Part of this work was conducted through collaboration with Prof. Hiroki R. Ueda (University of Tokyo), Prof. Etsuo A. Susaki (Juntendo University), Prof. Tetsuhiro Tanaka (Tohoku University), Prof. Masafumi Fukagawa, Dr. Takehiko Wada, and Dr. Hirotaka Komaba (Tokai University).

All experiments were approved by the University of Tokyo Institutional Review Board. All animal procedures were performed according to the National Institutes of Health guidelines. Male C57BL/6NJcl mice, 8 weeks old, were used for the present study. The mice were obtained from commercial sources (see Table of Materials).
1. Animal preparation and kidney fixation
<ol>
	<li>Perform perfusion fixation following the steps below.
	<ol>
		<li>Anesthetize the mouse...

<ol>
	<li>Velez-Fort, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+stimulus+selectivity+and+connectivity+of+layer+six+principal+cells+reveals+cortical+microcircuits+underlying+visual+processing.">The stimulus selectivity and connectivity of layer six principal cells reveals cortical microcircuits underlying visual processing.</a> Neuron. 83 (6), 1431-1443 (2014).</li><li>Susaki, E. A., 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=Whole-brain+imaging+with+single-cell+resolution+using+chemical+cocktails+and+computational+analysis.">Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis.</a> Cell. 157 (3), 726-739 (2014).</li><li>Erturk, A., 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=Three-dimensional+imaging+of+solvent-cleared+organs+using+3DISCO.">Three-dimensional imaging of solvent-cleared organs using 3DISCO.</a> Nature Protocols. 7 (11), 1983-1995 (2012).</li><li>Tainaka, K., 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=Chemical+Landscape+for+Tissue+Clearing+Based+on+Hydrophilic+Reagents.">Chemical Landscape for Tissue Clearing Based on Hydrophilic Reagents.</a> Cell Reports. 24 (8), 2196-2210 (2018).</li><li>Susaki, E. A., Ueda, H. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Whole-body+and+whole-organ+clearing+and+imaging+techniques+with+single-cell+resolution:+toward+organism-level+systems+biology+in+mammals.">Whole-body and whole-organ clearing and imaging techniques with single-cell resolution: toward organism-level systems biology in mammals.</a> Cell Chemical Biology. 23 (1), 137-157 (2016).</li><li>Keller, P. J., Dodt, H. U. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Light+sheet+microscopy+of+living+or+cleared+specimens.">Light sheet microscopy of living or cleared specimens.</a> Current Opinion in Neurobiology. 22 (1), 138-143 (2012).</li><li>Susaki, E. A., 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=Advanced+CUBIC+protocols+for+whole-brain+and+whole-body+clearing+and+imaging.">Advanced CUBIC protocols for whole-brain and whole-body clearing and imaging.</a> Nature Protocols. 10 (11), 1709-1727 (2015).</li><li>Kubota, S. I., 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=Whole-body+profiling+of+cancer+metastasis+with+single-cell+resolution.">Whole-body profiling of cancer metastasis with single-cell resolution.</a> Cell Reports. 20 (1), 236-250 (2017).</li><li>Hasegawa, S., 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=Comprehensive+three-dimensional+analysis+(CUBIC-kidney)+visualizes+abnormal+renal+sympathetic+nerves+after+ischemia/reperfusion+injury.">Comprehensive three-dimensional analysis (CUBIC-kidney) visualizes abnormal renal sympathetic nerves after ischemia/reperfusion injury.</a> Kidney International. 96 (1), 129-138 (2019).</li><li>Hasegawa, S., Inoue, T., Inagi, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Neuroimmune+interactions+and+kidney+disease.">Neuroimmune interactions and kidney disease.</a> Kidney Research and Clinical Practice. 38 (3), 282-294 (2019).</li><li>Hasegawa, S., 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=The+oral+hypoxia-inducible+factor+prolyl+hydroxylase+inhibitor+enarodustat+counteracts+alterations+in+renal+energy+metabolism+in+the+early+stages+of+diabetic+kidney+disease.">The oral hypoxia-inducible factor prolyl hydroxylase inhibitor enarodustat counteracts alterations in renal energy metabolism in the early stages of diabetic kidney disease.</a> Kidney International. 97 (5), 934-950 (2020).</li><li>Gage, G. J., Kipke, D. R., Shain, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Whole+animal+perfusion+fixation+for+rodents.">Whole animal perfusion fixation for rodents.</a> Journal of Visualized Experiments. (65), e3564 (2012).</li><li>Hasegawa, S., 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=Activation+of+sympathetic+signaling+in+macrophages+blocks+systemic+inflammation+and+protects+against+renal+ischemia-reperfusion+injury.">Activation of sympathetic signaling in macrophages blocks systemic inflammation and protects against renal ischemia-reperfusion injury.</a> Journal of the American Society of Nephrology. 32 (7), 1599-1615 (2021).</li><li>Renier, N., 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=iDISCO:+a+simple,+rapid+method+to+immunolabel+large+tissue+samples+for+volume+imaging.">iDISCO: a simple, rapid method to immunolabel large tissue samples for volume imaging.</a> Cell. 159 (4), 896-910 (2014).</li><li>Klingberg, A., 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=Fully+automated+evaluation+of+total+glomerular+number+and+capillary+tuft+size+in+nephritic+kidneys+using+lightsheet+microscopy.">Fully automated evaluation of total glomerular number and capillary tuft size in nephritic kidneys using lightsheet microscopy.</a> Journal of the American Society of Nephrology. 28 (2), 452-459 (2017).</li><li>Zhao, S., 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=Cellular+and+molecular+probing+of+intact+human+organs.">Cellular and molecular probing of intact human organs.</a> Cell. 180 (4), 796-812 (2020).</li><li>Susaki, E. A., 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=Versatile+whole-organ/body+staining+and+imaging+based+on+electrolyte-gel+properties+of+biological+tissues.">Versatile whole-organ/body staining and imaging based on electrolyte-gel properties of biological tissues.</a> Nature Communications. 11 (1), 1-22 (2020).</li></ol>

