D. program, all Ph.D. students must have a minimum of two 1-credit advanced (300 or 500) lecture, lab, or seminar courses. Before taking the qualifying examination, all Ph.D. students must have completed at least one course above the introductory level at Wesleyan (1-credit) or elsewhere (equivalent of 1-credit at Wesleyan) in each of five subject areas, with coursework approved by the PCC:
     1. Genetics/Genomics/Bioinformatics
        1. Students whose focus is bioinformatics may substitute two upper-level courses in computer science for one of these five areas
     2. Evolution/Ecology
     3. Physiology/Neurobiology/Behavior
     4. Cell Biology/Developmental Biology
     5. Biochemistry/Molecular Biology
        
        
  3. A grade of B- is required for a course to contribute to your PhD program of study.
• BIOL 557: Advanced Research Seminars in Biology

  You are required to enroll in BIOL 557 each semester and present your research annually in this seminar course which is attended by research faculty and other graduate students of the Biology Department. These presentations are opportunities to develop research presentation skills and gain critical feedback on your research hypotheses and data.

  ^{Students on Final Year Status are expected to enroll in and attend BIOL 557, but are not required to give a presentation.}

• Teaching Assistantships

  During your tenure as a Ph.D. student, you are required to serve at least 3 semesters as a teaching assistant (TA) to develop your teaching pedagogy and mentorship skills. Every Ph.D. student is required to TA two semesters drawn from any combination of BIOL 181/191 (fall semester) or BIOL 182/192 (spring semester), preferentially drawing from both fall and spring semesters in order to be exposed to the full range of our introductory Biology sequence.

  In addition, many Ph.D. students will TA for another large intro-level course such as BIOL/ENVS 197 and BIOL/NSB 213. Graduate students may also TA for courses outside of introductory Biology that are offered by department faculty or courses hosted by other departments that are cross-listed with Biology.

• Biology/MB&B Seminar Series
  Biology Graduate Students are strongly encouraged to attend Biology/MB&B seminars given by outside speakers. These seminars normally occur weekly during each semester. In addition, each graduate student is expected to attend at least two lunches with the guest speakers each academic year.

PROGRAM COMMITTEES

Biology graduate students will be guided by three committees during their time in the program: Pre-Candidacy Committee, Qualifying Committee, and Thesis Committee. Below are details about each committee, who serves on them, and how they can assist you.

• Pre-Candidacy Committee (PCC)
  1. The PCC is composed of three faculty members and one senior graduate student.
     1. If a student’s faculty advisor is on the PCC, that faculty member will be excused from part of the meeting.
        
        
  2. The PCC will mentor each cohort of graduate students from the start of their first semester in the grad program, through rotations in their initial 2-3 semesters, up until they schedule and complete their qualifying exam (i.e. qualifier) within 3 months of the end of their fourth semester.
     
     
  3. The PCC will review an incoming student’s academic history to identify gaps in their biological background. Based on this information, the PCC will work with the student to recommend or require specific courses to fill the gaps to ensure students have completed coursework in all areas outlined in General Requirements 2a-2e. The PCC will also help the student identify course(s) that would provide further training in their area of interest.
     
     
  4. The PCC will discuss possible research rotations with each student. Research rotations can help students explore Ph.D. options and enlarge their toolbox when they have an intended home lab.
     
     
  5. The committee will meet with each student 3 times during their first and second year in the program. Meeting schedule for each of the first two years:
     1. Before the first semester
        1. Based on PCC discretion, returning students may be given the option of having a short 10-15 minute check-in or a full-length 25-30 minute meeting for the pre-fall semester meeting
     2. In between the first and second semester
     3. At the end of the second semester
• Qualifying Examination Committee
  After settling into a lab for your thesis research, you are required to form a Qualifying Examination Committee of three members to facilitate completion of a qualifying examination. At least two of the members should be drawn from the Wesleyan Biology faculty, with one of them being your research advisor. One of the Committee members who is not the student’s research advisor will serve as the Chair of the Qualifying Committee, and it is the Chair’s role to keep the meeting on schedule and to report the results of the meeting. You are encouraged to consult with your research advisor as you consider which professors you will ask to join the committee.
• Thesis Committee
  1. Within a year of passing the qualifying exam, you must select your Thesis Committee. In consultation with your advisor, you will form a Thesis Committee with whom you will meet at least annually to discuss your proposed research and research progress. The Thesis Committee is comprised of four members. At least three of the members will be drawn from the Wesleyan Biology faculty, with one of them being your research advisor. One of the Committee members who is not the student’s research advisor will serve as the Chair of the Thesis Committee. It is the Chair’s role to keep the meeting on schedule and to report results of the meetings.
  2. Through yearly meetings with the Ph.D. candidate, the Thesis Committee determines when sufficient original research has been completed for the dissertation. Finally, you are required to obtain confirmation from the Thesis Committee for "Final Year" status. Within a year of this status, you are expected to deposit a final written thesis that has been examined and approved by the Thesis Committee and required to offer a public defense.

