Songbird organotypic culture as an in vitro model for interrogating sparse sequencing networks

Sparse sequences of neuronal activity are fundamental features of neural circuit computation; however, the underlying homeostatic mechanisms remain poorly understood. To approach these questions, we have developed a method for cellular-resolution imaging in organotypic cultures of the adult zebra finch brain, including portions of the intact song circuit. These in vitro networks can survive for weeks, and display mature neuron morphologies. Neurons within the organotypic slices exhibit a diversity of spontaneous and pharmacologically induced activity that can be easily monitored using the genetically encoded calcium indicator GCaMP6. In this study, we primarily focus on the classic song sequence generator HVC and the surrounding areas. We describe proof of concept experiments including physiological, optical, and pharmacological manipulation of these exposed networks. This method may allow the cellular rules underlying sparse, stereotyped neural sequencing to be examined with new degrees of experimental control

Aberrant Calcium Signaling in Astrocytes Inhibits Neuronal Excitability in a Human Down Syndrome Stem Cell Model.

Down syndrome (DS) is a genetic disorder that causes cognitive impairment. The staggering effects associated with an extra copy of human chromosome 21 (HSA21) complicates mechanistic understanding of DS pathophysiology. We examined the neuron-astrocyte interplay in a fully recapitulated HSA21 trisomy cellular model differentiated from DS-patient-derived induced pluripotent stem cells (iPSCs). By combining calcium imaging with genetic approaches, we discovered the functional defects of DS astroglia and their effects on neuronal excitability. Compared with control isogenic astroglia, DS astroglia exhibited more-frequent spontaneous calcium fluctuations, which reduced the excitability of co-cultured neurons. Furthermore, suppressed neuronal activity could be rescued by abolishing astrocytic spontaneous calcium activity either chemically by blocking adenosine-mediated signaling or genetically by knockdown of inositol triphosphate (IP3) receptors or S100B, a calcium binding protein coded on HSA21. Our results suggest a mechanism by which DS alters the function of astrocytes, which subsequently disturbs neuronal excitability

Contribution of GABAergic Interneurons to the Development of Spontaneous Activity Patterns in Cultured Neocortical Networks

Periodic synchronized events are a hallmark feature of developing neuronal networks and are assumed to be crucial for the maturation of the neuronal circuitry. In the developing neocortex, the early network oscillations coincide with an excitatory action of the neurotransmitter gamma-aminobutyric acid (GABA). A relationship between the emerging inhibitory action of GABA and the gradual disappearance of early synchronized network activity has been previously suggested. Therefore we investigate the interplay between the action of GABA and spontaneous activity in cultured networks of the lateral or dorsal embryonic rat neocortex, which show considerable difference in the content of GABAergic neurons. Here we present the results of long-term monitoring of spontaneous electrical activity of cultured networks growing on microelectrode arrays and the time course of changes in GABA action using calcium imaging. All cultures studied displayed stereotyped synchronized burst events at the end of the first week in vitro. As the GABAA depolarizing action decreases, naturally or after bumetanide treatment, network activity in lateral cortex cultures changed from stereotypic bursting to more clustered and asynchronous activity patterns. Dorsal cortex cultures and cultures lacking GABAA-receptor mediated synaptic transmission, retained an immature synchronous firing pattern, but developed prominent intraburst oscillations (∼3–10 Hz). Large, mostly parvalbumin positive, GABAergic neurons dominate the GABAergic population in lateral cortex cultures. These large interneurons were virtually absent in dorsal cortex cultures. Based on these results, we suggest that the richly interconnected large GABAergic neurons contribute to desynchronize and temporally differentiate the spontaneous activity of cultured cortical networks

Inhibition of de novo ceramide biosynthesis affects aging phenotype in an in vitro model of neuronal senescence.

Although aging is considered to be an unavoidable event, recent experimental evidence suggests that the process can be counteracted. Intracellular calcium (Ca2+i) dyshomeostasis, mitochondrial dysfunction, oxidative stress, and lipid dysregulation are critical factors that contribute to senescence-related processes. Ceramides, a pleiotropic class of sphingolipids, are important mediators of cellular senescence, but their role in neuronal aging is still largely unexplored. In this study, we investigated the effects of L-cycloserine (L-CS), an inhibitor of thede novoceramide biosynthesis, on the aging phenotype of cortical neurons cultured for 22 days, a setting employed as anin vitromodel of senescence. Our findings indicate that, compared to control cultures, 'aged' neurons display dysregulation of [Ca2+]ilevels, mitochondrial dysfunction, increased generation of reactive oxygen species (ROS), altered synaptic activity as well as the activation of neuronal death-related molecules. Treatment with L-CS positively affected the senescent phenotype, a result associated with recovery of neuronal [Ca2+]isignaling and reduction of mitochondrial dysfunction and ROS generation. The results suggest that thede novoceramide biosynthesis represents a critical intermediate in the molecular and functional cascade leading to neuronal senescence and identify ceramide biosynthesis inhibitors as promising pharmacological tools to decrease age-related neuronal dysfunctions

