Course Calendar

Spring 2017 --

Subject to change -- check announcements!


January 17 (Tu): Principles of neural circuits and systems; auditory localization as an example

    1. Konishi M (2006) Listening with two ears. Scientific American p28-35.

Topic I: Sensory systems and representations

January 19 (Th) Vision and Light

January 24 (Tu): Animal eyes Homework #1 DUE

    1. Animal Eyes, Land and Nilsson, Chapter 3: What makes a good eye?

    2. Animal Eyes, Land and Nilsson, Chapter 4: Aquatic eyes, the evolution of the lens

January 26 (Th): Retinal receptive fields and feature detectors

  1. Kuffler SW (1953) Discharge patterns and functional organization of mammalian retina. J. Neurophysiol. 16:37-68

  2. Zhang Y, Kim IJ, Sanes JR, Meister M. (2012) The most numerous ganglion cell type of the mouse retina is a selective feature detector. Proc Natl Acad Sci U S A. ;109:E2391-8.

  3. Review for background: Kevan Martin (1994): A brief history of the “feature detector” Cerebral Cortex 4:1-7.

Jan 31 (Tu): Mechanisms of retinal direction selectivity Homework #2 DUE

  1. Barlow HB and Levick, WR (1965) The mechanism of directionally selective units in rabbit's retina. J. Physiol. 178:477-504.

  2. Euler T, Detwiler PB and Denk W (2002) Directionally selective calcium signals in dendrites of starburst amacrine cells. Nature 418:845-852.

  3. Review for background: Demb (2007) Cellular mechanisms for direction selectivity in the retina. Neuron 55:179-186

  4. Review for background: Elstrott and Feller (2009) Vision and the establishment of direction selectivity; a tale of two circuits. Curr Opin Neurobiology

Feb 2 (Th): Mechanisms of retinal direction selectivity 2

  1. Briggman KL, Helmstaedter M, Denk W. (2011) Wiring specificity in the direction-selectivity circuit of the retina. Nature 471:183-8

  2. Kim/Green et al., (2014) Space–time wiring specificity supports direction selectivity in the retina. Nature 509:331-336.

Feb 7 (Tu): Visual cortex and functional architecture

  1. Hubel, DH and TN Wiesel (1962) Receptive fields, binocular interaction and functional architecture in the cat’s visual cortex. J. Physiol. 160:106-154.

  2. Ohki K, Chung S, Ch'ng YH, Kara P, Reid RC. (2005) Functional imaging with cellular resolution reveals precise micro-architecture in visual cortex. Nature 433:597-603.

  3. Review for background: Van Hooser SD, Nelson SB (2005) Visual system. Encyclopedia of the Life Sciences.

  4. Review for background: Van Hooser SD (2007): Similarity and diversity in visual cortex: is there a unifying theory of cortical computation? Neuroscientist 13:639-56.

  5. Video of recordings of simple/complex cells:

Febuary 9 (Th): SNOW DAY

February 14 (Th): Cortical Microcircuitry and Mechanisms of Selectivity 1 Homework #3 DUE

  1. Reid and Alonso (1995) Specificity of monosynaptic connections from thalamus to visual cortex. Nature 378:281-284

  2. Somers, Nelson, and Sur (1995) An emergent model of orientation selectivity in cat visual cortical simple cells. J Neurosci. 15:5488-5465

  3. Review for background: Ferster D, Miller KD. (2000) Neural mechanisms of orientation selectivity in the visual cortex. Annu. Rev. Neurosci. 23:441-71

February 16 (Tu): Cortical Microcircuitry and Mechanisms of Selectivity 2

  1. Anderson JS, Carandini M, Ferster D. (2000) Orientation tuning of input conductance, excitation, and inhibition in cat primary visual cortex. J. Neurophysiol. 84:909-26

  2. Ozeki H, Finn IM, Schaffer ES, Miller KD, Ferster D. (2009) Inhibitory stabilization of the cortical network underlies visual surround suppression. Neuron 62:578-92

  3. Review for background: Ferster D, Miller KD. (2000) Neural mechanisms of orientation selectivity in the visual cortex. Annu. Rev. Neurosci. 23:441-71

February 20 - 24 Winter recess - No class

Topic II: Neural codes: populations, rates, and timing

February 28 (Tu): Population codes 1

  1. Lee, Rohrer, and Sparks (1987): Population coding of saccadic eye movements by neurons in the superior colliculus. Nature 332:357-360

  2. Lewis and Kristan (1998) A neuronal network for computing population vectors in the leech. Nature 391:76-79

  3. MacEvoy, Tucker, and Fitzpatrick 2009:A precise form of divisive suppression supports population coding in the primary visual cortex. Nature Neuroscience: 12(5):637-45.

