This work was supported by Humboldt Universit&#228;t zu Berlin, the Bernstein Center for Computational Neuroscience Berlin, the German Center for Neurodegenerative Diseases (DZNE), the German Federal Ministry of Education and Research (BMBF, F&#246;rderkennzeichen 01GQ1001A), NeuroCure, and the Gottfried Wilhelm Leibniz prize of the DFG. We thank Shimpei Ishiyama for excellent graphic design and Juliane Diederichs for excellent technical assistance.

All experimental procedures were performed according to the German guidelines on animal welfare under the supervision of local ethics committees (LaGeSo). Human and bat brain data were derived from Naumann et al.5 The following procedure is performed on a male adult Wistar rat (strain: RJHan:WI).
1. Perfusion and Brain Extraction
NOTE: In order to obtain a homogenously fixed and blood-free brain, transcardial perfusion of the animal is...

<ol>
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Modularity in the cerebral cortex has been identified using a variety of techniques. The earliest studies typically identified cortical modules by either visualizing cell dense regions, or an absence of fibers1. Subsequent methods have utilized the presence of dendritic bundles24, afferents from a particular region25, or enrichment of neurotransmitters26. Here we demonstrate two techniques, (i) cytochrome oxidase histochemistr...

Some of the most significant changes in the brain structure across phylogeny can be observed in the cerebral cortex. Despite significant differences, the cortex of animals follows a common pattern and can be broadly divided in two distinct ways, by layers and areas1. Cortical layers lie parallel to the surface of the brain and vary in number from 3 layers in reptilian cortices2 to 6 layers in mammalian cortices1. Cortical areas on the other hand are distinct regions of the cortex which largely correspond to distinct functionalities, e.g., the somatosensory cortex is involved in the sensation of touch or the visual cortex in processing visual inputs. These cortical areas can often be subdivided into patches or modules3, which are regularly repeating anatomical structures, essentially found parallel to the pial surface of the brain. Cortical modules may be confined to a particular layer4, or extend across several layers5.
Standard sectioning methods of the brain involve sections normal to the surface of the brain, like coronal or sagittal. While these methods can be used to visualize cortical modules, a multitude of interesting features can be revealed when the cortical modules are visualized tangentially, in a plane parallel to the surface of the brain. For instance, somatosensory modules in the rodent brain representing whiskers, appear as barrels when visualized normal to the brain surface, and thus the regions derive the name barrel cortex. However, on visualizing the barrels in a tangential orientation, they reveal a whisker-map, with the barrels being laid out in a topographic orientation mirroring the exact layout of the whiskers on the external body surface. In certain cases, modular arrangement has even escaped detection for considerable periods, when visualized in a non-tangential manner. The medial entorhinal cortex, is known for the presence of grid cells, neurons which fire in a regular hexagonal pattern when an animal is traversing an environment. Even though it is a heavily investigated area, until recently, the presence of patches or modules of cells in the medial entorhinal cortex, which are physically laid out in a hexagonal pattern6, had escaped detection. The presence and arrangement of these modules, in the rat brain, was facilitated by making tangential sections of the medial entorhinal cortex and investigating the cytoarchitecture in a layer-wise manner.
Subsequent to sectioning, the particular aspect of visualization of cortical modules can also be realized in multiple ways. Classically, studies have delineated modules based on cell density or fiber layout1. Another popular approach is the use of cytochrome oxidase histochemistry, which reveals areas of higher activity8. Newer approaches include looking at genetically determined cell types, distinguished on the basis of their protein expression profiles6,8.
In this study, we highlight methods to isolate the cortex from mammalian brains, obtain flattened tangential sections, and visualize cortical modules based on cytochrome oxidase histochemistry and immunohistochemistry of cell-type specific proteins.

