Virus stamping for targeted single-cell infection in vitro and in vivo

Challenges in AAV-Based Retinal Gene Therapies and the Role of Magnetic Nanoparticle Platforms

Retinal diseases, leading to various visual impairments and blindness, are on the rise. However, the advancement of retinal gene therapies offers new hope for treatment of such diseases. Among different vector systems for conferring therapeutic genetic load to retinal cells, adeno-associated viruses (AAVs) have been most intensively explored and have already successfully gained multiple clinical approvals. AAV-based retinal gene therapies have shown great promise in treating retinal disorders, but usually rely on the heavily disruptive administration methods such as subretinal injection. This is because the clinically well-established, minimally invasive alternative of intravitreal injection (IVI) necessitates AAVs to traverse the retinal inner limiting membrane (ILM), which is hard to penetrate in higher eye models, like human or porcine eyes. Additionally, AAVs' natural transduction preference, known as tropism, is commonly not specific to cells of only one target retinal layer, which is another ongoing challenge in retinal gene therapy. This review examines strategies to overcome these obstacles with a focus on the potential of magnetic nanoparticles (MNPs) for improved retinal AAV delivery.

Magnetically Guided Adeno-Associated Virus Delivery for the Spatially Targeted Transduction of Retina in Eyes

Adeno-associated viruses (AAVs) are intensively explored for gene therapies in general and have found promising applications for treating retina diseases. However, controlling the specificity (tropism) and delivery of AAVs to selected layers, cell types, and areas of the retina is a major challenge to further develop retinal gene therapies. Magnetic nanoparticles (MNPs) provide effective delivery platforms to magnetically guide therapeutics to target cells. Yet, how MNPs can deliver AAVs to transfect particular retina layers and cells remains elusive. Here, it is demonstrated that MNPs can be used to transport different AAVs through the retina and to modulate the selective transduction of specific retinal layers or photoreceptor cells in ex vivo porcine explants and whole eyes. Thereby, transduction is triggered by bringing the viruses in close proximity to the target cell layer and by controlling their interaction time. It is shown that this magnetically guided approach to transport AAVs to selected areas and layers of the retina does not require the cell-specific optimization of the AAV tropism. It is anticipated that the new approach to control the delivery of AAVs and to selectively transduce cellular systems can be applied to many other tissues or organs to selectively deliver genes of interest.

Advances in optical molecular imaging for neural visualization

Iatrogenic nerve injury is a significant complication in surgery, which can negatively impact patients' quality of life. Currently, the main clinical neuroimaging methods, such as computed tomography, magnetic resonance imaging, and high-resolution ultrasonography, do not offer precise real-time positioning images for doctors during surgery. The clinical application of optical molecular imaging technology has led to the emergence of new concepts such as optical molecular imaging surgery, targeted surgery, and molecular-guided surgery. These advancements have made it possible to directly visualize surgical target areas, thereby providing a novel method for real-time identification of nerves during surgery planning. Unlike traditional white light imaging, optical molecular imaging technology enables precise positioning and identifies the cation of intraoperative nerves through the presentation of color images. Although a large number of experiments and data support its development, there are few reports on its actual clinical application. This paper summarizes the research results of optical molecular imaging technology and its ability to realize neural visualization. Additionally, it discusses the challenges neural visualization recognition faces and future development opportunities.

Organoids as a novel tool in modelling infectious diseases

Infectious diseases worldwide affect human health and have important societal impacts. A better understanding of infectious diseases is urgently needed. In vitro and in vivo infection models have brought notable contributions to the current knowledge of these diseases. Organoids are multicellular culture systems resembling tissue architecture and function, recapitulating many characteristics of human disease and elucidating mechanisms of host-infectious agent interactions in the respiratory and gastrointestinal systems, the central nervous system and the skin. Here, we discuss the applicability of the organoid technology for modeling pathogenesis, host response and features, which can be explored for the development of preventive and therapeutic treatments.