FIRST YEAR OVERVIEW

• PCC
  The committee will meet with each student 3 times during the first year. The PCC will also reach out to first-year students in mid-semester to ask about their progress or any difficulties they are encountering, encouraging the student to respond to whichever committee member they are most comfortable talking with (either a faculty member or the graduate student member).
• Academic Classes
  Classes are chosen with help from the PCC based on the student's prior experience in areas that the department considers to be essential for adequate background education. The PCC and student will also discuss advanced elective courses of interest they may wish to take.
• Graduate Pedagogy

  All incoming graduate students are required to take Wesleyan's graduate pedagogy course during their first semester. This course is offered only in the fall semester. If a graduate student has a spring start, they must take the graduate pedagogy course during their first fall semester.

SECOND YEAR OVERVIEW & QUALIFYING EXAM

• PCC
  The committee will meet with each student 3 times during the second year. The PCC and student will together determine the length of preparation time needed for study and writing related to the student's qualifying exam.
• Scheduling the Qualifying Exam
  The student should work with their Qualifying Committee to establish a date and time for the qualifying exam. Students should establish an exam date and that date should be before the beginning of their fifth semester (i.e., before the beginning of their third year). Once a date and time are established, the student should work with the department AA to book a location for the exam.
• The Qualifying Exam

  The Qualifying Exam consists of a written document and an oral examination that are both assessed by the Qualifying Committee. A student’s written document should be in the form of a grant proposal that outlines the rationale for a set of experiments. The oral exam will consist of questions posed to the student that are drawn from the coursework and research the student has completed at Wesleyan.

  If a student wishes to see examples of qualifying exam research proposals from previous students, they may contact the department AA. Digital copies of recent qualifying exam research proposals are available to share with permission from their authors.
  
  

• Qualifying Exam Outcomes
  1. Passing the Qualifying Exam: If a student successfully completes their qualifying exam, the Chair of the Qualifying Committee will notify the AA. The AA will put the note of passing in the student’s file and notify the PCC of the successful exam. Upon passing, the student will no longer be required to meet with the PCC.
  2. Incomplete Qualifying Exam: If a student passes only part of the exam (either written or oral), the student will be given 30 days to resubmit the written proposal or retake the oral exam.
  3. Failing the Qualifying Exam: If a student fails outright, one of two outcomes is possible:
     1. If the student has sufficient data, they will write a thesis to be submitted no later than the end of the subsequent semester for a Master’s Degree (see Addendum).
     2. The student leaves the program with no degree.

CANDIDACY & THESIS RESEARCH

• Becoming a Ph.D. Candidate
  After passing the qualifying exam, the student becomes a Ph.D. Candidate. Candidacy entails conducting thesis research, teaching if required, as well as taking journal club and BIOL 557 courses. The PCC will be replaced with a Thesis Committee, chosen by the student with the advice of their Ph.D. advisor and the PCC if desired.
• Thesis Committee & Meetings
  1. Once a student has established their Thesis Committee, the student should inform the department AA of its members. Students should also inform the AA of any committee meetings and are welcome to request scheduling assistance from the AA as needed to establish date, time, and/or location for any committee meetings.
  2. During a normal Thesis Committee meeting, the student will present the research and any findings they’ve made so far as well as research plans. The student should expect a conversational style of meeting with much constructive feedback as the student presents their work.

FINAL YEAR STATUS

• Determination of Status
  Based on a student’s progress, the full Thesis Committee will determine the appropriate timing for a student’s transition to final year (FY) status, which typically lasts one year. Final year status is conferred on the Ph.D. candidate when their thesis committee has determined that the candidate can complete and defend their thesis within one year of the start of FY status. Typically, FY status is given when the student has completed most if not all the data collection and is now ready to devote themselves to analysis and writing the dissertation. Though the Thesis Committee can decide whether the student is ready for FY status at any time during the year, the timing of FY status will follow the stipend schedule. This schedule dictates that a student’s FY status would begin on June 1 or January 1.
• Requirements for Final Year Status Students
  1. Students who are on FY status and who are paid by a university stipend will be given a TA assignment. Duties will be determined commensurate with FY status.
  2. Students on FY status are not required to enroll in Journal Club courses, but rather, they are required to at least audit those courses.
  3. In anticipation of the public defense, students on FY status will not be required to give a BIOL 557 presentation. However, given the power and importance of community, we expect FY status students to enroll in and attend 557.