The present protocol allowed whole-kidney 3D imaging of various structures such as sympathetic nerves, collecting ducts, arteries, proximal tubules, and glomeruli9,10,11. This staining method offered macroscopic observation and led to new biological discoveries, by visualizing the alteration in renal sympathetic nerves after ischemia-reperfusion injury9,10 and glomerulom...

The kidney is composed of various cell populations. Although conventional pathology gives us much information about the kidney microenvironment, three-dimensional (3D) imaging is needed to precisely understand the intercellular crosstalk during kidney disease progression. In the past, a huge number of serial sectioning and image reconstruction needed to be performed for the whole-organ 3D imaging1. However, this method required too much effort and had problems in terms of reproducibility.
Optical clearing is a good strategy to overcome this hurdle2,3. Tissue opacity is mainly due to light scattering and absorption because each organ consists of various substances, including water, protein, and lipids. Thus, the basic strategy of tissue clearing is replacing water and lipids in tissues with refractive index (RI) matching reagents that have the same optical properties as proteins4. In order to observe a transparent specimen, a light sheet fluorescent microscopy is useful5. Light sheets illuminate the transparent specimen from the side, and excitation signals are acquired through the objective lens located in a vertical position6. This microscopy obtains cross-section information in a single sweep, which is different from the confocal or multiphoton fluorescent microscopy. Thus, it can quickly acquire z-stack images with a low level of photobleaching.
Clear, Unobstructed Brain/Body Imaging Cocktails and Computational Analysis (CUBIC) is one of the tissue clearing methods which enables whole-organ imaging by light sheet fluorescent microscopy2,7,8. CUBIC and whole-mount immunofluorescent staining are optimized in the present study to visualize mouse kidney 3D structures9,10,11. Using this whole-mount staining method, the alteration in renal sympathetic nerves is visualized after ischemia-reperfusion injury9,10 and glomerulomegaly in the early stage of diabetic kidney disease11, as well as blood vessels, proximal tubules, and collecting ducts in a whole kidney9.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>14 mL Round Bottom High Clarity PP Test Tube</td>
			<td>Falcon</td>
			<td>352059</td>
			<td>Tissue clearing, staining, wash</td>
		</tr>
		<tr>
			<td>2,3-dimethyl-1-phenyl-5-pyrazolone/antipyrine</td>
			<td>Tokyo Chemical Industry</td>
			<td>D1876</td>
			<td>CUBIC-R+</td>
		</tr>
		<tr>
			<td>37%-Formaldehyde Solution</td>
			<td>Nacalai Tesque</td>
			<td>16223-55</td>
			<td>Post fixation</td>
		</tr>
		<tr>
			<td>4%-Paraformaldehyde Phosphate Buffer Solution</td>
			<td>Nacalai Tesque</td>
			<td>09154-85</td>
			<td>Kidney fixation</td>
		</tr>
		<tr>
			<td>Alexa Flour 555-conjugated donkey anti-sheep IgG antibody</td>
			<td>Invitrogen</td>
			<td>A-21436</td>
			<td>Secondary antibody (1:100)</td>
		</tr>
		<tr>
			<td>Alexa Flour 647-conjugated donkey anti-rabbit IgG antibody</td>
			<td>Invitrogen</td>
			<td>A-31573</td>
			<td>Secondary antibody (1:200)</td>
		</tr>
		<tr>
			<td>Anti-aquaporin 2 (AQP2) antibody</td>
			<td>Abcam</td>
			<td>ab199975</td>
			<td>Primary antibody (1:100)</td>
		</tr>
		<tr>
			<td>Anti-podocin antibody</td>
			<td>Sigma-Aldrich</td>
			<td>P0372</td>
			<td>Primary antibody (1:100)</td>
		</tr>
		<tr>
			<td>Anti-sodium glucose cotransporter 2 (SGLT2) antibody</td>
			<td>Abcam</td>
			<td>ab85626</td>
			<td>Primary antibody (1:100)</td>
		</tr>
		<tr>
			<td>Anti-tyrosine hydroxylase (TH) antibody</td>
			<td>Abcam</td>
			<td>ab113</td>
			<td>Primary antibody (1:100)</td>
		</tr>
		<tr>
			<td>Anti-&#945;-smooth muscle actin (&#945;-SMA) antibody</td>
			<td>Abcam</td>
			<td>ab5694</td>
			<td>Primary antibody (1:200)</td>
		</tr>
		<tr>
			<td>Blocker Casein in PBS</td>
			<td>Thermo Fisher Scientific</td>
			<td>37528</td>
			<td>Staining buffer</td>
		</tr>
		<tr>
			<td>Butorphanol Tartrate</td>
			<td>Meiji</td>
			<td>005526</td>
			<td>Anesthetic</td>
		</tr>
		<tr>
			<td>C57BL/6NJcl</td>
			<td>Nippon Bio-Supp.Center</td>
			<td>N/A</td>
			<td>Mouse strain</td>
		</tr>
		<tr>
			<td>Imaris</td>
			<td>Bitplane</td>
			<td>N/A</td>
			<td>Imaging analysis software</td>
		</tr>
		<tr>
			<td>Macro-zoom microscope</td>
			<td>OLYMPUS</td>
			<td>MVX10</td>
			<td>The observation unit of the custom-built microscope</td>
		</tr>
		<tr>
			<td>Medetomidine Hydrochloride</td>
			<td>Kyoritsu-Seiyaku</td>
			<td>008656</td>
			<td>Anesthetic</td>
		</tr>
		<tr>
			<td>Midazolam</td>
			<td>SANDOZ</td>
			<td>27803229</td>
			<td>Anesthetic</td>
		</tr>
		<tr>
			<td>Mineral oil</td>
			<td>Sigma-Aldrich</td>
			<td>M8410</td>
			<td>Immersion oil</td>
		</tr>
		<tr>
			<td>N-buthyldiethanolamine</td>
			<td>Tokyo Chemical Industry</td>
			<td>B0725</td>
			<td>CUBIC-L, CUBIC-R+</td>
		</tr>
		<tr>
			<td>Nicotinamide</td>
			<td>Tokyo Chemical Industry</td>
			<td>N0078</td>
			<td>CUBIC-R+</td>
		</tr>
		<tr>
			<td>Polyethylene glycol mono-p-isooctylphenyl ether/Triton X-100</td>
			<td>Nacalai Tesque</td>
			<td>12967-45</td>
			<td>CUBIC-L, PBST</td>
		</tr>
		<tr>
			<td>Silicon oil HIVAC-F4</td>
			<td>Shin-Etsu Chemical</td>
			<td>50449832</td>
			<td>Immersion oil</td>
		</tr>
		<tr>
			<td>Sodium azide</td>
			<td>Wako</td>
			<td>195-11092</td>
			<td>Staining buffer</td>
		</tr>
	</tbody>
</table>

