Category Archives: On Site

Display this course using the On-Site template (blue)

Neuro-vascular function in health and disease

Course overview

The neurovascular unit, composed of vascular cells, glial cells, and neurons is fundamental for the proper function of the brain. The NVU regulates supply of the cerebral blood flow (CBF) and maintains integrity of the blood-brain barrier (BBB).

Dysfunction of the neurovascular unit may result in devastating conditions such as dementia, cerebral ischemia, or brain oedema formation. This advanced experimental course will allow students to gain basic knowledge and hands-on experience on the most important techniques used to study the neurovascular unit, such as in vivo/in vitro high-resolution imaging, magnetic resonance imaging, and rodent models of cerebrovascular disease. The course will also focus on data reproducibility and open science.

Course partner

ERA-NET NEURON

Course directors

Ludwig Maximilian University, Germany

Bordeaux University, France

Sussex University, UK

Keynote Speakers

David Attwell – University College London, UK
Felipe Barros – Centro de Estudios Científicos, Chile
Serge Charpak – University of Paris, France
Turgay Dalkara – Hateceppe University, Turkey
Ali Ertürk – University of Munich, Germany
Jean Francois Ghersi-Egea – Lyon Neuroscience Research Centre, France
Anne Joutel – University of Paris, France
Martin Lauritzen – University of Copenhagen, Denmark
Malcolm MacLeod – University of Edinburgh, UK
Pierre Magistretti – University of Lausanne, Switzerland
Maiken Nedergaard – University of Copenhagen, Denmark
Mark Nelson – University of Burlington, USA
Andy Obenhaus – USI, USA
Andy Shih – Seattle Children’s Research Institute, USA
Robert Thorne – Denali Therapeutics / University of Wisconsin-Madison, USA
Susanne Van Veluw – Harvard Medical School, USA

Instructors

Silvia Anderle – University of Sheffield
Orla Bonnar – University of Sheffield
Gian-Marco Calandra – Massachusetts General Hospital
Audrey Chagnot – University of Sussex
Yulia Dembitskaia – University of Edinburgh
Maximillian Dorok – Johns Hopkins
Christophe Dubois – université de Bordeaux
Beth Eyre – University of Munich
Severin Filser – University of Munich
Jordan Girard – Université de Bordeaux
Clare Howarth – University of Munich
Malika Ihle – University of Munich
Igor Khalin – University of Munich
Tom Langdon – University of Munich
Guillaume Le Bourdelles – Inscopix
Axel Montagne – Université de Bordeaux
Burcu Seker – Université de Bordeaux
Josh Shrouder – University of Munich
Rebecca Sienel – University of Edinburgh
Jonathan Zapata – Johns Hopkins

Course content

This 3-week long course is a practical “hands-on” introduction to advanced methods for the investigation of the neuro-vascular unit in health and disease. The course will be structured in a theoretical and a practical part.

In the theoretical part world leading scientists in the neurovascular unit (NVU) research will give overview lectures about the function of the NVU and present techniques how to study the NVU in a reproducible manner. Such overview presentations will be paralleled by workshops. In the practical part of the course students will learn surgical techniques necessary to perform animal models of disease and to prepare cranial windows required for the study of cerebral vessels, will be trained to image cerebral vessel function in vitro and in vivo, and will learn how to analyse and display the acquired data.

Techniques

The following techniques will be taught at the course:

Chronic cranial window surgery
Habituation to the rig for awake imaging
Experimental design and presentation of stimuli
2 photon imaging of neurovascular coupling (neuronal activity, blood vessel dilations)
2 photon imaging of vascular function (vasomotion, calcium signals in vessels)
Wide field imaging and recording of neurovascular function and metabolism (2D OIS, laser speckle, haemoglobin spectrometry, laser doppler flowmetry – equipment to be loaned by Moor Instruments)
Data processing and analysis

Projects

The following projects will be taught at the course:

Two-photon microscopy imaging of blood vessels and neuronal activity in vivo
Brain imaging in freely moving mice using mini-scopes
Two-photon microscopy imaging of stroke
Widefield imaging of neurovascular relationships
Open Science
Correlative light-electron microscopy (CLEM)
Vascular signalling in pressurized brain slices
BBB permeability in mice and humans by MRI
SUSHI – evaluating the brain’s extracellular space by STED microscopy
Histological techniques for the analysis of cerebral vessels
Brain clearing for the analysis of cerebral vessels

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

Fee : 3.950 € (includes tuition fee, accommodation and meals)

Applications closed on 14 November 2022

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.

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

Champalimaud Foundation, Portugal

Sainsbury Wellcome Centre, UK

Keynote Speakers

Instructors

Stan Heinze – Lund University, Sweden
Chris Xu – Cornell University, USA
Michael Orger – Champalimaud Foundation, Portugal
Constanze Lenschow – Magdeburg University, Germany
Ana João Rodrigues – ICVS, Minho University, Portugal
Bob Datta – Harvard University, USA
Marta Moita – Champalimaud Foundation, Portugal
Botond Roska – Institute of Molecular and Clinical Ophthalmology Basel, Switzerland
Tobias Rose – University of Bonn Medical Center, Germany
Darcy Peterka – Columbia University, USA
Vanessa Ruta – Rockefeller University, USA
Eugenia Chiappe – Champalimaud Foundation, Portugal
Isaac Bianco – University College of London, UK
Christine Constantinople– New York University, USA
Valentina Emiliani – Institut de la Vision, France
Carsen Stringer – HHMI Janelia, USA

Hugo Marques – Champalimaud Foundation, Portugal
Ana Rita Mendes – Champalimaud Foundation, Portugal
João Frazão – Champalimaud Foundation, Portugal
Gokul Rajan – Champalimaud Foundation, Portugal
Matheus Farias – Champalimaud Foundation, Portugal

Course content

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.