<table>
	<tbody>
		<tr>
			<td>Cytochrome oxidase staining</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Cytochrome c from equine heart</td>
			<td>Sigma-Aldrich</td>
			<td>C2506</td>
			<td></td>
		</tr>
		<tr>
			<td>3,3&#39;Diaminobenzidine tetrahydrochloride hydrate</td>
			<td>Sigma-Aldrich</td>
			<td>D5637</td>
			<td></td>
		</tr>
		<tr>
			<td>D(+)-Saccharose</td>
			<td>Carl Roth&#160;</td>
			<td>4621.1</td>
			<td></td>
		</tr>
		<tr>
			<td>Ammonium nickel(II) sulfate hexahydrate</td>
			<td>Sigma-Aldrich</td>
			<td>A1827</td>
			<td></td>
		</tr>
		<tr>
			<td>HEPES</td>
			<td>Carl Roth&#160;</td>
			<td>9105.4</td>
			<td></td>
		</tr>
		<tr>
			<td>Name</td>
			<td>Company</td>
			<td>Catalog Number</td>
			<td>Comments</td>
		</tr>
		<tr>
			<td>Antigen retrieval</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Trisodium citrate dihydrate</td>
			<td>Sigma-Aldrich</td>
			<td>S1804</td>
			<td></td>
		</tr>
		<tr>
			<td>Citric acid monohydrate</td>
			<td>Sigma-Aldrich</td>
			<td>C1909</td>
			<td></td>
		</tr>
		<tr>
			<td>Name</td>
			<td>Company</td>
			<td>Catalog Number</td>
			<td>Comments</td>
		</tr>
		<tr>
			<td>Phosphate buffer/phosphate-buffered saline/prefix/PFA</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Potassium dihydrogen phosphate</td>
			<td>Carl Roth</td>
			<td>3904.2</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium chloride</td>
			<td>Carl Roth</td>
			<td>9265.1</td>
			<td></td>
		</tr>
		<tr>
			<td>Di-Sodium hydrogen phosphate dihydrate</td>
			<td>Carl Roth</td>
			<td>4984.3</td>
			<td></td>
		</tr>
		<tr>
			<td>Paraformaldehyde</td>
			<td>Carl Roth</td>
			<td>0335.3</td>
			<td></td>
		</tr>
		<tr>
			<td>TRITON-X 100</td>
			<td>Carl Roth</td>
			<td>3051.3</td>
			<td></td>
		</tr>
		<tr>
			<td>Name</td>
			<td>Company</td>
			<td>Catalog Number</td>
			<td>Comments</td>
		</tr>
		<tr>
			<td>Immunohistochemistry</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Calbindin D-28k puriefied from chicken gut, Mouse monoclonal</td>
			<td>Swant</td>
			<td>RRID: AB_10000347</td>
			<td></td>
		</tr>
		<tr>
			<td>Calbindin D-28k from recombinant rat calbindin D-28k, Rabbit polyclonal</td>
			<td>Swant</td>
			<td>RRID: AB_10000340</td>
			<td></td>
		</tr>
		<tr>
			<td>Albumin Fraction V, biotin free</td>
			<td>Carl Roth</td>
			<td>0163.4</td>
			<td></td>
		</tr>
		<tr>
			<td>Name</td>
			<td>Company</td>
			<td>Catalog Number</td>
			<td>Comments</td>
		</tr>
		<tr>
			<td>Mounting or freezing media</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Fluoromount (immunofluorescence)</td>
			<td>Sigma-Aldrich</td>
			<td>F4680</td>
			<td></td>
		</tr>
		<tr>
			<td>Eukitt (histochemistry)</td>
			<td>Sigma-Aldrich</td>
			<td>03989</td>
			<td></td>
		</tr>
		<tr>
			<td>Tissue freezing medium</td>
			<td>Leica Biosystems</td>
			<td>NC0696746</td>
			<td></td>
		</tr>
		<tr>
			<td>Name</td>
			<td>Company</td>
			<td>Catalog Number</td>
			<td>Comments</td>
		</tr>
		<tr>
			<td>Alcohol dehydration</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Ethanol 100%</td>
			<td>Carl Roth</td>
			<td>9065.3</td>
			<td></td>
		</tr>
		<tr>
			<td>Ethanol 96%</td>
			<td>Carl Roth</td>
			<td>P075.3</td>
			<td></td>
		</tr>
		<tr>
			<td>2-Propanol</td>
			<td>Carl Roth</td>
			<td>6752.4</td>
			<td></td>
		</tr>
		<tr>
			<td>Xylene substitute</td>
			<td>Fluka</td>
			<td>78475</td>
			<td></td>
		</tr>
		<tr>
			<td>Name</td>
			<td>Company</td>
			<td>Catalog Number</td>
			<td>Comments</td>
		</tr>
		<tr>
			<td>Devices/tools</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Microm HM 650V</td>
			<td>Thermo Scientific</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Jung RM2035</td>
			<td>Leica Biosystems</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Dumont #55 Forceps - Inox</td>
			<td>Fine Science Tools</td>
			<td>11255-20</td>
			<td></td>
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		<tr>
			<td>Dumont #5 Forceps - Inox Biology Tip</td>
			<td>Fine Science Tools</td>
			<td>11252-30</td>
			<td></td>
		</tr>
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			<td>Dumont #5SF Forceps - Inox Super Fine Tip</td>
			<td>Fine Science Tools</td>
			<td>11252-00</td>
			<td></td>
		</tr>
		<tr>
			<td>Bone Shears - 24 cm</td>
			<td>Fine Science Tools</td>
			<td>16150-24</td>
			<td></td>
		</tr>
		<tr>
			<td>Friedman Rongeur</td>
			<td>Fine Science Tools</td>
			<td>16000-14</td>
			<td></td>
		</tr>
		<tr>
			<td>Blunt Scissors</td>
			<td>Fine Science Tools</td>
			<td>14000-18</td>
			<td></td>
		</tr>
		<tr>
			<td>Surgical Scissors - Large Loops</td>
			<td>Fine Science Tools</td>
			<td>14101-14</td>
			<td></td>
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		<tr>
			<td>Surgical Scissors - Sharp-Blunt</td>
			<td>Fine Science Tools</td>
			<td>14001-13</td>
			<td></td>
		</tr>
		<tr>
			<td>Fine Iris Scissors</td>
			<td>Fine Science Tools</td>
			<td>14094-11</td>
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visualization of cortical modules in flattened mammalian cortices

