2008 - 2009 Courses

All trainees take a class related to developmental biology. This is a list of some offerings in the coming year.

HGEN 6040 Concepts in Developmental Biology:
1st half spring semester,
David Grunwald, Anthea Letsou, Shige Sakonju, Gabrielle Kardon.
Location: HSEB 2938

PREREQUISITES: Open to all graduate students. The course is primarily designed for first year graduate students. Advanced students, please note: We will offer a literature-based Developmental Biology course for advanced students in 2006 - 2007.

The course focuses on topics in developmental biology in a variety of organisms. A selected series of subjects will be covered, including: body plan patterning & specification of body axes, long range and short range intercellular signaling, cell fate and cell differentiation, morphogenesis and organogenesis, germ cell development, stem cells and regeneration, and evolutionary changes in development. The course consists of two lectures per week (Monday and Wednesday) followed by a discussion session (Friday) based on assigned readings from primary literature.

HGEN 6091 Evolution and Development:
2nd half spring semester,
Gabrielle Kardon, Mike Shapiro, Shige Sakonju.

This course will explore the molecular, developmental, and genetic mechanisms underlying evolutionary change, with an emphasis on current research in animal biology. Topics include regulatory networks and signaling pathways, modularity, developmental constraints, origin of animals, molecular/developmental origin of diverse body plans and appendages, and genetics of speciation. The class will consist of both lectures and discussions of current literature. Suitable for graduate students at all levels.

BIOL 6040 Cellular and Molecular Neuroscience (4)
Cross listed as NEUSC 6040, PHYSL 6040.

The bulk of this course will focus on the cellular mechanisms of signaling. The topics to be covered include basic neuronal/glial morphology and cell biology; neurostructural mapping and identification; basic neural development; cytoskeleton-structure and biochemistry; basic membrane biophysics; cable properties; ion channel biophysics and molecular biology; synaptic transmission; neurotransmitter gated ionotropic systems; and neurotransmitter gated metabotropic systems.

BIOL 6290 Fundamentals of Biological Microscopy (1)
PREREQUISITES: BIOL 2020.

Meets with BIOL 5290. Lecture course providing a foundation in the essentials of microscopy and imaging, including digital imaging, for advanced undergraduates and graduate students. Meets 2 hrs. per week for one half-semester.

BIOL 6420 Genetics and Genome (3)
Cross listed as MBIOL 6420.
PREREQUISITES: BIOL 3510 or equivalent.

This course covers transmission of the genetic analysis in humans and various model organisms. Some of the Molecular Biology Program students have not had adequate preparation in Genetics (such as a comprehensive undergraduate course in Genetics), and have struggled in the graduate course. To prevent such problems, all students will be given a simple exam the week before the semester begins. This entrance exam will cover basic concepts in Genetics. You should have no problem with this entrance exam if you review the CD-Rom/Booklet entitled Interactive Genetics. This review should include all of the problems on the pre-test. You can find the books on reserve at the campus libraries or you can check it out from the Program Office or buy it (ISBN 0-7380-1546-6) for $16.00 from Hayden-McNiel Publishing. To receive further details, please contact Barbara Saffel. For further information please go to: http://www.bioscience.utah.edu/curriculum/corecourses.html

BIOL 6510 Fundamental of Microbial Biology (1.5)
PREREQUISITES: Graduate standing or instructor consent.

This course is a graduate level introduction to the fundamentals of microbial biology. Topics include cell and sub-cell structure, basic metabolism, prokaryote genetics, DNA replication and cell cycle, regulation of transcription and translation, and genomics and diversity.

BIOL 6540 Biochemistry of Membrane Processes (3)
PREREQUISITES: CHEM 3510 or BIOL 3510.
Meets with BIOL 5540.

Explores membrane channels, receptors, and transporters, and associated cellular signaling processes. These are described from diverse perspectives ranging from molecular structure and biophysics to cellular and tissue-level physiology, with emphasis on the diversity of approaches use to understand mechanism. Extensive readings from the primary literature. A review paper is required of students enrolled in BIOL 6540.

