Biochemistry (Ph.D.)

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Program Coordinator/Contact

Douglas Raynie, Department Head
Jihong Cole-Dai, Graduate Program Coordinator
Department of Chemistry and Biochemistry
Avera Health and Science Center 131, Box 2202
605-688-5151

Program Information

The Department’s biochemistry faculty research programs focus on the chemistry and biochemistry of cell membranes, multi-scale modeling of signal transduction in macromolecular assemblies, development of FRET-imaging technologies to measure the location and dynamics of direct protein interactions, biophysical chemistry underlying cell-surface control of leukocyte function, structural biology, proteomics, protein function, the cellular biochemistry of disease and cancer, and photobiochemistry.

This program is unique in that a student can chose their dissertation research over a broad range of research projects available in the Department or in the laboratories of participating program faculty at the Sanford and Avera Research Institutes in Sioux Falls, SD. The partnerships with the biomedical research programs at these research institutes also provides a unique opportunity for research that translates basic science into clinical treatments that directly impact patients. For additional information about these options review the descriptions of current faculty research interests on the Department website.

Student Learning Outcomes

Comprehensive disciplinary knowledge: Graduate degree recipients will possess comprehensive disciplinary knowledge with high competence.
- Ph.D. degree recipients will be able to demonstrate knowledge of the chemistry discipline, appropriate sub-discipline and related scientific disciplines (e.g., biochemistry, biology, mathematics, physics, environmental science) and be cognizant of the disciplinary development frontier.
- Ph.D. degree recipients will be able to define scientifically meaningful research issues, develop competitive proposals, and contribute to knowledge creation through research.
- Graduate degree recipients will be prepared to demonstrate knowledge and technical skills in a large variety of professional fields, careers and endeavors.
- Graduate degree recipients will communicate effectively in an oral, written and visual manner to technical audiences and stakeholders.
- Graduate degree recipients will possess and practice high standards of scientific integrity and professional ethics. (Communication Skills)
Trans-disciplinary professional skills: Graduate degree recipients will possess trans-disciplinary professional skills.
- Graduate degree recipients will apply creativity to innovation.
- Graduate degree recipients will recognize the importance of workplace diversity in culture, gender, perspective, and experience.
- Graduate degree recipients will work effectively with peers and develop mentoring skills.
- Graduate degree recipients will develop an understanding of the intellectual property process and the business needs of their workplace. (Transferable Skill: Mentoring; Diversity Awareness; Entrepreneurship)
Familiar with research literature: Students will be familiar with the research literature of their chemistry subdiscipline and have the ability to keep abreast of major developments to acquire a working background in any area. (Communication Skills)
Recognize meaningful problems and questions: Students will be able to demonstrate skill in the recognition of meaningful problems and questions for research.
Technical laboratory skills: Students will possess technical skill in laboratory manipulation.
Design experiments and conduct research: Students will be able to demonstrate skill in designing experimental protocols and in conducting productive self-directed research.

Research Instrumentation

The Department is equipped with modern instrumentation core facilities to support its research program. These facilities are readily available to graduate students for hands-on experience after successfully completing a short training course.

NMR core facility includes 600, 400, and 200 MHz solution FT-NMR spectrometers and 400, 300, 100 MHz wide-bore solid-state NMR spectrometers
Core campus mass spectrometry facility consists of a high-resolution magnetic sector mass spectrometer with EI and CI sources and GC, HPLC, pyrolysis and fast-atom bombardment capabilities; a MALDI-TOF mass spectrometer; a Eksigent/Thermo LTQ ESI LC-MS/SM dedicated to “bottom-up” proteomics studies; and an Applied Biosystems SCIEX QTRAP ESI LC-MS/MS dedicated to small molecule and metablomics characterizations.
Core campus proteomics facility has all the necessary equipment to prepare samples for mass-spectrometry-based proteomics characterizations.
Optical Spectroscopy lab containing 2 FT-IR spectrometer with far-IR capabilities; time-resolved spectrofluorometer; atomic absorption and diode-array UV-Vis spectrophotometers.
The Department is home to multiple state of the art fluorescence microscopes for the analysis of biochemical reactions involving purified molecules and within living cells. These instruments including spinning disk confocal microscopy, total internal reflection fluorescence (TIRF) microscopy, targeted photo-bleaching, instrumentation of for ensemble and single-molecule fluorescence-resonance energy transfer (FRET) experiments and fluorescence-correlation spectroscopy, and optogenetics capabilities. The department also houses cell/tissue culture facilities, large- and small-scale protein-purification equipment and biophysical characterization capabilities including isothermal titration calorimetry. Campus computer facilities (including a Beowulf supercomputer cluster) are readily available. Individual groups maintain their own systems for molecular modeling, word processing or data manipulation. Direct, on-line computer access to chemical and biochemical literature databases such as Chemical Abstracts and Web of Science are provided by the Department.
In addition to these departmental resources, individual research groups also maintained instrumentation including supercritical fluid chromatography and extraction, thermal analysis, laser light scattering, and computational chemistry. Campus supercomputer facilities and on-line computer access to other on-line information sources are readily available.

