Course Syllabus - [PDF file]  last revised 5 / 28 / 2008

 

Lectures start at 9:00 a.m. -  Discussions start at 1:30 p.m.

 

WEEK ONE

 

Monday, August 25 (Link to John Heuser’s Web site – fine structure of neurons, synapses and molecules)
Lecture 1:              Nerve cells, genes and behavior (Herzog)

Chapters 1, 2 and 3. The Brain, Nerve Cells, Genes and Behavior. in Principles of Neural Science, 4th Edition, Kandel, Schwartz, and Jessell, Eds. McGraw-Hill, NY, NY. (2000).

Lecture 2:              Neuronal and glial cell biology (Huettner)

Chapter 4 and 5. The Cytology of Neurons and Synthesis and Trafficking of Neuronal Proteins. in Principles of Neural Science, 4th Edition, Kandel, Schwartz, and Jessell, Eds. McGraw-Hill, NY, NY. (2000).

Bhat MA, Rios JC, Lu Y, Garcia-Fresco GP, Ching W, St Martin M, Li J, Einheber S, Chesler M, Rosenbluth J, Salzer JL, Bellen HJ. (2001) Axon-glia interactions and the domain organization of myelinated axons requires neurexin IV/Caspr/Paranodin. Neuron 30(2):369-83.

Boyle ME, Berglund EO, Murai KK, Weber L, Peles E, Ranscht B. (2001) Contactin orchestrates assembly of the septate-like junctions at the paranode in myelinated peripheral nerve. Neuron 30(2):385-97.

Pedraza L, Huang JK, Colman DR. (2001) Organizing principles of the axoglial apparatus. Neuron 30(2):335-44.

Feng G, Mellor RH, Bernstein M, Keller-Peck C, Nguyen QT, Wallace M, Nerbonne JM, Lichtman JW, Sanes JR. (2000) Imaging neuronal subsets in transgenic mice expressing multiple spectral variants of GFP. Neuron 28:41-51.

Gan W-B, Grutzendler J, Wong WT, Wong ROL, Lichtman JW. (2000) Multicolor "DiOlistic" labeling of the nervous system using lipophilic dye combinations. Neuron 27:219-225.

Discussion 1:        Cellular Neurobiology (Huettner)

 

Tuesday, August 26  (Link to Molecular Neuroscience Study Questions)
Lecture 3:              DNA structure, transcription (Ramanan)

Alberts et al. Molecular Biology of the Cell. 4th ed. Chapters 4 and 6

Lecture 4:              Control of gene expression, translation (Ramanan)

Alberts et al. Molecular Biology of the Cell. 4th ed. Chapters 6 and 7

 

 

Wednesday, August 27

Lecture 5:              Protein targeting to the ER, quality control (Ramanan)

Alberts et al. Molecular Biology of the Cell. 4th ed. Chapters 6 and 12

Lecture 6:              DNA and protein techniques (Ramanan)

Alberts et al. Molecular Biology of the Cell. 4th ed. Chapters 8

Discussion 2: Channel Simulation (Huettner)

 

Thursday, August 28

Lecture 7:              Electrical signaling in the nervous system and basic electricity (Huettner)
from Principles of Neural Science, 4th Edition, Kandel, Schwartz, and Jessell, Eds. McGraw-Hill, NY, NY. (2000)

Appendix A - Current flow in neurons

Chapter 6 - Ion channels

Chapter 7 - Membrane potential

Chapter 8 - Local signaling: passive electrical properties of the neuron

Chapter 9 - Propagated signaling: the action potential

Lecture 8:              Channel structure and diversity (Huettner)

Background and supplemental reading (recommended, not required) Hille (3rd ed) Chapters 1, 10, 11, 13, 17

General References:

(Link to Amino Acid Properties)

Proteins: Structure and Molecular Properties, 2nd. Ed., by T. Creighton, Freeman Press, NY 1993

Protein Structure, by Branden and Tooze, Garland Publishing, N.Y. 1991.

