Optogenetics: 10 years of microbial opsins in neuroscience

Neural circuit mechanisms of epilepsy: Maintenance of homeostasis at the cellular, synaptic, and neurotransmitter levels

Epilepsy, a common neurological disorder, is characterized by recurrent seizures that can lead to cognitive, psychological, and neurobiological consequences. The pathogenesis of epilepsy involves neuronal dysfunction at the molecular, cellular, and neural circuit levels. Abnormal molecular signaling pathways or dysfunction of specific cell types can lead to epilepsy by disrupting the normal functioning of neural circuits. The continuous emergence of new technologies and the rapid advancement of existing ones have facilitated the discovery and comprehensive understanding of the neural circuit mechanisms underlying epilepsy. Therefore, this review aims to investigate the current understanding of the neural circuit mechanisms in epilepsy based on various technologies, including electroencephalography, magnetic resonance imaging, optogenetics, chemogenetics, deep brain stimulation, and brain-computer interfaces. Additionally, this review discusses these mechanisms from three perspectives: structural, synaptic, and transmitter circuits. The findings reveal that the neural circuit mechanisms of epilepsy encompass information transmission among different structures, interactions within the same structure, and the maintenance of homeostasis at the cellular, synaptic, and neurotransmitter levels. These findings offer new insights for investigating the pathophysiological mechanisms of epilepsy and enhancing its clinical diagnosis and treatment.

Human perception of ionizing radiation

Here we address the question of whether humans can perceive ionizing radiation. We conducted a thorough review of the clinical and experimental literature related to ionizing radiation, with a focus on its acute effects. Specifically, we examined the three domains of X-ray perception found in animals (abdominal, olfactory, and retinal), which led us to instances of ionizing radiation-induced hearing and taste sensory phenomena in humans thus suggesting that humans can perceive X-rays across various sensory modalities via multiple mechanisms. We also analyzed literature to understand the mechanisms associated with reported symptoms, this led us to the concept of radiomodulation, an understudied modulatory effect of sub-ablative ionizing radiation doses on neurons. Based on this review of the literature we propose the hypothesis that a significant radiomodulation mechanism is the formation of reactive oxygen species from radiolysis which activates immune and sensory signal transduction mechanisms specifically related to the redox activity in TRP and K+ channels. Additionally, we find evidence to support the previous claims of perception stemming from Cherenkov radiation and ozone production which are perceived using canonical sensory modalities. Finally, for we provide a concise summary of the applications of ionizing radiation in clinical imaging and therapy, as well as prospects for future developments of radiation technologies for biomedical and fundamental research.

Neurocounter - A deep learning framework for high-fidelity spatial localization of neurons

BACKGROUND

Many neuroscientific applications require robust and accurate localization of neurons. It is still an unsolved problem because of the enormous variation in intensity, texture, spatial overlap, morphology, and background artifacts. In addition, curating a large dataset containing complete manual annotation of neurons from high-resolution images for training a classifier requires significant time and effort. In this work, we presented Neurocounter, a deep learning network to detect and localize neurons.

NEW METHOD

Neurocounter contains an encoder, a decoder and an attention module. It is trained on images containing incompletely-annotated neurons having highly varied morphology, and control images containing artifacts and background structures. During training, Neurocounter progressively labels the un-annotated neurons in the training data. It detects centers of neuron soma as the output.

RESULTS

Neurocounter's self-learning ability reduces the need for time-intensive complete annotation and ensures high accuracy in the localization of neurons across various brain regions (approximately 94 % F1 score). Comparison with existing methods Neurocounter shows its efficacy over the state of the arts by significantly reducing false-positive detection (by at least 3 %).

CONCLUSIONS

Neurocounter offers precise neuron soma detection in various scenarios, such as with background artifacts, clutter and overlapped cell soma. This tool can be potentially used to reconstruct brain-wide 3D maps of activated neurons from 2D localization of neurons.

Integrating optical neuroscience tools into touchscreen operant systems

Unlocking the neural regulation of complex behavior is a foundational goal of brain science. Touchscreen-based assessments of behavior have been used extensively in the pursuit of this goal, with traditional pharmacological and neurochemical approaches being employed to provide key insights into underlying neural systems. So far, optically based approaches to measure and manipulate neural function, which have begun to revolutionize our understanding of relatively simple behaviors, have been less widely adopted for more complex cognitive functions of the type assessed with touchscreen-based behavioral tasks. Here we provide guidance and procedural descriptions to enable researchers to integrate optically based manipulation and measurement techniques into their touchscreen experimental systems. We focus primarily on three techniques, optogenetic manipulation, fiber photometry and microendoscopic imaging, describing experimental design adjustments that we have found to be critical to the successful integration of these approaches with extant touchscreen behavior pipelines. These include factors related to surgical procedures and timing, alterations to touchscreen operant environments and approaches to synchronizing light delivery and task design. A detailed protocol is included for each of the three techniques, covering their use from implementation through data analysis. The procedures in this protocol can be conducted in as short a time as a few days or over the course of weeks or months.

Multiplexing light-inducible recombinases to control cell fate, Boolean logic, and cell patterning in mammalian cells

Light-inducible regulatory proteins are powerful tools to interrogate fundamental mechanisms driving cellular behavior. In particular, genetically encoded photosensory domains fused to split proteins can tightly modulate protein activity and gene expression. While light-inducible split protein systems have performed well individually, few multichromatic and orthogonal gene regulation systems exist in mammalian cells. The design space for multichromatic circuits is limited by the small number of orthogonally addressable optogenetic switches and the types of effectors that can be actuated by them. We developed a library of red light-inducible recombinases and directed patterned myogenesis in a mesenchymal fibroblast-like cell line. To address the limited number of light-inducible domains (LIDs) responding to unique excitation spectra, we multiplexed light-inducible recombinases with our "Boolean logic and arithmetic through DNA excision" (BLADE) platform. Multiplexed optogenetic tools will be transformative for understanding the role of multiple interacting genes and their spatial context in endogenous signaling networks.

Spatially precise activation of the mouse cochlea with a multi-channel hybrid cochlear implant

Objective.Cochlear implants are among the few clinical interventions for people with severe or profound hearing loss. However, current spread during monopolar electrical stimulation results in poor spectral resolution, prompting the exploration of optical stimulation as an alternative approach. Enabled by introducing light-sensitive ion channels into auditory neurons (optogenetics), optical stimulation has been shown to activate a more discrete neural area with minimal overlap between each frequency channel during simultaneous stimulation. However, the utility of optogenetic approaches is uncertain due to the low fidelity of responses to light and high-power requirements compared to electrical stimulation.Approach.Hybrid stimulation, combining sub-threshold electrical and optical pulses, has been shown to improve fidelity and use less light, but the impact on spread of activation and channel summation using a translatable, multi-channel hybrid implant is unknown. This study examined these factors during single channel and simultaneous multi-channel hybrid stimulation in transgenic mice expressing the ChR2/H134R opsin. Acutely deafened mice were implanted with a hybrid cochlear array containing alternating light emitting diodes and platinum electrode rings. Spiking activity in the inferior colliculus was recorded during electrical-only or hybrid stimulation in which optical and electrical stimuli were both at sub-threshold intensities. Thresholds, spread of activation, and threshold shifts during simultaneous hybrid stimulation were compared to electrical-only stimulation.Main results.The electrical current required to reach activation threshold during hybrid stimulation was reduced by 7.3 dB compared to electrical-only stimulation (p< 0.001). The activation width measured at two levels of discrimination above threshold and channel summation during simultaneous hybrid stimulation were significantly lower compared to electrical-only stimulation (p< 0.05), but there was no spatial advantage of hybrid stimulation at higher electrical stimulation levels.Significance.Reduced channel interaction would facilitate multi-channel simultaneous stimulation, thereby enhancing the perception of temporal fine structure which is crucial for music and speech in noise.

