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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
  • Plant and Microbial Biochemistry
  • Synthetic Biology and Biotechnology
  • Biochemical Informatics

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 eight-week sessions during the semester (a third rotation may also be done during the summer before classes start or in the second semester). 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 four 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 members 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.

All CBC graduate students are required to take the following courses:

BIOC 836, Physical Basis of Macromolecular Function, 3 credits
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 take biochemistry seminar (BIOC 992k) each semester for a total of at least 8 credits. Each student will present two seminars per year, one of which is based on a current journal article of broad interest and the other a formal presentation of their laboratory research.

Students in the M.S. program take BIOC 992k for a total of at least 4 credits

Other course requirements are arranged in consultation with the Supervisory Committee. The student and advisor 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 involves 90 credit hours in which a third is coursework and the remainder thesis research. No more than 55 credit hours may be earned in dissertation research, and 35 credit hours must be in (PDF)Biochemistry offerings.

The Graduate Committee has prepared a (PDF) TABLE that outlines the graduate program requirements by semester. For convenience, this table also lists some sample specialty courses that can be chosen by students in consultation with their faculty mentor and supervisory committee. Questions can be addressed to the Graduate Committee Chair.

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 teach biochemistry laboratory courses for 2 semesters; additional teaching experiences in the undergraduate program are also available.

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 Allison Barnes asiekmanbarnes@gmail.com (Roston Lab),  or Sagar Patel sagar.patel1185@huskers.unl.edu (Becker Lab).

BGSA Meeting Minutes:
2015
2014

Departmental Equipment

 Joint with the Redox Biology Center, the department has Mass Spectrometry Instrumentation:

  • Bruker SolariX 7T Fourier Transform Ion Resonance SolariX - hybrid mass spectrometer allowing for simultaneous MS and MS/MS analysis using MALDI and ESI ionization sources for analysis of intact tissue molecular imaging for proteins and metabolites; peptide sequencing studies, structural determination of small molecules, and analysis of undigested intact proteins and their post-translational modifications (this unit is coupled with Agilent's nanoChip-HPLC for separation of complex mixtures in nano scale mode)
  • AB Sciex 4000 Q TRAP LC/MS/MS Systems equipped with nano flow LC-Packings UltiMate and Micro flow (Shimadzu UFLC XR) each equipped with an autosampler; Thermo-LCQ Fleet Ion Trap Mass Spectrometer – for routine analysis of complex samples
  • Thermo-LTQ Velos Pro Ion Trap Mass Spectrometer –for identification of post translational modifications and global proteomic profiling; Agilent 6410 Triple Quadrupole MS with Multimode Ionization Source (ESI, APCI, and ESI+APCI) linked to a 1200 Series Rapid Resolution LC (left stack: solvent tray, degasser, binary pump; right stack: RI detector, Diode array detector and equipped with a thermostatted column compartment, autosampler, and thermostat for autosampler.  
  • Agilent 7890A GC systems with SSL inlet linked to a 5975C VL inert MSD/DS Diffusion Pump EI System and equipped with autosamplers

Biophysical Instrumentation:

  • Jasco J-815 Spectropolarimeter with CD and ABS measurement modes (Wavelength range: 163 - 900nm; Scanning modes: Continuous scan, step-scan and auto-scan; Optics: Dual prism monochromator with collimated beam; Scanning Emission Monochromator, Wavelength range: 200-750nm; SFS-492 Stopped-Flow Accessory; Peltier thermoelectric temperature control system; and Fluorescence Polarization/Anisotropy Accessory)
  • MicroCal Microcalorimeters (Differential Scanning and Isothermal)
  • Inductively Coupled Plasma Mass Spectrometry (ICP-MS) for trace elemental analysis, equipped with an HPLC and an autosampler
  • Hi-Tech Stopped Flow System – for enzyme kinetics and equipped with sample handling unit, monochromator, photomultiplier power supply and diode array detector

Structural Biology Instrumentation:

  • Rigaku 007 Micromax generator with Osmic blue confocal optics and a Raxis IV++ detector. X-stream 2000 cryo assembly and Haskis water chiller
  • Robotic crystallization screening for small sample volumes; and incubators for crystallization trials

General Instrumentation housed within the Department of Biochemistry include: Bio-Rad Gel Doc systems; Li-Cor Odyssey imaging systems; BD X-Calibur flow cytometer with high throughput capabilities; Common Centrifuges (hi-speed and ultra, with a full complement of rotors); scintillation counters; gamma counter; constant temperature rooms (5˚C and 30˚C); darkrooms with automatic photoprocessors; 2 autoclaves and associated dishwashing capabilities

Center for Biotechnology Equipment

The Center for Biotechnology, housed within the Beadle Center provides:

  • Protein Core Facility has a Storm 860 Molecular Imager; a Beckman Optima Maz-XP and Optima TL 100 ultracentrifuges with 3 rotors each; a Beckman Proteome Lab XL-1 analytical ultracentrifuge; a Cary 14 spectrophotometer, and a Fuji Film FLA-5100 fluorescent scanner useful for imaging fluorescently labeled lipids on TLC plates.  The protein core also has 2-D protein gel systems, 2 Li-Cor Odyssey imaging systems, HPLC and FPLC systems useful for protein fractionation and purification.
  • Microscopy Facility that includes: Olympus FV500 Upright and Inverted Confocal Microscopes use confocal optics for high resolution, high contrast and increased resolution in the light axis direction. Acquisition functions include 3D construction, Z series sectioning, time series observations, sequential laser scan and image analysis functions. The confocal has 6 laser lines (405, 458, 488, 514, 543, and 633 nm) and can be used for multiple fluorescence labeling detection; Laser Capture Microdissection system (LCM, PixCell IIe from Aucturus) provides one of the best tools available to date for isolation of individual cells or specific populations of cells, or bacteria of interest from tissue sections for further molecular and biochemical analyse; and Advanced fluorescence microscopes with high-sensitivity digital cameras: Olympus AX70 upright fluorescence microscope and Nikon TE-300 inverted fluorescence microscope; and a Nikon SMZ-800 stereo fluorescence microscope.
  • Bioinformatics Core Research Facility (BCRF) provides computational support for molecular biology, genomics, proteomics and other biological related disciplines. The BCRF is equipped with high-performance computer hardware, specialized software, and advanced database systems. The main focus of the BCRF is on database systems and the various bioinformatics tools used to mine for useful information. Services of consultation, data analysis, software training, and database support are mainly provided to the University of Nebraska-Lincoln research community and its partners. We also assist in fostering collaborative projects seeking to integrate modern computational techniques in the research activities.  All members of the university academic community have access to the standard services of the BCRF at a cost-recovery rate.

Many additional common items are available in the Department of Biochemistry and Beadle Center, including  low-speed ultracentrifuges, floor shakers for large scale culture, spectrophotometers, conventional thermocyclers. Inquire!

Graduate Courses

All students are required to take:

  • BIOC 932 (Proteins)
  • BIOC 933 (Enzymes)
  • BIOC 934 (Genome Dynamics and Gene Expression)
  • BIOC 935 (Metabolic Function and Dysfunction)

All students in the Ph.D. program are required to take biochemistry seminar (BIOC 992k) each semester for a total of at least 8 credits. Each student will present two seminars per year, one of which is based on a current journal article of broad interest and the other a formal presentation of their laboratory research.

Students in the M.S. program take BIOC 992k for a total of at least 4 credits

Other course requirements are arranged in consultation with the Supervisory Committee. The student and advisor 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 involves 90 credit hours in which a third is coursework and the remainder thesis research. No more than 55 credit hours may be earned in dissertation research, and 35 credit hours must be in (PDF)Biochemistry offerings.

The Graduate Committee has prepared a (PDF) TABLE that outlines the graduate program requirements by semester. For convenience, this table also lists some sample specialty courses that can be chosen by students in consultation with their faculty mentor and supervisory committee. Questions can be addressed to the Graduate Committee Chair.