March 2 (Th): Rate codes and temporal codes 1 Homework #4 DUE

  1. O’Keefe (1976) Place Units in the hippocampus of the feely moving rat. Exper. Neurology 51:78-109

  2. Huxter, Burgess, and O’Keefe (2003) Independent rate and temporal coding in hippocampal pyramidal cells. Nature 425:828-832

  3. Mehta, Lee, and Wilson (2002) Role of experience and oscillations in transforming a rate code into a temporal code. Nature 417:741-746

March 7 (Tu): Rate codes and temporal codes 2 Term paper topic DUE

  1. Panzeri, Petersen, Schultz, Lebedev, and Diamond (2001) The role of spike timing in the coding of stimulus location in rat somatosensory cortex. Neuron 29:769-777

  2. Pouille and Scanziani (2001) Enforcement of temporal fidelity in pyramidal cells by somatic feed-forward inhibition. Science 293:1159-1163

  3. Review for background: Hull and Scanziani (2007) Its about time. Nat Neurosci 10:400-402

March 9 (Th): Decoding neural codes

  1. Handout!

  2. Softky and Koch (1993): The highly irregular firing of cortical cells is inconsistent with temporal integration of random EPSPs. J Neurosci 13:334-50

March 14 (Tu): Special guest - Frank Werblin!

  1. Congdon, N., B. O'Colmain, et al. (2004). "Causes and prevalence of visual impairment among adults in the United States." Arch Ophthalmol 122(4): 477-485

  2. Crossland, M. D., L. E. Culham, et al. (2005). "Preferred retinal locus development in patients with macular disease." Ophthalmology 112(9): 1579-1585

  3. Fletcher, D. C. and R. A. Schuchard (1997). "Preferred retinal loci relationship to macular scotomas in a low-vision population." Ophthalmology 104(4): 632-638

March 16 (Th): Decoding neural codes II

  1. Yang and Shadlen (2007) Probabilistic reasoning by neurons. Nature 447:1075-1080

  2. Shadlen and Newsome (1998): The variable discharge of cortical neurons: implications for connectivity, computation, and information coding. J Neurosci:18:3870-96.

Topic III: Neural basis of simple and complex behaviors

March 21 (Tu): Neural correlates of perception and decision making I Homework #5 DUE

  1. Newsome, Britten, Movshon (1989) Neural correlates of a perceptual decision. Nature 341:52-54

  2. Salzman, Britten, and Newsome (1990) Cortical microstimulation influences perceptual judgments of motion direction. Nature 346:174-177

  3. Yang and Shadlen (2007) Probabilistic reasoning by neurons. Nature 447:1075-1080

  4. Review for Background: Gold and Shadlen (2007) The Neural Basis of decision making. Ann Rev. Neurosci. 30: 535-57

March 23 (Th): Spatial codes and cognitive maps

  1. Leutgeb, Leutgeb, Marnes, Moser, McNaughton, and Moser (2005) Independent codes for spatial and episodic memory in hippocampal neuronal ensembles. Science 309:619-623

  2. Hafting, Fyhn, Molden, Moser, and Moser (2005) Microstructure of a spatial map in the entorhinal cortex. Nature 436:801-806

  3. Fyhn, Hafting, Treves, Moser, and Moser (2007) Hippocampal remapping and grid realignment in entorhinal cortex. Nature 446:190-194

  4. Reviews for Background: Leutgeb, Leutgeb, Moser, and Moser (2005) Place cell, spatial maps and the population code for memory. Curr Opin Neurobiol. 15:738-746; McNaughton, Battaglia, Jensen, Moser, and Moser (2006) Path integration and the neural basis of the ‘cognitive map’. Nat. Rev. Neurosci. 7:663-678

March 28 (Tu): Spatial codes and cognitive maps 2 Term anatomy/synaptic connection section DUE

  1. Leutgeb, Leutgeb, Moser, and Moser (2005) Place cell, spatial maps and the population code for memory. Curr Opin Neurobiol. 15:738-746

  2. McNaughton, Battaglia, Jensen, Moser, and Moser (2006) Path integration and the neural basis of the ‘cognitive map’. Nat. Rev. Neurosci. 7:663-678

March 30 (Th): Replay

  1. Dupret et al. (2010) The reorganization and reactivation of hippocampal maps predict spatial memory performance. Nat Neurosci 13:995-1002.

    1. Pfeiffer and Foster (2013) Hippocampal place-cell sequences depict future paths to remembered goals. Nature 497:74-79.

  2. Jadhav et al. (2012) Awake Hippocampal Sharp-Wave Ripples Support Spatial Memory. Science. 336:1454-8.

  3. Perspective: Carr et al. (2011) Hippocampal replay in the awake state: a potential substrate for memory consolidation and retrieval. Nat Neurosci. 14:147-153.