Chemogenetic modulation in stroke recovery: A promising stroke therapy approach

Stroke remains a leading cause of long-term disability and mortality worldwide, necessitating novel therapeutic strategies to enhance recovery. Traditional rehabilitation approaches, including physical therapy and pharmacological interventions, often provide limited functional improvement. Neuromodulation has emerged as a promising strategy to promote post-stroke recovery by enhancing neuroplasticity and functional reorganization. Among various neuromodulatory techniques, chemogenetics, particularly Designer Receptors Exclusively Activated by Designer Drugs (DREADDs), offers precise, cell-type-specific, and temporally controlled modulation of neuronal and glial activity. This review explores the mechanisms and therapeutic potential of chemogenetic modulation in stroke recovery. Preclinical studies have demonstrated that activation of excitatory DREADDs (hM3Dq) in neurons located within the peri-infarct area or contralateral M1 has been shown to enhance neuroplasticity, facilitate axonal sprouting, and lead to improved behavioral recovery following stroke. Conversely, stimulation of inhibitory DREADDs (hM4Di) suppresses stroke-induced excitotoxicity, mitigates peri-infarct spreading depolarizations (PIDs), and modulates neuroinflammatory responses. By targeting specific neuronal and glial populations, chemogenetics enables phase-specific interventions-early inhibition to minimize damage during the acute phase and late excitation to promote plasticity during the recovery phase. Despite its advantages over traditional neuromodulation techniques, such as optogenetics and deep brain stimulation, several challenges remain before chemogenetics can be translated into clinical applications. These include optimizing viral vector delivery, improving ligand specificity, minimizing off-target effects, and ensuring long-term receptor stability. Furthermore, integrating chemogenetics with existing stroke rehabilitation strategies, including brain-computer interfaces and physical therapy, may enhance functional recovery by facilitating adaptive neuroplasticity. Future research should focus on refining chemogenetic tools to enable clinical application. By offering a highly selective, reversible, and minimally invasive approach, chemogenetics holds great potential for revolutionizing post-stroke therapy and advancing personalized neuromodulation strategies.

A chemogenetic technology using insect Ionotropic Receptors to stimulate target cell populations in the mammalian brain

Chemogenetics uses artificially-engineered proteins to modify the activity of cells, notably neurons, in response to small molecules. Although a common set of chemogenetic tools are the G protein-coupled receptor-based DREADDs, there has been great hope for ligand-gated, ion channel-type chemogenetic tools that directly impact neuronal excitability. We have devised such a technology by exploiting insect Ionotropic Receptors (IRs), a highly divergent subfamily of ionotropic glutamate receptors that evolved to detect diverse environmental chemicals. Here, we review a series of studies developing and applying this "IR-mediated neuronal activation" (IRNA) technology with the Drosophila melanogaster IR84a/IR8a complex, which detects phenyl-containing ligands. We also discuss how variants of IRNA could be produced by modifying the composition of the IR complex, using natural or engineered subunits, which would enable artificial activation of different cell populations in the brain in response to distinct chemicals.

Optogenetic stimulation of cell bodies versus axonal terminals generate comparable activity and functional connectivity patterns in the brain

Optogenetic techniques are often employed to dissect neural pathways with presumed specificity for targeted projections. In this study, we used optogenetic fMRI to investigate the effective landscape of stimulating the cell bodies versus one of its projection terminals. Specifically, we selected a long-range unidirectional projection from the ventral subiculum (vSUB) to the nucleus accumbens shell (NAcSh) and placed two stimulating fibers-one at the vSUB cell bodies and the other at the vSUB terminals in the NAcSh. Contrary to the conventional view that terminal stimulation confines activity to the feedforward stimulated pathway, our findings reveal that terminal stimulation induces brain activity and connectivity patterns remarkably similar to those of vSUB cell body stimulation. This observation suggests that the specificity of optogenetic terminal stimulation may induce antidromic activation, leading to broader network involvement than previously acknowledged.

A subtype-selective photoswitchable agonist for precise manipulation of GABAA receptors

BACKGROUND AND PURPOSE

Neuronal inhibition is largely mediated by type-A GABA receptors (GABAARs), a family of ligand-gated chloride-permeable channels, which can be sub-classified by their subunit composition. Unravelling the function and distribution of each GABAAR subtype is essential for a holistic understanding of GABAergic inhibition in health and diseases. Photopharmacology, a technique that utilises light-sensitive compounds to precisely manipulate endogenous proteins, is powerful for this purpose. To resolve the molecular complexity of neuronal inhibition, we aimed to develop subtype-selective photoswitchable agonists for GABAARs.

EXPERIMENTAL APPROACH

Inspired by THIP (gaboxadol), an agonist selective for δ subunit-containing GABAARs (δ-GABAARs), we merged a photoswitch moiety (azobenzene) with an analogue of THIP (isoguvacine) to construct Az-IGU. Using whole-cell voltage-clamp recording, Az-IGU was tested on 13 GABAAR subtypes expressed in human embryonic kidney (HEK) cells. Optical activation of endogenous GABAARs was examined via electrophysiology in cultured cortical neurons.

KEY RESULTS

In HEK cells, Az-IGU exerted reversible photo-agonism selectively for α4β3δ and α6β3δ GABAARs, two major mediators of tonic inhibition. Pharmacological and mutagenesis studies suggested that activation of the α4β3δ GABAAR involves interaction between Az-IGU and the GABA-binding pocket and is strongly correlated with the spontaneous activity of the receptor. In cultured cortical neurons, photoisomerisation of Az-IGU triggered responses that enabled reversible control of action potential firing.

CONCLUSIONS AND IMPLICATIONS

GABAARs are potential therapeutic targets for many disorders. However, their physiological and pathophysiological roles remain largely unexplored. Az-IGU may enable photopharmacological studies of α4/6β3δ GABAARs, providing new opportunities for biomedical and neurobiological applications.

Stellate Ganglia: A Key Therapeutic Target for Malignant Ventricular Arrhythmia in Heart Disease

Malignant ventricular arrhythmias (VAs), such as ventricular tachycardia and ventricular fibrillation, are the cause of approximately half a million deaths per year in the United States, which is a common lethal event in heart disease, such as hypertension, catecholaminergic polymorphic ventricular tachycardia, takotsubo cardiomyopathy, long-QT syndrome, and progressing into advanced heart failure. A common characteristic of these heart diseases, and the subsequent development of VAs, is the overactivation of the sympathetic nervous system. Current treatments for VAs in these heart diseases, such as β-adrenergic receptor blockers and cardiac sympathetic ablation, aim at inhibiting cardiac sympathetic overactivation. However, these treatments do not translate into becoming efficacious as long-term suppressors of ventricular tachycardia/ventricular fibrillation events. As a key regulatory component in the heart, cardiac postganglionic sympathetic neurons residing in the stellate ganglia (SGs) release neurotransmitters (such as norepinephrine and NPY [neuropeptide Y]) to perform their regulatory role in dictating cardiac function. Growing evidence from animal experiments and clinical studies has demonstrated that the remodeling of the SG may be intimately involved in malignant arrhythmogenesis. This identifies the SG as a key potential therapeutic target for the treatment of malignant VAs in heart disease. Therefore, this review summarizes the role of SG in ventricular arrhythmogenesis and updates the novel targeting of SG for clinical treatment of VAs in heart disease.

Optogenetic therapy for retinal degenerative diseases: A review

Optogenetics, a cutting-edge tool in novel gene manipulation and drug discovery, holds significant therapeutic potential for a variety of neurological disorders, including retinal diseases. Retinal diseases such as age-related macular degeneration (AMD) and retinitis pigmentosa (RP), significantly impair quality of life and cause severe visual impairment due to limited treatment options and a general lack of awareness. The increasing incidence of these degenerative conditions underscores the need for innovative solutions, such as optogenetics. Optogenetic therapy introduces genes coding for light-sensitive proteins, which are controlled by light signals to make neurons photosensitive. This precise targeting approach does not require specific gene intervention and can bypass dysfunctional photoreceptors, offering a treatment option for various degenerative and dystrophic eye diseases. Successful outcomes in patients with late-stage genetic retinal diseases and numerous clinical trials suggest that optogenetics could be an effective treatment for humans. This review provides an overview of the current landscape of optogenetic therapy, discusses its challenges, and summarizes the findings of ongoing clinical trials for neural and visual restoration.

