Bioscience Curriculum, Fall 2009 and Spring 2009 Courses

SPRING Elective Possibilities (Possible Advanced Didatic Courses)

A TERM: Begins January 11: This course is intended to provide an overview of the methods of chemical analysis used to characterize biological samples. Topics will include a discussion of separations techniques, the spectroscopy of biological molecules, immunological and enzymatic assays, and surface analytical methods.

MWF 11:50-12:40 and Thursday 11:50-12:40 in HEB 2002

B TERM:  Begins March 3: Understanding the biology of a multicellular organism means understanding how its individual cells coordinate their development, behavior, proliferation and death. This is accomplished by intercellular signaling, the subject of this course. Lectures will cover the mechanisms of several eukaryotic signal transduction pathways, and describe how these pathways affect the behavior of cells within developing and adult tissues. The material will include readings and discussion of the primary literature, and emphasize experimental techniques and analyses.

MWF 10:45-11:35 in 4100C HSEB

FULL SEMESTER:   This course will educate physicians and graduate students on the fundamentals of biochemical genetics. Includes inborn errors of metabolism and several common disorders, such as diabetes and hypertension, which have biochemical bases correctable by diet or other medical intervention. Provides overview of biochemical pathways, practical experience on how the biochemical pathways can be studied in vivo and in vitro, the molecular bases of common metabolic problems, the mechanism of inheritance including recurrence risk, and how to rationally treat metabolic blocks.

Mondays: 4:00-6:00 and Wednesdays: 4:30-5:30 room TBD

B TERM:  Begins March 3: This course will review current understanding of the molecular and cellular biology of cancer and how this knowledge relates to the diagnosis, treatment and prevention of cancer.

MWF 3:00-4:00 in 4S HCI

FULL SEMESTER: Cellular and molecular biology of the nervous system development.

Tuesday and Thursday 1:30-2:30 and Friday 10:45-11:45 in 408 MREB

A TERM: Begins January 11: This course will provide students with a rigorous introduction to the theory and practice of DNA and protein sequence analysis. Subjects will include sequence alignment & genome annotation; quantitative models of sequence change; methods for inferring phylogenetic relationships; and linkage mapping. These subjects will be illustrated with examples drawn from a wide range of fields including medical genetics, anthropological genetics, and comparative genome analysis.

Tuesday and Thursday 1:30-3:00 in 2948 HSEB

B TERM:  This course will focus on molecular genetics and structural biology of influenza virus transmission and evolution, the host immune response, and vaccine strategies. Prerequisite: Graduate standing or Instructor's consent. Competence with, or willingness to quickly learn, molecular viewing and sequence comparison programs required. Limit: 12

Thursday 10:30-noon in 747 Wintrobe

FULL SEMESTER. This course will introduce you to polymer in Pharmaceutics and drug delivery, transport phenomena in drug delivery systems, macromolecular and vesicular carriers, biorecognition and drug targeting, protein, oligonucleotide, and gene delivery systems.

Tuesday and Thursday 9:40-11:35 in 421 Wakara Way Room 322

A TERM:  Begins January 11. This course will cover drug properties and chemical principles of drug design, discovery, and development. Emphasis on small molecule interactions with receptors, enzymes, and nucleic acids, library design methodology, computational chemistry, and pharmacological principles.

MWF 1:00-2:00 in 2600 HSEB

B TERM: Begins March 3: This course is intended for graduate students in chemistry, medicinal chemistry, biology, biochemistry, and pharmaceutics. The subject matter will attempt to bridge the gap between organic chemistry and biochemistry pertaining to nucleic acids. Students with no graduate background in organic chemistry should expect to do a little additional reading. Likewise, students with no background in biochemistry may need to do additional reading. Topics include chemical synthesis of DNA and RNA, nucleoside and oligomer analogs, chemistry of DNA damage and repair, nucleic acid-targeted drugs and binding agents.

MWHF 8:35-9:25 in 2006 HEB

B TERM:  Begins March 3: This is a didactic course focusing on the regulation of sugar, fat and protein metabolism in eukaryotes. The course will begin with a review of basic metabolic pathways, with an emphasis on pathway integration and regulation. We will then progress to an in-depth analysis of current research in specific areas of nutritional sensing, signaling and metabolic regulation. The overall goal of the course is to provide students with a foundation for understanding research and literature in the field of metabolism.

The review of basic metabolic pathways will be taught by Janet Lindsley (Biochemistry Department). The advanced lectures will be taught by Drs. Dale Abel (Endocrinology/Medicine/Biochemistry), Don McClain (Endocrinology/Medicine/Biochemistry), Jared Rutter (Biochemistry), Tim Graham (Endocrinology/Medicine/Biochemistry) and Carl Thummel (Human Genetics). Students will teach the final classes. Student assessment will be based on problem sets, classroom participation, and class teaching. Class limit is 20..

MWF 9:40-10:30 in 3420 HSEB

FULL SEMESTER: Understanding how the brain works is one of the deepest and most exciting challenges confronting modern science. This course will explore systems-level functioning of the nervous system, beginning with relatively concrete issues of sensory coding and motor control, and expanding into more abstract, but equally important, higher-order phenomena, such as language, cognitive and mood disorders, states of arousal, and experience-dependent modifications of neuronal operations.

Tuesday and Thursday 10:45-12:05 in 3420 HSEB and Friday 12:55-1:45 in 3430 HSEB

B TERM: Begins March 3. This course is a Continuation of 7891, but also a self-contained course. Focus on chemical biology, including now classical chemical biology and natural biomolecules such as carbohydrates, natural products, metals in biology, lipid signaling, and nucleic acids.