whole-kidney three-dimensional staining with cubic

Although conventional pathology provided numerous information about kidney microstructure, it was difficult to know the precise structure of blood vessels, proximal tubules, collecting ducts, glomeruli, and sympathetic nerves in the kidney due to the lack of three-dimensional (3D) information. Optical clearing is a good strategy to overcome this big hurdle. Multiple cells in a whole organ can be analyzed at single-cell resolution by combining tissue clearing and 3D imaging technique. However, cell labeling methods for whole-organ imaging remain underdeveloped. In particular, whole-mount organ staining is challenging because of the difficulty in antibody penetration. The present protocol developed a whole-mount mouse kidney staining for 3D imaging with the CUBIC (Clear, Unobstructed Brain/Body Imaging Cocktails and Computational analysis) tissue clearing method. The protocol has enabled visualizing renal sympathetic denervation after ischemia-reperfusion injury and glomerulomegaly in the early stage of diabetic kidney disease from a comprehensive viewpoint. Thus, this technique can lead to new discoveries in kidney research by providing a macroscopic perspective.

Using this staining method, sympathetic nerves [anti-tyrosine hydroxylase (TH) antibody] and arteries [anti-&#945;-smooth muscle actin (&#945;SMA) antibody] in a whole kidney (Figure 4A,B and Video 1) were visualized9. Abnormal renal sympathetic nerves were also visualized after ischemia/reperfusion injury (IRI)9,10 (Figure 4C). Moreover, visualiz...

Watch this Scientific Journal Video about Whole-Kidney Three-Dimensional Staining with CUBIC at JoVE.com

Whole-Kidney Three-Dimensional Staining with CUBIC

The present protocol describes a tissue clearing method and whole-mount immunofluorescent staining for three-dimensional (3D) kidney imaging. This technique can offer macroscopic perspectives in kidney pathology, leading to new biological discoveries.

Although conventional pathology provided numerous information about kidney microstructure, it was difficult to know the precise structure of blood ...

