Course Curriculum

Selected Courses Available for STTP Predoctoral Trainees, the GEMS Program,
and Courses offered by Participating Basic Science Departments

Selected courses available to STTP trainees that are most highly relevant to training in signal transduction, gene transcription and cellular endocrinology are listed below. These courses are designed to provide a strong foundation in the fundamental disciplines and in the interdisciplinary areas of the Training Program. These courses cover the areas of signal transduction and related fields, cell biology and cellular endocrinology, biochemistry and molecular genetics, structural biology and molecular biophysics, and importantly, course focused on training to succeed in a scientific career. Several of the courses were developed and implemented specifically for this training program and were not available before its inception, while others are more fundamental core courses taken by all incoming students in the GEMS program, regardless of their immediate or ultimate departmental affiliation. The list also includes the core GEMS curriculum taken by all graduate students in the College of Medicine, as well more specialized courses offered by the participating Departments, which includes courses meeting their individual Ph.D. requirements. The current core curriculum of the GEMS program was purposefully and completely redesigned and courses revamped for implementation of this interdepartmental/interdisciplinary program. After students choose their mentors, they must take other courses needed to fulfill the course requirements of the graduate programs in their respective departments, and these courses provide more specialized training in their chosen area of research.

I. COURSES SPECIFICALLY RELEVANT TO THIS TRAINING PROGRAM

i. Signal Transduction and Related Fields

Receptor Pharmacology & Cell Signaling (GCLS 515). Course Directors: T. Kozasa (STTP faculty member), T. Voyno-Yasenetskaya (STTP faculty member), and R. Ye (STTP faculty member). This is an advanced course on the molecular pharmacology of signal transduction mechanisms in cells. The course includes an overview of receptor theory, hands-on data analysis, lectures on various receptor-mediated signaling mechanisms, student presentations and discussions of selected papers. The emphasis is to provide fundamental knowledge of molecular mechanisms of cell signaling, as well as to expose students to the most updated progress in the field. Major topics covered include (1) Receptor Theory, (2) Signaling through G-protein coupled receptors; Heterotrimeric G proteins, Low molecular weight G proteins; Effectors and regulators of G-protein signaling pathways, (3) Signaling through enzyme-linked receptors; Receptors with tyrosine kinase activity; Cytokine receptor signaling, (4) Signaling through ion channels, and (5) Signaling through nuclear receptors.

Molecular Pharmacology of Platelets, Thrombosis and Vascular System (Pcol 510). Molecular mechanism and therapeutic approaches to: platelet functions, thrombosis, hemostasis, and vascular biology. The platelet as a model cell for molecular mechanisms of intracellular signal transduction and cell adhesion.

Ion Channels: Structure, Function, Pharmacology and Pathology (Pcol 540). The concept of ion channels is treated from the perspectives of their molecular structures and functions. Modulation, pathological conditions (channelopathies), and pharmacological intervention will also be addressed.

Advanced Immunology (MIm 551). Concepts in immunochemistry, immunogenetics, molecular immunology, cellular immunology and immunopathology.

Cellular and Systems Neurobiology (ANAT 527). Molecular and cellular properties of ion channels in neurons and sensory cells and their relationship to brain and sensory systems.

Cell and Molecular Neurobiology (ANAT 586). Structure and function of voltage-dependent and neurotransmitter-gated ion channels; the role of these ion channels in synaptic transmission, synaptic modification, and neuromodulation.

Biological Signal Analysis (BIOe 440). Analysis of signals of biological origin. Transient signals. Stability analysis. Control Mechanisms. Probabilities, stochastic processes, Medical applications.

Molecular Basis of Cell Growth and Differentiation (Gene 513). Oncogenes, tumor suppressor proteins and growth factors, and their roles in tumorigenesis, cell growth, differentiation and development.

Signal Transduction Colloquium: An approximately monthly informal series in which trainers and trainees, as well as invited speakers, meet to review and discuss new results and hot topics in signal transduction.

ii. Endocrinology:

Endocrinology (PhyB 501). Review of the field of endocrinology is followed by a systematic consideration of new concepts in endocrine gland and mechanisms of hormone action. Attention is on the most important areas of research currently being pursued in the field.

