German Research Foundation (FOR2240 "(Lymph) Angiogenesis and Cellular Immunity in Inflammatory Diseases of the Eye" to CC and LMH; HE 6743/2-1 and HE 7643/3-1 to LMH; CU47/6-1 to CC), German Cancer Aid (to LMH and CC), GEROK program University of Cologne (to SLS and LMH), and EU COST BM1302 "Joining Forces to Corneal Regeneration" (to CC).

The use of human tissues must be reviewed and approved by an institutional review board or the equivalent. The work described here was approved by the local ethics committee and had approval for scientific examination. This work was performed according to the Declaration of Helsinki. The human scleral specimens were obtained from the eyes of globe donors (maximum post-mortem time 24 hr) at the Eye Bank of the Department of Ophthalmology, University of Cologne, Germany.
1. Experimental Preparation
<ol>
	<li>Prepare 96% ethanol and phosphate buffered saline (PBS) in different tubes. Prepare the primary antibodies in the recommended dilution of PBS containing 2% bovine serum albumin (BSA) and keep all solutions on ice. Prepare 100 &#956;l per sample.</li>
	<li>Clean all instruments and use sharp scalpels. After repeated cutting with the same scalpel, change the scalpel.</li>
	<li>Obtain 1-2 colibri forceps, straight micro dissecting scissors, a #10 scalpel or ophthalmic scalpel micro feather, and four 26 G needles.</li>
	<li>Wrap aluminum foil around a polystyrene plate or use a cork plate to affix the tissue. Work underneath a binocular stereo microscope. Work sterile underneath a laminar airflow if needed.</li>
</ol>
2. Prepare the Sclera
<ol>
	<li>Gently hold the bulb and perform a perforating trepanation on the corneoscleral part, then rotate the trepan. Rotate the trepan carefully and evenly onto the surface to perform an equally round cut. Use a 15.5 mm sized trepan. Cut the remaining attachments with curved scissors. Remove the corneoscleral trepanation. This will result in an anteriorly opened bulb.
	<ol>
		<li>Put the sclera on a swab with the open part upwards. Remove the retina and uvea, using colibri forceps to pull off both layers (retina and uvea) from the sclera. Do not leave the pigmented uvea on the inner sclera. Use curved scissors to remove the retina and uvea from the papilla. Remove the remaining conjunctiva, extraocular muscles, and tenon&#39;s capsule from the superficial sclera.</li>
	</ol>
	</li>
	<li>Remove the scleral sample in the required size by using straight-type scissors and the colibri forceps. Take about 2 cm2 sized scleral samples from different locations. Because of the small size, hold the sclera gently and cut out the required size as squares using the straight-type scissors. The corneoscleral trepanation defines the anterior margin of the scleral samples.
	<ol>
		<li>Avoid repeated grabbing with the forceps as the area where the tissue was grabbed is not suitable for confocal microscopy analyses. Prepare the required number of samples depending on the experiment type (e.g. anteriorly vs. posteriorly, compare Figure 1) and the amount of antibodies used.</li>
	</ol>
	</li>
	<li>Put the samples in 1.5 ml tubes for later use. Fix the samples in 1.5 ml 96% ethanol for 15 min, and then wash them three times each for 5 min in 1.5 ml PBS on the shaker. If working with frozen tissue, perform this step before snap freezing.</li>
	<li>Use fresh tissue. However, if this is not possible, snap freeze the sclera in liquid nitrogen and keep it at -20 &#176;C for later use. If working with frozen tissue, thaw before use. Avoid repeated thawing and freezing cycles.</li>
	<li>Keep each sample in PBS containing 1.5 ml 5% BSA at room temperature for 2 hr. This step induces a swelling of the sample that is helpful for the laminating and also prevents unspecific binding.</li>
	<li>After the samples have swelled, prepare the scleral squares for lamination. Work underneath a microscope, e.g. a binocular stereo microscope. Affix the posterior scleral samples to the polystyrene membrane wrapped in aluminum foil or the cork plate using the 26 G needles.</li>
	<li>Bend the edges of the needles so they do not interfere with the visual field underneath the microscope.</li>
	<li>Laminate the full-thickness scleral samples.
	<ol>
		<li>First, hold the anterior scleral edge using colibri forceps. Then carefully cut a thin layer of the superficial sclera using the #10 scalpel, the ophthalmic scalpel micro feather, or a spatula blade. Hold the scalpel horizontally and cut the superficial layer as thinly as possible from the underlying layer.</li>
		<li>Dissect a thin scleral layer from the scleral square. This method is comparable to standard surgical techniques to prepare a flap during trabeculectomy and should result in 30-80 &#181;m thick layers (compare Figure 2).</li>
	</ol>
	</li>
	<li>Prevent drying of the sclera by adding small amounts of PBS to the tissue, e.g. 50 &#181;l PBS using a pipette.</li>
	<li>Put the cut layers into 100 &#181;l of PBS in the 96 well plate and label both the orientation (towards extern and intern) and the layer (superficial and profound) e.g. with a waterproof color.</li>
	<li>Repeat steps 2.7-2.9 until the tissue is fully laminated.</li>
</ol>
3. Perform Immunohistochemistry
<ol>
	<li>Add 100 &#181;l of the required primary antibodies into the recommended dilution. Here, e.g. use CD 31 (monoclonal mouse anti human) and LYVE1 antibody (rabbit anti human), both in a dilution of 1:100 in PBS (containing 2% BSA) and incubate at 4 &#176;C overnight. To change the medium in the 96 well plate, hold the pipette to the wall of the well and remove the fluid.</li>
	<li>The next day, wash the samples three times each for 5 min with 200-300 &#181;l PBS on the shaker. Add 100 &#181;l of the corresponding secondary antibodies; here use goat anti mouse fluorescein isothiocyanate (FITC) and goat anti rabbit cyanine dyes 3 (Cy3), and incubate the samples at room temperature for 1-2 hr. Dilute the secondary antibodies 1:300 in PBS containing 2% goat serum.</li>
	<li>Rinse the samples again three times each for 5 min in 200-300 &#181;l PBS on the shaker.</li>
	<li>Perform nucleus staining, e.g. 4&#39;,6-diamidino-2-phenylindole (DAPI) (dilution 1:2,000, 100 &#181;l in each well and incubate 10 min at room temperature), then wash again 2 times in 200-300 &#181;l PBS on the shaker.</li>
	<li>Transfer the samples onto microscope slides, embed them in 1-2 drops of fluorescent mounting medium, add a coverslip, seal it by covering the edges with transparent varnish, and store at 4 &#176;C for later use or directly examine the slides with the confocal microscope.</li>
	<li>Use a confocal microscope (or equivalent) to analyze the samples. Use the desired magnification, e.g. 10-40X magnification.</li>
	<li>To verify the thickness of the samples, measure with confocal microscopy using Z-Stacks. The amount of possible scleral sections depends on the location of the sclera, as the thickness differs equatorially and posteriorly (compare introduction).</li>
</ol>

