Program Description

Goals of the Program and Rationale for the Program Organization

Predoctoral trainees will be selected from a pool of graduate students who have been recruited by the Chemistry, Biochemistry, Molecular Biology & Biophysics, and Medicinal Chemistry Departments, at a stage in their graduate careers when their talents and motivations can be gauged by their performance in University of Minnesota coursework and their interactions with several of the faculty. Thus, trainees will generally be chosen from the pool of graduate students in participating departments at the end of their first or second year. Under unusual circumstances, new applications from students beyond their second year may be supported by the program.  However, applicants beyond their second year should consult with the PI before applying.

Once appointed, trainees will become immersed in an enriched menu of training experiences. After a maximum of two years’ support by the training grant, students will normally be supported by the NIH (or other) research grants of their primary advisors. The defining characteristic of our program will be to continue to allow first-rate students to grow into accomplished professionals both in their primary area of interest (e.g., synthetic/mechanistic chemistry, molecular biology, mechanistic enzymology, medicinal chemistry) and in a complementary field by cross-discipline research interactions and experiences.

Research Opportunities and Cross-Discipline Training

Research opportunities are available in each of 30 training faculty laboratories. Each trainee will have a research advisor in his/her major field of interest and a coadvisor in the complementary area chosen from among the members of the CBITG faculty. As an additional mechanism to ensure cross-training, the trainee will generally spend a significant period of time during their training period (i.e. ~3 months) in the laboratory of the co-advisor to learn skills in the other discipline. In other words, the trainee's project will be set up to have both chemistry and biology components, and the trainee will be involved in both aspects. Thus, trainees would not only develop skills corresponding to their natural background and interests, but also become knowledgeable and proficient in new research environments. By spending a significant amount of time in a laboratory other than that of their primary advisor, students would learn new techniques and experience first-hand the obstacles, failures, tricks, and triumphs of the ‘other half’ of the chemistry/biology interface.

Due to the unpredictable nature of scientific research, a trainee’s project may either move forward too slowly (e.g., a total synthesis is not completed in the first two years so biological testing is not possible), or move in a direction that is not compatible with hands-on cross training in the co-advisor’s lab during the 2-year period of training grant support. In these cases, the cross-training will be expected to occur later in the student’s graduate training. To ensure that significant exposure to the complementary discipline is still received during the period of training grant support, all trainees will be asked to attend group meetings in the co-advisor’s lab on a regular basis and also to present their work at regular intervals. Students will be expected to participate in the planning and running of the Annual Training Grant Symposium (see http://www.chem.umn.edu/bio/symposium2011) and attend appropriate seminars in the disciplines of their advisor and co-advisor. 

Coursework

Coursework: Trainees will be chosen from the Chemistry, Medicinal Chemistry, and BMBB graduate programs. Students in those programs are typically required to take six courses (24 credits) as the minimum for an acceptable graduate program. To provide a true interfacial training experience while retaining individual flexibility, trainees will be expected to take two courses from outside their department (within the other two departments participating in the training program).  This coursework plan significantly augments trainees' depth of knowledge of the chemistry-biology interface and provides them with the tools necessary to think more critically about their own research and that of others, while not introducing an overly onerous barrier to their research progress.

Flexibility in course selection is important given the diverse training needs for each trainee’s research. However, the majority of trainees enroll in CHEM 8411 (Foundations of Chemical Biology) to provide them with a basic understanding of methods and current problems in chemical biology. Thus, a possible course plan would include CHEM 8411, MCHEM 8001 (General Principles of Medicinal Chemistry) and BIOC 8007/8 (Molecular Biology of the Genome/Transcriptome). However, there is no prescribed list.  Exceptions for coursework outside the three departments that fulfills the goals of the interdisciplinary coursework such as computational, programming, or statistics courses can be approved by the Program Directors (see below). Beyond the above courses, the list below gives several popular alternatives taken by trainees but is not exhaustive:

A set of 3 suggested courses for trainees is listed below. Students taking all three of those courses would satisfy the above requirements.

A course in Biochemistry: BioC 4331, BioC 4332, BioC 8001 or BioC 8002

Chem 8411 Introduction to Chemical Biology: Covers the chemistry of proteins and nucleic acids with a focus on chemical methods used to study biological problems.

MedC 5245 Introduction to Drug Design: Concepts that govern design/discovery of drugs. Physical, bioorganic, medicinal chemical principles applied to rational design and mechanism of action.

