This work was supported by NIH-NINDS grant RO1-NS065895 and NIH-NINDS grant 5-F31-NS076250-02. 
We thank JHU SOM Microscope Facility for the use of the cryostat.

NOTE: All animal procedures described in this protocol were carried out in accordance with the recommendations in the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health26. The protocol (MO13M391) was approved by the Johns Hopkins University Animal Care and Use Committee.
1. Neonatal Mouse Sacrifice, Dissection, and Fixation
<ol>
	<li>Sacrifice a neonatal mouse by CO2 inhalation.</li>
	<li>Immediately cut off the hindlimb above the knee. Until approximately postnatal day 7, the leg bones are soft enough to cut through with large laboratory scissors or sharp blade and to subsequently section on a cryostat.</li>
	<li>Place the hindlimb in 10&#160;ml of ice cold 4% paraformaldehyde in phosphate-buffered saline (PBS) in a 15&#160;ml tube.</li>
	<li>Immersion fix the hindlimb in paraformaldehyde for 4-24&#160;hr at 4&#160;&#176;C. Embryonic tissue requires only several hours of fixation.
	<ol>
		<li>Avoid fixation longer than 24&#160;hr, as this may reduce TUNEL assay efficiency.</li>
	</ol>
	</li>
	<li>Cryoprotect the hindlimb by immersing it in sucrose solution.
	<ol>
		<li>Change paraformaldehyde to 10% sucrose in PBS in the same 15&#160;ml tube, incubate overnight at 4&#160;&#176;C.</li>
		<li>Change to 30% sucrose in PBS, incubate overnight at 4&#160;&#176;C or until the hindlimb sinks to the bottom of the tube. Tissue may be left in 30% sucrose for a longer period, provided that the sucrose has been sterile-filtered.</li>
	</ol>
	</li>
</ol>
2. Tissue Embedding
<ol>
	<li>Fill a labeled embedding mold half-way with embedding medium.</li>
	<li>Place hindlimb on top of the embedding medium, with the cut side as close as possible to one wall of the mold. Mark the orientation of the hindlimb on the outside of the mold.
	<ol>
		<li>Embed several hindlimbs and cut in the same block. However, it is important to ensure that all hindlimbs in the block are oriented parallel to each other to get sections at matching levels along the axis of the limb.</li>
	</ol>
	</li>
	<li>Cover hindlimbs with embedding medium. If hindlimbs shift while pouring the medium, re-orient them with blunt-tipped forceps or a toothpick.</li>
	<li>Allow embedding medium to infiltrate the tissue at room temperature for at least 15&#160;min.</li>
	<li>Place molds directly on dry ice or in isopentane on dry ice to freeze embedding medium. Make sure to keep the molds level at all times and avoid shifting of the embedded tissue.</li>
	<li>Keep frozen molds at -80&#160;&#176;C until ready to cut, for up to several months.</li>
</ol>
3. Cryosectioning Embedded Limbs
<ol>
	<li>Set cryostat chamber temperature to -20&#160;&#176;C, object temperature to -18&#160;&#176;C; adjust object temperature down as necessary.</li>
	<li>Equilibrate the tissue block inside the cryostat chamber for at least 30&#160;min. Correct block temperature is crucial for section quality.</li>
	<li>Cut transverse sections at a thickness of 10&#160;&#956;m or less. Thicker sections will not be fully penetrated by TUNEL reagents. Use the anti-roll plate, blades, and blade angle (typically 5&#176;) recommended for the cryostat.</li>
	<li>Collect sections onto gelatin- or vectabond-coated glass slides at room temperature. Place immediately into a slide box on dry ice. Keep the slide box in a separate container with dry ice placed near the cryostat within arm&#8217;s reach.
	<ol>
		<li>Cut transverse serial sections through the long axis of the limb, skipping 100-200&#160;&#956;m. Collect at least 3 adjacent sections at each serial level.</li>
	</ol>
	</li>
</ol>
4. TUNEL Assay on Hindlimb Sections Using a Commercially Available Kit (all steps at room temperature unless noted)
<ol>
	<li>Thaw slides with sections to room temperature and dry overnight or over the weekend.</li>
	<li>Rehydrate sections by immersing slides in PBS for 2&#160;x&#160;10&#160;min in a Coplin jar. Dry with a lab wipe, removing as much liquid around the section as possible.</li>
	<li>Permeabilize sections
	<ol>
		<li>Use either a non-proteolytic, saponin-based commercial reagent or 0.5% Tween20 and 0.05% Triton X100 in PBS.</li>
		<li>Place the slide into a humidity chamber. A simple humidity chamber is an empty pipette tip box with a tight lid, with just enough water added to cover the bottom of the box.</li>
		<li>Pipette enough reagent onto the slide to cover the section (50&#160;&#956;l is sufficient for neonatal mouse limbs). Do not pipette directly onto the section, as repeated agitation may cause the section to lift off the slide.</li>
		<li>Using blunt-tipped forceps, place a small rectangle of parafilm on top of the section to spread out the drop of reagent and completely cover the section. If any bubbles form under the parafilm, gently lift it off, dry, and reapply.</li>
		<li>Incubate slides with permeabilization reagent for 1&#160;hr in a covered humidity chamber. If sections begin to lift off from the slide, permeabilization time may be reduced to 30&#160;min.</li>
		<li>Wash slides in PBS in a Coplin jar 2&#160;x&#160;5&#160;min. The parafilm rectangles should float to the top and can then be removed and discarded.</li>
		<li>Using a lab wipe, dry as much liquid around the sections as possible.</li>
	</ol>
	</li>