This protocol allows a visualization of three-dimensional structures in full kidney, which can lead to innovative discoveries in kidney research by providing a macroscopic perspective. Whole-mount organ staining is challenging because of the difficulty in antibody penetration. This protocol has demonstrated the high quality, whole-mount staining of the kidneys by the antibodies.To begin, perform the immersion fixation immediately after the perfusion fixation and kidney sampling, by immersing the kidney in 4%paraformaldehyde at four degrees Celsius for 16 hours. Give three washes using PBS for two hours each. Perform the decolorization and delipidation process by immersing the fixed kidney in seven millimeters of 50%CUBIC-L in a 14 milliliter round-bottom tube, with gentle shaking at room temperature.After six hours, immerse the kidney in seven milliliters of CUBIC-L in a 14 millimeter round-bottom tube, with gentle shaking at 37 degrees Celsius for five days. Refresh CUBIC-L every day. Once the decolorization and delipidation are complete, use a dispensing spoon for sample handling and wash the kidney thrice with PBS at room temperature for two hours.Immunostain the delipidated kidney in primary antibodies diluted in staining buffer solution, with gentle shaking in an incubator shaker at 37 degrees Celsius for seven days. Then, wash the kidney with 0.5%Triton X-100 in PBS, also known as PBST, at room temperature for one day. For secondary antibodies staining, treat the kidney with secondary antibodies in the staining buffer, in the dark, with gentle shaking at 37 degrees Celsius for seven days.Fix the staining with a PBST wash at room temperature for one day. Post-fixation, immerse the kidney in 1%formaldehyde in PB for three hours, and wash it with PBS at room temperature for six hours. Perform the refractive index matching by immersing the kidney in seven milliliters of 50%CUBIC-R+in a 14 milliliter round-bottom tube with shaking for one day, followed by treatment with seven milliliters of CUBIC-R+with shaking at room temperature for two days.With the help of the immune staining method, sympathetic nerves and arteries in a whole kidney were visualized in 3D kidney imaging. Moreover, abnormal renal sympathetic nerves were visualized after ischemia-reperfusion injury. This protocol also facilitated visualizing sympathetic nerves in the whole spleen.The data quantification process for the three-dimensional immunofluorescent staining is displayed here. In addition, collecting ducts, the S1 segment of proximal tubules, and the glomeruli were successfully visualized in a whole kidney. The suppressed glomerulomegaly, resulting from drug administration in the early stages of diabetic kidney disease, was also visualized in 3D imaging.This protocol can label the specific molecule within an entire kidney. Thus, researchers can analyze structure alteration in the vasculature or find rare events in kidney tissues.

whole-kidney-three-dimensional-staining-with-cubic

Research

JoVE Journal

Medicine

3.3K vistas.  The University of Tokyo. Este protocolo permite una visualización de estructuras tridimensionales en el riñón completo, lo que puede conducir a descubrimientos innovadores en la investigación renal al proporcionar una perspectiva macroscópica. La tinción de órganos de montaje completo es un desafío debido a la dificultad en la penetración de anticuerpos. Este protocolo ha demostrado la tinción de alta calidad y montaje completo de los riñones por los anticuerpos.Para comenzar, realice la fijación p...

Video: Whole-Kidney Three-Dimensional Staining with CUBIC

The present protocol describes a tissue clearing method and whole-mount immunofluorescent staining for three-dimensional (3D) kidney imaging. This technique can offer macroscopic perspectives in kidney pathology, leading to new biological...

a whole-mount organ staining technique for three-dimensional imaging of the kidney

This video demonstrates an assay for the whole-mount staining of murine kidneys using a tissue-clearing method called CUBIC (clear, unobstructed brain/body imaging cocktails and computational analysis) and immunofluorescent staining. The kidney is subjected to tissue clearing, wherein the kidney is delipidated, decolorized, and treated with a refractive index matching solution to make the tissue transparent for optimum three-dimensional imaging. The tissue is stained with fluorescently labeled...

A Whole-Mount Organ Staining Technique for Three-Dimensional Imaging of the Kidney

After six hours, immerse the kidney in seven milliliters of CUBIC-L in a 14-millimeter round-bottom tube with gentle shaking at 37 degrees Celsius for five days. Refresh CUBIC-L every day. Once the decolorization and delipidation are complete, use a dispensing spoon for sample handling, and wash the kidney thrice with PBS at room temperature for two...

three-dimensional reconstruction for the whole lung with early multiple pulmonary nodules

Author Spotlight: Advancing 3D Modeling for Enhanced Diagnosis and Treatment of Pulmonary Nodules in Early-Stage Lung Cancer 

This study introduces a three-dimensional (3D) reconstruction method for the entire lung in patients with early multiple pulmonary nodules. It offers a comprehensive visualization of nodule distribution and their interplay with lung tissue, simplifying the assessment of diagnosis and prognosis for these...

Three-Dimensional Reconstruction for the Whole Lung with Early Multiple Pulmonary Nodules

high&#45;resolution three&#45;dimensional whole&#45;organ tomography of microbial infections

Author Spotlight: Unraveling Bacterial Responses to Antibiotics and Immune System in Tissues

Here, we describe a procedure that enables organ-wide detection of pathogenic bacteria during infection and quantification of fluorescent reporter...

High&#45;Resolution Three&#45;Dimensional Whole&#45;Organ Tomography of Microbial Infections

cubic protocol visualizes protein expression at single cell resolution in whole mount skin preparations

CUBIC Protocol Visualizes Protein Expression at Single Cell Resolution in Whole Mount Skin Preparations

This report describes a CUBIC protocol to clarify full thickness mouse skin biopsies, and visualize protein expression patterns, proliferating cells, and sebocytes at the single cell resolution in 3D. This method enables accurate assessment of skin anatomy and pathology, and of abnormal epidermal phenotypes in genetically modified mouse...

in vivo whole-brain imaging of zebrafish larvae using three-dimensional fluorescence microscopy

Author Spotlight: In Vivo Whole-Brain Imaging of Zebrafish Larvae Using Three-Dimensional Fluorescence Microscopy  

Presented here is a protocol for in vivo whole-brain imaging of larval zebrafish using three-dimensional fluorescence microscopy. The experimental procedure includes sample preparation, image acquisition, and...

