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The Graduate Studies Program
A critical mass of outstanding developmental biologists
trains new leaders in the attack on the fundamental problems of development
in a wide group of organisms; provides wider and more general teaching of developmental
biology; and provides a focal point for communication and collaboration among
scientists throughout the University.
These research activities impinge upon the problems of developmental biology. As knowledge of the molecular mechanisms controlling normal development grows, the department is expected to play an increasingly important role in interacting with clinically-oriented developmental biologists in devising the means for preventing and treating the abnormalities of human development.
Students in the PhD program in Developmental Biology may apply for an M.S. degree, assuming completion of their course requirements and the preparation of a written proposal. (The Masters degree awarded by the Department of Developmental Biology will not include the possibility of minors for graduate students enrolled in other departments or programs.)
Students are required to take, and satisfactorily complete,
at least six courses, including Developmental Biology (210), Advanced Genetics
(203), Frontiers in Biological Sciences (215) and an advanced molecular biology,
biochemistry or biophysics course. Students are also expected to attend Developmental
Biology seminars and journal clubs.
Entering students are normally offered research
assistantships that include payment of a stipend and remission of tuition.
Students are encouraged to apply for outside support from foundations and other
non-Stanford sources.
Graduate Students are required by the University to register for Autumn, Winter, Spring and Summer quarters each year until the degree is received. Registration is also required each quarter in which Stanford financial award is received. Leaves of absence require approval before departure.
Axess is a computerized service that students use from computers and terminals in University residences, labs, offices, and off-campus locations via modem to complete many administrative tasks. Through Axess, you can file your registration commitments, review your grades, request an offical transcript, review your status regarding degree requirements, give the University your correct address, file and amend your study list, apply for housing, etc. To get to AXESS go to the following website: http://axess.stanford.edu.
New Students use Axess at any time after receipt of the
registration packet from the Registrar's Office. You are free to update
addresses and phone numbers (including e-mail addresses), biodemographic information,
and elect your privacy options before you arrive for orientation.
Program of Study
The Department of Developmental Biology offers a Ph.D. program designed to prepare
men and women for careers in research and teaching. The program also includes
those pursuing the M.D./ Ph.D. combination.
The first year curriculum, which is carried out on the
quarter system, includes consecutive courses in Genetics, Biochemistry, Cell
Biology and Developmental Biology. Specialty courses are offered in the
second year. Students are also expected to attend the Developmental Biology
Seminar Series and Journal Club. Letter grades will be given for all core courses
except Frontiers. In addition to the required courses, many students also
take Cell Biology of Physiological Processes (MCP211; offered in the Winter
quarter). And may choose from a variety of elective courses that are offered
on a rotating basis. The first year students should meet with their Advisory
Committee to determine their course schedules. Course requirements are
fulfilled during the first two years of study; the latter years of the program
are devoted to full-time research and work on the dissertation. Admission
to candidacy for the Ph.D. degree requires completion of a qualifying examination
at the end of the second year. The University requires that a minimum
of three (3) units of coursework be taken with each four (4) or more Stanford
faculty members, not necessarily within the major department.
Curriculum
Course requirements for the Graduate Program in Developmental Biology are as
follows:
1) Research (DB399; 3 rotations during the
first year)
2) Frontiers in Biological Sciences (DB215; taken each of the first
two quarters during the first year).
3) Advanced Genetics (Genetics 203/ DB 203)
4) Developmental Biology (DB) 210
5) An advanced molecular biology, biochemistry, or biophysics
course. Possible courses that would fulfill this requirement
are: Graduate Molecular Biology (Biochem 201), Physical and Chemical
Principles of Biochemistry (Biochem 214), Computational Molecular
Biology (Biochem 218), Principles of Cell Physiology (MCP 210),
Protein and Nucleic Acid Structure, Dynamics and Engineering
(Structural Bio 228), Eukaryotic Chromosome (Structural Bio
229). Other courses not listed may be used to fulfill this
requirement contingent on prior approval of the faculty
coordinator. Alternatively, this requirement may be fulfilled
by acting as a T.A. for Biochemistry 200 or 203.
6) At least two additional courses.
Research rotations are an important part of the training
program, designed to broaden the research experience and to familiarize students
with the department's ongoing research efforts. First-year students spend
one quarter in each of three different laboratories. The Fall quarter
rotation must be in a laboratory within the Department of Developmental Biology.
Rotations during the Winter and Spring quarters may be in any laboratory within
the biosciences at Stanford. At the end of the third quarter, students
choose a laboratory in which to carry out dissertation research. It is
the student's responsibility to contact appropriate faculty members to arrange
lab rotations. Research is conducted in an environment that encourages
creativity, collaboration, open and continuous exchange of ideas and the highest
level of commitment to science.
