Bioscience Curriculum, Electives

SPRING 2012 Elective Possibilities (Possible Advanced Didatic Courses)

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

T,TH: 1:30-2:30 F: 10:30-11:30 in MREB 408

BIO C 6420

Kay

A TERM:  Begins January 9:  This course will focus on biochemical and biophysical approaches to studying proteins and their functional interactions. Topics covered will include: protein-ligand interactions, cooperativity and allostery, protein folding and design, spectroscopic techniques, analytical ultracentrifugation, calorimetry, biosensors, proteomics approaches, and protein structure prediction.

MWF 9:40-11:00 am in 2908 HSEB

BIO C 6600-001

B TERM:  Begins February 29: 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.

T/TH 9:30-11:00 am in 2908 HSEB

**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.

FULL SEMESTER:  This course addresses key concepts in the ecology and evolution of parasites and pathogens, such as: origins of parasitism, evolution of virulence, disease ecology, host-parasites co-evolution, influences on human history, and Darwinian medicine.

T, Th 10:45-12:05 JTB 230

Th 12:55-3:55

FULL SEMESTER:  Begins January 9:  Techniques of seminar presentation, data analysis, and communication of scientific information from new areas of microbial biology are taught by the Microbial Biology Program faculty.   .

Time/Place: TBA

FULL SEMESTER: Genomics Program Requirement. 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)

MW 1:00-2:20 in 2949 HSEB

B TERM: Begins February 29:  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.

MWThF 8:35 – 9:25am in 2006 HEB

A TERM: Begins January 9:  This course is intended for advanced undergraduate students in Chemistry, Biology, Biochemistry, Biotechnology, and Bioengineering. The subject matter will include a brief background on biomolecular structure and function, then focus on the use of organic chemistry as a tool for manipulating biomolecules, exploring the breakthrough technologies that have enabled recent advantages in fields including protein labeling, protein interactions, biosensors, and nanotechnology.

MWThF 10:45 – 11:35 am 2002 HEB

A TERM:  Begins January 9:  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.

MTWF 11:50-12:40 2010 HEB

S Sakonju
D Grunwald
A Letsou
G Stanfield

G Kardon

A TERM: Begins January 9:  Principles of and topics in developmental biology.  The course is based on reading and discussion of primary literature.  Registration is limited to 30 students.

MWF 1:00-2:30pm 2948 HSEB

N Longo

Pasquali

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.

M 3:30-4:30 W 4:30-5:30 2948 HSEB

Sakonju/Metzstein

B Term: Advanced Class: Classicaltransmission genetics continues to be a backbone of biological analysis. The development of multiple new tools is additing 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 intergrated into classical genetics, primarily looking at their utility in workhorse genetic organisms: Drosophila, C. elegans, zebrafish, and mice. Amongst topics to be dicussed are: new methods of mosaic analysis and lineage tracing; use of transpons 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.

MWF 2:00-3:30 PM 2908 HSEB

HGEN

Cell Biology II

Mechanisms of Signal Transduction

B TERM:  Begins February 29:  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 4100C 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.

T/TH 1:30-3:30 p.m. in 2938 HSEB

Weiss

B TERM: Genomics Program Requirement. Begins February 29:  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.

T Th 1-2:30 p.m. 3100CHSEB

HGEN 6421

A TERM:  Begins January 11: This course addresses issues relevant to the identification of genes that underlie susceptibility to complex diseases. Topics include: design of genome-wide association studies; utilization of affected sibling pairs, discordant sibling pairs and extended families; advantages and disadvantages of isolates versus large populations; gene-gene and gene-environment interaction; deep resequencing to find disease-causing mutations; use of the Utah Population Database.   Methods and principles will be illustrated with discussions of ongoing studies of complex diseases such as inflammatory bowel disease, juvenile idiopathic arthritis, hypertension, common cancers, and psychiatric diseases.
Meets with MDCRC 6420. Med-2-Grad core course.

T, 1:30-3:00PM, 2680 HSEB

MBIOL

Begins January 9.  This is a required course for the MBP students. 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.

