Center for Biological Chemistry
Graduate Handbook
Through a combination of coursework, seminars, and original research, CBC graduate students will complete a graduate degree and acquire the skills needed to become independent research scientists. Our four major research training areas are:
- Structural and chemical basis of protein function
- Metabolism and metabolic engineering
- Molecular mechanisms of disease
- Plant and microbial biochemistry and biotechnology
The CBC Graduate Program is constructed to satisfy disciplinary expectations for MS and PhD-level Biochemists according to American Society for Biochemistry and Molecular Biology (ASBMB), and National Academy for Science, Engineering, and Mathematics (NASEM)
1. Orientation
The Graduate Committee will assist all students in initial course selections and research rotation choices. A poster session will be held to allow students to interact with each faculty member and/or members of their labs to find out about their research and get an overview of the active research areas in Biochemistry. This will help students in choosing a research advisor and Supervisory Committee. Students will also have a one-on-one guidance interview with the Chair of the Graduate Committee to learn about the program in Biochemistry and choose courses for the first semester.
2. Courses
All CBC graduate students are required to take the following core courses:
- BIOC 932, Proteins, 2 credits
- BIOC 933, Enzymes, 2 credits
- BIOC 934, Genome Dynamics and Gene Expression, 3 credits
- BIOC 935, Metabolic Function and Dysfunction, 3 credits
- BIOC 836, Physical Basis of Macromolecular Function, 3 credits
- GRDC 901, Professional Ethics, 1 credit
In addition, all students in the Ph.D. program are required to register for the graduate seminar every semester throughout their program, receiving one credit per semester (BIOC 992k) for a total of 8 credits over four years.
Students in the M.S. program take BIOC 992k for at least two years (4 credits).
Other course requirements are arranged in consultation with the Supervisory Committee.
The student and advisor submit a Program of Studies (for the Ph.D.) or Memorandum of Courses (for the M.S.) that details the student’s course work requirements to the Graduate College before one half of the courses are complete. Forms can be found on the Graduate Studies website (http://www.unl.edu/gradstudies/home).
Successful completion of the Ph.D. degree requires 90 credit hours, of which 35 credits are coursework and the remainder thesis research. No more than 55 of the 90 credit hours may be dissertation research, and 45 credit hours must be in Biochemistry offerings (including dissertation research, BIOC 999). All courses counting toward the degree must receive a B or higher grade.
3. Rotation Selection Process and Thesis Advisor Selection
A Ph.D. in the Center for Biological Chemistry is granted for original research that makes a new contribution to biochemistry. This original contribution to scholarship is the product of years of mentored student research in the laboratory of an advisor that the student selects, culminating in a thesis containing published or publication-quality scholarship.
Students typically choose an advisor based on a shared research interests and a good rapport with that faculty member. The program is set up to allow students to rotate for two 8-week sessions during the first semester (a third rotation may be done in the second semester if the student is a part of the MMoD program, see below, or if there are extenuating circumstances). Each student is encouraged to contact potential mentors and discuss their interests and availability to serve as a rotation mentor. After these conversations but before the start of each 8-week rotation period, students will submit a list of three potential advisors to the Chair of the Graduate Program Committee. The Grad Chair and the Department Chair will consult and then inform students of their rotation mentor shortly after these lists are submitted. Every effort is made to ensure that students receive their first choice of rotation advisor. However, in rare cases, second or third-choice advisors will be chosen. Students are encouraged to communicate with the Grad Chair prior to rotation choices about preferences or special considerations. After the final rotation period, all students will submit their choices for an advisor to the Graduate Committee, and final assignments will be made upon consultation with the Chair of Biochemistry.
