Biological Sciences 300/301, Smith College | Neurophysiology

Schedule, Spring 2017   [also:]

UPDATED: April 18, 2017

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TOPICS, ASSIGNMENTS & LABS                                   COMPRESS SCHEDULE

Jan 26-31
and Feb 2


Neurons convey information: sensory receptors for touch.

Rapidly-adapting (phasic) vs. slowly-adapting (tonic) responses.
Code: bigger stimulus = more frequent action potentials.

Case discussion: How accurate is sensory reality?

Example: crustacean muscle receptor organ (MRO or "stretch receptor").
Intracellular recording using microelectrodes.
Electrical potential. Ohm's Law.
Resting, generator and action potentials.
Link between amplitude of generator potential and frequency of action potentials.

Reading: Purves et al, Neuroscience, 5th edition, 2012 ("N5e"), chapter 9, pages 189-196 (touch receptors), emphasizing aspects that correspond to the work we did in the first class, and chapter 2, pages 25-29 (neural signals).

The first weekly quiz will be on Thursday, February 2, at the start of class, on topics from this first reading assignment. Future quizzes will be on Tuesdays, beginning February 14.

Course requirements, textbook information, and other Administrative Information are posted online. The textbook has a companion website at:

     Lab 1: Using the oscilloscope.

Visualizing neurons.

An overview of some brains and neurons. Sections through the mammalian brain. CNS of arthropods as a comparison; structure of ganglia. Visualizing individual neurons: general stains, injecting fluorescent dye or dense marker, cobalt backfill, HRP backfill, lipid-soluble dyes, immunocytochemistry, genetically expressed green fluorescent protein, "brainbow," CLARITY technique, connectomics.

Reading: N5e, chapter 1, pages 4-16 (visualizing neurons).

   Collaborative Writing Project Chapter 1 ends here. DUE: Feb 9.

Feb 7-9


Ions, pumps, and membrane potentials.

Squid giant axon. Distribution of ions in axon and blood. Na/K pump: active transport of ions.

Case discussion: Why do red blood cells need pumps?

Forces acting on ions. Equilibrium between diffusion and electrical attraction. Equilibrium potential. Nernst equation.

Ions that can cross membrane carry charge until cell's potential matches the ion's equilibrium potential. Concentrations can be regarded as constant. Preview of the action potential.

Reading: N5e, chapter 4, pages 69-75 (pumps); chapter 2, pages 29, 32-40 (distribution of ions; skip box 2A for now).

View: Animations 4.2: The Sodium-Potassium Pump, 2.1: The Resting Membrane Potential, and 2.2: Electrochemical Equilibrium

     Lab 2: Circuits and amplifiers.

Membrane channels for Na+ and K+ ions.

Voltage clamping: command and measured potentials; inject current as needed to maintain constant conditions.
Axon: early inward current and late outward current follow depolarization.

Reading: N5e, chapter 3, pages 41-51 (voltage clamping).

View: five videos on the squid giant axon; Animations 3.1: The Voltage Clamp Method

Feb 14-16

Voltage clamping (continued)

Separating currents due to Na ions and K ions (low-Na, TTX, TEA). Na-inactivation.

Case discussion: A lethal shipboard snack.

Calculating conductance for each ion. Peak conductance vs. potential. Peak current vs. potential.

Reconstructing the action potential from voltage-clamp data. Threshold and refractory period.
Na/K pump is not a direct part of the action potential mechanism; it just "cleans up" afterward.

Patch clamping to look at individual channels.

Reading: N5e, chapter 4, pages 57-62 (patch clamping).

Animations 2.3: The Action Potential, 4.1: The Patch Clamp Method

  Collaborative Writing Project Chapter 2 ends here. DUE: Feb 21.

     Lab 3: Effect of potassium concentration on the resting potential.

 Propagation of the action potential.

Local circuit currents. Length constant. Conduction velocity. Strategies for faster conduction: giant fibers and myelination. Demyelinating diseases.

Case discussion: The case of the missing channels.

Reading: N5e, chapter 2, pages 30-31 (Box 2A, passive responses); chapter 3, pages 51-55 (propagation).

View: Animation 3.2: Impulse Conduction in Axons

  Collaborative Writing Project Chapter 3 (covering only one class) ends here. DUE: Feb 24.

Feb 21-23

Generator channels. Other voltage-dependent channels.

