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Neural circuit basis of computation and behaviour

Course overview

How does the activity of neural circuits govern information processing, enable memory formation, and give rise to behaviour? Tackling these questions is one of the great challenges in current neuroscience. To make progress, quantitative studies of both structure and function of neural circuits are required, which these days have become feasible with a collection of new and broad methods. Neural circuit research bridges the molecular-cellular level to the levels of large-scale brain operation and animal behaviour and thus promises to reveal principles of spatiotemporal circuit dynamics that underlie specific brain states and behaviours. The relevance and role of specific cell types and of local as well as long-range circuit motifs need to be understood. This course aims to bring students up-to-date with the most recent developments in this exciting and fundamental field of neuroscience research. The focus will be on the advanced experimental approaches that are available today for the dissection of neural circuit connectivity and activity in various animal models (mouse, fly, zebrafish).

The Cajal course is an intensive three-week course that guides participants through the theory and practice of state-of-the-art methods for addressing pertinent questions in this field of research. This course will teach the latest technological advances in optical, electrophysiological, genetic, viral tracing, anatomical, and optogenetic approaches for the study of neural circuits. Students will learn the current state of knowledge of how neural circuits are organized, especially in the mammalian mouse brain, and how information can be processed in biological circuits through population-based activity patterns. The faculty will consist of international experts in their respective fields, discussing fundamental concepts and their own research, introducing methods relevant for neural circuit research, and providing hands-on projects. Students will perform experimental projects to apply these methods to scientific problems, they will learn how to analyse acquired data, and they will discuss strengths and limitations of the various techniques. The course is designed for PhD students, postdoctoral researchers, and early-stage group leaders, and is aimed at providing them with an enhanced tool set for addressing their current and future research questions.

Course partner

Course directors

Brain Research Institute, University of Zurich, Switzerland

Neurocentre Magendie, INSERM U1215, University of Bordeaux, France

Keynote speakers

Antoine Adamantidis – University of Bern (Switzerland)
Athena Akrami – University College London (UK)
Matteo Carandini – University College London (UK)
Megan Carey – Champalimaud Research (Portugal)
Marie Carlen – Karolinska Institute (Sweden)
Valentina Emiliani – Vision Institute Paris (France)
Rainer Fiedrich – Friedrich Miescher Institute for Biomedical Research (Switzerland)
Nadine Gogolla – Max Planck Institute of Neurobiology (Germany)
Benjamin Grewe – ETH Zurich (Switzerland)
Johannes Kohl – Francis Crick Institute (UK)
Matthew E. Larkum – Humboldt University of Berlin (Germany)
Tommaso Patriarchi – University of Zurich (Switzerland)
Pavan Ramdya -EPFL Lausanne (Switzerland)
Nathalie Rochefort – The University of Edinburgh (UK)
Lisa Roux – Bordeaux Neurocampus (France)
Manuel Zimmer – University of Vienna (Austria)

Instructors

Jerôme Baufretton – Bordeaux Neurocampus (France)
Philipp Bethge – University of Zurich (Switzerland)
Roman Boehringer – ETH Zurich (Switzerland)
Cecilia Castelli – Bordeaux Neurocampus (France)
Simon d’Aquin – University of Zurich (Switzerland)
Lorena Delgado – Bordeaux Neurocampus (France)
Matthias Durrieu – EPFL (Switzerland)
Gabrielle Girardeau – Institut du Fer à Moulin (France)
Noelle Grosjean – Bordeaux Neurocampus (France)
Yann Humeau – Bordeaux Neurocampus (France)
Daniel Jercog – Bordeaux Neurocampus (France)
Jean-Sebastien Jouhanneau – MDC Berlin (Germany)
Marie Labouesse – ETH Zurich (Switzerland)
Frederic Lanore – Bordeaux Neurocampus (France)
Arthur Leblois – Bordeaux Neurocampus (France)
Christopher Lewis – University of Zurich (Switzerland)
Catherine Marneffe – Bordeaux Neurocampus (France)
Pavan Ramdya – EPFL (Switzerland)
Lisa Roux – Bordeaux Neurocampus (France)
Gwendolin Schoenfeld – University of Zurich (Switzerland)
Ourania Semelidou – Bordeaux Neurocampus (France)
Sandra Soukup – Bordeaux Neurocampus (France)
Naoya Takahashi – Bordeaux Neurocampus (France)
Roman Ursu – Bordeaux Neurocampus (France)
Nikita Vladimirov – University of Zurich (Switzerland)
Yuktiben Vyas – Bordeaux Neurocampus (France)
Nanci Winke – Bordeaux Neurocampus (France)
Jonathan Zapata (Inscopix)

Course content

Topics & Techniques

Participants will learn all basic requirements to perform:

– ex vivo optogenetic and patchclamp recordings in acute brain slices;

– in vivo calcium imaging experiments in freely moving mice using miniaturized microscopes;

– laser scanning lightsheet microscope by disassembling and reassembling a benchtop version of the mesoSPIM before preparing, acquiring and analysing various cleared neuronal samples;

– how to operate a two-photon microscope and how to do basic trouble-shooting;

– basics of electrode design, construction and instrumentation;

– basic requirements to perform extracellular recordings in singing birds using motorized micro-drive; basic procedures to image activity from individual dendrites of cortical pyramidal neurons in awake mice;

– basic spike data analysis (spike sorting, detection of tagged unit);

– dissection, microimplantation, and specimen preparation for live imaging; Calcium imaging data acquisition and computational data analysis;

Projects

The following projects are confirmed so far:

Project 1: “Imaging neural population activity along the gut-brain axis in adult Drosophila”

Project 2: “Two-photon targeted patch-clamp and calcium population imaging in mouse neocortex during tactile stimulation.”

Project 3: “Monitoring neuronal activity in the song-control circuits in freely behaving zebra finches.”

Project 4: “MesoSPIM light-sheet imaging of anatomical projections in the cleared mouse brain”

Project 5: “Functional Representations of Tactile Stimuli in the Cortex Using In Vivo 2-Photon Calcium Imaging”

Project 6: “Large scale multi-electrode recordings and optogenetic manipulations of neuronal subtypes in freely moving animals.”

Project 7: “All optical imaging and stimulation of neuromodulator release in freely moving mice (multiplex fiber photometry)”

Project 8: “Ex vivo optogenetic manipulations of basal ganglia circuits”

Project 9: “In vivo calcium imaging of hippocampal CA1 population activity in the freely moving mouse using miniaturized microscopes”

Project 10: “In vivo multimodal, multiscale physiology”

Project 11: “In vivo optogenetic manipulations of prefrontal circuits.”

Project 12: “Multi-site electrophysiological activities in a working memory task and related consolidation sleeping phases.”

Project 13: “Two-photon calcium imaging of cortical dendrites in awake head-fixed mice.

Project 14: ‘‘Birth of a memory: ex vivo optogenetic approach to study hippocampal engrams’’

Bordeaux School of Neuroscience, France

The Bordeaux School of Neuroscience is part of Bordeaux Neurocampus, the Neuroscience Department of the University of Bordeaux. Christophe Mulle, its current director, founded it in 2015. Throughout the year, renowned scientists, promising young researchers and many students from any geographical horizon come to the School.
The school works on this principle: training in neuroscience research through experimental practice, within the framework of a real research laboratory.

Facilities
Their dedicated laboratory (500m2), available for about 20 trainees, is equipped with a wet lab, an in vitro and in vivo electrophysiology room, IT facilities, a standard cellular imaging room, an animal facility equipped for behavior studies and surgery and catering/meeting spaces. They also have access to high-level core facilities within the University of Bordeaux. They offer their services to international training teams who wish to organize courses in all fields of neuroscience thanks to a dedicated staff for the full logistics (travels, accommodation, on-site catering, social events) and administration and 2 scientific managers in support of the experimentation.

