Bioscience Curriculum, Fall 2007 and Spring 2008 Courses

Elective Possibilities (Possible Advanced Didatic Courses)

A TERM:  Begins January 7:  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.

MWHF 11:50-12:40 in HEB 2010

B TERM:  Begins February 27: This course will introduce students to some of the major signaling pathways that regulate cell fate and behavior.  Both solid state and soluble signaling pathways will be covered.  Some of the featured pathways will include integrins, notch, receptor tyrosine kinases, Wnt, and nuclear hormone receptors. In addition to formal lectures, original papers will be read outside the classroom and discussed in class.

MWF 9:40-10:30 in 4100C HSEB

FULL SEMESTER course:.   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.

Monday 3:00-5:00 p.m. in HSEB 2948

B TERM:  Begins February 27:  The Clinical Cancer Biology course complements the Molecular Biology of Cancer course. It is designed for graduate students and post-doctoral fellows in basic science departments with an interest in modern principles and practice of oncology. The course will focus on general principles and new developments in cancer etiology, detection, diagnosis, treatment, and prevention. The course is organized around specific diseases, using advances in each area to highlight modern principles and practice of oncology.  Course Capacity:  37

MWF 11:00-Noon in 3C HCI

Cellular and molecular biology of the nervous system development.

Tuesday and Thursday 1:00-2:00 and Friday 2:00-3:00 in 408 MREB

A TERM:  Begins January 7:   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.

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

A TERM:  Begins January 7:   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 1:00-2:30 Room TBA

B TERM:  Begins February 27:    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.

MWF 3:00-3:50 in 2958 HSEB

B TERM:  Begins February 27:  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.

Tuesday and Thursday 1:00-2:30 room TBA

A TERM:  Begins January 7: This course will cover basics of drug discovery and development from a chemistry perspective. Topics to be covered include: Mechanisms and chemistry of representative major drug classes; genetics, genomics, and pharmacogenomics in drug discovery and development; natural products and carbohydrate chemistry; combinatorial and parallel synthesis: HTS; computer-assisted and structure-based drug design; pharmacokinetics and ADME. The course is aimed at chemists and Biological Chemistry Program students interested in expanding their knowledge of biological and medicinal chemistry, but it is also suitable for other graduate students with a basic background in organic chemistry and biochemistry.

MWF 1:00-2:00 in 2600 HSEB

B TERM: Begins February 27:  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.

MWF 8:35-9:25 in 2002 HEB and Thursday 11:50-12:40 in 2010 HEB

A TERM:  Begins January 7: 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.  Class Limit is 20.

MWF 1:00-2:00 in 2938 HSEB

A TERM: This graduate-level course will cover both the theoretical and practical aspects of using light microscopic techniques to analyze biological specimens. We will cover steps including sample preparation and staining, fluorescence and confocal microscopy, digital imaging, image analysis and quantitation, figure preparation, and electronic figure submission. There will be problem sets and a project, for which students are expected to use data from their own research. There will also be hands-on demonstrations in the core imaging facility. Prerequisites: second-year (or later) graduate students.

Tuesday and Thursday 10:45-12:05 and Friday 12:55-1:45 in 501 BPRB

FULL SEMESTER: Cellular and molecular bases of plant development.

Tuesday and Thursday 12:25-1:45 in 110 JTB

Advanced Seminars

Fall 2007

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.

Spring 2008

A TERM: The goal of this graduate seminar will be to read, critique, and debate current hypotheses of neural degeneration (eg. Alzheimer’s, Parkinson’s, Spinocerebellar Ataxia, MS) and explore why the CNS has a limited capacity to regenerate after acute or chronic damage.   

Course Format: The course will meet weekly at a time that will work for most participants. Each student taking the course for credit will give an oral presentation that synthesizes an assigned recent paper with our current understanding of the field of neural regeneration or degeneration, followed by discussion among all participants. A short organizational meeting (TBA) will be held prior to the beginning of class. 

Please contact Michael Bastiani (581-8605, bastiani@bioscience.utah.edu) for further information.

B TERM: The goal of this graduate seminar will be to read, critique, and debate current hypotheses of neural degeneration (eg. Alzheimer’s, Parkinson’s, Spinocerebellar Ataxia, MS) and explore why the CNS has a limited capacity to regenerate after acute or chronic damage. 