	<li>TdT-mediated DNA break labeling
	<ol>
		<li>Follow the kit instructions to make 1x TdT labeling buffer, pipette enough labeling buffer onto the slide to cover tissue section (50&#160;&#956;l is sufficient for neonatal mouse limbs). Incubate in the humidity chamber for 5&#160;min. Alternatively, immerse the slide in TdT labeling buffer in a coplin jar.</li>
		<li>Follow kit instructions to make TdT labeling mix. The kit includes cobalt, magnesium, and manganese cations; the manganese cation works well on a variety of tissues, including skeletal muscle, nervous system tissues, liver, skin, and bone.</li>
		<li>For a positive control, add DNase (labeled &#8220;nuclease&#8221; in the kit) to the TdT labeling mix. Alternatively, pre-treat a positive control section with DNase in nuclease buffer for 1&#160;hr at 37&#160;&#176;C, according to kit instructions. Keep DNase solution and DNase-treated sections away from other experimental sections to prevent cross-contamination.</li>
		<li>For a negative control, omit TdT enzyme from the labeling mix.</li>
		<li>Use a lab wipe to remove as much TdT labeling buffer from the slide as possible. Pipette TdT labeling mix onto the slide (50&#160;&#956;l per section), cover with a new rectangle of parafilm, and incubate in the humidity chamber at 37&#160;&#176;C for 1&#160;hr.</li>
		<li>Follow the kit instructions to make 1x stop buffer. Use a lab wipe to remove TdT labeling mix from the slide, and add 200-300&#160;&#956;l stop buffer to cover the tissue section, and incubate in the humidity chamber for 5&#160;min. Alternatively, immerse the slide in stop buffer in a Coplin jar.</li>
		<li>Wash the slide 2&#160;x&#160;2&#160;min in PBS. Use a lab wipe to remove as much PBS from the slide as possible.</li>
	</ol>
	</li>
	<li>Fluorescent labeling
	<ol>
		<li>Follow kit instructions to prepare fluorescein labeling solution to label dNTPs at DNA breaks. Pipette solution onto the slide (50&#160;&#956;l per section), cover with a new rectangle of parafilm, and incubate in the humidity chamber for 20&#160;min.</li>
		<li>Wash slide for 2&#160;min in PBS in a Coplin jar. Use a lab wipe to remove as much PBS as possible from the slide.</li>
		<li>Dilute Hoechst 33258 nuclear stain to 1&#160;&#956;g/ml in PBS and pipette onto the slide (100-200&#160;&#956;l is sufficient to cover section). Incubate in the humidity chamber for 5&#160;min.</li>
		<li>Wash 3x for 5&#160;min in PBS.</li>
		<li>Coverslip with antifade fluorescence mounting media and seal edges with nail polish.</li>
	</ol>
	</li>
</ol>
5. Digital Image Acquisition
<ol>
	<li>Acquire images using a conventional fluorescent microscope with DAPI, FITC, and Texas Red filters (or equivalent). Use a higher magnification objective (20X or 40X) to verify that the labeling was successful and nuclei (intact or fragmented) were labeled. A 10X objective is sufficient for quantitation of TUNEL-positive puncta.</li>
	<li>Collect images of the Hoechst staining, TUNEL staining, and autofluorescent signal as three separate false-color channels combined in one image. If the TUNEL fluorophore label is green, image autofluorescent signal in the red filter, and vise versa.
	<ol>
		<li>Keep all imaging settings equivalent between slides for subsequent thresholding and quantitation. For each filter, preset and record exposure times, gain, and binning (no binning is best); do not use automatic exposure or gain settings.</li>
		<li>Use trial-and-error to find exposure and gain settings that will best capture the range of intensities across all stained slides. Ensure that there are no saturated pixels in the acquired images, as this will bias quantitation.</li>
	</ol>
	</li>
	<li>Take images of the entire muscle group of interest. This may require multiple images to be &#8220;stitched&#8221; together.</li>
</ol>
6. Image Analysis
<ol>
	<li>Use commercially available image analysis programs to analyze digital images of TUNEL staining. Analysis using commercial software is shown here. Alternatively, the free software ImageJ from NIH can be used to analyze TUNEL staining.</li>
	<li>Stain a section adjacent to the TUNEL-stained section with hematoxylin and eosin (H&#38;E) and take a full-section digital image with a conventional brightfield microscope. Use this H&#38;E image in combination with an anatomy atlas5,18,19 to trace the anatomical structures to be quantified.</li>
	<li>With the TUNEL channel turned off, manually trace the outline of the area to be quantified, using Hoechst and autofluorescence channels for guidance. Convert the traced area into a mask (a set of selected pixel coordinates to be analyzed).</li>
	<li>Turn on the TUNEL channel. Using the intensity thresholding function in the image analysis program, set the lower threshold to exclude all autofluorescence signal.</li>
	<li>Apply the same threshold settings to all images in the study set. Convert thresholded selections into masks.</li>
	<li>For each image, combine the muscle area mask and the TUNEL mask. The new combination mask will represent TUNEL signal within the traced muscle area only.</li>
	<li>Perform mask quantitation on the combination mask to determine number of objects and object area of the TUNEL signal within the traced muscle area. Perform this using the Particle Analyzer function in ImageJ.</li>
</ol>

The authors have nothing to disclose.