M W F 10:45 -11:35 am 3515B HSEB

MD CH

A TERM:  Begins January 9.  In this half-semester course, we cover the basics of drug development and evaluation. The principles of pharmacokinetics, ADME and structure-activity relationships are emphasized. Students will leave the class with the ability to discuss major trends in drug discovery and development, understand the structure-activity relationships and mechanisms of action of major drug classes and appreciate the drug discovery and development process from a chemist’s perspective.

MWF 1:00-2:00 pm 2600 HSEB

MD CH

B TERM:  Begins February 29.  In this half-semester course, we cover several classes of therapeutically relevant biomolecules, including nucleic acids, peptides, carbohydrates, natural products and synthetic molecules. Key aspects of each class of molecules will be discussed, with an emphasis on recent scientific developments in the field. Students will leave the class able to explain the therapeutic relevance of several classes of molecules, analyze the primary literature and design experiments to test key questions at the interface between chemistry and biology.

MWF 1:00-2:00 2600 HSEB

MDCRC

J Shiffman

Personalized Health Care is the tailoring of medical treatment to the individual characteristic of each patient. This course will review the fundamental elements of Personalized Health Care, discuss relevant case studies of preventative and therapeutic applications of Personalized Health Care, and explore future developements. Students will also have the opportunity to devise ways in which Personalized Health Care can be advanced locally, nationally and globally.

M 4:30 PM- 6:10 PM, Rm. TBA

2813

NEUSC

G Clark

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.
Meets with BIOEN 6430

T Th 10:45-12:05 3420 HSEB

F 12:55-1:45 3430 HSEB

ONCSC
6520-002

K Thomas

B TERM:  Begins March 7th ends April 25th.   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).
Med-2-Grad core course.

W 1:00-2:30 p.m. 3515C HSEB

ONCSC
6520-001

Li

Trede

A TERM:  Med-2-Grad core course. Begins Jan. 9: Provides basic science trainees with an understanding of normal and abnormal human physiology and relevant clinical experiences so they can connect their reserach to human disease. The U2M2G faculty includes a cadre of successful physician-scientists to teach this course, which has been oversubscribed since its inception. Each topic/organ system covers: 1)anatomy, histology and embyology; 2)physiology; 3)pathophysiology; 4) current therapeutic challenges. Students make clinical rounds on the various services with faculty and clinical trainees.

MWF 1:00-2:30 p.m. 3515C HSEB

ONCSC

Topham

Trede

Engel

B TERM:  Begins February 29: In this course, participants will be provided with the clinician’s look at cancer:  How is the diagnosis made at the level of clinical exam, through imaging modalities and modern molecular tests?  What are new developments in treatment modalities available to the surgeon, radiotherapist and oncologist?  What are genetic risk factors and how should families be counseled?  A number of specific solid tumors are leukemias will be discussed and emphasis will be placed on bench-to-bedside efforts.  The course is designed for graduate students and post-doctoral fellows in basic science departments with an interest in modern principles and practice of oncology, and complements the Molecular Mechanisms of Cancer course offered in alternating years.  Pre-requisite:  Concurrent enrollment or equivalent 1st year cell biology, molecular biology and genetics.

MWF, 3-4PM, 3S HCI

A TERM:  Begins January 9:  Advanced Course:  This course aims to develop rigor and novelty in thinking about how to conduct hypothesisdriven drug discovery and clinical research. It is an Advanced Seminar in which students will read, analyze and discuss key publications on the development of modern cancer therapeutics. Discussions will include the definition and identification of viable drug targets, drug development hurdles, clinical trials, clinical endpoints, surrogate endpoints, pharmacokinetics, drug-drug interactions, data and safety monitoring, criteria for closure and single versus multi-institution trials. Grades will be based on class presentation and participation. The course is limited to 14.

Date, Time, Location TBA

B TERM:  Begins February 29:  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.

