BIO/CBI 282/283(282 Mechanisms of Development/ 283 Developmental
Genetics) - These two courses are targeted to first year graduate
students in the Biological Sciences. They are taught sequentially as two
half-semester minicourses, in the Fall semester. Mechanisms of development
will introduce basic concepts of cell specification, morphogenesis, induction,
and other mechanisms that enable cells, tissues and organs to assemble
the animal. Developmental genetics will focus on genetic approaches to
solve mechanistic problems of development. Coverage will focus on the
use of model organisms, mainly Drosophila, C. elegans, mouse and zebrafish,
in which genomics, mutational analysis, gene modifiers, epistatic relationships,
gene knockouts, and transgenics have yielded important insights into the
differentiation of cells and the development of complex organisms. T Th
10:55 - 12:10, 384 Nanaline Duke, McClay, Klingensmith, 2 units each.
BIOCHEM 258 – Structural Biochemistry I: Structure of Macromolecules
- Introduction to the principles of macromolecular protein structure
and function. Examples of methods of structure determination. This course
is intended to give a survey of protein structures and of how to use structural
analysis to understand how proteins work. Minicourse, 1st half-semester.
M W F 2:20 – 3:10.
BIOCHEM 259 – Structural Biochemistry II: Molecular Biology
I - Continuation of BIOCHEM 258. Structure/function analysis
of proteins as enzymes, multiple ligand binding, protein folding and stability,
allostery, protein-protein interactions. Prerequisites: BIOCHEM 258, organic
chemistry, physical chemistry, and introductory biochemistry. This is
an introductory course to learn how to use quantitative methods to understand
biological structure and function. Minicourse, 2nd half-semester. M W
F 2:20 – 3:10.
BIOCHEM 267 – Molecular Genetics I: DNA and Genome Stability
- Chromosome structure, replication, repair, genetic recombination,
mutation and chromosome rearrangement. Molecular Genetics I & II are
part of a 3 half-semester course series. This series is literature-based
and covers the subject in depth. The third part (Molecular Genetics III)
is taught in the spring and is listed as GENETICS 260. Minicourse, 1st
half-semester. T Th 10:55 – 12:10.
BIOCHEM/UPG/CBI 268 - Biochemical Genetics II: From
RNA to Protein - Mechanisms
of transcription, splicing, catalytic RNA, RNA editing, mRNA stability and translation.
Mini-course, 2nd half semester. Tu Th 10:05-11:20, (TBA), Steege and Staff.
and Genome Technology
BGT 200/STA 270 - Statistical Methods for Computational
Biology - Methods of statistical inference and stochatic modeling with application to
functional genomics and computational molecular biology. Topics include: statistical
theory underlying sequence analysis and database searching; Markov models; elements
of Bayesian and likelihood inference; discrete data models; applied linear regression
analysis; multivariate data decomposition methods (PCA, clustering); software
tools for statistical computing. This course presupposes previous exposure to
mathematics and statistics at the level of the BGT program prerequisites. W F
11:40-12:50, 143 Jones, Staff.
BGT 204/COMPSCI 260 - Algorithms in Computational
Biology - Provides
a systematic introduction to the algorithms behind the most commonly-used
tools in computational biology. Surveys a wide range of methods in the
field and provides a significant amount of exposure to actual tools,
but primary emphasis is on understanding and analyzing the algorithms
behind these tools. Introduction to common techniques in algorithmic
design and analysis, including design of data structures and analysis
of running time. Covers dynamic programming, string matching, probabilistic
techniques, geometric algorithms, hidden Markov models, data mining,
and complexity analysis. Topics explored in the context of applications
of genome sequence assembly, protein and DNA homology detection, gene
and promoter finding, protein structure prediction, motif identification,
analysis of gene expression data, functional genomics, and phylogenetic
trees. Tu Th 10:05-11:20, LSRC D106, Agarwal or Hartemink.
BGT/IMM 213S - Computational Immunology and Immunogenomics
will integrate empirical and computational perspectives on immunology
and host defense. Students are expected to have significant preparation
in either biomedicine or a quantitative science. Topics covered are intended
to provide an entree into the use of computational methods for research
and practice in immunology and infectious disease, from basic science
to medical applications. Consent of instructor required. Tu 4:30-7:00,
(TBA), Kepler and Cowell.