Neuroendocrinology (ANAT 554). Survey of neuroendocrine integration including neuroendocrine regulation of development, homeostasis, reproduction, and behavior. The hypothalamohypophyseal axis receives special attention from both morphologic and functional viewpoints.

iii. Cell Biology:

Cell Biology (PhyB 585). Functional and structural organization of the cell with emphasis on the cellular basis of physiological activity.

Cell Physiology (PhyB 586). Advanced functional and structural organization of the cell with emphasis on the cellular basis of physiological activity.

iv. Biochemistry and Molecular Genetics:

Biochemistry of Cellular Regulation (Bche 561). Membrane structure and function, transport, receptor and signal transduction mechanisms and growth factors. Cytoskeleton and motility, cell-cell communication, enzyme cascades and cellular control mechanisms are also covered.

Gene Structure and Function (Bche 562). DNA organization and gene structure, transcription and translational control of gene expression. Emphasis given to the regulation of gene expression in selected developmental systems.

Somatic Cell and Human Genetics (Gene 502). The genetics of somatic cells and advanced human genetics. Gene transfer, mutagenesis, drosophila genetics, genetic linkage and human disease, cancer genetics, and gene therapy.

Molecular Basis of Cell Growth and Differentiation (Gene 513). Oncogenes, tumor suppressors, proteins and growth factors, and their roles in tumorigenesis, cell growth, differentiation and development.

Molecular Aspects of Microbiology (MIm 554). Basic concepts of prokaryotic and eukaryotic genetics: gene structure and function; molecular aspects of mutation and recombination; chromosome structure and function.

v. Structural Biology and Molecular Biophysics:

Structure of Biopolymers (BCHe 513). Explores the relationship between structural stability, kinetic properties and function of biopolymers, with particular emphasis on proteins and nucleic acids. The course deals with the application of modern spectroscopic, crystallographic, kinetic, hydrodynamic, and thermodynamic methods to answering important biochemical questions at a molecular level.

vi. Training to Succeed in a Scientific Career:

Scientific Integrity and Responsible Research (GC401). Designed to meet NIH requirements for formal training in the responsible conduct of research. Ethical and legal issues in the conduct of research, and UIC research standards, regulations, and procedures. Good laboratory practices, academic integrity issues, including plagiarism, copyright, authorship, ownership of data, ideas, etc., and sexual harassment. Scientific integrity & conflict of interest, human subjects and survey research and ethical issues in the use of animals in research (See Table 6 for greater curriculum detail and other available seminars).

Strategies for Effective Scientific Communication (BCHe 522). Development of critical skills for evaluation, development, and execution of forms of scientific communication, including research and grant proposals, manuscripts describing original research, and review summaries.

Investigator 101 - What Researchers Need to Know Before Human Subjects Research Can Start. Offered throughout the year, Investigator 101 covers the history of research ethics, ethical principles and The Belmont Report, development and application of the federal regulations for human subject protections, UIC's Federal-wide assurance and policies, criteria for review of research, informed consent process, research protocol review processes, and the application of the ethical principles and regulatory requirements.

CITI "Core" Online Course. This web-based course takes three to six hours to complete depending on an individual's prior knowledge and experience with research, ethical principles and regulations about human subject protections and CITI course requirements.

Essentials for Animal Research (GC 470). Will acquaint the students with the regulations, sources of information, humane principles and ethical considerations involving the appropriate use of animals for research and teaching purposes. Completion of GC470 is a requirement for all graduate students at UIC using vertebrate animals for thesis research. As well, all investigators and research personnel including predoctoral trainees performing animal research on approved ACC protocols must complete the on-line training course "Animals and Research at UIC - What Investigators Need to Know and Why?

Experimental Animal Techniques (GC 471). Noninvasive and invasive techniques commonly used in laboratory animals are performed with emphasis placed upon the proper use of anesthetic, analgesics and aseptic techniques. Satisfactory/Unsatisfactory grading only. Animals used in instruction. Prerequisite(s): GC 470.

