Jordi Soriano

Model-free reconstruction of excitatory neuronal connectivity from calcium imaging signals.

A systematic assessment of global neural network connectivity through direct electrophysiological assays has remained technically infeasible, even in simpler systems like dissociated neuronal cultures. We introduce an improved algorithmic approach based on Transfer Entropy to reconstruct structural connectivity from network activity monitored through calcium imaging. We focus in this study on the inference of excitatory synaptic links. Based on information theory, our method requires no prior assumptions on the statistics of neuronal firing and neuronal connections. The performance of our algorithm is benchmarked on surrogate time series of calcium fluorescence generated by the simulated dynamics of a network with known ground-truth topology. We find that the functional network topology revealed by Transfer Entropy depends qualitatively on the time-dependent dynamic state of the network (bursting or non-bursting). Thus by conditioning with respect to the global mean activity, we improve the performance of our method. This allows us to focus the analysis to specific dynamical regimes of the network in which the inferred functional connectivity is shaped by monosynaptic excitatory connections, rather than by collective synchrony. Our method can discriminate between actual causal influences between neurons and spurious non-causal correlations due to light scattering artifacts, which inherently affect the quality of fluorescence imaging. Compared to other reconstruction strategies such as cross-correlation or Granger Causality methods, our method based on improved Transfer Entropy is remarkably more accurate. In particular, it provides a good estimation of the excitatory network clustering coefficient, allowing for discrimination between weakly and strongly clustered topologies. Finally, we demonstrate the applicability of our method to analyses of real recordings of in vitro disinhibited cortical cultures where we suggest that excitatory connections are characterized by an elevated level of clustering compared to a random graph (although not extreme) and can be markedly non-local.

Development of input connections in neural cultures

We introduce an approach for the quantitative assessment of the connectivity in neuronal cultures, based on the statistical mechanics of percolation on a graph. This allows us to monitor the development of the culture and to see the emergence of connectivity in the network. The culture becomes fully connected at a time equivalent to the expected time of birth. The spontaneous bursting activity that characterizes cultures develops in parallel with the connectivity. The average number of inputs per neuron can be quantitatively determined in units of m0, the number of activated inputs needed to excite the neuron. For m0 ≃ 15 we find that hippocampal neurons have on average ≈60–120 inputs, whereas cortical neurons have ≈75–150, depending on neuronal density. The ratio of excitatory to inhibitory neurons is determined by using the GABAA antagonist bicuculine. This ratio changes during development and reaches the final value at day 7–8, coinciding with the expected time of the GABA switch. For hippocampal cultures the inhibitory cells comprise ≈30% of the neurons in the culture whereas for cortical cultures they are ≈20%. Such detailed global information on the connectivity of networks in neuronal cultures is at present inaccessible by any electrophysiological or other technique.

Aberrant epigenome in iPSC‐derived dopaminergic neurons from Parkinson's disease patients

The epigenomic landscape of Parkinsons disease (PD) remains unknown. We performed a genomewide DNA methylation and a transcriptome studies in induced pluripotent stem cell (iPSC)‐derived dopaminergic neurons (DAn) generated by cell reprogramming of somatic skin cells from patients with monogenic LRRK2‐associated PD (L2PD) or sporadic PD (sPD), and healthy subjects. We observed extensive DNA methylation changes in PD DAn, and of RNA expression, which were common in L2PD and sPD. No significant methylation differences were present in parental skin cells, undifferentiated iPSCs nor iPSC‐derived neural cultures not‐enriched‐in‐DAn. These findings suggest the presence of molecular defects in PD somatic cells which manifest only upon differentiation into the DAn cells targeted in PD. The methylation profile from PD DAn, but not from controls, resembled that of neural cultures not‐enriched‐in‐DAn indicating a failure to fully acquire the epigenetic identity own to healthy DAn in PD. The PD‐associated hypermethylation was prominent in gene regulatory regions such as enhancers and was related to the RNA and/or protein downregulation of a network of transcription factors relevant to PD (FOXA1, NR3C1, HNF4A, and FOSL2). Using a patient‐specific iPSC‐based DAn model, our study provides the first evidence that epigenetic deregulation is associated with monogenic and sporadic PD.

Transfer Entropy Reconstruction and Labeling of Neuronal Connections from Simulated Calcium Imaging

Neuronal dynamics are fundamentally constrained by the underlying structural network architecture, yet much of the details of this synaptic connectivity are still unknown even in neuronal cultures in vitro. Here we extend a previous approach based on information theory, the Generalized Transfer Entropy, to the reconstruction of connectivity of simulated neuronal networks of both excitatory and inhibitory neurons. We show that, due to the model-free nature of the developed measure, both kinds of connections can be reliably inferred if the average firing rate between synchronous burst events exceeds a small minimum frequency. Furthermore, we suggest, based on systematic simulations, that even lower spontaneous inter-burst rates could be raised to meet the requirements of our reconstruction algorithm by applying a weak spatially homogeneous stimulation to the entire network. By combining multiple recordings of the same in silico network before and after pharmacologically blocking inhibitory synaptic transmission, we show then how it becomes possible to infer with high confidence the excitatory or inhibitory nature of each individual neuron.

