The Committee on Cancer Biology - Curriculum
The Committee on Cancer Biology offers a graduate
program of study leading to the Ph.D. in Cancer Biology. The
program provides multidisciplinary training for the student interested
in pursuing a research career in any aspect of Cancer Biology, focusing
on mammalian (particularly human) biology as well as the study of genes
and processes in other eukaryotic organisms. The program provides
doctoral students with the most up-to-date knowledge and research
training in molecular and cellular aspects of Cancer Biology and
prepares the students for leadership positions in the academic
community. The broad range of interests and expertise of the
faculty members of the Committee on Cancer Biology enables students to
concentrate specifically in one of several areas of Cancer Biology such
as apoptosis, cancer cytogenetics, cell cycle, chromosome
damage/repair, drug resistance, metastatic progression, signal
transduction, or tumor biology.
The Biomedical Sciences Cluster
The Committee on Cancer Biology is integrated within a
cluster of graduate programs from the Committee on Immunology, the
Committee on Microbiology, the Committee on Molecular Metabolism and
Nutrition and the Department of Pathology Molecular Pathogenesis and
Molecular Medicine Program. The five academic units share a joint
Admissions Committee, several common courses, a seminar series, and
additional common events for students and faculty within the cluster.
The goal of the cluster system is to encourage interdisciplinary
interactions among both trainees and faculty, and to allow students
flexibility in designing their particular course of study.
In addition, students will have extensive opportunities
for interaction with the three other clusters within the Biological
Sciences Division: the Molecular Biology Cluster: Biochemistry and
Molecular Biology, Developmental Biology, Genetics, Human Genetics and
Molecular Genetics and Cell Biology; the Ecology, Evolution, and
Integrative Biology Cluster; and the Neurobiology Cluster. These
clusters offer courses and sponsor seminars and symposia open to Cancer
Biology students. Many students from the Molbio and Neurobiology
Clusters with cancer research interests are very active in the life of
the Committee on Cancer Biology. The Cancer Biology student will thus
enjoy an exceptional training environment with extensive opportunities
for scientific interaction among a variety of students and faculty.
Formal Coursework
The academic program in Cancer Biology will require that
each student take at least nine graded courses, six quarters of
Introduction to Experimental Cancer Biology, and complete two research
rotations for a total of 10.5 course credits.
The Programmatic Core in Cancer Biology
A student must take the following Cancer Biology core courses:
Cancer Biology Programmatic Core
Cancer Biology 1:
Introduction to Cancer Biology (CABI 30800). Overview of
cancer biology, including epidemiology, pathology, diagnosis and
staging, and the basis for various therapeutic strategies.
Also covered are experimental models for cancer, including the
generation and validation of animal models. The course will
emphasize several tumor models, such as breast cancer, hematological
malignancies, cervical carcinoma, colon carcinoma, and sarcomas.
Conzen, Noffsinger. Autumn.
Cancer Biology 2:
Molecular Mechanisms in Cancer Biology (CABI 30900; MPMM 30900).
This course examines our current understanding of the processes leading
to malignant cell transformation. Topics include comparative
properties of normal cells and cells transformed spontaneously or by
chemicals, radiation, and viruses; multistage mechanisms of
carcinogenesis; genetic basis of cancer; oncogenes and tumor suppressor
genes; metabolic activation of chemical carcinogens; DNA adduct
formation; repair of DNA damage; metastasis/invasion; and mechanisms of
cancer therapeutics. Le Beau, Lingen, Macleod, Maki, Onel.
Winter.
Cancer Biology 3:
Signal Transduction and Cell Cycle Regulation (CABI 31200; NPHP 31200;
CPHY 31200). Topics include receptor ligands, membrane
receptor tyrosine kinases and phosphatases, G proteins,
proto-oncogenes, signaling pathways, cytoplasmic protein kinases and
phosphatases, transcription factors, receptor-nucleus signaling,
development and cancer, genetic dissection of signaling pathways,
oncogenes and tumor suppressor genes, cell growth and cell
proliferation, interplay of cell cycle regulators, cell cycle
progression and apoptosis. Du, Lin. Spring.
Cancer Biology 4:
Frontiers in Cancer Research (CABI 31500-01). This is a
lecture-discussion course on selected topics in Cancer Biology that
will vary from year to year but may include such subjects as
angiogenesis, metastatic progression, experimental animal models and
systems, DNA-mediated gene transfer, cancer cytogenetics, chromosome
damage and repair, growth factors, and cancer therapy.