Anisotropic light propagation in human brain white matter

Significance

Accurate modeling of light diffusion in the human brain is crucial for applications in optogenetics and spectroscopy diagnostic techniques. White matter tissue is composed of myelinated axon bundles, suggesting the occurrence of enhanced light diffusion along their local orientation direction, which however has never been characterized experimentally. Existing diffuse optics models assume isotropic properties, limiting their accuracy.

Aim

We aim to characterize the anisotropic scattering properties of human white matter tissue by directly measuring its tensor scattering components along different directions, and to correlate them with the local axon fiber orientation.

Approach

Using a time- and space-resolved setup, we image the transverse propagation of diffusely reflected light across two perpendicular directions in a ex vivo human brain sample. Local fiber orientation is independently determined using light sheet fluorescence microscopy (LSFM).

Results

The directional dependence of light propagation in organized myelinated axon bundles is characterized via Monte Carlo (MC) simulations accounting for a tensor scattering coefficient, revealing a lower scattering rate parallel to the fiber orientation. The effects of white matter anisotropy are further assessed by simulating a typical time-domain near-infrared spectroscopy measurement in a four-layer human head model.

Conclusions

This study provides a first characterization of the anisotropic scattering properties in ex vivo human white matter, highlighting its direct correlation with axon fiber orientation, and opening to the realization of quantitatively accurate anisotropy-aware human head 3D meshes for diffuse optics applications.

Exploring neuropharmacokinetics: mechanisms, models, and clinical implications

Neuropharmacokinetics is an emerging field dedicated to understanding the pharmacokinetics of drugs within the central nervous system (CNS), with a particular emphasis on overcoming the challenges posed by the blood-brain barrier. This paper reviews the latest advancements in drug delivery strategies, including nanoparticle-based systems, receptor-mediated transcytosis, and efflux transporter inhibition, which have been designed to enhance drug penetration into the brain. Additionally, the use of advanced imaging techniques such as positron emission tomography, functional magnetic resonance imaging, and magnetic resonance imaging with contrast agents has provided critical insights into drug distribution, receptor occupancy, and the functional impact of therapeutic agents within the CNS. These innovations not only enhance our understanding of CNS drug action but also pave the way for more effective treatments for neurological and psychiatric disorders.

The DMC-Behavior Platform: An Open-Source Framework for Auditory-Guided Perceptual Decision-Making in Head-Fixed Mice

Perceptual decision-making describes the process of selecting an appropriate action based on the sensory information present in the immediate environment and is hence an omnipresent factor in the life of animals. In preclinical research, a widespread approach to study the neuronal correlates of perceptual decision-making is to record (and manipulate) neuronal activity in head-fixed mice performing behavioral tasks. In contrast to the technologies used to record/manipulate neuronal activity, standardization of the behavioral training of mice is generally neglected, a circumstance that is particularly true for behavioral tasks involving auditory stimuli. Here, we present the DMC-Behavior Platform, an open-source, cost-efficient framework for training head-fixed mice in perceptual decision-making tasks involving auditory stimuli. Combining the DMC-Behavior Platform with strategies to record and manipulate neuronal activity offers many opportunities to test hypotheses on the neuronal underpinnings of cognitive processes. We demonstrate the utility of the platform by training mice on auditory variants of three behavioral tasks commonly used to study perceptual decision-making: a detection, a Go/NoGo, and a two-alternative forced choice task. The presented work establishes the seamless integration and synchronization of external devices to record neuronal activity, task-related, and nontask-related behavioral variables. Our platform provides a valuable tool for more standardized and reproducible investigations into the neuronal circuits underlying auditory-guided decision-making.

Neuromodulation in Small Animal fMRI

The integration of functional magnetic resonance imaging (fMRI) with advanced neuroscience technologies in experimental small animal models offers a unique path to interrogate the causal relationships between regional brain activity and brain-wide network measures-a goal challenging to accomplish in human subjects. This review traces the historical development of the neuromodulation techniques commonly used in rodents, such as electrical deep brain stimulation, optogenetics, and chemogenetics, and focuses on their application with fMRI. We discuss their advantageousness roles in uncovering the signaling architecture within the brain and the methodological considerations necessary when conducting these experiments. By presenting several rodent-based case studies, we aim to demonstrate the potential of the multimodal neuromodulation approach in shedding light on neurovascular coupling, the neural basis of brain network functions, and their connections to behaviors. Key findings highlight the cell-type and circuit-specific modulation of brain-wide activity patterns and their behavioral correlates. We also discuss several future directions and feature the use of mediation and moderation analytical models beyond the intuitive evoked response mapping, to better leverage the rich information available in fMRI data with neuromodulation. Using fMRI alongside neuromodulation techniques provide insights into the mesoscopic (relating to the intermediate scale between single neurons and large-scale brain networks) and macroscopic fMRI measures that correlate with specific neuronal events. This integration bridges the gap between different scales of neuroscience research, facilitating the exploration and testing of novel therapeutic strategies aimed at altering network-mediated behaviors. In conclusion, the combination of fMRI with neuromodulation techniques provides crucial insights into mesoscopic and macroscopic brain dynamics, advancing our understanding of brain function in health and disease. EVIDENCE LEVEL: 1 TECHNICAL EFFICACY: Stage 1.

Elucidation of Expression Patterns and Functional Properties of Archaerhodopsin Derived from Halorubrum sp. Ejinoor

This study elucidates the structural determinants and optogenetic potential of Archaerhodopsin HeAR, a proton pump from Halorubrum sp. Ejinoor isolated from Inner Mongolian salt lakes. Through heterologous expression in E. coli BL21 (DE3) and integrative biophysical analyses, we demonstrate that HeAR adopts a stable trimeric architecture (129 kDa) with detergent-binding characteristics mirroring bacteriorhodopsin (BR); however, it exhibits a 10 nm bathochromic spectral shift (λmax = 550 nm) and elevated proton affinity (Asp-95 pKa = 3.5 vs. BR Asp-85 pKa = 2.6), indicative of evolutionary optimization in its retinal-binding electrostatic microenvironment. Kinetic profiling reveals HeAR's prolonged photocycle (100 ms vs. BR's 11 ms), marked by rapid M-state decay (3.3 ms) and extended dark-adaptation half-life (160 min), a bistable behavior attributed to enhanced hydrogen bond persistence (80%) and reduced conformational entropy (RMSD = 2.0 Å). Functional assays confirm light-driven proton extrusion (0.1 ng H⁺/mg·s) with DCCD-amplified flux (0.3 ng H⁺/mg·s) and ATP synthesis (0.3 nmol/mg·s), underscoring its synergy with H⁺-ATPase. Phylogenetic and structural analyses reveal 95% homology with Halorubrum AR4 and conservation of 11 proton-wire residues, despite divergent Trp/Tyr/Ser networks that redefine chromophore stabilization. AlphaFold-predicted models (TM-score > 0.92) and molecular docking identify superior retinoid-binding affinity (ΔG = -12.27 kcal/mol), while spectral specificity (550-560 nm) and acid-stable photoresponse highlight its adaptability for low-irradiance neuromodulation. These findings position HeAR as a precision optogenetic tool, circumventing spectral overlap with excitatory opsins and enabling sustained hyperpolarization with minimized phototoxicity. By bridging microbial energetics and optobioengineering, this work expands the archaeal rhodopsin toolkit and provides a blueprint for designing wavelength-optimized photoregulatory systems.

