A half century of experimental neuroanatomical tracing

Viral Vectors for Neural Circuit Mapping and Recent Advances in Trans-synaptic Anterograde Tracers

Viral tracers are important tools for neuroanatomical mapping and genetic payload delivery. Genetically modified viruses allow for cell-type-specific targeting and overcome many limitations of non-viral tracers. Here, we summarize the viruses that have been developed for neural circuit mapping, and we provide a primer on currently applied anterograde and retrograde viral tracers with practical guidance on experimental uses. We also discuss and highlight key technical and conceptual considerations for developing new safer and more effective anterograde trans-synaptic viral vectors for neural circuit analysis in multiple species.

[Use of Transsynaptic Viral Tracers for Observing Neural Circuit Control of Physiological Responses]

Central neural circuits in the brain receive and integrate environmental and internal information to enable the animals to execute appropriate behaviors and physiological responses. Communication between the brain and peripheral organs via peripheral neural circuits maintains energy homeostasis in the body. Therefore it is important to investigate the anatomical organization of central and peripheral neural circuits for elucidating the mechanisms of energy homeostasis. Transsynaptic viral tracers can travel through connected neurons via synaptic connections and have been used to delineate the anatomical organization of neural circuits with specific functions. Herein, I review our recent studies investigating neural circuits and their involvement in physiological changes using transsynaptic tracers.

A Large-Scale High-Density Weighted Structural Connectome of the Macaque Brain Acquired by Predicting Missing Links

As a substrate for function, large-scale brain structural networks are crucial for fundamental and systems-level understanding of primate brains. However, it is challenging to acquire a complete primate whole-brain structural connectome using track tracing techniques. Here, we acquired a weighted brain structural network across 91 cortical regions of a whole macaque brain hemisphere with a connectivity density of 59% by predicting missing links from the CoCoMac-based binary network with a low density of 26.3%. The prediction model combines three factors, including spatial proximity, topological similarity, and cytoarchitectural similarity-to predict missing links and assign connection weights. The model was tested on a recently obtained high connectivity density yet partial-coverage experimental weighted network connecting 91 sources to 29 target regions; the model showed a prediction sensitivity of 74.1% in the predicted network. This predicted macaque hemisphere-wide weighted network has module segregation closely matching functional domains. Interestingly, the areas that act as integrators linking the segregated modules are mainly distributed in the frontoparietal network and correspond to the regions with large wiring costs in the predicted weighted network. This predicted weighted network provides a high-density structural dataset for further exploration of relationships between structure, function, and metabolism in the primate brain.

Modular output circuits of the fastigial nucleus for diverse motor and nonmotor functions of the cerebellar vermis

The cerebellar vermis, long associated with axial motor control, has been implicated in a surprising range of neuropsychiatric disorders and cognitive and affective functions. Remarkably little is known, however, about the specific cell types and neural circuits responsible for these diverse functions. Here, using single-cell gene expression profiling and anatomical circuit analyses of vermis output neurons in the mouse fastigial (medial cerebellar) nucleus, we identify five major classes of glutamatergic projection neurons distinguished by gene expression, morphology, distribution, and input-output connectivity. Each fastigial cell type is connected with a specific set of Purkinje cells and inferior olive neurons and in turn innervates a distinct collection of downstream targets. Transsynaptic tracing indicates extensive disynaptic links with cognitive, affective, and motor forebrain circuits. These results indicate that diverse cerebellar vermis functions could be mediated by modular synaptic connections of distinct fastigial cell types with posturomotor, oromotor, positional-autonomic, orienting, and vigilance circuits.

Labeling Dual Presynaptic Inputs using cFork Anterograde Tracing System

Understanding brain function-related neural circuit connectivity is essential for investigating how cognitive functions are decoded in neural circuits. Trans-synaptic viral vectors are useful for identifying neural synaptic connectivity because of their ability to be transferred from transduced cells to synaptically connected cells. However, concurrent labeling of multisynaptic inputs to postsynaptic neurons is impossible with currently available trans-synaptic viral vectors. Here, we report a neural circuit tracing system that can simultaneously label postsynaptic neurons with two different markers, the expression of which is defined by presynaptic input connectivity. This system, called “cFork (see fork)”, includes delivering serotype 1-packaged AAV vectors (AAV1s) containing Cre or flippase recombinase (FlpO) into two different presynaptic brain areas, and AAV5 with a dual gene expression cassette in postsynaptic neurons. Our in vitro and in vivo tests showed that selective expression of two different fluorescence proteins, EGFP and mScarlet, in postsynaptic neurons could be achieved by AAV1-mediated anterograde trans-synaptic transfer of Cre or FlpO constructs. When this tracing system was applied to the somatosensory barrel field cortex (S1BF) or striatum innervated by multiple presynaptic inputs, postsynaptic neurons defined by presynaptic inputs were simultaneously labeled with EGFP or mScarlet. Our new anterograde tracing tool may be useful for elucidating the complex multisynaptic connectivity of postsynaptic neurons regulating diverse brain functions.

hFRUIT: An optimized agent for optical clearing of DiI-stained adult human brain tissue

Here, we describe a new immersion-based clearing method suitable for optical clearing of thick adult human brain samples while preserving its lipids and lipophilic labels such as 1,1'-dioctadecyl-3,3,3',3'-tetramethylindocarbocyanine perchlorate (DiI). This clearing procedure is simple, easy to implement, and allowed for clearing of 5 mm thick human brain tissue samples within 12 days. Furthermore, we show for the first time the advantageous effect of the Periodate-Lysine-Paraformaldehyde (PLP) fixation as compared to the more commonly used 4% paraformaldehyde (PFA) on clearing performance.

