Tissue-based metabolic labeling of polysialic acids in living primary hippocampal neurons.

The posttranslational modification of neural cell-adhesion molecule (NCAM) with polysialic acid (PSA) and the spatiotemporal distribution of PSA-NCAM play an important role in the neuronal development. In this work, we developed a tissue-based strategy for metabolically incorporating an unnatural monosaccharide, peracetylated N-azidoacetyl-D-mannosamine, in the sialic acid biochemical pathway to present N-azidoacetyl sialic acid to PSA-NCAM. Although significant neurotoxicity was observed in the conventional metabolic labeling that used the dissociated neuron cells, neurotoxicity disappeared in this modified strategy, allowing for investigation of the temporal and spatial distributions of PSA in the primary hippocampal neurons. PSA-NCAM was synthesized and recycled continuously during neuronal development, and the two-color labeling showed that newly synthesized PSA-NCAMs were transported and inserted mainly to the growing neurites and not significantly to the cell body. This report suggests a reliable and cytocompatible method for in vitro analysis of glycans complementary to the conventional cell-based metabolic labeling for chemical glycobiology.

Feasibility Study of Extended-Gate-Type Silicon Nanowire Field-Effect Transistors for Neural Recording.

In this research, a high performance silicon nanowire field-effect transistor (transconductance as high as 34 µS and sensitivity as 84 nS/mV) is extensively studied and directly compared with planar passive microelectrode arrays for neural recording application. Electrical and electrochemical characteristics are carefully characterized in a very well-controlled manner. We especially focused on the signal amplification capability and intrinsic noise of the transistors. A neural recording system using both silicon nanowire field-effect transistor-based active-type microelectrode array and platinum black microelectrode-based passive-type microelectrode array are implemented and compared. An artificial neural spike signal is supplied as input to both arrays through a buffer solution and recorded simultaneously. Recorded signal intensity by the silicon nanowire transistor was precisely determined by an electrical characteristic of the transistor, transconductance. Signal-to-noise ratio was found to be strongly dependent upon the intrinsic 1/f noise of the silicon nanowire transistor. We found how signal strength is determined and how intrinsic noise of the transistor determines signal-to-noise ratio of the recorded neural signals. This study provides in-depth understanding of the overall neural recording mechanism using silicon nanowire transistors and solid design guideline for further improvement and development.

Axon-First Neuritogenesis on Vertical Nanowires.

In this work, we report that high-density, vertically grown silicon nanowires (vg-SiNWs) direct a new in vitro developmental pathway of primary hippocampal neurons. Neurons on vg-SiNWs formed a single, extremely elongated major neurite earlier than minor neurites, which led to accelerated polarization. Additionally, the development of lamellipodia, which generally occurs on 2D culture coverslips, was absent on vg-SiNWs. The results indicate that surface topography is an important factor that influences neuronal development and also provide implications for the role of topography in neuronal development in vivo.

Function of ezrin-radixin-moesin proteins in migration of subventricular zone-derived neuroblasts following traumatic brain injury.

Throughout life, newly generated neuroblasts from the subventricular zone migrate toward the olfactory bulb through the rostral migratory stream. Upon brain injury, these migrating neuroblasts change their route and begin to migrate toward injured regions, which is one of the regenerative responses after brain damage. This injury-induced migration is triggered by stromal cell-derived factor 1 (SDF1) released from microglia near the damaged site; however, it is still unclear how these cells transduce SDF1 signals and change their direction. In this study, we found that SDF1 promotes the phosphorylation of ezrin-radixin-moesin (ERM) proteins, which are key molecules in organizing cell membrane and linking signals from the extracellular environment to the intracellular actin cytoskeleton. Blockade of ERM activation by overexpressing dominant-negative ERM (DN-ERM) efficiently perturbed the migration of neuroblasts. Considering that DN-ERM-expressing neuroblasts failed to maintain proper migratory cell morphology, it appears that ERM-dependent regulation of cell shape is required for the efficient migration of neuroblasts. These results suggest that ERM activation is an important step in the directional migration of neuroblasts in response to SDF1-CXCR4 signaling following brain injury.

Cytoskeletal actin dynamics are involved in pitch-dependent neurite outgrowth on bead monolayers.

