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NEU466G, Dr. Harris · Class documents

Overview

The course meets once a week for one long class period that combines a lecture or discussion with a lab. It has four modules over 14 weeks. The dates are not set yet, so the weeks are numbered.

Each week below lists what to do before class, what happens in class, and what is due. Work listed under "Due" is due on Canvas by 11:59 PM on the Sunday before that week's class.

Most lectures are recorded: watch them on Canvas before class. In class, we discuss the lecture and reading, then you take a short open-book quiz and work in the lab. Lecture slides and quizzes are on Canvas. Reading links go to Readings, and each assignment is described in Assignments.

Every week: before you leave class, save your series and upload your .jser file on Canvas. This counts for attendance and data management.

Guides to use all term

Module 1: Postsynaptic structure and function

Week 1: Introduction to synapses, and why 3DEM

Before class

  • Download the class series and install PyReconstruct (Getting Started).
  • There is no reading this week.

In class

  • Lecture: introduction to synapses, and why we use 3D electron microscopy (3DEM).
  • Install check and a PyReconstruct demo.
  • Lab: Lab 1.1: Dendritic Spines.

Due

  • Nothing.

Week 2: Dendrites: excitatory postsynaptic structure

Before class

In class

Due

Module 2: Presynaptic structure and function

Week 3: Presynaptic boutons, vesicles, and mitochondria

Before class

  • Read the papers for the week: Week 3 readings.
  • Write your discussion question.

In class

Due

Week 4: Methods: sample preparation and imaging

Guest lecturer: Masa Kuwajima, Ph.D.

Before class

  • Read the papers for the week: Week 4 readings.
  • Write your discussion question.

In class

  • Lecture on how the tissue is prepared and imaged.
  • Lab: Lab 2.1, Part B (mitochondria).
  • Tour of the Harris Lab and its transmission-mode scanning electron microscope, the microscope that imaged your class series.

Due

  • Your discussion question for Week 4.

Module 3: Postsynaptic subcellular resources

Week 5: Smooth endoplasmic reticulum (SER) and recycling endosomes

Before class

  • Read the papers for the week: Week 5 readings.
  • Write your discussion question.

In class

Due

Week 6: Polyribosomes (PR) and local protein synthesis

Before class

  • Read the papers for the week: Week 6 readings.
  • Write your discussion question.

In class

Due

Module 4: Class research project

From Week 7 on, the class works on one research project in groups on dendrites from the dentate gyrus. Start with the project overview.

To be decided

The readings for Weeks 7 to 14 are chosen by Dr. Harris. Until then, Readings has no papers for these weeks, so check Canvas for any discussion question.

Week 7: Project introduction

Before class

In class

  • Introduction to the class research project.
  • Form project groups and get your group's dendrite.
  • Classify the synapses on your dendrite (Synapse categories).

Due

Week 8: Postsynaptic resources

Before class

  • Read the paper for the student-led paper discussion (on Canvas).

In class

Due

  • Nothing.

Week 9: Postsynaptic resources (continued)

In class

Due

  • Nothing.

Week 10: Class data

In class

  • Put the data from every group together (Class data).
  • Class discussion of the data so far.

Due

  • Nothing.

Week 11: Unbiased sampling and sources of variation

In class

  • Lecture and discussion on unbiased sampling and sources of variation.
  • Curate the class data (Data curation).

Due

  • Nothing.

Week 12: 3D exploration of synapse density and clustering

In class

  • Blender and 3D dendrite analysis (3D analysis).
  • Unblinding: learn the condition and time point of each dendrite.
  • The final lab report rubric is handed out.

Due

Week 13: Class data and discussion

In class

  • Class discussion of the unblinded data.
  • More Blender work (3D analysis).
  • Each group gets its figure for the oral presentation.

Due

  • Nothing.

Week 14: Student oral presentations

In class

Due