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L., 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=Absence+of+lymphatic+vessels+in+the+developing+human+sclera.">Absence of lymphatic vessels in the developing human sclera.</a> Exp Eye Res. 125, 203-209 (2014).</li><li>Hos, D., Cursiefen, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Lymphatic+vessels+in+the+development+of+tissue+and+organ+rejection.">Lymphatic vessels in the development of tissue and organ rejection.</a> Adv Anat Embryol Cell Biol. 214, 119-141 (2014).</li><li>Hos, D., Schlereth, S. L., Bock, F., Heindl, L. 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S., Sainz de la Maza, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> The sclera. , (2012).</li><li>Kiss, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Der+Blutkreislauf+des+Auges.">Der Blutkreislauf des Auges.</a> Ophthalmologica. 106, 225 (1943).</li><li>Ashton, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Anatomical+study+of+Schlemm's+canal+and+aqueous+veins+by+means+of+neoprene+casts.+Part+I.+Aqueous+veins.">Anatomical study of Schlemm's canal and aqueous veins by means of neoprene casts. Part I. 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The authors declare no financial disclosures. The contents of this article are solely the responsibility of the authors.

Laminating the human sclera is a method for performing confocal microscopy on this tissue. A critical step in this process is the use of ethanol instead of formalin for affixing the tissue. In our experience, better results are obtained when using ethanol instead of formalin for fixation. Blunt scalpels aggravate the procedure and should be avoided. Similarly, the drying up of the sclera should be avoided, as it complicates the procedure and reduces the quality of the images.
Regarding the imm...

The sclera is the rigid outer layer that covers the eye, which is made of dense connective tissue. It helps to protect intraocular structures and to maintain intraocular pressure. Thus, the sclera is essential for clear vision. It is devoid of lymphatic vessels 1,2 and thereby forms an outer lymphatic-free border between it and the lymphatic-free inner eye 3-7. It also provides attachment sites for extraocular muscles, thereby sharing anatomical similarities with tendons. Because the sclera mainly consists of dense bundles of type I collagen and has smaller numbers of collagen types III, IV, V, VI, VIII 8,9 and elastin 10,11, this tissue is not easy to use for immunohistochemistry.
Anatomically, the sclera can be separated into three main layers: (1) the superficial vascularized episclera, found underneath the conjunctiva and tenon&#39;s capsule and towards the sides and the back of the eye facing the orbit; (2) the scleral stroma, the main part of the sclera; and (3) the lamina fusca, which is a thin, pigmented layer located directly above the uvea. Our anatomical knowledge about the sclera stems mainly from the first half of the 20th century. At that time, researchers studied the anatomy of vasculature mainly by using India ink injections 12 and vascular casting 13-15. Later, it was researched in angiographic studies 16-19.
Since that time, older techniques have been improved and new ones have been developed that have allowed us to supplement previous anatomical knowledge. For example, it has only been about one decade since we have had such reliable lymphatic markers as lymphatic vascular endothelium specific hyaluronan receptor-1 (LYVE1) 20 or podoplanin 21. Confocal microscopy offers new possibilities for studying the anatomical features of the different tissues of the eye. It allows for multiple stains to be used for differentiating markers of cells or for the localization of cells in relation to blood vessels and other anatomical structures. It provides an overview when the sample is of a larger size and allows us to scan through a sample when in search of a specific cell type. With Z-Stack technology, confocal microscopy can be used for samples up to 100-200 &#181;m. The sclera differs in thickness between 0.3 mm behind the muscle insertions and 1 mm at the posterior pole 11. Due to both its thickness and opaqueness, the sclera is not suitable for confocal microscopy using traditional methods.
To remedy this, scleral tissues were laminated to allow for their analysis with confocal microscopy. This technology is useful for gaining a better understanding of both physiological and pathological situations in the human sclera.

