Curriculum

This course covers essential techniques used in genetic engineering. Assuming modest background in biology, the course introduces fundamental aspects of molecular biology including mechanisms for storage of information in DNA and transfer of this information to RNA and protein molecules. Manipulations of DNA molecules to rearrange or remodel genetic information (cloning) are described from both theoretical and practical viewpoints. Topics covered include the use of restriction endonucleases, amplification of DNA sequences using the polymerase chain reaction (PCR), detection of DNA and RNA using hybridization (Southern and Northern blotting), properties of cloning vectors and their use in constructing genomic and cDNA libraries, DNA sequencing and sequence analysis, creating and detecting mutations in DNA and introducing these mutations into a genome, and expression and characterization of proteins.

Fall 2021 Schedule

2.0 Credit Hours, Second Half Semester

Instructors: Greg Ducker & Matt Miller

BC Students should register for Section 001, Class 14692

This course covers transmission genetics, methods of genetic and genome analysis in model systems and humans, as well as transcriptional and post-transcriptional mechanisms of gene regulation. Lectures cover both classical achievements and recent advances in these fields, with readings based chiefly in the primary literature. Grades are based on exams and problem sets. 

In previous years, we have found that some students have struggled in this graduate level course in Genetics. Success in G3 requires a foundational understanding of transmission genetics (i.e. successful completion of an undergraduate course in genetics) as the course focuses heavily on genetic analysis. All students should review the basic concepts and students who have not taken a comprehensive undergraduate course in Genetics or have been working in a lab for a number of years should delay taking G3 until the following Fall and complete a prerequisite undergraduate course.

Fall 2021 Schedule

3.0 Credit Hours, Full Semester

Instructor: Anthea Letsou

MB Students should register for Section 001, Class 4525

Non-program students should contact instructor and Bioscience PhD Office for a permission code to register for Section 002, Class 8541

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.

Cross-listed with MBIOL 6410

Fall 2021 Schedule

2.0 Credit Hours, First Half Semester

Instructors: Paul Sigala and Brenda Bass

Non-program students should contact instructor and Bioscience PhD Office for a permission code to register.

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.

Cross-listed with BLCHM 6410

Fall 2021 Schedule

2.0 Credit Hours, First Half Semester

Instructors:  Paul Sigala and Brenda Bass

MB Students should register for Section 001, Class 4524

Non-program students should contact instructor and Bioscience PhD Office for a permission code to register for Section 002, Class 8540

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.

Cross-listed with CHEM 5440, & CHEM 7450

Fall 2021 Schedule

2.0 Credit Hours, Second Half Semester

Instructor: Jessica M Swanson-Voth

BC Students should register for Section 001, Class 1792

Non-program students should contact instructor for instructions and permission code to register for cross listed Chemistry Department Section

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.

Fall 2021 Schedule

1.5 Credit Hours, Second Half Semester

Instructors:  Adam Hughes and Minna Roh-Johnson

Non-program students should contact instructor and Bioscience PhD Office for a permission code to register for Section 002, Class 10748

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.

Cross-listed with CHEM 5460 & CHEM 7460

Fall 2021 Schedule

2.0 Credit Hours, First Half Semester

Instructor: Vahe Bandarian

BC Students should register for Section 001, Class 7133

Non-program students should contact instructor for instructions and permission code to register for cross listed Chemistry Department Section

Laboratory rotations for students in the Graduate Programs Biological Chemistry.

A signed Rotation Verification Form and a copy of the Rotation Report must be submitted to the Program Office in order to receive credit.

Rotation Schedule for 2021-22

(Please note: these dates do not correlate with the academic quarters.)

Fall 2021 Semester

1st Rotation: Monday, August 30, 2021 - Friday, October 22, 2021

2nd Rotation: Monday, October 25, 2021 - Thursday, December 9, 2021

Spring 2022 Semester

3rd Rotation: Monday, January 10, 2022 - Friday, March 4, 2022

Verbal Lab Commitments Begin: Monday, March 7, 2022

Laboratory rotations for students in Molecular Biology.

A signed Rotation Verification Form and a copy of the Rotation Report must be submitted to the Program Office in order to receive credit.

Rotation Schedule for 2021-22

(Please note: these dates do not correlate with the academic quarters.)

Fall 2021 Semester

1st Rotation: Monday, August 30, 2021 - Friday, October 22, 2021

2nd Rotation: Monday, October 25, 2021 - Thursday, December 9, 2021

Spring 2022 Semester

3rd Rotation: Monday, January 10, 2022 - Friday, March 4, 2022

Verbal Lab Commitments Begin: Monday, March 7, 2022

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.