Non-invasive in vivo bidirectional magnetogenetic modulation of pain circuits

Primary nociceptors in the dorsal root ganglion (DRG) receive sensory information from discrete parts of the body and are responsible for initiating signaling events that in supraspinal regions will be interpreted as physiological or pathological pain. Genetic, pharmacologic and electric neuromodulation of nociceptor activity in freely moving non-transgenic animals has been shown to be challenging due to many factors including the immunogenicity of non-mammalian proteins, procedure invasiveness and poor temporal precision. Here, we introduce a magnetogenetic strategy that enables remote bidirectional regulation of nociceptor activity. Magnetogenetics utilizes a source of direct magnetic field (DMF) to control neuronal activity in cells that express an anti-ferritin nanobody-TRPV1 receptor fusion protein (Nb-Ft-TRPV1). In our study, AAV2retro-mediated delivery of an excitatory Nb-Ft-TRPV1 construct into the sciatic nerve of wild-type mice resulted in stable long-term transgene expression accompanied by significant reduction of mechanical withdrawal thresholds during DMF exposure, place aversion of the DMF zone and activity changes in the anterior cingulate (ACC) nucleus. Conversely, delivery of an inhibitory variant of the Nb-Ft-TRPV1 construct, engineered to gate chloride ions in response to DMF, led to reversed behavioral manifestations of mechanical allodynia and showed place preference for the DMF zone, suggestive of functional pain relief. Changes in DRG activity were confirmed by post-mortem levels, immediately following DMF exposure, of the activity-induced gene cfos, which increased with the excitatory construct in normal mice and decreased with the inhibitory construct in pain models Our study demonstrates that magnetogenetic channels can achieve long-term expression in the periphery without losing functionality, providing a stable gene therapy system for non-invasive, magnetic field regulation of pain-related neurons for research and potential clinical applications.

Identifying Cardiovascular Risk by Nonlinear Heart Rate Dynamics Analysis: Translational Biomarker from Mice to Humans

BACKGROUND

The beat-by-beat fluctuation of heart rate (HR) in its temporal sequence (HR dynamics) provides information on HR regulation by the autonomic nervous system (ANS) and its dysregulation in pathological states. Commonly, linear analyses of HR and its variability (HRV) are used to draw conclusions about pathological states despite clear statistical and translational limitations.

OBJECTIVE

The main aim of this study was to compare linear and nonlinear HR measures, including detrended fluctuation analysis (DFA), based on ECG recordings by radiotelemetry in C57BL/6N mice to identify pathological HR dynamics.

METHODS

We investigated different behavioral and a wide range of pharmacological interventions which alter ANS regulation through various peripheral and/or central mechanisms including receptors implicated in psychiatric disorders. This spectrum of interventions served as a reference system for comparison of linear and nonlinear HR measures to identify pathological states.

RESULTS

Physiological HR dynamics constitute a self-similar, scale-invariant, fractal process with persistent intrinsic long-range correlations resulting in physiological DFA scaling coefficients of α~1. Strongly altered DFA scaling coefficients (α ≠ 1) indicate pathological states of HR dynamics as elicited by (1) parasympathetic blockade, (2) parasympathetic overactivation and (3) sympathetic overactivation but not inhibition. The DFA scaling coefficients are identical in mice and humans under physiological conditions with identical pathological states by defined pharmacological interventions.

CONCLUSIONS

Here, we show the importance of tonic vagal function for physiological HR dynamics in mice, as reported in humans. Unlike linear measures, DFA provides an important translational measure that reliably identifies pathological HR dynamics based on altered ANS control by pharmacological interventions. Central ANS dysregulation represents a likely mechanism of increased cardiac mortality in psychiatric disorders.

A new flavor of synthetic yeast communities sees the light

No organism is an island: organisms of varying taxonomic complexity, including genetic variants of a single species, can coexist in particular niches, cooperating for survival while simultaneously competing for environmental resources. In recent years, synthetic biology strategies have witnessed a surge of efforts focused on creating artificial microbial communities to tackle pressing questions about the complexity of natural systems and the interactions that underpin them. These engineered ecosystems depend on the number and nature of their members, allowing complex cell communication designs to recreate and create diverse interactions of interest. Due to its experimental simplicity, the budding yeast Saccharomyces cerevisiae has been harnessed to establish a mixture of varied cell populations with the potential to explore synthetic ecology, metabolic bioprocessing, biosensing, and pattern formation. Indeed, engineered yeast communities enable advanced molecule detection dynamics and logic operations. Here, we present a concise overview of the state-of-the-art, highlighting examples that exploit optogenetics to manipulate, through light stimulation, key yeast phenotypes at the community level, with unprecedented spatial and temporal regulation. Hence, we envision a bright future where the application of optogenetic approaches in synthetic communities (optoecology) illuminates the intricate dynamics of complex ecosystems and drives innovations in metabolic engineering strategies.

Principles and Design of Molecular Tools for Sensing and Perturbing Cell Surface Receptor Activity

Cell-surface receptors are vital for controlling numerous cellular processes with their dysregulation being linked to disease states. Therefore, it is necessary to develop tools to study receptors and the signaling pathways they control. This Review broadly describes molecular approaches that enable 1) the visualization of receptors to determine their localization and distribution; 2) sensing receptor activation with permanent readouts as well as readouts in real time; and 3) perturbing receptor activity and mimicking receptor-controlled processes to learn more about these processes. Together, these tools have provided valuable insight into fundamental receptor biology and helped to characterize therapeutics that target receptors.

Conceptual expansion of photomedicine for spatiotemporal treatment methods

Photomedicine has evolved from basic phototherapy to a broad range of light-based technologies to achieve precise and minimally invasive therapeutic outcomes. Recent advances in light sources, photochemical reactions, and photoswitches have facilitated the development of light-activated methodologies for modulating biological processes. This review discusses the history of light therapy that leads to the emergence of a new field known as photopharmacology, mode of actions in photopharmacology such as photodynamic, photo-uncaging and photoswitchable methods, a few representative examples in photopharmacology, and a brief overview of its associated challenges. The current developments in photopharmacology hold great promise for the treatment of diseases such as cancer, with enhanced therapeutic precision, and minimal side effects. We foresee further expansion of photomedicine for novel approaches in precision medicine and healthcare, and unprecedented treatment methods.

Theoretical analysis of low-power deep synergistic sono-optogenetic excitation of neurons by co-expressing light-sensitive and mechano-sensitive ion-channels

The present challenge in neuroscience is to non-invasively exercise low-power and high-fidelity control of neurons situated deep inside the brain. Although, two-photon optogenetic excitation can activate neurons to millimeter depth with sub-cellular specificity and millisecond temporal resolution, it can also cause heating of the targeted tissue. On the other hand, sonogenetics can non-invasively modulate the cellular activity of neurons expressed with mechano-sensitive proteins in deeper areas of the brain with less spatial selectivity. We present a theoretical analysis of a synergistic sono-optogenetic method to overcome these limitations by co-expressing a mechano-sensitive (MscL-I92L) ion-channel with a light-sensitive (CoChR/ChroME2s/ChRmine) ion-channel in hippocampal neurons. It is shown that in the presence of low-amplitude subthreshold ultrasound pulses, the two-photon excitation threshold for neural spiking reduces drastically by 73% with MscL-I92L-CoChR (0.021 mW/µm2), 66% with MscL-I92L-ChroME2s (0.029 mW/µm2), and 64% with MscL-I92L-ChRmine (0.013 mW/µm2) at 5 Hz. It allows deeper excitation of up to 1.2 cm with MscL-I92L-ChRmine combination. The method is useful to design new experiments for low-power deep excitation of neurons and multimodal neuroprosthetic devices and circuits.