Neurite outgrowth is an important preceding step for the development of nerve systems. Given that the in vivo environments of neurons consist of numerous hierarchical micro/nanotopographies, there have been many efforts to investigate the relationship between neuronal behaviors and surface topography. The acceleration of neurite outgrowth was recently reported on surfaces with a periodic nanotopography, but the biological mechanism has not yet been elucidated. In this work, the initial neurite development of hippocampal neurons on assembled silica beads with diameters ranging from 700 to 1800 nm was explored. The acceleration of neurite outgrowth increased with the surface-pitch size and leveled off after a pitch of 1 µm. Biochemical analysis indicated that cytoskeletal actin dynamics were primarily responsible for the recognition of surface topography. This work contributes to the emerging research field of topographical neurochemistry, as well as applied fields including neuroregeneration and neuroprosthetics.

A 3D neuronal network read-out interface with high recording performance using a neuronal cluster patterning on a microelectrode array.

In recent years, in vitro three-dimensional (3D) neuronal network models utilizing extracellular matrices have been advancing. To understand the network activity from these models, attempts have been made to measure activity in multiple regions simultaneously using a microelectrode array (MEA). Although there hve been many attempts to measure the activity of 3D networks using 2-dimensional (2D) MEAs, the physical coupling between the 3D network and the microelectrodes was not stable and needed to be improved. In this study, we proposed a neuronal cluster interface that improves the active channel ratio of commercial 2D MEAs, enabling reliable measurement of 3D network activity. To achieve this, neuronal clusters, which consist of a small number of neurons, were patterned on microelectrodes and used as mediators to transmit the signal between the 3D network and the microelectrodes. We confirmed that the patterned neuronal clusters enhanced the active channel ratio and SNR(signal-to-noise-ratio) about 3D network recording and stimulation for a month. Our interface was able to functionally connect with 3D networks and measure the 3D network activity without significant alternation of activity characteristics. Finally, we demonstrated that our interface can be used to analyze the differences in the dynamics of 3D and 2D networks and to construct the 3D clustered network. This method is expected to be useful for studying the functional activity of various 3D neuronal network models, offering broad applications for the use of these models.

Identification of feedback loops in neural networks based on multi-step Granger causality.

MOTIVATION: Feedback circuits are crucial network motifs, ubiquitously found in many intra- and inter-cellular regulatory networks, and also act as basic building blocks for inducing synchronized bursting behaviors in neural network dynamics. Therefore, the system-level identification of feedback circuits using time-series measurements is critical to understand the underlying regulatory mechanism of synchronized bursting behaviors. RESULTS: Multi-Step Granger Causality Method (MSGCM) was developed to identify feedback loops embedded in biological networks using time-series experimental measurements. Based on multivariate time-series analysis, MSGCM used a modified Wald test to infer the existence of multi-step Granger causality between a pair of network nodes. A significant bi-directional multi-step Granger causality between two nodes indicated the existence of a feedback loop. This new identification method resolved the drawback of the previous non-causal impulse response component method which was only applicable to networks containing no co-regulatory forward path. MSGCM also significantly improved the ratio of correct identification of feedback loops. In this study, the MSGCM was testified using synthetic pulsed neural network models and also in vitro cultured rat neural networks using multi-electrode array. As a result, we found a large number of feedback loops in the in vitro cultured neural networks with apparent synchronized oscillation, indicating a close relationship between synchronized oscillatory bursting behavior and underlying feedback loops. The MSGCM is an efficient method to investigate feedback loops embedded in in vitro cultured neural networks. The identified feedback loop motifs are considered as an important design principle responsible for the synchronized bursting behavior in neural networks.

Connectivity and network burst properties of in-vitro neuronal networks induced by a clustered structure with alginate hydrogel patterning.