Cross-listed with PHIL 7570

Fall 2021 Schedule

1.0 Credit Hour

Instructor: Joyce Havstad

Online, can be taken either First Half or Second Half

First Half, Section 001, Class 6095

Second Half, Section 002, Class 17138

In order to teach the skills required to be a successful independent scientist this course will teach students critical thinking strategies for successful research. This will include how to digest and analyze papers and problem solve, both of which will review and apply material from core courses. The instructors will develop specific course content. Topics may include: How to read a paper (read at home, discuss in class); Survey of the core services; Problem solving with open-ended problems posed on real-life or made-up situations. A focused effort will be made to help students identify topics that they can develop into grants in the Spring term. Grading will be based on participation and individual work.

Cross-listed with MBIOL 6200

Spring 2022 Schedule

2.0 Credit Hours, First Half Semester

T & TH 3:00PM-5:00PM, EHSEB 1750

Instructors: Darrell Davis & Eric Huang

BC Students should register for Section 001, Class 10621

In order to teach the skills required to be a successful independent scientist this course will teach students critical thinking strategies for successful research. This will include how to digest and analyze papers and problem solve, both of which will review and apply material from core courses. The instructors will develop specific course content. Topics may include: How to read a paper (read at home, discuss in class); Survey of the core services; Problem solving with open-ended problems posed on real-life or made-up situations. A focused effort will be made to help students identify topics that they can develop into grants in the Spring term. Grading will be based on participation and individual work.

Cross-listed with BLCHM 6200

Spring 2022 Schedule

2.0 Credit Hours, First Half Semester

T & TH 3:00PM-5:00PM, EHSEB 1750

Instructors: Darrell Davis & Eric Huang

MB Students should register for Section 001, Class 10619

Statistics is the underpinning of scientific research. This course offers a broad introduction to methods for statistical analysis of biological and biomedical data with emphasis on the fundamental concepts of probability analysis and statistical inference and the practical application of these concepts to experimental design and data analysis. The focus will be on real-world examples that students are likely to encounter in their own research. By the end of the course, students will gain a solid foundation for understanding how to apply statistical analysis to their own data, rigorously interpreting the biomedical literature, and seeking out additional knowledge when needed. An additional component of this class will be an introduction to the statistical software R, which is one of the most used statistical packages in many disciplines.

Spring 2022 Schedule

2.0 Credit Hours, First Half Semester

M 3:00PM-3:50PM & T, TH 9:00AM-10:20AM, EHSEB TBA

Instructors: Gillian Stanfield & Edgar Hernandez

MB Students should register for Section 001, Class 18952

To prepare students for their thesis research, prelims, and qualifying exams, we will offer a guided proposal preparation course in the second half of the Spring semester that builds on their experience earlier in the semester (critical thinking in research, reading of primary literature and problem solving). The guided proposal writing course will provide an opportunity for students to create an original research proposal by critical review of other grants, training in hypothesis generation, scientific writing, and experimental design. The written original grant proposal will be used as a basis for an oral qualifying examination by a faculty committee.

Cross-listed with MBIOL 6300

Spring 2022 Schedule

2.0 Credit Hours, Second Half Semester

T & TH 3:00PM-5:00PM, EHSEB 2938

Instructors: Clement Chow, Tim Formosa & Megan Williams

BC Students should register for Section 001, Class 10622

To prepare students for their thesis research, prelims, and qualifying exams, we will offer a guided proposal preparation course in the second half of the Spring semester that builds on their experience earlier in the semester (critical thinking in research, reading of primary literature and problem solving). The guided proposal writing course will provide an opportunity for students to create an original research proposal by critical review of other grants, training in hypothesis generation, scientific writing, and experimental design. The written original grant proposal will be used as a basis for an oral qualifying examination by a faculty committee.

Cross-listed with BLCHM 6300

Spring 2022 Schedule

2.0 Credit Hours, Second Half Semester

T & TH 3:00PM-5:00PM, EHSEB 2938

Instructors: Clement Chow, Tim Formosa & Megan Williams

MB Students should register for Section 001, Class 10620

The written original grant proposal prepared in the Guided Grant Preparation course will be used as a basis for an oral capstone examination by a faculty committee. This exam will ensure that students meet our standards for thesis work and review material from the core courses before they join a department and lab. Students will prepare an R21-style grant proposal (~6 single-spaced pages, covering 2 years of work) to be submitted 5 days before the exam. They will present and defend the proposal in front of a 3-member capstone exam committee.

Capstone exams will be held during Final Exam Week:

Thursday, April 28 - Wednesday, May 4

Frequent BC Elective (Biochemistry Research Track)

Frequent MB Elective

This half-semester course will begin with a review of carbohydrate and lipid metabolic pathways, with an emphasis on an integrated understanding the pathways and what is known about their regulation. The course will progress to an in-depth analysis of current research in specific areas of nutritional sensing and metabolic regulation.