Pneumonia-induced endothelial amyloids reduce dendritic spine density in brain neurons

Pseudomonas aeruginosa pneumonia elicits endothelial cell release of cytotoxic amyloids that can be recovered from the bronchoalveolar lavage and cerebrospinal fluids of critically ill patients. Introduction of these cytotoxic amyloids into the lateral ventricle impairs learning and memory in mice. However, it is unclear whether the amyloids of lung origin (1) are neurotropic, and (2) cause structural remodeling of hippocampal dendrites. Thus, we used electrophysiological studies in brain slices and structural analysis of post-mortem tissues obtained from animals exposed to endothelium-derived amyloids to assess these issues. The amyloids were administered via three different routes, by intracerebroventricular, intratracheal, and intraperitoneal injections. Synaptic long-term potentiation was abolished following intracerebroventricular amyloid injection. Fluorescence dialysis or Golgi-impregnation labeling showed reduced dendritic spine density and destabilized spines of hippocampal pyramidal neurons 4 weeks after intracerebroventricular amyloid injection. In comparison, endothelial amyloids introduced to the airway caused the most prominent dendritic spine density reduction, yet intraperitoneal injection of these amyloids did not affect spine density. Our findings indicate that infection-elicited lung endothelial amyloids are neurotropic and reduce neuronal dendritic spine density in vivo. Amyloids applied into the trachea may either be disseminated through the circulation and cross the blood-brain barrier to access the brain, initiate feed-forward amyloid transmissibility among cells of the blood-brain barrier or access the brain in other ways. Nevertheless, lung-derived amyloids suppress hippocampal signaling and cause injury to neuronal structure.

Neuroanatomical tract-tracing techniques that did go viral

Neuroanatomical tracing methods remain fundamental for elucidating the complexity of brain circuits. During the past decades, the technical arsenal at our disposal has been greatly enriched, with a steady supply of fresh arrivals. This paper provides a landscape view of classical and modern tools for tract-tracing purposes. Focus is placed on methods that have gone viral, i.e., became most widespread used and fully reliable. To keep an historical perspective, we start by reviewing one-dimensional, standalone transport-tracing tools; these including today's two most favorite anterograde neuroanatomical tracers such as Phaseolus vulgaris-leucoagglutinin and biotinylated dextran amine. Next, emphasis is placed on several classical tools widely used for retrograde neuroanatomical tracing purposes, where Fluoro-Gold in our opinion represents the best example. Furthermore, it is worth noting that multi-dimensional paradigms can be designed by combining different tracers or by applying a given tracer together with detecting one or more neurochemical substances, as illustrated here with several examples. Finally, it is without any doubt that we are currently witnessing the unstoppable and spectacular rise of modern molecular-genetic techniques based on the use of modified viruses as delivery vehicles for genetic material, therefore, pushing the tract-tracing field forward into a new era. In summary, here, we aim to provide neuroscientists with the advice and background required when facing a choice on which neuroanatomical tracer-or combination thereof-might be best suited for addressing a given experimental design.

Tracing the retina to analyze the integrity and phagocytic capacity of the retinal pigment epithelium

We have developed a new technique to study the integrity, morphology and functionality of the retinal neurons and the retinal pigment epithelium (RPE). Young and old control albino (Sprague-Dawley) and pigmented (Piebald Virol Glaxo) rats, and dystrophic albino (P23H-1) and pigmented (Royal College of Surgeons) rats received a single intravitreal injection of 3% Fluorogold (FG) and their retinas were analyzed from 5 minutes to 30 days later. Retinas were imaged in vivo with SD-OCT and ex vivo in flat-mounts and in cross-sections. Fifteen minutes and 24 hours after intravitreal administration of FG retinal neurons and the RPE, but no glial cells, were labeled with FG-filled vesicles. The tracer reached the RPE 15 minutes after FG administration, and this labeling remained up to 30 days. Tracing for 15 minutes or 24 hours did not cause oxidative stress. Intraretinal tracing delineated the pathological retinal remodelling occurring in the dystrophic strains. The RPE of the P23H-1 strain was highly altered in aged animals, while the RPE of the RCS strain, which is unable to phagocytose, did not accumulate the tracer even at young ages when the retinal neural circuit is still preserved. In both dystrophic strains, the RPE cells were pleomorphic and polymegathic.

Viral approaches to study the mammalian brain: Lineage tracing, circuit dissection and therapeutic applications

Viral vectors are widely used to study the development, function and pathology of neural circuits in the mammalian brain. Their flexible payloads with customizable choices of tool genes allow versatile applications ranging from lineage tracing, circuit mapping and functional interrogation, to translational and therapeutic applications. Different applications have distinct technological requirements, therefore, often utilize different types of virus. This review introduces the most commonly used viruses for these applications and some recent advances in improving the resolution and throughput of lineage tracing, the efficacy and selectivity of circuit tracing and the specificity of cell type targeting.

Optimizing techniques for injecting DiI into the brain nuclei of neonatal mice P6 - C57Bl6/CBA

DiI (1,1'-dioctadecyl-3,3,3'3'-tetramethylindocarbocyanine perchlorate) is a lipophilic dye used to research the intracerebral connections of neonatal animals. This dye is most frequently used in the form of dry crystals, but injections of the marker in this state into the mouse brain nuclei, such as MHb (2 cases), LHbM (2 cases), LPA (3 cases) and TS (1 case), clearly revealed excessive lateral diffusion marker into the tissue. Eventually, all the investigated cases except the LPA gave a false positive result. To find the optimal method of marker injection,DiI-kerosene liquid films (3 cases in the MHb); DiI-kerosene gelatinous paste (3 cases in the MHb); injections of insoluble DiI crystals from a solution of 99% dmso (3 cases in the MHb) and 70% ethanol (3 cases in the MHb, 2 cases in the LHbM, 4 cases in the TS) were tested. Injections of DiI in the form of undissolved crystals from a 70% ethanol solution gave a minimal level of side diffusion in all the studied cases. This method of injection is optimal and recommended for use.

Comparative neuroanatomy: Integrating classic and modern methods to understand association fibers connecting dorsal and ventral visual cortex

Comparative neuroanatomy studies improve understanding of brain structure and function and provide insight regarding brain development, evolution, and also what features of the brain are uniquely human. With modern methods such as diffusion MRI (dMRI) and quantitative MRI (qMRI), we are able to measure structural features of the brain with the same methods across human and non-human primates. In this review article, we discuss how recent dMRI measurements of vertical occipital connections in humans and macaques can be compared with previous findings from invasive anatomical studies that examined connectivity, including relatively forgotten classic strychnine neuronography studies. We then review recent progress in understanding the neuroanatomy of vertical connections within the occipitotemporal cortex by combining modern quantitative MRI and classical histological measurements in human and macaque. Finally, we a) discuss current limitations of dMRI and tractography and b) consider potential paths for future investigations using dMRI and tractography for comparative neuroanatomical studies of white matter tracts between species. While we focus on vertical association connections in visual cortex in the present paper, this same approach can be applied to other white matter tracts. Similar efforts are likely to continue to advance our understanding of the neuroanatomical features of the brain that are shared across species, as well as to distinguish the features that are uniquely human.

