We would like to thank Drs. Ed Callaway and Marty Usrey for allowing us to use the tissue prepared as a part of a prior study and Libby Fairless and Shiyuan Liu for help with neuronal reconstructions. This work was funded by the NIH (NEI: EY018683) and the Whitehall Foundation.

<ol>
	<li>Cajal, S. R. y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Histologie du systeme nerveaux de l'homme et des vertebres. , (1911).</li><li>Seung, H. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Toward+functional+connectomics.">Toward functional connectomics.</a> Nature. 471, 170-172 (2011).</li><li>Callaway, E. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Transneuronal+circuit+tracing+with+neurotropic+viruses.">Transneuronal circuit tracing with neurotropic viruses.</a> Current Opinion in Neurobiology. 18, 1-7 (2009).</li><li>Wickersham, I. R., Finke, S., Conzelmann, K. K., Callaway, E. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Retrograde+neuronal+tracing+with+a+deletion-mutant+rabies+virus.">Retrograde neuronal tracing with a deletion-mutant rabies virus.</a> Nature Methods. 4, 47-49 (2007).</li><li>Briggs, F., Kiley, C. W., Callaway, E. M., Usrey, W. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Morphological+substrates+for+parallel+streams+of+corticogeniculate+feedback+originating+in+both+V1+and+V2+of+the+macaque+monkey.">Morphological substrates for parallel streams of corticogeniculate feedback originating in both V1 and V2 of the macaque monkey.</a> Neuron. 90, 388-399 (2016).</li><li>Cauli, B., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Classification+of+fusiform+neocortical+interneurons+based+on+unsupervised+clustering.">Classification of fusiform neocortical interneurons based on unsupervised clustering.</a> PNAS. 97, 6144-6149 (2000).</li><li>Bragg, E. M., Fairless, E. A., Liu, S., Briggs, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Morphology+of+visual+sector+thalamic+reticular+neurons+in+the+macaque+monkey+sugests+retinotopically-specialized,+parallel+stream-mixed+input+to+the+lateral+geniculate+nucleus.">Morphology of visual sector thalamic reticular neurons in the macaque monkey sugests retinotopically-specialized, parallel stream-mixed input to the lateral geniculate nucleus.</a> J. Comparative Neurology. 525 (5), 1273-1290 (2017).</li><li>Osakada, F., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=New+rabies+virus+varients+for+monitoring+and+manipulating+activity+and+gene+expression+in+defined+neural+circuits.">New rabies virus varients for monitoring and manipulating activity and gene expression in defined neural circuits.</a> Neuron. 71, 617-631 (2011).</li><li>Callaway, E. M., Luo, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Monosynaptic+circuit+tracing+with+glycoprotein-deleted+rabies+viruses.">Monosynaptic circuit tracing with glycoprotein-deleted rabies viruses.</a> Journal of Neuroscience. 35, 8979-8985 (2015).</li><li>Nhan, H. L., Callaway, E. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Morphology+of+superior+colliculus-+and+middle+temporal+area-projecting+neurons+in+primate+primary+visual+cortex.">Morphology of superior colliculus- and middle temporal area-projecting neurons in primate primary visual cortex.</a> J. Comparative Neurology. 520, 52-80 (2012).</li><li>Pinault, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+thalamic+reticular+nucleus:+structure,+function+and+concept.">The thalamic reticular nucleus: structure, function and concept.</a> Brain Research Reviews. 46, 1-31 (2004).</li><li>Gage, G. J., Kipke, D. R., Shain, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Whole+Animal+Perfusion+Fixation+for+Rodents.">Whole Animal Perfusion Fixation for Rodents.</a> Journal of Visualized Experiments. 65, e3564 (2012).</li><li>Wong-Riley, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Changes+in+the+visual+system+of+monocularly+sutured+or+enucleated+cats+demonstrable+with+cytochrome+oxidase+histochemistry.">Changes in the visual system of monocularly sutured or enucleated cats demonstrable with cytochrome oxidase histochemistry.</a> Brain Research. 171, 11-28 (1979).</li><li>Gerfen, C. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Basic+neuroanatomical+methods.">Basic neuroanatomical methods.</a> Current Protocols in Neuroscience. Chapter 1, Unit 1.1 (2003).</li><li>Thorndike, R. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Who+belongs+in+the+family?.">Who belongs in the family?.</a> Psychometrika. 18, 267-276 (1953).</li><li>Talebi, V., Baker, C. I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Categorically+distinct+types+of+receptive+fields+in+early+visual+cortex.">Categorically distinct types of receptive fields in early visual cortex.</a> Journal of Neurophysiology. 115, 2556-2576 (2016).</li><li>Helmstaedter, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Connectomic+reconstruction+of+the+inner+plexiform+layer+in+the+mouse+retina.">Connectomic reconstruction of the inner plexiform layer in the mouse retina.</a> Nature. 500, 168-174 (2013).</li></ol>

The authors have nothing to disclose.