Registration

Registration fee: €3.500,00 (includes tuition fee, accommodation and meals)

Application closed on 13th December 2021

The CAJAL programme offers 4 stipends per course (waived registration fee, not including travel expenses). Please apply through the course online application form. In order to identify candidates in real need of a stipend, any grant applicant is encouraged to first request funds from their lab, institution or government.

Kindly note that if you benefited from a Cajal stipend in the past, you are no longer eligible to receive this kind of funding. However other types of funding (such as partial travel grants from sponsors) might be made available after the participants selection pro- cess, depending on the course.

Quantitative Approaches to Behaviour

Course overview

Quantitative studies of behaviour are fundamental in our effort to understand brain function and malfunction. Recently, the techniques for studying behaviour, along with those for monitoring and manipulating neural activity, have progressed rapidly. This course provides promising young scientists with a comprehensive introduction to state-of-the-art techniques in quantitative behavioural methods. This course’s content is complementary to other summer courses that focus on measuring and manipulation neurophysiological processes.

Our focus is on methodologies to acquire rich data representations of behavior, dissect them statistically, model their dynamics, and integrate behavioral measurements with other kinds of neurobiological data. To this end, students will 1) fabricate devices for recording the behavior experimental organisms, 2) learn, under the guidance of the scientists developing these methods, the modern tools to analyze behavioral data from these organisms, and 3) in a week-long independent project develop and conduct a behavioral study of their own design, with the support and guidance of the course instructors and teaching assistants.

This 3-week course is a practical “hands-on” introduction to advanced methods in behavioural tracking and analysis. Our educational goal is to cover sufficient background such that all participants will be able to establish these techniques in their home laboratories.

In the pedagogical portion of the course (blocks 1 and 2, see below) we will use two main experimental model systems: flies (Drosophila melanogaster) and zebrafish (Danio rerio). Several days of instruction will focus on analysis of video data, and on these days, students may use videos of flies and fish, videos we provide of mammals behaving, or videos of their own organism of choice. In the student project portion of the course (block 3), students may use these experimental organisms, as well as, subject to their availability, organisms in use at the Champalimaud.

We will cover data acquisition (software, hardware, tools), preprocessing (single animal, body parts and multiple animals tracking systems), data analysis (clustering, ethograms) and modeling.

Course directors

Emory University, USA

Harvard University, USA

Champalimaud Foundation, Portugal

University of Colorado, USA

VU University Amsterdam, The Netherlands
OIST Graduate University, Japan

Keynote speakers

Sama Ahmed, University of Washington, USA
Kristin Branson – hhmi, Janelia Research Campus, USA
Bing Brunton – University of Washington, USA
António C. Costa, Ecole Normale Supérieure de Paris, France
Serena Ding – Max Planck Institute of Animal Behavior, Germany
Giorgio Gilestro – Imperial College London, UK
Alex Jordan – Max Planck Institute of Animal Behavior, Germany
Ann Kennedy – Northwestern University, USA
Natasha Mhatre – Western University, Canada
Ilya Nemenman – Emory University, USA
Talmo Pereira – Salk Institute for Biological Studies, USA
Sam Reiter – Okinawa Institute of Science and Technology, Japan
Barbara Webb – University of Edinburgh, UK

Instructors

Tosif Ahamed – Mount Sinai Hospital, Toronto, Canada
Kanishk Jain – Emory University, USA
Ugne Klibaite – Center for Brain Science, Harvard University, USA
Chantal Nguyen – BioFrontiers Institute, University of Colorado Boulder, USA
Denise Yoon, Harvard University, USA
Akira Kawano, Okinawa Institute of Science and Technology, Japan
Adrien Jouary, Champalimaud Foundation, Portugal
Dean Rance, Champalimaud Foundation, Portugal
Francisco Romero, Veriff, Spain
Bruno Cruz, NeuroGEARS, UK

Course content

Schedule

Week 1

Sunday, May 22nd: Arrival & Welcome reception

Monday, May 23rd: Keynote lecture by Ben de Bivort / Afternoon tutorial: Build a rig & capture movies by Ben de Bivort & Giorgio Gilestro

Tuesday, May 24th: Keynote lecture by Giorgio Gilestro / Afternoon tutorial: Build a centroid tracker by Ben de Bivort & Giorgio Gilestro

Wednesday, May 25th: Keynote lecture by Alex Jordan / Afternoon tutorial: Multianimal idtracker.ai by Francisco Romero & Dean Rance

Thursday, May 26th: Morning tutorial by Gonzalo de Polavieja / Afternoon tutorial: Deep Learning notebooks applied to behaviour data sets by Gonzalo de Polavieja

Friday, May 27th: Keynote lecture by Talmo Pereira / Afternoon tutorial: Limb and body tracking by Talmo Pereira

Week 2

Sunday, May 29th: Keynote lecture by Kristin Branson / Afternoon tutorial: Supervised classification by Kristin Branson

Monday, May 30th: Keynote Lecture by Sam Reiter / Afternoon tutorial: Dynamics of behaviour by Greg Stephens & Tosif Ahamed

Tuesday, May 31st: Keynote lecture by Ben de Bivort & Gordon Berman / Afternoon tutorial: Unsupervised analysis of behaviour by Ugne Klibaite & Kanishk Jain

Wednesday, June 1st: Keynote lecture by Bing Brunton / Afternoon tutorial: Probabilistic models by Bing Brunton

Thursday, June 2nd: Keynote lecture by Barbara Webb & Orit Peleg / Afternoon tutorial: Braitenberg and agent-based models by Barbara Webb & Orit Peleg

Friday, June 3rd: Keynote lecture by António Costa / Afternoon: Project design

Week 3

Sunday June 5th Keynote lecture by Ilya Nemenman / Afternoon: Project development

Monday, June 6th: Keynote lecture by Serena Ding / Afternoon: Project development

Tuesday, June 7th: Keynote lecture by Ann Kennedy / Afternoon: Project development

Wednesday, June 8th: Keynote lecture by Natasha Mhatre / Afternoon: Project development

Thursday, June 9th: Keynote lecture by Sama Ahmed

Friday, June 10th: Project presentations

Saturday, June 11th: Departure

Projects

Projects from previous years:

The role of visual cues in social behaviour in flies;
Social learning in Drosophila melanogaster;
Mapping the behavioural repertoire of zebrafish larvae in response to tastants and neuroactive compounds;
Slfish: characterizing the collective behavior of larval zebrafish following acute social isolation;
Skinner’s flies: inducing superstitious microbehaviors via random operant rewards;
The role of lateralized latency asymmetry in virtual task performance;

Ideas for projects for the upcoming course:

Manifolds in dynamical representations of behavior;
Deep attention models of collective fish behavior;
Modelling behavior with different tradeoffs of accuracy and complexity using symbolic regression;
Unsupervised discovery of motifs in rodent vocalizations.

Champalimaud Centre for the Unknown, Portugal

The Champalimaud Foundation is a private, non-profit organization, established in 2005 and dedicated to research excellence in biomedical science. Completed in 2010, the Champalimaud Centre for the Unknown is a state-of-the-art centre that houses the Champalimaud Clinical Centre and the Champalimaud Research, with its three parallel programs – the Champalimaud Neuroscience Programme, the Physiology and Cancer Programme, and the Experimental Clinical Research Programme.
Initially focused on a system and circuit approach to brain function and behavior, the Centre expanded to incorporate molecular and cell biological expertise. The Centre comprises 26 research groups (circa 400 researchers) leading independent curiosity-based research.

