BMOL 514 (BIOL 514) FLOW CYTOMETRY RESEARCH TECHNIQUES (0-3-1) (F/S/SU). Provides a basic understanding of flow cytometry principles and applications in research and clinical setting. Students gain ‘hands-on’ experience including staining and separating blood cells, staining of DNA for cell cycle analysis, and purification of rare cell types using a cell sorter. Students will apply flow cytometry to a specific research topic. May be taken for BIOL or BMOL credit, but not both. PREREQ: BIOL 320 or equivalent.
BMOL 516 RESPONSIBLE CONDUCT IN RESEARCH (1-0-1)(F). Basic concepts, principles and practices governing research compliance and Responsible Conduct for Research (RCR) in the biomolecular and biomedical areas. Utilizes on-line Collaborative Institutional Training Initiative (CITI) training modules and group discussions of case studies or lectures presented by professionals in the field. PREREQ: Graduate standing.
BMOL 555 APPLIED CALCULUS FOR BIOMOLECULAR SCIENCES (1-0-1)(S). Review and practice of calculus methods and techniques relevant to qualitative and quantitative descriptions of complex phenomena in the biomolecular sciences. PREREQ: MATH 170; and PHYS 112 or PHYS 112.
BMOL 598 GRADUATE SEMINAR (1-0-1)(S). Seminars by scientists on a wide range of subjects in the areas of biomolecular sciences. PREREQ: Admission to program or PERM/INST. The course is graded Pass/Fail.
BMOL 601 BIOMOLECULES I (4-0-4)(F). An in-depth study of the metabolism of both DNA and RNA at the molecular/mechanistic level. This course will cover the mechanisms of DNA replication, transcription, translation, transposition and repair, as well as those for RNA interference, catalysis, silencing and splicing. Molecular genetics and bioinformatics approaches for studying DNA/RNA and their interactions with proteins will be discussed. PREREQ: BIOL 320, CHEM 431, MATH 170, PHYS 112.
BMOL 602 BIOMOLECULES II (4-0-4)(S). An in-depth study of proteins focusing on amino acid chemistry, protein structure, protein folding, protein function, membrane biochemistry as well as small molecules, lipids and carbohydrates. This course will discuss modern methods of protein characterization and the use of bioinformatics in understanding the chemistry/function of proteins. Recent developments in proteomics and high-throughput approaches to identifying and assessing protein function will be presented. PREREQ: BMOL 601.
BMOL 603 BIOPHYSICAL INSTRUMENTATION AND TECHNIQUES (3-3-4) (F/S).Applications and principles of key physical methods and instruments used for the characterization of the structural, functional, and dynamical properties of biological molecules and their interactions. Methods include single-molecule detection and manipulation; mass spectroscopy; X-ray, electron, and neutron diffraction; spectroscopy (optical, IR, UV, Raman); magnetic resonance (NMR, EPR, MRI); plasmon resonance; birefringence; electrophoresis; and hydrodynamic techniques. PREREQ: BIOL 320, CHEM 431, MATH 170, PHYS 112.
BMOL 605 CURRENT SCIENTIFIC LITERATURE (1-0-1)(F). Written and oral presentation of current topics from the published literature in areas of Biomolecular Sciences aimed at integrating material from the various related disciplines. Course will be multidisciplinary involving in depth discussion and critical analysis of current literature by the students. PREREQ: Graduate student status.
BMOL 606 PROPOSAL WRITING (0-2-2)(F/S). Written and oral presentation of a research proposal in an area of biomolecular sciences related to the student’s proposed dissertation research project. PREREQ: BMOL 601.
BMOL 607 GRADUATE RESEARCH PRESENTATION (1-0-1)(S). Oral presentation on research activity by third year students in the Biomolecular Sciences program. PREREQ: BMOL 601, BMOL 602, BMOL 603.
BMOL 613(BIOL 613) MOLECULAR GENETICS (3-0-3) (F/S). An advanced study of genetics in microbial, animal and plant systems, focused on the biochemical and molecular aspects of genetic structure and function. Information obtained from recent genomic analysis and comparisons will be included as well as discussion of contemporary molecular biology techniques and applications and an introduction to genomics. May be taken for BIOL or BMOL credit, but not both. PREREQ: BIOL 310 or equivalent.
BMOL 615 Research in the Biomolecular Sciences (0-3-1) (F). Research conducted by a graduate student under the supervision of faculty in the Biomolecular Sciences area. Students rotate through different research laboratories during the course of a semester to learn new research techniques, review relevant scientific literature, experience different mentoring styles and laboratory environments, and contribute to a research team’s generation of hypotheses and/or data interpretation. PREREQ: PERM/INST.