Neuroanatomical studies have remained a pillar of neuroscience and recent interest in connectomics and structure-function relationships has renewed enthusiasm for detailed morphological characterization of selective neuronal populations. Traditionally, neuroanatomical studies have relied on qualitative classifications of neurons into morphologically distinct classes of neurons defined by expert neuroanatomists. With advances in the techniques for reconstructing neurons and extracting morphological data, it is now possibl...

Neuroanatomy is one of the foundations of neuroscience1 and recent interest in &#34;connectomics&#34; has renewed enthusiasm for understanding the morphological diversity of neuronal populations and the connections between specific neurons2. Methods for labeling and reconstructing neurons have greatly improved with recent innovations, including genetic and virus-mediated circuit tracing approaches3,4, enabling more comprehensive morphological surveys of neuronal populations5. In addition to improvements in labeling individual neurons, quantitative data analysis techniques have also emerged that enable independent and unbiased classification of neurons into distinct subpopulations based on morphological data5,6. These unbiased techniques are an improvement upon more traditional qualitative classification methods that have been the standard in the field for over a century. The goal of this study is to outline, step-by-step, the combination of virus-mediated labeling of neurons within a selective population, large-scale reconstructions of a comprehensive sample of these neurons, and quantitative data analysis based on independent clustering with statistical evaluation. By combining these methods, we outline a novel approach toward the collection and analysis of neuroanatomical data to facilitate comprehensive sampling and unbiased classification of morphologically unique neuronal types within a selective neuronal population.
As an example of these methods, we describe our analysis of a large population of neurons within a single sector of the thalamic reticular nucleus (TRN) of the macaque monkey. These data are from a prior study7. Methods for selectively labeling TRN neurons projecting to the dorsal lateral geniculate nucleus of the thalamus (dLGN) using surgical injection of modified rabies virus encoding EGFP4,8 (see Table of Specific Materials/Equipment, row 2) are outlined. This modified rabies virus lacks the gene encoding an essential coat protein, eliminating trans-synaptic movement of the virus. Once the virus enters axon terminals at the injection site, it acts like a traditional retrograde tracer with the important benefit of driving EGFP expression throughout the full dendritic arborization of infected neurons5,9,10. Accordingly, this G-deleted rabies virus can be utilized to selectively infect and label any neuronal population following injection and retrograde transport.
In order to perform a comprehensive analysis of a specific neuronal population, it is important to sample from a broad distribution of neurons within the population. Because the virus-mediated labeling technique produces complete intracellular, &#34;Golgi-like&#34; fills of many neurons with axons at the virus injection site, it is possible to reconstruct a very large sample of neurons within the full extent of a brain structure. Additionally, because the modified rabies virus is so effective at infecting and labeling large numbers of neurons, it is possible to reconstruct hundreds of neurons per animal. Procedures for sampling 160 neurons throughout the visual sector of the TRN11 in order to generate a comprehensive sample of dLGN-projecting TRN neurons are outlined. The process of reconstructing individual neurons using a neuron reconstruction system including a microscope, camera, and reconstruction software is described. Also described are methods to determine positions of individual neurons within a brain structure (in this case within the TRN) and to verify virus injection site volume and location within a structure (in this case within the dLGN) using volumetric contour reconstructions. Steps to export morphological data and perform independent cluster analyses based on morphological metrics measured for each neuron are outlined. There are limitations to clustering methods and there are also a variety of different clustering algorithms available. Accordingly, these options and the benefits of some of the more commonly used algorithms are described. The cluster analysis does not provide statistical verification of the uniqueness of clusters. Therefore, additional steps are outlined to verify optimal clustering as well as the relationships between morphological data within and across clusters. Statistical methods for evaluating clusters for the TRN dataset to confirm that TRN neurons are grouped into three unique clusters based on 10 independent morphological metrics are described.
Thus, by outlining steps for selectively labeling, reconstructing, and analyzing morphological data from a specific neuronal population, we describe methods for quantifying morphological differences among neurons within a population. Prior findings of distinct neuronal types within the visual sector of the macaque monkey TRN are confirmed with separate statistical evaluation methods. Together, we hope these techniques will be broadly applicable to neuroanatomical datasets and help establish quantitative classification of the diversity of neuronal populations through the brain.