Facilities
The Centre provides Facilities dedicated for Training, some in their entirety, for use by the CAJAL Advanced Neuroscience Training Programme. These include the Teaching Laboratory, a fully equipped open lab space for 20-30 students that can be dynamically reconfigured to support a full range of neuroscience courses. It also overlooks, via floor to ceiling windows, a tropical garden and the river. The experimental spaces include: Imaging Lab: A dark-room containing a full size optical table is used for advanced imaging setups (two-photon microscopy, SPIM, etc.) and custom (course-designed) optical systems.

Registration

Fee : 3.500 € (includes tuition fee, accommodation and meals)

Applications closed on 20th December 2021

Single cell profiling and analysis in neuroscience

Course overview

Understanding the cellular complexity of the nervous system is a key endeavor in the pursuit to reveal the biological underpinnings of brain function. The recent methodological development of high-throughput single-cell profiling techniques and analysis has emerged as an essential tool for characterizing cellular diversity in the brain offering data sets that hold the promise of being complete, accurate and permanent. This course will teach central ideas, methods, and practices of single cell profiling and hands-on computational analysis through a combination of lectures from prominent international faculty speakers, experimental projects and data analysis workshops.

The course will include practical training in small groups of students on single cell methodologies and computational and statistical data analysis needed to interpret large data sets. This integration of data analysis with hands-on experiments will allow the students to gain knowledge in technical performance as well as biological interpretation of single cell data sets.

This advanced course is aimed for graduate students from a variety of disciplines, including neuroscience, physics, computer science and applied mathematics. Students are expected to have a keen interest and basic background in neurobiology, and to fully benefit from the data analysis it is expected that the students have at least a basic knowledge in programming.

Course partner

Course directors

Department of Medical Biochemistry and Biophysics, Karolinska Institute, Sweden

Biomedical Informatics, Harvard Medical School, USA

University of Cádiz/INiBICA, Spain

CNRS – IINS, University of Bordeaux, France

Keynote Speakers

Kenneth Harris – UCL Queen Square Institute of Neurology, UK
Ed Lein – Allen Institute for Brain Science, USA
John Marioni – European Bioinformatics Institute (EMBL-EBI), UK
Ana Martin-Villalba – University of Heidelberg, Germany
Rahul Satija – New York Genome Center (NYGC), USA
Kun Zhang – Department of Bioengineering, University of California, USA

Instructors

Marek Bartosovic – Karolinska Institutet (Sweden)
Lisa Bast – Karolinska Institutet (Sweden)
Pierre Boyeau – UC Berkeley (USA)
Hattie Chung – Broad Institute/MIT (USA)
Lisbeth Harder – Karolinska Institutet (Sweden)
Martin Häring – University Clinic Münster (Germany)
Hannah-Sophie Hochgerner – Technion (Israel)
Sergey Isaev – Moscow Institute of Physics and Technologies (Russia)
Danny Kitsberg – Jerusalem University (Israel)
Gioele La Manno – EPFL (Switzerland)
Christoffer Langseth – Stockholm University (Sweden)
Christian Mayer – Max Plank Institute (Germany)
Viktor Petukhov – University of Copenhagen (Denmark)
Anna Schaar – Helmholtz Zentrum München (Germany)
Milda Valiukonyte – Karolinska Institutet (Sweden)
Zinah Wassouf – Wellcome Sanger Institute (UK)

Course content

Topics & Techniques

During this course, students will get hands-on experience with entire single-cell transcriptomic projects from tissue dissociation to publishable figures. We will teach the use of different kinds of starting material, three different sequencing techniques, how to treat the raw sequencing data and a multitude of analytical tools. After attending the course, our goal is that the students should be able to go back to their institute and have enough knowledge and understanding to initiate well-designed single-cell sequencing projects to tackle important questions in Neuroscience.

The course will cover following topics:

Cell classification in the nervous system and its implication on how we do neuroscience
Discrete versus continuous variability in gene expression
Single-cell transcriptomics and analysis of disease
advantages and disadvantages of different techniques; RNA amplification, SmrtSeq, SplitSeq, Dropseq, 10X genomics,
What type of biological insights can be gained from single cell transcriptomics
multimodal analysis of single cell biology where transcriptomics is coupled with other biological parameters such as a cell’s morphology, tissue localization, epigenome, proteome and/or function
Preparation and isolation of single cell, nuclei isolation, RNA isolation, single cell RNA amplification procedures, library construction for sequence analysis and RNA sequencing.
experimental design considerations, data processing, data handling, quality control of the sequencing data, understanding the variances of the data, clustering of cell types
Nervous system development and other dynamical processes including lineage tracing including RNA-Velocity and pseudotime analysis

Projects

For more information on projects download the “Projects list”.

– Project 1: Visualization and quantification of cellular complexity of the CA1 region of the
mouse brain

– Project 2: Understanding cellular maturation during the development of the embryonic
nervous system by whole-cell RNA seq

– Project 3: GABAergic neuronal diversity across different forebrain structures

– Project 4: Single whole cells analysis of an Alzheimer’s disease mouse model

– Project 5: Single nuclei analysis of an Alzheimer’s disease mouse model

– Project 6: Single nuclei analysis of GABAergic cells in the dorsal horn in a chronic pain
model

– Project 7: Single whole cells analysis of GABAergic cells in the dorsal horn in a chronic pain model

– Project 8: Large scale single-cell RNA-sequencing of brain tissue using SPLiT-Seq

– Project 9: Single-cell profiling of histone modifications in the mouse cortex using scCUT&Tag

– Project 10: InCiteSeq

– Computational Projects: state-of-the-art approaches for computational analysis and interpretation of single-cell RNA-seq data.

Bordeaux School of Neuroscience, France

Registration

Fee : 3.500 € (includes tuition fee, accommodation and meals)

Applications closed on 21st February 2022

Course sponsors

Interacting with neural circuits

Course overview

Understanding the links between activity in neural circuits and behavior is a fundamental problem in neuroscience. Attacking this problem requires detailed information about the cell types in neural circuits and their connectivity, and recording the spatiotemporal patterns of activity in the intact brain during behaviour. Furthermore, probing causal relationships between cellular and circuit-level processes and behaviour requires perturbation of specific elements of the circuit in a temporally and spatially precise manner.

This course will highlight the new anatomical, genetic, optical, electrophysiological, optogenetic, and pharmacogenetic approaches that are available for addressing these challenges. The faculty will discuss tool development through to their implementation in diverse model systems, including mice and zebrafish. Students will learn the potential and limitations of these techniques, allowing them to both design and interpret experiments correctly.

Course directors

Wolfson Institute for Biomedical Research, UCL, UK

Paris Brain Institute, ICM, France

Sainsbury Wellcome Centre, UK

Champalimaud Foundation, Portugal

Keynote Speakers

Isaac Bianco, University College London, UK
Ed Boyden, Massachusetts Institute of Technology, USA
Michael Brecht, Bernstein Center for Computational Neuroscience, Germany
Megan Carey, Champalimaud Foundation, Portugal
Eugenia Chiappe, Champalimaud Foundation, Portugal
Winfried Denk, Max Planck Institute of Neurobiology, Germany
Emily Dennis, HHMI, Janelia, USA
Valentina Emiliani, Vision Institute, France
Ken Harris, University College London, UK
Greg Jefferis MRC Laboratory of Molecular Biology, UK
Na Ji, University of California, USA
Mackenzie Mathis, EPFL, Switzerland
Marta Moita, Champalimaud Foundation, Portugal
Francois St-Pierre, Baylor College of Medicine, USA

