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BMB Elective Courses

Fall 2017

BCH 515 - CRITICAL THINKING IN RESEARCH SCIENCE (1)

Students present a history of experimental work leading to their research project. This includes a selection of published and unpublished work from their advisor's lab and other labs in the same field, providing a rationale for the project. Students conclude with a report of their published and preliminary data. Focus will be on interpreting experimental data and engaging student interactions.

BCH 517 - TOPICS IN CELLULAR, BIOCHEMICAL AND MOLECULAR SCIENCE (1)

Students attend presentations in the Department of Biochemistry and Biophysics Seminar Series. Instructors and students select speakers and read 2-3 publications (suggested by the speaker) in depth. Students present these papers to the class, instructors and the speaker's faculty host in a journal club setting prior to the speaker's arrival. Finally, students attend a post-seminar class with the selected speaker.

BIO 422 - BIOLOGY OF AGING (4)

This course focuses on molecular mechanisms of aging. We will discuss popular theories of aging, model organisms used in aging research, evolution of aging, relation between aging and cancer, human progeroid syndromes, and interventions to slow aging.

BIO 426 - DEVELOPMENTAL BIOLOGY (4)

This course deals with the cellular and molecular aspects of animal development, with emphasis on processes and underlying mechanisms. Topics include embryonic cleavage, gastrulation, early development of model vertebrates and invertebrates, patterning of cell fates along embryonic axes of Drosophila and vertebrates, organogenesis and stem cells.

CHM 411 - INORGANIC CHEMISTRY I (4)

This course covers bonding in inorganic molecules, molecular symmetry, an introduction to solid-state chemistry, coordination chemistry and the properties of transition metal complexes. Two 75 minute lectures per week, 7 workshops, 6 problem sets, three midterm examinations and a final examination.

CHM 415 - GROUP THEORY (2)

Development of symmetry and group theory concepts and scope of applications to chemical problems. Applications include molecular orbital theory, ligand field theory and spectroscopy. (Fall, 1st half of semester.)

CHM 423 - NMR SPECTROSCOPY (2)

(Formerly CHM 422) - An introduction to NMR spectroscopy. Collection, processing, and interpretation of homonuclear and heteronuclear 1D and multidimensional spectra will be covered. Topics to be discussed include chemical shifts, relaxation, and exchange phenomena. Examples from organic, inorganic, and biological chemistry will be used. (Fall, 1st half of semester).

MBI 473 - IMMUNOLOGY (3)

Innate and adaptive immunity; structure and genetics of immunoglobulins and T cell receptors; lymphocyte development, immune regulation, immunological diseases, tumor immunity. Three Exams.

PHP 403 - HUMAN CELL PHYSIOLOGY (4)

This course is aimed at providing an introduction to the fundamental principles of modern cell physiology; the implications of cellular and molecular principles for the integrated physiological responses of intact organs and tissues, in both healthy and diseased states, will be discussed. The material will include basic concepts, principal research questions, and common methodologies - emphasis will be on a quantitative approach wherever possible. Course content will particularly focus on basic cellular physiology, including excitable cell physiology, and will emphasize intercellular interactions and responses to their tissue and organ environment. Recent literature relevant to the material will be reviewed and analyzed during the course.

BST 463 - INTRO TO BIOSTATISTICS (4)               

Introduction to statistical techniques with emphasis on applications in the health sciences. Summarizing and displaying data; introduction to probability; Bayes' theorem and its application in diagnostic testing; binomial, Poisson, and normal distributions; sampling distributions; estimation, confidence intervals, and hypothesis testing involving means and proportions; simple correlation and regression; contingency tables; use of statistical software.

BST 464 - APPLIED LINEAR REGRESSIONS (4)

One-way and two-way analysis of variance; multiple comparisons involving means; fixed and random effects; simple and multiple linear regression; analysis of covariance; interactions; correlation and partial correlation; multicollinearity; model selection; model checking.

Spring 2018

BIO 415 - MOLECULAR BIOLOGY OF CELL SIGNALLING (4)

This course offers an introduction to cell signaling. We will explore basic molecular mechanisms of signal transduction, and study how these mechanisms are used in different contexts to direct cell fate during development, physiology and disease. The course will draw heavily on experiments from the classic and most recent primary literature.