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

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 : 3.950 € (includes tuition fee, accommodation and meals)

Applications closed on 31 January 2023

Course overview

For over a century, the main focus of neuroscience research has been on neurons. It is however, becoming ever more clear that brain functions such as conceptual reasoning, memory, and processing speed depend on glial cells (microglia, astrocytes and oligodendrocytes).

The lack of understanding of the role of glia in normal brain development, function and disease is mainly due to lack of tools and methods to accurately study these cells. In recent years, neuroscience has seen a methodological revolution. The function of glia cells in neuronal circuit development, and neurodegenerative disease has become evident. The study of glial biology and the understanding on how glial cells impact on circuit function are key to understanding how the brain works and what goes wrong in brain disease. Advanced training of a new generation of neuroscientists with strong focus on glial function is crucial to make these studies a success in the coming decades.

Course directors

Cambridge University, UK

Duke University, US

Bordeaux Neurocampus, FR

Keynote Speakers

Amit Agarwal – Heidelberg University, Germany
Paola Arlotta – Harvard University, US
David Belin – University of Cambridge, UK
Bart J. L. Eggen – University Medical Center Groningen, The Netherlands
Sonia Garel – Institut de Biologie de l’Ecole Normale Superieure (IBENS), Paris, France
Soyon Hong – UCL, London, UK
Maarten Kole – Utrecht University, The Netherlands
Kelly Monk – The Vollum Institute, OHSU, US
Stéphane Oliet – Neurocentre Magendie, France
Thomas Papouin – Washington University School of Medicine in St. Louis, US
Nathalie Rouach – College de France, France
David Rowitch – University of Cambridge, UK
Mikael Simons – Technical University Munich, Germany

Instructors

Amit Agarwal – Heidelberg University, Germany
Liam Barry–Carroll – IMN, Bordeaux Neurocampus, France
Arne Battefeld – IMN, Bordeaux Neurocampus, France
Felipe Bodaleo – Heidelberg University, Germany
Sarah Bou Sader Nehme – IMN, Bordeaux Neurocampus, France
Sara Carracedo Vicente – IMN, Bordeaux Neurocampus, France
Omar De Faria – Stem Cell Institute, University of Cambridge, UK
Mohit Dubey – Netherlands Institute for Neuroscience, The Netherlands
Jiaxing Li – Oregon Health & Science University, US
Charlotte Madore-Delpech – INRAE, University of Bordeaux, France
Giampaolo Milior – College de France, France
Wiebke Möbius – Max Planck Institute for Multidisciplinary Sciences, Germany
Torben Ruhwedel – Max Planck Institute for Multidisciplinary Sciences, Germany
Kristina Sakers Hays – Duke University Medical Center, US
Caroline Smith – Boston College, US
Francesco Ulloa Severino – Duke University, US

Course content

This is a theoretical and practical training course on glial cells and their communication with neuronal circuits. It will provide an overview of the current concepts and knowledge of glial cell biology in central and peripheral nervous system development in several species, including zebrafish, mice, and humans, and their link to diseases.

It will combine lectures and hands-on projects on glial development including methods in cellular neuroscience (e.g. live and fixed tissue imaging), genetic modifications, -omics (e.g., scRNA seq, proteomics and bioinformatics), electrophysiology, optogenetic and chemogenetic manipulation of glial cells and methods to study behaviour.

Bordeaux School of Neuroscience, France

Registration

Fee : 3.950 € (includes tuition fee, accommodation and meals)

Machine learning for neuroscience

Course overview

Neuroscience has played an important role in the history of Artificial intelligence and Machine learning. Artificial neural networks are inspired by neuronal physiology and are today the core of Deep Learning. This common history continues today. Machine Learning methods are developed into tools that allow for a higher quality of data processing in the study of animal behavior and brain activity. Machine Learning is also used to model the brain as it can solve similar problems to what brains solve and the basic units of processing may be comparable.

The course gives a hands-on introduction to Artificial Intelligence and Machine Learning and how it can be used for data acquisition, analysis and modeling brain activity and behavior. Experts in the field will teach the basics of Machine Learning and how to apply it to Neuroscience and will also discuss the limits of the field, and what are the boundaries of application and how Neuroscience and Psychology could inform new systems.