<table><tbody><tr><td>96% ethanol</td><td>Merck Chemicals, Darmstadt, Germany</td><td>P075.4</td><td></td></tr><tr><td>binocular stereo microscope&amp;nbsp;</td><td>Motic, Hongkong, China</td><td>n.a</td><td></td></tr><tr><td>26 G needles&amp;nbsp;</td><td>Terumo, Leuven, Belgium</td><td>303800</td><td></td></tr><tr><td>15.5 mm trepan</td><td>Geuder, Heidelberg, Germany</td><td>n.a</td><td></td></tr><tr><td>no.10 scalpel&amp;nbsp;</td><td>Feather, pfm medical, Osaka, Japan</td><td>2E+08</td><td></td></tr><tr><td>ophthalmic scalpel micro feather&amp;nbsp;</td><td>Feather, pfm medical, Osaka, Japan</td><td>no. 7657BR</td><td></td></tr><tr><td>CD 31 antibody (monoclonal mouse anti human)</td><td>Dako, USA</td><td>IR610</td><td></td></tr><tr><td>LYVE1 antibody&amp;nbsp; (polyclonal rabbit anti human)</td><td>Zytomed, Germany</td><td>RBK014-05</td><td></td></tr><tr><td>goat anti mouse FITC antibody</td><td>Sigma Aldrich, Steinheim, Germany</td><td>F0257</td><td></td></tr><tr><td>goat anti rabbit Cy3 antibody</td><td>Dianova, Germany</td><td>111-165-003</td><td></td></tr><tr><td>Goat Serum normal</td><td>Dako, Glostrup, Denmark</td><td>X090710-8</td><td></td></tr><tr><td>DAPI</td><td>Carl Roth GmbH, Karlsruhe, Germany</td><td>6335.1</td><td></td></tr><tr><td>microscope slides&amp;nbsp;</td><td>Engelbrecht, Ederm&amp;uuml;nde, Germany</td><td>WC7695002</td><td></td></tr><tr><td>Coverslips 24 mm x 24 mm</td><td>Th. Gayer, Lohmar, Germany</td><td>7695026</td><td></td></tr><tr><td>DAKO fluorescent mounting medium&amp;nbsp;</td><td>DAKO, USA</td><td>S3023</td><td></td></tr><tr><td>LSM Meta 510 confocal microscopy&amp;nbsp;</td><td>Carl Zeiss AG, Jena, Germany</td><td>n.a</td><td></td></tr></tbody></table>

using a laminating technique to perform confocal microscopy of the human sclera

The sclera is a dense connective tissue that covers and protects the eye. It mainly consists of dense collagen bundles (types I, III, IV, V, VI, and VII). Due to its autofluorescence, opaqueness, and thickness, it has not been found suitable for confocal microscopy. An alternative approach to the one presented here, which uses formalin-fixed sclera embedded in paraffin for immunohistochemistry, has technical challenges, especially when preheating the tissue for antigen retrieval. Since the sclera is relatively poor in both cells and vessels, the use of larger tissue samples was explored to help prevent overlooking cells and to understand their localization in relation to vessels and other anatomical sites. To allow for the analysis of larger tissue samples under the confocal microscope, a laminating technique was performed to create thin layers from the sclera. Following the analysis of results of CD31 blood vessels and lymphatic vessel endothelial hyaluronan receptor 1 (LYVE1) positive cells, for which approval for scientific examination was obtained, the advantages and limitations of this method are discussed.

In the representative experiments performed here, there are demonstrable benefits derived from the use of this particular laminating technique. The first experiment illustrates the diverse network of the episcleral blood vessel plexus in three representative pictures (Figure 3). The vessels are positive for CD31.
The second experiment shows immune cells, in particular LYVE1 + cells of the episclera and their rel...

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Using a Laminating Technique to Perform Confocal Microscopy of the Human Sclera

Human sclera tissue is mainly collagen; therefore, it is not easily usable for immunohistochemistry. To achieve the goal of performing immunohistochemistry for confocal microscopy of scleral tissue, a laminating technique was used.


The sclera is a dense connective tissue that covers and protects the eye. It mainly consists of dense collagen bundles (types I, III, IV, V, VI, and ...

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Universidad de Cartagena UDEC

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Medicine

7.5K Views.  University of Cologne. Human sclera tissue is mainly collagen; therefore, it is not easily usable for immunohistochemistry. To achieve the goal of performing immunohistochemistry for confocal microscopy of scleral tissue, a laminating technique was used. 