<table border="0" cellpadding="0" cellspacing="0" width="818">
	<tbody>
		<tr height="60">
			<td height="60" style="height:60px;width:233px;">SAD&#916;G-EGFP</td>
			<td style="width:171px;">E.M. Callaway Laboratory, Salk Institute</td>
			<td style="width:133px;"></td>
			<td style="width:281px;">Prepared by Dr. F. Osakada. G-deleted rabies virus available through the Salk Institute Viral Core</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;width:233px;">Recording electrode: platinum/iridium or tungsten</td>
			<td style="width:171px;">FHC</td>
			<td style="width:133px;">UEPSGGSE1N2M</td>
			<td style="width:281px;">Visit website (www.fh-co.com) for alternative order specifications</td>
		</tr>
		<tr height="33">
			<td height="33" style="height:33px;width:233px;">Nanoject II</td>
			<td style="width:171px;">Drummod Scientific</td>
			<td style="width:133px;">3-000-204, 110V</td>
			<td style="width:281px;">Alternatives: picospritzer, Hamilton syringe</td>
		</tr>
		<tr height="38">
			<td height="38" style="height:39px;width:233px;">Freezing microtome</td>
			<td style="width:171px;">Thermo Scientific</td>
			<td style="width:133px;"></td>
			<td style="width:281px;"></td>
		</tr>
		<tr height="100">
			<td height="100" style="height:100px;width:233px;">DAB</td>
			<td style="width:171px;">Sigma Aldrich</td>
			<td style="width:133px;">D5905-50TAB</td>
			<td style="width:281px;">3,3&#39;-Diaminobenzidine tetrahydrochloride, tablet, 10 mg substrate per tablet. Caution: carcinogen - must be bleached before discarding</td>
		</tr>
		<tr height="36">
			<td height="36" style="height:36px;width:233px;">Cytochrome C</td>
			<td style="width:171px;">Sigma Aldrich</td>
			<td style="width:133px;">C2037-100MG</td>
			<td style="width:281px;"></td>
		</tr>
		<tr height="37">
			<td height="37" style="height:37px;width:233px;">Catalase</td>
			<td style="width:171px;">Sigma-Aldich</td>
			<td style="width:133px;">C9322-5G</td>
			<td style="width:281px;"></td>
		</tr>
		<tr height="60">
			<td height="60" style="height:60px;width:233px;">Rabbit anti-GFP</td>
			<td style="width:171px;">Life Technologies/Thermo Fisher</td>
			<td style="width:133px;">#A-11122&#160;</td>
			<td style="width:281px;">Primary antibody</td>
		</tr>
		<tr height="34">
			<td height="34" style="height:35px;width:233px;">Biotinylated goat anti-rabbit</td>
			<td style="width:171px;">Vector Laboratories</td>
			<td style="width:133px;">#BA-1000</td>
			<td style="width:281px;">Secondary antibody</td>
		</tr>
		<tr height="80">
			<td height="80" style="height:80px;width:233px;">Neurolucida System&#160;</td>
			<td style="width:171px;">MicroBrightField</td>
			<td style="width:133px;"></td>
			<td style="width:281px;">Software for neuron tracing and analysis. http://www.mbfbioscience.com/neurolucida</td>
		</tr>
		<tr height="38">
			<td height="38" style="height:39px;width:233px;">Neurolucida Explorer</td>
			<td style="width:171px;">MicroBrightField</td>
			<td style="width:133px;"></td>
			<td style="width:281px;">Data export software</td>
		</tr>
		<tr height="80">
			<td height="80" style="height:80px;width:233px;">Microfire Camera&#160;</td>
			<td style="width:171px;">Optronics</td>
			<td style="width:133px;"></td>
			<td style="width:281px;">2-Megapixel true color microscope camera. http://www.simicroscopes.com/pdfs/microfire.pdf</td>
		</tr>
		<tr height="60">
			<td height="60" style="height:60px;width:233px;">Nikon E800 Microscope</td>
			<td style="width:171px;">Nikon Instruments Inc.</td>
			<td style="width:133px;"></td>
			<td style="width:281px;">Biological research microscope. http://www.microscopyu.com/museum/eclipseE800.html</td>
		</tr>
		<tr height="60">
			<td height="60" style="height:60px;width:233px;">Matlab</td>
			<td style="width:171px;">The MathWorks Inc.&#160;</td>
			<td style="width:133px;"></td>
			<td style="width:281px;">Matrix-based computational mathematics software. http://www.mathworks.com</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;width:233px;">Microsoft Office Excel</td>
			<td style="width:171px;">Microsoft</td>
			<td style="width:133px;"></td>
			<td>Spreadsheet program</td>
		</tr>
	</tbody>
</table>