BIO 453 - COMPUTATIONAL BIOLOGY (4)

An introduction to the history, theory, and practice of using computers to conduct biological research. Topics include the fundamentals of Linux-based computing and perl programming, accessing and storing biological data, alignment of molecular sequences, and computer-based analysis of data.

BPH 411 - METHODS IN STRUCTURAL BIOLOGY (5)

An introduction to the theory and practical application of several major techniques used in the structural characterization of biological macromolecules.  These methods include: X-ray crystallography, Small Angle X-ray Scattering, Spectroscopic and Calorimetric Techniques, NMR and Comparative Modeling.  The goal is to enable non-specialists to become conversant in the language and principles of the field, as well as to understand the strengths and limitations of various techniques.  This course is a prerequisite to the literature-based course BPH592, “Advanced Topics in Biomolecular Diffraction and Scattering”.  Non-majors should also consider BCH 412 “Advanced Topics in Biological Macromolecules”.  Offered every other year (Even # years).

BPH 509 - MOLECULAR PHYSICS (5)

This course is designed to show how physical concepts and techniques are used to explore and understand biological phenomena. A major portion of the term focuses on thermo- dynamics of biological molecules and systems; the remainder covers the structure and physical properties of biological membranes and transport. Students are expected to have had basic courses in physics, chemistry, and biology, with an in-depth background in at least one of these areas. Offered every other year (Odd # years).

CHM 402 - BIOPHYSICAL CHEMISTRY I (4)

An introduction to the theory and practical application of several major techniques used in the structural characterization of biological macromolecules. These methods include: X-ray crystallography, Small Angle X-ray Scattering, Spectroscopic and Calorimetric Techniques, NMR and Comparative Modeling. The goal is to enable non-specialists to become conversant in the language and principles of the field, as well as to understand the strengths and limitations of various techniques. Paper and presentation. (even years)

CHM 414 - BIOLOGICAL INORGANIC CHEMISTRY (4)

Discussion of the role of metal ions in biological systems, especially enzymes. Uptake and regulation of metals, common spectroscopic techniques used for studying metals, and mechanisms through which they react. Other topics include metal ion toxicity, metal-based drugs, and interaction of metals with nucleic acids. Problem sets and proposal.

CHM 416 - X-RAY CRYSTALLOGRAPHY (2)

Students will learn the basic principles of X-ray diffraction, symmetry, and space groups. Students will also experience the single crystal diffraction experiment, which includes crystal mounting, data collection, structure solution and refinement, and the reporting of crystallographic data. Weekly assignments: problem sets, simple lab work, or computer work.

CHM 440 - BIO ORGANIC CHEMISTRY (4)

(Formerly CHM 437) An introduction to bioorganic chemistry and chemical biology. The course will present a survey of how the principles of organic chemistry have been applied to understand and exploit biological phenomena and address fundamental questions in life sciences. The course is primarily based upon the primary literature. Covered topics include the design and mechanism of enzyme mimics and small molecule catalysts (organocatalysts), synthesis and chemical modification of biomolecules (oligonucleotides, proteins, and oligosaccharides), design and application of oligonucleotide and peptide mimetics, and chemical approaches to proteomic and genetic analyses. Not open to freshmen and sophomores.

CHM 458 - MOLECULAR SPECTROSCOPY (2)

This 2 credit course covers the basic theory and experimental practice of spectroscopy in molecules and condensed matter. A general review of electromagnetic waves is followed by time dependent perturbation theory and a density matrix treatment of two-level systems. The basic principles are applied electronic, vibrational and rotational spectroscopy. The course draws heavily on literature studies that exemplify the material.

CHM 460 - CHEMICAL KINETICS (2)

Within the broad area of chemical kinetics, this course will focus on basic concepts of kinetics, photochemistry and electron-transfer (eT). In addition to studying bulk reaction rates, we will discuss Marcus's theory of eT, intramolecular vibrational energy redistribution (IVR) and vibrational cooling, and the fates of photoexcited species (radiative and non-radiative decay channels). We will address the experimental quantification of these kinetics using time-resolved spectroscopy and analysis of kinetic data. The course material will be somewhat continuous with that of CHM 458, Molecular Spectroscopy. (Spring, 2nd half of semester.)