Rinker-Schaeffer, Lingen. Spring.
Cancer Biology 5:
Introduction to Experimental Cancer Biology (CABI 39000).
This course is related to a seminar series sponsored by the Committee
on Cancer Biology and also incorporates seminars of interest from other
Cluster programs. Typically, students meet to discuss research
papers published by the following week’s seminar speaker, attend the
seminar, and then meet with the speaker afterward. The goal of
the course is to broaden the student’s exposure to current research and
encourage discussion of scientific ideas among peers. Onel,
Peter. Offered every quarter except summer.
The General Basic Science Core
Students will be required to take 1 course in 3 of the
following four areas:
Biochemistry
Proteins 1:
Protein Fundamentals (BCMB 30400). The course covers the
physico chemical phenomena that define protein structure and
function. Topics include: 1) the interactions/forces that
define polypeptide conformation; 2) the principles of protein folding,
structure and design; and 3) the concepts of molecular motion,
molecular recognition, and enzyme catalysis. Prereq: BCMB
30100, which may be taken concurrently, or equivalent. Koide,
Keenan. Autumn.
Fundamentals of
Structural Biology (BCMB 30500). This course emphasizes
the basic principles of protein structure determination by X-ray
crystallography and NMR spectroscopy. The underlying physical concepts
of these methods will be introduced and the capabilities of each will
be discussed and compared in context of their uses in de novo structure
determination and protein engineering studies. Kossiakoff,
Koide. Winter. (This course will not be offered in 2008.)
Proteins 2:
Structure and Function of Membrane Proteins (BCMB 32300).
This course will be an in depth assessment of the structure and
function of biological membranes. In addition to lectures, directed
discussions of papers from the literature will be used. The main topics
of the courses are: (1) Energetic and thermodynamic principles
associated with membrane formation, stability and solute transport (2)
membrane protein structure, (3) lipid-protein interactions, (4)
bioenergetics and transmembrane transportmechanisms, and (5) specific
examples of membrane protein systems and their function (channels,
transporters, pumps, receptors). Emphasis will be placed on biophysical
approaches in these areas. The primary literature will be the main
source of reading. Perozo, Roux. Winter
Cell Biology
Cell Biology 1
(MGCB 31600). Eukaryotic protein traffic and related
topics, including molecular motors and cytoskeletal dynamics, organelle
architecture and biogenesis, protein translocationand sorting,
compartmentalization in the secretory pathway, endocytosis and
exocytosis,and mechanisms and regulation of membrane fusion.
Glick, Turkewitz. Autumn.
Cell Biology 2
(MGCB 31700). This course will cover cell cycle
progression, cell growth, cell death, cytoskeletal polymers and motors,
cell motility, and cell polarity. Win: Glotzer, Kovar.
Genetics
General
Principles of Genetic Analysis (GENE 31400). Coverage of
the fundamental tools of genetic analysis as used to study biological
phenomena. Topics include genetic exchange in prokaryotes and
eukaryotes, analysis of gene function, and epigenetics. Bishop
and Staff. Autumn.
Genetic
Mechanisms (GENE 31500). Advanced coverage of genetic
mechanisms involved in genome stability and rearrangement in lower and
higher organisms. Topics include the genetics of mutagenesis, DNA
repair, homologous and site specific recombination, transposition and
chromosome segregation. Bishop. Winter.
Human Genetics 1:
Human Genetics (HGEN 47000). This course covers classical
and modern approaches to studying cytogenetic, Mendelian, and complex
human diseases. Topics include chromosome biology, human gene
discovery for single gene and complex disease, non-Mendelian
inheritance, mouse models of human disease, cancer genetics, and human
population genetics. The format includes lectures and student
presentations. Cox, Millen, Ober. Autumn.
Molecular Biology
Fundamentals in
Molecular Biology (MGCB 31000). The course covers nucleic
acid structure and DNAtopology, recombinant DNA technology, DNA
replication, DNA damage, mutagenesis and repair, Transposons and
site-specific recombination, prokaryotic and eukaryotic transcription
and its regulation, RNA structure, splicing and catalytic RNAs, protein
synthesis, and chromatin. Staley. Storb Winter.
