PhD Program

Course Descriptions

These courses include all required courses for the PhD in Pharmacology and Toxicology as well as those commonly taken as electives.

BCH 503 Biochemical Principles, 4 credits

One semester survey of the molecules in a cell, their interconversions and roles in sustaining and regulating cellular function, cell replication and information transfer.  The course is designed for Master's candidates in the biomedical sciences.

BCH 507 Protein Structure and Function, 2-3 credits

Prerequisites: BMS 503 or BCH 403/BCH 503
The primary objective of this course is for students to become familiar with the principal, broad questions in protein structural biology and the experimental strategies used to answer them. These strategies include kinetics, specific mutagenesis, and model design and analysis. Specific topics include steady-state and transient kinetics, protein origins of enzyme catalysis, folding pathways and protein design, and protein allostery in the gating function of ion channels.

BCH 508 Gene Expression, 2 credits

Familiarizes students with up-to-date concepts and experimental approaches used in the study of eukaryotic gene expression. Focuses on the molecular mechanisms involved in RNA polymerase II (RNAPII) transcription. Specific topics include the structure and function of RNAPII and required auxiliary factors, the molecular mechanisms of transcriptional activation and repression, the coupling of transcriptional elongation with mRNA processing, and specific examples of the role of regulated RNA polymerase II transcription in development and cellular differentiation. Each week, one to two selected papers from the scientific literature are discussed in class, with students taking turns presenting one or two figures and the instructor providing clarification and/or additional questions as appropriate.

BMS 501 Cell Biology I, 4 credits

This course concerns basic concepts and contemporary issues of cell structure and function. Topics covered include cell structure and function, protein sorting and trafficking, membrane transport and excitability, signal transduction and cell cycle. A combined lecture and conference format is used with lectures emphasizing basic principles derived from original journal articles. Conferences are used to review lecture concepts, present laboratory demonstrations, analyze original literature and solve problems.

BMS 509 PhD Program Laboratory Rotation, 4 credits

Laboratory rotations introduce students to disciplines, faculty, techniques and research strategies. Students participate in ongoing projects in the basic science departments. These courses are designed to assist students in identifying their research goals while enabling them to maintain a more comprehensive view of the integrative nature of life sciences.

BMS 510 PhD Program Laboratory Rotation, 4 credits

Laboratory rotations introduce students to disciplines, faculty, techniques and research strategies. Students participate in ongoing projects in the basic science departments. These courses are designed to assist students in identifying their research goals while enabling them to maintain a more comprehensive view of the integrative nature of life sciences.

BMS 511 Fundamentals in Biomedical Sciences - Critiquing Scientific Literature, 1 credit

The goal of this course is to introduce students to strategies for identifying, reading, critiquing and presenting scientific literature. Students will break into small group journal clubs in which they will present a paper from the primary literature.

BMS 514LEC Introduction to Scientific Investigation and Responsible Conduct, 2 credits

This course is required for all students in the PPBS program. Students will be introduced to topics relevant to their training and situations that pose potential ethical concerns. Class discussions led by faculty facilitators will explore appropriate and inappropriate ways to deal with these situations.

BMS 515LEC Fundamentals of Biomedical Research I, 4 credits

This lecture course is required for all students in the PPBS program. It will teach students fundamental concepts important to a broad range of biomedical research topics.

BMS 516LEC Fundamentals of Biomedical Research II, 3 credits

This course is a combination of lectures and research paper discussions and is required for all students in the PPBS program. This course will teach students to research methods, experimental design, data analysis and critical thinking.

BMS 600 Biomedical Sciences Seminar

Designed to expose students in the Natural Sciences Interdisciplinary masters program to current topics in the biomedical sciences. Students will be required to attend a one-hour seminar each week, chosen from the wide array of Jacobs School seminar series offered in both biomedical and clinical disciplines.

BMS 650 Project Guidance

Supervised culminating project for the Natural Sciences Interdisciplinary master's program. Students will present and discuss their work in progress in individual meetings with their advisor.

NRS 520 Cellular and Molecular Neuroscience, 4 credits

This course provides the Graduate Students in the Graduate Neuroscience Program and other life sciences with a comprehensive overview of the principles that control the development and function of the nervous system. These principles require knowledge that cuts across all scientific disciplines. Hence, topics will be team-taught at the molecular, cellular, and systems levels. The course covers the structure and development of the nervous system, formation and function of the synapse, and the general principles of neuronal function. The student is expected to gain 1) the necessary background to pursue in greater depth any selected facet of neuroscience and 2) an appreciation of the beauty and excitement offered by the intellectual challenge posed by analyzing how the nervous system functions. Malcolm Slaughter, PhD, is the course coordinator.

NRS 521 Neuroscience Intro 2, 4 credits

PHI 640 Research Ethics, 3 credits

The course offers a broad analysis of ethical issues in science including scientific misconduct, fraud and plagiarism, animal use and animal rights, clinical trials and informed consent, intellectual property rights, data handling and preservation, and issues around genetic diseases and information.

PMY 503 Fundamentals of Pharmacology

The goal of PMY 503 is to provide graduate students with an in-depth understanding of pharmacological principles as well as the ability to use and apply this information. Topics to be included: pharmacokinetic principles (e.g.,absorption, distribution, metabolism, excretion,drug dosing); receptor theory and drug-receptor interactions; non-receptor targets (eg,enzymes, biologics RNA-based therapy); pharmacogenetics; drug safety; quantifying drug effects; and target engagement and validation. Each topic will be introduced and necessary information provided through didactic lectures; subsequent sessions will focus on the use and application of this information. These sessions will involve a discussion of research papers or research problems using the Socratic Method with the faculty acting as discussion facilitators. For the more quantitative aspects of this course (e.g.,pharmacokinetics and the describing of drug effects), quantitative problem-solving will also be used.