Seminars and Journal Clubs (Anat 595; BMG 595; MIm 595; Pcol 595, PhyB 595). Department-based graduate student presentations and in-depth discussions of research subjects of current importance in anatomy, biochemistry, molecular genetics, molecular biology, bacteriology, virology, immunology, pharmacology, physiology, biophysics, and signal transduction.

Special Topics in Biochemistry and Molecular Geneticfs (BCHe 594). Topics of current interest in the field of biochemistry, and may include NMR structural studies, proteinases and their inhibitors, gene regulation, signal transduction, and transcription factors.

Special Topics in Microbiology, Immunology and Virology (Mim 594). Advanced topics are covered in depth. Topics vary yearly.

Special Topics in Pharmacology Research (Pcol 594). Organized presentation and discussion of rapidly developing research areas in molecular, cellular and systems pharmacology.

Special Topics in Physiology & Biophysics (PhyB 594). Topics may include bioengineering, endocrinology, membrance biology, ion transport and its regulation, muscle physiology, neurophysiology, molecular neurobiology, and others of current significance in physiology and biophysics.

II. CORE CURRICULUM OF THE GRADUATE EDUCATION IN MEDICAL SCIENCES PROGRAM (GEMS)

In the first year of the GEMS program, students take a core curriculum that provides them a strong base in the fundamentals of biochemistry, molecular and cell biology and integrated physiology. In the second semester, students pursue their own interests and choose from among several core courses that span a variety of advanced topics. In the first year students also have the opportunity to take four methods modules of their choice. In addition, students must take GC 401-Scientific Integrity and Responsible Research, and some students take GC 470-Essential for Animal Research if their research will involve animals.

Research Rotations:
An integral part of the new interdepartmental graduate program in the College of Medicine, GEMS, is the student research experience. As part of the new program we have students do 3 research rotations in the various academic departments associated with the GEMS program. These rotations not only provide students with valuable hands-on laboratory experience, but also allow them to make an informed decision about which laboratory to join for their Ph.D. research project.

Additional training experiences:
While participating in research rotations, first year students are also expected to attend departmental journal clubs and research seminars in the department in which they are performing their rotation.

Semester I: All courses required

Biochemistry (GCLS 501) Course Directors: P. Gettins (STTP faculty member), S. Lam. This course is taken by all basic science graduate students in the College of Medicine as well as students from other colleges, most prominently Bioengineering and Pharmacognosy. The course presents selected topics in depth, appropriate to a 500-level course. Whereas there is a heavy emphasis on metabolic pathways in traditional introductory Biochemistry courses, most of this has been removed in this course. The emphasis is on fundamental properties of bio-macromolecules in an aqueous environment, the thermodynamics underlying basic biochemical processes and the properties of enzymes, including the kinetics of operation, and regulation, illustrated with important examples. The course consists of 37 hours of lecture, with 5 hours of student conferences to discuss material that has been covered, and its application. These conferences will be evenly spaced and will give instructors a better opportunity to actively engage students. There are three exams.

Molecular Biology (GCLS 502). Course Directors: W. Walden and S. Mirkin. This is a core Molecular Biology course covering basic principles of gene expression, genome replication and molecular interactions important to biological processes in prokaryotes and eukaryotes. The goals of this course are to ensure that graduate students have a broad base of knowledge in the molecular biology of prokaryotes and eukaryotes. Students will learn the basic molecular principles of gene expression, genome replication, recombination and repair, RNA processing, translation and modification. Students will learn examples of important molecular interactions central to biological regulation. Students will gain an understanding of the principles, terminology and techniques of molecular biology important for most aspects of biomedical research. They will acquire fundamental skills that are necessary for reading current literature, critical analysis and for use in their own research.

Cell Biology & Integrated Physiology (GCLS 503). Course Directors: S. Appel, J. Art and K. Colley (STTP faculty member). This is an advanced course that will provide students with a solid background in fundamental aspects of cell biology and will expose them to recent advances in both general cell biology and human physiology. The course is divided into several topic areas including membrane structure, membrane transport of small molecules, electrical properties of membranes, intracellular compartments, protein trafficking, extracellular matrix, cell adhesion, cytoskeleton, cell communication, the cell cycle, and programmed cell death. Using the basic knowledge of cell biology and physiology obtained during lectures, students will be expected to critically read and discuss related primary scientific literature.