large-scale reconstructions and independent, unbiased clustering based on morphological metrics to classify neurons in selective populations

This protocol outlines large-scale reconstructions of neurons combined with the use of independent and unbiased clustering analyses to create a comprehensive survey of the morphological characteristics observed among a selective neuronal population. Combination of these techniques constitutes a novel approach for the collection and analysis of neuroanatomical data. Together, these techniques enable large-scale, and therefore more comprehensive, sampling of selective neuronal populations and establish unbiased quantitative methods for describing morphologically unique neuronal classes within a population.
The protocol outlines the use of modified rabies virus to selectively label neurons. G-deleted rabies virus acts like a retrograde tracer following stereotaxic injection into a target brain structure of interest and serves as a vehicle for the delivery and expression of EGFP in neurons. Large numbers of neurons are infected using this technique and express GFP throughout their dendrites, producing &#34;Golgi-like&#34; complete fills of individual neurons. Accordingly, the virus-mediated retrograde tracing method improves upon traditional dye-based retrograde tracing techniques by producing complete intracellular fills.
Individual well-isolated neurons spanning all regions of the brain area under study are selected for reconstruction in order to obtain a representative sample of neurons. The protocol outlines procedures to reconstruct cell bodies and complete dendritic arborization patterns of labeled neurons spanning multiple tissue sections. Morphological data, including positions of each neuron within the brain structure, are extracted for further analysis. Standard programming functions were utilized to perform independent cluster analyses and cluster evaluations based on morphological metrics. To verify the utility of these analyses, statistical evaluation of a cluster analysis performed on 160 neurons reconstructed in the thalamic reticular nucleus of the thalamus (TRN) of the macaque monkey was made. Both the original cluster analysis and the statistical evaluations performed here indicate that TRN neurons are separated into three subpopulations, each with unique morphological characteristics.

We have shown previously that large-scale reconstructions of neurons within a selective population is feasible following injection of modified rabies virus into the dLGN5. Recently, the same tissue was utilized to reconstruct 160 neurons in the visual sector of the TRN (Bragg et al., in review; Figure 2A-B) following the detailed methodological steps described above. In the TRN study, three unique clusters of TRN neurons were identified based on indepe...

Watch this Scientific Journal Video about Large-scale Reconstructions and Independent, Unbiased Clustering Based on Morphological Metrics to Classify Neurons in Selective Populations at JoVE.com

Large-scale Reconstructions and Independent, Unbiased Clustering Based on Morphological Metrics to Classify Neurons in Selective Populations

This protocol describes large-scale reconstructions of selective neuronal populations, labeled following retrograde infection with a modified rabies virus expressing fluorescent markers, and independent, unbiased cluster analyses that enable comprehensive characterization of morphological metrics among distinct neuronal subclasses.

This protocol outlines large-scale reconstructions of neurons combined with the use of independent and unbiased clustering analyses to create a ...

large-scale-reconstructions-independent-unbiased-clustering-based-on

Research

JoVE Journal

Neuroscience

6.8K Views.  Geisel School of Medicine at Dartmouth. This protocol describes large-scale reconstructions of selective neuronal populations, labeled following retrograde infection with a modified rabies virus expressing fluorescent markers, and independent, unbiased cluster analyses that enable comprehensive characterization of morphological metrics among distinct neuronal subclasses.