and Molecular Biology
CMB 201 Elements of Molecular Biology and Genetics - T/Th
4:00-5:15pm; TBA; 208 CARL Bldg **Not listed in ACES
CMB 297 Modern Techniques in Molecular Biology - This course
is divided into two sections. One section deals primarily with techniques
used for protein purification and analysis, and for the study of protein-protein
interactions. The second deals with the molecular biology aspects, including
discussions of nucleic acid sequencing and manipulation, cloning strategies,
vectors, expression, hybridization and blotting methods, PCR, etc. Minicourse,
1st half-semester, MWF 9:10-10:00am; Casey;147 Nanaline Duke Bldg; 2
CMB 247 Macromolecular Synthesis - The macromolecular
synthesis course covers basic mechanisms of DNA synthesis, RNA transcription,
protein translation, and protein stability. The material will be covered
through discussion sections on both review articles (to provide adequate
background) and current primary literature. Students will be expected
to present data from papers covered in class and to participate in detailed
discussions of those papers. Students will also write minireviews on
current topics in DNA/RNA/protein synthesis. Minicourse, 2nd half-semester
MWF 8-9 Kornbluth; 147 Nanaline Duke Bldg; 2 units.
CBI 212 Cell & Molecular Biology of Reproduction - This
course focuses on the recent cellular and molecular investigations that
have dramatically advanced our understanding of reproduction. The general
areas to be covered include neuroendocrinology, reproductive endocrinology,
gametogenesis, and fertilization; within these topics, studies in areas
such as gene regulation, intercellular communication, hormones, growth
factors and signalling will be emphasized. In addition to didactic presentations,
students are expected to read and present selections from the primary
literature. An interactive approach is encouraged. Meeting time is arranged
each year for maximum compatibility with the participants' schedules.
Time: Variable Saling & Schomberg
ENVIRON 212 - Environmental Toxicology - Study of environmental contaminants
from a broad perspective encompassing biochemical, ecological, and toxicological
principles and methodologies. Discussion of sources, environmental transport
and transformation phenomena, accumulation in biota and ecosystems. Impacts
at various levels of organization, particularly biochemical and physiological
effects. Prerequisites: organic chemistry and vertebrate physiology or consent
of instructor. M W 11:40 AM-12:55 PM, LSRC A312, Di Giulio.
Program in Genetics
UPG 224 Fundamentals of Human and Mouse Genetics - The
genomic resources and technologies associated with the Human Genome Initiative
provide opportunities for understanding and treating human genetic disease.
In addition, these resources have vast implications for research in all
biologic and biomedical science. This course is aimed at scientists with
limited genetic background who desire a broader understanding of the
concepts and tools available to the geneticist. Topics range from review
of meiosis, linkage and recombination, relationships between phenotype
and genotype, and inheritance patterns, to mapping of genes via genetic
and physical mapping tools, to mouse models of human disease (strains
and crosses, knock-outs and transgenics). The social, legal, and ethical
implications of understanding genetic disease will also be reviewed.
Minicourse, 1st half semester, T. Th. 9:10 - 10:25, Speer and Capel,
UPG 225 - Readings in Human Statistical Genetics
- In-depth readings
of classical human statistical genetics papers that shaped the field
including Morton's lod score analysis, Penrose's affected sibling pair
studies, and the Elston-Stewart algorithm, among others. Student-led
discussions of content. W 8:30 AM-10:00, Speer and Scott.
UPG 278 Genetics - Solutions to Biological Problems - This
course provides an in-depth grounding in the use of genetic approaches
to address research problems in cell and developmental biology. It begins
with genetic fundamentals including dominance, linkage, complementation,
types of mutants (loss of function, conditional, partial-function, dominant
active & dominant negative), and genetic interactions (epistasis,
suppression, synthetic lethality, intragenic complementation, nonallelic
noncomplementation). There is a focus on the devising and interpretation
of genetic screens, the application of reverse genetic approaches, and
the use of mosaic analysis. All are covered with emphasis on how they
are applied to address research problems, and are repeatedly encountered
in both classical and modern molecular context (e.g. enhancer traps,
PCR mutagenesis, etc.). Students gain familiarity with several major
genetic model organisms, and encounter topics at the cutting edge of
modern genetics. Classes are held three afternoons per week: two are
socratic-style discussions and one is literature-based. 4 credits. M
W 2:00- 3:45; Kiehart; 4 units.
UPG/BIO 281 - DNA, Chromosomes, and History - Past and
present research on evolution, genetics, and chromosome biology. The
curious path to our present understanding of inheritance including how
genes got put on chromosomes and the fluctuating fortunes of DNA. Implications
of current research on chromosome and genome organization for evolutionary
biology. Prerequisite: an introductory course in genetics or cell or
molecular biology, or consent of instructor. Tu Th 2:50-4:05, LSRC A155,
UPG 287/BIO 187 - Evolutionary Genetics - An introduction to the principles
of evolutionary genetics, with discussion of the current literature.