A Student's Guide to Neural Circuit Tracing

The mammalian nervous system is comprised of a seemingly infinitely complex network of specialized synaptic connections that coordinate the flow of information through it. The field of connectomics seeks to map the structure that underlies brain function at resolutions that range from the ultrastructural, which examines the organization of individual synapses that impinge upon a neuron, to the macroscopic, which examines gross connectivity between large brain regions. At the mesoscopic level, distant and local connections between neuronal populations are identified, providing insights into circuit-level architecture. Although neural tract tracing techniques have been available to experimental neuroscientists for many decades, considerable methodological advances have been made in the last 20 years due to synergies between the fields of molecular biology, virology, microscopy, computer science and genetics. As a consequence, investigators now enjoy an unprecedented toolbox of reagents that can be directed against selected subpopulations of neurons to identify their efferent and afferent connectomes. Unfortunately, the intersectional nature of this progress presents newcomers to the field with a daunting array of technologies that have emerged from disciplines they may not be familiar with. This review outlines the current state of mesoscale connectomic approaches, from data collection to analysis, written for the novice to this field. A brief history of neuroanatomy is followed by an assessment of the techniques used by contemporary neuroscientists to resolve mesoscale organization, such as conventional and viral tracers, and methods of selecting for sub-populations of neurons. We consider some weaknesses and bottlenecks of the most widely used approaches for the analysis and dissemination of tracing data and explore the trajectories that rapidly developing neuroanatomy technologies are likely to take.

Retinal ganglion cell topography and spatial resolution estimation in the Japanese tree frog Hyla japonica (Günther, 1859)

Tree frogs are an interesting and diverse group of frogs. They display a number of unique adaptations to life in the arboreal environment. Vision plays a crucial role in their ecology. The topography of retinal ganglion cells (GCs) is closely related to a species' visual behavior. Despite a large amount of research addressing GC topography in vertebrates, there is scarce data on this subject in tree frogs. I studied the topography of GCs in the retina of the Japanese tree frog Hyla japonica. The GC density distribution was locally fairly homogeneous, with spatial density increasing gradually from the dorsal and ventral periphery towards the equator. A moderately pronounced visual streak was found close to the equator in the dorsal hemiretina, with a distinct area retinae temporalis in the dorsotemporal quadrant potentially subserving binocular vision. The minimum GC density (mean ± SEM, n = 5) was 3060 ± 60 and the maximum 12 800 ± 170 cells/mm² . The total number of GCs was 292 ± 7 × 10³ . The theoretical anatomical spatial resolution estimated from GC densities and eye optics was lowest in the ventral periphery (ca. 0.9 and 1.3 cycles/degree in air and water, respectively) and highest in the area retinae temporalis (ca. 2.1 and 2.8 cycles/degree). The relatively high GC density and presence of specialized retinal regions in Hyla japonica are consistent with its highly visual behavior. The present findings contribute to our understanding of the relative role of common ancestry and environmental pressure in GC topography variation within Anura.

Review of micro-optical sectioning tomography (MOST): technology and applications for whole-brain optical imaging [Invited]

Elucidating connectivity and functionality at the whole-brain level is one of the most challenging research goals in neuroscience. Various whole-brain optical imaging technologies with submicron lateral resolution have been developed to reveal the fine structures of brain-wide neural and vascular networks at the mesoscopic level. Among them, micro-optical sectioning tomography (MOST) is attracting increasing attention, as a variety of technological variations and solutions tailored toward different biological applications have been optimized. Here, we summarize the recent development of MOST technology in whole-brain imaging and anticipate future improvements.

Decoding the microstructural correlate of diffusion MRI

Diffusion imaging has evolved considerably over the past decade. While it provides valuable information about the structural connectivity at the macro- and mesoscopic scale, bridging the gap to the microstructure at the level of single nerve fibers poses an enormous challenge. This is particularly true for the human brain with its large size, its large white-matter volume and availability of histological techniques for studying human whole-brain sections and subsequent 3D reconstruction. Classic post-mortem techniques for studying the fiber architecture of the brain, such as myeloarchitectonic staining or dye tracing, are complemented by novel histological approaches, such as 3D polarized light imaging or optical coherence tomography, enabling unique insight into the fiber architecture from large fiber bundles within deep white matter to single nerve fibers in the cortex. The present review discusses the benefits and challenges of these latest developments in comparison with the classic techniques, with particular focus on the mutual exchange between in vivo and post-mortem diffusion imaging and post-mortem microstructural approaches for understanding the wiring of the brain across different scales.

MemBright: A Family of Fluorescent Membrane Probes for Advanced Cellular Imaging and Neuroscience

The proper staining of the plasma membrane (PM) is critical in bioimaging as it delimits the cell. Herein, we developed MemBright, a family of six cyanine-based fluorescent turn-on PM probes that emit from orange to near infrared when reaching the PM, and enable homogeneous and selective PM staining with excellent contrast in mono- and two-photon microscopy. These probes are compatible with long-term live-cell imaging and immunostaining. Moreover, MemBright label neurons in a brighter manner than surrounding cells, allowing identification of neurons in acute brain tissue sections and neuromuscular junctions without any use of transfection or transgenic animals. In addition, MemBright probes were used in super-resolution imaging to unravel the neck of dendritic spines. 3D multicolor dSTORM in combination with immunostaining revealed en-passant synapse displaying endogenous glutamate receptors clustered at the axonal-dendritic contact site. MemBright probes thus constitute a universal toolkit for cell biology and neuroscience biomembrane imaging with a variety of microscopy techniques. VIDEO ABSTRACT.