The cortex of mammalian brains is parcellated into distinct substructures or modules. Cortical modules typically lie parallel to the cortical sheet, and can be delineated by certain histochemical and immunohistochemical methods. In this study, we highlight a method to isolate the cortex from mammalian brains and flatten them to obtain sections parallel to the cortical sheet. We further highlight selected histochemical and immunohistochemical methods to process these flattened tangential sections to visualize cortical modules. In the somatosensory cortex of various mammals, we perform cytochrome oxidase histochemistry to reveal body maps or cortical modules representing different parts of the body of the animal. In the medial entorhinal cortex, an area where grid cells are generated, we utilize immunohistochemical methods to highlight modules of genetically determined neurons which are arranged in a grid-pattern in the cortical sheet across several species. Overall, we provide a framework to isolate and prepare layer-wise flattened cortical sections, and visualize cortical modules using histochemical and immunohistochemical methods in a wide variety of mammalian brains.

We obtained flattened cortical sections of the somatosensory cortex in a variety of brains, and processed them for cytochrome oxidase histochemistry to visualize the somatotopic modules representing different body parts. This comparative approach allows studying the evolutionary forces that shape cortex, e.g., showing highly conserved representation of mystacial vibrissae in rodents and lagomorpha as barrels21 (Figure 2). In c...

Watch this Scientific Journal Video about Visualization of Cortical Modules in Flattened Mammalian Cortices at JoVE.com

Visualization of Cortical Modules in Flattened Mammalian Cortices

This article describes a detailed methodology to obtain flattened tangential sections from mammalian cortices and visualize cortical modules using histochemical and immunohistochemical methods.

The cortex of mammalian brains is parcellated into distinct substructures or modules. Cortical modules typically lie parallel to the cortical sheet, and ...

The overall goal for this procedure for cortex flattening and staining is to visualize cellular modules in the cortical regions in a layer-wise manner. This method can answer key questions in neuroscience, like how cortical structure spreads into the brain, and how it might relate to function. The main advantage of this technicque is you can compare cortical architecture in a laminal fashion, and compare various aspects of it, like how it's conserved the class evolution, or how it varies in function.Demonstrating the technique will be Simon Lauer, and Undine Schneeweib, a student and a technician from the lab of Professor Michelle Black. To begin, transcardially perfuse the animal to obtain a homogeneously fixed and blood-free brain. After removing the brain, submerge it in 0.1 molar phosphate buffer.If sections with large cortical areas are desired, flatten the brain prior to further postfixation. However, to obtain sections of harder-to-reach areas, like the medial entorhinal cortex, postfix the brain in 4%PFA for 24 hours before flattening. Prepare to keep the brain moist with buffer during the whole dissection.To begin, separate the hemispheres using a scalpel. If the brain has not been postfixed, be careful when handling it. Next, while securing the brain by the cerebellum, gently insert the spatula to open a dissection plane in the corpus callosum.The round tip of spatula should point away from the cortex. Then, manipulate the spatula to divide the thalamus and cortex. Next, separate the subcortical structures using a razor blade.Next, separate the subcortical structures using a scalpel or the edge of the spatula. To improve the flattening, make a clean cut through the striatum, nucleus accumbens, and orbital frontal cortex, since they increase the thickness of the cortex in the lateral region. Then add a relieving cut at the base of the inner region of prefrontal cortex.This will allow for unfolding of medial portions of the cortex. Now, place a hemisphere cortex down on a glass slide. Then, place two clay cylinders on either side of the tissue.The clay must a 10 to 20%thinner than the brain tissue, as the clay defines the extent of flattening. Next, place a glass side tangentially onto the cortex, contacting the lateral portion first. Then, set a weight on the glass, with the mass centered over the lateral portion.Now, let the assembly sit for three to five hours in phosphate buffer at four degrees Celsius. The real key to this preparation is to get the brain as flat as possible, as this has the greatest impact on viewing the cortical map. Lastly, if needed, postfix the brain.Transfer the flattened hemisphere to 1%PFA, or 2%PFA if it was not taken from a perfused animal. Then, let it fix for 24 hour at 4 degrees Celsius, with gentle agitation. First, wash the flattened hemisphere in phosphate buffer for 15 minutes.Then, slice the hemisphere tangentially on a Vibratome. Fix the tissue in position using a small volume of cyanoacrylate and gentle pressing. Be careful, as too much glue can lead to cutting artifacts.Now, cut the hemisphere from the thicker and more stable end towards the thinner end at the required thickness. If low fixative concentrations were used, cut the tissue slowly with a high amplitude. Next, wash the sectioned tissue in hepes buffer for 15 minutes with gentle agitation.During the wash, prepare fresh cytochrome oxidase staining solution. And add the DAB component just before using it. Now, incubate the sections in the freshly made staining solution at room temperature with shaker and keep watch.Depending on the amount of fixation, staining could be observable in 10 minutes or it make take several hours. If the reaction is going too slow, increase the temperature to 37 degrees Celsius. To stop the reaction, transfer the sections to a bath of 4%PFA and let them incubate for 15 minutes with gentle agitation.Then, wash the sections three times, with hepes buffer for 10 minutes per wash. Now, mount and dry the sections on glass slides. And dehydrate them using progressively stronger ethanol baths.Then, wash the slides in Isopropanol for five minutes, followed by Xylene for five minutes. After the Xylene bath, immediately add a quick-hardening, non water-based mounting medium. Water-based mediums will degrade the stain.After adding a cover slip, store the slides at four degrees Celsius until imaged. Cortical sections of the somatosensory cortex in a variety of brain were processed, using the described procedures. This comparative approach allows for the study of the evolutionary forces that shape cortex, such as the highly conserved representation of mistacial vibrissaer in rodents and lagomorpha as barrels.The architecture of the medial entorhinal cortex was observed sections parallel to the peel surface, using tangential sectioning of the medical entorhinal cortex in mice, rats, and Egyptian fruit bats. In addition, human brains were processed using gentle flattening of the cortex and tangential slices. All of the brains were cryopreserved, and sectioned on a cryostat at 60 microns.Immunostaining was used to label calbindin-positive parameatal cell modules. In the entorhinal cortex the calbindin modules show a remarkable periodicity in each species, and vary in size by only a factor of 10, across a 20, 000-fold variation in brain size. After watching this video you should have a good understanding of how to obtain tangential sections for analysis.Once mastered, this technique can be completed in a couple of hours. While attempting this procedure, it's important to remember to flatten the brain properly, instead the size, the quality, or the final results. Don't forget that working with the agents like PFA and DAB can be extremely hazardous, and you should always wear protective clothing and work under the field light.