Michael Orger, Champalimaud Foundation, Portugal
Marius Pachitariu, HHMI, Janelia, USA
Darcy Peterka, Columbia University, USA
Pavan Ramdya, EPFL, Switzerland
Ana João Rodrigues, ICVS, Minho University, Portugal
Botond Roska, Institute of Molecular and Clinical Ophthalmology, Switzerland
Nick Steinmetz, University of Washington, USA
Carsen Stringer, HHMI, Janelia, USA
Karel Svoboda, HHMI, Janelia, USA
Scott Waddell, Oxford University, UK
Chris Xu, Cornell University, USA
Ofer Yizhar, Weizmann Institute of Science, Israel

Instructors

Dustin Herrmann, Wolfson Institute for Biomedical Research, UCL, UK
Maxime Beau, Wolfson Institute for Biomedical Research, UCL, UK
Edgar Baumler, Wolfson Institute for Biomedical Research, UCL, UK
Moritz Buchholz, Wolfson Institute for Biomedical Research, UCL, UK
Maha Dhanasekar, Paris Brain Institute, ICM, France
Pierre Tissier, Paris Brain Institute, ICM, France
Martin Carbó-Tano, Paris Brain Institute, ICM, France
Olivier Mirat, Paris Brain Institute, ICM, France
Dario Campagner, Sainsbury Wellcome Centre, UK
Tan YuLin, Sainsbury Wellcome Centre, UK
Hugo Marques, Champalimaud Foundation, Portugal
Ana Gonçalves, Champalimaud Foundation, Portugal

Course content

Schedule

Week 1

Sunday, June 19th: Arrival & Welcome reception

Monday, June 20th: Keynote lecture by Chris Xu / Ed Boyden Afternoon: Student presentations & Poster session I

Tuesday, June 21st: Keynote lecture by Eugenia Chiappe / Pavan Ramdya Afternoon: TA & Experimental Resources presentation & Poster session II

Wednesday, June 22nd: Keynote lecture by Greg Jefferis / Tiago Branco Afternoon TA & Experimental Resources presentation / Project Design & Discussion

Thursday, June 23rd: Morning tutorial by Scott Waddell / Na Ji Afternoon: Rig rotation / Project Design & Discussion

Friday, June 24th: Keynote lecture by Winfried Denk / Susana Lima Afternoon: Rig rotation/ Project Design & Discussion

Friday, June 25th: Surf/Beach Day

Week 2

Sunday, June 26th: Keynote lecture by Darcy Peterka / Nick Steinmetz / Botond Roska Afternoon: Rig rotation

Monday, June 27th: Keynote Lecture by Marius Pachitariu / Carsen Stringer Afternoon: Miniprojects

Tuesday, June 28th: Keynote lecture by Karel Svoboda / Ana João Rodrigues Afternoon: Miniprojects

Wednesday, June 29th: Keynote lecture by Isaac Bianco Afternoon: Miniprojects

Thursday, June 30th: Keynote lecture by Michael Brecht / Marta Moita Afternoon: Miniprojects

Friday, July 1st: Keynote lecture by Megan Carey Afternoon: Miniprojects

Saturday July 2nd: Keynote lecture by Francois St. Pierre / Michael Hausser / Afternoon: Free/Social

Week 3

Sunday July 3rd: Keynote lecture by Emily Dennis / Claire Wyart / Valentina Emiliani / Afternoon: Miniprojects

Monday, July 4th: Keynote lecture by Ofer Yizhar/ Afternoon: Miniprojects

Tuesday, July 5th: Keynote lecture by Michael Orger / Afternoon: Miniprojects

Wednesday, July 6th: Keynote lecture by Ken Harris / Afternoon: Miniprojects

Thursday, July 7th: Keynote lecture by Mackenzie Mathis Afternoon: Miniprojects

Friday, July 8th: Miniproject presentation

Saturday, July 9th: Departure

Topics & Techniques

The course combines a lecture series featuring top speakers from around the world with a practical “hands-on” introduction to the latest methods for probing neural circuits, using drosophila, zebrafish, and (transgenic) mice. The course will focus on anatomy and connectivity, recording and manipulation, and the relation between circuits and behavior. During the course, each student will carry out a ‘mini-project’, executed under the guidance and supervision of experienced researchers and teaching assistants. Techniques used during the course include:

Zebrafish

optogenetic manipulation using digital holography;
behavior & population calcium imaging using 2-photon microscopy;

Mice

In vivo 2-photon and 3-photon imaging;
all-optical interrogation (simultaneous 2-photon optogenetics and 2-photon imaging);
miniscope imaging;
extracellular recordings of neural population activity using Neuropixels probes in head-fixed and freely behaving animals;
intracellular electrophysiological recordings using whole-cell patch-clamp;
viral tracing, histology preparation, expansion microscopy, and fluorescence imaging techniques.

For more information on the course programme, you can visit the past course website.

Champalimaud Centre for the Unknown, Portugal

Registration

Fee : 3.500 € (includes tuition fee, accommodation and meals)

Application closed on 24th January 2022

Course overview

Computational Neuroscience is a rapidly evolving field whose methods and techniques are critical for understanding and modelling the brain, and also for designing and interpreting experiments. Mathematical modelling is an essential tool to cut through the vast complexity of neurobiological systems and their many interacting elements.

The course teaches the central ideas, methods, and practices of modern computational neuroscience through a combination of lectures and hands-on project work. During the course’s mornings, distinguished international faculty deliver lectures on topics across the entire breadth of experimental and computational neuroscience. For the remainder of the time, students work on research projects in teams of 2 to 3 people under close supervision of expert tutors and faculty. Research projects are proposed by faculty before the course, and include the modeling of neurons, neural systems, and behavior, the analysis of state-of-the-art neural data (behavioral data, multi-electrode recordings, calcium imaging data, connectomics data, etc.), and the development of theories to explain experimental observations.

Course directors

University of Chicago, USA

University of Pennsylvania, USA

Technical University of Munich, Germany

Champalimaud Foundation, Portugal

Keynote Speakers

Alex Cayco-Gajic – École Normale Supérieure, France
John Krakauer – Johns Hopkins University, USA
Maté Lengyel – Cambridge University, UK
Ashok Litwin-Kumar – Columbia University, USA
Christian Machens – Champalimaud Foundation, Portugal
Olivier Marre – Vision Institute, France
Ken Miller – Columbia University, USA
Srdjan Ostojic – École Normale Supérieure, France
Anne-Marie Oswald – University of Pittsburgh, USA
Saskia de Vries, Allen Institute, USA
Alfonso Renart – Champalimaud Foundation, Portugal
Megan Carey – Champalimaud Foundation, Portugal
Gilles Laurent – Max Planck Institute for Brain Research, Germany
Wiktor Młynarski, Institute of Science and Technology, Austria
Ann Kennedy, Northwestern University, USA

Instructors

Dylan Festa – Technical University of Munich, Germany
Francesca Mastrogiuseppe – Champalimaud Foundation, Portugal
Carlos Stein – Champalimaud Foundation, Portugal
Janaki Sheth – University of Pennsylvania, USA

Course content

Projects

Project 1. Emergence of selectivity through the interplay of Hebbian and homeostatic plasticity in neuronal networks (Gjorgjieva)

Project 2. Neural circuits for the generation of locomotor behavior (Gjorgjieva)

Project 3. Analysis of multi-neuron spike time series data from the locust olfactory system (Laurent)

Project 4. Reinforcement learning as a model for decision making (Paton & Lloyd)

Project 5. Finding structure in natural behavior (Murthy)

Project 6. The SSN: Dynamic behavior, effects of adaptive and saturating mechanisms and of network noise (Miller & Doiron)

Project 7. Uncovering synaptic plasticity rules from experiments (Stein)

Project 8. Implementing linear, nonlinear, and chaotic computations in spike coding networks (Keemink)

Project 9.Teaching animals to respond without bias by teaching algorithms to find bias (Macke)

Project 10.Predicting responses of single neuron in vitro: Mechanistic vs LIF models (Gonçalves & Macke)

Project 11. The role of inhibitory neurons in sound adaptation (Geffen)

Project 12. The neuronal circuit for hearing under uncertainty (Geffen)

Preliminary programme

All days are structured with lectures in the morning and experimental learning & tutorials – followed by discussion – in the afternoon

Week 1

17-22 July

Arrival and Welcome reception
Introduction and Single-Neuron Dynamics
Statistical analysis of neural data
Network dynamics
Normative models
Physical Constraints on Computing

23-24 July

Social event and free time

Week 2

25-29 July

Sensory coding and receptive fields
Spatial coding and memory
Vision
Neural Circuits and Synaptic Plasticity
Map formation and self-organization

30-31 July

Social event and free time

Week 3

1-5 August

Balanced Networks & Efficient Population Coding
Dendritic Computations & Birdsong Production
Reinforcement learning
Project work and presentations

6 August

Departure

For more information on the course programme, you can visit the past course website.