Modularity is one of the important structural properties that affect information processing and other functionalities of neuronal networks. Researchers have developed in-vitro clustered network models for reproducing the modularity, but it is still challenging to control the segregation and integration of several sub-populations of them. We cultured clustered networks with alginate patterning and collected the electrophysiological signals to investigate the changes in functional properties during the development. We built inter-connected neuronal clusters using alginate micro-patterning with a circular shape on the surface of the micro-electrode array. The neuronal clusters were enabled to be connected at 3 or 10 days-in-vitro (DIV) by removing the barrier. The neuronal signals from different types of networks were collected from 16 to 34 DIV, and functional characteristics were examined. Connectivity and burst motif analysis were carried out to find out the relation between the structure and function of the networks. Neuronal networks with clustered structure showed different activity properties from the random networks along the development. The clustered networks had more short-range connections compared to the random networks. In the network burst motif analysis, the clustered networks showed more various patterns and a slower propagation of the activation patterns. In this study, we successfully cultured neuronal networks with clustered structure, and the structure affected the functional properties. The network model suggested in this study will be a good solution for observing the effect of structure on function during their development. Supplementary Information: The online version contains supplementary material available at 10.1007/s13534-023-00289-5.

Electrochemically driven, electrode-addressable formation of functionalized polydopamine films for neural interfaces.

The electrode-specific formation of polydopamine films is achieved by applying positive voltage to the target electrodes at pH 6.0. The functionalization of the films is simultaneously carried out by co-depositing dopamine with molecules of interest onto the electrode.

Neurons-on-a-Chip: In Vitro NeuroTools.

Neurons-on-a-Chip technology has been developed to provide diverse in vitro neuro-tools to study neuritogenesis, synaptogensis, axon guidance, and network dynamics. The two core enabling technologies are soft-lithography and microelectrode array technology. Soft lithography technology made it possible to fabricate microstamps and microfluidic channel devices with a simple replica molding method in a biological laboratory and innovatively reduced the turn-around time from assay design to chip fabrication, facilitating various experimental designs. To control nerve cell behaviors at the single cell level via chemical cues, surface biofunctionalization methods and micropatterning techniques were developed. Microelectrode chip technology, which provides a functional readout by measuring the electrophysiological signals from individual neurons, has become a popular platform to investigate neural information processing in networks. Due to these key advances, it is possible to study the relationship between the network structure and functions, and they have opened a new era of neurobiology and will become standard tools in the near future.

Optical recording of neural responses to gold-nanorod mediated photothermal neural inhibition.

BACKGROUND: Photothermal stimulation is a heat-mediated neuromodulation technique. When photothermal effects are induced on neuronal membrane, it can either excite or inhibit neural spiking activities. It has been demonstrated that gold nanorod mediated photothermal stimulation could decrease the electrical activity of cultured neural network. We investigated the effect of photothermal inhibition on neural activity using calcium imaging technique. NEW METHOD: Hippocampal neurons were cultured on a gold-nanorod-coated-microelectrode array and near-infrared laser was illuminated to induce neural inhibition. The neuronal responses at a single-cell resolution were measured by an extracellular recording and calcium imaging simultaneously. RESULTS: The photothermal effect on neural spikes were confirmed by electrical recording and calcium imaging. The decrease in neural spikes in electrical recordings during NIR illumination was correlated with the neighboring neural activity quantified by calcium spikes. COMPARISON WITH EXISTING METHOD(S): Optical recording at the single cell resolution was attempted during photothermal stimulation to confirm the neural suppression effect. CONCLUSIONS: Heat mediated suppression of neural activity was optically validated in single cell level. The present study will be helpful to understand the emerging photothermal neuromodulation technology.

Enhancement of Thermoplasmonic Neural Modulation Using a Gold Nanorod-Immobilized Polydopamine Film.

Photothermal neural activity inhibition has emerged as a minimally invasive neuromodulation technology with submillimeter precision. One of the techniques involves the utilization of plasmonic gold nanoparticles (AuNPs) to modulate neural activity by photothermal effects ("thermoplasmonics"). A surface modification technique is often required to integrate AuNPs onto the neural interface. Here, polydopamine (pDA), a multifunctional adhesive polymer with a wide light absorption spectrum, is introduced both as a primer layer for the immobilization of gold nanorods (GNRs) on the neural interface and as an additional photothermal agent by absorbing near-infrared red (NIR) lights for more efficient photothermal effects. First, the optical and photothermal properties of pDA as well as the characteristics of GNRs attached onto the pDA film are investigated for the optimized photothermal neural interface. Due to the covalent bonding between GNR surfaces and pDA, GNRs immobilized on pDA showed strong attachment onto the surface, yielding a more stable photothermal platform. Lastly, when photothermal neural stimulation was applied to the primary rat hippocampal neurons, the substrate with GNRs immobilized on the pDA film allowed more laser power-efficient photothermal neuromodulation as well as photothermal cell death. This study suggests the feasibility of using pDA as a surface modification material for developing a photothermal platform for the inhibition of neural activities.