BMOL 687 DOCTORAL PRELIMINARY EXAMINATION (Variable Credit). An early assessment of a student’s potential to complete a doctoral program satisfactorily. Considerable autonomy is granted to the academic unit in the design, administration, and evaluation of the preliminary examination. Pass/fail only.
Written assessments of foundational knowledge gained from the core curriculum, experimental design skills, and ability to interpret and communicate scientific data. Students enroll in this course during the summer semester after completion of their second academic year of study. Examinations will be evaluated by an assembled panel of Biomolecular Sciences program faculty. PREREQ: PERM/INST. The course is graded Pass/Fail, is offered during the summer and is one credit.
BMOL 691 DOCTORAL COMPREHENSIVE EXAMINATION (Variable Credit).
Taken when the doctoral student is in Regular Status and has completed a significant number of course credits applicable to the degree requirements. Considerable autonomy is granted to the academic unit in the design, administration, and evaluation of the comprehensive examination. Pass/fail only.
Students enrolled in this course prepare a research proposal on a topic other than their dissertation work and submit it to an examining committee. An oral defense of the proposal is scheduled during the semester to assess familiarity with the grant topic as well as material covered in core curriculum and prerequisite courses. Successful completion of this course is required for the student to advance to candidacy. PREREQ: PERM/INST. The course is graded Pass/Fail, is offered in the fall, and is one credit.
BIOCHEM 513 ADVANCED ENZYMOLOGY (3-0-3)(S)(Alternate years). A deeper look into the catalytic and kinetic mechanisms of enzymes. Modern methods for studying enzymes will be included as well as learning strategies for studying steady state and transient enzyme kinetics. Students will make extensive use of primary literature. PREREQ: CHEM 322 and CHEM 433 or PERM/INST.
BIOL 503 ADVANCED BIOMETRY (3-3-4)(S)(Even years). A survey of experimental design and selected multivariate techniques. The course is designed to assist students in selecting proper statistical techniques for gathering and analyzing biological data, and correctly interpreting the statistical analysis of their data. Prior experience with Statistical Analysis System (SAS) is helpful. PREREQ: BIOL 501 or PERM/INST.
BIOL 509 MOLECULAR ECOLOGY (3-0-3)(F)(Odd years). Theory and methodologies. Use of molecular genetic markers to study ecological phenomena (e.g., mating systems, parentage and kinship, population structure, gene flow, dispersal, natural selection). Emphasis on an hypothesis-testing approach. Appropriateness of particular molecular techniques to specific research questions. PREREQ: BIOL 323 and BIOL 310 or PERM/INST.
BIOL 510 PATHOGENIC BACTERIOLOGY (2-6-4)(S). Medically important bacteria, rickettsia, and chlamydia are surveyed with emphasis on their pathogenicity, host-parasite relationships, and the clinical and diagnostic aspects of the diseases they produce in humans and animals. PREREQ: BIOL 320 and BIOL 303.
BIOL 511 (BMOL 511) ADVANCED CELL BIOLOGY (3-0-3) (S). Contemporary and frontier topics in the biology of microbial, plant, and animal cells covering signal transduction, protein trafficking, membrane structure and transport, cell to cell communication, cellular compartmentalization, and cell biotechnology applications. May be taken for BIOL or BMOL credit, but not both. PREREQ: BIOL 3020or PERM/INST.
BIOL 514 (BMOL 514) FLOW CYTOMETRY RESEARCH TECHNIQUES (0-3-1) (F/S/SU). Provides a basic understanding of flow cytometry principles and applications in research and clinical setting. Students gain ‘hands-on’ experience including staining and separating blood cells, staining of DNA for cell cycle analysis, and purification of rare cell types using a cell sorter. Students will apply flow cytometry to a specific research topic. May be taken for BIOL or BMOL credit, but not both. PREREQ: BIOL 320 or equivalent.
BIOL 520 IMMUNOLOGY (3-0-3)(S). Principles of immunology, host defense mechanisms, the immune response, immune disorders, serology, and related topics. PREREQ: BIOL 320 or equivalent.
BIOL 521 IMMUNOLOGY LABORATORY (0-6-2)(F/S). Modern immunological laboratory techniques including flow cytometry, immune system physiology, antibody-based assays including ELISA, vaccine design, and immuno-bioinformatics. COREQ: BIOL 520.