Exploring the limits of network topology estimation using diffusion-based tractography and tracer studies in the macaque cortex

Reconstructing the anatomical pathways of the brain to study the human connectome has become an important endeavour for understanding brain function and dynamics. Reconstruction of the cortico-cortical connectivity matrix in vivo often relies on noninvasive diffusion-weighted imaging (DWI) techniques but the extent to which they can accurately represent the topological characteristics of structural connectomes remains unknown. We addressed this question by constructing connectomes using DWI data collected from macaque monkeys in vivo and with data from published invasive tracer studies. We found the strength of fiber tracts was well estimated from DWI and topological properties like degree and modularity were captured by tractography-based connectomes. Rich-club/core-periphery type architecture could also be detected but the classification of hubs using betweenness centrality, participation coefficient and core-periphery identification techniques was inaccurate. Our findings indicate that certain aspects of cortical topology can be faithfully represented in noninvasively-obtained connectomes while other network analytic measures warrant cautionary interpretations.

In Vivo Genetic Strategies for the Specific Lineage Tracing of Stem Cells

BACKGROUND

Characterization of the fate changes of stem cells is essential to understand the roles of certain stem cells both during development and in diseases, such as cancer. In the past two decades, more and more importance has been paid to the studies of in vivo lineage tracing, because they could authentically reveal the differentiation, migration and even proliferation of stem cells. However, specific genetic tools have only been developed until recently.

OBJECTIVE

To summarize the progresses of genetic tools for specific lineage tracing with emphasis on their applications in investigating the stem cell niche signals.

RESULTS

Three major genetic strategies have been reviewed according to the development of technique, particularly the advantages and disadvantages of individual methods.

CONCLUSION

In vivo specific lineage tracing of stem cells could be achieved by comprehensive application of multiple genetic tools.

A brand-new generation of fluorescent nano-neural tracers: biotinylated dextran amine conjugated carbonized polymer dots

We develop a novel fluorescent nano-neural tracer: BDA–CPDs, which can be anterogradely transported within the peripheral nervous system of rats.

Did you choose appropriate tracer for retrograde tracing of retinal ganglion cells? The differences between cholera toxin subunit B and Fluorogold

Cholera toxin subunit B (CTB) and Fluorogold(FG) are two widely utilized retrograde tracers to assess the number and function of retinal ganglion cells (RGCs). However, the relative advantages and disadvantages of these tracers remain unclear, which may lead to their inappropriate application. In this study, we compared these tracers by separately injecting the tracer into the superior Colliculi (SC) in rats, one or 2 weeks later, the rats were sacrificed, and their retinas, brains, and optic nerves were collected. From the first to second week, FG displayed a greater number of labeled RGCs and a larger diffusion area in the SC than CTB; The number of CTB labeled RGCs and the diffusion area of CTB in the SC increased significantly, but there was no distinction between FG; Furthermore, CTB exhibited more labeled RGC neurites and longer neurites than FG, but no difference was evident between the same trace; The optic nerves labeled using CTB were much clearer than those labeled using FG. In conclusion, both CTB and FG can be used for the retrograde labeling of RGCs in rats at 1 or 2 weeks. FG achieves retrograde labeling of a greater number of RGCs than CTB, whereas CTB better delineates the morphology of RGCs. Furthermore, CTB seems more suitable for retrograde labeling of some small, non-image forming nuclei in the brain to which certain RGC subtypes project their axons.

Differential innervation of tissues located at traditional acupuncture points in the rat forehead and face

OBJECTIVES

To compare the neural pathways associated with the tissues located at different traditional acupuncture points in the rat forehead and face using the cholera toxin B subunit (CTB) neural tracing technique.

METHODS

After injection of CTB into the tissues at GB14, ST2 and ST6 in the rat, the neural labelling associated with each acupuncture point was revealed by fluorescent immunohistochemistry of the nervous system, including the trigeminal ganglion (TRG), cervical dorsal root ganglia (DRG), spinal cord and brain.

RESULTS

The CTB labelling included sensory neurons and their transganglionic axonal terminals, as well as motor neurons. The labelled sensory neurons associated with GB14, ST2 and ST6 were distributed in both the TRG and cervical DRG, and their centrally projected axons terminated in an orderly fashion at their corresponding targets in the spinal trigeminal nucleus and cervical spinal dorsal horn. In addition, labelled motor neurons were observed in the facial motor nucleus, trigeminal motor nucleus and cervical spinal ventral horn, in which facial motor neurons projected to the tissues located at all three acupuncture points. Trigeminal motor neurons innervated both ST2 and ST6, while spinal motor neurons only correlated with ST6.

CONCLUSIONS

These results indicate that the tissues located at each of these three traditional acupuncture points in the rat forehead and face has its own sensory and motor connection with the nervous system in a region-specific pattern through distinct neural pathways. Understanding the neuroanatomical characteristics of acupuncture points from the peripheral nervous system to the central nervous system should help inform acupuncture point selection according to the demands of the clinical situation.

Differential Ascending Projections From the Male Rat Caudal Nucleus of the Tractus Solitarius: An Interface Between Local Microcircuits and Global Macrocircuits

To integrate and broadcast neural information, local microcircuits and global macrocircuits interact within certain specific nuclei of the central nervous system. The structural and functional architecture of this interaction was determined for the caudal nucleus of the tractus solitarius (NTS) at the level of the area postrema (AP), a relay station of peripheral viscerosensory information that is processed and conveyed to brain regions concerned with autonomic-affective and other interoceptive reflexive functions. Axon collaterals of most small NTS cells (soma <150 μm²) establish excitatory or inhibitory local microcircuits likely to control the activity of nearby NTS cells and to transfer peripheral signals to efferent projection neurons. At least two types of cells that constitute efferent pathways from the caudal NTS (cNTS) were distinguished: (1) a greater numbers of small cells, seemingly forming local excitatory microcircuits via recurrent axon collaterals, that project specifically and unidirectionally to the lateral parabrachial nucleus; and (2) a much smaller numbers of cells likely to establish multiple global connections, mostly via the medial forebrain bundle (MFB) or the dorsal longitudinal fascicle (DLF), with a wide range of brain regions, including the ventrolateral medulla (VLM), hypothalamus, central nucleus of the amygdala (ACe), bed nucleus of the stria terminalis (BNST), spinal cord dorsal horn, brainstem reticular formation, locus coeruleus (LC), periaqueductal gray (PAG) and periventricular diencephalon (including the epithalamus). The evidence presented here suggests that distinct cNTS cell types distinguished by projection pattern and related structural and functional features participate differentially in the computation of viscerosensory information and coordination of global macro-networks in a highly organized manner.