ONCSC 6520-001 Physiology & Medicine for the Molecular Biologist
Course leader: Dean Li
FALL - 2008 (2nd half semester) October 20 - December 12

The goal of this course is to provide graduate students in the basic sciences with a richer understanding of human physiology and pathophysiology. This information is critical for understanding the importance of any molecular mechanism at the level of cells, organs and whole animals, and applying this information to humans. This course is aimed for students interested in:

  1. Gaining an understanding on the broad implications of their research and basic science.
  2. Learning how their focus in molecular mechanisms translates to medical interventions.
  3. Obtaining a foundation in anatomy and physiology necessary that is critical for understanding how to characterize genetic engineered animal models
  4. Preparing themselves scientifically for careers in biotech or pharma industry. We will teach the anatomy, physiology and pathophysiology relevant to a given organ system (heart, lung, kidney etc.). The relationship between molecular mechanism, pathophysiology and medicine will be emphasized. Each sections will be organized into three-1 hour lectures. Lectures will include up to date molecular details of interest and relevance to this audience. Though the course will utilize a textbook, McCance and Huether Pathophysiology, class participation is key as we will synthesize information to develop therapeutic strategies of today and tomorrow.

ONCSC 6700-001 Oxidative Stress, Inflammation & Cancer (Advanced Seminar)
Course leaders: Frank Fitzpatrick & Doug Grossman
FALL - 2008 (2nd half semester) October 20 - December 12.
Location: Huntsman Cancer Institute 3rd Floor, Conference Room
Day/Time: Wednesdays 1:30 - 3:30 p.m.

There is increasing recognition of the role of oxidative stress and inflammation in the development of many cancers. This seminar course will focus on basic mechanisms of oxidative damage resulting from environmental exposures and inflammation, cellular response pathways, links to carcinogenesis, and opportunities for chemoprevention in cancer. Students will have the opportunity to read, critique, present and discuss current articles from the literature. There will be no written exam.

ANAT 6010 Gross Anatomy (9)
Anatomy of the thorax, abdomen, pelvis, lower limbs, upper limbs, head, and neck. Includes lectures, dissection, and clinical correlations.

ANAT 6050 Neuroanatomy (3)
Gross and microscopic study of the central nervous system.

ANAT 6060 Embryology (2)
Origin and development of the fertilized egg, development of early tissues and organs, and transformation of the embryo into a fetus. Includes clinical correlations.

ONCSC / TBN Tumor Microenvironment & Hypoxia (Advanced Seminar)
Course Leaders: Eric Huang & Betty Leibold.
SPRING - 2009 (1st half semester) January 12 - March 3

The tumor microenvironment plays an essential role in promoting tumor growth and development. Recent advances in the understanding of oxygen deficiency (hypoxia) at the molecular level have provided new insights into the underlying mechanisms of tumor progression. This seminar course will explore up-to-date literatures on the basic mechanisms and biology of hypoxic responses, with emphasis on their roles in tumor metabolism, signaling, angiogenesis, genetic instability, and metastasis. Students will participate in presentation, discussion, and critique of the literatures.

ONCSC 6150-002 Molecular Mechanisms of Cancer (Didactic)
Course Leader: Steve Lessnick
SPRING - 2009 (2nd half semester) March 4 - April 29

Course Aim: Review current understanding of the molecular and cellular biology of cancer and how this knowledge relates to the diagnosis, treatment and prevention of cancer. Prerequisites: Concurrent enrollment or equivalent 1st year Cell Biology, Molecular Biology and Genetics

ONCSC 6700-011 Utilization of Animal Models in the Development of Clinical Models*
Course Leaders: Dean Li & Kirk Thomas.
SPRING - 2009 (2nd half semester) March 4 - April 29

It is now possible to precisely modify any DNA sequence within the genome of the mouse. This course emphasizes using mouse models to dissect the genetic basis of human disease. Modification of genes using homologous recombination will be covered extensively as will other methods of gene inactivation (anti-sense constructs, inhibitory RNA, etc.). New experimental systems for modeling human disease in zebrafish and drosophila will also be covered. We will use genes of interest from clinical and scientific studies of the class participants as examples (e.g. If you want to knockout a gene for your project, in preparation for your prelims or scientific edification-we will develop the strategy).