CRISPR-clear imaging of melanin-rich B16-derived solid tumors

Tissue clearing combined with deep imaging has emerged as a powerful technology to expand classical histological techniques. Current techniques have been optimized for imaging sparsely pigmented organs such as the mammalian brain. In contrast, melanin-rich pigmented tissue, of great interest in the investigation of melanomas, remains challenging. To address this challenge, we have developed a CRISPR-based gene editing approach that is easily incorporated into existing tissue-clearing workflows such the PACT clearing method. We term this method CRISPR-Clear. We demonstrate its applicability to highly melanin-rich B16-derived solid tumors, including one made transgenic for HER2, constituting one of very few syngeneic mouse tumors that can be used in immunocompetent models. We demonstrate the utility in detailed tumor characterization by staining for targeting antibodies and nanoparticles, as well as expressed fluorescent proteins. With CRISPR-Clear we have unprecedented access to optical interrogation in considerable portions of intact melanoma tissue for stained surface markers, expressed fluorescent proteins, of subcellular compartments, and of the vasculature.

Integrating Micro and Nano Technologies for Cell Engineering and Analysis: Toward the Next Generation of Cell Therapy Workflows

The emerging field of cell therapy offers the potential to treat and even cure a diverse array of diseases for which existing interventions are inadequate. Recent advances in micro and nanotechnology have added a multitude of single cell analysis methods to our research repertoire. At the same time, techniques have been developed for the precise engineering and manipulation of cells. Together, these methods have aided the understanding of disease pathophysiology, helped formulate corrective interventions at the cellular level, and expanded the spectrum of available cell therapeutic options. This review discusses how micro and nanotechnology have catalyzed the development of cell sorting, cellular engineering, and single cell analysis technologies, which have become essential workflow components in developing cell-based therapeutics. The review focuses on the technologies adopted in research studies and explores the opportunities and challenges in combining the various elements of cell engineering and single cell analysis into the next generation of integrated and automated platforms that can accelerate preclinical studies and translational research.

Nanomaterials for virus sensing and tracking

The effect of the on-going COVID-19 pandemic on global healthcare systems has underlined the importance of timely and cost-effective point-of-care diagnosis of viruses. The need for ultrasensitive easy-to-use platforms has culminated in an increased interest for rapid response equipment-free alternatives to conventional diagnostic methods such as polymerase chain reaction, western-blot assay, etc. Furthermore, the poor stability and the bleaching behavior of several contemporary fluorescent reporters is a major obstacle in understanding the mechanism of viral infection thus retarding drug screening and development. Owing to their extraordinary surface-to-volume ratio as well as their quantum confinement and charge transfer properties, nanomaterials are desirable additives to sensing and imaging systems to amplify their signal response as well as temporal resolution. Their large surface area promotes biomolecular integration as well as efficacious signal transduction. Due to their hole mobility, photostability, resistance to photobleaching, and intense brightness, nanomaterials have a considerable edge over organic dyes for single virus tracking. This paper reviews the state-of-the-art of combining carbon-allotrope, inorganic and organic-based nanomaterials with virus sensing and tracking methods, starting with the impact of human pathogenic viruses on the society. We address how different nanomaterials can be used in various virus sensing platforms (e.g. lab-on-a-chip, paper, and smartphone-based point-of-care systems) as well as in virus tracking applications. We discuss the enormous potential for the use of nanomaterials as simple, versatile, and affordable tools for detecting and tracing viruses infectious to humans, animals, plants as well as bacteria. We present latest examples in this direction by emphasizing major advantages and limitations.

All-viral tracing of monosynaptic inputs to single birthdate-defined neurons in the intact brain

Neuronal firing patterns are the result of inputs converging onto single cells. Identifying these inputs, anatomically and functionally, is essential to understand how neurons integrate information. Single-cell electroporation of helper genes and subsequent local injection of recombinant rabies viruses enable precise mapping of inputs to individual cells in superficial layers of the intact cortex. However, access to neurons in deeper structures requires more invasive procedures, including removal of overlying tissue. We developed a method that, through a combination of virus injections, allows us to target 4 or fewer hippocampal cells 48% of the time and a single cell 16% of the time in wild-type mice without use of electroporation or tissue aspiration. We identify local and distant monosynaptic inputs that can be functionally characterized in vivo. By expanding the toolbox for monosynaptic circuit tracing, this method will help further our understanding of neuronal integration at the level of single cells.