The Establishment of a CSF-Contacting Nucleus "Knockout" Model Animal

To establish an entirely cerebrospinal fluid (CSF)-contacting nucleus-deficient model animal, we used cholera toxin B subunit (CB)- saporin (SAP), which is an analog of CB-HRP that specifically labels the CSF-contacting nucleus, to exclusively damage the nucleus. The effectiveness and specificity of the ablation were evaluated upon days 1-10 after CB-SAP microinjection into the brain ventricular system. The vital status, survival, and common physiological parameters of the model animals were also assessed during the experimental period. The results demonstrated that CB-SAP damaged only the CSF-contacting nucleus, but not other functional structures, in the brain. The complete ablation occurred by day 7 after CB-SAP microinjection. A model animal that had no CSF-contacting nucleus was established after survival beyond that time point. No obvious effects were observed in the vital status of the model animals, and their survival was ensured. The common physiological parameters of model animals were stable. The present study provides a method to establish a CSF-contacting nucleus "knockout" model animal, which is similar to a gene knockout model animal for studying this particular nucleus in vivo.

Surface Chemistry and Spectroscopic Study of a Cholera Toxin B Langmuir Monolayer

In this article, we explored the surface chemistry properties of a cholera toxin B (CTB) monolayer at the air-subphase interface and investigated the change in interfacial properties through in situ spectroscopy. The study showed that the impact of the blue shift was negligible, suggesting that the CTB molecules were minimally affected by the subphase molecules. The stability of the CTB monolayer was studied by maintaining the constant surface pressure for a long time and also by using the compression-decompression cycle experiments. The high stability of the Langmuir monolayer of CTB clearly showed that the driving force of CTB going to the amphiphilic membrane was its amphiphilic nature. In addition, no major change was detected in the various in situ spectroscopy results (such as UV-vis, fluorescence, and IR ER) of the CTB Langmuir monolayer with the increase in surface pressure. This indicates that no aggregation occurs in the Langmuir monolayer of CTB.

New dimensions of connectomics and network plasticity in the central nervous system

Cellular network architecture plays a crucial role as the structural substrate for the brain functions. Therefore, it represents the main rationale for the emerging field of connectomics, defined as the comprehensive study of all aspects of central nervous system connectivity. Accordingly, in the present paper the main emphasis will be on the communication processes in the brain, namely wiring transmission (WT), i.e. the mapping of the communication channels made by cell components such as axons and synapses, and volume transmission (VT), i.e. the chemical signal diffusion along the interstitial brain fluid pathways. Considering both processes can further expand the connectomics concept, since both WT-connectomics and VT-connectomics contribute to the structure of the brain connectome. A consensus exists that such a structure follows a hierarchical or nested architecture, and macro-, meso- and microscales have been defined. In this respect, however, several lines of evidence indicate that a nanoscale (nano-connectomics) should also be considered to capture direct protein-protein allosteric interactions such as those occurring, for example, in receptor-receptor interactions at the plasma membrane level. In addition, emerging evidence points to novel mechanisms likely playing a significant role in the modulation of intercellular connectivity, increasing the plasticity of the system and adding complexity to its structure. In particular, the roamer type of VT (i.e. the intercellular transfer of RNA, proteins and receptors by extracellular vesicles) will be discussed since it allowed us to introduce a new concept of 'transient changes of cell phenotype', that is the transient acquisition of new signal release capabilities and/or new recognition/decoding apparatuses.

Anterograde Tract Tracing for Assaying Axonopathy and Transport Deficits in Glaucoma

Whether to stage degeneration or investigate early pathology in glaucoma, examination of axonal structure and function is essential. There are a wide variety of methods available to investigators using animal models of glaucoma, with varying utilities depending on the questions asked. Here, we describe the use of anterograde neuronal tract tracing using cholera toxin B (CTB) for the determination of axon transport integrity of the retinofugal projection. This method reveals the structure of the retinal axons as well as the functional integrity of anterograde transport systems.

Simultaneous acquisition of neuronal morphology and cytoarchitecture in the same Golgi-stained brain

Acquiring an accurate orientation reference is a prerequisite for precisely analysing the morphological features of Golgi-stained neurons in the whole brain. However, the same reflective imaging contrast of Golgi staining for morphology and Nissl staining for cytoarchitecture leads to the failure of distinguishing soma morphology and simultaneously co-locate cytoarchitecture. Here, we developed the dual-mode micro-optical sectioning tomography (dMOST) method to simultaneously image the reflective and fluorescent signals in three dimensions. We evaluated the feasibility of real-time fluorescent counterstaining on Golgi-stained brain tissue. With our system, we acquired whole-brain data sets of physiological and pathological Golgi-stained mouse model brains with fluorescence-labelled anatomical annotation at single-neuron resolution. We also obtained the neuronal morphology of macaque monkey brain tissue using this method. The results show that real-time acquisition of the co-located cytoarchitecture reference in the same brain greatly facilitates the precise morphological analysis of Golgi-stained neurons.

An Implantable Micro-Caged Device for Direct Local Delivery of Agents

Local and controlled delivery of therapeutic agents directly into focally afflicted tissues is the ideal for the treatment of diseases that require direct interventions. However, current options are obtrusive, difficult to implement, and limited in their scope of utilization; the optimal solution requires a method that may be optimized for available therapies and is designed for exact delivery. To address these needs, we propose the Biocage, a customizable implantable local drug delivery platform. The device is a needle-sized porous container capable of encasing therapeutic molecules and matrices of interest to be eluted into the region of interest over time. The Biocage was fabricated using the Nanoscribe Photonic Professional GT 3D laser lithography system, a two-photon polymerization (2PP) 3D printer capable of micron-level precision on a millimeter scale. We demonstrate the build consistency and features of the fabricated device; its ability to release molecules; and a method for its accurate, stable delivery in mouse brain tissue. The Biocage provides a powerful tool for customizable and precise delivery of therapeutic agents into target tissues.

