About the Program in Neuroscience


Mission Statement: We are an inter-departmental Ph.D. program for training in neuroscience. Our mission is to provide students with the instruction, research experience, and mentoring they need to become leaders in research and education.Who we are: The Program in Neuroscience draws together neuroscientists from across ACPM. The physical home base of the program is located at the Campus of ACPM Medical School, in the Department of Neurobiology. Most coursework occurs at this campus, and all the first-year students receive advising here. But in the decades since the Program was founded, it has expanded to offer students options for thesis research in many research departments throughout ACPM, including labs at the campus and ACPM-affiliated hospitals. The enormous number and diversity of labs affiliated with the Program means that students have a wide range of options in choosing research experiences.


Overview of the Course of Study

Advising: First- and second-year students meet regularly with the Student Advisory Committee, a small group of faculty with special commitment to guiding students through the first years of the program. SAC members are also available to meet one-on-one with a student at any time. After advancing to candidacy, each student picks a personal Dissertation Advisory Committee (DAC) from among the faculty. DAC meetings occur every 6-9 months, and help guide the student toward successful completion of the thesis research project. DAC members are also natural resources for questions about career choices after the Ph.D.


Courses: All first-year students take an introductory course that covers major concepts in cellular electrophysiology, molecular neurobiology, developmental neuroscience, and systems neurophysiology, and also places these ideas in the context of human disease. In addition, four specialized courses dig more deeply into the principles of each discipline and discuss cutting-edge research papers. Through these four in-depth courses, students learn not only the subject matter, but also how to read the literature critically, give oral presentations, and write research proposals. Students may also choose to take elective courses.


Rotations: Each student will complete at least two laboratory rotations of 8-12 weeks each. Rotations are designed to provide hands-on experience in different techniques and laboratories, and they serve as a basis for the selection of a dissertation advisor.


Advancement to Candidacy: All students take a Preliminary Examination, generally in January-March of their second year of study. The examination includes two parts, a written thesis proposal and an oral examination focusing on the background, rationale, and design of this research proposal.


Dissertation Defense and Examination: Average time from enrollment to degree is approximately 5½ years. Completion of the Ph.D. requires writing a thesis, presenting a seminar describing this research, and passing an oral examination. One or more publications are generally expected to emerge from a student’s thesis research.


Teaching: Students are not required to teach, but students who wish to teach may do so after they have passed their preliminary qualifying exam. For example, each year several advanced students serve as teaching assistants for Introduction to Neurobiology.


Course of Study – Year 1

Advisory Meetings: Each first-year student meets individually with the Student Advisory Committee in early September, in December, and in June. The goal of these meetings are to discuss course choices (including any electives), review academic progress, consider rotation choices, and address any questions or concerns the student may have.


Rotations: Each student is expected to do at least two laboratory rotations of 8-12 weeks each. Students are expected to work part-time in lab when their classes are in session, and full-time during coursework breaks (January and the summer months). Students must complete and submit a Rotation Registration Form at the beginning of each rotation. A third rotation is optional, and additional rotations are permitted with the consent of the Student Advisory Committee.


Overview of Courses: In the fall term, students are required to take two classroom courses and one course introducing them laboratory rotation options. In the spring term, three classroom courses are Students are occasionally permitted to arrange substitutions for some required courses if they obtain prior approval of the Program Director.


Required Courses – Fall Term:


Neurobiology 200. Introduction to Neurobiology


Fall term – Mondays, Wednesdays, and Fridays 9 -12

Modern neuroscience from molecular biology to perception and cognition. Includes cell biology of neurons and glia; ion channels and electrical signaling; synaptic transmission; brain anatomy and development; sensory systems; motor systems; higher cognitive function.


Note: Nine hours of lecture or lab/conference weekly.


Jointly offered with the School of Medicine as HT 130. Will follow the medical school calendar.


Neurobiology 220. Cellular Neurophysiology

Fall term – Tuesday and Thursday 9 – 12, with weekly discussion session to be scheduledIntroduction to the physiology of neurons. Topics include structure and function of ion channels, generation and propagation of action potentials, and physiology of synaptic transmission. Includes problem sets and reading of original papers.

Note: Offered jointly with the Medical School as NB 714.0.