Video: Large-scale Reconstructions and Independent, Unbiased Clustering Based on Morphological Metrics to Classify Neurons in Selective Populations

Fluorescence Recovery After Photobleaching (FRAP) of Fluorescence Tagged Proteins in Dendritic Spines of Cultured Hippocampal Neurons

FRAP has been used to quantify the mobility of GFP-tagged proteins. Using a strong excitation laser, the fluorescence of a GFP-tagged protein is bleached in the region of interest. The fluorescence of the region recovers when the unbleached GFP-tagged protein from outside of the region diffuses into the region of interest. The mobility of the protein is then analyzed by measuring the fluorescence recovery rate. This technique could be used to characterize protein mobility and turnover rate.
In this study, we express the (enhanced green fluorescent protein) EGFP vector in cultured hippocampal neurons. Using the Zeiss 710 confocal microscope, we photobleach the fluorescence signal of the GFP protein in a single spine, and then take time lapse images to record the fluorescence recovery after photobleaching. Finally, we estimate the percentage of mobile and immobile fractions of the GFP in spines, by analyzing the imaging data using ImageJ and Graphpad softwares.
This FRAP protocol shows how to perform a basic FRAP experiment as well as how to analyze the data.

Fluorescence Recovery After Photobleaching FRAP of Fluorescence Tagged Proteins in Dendritic Spines of Cultured Hippocampal Neurons

FRAP has been used to quantify the mobility of Green Fluorescence Protein (GFP)-tagged proteins in cultured cells. We examined the mobile/immobile fractions of the GFP by analyzing the fluorescence recovery percentage after photobleaching. In this study, FRAP was performed at spines of hippocampal neurons.

FRAP has been used to quantify the mobility of GFP-tagged proteins. Using a strong excitation laser, the fluorescence of a GFP-tagged protein is bleached ...

Physiological, Morphological and Neurochemical Characterization of Neurons Modulated by Movement

The role of individual neurons and their function in neuronal circuits is fundamental to understanding the neuronal mechanisms of sensory and motor functions. Most investigations of sensorimotor mechanisms rely on either examination of neurons while an animal is static1,2 or record extracellular neuronal activity during a movement.3,4 While these studies have provided the fundamental background for sensorimotor function, they either do not evaluate functional information which occurs during a movement or are limited in their ability to fully characterize the anatomy, physiology and neurochemical phenotype of the neuron. A technique is shown here which allows extensive characterization of individual neurons during an in vivo movement. This technique can be used not only to study primary afferent neurons but also to characterize motoneurons and sensorimotor interneurons. Initially the response of a single neuron is recorded using electrophysiological methods during various movements of the mandible followed by determination of the receptive field for the neuron. A neuronal tracer is then intracellularly injected into the neuron and the brain is processed so that the neuron can be visualized with light, electron or confocal microscopy (Fig. 1). The detailed morphology of the characterized neuron is then reconstructed so that neuronal morphology can be correlated with the physiological response of the neuron (Figs. 2,3). In this communication important key details and tips for successful implementation of this technique are provided. Valuable additional information can be determined for the neuron under study by combining this method with other techniques. Retrograde neuronal labeling can be used to determine neurons with which the labeled neuron synapses; thus allowing detailed determination of neuronal circuitry. Immunocytochemistry can be combined with this method to examine neurotransmitters within the labeled neuron and to determine the chemical phenotypes of neurons with which the labeled neuron synapses. The labeled neuron can also be processed for electron microscopy to determine the ultrastructural features and microcircuitry of the labeled neuron. Overall this technique is a powerful method to thoroughly characterize neurons during in vivo movement thus allowing substantial insight into the role of the neuron in sensorimotor function.

A technique is described to quantify the in vivo physiological response of mammalian neurons during movement and correlate the physiology of the neuron with neuronal morphology, neurochemical phenotype and synaptic microcircuitry.

The role of individual neurons and their function in neuronal circuits is fundamental to understanding the neuronal mechanisms of sensory and motor ...

Vibrodissociation of Neurons from Rodent Brain Slices to Study Synaptic Transmission and Image Presynaptic Terminals

Mechanical dissociation of neurons from the central nervous system has the advantage that presynaptic boutons remain attached to the isolated neuron of interest. This allows for examination of synaptic transmission under conditions where the extracellular and postsynaptic intracellular environments can be well controlled. A vibration-based technique without the use of proteases, known as vibrodissociation, is the most popular technique for mechanical isolation. A micropipette, with the tip fire-polished to the shape of a small ball, is placed into a brain slice made from a P1-P21 rodent. The micropipette is vibrated parallel to the slice surface and lowered through the slice thickness resulting in the liberation of isolated neurons. The isolated neurons are ready for study within a few minutes of vibrodissociation. This technique has advantages over the use of primary neuronal cultures, brain slices and enzymatically isolated neurons including: rapid production of viable, relatively mature neurons suitable for electrophysiological and imaging studies; superior control of the extracellular environment free from the influence of neighboring cells; suitability for well-controlled pharmacological experiments using rapid drug application and total cell superfusion; and improved space-clamp in whole-cell recordings relative to neurons in slice or cell culture preparations. This preparation can be used to examine synaptic physiology, pharmacology, modulation and plasticity. Real-time imaging of both pre- and postsynaptic elements in the living cells and boutons is also possible using vibrodissociated neurons. Characterization of the molecular constituents of pre- and postsynaptic elements can also be achieved with immunological and imaging-based approaches.