In vitro microelectrode array technology and neural recordings.

In vitro microelectrode array (MEA) technology has evolved into a widely used and effective methodology to study cultured neural networks. An MEA forms a unique electrical interface with the cultured neurons in that neurons are directly grown on top of the electrode (neuron-on-electrode configuration). Theoretical models and experimental results suggest that physical configuration and biological environments of the cell-electrode interface play a key role in the outcome of neural recordings, such as yield of recordings, signal shape, and signal-to-noise ratio. Recent interdisciplinary approaches have shown that MEA performance can be enhanced through novel nanomaterials, structures, surface chemistry, and biotechnology. In vitro and in vivo neural interfaces share some common factors, and in vitro neural interface issues can be extended to solve in vivo neural interface problems of brain-machine interface or neuromodulation techniques.

Closed-loop control of neural spike rate of cultured neurons using a thermoplasmonics-based photothermal neural stimulation.

Objective.Photothermal neural stimulation has been developed in a variety of interfaces as an alternative technology that can perturb neural activity. The demonstrations of these techniques have heavily relied on open-loop stimulation or complete suppression of neural activity. To extend the controllability of photothermal neural stimulation, combining it with a closed-loop system is required. In this work, we investigated whether photothermal suppression mechanism can be used in a closed-loop system to reliably modulate neural spike rate to non-zero setpoints.Approach. To incorporate the photothermal inhibition mechanism into the neural feedback system, we combined a thermoplasmonic stimulation platform based on gold nanorods (GNRs) and near-infrared illuminations (808 nm, spot size: 2 mm or 200µm in diameter) with a proportional-integral (PI) controller. The closed-loop feedback control system was implemented to track predetermined target spike rates of hippocampal neuronal networks cultured on GNR-coated microelectrode arrays.Main results. The closed-loop system for neural spike rate control was successfully implemented using a PI controller and the thermoplasmonic neural suppression platform. Compared to the open-loop control, the target-channel spike rates were precisely modulated to remain constant or change in a sinusoidal form in the range below baseline spike rates. The spike rate response behaviors were affected by the choice of the controller gain. We also demonstrated that the functional connectivity of a synchronized bursting network could be altered by controlling the spike rate of one of the participating channels.Significance.The thermoplasmonic feedback controller proved that it can precisely modulate neural spike rate of neural activityin vitro. This technology can be used for studying neuronal network dynamics and might provide insights in developing new neuromodulation techniques in clinical applications.

Laser Power Determination Using Light-to-Heat Conversion Rate of Nanoplasmonic Substrates for Neural Stimulation.

Since neurons have temperature sensitive properties, gold nanorod (GNR)-mediated photothermal stimulation has been developed as a neuromodulation application. As an in vitro photothermal platform, GNR-layer was integrated with substrates to effectively apply heat stimulation to the cultured neurons. However, identifying optimal laser power for a targeted temperature on the substrate requires the consideration of thermal properties of the GNR-coated substrates. In this report, we suggest a simple numerical method to determine incident laser power on the substrates for a targeted temperature.

Development of the micro-patterned 3D neuronal-hydrogel model using soft-lithography for study a 3D neural network on a microelectrode array.

In vitro patterned neuronal models have been studied as one of the strategies to investigate the relationship between structural connectivity and functional activity of neural network. Despite the importance of three-dimensional (3D) cell models, most of these studies have been performed on two-dimensional models. In this study, we present a technique to construct the micro-pattern to 3D neuronal-hydrogel model using a micromolding in capillaries (MIMIC) technique on microelectrode array (MEA). Our technique was suitable to prevent the deformation of micro-patterned collagen model against the neuronal contracted tension during the network formation. The relationship between the growth directions of glial cells and micro-pattern direction was investigated. Lastly, we confirmed that our 3D model had synchronized activity among neurons in 3D. This model is expected to be used as a tool to study the relationship between structural connectivity and functional activity in the 3D environment.