visualization-of-cortical-modules-in-flattened-mammalian-cortices

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Neuroscience

12.5K ビュー.  Humboldt University of Berlin. The overall goal for this procedure for cortex flattening and staining is to visualize cellular modules in the cortical regions in a layer-wise manner. This method can answer key questions in neuroscience, like how cortical structure spreads into the brain, and how it might relate to function. The main advantage of this technicque is you can compare cortical architecture in a laminal fashion, and compare various aspects of it, like how it's conserved the class evolution, or how it varies in f...

ビデオ: Visualization of Cortical Modules in Flattened Mammalian Cortices

This article describes a detailed methodology to obtain flattened tangential sections from mammalian cortices and visualize cortical modules using histochemical and immunohistochemical...

visualization of endoplasmic reticulum localized mrnas in mammalian cells

Visualization of Endoplasmic Reticulum Localized mRNAs in Mammalian Cells

Here we describe a method to visualize endoplasmic reticulum-associated mRNAs in mammalian tissue culture cells. This technique involves the selective permeabilization of the plasma membrane with digitonin to remove cytoplasmic contents followed by fluorescent in situ hybridization to detect either bulk poly(A) mRNA or specific...

fabrication of micro-tissues using modules of collagen gel containing cells

Fabrication of Micro-tissues using Modules of Collagen Gel Containing Cells

Creation of micro-tissues using cylindrical collagen gels, called modules, that contain embedded cells and which surface is coated with endothelial...

reconstitution of membrane-tethered minimal actin cortices on supported lipid bilayers

Reconstitution of Membrane-Tethered Minimal Actin Cortices on Supported Lipid Bilayers

This protocol describes the formation of supported lipid bilayers and the addition of cytoskeletal filaments and motor proteins to study the dynamics of reconstituted, membrane-tethered cytoskeletal networks using fluorescence...

electrophysiology of laminar cortical activity in the common marmoset

Author Spotlight: Optimizing Micro-Drive Systems for Precise Electrode Positioning in Marmoset

Custom-built micro-drives enable the sub-millimeter targeting of cortical recording sites with linear silicon...

Electrophysiology of Laminar Cortical Activity in the Common Marmoset

nuclear transport assays in permeabilized mouse cortical neurons

Nuclear Transport Assays in Permeabilized Mouse Cortical Neurons

We have developed a reliable method of selective plasma membrane permeabilization of primary mouse cortical neurons for high content automated analysis of neuronal nucleocytoplasmic...

in vivo two-photon imaging of cortical neurons in neonatal mice

In Vivo Two-photon Imaging of Cortical Neurons in Neonatal Mice

We present an in vivo two-photon imaging protocol for imaging the cerebral cortex of neonatal mice. This method is suitable for analyzing the developmental dynamics of cortical neurons, the molecular mechanisms that control the neuronal dynamics, and the changes in neuronal dynamics in disease...

In Vivo Two-photon Imaging of Cortical Neurons in Neonatal Mice

neurophysiology recordings in cortical tissue of marmoset

Neurophysiology Recordings in Cortical Tissue of Marmoset

electroporation of sliced human cortical organoids for studies of gene function

Author Spotlight: Studying Gene Function in Neural Progenitors via Electroporation of Cortical Organoids

Here, we present the acute genetic manipulation of sliced human cortical organoids by electroporation. These cortical organoid models are particularly amenable to injection as ventricle-like structures can be readily identified after slicing, enabling the functional investigation of human cortical development, neurodevelopmental disorders, and cortical evolution.