A method to detect and quantitatively analyze DNA damage-associated apoptosis in mouse skeletal muscle is described. The procedure includes tissue harvesting, TUNEL staining, digital image acquisition, and image analysis. Common histological supplies and tools are needed, and a special commercial TUNEL kit is necessary. The essential big equipment items needed are a cryostat, epifluorescent microscope with digital image capability, and a computer system for image analysis.
The experimenter sho...

Terminal deoxynucleotidyl transferase (TdT) dUTP nick end labeling (TUNEL) is the process of using the TdT enzyme to attach dUTP to 3&#8217; ends of double and single-stranded DNA breaks12,23. The TUNEL method for detection of apoptosis and DNA damage was first reported over 20 years ago by Gavrieli et al.1,12,24. It has since been evaluated and optimized in different tissue preparations7,23,27,40. TUNEL has been used to study ischemia-induced cell death of neurons6,14,29 and cardiomyocytes43,44, excitotoxic neuronal cell death30,31, and as a biomarker in arthritis treatment39. It has also been used as a prognostic factor and tumor cell marker in various human cancers2,3,15,32,37,38,42.
Alternative methods exist for DNA damage and cell death detection, but they have technical challenges and caveats. Southern blotting may be used to quantify DNA damage in whole tissue lysates7,9-11, but this method does not provide cellular-level resolution and is difficult to quantify. The comet assay is an alternative cell-based method that requires extracting preserved nuclei from cells4,20,28,36. Although the comet assay works well on cultured isolated cells, it is much more difficult to prepare intact nuclei from skeletal muscle tissue8,21. As with Southern blot, the comet assay does not provide cell-type-specific information from a whole muscle tissue homogenate. Another alternative to the TUNEL method is immunohistochemistry using antibodies against single-stranded DNA25,33,41 or against proteins that participate in DNA damage response and cell death pathways (e.g. p53, H2AX, and caspases)13,17,22,40. Such antibody-based methods require thorough characterization of antibodies and excellent antibody specificity to yield a high signal-to-background ratio. Even when specific antibodies exist, they may require denaturation of the target protein through antigen retrieval procedures34,35. As we discuss here, antigen retrieval in muscle tissue results in unacceptably high autofluorescence. Unlike the alternative methods, TUNEL achieves DNA damage detection with a high signal and low background, excellent specificity that can be tested with simple positive and negative controls, good tissue penetration that does not require antigen retrieval, and cellular-level resolution. In addition, the TUNEL method takes about 4 hours to complete, whereas alternative methods typically require overnight incubations.
We study skeletal muscle cell death in a mouse model of spinal muscular atrophy (SMA)10 that was generated by Hsieh-Li and colleagues16. To quantify apoptotic cells in the muscle, we have developed a method of tissue preparation, staining, and quantitation that works robustly across different skeletal muscle groups at different developmental time points in mice. We use a commercially available TUNEL-labeling kit and commercially available image analysis software. We have also successfully used the TUNEL assay in combination with immunofluorescent staining in the spinal cord10.
The methods described here are useful for investigators who want to assess tissue pathology,&#160;mechanisms&#160;of disease, mechanisms&#160;of aging, and developmental (pre- and post-natal) cell death in skeletal muscle. The TUNEL technique is especially useful for studies of DNA damage and repair and cell death in model systems where only a subset of cells is affected and cellular level resolution is necessary.
This video describes dissection, tissue processing, sectioning, and fluorescence-based TUNEL labeling of mouse skeletal muscle. It also describes a method of semi-automated TUNEL signal quantitation.