PMY 503 is dual-listed with PMY 405, intended for undergraduates, and PMY 511, for pharmacy students. These courses share a central syllabus and include a one-hour recitation tailored to the needs of each group of students.

PMY 505/506 Pharmacology Seminar, 2 credits each

In this course, you will learn, under supervision, how to evaluate and present original research from biomedical scientific literature.  Typically, one to two published papers are presented in a seminar (approximately 50 minutes long).  In consultation with the course director, students choose papers to be presented within the general fields of pharmacology and toxicology. A brief question and answer session follows each presentation, involving students and faculty from the Department of Pharmacology and Toxicology.

You will learn to formulate a seminar abstract, deliver work effectively in a seminar, prepare quality slides, use background information well, and evaluate papers’ methods, results and conclusions.  Your presentation will also be evaluated on your critical assessment of the presented research, ability to respond to audience questions and extent to which you place the results in a broader context of ongoing research.

PMY 516 Molecular Neuropsychopharmacology, 3 credits

The neuropharmacology course will discuss the drug actions on the nervous system. The particular focus of this course will be to provide a description of the cellular and molecular actions of drugs on synaptic transmission. This course will also refer to specific disorders of the nervous systems and their treatment in addition to giving an overview of the techniques used for the study of neuropharmacology.

The course will focus on human diseases involving chronic pain, drugs of abuse, and neurodegeneration (such as Parkinson's and Multiple Sclerosis). The course comprises both lectures and recitation periods which will vary by instructor and are designed to foster class participation, reading of primary literature (as well as textbook reading) and critical evaluation of research data to develop knowledge in the discipline of neuropharmacology.

PMY 525 Discoveries in Pharmacological Sciences, 2 credits

The goal of this 2-credit course is to learn and appreciate the history behind key discoveries that lead to modern pharmacotherapies of clinical disorders. At the end of the course students will 1) Learn the historical discoveries of various pharmacological topics and 2) Appreciate the importance of basic sciences toward significant clinical treatments.

PMY 526 Trends In Pharmacological Sciences, 2 credits

In this graduate course, students will learn to critically evaluate scientific papers using examples of recent high impact findings in the area of pharmacology. With guidance from experts in the field, students will learn to summarize the core concepts, data and implications of these papers. Emphasis will be placed on developing skills in analytical thinking, experimental design and critical paper reading. Secondary goals of the course are to improve technological fluency and knowledge in different areas of pharmacology.  

PMY 527 Modern Approaches to Drug Discovery, 2 credits

This course will provide students with hands-on experience in genomic techniques for target identification and validation, and computational techniques for the assessment of target “drugability” and structure-assisted drug discovery. Students are required to bring a notebook computer to class, as the course provides hands-on training using open-source software packages for the analysis of genomic data and molecular visualization. Before these two sections, students are introduced to the receptor and ion-channel basis of drug action, including receptor theory and genetic techniques for studying ion channel function.

PMY 540 Pharmacology Research Proposal, 2 credits

This course teaches you to prepare a research proposal and is connected to the pharmacology Proposition Exam. You will choose a topic related to your intended thesis work, make a Journal Club presentation on the topic, and present a pre-proposal to the Proposition Examination Committee. You will then write a complete proposal addressing the comments you receive from the Committee, and, on approval of the proposal by the Committee, defend your proposal in an oral examination. Your grade will be based on your performance in the Journal Club presentation, the written proposal and the oral defense of the proposal. To continue in the program, you must receive grade B or better.

PMY 605 Introduction to Bioethics, 2 credits

In this graduate course students will learn to critically evaluate scientific papers using examples of recent high impact findings in neuropharmacology, cancer, toxicology and drug discovery. With guidance from experts in the field, students will learn to summarize the core concepts, data and implications of these papers. Emphasis will be placed on pushing concepts past the literature and transitioning from published work to novel drug discovery and development.

PMY 626 Toxicology—Principles and Practice, 2 credits

An introduction to the basic principles and practice of toxicology, including dose-response and toxicokinetic analysis.  We will also cover chemical mutagenesis and carcinogenesis, with an emphasis on understanding mechanisms for these responses.  An overview of risk assessment will include quantitative aspects of cancer and non-cancer based risk assessments.

PMY 627 Target Organ Toxicity, 2 credits

This course takes a systemic approach to toxicology, including developmental toxicology.  We will investigate the adverse effects of several classes of chemicals at specific target organs, including the liver, lung and kidney, and the endocrine, nervous, reproductive and immune systems.  The course emphasizes understanding the mechanism(s) for the adverse responses of specific agents at a given target site.

STA 527 Introduction to Medical Statistics, 4 credits

This course is designed for students concerned with medical data. The material covered includes the design of clinical trials and epidemiological studies, data collection, summarizing and presenting data, probability, standard error, confidence intervals and significance tests, techniques of data analysis including multifactorial methods and the choice of statistical methods, problems of medical measurement and diagnosis, vital statistics and calculation of sample size. The design and analysis of medical research studies will be illustrated. MINITAB is used to perform some data analysis. Descriptive statistics, probability distributions, estimation, tests of hypothesis, categorical data, regression model, analysis of variance, nonparametric methods, and others will be discussed as time permits.