CRISPR/Cas9 Gene Knockout in Sliced Human Cortical Organoids via Electroporation

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functional calcium imaging in developing cortical networks

Functional Calcium Imaging in Developing Cortical Networks

Spontaneous activity of developing neuronal networks can be measured using AM-ester forms of calcium-sensitive indicator dyes. Changes in intracellular calcium, indicating neuronal activation, are detected as transient changes in indicator fluorescence with one- or two-photon imaging. This protocol can be adapted for a range of developmentally-dependent neuronal networks in...

subtype-selective electroporation of cortical interneurons

Subtype-selective Electroporation of Cortical Interneurons

This procedure shows how to target interneurons in the developing mouse forebrain by means of in utero electroporation. This technique was particularly efficient to achieve selective gene expression in interneuron subtypes destined to the superficial layers of the...

chronic implantation of whole-cortical electrocorticographic array in the common marmoset

Chronic Implantation of Whole-cortical Electrocorticographic Array in the Common Marmoset

We have developed a whole-cortical electrocorticographic array for the common marmoset that continuously covers almost the entire lateral surface of cortex, from the occipital pole to the temporal and frontal poles. This protocol describes a chronic implantation procedure of the array in the epidural space of the marmoset...

deepomicsae: representing signaling modules in alzheimer's disease with deep learning analysis of proteomics, metabolomics, and clinical data

Author Spotlight: Advancing Alzheimer&#039;s Research &amp;#8211; Exploring Early Detection and Multi-Omics Approaches

DeepOmicsAE is a workflow centered on the application of a deep learning method (i.e., an autoencoder) to reduce the dimensionality of multi-omics data, providing a foundation for predictive models and signaling modules representing multiple layers of omics...

DeepOmicsAE: Representing Signaling Modules in Alzheimer's Disease with Deep Learning Analysis of Proteomics, Metabolomics, and Clinical Data

quantitative assessment of cortical auditory-tactile processing in children with disabilities

Quantitative Assessment of Cortical Auditory-tactile Processing in Children with Disabilities

Objective and easy measurement of sensory processing is extremely difficult in nonverbal or vulnerable pediatric patients. We developed a new methodology to quantitatively assess infants and children&#39;s cortical processing of light touch, speech sounds, and the multisensory processing of the 2 stimuli, without requiring active subject participation or causing discomfort in vulnerable...

measurement of heme synthesis levels in mammalian cells

Measurement of Heme Synthesis Levels in Mammalian Cells

Altered intracellular heme levels are associated with common diseases such as cancer. Thus, there is a need to measure heme biosynthesis levels in diverse cells. The goal of this protocol is to provide a fast and sensitive method to measure and compare the levels of heme synthesis in different...

cortical source analysis of high-density eeg recordings in children

Cortical Source Analysis of High-Density EEG Recordings in Children

In recent years, there has been increasing interest in estimating the cortical sources of scalp measured electrical activity for cognitive neuroscience experiments. This article describes how high density EEG is acquired and how recordings are processed for cortical source estimation in children from the age of 2 years at the London Baby...

in vivo imaging of deep cortical layers using a microprism

In vivo Imaging of Deep Cortical Layers using a Microprism

Right-angle microprisms inserted into the mouse neocortex allows for deep imaging of multiple cortical layers with a viewpoint typically found in slice.  One-millimeter microprisms offer a wide field-of-view (~900 &mu;m) and spatial resolutions sufficient to resolve dendritic spines.  We demonstrate layer V neuronal imaging and neocortical vascular imaging using...

In vivo Imaging of Deep Cortical Layers using a Microprism

engineering intracellular protein sensors in mammalian cells

Engineering Intracellular Protein Sensors in Mammalian Cells

Here, we present a protocol for engineering genetically-encoded intracellular protein sensor-actuator(s). The device specifically detects target proteins through intracellular antibodies (intrabodies) and responds by switching on gene transcriptional output. A general framework is built to rapidly replace intrabodies, enabling rapid detection of any desired protein, without altering the general...

in vivo two-photon imaging of experience-dependent molecular changes in cortical neurons

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...

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

quantification of filamentous actin (f-actin) puncta in rat cortical neurons

Quantification of Filamentous Actin F-actin Puncta in Rat Cortical Neurons

Filamentous actin (F-actin) plays an important role in spinogenesis, synaptic plasticity, and synaptic stability. Quantification of F-actin puncta is therefore a useful tool to study the integrity of synaptic structures. This protocol describes the procedures of quantifying F-actin puncta labeled with Phalloidin in low-density primary cortical neuronal...