Pre-school in Mathematics and Programming (12-15 July)

The Computational Neuroscience course targets both students with a biological/experimental background (“experimentalists”) and ones with a quantitative background (“theorists”). Two primary objectives of the course are to help students cross the traditional discipline boundaries that most are still trained in, and to get experimentalists and theorists to collaborate on a research project.

For the experimentalists, this often means catching up on their math and programming skills; for the theorists, on their (neuro-)biology. Because course projects will be computer-based, “catching up” is asymmetrical. When theorists engage on a course project, they can usually get by with limited neurobiological background. When experimentalists engage on a course project, however, they need some proficiency in programming and a solid understanding of the underlying mathematics.

To level the playing field and counterbalance this asymmetry, we offer an optional pre-school that teaches students with little or no programming skills the basics of modern programming languages (e.g., MATLAB or Python). The pre-school will also provide refreshers on standard math topics such as linear algebra and calculus, important to better follow the course. While a four-day school cannot be a replacement for the mathematical education that students from quantitative disciplines enjoy, it will give students a sufficient head-start to focus on lecture contents and the research projects, once the main course starts.

Unsure on whether to attend the preschool? It’s easy: if you have no knowledge of MATLAB or Python, then you should take the preschool. If you do know how to program in these languages, then it depends on your math background. Check out our little exam here to test your skills. Try to answer as many questions as possible within twenty minutes. The solutions are here.

Self-evaluation:

If you managed to do all exercises (and you have some knowledge of MATLAB/Python) then you should skip the pre-school.
If you more or less managed everything, with a few difficulties here or there (but you do know how to work in MATLAB/Python) then the pre-school may be a good idea, but you should consider it optional.
If you managed to solve exercises 1 to 6, but had difficulties afterwards, then you should take the pre-school.
If you had many problems in exercises 1 to 6, and the rest was pretty incomprehensible, then we’d strongly recommend to catch up on your high school math first before taking either the pre-school or the main course. Experience has shown that you will get very little out of the course without a solid background in quantitative thinking

Please note, that there is an additional fee for the pre-school: 500 EUR , which covers tuition, housing, and boarding for the extra days. Applications to the pre-school are part of the application to the main course.

Champalimaud Centre for the Unknown, Portugal

Registration

Fee : 2.500 € (includes tuition fee, accommodation and meals)

Pre-school fee: 500 €

Applications closed on 28th March 2022

Course overview

This course is a theoretical and practical training course on neurodevelopment and its evolution. It will provide an overview of the current concepts and knowledge on central nervous system development in several species, including invertebrates, mice, and humans, and their link to diseases. It will combine lectures and hands-on projects on convergent and divergent developmental processes across species at the molecular, cellular, circuit, and behavioural levels, including those relevant for human disease. It will include methods in genetics and molecular biology (e.g. genome editing), cellular neuroscience (e.g. transplantations), circuit neuroscience (e.g. live imaging) and -omics (e.g scRNA seq and bioinformatics).

This course will provide participants with a broad yet practical understanding of how the brain develops in different species, and how modern genetic approaches now allow cross-species comparisons to identify key developmental mechanisms. It is intended for PhD students and early-career postdocs.

Course directors

Faculty of Medicine,
University of Geneva, Switzerland

Paris Brain Institute, Institut du Cerveau (ICM), France

Department of Biology, NYU New York, USA

Neurocentre Magendie, University of Bordeaux, France

Keynote Speakers

Laure Bally-Cuif – Institut Pasteur, France
Sonia Garel – Ecole Normale Superieure (ENS), France
Simon Hippenmeyer – Institute of Science and Technology (IST), Austria
Oliver Hobert – Columbia University , USA
Guillermina Lopez Bendito – Instituto de Neurociencias – UMH-CSIC, Spain
Shubha Tole – Tata Institute of Fundamental Research, India

Instructors

Alexandre Baffet – Institut Curie, France
Nathan Benac – University of Bordeaux, France
Sara Bizzotto – Paris Brain Institute, France
Boyan Bonev – Helmholtz Zentrum München, Germany
Antoine de Chevigny – INMED, Univeristy of Marseille, France
Fernando García-Moreno, Achucarro Basque Center for Neuroscience, Bilbao, Spain
Juliette Godin – IGBMC Univeristy of Strasbourg, France
Isabel Holguera – New York University, USA
Nathalie Jurisch – Kavli Institute for Systems Neuroscience – NTNU, Norway
Karine Loulier – Institute for Neurosciences of Montpellier, France
Esther Klingler – UNIGE, Switzerland
Nikos Konstantinides – Institut Jacques Monod, France
Pierre Mortessagne – Neurocentre Magendie, Univeristy of Bordeaux, France
Homaira Nawabi – Grenoble Institute of Neuroscience, France
Stéphane Nédélec – Institut du Fer à Moulin, France
Sergi Roigg Puigros – UNIGE, Switzerland
Julie Stoufflet – Giga Liège, Belgium
Emre Yaksi – Kavli Institute for Systems Neuroscience – NTNU, Norway

Course content

Techniques

Crispr-CAS9 mediated genome editing to tag endogenous actin
Dissection and dissociation of mouse cortex
Fly husbandry
Human induced pluripotent stem cells culture
In utero/ex-utero electroporation
Analyses of cell position and protein expression using ImageJ
analyses of migration
ATAC-seq library preparation
Cell culture (dissociated hippocampal neurons, COS-7), cell transfection
Comparative neuroanatomy
Confocal microscopy and image analysis
Culture of organotypic brain slices
Drosophila brain dissection at L3 stage
Functional brain imaging in adult, juvenile and larval zebrafish and associated data analysis
Genetic manipulation of tTFs in neuroblasts using MARCM
Immunofluorescence
Image reconstructions and 3D analysis
Immunohistochemistry
Immunostaining
Intravitreal & in utero injections
Introduction to bioinformatics and scRNAseq analysis
Live birth-dating of neurons and functional imaging of their activity
Microtome / Vibratome sectioning
Retina, optic nerve dissection & explant culture
Spheroid generation and differentiation
Tissue freezing and cryostat slicing
Videomicroscopy,time lapse recording

See more techniques in the projects list.