Lodish et al., Molecular Cell Biology, Chapter 3 pg. 51-100.

The Protein Data Bank for getting coordinates: http://www.rcsb.org/pdb/

Rasmol and Protein Explorer (new version of Rasmol): http://www.umass.edu/microbio/rasmol/

Cn3D from NCBI: http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml

Swiss pdb viewer (most powerful, a bit harder to use but well worth while): http://www.expasy.ch/spdbv/text/download.htm

Problem Set 1.3 (Huettner)

Problem Set 2.1 (Huettner)

 

Friday, August 29

Lecture 9:              Channel gating - voltage gated channels (Huettner)
Lecture 10:            Na and K channels - Action potential generation (Huettner)

Doyle DA, Morais Cabral J, Pfuetzner RA, Kuo A, Gulbis JM, Cohen SL, Chait BT, MacKinnon R (1998 - PDF file of the paper) The structure of the potassium channel: molecular basis of K+ conduction and selectivity. Science 280:69-77

Jiang Y, Lee A, Chen J, Cadene M, Chait BT, MacKinnon R. (2002 - PDF file of the paper) The open pore conformation of potassium channels. Nature 417:523-6.

Jiang Y, Lee A, Chen J, Cadene M, Chait BT, MacKinnon R. (2002 - PDF file of the paper) Crystal structure and mechanism of a calcium-gated potassium channel. Nature 417:515-22.

Discussion 3:        Parkinson’s Disease  (Ramanan)

Main paper for discussion:

Cooper AA, Gitler AD, Cashikar A, Haynes CM, Hill KJ, Bhullar B, Liu K, Xu K, Strathearn KE, Liu F, Cao S, Caldwell KA, Caldwell GA, Marsischky G, Kolodner RD, Labaer J, Rochet JC, Bonini NM, Lindquist S. (2006) Alpha-synuclein blocks ER-Golgi traffic and Rab1 rescues neuron loss in Parkinson's models. Science. Jul 21;313(5785):324-8. Epub 2006 Jun 22. (Supplementary information). 

Background reading for the discussion paper:
Outeiro TF, Lindquist S. (2003) Yeast cells provide insight into alpha-synuclein biology and pathobiology. Science. Dec 5;302(5651):1772-5. (Supplementary information).

 

WEEK TWO


Monday, September 1        Labor Day – No class

 

Tuesday, September 2 

Lecture 1:              Action potential propagation / myelination (Huettner)
Lecture 2:              Additional v-gated currents / frequency coding (Huettner)

Principles of Neural Science, Kandel, Schwartz, and Jessell, Eds. McGraw-Hill, NY, NY.

Chapter 8: Local signaling: passive electrical properties of the neuron
Chapter 9: Propagated signaling: the action potential

Recommended:

Hille, Ion Channels of Excitable Membranes. Third Edition, Sinauer, 2001.
Chapter 2: Classical Biophysics of the Squid Giant Synapse
Chapter 4: Voltage-gated calcium channels
Chapter 5: Potassium and chloride channels

Aidley, The Physiology of Excitable Cells, Fourth Edition, Cambridge University Press, 1998. Chapter 4: Electrical properties of the nerve axon

                Nicholls, Martin, Wallace, and Fuchs. From Neuron to Brain. Fourth Edition, Sinauer, 2001. Chapter 7: Neurons as conductors of electricity 

Discussion 1:        Channel Inactivation (Huettner)

Hoshi, Zagotta, and Aldrich (1990) Biophysical and molecular mechanisms of Shaker potassium channel inactivation. Science 250:533-538.

Zagotta, Hoshi, and Aldrich (1990) Restoration of inactivation in mutant Shaker potassium channels by a peptide derived from ShB. Science 250:568-571.