Spring 2022 Schedule

1.5 Credit Hours, Second Half Semester

Instructor: Janet Lindsley

T, Th 9:30AM - 11:00AM, EHSEB 2958, Class 3476

Frequent MB Elective

(Counts as 2 electives)

This course 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 is based on the R programming language.

Spring 2022 Schedule

3.0 Credit Hours, Full Semester

Instructor: Donald Feener

M, W 2:00PM-3:30PM, SFEBB 5160A, Class 14845

Frequent BC Elective

Students should gain an understanding of NMR theory, experimental set-up and spectral interpretation/identification of organic molecules from 1D and 2D solution NMR spectra. Specifically:

• Fundamentals of organic structural determination
• Components of the NMR spectrometer, data acquisition and sample considerations
• Chemical shift theory and estimation of 1H and 13C chemical shift through empirical formulas
• J-coupling theory, magnetic equivalence and higher order spectra, and use of spin decoupling for signal enhancement
• NMR relaxation – theory of longitudinal (T1) and transverse (T2) relaxation, experimental measurements of T1 and T2 (inversion-recovery, spin-echo, CPMG), quadrapolar relaxation effects, use of relaxation properties in spectral assignment
• Nuclear Overhauser Effect (NOE) – theory and application
• Multinuclear NMR – spectral interpretation for direct detection of 15N, 19F, and 31P nuclei
• Advanced 1D NMR techniques – theory and spectral interpretation of INEPT, DEPT, TOCSY, NOESY/ROESY data
• 2D NMR techniques – theory and spectral interpretation of homonuclear: COSY, TOCSY, NOESY/ROESY, INADEQUATE; and heteronuclear: 13C/1H HMQC, HSQC, HMBC data

Spring 2022 Schedule

2.0 Credit Hours, First Half Semester

Instructor: Peter Flynn

M, W, F 11:00AM - 12:05PM, JTB 130, Class 15575

Frequent BC Elective (Biochemistry Research Track)

Frequent MB Elective

Prerequisite: 2 semesters undergraduate organic chemistry.

Three lectures, one discussion per week for 7.5 weeks. 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. 

Spring 2022 Schedule

2.0 Credit Hours, Second Half Semester

Instructor: Ming Hammond

M, W, F, 8:20AM - 9:25AM, MCD 230, Class 15769

Frequent MB Elective

Seminar for graduate students. Faculty and topics will change yearly. Consult instructor before registration.

Spring 2022 Schedule

1.0 Credit Hours, Full Semester

Instructors: Mark Metzstein & David Grunwald

W 2:00PM-4:00PM, HSEB 4100D, Class 15682

Frequent BC Elective

Frequent MB Elective

(Counts as 2 electives)

Prerequisites: Complete "Learn the Command Line" from codeacademy.com

This course will provide a comprehensive introduction to fundamental concepts and experimental approaches in the analysis and interpretation of experimental genomics data. It will be structured as a series of lectures covering key concepts and analytical strategies. A diverse range of biological question enabled by modern DNA sequencing technologies will be explored including sequence alignment, the identification of genetic variation, structural variation, and ChIP-seq and RNA-seq analysis. Students will learn and apply the fundamental data formats and analysis strategies that underlie computational genomics research. The primary goal of the course is for students to be grounded in theory and have the ability to conduct independent genomic analyses.

Spring 2022 Schedule

2.0 Credit Hours, Full Semester

Instructor: Aaron Quinlan

T, Th, 9:10AM - 10:30AM, EIHG Gesteland- White Auditorium, Class 15369

Frequent MB Elective

Course work addresses issues relevant to the identification of genes underlying susceptibility to complex disorders. Subjects covered include advantages and disadvantages of isolates versus large population, utilization of affected sibling pairs, discordant sibling pairs and extended families.  Methods taught include traditional case-control association methods and family based methods.  Other subjects include locus and allelic heterogeneity, phenotypic heterogeneity, gene-gene and gene-environment interactions and density of polymorphic markers.

Spring 2022 Schedule

1.5 Credit Hours, First Half Semester

Instructor: Lynn Jorde

W 1:30PM - 3:30PM, EHSEB 2969, Class 7958

Frequent MB Elective

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.

Spring 2022 Schedule

1.5 Credit Hours, Second Half Semester

Instructor: Gabrielle Kardon & Michael Shapiro

T, Th 1:15-2:45, EHSEB 2962, Class 13604

Frequent MB Elective

This course will examine the mechanisms of a variety of eukaryotic signal transduction pathways, and explore 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.

Spring 2022 Schedule

1.5 Credit Hours, First Half Semester

Instructor: Charles Murtaugh

M, W, F 10:45AM-11:35AM, EHSEB 3515B, Class 5554

Frequent BC Elective (Chemical Biology / Medicinal Chemistry Track)

In this half-semester course, we will introduce key concepts in Chemical Biology with an emphasis on examples from the primary literature. Topics will include chemical and biological compound library development, chemical genetics and target identification, and strategies for the development of chemical probes and therapeutic compounds. Students will leave the class with a working knowledge of the field of Chemical Biology and its relationship to medicinal chemistry and drug development, the ability to analyze the primary literature and to design experiments to test key questions at the interface between chemistry and biology.