Human Brain Organoids as Models for Central Nervous System Viral Infection

Pathogenesis of viral infections of the central nervous system (CNS) is poorly understood, and this is partly due to the limitations of currently used preclinical models. Brain organoid models can overcome some of these limitations, as they are generated from human derived stem cells, differentiated in three dimensions (3D), and can mimic human neurodevelopmental characteristics. Therefore, brain organoids have been increasingly used as brain models in research on various viruses, such as Zika virus, severe acute respiratory syndrome coronavirus 2, human cytomegalovirus, and herpes simplex virus. Brain organoids allow for the study of viral tropism, the effect of infection on organoid function, size, and cytoarchitecture, as well as innate immune response; therefore, they provide valuable insight into the pathogenesis of neurotropic viral infections and testing of antivirals in a physiological model. In this review, we summarize the results of studies on viral CNS infection in brain organoids, and we demonstrate the broad application and benefits of using a human 3D model in virology research. At the same time, we describe the limitations of the studies in brain organoids, such as the heterogeneity in organoid generation protocols and age at infection, which result in differences in results between studies, as well as the lack of microglia and a blood brain barrier.

Red Light Optogenetics in Neuroscience

Optogenetics, a field concentrating on controlling cellular functions by means of light-activated proteins, has shown tremendous potential in neuroscience. It possesses superior spatiotemporal resolution compared to the surgical, electrical, and pharmacological methods traditionally used in studying brain function. A multitude of optogenetic tools for neuroscience have been created that, for example, enable the control of action potential generation via light-activated ion channels. Other optogenetic proteins have been used in the brain, for example, to control long-term potentiation or to ablate specific subtypes of neurons. In in vivo applications, however, the majority of optogenetic tools are operated with blue, green, or yellow light, which all have limited penetration in biological tissues compared to red light and especially infrared light. This difference is significant, especially considering the size of the rodent brain, a major research model in neuroscience. Our review will focus on the utilization of red light-operated optogenetic tools in neuroscience. We first outline the advantages of red light for in vivo studies. Then we provide a brief overview of the red light-activated optogenetic proteins and systems with a focus on new developments in the field. Finally, we will highlight different tools and applications, which further facilitate the use of red light optogenetics in neuroscience.

AAV capsid variants with brain-wide transgene expression and decreased liver targeting after intravenous delivery in mouse and marmoset

Genetic intervention is increasingly being explored as a therapeutic option for debilitating disorders of the central nervous system. The safety and efficacy of gene therapies rely upon expressing a transgene in affected cells while minimizing off-target expression. Here we show organ-specific targeting of adeno-associated virus (AAV) capsids after intravenous delivery, which we achieved by employing a Cre-transgenic-based screening platform and sequential engineering of AAV-PHP.eB between the surface-exposed AA452 and AA460 of VP3. From this selection, we identified capsid variants that were enriched in the brain and targeted away from the liver in C57BL/6J mice. This tropism extends to marmoset (Callithrix jacchus), enabling robust, non-invasive gene delivery to the marmoset brain after intravenous administration. Notably, the capsids identified result in distinct transgene expression profiles within the brain, with one exhibiting high specificity to neurons. The ability to cross the blood-brain barrier with neuronal specificity in rodents and non-human primates enables new avenues for basic research and therapeutic possibilities unattainable with naturally occurring serotypes.

Magnetically Single-Cell Virus Stamping

Single-cell engineering via virus based genetic manipulation allows the possibility of understanding of complex tissues. However, current delivery methods for the genetic engineering of single cells via viral transduction suffer from limitations that restrict their application. Here I present a protocol describing a precise technique which can be used for the targeted virus infection of single cells in a monolayer of cells that is optically accessible. The protocol, demonstrated here by stamping cultured Hela cells with lentiviruses (LVs), completes in a few minutes and allows stable transgene expression within a few days, at success rates approaching 80%.