Course directors

Champalimaud Foundation, PT

HHMI Janelia, USA

Champalimaud Foundation, PT

Keynote Speakers

Ann Kennedy – Northwestern University, US
N. Alex Cayco Gajic – École Normale Supérieure, France
Ben Cowley – Cold Spring Harbor, US
Kim Stachenfeld – DeepMind, UK
Jennifer Sun – Caltech, US
Josue Nassar – Stony Brook University, US
Laura Driscoll – Stanford University, US
Maneesh Sahani – Gatsby Computational Neuroscience Unit, UK
Nakul Verma – Columbia University, US
Patrick Mineault – xcorr, Canada
Rui Ponte Costa – University of Bristol, UK
Sara Solla – Northwestern University, US
Sophie Deneve – Ecole Normale Superieure, France
Surya Ganguli – Stanford University, US

Instructors

Alice Robie – HHMI Janelia, USA
Brad Hulse – HHMI Janelia, USA
Joao Barbosa – Ecole Normale Superieure, France
Tiago Marques – Champalimaud Foundation, Portugal

More information to come soon.

Course content

Programme

During the first two weeks, there will be lectures in the morning, and evening tutorials will consist of analytical and computational application of the concepts learned in the morning. The third week consists of lectures in the mornings and projects in the evening.

First week

The first week will consist of a mini-course in Machine Learning, especially those techniques used in Neuroscience. This will include supervised and unsupervised learning, learning for time series and Reinforcement Learning, as well as a day dedicated to practical aspects in the use of Machine Learning Techniques.

Day 1: History of AI and the relationship between Machine Learning and Neuroscience
Day 2: Supervised Learning
Day 3: Unsupervised Learning
Day 4: Practical consideration of the use of Machine Learning
Day 5: Learning for Time Series
Day 6: Reinforcement Learning

Second Week

The second week discusses how Machine Learning techniques are applied in Neuroscience. This will include the Machine Learning tools used to extract information from datasets of animal behavior and brain activity, Machine Learning models from brain activity and behavior, models using spiking neural networks and which are the limits ofML techniques.

Day 7: ML tools in animal behavior
Day 8: ML tools in brain activity
Day 9: Models derived from the brain and behavior
Day 10: ML-based models of the brain & discrepancies
Day 11: Theory-based modeling, and its connection to ML
Day 12: Bio-inspired ML/spiking networks

Third week

The third week has lectures on more advanced topics and evenings on projects.

Students will design projects applying machine learning (ML) methods to neural recording and animal behavior data sets. Neural recording data sets provided will be from a variety of techniques, including electrophysiology, calcium imaging, and fMRI. Behavior data sets provided will be from video. Students may focus on developing new ML algorithms for improving automated tracking, segmentation, categorization, or representation learning. Alternatively, they may focus on applying these ML methods to large data sets to discover new biological insights. A third option is to explore ML-based computational models of neural activity or behavior. Through these projects, students will gain hands-on experience using modern ML approaches, coding in PyTorch, and gain a deeper understanding of the power and potential failures of ML.

Datasets

Behavioral Datasets

Fish Fish in groups, raw and tracked
Some rodents and ants, raw and tracked
Flies data from Maabe and other datasets.

Neural Datasets (spike trains)

Neural Latent Benchmark ones
Neuromatch ones (e.g. Steinmetz)
Brain machine interface related datasets
IBL datasets

Other Neural Datasets ( LFP, fMRI, etc)

Computational models (not datasets but used as input for further analysis or modeling)

RNNs trained on tasks
Models trained on fish in collectives

Techniques

Deep learning tools for analyzing complex behavior data
Neural manifolds
Modeling neural computation with recurrent neural networks
State space modeling of neural time series
Probabilistic modeling of neural data and behavior
Deep learning models of brain activity and behavior
Spiking neural networks
Best practices for high quality neuroscience research using machine learning

Champalimaud Centre for the Unknown, Portugal

Registration

Fee : €2.950,00 (includes tuition fee, accommodation and meals)

Applications closed on 23rd January 2023

Connectomics from micro- to meso- and macro-scales

Course overview

The biological factors shaping the synaptic connectivity of neuronal circuits are complex and multifaceted, depending on cell types, functional activity, homeostasis, and more. Mapping brain wiring at the level of both local circuits and across brain-wide projections is a key aspect of understanding how nervous systems develop, learn, process information and generate behaviour. Recent advances in molecular biology, tissue processing, computational methods, and microscopy have enabled a revolution in understanding structural connectivity with cellular and synaptic resolution. Large-scale electron microscopy volumes provide nanometer-scale maps of anatomy and connectivity of whole invertebrate brains and millimetre-scale regions of vertebrate brains, while light-microscopic methods can highlight genetically defined connections and enable brain-wide reconstruction of neurons. Together, these complementary approaches yield powerful insight into the neuroanatomy and connectivity of the nervous system with single-cell resolution.

This course will provide students with a broad introduction to contemporary methods of studying neuronal connectivity with lectures from experts in the field. It also provides practical project-based instruction in experimental methods of circuit tracing and reconstruction with light microscopy (light sheet or 2-photon), as well as the computational analysis of rich electron microscopy connectomes in flies and mice. Students will consider the strengths and limitations of different techniques and how they can be used to address key problems in circuit neuroscience.