April 4 (Tu): Birdsong and vocal learning Term paper physiology of synaptic inputs/outputs section DUE

  1. Marler P, Peters S (1977) Selective vocal learning in a sparrow. Science 198:519-521

  2. Leonardo A, Konishi M (1999). Decrystallization of adult birdsong by perturbation of auditory feedback. Nature 399:466-70.

  3. Brainard, M.S. and Doupe, A. J. (2000) Interruption of a basal ganglia-forebrain circuit prevents plasticity of learned vocalizations. Nature 404:762-766

  4. Review for background: Brainard and Doupe (2000) Auditory feelback in learning and maintenance of vocal behavior. Nat. Rev. Neurosci 1:31-40

Topic IV: Activity-dependent plasticity in circuits

April 6 (Th): Development of visual responses -- experience-independent and -dependent features

  1. Li Y, Fitzpatrick D, White LE. (2006) The development of direction selectivity in ferret visual cortex requires early visual experience. Nat Neurosci 9:676-81.

  2. Li Y/Van Hooser SD, Mazurek M, White LE, Fitzpatrick D. (2008) Experience with moving visual stimuli drives the early development of cortical direction selectivity. Nature 456:952-6.

April 10 - April 18 Spring recess - No class

April 20 (Th): Visual Deprivation and amblyopia Term paper role in perception/behavior section and PR DUE

  1. Wiesel TN, Hubel DH (1965) Comparison of the effects of unilateral and bilateral eye closure on cortical unit responses in kittens. J Neurophysiol 1965, 28:1029-1040

  2. Wiesel TN, Hubel DH (1965) Extent of recovery from the effects of visual deprivation in kittens. J Neurophysiol 1965, 28:1060-1072

  3. Review for background: Huberman, Feller, and Chapman (2008) Mechanisms underlying development of visual maps and receptive fields. Ann Rev Neurosci 31:479-509.

April 25 (Tu): Visual deprivation: mechanisms

  1. Heynen AJ, Yoon BJ, Liu CH, Chung HJ, Huganir RL, Bear MF (2003) Molecular mechanism for loss of visual cortical responsiveness following brief monocular deprivation. Nat Neurosci. 6(8):854-62

  2. Maffei, Nataraj, Nelson, and Turrigiano (2006) Potentiation of Cortical inhibition by visual deprivation. Nature 443:81-84

April 27 (Th): Homeostatic plasticity in circuits Term paper disease section draft DUE (returned to you by Wednesday May 2)

  1. Desai et al. (2002) Critical periods for experience-dependent synaptic scaling in visual cortex. Nature Neurosci. 5:783-789

  2. Mrsic-Flogel et al. (2007) Homeostatic regulation of eye specific responses in visual cortex during ocular dominance plasticity. Neuron 54:961

May 02 (Tu): Map registration: aligning visual and auditory maps

  1. Knudsen EI (1983) Early Auditory Experience Aligns the Auditory Map of Space in the Optic Tectum of the Barn Owl. Science, 222:939-942.

  2. Bergen et al. (2005) Hunting increases adaptive auditory map plasticity in barn owls. J Neurosci. 25:9816-9820

  3. Review for background: Knudsen EI (2002) Instructed learning in the auditory localization pathway of the barn owl. Nature 417:322-8.

Final deadline:

May 5 (F) at midnight (that is, 1 second after 2017-05-05 11:59pm), revised term paper due

No time (): Miscellaneous cool papers, previous papers

  1. Bogen and Campbell (1962) Recovery of of foreleg placing after ipsilateral frontal lobectomy in the hemicerebrectomized cat. Science. 135:309-10.

  2. Ramirez et al. (2013) Creating a false memory in the hippocampus. 341:387-91.

  3. Wilson MA, McNaughton BL. (1994) Reactivation of hippocampal ensemble memories during sleep. Science. 265:676-9.

  4. Perspective: Schwartz (2003) Are life episodes replayed during dreaming? Trends Cogn Sci. 7:325-327

  5. Ziv et al. 2013 Long-term dynamics of CA1 hippocampal place codes Nature 16: 264–266

Next time? (): Molecular cues and activity-dependent mechanisms role in development

  1. Fukuchi-Shimogori T, Grove EA (2001) Neocortex patterning by the patterning molecule FGF8. Science 294:1071-1074

  2. Cang J, Niell CM, Liu X, Pfeiffenberger C, Feldheim DA, Stryker MP (2008) Selective disruption of one cartesian axis of cortical maps and receptive fields by deficiency in Ephrin-As and structured activity. Neuron 57:511-23

Steve to do: Peer review form, perhaps update grid cell papers, do figure lists