On brain stimulation in epilepsy

Brain stimulation has, for many decades, been considered as a potential solution for the unmet needs of the many people living with drug-resistant epilepsy. Clinically, there are several different approaches in use, including vagus nerve stimulation, deep brain stimulation of the thalamus, and responsive neurostimulation. Across populations of patients, all deliver reductions in seizure load and sudden unexpected death in epilepsy risk, yet do so variably, and the improvements seem incremental rather than transformative. In contrast, within the field of experimental neuroscience, the transformational impact of optogenetic stimulation is evident; by providing a means to control subsets of neurons in isolation, it has revolutionized our ability to dissect out the functional relations within neuronal microcircuits. It is worth asking, therefore, how preclinical optogenetics research could advance clinical practice in epilepsy? Here, we review the state of the clinical field, and the recent progress in preclinical animal research. We report various breakthrough results, including the development of new models of seizure initiation, its use for seizure prediction, and for fast, closed-loop control of pathological brain rhythms, and what these experiments tell us about epileptic pathophysiology. Finally, we consider how these preclinical research advances may be translated into clinical practice.

Analyzing the brain's dynamic response to targeted stimulation using generative modeling

Generative models of brain activity have been instrumental in testing hypothesized mechanisms underlying brain dynamics against experimental datasets. Beyond capturing the key mechanisms underlying spontaneous brain dynamics, these models hold an exciting potential for understanding the mechanisms underlying the dynamics evoked by targeted brain stimulation techniques. This paper delves into this emerging application, using concepts from dynamical systems theory to argue that the stimulus-evoked dynamics in such experiments may be shaped by new types of mechanisms distinct from those that dominate spontaneous dynamics. We review and discuss (a) the targeted experimental techniques across spatial scales that can both perturb the brain to novel states and resolve its relaxation trajectory back to spontaneous dynamics and (b) how we can understand these dynamics in terms of mechanisms using physiological, phenomenological, and data-driven models. A tight integration of targeted stimulation experiments with generative quantitative modeling provides an important opportunity to uncover novel mechanisms of brain dynamics that are difficult to detect in spontaneous settings.

Neuronal mechanisms of nociceptive-evoked gamma-band oscillations in rodents

Gamma-band oscillations (GBOs) in the primary somatosensory cortex (S1) play key roles in nociceptive processing. Yet, one crucial question remains unaddressed: what neuronal mechanisms underlie nociceptive-evoked GBOs? Here, we addressed this question using a range of somatosensory stimuli (nociceptive and non-nociceptive), neural recording techniques (electroencephalography in humans and silicon probes and calcium imaging in rodents), and optogenetics (alone or simultaneously with electrophysiology in mice). We found that (1) GBOs encoded pain intensity independent of stimulus intensity in humans, (2) GBOs in S1 encoded pain intensity and were triggered by spiking of S1 interneurons, (3) parvalbumin (PV)-positive interneurons preferentially tracked pain intensity, and critically, (4) PV S1 interneurons causally modulated GBOs and pain-related behaviors for both thermal and mechanical pain. These findings provide causal evidence that nociceptive-evoked GBOs preferentially encoding pain intensity are generated by PV interneurons in S1, thereby laying a solid foundation for developing GBO-based targeted pain therapies.

Post-stroke depression: exploring gut microbiota-mediated barrier dysfunction through immune regulation

Post-stroke depression (PSD) is one of the most common and devastating neuropsychiatric complications in stroke patients, affecting more than one-third of survivors of ischemic stroke (IS). Despite its high incidence, PSD is often overlooked or undertreated in clinical practice, and effective preventive measures and therapeutic interventions remain limited. Although the exact mechanisms of PSD are not fully understood, emerging evidence suggests that the gut microbiota plays a key role in regulating gut-brain communication. This has sparked great interest in the relationship between the microbiota-gut-brain axis (MGBA) and PSD, especially in the context of cerebral ischemia. In addition to the gut microbiota, another important factor is the gut barrier, which acts as a frontline sensor distinguishing between beneficial and harmful microbes, regulating inflammatory responses and immunomodulation. Based on this, this paper proposes a new approach, the microbiota-immune-barrier axis, which is not only closely related to the pathophysiology of IS but may also play a critical role in the occurrence and progression of PSD. This review aims to systematically analyze how the gut microbiota affects the integrity and function of the barrier after IS through inflammatory responses and immunomodulation, leading to the production or exacerbation of depressive symptoms in the context of cerebral ischemia. In addition, we will explore existing technologies that can assess the MGBA and potential therapeutic strategies for PSD, with the hope of providing new insights for future research and clinical interventions.

A brief guide for gene delivery to the brain using adeno-associated viral vectors

The advent of recombinant adeno-associated viral (rAAV) vector-mediated gene delivery has accelerated the comprehensive analysis and manipulation of the nervous system owing to its ability to regulate gene expression in a spatiotemporal manner, thereby facilitating the study of brain physiology and the investigation of the pathophysiology of neurological disorders. Here, we provide a concise guide to stereotaxic gene delivery into the mouse brain using rAAV vectors. Key considerations for designing a customized rAAV vector are discussed, along with an overview of the surgical procedures of intracranial stereotaxic injection. This article aims to assist neuroscientists in establishing experimental setups for genetic manipulation in the mouse brain.

Luminos: open-source software for bidirectional microscopy

Bidirectional microscopy (BDM) combines simultaneous targeted optical perturbation and imaging of biophysical or biochemical signals (e.g. membrane voltage, Ca2+, or signaling molecules). A core challenge in BDM is precise spatial and temporal alignment of stimulation, imaging, and other experimental parameters. Here we present Luminos, an open-source MATLAB library for modular and precisely synchronized control of BDM experiments. The system supports hardware-triggered synchronization across stimulation, recording, and imaging channels with microsecond accuracy. Source code and documentation for Luminos are available online at https://www.luminosmicroscopy.com and https://github.com/adamcohenlab/luminos-microscopy. This library will facilitate development of bidirectional microscopy methods across the biological sciences.

Structural insights into light-gating of potassium-selective channelrhodopsin

Structural information on channelrhodopsins' mechanism of light-gated ion conductance is scarce, limiting its engineering as optogenetic tools. Here, we use single-particle cryo-electron microscopy of peptidisc-incorporated protein samples to determine the structures of the slow-cycling mutant C110A of kalium channelrhodopsin 1 from Hyphochytrium catenoides (HcKCR1) in the dark and upon laser flash excitation. Upon photoisomerization of the retinal chromophore, the retinylidene Schiff base NH-bond reorients from the extracellular to the cytoplasmic side. This switch triggers a series of side chain reorientations and merges intramolecular cavities into a transmembrane K+ conduction pathway. Molecular dynamics simulations confirm K+ flux through the illuminated state but not through the resting state. The overall displacement between the closed and the open structure is small, involving mainly side chain rearrangements. Asp105 and Asp116 play a key role in K+ conductance. Structure-guided mutagenesis and patch-clamp analysis reveal the roles of the pathway-forming residues in channel gating and selectivity.

The neuroimmune connectome in health and disease

The nervous and immune systems have complementary roles in the adaptation of organisms to environmental changes. However, the mechanisms that mediate cross-talk between the nervous and immune systems, called neuroimmune interactions, are poorly understood. In this Review, we summarize advances in the understanding of neuroimmune communication, with a principal focus on the central nervous system (CNS): its response to immune signals and the immunological consequences of CNS activity. We highlight these themes primarily as they relate to neurological diseases, the control of immunity, and the regulation of complex behaviours. We also consider the importance and challenges linked to the study of the neuroimmune connectome, which is defined as the totality of neuroimmune interactions in the body, because this provides a conceptual framework to identify mechanisms of disease pathogenesis and therapeutic approaches. Finally, we discuss how the latest techniques can advance our understanding of the neuroimmune connectome, and highlight the outstanding questions in the field.