Course directors

MRC LMB and University of Cambridge, UK

Korea Institute of Science and Technology, Korea

Paris Brain Institute, France

Allen Institute of Brain Science, US

Keynote Speakers & Instructors

Keynote Speakers

Christel Genoud – University of Lausanne, Switzerland
Moritz Hemlstaedter – Max Plank Institute for Brain Research, Germany
Alexandra Pacureanu – European Synchrotron Radiation Facility, France
Hiroki Ueda – Laboratory for Synthetic Biology, Japan
Claire Wyart – ICM Institute for Brain and Spinal Cord, France

Instructors

Will be announced soon

Course content

Light Microscopy and functional, molecular methods:

– Choice of labelling strategy: use of specific cre lines (for instance, the GENSAT project); finding specific markers for cell populations; using viral vectors and intersectional genetics (Dual or triple injections, transsynaptic tracing, Tango system, mGRASP, etc.).

– Tissue preparation for imaging: tissue clearing: choice of methods, considerations for the resolution needed and type of molecular labelling (Ueda, Renier); expansion microscopy methods: when to use them, and which iteration (Jae-Byum Chang)

– Imaging strategy: use of scanning microscopes: confocal or 2p, in intact samples or using serial sectioning; use of light sheet microscopy: commercial systems (eg. Miltenyi’s Blaze or Zeiss Z7), and custom systems (Mesospim).

– Analysis of imaging data: use of neuron mapping pipelines for whole brain data obtained from light sheet microscopy or from sections (eg. ClearMap, TrailMap, WholeBrain, etc). (Ueda, Renier, Carlen); se of virtual reality-assisted tools for single neuron reconstructions from 3D datasets (eg. SyGlass, Vision4D…).

Electron microscopy synaptic connectomics:

At the end of this course, the students will be familiar with all of the steps that go into producing and analysing large scale, synaptic resolution EM connectomics datasets, summarised as below. Detailed analysis projects tailored by student interest will use public datasets and open source tools in which their directors and their colleagues are experts. These include the microns mouse cortical cubic millimetre dataset (https://www.microns-explorer.org/) and fly CNS datasets including the hemibrain, flywire.

Techniques

EM imaging for connectomics (theory, image analysis)
X-ray imaging for connectomics (theory, image analysis)
EM connectomics data analysis (detailed hands on coverage for latest public whole brain fly and mouse cortex datasets; other organisms pending)
In vivo calcium imaging

In vivo 2-photon microscopy
Light sheet microscopy
Tissue Clearing
Brain mapping of cleared tissue (image analysis, commercial and academic softwares)

Projects

Mapping of axonal projections with light sheet microscopy in the mouse brain
Assembly of a Mesospim microscope for whole brain mapping with tissue clearing
Brain mapping of cellular markers with HCR-fish, tissue clearing and light sheet microscopy
In vivo recording of activity and connectivity in the Zebrafish larva
Inference of information flow in Zebrafish larva using calcium imaging and Granger Causality

Bordeaux School of Neuroscience, France

Registration

Fee : 3.950 € (includes tuition fee, accommodation and meals)

Applications open from 21 Feb – 3 April 2023

Advanced techniques for synapse biology

Course overview

Synapses are sites of information transfer and storage in the brain. These specialised structures integrate complex signals and undergo functional changes that underlie the formation of memories. Synaptic dysfunction is associated with early stages of neurodegenerative disorders such as Alzheimer’s disease, and underlies neurodevelopmental disorders such as autism spectrum disorders and intellectual disability.

Studying synapse function and plasticity is key to understanding brain circuits that underlie behaviour, and to identify synaptic malfunction mechanisms underpinning brain diseases. This course will allow students to integrate theoretical and methodological concepts on synapse biology with hands-on experience on state-of-the art imaging, functional and computational methodologies. The course provides an in-depth understanding to many concepts such as synapse formation and maintenance, pre- and postsynaptic mechanisms, structural and functional synaptic plasticity, synaptic integration in neuronal networks and synaptopathies. Hands-on experimental projects conducted in small groups with the support of senior scientists will expose the students to methodologies at the forefront of research in this field.

Course directors

CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Portugal

IINS, University of Bordeaux, France

The Zanvyl Krieger Mind/Brain Institute, The Johns Hopkins University, USA

Keynote Speakers

Alfredo Kirkwood – Johns Hopkins University, USA
Brian D McCabe – EPFL, Lausanne, Switzerland
Cécile Charrier – Institute of Biology, École Normale Supérieure, France
Christian Lohmann – University of Amsterdam, Holland
Daniel Choquet – IINS, University of Bordeaux, France
Joseph Kittler – University College London, UK
Juan Burrone – King’s College London, UK
Julie Perroy – IGF, University of Montpellier, France
Julijana Gjorgjieva – Max Planck Institute for Brain Research, Germany
Marina Mikhaylova – Center for Molecular Neurobiology Hamburg (ZMNH), Germany
Nael Nadif Kasri – Radboudumc Donders Institute for Brain, Cognition and Behaviour, Holland
Noa Lipstein – FMP-Berlin, Germany
Rosa Paolicelli – University of Lausanne, Switzerland