MD CH 6560 Biomedical Applications of Mass Spectrometry (2)
Basic principles of mass spectrometry and its application to the determination of molecular structure in chemical and biological problems; uses of stable isotopes, quantitative analyses of drugs by GC/MS and LC/MS. Discussion and problems taken from recent literature.

MBIOL 6440 Gene Expression (1.5)
PREREQUISITES: BIOL 3510 or equivalent.

This course covers both transcriptional and post-transcriptional mechanisms of gene regulation. Lectures cover recent advances in these fields with material based on the primary literature. The transcriptional regulation section covers, basic mechanisms of gene activation and repression, chromatin remodeling machines, regulation of transcription activation by signal transduction cascades. The post-transcriptional section covers mechanisms regulating RNA processing (splicing, editing, and transport), translation and mRNA stability. Grades are based on in-class exams and problem sets.

MBIOL 6480 Cell Biology (1.5)
PREREQUISITES: BIOL 3510 or equivalent.
This course covers basic and advanced topics related to cell structure and function including cytoskeleton, membrane trafficking, protein targeting/modification and degradation, cell cycle regulation, and signal transduction.

MBIOL 6481 Cell Biology II (1.5)
This course will focus on mechanisms regulating cell growth and depth in eukaryotic cells.

MBIOL 7570 Case Studies and Research Ethics (1)
Cross listed as PHIL 7570.

An examination of research integrity and other ethical issues involved in scientific research. Topics may include scientific fraud, conflicts of interest, plagiarism and authorship designation, and the role of science in formulating social policy. This course is designed for graduate students, post-docs and regular faculty in the sciences.

MD CH 5110 Physiological Chemistry I (4)
Prerequisite: CHEM 2320.
Introduction to acid-base theory, amino acid structure and metabolism, stereochemistry, enzyme structure and kinetics, carbohydrate structure and metabolism, lipid structure and metabolism, nutrition.

MD CH 5120 Physiological Chemistry II (3)
PREREQUISITES: MD CH 5110.

Continuation of MD CH 5110. Structure of nucleosides, nucleotides, and nucleic acids, nucleic acid and protein synthesis, genetic engineering, pharmaceutical biotechnology.

MDCRC 6030 Computer Practicum (1)
Practice with statistical software (e.g. Stata) to merge datasets, analyze data, scientific graphing, Monte Carlo simulation, and sensitivity analysis.

MDCRC 6200 Meta Analysis (1)
Meta-analysis approach of combining quantitative, including statistical methods, eligibility criteria of studies, tests of homogeneity, summary measures, sources of variation, and sensitivity analysis.

MDCRC 6210 Regression Models (2)
PREREQUISITES: MDCRC 6000, MDCRC 6010

Linear regression, logistic regression, Poisson regression, Cox regression, including: methods for correlated data (generalized estimating equations and mixed models), testing model assumptions, and assessment of model fit.

MDCRC 6220 Survey Methods (2)
PREREQUISITES: MDCRC 6210.

Design of surveys used in research and practical issues related to their development, application, and interpretation. Topics include methods of data collection, sampling strategies, measurement error, error associated with sampling and non-response, questionnaire format, interview effects and training, and survey evaluation.

BMI 6030 Foundations of Bioinformatics (1.5)
PREREQUISITES: Admission to program or permission from department.

