Question
How do collective neuronal dynamics relate to function?

Challenges
Most brain functions are supported by the activity of neuronal ensembles distributed across brain regions. Understanding the structure of these representations, how they are learned, and how they lead to behavior is one of the main challenges facing neuroscientists. In the recent years, technology, in particular imaging, high throughput electrophysiology and transcriptomics, have revolutionized our way to analyze structure and function in the brain and how it relates to behavior. Neuroscience is flooded by a deluge of complex data describing a system that is, itself, already complex. Never has the need been greater for theoretical models and data analysis. Future progress requires developing the ability to extract meaningful knowledge from these data through analyses and modeling.

Type of data
Activity dynamics from multiple neurons in awake behaving rodents (prefrontal cortex, hippocampus and striatum):

- Electrophysiological signals
- Calcium fluorescence movies

Methods
Two-photon and endoscopic calcium imaging, Image analysis, signal processing, functional connectivity, clustering

Type of data

Fluorescence images of single-cell anatomy and whole brain distribution

Multivariate morphometric neuronal

Single-cell electrophysiological recordings

Question

What is a neuronal cell-type?

Methods

Electrophysiology and cell labelling

Light-sheet imaging

Image analysis

Signal processing

Data mining and clustering

Question
How do B lymphocytes progress through multiple functional states to gain the ability to produce high affinity antibodies?

Challenges
Antibodies are lifesaving biomolecules – major effectors of vaccines efficacy and popular therapeutics for cancer treatment. In natural immunity, highly potent antibodies are produced by the descendants of a single antigen-specific B cell after a process of cellular and molecular maturation. In the aim of designing new therapies for challenging infections and cancers, understanding the distinct steps of B lymphocyte maturation is a major focus of immunology research.
Novel analytical methods enable the parallel analysis of antibody gene sequences and genome-wide gene expression in hundreds to thousands of single B cells, opening new avenues to dissect the mechanisms of B cell maturation. Integrating and analyzing the massive amount of data produced in those experiments will be an exciting challenge in the coming years.

Type of data
For thousands of B cells, sorted from healthy human lymphoid organs, human tumors, and mouse lymphoid organs after vaccination:

- Gene expression data (single-cell RNAseq)
- Cell surface phenotype and size/aspect characteristics (flow cytometry)
- Antibody gene sequence (computed from single-cell RNAseq)

Methods
Fluorescence-activated Cell Sorting (FACS), single-cell RNA sequencing, sequence alignment and mapping on genome, sequence reconstruction from short read RNAseq, dimensionality reduction and clustering, pseudotime analysis, cell – cell interaction networks, gene – gene interaction networks.

Question

How to image living cells and tissues in 3D, with sub-cellular resolution?

Challenges

Many systems in biology involve an assembly of cells that are arranged spatially and the interaction between these cells to achieve a variety of functions. Therefore modern imaging tools need to address both the architecture and the function of biological systems. This optical imaging module will concentrate on multiphoton imaging techniques that are able to image a variety of fluorophores but also endogenous molecular structure and chemical bonds such as collagen, and lipids. Interestingly these techniques use ultra-short laser pulses whose interaction with biological media are localized in space such that 3D resolution is possible. The module will concentrate on multiphoton imaging techniques (2photon, harmonic generations and coherent Raman) from concepts to technical implementations and applications in the field of neurosciences, immunology and development biology. Hands-on of running setup will be organized.

Type of data

2photon, harmonic generations (SHG, THG) and coherent Raman (CARS, SRS) images coming from cell and tissues imaging.

Methods

2photon, harmonic generations (SHG, THG) and coherent Raman (CARS, SRS)

Question

Neuronal development relies on both a predetermined genetic program and sensory informations from the external environment. What are the mechanisms that link these 2 modalities and how do they interact to control morphology, survival and ultimately function of developing neurons?

Challenges

Neuronal development is controlled by intricate interactions between a genetic program and informations from sensory environment. What are the rules and the mechanism controlling the interaction of these two modalities is not clear. The rodent olfactory system represents a powerful model to approach these questions. It allows us to use genetic manipulations in combination with chronic in vivo imaging and olfactory behavioral paradigm to obtain unprecedented new sets of complex data on neuronal development. Statistical analysis and computational modeling are required to fully understand these results and to establish new hypothesis and predictions on the complex mechanisms that control neuronal development.

Type of data

In vivo imaging of developing olfactory bulb neurons in anesthetized and awake mice in various sensory environments (enriched, deprived, during learning):

• Activity dynamics (calcium imaging)
• Morphological imaging
• Whole brain imaging

Methods

Two-photon in vivo chronic structural imaging; Two-photon in vivo chronic calcium imaging; Light-sheet imaging; Image analysis; Signal processing; modeling