MWF 1:00-2:00 p.m. in 2600 HSEB

FULL SEMESTER: Begins January 11: The use of optics in biology has evolved from the simple light microscope used by Darwin to the complex cryo-electron and live cell high resolution microscopes used today. With all these advances it can now be argued that we stand at the dawn of quantitative biology and optics provides an essential tool in this pursuit. This course is designed to give students a good understanding of physics involved in advanced optics while focusing their attention on the biological problems amenable to these techniques. Students with backgrounds in biology, chemistry or physics are equally encouraged however knowing algebra is a requirement for taking this course. Each section of the course would deal specifically with a special kind of microscopy followed with a case study in a biological problem that is most amenable to the use of the techniques discussed.

Monday and Wednesday 1:30-2:50 in 102 JFB (Physics Bldg)

B TERM: Begins March 3. 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)

Wednesday 1:00-2:30 in 3515C HSEB

A TERM: Begins January 11: This course serves as the introductory microbiology course for graduate students in the Microbial Biology Program. The course begins with lectures on the history of microbiology. 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. In general, lectures are then derived from the primary literature and cover the basics of modern microbiology.

Tuesday and Thursday 12:25-1:45 in 320 JTB

B TERM: Begins March 3: Topics in this course vary each year. Typically, three different faculty members from the Microbial Biology Program present lectures on a current topic in molecular microbiology. Students are encouraged to suggest topics to a faculty member prior to the start of the course.

Tuesday and Thursday 12:25-1:45 in 320 JTB

B TERM: Begins March 3: Basic programming skills are rapidly becoming an essential skill for research in genetics, genomics, and molecular/developmental biology. Emphasis in this course will be on programming essentials for bioinformatics; no prior knowledge will be required. Students will learn the basics of the UNIX operating system, simple command line programming with sed & awk and how to write their own Perl programs. Topics will include manipulating mircoarray data, sequence files, and how to post-process database search results. Skills taught will include: getting around in the UNIX operating system, vi, basic scripting, file IO, regular expressions, subroutines, modules, and object oriented programming. Students will also learn how to leverage existing Perl-based bioinformatics software libraries such as Bioperl. Students will leave the class with their own self-designed programming tool-kit that will provide a starting point for bioinformatics analyses during the remainder of their graduate careers..

Tuesdays and Thursdays 1:00-2:30 in 3100C HSEB

Advanced Seminars

Fall 2009

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.

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. Optaining 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 interaction between molecular mechanism and medicine will be emphasized. Sections are in three one hour lectures. Lectures will include up-to-date molecular details of interest and relevance to this audience. We will emphasize class participation. The course will utilize a textbook, McCance and Huether Pathophysiology.

All graduate student, post doctoral fellows and basic science faculty are welcome.

Please contact Dr. Rutter for the registration number at rutter@biochem.utah.edu and information concerning the course.

A weekly writing workshop and discussion in which you will 1) improve your writing by learning and applying key cocepts in rhetoric, argumentation, and style and 2) turn your term paper, thesis, or dissertation chapter into a publishable scholarly article.

For more information, contact Dr. Natalie Stillman-Webb, University Writing Program at ns13@utah.edu or 581-5623

There are two sessions. Thursdays 6:00-8:00 p.m. and 3:00-5:00 p.m.

Spring 2009

None at this time - 11/20/09

OTHER POSSIBLE DIDACTICS

Fall 2009

The focus of the course is protein NMR spectroscopy and its applications in structural biology. The Textbook is Protein MNR Spectroscopy (Cavanaugh, Fairbrother, Palmer, Rance, Skelton; 2nd Edition 2007). The course will be taught using conventional lectures, student-led topic discussions, and a group or individual NMR project.

The class will meet in the second half of Fall Semester at mutually agreed upon dates, time and place. An organization meeting is planned for early in the semester: 12:00 noon on September 1st in the 3rd floor conference room in EEJMRB.

If you have any questions, please contact one of the instructors before registering.

Instructors: Jack Skalicky (585-7363) and Steve Alam (585-0583)

skalicky@biochem.utah.edu and alam@biochem.utah.edu

Spring 2009

A TERM: Begins January 11. Advanced course

Tuesday and Thursday 3:00-4:00 Room TBD

B TERM: Begins March 3: Classical transmission genetics continues to be a backbone of biological analysis. The development of multiple new tools is adding considerably to the power of transmission genetic analysis, transforming the speed, scale, and resolution of research that can be carried out. This class will focus on how these new methods have been integrated into classical genetics, primarily looking at their utility in workhorse genetic organisms: Drosophila, C. elegans, zebrafish, and mice. Amongst topics to be discussed are: new methods of mosaic analysis and lineage tracing; use of transposons to transform and engineer the genome; logic and design of forward and reverse genetic screens; suppressor and enhancer screens; use of high throughput sequencing methods in gene identification and population analysis; and using genetics in a systems level analysis of biological processes. Not available for 1st year students.

Thursday 2:00-3:30 3420 HSEB

B TERM: Begins March 3: This course will examine the mechanisms and consequences of microbial interactions with host cells and tissues. The means by which microbial pathogens stimulate and overcome host defenses in order to cause disease will be explored. This course is suitable for all graduate students and can be repeated up to three times for credit. Topics change annually. This is a half semester course, offered in the spring.

Monday, Wednesday, Friday 3:00-3:50 Room TBD

Descriptions of other possible coursese are listed above as first-year electives.