Projects

Project 1 : “Live imaging of microtubule dynamics in mouse brain slices”
Project 2 : “Role of dopamine-glutamate interplay during synaptogenesis”
Project 3 : “Studying a developmental mosaic brain disorder in human cortical spheroids”
Project 4: “Histological and transcriptional analysis of isochronically labelled cortical neurons”.
Project 5: “Studying the morphological properties of developmentally- and adult-born dentate granule neurons”
Project 6: “RGC manipulation to modulate CNS regeneration”
Project 7: “Study of neuronal migration after prenatal alcohol exposure”
Project 8 : “Genome-wide profiling of the epigenome and the transcriptome of major cell types from the developing mouse cortex”
Project 9: “Emergence of intracortically-projecting neuron diversity”
Project 10 : “Studying the effect of temporal series in the proliferative capacity of Drosophila neural stem cells”
Project 11: “MAGIC Markers strategies to investigate neuron-astrocyte anatomical relationships during cortical development”
Project 12: “ Differentiation of spinal organoids and motor neuron subtypes from human induced pluripotent stem cells”
Project 13: “Inferring ligand-receptor interactions between GABAergic and Glutamatergic cells during Somatosensory Cortex Development”
Project 14: “Imaging actin cytoskeleton dynamics during radial migration of projection neurons in the mouse developing cortex”.
Project 15: “Neurogenesis in the Drosophila optic lobe by temporal patterning”
Project 16: “Fluid dynamics in the brain of zebrafish and medaka larvae”
Project 17: “Imaging function, connectivity, and development of brain circuits in zebrafish”
Project 18: “Comparative neurodevelopment of mouse and chick brains”

Bordeaux School of Neuroscience, France

Registration

Fee : 3.500 € (includes tuition fee, accommodation and meals)

Brain Organoids

Course overview

Recent advancement in the stem cell field has led to the development of novel 3D cell culture models called organoids that mimic cell type diversity and architecture during organogenesis. Brain organoids, derived from human embryonic stem cells or induced pluripotent stem cells, capture key features of the developing human brain, including stem cell pool expansion, neurogenesis, gliogenesis, synaptogenesis and cytoarchitecture formation with cellular diversity and complexity. Organoids can also be derived from patient tumor samples, such as glioblastoma, for modelling brain tumors. In less than a decade, brain organoids have already been shown to be an extremely valuable tool to understand the human brain, and novel insights have been gained in deciphering evolution, human-specific features related to the brain development and neurological diseases resulted from pathogen infection, environmental insult, or genetic mutations.

In this course, we will take a multi-disciplinary approach to show what we could learn from brain organoid technology and what the future holds. The keynote speakers are all leaders in the field and will showcase the most up-to-date knowledge of brain organoids.

Course directors

University of Pennsylvania, USA

Friedrich-Alexander University of Erlangen-Nürnberg, Germany

Keynote Speakers

Alex Baffet – Institute Curie, Paris, France
Gray Camp – Roche Institute, Basel, Switzerland
Silvia Cappello – MPI Psychaitry, Munich, Germany
Mike Karl – CRTD, Dresden, Germany
Agnete Kirkeby – reNEW, Copenhagen, Denmark
Jürgen Knoblich – IMBA, Vienna, Austria
Matthias Lütolf – Roche Institute, Basel, Switzerland
Abed Mansour – The Hebrew University of Jerusalem, Israel
Sergiu Pasca – Wu Tsai Neurosciences Institute, Stanford, US
Lorenz Studer – Memorial Sloan-Kettering Cancer Center, US
Barbara Treutlein – ETH, Zurich, Switzerland

Instructors

Giovanna Brancati – BSSE, ETH Zürich, Basel, Switzerland
Clarisse Brunet – Institut Curie, Paris, France
Maren Büttner – DZNE, Bonn, Germany
Francesco Di Matteo – Max Planck Institute for Psychiatry, Munich, Germany
Sarah Frank – FAU Erlangen-Nürnberg, Institute of Biochemistry, Erlangen, Germany
Federica Furlanetto – FAU Erlangen-Nürnberg, Institute of Biochemistry, Erlangen, Germany
Yan Hong – Perelman School of Medicine at the University of Pennsylvania, Philadelphia, USA
Richard O’Laughlin – Perelman School of Medicine at the University of Pennsylvania, Philadelphia, USA
Laura Pellegrini – MRC Laboratory of Molecular Biology, Cambridge, UK
Fides Zenk – BSSE, ETH Zürich, Basel, Switzerland
Ting Zhao – Perelman School of Medicine at the University of Pennsylvania, Philadelphia, USA

Course content

Topics & Techniques

The following techniques will be taught at the course:

• Generation of organoids and assembloids
• Organoids characterization
• CSF sampling from choroid plexus organoids
• Viral infection (transduction)
• Live-cell imaging (spinning-disk confocal microscope)
• Setting up of a microfluidic device
• Evaluation of the performance of microfluidic devices
• Extracellular multielectrode array (MEA) recordings
• FACS sorting
• Single cell RNA sequencing
• Generation of retina organoids
• Single cell analysis
• SCANPY framework
• Confocal microscopy
• Surgical procedure of organoid transplantation
• Animal perfusion
• Immunofluorescence
• Image analysis

Projects

Project 1: Generation and characterization of brain organoid of different regional identities and assembloids derived
Project 2: Microfluidic methods for patterning brain organoids
Project 3: Different approaches to perform Electrophysiological recordings in mature human cerebral organoids
Project 4: Using single cell RNA sequencing to decipher cellular heterogeneity of cerebral organoids
Project 5: Transplantation of hPSC-derived brain organoids into mouse brain
Project 6: A sneak peek into retinal organoids
Project 7: Generation and characterization of specialized organoids: cerebral and choroid plexus organoids
Project 8: Revealing neuronal activity in brain organoids using microelectrode array (MEA)
Project 9: Single cell analysis in brain organoids
Project 10: Investigate the Neurogenesis of Transplanted Forebrain Organoids In Vivo with Immunostaining
Project 11: To Fate or Not To Fate: live-cell imaging of neural progenitor cells to study cell fate decisions in the human developing neocortex

Get more information on the projects in the projects list file below.

Bordeaux School of Neuroscience, France

Registration

Fee : 3.500 € (includes tuition fee, accommodation and meals)

Applications closed on 30 May 2022

Course sponsors

The Tianqiao and Chrissy Chen Institute is a science foundation dedicated to advancing our understanding of the full complexity of the brain and mind. The foundation’s mission is implemented through partnerships with world-leading universities and major scientific societies.

Optogenetics, chemogenetics and biosensors for cellular and circuit neuroscience

Course overview

Spatio-temporally precise manipulation and read-out of brain circuit function has been one of the longest-standing challenges in neuroscience. The recent explosion in the field of genetically encoded tools to control and measure neuronal activity has greatly facilitated investigation of brain function, ranging from single synapses to large-scale circuits. Both control and readout of neuronal activity can now be achieved over orders of magnitude in space and time, ranging from micrometers to entire brain regions and from milliseconds to days.

This course will provide participants with the opportunity to gain hands-on experience using the latest genetically encoded tools and state-of-the-art equipment for brain circuit investigation. A particular focus will lie on multiplexed manipulations and read-out of brain circuits. Participants will be familiarized with the biophysical principles behind the sensors and actuators, and given training complementary to their background in the technical aspects of experimental approaches.

Hands-on experiments will employ optogenetic and chemogenetic actuators, including excitatory and inhibitory ion channels, pumps, enzymes and G-protein coupled receptors. These actuators will be complemented by genetically encoded indicators of neural activity, including calcium and voltage indicators as well as indicators for neurotransmitters and neuromodulators such as glutamate, dopamine and norepinephrine.

The course will cover a wide range of experimental systems with an emphasis on functional brain circuits in vivo. Finally, participants will be guided through data analysis and conceptual interpretations of their experiments.

