Columbia University

Kavli Institute for Brain Science

W3005y/W4005 Neurobiology II: Neural circuits                                                                                                                                         Spring 2015



Lectures: Tu./Th. 4:10-5:25 Room: FAYERWEATHER 310

Course website:

Undergraduate instructor: Rafael Yuste, Graduate student instructor: Darcy Kelley, Guest lecturers: Darcy Peterka, Thomas Jessell & Eric Kandel

Office Hours: Tuesdays and Thursdays from 3-4 pm, 906 NWC building or by appointment Teaching Assistants:

Georgia Pierce <>, Wujie Zhang (  Rebecca Rabinovich <>, Shuting Han <>

Auditors: allowed only after permission is granted by Professor



REQUIREMENTS:  This  course  is  the  "capstone"  course  for  the  Neurobiology  and  Behavior undergraduate major at Columbia University and will be taught by the Directors of the Kavli Institute for Brain Science at Columbia. It is designed for advanced undergraduate and graduate students. Knowledge of Cellular Neuroscience (how an action potential is generated and how a synapse works) will be assumed. It is strongly recommended that students take w3004 Neurobiology 1: Molecular and Cellular Neuroscience, or a similar course, before enrolling in w3005. Students unsure about their backgrounds should check a representative syllabus of w3004 in



Required: Kandel et al., Principles of Neural Science, Fifth Edition, McGraw Hill

During the course we will cover the book, reading most of the chapters. The text is available at the Columbia Bookstore and in also in Book Culture. Several copies should be on reserve at the NWC Science Library.

Hardcover: Kandel/dp/0071390111/ref=tmm_hrd_title_0



Also recommended: Kandel, In Search of Memory, Norton.

Kindle:                                    ebook/dp/B002PQ7B5O/ref=tmm_kin_title_0?_encoding=UTF8&sr=&qid=

Papeback:                                                  Science/dp/0393329372/ref=tmm_pap_title_0


PAPERS: During the weekly recitations, students will present and discuss papers from the primary literature posted on the course website:

EXAMS: Three tests will be given, without a final exam. The first two tests covers material discussed in class. Extra credit will be given for questions related to additional reading of material not covered in class. The last test will also include the research articles discussed in the recitations. The tests take place during class. Rescheduling is only granted under exceptional circumstances, in cases of serious illness or personal crisis, and the student is required to present a letter from the undergraduate dean as well as other supporting evidence (such as doctor’s notes, etc.). Please note all test dates ASAP and make travel arrangements accordingly.


RECITATIONS: Students read and discuss in depth selected research papers posted in the Courseworks website. Weekly attendance at the recitations is mandatory for a passing grade and active participation counts in the final grade. Recitation material will also be part of the third test. Recitations will take place on:

Mondays 5:45-7pm, Fairchild 9000, TBA Tuesdays 5:45-7pm, Fairchild 1000, TBA Wednesdays 5:45-7pm, Fairchild 1000, TBA Thursdays 5:45-7pm, Fairchild 1000, TBA

Graduate students recitation, Thursdays 5:45-7pm, Fairchild 9000, Darcy Kelley


All students need to sign up for one recitation with the corresponding TA and are required to attend that recitation till the end of the semester. The first recitations will be January 26th-29th


GRADING: Each exam will contribute 30% towards the final grade. Participation in the recitations is required for a passing grade and will determine the remaining 10%.




Part I: Introduction


Introduction (Ch. 1- 3)                                                                                                                                              Jan 20th

Neuroscience Laboratory Visit (902 NWC): Peterka                                                                                                                      Jan 22nd Recitation 1: Jan 26th- 29th: Markram et al 1997

Part II: Cell and Molecular Biology of neurons (Ch. 4-7)                                                                                                                                              Jan 27th

Part III: Synaptic transmission (Ch. 8-14)                                                                                                                      Jan 29th Recitation 2: Feb 2nd-5th: Sperry 1945

Part VIII: Development


Patterning and differentiation (Ch. 52, 53)                                                                                                                                              Feb 3rd

Axonal growth and Synaptogenesis (Ch. 54, 55)                                                                                                                   Feb 5th Recitation 3: Feb 9th- 12th Zuo et al 2005

Spinal Cord Development -Jessell                                                                                                                                              Feb 10th