Video: Using a Laminating Technique to Perform Confocal Microscopy of the Human Sclera

Three-dimensional Rendering and Analysis of Immunolabeled, Clarified Human Placental Villous Vascular Networks

Nutrient and gas exchange between mother and fetus occurs at the interface of the maternal intervillous blood and the vast villous capillary network that makes up much of the parenchyma of the human placenta. The distal villous capillary network is the terminus of the fetal blood supply after several generations of branching of vessels extending out from the umbilical cord. This network has a contiguous cellular sheath, the syncytial trophoblast barrier layer, which prevents mixing of fetal blood and the maternal blood in which it is continuously bathed. Insults to the integrity of the placental capillary network, occurring in disorders such as maternal diabetes, hypertension and obesity, have consequences that present serious health risks for the fetus, infant, and adult. To better define the structural effects of these insults, a protocol was developed for this study that captures capillary network structure on the order of 1 - 2 mm3 wherein one can investigate its topological features in its full complexity. To accomplish this, clusters of terminal villi from placenta are dissected, and the trophoblast layer and the capillary endothelia are immunolabeled. These samples are then clarified with a new tissue clearing process which makes it possible to acquire confocal image stacks to z- depths of ~1 mm. The three-dimensional renderings of these stacks are then processed and analyzed to generate basic capillary network measures such as volume, number of capillary branches, and capillary branch end points, as validation of the suitability of this approach for capillary network characterization.

This study presents a protocol for the reversible tissue clearing, immunostaining, 3D-rendering and analysis of vascular networks in human placenta villi samples on the order of 1 - 2 mm3.

Nutrient and gas exchange between mother and fetus occurs at the interface of the maternal intervillous blood and the vast villous capillary network that ...

Developmental Biology

Light-sheet Microscopy for Three-dimensional Visualization of Human Immune Cells

In vivo, activation, proliferation, and function of immune cells all occur in a three-dimensional (3D) environment, for instance in lymph nodes or tissues. Up to date, most in vitro systems rely on two-dimensional (2D) surfaces, such as cell-culture plates or coverslips. To optimally mimic physiological conditions in vitro, we utilize a simple 3D collagen matrix. Collagen is one of the major components of extracellular matrix (ECM) and has been widely used to constitute 3D matrices. For 3D imaging, the recently developed light-sheet microscopy technology (also referred to as single plane illumination microscopy) is featured with high acquisition speed, large penetration depth, low bleaching, and photocytotoxicity. Furthermore, light-sheet microscopy is particularly advantageous for long-term measurement. Here we describe an optimized protocol how to set up and handle human immune cells, e.g. primary human cytotoxic T lymphocytes (CTL) and natural killer (NK) cells in the 3D collagen matrix for usage with the light-sheet microscopy for live cell imaging and fixed samples. The procedure for image acquisition and analysis of cell migration are presented. A particular focus is given to highlight critical steps and factors for sample preparation and data analysis. This protocol can be employed for other types of suspension cells in a 3D collagen matrix and is not limited to immune cells.

Here, we present a protocol to visualize immune cells embedded in a three-dimensional (3D) collagen matrix using light-sheet microscopy. This protocol also elaborates how to track cell migration in 3D. This protocol can be employed for other types of suspension cells in the 3D matrix.

In vivo, activation, proliferation, and function of immune cells all occur in a three-dimensional (3D) environment, for instance in lymph nodes or ...

Immunology and Infection

Near Simultaneous Laser Scanning Confocal and Atomic Force Microscopy (Conpokal) on Live Cells

Techniques available for micro- and nano-scale mechanical characterization have exploded in the last few decades. From further development of the scanning and transmission electron microscope, to the invention of atomic force microscopy, and advances in fluorescent imaging, there have been substantial gains in technologies that enable the study of small materials. Conpokal is a portmanteau that combines confocal microscopy with atomic force microscopy (AFM), where a probe &#8220;pokes&#8221; the surface. Although each technique is extremely effective for the qualitative and/or quantitative image collection on their own, Conpokal provides the capability to test with blended fluorescence imaging and mechanical characterization. Designed for near simultaneous confocal imaging and atomic force probing, Conpokal facilitates experimentation on live microbiological samples. The added insight from paired instrumentation provides co-localization of measured mechanical properties (e.g., elastic modulus, adhesion, surface roughness) by AFM with subcellular components or activity observable through confocal microscopy. This work provides a step by step protocol for the operation of laser scanning confocal and atomic force microscopy, simultaneously, to achieve same cell, same region, confocal imaging, and mechanical characterization.

Near Simultaneous Laser Scanning Confocal and Atomic Force Microscopy Conpokal on Live Cells

Presented here is the protocol of the Conpokal technique, which combines confocal and atomic force microscopy into a single instrument platform. Conpokal provides same cell, same region, near simultaneous confocal imaging and mechanical characterization of live biological samples.

Techniques available for micro- and nano-scale mechanical characterization have exploded in the last few decades. From further development of the scanning ...