In Vivo Whole-Brain Imaging of Zebrafish Larvae Using Three-Dimensional Fluorescence Microscopy

staining and high-resolution imaging of three-dimensional organoid and spheroid models

Staining and High-Resolution Imaging of Three-Dimensional Organoid and Spheroid Models

Here, we provide detailed, robust, and complementary protocols to perform staining and subcellular resolution imaging of fixed three-dimensional cell culture models ranging from 100 &#181;m to several millimeters, thus enabling the visualization of their morphology, cell-type composition, and...

eosin staining of soft-tissue samples: an eosin-based procedure for whole mouse kidney staining to visualize specific tissue microstructures

After refrigeration, wash the soft tissue sample with DPBS solution for 1 hour. Then, stain the sample by placing it in 2 milliliters of eosin Y-staining solution, and incubate it on a horizontal shaking plate for 24...

Eosin Staining of Soft-Tissue Samples: An Eosin-Based Procedure for Whole Mouse Kidney Staining to Visualize Specific Tissue Microstructures

This video demonstrates the procedure for the acidification of the whole mouse kidney with fixation followed by Eosin Y staining. This cytoplasm-specific Eosin staining method helps visualize and identify anatomical structures in the...

basic three-dimensional (3d) intestinal model system with an immune component

Author Spotlight: Investigating the Effects of Compounds on Intestinal Tissue Using 3D Human Cell Line Models 

Here we describe constructing a basic three-dimensional (3D) intestinal cell line model system and a paraffin embedding protocol for light microscopic evaluation of fixed intestinal equivalents. Staining of selected proteins permits the analysis of multiple visual parameters from a single experiment for potential use in preclinical drug screening...

Basic Three-Dimensional (3D) Intestinal Model System with an Immune Component

construction of a realistic, whole-body, three-dimensional equine skeletal model using computed tomography data

Construction of a Realistic, Whole-Body, Three-Dimensional Equine Skeletal Model using Computed Tomography Data

The purpose of this protocol is to describe the method of creation of a realistic, whole-body, skeletal model of a horse that can be used for functional anatomical and biomechanical modeling to characterize whole-body...

high-resolution, high-speed, three-dimensional video imaging with digital fringe projection techniques

High-resolution, High-speed, Three-dimensional Video Imaging with Digital Fringe Projection Techniques

This video describes the fundamentals of digital fringe projection techniques, which provide dense 3D measurements of dynamically changing surfaces.&#160;It also demonstrates the design and operation of a high-speed binary defocusing system based on these...

three-dimensional (3d) tumor spheroid invasion assay

Three-Dimensional 3D Tumor Spheroid Invasion Assay

Invasion of surrounding normal tissues is a defining characteristic of malignant tumors. We provide here a simple, semi-automated micro-plate assay of invasion into a natural 3D biomatrix that has been exemplified with a number of models of advanced human...

Three-Dimensional (3D) Tumor Spheroid Invasion Assay

fret imaging in three-dimensional hydrogels

FRET Imaging in Three-dimensional Hydrogels

F&#246;rster resonance energy transfer (FRET) imaging is a powerful tool for real-time cell biology studies. Here a method for FRET imaging cells in physiologic three-dimensional (3D) hydrogel microenvironments using conventional epifluorescence microscopy is presented. An analysis for ratiometric FRET probes that yields linear ratios over the activation range is...

three-dimensional ultrasonic needle tip tracking with a fiber-optic ultrasound receiver

Three-Dimensional Ultrasonic Needle Tip Tracking with a Fiber-Optic Ultrasound Receiver

Accurate and efficient visualization of invasive medical devices is extremely important in many ultrasound-guided minimally invasive procedures. Here, a method for localizing the spatial position of a needle tip relative to the ultrasound imaging probe is...

estimation of nephron number in whole kidney using the acid maceration method

Estimation of Nephron Number in Whole Kidney using the Acid Maceration Method

Estimates of whole kidney nephron number are important clinically and experimentally, as there is an inverse association between nephron number and an enhanced risk of renal and cardiovascular disease.Herein, the use of the acid maceration method, which provides fast and reliable estimates of whole kidney nephron number, is...

three-dimensional imaging of aortic tissues in atherosclerosis

Author Spotlight: Advanced Imaging Techniques for Investigating Nervous System Interactions in Atherosclerosis Progression

Here, we present optimized tissue-clearing protocols to image the murine aorta in three dimensions (3D). We delineate state-of-the-art procedures for immunostaining, optical clearing, and imaging with the intent to define the anatomical proximity of the peripheral nervous system with atherosclerotic plaques and the adventitia in...

Three-Dimensional Imaging of Aortic Tissues in Atherosclerosis

transplantation of whole kidney marrow in adult zebrafish

Transplantation of Whole Kidney Marrow in Adult Zebrafish

In this article, we demonstrate a method to perform HCT in adult...

three-dimensional patterning of engineered biofilms with a do-it-yourself bioprinter

Three-dimensional Patterning of Engineered Biofilms with a Do-it-yourself Bioprinter

This article describes a method of transforming a low-cost commercial 3D printer into a bacterial 3D printer that can facilitate printing of patterned biofilms. All necessary aspects of preparing the bioprinter and bio-ink are described, as well as verification methods to assess the formation of...