Quantification of Filamentous Actin (F-actin) Puncta in Rat Cortical Neurons

Automated Interactive Video Playback for Studies of Animal Communication

Video playback is a widely-used technique for the controlled manipulation and presentation of visual signals in animal communication. In particular, parameter-based computer animation offers the opportunity to independently manipulate any number of behavioral, morphological, or spectral characteristics in the context of realistic, moving images of animals on screen. A major limitation of conventional playback, however, is that the visual stimulus lacks the ability to interact with the live animal. Borrowing from video-game technology, we have created an automated, interactive system for video playback that controls animations in response to real-time signals from a video tracking system. We demonstrated this method by conducting mate-choice trials on female swordtail fish, Xiphophorus birchmanni. Females were given a simultaneous choice between a courting male conspecific and a courting male heterospecific (X. malinche) on opposite sides of an aquarium. The virtual male stimulus was programmed to track the horizontal position of the female, as courting males do in the wild. Mate-choice trials on wild-caught X. birchmanni females were used to validate the prototype's ability to effectively generate a realistic visual stimulus.

Video playback is a widely used technique in animal behavior. We created and evaluated a program that applies rules-based, interactive playback of 3-D computer animations in response to real-time, automated data on subject behavior.

Video playback is a widely-used technique for the controlled manipulation and presentation of visual signals in animal communication. In particular, ...

Determination of Mitochondrial Membrane Potential and Reactive Oxygen Species in Live Rat Cortical Neurons

Mitochondrial membrane potential (&Delta;&Psi;m) is critical for maintaining the physiological function of the respiratory chain to generate ATP. A significant loss of &Delta;&Psi;m renders cells depleted of energy with subsequent death. Reactive oxygen species (ROS) are important signaling molecules, but their accumulation in pathological conditions leads to oxidative stress. The two major sources of ROS in cells are environmental toxins and the process of oxidative phosphorylation. Mitochondrial dysfunction and oxidative stress have been implicated in the pathophysiology of many diseases; therefore, the ability to determine &Delta;&Psi;m and ROS can provide important clues about the physiological status of the cell and the function of the mitochondria. 
Several fluorescent probes (Rhodamine 123, TMRM, TMRE, JC-1) can be used to determine &Delta;&psi;m in a variety of cell types, and many fluorescence indicators (Dihydroethidium, Dihydrorhodamine 123, H2DCF-DA) can be used to determine ROS. Nearly all of the available fluorescence probes used to assess &Delta;&Psi;m or ROS are single-wavelength indicators, which increase or decrease their fluorescence intensity proportional to a stimulus that increases or decreases the levels of &Delta;&Psi;m or ROS. Thus, it is imperative to measure the fluorescence intensity of these probes at the baseline level and after the application of a specific stimulus. This allows one to determine the percentage of change in fluorescence intensity between the baseline level and a stimulus. This change in fluorescence intensity reflects the change in relative levels of &Delta;&Psi;m or ROS. In this video, we demonstrate how to apply the fluorescence indicator, TMRM, in rat cortical neurons to determine the percentage change in TMRM fluorescence intensity between the baseline level and after applying FCCP, a mitochondrial uncoupler. The lower levels of TMRM fluorescence resulting from FCCP treatment reflect the depolarization of mitochondrial membrane potential. We also show how to apply the fluorescence probe H2DCF-DA to assess the level of ROS in cortical neurons, first at baseline and then after application of H2O2. This protocol (with minor modifications) can be also used to determine changes in &#x2206;&#x03A8;m and ROS in different cell types and in neurons isolated from other brain regions.

We demonstrate application of the fluorescence indicator, TMRM, in cortical neurons to determine the relative changes in TMRM fluorescence intensity before and after application of a specific stimulus. We also show application of the fluorescence probe H2DCF-DA to assess the relative level of reactive oxygen species in cortical neurons.

Mitochondrial membrane potential (&Delta;&Psi;m) is critical for maintaining the physiological function of the respiratory chain to generate ATP.  A ...

A hallmark pattern of activity in developing nervous systems is spontaneous, synchronized network activity. Synchronized activity has been observed in intact spinal cord, brainstem, retina, cortex and dissociated neuronal culture preparations. During periods of spontaneous activity, neurons depolarize to fire single or bursts of action potentials, activating many ion channels. Depolarization activates voltage-gated calcium channels on dendrites and spines that mediate calcium influx. Highly synchronized electrical activity has been measured from local neuronal networks using field electrodes. This technique enables high temporal sampling rates but lower spatial resolution due to integrated read-out of multiple neurons at one electrode. Single cell resolution of neuronal activity is possible using patch-clamp electrophysiology on single neurons to measure firing activity. However, the ability to measure from a network is limited to the number of neurons patched simultaneously, and typically is only one or two neurons. The use of calcium-dependent fluorescent indicator dyes has enabled the measurement of synchronized activity across a network of cells. This technique gives both high spatial resolution and sufficient temporal sampling to record spontaneous activity of the developing network.
A key feature of newly-forming cortical and hippocampal networks during pre- and early postnatal development is spontaneous, synchronized neuronal activity (Katz &amp; Shatz, 1996; Khaziphov &amp; Luhmann, 2006). This correlated network activity is believed to be essential for the generation of functional circuits in the developing nervous system (Spitzer, 2006). In both primate and rodent brain, early electrical and calcium network waves are observed pre- and postnatally in vivo and in vitro (Adelsberger et al., 2005; Garaschuk et al., 2000; Lamblin et al., 1999). These early activity patterns, which are known to control several developmental processes including neuronal differentiation, synaptogenesis and plasticity (Rakic &amp; Komuro, 1995; Spitzer et al., 2004) are of critical importance for the correct development and maturation of the cortical circuitry.
In this JoVE video, we demonstrate the methods used to image spontaneous activity in developing cortical networks. Calcium-sensitive indicators, such as Fura 2-AM ester diffuse across the cell membrane where intracellular esterase activity cleaves the AM esters to leave the cell-impermeant form of indicator dye. The impermeant form of indicator has carboxylic acid groups which are able to then detect and bind calcium ions intracellularly.. The fluorescence of the calcium-sensitive dye is transiently altered upon binding to calcium. Single or multi-photon imaging techniques are used to measure the change in photons being emitted from the dye, and thus indicate an alteration in intracellular calcium. Furthermore, these calcium-dependent indicators can be combined with other fluorescent markers to investigate cell types within the active network.