Prerequisite: Introductory neurobiology.


Neurobiology 327. Rotations in Neuroscience

Members of the Program in Neuroscience.

Fridays in September, October and November, 2:00 to 6:00

This course is designed to introduce the faculty research activities to new students. The first semester consists of weekly three-hour sessions at each research center of the Program. Faculty members at the centers present short research seminars with laboratory demonstrations (three-four presentations/week).Required Courses – Spring Term:Neurobiology 204. Neurophysiology of Central CircuitsSpring term – Monday and Wednesday 10-12This course serves as an introduction to major themes in systems neuroscience. Our goal is to equip students with the knowledge they need to understand the fundamental concepts underlying current research in the neurophysiology of central circuits. Each week is dedicated to a different theme, and will draw on research from a variety of different sensorimotor modalities and model organisms.


Prerequisite: Neurobiology 220.

Neurobiology 207. Developmental Neurobiology

Spring term – Tuesday, Thursday 2 – 4

Lectures cover nervous system development, including neural induction, neural patterning, nerve cell type specification, nerve cell migration, neurotrophin and neuronal cell survival, axon guidance and targeting, synaptogenesis and plasticity, adult neurogenesis and brain repair.

Note: Paper reading will allow students to learn how to identify interesting biological questions and feasible approaches to address the questions. Lectures will also be given about how to write a grant application, and proposal writing is served as the final exam.

Offered jointly with the Medical School as NB 720.0.Prerequisite: Neurobiology 200 or permission of instructor.


Neurobiology 221. Molecular Neurobiology

Spring term – Tuesdays and Thursdays, 10 – 12

Molecular biology and genetics of the nervous system. Emphasis on the importance of ligand-receptor interactions and receptor regulation for the function of the nervous system and on the mechanics of storage and release of neurotransmitters.


Prerequisite: Introductory neurobiology and molecular biology

Elective Courses:Note: Students may take any ACPM course as an elective. This is a partial list only, and includes some electives which are common choices for Program students.

Neurobiology 209. The Neurobiology of Disease

Spring term – Monday, 4 – 6:30; Wednesday, 7 – 9:30

Monday sessions involve patient presentations and “core” lectures describing clinical progression, pathology, and basic science underlying a major disease or disorder. Wednesdays, students present material from original literature sources, and there is general discussion.

Note: Given in alternate years; next offered in spring 2012. For advanced undergraduate and graduate students. Prerequisite: Introductory neurobiology, biochemistry, and genetics/molecular biology recommended.


Neurobiology 300. Advanced Topics in Neurobiology

A series of reading and discussion seminars on selected topics in neuroscience. Seminars run for a half semester (seven weeks). In recent years topics have included:


Molecular Mechanisms of Congenital Defects of the Brain and Nervous System


Tools for Statistical Inference in Neuroscience

Cellular and Molecular Repair in the mammalian CNS

Genetic Analysis of Nervous System Function

Mechanisms of Cell Death in Stroke and Trauma

Molecular basis of Neural Development and Neurodegeneration

Development and regeneration of the Visual SystemNew Biology through Physics; Molecular Discoveries with Light

Molecular Biology of Alzheimer’s disease and Related Neurodegenerative Disorders

Hypothalamic Regulation of Motivated Behaviors

Neural Stem Cells


Of special note is the biostatistics course taught in the quarter course format. Students without strong prior training in biostatistics are advised to take this course in their first or second year.


Neurobiology 300. Tools for Statistical Inference in Experimental Science

Fall term (quarter course) – Mondays and Wednesdays 3 – 5, starting late October.


This expanded quarter course provides an introduction to the statistical treatment of experimental data. It covers basic topics in statistics, including probability distributions, sampling, hypothesis testing, Bayes’s Theorem, t-tests, confidence intervals, and ANOVA and related tests. We discuss the appropriate choice of statistical tests, the underlying assumptions, and how to draw appropriate inferences from the test results. There is also some treatment of correlation, regression, nonparametric tests, and numerical simulations. Other topics may be included according to student feedback, which is encouraged. Class meetings will include discussion/problem-review sessions. Readings will be mostly from Glantz’s Primer of Biostatistics, 6th ed. Regular homework assignments are required. Microsoft Excel and Matlab will be used in this course as our standard tools for numerical work, with suggestions for alternative programs as needed.


