BIPN148 Main Page

Cellular Basis of Learning & Memory

BIPN148

Prof. Anirvan Ghosh
Prof. Massimo Scanziani

CSB 002

Announcement
Final Exam: June 12th, 3:00-5:00pm, CSB002.

Beginning next week, the TA-led discussion sessions will be held at 4pm on Wednesday and Thursday at the following location:

Wednesdays - Pacific Hall Room 3501
**For Wednesday, May 16th only - Meet in Pacific Hall 3500.**
Thursdays - The discussion section will remain in Pacific Hall 1115.

.COURSE OUTLINE.
Cellular Basis of Learning and Memory
BIPN 148
Spring 2007
April 2-June 8, 2007

This course will examine the cellular and molecular mechanisms that underlie learning and memory. Topics covered will include the role of the hippocampus in learning and memory, neurotransmitter systerms and receptors involved in learning and memory, and biochemical mechanisms of synaptic plasticity. Emphasis will be placed on discussing experiments from the primary literature. A solid background in cell and molecular biology is expected.

Prerequisites: BILD 1; BILD 2; BIBC 100/102; BIPN 140 highly recommended.

Times:                      MWF at 3:00
Location:                   CSB 002
Web Site:                http://www.biology.ucsd.edu/classes/bipn148.SP07

Recommeded Text:   Ghosh and Scanziani 2007 Lecture Notes
Lecture notes are available for purchase through University Readers at http://www.universityreaders.com/students .

Grading:                    Weekly Quizzes: 40%
                                  Group paper: 20%
                                  Group presentation: 10%
                                  Final Exam: 30%
                                  Grading is on a curve.

Discussion Sessions/TA office hours (optional): TBD

CONTACT INFORMATION
Professors:
Anirvan Ghosh, Pacific Hall 1123, aghosh@ucsd.edu, 822 4142
Massimo Scanziani, CMG 2nd Floor, massimo@ucsd.edu, 822 3839

TEACHING ASSISTANTS:
Dan Keller, dkeller@salk.edu
Lara Pickle, larapickle@gmail.com
Lauren Hollingsworth, lholling@ucsd.edu

Office Hours for Professors by appointment.

.COURSE OUTLINE.

Week 1: Role of Hippocampus in learning and memory (Ghosh)
April 2: Ghosh ∞
April 4: Ghosh ∞
April 6: Paper presentation: TA

Week 2: Organization of the Hippocampal circuit (Scanziani)
April 9: Scanziani ∞
April 11: Scanziani ∞
April 13: Quiz 1; Paper presentation: TA ∞

Week 3: Synaptic plasticity 1 (Scanziani)
April 16: Scanziani ∞
April 18: Scanziani ∞
April 20: Quiz 2; Paper presentation: Group 1

Week 4: Synaptic plasticity II (Scanziani)
April 23: Scanziani ∞
April 25: Scanziani ∞
April 27: Quiz 3; Paper presentation: Group 2

Week 5: Biochemical mechanisms of LTP expression: Receptor trafficking I (Ghosh)
April 30: Ghosh ∞
May 2: Ghosh ∞
May 4: Quiz 4; Paper presentation: Group 3

Week 6: Biochemical mechanisms of LTP expression: Receptor trafficking II (Ghosh)
May 7: Ghosh ∞
May 9: Ghosh ∞
May 11: Quiz 5; Paper presentation: Group 4

Week 7: Biochemical mechanisms of LTP induction: Role of CaM kinase II (Ghosh)
May 14: Ghosh ∞
May 16: Ghosh ∞ Qiuz 6; Paper presentation: Group 5
May 18: NO CLASS

Week 8: Biochemical mechanisms of long-term memory: Transcriptional Mechanisms (Ghosh)
May 21: Ghosh ∞
May 23: Ghosh ∞
May 25: Quiz 7; Paper presentation: Group 6

Week 9: Biochemical mechanisms of long-term memory: Translational mechanisms (Ghosh)
May 28: NO CLASS - Memorial Day
May 30: NO CLASS - Kuffler Lecture - Richard Axel (Liebow Auditorium, 4pm)
June 1: Quiz 8; Paper presentation: Group 7

Week 10: Genetic Analysis of Memory
June 4: Ghosh
June 6: Group 8; Final written reports due
............Sample Reports - #1 & #2
June 8: In-class review for Finals

Lectures are either in powerpoint or pdf format.
Lectures are indicated with the following icon: ∞

.BIPN148 PAPERS.