Spontaneous activity of developing neuronal networks can be measured using AM-ester forms of calcium-sensitive indicator dyes. Changes in intracellular calcium, indicating neuronal activation, are detected as transient changes in indicator fluorescence with one- or two-photon imaging. This protocol can be adapted for a range of developmentally-dependent neuronal networks in vitro.

A hallmark pattern of activity in developing nervous systems is spontaneous, synchronized network activity. Synchronized activity has been observed in ...

Visualization of Proprioceptors in Drosophila Larvae and Pupae

Proprioception is the ability to sense the motion, or position, of body parts by responding to stimuli arising within the body. In fruitflies and other insects proprioception is provided by specialized sensory organs termed chordotonal organs (ChOs) 2. Like many other organs in Drosophila, ChOs develop twice during the life cycle of the fly. First, the larval ChOs develop during embryogenesis. Then, the adult ChOs start to develop in the larval imaginal discs and continue to differentiate during metamorphosis.
The development of larval ChOs during embryogenesis has been studied extensively 10,11,13,15,16. The centerpiece of each ChO is a sensory unit composed of a neuron and a scolopale cell. The sensory unit is stretched between two types of accessory cells that attach to the cuticle via specialized epidermal attachment cells 1,9,14. When a fly larva moves, the relative displacement of the epidermal attachment cells leads to stretching of the sensory unit and consequent opening of specific transient receptor potential vanilloid (TRPV) channels at the outer segment of the dendrite 8,12. The elicited signal is then transferred to the locomotor central pattern generator circuit in the central nervous system.
Multiple ChOs have been described in the adult fly 7. These are located near the joints of the adult fly appendages (legs, wings and halters) and in the thorax and abdomen. In addition, several hundreds of ChOs collectively form the Johnston's organ in the adult antenna that transduce acoustic to mechanical energy 3,5,17,4.
In contrast to the extensive knowledge about the development of ChOs in embryonic stages, very little is known about the morphology of these organs during larval stages. Moreover, with the exception of femoral ChOs 18 and Johnston's organ, our knowledge about the development and structure of ChOs in the adult fly is very fragmentary.
Here we describe a method for staining and visualizing ChOs in third instar larvae and pupae. This method can be applied together with genetic tools to better characterize the morphology and understand the development of the various ChOs in the fly.

Visualization of Proprioceptors in Drosophila Larvae and Pupae

A method to immunostain and visualize chordotonal organs in larvae and pupae of Drosophila melanogaster is described.

Proprioception is the ability to sense the motion, or position, of body parts by responding to stimuli arising within the body. In fruitflies and other ...

Thinned-skull Cortical Window Technique for In Vivo Optical Coherence Tomography Imaging

Optical coherence tomography (OCT) is a biomedical imaging technique with high spatial-temporal resolution. With its minimally invasive approach OCT has been used extensively in ophthalmology, dermatology, and gastroenterology1-3. Using a thinned-skull cortical window (TSCW), we employ spectral-domain OCT (SD-OCT) modality as a tool to image the cortex in vivo. Commonly, an opened-skull has been used for neuro-imaging as it provides more versatility, however, a TSCW approach is less invasive and is an effective mean for long term imaging in neuropathology studies. Here, we present a method of creating a TSCW in a mouse model for in vivo OCT imaging of the cerebral cortex.

Thinned-skull Cortical Window Technique for In Vivo Optical Coherence Tomography Imaging

We present a method of creating a thinned-skull cortical window (TSCW) in a mouse model for in vivo OCT imaging of the cerebral cortex.

Optical coherence tomography (OCT) is a biomedical imaging technique  with high spatial-temporal resolution. With its minimally invasive approach OCT  has ...