 Course Format: The course will meet weekly at a time that will work for most participants. Each student taking the course for credit will give an oral presentation that synthesizes an assigned recent paper with our current understanding of the field of neural regeneration or degeneration, followed by discussion among all participants. A short organizational meeting (TBA) will be held prior to the beginning of class. 

Please contact Michael Bastiani (581-8605, bastiani@bioscience.utah.edu) for further information.

PATH 7850

Research presentations and discussions by students in the genetics training program.
Prerequisite: Instructor's permission required.

B TERM:  Begins February 27:  The metabolism of cancer cells is reprogrammed which provides them with a growth and survival advantage.  This course will cover the mechanisms underlying these metabolic changes and how metabolic changes provide advantages to cancer cells.  Finally, we will cover how the altered metabolism of cancer cells might be exploited therapeutically.  This is an advanced seminar course with a focus of primary literature.  

Pre-requisites:  Cell Biology I & II.  Course Capacity:  15

Tuesday and Thursday 2:30-3:30 in 4C HCI

A TERM:  Begins January 7:  Transcription factors and their interacting proteins are critical regulators of development. This seminar course will explore how transcriptional regulation impacts developmental processes, with particular emphasis on chromatin. In each class, we will explore a paper that makes a conceptual leap in our understanding of transcriptional regulation and then discuss a paper that shows how this concept is applied during cell fate specification and differentiation.   We will examine the role of chromatin in X chromosome inactivation, muscle and neuronal differentiation, organ specification, pluripotency in germ and ES cells, and imprinting/epigenetics. 

Pre-requisite:  Gene Expression  Course Capacity:  14

Friday 9:30--Noon in 2C HCI

B TERM: 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 clinic al 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).

Course Capacity: 15

Wednesday 1:00-2:30 in 4120 EIHG

FULL TERM: This course will provide a brief overview of professional skills for graduate students and postdoctoral fellows, and will focus on how to write grant proposals in the biomedical sciences.

Contact Tracy Marble <tracy.marble@hsc.utah.edu> 1-4820 with any questions.

Thursday 2:00-4:00 in 5100B HSEB

Join us as we read some of the recent intriguing papers discussing the variable roles of the Wnt, Notch, TGF-b, and FGF signaling pathways, in development and disease.  We will think about the properties of these fundamental signaling cascades, and discuss how they interact with each other during development and in disease states. The potential for biomedical interventions in these diseases using the signaling pathways discussed above will also be addressed. 
We welcome any interested students, postdocs and faculty!  The more people, the better!

Contact Sarah <sarah.hutchinson@hci.utah.edu> or Kathy <kmoore@neuro.utah.edu> with any questions.

Wednesday 3:30-4:30 in 408 MREB

OTHER POSSIBLE DIDACTICS

Fall 2007

No Descriptions Available

Spring 2008

A TERM: This graduate-level course will cover both the theoretical and practical aspects of using light microscopic techniques to analyze biological specimens. We will cover steps including sample preparation and staining, fluorescence and confocal microscopy, digital imaging, image analysis and quantitation, figure preparation, and electronic figure submission. There will be problem sets and a project, for which students are expected to use data from their own research. There will also be hands-on demonstrations in the core imaging facility.

Prerequisites: second-year (or later) graduate students.

Full Semester: This course covers basic and clinical aspects of human physiology. All major organ systems including nervous, cardiovascular, respiratory, gastrointestinal, endocrine, and renal will be presented by physiologists with expertise in each respective area. The course is open to graduate students from all science majors.

Course Capacity: 25

Tuesday and Thursday 1:00-3:30 in suite 1420, 420 Chipeta Way (Reseach Park)

FULL TERM: This course will provide a brief overview of professional skills for graduate students and postdoctoral fellows, and will focus on how to write grant proposals in the biomedical sciences.

Contact Tracy Marble <tracy.marble@hsc.utah.edu> 1-4820 with any questions.

Thursday 2:00-4:00 in 5100B HSEB

In this session we will cover the fundamentls of microbial bilogy. This includes cell and sub-cell structure, metabolism, genetics, DNA replication and cell cycle, DNA repair and recombination, regulations of gene expression, and genomics and diversity. For more information about this course contact Stan at williams@biology.utah.edu

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

Four different, specialized topics will be offered each spring. This year's topics are: 1) Chemotaxis by Sandy Parkinson; 2) Endosymbionts by Colin Dale; 3) Biological Motors by David Blair; 4) Phage Biology by Sherwood Casjens

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