The Roles of Discrete Populations of Neurons Expressing Short Neuropeptide F in Sleep Induction in Drosophila melanogaster

Sleep is of vital importance in our lives, yet we are far from understanding the neuronal networks that control the amount and timing of sleep. There is substantial conservation of known sleep-regulating transmitters, allowing for studies in simpler organisms to lead the way in gaining insight into the organization of sleep control circuits. In Drosophila melanogaster, we recently showed that optogenetic activation of neurons that produce the neuropeptide Y (NPY)-related transmitter short neuropeptide F (sNPF) increases time spent asleep. However, sNPF is expressed in several neuronal populations, and thus it is unknown which of those populations play roles in the sleep-promoting effect. In this study, we addressed this issue using a genetic approach to limit optogenetic activation to subsets of sNPF-expressing neurons. We found that sleep promotion was shorter-lived when cryptochrome (CRY)-positive neurons were excluded from being activated. Pigment-dispersing factor (PDF) neurons were not required for sleep promotion, nor were mushroom body (MB) neurons. Acute reactions to a short, 10-s period of optogenetic activation were largely unchanged by excluding activation of the three neuronal populations mentioned above. Together, these results suggest that clock neurons that are CRY-positive and PDF-negative are important contributors to the long-lasting sleep promotion produced by sNPF neuron activation. However, other neurons targeted by the sNPF-GAL4 driver appear to mediate the more rapid behavioral responses. Future studies will seek to identify these additional sNPF neuron populations and to determine how sNPF-expressing clock neurons act in concert with other neuronal circuits to promote sleep.

H-bonded organic frameworks as ultrasound-programmable delivery platform

The precise control of mechanochemical activation within deep tissues using non-invasive ultrasound holds profound implications for advancing our understanding of fundamental biomedical sciences and revolutionizing disease treatments1-4. However, a theory-guided mechanoresponsive materials system with well-defined ultrasound activation has yet to be explored5,6. Here we present the concept of using porous hydrogen-bonded organic frameworks (HOFs) as toolkits for focused ultrasound (FUS) programmably triggered drug activation to control specific cellular events in the deep brain, through on-demand scission of the supramolecular interactions. A theoretical model is developed to potentially visualize the mechanochemical scission and ultrasound mechanics, providing valuable guidelines for the rational design of mechanoresponsive materials to achieve programmable control. To demonstrate the practicality of this approach, we encapsulate the designer drug clozapine N-oxide (CNO) into the optimal HOF nanocrystals for FUS-gated release to activate engineered G-protein-coupled receptors in the ventral tegmental area (VTA) of mice and rats and hence achieve targeted neural circuit modulation even at depth 9 mm with a latency of seconds. This work demonstrates the capability of ultrasound to precisely control molecular interactions and develops ultrasound-programmable HOFs to non-invasively and spatiotemporally control cellular events, thereby facilitating the establishment of precise molecular therapeutic possibilities.

Optogenetic calcium modulation in astrocytes enhances post-stroke recovery in chronic capsular infarct

Stroke is caused by disruption of cerebral blood flow, leading to neuronal death and dysfunction in the interconnected areas, which results in a wide range of severe symptoms depending on the specific brain regions affected. While previous studies have primarily focused on direct modulation of neuronal activity for post-stroke treatment, accumulating evidence suggests that astrocytes may play a critical role in post-stroke progression and could serve as a potential therapeutic target for recovery. In this study, we investigate the effects of selective modulation of astrocytic calcium signals on chronic stroke using OptoSTIM1, an optogenetic tool that activates endogenous calcium channels. In contrast to channelrhodopsin-2 (ChR2), OptoSTIM1 robustly elevates astrocytic calcium levels, sustaining the increase for over 10 min upon a single activation. The calcium elevation in astrocytes in the ipsilesional sensory-parietal cortex leads to remarkable recovery from post-stroke impairment. Thus, manipulating intracellular calcium levels in astrocytes holds promise as a potential therapeutic strategy for improving recovery following a stroke.

Viroporin activity is necessary for intercellular calcium signals that contribute to viral pathogenesis

Viruses engage in a variety of processes to subvert host defenses and create an environment amenable to replication. Here, using rotavirus as a prototype, we show that calcium conductance out of the endoplasmic reticulum by the virus encoded ion channel, NSP4, induces intercellular calcium waves that extend beyond the infected cell and contribute to pathogenesis. Viruses that lack the ability to induce this signaling show diminished viral shedding and attenuated disease in a mouse model of rotavirus diarrhea. This implicates nonstructural protein 4 (NSP4) as a virulence factor and provides mechanistic insight into its mode of action. Critically, this signaling induces a transcriptional signature characteristic of interferon-independent innate immune activation, which is not observed in response to a mutant NSP4 that does not conduct calcium. This implicates calcium dysregulation as a means of pathogen recognition, a theme broadly applicable to calcium-altering pathogens beyond rotavirus.

Advancing Neuroscience and Therapy: Insights into Genetic and Non-Genetic Neuromodulation Approaches

Neuromodulation stands as a cutting-edge approach in the fields of neuroscience and therapeutic intervention typically involving the regulation of neural activity through physical and chemical stimuli. The purpose of this review is to provide an overview and evaluation of different neuromodulation techniques, anticipating a clearer understanding of the future developmental trajectories and the challenges faced within the domain of neuromodulation that can be achieved. This review categorizes neuromodulation techniques into genetic neuromodulation methods (including optogenetics, chemogenetics, sonogenetics, and magnetogenetics) and non-genetic neuromodulation methods (including deep brain stimulation, transcranial magnetic stimulation, transcranial direct current stimulation, transcranial ultrasound stimulation, photobiomodulation therapy, infrared neuromodulation, electromagnetic stimulation, sensory stimulation therapy, and multi-physical-factor stimulation techniques). By systematically evaluating the principles, mechanisms, advantages, limitations, and efficacy in modulating neuronal activity and the potential applications in interventions of neurological disorders of these neuromodulation techniques, a comprehensive picture is gradually emerging regarding the advantages and challenges of neuromodulation techniques, their developmental trajectory, and their potential clinical applications. This review highlights significant advancements in applying these techniques to treat neurological and psychiatric disorders. Genetic methods, such as sonogenetics and magnetogenetics, have demonstrated high specificity and temporal precision in targeting neuronal populations, while non-genetic methods, such as transcranial magnetic stimulation and photobiomodulation therapy, offer noninvasive and versatile clinical intervention options. The transformative potential of these neuromodulation techniques in neuroscience research and clinical practice is underscored, emphasizing the need for integration and innovation in technologies, the optimization of delivery methods, the improvement of mediums, and the evaluation of toxicity to fully harness their therapeutic potential.

Flexible modeling of large-scale neural network stimulation: electrical and optical extensions to The Virtual Electrode Recording Tool for EXtracellular Potentials (VERTEX)

Background

Computational models that predict effects of neural stimulation can be used as a preliminary tool to inform in-vivo research, reducing the costs, time, and ethical considerations involved. However, current models do not support the diverse neural stimulation techniques used in-vivo, including the expanding selection of electrodes, stimulation modalities, and stimulation paradigms.

New Method

To develop a more comprehensive software, we created several extensions to The Virtual Electrode Recording Tool for EXtracellular Potentials (VERTEX), the MATLAB-based neural stimulation tool from Newcastle University. VERTEX simulates input currents in a large population of multi-compartment neurons within a small cortical slice to model electric field stimulation, while recording local field potentials (LFPs) and spiking activity. Our extensions to its existing electric field stimulation framework include allowing multiple pairs of parametrically defined electrodes and biphasic, bipolar stimulation delivered at programmable delays. To support the growing use of optogenetic approaches for targeted neural stimulation, we introduced a feature that models optogenetic stimulation through an additional VERTEX input function that converts irradiance to currents at optogenetically responsive neurons. Finally, we added extensions to allow complex stimulation protocols including paired-pulse, spatiotemporal patterned, and closed-loop stimulation.