BIOL 531 PHARMACOLOGY (3-0-3)(F). Basic pharmacological principles including mechanisms of drug action in relation both to drug- receptor interactions and to the operation of physiological and biochemical systems. Pharmacokinetics, metabolism, receptor theory and an examination of major classes of therapeutic agents used in humans. PREREQ: BIOL 227-228 or BIOL 191-192, and BIOL 320.
BIOL 539 VACCINOLOGY (3-0-3)(S). Discussion of the history, safety, epidemiology, molecular biology and immunology of vaccines. Development of the next generation of vaccines to combat infectious disease of global importance, such as HIV, malaria and tuberculosis, also will be discussed. PREREQ: BIOL 320 or PERM/INST.
BIOL 540 GENERAL AND MOLECULAR TOXICOLOGY (3-0-3)(F/S). General and molecular principles of mammalian toxicology including toxicant disposition, mechanisms of toxicity, target organ toxicity, and major classes of toxic agents. PREREQ: BIOL 320 OR PERM/INST.
BIOL 541 MOLECULAR BIOLOGY OF CANCER (3-0-3)(S). A treatment of the basic biology of cancer and the process of tumor progression. Topics examined will include oncogenes, tumor suppressor genes, and the causes of cancer. PREREQ: BIOL 320, BIOL 310.
BIOL 542 MOLECULAR NEUROBIOLOGY (3-0-3)(F). Emphasis will be on the molecular aspects of neurobiology. Topics will include: cells of the nervous system, neurochemical transmission, nerve terminals, membrane structure and function, electrical signaling, neural development, process outgrowth and myelination and glia, and specific neural diseases including Alzheimer’s disease, Parkinson’s disease, and Lou Gehrig’s disease. PREREQ: BIOL 320 and PHYS 112, or PERM/INST.
BIOL 543 ADVANCED DEVELOPMENTAL BIOLOGY (1-6-2)(F)(Odd years). Application of molecular and cellular methods to current topics in developmental biology. Analysis of current literature in biology with emphasis on the coordinated regulation of gene expression, cellular differentiation and migration. Laboratory studies include model systems such as chick, zebrafish, sea urchin and mouse, utilizing cell/tissue culture, histology, immunohistochemistry, RT-PCR, protein purification, SDS-PAGE, western blot and others. Previous enrollment in BIOL 344 and ZOOL 351 recommended.
BIOL 546 BIOINFORMATICS (2-3-3)(F). Practical training in bioinformatics methods: accessing sequence data bases, BLAST tools, analysis of nucleic acid and protein sequences, detection of motifs and domains of proteins, phylogenetic analysis, gene arrays, and gene mapping. PREREQ: BIOL 310 or PERM/INST.
BIOL 547 FORENSIC BIOLOGY (3-0-3)(F). Analysis and interpretation of biological evidence in forensic contexts. Topics include entomology, botany, fingerprints, toxicology, DNA, pathology, anthropology and odontology. PREREQ: BIOL 310.
BIOL 548 PERL FOR BIOINFORMATICS APPLICATIONS (3-0-3)(F/S). The PERL programming language is used to introduce skills and concepts to process and interpret data from high-throughput technologies in the biological sciences. Key bioinformatics concepts are reinforced through lectures, computer demonstrations, weekly readings, and programming exercises from biological sequence analysis and real-world problems in proteomics and genetics. PREREQ: BIOL 446 or PERM/INST.
BIOL 549 GENOMICS (3-0-3)(F/S). A fusion of biology, computer science, and mathematics to answer biological questions. Topics include analyzing eukaryotic, bacterial, and viral genes and genomes; locating genes in genomes and identifying their biological functions; predicting regulatory sites; assessing gene and genome evolution; and analyzing gene expression data. PREREQ: BIOL 310 and MATH 254, or PERM/INST.
BIOL 551 DEVELOPMENTAL BIOLOGY (2-6-4)(S)(Odd years). Germ cell development, comparative patterns of cleavage and gastrulation, neurulation and induction, and development of human organ systems with emphasis on molecular and cellular mechanisms. Laboratory studies of sea urchin, frog, chick, and pig development. PREREQ: BIOL 191-192 or PERM/INST.
BIOL 565 ADVANCED TOPICS IN MOLECULAR BIOLOGY TECHNIQUES (1-0-1)(F). Discussion of scientific literature with emphasis on modern molecular biology techniques. Students lead discussions and present articles from relevant primary literature. May be repeated once for credit. PREREQ: BIOL 310 and PERM/INST.