 In addition to the above courses, the list below gives a number of popular alternatives. However, this list is not exhaustive.

Chem 8011 Mechanisms of Chemical Reactions: Covers principles that govern organic, inorganic, and enzyme reaction mechanisms and how reactions are studied.

Chem 8412 Chemical Biology of Enzymes: Covers structure, thermodynamics, dynamics and kinetics of enzymes with an emphasis on how enzymes catalyze chemical reactions.

Chem 8765 Bioinorganic Chemistry: Covers metalloenzyme structure and function, model complexes, metal-nucleic acid interactions, and metals in medicine.

Chem 8134 Bioanalytical Chemistry: Covers analytical techniques  with  important  applications  to biochemical  problems. 

BioC 5527 Introduction to Modern Structural Biology: Methods employed in modern structural biology to elucidate macromolecular structures. Primary focus on X-ray diffraction, nuclear magnetic resonance (NMR) and mass spectrometry. Principles underlying structural biology and structure/function relationships.

BioC 5528 Spectroscopy and Kinetics: Biochemical  dynamics  from  perspectives  of   kinetics  and spectroscopy. Influence of structure, molecular interactions, and chemical transformations on biochemical reactions. Focuses on computational, spectroscopic, and physical methods. Steady-state and transient kinetics. Optical and magnetic resonance spectroscopies.

BioC 5331 Macromolecular Crystallography I: Fundamentals and Techniques. Macromolecular crystallography for protein structure determination/engineering. Determining  macromolecule  structure  by diffraction.

BioC 5332 Macromolecular Crystallography II: Techniques and Applications. Determining structure of macromolecule by diffraction. Using software in macromolecular crystallography.

MedC 8413 Nucleic Acids: Covers the chemistry and biology of nucleic acids, including structure, thermodynamics, reactivity, DNA repair, chemical oligonucleotide synthesis, antisense approaches, ribozymes, techniques used in nucleic acid research, interactions with small molecules and proteins.

MedC 8700 Combinatorial Methods in Chemical Biology: The  emphasis  in  this  course  is  on understanding the general principles of current combinatorial methods for the generation of  biological  and chemical libraries with an emphasis on their utility in biology and drug design.

Given the growing needs of trainees in diverse disciplines and differences in trainee backgrounds including computation and statistics, trainees may opt to replace one course outside of the three departments with permission of the Program Directors.  Recommended examples include:

BICB 8510 Computation and Biology: Provides topic overviews in molecular biology and genetics; mathematics, statistics and biostatistics; programming in FORTRAN and C/C++; programming in Perl; data management; data mining.

CSCI 5465 Introduction to Computing for Biologists: Teaches fundamental computing skills for developing computational approaches for interpretation of scientific data using Python and R.

PUBH 6450 Biostatistics I: Explores the basic concepts of statistical inference, including: descriptive statistics, hypothesis testing, ANOVA, simple regression/correlation, multiple regression, uses output from statistical packages, and teaches R programming language skills.

Trainee Candidates

Trainees are selected by an ad hoc committee appointed by the CBITG Director.

Nomination materials will consist of the results of all courses taken during the first year, two nomination letters (typically from the advisor and the co-advisor), and a short (1-2 page) description of the research project that is written by the candidate and clearly outlines the goals of the research project and its cross-disciplinary features. A candidate will not be appointed a trainee unless the project has both chemistry and biology components. Because of the large number of highly qualified candidate trainees anticipated, each trainee will be appointed with the likelihood of receiving two years (24 months) of support.

Monitoring Trainee Progress

Re-appointment for the second year of CBITG support requires that the trainee submit evidence that satisfactory progress has been made toward meeting the departmental requirements for completion of written and oral Ph. D. candidacy examinations and that the trainee has actively participated in training activities. Each year, the trainee will submit a short written report to the training grant Director detailing research progress, current and future directions, and efforts to incorporate cross-disciplinary training. A meeting between the trainee, the trainee’s advisor and co-advisor, and the steering committee will be held to discuss the report and the trainee’s progress. These meetings will provide another opportunity for trainees to discuss their research with faculty in an informal setting, and will also provide students with valuable feedback at a relatively early stage in their graduate training. Re-appointment for a second year will be denied if there is not satisfactory progress or a plan in place to incorporate cross-disciplinary training.