<table border="0" cellpadding="0" cellspacing="0" width="916">
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Name of Reagent/ Equipment</td>
			<td style="width:121px;">Company</td>
			<td style="width:119px;">Catalog Number</td>
			<td style="width:460px;">Comments/Description</td>
		</tr>
		<tr height="147">
			<td height="147" style="height:147px;width:216px;">4% Paraformaldehyde in phosphate buffered saline</td>
			<td style="width:121px;">Electron Microscopy Sciences</td>
			<td style="width:119px;">19202</td>
			<td style="width:460px;">For procedures described here, 4% solution was prepared fresh from powder. Paraformaldehyde from any supplier may be used. Prepared formaldehyde solution should be stored at 4 &#176;C and should not be used after its expiration date (up to several months). Paraformaldehyde is a carcinogen and a toxin by inhalation and skin contact. Please follow precautions specified in the MSDS when handling paraformaldehyde.</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Sucrose</td>
			<td style="width:121px;">Sigma</td>
			<td style="width:119px;">S0389</td>
			<td style="width:460px;">Used for cryoprotecting tissue before freezing. Sucrose from any supplier may be used.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">O.C.T. compound&#160;</td>
			<td style="width:121px;">Tissue-Tek</td>
			<td style="width:119px;">4583</td>
			<td>Embedding medium for cryosectioning.</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Cryostat</td>
			<td style="width:121px;">Leica</td>
			<td style="width:119px;">CM 3050S</td>
			<td style="width:460px;">A Leica CM3050S cryostat was used for the preparations described here. Any cryostat capable of cutting 10 &#956;m sections may be used.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Glass slides, 25 x 75 x 1 mm</td>
			<td style="width:121px;">Fisher</td>
			<td style="width:119px;">12-552-3</td>
			<td>Slides from any supplier may be used.</td>
		</tr>
		<tr height="105">
			<td height="105" style="height:105px;width:216px;">Gelatin</td>
			<td style="width:121px;">Sigma</td>
			<td style="width:119px;">G-9391</td>
			<td style="width:460px;">Gelatin is used to promote tissue section adhesion to glass slides. To coat glass slides with gelatin, dissolve 2.75 g gelatin and 0.275 g chrome alum in 500 mL distilled water, warm to 60 &#176;C, dip slides for several seconds, and let dry. Gelatin from any supplier may be used. Alternatively, gelatin-precoated slides may be purchased.</td>
		</tr>
		<tr height="84">
			<td height="84" style="height:84px;width:216px;">Chromium(III) potassium sulfate dodecahydrate (chrome alum)</td>
			<td style="width:121px;">Sigma</td>
			<td style="width:119px;">243361</td>
			<td style="width:460px;">Chrome alum is added to gelatin solution to promote tissue adhesion on glass slides. It is a possible carcinogen and a toxin by inhalation and skin contact. Please follow precautions specified in the MSDS when handling chrome alum.</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Vectabond tissue adhesion reagent</td>
			<td style="width:121px;">Vector Labs</td>
			<td style="width:119px;">SP-1800</td>
			<td style="width:460px;">Optional substrate for better tissue adhesion to glass slides; gellatin-coated slides may be used instead.</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Tween20</td>
			<td style="width:121px;">Sigma</td>
			<td style="width:119px;">P9416</td>
			<td style="width:460px;">A detergent used to permeabilize tissue. Tween20 from any supplier may be used.</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Triton X100</td>
			<td style="width:121px;">Sigma</td>
			<td style="width:119px;">T8787</td>
			<td style="width:460px;">A detergent used to permeabilize tissue. Triton X100 from any supplier may be used.</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">TACS 2 TdT fluorescein in situ apoptosis detection kit</td>
			<td style="width:121px;">Trevigen</td>
			<td style="width:119px;">4812-30-K</td>
			<td>Commercial kit for fluorescence-based TUNEL labeling.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">DNase/nuclease</td>
			<td style="width:121px;">Trevigen</td>
			<td style="width:119px;">4812-30-K</td>
			<td>(included with kit)</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">DNase/nuclease buffer</td>
			<td style="width:121px;">Trevigen</td>
			<td style="width:119px;">4812-30-K</td>
			<td>(included with kit)</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">10x phosphate buffered saline (PBS), pH 7.4</td>
			<td style="width:121px;">Amresco</td>
			<td style="width:119px;">780</td>
			<td style="width:460px;">Make 1x PBS for washes and dilutions. PBS from any supplier may be used.</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">DNase-free water</td>
			<td style="width:121px;">Quality Biologicals</td>
			<td style="width:119px;">351-029-131</td>
			<td>Water from any supplier may be used.</td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:216px;">Hoechst 33258</td>
			<td style="width:121px;">Sigma</td>
			<td style="width:119px;">94403</td>
			<td style="width:460px;">Nuclear dye. Any blue fluorescent nuclear dye may be used. As a DNA-binding dye, Hoechst is a suspected carcinogen and should be handled with protective equipment to minimize skin contact.</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Parafilm M</td>
			<td style="width:121px;">multiple</td>
			<td style="width:119px;">807</td>
			<td style="width:460px;">Any other hydrophobic film or cover slip may be used. Available from multiple suppliers.&#160;</td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:216px;">Fluorescent microscope with digital camera</td>
			<td style="width:121px;">&#160;--</td>
			<td style="width:119px;">&#160;--</td>
			<td style="width:460px;">Any fluorescent microscope capable of digitally capturing red, green, and blue fluorescence in separate channels may be used.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Vectashield antifade media</td>
			<td style="width:121px;">Vector Labs</td>
			<td style="width:119px;">H-1000</td>
			<td>Antifade media from any supplier may be used.</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">glass coverslips, No.1 thickness</td>
			<td style="width:121px;">Brain Research Labs</td>
			<td style="width:119px;">2222-1</td>
			<td style="width:460px;">Cover slips from any supplier may be used. The smallest size of 22x22 mm is sufficient for neonatal mouse leg sections.</td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:216px;">Nail polish</td>
			<td style="width:121px;">Ted Pella</td>
			<td style="width:119px;">114-8</td>
			<td style="width:460px;">Used to seal coverslips. Nail polish from any supplier (including regular retailers) may be used. Avoid using nail polish with color or additives that may reflect light during fluorescent imaging.&#160;</td>
		</tr>
	</tbody>
</table>

detection and analysis of dna damage in mouse skeletal muscle in situ using the tunel method