Synaptic refinement and repair (Ch. 56, 57)                                                                                                                          Feb 12th Recitation 4: Feb 16th- 19th: Wiesel and Hubel 1965

Sexual differentiation and aging (Ch. 58, 59)                                                                                                                                              Feb 17th

Open Q&A Review                                                                                                                                              Feb 19th

No recitations: Feb 23rd- 26th

FIRST TEST                                                                                                                                              Feb 24th


Part V: Perception


The Retina (Ch. 26)                                                                                                                                              Feb 26st

Recitation 5: March 2nd- 5th Hopfield and Tank 1986

Visual Processing (Ch. 25, 27- 29)                                                                                                                                             Mar 3rd

Auditory System (Ch. 30, 31)                                                                                                                                             Mar 5th

Recitation 6: March 9th- 12th Hafting et al 2005

Chemical Senses (Ch. 32)                                                                                                                                             Mar 10th

Somatosensory system and Pain (Ch. 21-24)                                                                                                                                             Mar 12th

SPRING BREAK                                                                                                                                             Mar 17-20th

Recitation 7: March 23rd- 26th Harvey et al 2012 Part VI: Movement

Motor system 1 (Ch. 16, 33-36)                                                                                                                                             Mar 24th

Motor system 2 (Ch. 37 and 38)                                                                                                                                             Mar 26th

Recitation 8: March 30th- April 2nd: Hahnloser et al., 2002

Cerebellum (Ch. 42)                                                                                                                                             Mar 31st

Open Q&A Review                                                                                                                                           April 2nd

No Recitations: April 6th- 9th

SECOND TEST                                                                                                                                           April 7th

Part VII: Information Processing


Emotions and feelings (Ch. 48)                                                                                                                                           April 9th

Recitation 9: April 13th- 16th: Xie et al 2013

Sleep and internal states (Ch. 51)                                                                                                                                           April 14th


Part IX: Language, thought, learning


Learning and memory (Ch. 65-67)                                                                                                                                           April 16th

Recitation 10: April 20-23rd:: Liu et al 2012

Neural Networks (Appendix E, F)                                                                                                                                           April 21st

Memory (Ch. 65-66)-Kandel                                                                                                                                           April 23rd

No Recitations: April 27th-30th


Open Q&A Review                                                                                                                                           April 28th

THIRD TEST                                                                                                                                           April 30th

Recitation papers:



Markram H, Lubke J, Frotscher M, Sakmann B. (1997) Regulation of synaptic efficacy by coincidence of postsynaptic APs and EPSPs. Science 275:213-5.


Sperry, RW (1945). Restoration of vision after crossing of optic nerves and after contralateral transplantation of eye. J. Physiology, Vol. 8no. 1, 15.


Zuo Y, Yang G, Kwon E, Gan WB. (2005) Long-term sensory deprivation prevents dendritic spine loss in primary somatosensory cortex. Nature 436 :261-5.


Wiesel TN, Hubel DH. (1965). Comparison of the effects of unilateral and bilateral eye closure on cortical unit responses in kittens. J Neurophysiol. Nov;28(6):1029-40.


Hopfield JJ, Tank DW. (1986) Computing with neural circuits: a model. Science 233: 625-33.


Hafting T1, Fyhn M, Molden S, Moser MB, Moser EI. (2005). Microstructure of a spatial map in the entorhinal cortex. Nature Aug 11;436(7052):801-6.


Harvey CD, Coen P, Tank DW. (2012). Choice-specific sequences in parietal cortex during a virtual- navigation decision task. Nature Mar 14;484(7392):62-8


Hahnloser RH, Kozhevnikov AA, Fee MS.  (2002) An ultra-sparse code underlies the generation of neural sequences in a songbird. Nature 419:65-70.


Xie L, Kang H, Xu Q, Chen MJ, Liao Y, Thiyagarajan M, O'Donnell J, Christensen DJ, Nicholson C, Iliff JJ, Takano T, Deane R, Nedergaard M.(2013). Sleep drives metabolite clearance from the adult brain. Science. 2013 Oct 18;342(6156):373-7.


Liu X, Ramirez S, Pang PT, Puryear CB, Govindarajan A, Deisseroth K, Tonegawa S. (2012). Optogenetic stimulation of a hippocampal engram activates fear memory recall. Nature Mar 22;484(7394):381-5.