Bioengineering

Second Harmonic Generation Signals in Rabbit Sclera As a Tool for Evaluation of Therapeutic Tissue Cross-linking (TXL) for Myopia

Methods to strengthen tissue by introducing chemical bonds (non-enzymatic cross-linking) into structural proteins (fibrillar collagens) for therapy include photochemical cross-linking and tissue cross-linking (TXL) methods. Such methods for inducing mechanical tissue property changes are being employed to the cornea in corneal thinning (mechanically weakened) disorders such as keratoconus as well as the sclera in progressive myopia, where thinning and weakening of the posterior sclera occurs and likely contributes to axial elongation. The primary target proteins for such tissue strengthening are fibrillar collagens which constitute the great majority of dry weight proteins in the cornea and sclera. Fortuitously, fibrillar collagens are the main source of second harmonic generation signals in the tissue extracellular space. Therefore, modifications of the collagen proteins, such as those induced through cross-linking therapies, could potentially be detected and quantitated through the use of second harmonic generation microscopy (SHGM). Monitoring SHGM signals through the use of a laser scanning microscopy system coupled with an infrared excitation light source is an exciting modern imaging method that is enjoying widespread usage in the biomedical sciences. Thus, the present study was undertaken in order to evaluate the use of SHGM microscopy as a means to measure induced cross-linking effects in ex vivo rabbit sclera, following an injection of a chemical cross-linking agent into the sub-Tenon&#39;s space (sT), an injection approach that is standard practice for causing ocular anesthesia during ophthalmologic clinical procedures. The chemical cross-linking agent, sodium hydroxymethylglycinate (SMG), is from a class of cosmetic preservatives known as formaldehyde releasing agents (FARs). Scleral changes following reaction with SMG resulted in increases in SHG signals and correlated with shifts in thermal denaturation temperature, a standard method for evaluating induced tissue cross-linking effects.

Second Harmonic Generation Signals in Rabbit Sclera As a Tool for Evaluation of Therapeutic Tissue Cross-linking TXL for Myopia

This protocol describes techniques for evaluating chemical cross-linking of the rabbit sclera using&#160;second harmonic generation imaging and differential scanning calorimetry.

Methods to strengthen tissue by introducing chemical bonds (non-enzymatic cross-linking) into structural proteins (fibrillar collagens) for therapy ...

Full-Circle Cauterization of Limbal Vascular Plexus for Surgically Induced Glaucoma in Rodents

Glaucoma, the second leading cause of blindness worldwide, is a heterogeneous group of ocular disorders characterized by structural damage to the optic nerve and retinal ganglion cell (RGC) degeneration, resulting in visual dysfunction by interrupting the transmission of visual information from the eye to the brain. Elevated intraocular pressure is the most important risk factor; thus, several models of ocular hypertension have been developed in rodents by either genetic or experimental approaches to investigate the causes and effects of the disease. Among those, some limitations have been reported such as surgical invasiveness, inadequate functional assessment, requirement of extensive training, and highly variable extension of retinal damage. The present work characterizes a simple, low-cost, and efficient method to induce ocular hypertension in rodents, based on low-temperature, full-circle cauterization of the limbal vascular plexus, a major component of aqueous humor drainage. The new model provides a technically easy, noninvasive, and reproducible subacute ocular hypertension, associated with progressive RGC and optic nerve degeneration, and a unique post-operative clinical recovery rate that allows in vivo functional studies by both electrophysiological and behavioral methods.

The goal of this protocol is to characterize a novel model of glaucomatous neurodegeneration based on 360&#176; thermic cauterization of limbal vascular plexus, inducing subacute ocular hypertension.

Glaucoma, the second leading cause of blindness worldwide, is a heterogeneous group of ocular disorders characterized by structural damage to the optic ...

Neuroscience

A Tissue Clearing Method for Neuronal Imaging from Mesoscopic to Microscopic Scales

A detailed protocol is provided here to visualize neuronal structures from mesoscopic to microscopic levels in brain tissues. Neuronal structures ranging from neural circuits to subcellular neuronal structures are visualized in mouse brain slices optically cleared with ScaleSF. This clearing method is a modified version of ScaleS and is a hydrophilic tissue clearing method for tissue slices that achieves potent clearing capability as well as a high-level of preservation of fluorescence signals and structural integrity. A customizable three dimensional (3D)-printed imaging chamber is designed for reliable mounting of cleared brain tissues. Mouse brains injected with an adeno-associated virus vector carrying enhanced green fluorescent protein gene were fixed with 4% paraformaldehyde and cut into slices of 1-mm thickness with a vibrating tissue slicer. The brain slices were cleared by following the clearing protocol, which include sequential incubations in three solutions, namely, ScaleS0 solution, phosphate buffer saline (&#8211;), and ScaleS4 solution, for a total of 10.5&#8211;14.5 h. The cleared brain slices were mounted on the imaging chamber and embedded in 1.5% agarose gel dissolved in ScaleS4D25(0) solution. The 3D image acquisition of the slices was carried out using a confocal laser scanning microscope equipped with a multi-immersion objective lens of a long working distance. Beginning with mesoscopic neuronal imaging, we succeeded in visualizing fine subcellular neuronal structures, such as dendritic spines and axonal boutons, in the optically cleared brain slices. This protocol would facilitate understanding of neuronal structures from circuit to subcellular component scales.

The protocol provides a detailed method of neuronal imaging in brain slice using a tissue clearing method, ScaleSF. The protocol includes brain tissue preparation, tissue clarification, handling of cleared slices and confocal laser scanning microscopy imaging of neuronal structures from mesoscopic to microscopic levels.

A detailed protocol is provided here to visualize neuronal structures from mesoscopic to microscopic levels in brain tissues. Neuronal structures ranging ...