"Generator-type" channels: not electrically excitable. Examples: stretch-activated channels. Reversal potential suggests small positive ions go through the channels.

Initiation of action potentials at nearest low-threshold site.

Calcium and potassium channels (IA, IC) that modulate firing rate of neurons. Optogenetics: artificial channels to control neuron firing.

Reading: N5e, chapter 4, pages 63-66 (other channels).

     Lab 4: Action potentials in earthworm giant axons.

Molecular structure of voltage-dependent channels.

Physiological and genetic insights to structure of membrane channels. TTX binding at selectivity filter, pronase attack on inactivation gate. Purification of Na channel protein, sequencing of gene. Deductions about structure and function, S4 helix as probable voltage sensor.

Solving the molecular structure of the bacterial KcsA channel. Location of selectivity filter. Structure of the voltage-gated Shaker channel. Evolution of Ca and Na channels: four domains resembling Shaker channel.

Reading: N5e, chapter 4, pages 66-69 (channel structure).

Videos on K channel structure.

  Collaborative Writing Project Chapter 4 ends here. DUE: Mar 7, but you may wish to complete at least a rough draft prior to the exam on Mar 2.

Feb 28
-Mar 2


Feb 28: No class. The following two topics will be covered instead in online lessons hosted on our Moodle site. Those lessons and the reading assignment will be the topics for a quiz the following Tuesday.

Electrical synapses: structure of gap junctions, examples of electrical conduction.
Neuromuscular junction: structure of pre- and post-synaptic components.

Reading: N5e, chapter 5, pages 77-86 (electrical synapses, presynaptic aspects of chemical synapses [part 1]).

View: Animation 5.1: Synaptic Transmission

      Lab 5: Computer simulations of membrane potentials.

Mar 2, in class: EXAM on membrane potentials (topics through Feb 23 classes and readings).
A copy of a recent exam is posted on our Moodle site.

Mar 7-9

Presynaptic release of vesicles. Endplate potential. "Minepps." Quantal release..
Release requires depolarization, entry of extracellular calcium through excitable Ca-channels.
Timing and synaptic delay.

     Lab 6: Electroretinogram of the crayfish eye.

Postsynaptic receptors for acetylcholine.
Molecular structure: 5 homologous subunits. Patch clamping: selectivity for small positive ions.

ACh degradation: acetylcholine esterase. Synthesis: choline acetyl transferase. Reuptake and repackaging in vesicles via transporters. Pharmacology of the neuromuscular junction.

Reading: N5e, chapter 5, pages 86-96 (presynaptic); 96-101 (postsynaptic); chapter 6, pages 109-115 (nAChR);

  Collaborative Writing Project Chapter 5 ends here. DUE: Mar 23.

Mar 11-19

Spring break

Mar 21-23

Neuron-to-neuron synapses: spinal motoneurons.
Temporal and spatial summation.
Excitatory synapses. EPSPs. Reversal potential impies Na and K ions involved.
Transmitter: glutamate. AMPA and NMDA subtypes of glutamate receptor
Inhibitory synapses, IPSPs. Reversal potential = Cl ions.
Transmitter: glycine and GABA. Receptors structurally similar to AChR.
Interaction of excitation and inhibition = synaptic integration. Weighting of synapses by location.

     Lab 7: Motor units in the crayfish nerve cord.

Transmitters activating second messengers (metabotropic receptors).

Classical ionotropic (fast) vs. metabotropic receptors (slow).
Three groups of metabotropic second messengers.

Example: autonomic nervous system.
Pre- and post-ganglionic neurons. Parasympathetic and sympathetic innervation of heart. Multiple transmitters create PSPs of different durations (sympathetic ganglion)

Mechanisms of action: collision-coupling to channels, second messengers causing phosphorylation of channels, opening or closing channels.

Modulation at synapses: Multiple second-messenger systems, overlapping pathways, pre- and post-synaptic modulation.

Reading: N5e, chapter 5, pages 101-106 (epsps & ipsps); Appendix A, pages 720-722 (spinal cord); chapter 6, pages 116-125 (glutamate and GABA); chapter 7, pages 141-153 (second messengers); chapter 21, pages 454-461 (autonomic nervous sytem); chapter 6, pages 132-139 (other transmitters).

View: Animations 5.2 - Summation of Postsynaptic Potentials, 5.3: Ionotropic and Metabotropic Receptors

  Collaborative Writing Project Chapter 6 ends here. DUE: Mar 30.

