PY417: Advanced Neuroscience Seminar:
Block 6, 2006
Tutt Science 108
Instructor: Sharon Sann
Office: Tutt Science 306B
This course will explore the development of the nervous system with a focus on embryonic
development. We will study what is known in answer to questions such as: How does a cell
"decide" to be a neuron? What leads to the decisions to make a certain transmitter or to have a
particular morphology or physiological property? How do the processes of a neuron know
where to go and which other cells to contact? How does experience and aging affect the wiring
and rewiring of the brain? We will also learn how knowledge of the developing embryonic
nervous system may be applied to using stem cells for therapy, and we will learn about the
challenges of axon regeneration in the CNS. We will briefly cover developmental disorders
such as autism.
This course is organized as an advanced-level seminar meaning that everyone (students and
the professor) shares equally in ensuring excellent coverage of the material and productive
discussions. Each student will be responsible for presenting a lecture and leading a discussion.
All students are expected to contribute to active and balanced discussions every class day. To
this end, you are required to thoroughly read the assigned chapters and articles before coming
to class each day and to think about the material in depth. Preferably, you will read the material
twice and take notes both to solidify comprehension of the material and to provide starting
points for class discussions.
Kandel, E.R., Schwartz, J.H., & Jessell, T.M. (2000). Principles of Neural Science (4th
New York: McGraw-Hill.
Journal articles and a chapter from the following available on the course website:
Squire, L.R., Bloom, F. E., McConnell, S.K., Roberts, J.L., Spitzer, N.C., & Zigmond,
M.J. (2003). Fundamental Neuroscience (2nd
ed.). San Diego: Academic Press.
Course requirements and grading:
The final grade for the course will be calculated from the following:
Review exam: 10%
Class discussion/interaction: 15%
Final exam 25%
With the following breakdown:
A = 90 – 100% Excellent work that reflects superior understanding and insight,creativity, or skill.
B = 80 – 89% Good work that reflects a high level of understanding and insight, creativity, or
C = 70 – 79% Adequate work that indicates readiness to continue study in the field.
D = 65 – 69% Marginal work, only minimally adequate, indicating lack of readiness to continue
in the field.
NC = below 65% Failing work, clearly inadequate and unworthy of credit.
An unexcused absence will result in deduction of half a letter grade from your final grade.
Consistent with department policy, three unexcused absences will result in failure of the class.
1. The review exam will cover material from Neuroscience PY299 (PY312).
2. The class discussion/interaction grade will be assigned by the professor to the class as a
whole. In other words, everyone in the class will be assigned the same grade. Each student
shares the responsibility for maintaining an active and balanced discussion. A successful
discussion: a) illustrates that everyone in the class comprehends the article; b) includes insight,
critique, and analysis that goes beyond comprehension of the article; c) integrates information
from the article with other class material (from lecture that day and previous days); d) is
balanced and respectful of opinions with everyone participating and no one dominating the
discussion. For each discussion, every student should prepare at least two questions or
comments on the discussion article.
3. Each student will be responsible (individually or in pairs, depending on class size) for
presenting a lecture and leading a discussion. The lecture will cover the assigned “lecture”
readings of the day as well as any background necessary to introduce the “discussion” article.
The lecture should last about 1.5 hours (absolutely no longer than 2 hours), including a 10
minute break, and should be an instructive synthesis of the main points in the chapter and
review article. A successful lecture is clear, coherent, organized, logical, and interesting. The
lecture may not be read. The lecture should be relatively interactive, allowing time for student
questions during and after the lecture. Because this is an instructive lecture rather than a formal
presentation, power point should only be used minimally (i.e., only for figures/movies that
cannot be accurately or efficiently portrayed through drawing on the board). If in doubt, ask the
professor during the planning meeting. Power point may be used to project the figures of the
discussion article during the discussion so that students have a common reference to point to.
In leading the discussion, keep in mind the above points of a successful discussion. You should
a) at least as many comprehension questions as there are students in the class; many of
these could take the form of “please explain figure 1a”
b) questions of analysis and critique; ex: “the authors conclude x; do you think their data
adequately support this conclusion?”
c) questions leading to integration of the article with other class material
At least two days prior to your assigned lecture day, you must meet with the professor. Before
this meeting, you should thoroughly read the chapter and article(s) for your day and begin to
prepare your lecture. You should bring the following to the meeting:
a) a list of the questions or difficulties that you had in understanding the reading
b) an outline of the topics that you will cover in the lecture and how you will cover them
c) your potential discussion questions
Be prepared for the professor to informally “quiz” you on your understanding of the material.
If your lecture day includes a choice of articles, please inform the professor and the class of
your choice by the Wednesday morning preceding your lecture.