Molecular Biology
1 (MGCB 31200). Nucleic acid structure and DNA topology;
methodology; nucleic-acid protein interactions; mechanisms and
regulation of transcription in eubacteria, and of replication in
eubacteria and eukaryotes; mechanisms of genome and plasmid segregation
in eubacteria. Rothman-Denes. Winter.
Molecular Biology
2 (MGCB 31300). The content of this course will
cover the mechanisms and regulation of eukaryotic gene expression at
the transcriptional and post-transcriptional levels. Our goal is to
explore with you research frontiers and evolving methodologies. Rather
than focusing on the elemental aspects of a topic, the lectures and
discussions will focus on the most significant recent developments,
their implications and future directions. Singh, Staley. Spring.
Electives
The student will take two elective courses in an area,
or areas, of specific interest to the student, in consultation with the
Curriculum Committee, which will keep the individual interests and the
goals of the student in mind. Students may take additional
electives according to their specific interests. All course
requirements should be completed by the end of the student's second
year.
Genomics and
Systems Biology (CABI 47300). Genomics is a new
field that addresses biological questions by combining large scale
collection of biological data with rigorous mathematical and
statistical design and analysis. This lecture course will explore
the technologies that enable high-throughput collection of
genomic-scale data, including sequencing, genotyping, gene expression
profiling, assays of copy number variation, protein design and
statistical analysis of large data sets, as well as how data from
different sources can be used to understand regulatory networks, i.e.,
systems. Statistical tools that will be introduced include linear
models, likelihood-based inference, supervised and unsupervised
learning techniques, methods for assessing quality of data, hidden
Markov models, and controlling for false discovery rates in large data
sets. Readings will be drawn from the primary literature.
Evaluation will be based primarily on problem sets. Gilad.
Spring.
Laboratory Rotations
The student will complete at least two research
rotations (CABI 30100: Introduction to Research) in different
laboratories. Each rotation will be graded. At the end of
the first year (4 quarters of residence) the student will select an
advisor in whose lab he or she will conduct research.
Preliminary Examination
All first year Ph.D. students will be required to take
an oral preliminary exam in the late summer of their first year.
The exam will take the form of a research proposal. Concepts,
experimental design and interpretation, and the ability to synthesize
and integrate knowledge will be evaluated.
The purpose of the Preliminary Examination is to help both the student
and the Program determine whether he/she has received adequate training
in core areas prior to progression to thesis research. The
Preliminary Examination will be given just prior to the Autumn Quarter
of the student’s second year. By this time it is expected that
the student will have taken a minimum of seven of the nine required
courses (three general core courses; four programmatic core courses)
prior to the exam. An overall grade average of "B" or better from
all courses taken to date is required before taking the Preliminary
Examination.
Purpose: The student must demonstrate that he/she is qualified to
begin independent research by preparing and defending an original
research proposal not in an area directly related to rotation or thesis
research. The student should be able to define a scientific
problem of significance, design experiments to address it, anticipate
possible problems and results, and discuss the significance of
anticipated results. The preliminary examination consists of a
written research proposal, a short oral presentation based on the
proposal, and an oral examination.
Dissertation Committee
All students who pass their preliminary examinations
will set up a dissertation committee within six months of choosing a
thesis advisor. Students will pursue original research (CABI 40100:
Research in Cancer Biology) in the laboratory of their advisor.
During this time students will participate in the Introduction to
Experimental Cancer Biology course, Cancer Biology Journal Club,
Student Research Presentations, Student Seminar Series, and Symposia,
and should consider taking additional courses of interest.
Thesis Proposal
The thesis proposal will be taken preferably in the
Spring Quarter of the student's second year and no later than in the
Autumn Quarter of the student's third year. The thesis proposal will
consist of an oral defense of the student's written research proposal
before the student's dissertation committee. The purpose of the thesis
proposal is twofold, to evaluate the project and the student's
understanding of it, and to evaluate the student's bench skills as
exemplified in research rotations and pursuit of the research project.
Following satisfactory performance in the thesis proposal, the student
will be formally admitted to Ph.D. candidacy. After approval of
the thesis proposal, students are required to meet
with their thesis committee at least once a year. Meetings are
meant
to facilitate and monitor progress in the project and thus can be
scheduled more frequently, if faculty input is sought on particular
problems or choices in research direction.
Dissertation Defense
The Ph.D. will be awarded when the student, working in
concert with his or her doctoral committee, has prepared a dissertation
based upon original research which has been presented in a public
seminar and defended successfully before the doctoral committee.
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