Terminal deoxynucleotidyl transferase (TdT) deoxyuridine triphosphate (dUTP) nick end labeling (TUNEL) is the method of using the TdT enzyme to covalently attach a tagged form of dUTP to 3&#8217; ends of double- and single-stranded DNA breaks in cells. It is a reliable and useful method to detect DNA damage and cell death in situ. This video describes dissection, tissue processing, sectioning, and fluorescence-based TUNEL labeling of mouse skeletal muscle. It also describes a method of semi-automated TUNEL signal quantitation. Inherent normal tissue features and tissue processing conditions affect the ability of the TdT enzyme to efficiently label DNA. Tissue processing may also add undesirable autofluorescence that will interfere with TUNEL signal detection. Therefore, it is important to empirically determine tissue processing and TUNEL labeling methods that will yield the optimal signal-to-noise ratio for subsequent quantitation. The fluorescence-based assay described here provides a way to exclude autofluorescent signal by digital channel subtraction. The TUNEL assay, used with appropriate tissue processing techniques and controls, is a relatively fast, reproducible, quantitative method for detecting apoptosis in tissue. It can be used to confirm DNA damage and apoptosis as pathological mechanisms, to identify affected cell types, and to assess the efficacy of therapeutic treatments in vivo.

With successful staining, TUNEL-positive signal should be bright enough to isolate from autofluorescence by setting intensity thresholds. TUNEL-positive objects at low magnification may appear as bright irregular fragments in skeletal muscle (Figure 1A). However, at higher magnification, some TUNEL-positive objects with the classic apoptotic morphology should be observed, if the cell death type involved is apoptosis (Figure 1B). The positive control (DNase added) should exhibit abundant ...

Watch this Scientific Journal Video about Detection and Analysis of DNA Damage in Mouse Skeletal Muscle In Situ Using the TUNEL Method at JoVE.com

Detection and Analysis of DNA Damage in Mouse Skeletal Muscle In Situ Using the TUNEL Method

This video describes dissection, tissue processing, sectioning, and fluorescence-based TUNEL labeling of mouse skeletal muscle. It also describes a method for semi-automated analysis of TUNEL labeling.

Detection and Analysis of DNA Damage in Mouse Skeletal Muscle In Situ Using the TUNEL Method

Terminal deoxynucleotidyl transferase (TdT) deoxyuridine triphosphate (dUTP) nick end labeling (TUNEL) is the method of using the TdT enzyme to covalently ...

detection-analysis-dna-damage-mouse-skeletal-muscle-situ-using-tunel

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JoVE Journal

Biology

16.2K Views.  Johns Hopkins School of Medicine. This video describes dissection, tissue processing, sectioning, and fluorescence-based TUNEL labeling of mouse skeletal muscle. It also describes a method for semi-automated analysis of TUNEL labeling. 

Video: Detection and Analysis of DNA Damage in Mouse Skeletal Muscle In Situ Using the TUNEL Method

Procedures for Rat in situ Skeletal Muscle Contractile Properties

There are many circumstances where it is desirable to obtain the contractile response of skeletal muscle under physiological circumstances: normal circulation, intact whole muscle, at body temperature. This includes the study of contractile responses like posttetanic potentiation, staircase and fatigue. Furthermore, the consequences of disease, disuse, injury, training and drug treatment can be of interest. This video demonstrates appropriate procedures to set up and use this valuable muscle preparation.
To set up this preparation, the animal must be anesthetized, and the medial gastrocnemius muscle is surgically isolated, with the origin intact. Care must be taken to maintain the blood and nerve supplies. A long section of the sciatic nerve is cleared of connective tissue, and severed proximally. All branches of the distal stump that do not innervate the medial gastrocnemius muscle are severed. The distal nerve stump is inserted into a cuff lined with stainless steel stimulating wires. The calcaneus is severed, leaving a small piece of bone still attached to the Achilles tendon. Sonometric crystals and/or electrodes for electromyography can be inserted. Immobilization by metal probes in the femur and tibia prevents movement of the muscle origin. The Achilles tendon is attached to the force transducer and the loosened skin is pulled up at the sides to form a container that is filled with warmed paraffin oil. The oil distributes heat evenly and minimizes evaporative heat loss. A heat lamp is directed on the muscle, and the muscle and rat are allowed to warm up to 37&deg;C. While it is warming, maximal voltage and optimal length can be determined. These are important initial conditions for any experiment on intact whole muscle. The experiment may include determination of standard contractile properties, like the force-frequency relationship, force-length relationship, and force-velocity relationship.
With care in surgical isolation, immobilization of the origin of the muscle and alignment of the muscle-tendon unit with the force transducer, and proper data analysis, high quality measurements can be obtained with this muscle preparation.

Procedures for Rat in situ Skeletal Muscle Contractile Properties

This video demonstrates the surgical preparation and procedures needed to study the contractile responses of the rat medial gastrocnemius muscle preparation in situ. This preparation allows measurement of skeletal muscle contractile properties under physiological conditions. The animal is anesthetized and the muscle is separated from surrounding tissue at its distal end. The Achilles tendon is attached to a force transducer, allowing measurement of the muscle&#x2019;s contractile response at 37 degrees C with an intact circulation.