The spontaneous activity of organotypic and dissociated networks

In the absence of external stimuli, the nervous system exhibits a spontaneous electrical activity whose functions are not fully understood, and that represents the background noise of brain operations. In vitro models have long represented a simple and useful tool for studying the basic properties of neurons and networks. This study provides a detailed characterization of spontaneous activity of neuronal networks in different in vitro models. In particular, it clarifies the role of the extra-cellular environment and of the intrinsic architecture in shaping the spontaneous activity of networks by means of calcium imaging techniques. The results presented within this study come from three experimental works, each one addressing a particular feature of the network model: \u2022 Chemical composition of the extra-cellular environment: a comparison of dissociated hippocampal cultures grown in three different culturing media revealed that the use of an astrocyte-conditioned medium improves significantly the frequency and synchronization of neuronal signaling. \u2022 Mechanical and topographical properties of the extra-cellular environment: the design of a hybrid micro-nano substrate for dissociated hippocampal cultures revealed that nano-scaled patterns provide an improved artificial extra-cellular matrix for obtaining neuronal networks with a frequent spontaneous signaling. \u2022 Network architecture: synchronized events called Global Up states - involving the totality of neurons in the network - are observed in both organotypic and dissociated neurons; the duration of Global Up states increases by increasing the complexity of the network, while their frequency decreases. Simulations with simplified models of single- and multilayered networks confirm the experimental data. Taken together, these results show that the spontaneous synchronous activity of neurons is a result of their intrinsic biophysical properties, arising also after disruption of the original network architecture. However, dissociated neurons show different levels of synchrony depending on the chemical and topographical composition of the surrounding artificial extra-cellular matrix. Moreover, the specific architecture of the network and its single- or multilayered composition has an influence on the frequency and duration of spontaneous events, suggesting a potential explanation for the diversity of oscillatory rhythms observed in the brain

Sustained synchronized neuronal network activity in a human astrocyte co-culture system

Impaired neuronal network function is a hallmark of neurodevelopmental and neurodegenerative disorders such as autism, schizophrenia, and Alzheimer's disease and is typically studied using genetically modified cellular and animal models. Weak predictive capacity and poor translational value of these models urge for better human derived in vitro models. The implementation of human induced pluripotent stem cells (hiPSCs) allows studying pathologies in differentiated disease-relevant and patient-derived neuronal cells. However, the differentiation process and growth conditions of hiPSC-derived neurons are non-trivial. In order to study neuronal network formation and (mal) function in a fully humanized system, we have established an in vitro co-culture model of hiPSC-derived cortical neurons and human primary astrocytes that recapitulates neuronal network synchronization and connectivity within three to four weeks after final plating. Live cell calcium imaging, electrophysiology and high content image analyses revealed an increased maturation of network functionality and synchronicity over time for co-cultures compared to neuronal monocultures. The cells express GABAergic and glutamatergic markers and respond to inhibitors of both neurotransmitter pathways in a functional assay. The combination of this co-culture model with quantitative imaging of network morphofunction is amenable to high throughput screening for lead discovery and drug optimization for neurological diseases

Tetramethylenedisulfotetramine alters Ca²⁺ dynamics in cultured hippocampal neurons: mitigation by NMDA receptor blockade and GABA(A) receptor-positive modulation.

Tetramethylenedisulfotetramine (TETS) is a potent convulsant that is considered a chemical threat agent. We characterized TETS as an activator of spontaneous Ca²⁺ oscillations and electrical burst discharges in mouse hippocampal neuronal cultures at 13-17 days in vitro using FLIPR Fluo-4 fluorescence measurements and extracellular microelectrode array recording. Acute exposure to TETS (≥ 2 µM) reversibly altered the pattern of spontaneous neuronal discharges, producing clustered burst firing and an overall increase in discharge frequency. TETS also dramatically affected Ca²⁺ dynamics causing an immediate but transient elevation of neuronal intracellular Ca²⁺ followed by decreased frequency of Ca²⁺ oscillations but greater peak amplitude. The effect on Ca²⁺ dynamics was similar to that elicited by picrotoxin and bicuculline, supporting the view that TETS acts by inhibiting type A gamma-aminobutyric acid (GABA(A)) receptor function. The effect of TETS on Ca²⁺ dynamics requires activation of N-methyl-D-aspartic acid (NMDA) receptors, because the changes induced by TETS were prevented by MK-801 block of NMDA receptors, but not nifedipine block of L-type Ca²⁺ channels. Pretreatment with the GABA(A) receptor-positive modulators diazepam and allopregnanolone partially mitigated TETS-induced changes in Ca²⁺ dynamics. Moreover, low, minimally effective concentrations of diazepam (0.1 µM) and allopregnanolone (0.1 µM), when administered together, were highly effective in suppressing TETS-induced alterations in Ca²⁺ dynamics, suggesting that the combination of positive modulators of synaptic and extrasynaptic GABA(A) receptors may have therapeutic potential. These rapid throughput in vitro assays may assist in the identification of single agents or combinations that have utility in the treatment of TETS intoxication

Model-free reconstruction of neuronal network connectivity from calcium imaging signals