Research Methods I (GCLS 504). Course Directors: Y.K. Ho, P. DeLanerolle (STTP faculty member). This course is organized into ten modules focusing on the theory and practice of the major research techniques in biochemistry, molecular biology, spectroscopy, structural biology, genetics, bio-imaging, immunology, separation, kinetics, synthesis and sequencing of biopolymers, bio-informatics, combinatory chemistry and high through-put screening technology. The ten modules are given in two semesters, GCLS 504 in fall semester and GCLS 505 in spring semester. Each module consists of 9-11 lectures and is assigned 0.5 credit hours. The first year GEMS graduate students are expected to take four modules during their first year to fulfill the requirement of 2 credit hours. The remaining modules will become electives and a total of 5 credits will be awarded if the student takes all ten modules in their graduate career. Students will choose 2 modules in the first semester from those listed below.

Module I - Separation Techniques
Techniques involved in separation of cells, organelles and membranes; in the extraction of bio-molecules; and in purification of proteins and nucleic acids will be systematically examined. Principles and practical usage of fluorescence activated cell sorting (FACS), magnetic beads sorting, differential centrifugation, chromatography and electrophoresis will be discussed.

Module II Physical Methods I - Spectroscopic Analysis
The theory and application of x-ray absorption, UV-Visible, fluorescence, circular dichroism, light scattering, infrared and Raman, nuclear magnetic resonance and electron spin resonance will be discussed. Special emphases will be focused on the quantitative aspects in structural and dynamic characterization of biopolymers.

Module III - Basic Molecular Biology Techniques
This module will provide students with an overview of selected techniques commonly used in molecular biology research. Lecture will emphasize the principles and practical application of specific techniques and interpretation of data related to studies focused on gene structure and function.

Module IV - Methods for Studying Biological Membranes
This module provides a systematic evaluation of the fundamental techniques used to examine membrane function. Methods in studying biological membrane organization and dynamics, in characterizing active and passive transport, in assessing membrane potentials and channel activity will be presented.

Module V - Discovery Bioinformatics and Proteomics
Basic knowledge of bioinformatics and application tools in DNA and protein sequence analysis, micro-array analysis, and protein structure analysis will be discussed. The goal is to enable students to use bioinformatics tools and databases available on the web for their own research, and develop essential sophistication in interpreting bioinformatics results.

GEMS Research Rotation (GCLS 506). One rotation required in the fall semester. This course is designed for graduate students in the first year of the GEMS interdepartmental graduate program. Students participate in research rotations in laboratories that are affiliated with the GEMS program. Students are expected to participate directly in laboratory research, and in so doing, gain an appreciation of how to approach a scientific problem and how to perform the various experimental techniques to investigate that problem. In second half of the first semester, students will do one rotation.

Semester II: Required Courses

Research Methods II (GCLS 505). Course Directors: Y.K. Ho, P. DeLanerolle (STTP faculty member).
Please see the general description of GCLS 504 and 505, Research Methods I and II under First semester courses (above). In the second semester, students will choose 2 modules from those listed below to complete their 4 module requirement for the first year.

Module VI - Bio-imaging
This module provides a basic understanding of bioimaging techniques at different levels of resolution. The theory and practice of light, fluorescence/confocal, electron and atomic force microscopy as well as magnetic resonance imaging will be highlighted. Practical use of antibodies and molecular probes such as green fluorescence protein (GFP) to track the location and movement of protein molecules, and spectroscopic indicator dyes to monitor changes in concentration of intracellular ions and bioactive compounds will be discussed. We will introduce advanced techniques of single molecule fluorescence imaging and structural reconstruction with cryo-EM that allow direct probing of enzyme mechanisms, and the analysis of 3D structure of protein complexes.