Three-dimensional Imaging of Nociceptive Intraepidermal Nerve Fibers in Human Skin Biopsies

A punch biopsy of the skin is commonly used to quantify intraepidermal nerve fiber densities (IENFD) for the diagnosis of peripheral polyneuropathy 1,2. At present, it is common practice to collect 3 mm skin biopsies from the distal leg (DL) and the proximal thigh (PT) for the evaluation of length-dependent polyneuropathies 3. However, due to the multidirectional nature of IENFs, it is challenging to examine overlapping nerve structures through the analysis of two-dimensional (2D) imaging. Alternatively, three-dimensional (3D) imaging could provide a better solution for this dilemma.
In the current report, we present methods for applying 3D imaging to study painful neuropathy (PN). In order to identify IENFs, skin samples are processed for immunofluorescent analysis of protein gene product 9.5 (PGP), a pan neuronal marker. At present, it is standard practice to diagnose small fiber neuropathies using IENFD determined by PGP immunohistochemistry using brightfield microscopy 4. In the current study, we applied double immunofluorescent analysis to identify total IENFD, using PGP, and nociceptive IENF, through the use of antibodies that recognize tropomyosin-receptor-kinase A (Trk A), the high affinity receptor for nerve growth factor 5. The advantages of co-staining IENF with PGP and Trk A antibodies benefits the study of PN by clearly staining PGP-positive, nociceptive fibers. These fluorescent signals can be quantified to determine nociceptive IENFD and morphological changes of IENF associated with PN. The fluorescent images are acquired by confocal microscopy and processed for 3D analysis. 3D-imaging provides rotational abilities to further analyze morphological changes associated with PN. Taken together, fluorescent co-staining, confocal imaging, and 3D analysis clearly benefit the study of PN.

In order to study the changes of nociceptive intraepidermal nerve fibers (IENFs) in painful neuropathies (PN), we developed protocols that could directly examine three-dimensional morphological changes observed in nociceptive IENFs. Three-dimensional analysis of IENFs has the potential to evaluate the morphological changes of IENF in PN.

A punch biopsy of the skin is commonly used to quantify intraepidermal nerve fiber densities (IENFD) for the diagnosis of peripheral polyneuropathy 1,2. ...

Quantification of Breast Cancer Cell Invasiveness Using a Three-dimensional (3D) Model

It is now well known that the cellular and tissue microenvironment are critical regulators influencing tumor initiation and progression. Moreover, the extracellular matrix (ECM) has been demonstrated to be a critical regulator of cell behavior in culture and homeostasis in vivo. The current approach of culturing cells on two-dimensional (2D), plastic surfaces results in the disturbance and loss of complex interactions between cells and their microenvironment. Through the use of three-dimensional (3D) culture assays, the conditions for cell-microenvironment interaction are established resembling the in vivo microenvironment. This article provides a detailed methodology to grow breast cancer cells in a 3D basement membrane protein matrix, exemplifying the potential of 3D culture in the assessment of cell invasion into the surrounding environment. In addition, we discuss how these 3D assays have the potential to examine the loss of signaling molecules that regulate epithelial morphology by immunostaining procedures. These studies aid to identify important mechanistic details into the processes regulating invasion, required for the spread of breast cancer.

Quantification of Breast Cancer Cell Invasiveness Using a Three-dimensional 3D Model

This article provides detailed methodologies for the use of three-dimensional (3D) assays to quantify breast cancer cell invasion. Specifically, we discuss the procedures required to set up such assays, quantification, and data analysis, as well as methods to examine the loss of membrane integrity that occurs when cells invade.

It is now well known that the cellular and tissue microenvironment are critical regulators influencing tumor initiation and progression. Moreover, the ...

Three-dimensional Co-culture Model for Tumor-stromal Interaction

Cancer progression (initiation, growth, invasion and metastasis) occurs through interactions between malignant cells and the surrounding tumor stromal cells. The tumor microenvironment is comprised of a variety of cell types, such as fibroblasts, immune cells, vascular endothelial cells, pericytes and bone-marrow-derived cells, embedded in the extracellular matrix (ECM). Cancer-associated fibroblasts (CAFs) have a pro-tumorigenic role through the secretion of soluble factors, angiogenesis and ECM remodeling. The experimental models for cancer cell survival, proliferation, migration, and invasion have mostly relied on two-dimensional monocellular and monolayer tissue cultures or Boyden chamber assays. However, these experiments do not precisely reflect the physiological or pathological conditions in a diseased organ. To gain a better understanding of tumor stromal or tumor matrix interactions, multicellular and three-dimensional cultures provide more powerful tools for investigating intercellular communication and ECM-dependent modulation of cancer cell behavior. As a platform for this type of study, we present an experimental model in which cancer cells are cultured on collagen gels embedded with primary cultures of CAFs.

Here we present a protocol to co-culture in three-dimensions, which is useful for investigating multicellular interactions and extracellular matrix-dependent modulation of cancer cell behavior. In this experimental model, cancer cells are cultured on collagen gels embedded with human cancer-associated fibroblasts.

Cancer progression (initiation, growth, invasion and metastasis) occurs through interactions between malignant cells and the surrounding tumor stromal ...