Real Time In Vivo Tracking of Thymocytes in the Anterior Chamber of the Eye by Laser Scanning Microscopy

The purpose of the method being presented is to show, for the first time, the transplant of newborn thymi into the anterior eye chamber of isogenic adult mice for in vivo longitudinal real-time monitoring of thymocytes&#180; dynamics within a vascularized thymus segment. Following the transplantation, laser scanning microscopy (LSM) through the cornea allows in vivo noninvasive repeated imaging at cellular resolution level. Importantly, the approach adds to previous intravital T-cell maturation imaging models the possibility for continuous progenitor cell recruitment and mature T-cell egress recordings in the same animal. Additional advantages of the system are the transparency of the grafted area, permitting macroscopic rapid monitoring of the implanted tissue, and the accessibility to the implant allowing for localized in addition to systemic treatments. The main limitation being the volume of the tissue that fits in the reduced space of the eye chamber which demands for lobe trimming. Organ integrity is maximized by dissecting thymus lobes in patterns previously shown to be functional for mature T-cell production. The technique is potentially suited to interrogate a milieu of medically relevant questions related to thymus function that include autoimmunity, immunodeficiency and central tolerance; processes which remain mechanistically poorly defined. The fine dissection of mechanisms guiding thymocyte migration, differentiation and selection should lead to novel therapeutic strategies targeting developing T cells.

Real Time In Vivo Tracking of Thymocytes in the Anterior Chamber of the Eye by Laser Scanning Microscopy

The goal of the protocol is to show longitudinal intravital real-time tracking of thymocytes by laser scanning microscopy in thymic implants in the anterior chamber of the mouse eye. The transparency of the cornea and vascularization of the graft allows for continuously recording progenitor cell recruitment and mature T-cell egress.

The purpose of the method being presented is to show, for the first time, the transplant of newborn thymi into the anterior eye chamber of isogenic adult ...

Biology

Stria Vascularis Microdissection for Single-Nucleus Sequencing or Immunostaining

Dissection of Adult Mouse Stria Vascularis for Single-Nucleus Sequencing or Immunostaining

Endocochlear potential, which is generated by the stria vascularis, is essential to maintain an environment conducive to appropriate hair cell mechanotransduction and ultimately hearing. Pathologies of the stria vascularis can result in a decreased hearing. Dissection of the adult stria vascularis allows for focused single-nucleus capture and subsequent single-nucleus sequencing and immunostaining. These techniques are used to study stria vascularis pathophysiology at the single-cell level. 
Single-nucleus sequencing can be used in the setting of transcriptional analysis of the stria vascularis. Meanwhile, immunostaining continues to be useful in identifying specific populations of cells. Both methods require proper stria vascularis dissection as a prerequisite, which can prove to be technically challenging.

Author Spotlight: Dissection of Adult Mouse Stria Vascularis for Single-Nucleus Sequencing or Immunostaining  

The stria vascularis is vital to the generation of endocochlear potential. Here, we present the dissection of the adult mouse stria vascularis for single-nucleus sequencing or immunostaining.

Endocochlear potential, which is generated by the stria vascularis, is essential to maintain an environment conducive to appropriate hair cell ...

Preparation and Imaging of Murine Ocular Lens Whole Mounts

Whole Mount Imaging to Visualize and Quantify Peripheral Lens Structure, Cell Morphology, and Organization

The ocular lens is a transparent flexible tissue that alters its shape to focus light from different distances onto the retina. Aside from a basement membrane surrounding the organ, called the capsule, the lens is entirely cellular consisting of a monolayer of epithelial cells on the anterior hemisphere and a bulk mass of lens fiber cells. Throughout life, epithelial cells proliferate in the germinative zone at the lens equator, and equatorial epithelial cells migrate, elongate, and differentiate into newly formed fiber cells. Equatorial epithelial cells substantially alter morphology from randomly packed cobble-stone-shaped cells into aligned hexagon-shaped cells forming meridional rows. Newly formed lens fiber cells retain the hexagonal cell shape and elongate toward the anterior and posterior poles, forming a new shell of cells that are overlaid onto previous generations of fibers. Little is known about the mechanisms that drive the remarkable morphogenesis of lens epithelial cells to fiber cells. To better understand lens structure, development, and function, new imaging protocols have been developed to image peripheral structures using whole mounts of ocular lenses. Here, methods to quantify capsule thickness, epithelial cell area, cell nuclear area and shape, meridional row cell order and packing, and fiber cell widths are shown. These measurements are essential for elucidating the cellular changes that occur during lifelong lens growth and understanding the changes that occur with age or pathology.

Author Spotlight: In-Depth Morphometric Examination and Quantification of Native Lens Structure Using Whole Mount Imaging 

The present protocols describe novel whole mount imaging for the visualization of peripheral structures in the ocular lens with methods for image quantification. These protocols can be used in studies to better understand the relationship between lens microscale structures and lens development/function.

The ocular lens is a transparent flexible tissue that alters its shape to focus light from different distances onto the retina. Aside from a basement ...