	BIPN148 Papers 2007 (The papers listed first [in italics] should be presented in class. Each presentation should be no more than 20 minutes. The subgroups are responsible for writing written reports on the papers they are assigned. The reports are due on June 6th. Two hard copies needs to be turned in class, and an electronic copy [Word or PDF file] needs to be emailed to Dr. Ghosh at aghosh@ucsd.edu)
April 6 (Dan Keller, TA)	Zola, SM, Squire, LR, Teng, E, Stefanacci, L, Buffalo, EA, Clark, RE (2000) Impaired recognition memory in monkeys after damage limited to the hippocampal region. J. Neurosci, 20:451–463. Manns, JR, Hopkins, RO, Squire, LR (2003) Semantic memory and the human hippocampus. Neuron, 38:127–133.
April 13 (Lauren Hollingsworth and Lara Pickle, TAs)	Bliss TV, Lomo T. Long-lasting potentiation of synaptic transmission in the dentale area of the anaesthetized rabbit following stimulation of the perforant path. J Physiol. 1973 Jul;232(2):331-56.
April 20 (Group 1)	1A: Morris RG, Anderson E, Lynch GS, Baudry M. Selective impairment of learning and blockade of long-term potentiation by an N-methyl-D-aspartate receptor antagonist, AP5. Nature. 1986 Feb 27-Mar 5;319(6056):774-6. 1B: Megias M, Emri Z, Freund TF, Gulyas Al. Total number and distribution of inhibitory and excitatory synapses on hippocampal CA1 pyramidal cells. Neuroscience. 2001;102(3):527-40. 1C: Davis S, Butcher SP, Morris RG. The NMDA receptor antagonist D-2-amino-5-phosphonopentanoate (D-AP5) impairs spatial learning and LTP in vivo at intracerebral concentrations comparable to those that block LTP in vitro. J Neurosci. 1992 Jan;12(1):21-34.
April 27 (Group 2)	2A: Kauer J. A., Malenka R.C. & Nicoll R. A. A persistent postsynaptic modification mediates long-term potentiation in the hippocampus. Neuron 1, 911-917 (1988). 2B: Lynch G, Larson J, Kelso S, Barrionuevo G, Schottler F. Intracellular injections of EGTA block induction of hippocampal long-term potentiation. Nature. 1983 Oct 20-26;305(5936):719-21. 2C: Regehr WG, Tank DW. Postsynaptic NMDA receptor-mediated calcium accumulation in hippocampal CA1 pyramidal cell dendrites. Nature. 1990 Jun 28;345(6278):807-10.
May 4 (Group 3)	3A: Perkel DJ, Petrozzino JJ, Nicoll RA, Connor JA. The role of Ca2+ entry via synaptically activated NMDA receptors in the induction of long-term potentiation. Neuron. 1993 Nov;11(5):817-23. 3B: Takumi Y, Ramirez-Leon V, Laake P, Rinvik E, Ottersen OP. Different modes of expression of AMPA and NMDA receptors in hippocampal synapses. Nat Neurosci. 1999 Jul;2(7):618-24. 3C: Zalutsky RA, Nicoll RA. Comparison of two forms of long-term potentiation in single hippocampal neurons. Science. 1990 Jun 29;248(4963):1619-24