There are many circumstances where it is desirable to obtain the contractile response of skeletal muscle under physiological circumstances: normal ...

Visualization and Analysis of mRNA Molecules Using Fluorescence In Situ Hybridization in Saccharomyces cerevisiae

The Fluorescence in situ Hybridization (FISH) method allows one to detect nucleic acids in the native cellular environment. Here we provide a protocol for using FISH to quantify the number of mRNAs in single yeast cells. Cells can be grown in any condition of interest and then fixed and made permeable. Subsequently, multiple single-stranded deoxyoligonucleotides conjugated to fluorescent dyes are used to label and visualize mRNAs. Diffraction-limited fluorescence from single mRNA molecules is quantified using a spot-detection algorithm to identify and count the number of mRNAs per cell. While the more standard quantification methods of northern blots, RT-PCR and gene expression microarrays provide information on average mRNAs in the bulk population, FISH facilitates both the counting and localization of these mRNAs in single cells at single-molecule resolution.

Visualization and Analysis of mRNA Molecules Using Fluorescence In Situ Hybridization in Saccharomyces cerevisiae

This protocol describes an experimental procedure for performing Fluorescence in situ Hybridization (FISH) for counting mRNAs in single cells at single-molecule resolution.

The Fluorescence in situ Hybridization (FISH) method allows one to detect nucleic acids in the native cellular environment. Here we provide a protocol for ...

Assessment of Calcium Sparks in Intact Skeletal Muscle Fibers

Maintaining homeostatic Ca2+ signaling is a fundamental physiological process in living cells. Ca2+ sparks are the elementary units of Ca2+ signaling in the striated muscle fibers that appear as highly localized Ca2+ release events mediated by ryanodine receptor (RyR) Ca2+ release channels on the sarcoplasmic reticulum (SR) membrane. Proper assessment of muscle Ca2+ sparks could provide information on the intracellular Ca2+&#160;handling properties of healthy and diseased striated muscles. Although Ca2+ sparks events are commonly seen in resting cardiomyocytes, they are rarely observed in resting skeletal muscle fibers; thus there is a need for methods to generate and analyze sparks in skeletal muscle fibers.
Detailed here is an experimental protocol for measuring Ca2+ sparks in isolated flexor digitorm brevis (FDB) muscle fibers using fluorescent Ca2+ indictors and laser scanning confocal microscopy. In this approach, isolated FDB fibers are exposed to transient hypoosmotic stress followed by a return to isotonic physiological solution. Under these conditions, a robust Ca2+ sparks response is detected adjacent to the sarcolemmal membrane in young healthy FDB muscle fibers. Altered Ca2+ sparks response is detected in dystrophic or aged skeletal muscle fibers. This approach has recently demonstrated that membrane-delimited signaling involving cross-talk between inositol (1,4,5)-triphosphate receptor (IP3R) and RyR contributes to Ca2+ spark activation in skeletal muscle. In summary, our studies using osmotic stress induced Ca2+ sparks showed that this intracellular response reflects a muscle signaling mechanism in physiology and aging/disease states, including mouse models of muscle dystrophy (mdx mice) or amyotrophic lateral sclerosis (ALS model).

Described here is a method to directly measure calcium sparks, the elementary units of Ca2+ release from sarcoplasmic reticulum&#160;in intact skeletal muscle fibers. This method utilizes osmotic-stress-mediated triggering of Ca2+ release from ryanodine receptor in isolated muscle fibers. The dynamics and homeostatic capacity of intracellular Ca2+ signaling can be employed to assess muscle function in health and disease.

Maintaining homeostatic Ca2+ signaling is a fundamental physiological process in living cells. Ca2+ sparks are the elementary units of Ca2+ signaling in ...

Filtration Isolation of Nucleic Acids:  A Simple and Rapid DNA Extraction Method

FINA, filtration isolation of nucleic acids, is a novel extraction method which utilizes vertical filtration via a separation membrane and absorbent pad to extract cellular DNA from whole blood in less than 2 min. The blood specimen is treated with detergent, mixed briefly and applied by pipet to the separation membrane. The lysate wicks into the blotting pad due to capillary action, capturing the genomic DNA on the surface of the separation membrane. The extracted DNA is retained on the membrane during a simple wash step wherein PCR inhibitors are wicked into the absorbent blotting pad. The membrane containing the entrapped DNA is then added to the PCR reaction without further purification. This simple method does not require laboratory equipment and can be easily implemented with inexpensive laboratory supplies. Here we describe a protocol for highly sensitive detection and quantitation of HIV-1 proviral DNA from 100 &#181;l whole blood as a model for early infant diagnosis of HIV that could readily be adapted to other genetic targets.

We describe here a simple and rapid paper-based DNA extraction method of HIV proviral DNA from whole blood detected by quantitative PCR. This protocol can be extended for use in detecting other genetic markers or using alternative amplification methods.

FINA, filtration isolation of nucleic acids, is a novel extraction method which utilizes vertical filtration via a separation membrane and absorbent pad ...