Isolation and Culture of Mouse Cortical Astrocytes

Astrocytes are an abundant cell type in the mammalian brain, yet much remains to be learned about their molecular and functional characteristics. In vitro astrocyte cell culture systems can be used to study the biological functions of these glial cells in detail. This video protocol shows how to obtain pure astrocytes by isolation and culture of mixed cortical cells of mouse pups. The method is based on the absence of viable neurons and the separation of astrocytes, oligodendrocytes and microglia, the three main glial cell populations of the central nervous system, in culture. Representative images during the first days of culture demonstrate the presence of a mixed cell population and indicate the timepoint, when astrocytes become confluent and should be separated from microglia and oligodendrocytes. Moreover, we demonstrate purity and astrocytic morphology of cultured astrocytes using immunocytochemical stainings for well established and newly described astrocyte markers. This culture system can be easily used to obtain pure mouse astrocytes and astrocyte-conditioned medium for studying various aspects of astrocyte biology.

Astrocytes have been recognized to be versatile cells participating in fundamental biological processes that are essential for normal brain development and function, and central nervous system repair. Here we present a rapid procedure to obtain pure mouse astrocyte cultures to study the biology of this major class of central nervous system cells.

Astrocytes  are an abundant cell type in the mammalian brain, yet much remains to be  learned about their molecular and functional characteristics. In ...

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.

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 ...

The study of central nervous system (CNS) maturation relies on genetic targeting of neuronal populations. However, the task of restricting the expression of genes of interest to specific neuronal subtypes has proven remarkably challenging due to the relative scarcity of specific promoter elements. GABAergic interneurons constitute a neuronal population with extensive genetic and morphological diversity. Indeed, more than 11 different subtypes of GABAergic interneurons have been characterized in the mouse cortex1. Here we present an adapted protocol for selective targeting of GABAergic populations. We achieved subtype selective targeting of GABAergic interneurons by using the enhancer element of the homeobox transcription factors Dlx5 and Dlx6, homologues of the Drosophila distal-less (Dll) gene2,3, to drive the expression of specific genes through in utero electroporation.

This procedure shows how to target interneurons in the developing mouse forebrain by means of in utero electroporation. This technique was particularly efficient to achieve selective gene expression in interneuron subtypes destined to the superficial layers of the cortex.

The study of central nervous system (CNS) maturation relies on genetic targeting of neuronal populations. However, the task of restricting the expression ...

Filamentous actin protein (F-actin) plays a major role in spinogenesis, synaptic plasticity, and synaptic stability. Changes in dendritic F-actin rich structures suggest alterations in synaptic integrity and connectivity. Here we provide a detailed protocol for culturing primary rat cortical neurons, Phalloidin staining for F-actin puncta, and subsequent quantification techniques. First, the frontal cortex of E18 rat embryos are dissociated into low-density cell culture, then the neurons grown in vitro for at least 12-14 days. Following experimental treatment, the cortical neurons are stained with AlexaFluor 488 Phalloidin (to label the dendritic F-actin puncta) and microtubule-associated protein 2 (MAP2; to validate the neuronal cells and dendritic integrity). Finally, specialized software is used to analyze and quantify randomly selected neuronal dendrites. F-actin rich structures are identified on second order dendritic branches (length range 25-75 &#181;m) with continuous MAP2 immunofluorescence. The protocol presented here will be a useful method for investigating changes in dendritic synapse structures subsequent to experimental treatments.

Filamentous actin (F-actin) plays an important role in spinogenesis, synaptic plasticity, and synaptic stability. Quantification of F-actin puncta is therefore a useful tool to study the integrity of synaptic structures. This protocol describes the procedures of quantifying F-actin puncta labeled with Phalloidin in low-density primary cortical neuronal cultures.

Filamentous actin protein (F-actin) plays a major role in spinogenesis, synaptic plasticity, and synaptic stability. Changes in dendritic F-actin rich ...

Two-photon imaging is a powerful tool for the in vivo analysis of neuronal circuits in the mammalian brain. However, a limited number of in vivo imaging methods exist for examining the brain tissue of live newborn mammals. Herein we summarize a protocol for imaging individual cortical neurons in living neonatal mice. This protocol includes the following two methodologies: (1) the Supernova system for sparse and bright labeling of cortical neurons in the developing brain, and (2) a surgical procedure for the fragile neonatal skull. This protocol allows the observation of temporal changes of individual cortical neurites during neonatal stages with a high signal-to-noise ratio. Labeled cell-specific gene silencing and knockout can also be achieved by combining the Supernova with RNA interference and CRISPR/Cas9 gene editing systems. This protocol can, thus, be used for analyzing the developmental dynamics of cortical neurons, molecular mechanisms that control the neuronal dynamics, and changes in neuronal dynamics in disease models.

We present an in vivo two-photon imaging protocol for imaging the cerebral cortex of neonatal mice. This method is suitable for analyzing the developmental dynamics of cortical neurons, the molecular mechanisms that control the neuronal dynamics, and the changes in neuronal dynamics in disease models.

Two-photon imaging is a powerful tool for the in vivo analysis of neuronal circuits in the mammalian brain. However, a limited number of in vivo imaging ...