COMPLETION OF PH.D.

• Requirements to Complete & Graduate

  Completion of a Ph.D. thesis is a complex process and there are various requirements that are clearly explained by the Office of Graduate Student Services’ Graduation Requirements - Ph.D. webpage. Getting fully acquainted with the process will help you successfully negotiate it in a professional manner, and with minimal stress. The requirements outlined by the Office of Graduate Student Services include information about submission deadlines, how to purchase graduation regalia, and how to schedule your mandatory Office of Graduate Student Services exit interview.

  Timing can be more flexible if the graduate student does not try to complete their thesis during the spring exit period. If a student completes the degree requirements after Commencement of the current year (e.g. does not complete their degree during the spring exit period), the degree will be received the following May.
  
  

• Writing a Dissertation

  Students should consult with their mentors and/or Thesis Committee members if they have questions about expectations for the quality of a dissertation.

  Publications: Many students will have at least one publication by the time they enter FY status, but this is not a requirement and depends on the field and the opinion of the Thesis Committee. First-author publications can be used as chapters of the dissertation.
  
  

• Setting a Thesis Defense Date

  Given the wide variety of availability among Thesis Committee members, it is advisable to determine a thesis defense date before distribution of the thesis. This is especially recommended for students who will be defending during the spring exit period.

  When establishing a date for the Thesis Defense Examination (closed defense), the student and committee members should also consider establishing a date and time for the public seminar (open defense). This ensures that the Thesis Committee members are all available and that the student can adequately prepare.
  
  

• Distribution of Thesis
  Once a satisfactory copy of the thesis has been produced, it will be distributed to the student’s full Thesis Committee. The Ph.D. candidate must submit their dissertation to the committee at least 2 weeks prior to the established closed defense date to allow the committee time to read and critique the candidate’s thesis.
• Closed Thesis Defense
  1. The purpose of the closed defense is to offer feedback about the written thesis and ensure that the student is able to answer questions regarding the topics presented in the thesis. The Thesis Defense Examination will consist of a presentation of the thesis research by the Ph.D. candidate, interrupted by questions and comments from the Thesis Committee. The presentation should include slides that include a brief introduction, methods, results, and conclusions. This presentation should last 15-20 minutes without interruption. The Ph.D. candidate should expect the committee to ask the student to skip over some work or briefly summarize important, older findings. Typically, the Thesis Defense Examination will focus on the graduate student’s most recent work in greater detail, since older work has already been reviewed.
     
     
  2. The Thesis Committee members will communicate recommendations for additional work or thesis revisions to the Ph.D. candidate and their Ph.D. advisor. Such feedback is typically given by the committee members via a copy of the candidate’s thesis marked with their comments and edits. In addition, the Thesis Committee will discuss the thesis and the candidate’s defense during the closed defense. These discussions take place at the very start and end of the Thesis Defense Examination without the Ph.D. candidate present. During the end discussion, the Thesis Committee will vote on the outcome with the following three options: pass, conditional pass, or fail. The committee will call the candidate back into the room, and the Chair and other members of the committee will inform the candidate of the voted outcome as well as any required revisions to the dissertation.
     
     
  3. There are three possible outcomes after a closed defense. They are:
     1. Passing the Defense: A pass is contingent on satisfactory completion of minor recommended changes to the thesis. The Ph.D. advisor will usually oversee this on behalf of the Thesis Committee.
     2. Conditional Pass: A conditional pass may be given if the Thesis Committee feels additional work is needed to complete the thesis. This outcome may or may not necessitate a second closed defense meeting depending on the importance of the outstanding work. Again, the Ph.D. advisor usually monitors and confirms the completion of this work, without another meeting.
     3. Failing the Defense: A failing determination is made if the thesis is poorly conceived or written, or alternatively, if the student is unable to adequately orally defend it. This is very unusual as these kinds of problems will have been addressed in earlier Thesis Committee meetings. In either case, this outcome will necessitate a second closed defense meeting.
        
        
  4. The Ph.D. candidate is responsible for filling out graduate exit forms before their thesis defense occurs. These forms can be found in the student’s WesPortal/Academics/Graduate Exit forms. Students should familiarize themselves with the requirements for graduation as stipulated in the Office of Graduate Studies. The Ph.D. candidate obtains the Ph.D. degree status upon completion of the defense and after the Thesis Committee signs the defense form that specifies that they have met all degree requirements. The graduate with their newly earned Ph.D. is then eligible to begin post-doctoral work (or other employment), even if their formal graduation occurs at the following year’s Commencement.
• Public Seminar (open defense)
  After successful completion of the closed Thesis Defense Examination, a graduate student will schedule their Public Seminar, typically within two weeks of the Thesis Defense Examination. The Ph.D. candidate is encouraged to ask the Biology AA for help with room scheduling, as well as advertising the event.