Invasion of surrounding normal tissues is generally considered to be a key hallmark of malignant (as opposed to benign) tumors. For some cancers in particular (e.g., brain tumors such as glioblastoma multiforme and squamous cell carcinoma of the head and neck &#8211; SCCHN) it is a cause of severe morbidity and can be life-threatening even in the absence of distant metastases. In addition, cancers which have relapsed following treatment unfortunately often present with a more aggressive phenotype. Therefore, there is an opportunity to target the process of invasion to provide novel therapies that could be complementary to standard anti-proliferative agents. Until now, this strategy has been hampered by the lack of robust, reproducible assays suitable for a detailed analysis of invasion and for drug screening. Here we provide a simple micro-plate method (based on uniform, self-assembling 3D tumor spheroids) which has great potential for such studies. We exemplify the assay platform using a human glioblastoma cell line and also an SCCHN model where the development of resistance against targeted epidermal growth factor receptor (EGFR) inhibitors is associated with enhanced matrix-invasive potential. We also provide two alternative methods of semi-automated quantification: one using an imaging cytometer and a second which simply requires standard microscopy and image capture with digital image analysis.

Invasion of surrounding normal tissues is a defining characteristic of malignant tumors. We provide here a simple, semi-automated micro-plate assay of invasion into a natural 3D biomatrix that has been exemplified with a number of models of advanced human cancers.

Invasion of surrounding normal tissues is generally considered to be a key hallmark of malignant (as opposed to benign) tumors. For some cancers in ...

Three-dimensional Alginate-bead Culture of Human Pituitary Adenoma Cells

A three-dimensional culture method is described in which primary pituitary adenoma cells are grown in alginate beads. Alginate is a polymer derived from brown sea algae. Briefly, the tumor tissue is cut into small pieces and submitted to an enzymatic digestion with collagenase and trypsin. Next, a cell suspension is obtained. The tumor cell suspension is mixed with 1.2% sodium alginate and dropped into a CaCl2 solution, and the alginate/cell suspension is gelled on contact with the CaCl2 to form spherical beads. The cells embedded in the alginate beads are supplied with nutrients provided by the culture media enriched with 20% FBS. Three-dimensional culture in alginate beads maintains the viability of adenoma cells for long periods of time, up to four months. Moreover, the cells can be liberated from the alginate by washing the beads with sodium citrate and seeded on glass coverslips for further immunocytochemical analyses. The use of a cell culture model allows for the fixation and visualization of the actin cytoskeleton with minimal disorganization. In summary, alginate beads provide a reliable culture system for the maintenance of pituitary adenoma cells.

Three-dimensional culture in alginate beads, due to its simplicity and reproducibility, was chosen to maintain the pituitary adenoma cells. The procedures included an initial enzymatic digestion and mechanical dissociation of the tumor tissue, and the subsequent cell suspension was encapsulated in alginate beads.

A three-dimensional culture method is described in which primary pituitary adenoma cells are grown in alginate beads. Alginate is a polymer derived from ...

Three-Dimensional Printing of a Complex Aortic Anomaly

Complex congenital aortic anomalies include diverse types of malformations that may be clinically asymptomatic or present with respiratory or esophageal symptoms. These anomalies may be associated with other congenital heart diseases. It is hard to identify the accurate anatomic vessel location from two-dimensional imaging data, such as computed tomography. As an additive manufacturing method, three-dimensional (3-D) printing can covert the acquired imaging data into 3-D physical models. This protocol describes the procedure for modeling the volumetric DICOM imaging into 3-D data and printing it as an anatomically realistic 3-D model. Using this model, surgeons can identify the vessel location of complex aortic anomalies, which is helpful for pre-operative planning and intra-operative guidance.

Here, we present a protocol to use three dimensional printed models for pre-operative planning and intra-operative reorganization of complicated vascular locations when handling a congenital aortic anomaly.

Complex congenital aortic anomalies include diverse types of malformations that may be clinically asymptomatic or present with respiratory or esophageal ...

Nephron endowment refers to the total number of nephrons an individual is born with, as nephrogenesis in humans is completed by 36 weeks of gestation and no new nephrons are formed post-birth. Nephron number refers to the total number of nephrons measured at any point in time post-birth. Both genetic and environmental factors influence both nephron endowment and number. Understanding how specific genes or factors influence the process of nephrogenesis and nephron loss or demise is important as individuals with lower nephron endowment or number are thought to be at a higher risk of developing renal or cardiovascular disease. Understanding how environmental exposures over the course of a person's lifetime affects nephron number will also be vital in determining future disease risk. Thus, the ability to assess whole kidney nephron number quickly and reliably is a basic experimental requirement to better understand mechanisms that contribute to or promote nephrogenesis or nephron loss. Here, we describe the acid maceration method for the estimation of whole kidney nephron number based on the procedure described by Damadian, Shawayri, and Bricker, with slight modifications. The acid maceration method provides fast and reliable estimates of nephron number (as assessed by counting glomeruli) that are within 5% of those determined using more advanced, albeit expensive, methods such as magnetic resonance imaging. Moreover, the acid maceration method is an excellent high-throughput method to assess nephron number in large numbers of samples or experimental conditions.

Estimates of whole kidney nephron number are important clinically and experimentally, as there is an inverse association between nephron number and an enhanced risk of renal and cardiovascular disease.Herein, the use of the acid maceration method, which provides fast and reliable estimates of whole kidney nephron number, is demonstrated.