This report demonstrates a technique for mechanical isolation of individual viable neurons retaining attached presynaptic boutons. Vibrodissociated neurons have the advantages of rapid production, excellent pharmacological control and improved space-clamp without influence from neighboring cells. This method can be used for imaging of synaptic elements and patch-clamp recording.

Mechanical dissociation of neurons from the central nervous system has the advantage that presynaptic boutons remain attached to the isolated neuron of ...

Recording Large-scale Neuronal Ensembles with Silicon Probes in the Anesthetized Rat

Large scale electrophysiological recordings from neuronal ensembles offer the opportunity to investigate how the brain orchestrates the wide variety of behaviors from the spiking activity of its neurons. One of the most effective methods to monitor spiking activity from a large number of neurons in multiple local neuronal circuits simultaneously is by using silicon electrode arrays1-3.
Action potentials produce large transmembrane voltage changes in the vicinity of cell somata. These output signals can be measured by placing a conductor in close proximity of a neuron. If there are many active (spiking) neurons in the vicinity of the tip, the electrode records combined signal from all of them, where contribution of a single neuron is weighted by its 'electrical distance'. Silicon probes are ideal recording electrodes to monitor multiple neurons because of a large number of recording sites (+64) and a small volume. Furthermore, multiple sites can be arranged over a distance of millimeters, thus allowing for the simultaneous recordings of neuronal activity in the various cortical layers or in multiple cortical columns (Fig. 1). Importantly, the geometrically precise distribution of the recording sites also allows for the determination of the spatial relationship of the isolated single neurons4. Here, we describe an acute, large-scale neuronal recording from the left and right forelimb somatosensory cortex simultaneously in an anesthetized rat with silicon probes (Fig. 2).

Extracellular recordings of neuronal activity using silicon probes in the anesthetized rat will be described. This technique allows information to be obtained across multiple brain areas from more than 100 neurons simultaneously. It provides information with single cell resolution about neuronal ensembles dynamics in multiple local circuits.

Large scale electrophysiological recordings from neuronal ensembles offer the opportunity to investigate how the brain orchestrates the wide variety of ...

Selective Viral Transduction of Adult-born Olfactory Neurons for Chronic in vivo Optogenetic Stimulation

Local interneurons are continuously regenerated in the olfactory bulb of adult rodents1-3. In this process, called adult neurogenesis, neural stem cells in the walls of the lateral ventricle give rise to neuroblasts that migrate for several millimeters along the rostral migratory stream (RMS) to reach and incorporate into the olfactory bulb. To study the different steps and the impact of adult-born neuron integration into preexisting olfactory circuits, it is necessary to selectively label and manipulate the activity of this specific population of neurons. The recent development of optogenetic technologies offers the opportunity to use light to precisely activate this specific cohort of neurons without affecting surrounding neurons4,5. Here, we present a series of procedures to virally express Channelrhodopsin2(ChR2)-YFP in a temporally restricted cohort of neuroblasts in the RMS before they reach the olfactory bulb and become adult-born neurons. In addition, we show how to implant and calibrate a miniature LED for chronic in vivo stimulation of ChR2-expressing neurons.

Selective Viral Transduction of Adult-born Olfactory Neurons for Chronic in vivo Optogenetic Stimulation

Adult-born neurons of the olfactory bulb can be optogenetically controlled using Channelrhodopsin2-expressing lentiviral injection in the rostral migratory stream and chronic photostimulation with an implanted miniature LED.

Local interneurons are continuously regenerated in the olfactory bulb of adult rodents1-3. In this process, called adult neurogenesis, neural stem cells ...