May 11 (Group 4)	4A: Shi et al. Rapid Spine Delivery and Redistribution of AMPA Receptors After Synaptic NMDA Receptor Activation. Science 284;1811 (1999) 4B: Nusser, Z. et al. Cell type and pathway dependence of synaptic AMPA receptor number and variability in the hippocampus. Neuron 21, 545–559 (1998). 4C: Isaac, J.T., Nicoll, R.A. & Malenka, R.C. Evidence for silent synapses: implications for the expression of LTP. Neuron 15, 427-434 (1995).
May 18 (Group 5)	5A: Giese Kp, Fedorov NB, Filipkowski RK, Silva AJ. Autophosphorylation at Thr286 of the alpha calcium-calmodulin kinase II in LTP and learning. Science. 1998 Feb 6;279(5352):870-3 5B: Liao, D., Hessler, N. A. & Malinow, R. Activation of postsynaptically silent synapses during pairing-induced LTP in CA1 region of hippocampal slice. Nature 375, 400–404 (1995). 5C: Barria A, Muller D, Derkach V, Griffith LC, Soderling TR. Regulatory phosphorylation of AMPA-type glutamate receptors by CaM-KII during long-term potentiation. Science. 1997 June 27;276(5321):2042-5.
May 25 (Group 6)	6A: Marie, H., Morishita, W., Yu, X., Calakos, N., and Malenka, R C. (2005). Generation of silent synapses by acute in vivo expression of CAMKIV and CREB. Neuron 45, 741-752. 6B: Barco A, Alarcon JM, Kandel ER. Expression of constitutively active CREB protein facilitates the late phase of long-term potentiation by enhancing synaptic capture. Cell. 2002 Mar 8;108(5):689-703. Pittenger C, Huang YY, Paletzki RF, Bourtchouladze R, Scanlin H, Vronskaya S, Kandel ER. Reversible inhibition of CREB/ATF transcription factors in region CA1 of the dorsal hippocampus disrupts hippocampus-dependent spatial memory. Neuron. 2002 Apr 25;34(3):447-62.
June 1 (Group 7)	7A: Flavell, S. W., Cowan, C. W., Kim, T. K., Greer, P. L., Lin, Y., Paradis, S., Griffith, E. C., Hu, L. S., Chen, C., and Greenberg, M. E. (2006). Activity-dependent regulation of MEF2 transcription factors suppresses excitatory synapse number. Science 311, 1008-1012. 7B: Sutton MA, Wall NR, Aakalu GN, Schuman EM. Regulation of dendritic protein synthesis by miniature synaptic events. Science. 2004 Jun 25;304(5679):1979-83. 7C: Ince-Dunn, G., Hall, B. J., Hu, S. C., Ripley, B., Huganir, R. L., Olson, J. M., Tapscott, S. J., and Ghosh, A. (2006). Regulation of thalamocortical patterning and synaptic maturation by NeuroD2. Neuron 49, 683-695.
June 8 (Group 8)	8A: Fonseca R, Nagerl UV, Bonhoeffer T. Neuronal activity determines the protein synthesis dependence of long-term potentiation. Nat Neurosci. 2006 Apr,9(4):478-80. 8B: Fonseca R, Vabulas RM, Hartl FU, Bonhoeffer T, Nagerl UV. A balance of protein synthesis and proteasome-dependent degradation determines the maintenance of LTP. Neuron. 2006 Oct 19;52(2):239-45. 8C: Costa-Mattioli M, Gobert D, Harding H, Herdy B, Azzi M, Bruno M, Bidinosti M, Ben Mamou C, Marcinkiewicz E, Yoshida M, Imataka H, Cuello AC, Seidah N, Sossin W, Lacaille JC, Ron D, Nader K, Sonenberg N. Translational control of hippocampal synaptic plasticity and memory by the eIF2alpha kinase GCN2. Nature. 2005 Aug 25;436(7054):1166-73.