4. Molecular Mechanisms of Disease (MMoD) Students
Per NIH policy, only US citizens or permanent residents are eligible for direct support through MMoD. However, all students are invited to participate in MMoD sponsored activities including the annual symposium, seminars and workshops. Students selected for the MMoD program will follow the same trajectory as all other CBC graduate students with some minor differences. First year MMoD students will do three rotations, the third of which will be performed at the start of the Spring semester of their first year. As the MMoD program focuses on interdisciplinary training with two co-mentors, it will be important to rotate in diverse laboratories so that the student gains the information that they will need to choose both co-mentors. MMoD fellowships for years 2 and 3 of the Ph.D. degree program are awarded based on a competitive application process. Applications for MMoD fellowships are due in April/May of the Spring semester with funding decisions completed in June.
Additional requirements for MMoD students include participation in MMoD monthly works-in-progress seminar, career development workshops, and annual symposium. All CBC students typically attend MMoD activities as well. Because the MMoD training grant prohibits teaching during the two-year period of support, students in MMoD will need to perform their required teaching starting in their fourth year in the Ph.D. program.
5. Supervisory Committee
Shortly after students have chosen a mentor and started working in their lab (i.e. in the second semester), students will confer with their research mentor to form a Supervisory Committee. The approval form for the Supervisory Committee can be downloaded from the Graduate Studies website (https://graduate.unl.edu/academics/program-steps/doctoral-degree-steps-to-completion#degapp). The purpose of this committee is to evaluate student progress in the degree program, to offer a support network within the University, and to assist students with practical guidance in their research project. The supervisory committee is chaired by the primary research advisor and must consist additionally of three other Biochemistry faculty and one faculty member from outside the Department.
Each year, students will schedule a meeting with their Supervisory Committee. At the meeting, the student will present a ~30-minute talk about their research progress to date, and their goals for the coming year. The Committee will ask questions during the presentation to ascertain the student’s level of development as a scientist, and will advise the Graduate Program Committee whether the student is making satisfactory progress toward the degree objective. Students should bring a CBC Annual Meeting Form (available from the Biochemistry office) to each committee meeting. The Supervisory Committee will check a box indicating either “satisfactory” or “unsatisfactory” progress, and then sign this form. If progress is deemed unsatisfactory, it is the responsibility of the Supervisory Committee to provide recommendations for improvement, probation, or termination (where warranted) to the student and to notify the Grad Chair.
5b. Mentoring: The student and mentor will fill out an annual Individual Professional Development Plan with a record of this conversation kept in the student file. This is for both the student’s and professor’s benefit in that their goals are aligned and to keep the flow of communication open.
6. Comprehensive Exam
Students are required to pass a Comprehensive Examination consisting of written and oral components. This exam must be taken in the fifth semester. If the exam is not completed by the end of the 5th semester, the Supervisory Committee should issue an “unsatisfactory” evaluation on the student’s CBC Annual Meeting Form. Brief delays for life-altering events can be made by the Graduate Chair only in extreme circumstances. The exam consists of both a written and oral portion, although the details of the exam are determined by the Supervisory Committee. Typically, students are required to write a research proposal in the style of an external grant application on a topic of their choosing. The topic must be different from the student’s research area. The student will then schedule a meeting with their Supervisory Committee, give a presentation of the proposal, and defend it against the Committee’s questions. We ask that students circulate the proposal to the members of your committee at least two weeks before the meeting. The exam will probe the depth and breadth of the student’s biochemistry knowledge, and the sophistication of their scientific thought process. There is a handbook for the written portion of this exam which will be made available.
Passing the Comprehensive Examination results in the student being recommended for Ph.D. candidacy. The student must be admitted to candidacy at least seven months prior to the final oral dissertation defense. Also, the Graduate College stipulates that if a student does not graduate within three years of passing the Comprehensive Examination, the Supervisory Committee must give another such exam.
7. Seminars
The development of oral communication skills is an essential component of professional development. Students give regular presentations in laboratory meetings, journal clubs, and other informal settings. The required credit hours in seminar courses (BIOC 992k) are expected to give the student experience in formal presentations. All Ph.D. students are required to give a formal, research-based, public seminar related to their dissertation research.