Confocal Fluorescence Microscopy: A Technique to Determine the Localization of Proteins in Mouse Fibroblasts

Source: Dominique R. Bollino1, Eric A. Legenzov2, Tonya J. Webb1 
1 Department of Microbiology and Immunology, University of Maryland School of Medicine and the Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, Maryland 21201 
2 Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, Maryland 21201
Confocal fluorescence microscopy is an imaging technique that enables increased optical resolution as compared to conventional &#34;wide-field&#34; epifluorescence microscopy. Confocal microscopes are able to achieve improved x-y optical resolution through &#34;laser scanning&#34;- typically a set of voltage-controlled mirrors (galvanometer or &#34;galvo&#34; mirrors) that direct laser-illumination to each pixel of the specimen at a time. More importantly, confocal microscopes achieve superior z-axial resolution by using a pinhole to remove out of focus light originating from locations that are not in the z-plane being scanned, thus enabling the detector to collect data from a specified z-plane. Because of the high z-resolution achievable in confocal microscopy, it is possible to collect images from a series of z-planes (also-called z-stack) and construct a 3D image through software.
Before discussing the mechanism of a confocal microscope, it is important to consider how a sample interacts with light. Light is composed of photons, packets of electromagnetic energy. A photon impinging on a biological sample can interact with the molecules comprising the sample in one of four ways: 1) the photon does not interact and passes through the sample; 2) the photon is reflected/scattered; 3) the photon is absorbed by a molecule and the absorbed energy is released as heat through processes collectively known as nonradiative decay; and 4) the photon is absorbed and the energy is then rapidly reemitted as a secondary photon through the process known as fluorescence. A molecule whose structure permits fluorescence emission is called a fluorophore. Most biological samples contain negligible endogenous fluorophores; therefore exogenous fluorophores must be used to highlight features of interest in the sample. During fluorescence microscopy, the sample is illuminated with light of the appropriate wavelength for absorption by the fluorophore. Upon absorbing a photon, a fluorophore is said to be &#34;excited&#34; and the process of absorption is referred to as &#34;excitation&#34;. When a fluorophore gives up energy in the form of a photon, the process is known as &#34;emission&#34;, and the emitted photon is called fluorescence.
The light beam used to excite a fluorophore is focused by the objective lens of a microscope and converges at a &#34;focal point&#34; where it is maximally focused. Beyond the focal point the light again diverges. The entering and exiting beams may be visualized as a pair of cones touching at the focal point (see Figure 1, left panel). The phenomenon of diffraction imposes a limit on how tightly a beam of light can be focused - the beam actually focuses to a spot of finite size. Two factors determine the size of the focal spot: 1) the wavelength of the light, and 2) the light-gathering ability of the objective lens, which is characterized by its numerical aperture (NA). The focal &#34;spot&#34; extends not only in the x-y plane, but also in the z direction, and is in reality a focal volume. The dimensions of this focal volume define the maximum resolution achievable by optical imaging. Although the number of photons is greatest within the focal volume, the conical light paths above and below the focus also contain a lower density of photons. Any fluorophore in the light path can thus be excited. In conventional (wide-field) epifluorescence microscopy, emission from fluorophores above and below the focal plane contribute out-of-focus fluorescence (a &#34;hazy background&#34;), which reduces image resolution and contrast, as demonstrated in Figure 1, with the red cube representing fluorophore emission above the focal plane (red star) that results in out-of-focus fluorescence (top right). This problem is ameliorated in confocal microscopy, due to the utilization of a pinhole. (Figure 2, bottom right). As depicted in Figure 3, the pinhole allows emissions originating from the focal place to reach the detector (left), while blocking the out-of-focus fluorescence (right) from reaching the detector, thus improving both resolution and contrast.
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/10501/10501fig1.jpg" /> 
Figure 1. Optical resolution of epifluorescence versus confocal microscopy. <a href="https://jove.unicartagenaproxy.elogim.com/files/ftp_upload/10501/10501fig1large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
The light beam used to excite a fluorophore is focused by the objective lens of a microscope and converges at a focal volume and then diverges (left). The red star represents the focal plane of a sample that is being imaged while the red square represents fluorophore emission above the focal plane. When capturing an image of this sample using an epifluorescent microscope, the emission from the out-of-focus red square will visible and contribute to a &#34;hazy background&#34; (top right). Confocal microscopes have a pinhole which prevents the detection of light emitted outside of the focal plane, eliminating the &#34;hazy background&#34; (bottom right).
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/10501/10501fig2.jpg" /> 
Figure 2. Pinhole effect in confocal microscopy. <a href="https://jove.unicartagenaproxy.elogim.com/files/ftp_upload/10501/10501fig2large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
Although the highest intensity of the excitation light is at the focal point of the lens (left, red oval), other parts of the sample not in the focal point (right, red star) will get light and fluoresce. To prevent light emitted from these out-of-focus regions to reach the detector, a screen with a pinhole is present in front of the detector. Only the in-focus light (left) emitting from the focal plane is able to travel through the pinhole and reach the detector. The out-of-focus light (right) is blocked with the pinhole and fails to reach the detector.
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/10501/10501fig3.jpg" /> 
Figure 3. Principal components of a confocal laser scanning microscope. <a href="https://jove.unicartagenaproxy.elogim.com/files/ftp_upload/10501/10501fig3large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
For the sake of simplicity, the mechanistic description of a confocal microscope will be limited to that of the Nikon Eclipse Ti A1R. Although there may be minor technical differences between different confocal microscopes, the A1R serves well as a good model for describing confocal microscope function. The excitation light beam, produced by an array of diode lasers, is reflected by the primary dichroic mirror into the objective, which focuses the light onto the specimen being imaged. The primary dichroic mirror selectively reflects the excitation light while allowing light at other wavelengths to pass through. The light then encounters the scanning mirrors that sweep the light beam across the specimen in an x-y manner, illuminating a single (x,y) pixel at a time. Fluorescence emitted by fluorophores at the illuminated pixel is collected by the objective lens and passes through the primary dichroic mirror to reach an array of photomultiplier tubes (PMTs). Secondary dichroic mirrors direct the emission light to the appropriate PMT. Excitation light scattered by the sample back into the objective is reflected by the primary dichroic mirror back towards the specimen, and thus prevented from entering the detection light path and reaching the PMTs (see Figure 3). This allows the relatively feeble fluorescence to be quantified without contamination by light scattered from the excitation light beam, which is typically orders of magnitude more intense than the fluorescence. Because the pinhole blocks light from outside of the focal volume, the light arriving at the detector comes from a narrow, selected z-plane. Therefore, images can be collected from a series of adjacent z-planes; this series of images is often referred to as a &#39;z-stack&#39;. By using the appropriate software, a z-stack can be processed to generate a 3D image of the specimen. A particular advantage of confocal microscopy is the ability to distinguish the subcellular localization of staining. For example, the differentiation between membrane staining from intracellular staining, which is very challenging with conventional epifluorescence microscopy (1, 2, 3).
Sample preparation is an important facet of confocal imaging. A strength of optical microscopy techniques is the flexibility to image live or fixed cells. When attempting to produce 3D images, because of the number of images that must be acquired for a z-stack, the difficulty of maintaining cell health, and the movement of live cells and their organelles, the use of fixed cells is typical. The procedure for fixing and staining cells for confocal fluorescence is similar to that conventionally used in immunofluorescence. After culture in chamber slides or on coverslips, cells are fixed using paraformaldehyde to preserve cellular morphology. Non-specific antibody binding is blocked using bovine serum albumin, milk, or normal serum. In order to maintain the specificity of the secondary antibodies, the solution used should not originate from the same species in which the primary antibodies were generated. The cells are incubated with primary antibodies that bind the antigen of interest. When labeling several cellular targets, the primary antibodies must each be derived from a different species. Antibodies tagging an antigen are then bound by fluorophore-conjugated secondary antibodies. Fluorophore-conjugated secondary antibodies should be selected so that they are compatible with the wavelengths of laser excitation available in the confocal microscope. When visualizing multiple antigens, the excitation/emission spectra of the fluorophores should differ enough so that their signals can be discriminated by microscopic analysis. The stained specimen is then mounted on a slide for imaging. A mounting medium is used to prevent photobleaching and specimen dehydration. If desired, a mounting medium containing a nuclear counterstain (e.g. DAPI or Hoechst) can be used (4).
In the following protocol, mouse fibroblasts transfected to express CD1d (LCD1) were stained with antibodies recognizing CD1d and CD107a (LAMP-1). CD1d is a major histocompatibility complex 1 (MHC 1)-like receptor present on the surface of antigen presenting cells that presents lipid antigens. LAMP-1 (lysosomal associated membrane protein-1) is a transmembrane protein primarily present in lysosomal membranes. For proper antigen presentation, CD1d is trafficked through the low pH lysosomal compartment, so LAMP-1 is being used as a marker of the lysosomal compartment for this protocol. By probing the LCD1 cells with anti-CD1d and anti- LAMP-1 that were produced in different species, secondary antibodies with unique fluorophores can be used to determine the localization of each protein in the cell and whether CD1d is present in the LAMP-1 positive lysosomal compartments.