Instructors

Anne-Claire Compagnion – Univ. Lausanne, Switzerland

Elena Baz-Badillo – IINS, Univ Bordeaux, France

Frederic Gambino – IINS, Univ Bordeaux, France

Joana Ferreira – CNC, Univ Coimbra, Portugal

Julia Bär – Center for Molecular Neurobiology Hamburg (ZMNH), Germany

Julien Dupuis – IINS, Univ Bordeaux, France

Kevin Crosby – University of Colorado Denver, Department of Pharmacology, USA

Léa Sarzynski – IINS, Univ Bordeaux, France

Luís Ribeiro – CNC, Univ Coimbra, Portugal

Marie-Lise Jobin – IINS, Univ Bordeaux, France

Marina Hommersom – Radboudumc Donders Institute for Brain, Cognition and Behaviour, Holland

Michelle Bridi – West Virginia University, USA

Mónica Santos – CNC, Univ Coimbra, Portugal

Olivier Nicole – IINS, Univ Bordeaux, France

Tamara Buijs – Univ Amsterdam, Holland

Vivek Belapurkar – IINS, Univ Bordeaux, France

Course content

Exposure to central topics in synapse biology, and hands-on experience with exciting projects with innovative techniques

The research in synapse biology holds a central place in Neuroscience, as it connects findings in molecular and cellular Neuroscience to the understanding of circuits and behaviour. In addition, synaptopathy is a major pathogenic mechanism in both neuropsychiatric and neurodegenerative disorders. The last decades have brought enormous advances in the methodologies used to study synapses, and which endow researchers with the possibility to bridge from the molecular analyses of synapses to cellular, circuits and behaviour approaches to tackle central questions about how the brain works.

This course provides the opportunity to learn from experts in the field about questions at the forefront of synapse biology, and to obtain hands-on experience with innovative techniques to study synapses. These include gene transfer, live imaging of proteins and signalling molecules (including in vivo 2 photon microscopy), superresolution microscopy for cellular imaging of proteins at excitatory and inhibitory synapses, electrophysiology, animal behaviour and computational methods.

Topics

Synaptic traficking
Synaptogenesis, synapse adhesion and synapse maintenance
Presynaptic mechanisms
Inhibitory synapses
Structural and functional synaptic plasticity
Synaptic integration in neuronal networks
Calcium dynamics and signaling
Microglia in the shaping of neural circuits
Synaptic dysfunction in disease
Synaptic computation

Course format

Three weeks of intensive training, with students in the lead, supported by senior scientists

The course includes both lectures by leading scientists in synapse biology, and hands-on training in two projects of about 9 days each, supported by senior scientists. Students (20 maximum) will attend theoretical and methodological lectures during the morning sessions, and spend the afternoon period in the Neuroscience Training Lab at the Neurocampus performing projects in groups of 2-3 students. The training laboratory is dedicated to the course and it is equipped with a wet lab for cellular and molecular biology, cell culture and animal rooms, electrophysiology rigs and behavior set-ups. Students will have access to core facilities at the University of Bordeaux, including to the Bordeaux Imaging Center, the Functional Genomics and the Biochemistry facilities. Support and expertise to carry out the projects is provided by external instructors coming from leading international laboratories in synapse biology, who will be present throughout the duration of the projects and assist students in their experiments (one instructor per group). Students are encouraged to participate in the design of projects, ahead of the course, through interaction with their project instructor. Students are welcome to bring their constructs or models, to be integrated in the project to be conducted. At the end of each project, students will present their findings and discuss with colleagues and instructors. Extracurricular activities (such as panel discussions on ethics, diversity and equity in Neuroscience), outreach activities and social events are also planned.

Techniques

Whole cell patch clamp recordings in brain slices
Patch-seq / RNAseq
Co-culture synaptogenic assay
Synaptic interactome analysis through proximity-dependent labeling
Stereotaxic surgery with cannulae implantation
Behavior analysis
Confocal time-lapse imaging and FRAP measurements
FLIM-FRET measurements for activity sensors
Single-molecule tracking and PALM studies
Direct stochastic optical reconstruction microscopy (dSTORM)
hiPSC culturing and neuronal differentiation
MEA recording: Axion Maestro Pro
Two photon imaging

Experimental projects:

Nanoscale organization of the synapse
Superresolution microscopy in the analysis of transsynaptic interactions
Interactome of synaptic cell-adhesion molecules
Architectural and signalling dynamics at the inhibitory synapse
Regulation of inhibitory synaptic transmission by wake-active neuromodulators
Measuring spontaneous network activity of human iPSC-derived neurons using micro-electrode arrays
Microglia-mediated synapse engulfment
Membrane trafficking/endo/exocytosis
In vivo imaging of boutons related to behavior
Pharmacological modulation of fear extinction
Mitochondrial dynamics and dendritic calcium imaging
Multimodal profiling of synaptic connectivity through patch-seq

Bordeaux School of Neuroscience, France

Registration

Fee : 3.950 € (includes tuition fee, accommodation and meals)

Applications open from 30 March to 15 May.

Machine Learning/Articfical intelligence course

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
Ilona Kadow – Technical University of Munich, Germany
Ann Kennedy – Northwestern University, USA
Natasha Mhatre – Western University, Canada
Mala Murthy, Princeton University, USA
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
Jake Graving – Max Planck Institute of Animal Behavior, Germany
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
Adrien Jouary, Champalimaud Foundation, Portugal
Dean Rance, Champalimaud Foundation, Portugal
Francisco Romero, Veriff, Spain
Bruno Cruz, NeuroGEARS, UK

Course content

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.