Course Delivery Format

Courses offered in the Ph.D. in Biochemistry curriculum are taught in a variety of formats which address student learning outcomes. Didactic (lecture) methods ensure the development of advanced knowledge of chemistry. Practical (laboratory) methods ensure the development and maturation of laboratory skills and training and these opportunities are developed in the research laboratory. A combination of didactic and practical methods ensures the successful completion of the graduate dissertation research project.

Facilities and Services

The Department is housed in the Avera Health and Science Center, which provides 100,000 sq. ft. of research and instructional space.

Available Options for Graduate Degrees

Doctor of Philosophy	60 Credit Plan
	90 Credit Plan

Core Requirements

60 Credit Plan

CHEM 790 - Seminar (COM) Credits: 1 (2 credits required)
CHEM 898D - Dissertation - PhD (COM) Credits: 1-12 (minimum of 18 credits)
and/or other coursework as required by Graduate Student Advisory Committee

90 Credit Plan

The core coursework (12 credits of coursework and 3 credits of laboratory rotations) covering basic concepts in biochemistry and research ethics provides disciplinary breadth and a foundation for a student’s plan of study. To support the interdisciplinary nature of the planned dissertation research project and provide depth in a subspecialty within the field, 9 credits of elective coursework are chosen by the student and their graduate advisory committee. Three additional credits of seminar are required. The remaining credits in the 90 credit plan of study are dissertation research. Students must develop their program of study in consultation with their graduate research advisor and graduate advisory committee during the first semester in residence.

BIOS 662 - Advanced Molecular Biology Credits: 3 (3 credits required)
BIOL 743 - Cell Biology (COM) Credits: 3
CHEM 548 - Biophysical Chemistry Credits: 3
CHEM 705 - Principles of Biochemistry Credits: 2-5 (3 credits required)
CHEM 760 - Laboratory Rotations in Biochemistry Credits: 1-2 (3 credits required)
CHEM 790 - Seminar (COM) Credits: 1 (3 credits required)
CHEM 898D - Dissertation - PhD (COM) Credits: 1-12 (62 credits required)
GSR 601 - Research Regulations Compliance Credits: 1
Electives Credits: 9
Courses may be selected from STEM disciplines (e.g. BIOL, BIOS, CHEM, MATH, or STAT prefixes)

Candidacy Examinations

The Department uses a comprehensive examination process as its written candidacy examination for the doctorate in Biochemistry. The exam is offered annually with all biochemistry faculty contributing equally to the exam. The exam is to be taken after the student has substantially completed the required coursework and the exam will cover the content presented in the required coursework. The oral candidacy exam takes place within a year of completion of the cumulative exams. For the oral examination, students are required to develop and write an original research proposal and defend it orally. In order to successfully defend such a proposal the student must be able to integrate their coursework into the proposed research, and the oral defense reflects that expectation.

Additional Admission Requirements

GRE: General and subject score are recommended but not required
TOEFL: Score of 580 paper-based, 92-93 Internet-based
IELTS: 5.5

Applications are accepted for admission to the Ph.D. program in fall only. Students are strongly encouraged to submit their applications for admission no later than January 15. Initial offers of admission will be made no later than the first week of February.

In addition to the materials required by the Graduate School, the Department of Chemistry and Biochemistry requires the following application materials:

A one- to two-page personal statement which includes a description of undergraduate research, work experience, or other factors demonstrating a propensity toward graduate studies. The personal statement should also include a statement of the applicant’s career goals. The applicant may upload this statement while completing the Graduate School’s online application.
Three letters of recommendation, preferably at least one from faculty at the applicant’s undergraduate institution. Letters should come from faculty who are directly familiar with the applicant’s academic work. They must address the applicant’s scholarly potential and may also speak to the applicant’s potential for graduate studies in the discipline. Letters should come directly from the recommenders, who may submit their letters electronically along with the personal recommendation form provided by the Graduate School. The Graduate School will email recommenders detailed instructions for submitting their recommendations using the contact information provided by the applicant.

General Requirements

Graduate students must consult with their advisor before registering for graduate coursework.

For additional information refer to the Doctor of Philosophy Degree Requirements .