Course partner

Course directors

Weizmann Institute of Science

Israel

Stanford University

USA

Center for Molecular Neurobiology Hamburg (ZMNH)

Germany

University of Bordeaux

France

Keynote speakers

Adam Cohen – Harvard University, USA
Stephane Dieudonne – University of Marseille, France
Valentina Emiliani – Institut de la vision, France
Stefan Herlitze – University of Bochum, Germany
Na Ji – University of Berkeley, USA
Tom Kash – University of North Carolina, USA
Tatiana Korotkova – MPI Köln, Germany
Adam Packer – University of Oxford, UK
Tommaso Patriarchi – ETH Zurich, Switzerland
Jonas Wietek – Weizmann Institute of science, Israel
Yaniv Ziv – Weizmann Institute of science, Israel

Instructors

Yoann Atlas – Institut de la vision, France
Imane Bendifallah – Institut de la vision, France
Miklos Boldogkoi – Institute of Molecular and Clinical Ophthalmology Basel IOB, Switzerland
Martina De Gennaro – Institute of Molecular and Clinical Ophthalmology Basel IOB, Switzerland
Alexander Dieter – Center for Molecular Neurobiology Hamburg – ZMNH, Germany
Andrey Formozov – Center for Molecular Neurobiology Hamburg ZMNH, Germany
Nitzan Geva – Weizmann Institute of science, Israel
Christianne Grimm – Institut de la vision, France
J. Quinn Lee – McGill University, Canada
Maxime Maheu – University Medical Center Hamburg-Eppendorf, Germany
Mathias Mahn – Friedrich Miescher Institute of Basel, Switzerland
Vasyl Mykytiuk – Max Plank Institute, Germany
Praneeth Namburi – Massachusetts Institute of Technology, USA
Mauro Pulin – Center for Molecular Neurobiology Hamburg – ZMNH, Germany
Inbar Saraf-Sinik – Weizmann Institute of science, Israel
Robson Scheffer Teixeira – University of Cologne, Germany
Guilherme Silva – University of Harvard, USA
Dimitrii Tanese – Institut de la vision, France

Course content

Topics & Techniques

The following techniques will be covered during the course:

implantation of optical fibers, stereotactic injection of viruses in mice.
optogenetic stimulation (BIPOLES) and monitoring of pupil size and mouse behavior.
imaging of calcium responses, building of a reward delivery system and a head-fixation system for mice either immobilized in a tube or running on a treadmill.
in vitro exploration of FLARE technique
2-photon holographic illumination to achieve single-cell resolved optogenetic activation of presynaptic cells and patch-clamp recording of the post-synaptic neuron
concurrent photostimulation and calcium imaging of the presynaptic cells, and voltage imaging on the post-synaptic cell
use of miniature head-mounted microscopes (Inscopix).
perform population level data analysis on data that was collected across multiple days
behavioral assays including the elevated plus maze, the open field test, consumption of water, sucrose, quinine and food, as well as mild foot shocks
head-bar implantation, stereotaxic intracerebral virus injection, and craniotomy preparation for long-term recordings
head-fixed electrophysiology setup building
silicon-probe recordings, in head-fixed mice during behavior, using multi-shank, high-density silicon probes (128-512 channels) & Physiological monitoring
opto-tagging and optogenetic manipulations of specific cell-types.
open-source hardware and software for the acquisition and processing of the data, including OpenEphys, Bonsai, PulsePal, Cyclops, Arduino, Linux, KiloSort, and MountainSort
construct microdrives, mount the silicon probes onto them, make optical fibers of custom length

Projects

Project 1: “Optogenetic control of neuromodulation ”
Project 2: “Optical tool exploration in culture, in slice, and in vivo”
Project 3: “Optical tool exploration in culture, in slice, and in vivo”
Project 4: “Probing neuronal excitability with Arch-derived voltage sensors ”
Project 5: “Longitudinal calcium imaging in freely behaving mice using Inscopix system”
Project 6: “In vivo imaging of divergent neural populations using dual-color fiber photometry”
Project 7: “All optical characterization of eOPN3 mediated terminal inhibition in vivo”
Project 8: “Large-scale electrophysiology and optogenetics during head-fixed behavior”
Project 9: “In vivo calcium imaging with open-source Miniscopes”
Project 10: “Combining in vivo electrophysiology and optogenetics in freely moving mice”
Project 11: “All optical interrogation of dopamine circuits in freely moving mice using multiplexfiber photometry and biosensors”
Project 12: “All-optical manipulation and read-out of synaptic transmission”

For more information on projects and techniques which will be taught at the course, download the projects list.

Bordeaux School of Neuroscience, France

Registration

Fee : 3.500 € (includes tuition fee, accommodation and meals)

Application closed on 7 December 2020

COVID-19 update: In case the Optogenetics, chemogenetics and biosensors for cellular and circuit neuroscience course is postponed due to the pandemic, all applicants will have the choice to maintain their application or cancel it. Applicants who were already selected to attend will not have to reapply and will automatically be enrolled in the rescheduled course.

In addition, the Cajal Programme will not, as far as possible, request the registration fee from selected applicants until the course has been secured and confirmed. Nevertheless, should the course be cancelled before the course dates and the registration fees already collected, participants will be reimbursed.

Course sponsors

Neuroepigenetics: writing, reading and erasing the epigenome

Course overview

This course is a theoretical and practical training on the recently emerged field of neuroepigenetics. It will provide an overview of the current concepts and knowledge on the nature and functions of the epigenome in the nervous system, its modes of regulation and its link to brain health and disease. It will combine lectures and hands-on projects to learn about state-of-the-art approaches and methodologies to study how the epigenome is established and modulated by behaviour in rodents and invertebrates, what machinery is involved and what is its causal relationship to functions. It will include methods in behaviour, epigenetics, (epi)genome editing, molecular and cell biology, -omics and bioinformatics.

This course wishes to foster the development of neuroepigenetics as a key discipline in the neurosciences, and train and educate young researchers expected to contribute to the field in the near future. It is intended for PhD students and early career postdocs who wish to acquire good bases and broad knowledge of the field.

Course partner

ERA-NET NEURON

Course directors

CNRS – LNCA, University of Strasbourg, France

Neurosciences Institute (UMH-CSIC), Spain

German Center for Neurodegenerative diseases (DZNE), Germany

Institute of Informatics, University of Warsaw, Poland

Keynote Speakers

Elisabeth Binder – Max Planck Institute of Psychiatry, Munich, Germany
Anne-Laurence Boutillier – LNCA, Strasbourg, France
Goncalo Castelo Branco – Karolinska Institute, Stockholm, Sweden
Johannes Gräff – EPFL, Lausanne, Switzerland
Elizabeth A Heller – Penn Epigenetics Institute, Philadelphia, USA
Denes Hnisz – Max Planck Institute for Molecular Genetics, Berlin, Germany
Aleksandra Pekowska – Dioscuri Center of Chromatin Biology and Epigenomics, Poland

Instructors

Rafael Alcala Vida – Instituto de Neurociencias UMH-CSIC, Spain
Mykhailo Batiuk – EPFL, Lausanne, Switzerland
Davide Coda – EPFL, Lausanne, Switzerland
Charles Decraene – LNCA, Strasbourg, France
Beatriz del Blanco Pablos – Instituto de Neurociencias UMH-CSIC, Spain
Aleksander Jankowski – Institute of informatics, Warsaw, Poland
Lalit Kaurani – DZNE, Göttingen, Germany
Marta Kullis – IDIBABS, Barcelona, Spain
Stéphanie Legras – IGBMC, Strasbourg, France
Jose Lopez Atalaya – Instituto de Neurociencias UMH-CSIC, Spain
Pierre-Eric Lutz – INCI, Strasbourg, France
Magdalena Machnicka – Institute of informatics, Warsaw, Poland
Marta Alaiz Noya – Instituto de Neurociencias UMH-CSIC, Spain
Isabel Paiva – LNCA, Strasbourg, France
Jose Sanchez-Mut – Instituto de Neurociencias UMH-CSIC, Spain
Sophie Schroeder – DZNE, Göttingen, Germany
Tanya Vavouri – Pujol Research Institute, Badalona, Spain

Course content

Topics & Techniques

State-of-the-art approaches to produce and analyze cell-type-specific epigenomic data in the brain in physiological and disease contexts will be taught, as well as approaches to manipulate the epigenome in brain cells.