Optimized Adeno-Associated Virus Vectors for Efficient Transduction of Human Retinal Organoids

The most widely used vectors for gene delivery in the retina are recombinant adeno-associated virus (rAAV) vectors. They have proven to be safe and effective in retinal gene therapy studies aimed to treat inherited retinal dystrophies, although with various limitations in transduction efficiency. Novel variants with modified capsid sequences have been engineered to improve transduction and overcome limitations of naturally occurring variants. Although preclinical evaluation of rAAV vectors based on such novel capsids is mostly done in animal models, the use of human induced pluripotent stem cell (hiPSC)-derived organoids offers an accessible and abundant human testing platform for rAAV evaluation. In this study, we tested the novel capsids, AAV9.GL and AAV9.NN, for their tropism and transduction efficiency in hiPSC-derived human retinal organoids (HROs) with all major neuronal and glial cell types in a laminated structure. These variants are based on the AAV9 capsid and were engineered to display specific surface-exposed peptide sequences, previously shown to improve the retinal transduction properties in the context of AAV2. To this end, HROs were transduced with increasing concentrations of rAAV9, rAAV9.GL, or rAAV9.NN carrying a self-complementary genome with a cytomegalovirus-enhanced green fluorescent protein (eGFP) cassette and were monitored for eGFP expression. The rAAV vectors transduced HROs in a dose-dependent manner, with rAAV9.NN achieving the highest efficiency and fastest onset kinetics, leading to detectable eGFP signals in photoreceptors, some interneurons, and Müller glia already at 2 days post-transduction. The potency-enhancing effect of the NN peptide insert was replicated when using the corresponding AAV2-based version (rAAV2.NN). Taken together, we report the application of an HRO system for screening novel AAV vectors and introduce novel vector candidates with enhanced transduction efficiency for human retinal cells.

Materials promoting viral gene delivery

Therapeutic viral gene delivery is an emerging technology which aims to correct genetic mutations by introducing new genetic information to cells either to correct a faulty gene or to initiate cell death in oncolytic treatments. In recent years, significant scientific progress has led to several clinical trials resulting in the approval of gene therapies for human treatment. However, successful therapies remain limited due to a number of challenges such as inefficient cell uptake, low transduction efficiency (TE), limited tropism, liver toxicity and immune response. To adress these issues and increase the number of available therapies, additives from a broad range of materials like polymers, peptides, lipids, nanoparticles, and small molecules have been applied so far. The scope of this review is to highlight these selected delivery systems from a materials perspective.

Rational Design of a Replication-Competent and Inheritable Magnetic Viruses for Targeting Biomedical Applications

Infection with live-attenuated vaccines always inevitably induces side effects that reduce their safety. This study suggests a concept of magnetic virus produced by genetically modifying viral surfaces with Fe₃ O₄ nanoparticles (NPs) to control their tropisms. An iron-affinity peptide is designed to be displayed on the viral surface protein (VP1) of human enterovirus type 71 (EV71), a typical nonenveloped picornavirus, as the model. The modified EV71 can self-bind with Fe₃ O₄ NPs under physiological conditions, resulting in novel EV71-Fe₃ O₄ hybrid materials. This rationally engineered EV71 with Fe₃ O₄ retains its original biological infectivity, but its tropism can be precisely controlled by magnetism. Both in vitro and in vivo experiments demonstrate that EV71-Fe₃ O₄ can infect only a desired area within the limit of the applied magnetic field, which effectively reduces its pathological damage. More importantly, this characteristic of EV71 can be inherited due to the gene-induced coassembly of viruses and NPs. This achievement provides a proof of concept in virus vaccine improvement by a combination of gene modification and material incorporation, leading to great potential for biomedical developments.

New Optical Tools to Study Neural Circuit Assembly in the Retina

During development, neurons navigate a tangled thicket of thousands of axons and dendrites to synapse with just a few specific targets. This phenomenon termed wiring specificity, is critical to the assembly of neural circuits and the way neurons manage this feat is only now becoming clear. Recent studies in the mouse retina are shedding new insight into this process. They show that specific wiring arises through a series of stages that include: directed axonal and dendritic growth, the formation of neuropil layers, positioning of such layers, and matching of co-laminar synaptic partners. Each stage appears to be directed by a distinct family of recognition molecules, suggesting that the combinatorial expression of such family members might act as a blueprint for retinal connectivity. By reviewing the evidence in support of each stage, and by considering their underlying molecular mechanisms, we attempt to synthesize these results into a wiring model which generates testable predictions for future studies. Finally, we conclude by highlighting new optical methods that could be used to address such predictions and gain further insight into this fundamental process.