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)

Applications closed on 20th December 2021

Bioenergetics for Brain Function

Course overview

The brain is one of the most energy-consuming organs of the body. Indeed, one could say that the main difference between the brain and a computer is the plug: once plugged, energy is not an issue for the computer, but it is a constant burden for each cell of the brain. As such, energy metabolism in the brain is not just a mere housekeeping and survival service, but it constitutes an essential element directly participating in signaling, computation and behavior.

This course will address the different ways by which energy metabolism participates to high-order brain functions and the underlying cellular, molecular and circuit mechanisms.

Course directors

University of Salamanca,

Spain

NeuroCentre Magendie – INSERM
University of Bordeaux
France

Centre RMSB – CNRS
University of Bordeaux
France

Keynote Speakers

Felipe Barros – Centro de Estudios Cientificos, Valdivia, Chile
Juan Pedro Bolaños – University of Salamanca, Spain
Gilles Bonvento – CNRS, MIRCen, Paris, France
Anne-Karine Bouzier-Sore – CNRS, Centre RMSB, Bordeaux, France
Daniela Cota – INSERM, Neurocentre Magendie, Bordeaux, France
Jaime De Juan-Sanz – Institut du Cerveau, Paris, France
Stephanie Fulton – University of Montreal, Canada
Ralf Jockers – Inserm, Institut Cochin, Paris, France
Giovanni Marsicano – INSERM, Neurocentre Magendie, Bordeaux, France
Aude Panatier – INSERM, Neurocentre Magendie, Bordeaux, France
Luc Pellerin – IRTOMIT, Poitiers, France
Carmen Sandi – EPFL, Lausanne, Switzerland

Instructors

Felipe Baeza-Lehnert – University of Leipzig, Germany + Centro de Estudios Científicos, Valdivia, Chile
Jerome Baufreton – University of Bordeaux, France
Luigi Bellocchio – University of Bordeaux, France
Giovanni Bénard – MRGM Laboratoty, Bordeaux, France
Abel Eraso Pichot – University of Bordeaux, France
Ignacio Fernandez-Moncada – University of Bordeaux, France
Marina Garcia Macia – University of Salamanca, Spain
Anna Hadjichambi – Institute of Hepathology, London, UK
Morgane Jego – University of Bordeaux, France
Daniel Jimenez – University of Salamanca, Spain
Christos Konstantinou – Institute of Hepathology, London, UK
Rodrigo Lerchundi – MIRCen, CNRS, Paris, France
Shingo Nakajima – University of Montreal, Canada
Antonio Pagano-Zottola – Institut de Biochimie Génétique et Cellulaires, Bordeaux, France
Sandrine Pouvreau – University of Bordeaux, France
Rubén Quintana-Cabrera – University of Salamanca, Spain

Course content

Topics & Techniques

The following techniques will be covered during the course:

Cultures of mouse primary astrocytes and neurons.
Bioenergetic profiles in mouse primary astrocytes and neurons using the Seahorse equipment.
Isolation of neurons and astrocytes from adult mice using immunomagnetic approach.
Flow cytometric analysis of mitochondrial membrane potential and mitochondrial ROS production in cultured primary brain cells and in acute immunomagnetically isolated brain cells.
Purification of mitochondrial fraction using differential centrifugation and immunomagnetic mitochondrial isolation approach.
Analysis of the mitochondrial respiratory chain organization using blue native gel electrophoresis from mitochondria isolated from either cultured cells, acutely isolated brain cells and brain-specific regions.
Study of real-time changes in mitochondrial membrane potential using confocal microscopy in cells expressing genetic ATP and ROS probes.
Classical techniques for the determination of common energy metabolites and enzyme activities in including the MRC complexes
Glucose and lactate metabolism in neurons: comparison of [1-13C]glucose and [3-13C]lactate metabolism in neuronal cultures, followed by 13C-NMR spectroscopy.
Glucose and lactate metabolism in astrocytes : comparison of [1-13C]glucose and [3-13C]lactate metabolism in astrocytic cultures, followed by 13C-NMR spectroscopy.
Metabolic changes during brain activity: in vivo functional MRI and MRS during whisker stimulation: visualisation of the barrel cortex and quantification of the lactate increase during brain activity in rat
Impact of metabolism for neuroprotection: longitudinal study (diffusion MRI) to follow brain lesions and regression following different injected substrates (pyruvate, glucose, lactate etc…)
Electrophysiology of hippocampal and cortical slices: comparison of population spike amplitudes and duration of activity with different substrates (glucose, ketone bodies, lactate, glucose+lactate…)
Analysis of mitochondrial respiration in ex vivo brain areas using the Oroboros technology
Mitochondrial calcium analysis by in vitro and in vivo imaging using Fiber photometry
Use of metabolic biosensors by in vitro and in vivo imaging using Fiber photometry
Impact of modulation of brain mitochondrial metabolism on behavior in mouse
Investigation of mitochondrial proteins trafficking using unconventional genetic tools
Impact of brain mitochondrial activity on whole-body energy balance.