Large-scale Recording of Neurons by Movable Silicon Probes in Behaving Rodents

A major challenge in neuroscience is linking behavior to the collective activity of neural assemblies. Understanding of input-output relationships of neurons and circuits requires methods with the spatial selectivity and temporal resolution appropriate for mechanistic analysis of neural ensembles in the behaving animal, i.e. recording of representatively large samples of isolated single neurons. Ensemble monitoring of neuronal activity has progressed remarkably in the past decade in both small and large-brained animals, including human subjects1-11. Multiple-site recording with silicon-based devices are particularly effective because of their scalability, small volume and geometric design.
Here, we describe methods for recording multiple single neurons and local field potential in behaving rodents, using commercially available micro-machined silicon probes with custom-made accessory components. There are two basic options for interfacing silicon probes to preamplifiers: printed circuit boards and flexible cables. Probe supplying companies (<a href="http://www.neuronexustech.com/" >http://www.neuronexustech.com/</a>; <a href="http://www.sbmicrosystems.com/">http://www.sbmicrosystems.com/</a>; <a href="http://www.acreo.se/">http://www.acreo.se/</a>) usually provide the bonding service and deliver probes bonded to printed circuit boards or flexible cables. Here, we describe the implantation of a 4-shank, 32-site probe attached to flexible polyimide cable, and mounted on a movable microdrive. Each step of the probe preparation, microdrive construction and surgery is illustrated so that the end user can easily replicate the process.

We describe methods for large-scale recording of multiple single units and local field potential in behaving rodents with silicon probes. Drive fabrication, probe attachment to the drive and probe implantation processes are illustrated in sufficient details for easy replication.

A major challenge in neuroscience is linking behavior to the collective activity of neural assemblies. Understanding of input-output relationships of ...

In Vivo Two-photon Imaging Of Experience-dependent Molecular Changes In Cortical Neurons

The brain's ability to change in response to experience is essential for healthy brain function, and abnormalities in this process contribute to a variety of brain disorders1,2. To better understand the mechanisms by which brain circuits react to an animal's experience requires the ability to monitor the experience-dependent molecular changes in a given set of neurons, over a prolonged period of time, in the live animal. While experience and associated neural activity is known to trigger gene expression changes in neurons1,2, most of the methods to detect such changes do not allow repeated observation of the same neurons over multiple days or do not have sufficient resolution to observe individual neurons3,4. Here, we describe a method that combines in vivo two-photon microscopy with a genetically encoded fluorescent reporter to track experience-dependent gene expression changes in individual cortical neurons over the course of day-to-day experience. 
One of the well-established experience-dependent genes is Activity-regulated cytoskeletal associated protein (Arc)5,6. The transcription of Arc is rapidly and highly induced by intensified neuronal activity3, and its protein product regulates the endocytosis of glutamate receptors and long-term synaptic plasticity7. The expression of Arc has been widely used as a molecular marker to map neuronal circuits involved in specific behaviors3. In most of those studies, Arc expression was detected by in situ hybridization or immunohistochemistry in fixed brain sections. Although those methods revealed that the expression of Arc was localized to a subset of excitatory neurons after behavioral experience, how the cellular patterns of Arc expression might change with multiple episodes of repeated or distinctive experiences over days was not investigated. 
In vivo two-photon microscopy offers a powerful way to examine experience-dependent cellular changes in the living brain8,9. To enable the examination of Arc expression in live neurons by two-photon microscopy, we previously generated a knock-in mouse line in which a GFP reporter is placed under the control of the endogenous Arc promoter10. This protocol describes the surgical preparations and imaging procedures for tracking experience-dependent Arc-GFP expression patterns in neuronal ensembles in the live animal. In this method, chronic cranial windows were first implanted in Arc-GFP mice over the cortical regions of interest. Those animals were then repeatedly imaged by two-photon microscopy after desired behavioral paradigms over the course of several days. This method may be generally applicable to animals carrying other fluorescent reporters of experience-dependent molecular changes4.

In Vivo Two-photon Imaging Of Experience-dependent Molecular Changes In Cortical Neurons

Experience-dependent molecular changes in neurons are essential for the brain's ability to adapt in response to behavioral challenges. An in vivo two-photon imaging method is described here that allows the tracking of such molecular changes in individual cortical neurons through genetically encoded reporters.

The brain's ability to change in response to experience is essential for healthy brain function, and abnormalities in this process contribute to a variety ...