Electroporation of Plasmid DNA into Mouse Skeletal Muscle

Transient gene expression modulation in murine skeletal muscle by plasmid electroporation is a useful tool for assessing normal and pathological physiology. Overexpression or knockdown of target genes enables investigators to manipulate individual molecular events and, thus, better understand the mechanisms that impact muscle mass, muscle metabolism, and contractility. In addition, electroporation of DNA plasmids that encode fluorescent tags allows investigators to measure changes in subcellular localization of proteins in skeletal muscle in vivo. A key functional assessment of skeletal muscle includes the measurement of muscle contractility. In this protocol, we demonstrate that whole muscle contractility studies are still possible after plasmid DNA injection, electroporation, and gene expression modulation. The goal of this instructional procedure is to demonstrate the step-by-step method of DNA plasmid electroporation into mouse skeletal muscle to facilitate uptake and expression in the myofibers of the tibialis anterior and extensor digitorum longus muscles, as well as to demonstrate that skeletal muscle contractility is not compromised by injection and electroporation.

Electroporation of plasmid DNA into skeletal muscle is a viable method to modulate gene expression without compromising muscle contractility in mice.

Transient gene expression modulation in murine skeletal muscle by plasmid electroporation is a useful tool for assessing normal and pathological ...

Quantification of Skeletal Muscle Fatty Infiltration via Decellularization

Decellularization-Based Quantification of Skeletal Muscle Fatty Infiltration

Fatty infiltration is the accumulation of adipocytes between myofibers in skeletal muscle and is a prominent feature of many myopathies, metabolic disorders, and dystrophies. Clinically in human populations, fatty infiltration is assessed using noninvasive methods, including computed tomography (CT), magnetic resonance imaging (MRI), and ultrasound (US). Although some studies have used CT or MRI to quantify fatty infiltration in mouse muscle, costs and insufficient spatial resolution remain challenging. Other small animal methods utilize histology to visualize individual adipocytes; however, this methodology suffers from sampling bias in heterogeneous pathology. This protocol describes the methodology to qualitatively view and quantitatively measure fatty infiltration comprehensively throughout intact mouse muscle and at the level of individual adipocytes using decellularization. The protocol is not limited to specific muscles or specific species and can be extended to human biopsy. Additionally, gross qualitative and quantitative assessments can be made with standard laboratory equipment for little cost, making this procedure more accessible across research laboratories.

Author Spotlight: Decellularization-Based Quantification of Skeletal Muscle Fatty Infiltration  

The present study describes decellularization-based methodologies for visualizing and quantifying intramuscular adipose tissue (IMAT) deposition through intact muscle volume, as well as quantifying metrics of individual adipocytes that comprise IMAT.

Fatty infiltration is the accumulation of adipocytes between myofibers in skeletal muscle and is a prominent feature of many myopathies, metabolic ...

Single-Cell CyTOF Analysis of Myogenic Progenitors in Muscle Regeneration

Identification and Analysis of Myogenic Progenitors In Vivo During Acute Skeletal Muscle Injury by High-Dimensional Single-Cell Mass Cytometry

Skeletal muscle regeneration is a dynamic process driven by adult muscle stem cells and their progeny. Mostly quiescent at a steady state, adult muscle stem cells become activated upon muscle injury. Following activation, they proliferate, and most of their progeny differentiate to generate fusion-competent muscle cells while the remaining self-renews to replenish the stem cell pool. While the identity of muscle stem cells was defined more than a decade ago, based on the co-expression of cell surface markers, myogenic progenitors were identified only recently using high-dimensional single-cell approaches. Here, we present a single-cell mass cytometry (cytometry by time of flight [CyTOF]) method to analyze stem cells and progenitor cells in acute muscle injury to resolve the cellular and molecular dynamics that unfold during muscle regeneration. This approach is based on the simultaneous detection of novel cell surface markers and key myogenic transcription factors whose dynamic expression enables the identification of activated stem cells and progenitor cell populations that represent landmarks of myogenesis. Importantly, a sorting strategy based on detecting cell surface markers CD9 and CD104 is described, enabling prospective isolation of muscle stem and progenitor cells using fluorescence-activated cell sorting (FACS) for in-depth studies of their function. Muscle progenitor cells provide a critical missing link to study the control of muscle stem cell fate, identify novel therapeutic targets for muscle diseases, and develop cell therapy applications for regenerative medicine. The approach presented here can be applied to study muscle stem and progenitor cells in vivo in response to perturbations, such as pharmacological interventions targeting specific signaling pathways. It can also be used to investigate the dynamics of muscle stem and progenitor cells in animal models of muscle diseases, advancing our understanding of stem cell diseases and accelerating the development of therapies.

Author Spotlight: Investigating Cellular and Molecular Dynamics During Muscle Regeneration Using Cutting-Edge Single-Cell Technologies

The protocol presented here enables the identification and high-dimensional analysis of muscle stem and progenitor cells by single-cell mass cytometry and their purification by FACS for in-depth studies of their function. This approach can be applied to study regeneration dynamics in disease models and test the efficacy of pharmacological interventions.

Skeletal muscle regeneration is a dynamic process driven by adult muscle stem cells and their progeny. Mostly quiescent at a steady state, adult muscle ...