In addition to giving seminars, it is equally important for students to educate themselves by attending seminars. External speakers are regularly invited in to several seminar series and annual symposia that we urge our students to attend. In particular, you should attend the weekly Biochemistry Departmental Seminar, at which eminent speakers present their research at the invitation of our own faculty.
8. Teaching
Learning to communicate effectively as a teacher is also critical to a student’s future career as a scientist. To facilitate this aspect of their development, students will be required to assist with teaching biochemistry courses for two semesters. This responsibility may be fulfilled in some cases by providing teaching assistance in a lab course, or in others by assisting course instructors with grading and fielding student questions. Teaching assignments are coordinated by Dr. Jing Zhang.
International students who earned their degree in a language other than English must attend and pass a three-week intensive training session (ITA training) in the summer after their first year to prepare for their teaching assignments. Information can be found online.
9. Research grades
The IP and XP grades shall be used exclusively for thesis and dissertation hours (course number 899 and 999, respectively) prior to the student’s final semester.
The IP grade indicates satisfactory work in progress or effort as determined by the student’s advisor and/or supervisory committee. The IP grade will stand until the final examination, at which time a grade of P or a letter grade for all thesis and dissertation hours is submitted to the Office of the University Registrar.
The XP grade indicates lack of satisfactory progress as determined by the student’s advisor and/or supervisory committee. Consecutive XP grades may result in the graduate committee taking action to inform the student and Graduate Studies regarding continuation of the student’s graduate study. No direct academic action will be imposed for earning one or more XP grades. However, departments may use a series of XP grades as a basis for recommending termination of the student from a graduate program. Criteria for XP grades include one or more of the following in any semester (list is not exhaustive):
- Academic issues (GPA below 3.0, dropped courses without prior approval, etc)
- Lack of technical research progress
- Inability to satisfactorily complete program benchmarks and deadlines (annual reports, committee meetings, timely completion of comprehensive exam or thesis defense)
- Unexplained absences or chronic unapproved absences
- Infractions of the Student and/or Employee Code of Conduct
10. Dissertation
The dissertation must be submitted and approved by Graduate Studies two weeks prior to the semester deadline. The doctoral candidate should allow the thesis committee at least two weeks to read and review the dissertation prior to the defense. All committee members should read and comment on the document. During this time, the committee is advised to make recommendation for any corrections that need to be made on the written document. On the day of the thesis defense, there should be at most only minor corrections (syntax, spelling, grammar) to the written document. An example of how this would look is if the semester deadline is April 22, the dissertation should be submitted and approved by OGS by April 8, and the written thesis distributed to the committee members by March 25. Between March 25 and April 8, major changes may be made at the request of the committee. The oral defense and minor corrections to the written thesis (if needed) may be completed anytime up to April 21.
11. Timeline for Ph.D.
Average time to completion of a Ph.D. is a little over 5 years. Trainees will complete an Annual Report each year and submit to their Advisor and Supervisory Committee documenting their cumulative research, academic, and professional development activities. Completed and signed Annual Reports are Due to the Graduate Program Chair September 15. This is how that breaks down as milestones for students, with mandatory UNL Graduate Studies paperwork in italics:
See: https://www.unl.edu/gradstudies/academics/degrees/doctoral#finalize
First year: complete core courses in Biochemistry; first year of seminar
- First semester: rotations and selection of a lab.
- OPTIONAL: Apply for Graduate Research Fellowships (see Adviser)
- Second semester: select supervisory committee
- Complete IPDP
- Complete Appointment of Supervisory Committee form and file with Graduate Studies
- First meeting of supervisory committee
- Complete Program of Study form, and file with Graduate Studies
- Select coursework for second year of study.
- · TA option (see Adviser)
Second year: continue/complete all coursework; continue meeting research and seminar requirements
- First semester: Annual Report due.
- Second semester: second meeting of supervisory committee
- Select format / topic for written and oral portions of comprehensive exam.
