Labeling neurons in vivo for morphological and functional studies

Multi-Beam Scanning Electron Microscopy for High-Throughput Imaging in Connectomics Research

Major progress has been achieved in recent years in three-dimensional microscopy techniques. This applies to the life sciences in general, but specifically the neuroscientific field has been a main driver for developments regarding volume imaging. In particular, scanning electron microscopy offers new insights into the organization of cells and tissues by volume imaging methods, such as serial section array tomography, serial block-face imaging or focused ion beam tomography. However, most of these techniques are restricted to relatively small tissue volumes due to the limited acquisition throughput of most standard imaging techniques. Recently, a novel multi-beam scanning electron microscope technology optimized to the imaging of large sample areas has been developed. Complemented by the commercialization of automated sample preparation robots, the mapping of larger, cubic millimeter range tissue volumes at high-resolution is now within reach. This Mini Review will provide a brief overview of the various approaches to electron microscopic volume imaging, with an emphasis on serial section array tomography and multi-beam scanning electron microscopic imaging.

Generation and Screening of Transgenic Mice with Neuronal Labeling Controlled by Thy1 Regulatory Elements

Major progress has been made using in vivo imaging in mice to study mammalian nervous system development, plasticity, and disease. This progress has depended in part on the wide availability of two-photon microscopy, which is capable of penetrating deep into scattering tissue. Equally important, however, is the generation of suitable transgenic mouse models, which provide a "Golgi staining"-like labeling of neurons that is sparse and bright enough for in vivo imaging. Particularly prominent among such transgenic mice are the so-called Thy1-XFP mice (in which XFP stands for any fluorescent protein) that are used in numerous studies, especially to visualize spine plasticity in the cortex and remodeling in peripheral synapses. New generations of Thy1-XFP mice are now being generated at a high rate, and these have allowed previously difficult experiments to become feasible. Moreover, with easy access to core facilities or commercial providers of pronuclear injections, generating simple Thy1 transgenic mice is now a possibility even for small laboratories. In this introduction, we discuss the Thy1 regulatory elements used to generate transgenic lines with neuronal labeling. We provide a brief overview of currently available Thy1 transgenic mice, including lines labeling neuronal organelles or reporting neuronal function.

Optogenetic approaches for functional mouse brain mapping

To better understand the connectivity of the brain, it is important to map both structural and functional connections between neurons and cortical regions. In recent years, a set of optogenetic tools have been developed that permit selective manipulation and investigation of neural systems. These tools have enabled the mapping of functional connections between stimulated cortical targets and other brain regions. Advantages of the approach include the ability to arbitrarily stimulate brain regions that express opsins, allowing for brain mapping independent of behavior or sensory processing. The ability of opsins to be rapidly and locally activated allows for investigation of connectivity with spatial resolution on the order of single neurons and temporal resolution on the order of milliseconds. Optogenetic methods for functional mapping have been applied in experiments ranging from in vitro investigation of microcircuits, to in vivo probing of inter-regional cortical connections, to examination of global connections within the whole brain. We review recently developed functional mapping methods that use optogenetic single-point stimulation in the rodent brain and employ cellular electrophysiology, evoked motor movements, voltage sensitive dyes (VSDs), calcium indicators, or functional magnetic resonance imaging (fMRI) to assess activity. In particular we highlight results using red-shifted organic VSDs that permit high temporal resolution imaging in a manner spectrally separated from Channelrhodopsin-2 (ChR2) activation. VSD maps stimulated by ChR2 were dependent on intracortical synaptic activity and were able to reflect circuits used for sensory processing. Although the methods reviewed are powerful, challenges remain with respect to finding approaches that permit selective high temporal resolution assessment of stimulated activity in animals that can be followed longitudinally.

High resolution imaging of neuronal connectivity

Connectomics is an emerging field that aims to generate and analyse neuronal connectivity data with high-throughput to gain knowledge about the brain. The realization of this goal largely depends on the development of innovative microscopy techniques that can produce large-scale three-dimensional images of brain tissue at nanoscale resolution and automated analysis tools that can extract relevant information from these images. This review surveys the challenges associated with generating the images needed for neuronal connectivity maps and how these challenges may be overcome by novel optical methods that allow sub-diffraction-limit imaging.