 

Wednesday, September 3

Lecture 3:              Transmission and neurotransmitters (Huettner)
Lecture 4:              M-current (Huettner)

Part III: Elementary interactions between neurons: synaptic transmission in Principles of Neural Science, 4th Edition, Kandel, Schwartz, and Jessell, Eds. McGraw-Hill, NY, NY. (2000)

Chapter 10 - Overview of Synaptic Transmission

Chapter 11 - Signaling at the Nerve-Muscle Synapse: Directly Gated Transmission

Chapter 14 - Transmitter Release

Discussion 2:        Channel Structure (Huettner)

Long SB, Campbell EB, Mackinnon R.  Crystal structure of a mammalian voltage-dependent Shaker family K+ channel. Science. 2005 Aug 5;309(5736):897-903. 
Long SB, Campbell EB, Mackinnon R.  Voltage sensor of Kv1.2: structural basis of electromechanical coupling.
Science. 2005 Aug 5;309(5736):903-8.

 

Thursday, September 4
Lecture 5:              Synapse molecular properties I (Hanson)
Lecture 6:              Synapse molecular properties II (Hanson)

Jahn R, Scheller RH. (2006) SNAREs - engines for membrane fusion. Nat Rev Mol Cell Biol. 7(9):631-43.

 
Friday, September 5

Lecture 7:              Ligand-gated ion channels (Mennerick)

Lecture 8:              Ligand-receptor interactions (Mennerick)

Discussion 3:        Vesicle Release (Hanson)

Schaub JR, Lu X, Doneske B, Shin YK, McNew JA. (2006) Hemifusion arrest by complexin is relieved by Ca2+-synaptotagmin I. Nat Struct Mol Biol. 13(8):748-50 (Supplemental Information).
Giraudo CG, Eng WS, Melia TJ, Rothman JE. (2006) A clamping mechanism involved in SNARE-dependent exocytosis. Science. 313(5787):676-80 (Supplemental Information).

 

WEEK THREE

 

Monday, September 8

Lecture  1:             Calcium dependence (Mennerick)

Lecture 2:              Quantal analysis (Mennerick)

Required:

Principles of Neural Science, 4th Edition, Kandel, Schwartz, and Jessell, Eds. McGraw-Hill, NY, NY. (2000).
Chapter 11 Signaling at the Nerve-Muscle Synapse
Chapter 15 Neurotransmitters
Chapter 13 Modulation of Synaptic Transmission: Second Messengers

Recommended:

Hall, An Introduction to Molecular Neurobiology Chapters 6 and 7

Purves, et al.; Neuroscience.  Chapters 6, 7 and 8

Discussion # 1:     Binding and Gating (Mennerick)

Chang Y, Weiss DS (1999) Channel opening locks agonist onto the GABAC receptor. Nature Neurosci  2(3):219-25.

 

Tuesday, September 9
Lecture 3:              Metabotropic receptors (Gereau)
Lecture 4:              Metabotropic effector pathways (Gereau)

Principles of Neural Science, 4th Edition, Kandel, Schwartz, and Jessell, Eds. McGraw-Hill, NY, NY. (2000).
Chapter 13  Modulation of Synaptic Transmission: Second Messengers

 

Wednesday, September 10
Lecture 5:              Glutamatergic Transmission (Huettner)
Lecture 6:              LTP / LTD (Huettner)

Bliss and Collingridge (1993) A synaptic model of memory: long-term potentiation in the hippocampus. Nature 361:31-39.

PDF file of a provocative paper!

PDF file of another provocative paper!

The Debate Continues – PDF File of two commentaries from November 2003

Discussion 2:        Analog and Action Potential transmission (Mennerick)

Alle H, Geiger JR. (2006) Combined analog and action potential coding in hippocampal mossy fibers. Science 311(5765):1290-3 (Supplemental Information).

 

Thursday, September 11

Lecture 7:              Dendritic Integration (Huettner)

Yuste R. and Tank D.W. (1996 - PDF file of the paper) Dendritic integration in mammalian neurons, a century after Cajal. Neuron 16:701-716.