Results

We demonstrated our novel features using VERTEX's built-in functionalities, with results in alignment with other models and experimental work.

Conclusions

Our extensions provide an all in one platform to efficiently and systematically test diverse, targeted, and individualized stimulation patterns.

Cortical Response to Acute Implantation of the Utah Optrode Array in Macaque Cortex

Optogenetics has transformed the study of neural circuit function, but limitations in its application to species with large brains, such as non-human primates (NHPs), remain. A major challenge in NHP optogenetics is delivering light to sufficiently large volumes of deep neural tissue with high spatiotemporal precision, without simultaneously affecting superficial tissue. To overcome these limitations, we recently developed and tested in vivo in NHP cortex, the Utah Optrode Array (UOA). This is a 10×10 array of penetrating glass shanks, tiling a 4×4mm 2 area, bonded to interleaved needle-aligned and interstitial µLED arrays, which allows for independent photostimulation of deep and superficial brain tissue. Here, we investigate the acute biological response to UOA implantation in NHP cortex, with the goal of optimizing device design for reduced insertion trauma and subsequent chronic response. To this goal, we systematically vary UOA shank diameter, surface texture, tip geometry, and insertion pressure, and assess their effects on astrocytes, microglia, and neuronal viability, following acute implantation. We find that UOAs with shanks of smaller diameter, smooth surface texture and round tips cause the least damage. Higher insertion pressures have limited effects on the inflammatory response, but lead to greater tissue compression. Our results highlight the importance of balancing shank diameter, tip geometry, and insertion pressure in UOA design for preserving tissue integrity and improving long-term UOA performance and biocompatibility.

Strategy and Design of In Situ Activated Protein Hydrolysis Targeted Chimeras

Protein hydrolysis targeted chimeras (PROTACs) represent a different therapeutic approach, particularly relevant for overcoming challenges associated with traditional small molecule inhibitors. These challenges include targeting difficult proteins that are often deemed "undruggable" and addressing issues of acquired resistance. PROTACs employ the body's own E3 ubiquitin ligases to induce the degradation of specific proteins of interest (POIs) through the ubiquitin-proteasome pathway. This process is cyclical, allowing for broad applicability, potent protein degradation, and selective targeting. Despite their effectiveness, PROTACs can inadvertently target and degrade nonspecific proteins, potentially resulting in significant side effects and off-target toxicity. To address this concern, researchers have created stimuli-activated PROTACs that enhance targeted protein degradation while minimizing potential harm to healthy cells. These advanced PROTACs aim to improve the precision of degradation in both time and space. This article reviews the strategies for in situ activated PROTACs, highlighting key compounds and research advancements associated with various mechanisms of action. The insights presented here aim to guide further exploration in the field of activated PROTACs.

NIR-photoactivatable DNA nanomachines for spatiotemporally controllable monitoring of microRNA-21 in living cells based on signal amplification strategy

Precise and spatiotemporally controllable analysis of microRNA-21 in living cells is crucial for accurate diagnosis and effective treatment of related diseases. Herein, a near-infrared (NIR)-photoactivatable DNA nanomachine (PUCNPs-NH2/PEG-ZL-DNA) was constructed for the precise analysis and diagnosis of microRNA-21 in tumor cells. Peanut-shaped upconversion nanoparticles (PUCNPs) were employed as the carriers and activators for the intelligent DNA probe, specifically enabling the cleavage of the photocleavable linker (PC-linker) from the hairpin DNA probe (Hp-Dzy) upon exposure to 808 nm irradiation. In the presence of the target microRNA-21, the locker DNA hybridized with microRNA-21 and the DNAzymes was freed to hybridize with the looped portion of the hairpin DNA (Hp-1). Mg2+ was employed as the cofactor, facilitating the precise cleavage of Hp-1, which triggered the restoration of fluorescence signals. Subsequently, DNAzymes exhibited the competency to selectively recognize and engage with additional Hp-1, and the fluorescence signals were effectively amplified by the recycling process. Consequently, the DNA nanomachine exhibited a linear response to microRNA-21 concentrations ranging from 0.5 nM to 1.0 μM, achieving a remarkable detection limit (LOD) of 1.19 nM under the optimal conditions. This strategy is realized through the integration of photocontrollable upconversion nanotechnology with the signal amplification approach, showing feasible prospects for spatiotemporally precise and highly sensitive monitoring of microRNA in tumor cells.

The mechanisms of electrical neuromodulation

The central and peripheral nervous systems are specialized to conduct electrical currents that underlie behaviour. When this multidimensional electrical system is disrupted by degeneration, damage, or disuse, externally applied electrical currents may act to modulate neural structures and provide therapeutic benefit. The administration of electrical stimulation can exert precise and multi-faceted effects at cellular, circuit and systems levels to restore or enhance the functionality of the central nervous system by providing an access route to target specific cells, fibres of passage, neurotransmitter systems, and/or afferent/efferent communication to enable positive changes in behaviour. Here we examine the neural mechanisms that are thought to underlie the therapeutic effects seen with current neuromodulation technologies. To gain further insights into the mechanisms associated with electrical stimulation, we summarize recent findings from genetic dissection studies conducted in animal models. KEY POINTS: Electricity is everywhere around us and is essential for how our nerves communicate within our bodies. When nerves are damaged or not working properly, using exogenous electricity can help improve their function at distinct levels - inside individual cells, within neural circuits, and across entire systems. This method can be tailored to target specific types of cells, nerve fibres, neurotransmitters and communication pathways, offering significant therapeutic potential. This overview explains how exogenous electricity affects nerve function and its potential benefits, based on research in animal studies. Understanding these effects is important because electrical neuromodulation plays a key role in medical treatments for neurological conditions.

Magnetic Resonance Imaging of Gastric Motility in Conscious Rats

INTRODUCTION

Gastrointestinal (GI) magnetic resonance imaging (MRI) enables simultaneous assessment of gastric peristalsis, emptying, and intestinal filling and transit. However, GI MRI in animals typically requires anesthesia, which complicates physiology and confounds interpretation and translation to humans. This study aimed to establish GI MRI in conscious rats, and for the first time, characterize GI motor functions in awake versus anesthetized conditions.

METHODS

Fourteen Sprague-Dawley rats were acclimated to remain awake, still, and minimally stressed during MRI. GI MRI was performed under both awake and anesthetized conditions following voluntary consumption of a contrast-enhanced test meal.

RESULTS

Awake rats remained physiologically stable during MRI, giving rise to gastric emptying of 23.7% ± 1.4% at 48 min and robust peristaltic contractions propagating through the antrum at 0.72 ± 0.04 mm/s, with a relative amplitude of 40.7% ± 2.3% and a frequency of 5.1 ± 0.1 cycles per minute. Under anesthesia, gastric emptying was approximately halved, mainly due to a significant reduction in peristaltic contraction amplitude, rather than the change in propagation speed, whereas the contraction frequency remained unchanged. Additionally, the small intestine showed faster filling and stronger motility in awake rats.

CONCLUSION

This study demonstrates the feasibility of GI MRI in awake rats and highlights notable differences in gastric and intestinal motility between awake and anesthetized states. Our protocol provides a novel and valuable framework for preclinical studies of GI physiology and pathophysiology.

Opto-Avoidance-Elevated Plus Maze protocol to study positive or negative valence upon optogenetic stimulation in the mouse brain

The elevated plus maze (EPM) apparatus consists of two open arms that provide aversive spaces and two closed arms that provide protective and welcoming spaces. Here, we present a protocol to implement the classical EPM apparatus in a real-time optogenetic environment to address behavioral avoidance in mice. We describe steps for performing stereotaxic surgery, mouse manipulation, and experimental setup. Finally, we detail the procedures required for the Opto-Avoidance-EPM test in which the naturally preferred closed arms are selectively paired with optogenetic stimulation. For complete details on the use and execution of this protocol, please refer to Serra et al.1.