Radial displacement of a fluid annulus in a rotating Hele-Shaw cell

The radial displacement of a fluid annulus in a rotating circular Hele–Shaw cell has been investigated experimentally. It has been found that the flow depends sensitively on the wetting conditions at the outer interface. Displacements in a prewet cell are well described by Darcy’s law in a wide range of experimental parameters, with little influence of capillary effects. In a dry cell, however, a more careful analysis of the interface motion is required; the interplay between a gradual loss of fluid at the inner interface, and the dependence of capillary forces at the outer interface on interfacial velocity and dynamic contact angle, result in a constant velocity for the interfaces. The experimental results in this case correlate in the form of an empirical scaling relation between the capillary number Ca and a dimensionless group, related to the ratio of centrifugal to capillary forces, which spans about three orders of magnitude in both quantities. Finally, the relative thickness of the coating film lef...

Interfacial instabilities of a fluid annulus in a rotating Hele–Shaw cell

We have studied the interfacial instabilities experienced by a liquid annulus as it moves radially in a circular Hele–Shaw cell rotating with angular velocity Ω. The instability of the leading interface (oil displacing air) is driven by the density difference in the presence of centrifugal forcing, while the instability of the trailing interface (air displacing oil) is driven by the large viscosity contrast. A linear stability analysis shows that the stability of the two interfaces is coupled through the pressure field already at a linear level. We have performed experiments in a dry cell and in a cell coated with a thin fluid layer on each plate, and found that the stability depends substantially on the wetting conditions at the leading interface. Our experimental results of the number of fingers resulting from the instability compare well with the predictions obtained through a numerical integration of the coupled equations derived from a linear stability analysis. Deep in the nonlinear regime we observ...

Identification of neuronal network properties from the spectral analysis of calcium imaging signals in neuronal cultures

Neuronal networks in vitro are prominent systems to study the development of connections in living neuronal networks and the interplay between connectivity, activity and function. These cultured networks show a rich spontaneous activity that evolves concurrently with the connectivity of the underlying network. In this work we monitor the development of neuronal cultures, and record their activity using calcium fluorescence imaging. We use spectral analysis to characterize global dynamical and structural traits of the neuronal cultures. We first observe that the power spectrum can be used as a signature of the state of the network, for instance when inhibition is active or silent, as well as a measure of the networks connectivity strength. Second, the power spectrum identifies prominent developmental changes in the network such as GABAA switch. And third, the analysis of the spatial distribution of the spectral density, in experiments with a controlled disintegration of the network through CNQX, an AMPA-glutamate receptor antagonist in excitatory neurons, reveals the existence of communities of strongly connected, highly active neurons that display synchronous oscillations. Our work illustrates the interest of spectral analysis for the study of in vitro networks, and its potential use as a network-state indicator, for instance to compare healthy and diseased neuronal networks.

An Osmoregulatory Basis for Shape Oscillations in Regenerating Hydra

The freshwater polyp Hydra has considerable regeneration capabilities. A small fragment of tissue excised from an adult animal is sufficient to regenerate an entire Hydra in the course of a few days. During the initial stages of the regeneration process, the tissue forms a hollow sphere. Then the sphere exhibits shape oscillations in the form of repeated cycles of swelling and collapse. We propose a biophysical model for the swelling mechanism. Our model takes the osmotic pressure difference between Hydras inner and outer media and the elastic forces of the Hydra shell into account. We validate the model by a comprehensive experimental study including variations in initial medium concentrations, Hydra sphere sizes and temperatures. Numerical simulations of the model provide values for the swelling rates that are in agreement with the ones measured experimentally. Based on our results we argue that the shape oscillations are a consequence of Hydras osmoregulation.

Anomalous roughening of viscous fluid fronts in spontaneous imbibition.

We report experiments on spontaneous imbibition of a viscous fluid by a model porous medium in the absence of gravity. The average position of the interface satisfies Washburns law. Scaling of the interface fluctuations provides a dynamic exponent z \simeq 3, indicative of global dynamics driven by capillary forces. The complete set of exponents clearly shows that interfaces are not self-affine, exhibiting distinct local and global scaling, both for time (b=0.64\pm 0.02, b* =0.33 \pm 0.03) and space (a=1.94 \pm 0.20, a_loc=0.94 \pm 0.10). These values are compatible with an intrinsic anomalous scaling scenario.

Magnetite-Amyloid- β deteriorates activity and functional organization in an in vitro model for Alzheimer’s disease

The understanding of the key mechanisms behind human brain deterioration in Alzheimer’ disease (AD) is a highly active field of research. The most widespread hypothesis considers a cascade of events initiated by amyloid-β peptide fibrils that ultimately lead to the formation of the lethal amyloid plaques. Recent studies have shown that other agents, in particular magnetite, can also play a pivotal role. To shed light on the action of magnetite and amyloid-β in the deterioration of neuronal circuits, we investigated their capacity to alter spontaneous activity patterns in cultured neuronal networks. Using a versatile experimental platform that allows the parallel monitoring of several cultures, the activity in controls was compared with the one in cultures dosed with magnetite, amyloid-β and magnetite-amyloid-β complex. A prominent degradation in spontaneous activity was observed solely when amyloid-β and magnetite acted together. Our work suggests that magnetite nanoparticles have a more prominent role in AD than previously thought, and may bring new insights in the understanding of the damaging action of magnetite-amyloid-β complex. Our experimental system also offers new interesting perspectives to explore key biochemical players in neurological disorders through a controlled, model system manner.