Synaptic Integration . Chapter 12 in Principles of Neural Science, Kandel, Schwartz, and Jessell, Eds. McGraw-Hill, NY, NY.

Lecture 8:              Gap junctions and electrical synapses (Lukasiewicz)

Pages 301-304, Principals of Neuroscience, Kandel et al. 4th ed.

Nicholls et al., From Neuron to Brain & Hille, Ionic Channels of Excitable Membranes.  Read appropriate sections on Gap Junctions and Electrical Synapses.

Bruzzone & Ressot (1997) Connexins, gap junctions and cell-cell signaling in the nervous system.  European J. Neurosci.  9:1-6

Deans MR, Volgyi B, Goodenough DA, Bloomfield SA and Paul DL (2002) Connexin36 Is Essential for Transmission of Rod-Mediated Visual Signals in the Mammalian Retina. Neuron 36: 703-712

 

Friday, September 12

Lecture 9:              TRP channels(Story)

Lecture 10:            Pain (Story)

Discussion 3:        Long-Term Depression (Huettner)

Oliet, S.H.R., Malenka, R.C. and Nicoll, R.A. (1997) Two distinct forms of long-term depression coexist in CA1 hippocampal pyramidal cells. Neuron 18:969-982.


EXAM 1: Handed out today – due back by noon Tuesday, September 16th.

 

WEEK FIVE

 

Monday, September 22
Lecture 1:              Sensory Transduction and Sensory Maps I (Kefalov)
Lecture 2:              Sensory Transduction and Sensory Maps II (Kefalov)

Hille, 3rd ed. Chapter 8, Pages 237-261.

Torre et al., (1995) Transduction and adaptation in sensory receptor cells.  J. Neurosci. 15:7757-7768.

  Photoreceptors:

Chapter 16, From Neuron to Brain, 3rd Ed.,  Nichols et al.

Chapter 26, Principals of Neuroscience, Kandel et al. 4th ed.

Baylor (1996 - PDF file of the paper) How Photons Start Vision.  PNAS  93:560-565.

  Hair Cells:

Chapters 30 and 31, Principals of Neuroscience, Kandel et al. 4th ed.

Chapter 14, From Neuron to Brain, 3rd Ed., Nichols et al.

Hudspeth (1997 - PDF file of the paper) How hearing happens.  Neuron 19:947-950

  Olfactory Receptor Neurons:

Chapters 32, Principals of Neuroscience, Kandel et al. 4th ed.

Chapter 14, From Neuron to Brain, 3rd Ed.,  Nichols et al.

Firestein S. How the olfactory system makes sense of scents. Nature. 2001 Sep 13;413(6852):211-8.

Discussion # 1:     TRP channels and Pain (Story)

Bandell M, Dubin AE, Petrus MJ, Orth A, Mathur J, Hwang SW, Patapoutian A. (2006) High-throughput random mutagenesis screen reveals TRPM8 residues specifically required for activation by menthol. Nat Neurosci. Apr;9(4):493-500 (supplemental information).

 


Tuesday, September 23

Lecture 3:              Sensory Transduction and Sensory Maps III (Holy)
Lecture 4:              Sensory Transduction and Sensory Maps IV (Holy)

Firestein S. How the olfactory system makes sense of scents. Nature. 2001 Sep 13;413(6852):211-8.

Buck LB (2000) Smell and Taste: The chemical senses. Chapter 32 in Principles of Neural Science, Kandel, Schwartz, and Jessell, Eds. McGraw-Hill, NY, NY.

 

Wednesday, September 24
Lecture 5:              Retinal Networks I (Lukasiewicz)
Lecture 6:              Retinal Networks II (Lukasiewicz)

Visual Processing by the Retina, Chapter 26, Principles of Neural Science, 4th Edition, Kandel et al.

Retina and Lateral Geniculate Nucleus, Chapter 16, From Neuron to Brain, 3rd Addition, Nicholls et al.