Levels of selection; neutral theory; variation in populations; speciation.
Reconstructing evolutionary history; genomic evolution. W F 1:15-2:30,
Bio Sci 144, Staff.
IMM244 Principles of Immunology - This is a graduate
level course that is open to both graduate students and advanced undergraduates.
It is an introduction to the molecular and cellular basis of the immune
response. Topics include anatomy of the lymphiod system, lymphocyte biology,
antigen-antibody interactions, humoral and cellular effector mechanisms,
and control of immune responses. The last third of the course focuses
on special topics and application such as transplantation, autoimmunity,
immunodeficiency, and tumor immunity. On selected days, the class is
broken down into small discussion groups of approximately 15 students
to discuss material introduced in the lectures or to work on problem
sets. Graduate students in the Department of Immunology lead these sections.
M W F 1:10 – 2:00; Dawson; 143 Jones Bldg; 3 units.
MCB/PHARM 418 - Molecular Mechanisms of Oncogenesis - Lectures, oral
presentations, and discussions on advanced topics and recent advances
in the molecular biology of cancer. Particular emphasis on strategies
to exploit this information in the design of intervention strategies
to selectively block the growth of cancer cells. Prerequisite: Cell Biology
417. M W 10:05 AM-11:20, LSRC C335, Counter and staff.
Genetics & Microbiology
MGM/GEN 300 - Gene Regulation - Principles of prokaryotic
and eukaryotic gene regulation at transcriptional and post-transcriptional
levels. Topics include promoter sturcture and transcription factor function;
processing, transport, and degradation of mRNA; translation. Gene regulatory
pathways will be discussed. Time and place TBA; Matsunami, Nevins, Keene,
Cullen, Gromeier; 3 units.
PHR233 Essentials in Pharmacology & Toxicology - This
is a graduate level course that is open to both graduate students and
advanced undergraduates. This course will discuss in depth how drugs
and toxins affect living organisms by interacting with specific receptors.
The emphasis is on general principles and mechanisms rather than specific
examples. Topics include: Kinetics of Drug Action; Blood-brain and placental
barriers; Biotransformation; General Principles of Receptor Action; Receptor
Families; Signal Transduction; Intracellular Targets Tolerance and Dependence;
Discovery of New Drugs; Developing Lead Compounds; Structure-Activity
Relationships; Chemical Libraries, Structure-Based Design. M W F 3:55-5:10;
Slotkin; room A156 LSRC, 4 units.
BIOCHEM 222 Structure of Biological Macromolecule - Computer
graphics intensive study of some of the biological macromolecules whose
three-dimensional structures have been determined at high resolution.
Emphasis on the patterns and determinants of protein structure. Two-hour
discussion session each week along with computer-based lessons and projects.
Th 2:00 – 4:00.
BIOCHEM 291 Physical Biochemistry - Basic principles
of physical chemistry as applied to biological systems. Topics include
thermodynamics, kinetics, statistical mechanics, spectroscopy, and diffraction
theory. Concepts discussed in the context of the biochemistry and behavior
of biological macromolecules. Emphasis on quantitative understanding of
biochemical phenomena, with extensive problem solving as an instructive
tool. Prerequisite: undergraduate physical chemistry and one year of calculus.
M W F 11:30 – 12:20.
BIOCHEM 417 Cellular Signaling - Mechanism of action
of hormones at the cellular level including hormone-receptor interactions,
secondary messenger systems for hormones, mechanisms of regulation of
hormone responsiveness, regulation of growth, differentiation and proliferation,
mechanisms of transport and ion channels, stimulus sensing and transduction.
Some lectures stress the clinical correlation of the basic course concepts.
M W F 8:00 – 8:50.
and Genome Technology
206 - Genome Technologies - This course introduces the laboratory and computational
methodologies for genetic and protein sequencing, mapping and expression measurement.
Tu Th 10:05-11:20, Sanford 224, Staff.
BGT 207/STA 277 - Computational Methods for Macromolecular
Structure - This course covers concepts of modeling and computation in approaches
to structure prediction in modern proteomics. It introduces advanced
probabilistic models and associated inference tools and will involve
custom computer programming in standard languages. M W 1:15-2:30, Perkins
BGT 208/STA 278 - Gene Expression Analysis - This course covers topics
spanning the technological and computational areas of modern gene expression
analysis, developing computational methods in important and current problems
of clinical and physiological phenotyping, including custom computation
and algorithmic development. M 2:50-5:30, Languages 08, Staff.