Developmental
Biology Course Offerings
(Same as Genetics 203, Biological Sciences 203). This course will focus on the underlying genetic logic used to dissect apart diverse biological phenomena. The course explores the genetic toolbox through studies of analytic methods and modern synthetic genetic manipulation, including original papers. Emphasis is on use of genetic tools in dissecting complex biological pathways, developmental processes, and regulatory systems. We will discuss classical genetic approaches as well as newer approaches being developed in the post-genome era (in which the entire genomic sequence of an organism is known.) Graduate students in any one of the biological sciences are welcome, but those with minimal experience in genetics should prepare themselves by working through problems in Hartl, et al and Jones. (4 units, Aut)
(Same as Biological Sciences 204 and Genetics 204). Continues exploration, begun in Genetics 203, of basic concepts and experimental design in modern Genetics. Emphasis is placed on studying genetic systems in detail from original papers as well as the impact of genomics on experimental design and practice. Prerequisite: Genetics 203. (3 units, Win) offered upon request of students
This course focuses on the mechanisms that direct human development, from conception to birth. Conserved molecular and cellular pathways regulate tissue and organ development in humans and other species. Errors in these pathways result in congenital anomalies, and common human diseases. Topics include: molecules regulating development, cell induction, developmental gene regulation, cell migration, programmed cell death, pattern formation, stem cells, cell lineage, and development of major organ systems. Emphasis is devoted to links between development and clinically significant topics, including infertility, assisted reproductive technologies, contraception, pre-natal diagnosis, multiparity, teratogenesis, inherited birth defects, and fetal therapy. Lectures connect fundamental discoveries in developmental biology to advances in disease diagnosis, therapy, and prevention in clinical medicine. (2 units, Autumn)
(Same as Biological Sciences 208). The goal of the course is to discover unifying themes in how organismic complexity is generated during embryonic and post-embryonic development. The roles of genetic hierarchies, induction events, cell lineage, maternal inheritance, cell-cell communication and hormonal control in developmental processes in well-studied organisms such as mammals, zebrafish, insects and nematodes will be discussed. This course is designed to acquaint graduate students and advanced undergraduates (with permission of the instructor only) with important current areas of research in developmental biology. It is recommended that preparation for the course include familiarity with basic techniques and experimental rationales of molecular biology, biochemistry and genetics. Two lectures each week will be accompanied by a third meeting during which small groups of students will meet with faculty to discuss current papers from the literature in depth. Team taught by members of the faculty of Developmental Biology. (5 units, Spr)
(Same as Biochemistry 215). Faculty-student discussion course with emphasis on how to critically evaluate primary research literature in many different areas of biological research. Held in conjunction with a Wednesday seminar series, hosted in alternate weeks by the departments of Biochemistry, Genetics, Developmental Biology. Each Wednesday a distinguished investigator will present their current work at the frontiers of biological research. Before the seminar, students and course faculty will meet and discuss in depth one or more papers from the primary research literature on a related topic. After the Wednesday seminar, students will have the opportunity to meet informally with the seminar speaker to discuss their research and future directions. Emphasis is on how to read papers in the primary research literature, the set of techniques most commonly used to study problems in biology and a comparison between genetic and biochemical approaches in biological research. (1 unit, Aut, Win)
Topics: imprinting, early development and implantation, germ cell allotment, phenotypic consequences of targeted knockouts of developmental genes, hox genes and other developmental genes in mammals, tumorigenesis, coat color mutations, classical mutations and positional cloning, mutagenesis and insertional and gene traps, growth controls, muscle and limb development, sex determination, classical genetics and gene mapping and inbred strains, segregation and T locus, and germ and embryonic stem cells and teratocarcinomas. One lecture per week, plus either one guest lecture or a literature discussion. (2 units, Win) offered every two years, not offered 2000-01
(Same as Biochemistry 225). The molecular basis of energy transduction that leads to movements generated by microfilament-based and microtubule-based motors. In depth analysis of forms of myosin, dynein, and kinesin and their roles in the cell, as a model for understanding the structural, biochemical, and functional properties of biological machines in general. Topics: structure of the molecular motors and their accessory proteins: regulation of the function of motile assemblies; functions of molecular motors in cells. Experimental approaches: genetic analysis, DNA cloning and expression, reconstitution of functional assemblies from purified proteins, x-ray diffraction, three-dimensional reconstitution of electron microscope images, spectroscopic methods, and high-resolution light microscopy. Focuses on how a complex cellular process is analyzed at the molecular level by a multifaceted approach using biomedical, biophysical, and genetic techniques. Prerequisites: knowledge of basic biochemistry and cell biology. (3 units, Aut) not offered 2000-01
(Same as Biochemistry 237, Biological Sciences 237, Biophysics 237, Chemistry 237, Civil Engineering 237, Developmental Biology 237, and Structural Biology 237). Faculty from the Departments of Biochemistry, Biological Sciences, Chemical Engineering, Chemistry, Civil Engineering, Civil Sciences, Developmental Biology, and Structural Biology and invited industrial speakers review the interrelated elements of modern biotechnology. Topics: protein structure and dynamics, protein engineering, biocatalysis, gene expression, cellular metabolism and metabolic engineering, fermentation technology, and purification of biomolecules. Prerequisite: graduate student or upper-division undergraduate in the sciences and engineering. (3 units, Spr)
Prerequisite(s): consent of instructor. See faculty list for
section numbers.
