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 Graduate Program Handbook

Center for Biological Chemistry
Graduate Program Description

Through a combination of coursework, seminars, and original research, you will complete a Graduate degree and acquire the skills needed to become an independent research scientist. Our four major training areas emphasize:

  • Structural and chemical basis of protein function
  • Metabolism and metabolic engineering
  • Molecular mechanisms of disease
  • Plant biochemistry and applied agriculture

                    Orientation

The Graduate Committee will assist you in your initial course selections and research rotation choices. You will have a guidance interview with the Graduate Committee to learn about the program in Biochemistry and choose courses for the first semester. A poster session will be held to allow you the opportunity 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 you think about choosing a research advisor and Supervisory Committee.

                    Thesis advisor selection

The major component of your graduate degree is a thesis that describes original research YOU conduct in the lab of a faculty advisor YOU select.
          Students typically choose an advisor based on a shared research interest and/or a good rapport with that faculty member. Many students entering the graduate program will have limited experience upon which to base this important career decision. We recommend that you do at least two “rotations” in your first semester, i.e.; work in a lab for a short time on a trial basis. The program is set up to allow you to rotate for two 8-week sessions during the semester (a third rotation may also be done during the summer before classes start). You will choose your first rotation after interviewing faculty whose research attracted you during the poster presentations, and make your second choice at the end of the first 4 weeks when you have had an opportunity to acclimate. After the second rotation, all students will submit their choices for an advisor to the Graduate Committee, and final assignments will be made.

                    Supervisory committee

Sometime in your second semester, you will confer with your research mentor to form a Supervisory Committee. The purpose of this committee is to evaluate your progress in the degree program, to offer a support network within the University, and to assist you with practical guidance in your research project. Your committee is chaired by your research advisor and must consist additionally of three other Biochemistry faculty and one faculty member from outside the Department.
          In May of each year, you will schedule a meeting with your Supervisory Committee. At the meeting, you will present a 20-30-minute talk about your research progress to date, and your goals for the coming year. The Committee will question you during your presentation to ascertain your level of development as a scientist, and will advise the Graduate Program Committee whether you are making satisfactory progress toward the degree objective. If progress is deemed insufficient, it is also the responsibility of the Supervisory Committee to forward recommendations for improvement, probation or termination where warranted.

                    Courses

All CBC graduate students are required to take the following 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

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 then submit a Program of Studies that details the student’s course work requirements to the Graduate College before one half of the courses are complete.

Successful completion of the Ph.D. degree requires 90 credit hours, of which 35 cr 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).

                    Comprehensives

Students in their fifth semester must pass a Comprehensive Examination consisting of written and oral components. The exact nature of this Exam is determined by the Supervisory Committee. Typically, you are asked to write a research proposal in the style of an external grant application on a topic of your choosing. The topic must be different from your advisor’s and your own research area. You then schedule a meeting with your Supervisory Committee at which you will give a presentation of your proposal and defend against the Committee’s questions. We ask that you circulate the proposal to the members of your committee approximately two weeks before the meeting. The exam will probe the depth and breadth of your biochemistry knowledge, and the sophistication of your scientific thought process.
          Passing the Comprehensive Examination results in your being recommended for Ph.D. candidacy. You must be admitted to candidacy at least 7 months prior to your final oral dissertation defense. Also, the Graduate College has a rule that if a student does not graduate within three years of passing the Comprehensive Examination, the Supervisory Committee must give another such exam.

                    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, publicized 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 of international renown present their research at the invitation of our own faculty.

                    Teaching

Learning to communicate effectively in a teaching capacity is also critical to your future career as a scientist. To facilitate this aspect of your development, you will be required to assist with teaching biochemistry courses for 2 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. Madhavan.
          International students 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.

                    Timeline for Ph.D.

Average time to completion of a Ph.D. is a little over 5 years. How does that break down in milestones for students?
First year: complete core courses in Biochemistry; first year of seminar
          • First semester: rotations and selection of a lab
          • Second semester: selection and first meeting of supervisory committee; select coursework for second year of study.
Second year: continue/complete all coursework; continue meeting research and seminar requirements
          • Second semester: second meeting of supervisory committee; select format / topic for written and oral comprehensive exams.
Third year: continue meeting research and seminar requirements; first semester of teaching
          • First semester: complete written and oral comprehensive exams
          • Second semester: third meeting of supervisory committee
Fourth year: continue meeting research and seminar requirements; complete teaching assignment
          • Second semester: fourth meeting of supervisory committee; discussion of time to graduation
Fifth year: complete research; write thesis; final defense of thesis work; final examination by supervisory committee; Ph.D. conferred

                    BGSA

Graduate students in the Department formed the Biochemistry Graduate Student Association (BGSA). The purpose of this organization is to represent our graduate students in communications among members of the Biochemistry community, 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 Co-Chairs Caitlin McAtee (Simpson Lab, comcatee@huskers.unl.edu) or Annastasia Hyde (Barycki/Simpson Lab, annastasia.harris@huskers.unl.edu).

Research equipment

                    Core facilities

Bioinformatics (http://bioinformatics.unl.edu)
Mass Spectrometry and Metabolomics (contact Renu Nandakumar rnandakumar2@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 (conact Charles Kuszynski ckuszyns@unmc.edu)

                    Departmental Equipment

The Biochemistry Department has numerous pieces of shared equipment available for
use by any member of the Department. Below is a list of this equipment and its current
location. Please contact the appropriate lab before using instruments.

Analytical ultracentrifuge - - - - - Dr. Don Becker
Dynamic Light Scattering - - - - - Barycki lab
Absorbance plate reader - - - - - Simpson lab
Fluorescence plate reader - - - - - Barycki lab
Luminescence plate reader - - - - - Simpson lab
Real time PCR thermocycler - - - - - Simpson lab
Flow cytometer - - - - - 2nd floor common room, far north corridor
FPLC - - - - - Becker lab, Barycki lab
HPLC - - - - - Fomenko (?) lab
GC/MS - - - - - Madhavan, Cahoon, Black/DiRusso labs
Bio-Rad Gel Doc - - - - - 1st floor, 2nd floor common rooms
Odyssey near-infrared imager - - - - - 2nd floor common room
Film developing equipment - - - - - 1st floor, 2nd floor common corridors
Stopped flow spectrofluorimeter - - - - - Barycki lab, contact Javier Seravalli
Sonicator - - - - - Becker, Barycki labs and others
Hypoxic cell culture - - - - - Simpson lab
Anaerobic glove box - - - - - Becker lab
High-speed centrifuge - - - - - Stone, Lee, Barycki labs and others
X-ray generator - - - - - Barycki 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!