BIO 284 - Molecular Population Genetics - Genetic mechanisms
of evolutionary change at the DNA sequence level. Models of nucleotide
and amino acid substitution; linkage disequilibrium and joint evolution
of multiple loci; analysis of evolutionary processes, including neutrality,
adaptive selection, and hitchhiking; hypothesis testing in molecular
evolution; estimation of evolutionary parameters; case histories of molecular
evolution. For graduate students and undergraduates with interests in
genetics, evolution, or mathematics. Tu Th 8:30-9:45, Bio Sci 0018, Uyenoyama.
BIO/UPG 286 - Evolutionary Mechanisms - Population ecology
and population genetics of plants and animals. Fitness concepts, life history
evolution, mating systems, genetic divergence, and causes and maintenance of
genetic diversity. Prerequisites: Biology 25L and 120 orequivalents. Tu Th 10:55-12:10,
Bio Sci 144, Rausher and Uyenoyama.
CBI 203 Introduction to Physiology - The objective of
the course is to provide an introduction to Human Physiology. The course
is intended for students who have not had human physiology. At the end
of class, students should be able to understand how the basic organ systems
(lung, cardiovascular, gastrointestinal, endocrine, and kidney) of the
body work and how the systems are coordinated. M W F 9:00–10:00;
Jakoi/Wright; 439 Nanaline Duke Bldg; 2 units, first half-semester.
MCB/CBI 208: Stem Cell Biology. This course is designed
for first-year graduate students to learn the fundamentals of stem cell
biology and to gain familiarity with current research in the field. The
course will be presented in a lecture and discussion format based on
the primary literature. Topics include: stem cell concepts, methodologies
for stem cell research, embryonic stem cells, adult stem cells, cloning
and stem cell reprogramming, and clinical applications of stem cell research.
Prerequisites: undergraduate level cell biology, molecular biology, and
genetics. Instructors: Tannishtha Reya, Brigid Hogan. Tentative
schedule: T Th 9:00-10:30. 3 units.
CBI 296 Developmental Biology Colloquium - Covers a broad range
of problems in developmental biology and is guided by the interests of
developmental biologists who will be speaking at Duke University during
that particular semester. Example of topics are axis specification, embryogenesis,
tissue polarity, RNA localization, axon guidance, plant developmental
timing, and signaling pathways such as Notch, wingless, hedgehog. M 5:00-600
W 4:00-6:00; Klingensmith; 3 units.
Program in Genetics
UPG 200 - Genetic Analysis for Human Disease - Quantitative and molecular
aspects in the identification of human disease genes, implications for genetic
counseling and risk assessment, and legal and social issues associated with
the human genome initiative. Concepts of linkage analysis in Mendelian and
complex disease, molecular approaches to disease gene cloning, molecular mechanisms
of disease gene expression, gene therapy, and the utility of animal models
for understanding human disease. Prerequisite: University Program in Genetics
278 or equivalent, and graduate status or consent of instructor. W 10:30-12:00,
LSRC B102, Marchuk.
UPG 222 Genetic Analysis of Cellular Function - This
class uses studies of fungi as a basis to discuss genetic approaches
to cell biological problems. Topics covered include signal transduction,
cell cycle, nutrient sensing, prions and genomics. 2-3 papers are assigned
for each class and the class is driven by in-depth, critical discussion
of these papers T Th 4:00-5:30; Heitman and Lew; 3 units.
Genetics & Microbiology
MGM/UPG 232 - Human Genetics - Topics include segregation, genetic linkage,
population genetics, multifactorial inheritance, biochemical genetics, cytogenetics,
somatic cell genetics, neurogenetics, cancer genetics, clinical genetics, positional
cloning, complex disease. Lectures plus weekly discussion of assigned papers
from the research literature. Prerequisites: University Program in Genetics
278 or equivalent, and graduate status or consent of instructor. Tu Th 8:30
AM-9:45, (TBA), Marchuk, Pericak-Vance, and Speer.
MGM 252 General Virology and Viral Oncology - (Summary
[Graduate core course]) - This course explores the molecular
biology of mammalian viruses, with major emphasis on mechanisms of virus
replication, virus-host-interactions, viral pathogenicity, and the relationships
between virus infections and cancers. M W F 10:30 -11:20; Keene; 418
Jones Bldg; 3 units.
MGM 282 Microbial Pathogenesis - (Summary [Graduate
Core Course]) Modern molecular genetic approaches to
understanding the pathogenic bacteria and fungi. The course also examines
underlying mechanisms of pathogenesis and host- parasite relationships
that contribute to the infectious disease process. M W F 3:55 - 4:45;
Kreuzer & McCusker;
418 Jones Bldg; 3 units.