PROTAC unleashed: Unveiling the synthetic approaches and potential therapeutic applications

Proteolysis-Targeting Chimeras (PROTACs) are a novel class of bifunctional small molecules that alter protein levels by targeted degradation. This innovative approach uses the ubiquitin-proteasome system to selectively eradicate disease-associated proteins, providing a novel therapeutic strategy for a wide spectrum of diseases. This review delineates detailed synthetic approaches involved in PROTAC building blocks, including the ligand and protein binding parts, linker attached structural components of PROTACs and the actual PROTAC molecules. Furthermore, the recent advancements in PROTAC-mediated degradation of specific oncogenic and other disease-associated proteins, such as those involved in neurodegenerative, antiviral, and autoimmune diseases, were also discussed. Additionally, we described the current landscape of PROTAC clinical trials and highlighted key studies that underscore the translational potential of this emerging therapeutic modality. These findings demonstrate the versatility of PROTACs in modulating the levels of key proteins involved in various severe diseases.

Optogenetic Stimulation Recruits Cortical Neurons in a Morphology-Dependent Manner

Single-photon optogenetics enables precise, cell-type-specific modulation of neuronal circuits, making it a crucial tool in neuroscience. Its miniaturization in the form of fully implantable wide-field stimulator arrays enables long-term interrogation of cortical circuits and bears promise for brain-machine interfaces for sensory and motor function restoration. However, achieving selective activation of functional cortical representations poses a challenge, as studies show that targeted optogenetic stimulation results in activity spread beyond one functional domain. While recurrent network mechanisms contribute to activity spread, here we demonstrate with detailed simulations of isolated pyramidal neurons from cats of unknown sex that already neuron morphology causes a complex spread of optogenetic activity at the scale of one cortical column. Since the shape of a neuron impacts its optogenetic response, we find that a single stimulator at the cortical surface recruits a complex spatial distribution of neurons that can be inhomogeneous and vary with stimulation intensity and neuronal morphology across layers. We explore strategies to enhance stimulation precision, finding that optimizing stimulator optics may offer more significant improvements than the preferentially somatic expression of the opsin through genetic targeting. Our results indicate that, with the right optical setup, single-photon optogenetics can precisely activate isolated neurons at the scale of functional cortical domains spanning several hundred micrometers.

Application of biomechanics in tumor epigenetic research

The field of cancer research is increasingly recognizing the complex interplay between biomechanics and tumor epigenetics. Biomechanics plays a significant role in the occurrence, development, and metastasis of cancer and may exert influence by impacting the epigenetic modifications of tumors. In this review, we investigate a spectrum of biomechanical tools, including computational models, measurement instruments, and in vitro simulations. These tools not only assist in deciphering the mechanisms behind these epigenetic changes but also provide novel methods for characterizing tumors, which are significant for diagnosis and treatment. Finally, we discuss the potential of new therapies that target the biomechanical properties of the tumor microenvironment. There is hope that by altering factors such as the stiffness of the extracellular matrix or interfering with mechano-sensing pathways, we can halt tumor progression through epigenetic mechanisms. We emphasize the necessity for multidisciplinary efforts to integrate biomechanics with tumor epigenetics more comprehensively. Such collaboration is anticipated to advance therapeutic strategies and enhance our understanding of cancer biology, signaling the dawn of a new era in cancer treatment and research.

Multifunctional Tetrode-like Drug delivery, Optical stimulation, and Electrophysiology (Tetro-DOpE) probes

Having reliable tools for recording and manipulating circuit activity are essential to understand the complex patterns of neural dynamics that underlie brain function. We present Tetro-DOpE (Tetrode-like Drug delivery, Optical stimulation, and Electrophysiology) probes that can simultaneously record and manipulate neural activity in behaving rodents. We fabricated thin multifunctional fibers (<50 μm) using the scalable convergence thermal drawing process. Then, the thin fibers are bundled, similar to tetrode fabrication, to produce Tetro-DOpE probes. We demonstrated the multifunctionality (i.e., electrophysiology, optical stimulation, and drug delivery) of our probe in head-fixed behaving mice. Furthermore, we assembled a six-shank probe mounted on a microdrive which enabled stable recordings of over months when chronically implanted in freely behaving mice. These in vivo experiments demonstrate the potential of customizable, low cost, and accessible multifunctional Tetro-DOpE probes for investigation of neural circuitry in behaving animals.

Disentangling the Neural Circuits of Arousal and Anxiety-Like Behavior

Anxiety disorders are prevalent and debilitating conditions characterized by excessive concern and fear, affecting thoughts, behaviors, and sensations. A critical component of anxiety is arousal, a complex process involving alertness regulation and stimulus salience modulation. While arousal is adaptive in normal circumstances, dysregulation can lead to hypoarousal or hyperarousal, affecting response selection and threat perception. This chapter reviews challenges in studying arousal in preclinical anxiety models, emphasizing the need for multicomponent measurement and analysis. Novel methodologies integrating physiological measurement with activity tracking of neurons with single-cell resolution in awake animals are discussed, with emphasis in current challenges. Understanding these mechanisms is crucial for developing effective treatments for anxiety disorders.

Large-Scale, High-Density MicroLED Array-Based Optogenetic Device for Neural Stimulation and Recording

Optogenetics has emerged as a pivotal tool in neuroscience, enabling precise control of neural activity through light stimulation. However, the current microLED arrays lack sufficient density and scalability. This study proposes an innovative optogenetic device capable of integrating hundreds of microLEDs and electrocorticography (ECOG) electrodes. Individual or multiple microLEDs in the device can be selectively controlled with a custom controller. The light intensity of microLEDs decreases with increasing brain tissue penetration while maintaining a low temperature rise during pulse stimulations. In addition, interference from microLED pulses on ECOG electrode recordings could be alleviated with local mean subtraction data processing. The optogenetic device enables high-quality neural signal recording and triggers a significant enhancement in neural activity following light stimulation. Integration of microLED arrays and ECOG electrodes in the optogenetic device represents a promising advancement in neuroscientific research, providing improved spatial and temporal recording and control over neural activity.

Interaction between corticotropin-releasing factor, orexin, and dynorphin in the infralimbic cortex may mediate exacerbated alcohol-seeking behavior

A major challenge for the treatment of alcohol use disorder (AUD) is relapse to alcohol use, even after protracted periods of self-imposed abstinence. Stress significantly contributes to the chronic relapsing nature of AUD, given its long-lasting ability to elicit intense craving and precipitate relapse. As individuals transition to alcohol dependence, compensatory allostatic mechanisms result in insults to hypothalamic-pituitary-adrenal axis function, mediated by corticotropin-releasing factor (CRF), which is subsequently hypothesized to alter brain reward pathways, influence affect, elicit craving, and ultimately perpetuate problematic drinking and relapse vulnerability. Orexin (OX; also called hypocretin) plays a well-established role in regulating diverse physiological processes, including stress, and has been shown to interact with CRF. Interestingly, most hypothalamic cells that express Ox mRNA also express Pdyn mRNA. Both dynorphin and OX are located in the same synaptic vesicles, and they are co-released. The infralimbic cortex (IL) of the medial prefrontal cortex (mPFC) has emerged as being directly involved in the compulsive nature of alcohol consumption during dependence. The IL is a CRF-rich region that receives OX projections from the hypothalamus and where OX receptor mRNA has been detected. Although not thoroughly understood, anatomical and behavioral pharmacology data suggest that CRF, OX, and dynorphin may interact, particularly in the IL, and that functional interactions between these three systems in the IL may be critical for the etiology and pervasiveness of compulsive alcohol seeking in dependent subjects that may render them vulnerable to relapse. The present review presents evidence of the role of the IL in AUD and discusses functional interactions between CRF, OX, and dynorphin in this structure and how they are related to exacerbated alcohol drinking and seeking.