Neuroscience: cellular and circuit mechanisms

The course BIO-482 "Neuroscience: cellular and circuit mechanisms" focuses on the biophysical mechanisms of mammalian brain function. We will study how neurons communicate through synaptic transmission in order to process sensory information ultimately leading to motor behavior.

The brain processes information through the concerted activity of many neurons, which communicate with each other through synapses organised in highly dynamic networks. The first goal of this course is to gain a detailed understanding of the structure and function of the fundamental building blocks of the brain, its synapses and neurons. In considering this goal, we will also examine some basic methods including cellular electrophysiology and optical imaging. This will enable the student to critically evaluate how neurons are studied. The second goal is to learn how synaptic input is integrated and processed in single neurons based on the active and passive properties of axons and dendrites. Students will assemble their knowledge of synapses and neurons into a coherent picture of neuronal network function, with specific emphasis on the interactions of excitatory glutamatergic and inhibitory GABAergic neurons, plasticity and neuromodulation. The third goal, will be to place neuronal networks in the context of how they contribute to associative learning and sensory processing ultimately leading to behavioural decisions and motor output. These topics will be examined during Week 9 of the semester in a written exam. After the exam, in the second part of the semester, students will carry out a miniproject analysing a neurophysiological dataset. Each student must submit their miniproject report by the end of the semester.

The course is divided into two major parts a) MOOC (online video lectures) and b) Mini-project (neurophysiological data analysis):

a) MOOC - The first part of this course (Weeks 1-7) is based on the 'Cellular Mechanisms of Brain Function' Massive Open Online Course (MOOC) in the form of video lectures and lecture notes (which you should study in your own time), along with exercise questions and discussion sessions taking place in CE1106 on Fridays 13:15-15:00. In Week 8, you will have a Mock exam in CM1105 on Wednesday 6^th November 13:15-16:00, followed by answers to the Mock exam questions in CE1106 on Friday 8^th November 13:15-15:00. In Week 9, you will have the main Written exam for this course, (Room to be announced) on Wednesday 13^th November 13:15-16:00.

The videos for each week of the MOOC can be found at 4 different locations:
https://www.epfl.ch/labs/lsens/mooc/
https://www.edx.org/course/cellular-mechanisms-of-brain-function
https://www.swissmooc.ch/courses/bio482/
https://doi.org/10.5281/zenodo.3974482

b) Mini-project - The second part of this course is a Mini-project to enhance quantitative understanding of neuronal function, as well as providing important transversal skills in computer coding and data analysis. It begins with introductory lectures in CE1106 on Friday 15^th November 13:15-15:00. In Weeks 10-14, you will meet to analyse neurophysiological data on Wednesdays (in room CM1105) and Fridays (in room CE1106) 13:15-15:00. There will be a final data analysis session in CE1106 on Friday 20^th December 13:15-15:00. Before the end of Friday 20^th December, you will need to submit your mini-project.

The week-by-week schedule and MOOC lecture notes are available as pdf files for download (see below).

11 September, 13:15-14:00 – Course introduction (Sylvain Crochet, CM1105)

Week 1 MOOC videos:

• 1.1 Introduction
  
• 1.2 The cell membrane
  
• 1.3 Ion channels
  
• 1.4 Membrane potential
  
• 1.5 Cable properties

13 September, 13:15-15:00 – Exercises (CE1106) - MOOC #1 Questions (download pdf file below)

Week 2 MOOC videos:

• 2.1 Voltage-gated channels
  
• 2.2 Voltage-gating kinetics
  
• 2.3 The action potential
  
• 2.4 Action potential propagation
  
• 2.5 Whole-cell recordings
  

Week 3 MOOC videos:

• 3.1 Synaptic transmission
  
• 3.2 Neurotransmitter release
  
• 3.3 Presynaptic dynamics
  
• 3.4 Presynaptic modulation
  
• 3.5 Electron microscopy
  

27 September, 13:15-15:00 – Exercises (CE1106) - MOOC #3 Questions (download pdf file below)

Week 4 MOOC videos:

• 4.1 Glutamate receptors
  
• 4.2 Postsynaptic potentials
  
• 4.3 Glutamatergic circuits
  
• 4.4 Synaptic plasticity
  
• 4.5 Dendritic spines
  

Week 5 MOOC videos:

• 5.1 GABAergic inhibition
  
• 5.2 Inhibitory synaptic conductances
  
• 5.3 Benzodiazepines
  
• 5.4 GABAergic projections
  
• 5.5 Neocortical inhibition
  

Week 6 MOOC videos:

• 6.1 Brain function and behavior
  
• 6.2 Man and mouse
  
• 6.3 Imaging the brain in action
  
• 6.4 In vivo electrophysiology
  
• 6.5 Controlling brain function
  

Week 7 MOOC videos:

• 7.1 Sensorimotor interactions
  
• 7.2 Sensory perception
  
• 7.3 Learning
  
• 7.4 Brain dysfunction
  
• 7.5 Concluding remarks
  

6 November, 13:15-15:00 – Mock exam (CM1105)

8 November, 13:15-15:00 – Answers to Mock exam (CE1106)

Week 9 – Exam and Mini-project introduction

13 November, 13:15-16:00 – Written Exam (Room CM1105 and CM1121)

The written exam will account for two-thirds of your final grade.

Please check the exam instructions document before the exam.

15 November, 13:15-15:00 – Mini-project introduction (CE1106)

In the mini-project, you will use Matlab/Python to analyse a database of in vivo recordings of membrane potential during mouse behavior. The data are published:

Kiritani T, Pala A, Gasselin C, Crochet S, Petersen CCH (2023) Membrane potential dynamics of excitatory and inhibitory neurons in mouse barrel cortex during active whisker sensing. PLOS ONE 18: e0287174. doi: 10.1371/journal.pone.0287174

Kiritani T, Pala A, Gasselin C, Crochet S, Petersen CCH (2023) Data set for “Membrane potential dynamics of excitatory and inhibitory neurons in mouse barrel cortex during active whisker sensing.” [Data set]. Zenodo. https://doi.org/10.5281/zenodo.7833080

* Please install Matlab/Python on your computer before the beginning of the mini-project.

* Please download the dataset before coming to class:

Dataset and Matlab and Python versions of the codes:

https://drive.google.com/drive/folders/0ALc1PIvbCTdKUk9PVA

* Please download the mini-project questions in your favorite format.

20 November, 13:15-15:00 – Mini-project (CM1105)

22 November, 13:15-15:00 – Mini-project (CE1106)

27 November, 13:15-15:00 – Mini-project (CM1105)

29 November, 13:15-15:00 – Mini-project (CE1106)

4 December, 13:15-15:00 – Mini-project (CM1105)

6 December, 13:15-15:00 – Mini-project (CE1106)

Week 13 – Mini-project: Neurophysiological data analysis

11 December, 13:15-15:00 – Mini-project (CM1105)

13 December, 13:15-15:00 – Mini-project (CE1106)

18 December, 13:15-15:00 – Mini-project (CM1105)

20 December, 13:15-15:00 – Mini-project (CE1106)

Please submit your Mini-project report as a single pdf file  by Friday 20 December midnight.

Email to: sylvain.crochet@epfl.ch

The Mini-project will count towards one-third of your final grade.