Tuesday and Thursday 3:00-3:50 p.m., location TBA

Weis,Janis
Mulvey

A Term:  Begins January 9:  This course will provide an introduction to bacterial pathogenesis, with emphasis on molecular and genetic determinants of virulence. Topics will include: bacterial toxins, secretion systems and virulence, interaction with host defenses and immune evasion, genetic regulation and exchange of virulence determinants, tissue specific interaction with host receptors, the microbiome, antibiotics and resistance, vaccination, and bioterrorism.  This class is open to advanced undergraduates and to graduate students.

M W Th F, 2:00-3:00 p.m., 2600 HSEB

B TERM:  Begins February 29:  This survey course, including a hands-on component, will cover computational and simulation methods for understanding the structure, dynamics and interactions of biological molecules with an emphasis on topics relevant to therapeutic design, delivery and disposition. Possible topics will include molecular modeling, atomistic simulation, molecular docking, drug design, ADME, homology modeling, high performance computing, and protein structure prediction. We will first review fundamental principles of molecular interaction and then survey various modeling approaches to highlight their ranges of applicability and limitations. Experience with computers is desirable for the laboratory component.

Date, time and location TBA

*Once registered, instructor will decide on a time and place around student's schedule.

A TERM: Genome Science Program core course requirement
Begins January 9: The Applied Genomics class serves tointroduce students to different genomic data types and their analyses. In particular, the use of microarray and next-generation sequencing data in prediction and mutation analysis will be examined. This is an introductory class, and a background in programming or bioinformatics is not required. Class is limited to 14.

4:00-5:00 PM, Day TBA, 3100B HSEB

B TERM: Genome Science Program core course requirement.
Begins February 29: The Applied Genomics class serves to introduce students to different genomic data types and their analyses. In particular, the use of microarray and next-generation sequencing data in prediction and mutation analysis will be examined. This is an introductory class, and a background in programming or bioinformatics is not required. Class is limited to 14

4:00-5:00 PM, Day TBA, 3100B HSEB

Optics in Biology

S.

B TERM:  Begins February 29: 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 basic calculus is a requirement for taking this course. This is a half semester course will meet with 6210 and 4210. 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.

Tuesday and Thursday 10:45-12:05 pm, location TBA

PHYS

A Term: Begins January 9:  This course will provide an overview of the structure and biological function of microtubule- and actin-based motors (including topics of motor regulation). Students with backgrounds in biology or physics are equally encouraged. The class will outline the biological context of motor activity, discuss motor families and details of their mechano-chemical activity as well as related advanced topics.  Cross-listed with 6230 which is a full term course.

Tuesday and Thursday 2:00-3:20 p.m., MLI 1725

S.

FULL TERM:  Begins January 9:  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.
 
Main Textbook:
Bioimaging: Current Techniques in Light & Electron Microscopy by Douglas Chandler  and Robert W. Roberson

Tuesday and Thursday 10:45-12:05 p.m., 207 WBB

Advanced Courses Spring 2011

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

Spring 2011

B TERM: Begins March 2: This is an advanced lecture and seminar course addressing topics of cell biology research and interest.  The course will focus upon original research articles, not a textbook.  Students will be expected to participate in discussions.  Class grade will be determined based upon classroom participation and article presentation based upon some aspect of cell biology covered in this course.

Prerequisite: A course in Cell Biology and exposure to Biochemistry, Immunology, Molecular Biology and Genetics.

Questions can be directed to Diane McVey Ward at diane.mcveyward@path.utah.edu

Tuesday and Thursday – 1:30-3:00 PM – Room TBD

A landscape course surveying the major problems in vision research and ophthalmology, integrating basic principles of visual pathways, significant unsolved problems in the field, clinical correlations, and profiles of key research projects on campus. Interested undergraduate and graduate students are welcomed to this interdisciplinary course cross-linking clinical ophthalmology, genetics, pharmaceutical sciences, neurobiology, and bioengineering.

This will be a survey of the frontiers of vision research going on at Moran and on campus, with each of the (or at least most) sessions correlating a major disease or clinical problem with active areas of research. This should be a fun interdisciplinary course drawing from multiple disciplines.