In vivo imaging and noninvasive ablation of pyramidal neurons in adult NEX-CreERT2 mice

To study the function of individual neurons that are embedded in a complex neural network is difficult in mice. Conditional mutagenesis permits the spatiotemporal control of gene expression including the ablation of cells by toxins. To direct expression of a tamoxifen-inducible variant of Cre recombinase (CreERT2) selectively to cortical neurons, we replaced the coding region of the murine Nex1 gene by CreERT2 cDNA via homologous recombination in embryonic stem cells. When injected with tamoxifen, adult NEX-CreERT2 mice induced reporter gene expression exclusively in projection neurons of the neocortex and hippocampus. By titrating the tamoxifen dosage, we achieved recombination in single cells, which allowed multiphoton imaging of neocortical neurons in live mice. When hippocampal projection neurons were genetically ablated by induced expression of diphteria toxin, within 20 days the inflammatory response included the infiltration of CD3+ T cells. This marks a striking difference from similar studies, in which dying oligodendrocytes failed to recruit cells of the adaptive immune system.

Efficient inducible Pan-neuronal cre-mediated recombination in SLICK-H transgenic mice

Large-scale functional genomics in mice is becoming feasible through projects to develop conditional knockout alleles for every gene. Inducible neuron-specific gene knockout in such mice will permit the analysis of neuronal phenotypes while circumventing developmental defects or embryonic lethality. Here we describe a transgenic line, termed SLICK-H, that facilitates widespread inducible conditional genetic manipulation within most populations of projection neurons. In SLICK-H mice, the Thy1 promoter drives robust and relatively uniform expression of a drug-inducible form of cre recombinase throughout the peripheral and central nervous system. This permits efficient induction of cre-mediated genetic manipulation upon tamoxifen administration in adult mice. Importantly, cre activity in the absence of tamoxifen is minimal, permitting tight control of recombination. In the present study, we catalog in detail the transgene expression patterns and recombination efficiencies in SLICK-H mice. Our results highlight the utility of SLICK-H mice for functional genomics in the nervous system.

Simultaneous visualization of multiple neuronal properties with single-cell resolution in the living rodent brain

To understand the fine-scale structures and functional properties of individual neurons in vivo, we developed and validated a rapid genetic technique that enables simultaneous investigation of multiple neuronal properties with single-cell resolution in the living rodent brain. Our technique PASME (promoter-assisted sparse-neuron multiple-gene labeling using in uteroelectroporation) targets specific small subsets of sparse pyramidal neurons in layer 2/3, layer 5 of the cerebral cortex and in the hippocampus with multiple fluorescent reporter proteins such as postsynaptic PSD-95-GFP and GFP-gephyrin. The technique is also applicable for targeting independently individual neurons and their presynaptic inputs derived from surrounding neurons. Targeting sparse layer 2/3 neurons, we uncovered a novel subpopulation of layer 2/3 neurons in the mouse cerebral cortex. This technique, broadly applicable for probing and manipulating neurons with single-cell resolution in vivo, should provide a robust means to uncover the basic mechanisms employed by the brain, especially when combined with in vivo two-photon laser-scanning microscopy and/or optogenetic technologies.

Single neuron electroporation in manipulating and measuring the central nervous system

The development and application of single neuron electroporation largely advanced the use of traditional genetics in investigations of the central nervous system. This quick and accurate manipulation of the brain at individual neuron level allowed the gain and loss of functional analyses of different genes and/or proteins. This manuscript reviewed the development of the technique and discussed some technical aspects in practical manipulations. Then the manuscript summarized the potential applications with this technique. Last but not least, the technique showed prospective future when combined with other modern methods in neuroscience research.

Fluorescent proteins and their applications in imaging living cells and tissues

Green fluorescent protein (GFP) from the jellyfish Aequorea victoria and its homologs from diverse marine animals are widely used as universal genetically encoded fluorescent labels. Many laboratories have focused their efforts on identification and development of fluorescent proteins with novel characteristics and enhanced properties, resulting in a powerful toolkit for visualization of structural organization and dynamic processes in living cells and organisms. The diversity of currently available fluorescent proteins covers nearly the entire visible spectrum, providing numerous alternative possibilities for multicolor labeling and studies of protein interactions. Photoactivatable fluorescent proteins enable tracking of photolabeled molecules and cells in space and time and can also be used for super-resolution imaging. Genetically encoded sensors make it possible to monitor the activity of enzymes and the concentrations of various analytes. Fast-maturing fluorescent proteins, cell clocks, and timers further expand the options for real time studies in living tissues. Here we focus on the structure, evolution, and function of GFP-like proteins and their numerous applications for in vivo imaging, with particular attention to recent techniques.

A time for atlases and atlases for time

Advances in neuroanatomy and computational power are leading to the construction of new digital brain atlases. Atlases are rising as indispensable tools for comparing anatomical data as well as being stimulators of new hypotheses and experimental designs. Brain atlases describe nervous systems which are inherently plastic and variable. Thus, the levels of brain plasticity and stereotypy would be important to evaluate as limiting factors in the context of static brain atlases. In this review, we discuss the extent of structural changes which neurons undergo over time, and how these changes would impact the static nature of atlases. We describe the anatomical stereotypy between neurons of the same type, highlighting the differences between invertebrates and vertebrates. We review some recent experimental advances in our understanding of anatomical dynamics in adult neural circuits, and how these are modulated by the organism's experience. In this respect, we discuss some analogies between brain atlases and the sequenced genome and the emerging epigenome. We argue that variability and plasticity of neurons are substantially high, and should thus be considered as integral features of high-resolution digital brain atlases.