Nephron endowment refers to the total number of nephrons an individual is born with, as nephrogenesis in humans is completed by 36 weeks of gestation and ...

Three-Dimensional Printing Guide Template Assisted Percutaneous Vertebroplasty (PVP)

Percutaneous vertebroplasty (PVP) is considered an effective treatment for the back pain caused by osteoporotic vertebral compression fracture. The accuracy of PVP mainly depends on the surgeons&#39; experience and multiple fluoroscopes during a traditional procedure. Puncture related complications were reported all over the world. To make the surgical procedure more precise and decrease the rate of puncture-related complications, our team applied a three-dimensional printing guide template to PVP to modify the traditional procedure. This protocol introduces how to model target vertebrae DICOM imaging data into three-dimensions in the software, how to simulate operation in this 3-D model, and how to use all of the surgical data to reconstruct a patient specific template for application. Using this template, surgeons can identify suitable puncture points accurately to improve the accuracy of the operation. The whole protocol includes: 1) diagnosis of the osteoporotic vertebral compression fracture; 2) acquisition of CT imaging of the target vertebra; 3) simulation of the operation in the software; 4) design and fabrication of the 3-D printing guide template; and 5) application of the template into an operation procedure.

Three-Dimensional Printing Guide Template Assisted Percutaneous Vertebroplasty PVP

Herein, we present a three-dimensional printing guide template for percutaneous vertebraplasty. A patient with a T11 vertebral compression fracture was selected as a case study.

Percutaneous vertebroplasty (PVP) is considered an effective treatment for the back pain caused by osteoporotic vertebral compression fracture. The ...

Three-Dimensional Collagen Matrix Scaffold Implantation as a Liver Regeneration Strategy

Liver diseases are the leading cause of death worldwide. Excessive alcohol consumption, a high-fat diet, and hepatitis C virus infection promote fibrosis, cirrhosis, and/or hepatocellular carcinoma. Liver transplantation is the clinically recommended procedure to improve and extend the life span of patients in advanced disease stages. However, only 10% of transplants are successful, with organ availability, presurgical and postsurgical procedures, and elevated costs directly correlated with that result. Extracellular matrix (ECM) scaffolds have emerged as an alternative for tissue restoration. Biocompatibility and graft acceptance are the main beneficial characteristics of those biomaterials. Although the capacity to restore the size and correct function of the liver has been evaluated in liver hepatectomy models, the use of scaffolds or some kind of support to replace the volume of the extirpated liver mass has not been assessed.
Partial hepatectomy was performed in a rat liver with the xenoimplantation of a collagen matrix scaffold (CMS) from a bovine condyle. Left liver lobe tissue was removed (approximately 40%), and an equal proportion of CMS was surgically implanted. Liver function tests were evaluated before and after the surgical procedure. After days 3, 14, and 21, the animals were euthanized, and macroscopic and histologic evaluations were performed. On days 3 and 14, adipose tissue was observed surrounding the CMS, with no clinical evidence of rejection or infection, as was vessel neoformation and CMS reabsorption at day 21. There was histologic evidence of an insignificant inflammation process and migration of adjacent cells to the CMS, observed with the hematoxylin and eosin (H&#38;E) and Masson&#39;s trichrome staining. The CMS was shown to perform well in liver tissue and could be a useful alternative for studying tissue regeneration and repair in chronic liver diseases.

Liver diseases are induced by many causes that promote fibrosis or cirrhosis. Transplantation is the only option for recovering health. However, given the scarcity of transplantable organs, alternatives must be explored. Our research proposes the implantation of collagen scaffolds in liver tissue from an animal model.

Liver diseases are the leading cause of death worldwide. Excessive alcohol consumption, a high-fat diet, and hepatitis C virus infection promote fibrosis, ...

Three-Dimensional Preoperative Virtual Planning in Derotational Proximal Femoral Osteotomy

Anterior knee pain (AKP) is a common pathology among adolescents and adults. Increased femoral anteversion (FAV) has many clinical manifestations, including AKP. There is growing evidence that increased FAV plays a major role in the genesis of AKP. Furthermore, this same evidence suggests that derotational femoral osteotomy is beneficial for these patients, as good clinical results have been reported. However, this type of surgery is not widely used among orthopedic surgeons.
The first step in attracting orthopedic surgeons to the field of rotational osteotomy is to give them a methodology that simplifies preoperative surgical planning and allows for the previsualization of the results of surgical interventions on computers. To that end, our working group uses 3D technology. The imaging dataset used for surgical planning is based on a CT scan of the patient. This 3D method is open access (OA), meaning it is accessible to any orthopedic surgeon at no economic cost. Furthermore, it not only allows for the quantification of femoral torsion but also for carrying out virtual surgical planning. Interestingly, this 3D technology shows that the magnitude of the intertrochanteric rotational femoral osteotomy does not present a 1:1 relationship with the correction of the deformity. Additionally, this technology allows for the adjustment of the osteotomy so that the relationship between the magnitude of the osteotomy and the correction of the deformity is 1:1. This paper outlines this 3D protocol.

This work presents a detailed surgical planning protocol using 3D technology with free open-source software. This protocol can be used to correctly quantify femoral anteversion and simulate derotational proximal femoral osteotomy for the treatment of anterior knee pain.