GEN 507 - ADVANCED GENETICS (4)

This course offers in-depth discussions of theoretical concepts and experimental strategies in genetics and genomics.  Lectures will cover genetically tractable model organisms, including yeast, Drosophila, Caenorhabditis elegans (a nematode), mouse, and human and their analyses from gene to genome and systems level.  Examples of the particular questions that can be addressed with advantage in each genetic model will be presented, and the special genetic approaches feasible in these respective systems will be emphasized.  The course builds upon a strong prior background in Mendelian and molecular genetics.  Topics covered include the genetic basis of pattern formation, cell-fate determination, control of cell function, structure-function relationships in macromolecules, and searching for genes important in human health.  Additional topics incorporated recently into the course include genome structure & evolution, small RNAs & mobile genetic elements, epigenetics and genomics, proteomics, and other studies at the whole genome level.

IND 419 - Introduction to Quantitative Biology (3)

This is a graduate-level survey course that introduces concepts for the analysis of high volume biological data in the context of important current biological questions. No previous computational experience is required. Course Aims and Objectives: At the end of this course, students should have a deeper understanding of the computational tools involved in the analysis of high volume biological data, focusing on web-based resources but also introducing core approaches in bioinformatics. As an advanced-level course, we will emphasize critical thinking and reading of the primary literature to understand original experiments, rather than abstract facts and memorization. Students’ knowledge, understanding and ability to formulate new ideas will be evaluated through homework and discussions.

IND 443 - EUKARYOTIC GENE REGULATIONS (4)

This advanced course examines mechanisms of chromatin-mediated regulation of gene expression, relating molecular structures, dynamic interactions, nuclear processes, 3-D nuclear organization to biological functions. Topics include DNA structures, packaging and higher order chromatin organization in the nucleus, the transcription machinery, eukaryotic chromosome structure and its modifications, epigenetics and functional genomics, dynamics of nuclear processes, nuclear reprogramming, development and applications of genome manipulation technology. Lectures and readings draw heavily on primary literature both classic and most recent.

IND 447 - SIGNAL TRANSDUCTION (4)

Cellular signal transduction is one of the most widely studied topics in the biomedical sciences. It has become clear that cells have multiple mechanisms for sensing the environment and converting the external signals into intracellular responses. The goal of this course will be for students to learn modern concepts in signal transduction. The lectures will cover a spectrum of topics ranging from basic principles and mechanisms of signal transduction to contemporary techniques for doing research in this area.

MBI 456 - GENERAL VIROLOGY (4)

Provides an introduction to animal virology, with emphasis on human disease. Topics covered include the following: general properties of viruses, methods in viral research, virus structure, biochemistry of virus replication, virus- host cell interactions, pathogenesis, HIV/AIDS, emerging infections, vaccines, antivirals, and viral vectors and gene therapy.  Three exams.

MBI 421 - MICROBIAL GENETICS (3)

This course provides an in-depth examination of representative genetic systems in bacteria and bacterial viruses. Emphasis is placed on the methods of genetic analysis used to study biological function. The material covered includes: the nature of bacterial variation, processes affecting gene synthesis and integrity, the nature of gene transfer in bacteria, the regulation of gene expression in prokaryotes and genomic approaches to the study of microbial genetics. (Graduate students register for MBI 521 Seminar).

PTH 507 - CANCER BIOLOGY (3)

The lectures will provide historical perspectives of cancer incidence, treatment, and early scientific inquiry as a foundation for understanding the current state of cancer research. Leading basic and translational scientists will discuss the genetic basis of cancer in both familial cancer syndromes and acquired somatic mutations. Research on the normal cellular functions such as cell cycle control, apoptosis, and signal transduction that become aberrant in cancer progression will also be discussed. Additionally, the mechanism of chemical and viral induction of cancer will also be explored. 

The second half of the course will focus on clinical identification and treatment of cancer as well as the mechanism of therapeutic action in prevention of carcinogenesis. Lectures from leading clinician-scientists will provide insight for cancer treatment with goals of understanding the human impact of the disease and identifying common themes, as well as distinctive characteristics of cancer. 

PHP 404 - PRINCIPLES OF PHARMACOLOGY (4)      

Pharmacology is one of the vital disciplines in biomedical sciences. It employs the multidisciplinary knowledge in biochemistry, cell biology, chemistry, genetics, neuroscience, pathology, physiology, toxicology, and clinical medicine, to elucidate the mechanisms of action of drugs in treating human diseases. This course represents a collective endeavor of our faculty to the teaching of graduate and senior undergraduate students in UR. It focuses on the fundamental principles of pharmacology, neuropharmacology, cardiovascular pharmacology, and contemporary approaches to drug discovery and design.