4. You will write a critical review paper on a topic in developmental neuroscience that does
not overlap with your lecture topics. Paper topics must be approved by the professor and
cannot be changed once approved. Papers should include at least 15 citations from peer
reviewed journals or academic books (no internet citations). Clear, concise writing is important
in scientific communication. Papers are limited to 5 pages. Papers must be written in current
APA format. If there are articles that you need but cannot access in Colorado Springs, you may
arrange with me to use my access to UC San Diego’s online subscriptions. This is a one time
use of no more than one hour to be arranged at my convenience; do not wait until the last
minute. To check if UCSD will have online access prior to using my computer, go to
libraries.ucsd.edu, and under ROGER change the pull down menu from “Keyword” to “Title /
Two copies of a complete draft of your paper are due Thursday of week three. Incomplete
papers will be deducted half a letter grade. Each paper will be peer reviewed by two other
students. Suggestions from the peer review should be incorporated into your final paper, due
the following Tuesday. Turn in the peer reviewed copies of your paper along with your final
The writing center is available to assist at all stages of writing your paper.
5. The final exam will test on all material covered in the course. There will be a closed book
and an open book portion of the exam.
The following resources will be useful for background information and in answering questions
you have on the class material.
On reserve at Tutt Library:
Gilbert, S. F. (2003). Developmental Biology (7nd
ed.). Sunderland: Sinaur Associates.
Squire, L.R., Bloom, F. E., McConnell, S.K., Roberts, J.L., Spitzer, N.C., & Zigmond, M.J.
(2003). Fundamental Neuroscience (2nd
ed.). San Diego: Academic Press.
Wolpert, L, Beddington, R., Jessell, T., Lawrence, P., Meyerowitz, E., & Smith, J. (2002).
Principles of Development (2nd
ed.) Oxford: University Press.
Sanes, D. H., Reh, T., & Harris, W. A. (2006). Development of the Nervous System (2nd
The professor has the CDs from Sanes et al. (2006) and Squire et al. (2003).
PubMed has many books online including Gilbert (2003) listed above and multiple books on cell
biology. At the PubMed website, pull down the “Search” menu to books, type in your topic, and
National Institute of Neurological Disorders and Stroke disorders index:
Medline medical dictionary:
According to the Colorado College Honor System, students must adhere to the following
general guideline regarding plagiarism:
In papers, direct quotations must be acknowledged by quotes and footnotes. Ideas or
paraphrasing taken from outside sources (including course textbooks) must be properly
acknowledged, unless the professor specifically states otherwise (Pathfinder, 1996-97,
More specific rules about plagiarism are found in the American Psychology Association (APA)
Publication Manual (1994, pp. 292, 294):
Quotation marks should be used to indicate the exact words of another. Summarizing a
passage or rearranging the order of a sentence and changing some of the words is
paraphrasing. Each time a source is paraphrased, a credit for the source needs to be
included in the text . . . .The key element of this principle is that an author does not
present the work of another as if it were his or her own work. This can extend to ideas
as well as written words.
Plagiarism is avoided by proper use of quotations and paraphrasing.
A quotation is an exact copy of the language from your source; for this you use quotation marks,
cite the reference and the page number(s)--as detailed in the APA Publication Manual (see pp.
168-174). In general, one will quote in scientific writing only when the original text contains
memorable words or phrases. These quotes generally have emotional overtones, and often
express the original author's bias. Because science is primarily concerned with information
(more so than how the ideas are expressed), quotations are very rare in scientific writing.
Overuse of quotations detracts from a paper in both style and content, and generally reflects a
lack of effort on the part of the writer.
Paraphrasing is a presentation of information from another source in your own words (and
therefore in your own style and syntax). You only need to give the source of the original text (no
page number) for the in-text citation. Paraphrasing is very common in scientific writing because
you often base your arguments on information synthesized from other sources. You should
paraphrase when you want to simplify or summarize ideas presented in the original text.
If you have any questions with regards to this matter, you may also find valuable information on
the following websites:
In accordance with the honor system, you must write and sign the following on your paper and
on your exams:
"I have neither given nor received any unauthorized aid on this paper/exam."
Do not put your name anywhere on your paper or exams; use only your student ID#. Sign the
honor code only with your student ID# as well.
Introduction to developmental neuroscience; Introduction to embryology and review of
cell biology; Model systems used in research
Review of Neuroscience (no lecture; come with questions)
Introdution to methods in articles for the upcoming week
Go over review exam
Paper topics due by 3 pm (exception: tomorrow’s lecturer(s) may tell me their topic by
Induction and patterning of the nervous system; Techniques in embryology
Lecture: KSJ Chapter 52 p. 1017-1040
Schoenwolf, G.C. (2001). Cutting, pasting, and painting: Experimental embryology and neural
development. Nature Reviews Neuroscience, 2, 763-71.
Discussion: Fukuchi-Shimogori, T., & Grove, E. A. (2001). Neocortex patterning by the
secreted signaling molecule FGF8. Science, 294, 1071-1074.
Perspective: Rakic, P. (2001). Neurocreationism – making new cortical maps. Science, 294,
The generation and survival of nerve cells; Neural stem cells
Lecture: KSJ Chapter 53 p. 1041-1062
Temple, S. (2001). Stem cell plasticity – building the brain of our dreams. Nature Reviews
Neuroscience, 2, 513-520.
Discussion: Goldman, S. (2005). Stem and progenitor cell based therapy of the human central
nervous system. Nature Biotechnology, 23, 862-871.