TBD-Check with Neuroscience Program

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)

A TERM: Begins January 10:  There are many cancers where family history is one of the strongest predictors of an individual’s lifetime risk.  While shared environment certainly contributes to familial risk of specific cancers, inherited susceptibility is the major component.  In the first few weeks of this course, we will explore key papers that describe the identification of various classes of cancer susceptibility genes and/or types of pathogenic sequence variants that they harbor.  This element of the course will survey the spectrum from the high-risk cancer susceptibility genes discovered in the 1990s by linkage analysis to modest-risk SNPs identified by recent Genome-Wide Association Studies.  Later in the course, we look at papers that explore challenges arising from clinical application of cancer genetics knowledge such as the problem of unclassified variants in high-risk genes and the question of why SNP profiles are not yet used in the clinic.  Finally, we look at ways that massively parallel sequencing based techniques such as expression profiling by RNA-seq and mutation screening by whole exome sequencing might power a new generation of susceptibility gene discoveries.

Fall 2011

Spontaneous spreading of tumor cells to distant organs, known as metastasis, is the leading cause of death in cancer patients. Understanding how metastasis occurs is critical for success in developing therapies that prevent dissemination of tumor cells and/or destroy secondary tumors.  In the last decade, a number of new discoveries have greatly contributed to our understanding of metastasis at the cell biological and molecular level.  Importantly, these findings provide the framework for future genetic, molecular and biochemical studies to fully elucidate the mechanisms underlying metastasis and how these mechanisms could be subverted for therapeutic intervention. In this course we will cover known molecular and cellular mechanisms of metastasis, and will discuss the implications for drug development and clinical care.

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

Class meets in 615 Arapeen, #200. First class will meet Sept. 10th (after Labor Day)

Other Advanced Courses Fall 2011

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.

Course dates: October 18 - December 10, 2010

This course will provide a comprehensive introduction into basic cellular and molecular immunology and is suitable for both upper division undergraduate students (5030) having a good general biology background and graduate students (7330) seeking to complement their biological science training. The course will cover innate and adaptive immunity, lymphocyte and macrophage biology, host defense mechanisms against disease, autoimmunity, and immune deficiencies.

HSEB 1730 2:00 – 3:30 PM Tuesday and Thursdays

The primary aim of this course is to provide students with a thorough understanding of contemporary phylogenetic analysis. By integrating methodological, theoretical and philosophical training in phylogenetics, this course provides a unique and interdisciplinary pedagogical approach. These different components complement each other, helping students develop a deeper understanding of phylogenetics that cannot be accomplished with a simple course on methods. This approach reflects the state of the art of the field. In phylogenetics, most contemporary debates concern conceptual issues that must be understood in order to properly design and analyze data. A thorough command of methodology without solid theoretical and philosophical underpinnings can result in misinterpretation of trees or even erroneous inferences of evolutionary history.

Computer lab sessions will coordinate with weekly lectures to provide training in classic and in very new methods in molecular phylogenetic techniques and in the context of philosophical approaches to the problems of tree inference. The student will implement lessons using PAUP, MrBayes, phylogenetics in R, Beast, SplitsTree, Phyml, Muscle, T-Coffee and more.

No previous experience with either philosophy or phylogenetics is required for this course.

Mondays and Wednesdays, 11:50 AM -1:10 PM

The Course: Advanced statistical modeling for biologists is designed for life science graduate students with a perhaps rusty background in mathematics and statistics who wish to become real practitioners of the art of modern statistics. The course will be based on the R programming language, and have the following elements, subject to change by popular demand:
• Introduction to the R language
• Simulating experiments in R
• Analyzing time-to-event data
• General linear models and contingency tables
• Likelihood and modern model fitting techniques

Throughout, the focus will be on the tight link between experimental design, explicit model building, and statistical analysis.

Projects. The project is central to the course, and involves choosing a topic, and presenting the idea, a progress report, and a full poster (or talk) at the end of the semester, along with a formal write-up. These projects should be based on each student’s own area of research or area of research interest, and involve analysis of real or simulated data.

TH 10:45 a.m. – 12:05 p.m., LCB 222