Spectral unmixing: analysis of performance in the olfactory bulb in vivo

Background

The generation of transgenic mice expressing combinations of fluorescent proteins has greatly aided the reporting of activity and identification of specific neuronal populations. Methods capable of separating multiple overlapping fluorescence emission spectra, deep in the living brain, with high sensitivity and temporal resolution are therefore required. Here, we investigate to what extent spectral unmixing addresses these issues.

Methodology/Principal Findings

Using fluorescence resonance energy transfer (FRET)-based reporters, and two-photon laser scanning microscopy with synchronous multichannel detection, we report that spectral unmixing consistently improved FRET signal amplitude, both in vitro and in vivo. Our approach allows us to detect odor-evoked FRET transients 180–250 µm deep in the brain, the first demonstration of in vivo spectral imaging and unmixing of FRET signals at depths greater than a few tens of micrometer. Furthermore, we determine the reporter efficiency threshold for which FRET detection is improved by spectral unmixing.

Conclusions/Significance

Our method allows the detection of small spectral variations in depth in the living brain, which is essential for imaging efficiently transgenic animals expressing combination of multiple fluorescent proteins.

Single-neuron labeling with inducible Cre-mediated knockout in transgenic mice

To facilitate a functional analysis of neuronal connectivity in a mammalian nervous system that is tightly packed with billions of cells, we developed a new technique that uses inducible genetic manipulations in fluorescently labeled single neurons in mice. Our technique, single-neuron labeling with inducible Cre-mediated knockout (SLICK), is achieved by coexpressing a drug-inducible form of Cre recombinase and a fluorescent protein in a small subsets of neurons, thus combining the powerful Cre recombinase system for conditional genetic manipulation with fluorescent labeling of single neurons for imaging. Here, we demonstrate efficient inducible genetic manipulation in several types of neurons using SLICK. Furthermore, we applied SLICK to eliminate synaptic transmission in a small subset of neuromuscular junctions. Our results provide evidence for the long-term stability of inactive neuromuscular synapses in adult animals and demonstrate a Cre-loxP compatible system for dissecting gene functions in single identifiable neurons.

Genetically encoded fluorescent sensors for studying healthy and diseased nervous systems

Neurons and glia are functionally organized into circuits and higher-order structures via synaptic connectivity, well-orchestrated molecular signaling, and activity-dependent refinement. Such organization allows the precise information processing required for complex behaviors. Disruption of nervous systems by genetic deficiency or events such as trauma or environmental exposure may produce a diseased state in which certain aspects of inter-neuron signaling are impaired. Optical imaging techniques allow the direct visualization of individual neurons in a circuit environment. Imaging probes specific for given biomolecules may help elucidate their contribution to proper circuit function. Genetically encoded sensors can visualize trafficking of particular molecules in defined neuronal populations, non-invasively in intact brain or reduced preparations. Sensor analysis in healthy and diseased brains may reveal important differences and shed light on the development and progression of nervous system disorders. We review the field of genetically encoded sensors for molecules and cellular events, and their potential applicability to the study of nervous system disease.

Electrophysiological evaluation of engrafted stem cell-derived neurons

Recent advances in the neural stem cell field have provided a wealth of methods for generating large amounts of purified neuronal precursor cells. It has become a question of paramount importance to determine whether these cells integrate and interact with established neural circuitry after engraftment. In principle, neurons have to fulfill three basic functions: receive incoming signals via synapses, compute and forward processed information to other neurons or effector cells. It is anticipated that functionally integrating stem cell-derived donor neurons perform accordingly. Here we provide protocols for the efficient electrophysiological evaluation of engrafted cells and highlight current limitations thereof.

Comprehensive maps of Drosophila higher olfactory centers: spatially segregated fruit and pheromone representation

In Drosophila, ∼50 classes of olfactory receptor neurons (ORNs) send axons to 50 corresponding glomeruli in the antennal lobe. Uniglomerular projection neurons (PNs) relay olfactory information to the mushroom body (MB) and lateral horn (LH). Here, we combine single-cell labeling and image registration to create high-resolution, quantitative maps of the MB and LH for 35 input PN channels and several groups of LH neurons. We find (1) PN inputs to the MB are stereotyped as previously shown for the LH; (2) PN partners of ORNs from different sensillar groups are clustered in the LH; (3) fruit odors are represented mostly in the posterior-dorsal LH, whereas candidate pheromone-responsive PNs project to the anterior-ventral LH; (4) dendrites of single LH neurons each overlap with specific subsets of PN axons. Our results suggest that the LH is organized according to biological values of olfactory input.