- Complete IPDP
- · TA option (see Adviser)
Third year: continue meeting research and seminar requirements; first semester of teaching
- First semester: complete comprehensive exam
- Complete Application for Admission to Candidacy and file with Graduate Studies.
- Annual Report due.
- Second semester: third meeting of supervisory committee.
- Complete IPDP
- OPTIONAL: Apply for Graduate Research Fellowships or Internships (see Adviser)
- TA option (see Adviser)
Fourth year: continue meeting research and seminar requirements; complete teaching assignment
- First semester: Annual Report due.
- Second semester: fourth meeting of supervisory committee; discuss time to graduation
- Complete IPDP
- TA option (see Adviser)
- OPTIONAL any semester: Apply for Graduate Research Fellowships or Internships (see Adviser)
Fifth year: complete research; write thesis; final defense of thesis work; final examination by supervisory committee; Ph.D. conferred
- First semester: Annual Report due.
- In the graduation year, complete Application for Graduation and Application for Final Oral Exam forms and file with Graduate Studies.
- TA option (see Adviser)
- OPTIONAL any semester: Apply for Postdoctoral Research Fellowships or next-stage
- employment (see Adviser)
12. Biological Chemistry Graduate Student Association (BCGSA)
Graduate students in the Center for Biological Chemistry (CBC) form the Biological Chemistry Graduate Student Association (BCGSA). The purpose of this organization is to represent our graduate students in communications among members of the Biochemistry community, the college and also to promote unity, camaraderie, and active participation in departmental affairs. Membership is open to all Biochemistry graduate students. Meetings are typically on a monthly basis. To join the group or seek additional information, contact President Tristen Mier, email: tmier2@huskers.unl.edu
13. Research Equipment
Core Facilities
Bioinformatics (http://bioinformatics.unl.edu)
Mass Spectrometry and Metabolomics (contact Dr. Bob Powers in Chemistry: rpowers3@unl.edu )
Biophysical instrumentation (contact Javier Seravalli: jseravalli1@unl.edu )
Microscopy (contact Joe Zhou: yzhou2@unl.edu )
Plant Transformation (contact Tom Clemente: tclemente1@unl.edu )
Flow Cytometry (contact Dirk Anderson: dirk.anderson@unl.edu )
Departmental Equipment
The Biochemistry Department has numerous pieces of shared equipment available for use by any member of the Department. Below is a partial list of this equipment and its current location. Please contact the appropriate lab before using instruments.
- Analytical ultracentrifuge Biophysical Core: contact Javier Seravalli
- Dynamic Light Scattering Biophysical Core: contact Javier Seravalli
- Real time PCR thermocycler Sun, Harris, Glowacka, others labs
- Flow cytometer 2nd floor common room, far north corridor
- FPLC Becker, Wilson labs
- HPLC/UPLC Khalimonchuk and Harris labs
- Seahorse Flux Analyzer Khalimonchuk lab
- Clarity RSM-spectrometer Becker and Khalimonchuk labs
- Microinjection system Khalimonchuk lab
- GC/MS Cahoon lab
- Bio-Rad Gel Doc 1st floor, 2nd floor common rooms
- Odyssey near-infrared imager 2nd floor common room and VanDyke lab
- Film developing equipment 2nd floor common corridors
- Stopped flow spectrofluorimeter Biophysical Core: contact Javier Seravalli
- Circular Dichroism Biophysical Core: contact Javier Seravalli
- ITC and DSC (calorimeters) Biophysical Core: contact Javier Seravalli
- Sonicator Becker, Wilson labs, and others
- Anaerobic glove box Becker lab
- High-speed centrifuge Lee lab, and others
- X-ray generator Zhang, and Wilson, first floor
Many additional common items are available, including autoclaves, dishwashers, walk-in warm and cold rooms, scintillation counters, low-speed ultracentrifuges, floor shakers for large scale culture, spectrophotometers, conventional thermocyclers. Inquire!