Bordeaux School of Neuroscience, France

Registration

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

Application closed on 1 March 2021

COVID-19 update: in case the Bioenergetics for Brain Function 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

Ageing cognition

Course overview

The normal aging process is associated with reduced performance on cognitive tasks that require one to quickly process or transform information to make a decision, including measures of speed of processing, executive cognitive function, working and relational memories. Structural and functional alterations in the brain correlate with these age-related cognitive changes, such as loss of synapses, and dysfunction of neuronal networks. It is crucial to develop new approaches that consider the whole neuroanatomical, endocrine, immunological, vascular and cellular changes impacting on cognition.

This 3-week course will cover the fundamentals of cognitive aging -including inter-individual differences, cognitive and brain reserve and risk factors- and highlight the newest functional imaging methods to study human brain function. The Faculty will share the state-of-the-art molecular, optical, computational, electrophysiological, behavioral and epidemiological approaches available for studying the aging brain in diverse model systems.

Students will learn the potential and limitations of these methods, through practical experience in a combination of lectures addressing aging in both humans and animal models and hands-on-projects. They will acquire sufficient practical experience to model, design and interpret experiments and brainstorm on novel technologies and hypotheses to explore the aging of the brain using more integrative and creative approaches.

Course directors

Neurobiology of Ageing & Disease
iMM Lisboa
Portugal

The Rotman Research Institute, Baycrest
& University Toronto
Canada

Neurocentre Magendie
INSERM U 1215 – University of Bordeaux
France

Keynote Speakers

Hélène Amieva – Bordeaux population Health Center, France
Adam Antebi – Max Planck Institute for Biology of Ageing, Germany
Carol Barnes – University of Arizona, USA
Luc Buée – University of Lille, France
Gwenaëlle Catheline – INCIA, Bordeaux, France
Maria Llorens-Martin – Universidad Autonoma Madrid, Spain
Aline Marighetto – Neurocentre Magendie, Bordeaux, France
Lars Nyberg – Umeå University, Sweden
Laure Rondi-Reig – Sorbonne Université, Paris, France
Yaakov Stern – Columbia University, USA

Instructors

Claudia Almeida – CEDOC, UNL, Lisbon, Portugal
Nicolas Blin – Neurocentre Magendie, Bordeaux, France
Vanessa Charrier – Neurocentre Magendie, Bordeaux, France
Joana Coelho – IMM, Lisbon, Portugal
Miguel De la Flor Garcia – Universidad Autónoma de Madrid , Spain
Nicole Etchamendy – Neurocentre Magendie, Bordeaux, France
David Koss – University of New castle, UK
Nuno Morais – IMM, Lisbon, Portugal
Paula Pousinha – IPMC, Nice, France
Miguel Remondes – IMM, Lisbon, Portugal
Jenny Rieck – Baycrest & Univ. Toronto,
Azza Sellami – Neurocentre Magendie, Bordeaux, France
Jean Vincent – Sorbonne Université, Paris, France

Course content

Projects

The following projects are confirmed so far:

Project 1: Is lysosome dysfunction a mechanism of synapse aging?
Project 2: Physiological signatures of cognitive aging
Project 3: Recording neuronal activity on hippocampal slices from aged mice
Project 4: Inter-individual variability of declarative memory decline in healthy aging: a brain network analysis in humans based on a virtual radial-maze task.
Project 7: Immunohistochemistry on brain tissue obtained from aged humans and rodents
Project 8: Unveiling the transcriptomic signatures of human brain ageing
Project 9: In vivo optogenetic to manipulate adult neurogenesis
Project 10: Inducing Neurons (iNs) from human fibroblasts to preserved the cellular synaptic ageing-signature
Project 11 and 12: Inter-individual variability of declarative memory decline in healthy aging: a brain network analysis in mice on a radial-maze task.
Project 13 and 14: Quantification of cortical DNA damage in age-associated neurodegenerative diseases.

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 21 June 2021

Advanced imaging techniques for cellular and systems neuroscience (rescheduled)

Course overview

Rapid advances in live imaging of targeted cellular morphologies and functions underpin the emerging revolution in our understanding of synapses, circuits, and behaviour. This Cajal course will assemble, as international faculty, leading experts in developing and exploiting cutting-edge imaging techniques that have been propelling such advances. How to combine genetically encoded fluorescence labelling with behavioural designs, micro-circuit monitoring, or single-molecule tracking, how to avoid pitfalls of having false-positive observations and inherent noise, how to best analyse your multi-dimensional data will be, among others, the recurrent subjects of the course. An intense programme of lectures and seminars will be combined with supervised, hands-on practical training modules and group assignments using experimental setups and tools provided by the world-leading research environment of the Bordeaux School of Neuroscience.