1 to 18 units, any quarter, by arrangement
1-18 units, any quarter (Staff) by arrangement; must register by sections numbers
Cross-listed in multiple departments in the schools of Humanities and Sciences, Engineering, and Medicine; students should enroll directly through their affiliated department, if at all possible.) Introduction to cutting-edge research involving interdisciplinary approaches to bioscience and biotechnology; for specialists and non-specialists. Associated with Stanford's Clark Center for Interdisciplinary Bioscience, and held in conjunction with a seminar series meeting twice monthly during 2000-01. Leading investigators from Stanford and throughout the world speak on their research; students also meet separately to present and discuss the ever-changing subject matter, related literature, and future directions. Prerequisite: keen interest in all of science, with particular interest in life itself. Recommended: basic knowledge of biology, chemistry, and physics. 2 units
Frontiers
Lecture Schedule
The Departments of Developmental Biology and Biochemsitry each sponsor a biweekly
departmental seminar series held on alternating Wednesday afternoons.
The "frontiers in Developmental biology and "Frontiers in Biochemistry" seminar
series bring outstanding developmental biologists and biochemists, both nationally
and internationally recognized, to Stanford to present their work. To
recognize and promote participation by the students, the departments jointly
offer one unit of credit for a seminar course, "frontiers in Biological Research"
associated with these seminar series. In this course, students will read
and discuss literacute related to the topic being presented. Students
have the opportunity to meet with each speaker after the seminar for an informal
discussion.
The Frontiers in Developmental Biology seminars take
place at 4pm in the Clark Center Auditorium. Coffee and cookies
are served at 3:45pm. A reception with the speaker follows in the presenting
their experiments and/or discussing papers from the literature.
An important aspect of the training of every graduate student is the development of speaking skills. The department provides numerous opportunities for trainees to speak about their research in a seminar setting. Once students begin their dissertation work in the second year, they will be asked to give a talk in the department about once a year. Student talks can be given in one of the many research interest groups, such as the Microbial Data or "Dev Bio Departmental Data Club ("3D") or RAVE, or at the departmental conference. This is a valuable experience because all members of the department, including faculty attend the seminars. These seminars will be concerned with ongoing and unfinished work and consequently are expected to generate considerable discussion. The speaker must organize the work, present it clearly, answer questions, and discuss other ideas raised by the listeners.
3D, Discussing Developmental Data: 3D is an informal research meeting at which graduate students and postdocs present their latest results and ideas to the entire department. These lunch-time discussions are lively and informative, reflecting the enthusiasm and cutting-edge research of graduate students, postdoctoral fellows, and faculty of the Department.
Most students participate in journal clubs that meets on a regular schedule to discuss published reports from the literature. The goal of these Journal Clubs is to teach students to read, analyze and criticize scientific papers. Students are exposed to a broad sampling of research interests and experimental approaches. All students participate actively in critiquing the papers, and each student is given the responsibility for leading discussions several times throughout the year.
The Microbial Data Club is an informal gathering of approximately 50 graduate students, postdocs and faculty who have a research interest in prokaryotic and eukaryotic microbes. The "Bug Club" meets the second Thursday of every month from 6-8 pm in the Developmental Biology library. Dinner can be purchased inexpensively for the first half-hour. Two talks of about 20-30 minutes are presented and there is plenty of time for questions. In the past year, participants from the following departments have taken part: Biological Sciences, Biochemistry, Developmental Biology, Genetics, and Microbiology and Immunology.
Research About Vertebrate Embryos (RAVE): Every month Bay Area labs working on vertebrate development meet to discuss ongoing research projects utilizing fish, frogs, chicks, mice, and humans. Two half-hour research talks are usually presented, with lots of time for questions and discussion. Meetings alternate between Stanford, Berkeley, and UCSF.
Pizza and soft drinks provided. Meeting times and topics posted near B307 and on departmental bulletin boards. Contact the Kingsley laboratory for more information.
Each faculty member in the department schedules weekly group meetings in which the students and postdoctoral fellows take turns presenting their experiments and/or discussing papers from the literature.
Every 2-3 years, students and postdocs organize a two-day symposium focused on a particular topic in Developmental Biology. Expert scientists in the field are brought together to probe the subject in depth. The Symposium will be held on April 17-18. Previous symposia topics include: "Cell Migration During Development", and "Evolution of Genetic and Developmental Programs". And "Cellular Asymmetry".
Two long-standing DB traditions are snacks provided by the department at 4:30 p.m. on Mondays and on Wednesdays when there is no seminar, and a Social Hour held Friday afternoons at 5:30 p.m. (sponsored by different lab groups on a rotating basis). Both gatherings are held in the 3rd Floor lobby.