Module VII - Physical Methods II - Structural Biology Techniques
Major structural biology techniques of x-ray crystallography and multi-dimensional NMR will be highlighted. From the initial experimental approach, such as crystallization and isotope labeling of proteins, to the data collection and the final resolution of the three-dimensional structure will be illustrated. The advance of mass spectrometry in protein structural analysis and its role in proteomics research will be discussed. The uses of sedimentation and calorimetry to study the hydrodynamics property and stability of proteins will be integrated in this module.

Module VIII - Advanced Molecular Biology Techniques
This module covers the general rationale for genetic manipulations to focused biological studies using animal models. The discussion focuses on genetically engineered mice. Technologies in transgenic expression, mutagenesis, gene knockout/silencing will be highlighted. Basic system biology using genetic mouse models in elucidating gene functions in embryology, endocrinology, cancer, metabolism, immuno-response and the use of stem cell technology will be presented.

Module IX - Biochemical Analyses
The quantitative use of radioactive isotopes in life science research will be examined. Immunological techniques in biochemical analyses will be discussed from the production and characterization of antibodies to various blotting and detection methods. Using enzymes as analytical tool from coupled enzyme assays to enzyme electrodes will be discussed. Methods studying kinetics of biochemical reactions as well as the basic enzyme kinetic treatment will be summarized. Methodology in characterizing ligand binding and protein-protein interaction will be presented.

Module X Chemical Methods
Methodology in chemical sequencing and synthesis of nucleic acids and peptides will be presented. Chemical modifications of biopolymers and its application in inhibitor design, affinity labeling and tagging of molecular probes will be discussed. Bio-conjugation in chemical cross-linking, immobilized enzyme, molecular tagging, artificial protein complex formation and manufacturing of microchip and micro-array will be outlined. Chemical strategy and the use of combinatory chemistry in rational drug design will be summarized focusing on the industrial, pharmaceutical and diagnostic applications.

GEMS Research Rotations (GCLS 506). Two rotations required in the Spring semester. An additional lab rotation can be taken in the summer before or after the first year.

Semester II: Core Courses (2 required from the following)

Integrative Biology - Development, Cancer, Immunology (GCLS 510). Course Directors: D. Ucker, A. Tyner, P (STTP faculty member), P. Raychaudhuri (STTP faculty member), and B. Hales. This a dvanced level course will explore issues of development, immunity, and cancer, especially from a molecular and cellular perspective. The course will provide students with rigorous fundamentals as well as in-depth explorations of critical topics and recent advances within each of these areas. A unique aspect of this course will be the focus on common thematic issues, including regulated gene expression, the control of genome stability, specificity and discrimination in cellular interactions, and selective cell death, that integrate these subjects. This approach is designed to foster critical and integrative thinking skills.

Molecular Genetics (GCLS 511). Course Directors: A. Katzen (STTP faculty member), T. Hope. Core molecular genetics course covering classical and molecular principles of microbial and Mendelian genetics. Systems covered include bacteria, bacteriophage, animal viruses, yeast, Drosophila, mouse, and human. The goals of this course are to ensure that graduate students have a broad base of knowledge in the molecular genetics of prokaryotic, eukaryotic, and viral genetic systems. Students will gain an understanding of the principles, terminology and techniques of molecular genetics important for most aspects of biomedical research. Students will acquire fundamental skills that are necessary for reading current literature, critical analysis and for use in their own research.

Cell Physiology (PhyB 586). Course Directors: J. Garcia-Martinez (STTP faculty member). Advanced functional and structural organization of the cell with emphasis on the cellular basis of physiological activity.

Structure of Biopolymers (BCHE 513). Course Directors: A. Lavie (STTP faculty member), M. Caffrey (STTP faculty member), A. Mesecar. This course provides an overview of structural and bioinformatic approaches used to characterize proteins and nucleic acids. Lectures emphasize X-ray crystallography and NMR spectroscopy and their application to the study of protein structure/function relationships, drug design, and structural genomics.

SECOND YEAR CURRICULUM AND BEYOND:
Please note that students whose research involves animals must take Essentials of Animal Research (GC 470). In addition, some students will profit from a course in statistics.