GROUP ASSIGNMENTS
Group 1 Group Leader: David Alexanian (dalexanian@ucsd.edu)	AAA-Chang	April 20th
Group 2 Group Leader: Deepak Dhaliwal (ddwaliwa@ucsd.edu)	Chen-Douzjian	April 27th
Group 3 Group Leader: Joe Gram (joegram119@hotmail.com)	Evans-Ho	May 4th
Group 4 Group Leader: My Hanh Huynh (myhanh2@gmail.com)	Hodge-Landreth	May 11th
Group 5 Group Leader: Cem Mangir (cmangir@gmail.com	Lee-Martony	May 19th (note date)
Group 6 Group Leaders: Krishna Nemani (knemani@gmail.com) Albert Noniyev (anoniyev@ucsd.edu)	Mashwood-Okada	May 25th
Group 7 Group Leader: Ella Shaviv (eshaviv@ucsd.edu)	Page-Sprague	June 1st
Group 8 Group Leader: Victor Tung (vtung@ucsd.edu)	Tanaka-ZZZ	June 6th

Week 11: FINALS

.GRADING COMPONENTS.

Student Group Presentation and Written Reports (30%)

30% of the grade will be determined by student group presentations and written reports on assigned papers. Each group will typically be assigned 2 papers on which they need to write reports and deliver an oral presentation. Students will be assigned to a group during the second week of class and assigned a paper or topic to present.

Each group will need to select a project manager and develop a plan to meet outside of class to discuss the paper(s) and to come up with a presentation plan. In your first meeeting you should come up with a division of responsibility (e.g. literature search, drafts for various sections, oral presenters etc).

Student Group Presentation (10%)

Each presentation should be 20 minutes long plus 5 minutes for questions at the end. Bring your presentation as a powerpoint file on a laptop, CD, or USB memory card. The group may select one or more members to make the presentation. It is a good idea to have a TA review your presentation before presenting it to the class.

The presentation must include the following:

Background
Description of Methods
Description of Results
Interpretation of Results and Conclusions

The main goal of this assignment is to develop your skills in evaluating the scientific literature and expressing your views in an effective and coherent manner.

Written Reports (20%)

The written reporst are due in class on June 6, 2007. Each assigned paper needs to have its own written report, which should be between 8 and 10 double-spaced pages in length. You may include up to two explanatory figures in each report if you choose.

Each report should have the following sections:

Group number, Title of paper, and names of all students who contributed to the report
Signatures of all contributing members of the group indicating that the students listed contributed to the report
Background and statement of problem
Descripton of approach and methods
Description of results
Discussion of findings and interpretation and conclusions
References/Bibliography

Each report should begin with a brief summary of past work on the topic and introduce the paper(s) being reviewed. This should be followed by the methods used and your review of the paper(s). Here you should summarize the main findings of the papers, and discuss whether the evidence justifies the principal conclusions of the study. If you discover weaknesses in the study, you should discuss those as well. End your report with a few concluding paragrahs that place the new findings in the context of previous work on the topic and identify areas that would be important to investigate in the future. Your report should refer to 5-10 key papers in the field that relate to the paper.

In preparing your report please pay close attention to the following:
1. Make sure the writing is grammatically correct and clear (have someone else read it before submitting it for grading).
2. Express your ideas simply and concisely (Strunk and White, "Elements of Style" is an excellent introduction to good writing, and is worth purchasing.
3. Try to make your review informative and interesting.

Quizzes (40%)
There will be eight 10-minute quizzes during the course. Each quiz will be based on topics covered that week and on the previous student presentation. The top 6 quiz scores will be used to calculate your overall quiz score, which will be worth 40% of the grade. There will be a make-up quiz at 5pm on June 7th (right after the TA-led discussion) for students who had to miss a quiz due to a UCSD-related activity (eg. playing on a sports team). If you take the make-up quiz, you need to submit a letter explaining the reason for the make-up (signed by the faculty member or official in charge of the event) along with the quiz.

Final Exam (30%)

The final exam will be a comprehensive exam that will test your command of material and concepts presented in class.

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Questions and concerns about the website, email Ria del Rosario at rvdelros@ucsd.edu.
**Updated .06.08.07 8:16am**