Fly MARCM and mouse MADM: genetic methods of labeling and manipulating single neurons

The Golgi staining method has served neuroscience well for more than a century. In this assay I review recent progresses using genetic methods to recapitulate and extend the Golgi staining method. These methods enable new discoveries on organization and development of neuronal circuits in the fly and mouse brains.

Characterization of mRNA expression in single neurons

How neurons differ from each other is largely determined by their specific repertoire of mRNAs. The genes expressed by a given neuron reflect its developmental history, its interaction with other cells, and its synaptic activity. Since the introduction of reverse transcription polymerase chain reaction (RT-PCR), it has been possible to identify specific mRNAs present in small samples of total RNA. But isolating RNA from only those cells of interest, and not others, represents a significant challenge. Several approaches can be used to isolate RNA from selected neurons. Following whole-cell patch-clamp recording, mRNA can be harvested from living cells by aspirating the cytoplasm into the patch-clamp pipette. Transcripts expressed in the recorded neuron can then be amplified by RT-PCR. Another way of isolating identified neurons is to use cell-specific promoters to drive the expression of a marker gene such as green fluorescent protein (GFP). RNA can then be isolated from GFP-positive cells. In a tissue context, laser microdissection can also be used to excise the cells of interest directly into an RNA isolation solution. The above methods of RNA isolation can also be combined with RNA amplification and microarray technology to identify specific transcripts that are unique to the cell type being studied. Here we provide detailed protocols for harvesting RNA from single cells, methods for RNA purification, and PCR amplification.

Next-generation optical technologies for illuminating genetically targeted brain circuits

Emerging technologies from optics, genetics, and bioengineering are being combined for studies of intact neural circuits. The rapid progression of such interdisciplinary "optogenetic" approaches has expanded capabilities for optical imaging and genetic targeting of specific cell types. Here we explore key recent advances that unite optical and genetic approaches, focusing on promising techniques that either allow novel studies of neural dynamics and behavior or provide fresh perspectives on classic model systems.

In vivo imaging of the diseased nervous system

In vivo microscopy is an exciting tool for neurological research because it can reveal how single cells respond to damage of the nervous system. This helps us to understand how diseases unfold and how therapies work. Here, we review the optical imaging techniques used to visualize the different parts of the nervous system, and how they have provided fresh insights into the aetiology and therapeutics of neurological diseases. We focus our discussion on five areas of neuropathology (trauma, degeneration, ischaemia, inflammation and seizures) in which in vivo microscopy has had the greatest impact. We discuss the challenging issues in the field, and argue that the convergence of new optical and non-optical methods will be necessary to overcome these challenges.

In vivo imaging of juxtaglomerular neuron turnover in the mouse olfactory bulb

As a consequence of adult neurogenesis, the olfactory bulb (OB) receives a continuous influx of newborn neurons well into adulthood. However, their rates of generation and turnover, the factors controlling their survival, and how newborn neurons intercalate into adult circuits are largely unknown. To visualize the dynamics of adult neurogenesis, we produced a line of transgenic mice expressing GFP in approximately 70% of juxtaglomerular neurons (JGNs), a population that undergoes adult neurogenesis. Using in vivo two-photon microscopy, time-lapse analysis of identified JGN cell bodies revealed a neuronal turnover rate of approximately 3% of this population per month. Although new neurons appeared and older ones disappeared, the overall number of JGNs remained constant. This approach provides a dynamic view of the actual appearance and disappearance of newborn neurons in the vertebrate central nervous system, and provides an experimental substrate for functional analysis of adult neurogenesis.

Deep tissue two-photon microscopy

With few exceptions biological tissues strongly scatter light, making high-resolution deep imaging impossible for traditional-including confocal-fluorescence microscopy. Nonlinear optical microscopy, in particular two photon-excited fluorescence microscopy, has overcome this limitation, providing large depth penetration mainly because even multiply scattered signal photons can be assigned to their origin as the result of localized nonlinear signal generation. Two-photon microscopy thus allows cellular imaging several hundred microns deep in various organs of living animals. Here we review fundamental concepts of nonlinear microscopy and discuss conditions relevant for achieving large imaging depths in intact tissue.

Time-lapse analysis of retinal differentiation

The availability of new vital markers and the improvements in time-lapse video microscopy have increased our ability to observe developmental events in the retina while they are happening. Using this approach, advances have been made in the understanding of important issues such as how division patterns relate to cell fate determination, how post-mitotic progenitors reach their correct retinal layers, and finally, how retinal ganglion cell axons navigate out of the retina and to their final targets in the midbrain.