Simultaneous Electrophysiological Recording and Calcium Imaging of Suprachiasmatic Nucleus Neurons

Simultaneous electrophysiological and fluorescent imaging recording methods were used to study the role of changes of membrane potential or current in regulating the intracellular calcium concentration. Changing environmental conditions, such as the light-dark cycle, can modify neuronal and neural network activity and the expression of a family of circadian clock genes within the suprachiasmatic nucleus (SCN), the location of the master circadian clock in the mammalian brain. Excitatory synaptic transmission leads to an increase in the postsynaptic Ca2+ concentration that is believed to activate the signaling pathways that shifts the rhythmic expression of circadian clock genes. Hypothalamic slices containing the SCN were patch clamped using microelectrodes filled with an internal solution containing the calcium indicator bis-fura-2. After a seal was formed between the microelectrode and the SCN neuronal membrane, the membrane was ruptured using gentle suction and the calcium probe diffused into the neuron filling both the soma and dendrites. Quantitative ratiometric measurements of the intracellular calcium concentration were recorded simultaneously with membrane potential or current. Using these methods it is possible to study the role of changes of the intracellular calcium concentration produced by synaptic activity and action potential firing of individual neurons. In this presentation we demonstrate the methods to simultaneously record electrophysiological activity along with intracellular calcium from individual SCN neurons maintained in brain slices.

Procedures are described to perform simultaneous recordings of membrane potential or current and changes of intracellular calcium concentration. Suprachiasmatic nucleus neurons are filled with the calcium indicator bis-fura-2 using a patch clamp electrode in the whole cell patch clamp configuration.

Simultaneous electrophysiological and fluorescent imaging recording methods were used to study the role of changes of membrane potential or current in ...

Functional and Morphological Assessment of Diaphragm Innervation by Phrenic Motor Neurons

This protocol specifically focuses on tools for assessing phrenic motor neuron (PhMN) innervation of the diaphragm at both the electrophysiological and morphological levels. Compound muscle action potential (CMAP) recording following phrenic nerve stimulation can be used to quantitatively assess functional diaphragm innervation by PhMNs of the cervical spinal cord in vivo in anesthetized rats and mice. Because CMAPs represent simultaneous recording of all myofibers of the whole hemi-diaphragm, it is useful to also examine the phenotypes of individual motor axons and myofibers at the diaphragm NMJ in order to track disease- and therapy-relevant morphological changes such as partial and complete denervation, regenerative sprouting and reinnervation. This can be accomplished via whole-mount immunohistochemistry (IHC) of the diaphragm, followed by detailed morphological assessment of individual NMJs throughout the muscle. Combining CMAPs and NMJ analysis provides a powerful approach for quantitatively studying diaphragmatic innervation in rodent models of CNS and PNS disease.

Compound muscle action potential recording quantitatively assesses functional diaphragm innervation by phrenic motor neurons. Whole-mount diaphragm immunohistochemistry assesses morphological innervation at individual neuromuscular junctions. The goal of this protocol is to demonstrate how these two powerful methodologies can be used in various rodent models of spinal cord disease.

This protocol specifically focuses on tools for assessing phrenic motor neuron (PhMN) innervation of the diaphragm at both the electrophysiological and ...

Method for High Speed Stretch Injury of Human Induced Pluripotent Stem Cell-derived Neurons in a 96-well Format

Traumatic brain injury (TBI) is a major clinical challenge with high morbidity and mortality. Despite decades of pre-clinical research, no proven therapies for TBI have been developed. This paper presents a novel method for pre-clinical neurotrauma research intended to complement existing pre-clinical models. It introduces human pathophysiology through the use of human induced pluripotent stem cell-derived neurons (hiPSCNs). It achieves loading pulse duration similar to the loading durations of clinical closed head impact injury. It employs a 96-well format that facilitates high throughput experiments and makes efficient use of expensive cells and culture reagents. Silicone membranes are first treated to remove neurotoxic uncured polymer and then bonded to commercial 96-well plate bodies to create stretchable 96-well plates. A custom-built device is used to indent some or all of the well bottoms from beneath, inducing equibiaxial mechanical strain that mechanically injures cells in culture in the wells. The relationship between indentation depth and mechanical strain is determined empirically using high speed videography of well bottoms during indentation. Cells, including hiPSCNs, can be cultured on these silicone membranes using modified versions of conventional cell culture protocols. Fluorescent microscopic images of cell cultures are acquired and analyzed after injury in a semi-automated fashion to quantify the level of injury in each well. The model presented is optimized for hiPSCNs but could in theory be applied to other cell types.

Here we present a method for a human in vitro model of stretch injury in a 96-well format on a timescale relevant to impact trauma. This includes methods for fabricating stretchable plates, quantifying the mechanical insult, culturing and injuring cells, imaging, and high content analysis to quantify injury.