TRAVEL & CONFERENCES

Students are encouraged to attend scientific meetings or conferences to present their work each year, especially after passing the qualifying exam. Advice about appropriate conferences to attend can be sought from research mentors and members of the PCC. Meetings and conferences provide valuable exposure to cutting edge scientific work in particular fields of Biology, opportunities to directly interact with other scientists and their research groups to form the networks that will enhance the graduate student’s career, and opportunities to attend professional development workshops.

• Available Department Funding

  The Biology Department will provide funds per academic year for each Ph.D. student to attend scientific meetings or conferences for a maximum of $1000 per academic year provided that the student applies for the funds and is approved before attending the meeting/conference. If the student is attending a meeting or conference and they are not speaking or presenting, then the department can provide up to $800. If the student is attending a meeting or conference and is also speaking or presenting, the department can provide up to $1000.

  If a student requires more funds than the department provides, it must be from alternative sources (e.g. grants). The student must speak with their faculty advisor if the meeting or conference will cost more than the $800 or $1000 provided by the department.

• Receiving Department Funding

  To receive access to these funds, a student will need to identify a meeting or conference they wish to attend, then provide the following written information to their faculty advisor with the Accounting Specialist copied:

  a. A written explanation of the purpose of the meeting or conference

  b. An estimated travel expense budget

  c. An agenda from the meeting or conference
• Booking Travel for Non-US Citizens
  Students who are not U.S. citizens should utilize the Biology Department expense cards held by the AA and the Accounting Specialist to pay for conference registration, travel costs (ex: flight or train tickets), and hotels. If a non-U.S. citizen student pays for these items on their own and later seeks reimbursement, they will be subject to a 14% tax on the amount reimbursed to them.

VACATIONS & LEAVES OF ABSENCE

• Vacation Time

  Students are allowed 3 weeks of vacation per year. Graduate students should communicate about their intended vacation time with their thesis or rotation advisor so that work can be coordinated around their absence.

  Due to the cost of international travel, foreign students may accumulate their annual vacation time for 2 years (a total of 6 weeks maximum). If any visa issues are anticipated, a foreign student should get help and advice from the Office of Graduate Student Services. In the past, some of our students have experienced lengthy delays in re-entry into the US, and this could delay progress through our program.

• Parental Leave
  Graduate students who receive University-funded stipends are eligible for a 12-week paid parental leave. This applies to both birth and adoption. In most cases, the 12-week leave should be taken when the child is born or adopted. In some instances, subject to approval, the leave may be delayed but not usually beyond six months of the child coming into the home. Additional information can be found in the Graduate Studies Handbook provided by Office of Graduate Student Services, which includes contact information for the State of Connecticut Paid Leave Program.
• End of Year Time Off (12/25-1/1)
  Graduate students are not required to be in lab during the week between Christmas and New Year’s Day. This time away is separate from the three weeks of vacation time described above.
• Other Leaves of Absence
  For any medical or non-medical leave of absence not noted above, the department will follow the same policies outlined in the Graduate Studies Handbook provided by the Office of Graduate Student Services.

ADDENDUM

Departing the Program Before Ph.D. Completion

• Option of Leaving with a Master's Degree
  1. While not the goal of this program, occasionally students leave our program earlier than anticipated and prior to the completion of the requirements needed for a Ph.D.. If a student, mentor, and/or the Biology Department decides on this course of action, then their mentor needs to notify the Chair of the Biology Department and the Office of Graduate Student Services. In addition, the PCC should be notified if the student has not completed their qualifier exam. The Chair of the Biology department will ensure that the appropriate AAs are notified (i.e., our Financial Analysis and AA for Biology).
  2. In order to obtain the Master’s degree, the student will also need to form a Master’s committee of at least three faculty members (two Wesleyan Biology faculty members and a third in Biology or another appropriate department), write a Master’s thesis, and defend that thesis during a meeting with the Master’s committee. Thus, there should be sufficient time between the student’s notification of their intention to depart and their departure date such that all the above can be accomplished prior to departure. The thesis should pertain to any research that has been done, including the usual sections of a thesis that include an abstract, introduction, materials and methods, results, and discussion. If there is insufficient research accomplished at the time of departure, then the student may also include designs of future experiments that would support the goals of the research, including descriptions and rationales for those experiments.