Laminar fMRI and computational theories of brain function

Recently developed methods for functional MRI at the resolution of cortical layers (laminar fMRI) offer a novel window into neurophysiological mechanisms of cortical activity. Beyond physiology, laminar fMRI also offers an unprecedented opportunity to test influential theories of brain function. Specifically, hierarchical Bayesian theories of brain function, such as predictive coding, assign specific computational roles to different cortical layers. Combined with computational models, laminar fMRI offers a unique opportunity to test these proposals noninvasively in humans. This review provides a brief overview of predictive coding and related hierarchical Bayesian theories, summarises their predictions with regard to layered cortical computations, examines how these predictions could be tested by laminar fMRI, and considers methodological challenges. We conclude by discussing the potential of laminar fMRI for clinically useful computational assays of layer-specific information processing.

Fragile X Mental Retardation Protein Restricts Small Dye Iontophoresis Entry into Central Neurons

Fragile X mental retardation protein (FMRP) loss causes Fragile X syndrome (FXS), a major disorder characterized by autism, intellectual disability, hyperactivity, and seizures. FMRP is both an RNA- and channel-binding regulator, with critical roles in neural circuit formation and function. However, it remains unclear how these FMRP activities relate to each other and how dysfunction in their absence underlies FXS neurological symptoms. In testing circuit level defects in the Drosophila FXS model, we discovered a completely unexpected and highly robust neuronal dye iontophoresis phenotype in the well mapped giant fiber (GF) circuit. Controlled dye injection into the GF interneuron results in a dramatic increase in dye uptake in neurons lacking FMRP. Transgenic wild-type FMRP reintroduction rescues the mutant defect, demonstrating a specific FMRP requirement. This phenotype affects only small dyes, but is independent of dye charge polarity. Surprisingly, the elevated dye iontophoresis persists in shaking B mutants that eliminate gap junctions and dye coupling among GF circuit neurons. We therefore used a wide range of manipulations to investigate the dye uptake defect, including timed injection series, pharmacology and ion replacement, and optogenetic activity studies. The results show that FMRP strongly limits the rate of dye entry via a cytosolic mechanism. This study reveals an unexpected new phenotype in a physical property of central neurons lacking FMRP that could underlie aspects of FXS disruption of neural function.SIGNIFICANCE STATEMENT FXS is a leading heritable cause of intellectual disability and autism spectrum disorders. Although researchers established the causal link with FMRP loss >;25 years ago, studies continue to reveal diverse FMRP functions. The Drosophila FXS model is key to discovering new FMRP roles, because of its genetic malleability and individually identified neuron maps. Taking advantage of a well characterized Drosophila neural circuit, we discovered that neurons lacking FMRP take up dramatically more current-injected small dye. After examining many neuronal properties, we determined that this dye defect is cytoplasmic and occurs due to a highly elevated dye iontophoresis rate. We also report several new factors affecting neuron dye uptake. Understanding how FMRP regulates iontophoresis should reveal new molecular factors underpinning FXS dysfunction.

Structure and diversity of human dendritic spines evidenced by a new three-dimensional reconstruction procedure for Golgi staining and light microscopy

BACKGROUND

Different approaches aim to unravel detailed morphological features of neural cells. Dendritic spines are multifunctional units that reflect cellular connectivity, synaptic strength and plasticity.

NEW METHOD

A novel three-dimensional (3D) reconstruction procedure is introduced for visualization of dendritic spines from human postmortem brain tissue using brightfield microscopy. The segmentation model was based on thresholding the intensity values of the dendritic spine image along 'z' stacks. We used median filtering and removed false positives. Fine adjustments during image processing confirmed that the reconstructed image of the spines corresponded to the actual original data.

RESULTS

Examples are shown for the cortical amygdaloid nucleus and the CA3 hippocampal area. Structure of spine heads and necks was evaluated at different angles. Our 3D reconstruction images display dendritic spines either isolated or in clusters, in a continuum of shapes and sizes, from simple to more elaborated forms, including the presence of spinule and complex 'thorny excrescences'.

COMPARISON WITH EXISTING METHODS

The procedure has the advantages already described for the adapted "single-section" Golgi method, since it provides suitable results using human brains fixed in formalin for long time, is relatively easy, requires minimal equipment, and uses an algorithm for 3D reconstruction that provides high quality images and more precise morphological data.

CONCLUSION

The procedure described here allows the reliable visualization and study of human dendritic spines with broad applications for normal controls and pathological studies.

Chemical Probes for Visualizing Intact Animal and Human Brain Tissue

Newly developed tissue clearing techniques can be used to render intact tissues transparent. When combined with fluorescent labeling technologies and optical sectioning microscopy, this allows visualization of fine structure in three dimensions. Gene-transfection techniques have proved very useful in visualizing cellular structures in animal models, but they are not applicable to human brain tissue. Here, we discuss the characteristics of an ideal chemical fluorescent probe for use in brain and other cleared tissues, and offer a comprehensive overview of currently available chemical probes. We describe their working principles and compare their performance with the goal of simplifying probe selection for neuropathologists and stimulating probe development by chemists. We propose several approaches for the development of innovative chemical labeling methods which, when combined with tissue clearing, have the potential to revolutionize how we study the structure and function of the human brain.

Rapid fluorescence imaging of spinal cord following epidural administration of a nerve-highlighting fluorophore

Iatrogenic spinal cord injury (SCI) is the most devastating complication of spine surgery, which usually results in permanent and serious disabilities of patients. Improvement of the visualization and discrimination of the spinal cord is critical for accuracy and safety during surgery; however, to date, there is no suitable technology to fulfill this clinical need. Here, we first show an efficient and rapid fluorescence imaging of the spinal cord in rabbit by epidural administration of a nerve-highlighting fluorophore, i.e. (E, E)-1,4-bis(p-aminostryl)-2-methoxy benzene (BMB). The BMB is firstly encapsulated into polymeric micelles to form a BMB-micelle (BMB-m) formulation with well-dispersion in normal saline solution. After epidural administration of BMB-m, BMB is transported by the flow of cerebrospinal fluid (CSF) and binds to the peripheral region of the white matter thus facilitating rapid staining of the spinal cord. Furthermore, this BMB imaging technology also holds great potential for visually monitoring the integrity of the spinal cord in real time and promptly identifying acute SCI during spine surgery.