The Benefits of Going Small: Nanostructures for Mammalian Cell Transfection

Nanostructures, with their localized interactions with mammalian cells, can offer better efficiency and lower cell perturbation than conventional viral, biochemical, and electroporation transfection techniques. In this Perspective, I describe the different stages of transfection and provide a comparison of transfection techniques based on their mechanisms. Focusing on specific aims of transfection, I also illustrate how recent developments in high-aspect-ratio nanostructures have endowed them with properties that are superior to existing viral, biochemical, and electroporation methods as a versatile technique to deliver a variety of cargoes and to interface with different mammalian cell types for biomedical applications. Finally, I describe the challenges associated with transfection that need to be overcome to enhance cargo delivery efficiency and clinical translation.

Near-Infrared Laser-Based Spatially Targeted Nano-enhanced Optical Delivery of Therapeutic Genes to Degenerated Retina

Non-viral delivery of therapeutic genes into targeted areas of retina is essential for re-functionalizing the retinal circuitry. While a focused ultrafast laser beam has been recently used for intra-ocular delivery of molecules, it poses the significant technical challenge of overcoming aberrations of the eye and maintaining a tightly focused spot on the retinal cell membrane. Furthermore, to minimize collateral damage and increase the throughput of gene delivery, we introduced a weakly focused near-infrared (NIR) continuous wave (CW) or pulsed laser beam on to the cells wherein the intensity is locally enhanced by gold nanorods bound to the cell membranes to permit gene insertion. Parametric optimization of nano-enhanced optical delivery (NOD) was carried out by varying the exposure time, as well as the power of the CW NIR beam or the energy of the pulsed NIR beam. Using this NOD method, therapeutic genes encoding for multi-characteristic opsins (MCOs) were delivered to spatially targeted regions of degenerated retina ex vivo as well as in vivo. NOD-mediated cell membrane-specific expression of MCOs in targeted retinal regions with photoreceptor degeneration will allow functional recovery in an ambient light environment.

BATTLE: Genetically Engineered Strategies for Split-Tunable Allocation of Multiple Transgenes in the Nervous System

Elucidating fine architectures and functions of cellular and synaptic connections requires development of new flexible methods. Here, we created a concept called the “battle of transgenes,” based on which we generated strategies using genetically engineered battles of multiple recombinases. The strategies enabled split-tunable allocation of multiple transgenes. We demonstrated the versatility of these strategies and technologies in inducing strong and multi-sparse allocations of multiple transgenes. Furthermore, the combination of our transgenic strategy and expansion microscopy enabled three-dimensional high-resolution imaging of whole synaptic structures in the hippocampus with simultaneous visualizations of endogenous synaptic proteins. These strategies and technologies based on the battle of genes may accelerate the analysis of whole synaptic and cellular connections in diverse life science fields.

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Generation of BATTLE-recombinase systems for allocation of multiple transgenes

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Split-tunable allocation in BATTLE-1 and multi-sparse allocation in BATTLE-2

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Clear and strong labeling of dendrites and axons using BATTLE-2

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3D high-resolution imaging of whole synapses in hippocampus in BATTLE-1EX

Kin discrimination in social yeast is mediated by cell surface receptors of the Flo11 adhesin family

Microorganisms have evolved specific cell surface molecules that enable discrimination between cells from the same and from a different kind. Here, we investigate the role of Flo11-type cell surface adhesins from social yeasts in kin discrimination. We measure the adhesion forces mediated by Flo11A-type domains using single-cell force spectroscopy, quantify Flo11A-based cell aggregation in populations and determine the Flo11A-dependent segregation of competing yeast strains in biofilms. We find that Flo11A domains from diverse yeast species confer remarkably strong adhesion forces by establishing homotypic interactions between single cells, leading to efficient cell aggregation and biofilm formation in homogenous populations. Heterotypic interactions between Flo11A domains from different yeast species or Saccharomyces cerevisiae strains confer weak adhesive forces and lead to efficient strain segregation in heterogenous populations, indicating that in social yeasts Flo11A-mediated cell adhesion is a major mechanism for kin discrimination at species and sub-species levels. These findings, together with our structure and mutation analysis of selected Flo11A domains, provide a rationale of how cell surface receptors have evolved in microorganisms to mediate kin discrimination.