Confocal Fluorescence Microscopy and Localization of Proteins

Source: Dominique R. Bollino1, Eric A. Legenzov2, Tonya J. Webb1
1 Department of Microbiology and Immunology, University of Maryland School of Medicine ...

Using a Laminating Technique to Perform Confocal Microscopy of the Human Sclera

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Light-sheet Microscopy for Three-dimensional Visualization of Human Immune Cells

Near Simultaneous Laser Scanning Confocal and Atomic Force Microscopy (Conpokal) on Live Cells

Second Harmonic Generation Signals in Rabbit Sclera As a Tool for Evaluation of Therapeutic Tissue Cross-linking (TXL) for Myopia

Full-Circle Cauterization of Limbal Vascular Plexus for Surgically Induced Glaucoma in Rodents

A Tissue Clearing Method for Neuronal Imaging from Mesoscopic to Microscopic Scales

Real Time In Vivo Tracking of Thymocytes in the Anterior Chamber of the Eye by Laser Scanning Microscopy

Dissection of Adult Mouse Stria Vascularis for Single-Nucleus Sequencing or Immunostaining

Whole Mount Imaging to Visualize and Quantify Peripheral Lens Structure, Cell Morphology, and Organization

Confocal Fluorescence Microscopy: A Technique to Determine the Localization of Proteins in Mouse Fibroblasts