Kamermans M, Fahrenfort I, Schultz K, Janssen-Bienhold U, Sjoerdsma T, and Weiler R (2001) Hemichannel-Mediated Inhibition in the Outer Retina. Science 292: 1178-1180.

Discussion 2 :       Odor Receptors  (Holy) 

Feinstein P, Bozza T, Rodriguez I, Vassalli A, Mombaerts P. Axon guidance of mouse olfactory sensory neurons by odorant receptors and the beta2 adrenergic receptor. Cell. 2004 Jun 11;117(6):833-46.

 

Thursday, September 25
Lecture 7:              Early Development I (Gray/Taghert)

Lecture 8:              Early Development II (Gray/Taghert)

 

Friday, September 26

Lecture 9:              Early Development III (Gray/Taghert)

Lecture 10:            Neural Stem Cells (Gray/Taghert)

Temple, S. (2001) The development of neural stem cells. Nature 414, page 112

Discussion # 3: Receptive Fields - PDF file of the paper (Lukasiewicz)

McReynolds, J.S. and Cook, P.B. (1998) Lateral inhibition in the inner retina is important for spatial tuning of ganglion cells. Nature Neuroscience, Volume 1 Number 8 pp 714-719.

  

WEEK SIX

 

Monday, September 29

Lecture 1:              Cell fate I  (Taghert)

Lecture 2:              Cell fate II  (Taghert)

Discussion 1:        Stem Cells in the CNS (Gray/Taghert)

Zhou Q, Anderson DJ. (2002) The bHLH transcription factors OLIG2 and OLIG1 couple neuronal and glial subtype specification. Cell. Apr 5;109(1):61-73.

 

Tuesday, September 30
Lecture  3:                   Early development (gradients, rhombomeres, hox code) (Gray)

Lecture  4:                   Early development (spinal cord dorsal-ventral pattern) (Gray)

Goridis C, Rohrer H  (2002) Specification of catecholaminergic and serotonergic neurons.  Nat Rev Neurosci.  Jul;3(7):531-41.
Edlund T and Jessell TM (1999 - PDF file of the paper)  Progression from extrinsic to intrinsic signaling in cell fate specification: a view from the nervous system.  Cell 96, 211-224.

Jessell, TM and Sanes JR (2000) The generation and survival of nerve cells. Chapter 53 in Principles of Neural Science, Kandel, Schwartz, and Jessell, Eds. McGraw-Hill, NY, NY.

 

Wednesday, October 1
Lecture 5:              Neurogenesis and migration (Corbo)

Lecture 6:              Axon pathfinding (Corbo)

Bronner-Fraser, M and Hatten, MB (2003) Neurogenesis and Migration. Chapter 15 in Fundamental Neuroscience, Squire, Bloom, McConnell, Roberts, Spitzer and Zigmond, Eds. Academic Press (2nd edition).

Sanes, JR and Jessell, TM (2000) The guidance of axons to their targets. Chapter 54 in Principles of Neural Science, Kandel, Schwartz, and Jessell, Eds. McGraw-Hill, NY, NY.

Optional

Dickson BJ (2002) Molecular mechanisms of axon guidance. Science. 298(5600):1959-64.

Discussion 2:        Early development (Gray)
Gavalas A, Ruhrberg C, Livet J, Henderson CE, Krumlauf R. (2003) Neuronal defects in the hindbrain of Hoxa1, Hoxb1 and Hoxb2 mutants reflect regulatory interactions among these Hox genes. Development. 2003 Dec;130(23):5663-79. Epub 2003

 

Thursday, October 2

Lecture 7:              Diversity of synapses (Nonet)
Lecture 8:              Synaptogenesis: cellular view (Nonet)

Movie 1 (right click and choose open in a new window)
Movie 2 (right click and choose open in a new window)
Movie 3 (double left click should work, but if not, try right click and open in a new window)