This course includes an introduction to fundamental concepts in bioinformatics and will introduce students to the data that is being managed, databases where this data resides, knowledge bases which are used to associate concepts with each other, and tools of analysis of this data. The course will have a short introduction to terminology and concepts, although it is strongly recommended that students will have had an introduction to molecular biology and genetics concepts in their undergraduate coursework. This course serves as the first course for students who wish to take more advanced courses in these topics. (Required for all biomedical informatics graduate students.

BMI 6105 Statistics for Biomedical Informatics (3)
This course covers a range of statistical methods from classical hypothesis testing to more modern computational methods. The emphasis is on application and practice rather than extensive theoretical derivations. Simulation is used to illustrate properties of distributions, tests and methods. Students are expected to have access to a personal computer and the "R" environment for statistics and computation. (Required for all biomedical informatics graduate students)

BMI 6300 Medical Decision-Making and Knowledge Engineering (3)
PREREQUISITES: BMI 6010.

Quantitative and symbolic approaches to medical decision-making. Statistical methods (discriminant functions, Bayes theorem), decision analysis, utility theory, artificial intelligence, and expert systems. Survey of operational decision-making systems; strengths and weaknesses of a group of approaches. Expert system techniques used in medical decision-making. Conceptual framework for computer-based medical decision-making. Student works with an expert in a medical discipline to conceive and develop an operational expert system.

BMI 6420 Advanced Biomedical Computing (2)
PREREQUISITES: Instructor's consent.

This course presents a survey of advanced techniques for computational science and their application to biomedical problems. The computational techniques presented will include: parallel, distributed and Grid computing. New emerging techniques will be incorporated to the course as appropriate. The course will review all the aspects of these techniques efficiency, portability, scalability, extensibility, security, etc. and provide both hands-on experience and conceptual frameworks to apply advanced computing techniques to problems of interest to the students enrolled in the class.

BLCHM 6410 Protein and Nucleic Acid Biochemistry (2)
Cross listed as MBIOL 6410.
PREREQUISITES: BIOL 3510 or equivalent.

The Biochemistry course covers the structure and function of nucleic acids and proteins, as well as the thermodynamics and kinetics of their interactions with each other and with other biologically important molecules. It is expected that all students have taken an undergraduate course in Biochemistry, and you may find it useful to review chapters discussing the above-mentioned subjects in an undergraduate Biochemistry textbook. You will also need to have a basic working knowledge of kinetics and thermodynamics. (So, if you are not comfortable working with equilibrium constants, free energies, and rate constants, please review these topics in an undergraduate chemistry text.) There are no required texts for this class; readings from various texts will be made available to the class. Some professors may administer a pre-quiz at the start of their lectures to make sure you are adequately prepared for the material to be covered. To receive further details and updates, please contact Barbara Saffel. For more information please go to: http://www.bioscience.utah.edu/curriculum/corecourses.html

BLCHM 6430 Structural Methods (1.5)
PREREQUISITES: BIOL 3510 or equivalent.

This course provides an integrated approach to the applications of NMR and X-ray crystallography in structural biology. Topics covered include: basic NMR theory, and the application of 2D and 3D NMR methods for the determining protein and RNA structures; methods of macromolecular crystallization and crystal structure determination.

BLCHM 6450 Biophysical Chemistry (2)
Cross listed as CHEM 7450.
PREREQUISITES: BIOL 3510 or equivalent.

Topics covered include: Basics of thermodynamics and statistical mechanics, with applications in biochemistry; transport phenomena; enzyme kinetics and inhibition; kinetic isotope effects; principles and applications of absorbance, fluorescence, and CD spectroscopies.

BLCHM 6460 Protein Chemistry (2)
Cross listed as CHEM 7460.
PREREQUISITES: CHEM 2310 and 2320 or equivalent.

This is a one half semester course which focuses on the mechanisms of chemical reactions involving peptides and proteins and methods for their study. Subject matter includes enzyme mechanisms, chemical modification of proteins and cofactor chemistry. Prerequisite: organic chemistry.