A systematic assessment of global neural network connectivity through direct electrophysiological assays has remained technically unfeasible even in dissociated neuronal cultures. We introduce an improved algorithmic approach based on Transfer Entropy to reconstruct approximations to network structural connectivities from network activity monitored through calcium fluorescence imaging. 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 effective network topology revealed by Transfer Entropy depends qualitatively on the time-dependent dynamic state of the network (e.g., bursting or non-bursting). We thus demonstrate how conditioning with respect to the global mean activity improves the performance of our method. [...] 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 reconstruction of the network clustering coefficient, allowing to discriminate between weakly or strongly clustered topologies, whereas on the other hand an approach based on cross-correlations would invariantly detect artificially high levels of clustering. Finally, we present the applicability of our method to real recordings of in vitro cortical cultures. We demonstrate that these networks are characterized by an elevated level of clustering compared to a random graph (although not extreme) and by a markedly non-local connectivity.Comment: 54 pages, 8 figures (+9 supplementary figures), 1 table; submitted for publicatio

Construction of carbon-based three-dimensional neural scaffolds and their structural regulation

Motivation The brain is formed by an intricate assembly of cellular networks, where neurons are embedded in an extracellular matrix (ECM) consisting of an intricate three-dimensional (3D) mesh of proteins that provides complex chemical, electrical and mechanical signalling.1 Given this complexity as well as the limitations of in vivo studies,2 it is important to develop in vitro models able to recapitulate the brain connectivity at various levels and ultimately, provide a mimic of the human brain suitable for preclinical applications.3 By reproducing cell to cell and cell to ECM interactions so to mimic the in vivo microenvironment, 3D tissue engineering promotes more physiological responses than conventional 2D cultures.4 Toward this goal, several 3D supporting materials or scaffolds have been developed, tested and applied.5 Among them, emerging carbon-based materials, such as carbon nanotubes (CNTs) 6, graphene oxide 7 and graphene foam (GF) 8 have high mechanical stability, high porosity and dense interconnectivity, providing a 3D microenvironment beneficial for cell growth and interaction.9 My Work In my Ph.D., I aimed to construct 3D neural scaffolds based on carbon materials especially graphene and carbon nanotubes (CNTs) and explore the regulation of these scaffolds for specific application in neural cultures. To achieve these goals, I combined chemical vapor deposition (CVD) and nano-fabrication for the preparation of different kinds of scaffolds and then used these scaffolds for the neural cultures. In the characterization of neural culture part, I mainly used optical imaging methods, particularly immunochemistry and calcium imaging, to investigate the neuronal network morphology and electrical dynamics of reconstructed 3D primary cultures from rats. These are my main results: 1) By using Fe nanoparticles confined to the interlamination of graphite as catalyst, we have obtained a fully 3D interconnected CNT web through the pores of graphene foam (GCNT web) by in situ chemical vapor deposition. This 3D GCNT web has a thickness up to 1.5 mm and a completely geometric, mechanical and electrical interconnectivity. Dissociated cortical cells cultured inside the GCNT web form a functional 3D cortex-like network exhibiting a spontaneous electrical activity that is closer to what is observed in vivo. Moreover, we have explored the application of this functional 3D cortex-like network: 2) By co-culturing and fluorescently labelling glioma and healthy cortical cells with different colours, a new in vitro model is obtained to investigate malignant glioma infiltration. This model allows reconstruction of the 3D trajectories and velocity distribution of individual infiltrating glioma with an unprecedented precision. The model is cost-effective and allows a quantitative and rigorous screening of anti-cancer drugs. 3) We have fabricated a 3D free-standing ordered graphene (3D-OG) network with the pore size of 20 \u3bcm, the skeleton width of 20 \u3bcm and an exact 90\ub0 orientation angle between the building blocks. Extensive interconnectivity of graphene sheets allows 3D-OG scaffolds to be free-standing and to be easily manipulated. When primary cortical cells are cultured on 3D-OG scaffolds, the cells form well-defined 3D connections with a cellular density similar to that observed when cells were cultured on 2D coverslip. In contrast to the 2D coverslips culture, astrocytes cultured on 3D-OG scaffolds did not have a flat morphology but had a more ramified shape similar to that seen in vivo conditions. Moreover, neurons on 3D-OG scaffolds had axons and dendrites aligned along the graphene skeleton allowing the formation of neuronal networks with highly controlled connections. Neuronal networks grown on 3D-OG scaffolds had a higher electrical activity with functional signaling over a long distance. 4) We have constructed a novel scaffold of three-dimensional bacterial cellulose-graphene foam (3D-BC/G) for neural stem cells (NSCs) in vitro, which was prepared via in situ bacterial cellulose interfacial polymerization on the skeleton surface of porous graphene foam. We found that 3D-BC/G can not only support NSCs growth and adhesion, but also keep NSCs stemness and enhanced its proliferative capacity. Further phenotypic analysis indicated that 3D-BC/G can induce NSCs selectively to differentiate into neurons, forming a neural network in short time. It was also meanwhile demonstrated to have good biocompatibility for primary cortical neurons and enhanced neuronal network activities by measuring calcium transient