Spring 2022 Schedule

2.0 Credit Hours, First Half Semester

Instructor: Eric Schmidt

M, W, F 1:00PM - 2:00PM, EHSEB 4100C, Class 19107

Frequent MB Elective

Med-2-Grad Core Course Requirement

(Counts as 2 electives)

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. Deletion 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 zebra fish and C. elegans will also be covered.

 Spring 2022 Schedule

2.0 Credit Hours, Full Semester

Instructor: Anthea Letsou

W 1:00PM - 2:30PM, EHSEB 4100A, Class 12844

Frequent MB Elective

This class is specifically geared toward 1st year MB students.

This course will address core topics in immunology including cellular and molecular mechanisms of innate and adaptive immune responses to infection, vaccines, autoimmunity and cancer immunology and immunotherapies.

Spring 2022 Schedule

1.5 Credit Hours, First Half Semester

Instructor: Scott Hale

T, TH 1:00PM - 2:30PM, EEJMRB Conference RM 5420, Class 15402

Frequent BC Elective

(Counts as 2 electives)

Prerequisite: PHCEU 7010, or Special Permission from Instructor

This course will review fundamental aspects of pharmacokinetics with an emphasis on understanding concepts for compartmental and non-compartmental modeling, physiologic modeling, and modeling of targeted drug delivery systems. The goal of the course is to understand how these techniques can be used to optimize drug delivery.

Spring 2022 Schedule

3.0 Credit Hours, Full Semester

Instructor: James Herron & Shawn Owen

W, F 10:30AM - 12:00PM, EHSEB 2680, Class 11202

Frequent BC Elective (Structural Biology / Biophysics Research Track)

Frequent MB Elective

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.

Not Offered Spring 2022

1.5 Credit Hours, First Half Semester

Instructor: Chris Hill

M, W, F 9:40AM - 10:30AM, Canvas, Class 16992

Frequent BC Elective

Meets with CHEM 5150. This course provides a broad overview of metal sites in biology and is intended for students at the interface of Chemistry, Biology, Biophysics, and related disciplines. It focuses on our current understanding of the role of metals in the structure and function of proteins and nucleic acids, metalloproteins as elaborated inorganic complexes, physical methods used to study metal sites with emphasis on the synergism between model complexes and biochemical studies, and applications in medicine. Three lectures, one discussion per week for 7.5 weeks.

 Not Offered Spring 2022

2.0 Credit Hours, Second Half Semester

Instructor: Matt Kieber-Emmons

M, W, F 9:35AM - 10:40AM

Frequent BC Elective

Frequent MB Elective

Prerequisites: Concurrent enrollment or equivalent 1st year Cell Biology, Molecular Biology and Genetics.

In alternating years, this course is focused on the current understanding of the molecular and cellular biology of cancer along with how this knowledge relates to the diagnosis, treatment and prevention of cancer. The complementary sister-course is focused on clinical cancer biology. It is designed for graduate students and post-doctoral fellows in basic science departments with an interest in modern principles and practice of oncology. It will cover 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.

Not Offered Spring 2022

1.5 Credit Hours, Second Half Semester

Instructor: Sean Tavtigian

M, W, F 3:00PM - 4:00PM

Frequent MB Elective

Basic knowledge of molecular biology is required. The molecular biology of virus lifestyle strategies, including cell entry, nucleic acid replication, gene expression, assembly of progeny virions, interaction with the host cell, and molecular epidemiology. The course will provide both a general introduction to the diversity of virus lifestyles and a detailed analysis of several of these strategies.

Not Offered Spring 2022

1.5 Credit Hours, First Half Semester

Instructor: Vicente Planelles

M, W 1:00PM - 2:30PM

Frequent MB Elective

Prerequisite: A survey course in Immunology (such as PATH 5030) and some exposure to Biochemistry, Cell Biology, and Genetics.

This is an advanced lecture and seminar course addressing topics of immunological 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 a research proposal based upon some aspect of immunology covered in this course.

Not Offered Spring 2022

1.5 Credit Hours, First Half Semester

Instructor: Dean Tantin

T, TH 2:00PM - 3:30PM

Frequent BC Elective (Biochemistry Research Track)

Frequent MB Elective

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.

Not Offered Spring 2022

1.5 Credit Hours, First Half Semester

Instructors: Michael Kay and Wes Sundquist

T, TH 9:40AM - 11:00PM

Med-2-Grad Core Course Requirement

Frequent MB Elective

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.

 Not Offered Spring 2022