Mapping brain structure and function: cellular resolution, global perspective

A comprehensive understanding of the brain requires analysis, although from a global perspective, with cellular, and even subcellular, resolution. An important step towards this goal involves the establishment of three-dimensional high-resolution brain maps, incorporating brain-wide information about the cells and their connections, as well as the chemical architecture. The progress made in such anatomical brain mapping in recent years has been paralleled by the development of physiological techniques that enable investigators to generate global neural activity maps, also with cellular resolution, while simultaneously recording the organism's behavioral activity. Combination of the high-resolution anatomical and physiological maps, followed by theoretical systems analysis of the deduced network, will offer unprecedented opportunities for a better understanding of how the brain, as a whole, processes sensory information and generates behavior.

Gene Expression Profiling with Cre-Conditional Pseudorabies Virus Reveals a Subset of Midbrain Neurons That Participate in Reward Circuitry

The mesolimbic dopamine pathway receives inputs from numerous regions of the brain as part of a neural system that detects rewarding stimuli and coordinates a behavioral response. The capacity to simultaneously map and molecularly define the components of this complex multisynaptic circuit would thus advance our understanding of the determinants of motivated behavior. To accomplish this, we have constructed pseudorabies virus (PRV) strains in which viral propagation and fluorophore expression are activated only after exposure to Cre recombinase. Once activated in Cre-expressing neurons, the virus serially labels chains of presynaptic neurons. Dual injection of GFP and mCherry tracing viruses simultaneously illuminates nigrostriatal and mesolimbic circuitry and shows no overlap, demonstrating that PRV transmission is confined to synaptically connected neurons. To molecularly profile mesolimbic dopamine neurons and their presynaptic inputs, we injected Cre-conditional GFP virus into the NAc of (anti-GFP) nanobody-L10 transgenic mice and immunoprecipitated translating ribosomes from neurons infected after retrograde tracing. Analysis of purified RNA revealed an enrichment of transcripts expressed in neurons of the dorsal raphe nuclei and lateral hypothalamus that project to the mesolimbic dopamine circuit. These studies identify important inputs to the mesolimbic dopamine pathway and further show that PRV circuit-directed translating ribosome affinity purification can be broadly applied to identify molecularly defined neurons comprising complex, multisynaptic circuits.SIGNIFICANCE STATEMENT The mesolimbic dopamine circuit integrates signals from key brain regions to detect and respond to rewarding stimuli. To further define this complex multisynaptic circuit, we constructed a panel of Cre recombinase-activated pseudorabies viruses (PRVs) that enabled retrograde tracing of neural inputs that terminate on Cre-expressing neurons. Using these viruses and Retro-TRAP (translating ribosome affinity purification), a previously reported molecular profiling method, we developed a novel technique that provides anatomic as well as molecular information about the neural components of polysynaptic circuits. We refer to this new method as PRV-Circuit-TRAP (PRV circuit-directed TRAP). Using it, we have identified major projections to the mesolimbic dopamine circuit from the lateral hypothalamus and dorsal raphe nucleus and defined a discrete subset of transcripts expressed in these projecting neurons, which will allow further characterization of this important pathway. Moreover, the method we report is general and can be applied to the study of other neural circuits.

Fluoro-Ruby as a reliable marker for regenerating fiber tracts

Axon visualization techniques are important in assessing the efficacy of interventional approaches to stimulate neural regeneration. Whereas the labeling of descending tracts in the spinal cord has been well established using the intracortical injection of biotin dextran amine (BDA), the labeling of ascending sensory fibers of the dorsal funiculus is more problematic. Fluoro-Ruby (FR; dextran tetramethylrhodamine; MW 10,000) is a bidirectional permanent tracer, but the retrograde tracing of fibers is particularly prominent, and FR is a highly sensitive tracer that can be applied in discrete injection sites. In the present report, we used FR to efficiently label ascending fibers in the dorsal columns of the rat spinal cord. After transplantation of olfactory ensheathing cells into the transected dorsal funiculus, the application of FR was able to detect regenerating ascending fibers in the spinal cord. Regenerated fibers crossing the injury site were labeled and easily identified. It is likely that the tracer was taken up by damaged fibers. As additional advantages, the labeling is resistant to photobleaching and no additional tissue processing is necessary for visualization. It can be used for in vivo as well as in vitro injections. The findings indicate that FR can be used as a reliable fluorescent marker to study ascending regenerated fibers in the spinal cord axonal regeneration.

A Single Vector Platform for High-Level Gene Transduction of Central Neurons: Adeno-Associated Virus Vector Equipped with the Tet-Off System

Visualization of neurons is indispensable for the investigation of neuronal circuits in the central nervous system. Virus vectors have been widely used for labeling particular subsets of neurons, and the adeno-associated virus (AAV) vector has gained popularity as a tool for gene transfer. Here, we developed a single AAV vector Tet-Off platform, AAV-SynTetOff, to improve the gene-transduction efficiency, specifically in neurons. The platform is composed of regulator and response elements in a single AAV genome. After infection of Neuro-2a cells with the AAV-SynTetOff vector, the transduction efficiency of green fluorescent protein (GFP) was increased by approximately 2- and 15-fold relative to the conventional AAV vector with the human cytomegalovirus (CMV) or human synapsin I (SYN) promoter, respectively. We then injected the AAV vectors into the mouse neostriatum. GFP expression in the neostriatal neurons infected with the AAV-SynTetOff vector was approximately 40-times higher than that with the CMV or SYN promoter. By adding a membrane-targeting signal to GFP, the axon fibers of neostriatal neurons were clearly visualized. In contrast, by attaching somatodendritic membrane-targeting signals to GFP, axon fiber labeling was mostly suppressed. Furthermore, we prepared the AAV-SynTetOff vector, which simultaneously expressed somatodendritic membrane-targeted GFP and membrane-targeted red fluorescent protein (RFP). After injection of the vector into the neostriatum, the cell bodies and dendrites of neostriatal neurons were labeled with both GFP and RFP, whereas the axons in the projection sites were labeled only with RFP. Finally, we applied this vector to vasoactive intestinal polypeptide-positive (VIP+) neocortical neurons, one of the subclasses of inhibitory neurons in the neocortex, in layer 2/3 of the mouse primary somatosensory cortex. The results revealed the differential distribution of the somatodendritic and axonal structures at the population level. The AAV-SynTetOff vector developed in the present study exhibits strong fluorescence labeling and has promising applications in neuronal imaging.