ChIP seq
CUT & Tag seq
ATAC seq
Single nuclei DNA methylome (snmC-seq2)
Single nuclei RNA seq
Sample preparation for simultaneous RNAseq, WGBSseq and/or singe-nuclei ATAC-RNAseq (multiome)
Design, production and manipulation of epi-editing tools using viral constructs and CRISPR system, and analysis of transcriptional changes at targeted loci
Mouse brain subregion dissection, tissue sectioning
Fluorescently activated nuclear sorting (FANS) of neuronal and non-neuronal cell populations from mouse brain tissue
Isolation of glial cells (astrocytes) from mouse brain tissue using magnetic beads (MACS)
RNAscope
Confocal microscopy
Primary cultures of hippocampal neurons.

Projects

Project 1: Cell-type-specific epigenetic profiling using Fluorescence-Activated Nuclear Sorting (FANS) from brain tissue

Project 2: Astrocyte epigenome of mouse hippocampus

Project 3: Transcriptomic profiling of adult mouse brain tissue using 10X Genomics single-nuclei RNA-sequencing

Project 4: Cell type-specific detection of lncRNAs in the mouse brain using RNAscope and immunofluorescence

Project 5: Investigation of single cell DNA methylome landscape of cortical brain cells

Project 6: Cell-type and brain-region specific epigenetic manipulation in Alzheimer’s disease models

Project 7: CRISPR-dCas9 systems for targeted epigenetic repression

Project 8: Epigenome editing technology based on the CRISPR/dCas9 system.

Computational projects: State-of-the-art approaches for bioinformatic analysis and interpretation of the next generation sequencing (NGS) data obtained in the epigenomic experiments covered in the first block.

Bordeaux School of Neuroscience, France

Registration

Fee : 3.500 € (includes tuition fee, accommodation and meals)

Applications closed on 5th September 2022

Our partner, ERA-NET NEURON, will also offer grants to participants who are part of an ERA-NET Neuron research group. Please indicate in the application form if you are a member of the network.

Course overview

Course partner

Course directors

Keynote speakers

Instructors

Course content

Topics & Techniques

Projects

Bordeaux School of Neuroscience, France

Registration

Course overview

Course directors

Keynote speakers

Instructors

Course content

Schedule

Sunday, May 22nd: Arrival & Welcome reception

Monday, May 23rd: Keynote lecture by Ben de Bivort / Afternoon tutorial: Build a rig & capture movies by Ben de Bivort & Giorgio Gilestro

Tuesday, May 24th: Keynote lecture by Giorgio Gilestro / Afternoon tutorial: Build a centroid tracker by Ben de Bivort & Giorgio Gilestro

Wednesday, May 25th: Keynote lecture by Alex Jordan / Afternoon tutorial: Multianimal idtracker.ai by Francisco Romero & Dean Rance

Thursday, May 26th: Morning tutorial by Gonzalo de Polavieja / Afternoon tutorial: Deep Learning notebooks applied to behaviour data sets by Gonzalo de Polavieja

Friday, May 27th: Keynote lecture by Talmo Pereira / Afternoon tutorial: Limb and body tracking by Talmo Pereira

Sunday, May 29th: Keynote lecture by Kristin Branson / Afternoon tutorial: Supervised classification by Kristin Branson

Monday, May 30th: Keynote Lecture by Sam Reiter / Afternoon tutorial: Dynamics of behaviour by Greg Stephens & Tosif Ahamed

Tuesday, May 31st: Keynote lecture by Ben de Bivort & Gordon Berman / Afternoon tutorial: Unsupervised analysis of behaviour by Ugne Klibaite & Kanishk Jain

Wednesday, June 1st: Keynote lecture by Bing Brunton / Afternoon tutorial: Probabilistic models by Bing Brunton

Thursday, June 2nd: Keynote lecture by Barbara Webb & Orit Peleg / Afternoon tutorial: Braitenberg and agent-based models by Barbara Webb & Orit Peleg

Friday, June 3rd: Keynote lecture by António Costa / Afternoon: Project design

Sunday June 5th Keynote lecture by Ilya Nemenman / Afternoon: Project development

Monday, June 6th: Keynote lecture by Serena Ding / Afternoon: Project development

Tuesday, June 7th: Keynote lecture by Ann Kennedy / Afternoon: Project development

Wednesday, June 8th: Keynote lecture by Natasha Mhatre / Afternoon: Project development

Thursday, June 9th: Keynote lecture by Sama Ahmed

Friday, June 10th: Project presentations

Saturday, June 11th: Departure

Projects

Champalimaud Centre for the Unknown, Portugal

Registration

Course overview

Course partner

Course directors

Keynote Speakers

Instructors

Course content

Topics & Techniques

Projects

Bordeaux School of Neuroscience, France

Registration

Course sponsors

Course overview

Course directors

Keynote Speakers

Instructors

Course content

Schedule

Sunday, June 19th: Arrival & Welcome reception

Monday, June 20th: Keynote lecture by Chris Xu / Ed Boyden Afternoon: Student presentations & Poster session I

Tuesday, June 21st: Keynote lecture by Eugenia Chiappe / Pavan Ramdya Afternoon: TA & Experimental Resources presentation & Poster session II

Wednesday, June 22nd: Keynote lecture by Greg Jefferis / Tiago Branco Afternoon TA & Experimental Resources presentation / Project Design & Discussion

Thursday, June 23rd: Morning tutorial by Scott Waddell / Na Ji Afternoon: Rig rotation / Project Design & Discussion

Friday, June 24th: Keynote lecture by Winfried Denk / Susana Lima Afternoon: Rig rotation/ Project Design & Discussion

Friday, June 25th: Surf/Beach Day

Sunday, June 26th: Keynote lecture by Darcy Peterka / Nick Steinmetz / Botond Roska Afternoon: Rig rotation

Monday, June 27th: Keynote Lecture by Marius Pachitariu / Carsen Stringer Afternoon: Miniprojects

Tuesday, June 28th: Keynote lecture by Karel Svoboda / Ana João Rodrigues Afternoon: Miniprojects

Wednesday, June 29th: Keynote lecture by Isaac Bianco Afternoon: Miniprojects

Thursday, June 30th: Keynote lecture by Michael Brecht / Marta Moita Afternoon: Miniprojects

Friday, July 1st: Keynote lecture by Megan Carey Afternoon: Miniprojects

Saturday July 2nd: Keynote lecture by Francois St. Pierre / Michael Hausser / Afternoon: Free/Social

Sunday July 3rd: Keynote lecture by Emily Dennis / Claire Wyart / Valentina Emiliani / Afternoon: Miniprojects

Monday, July 4th: Keynote lecture by Ofer Yizhar/ Afternoon: Miniprojects

Tuesday, July 5th: Keynote lecture by Michael Orger / Afternoon: Miniprojects

Wednesday, July 6th: Keynote lecture by Ken Harris / Afternoon: Miniprojects

Thursday, July 7th: Keynote lecture by Mackenzie Mathis Afternoon: Miniprojects

Friday, July 8th: Miniproject presentation

Saturday, July 9th: Departure

Topics & Techniques

Champalimaud Centre for the Unknown, Portugal

Registration

Sponsors