A new colitis therapy strategy via the target colonization of magnetic nanoparticle-internalized Roseburia intestinalis

The homeostasis process in the gut tissue of humans relies on intestinal bacteria. However, the intestine is a complex structural tissue with a huge superficial area, and thus the effective application of probiotics in the treatment of Crohn's disease (CD) is still challenging. Herein, we show the feasibility of probiotic target delivery and retention using magnetic iron oxide nanoparticle-internalized Roseburia intestinalis, which can be easily directed by a magnetic field in vitro and in vivo. Subsequently, the increased colonization of this core profitable flora not only resulted in a better therapy effect than traditional intragastric administration but also altered the bacterial composition, leading to a higher diversity in microbial taxa in rats with colitis. Our findings illustrate the exciting opportunities that nanotechnology offers for alternative strategies to modulate biological systems remotely and precisely, which represent a step towards the wireless magnetic manipulation of living biological entities in microbiology.

New Technologies for Outcome Measures in Glaucoma: Review by the European Vision Institute Special Interest Focus Group

Glaucoma is the leading cause of irreversible blindness worldwide, with an increasing prevalence. The complexity of the disease has been a major challenge in moving the field forward with regard to both pathophysiological insight and treatment. In this context, discussing possible outcome measures in glaucoma trials is of utmost importance and clinical relevance. A recent meeting of the European Vision Institute (EVI) special interest focus group was held on "New Technologies for Outcome Measures in Retina and Glaucoma," addressing both functional and structural outcomes, as well as translational hot topics in glaucoma and retina research. In conjunction with the published literature, this review summarizes the meeting focusing on glaucoma.

Genetic Modification of Brain Organoids

Brain organoids have become increasingly used systems allowing 3D-modeling of human brain development, evolution, and disease. To be able to make full use of these modeling systems, researchers have developed a growing toolkit of genetic modification techniques. These techniques can be applied to mature brain organoids or to the preceding embryoid bodies (EBs) and founding cells. This review will describe techniques used for transient and stable genetic modification of brain organoids and discuss their current use and respective advantages and disadvantages. Transient approaches include adeno-associated virus (AAV) and electroporation-based techniques, whereas stable genetic modification approaches make use of lentivirus (including viral stamping), transposon and CRISPR/Cas9 systems. Finally, an outlook as to likely future developments and applications regarding genetic modifications of brain organoids will be presented.

Next-generation interfaces for studying neural function

Monitoring and modulating the diversity of signals used by neurons and glia in a closed-loop fashion is necessary to establish causative links between biochemical processes within the nervous system and observed behaviors. As developments in neural-interface hardware strive to keep pace with rapid progress in genetically encoded and synthetic reporters and modulators of neural activity, the integration of multiple functional features becomes a key requirement and a pressing challenge in the field of neural engineering. Electrical, optical and chemical approaches have been used to manipulate and record neuronal activity in vivo, with a recent focus on technologies that both integrate multiple modes of interaction with neurons into a single device and enable bidirectional communication with neural circuits with enhanced spatiotemporal precision. These technologies not only are facilitating a greater understanding of the brain, spinal cord and peripheral circuits in the context of health and disease, but also are informing the development of future closed-loop therapies for neurological, neuro-immune and neuroendocrine conditions.

Molecular Cloning, Lentiviral Transduction, and Expression of Recombinant ADAMTSL2 and ADAMTSL4

Lentiviral systems have proven advantageous in the delivery and long-term integration of gene sequences into the genome of several cell types in vitro, in vivo, as well as in clinical trials. Here we detail the protocols involved in the molecular cloning of ADAMTSL2 and ADAMTSL4 into the human immunodeficiency virus (HIV)-derived pCDH lentiviral system. We also describe the lentiviral transduction of ADAMTSL2 and ADAMTSL4 into mammalian HEK293-EBNA cells to create stable cell lines, as well as their recombinant expression.