Course partner

Course directors

UCL Queen Square
Institute of Neurology
United Kingdom

Neuronal circuits and behaviour
MPI for Metabolism Research
Germany

CNRS, IINS UMR 5297
University of Bordeaux
France

Keynote speakers

Thomas Blanpied – University of Maryland School of Medicine, USA
Daniel Choquet – IINS, University of Bordeaux, France
Rosa Cossart – CNRS, Inserm – INMED, Aix-Marseille Université, France
Olga Garaschuk – University of Tuebingen, Germany
Laurent Groc – IINS, University of Bordeaux, France
Michael Hausser – University College London, UK
Christian Henneberger – University of Bonn, Germany
Christophe Leterrier – INP CNRS-AMU UMR 7051,
Aix-Marseille Université, France
Valentin Nagerl – University of Bordeaux, France
Tim Ryan – Weill Cornell Medical College, USA
Ilaria Testa – KTH Royal Institute of Technology, Sweden
Andrea Volterra – University of Lausanne, Switzerland
Kirill Volynski – University College London, UK

Instructors

Stephane Bancelin – University of Bordeaux, France
Francisco de los Santos – MPI Cologne, Germany
Yulia Dembitskaya – University of Bordeaux, France
Ani Jose – IINS, University of Bordeaux, France
Olga Kopach – University College London, UK
Philipe R. F. Mendonça – University College London, UK
Dragomir Milovanovic – Charité University Clinic, Berlin, Germany
Christian Hoffmann – Charité University Clinic, Berlin, Germany
Jakob Rentsch– Charité University Clinic, Berlin, Germany
Petr Unichenko – University College London, UK
Olga Tiurikova – University College London, UK
Hanna Van Den Munkhof – MPI Cologne, Germany
Kaiyu Zheng – University College London, UK
Olivier Nicole – IINS, University of Bordeaux, France
Julien Dupuis – IINS, University of Bordeaux, France
Xuesi Zhou – IINS, University of Bordeaux, France

Course content

Topics & Techniques

Students will learn:

– Super-resolved organisation of the synaptic cleft.

– Nanoscale monitoring and probing of NMDA receptors.

– Super-Resolution probing of the axonal initial segment.

– RESOLFT nanoscopy.

– Super-Resolution Imaging of Brain Nano-Structure In Vivo.

– Nanoscale imaging and manipulation of synapse function to study the brain.

– Monitoring molecular machinery of synaptic plasticity.

– Probing the molecular basis of synaptic transmission.

– Optical sensors for neurotransmitters.

– Multiplexed imaging of presynaptic function.

– Ca2+ regulation of synaptic vesicle fusion in central synapses.

– Optical monitoring of volume transmission.

– Studying astrocytes in synaptic function with 1D-to-3D two-photon Ca2+ imaging.

Projects

For more information on projects download the “Programme info”

Project 1: “Imaging prefrontal cortex neurons encoding social information”.
Project 2: “Imaging hippocampal place cells in freely moving animals”.
Project 3: “FRET imaging of NMDA receptor co-agonists dynamics”.
Project 4: “Assessing the mechanosensitive properties of the membrane periodic skeleton
(MPS) in neurons”.
Project 5: “RESOLFT nanoscopy to study the fast reorganization of dendritic spines”.
Project 6: “Single synapse imaging of glutamate release and pre-synaptic Ca2+ for study of
pre-synaptic receptor function and short-term synaptic plasticity”.
Project 7: “Quantitative intracellular calcium measurements using fluorescent lifetime
imaging microscopy”.
Project 8: “A viral strategy for targeting and manipulating principal neurons: probing the
glutamatergic synapse function at multi-synapse imaging approach”.
Project 9: “Probing of astroglial Ca2+ dynamics in organised brain tissue through
fluorescent intensity and lifetime measurements”.
Project 10: “Multicolor multiphoton imaging of single synaptic release sites in vivo”.
Project 11: “High spatial-temporal imaging of a heterogeneous population of synapses in
neuronal cultures using the iGluSnFR probe”.
Project 12: “Super-resolution shadow imaging in the mouse brain”.
Project 13: “Dual color single particle tracking to study membrane receptors dynamics”.
Project 14: “Imaging tripartite synapses using super-resolution microscopy”.
Project 15: “Nanoscale organization and dynamics of synapsin condensates”

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

Course overview

Course partner

Course directors

Keynote Speakers

Instructors

Course content

Techniques

Projects

Bordeaux School of Neuroscience, France

Registration

Course sponsors

Course overview

Course directors

Keynote Speakers

Instructors

Course content

Champalimaud Centre for the Unknown, Portugal

Registration

Sponsors

Course overview

Course directors

Keynote Speakers

Instructors

Course content

Bordeaux School of Neuroscience, France

Registration

Course overview

Course directors

Keynote Speakers

Instructors

Course content

Programme

Datasets

Techniques

Champalimaud Centre for the Unknown, Portugal

Registration

Course overview

Course directors

Keynote Speakers & Instructors

Keynote Speakers

Instructors

Course content

Techniques

Projects

Bordeaux School of Neuroscience, France

Registration

Course overview

Course directors

Keynote Speakers

Instructors

Course content

Topics

Course format

Techniques

Experimental projects:

Bordeaux School of Neuroscience, France

Registration

Course overview

Course directors

Keynote speakers

Instructors

Course content

Projects

Champalimaud Centre for the Unknown, Portugal

Registration

Course overview

Course directors

Keynote Speakers

Instructors

Course content

Topics & Techniques

Bordeaux School of Neuroscience, France

Registration

Course sponsors

Course overview

Course directors

Luísa V. Lopes

Cheryl L. Grady

Nora Abrous

Keynote Speakers