Contribution of Extracellular Matrix Component Landscapes in the Adult Subventricular Zone to the Positioning of Neural Stem/Progenitor Cells.

Neurogenesis persists in restricted regions of the adult brain, including the subventricular zone (SVZ). Adult neural stem cells (NSCs) in the SVZ proliferate and give rise to new neurons and glial cells depending on intrinsic and environmental cues. Among the multiple factors that contribute to the chemical, physical, and mechanical components of the neurogenic niche, we focused on the composition of the extracellular matrix (ECM) of vasculature and fractones in the SVZ. The SVZ consists of ECM-rich blood vessels and fractones during development and adulthood, and adult neural stem/progenitor cells (NS/PCs) preferentially attach to the laminin-rich basal lamina. To examine the ECM preference of adult NS/PCs, we designed a competition assay using cell micropatterning. Although both laminin and collagen type IV, which are the main components of basal lamina, act as physical scaffolds, adult NS/PCs preferred to adhere to laminin over collagen type IV. Interestingly, the ECM preference of adult NS/PCs could be manipulated by chemokines such as stromal-derived factor 1 (SDF1) and α6 integrin. As SDF1 re-routes NSCs and their progenitors toward the injury site after brain damage, these results suggest that the alteration in ECM preferences may provide a molecular basis for contextdependent NS/PC positioning.

Label-free monitoring of 3D cortical neuronal growth in vitro using optical diffraction tomography.

The highly complex central nervous systems of mammals are often studied using three-dimensional (3D) in vitro primary neuronal cultures. A coupled confocal microscopy and immunofluorescence labeling are widely utilized for visualizing the 3D structures of neurons. However, this requires fixation of the neurons and is not suitable for monitoring an identical sample at multiple time points. Thus, we propose a label-free monitoring method for 3D neuronal growth based on refractive index tomograms obtained by optical diffraction tomography. The 3D morphology of the neurons was clearly visualized, and the developmental processes of neurite outgrowth in 3D spaces were analyzed for individual neurons.

Systematic analysis of synchronized oscillatory neuronal networks reveals an enrichment for coupled direct and indirect feedback motifs.

MOTIVATION: Synchronized bursting behavior is a remarkable phenomenon in neural dynamics. So, identification of the underlying functional structure is crucial to understand its regulatory mechanism at a system level. On the other hand, we noted that feedback loops (FBLs) are commonly used basic building blocks in engineering circuit design, especially for synchronization, and they have also been considered as important regulatory network motifs in systems biology. From these motivations, we have investigated the relationship between synchronized bursting behavior and feedback motifs in neural networks. RESULTS: Through extensive simulations of synthetic spike oscillation models, we found that a particular structure of FBLs, coupled direct and indirect positive feedback loops (PFLs), can induce robust synchronized bursting behaviors. To further investigate this, we have developed a novel FBL identification method based on sampled time-series data and applied it to synchronized spiking records measured from cultured neural networks of rat by using multi-electrode array. As a result, we have identified coupled direct and indirect PFLs. CONCLUSION: We therefore conclude that coupled direct and indirect PFLs might be an important design principle that causes the synchronized bursting behavior in neuronal networks although an extrapolation of this result to in vivo brain dynamics still remains an unanswered question.

Directional neurite growth using carbon nanotube patterned substrates as a biomimetic cue.

Researchers have made extensive efforts to mimic or reverse-engineer in vivo neural circuits using micropatterning technology. Various surface chemical cues or topographical structures have been proposed to design neuronal networks in vitro. In this paper, we propose a carbon nanotube (CNT)-based network engineering method which naturally mimics the structure of extracellular matrix (ECM). On CNT patterned substrates, poly-L-lysine (PLL) was coated, and E18 rat hippocampal neurons were cultured. In the early developmental stage, soma adhesion and neurite extension occurred in disregard of the surface CNT patterns. However, later the majority of neurites selectively grew along CNT patterns and extended further than other neurites that originally did not follow the patterns. Long-term cultured neuronal networks had a strong resemblance to the in vivo neural circuit structures. The selective guidance is possibly attributed to higher PLL adsorption on CNT patterns and the nanomesh structure of the CNT patterns. The results showed that CNT patterned substrates can be used as novel neuronal patterning substrates for in vitro neural engineering.