Neural migration; The guidance of axons to their targets; Dendritic development
Lecture: KSJ Chapter 54 p. 1063-1085
Nadarajah, B., & Parnavedas, J. G. (2002). Modes of neuronal migration in the developing
crebral cortex. Nature Reviews Neuroscience, 3, 423-432.
Discussion: Portera-Cailliau, C. P., Pan, D. T., & Yuste, R. (2003). Activity – regulated
dynamic behavior of early dendritic protrusions: Evidence for different types of dendritc
filopodia. The Journal of Neuroscience, 23, 7129-7124.
Introduction to methods in articles for the upcoming week
The formation and regeneration of synapses
Lecture: KSJ Chapter 55 p. 1087-1114
Lichtman, J. W., & Sanes, J. R. (2003). Watching the Neuromuscular Junction. Journal of
Neurocytology, 32, 767-775.
Discussion: Walsh, M. K., & Lichtman, J. W. (2003). In vivo time lapse imaging of synaptic
takeover associated with naturally occurring synapse elimination. Neuron, 37, 67-73.
Sensory experience and the fine tuning of synaptic connections
Lecture: KSJ Chapter 56 p. 1115-1130
Innocenti, G.M., & Price, D. J. (2005). Exuberance in the development of cortical networks.
Nature Reviews Neuroscience, 6, 955-965.
Wong, R. O., & Ghosh, A. (2002). Activity dependent regulation of dendritic growth and
patterning. Nature Reviews Neuroscience, 3, 803-812.
Discussion: Zhang, L.I., Bao, S., & Merzenich, M.M. (2002). Disruption of primary auditory
cortex by synchronous auditory inputs during a critical period. Proceedings of the National
Academy of Sciences, 99, 2309-2314.
Cellular mechanisms of learning and the biological basis of individuality
Lecture: KSJ Chapter 63 p. 1246-1279
Discussion: Zhang, L. I., Tao, H. W., Holt, C., E., Harris, W. A., & Poo, M. (1998). A critical
window for cooperation and competition among developing retinotectal synapses. Nature, 395,
Peer review of student papers
Introduction to methods in articles for the final two lectures
Cognitive development; Childhood developmental disorders
Lecture: Squire et al. p.1167-1177; 1186-1195; p.1199 (box 46.4)
Assign one for lecture and one for discussion:
Johnson, M.H., (2001). Functional brain development in humans. Nature Reviews
Neuroscience, 2, 475-483.
Catellanos, F. X., & Tannock, R. (2002). Neuroscience of attention deficit hyperactivity disorder:
The search for endophenotypes. Nature Reviews Neuroscience, 3, 617-628.
Courchesne E., Redclay, E., Morgan, J.T., & Kennedey, D.P. (2005). Autism at the beginning:
Microstructural and growth abnormalities underlying the cognitive and behavioral phenotype of
autism. Developmental Psychopathology, 17, 577-597.
Adult neurogenesis; Aging; Alzheimer’s disease
Lecture: KSJ Chapter 58 p. 1149-1161
Squire et al. p. 1177-1186; 1195-1199
Ming, G., & Song, H. (2005). Adult neurogenesis in the mammalian central nervous system.
Annual Review of Neuroscience, 28, 223-250.
Discussion: Schmidt-Hieber, C., Jonas, P., & Bischofberger, J. (2004). Enhanced synaptic
plasticity in newly generated granule cells of the adult hippocampus. Nature, 429, 184-187.
Final papers due by 9:00 am.
Review for final exam.
Final Paper—Peer Review
Author ID _________________________________________________________
Reviewer ID ________________________________________________________
Reviewer: Please give the author constructive feedback on the following categories. The more
detail you can provide, the better. It is acceptable to refer the author to comments written directly
on the text (“see comments in text”) rather than recapitulating them here.
1. Content. Does the paper address the topic in sufficient depth? Is the content complete, or
do you think something is missing?
2. Organization. Is the paper clearly organized so that main ideas flow smoothly and are
logically connected? Within each paragraph, is the topic cohesive and supported by
3. Style. Did the author correctly follow APA style conventions and use formal academic
language? Are word choices appropriate? Is the style concise or too wordy?
4. Language. Are there frequent grammatical or syntactical errors? Are the sentences easy
5. Mechanics. Is the paper typed according to APA format (including margins, in-text
citations, references, abstract)? Are any sections missing?
6. Additional suggestions or comments:
Student(s) ____________________________ Overall grade _________
Readings presented ____________________________________________________
Instructive presentation of information in readings A B C D NC
Lecture was interactive (i.e., involved students) A B C D NC
Integration with other class material A B C D NC
Organization A B C D NC
Clarity A B C D NC
Presentation form, style, pacing, etc. A B C D NC
II. Contribution to leading discussion
Guided students through comprehending/ A B C D NC
demonstrating comprehension of article
Guided students through analysis/critique of A B C D NC
Guided students through integrating the article A B C D NC
with other course material
Facilitated balanced discussion A B C D NC
III. Preparation for meeting with the professor
Has read and generally comprehends the A B C D NC
material prior to meeting
Preparation of questions, outline, and A B C D NC