The missing link: Predicting connectomes from noisy and partially observed tract tracing data

Our understanding of the wiring map of the brain, known as the connectome, has increased greatly in the last decade, mostly due to technological advancements in neuroimaging techniques and improvements in computational tools to interpret the vast amount of available data. Despite this, with the exception of the C. elegans roundworm, no definitive connectome has been established for any species. In order to obtain this, tracer studies are particularly appealing, as these have proven highly reliable. The downside of tract tracing is that it is costly to perform, and can only be applied ex vivo. In this paper, we suggest that instead of probing all possible connections, hitherto unknown connections may be predicted from the data that is already available. Our approach uses a 'latent space model' that embeds the connectivity in an abstract physical space. Regions that are close in the latent space have a high chance of being connected, while regions far apart are most likely disconnected in the connectome. After learning the latent embedding from the connections that we did observe, the latent space allows us to predict connections that have not been probed previously. We apply the methodology to two connectivity data sets of the macaque, where we demonstrate that the latent space model is successful in predicting unobserved connectivity, outperforming two baselines and an alternative model in nearly all cases. Furthermore, we show how the latent spatial embedding may be used to integrate multimodal observations (i.e. anterograde and retrograde tracers) for the mouse neocortex. Finally, our probabilistic approach enables us to make explicit which connections are easy to predict and which prove difficult, allowing for informed follow-up studies.

Connectomic Analysis of Brain Networks: Novel Techniques and Future Directions

Brain networks, localized or brain-wide, exist only at the cellular level, i.e., between specific pre- and post-synaptic neurons, which are connected through functionally diverse synapses located at specific points of their cell membranes. "Connectomics" is the emerging subfield of neuroanatomy explicitly aimed at elucidating the wiring of brain networks with cellular resolution and a quantified accuracy. Such data are indispensable for realistic modeling of brain circuitry and function. A connectomic analysis, therefore, needs to identify and measure the soma, dendrites, axonal path, and branching patterns together with the synapses and gap junctions of the neurons involved in any given brain circuit or network. However, because of the submicron caliber, 3D complexity, and high packing density of most such structures, as well as the fact that axons frequently extend over long distances to make synapses in remote brain regions, creating connectomic maps is technically challenging and requires multi-scale approaches, Such approaches involve the combination of the most sensitive cell labeling and analysis methods available, as well as the development of new ones able to resolve individual cells and synapses with increasing high-throughput. In this review, we provide an overview of recently introduced high-resolution methods, which researchers wanting to enter the field of connectomics may consider. It includes several molecular labeling tools, some of which specifically label synapses, and covers a number of novel imaging tools such as brain clearing protocols and microscopy approaches. Apart from describing the tools, we also provide an assessment of their qualities. The criteria we use assess the qualities that tools need in order to contribute to deciphering the key levels of circuit organization. We conclude with a brief future outlook for neuroanatomic research, computational methods, and network modeling, where we also point out several outstanding issues like structure-function relations and the complexity of neural models.

Anti-correlations in the degree distribution increase stimulus detection performance in noisy spiking neural networks

Neuronal circuits in the rodent barrel cortex are characterized by stable low firing rates. However, recent experiments show that short spike trains elicited by electrical stimulation in single neurons can induce behavioral responses. Hence, the underlying neural networks provide stability against internal fluctuations in the firing rate, while simultaneously making the circuits sensitive to small external perturbations. Here we studied whether stability and sensitivity are affected by the connectivity structure in recurrently connected spiking networks. We found that anti-correlation between the number of afferent (in-degree) and efferent (out-degree) synaptic connections of neurons increases stability against pathological bursting, relative to networks where the degrees were either positively correlated or uncorrelated. In the stable network state, stimulation of a few cells could lead to a detectable change in the firing rate. To quantify the ability of networks to detect the stimulation, we used a receiver operating characteristic (ROC) analysis. For a given level of background noise, networks with anti-correlated degrees displayed the lowest false positive rates, and consequently had the highest stimulus detection performance. We propose that anti-correlation in the degree distribution may be a computational strategy employed by sensory cortices to increase the detectability of external stimuli. We show that networks with anti-correlated degrees can in principle be formed by applying learning rules comprised of a combination of spike-timing dependent plasticity, homeostatic plasticity and pruning to networks with uncorrelated degrees. To test our prediction we suggest a novel experimental method to estimate correlations in the degree distribution.

CLARITY-compatible lipophilic dyes for electrode marking and neuronal tracing

Fluorescent lipophilic dyes, such as DiI, stain cellular membranes and are used extensively for retrograde/anterograde labeling of neurons as well as for marking the position of extracellular electrodes after electrophysiology. Convenient histological clearing techniques, such as CLARITY, enable immunostaining and imaging of large volumes for 3D-reconstruction. However, such clearing works by removing lipids and, as an unintended consequence, also removes lipophilic dyes. To remedy this wash-out, the molecular structure of the dye can be altered to adhere to both membranes and proteins so the dye remains in the tissue after lipid–clearing. Nevertheless, the capacity of such modified dyes to remain in tissue has not yet been tested. Here, we test dyes with molecular modifications that make them aldehyde-fixable to proteins. We use three Dil–analogue dyes, CM-DiI, SP-DiI and FM 1–43FX that are modified to be CLARITY-compatible candidates. We use the challenging adult, myelin-rich spinal cord tissue, which requires prolonged lipid–clearing, of rats and mice. All three dyes remained in the tissue after lipid–clearing, but CM-DiI had the sharpest and FM 1–43FX the strongest fluorescent signal.