Department of Anatomy & Cellular Biology

Six credits hours of 500 level courses appropriate to the general area of the dissertation are usually taken in the second year.
Students will also take basic departmental courses that are most directly related to success in their research program or preliminary examination. All students are required to register for Seminar and Journal Club- ANAT 595 throughout their time in the graduate program. Recommendations for first year courses: Students interested in joining the Department of Anatomy and Cell Biology are free to take those courses that best suit their research interests.

Department of Biochemistry & Molecular Genetics

Topics in Biochemistry and Molecular Genetics (BCMG 575). This is an advanced course in which students will be exposed to, present and discuss recent scientific papers in biochemistry and molecular genetics. Students will learn about recent advances in these broad fields and learn how to critically evaluate and discuss scientific literature related to these areas.
One additional 500 level elective.
Students will also participate in student research seminars and journal clubs throughout their time in the department. Recommendation for first year courses: Students interested in joining the Department of Biochemistry and Molecular Genetics are free to take those courses that best suit their research interests.

Department of Microbiology & Immunology

Molecular Biology of Cells and Viruses (MIM 553). Animal viruses including basic structure and viral nucleic acids; emphasizes molecular organization of viral genomes; cellular and molecular events during virus replication and viral transformation.
Immunology (MIM 551). Concepts in immunochemistry, immunogenetics, molecular immunology, cellular immunology and immunopathology at the intermediate level.

Molecular Microbiology (MIM 552). Advanced microbial genetics and molecular biology. Topics include microbial pathogenesis, microbial cell biology, diversity of microorganisms, gene regulation, genetic structure, and genomics.
Special Topics (MIM 594). The department currently uses this course to develop presentation and grant-writing skills. Students develop research grants and present them to a "study section" of departmental faculty.

Other courses may be substituted or added based on a student's background an interests. Recommendation for first year courses: Students interested in joining the Department of Microbiology and Immunology are urged to take GCLS 510- Integrative Biology and GCLS 511-Molecular Genetics as core electives in Semester II of the first year. Other courses may be substituted based on a student's background and interests.

Department of Pharmacology

Medical Pharmacology (Pcol 425). A comprehensive course on human pharmacology. Drug mechanisms, toxicities and kinetics are presented as a foundation to therapeutic application. This is a College of Medicine course and as such does not follow the Graduate College academic calendar.
One 500 Level Elective chosen from the following

Drug Metabolism and Disposition (Pcol 508). Basic principles underlying the metabolism and disposition of drugs. Biochemical mechanisms influencing the therapeutic and/or toxic effects of drugs and other foreign compounds.
Molecular Pharmacology of the Cardiovascular System and Platelets (Pcol 510). Novel therapeutic approaches to: failing or dysrhythmic heart, prevention/dissolution of thrombi, vascular tone regulation, platelet dysfunction and platelets as model cells for excitation mechanisms.

Pharmacology and Biology of the Vessel Wall (Pcol 530). Regulation of physiological and pathological processes in the cardiovascular system; e.g. endothelial barrier, cell adhesion, smooth muscle proliferation, angiogenesis, endothelial gene expression. Pharmacological treatment of cardiovascular diseases.

Ion channels (Pcol 540).
Recommendations for first year courses: Students interested in joining the Department of Pharmacology are asked to take Receptor Pharmacology and Cell Signaling-GCLS 515 as one of their core electives in Semester II of the first year.

Department of Physiology & Biophysics

Semester 1:
Medical Physiology (PhyB 551). Lectures and conferences in human physiology. Emphasis is on cellular, nerve-muscle, cardiovascular, respiratory, and renal physiology.

Seminars in Physiology (PhyB 591).

Semester 2:
Medical Physiology (PhyB 552). Emphasizes gastrointestinal physiology and physiology of the central nervous system, endocrine and reproductive systems.

Seminars in Physiology (PhyB 591).
Note: Seminars in Physiology PhyB 591 is required for every semester for remainder of program.
Recommendations for first year courses: Students interested in joining the Department of Physiology and Biophysics are strongly urged to take Cell Physiology-PhyB 586 and Integrative Biology-GCLS 510 in Semester II of the first year. If not taken in the first year, students must take these courses in subsequent semesters.