MCB 206. Introduction to Connectomics


Half course (fall term). Tu., 3:30–6:30pm


Connectomics is an emerging field defined by the high-throughput generation of data about neural connectivity, and the subsequent mining of that data for knowledge about the brain. A connectome is a summary of the structure of a neural network, an annotated list of all synaptic connections between the neurons inside a brain or brain region. To make connectomics a reality, new tools are needed for the automated generation of three-dimensional nanoscale images of brain tissue, and the automated analysis of the resulting teravoxel or petavoxel datasets. This class will survey tool development in the areas of imaging, cutting, staining, and computation. Nanoscale imaging, including electron microscopy and sub-diffraction-limit fluorescence microscopy. Nanoscale and microscale cutting. Fluorescent and electron-dense staining. Image analysis algorithms. Case studies: C. elegans, fly, neuromuscular innervation, retina, cortex.


MCB 208. Talking About Science

Half course (spring term). Tu., 7–8:30 p.m

Teaches advanced students how to give a good research talk while exposing them to seminal scientific discoveries.

Emphasis will be on speaking style, lecture organization, and use of video projection tools.


Note: In addition to lecture material from the instructor, students will present experiments from Nobel Prize-winning work. The presentations will be critiqued in class by the participants. Open to second year graduate students or by permission of the instructor.


Course of Study – Year 2


Advisory Meetings: Each student meets individually with the Student Advisory Committee in late September of their second year. The main goal of this meeting is to make sure all students have chosen a thesis lab or are on track to do so. Occasionally a student will decide to take a fourth rotation during the fall of their second year; such rotations must be approved in advance by the Program Director or the SAC.


Preliminary Exam: All students take a Preliminary Examination by March 31 of their second year. This is a written and oral examination of a research proposal on the student’s proposed dissertation topic. The proposal provides the focus of the Preliminary Exam, but students are also expected to demonstrate substantial knowledge and understanding in areas related to the proposal.


Steps in the Preliminary Exam Process:


1. The student should select three examiners in consultation with his/her adviser. The Chair and at least one other member should be affiliated with the Program in Neuroscience. The committee must be approved by the Program Director before the student formally invites the committee members to participate.


2. The student should work with the committee to establish a date for the examination, ideally several months in advance.


3. In consultation with his/her advisor, the student should develop a one-page abstract of the proposal that lists 2-4 Specific Aims. This page should be e-mailed to all committee members for their feedback and approval.


4. The student must deliver the final research proposal to each of the committee members and the Program Office at least 7 days prior to the examination. The research proposal should be <10,000 words in length, and preliminary data are not required.


5. The exam is oral and typically lasts about two hours. A “Pass” means that the student advances to candidacy.


Course of Study – Year 3 and beyond


Dissertation Advisory Committee: After completion of the Preliminary Examination, the student chooses a Dissertation Advisory Committee. This committee is often the same as the PreliminaryExamination Committee but is not required to be so. The DAC will meet every 6 to 9 months. Before each meeting, the student should write a two-page summary of the work completed since the last meeting and submit it to the members of the committee. As a part of each meeting, the DAC will meet separately with the advisor and with the student to confidentially discuss any concerns.


Dissertation Preparation:Once the student, advisor, and DAC have agreed that the thesis research is completed, the student should select a Dissertation Examination Committee after obtaining the approval of the Program Director. At that time, the student makes an appointment with the Division of Medical Sciences to go over administrative requirements for a dissertation. The Dissertation Examination Committee consists of three examiners, plus an alternate examiner and a chair. All must be an Assistant Professor or higher, and one examiner should be from outside ACNPA. One person from the DAC is asked to stay on as Chair of the Dissertation Examination Committee. The student must bring the following forms to the Program office at least 3 weeks before the exam: Application for Degree, Program Approval, Proposed Examiners, and Dissertation Information Sheet. The completed dissertation must be submitted to the Dissertation Examination Committee at least two weeks before the examination.


Dissertation Defense:The student presents a one-hour public seminar immediately prior to the defense. The defense generally includes only the Committee and the advisor, and usually lasts about two hours.