Large-Scale, High-Resolution Microelectrode Arrays for Interrogation of Neurons and Networks

High-density microelectrode arrays (HD-MEAs) are increasingly being used for the observation and manipulation of neurons and networks in vitro. Large-scale electrode arrays allow for long-term extracellular recording of the electrical activity from thousands of neurons simultaneously. Beyond population activity, it has also become possible to extract information of single neurons at subcellular level (e.g., the propagation of action potentials along axons). In effect, HD-MEAs have become an electrical imaging platform for label-free extraction of the structure and activation of cells in cultures and tissues. The quality of HD-MEA data depends on the resolution of the electrode array and the signal-to-noise ratio. In this chapter, we begin with an introduction to HD-MEA signals. We provide an overview of the developments on complementary metal-oxide-semiconductor or CMOS-based HD-MEA technology. We also discuss the factors affecting the performance of HD-MEAs and the trending application requirements that drive the efforts for future devices. We conclude with an outlook on the potential of HD-MEAs for advancing basic neuroscience and drug discovery.

New Technologies for Outcome Measures in Retinal Disease: Review from the European Vision Institute Special Interest Focus Group

Novel diagnostic tools to measure retinal function and structure are rapidly being developed and introduced into clinical use. Opportunities exist to use these informative and robust measures as endpoints for clinical trials to determine efficacy and to monitor safety of therapeutic interventions. In order to inform researchers and clinician-scientists about these new diagnostic tools, a workshop was organized by the European Vision Institute. Invited speakers highlighted the recent advances in state-of-the-art technologies for outcome measures in the field of retina. This review highlights the workshop's presentations in the context of published literature.

Imaging: Gear up for mechano-immunology

Immune cells including B and T lymphocytes have a remarkable ability to sense the physical perturbations through their surface expressed receptors. At the advent of modern imaging technologies paired with biophysical methods, we have gained the understanding of mechanical forces exerted by immune cells to perform their functions. This review will go over the imaging techniques already being used to study mechanical forces in immune cells. We will also discuss the dire need for new modern technologies for future work.

PatcherBot: a single-cell electrophysiology robot for adherent cells and brain slices

OBJECTIVE

Intracellular patch-clamp electrophysiology, one of the most ubiquitous, high-fidelity techniques in biophysics, remains laborious and low-throughput. While previous efforts have succeeded at automating some steps of the technique, here we demonstrate a robotic 'PatcherBot' system that can perform many patch-clamp recordings sequentially, fully unattended.

APPROACH

Comprehensive automation is accomplished by outfitting the robot with machine vision, and cleaning pipettes instead of manually exchanging them.

MAIN RESULTS

the PatcherBot can obtain data at a rate of 16 cells per hour and work with no human intervention for up to 3 h. We demonstrate the broad applicability and scalability of this system by performing hundreds of recordings in tissue culture cells and mouse brain slices with no human supervision. Using the PatcherBot, we also discovered that pipette cleaning can be improved by a factor of three.

SIGNIFICANCE

The system is potentially transformative for applications that depend on many high-quality measurements of single cells, such as drug screening, protein functional characterization, and multimodal cell type investigations.

The first steps in vision: cell types, circuits, and repair

Dysfunction of the key sense of vision, leading to visual handicap or blindness, has a crucial effect on day-to-day life. In this commentary, I will summarize the work in my laboratory that is focused on a basic understanding of visual processing and the use of this information to understand disease mechanism and to develop correcting therapies. We are beginning to understand how cell types of the visual system interact in local circuits and compute visual information. This has brought insight into mechanisms of cell-type-specific diseases and has allowed us to design new therapies for restoring vision in genetic forms of blindness.