BIOL 566 ADVANCED TOPICS IN MOLECULAR, CELLULAR AND DEVELOPMENTAL BIOLOGY (1-0-1)(S). Discussion of current research. Students lead discussions and present articles, as well as monitor recent relevant primary literature. Previous enrollment in BIOL 465 or BIOL 565 recommended. May be repeated once for credit. PREREQ: BIOL 310 and PERM/INST.
BIOL 570 GENETIC ENGINEERING AND BIOTECHNOLOGY (3-0-3)(F/S). Applications of biotechnology, genetic engineering, and recombinant DNA technology in medical diagnosis and therapy, agriculture, microbial biology and environmental systems. The principles and application of recombinant DNA technology in industrial, agricultural, pharmaceutical, and biomedical fields are discussed. PREREQ: BIOL 310.
BIOL 613 (BMOL 613) MOLECULAR GENETICS (3-0-3) (F/S). An advanced study of genetics in microbial, animal and plant systems, focused on the biochemical and molecular aspects of genetic structure and function. Information obtained from recent genomic analysis and comparisons will be included as well as discussion of contemporary molecular biology techniques and applications and an introduction to genomics. May be taken for BIOL or BMOL credit, but not both. PREREQ: BIOL 310 or equivalent.
BIOL 623 ADVANCED IMMUNOLOGY (1-0-1)(S). An advanced study of the cellular and molecular regulation of the immune response. The course will include formal lectures, student presentations, in-depth discussion of selected topics using the current literature. PREREQ: BIOL 520 or PERM/INST.
CHEM 509 INTRODUCTION TO POLYMER CHEMISTRY (3-0-3) (F)(Alternate years). An introduction to the concepts of polymer synthesis, characterization, structure, properties, and basic fabrication processes. Emphasis is on practical polymer preparation, on the fundamental kinetics and mechanisms of polymerization, and on structure-property relationship. PREREQ: CHEM 309 or PERM/INST.
CHEM 510 ORGANIC POLYMER SYNTHESIS (3-0-3)(S) (Alternate years). A study of the synthesis and reactions of polymers. Emphasis is on practical polymer preparation and on the fundamental kinetics and mechanisms of polymerization reactions. Topics include relationship of synthesis and structure, characterization of polymer structure, step-growth polymerization, chain-growth polymerization via radical, ionic and coordination intermediates, copolymerization. PREREQ: CHEM 309 or PERM/INST.
CHEM 511 ADVANCED ANALYTICAL CHEMISTRY (3-0-3)(F). Stoichiometry involved in separations and instrumental methods of analysis. The course will be flexible in nature to adapt to the varied background of the students. PREREQ: CHEM 322 or PERM/INST.
CHEM 521 QUANTUM CHEMISTRY (3-0-3)(F)(Alternate years). Formal introduction to quantum mechanics, Dirac notation, angular momentum and operator algebra. Emphasis will be placed on electronic structure theory, reaction mechanisms and the use of modern quantum chemistry theoretical packages. PREREQ: CHEM 322, or PHYS 309 and PHYS 432, or PERM/INST.
CHEM 522 SPECTROSCOPY (3-0-3)(F)(Alternate years). Concepts and practical usage of modern chemical spectroscopic techniques, including electronic absorption, infrared/Raman, X-Ray/ EXAFS, magnetic resonance and magnetic circular dichroism. Emphasis will be placed on the application of these techniques to the structure/function characterization of chemical and biochemical systems. PREREQ: CHEM 521 or PERM/INST.
CHEM 523 CHEMICAL KINETICS (3-0-3)(F)(Alternate years). A comprehensive study of the role of quantum chemistry and thermodynamics in chemical reactions. Emphasis will be placed on determining reaction coordinates and transition states. Extensive use will be made of modern computational chemical computer programs for calculating potential energy surfaces and transition states. PREREQ: CHEM 322, or PHYS 309 and PHYS 432, or PERM/INST.
CHEM 540 SPECTROMETRIC IDENTIFICATION (3-0-3)(S). dentification of compounds using modern spectrometric techniques. PREREQ: CHEM 309 and CHEM 321.
CHEM 551 BIOINORGANIC CHEMISTRY (3-0-3)(S)(Alternate years). Exploration of the vital roles that metals play in biochemical systems. Emphasis is on transition metals in biology. Course will focus on structural, regulatory, catalytic, transport and redox functions of bioinorganic systems. PREREQ: CHEM 322 or PERM/INST.
