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South Dakota State University    
 
    
 
  Sep 24, 2017
 
2017-2018 Graduate Catalog

Biochemistry (Ph.D.)


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Program Coordinator/Contact
Douglas Raynie, Department Head
Matthew Miller, Graduate Program Coordinator
Department of Chemistry and Biochemistry
Avera Health Science Center 131, Box 2202
605-688-5151
E-mail: gradchem@sdstate.edu
www.sdstate.edu/chemistry-biochemistry

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 photo-biochemistry.

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 Sanford Research and the Avera Research Institute in Sioux Falls, SD. The partnerships with the biomedical research programs at Sanford Research and the Avera Research Institute also provide a unique opportunity for research that translation basic science into clinical treatments that directly impact patient treatment. For additional information about these options student should review the descriptions of current faculty research interests at chembiochem.sdatete.edu.

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 7T ESI FTMS; 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; and a Varian GCMS.
  • 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.
  • Powder x-ray diffractometer
  • 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 microscope, 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 an Isothermal Titration Calorimetry. Campus computer facilities (including a Beowulf supercomputer cluster) are readily available.  Individual groups maintain their own system 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, for FRET microscopy, laser light scattering, and computational chemistry. Campus super-computer facilities and on-line computer access to Web of Science, Chemical Abstracts Services and 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 newly constructed Avera Health Science Center South and newly renovated Avera Health and Science Center North. Combined, these connected facilities provide 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


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.

Candidacy Examinations


The Department uses a cumulative examination process as its written candidacy (comprehensive) examination for the doctorate in Biochemistry. A student must pass a total of five cumulative examinations: two in biochemistry and one in biophysical (or one in biochemistry and two in biophysical) with the remaining cumulative exams completed across two of the three remaining subdisciplines of biochemistry (e.g., molecular biology, structural biology, or cellular biology).  These exams must be passed over a period of two calendar years (24 possible tests). The oral candidacy (comprehensive) 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.

General Requirements


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

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

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