Accurate signal-source localization in brain slices by means of high-density microelectrode arrays

Extracellular recordings by means of high-density microelectrode arrays (HD-MEAs) have become a powerful tool to resolve subcellular details of single neurons in active networks grown from dissociated cells. To extend the application of this technology to slice preparations, we developed models describing how extracellular signals, produced by neuronal cells in slices, are detected by microelectrode arrays. The models help to analyze and understand the electrical-potential landscape in an in vitro HD-MEA-recording scenario based on point-current sources. We employed two modeling schemes, (i) a simple analytical approach, based on the method of images (MoI), and (ii) an approach, based on finite-element methods (FEM). We compared and validated the models with large-scale, high-spatiotemporal-resolution recordings of slice preparations by means of HD-MEAs. We then developed a model-based localization algorithm and compared the performance of MoI and FEM models. Both models provided accurate localization results and a comparable and negligible systematic error, when the point source was in saline, a condition similar to cell-culture experiments. Moreover, the relative random error in the x-y-z-localization amounted only up to 4.3% for z-distances up to 200 μm from the HD-MEA surface. In tissue, the systematic errors of both, MoI and FEM models were significantly higher, and a pre-calibration was required. Nevertheless, the FEM values proved to be closer to the tissue experimental results, yielding 5.2 μm systematic mean error, compared to 22.0 μm obtained with MoI. These results suggest that the medium volume or "saline height", the brain slice thickness and anisotropy, and the location of the reference electrode, which were included in the FEM model, considerably affect the extracellular signal and localization performance, when the signal source is at larger distance to the array. After pre-calibration, the relative random error of the z-localization in tissue was only 3% for z-distances up to 200 μm. We then applied the model and related detailed understanding of extracellular recordings to achieve an electrically-guided navigation of a stimulating micropipette, solely based on the measured HD-MEA signals, and managed to target spontaneously active neurons in an acute brain slice for electroporation.

Cell-type-specific and projection-specific brain-wide reconstruction of single neurons

We developed a dual-adeno-associated-virus expression system that enables strong and sparse labeling of individual neurons with cell-type and projection specificity. We demonstrated its utility for whole-brain reconstruction of midbrain dopamine neurons and striatum-projecting cortical neurons. We further extended the labeling method for rapid reconstruction in cleared thick brain sections and simultaneous dual-color labeling. This labeling system may facilitate the process of generating mesoscale single-neuron projectomes of mammalian brains.

Fluorinated Oligoethylenimine Nanoassemblies for Efficient siRNA-Mediated Gene Silencing in Serum-Containing Media by Effective Endosomal Escape

Efficient small interfering RNA (siRNA) delivery in the presence of serum is of crucial importance for effective gene therapy. Fluorinated vectors are considered to be attractive candidates for siRNA-mediated gene therapy because of their delivery efficacy in serum-containing media. However, the mechanisms driving the superior gene transfection behavior of fluorinated vectors are still not well-understood, and comprehensive investigations are warranted. Herein, we fabricated a library of perfluorooctanoyl fluoride-fluorinated (PFF-fluorinated) oligoethylenimines (f _xOEIs, x is the PFF:OEI feeding ratio), which can readily form nanoassemblies (f _xOEI NAs) capable of efficient siRNA delivery in cells cultured in medium both devoid of and supplemented with fetal bovine serum (FBS). The gene silencing test in serum-containing medium revealed that the f_0.7OEI/siRNA NAs achieved a luciferase silencing of ∼88.4% in Luc-HeLa cells cultured in FBS-containing medium, which was almost 2-fold greater than the silencing efficacy of siRNA delivered by the commercially available vector Lipo 2000 (∼48.8%). High levels of apolipoprotein B silencing were also achieved by f_0.7OEI/siRNA NAs in vivo. For an assessment of the underlying mechanisms of the efficacy of gene silencing of fluorinated vectors, two alkylated OEIs, aOEI-C8 and aOEI-C12, were fabricated as controls with similar molecular structure and hydrophobicity to that of f_0.7OEI, respectively. In vitro investigations showed that the superior gene delivery exhibited by f_0.7OEI NAs derived from the potent endosomal disruption capability of fluorinated vectors in the presence of serum, which was essentially attributed to the serum protein adsorption resistance of the f_0.7OEI NAs. Therefore, this work provides an innovative approach to siRNA delivery as well as insights into fluorine-associated serum resistance.