CHEM 560 INTRODUCTION TO NMR SPECTROSCOPY (1-3-2) (Offered intermittently). This course will instruct students on the theory and practice of one- and two-dimensional NMR spectroscopy. Emphasis will be placed on using the NMR spectrometer to solve a variety of chemical and biological problems. PREREQ: CHEM 322, or PHYS 309 and PHYS 432, or PERM/INST.
CHEM 561 INTRODUCTION TO MOLECULAR MODELING AND COMPUTATIONAL CHEMISTRY (1-3-2)( Offered intermittently). Overview of modern computational chemistry. Use of computational chemistry tools and their application to problems of chemical and biological interest. PREREQ: CHEM 322, or PHYS 309 and PHYS 432, or PERM/INST.
COMPSCI 521 DESIGN AND ANALYSIS OF ALGORITHMS (3-0-3)(F). Design techniques such as amortized analysis, dynamic programming, and greedy algorithms. Computational geometry, graph algorithms, primality and other number-theoretic algorithms, specialized data structure techniques such as augmenting data structures, combinatorial graph reduction and functional repetition. NP completeness and approximation algorithms. PREREQ: COMPSCI 242.
COMPSCI 530 PARALLEL COMPUTING (4-0-4)(F). Motivation for parallel computation and survey of different models. Fundamental techniques used in parallel algorithms. Implementation on parallel machines and simulations on clusters of workstations. Distributed computing versus parallel computing. Examples of distributed programming environments. PREREQ: COMPSCI 242 or PERM/INST.
COMPSCI 557 ARTIFICIAL INTELLIGENCE (3-0-3)(F/S). Course will include a survey of some of the following topics, plus a project: Principles of knowledge-based search techniques; automatic deduction; knowledge representation using predicate logic, semantic networks, connectionist networks, frames, rules; applications in problem solving, expert systems, game playing, vision, natural language understanding, learning, robotics; LISP programming. PREREQ: COMPSCI 242 and COMPSCI 354 or PERM/INST.
MATH 572 COMPUTATIONAL STATISTICS (3-0-3)(F)(Even numbered years). Introduction to the trend in modern statistics of basic methodology supported by state-of-art computational and graphical facilities, with attention to statistical theories and complex real world problems. Includes: data visualization, data partitioning and resampling, data fitting, random number generation, stochastic simulation, Markov chain Monte Carlo, the EM algorithm, simulated annealing, model building and evaluation. A statistical computing environment will be used for students to gain hands-on experience of practical programming techniques. PREREQ: MATH 361.
PHYS 520 NANOBIOTECHNOLOGY (3-0-3)(F/S). An introduction to the biological and biomedical uses of nanotechnology, including the nature and applications of nanostructures to cell biology, imaging, biosensors, medical therapy (including anti-cancer therapies and drug delivery), and biotechnology. PREREQ: BMOL 603.
PHYS 523 PHYSICAL METHODS OF MATERIALS CHARACTERIZATION (3-0-3)(S). Physical principles and practical methods used in determining the structural, electronic optical, and magnetic properties of materials. Course topics will include optical, electron, and scanning microscopies, diffraction, surface analysis, optical spectroscopy, electrical transport, and magnetometry. Individual projects will focus on the application of an analytical technique to solve a specific problem. PREREQ: PHYS 309 or PERM/INST.
PHYS 536 SOFT MATTER (3-0-3)(F/S). Examples of soft matter include glues, paints, soaps, rubber, foams, gelatin, milk, and most materials of biological origin. Introduction to the principles underlying the physical properties and behaviors of soft matter, including colloids, polymers, gels, and liquid crystals. Expected background: one semester of upper-level thermodynamics from any department. PREREQ: PERM/INST.
PHYS 537 Radiation Biophysics (3-0-3)(F/S). Physical properties and biological effects of different kinds of radiation: action of radiation on various cellular constituents: target theory, genetic effects, repair of radiation damage, physics of radiology and radiotherapy, isotopic tracers. PREREQ: PHYS 307 or PERM/INST.
PHYS 624 Membrane Biophysics (3-0-3)(F/S) Membranes are of fundamental importance for biological systems due to their roles in cellular compartmentalization, signal transduction, metabolism, and energy synthesis. Topics include structures and functions of membrane bilayers and of membrane proteins, physics of membrane fusion, and mechanisms of cell signaling and energy transduction. PREREQ: BMOL 602, PHYS 611.