Mar 28-30


Levels of control: within muscle cells (graded depolarization and calcium levels). Control at the motor unit (firing frequency and recruitment).

Feedback from spindles and Golgi tendon organs.

     Lab 7A: an extra techniques lab to prepare for Projects on the crayfish swimmeret system.
     Learn to isolate the crayfish nerve cord and record from first roots using pin electrodes.

Central control of posture and locomotion: command interneurons in crayfish, central pattern generators for locomotion in Tritonia, crayfish, roaches and cats. Role of sensory feedback in CPGs.

Case discussion: Swimming blindly (based on your response papers -- see the Special Assignment below).

Reading: N5e, chapter 16, pages 353-374 (motor control); chapter 9, pages 196-198 (spindle and GTO structure).

View: Animation 16.1: The Stretch Reflex

Special Assignment: Read a brief, classic paper on a central pattern generator that will be distributed in class Tuesday. Come to class Thursday with a one-paragraph response to the question: Does sensory feedback play a role in the swimming behavior of Tritonia?

  Collaborative Writing Project Chapter 7 ends here. DUE: Apr 6.

Apr 4-6


Structure of eyes and retinas. This introductory topic will be covered by two online lessons hosted on our Moodle site. Please view these lessons before Tuesday's class. The remaining topics will be covered in class:

The retina. Visual pigments, responses of photoreceptors to light. Synaptic network. Horizontal cells. Center-surround receptive fields of bipolar cells.

      Lab 8: Discussion: Crayfish swimmeret system.
      A paper is due (in lab) on the crayfish swimmeret system (see lab instructions).

Retinal ganglion cells. Transient (Y) and sustained (X) ganglion cells. Spatial distribution of retinal ganglion cells.

  Collaborative Writing Project Chapter 8 ends here. DUE: Apr 18.

Reading: N5e, chapter 11, pages 229-245 (eye, retina, photoreceptors; read box B, on the blind spot; boxes A, C & D are optional), 249-256 (retinal circuits).

View: Animations 11.1: Anatomy of the Human Eye, 11.2: Phototransduction, 11.3: Information Processing in the Retina

Apr 11-13

Visual pathway: lateral geniculate nucleus and visual cortex. Simple, complex and "hypercomplex" cells in striate cortex.

     Lab 9: Projects: Crayfish swimmeret system.

Primary visual cortex. Binocular (stereo) vision. Computer-based receptive field mapping. Spatial frequency selectivity.

Reading: N5e, chapter 12, pages 257-265 (visual cortex); Appendix A, pages 728-735 (thalamus and cortex).

View: Animation 12.1: Visual Pathway. View: Video about Hubel and Wiesel's experiments.

Apr 18-20

Cortical anatomy: Retinotopic map, ocular dominance columns, orientation pinwheels, spatial frequency patches, blobs, cortical layers.

  Collaborative Writing Project Chapter 9 ends here. DUE: Apr 25.

     Lab 10: Projects.

Extrastriate cortex: Pathways for motion and form. Dorsal pathway, area MT, direction and disparity selectivity.

Reading: N5e, chapter 12, pages 265-272 (cortical anatomy), pages 272-275 (extrastriate cortex); chapter 24, page 544 (box 24C, labeling method); and:
Hubel, D.H. (1982) Exploration of the primary visual cortex, 1955-1975. Nature 299: 515-524.

Apr 25-27

Inferotemporal cortex: Ventral pathway to inferotemporal lobe. Objects and faces. Visual perception.

Case discussion: Signaling by a face-selective neuron.
  Collaborative Writing Project Chapter 10 ends here. DUE: May 2.

     Lab 11: Projects.

Top-down and bottom-up components of visual perception.

Readings: (distributed as a packet)
    Gross, CG (2008) Single neuron studies of interior temporal cortex.
           Neuropsychologia 46: 841-852.
    de Haan, EHF and A Cowey (2011) On the usefulness of 'what' and 'where' pathways in vision.
           Trends in Cognitive Sciences 15: 460-466.

May 2-4

Color vision: retina, LGN, V1. Color patches and blobs. V4: color constancy.

     Lab 12: Projects: informal presentations.
            (See Lab 9 for assignment and due date.)

Cumulative review session. Bring questions!

Reading: N5e, chapter 11, pages 245-249 (color vision).

May 9-12

Final exam (self-scheduled).
A copy of a recent exam is posted on our Moodle site.

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