Confocal Microscopic Analysis of Rat Muscle Mitochondria

Analysis of the Mitochondrial Density and Longitudinal Distribution in Rat Live-Skeletal Muscle Fibers by Confocal Microscopy

The mitochondrion is an organelle that can be elongated, fragmented, and renovated according to the metabolic requirements of the cells. The remodeling of the mitochondrial network allows healthy mitochondria to meet cellular demands; however, the loss of this capacity has been related to the development or progression of different pathologies. In skeletal muscle, mitochondrial density and distribution changes are observed in physiological and pathological conditions such as exercise, aging, and obesity, among others. Therefore, the study of the mitochondrial network may provide a better understanding of mechanisms related to those conditions.
Here, a protocol for mitochondria imaging of live-skeletal muscle fibers from rats is described. Fibers are manually dissected in a relaxing solution and incubated with a fluorescent live-cell imaging indicator of mitochondria (tetramethylrhodamine ethyl ester, TMRE). The mitochondria signal is recorded by confocal microscopy using the XYZ scan mode to obtain confocal images of the intermyofibrillar mitochondrial (IMF) network. After that, the confocal images are processed by thresholding and binarization. The binarized confocal image accounts for the positive pixels for mitochondria, which are then counted to obtain the mitochondrial density. The mitochondrial network in skeletal muscle is characterized by a high density of IMF population, which has a periodic longitudinal distribution similar to that of T-tubules (TT).&#160;The Fast Fourier Transform (FFT) is a standard analysis technique performed to evaluate the distribution of TT that allows finding the distribution frequency and the level of their organization. In this protocol, the implementation of the FFT algorithm is described for the analysis of the longitudinal mitochondrial distribution in skeletal muscle.

Author Spotlight: Mitochondrial Remodeling in Skeletal Muscle 

Here, we present a protocol to analyze changes in mitochondrial density and longitudinal distribution by live-skeletal muscle imaging using confocal microscopy for mitochondrial network scanning.

The mitochondrion is an organelle that can be elongated, fragmented, and renovated according to the metabolic requirements of the cells. The remodeling of ...

Assessing Protein Interaction and Localization in DNA Damage

Proximity Ligand Assay to Localize Proteins in DNA Damage Sites

The DNA damage response is a genetic information safeguard that protects cells from perpetuating damaged DNA. The characterization of the proteins that cooperate in this process allows the identification of alternative targets for therapeutic intervention in several diseases, such as cancer, aging-related diseases, and chronic inflammation. The Proximity Ligand Assay (PLA) emerged as a tool for estimating interaction between proteins as well as spatial proximity among organelles or cellular structures and allows the temporal localization and co-localization analysis under stress conditions, for instance. The method is simple because it is similar to conventional immunofluorescence and allows the staining of an organelle, cellular structure, or a specific marker such as mitochondria, endoplasmic reticulum, PML bodies, or DNA double-strand marker, yH2AX simultaneously. The phosphorylation of the S139 at Histone 2A variant, H2AX, then referred to as yH2AX, is widely used as a very sensitive and specific marker of DNA double-strand breaks. Each focus of yH2AX staining corresponds to one break in DNA that occurs a few minutes after the damage. The analysis of changes in yH2AX foci is the most common assay for studying if the protein of interest is implicated in DNA damage response (DDR). Whether a direct role in the DNA damage site is expected, fluorescence microscopy is used to verify the colocalization of the protein of interest with yH2AX foci. However, except for the new super-resolution fluorescence methods, to conclude, the local interaction with DNA damage sites can be a little subjective. Here, we show an assay to evaluate the localization of proteins in the DDR pathway using yH2AX as a marker of the damage site. This assay can be used to characterize the temporal localization under different insults that cause DNA damage.

Author Spotlight: Combining Proximity Ligand Assay with Gamma-H2AX Staining to Characterize Protein Interactions in DNA Damage Response

Here, we present a simple and rapid protocol for the detection of protein interaction at DNA damage sites.

The DNA damage response is a genetic information safeguard that protects cells from perpetuating damaged DNA. The characterization of the proteins that ...

Cerebellar Purkinje Cells: DNA Damage Response in Organotypic Cultures

Visualizing the DNA Damage Response in Purkinje Cells Using Cerebellar Organotypic Cultures

Cerebellar Purkinje cells (PCs) exhibit a unique interplay of high metabolic rates, specific chromatin architecture, and extensive transcriptional activity, making them particularly vulnerable to DNA damage. This necessitates an efficient DNA damage response (DDR) to prevent cerebellar degeneration, often initiated by PC dysfunction or loss. A notable example is the genome instability syndrome, ataxia-telangiectasia (A-T), marked by progressive PC depletion and cerebellar deterioration. Investigating DDR mechanisms in PCs is vital for elucidating the pathways leading to their degeneration in such disorders. However, the complexity of isolating and cultivating PCs in vitro has long hindered research efforts. Murine cerebellar organotypic (slice) cultures offer a feasible alternative, closely mimicking the in vivo tissue environment. Yet, this model is constrained to DDR indicators amenable to microscopic imaging. We have refined the organotypic culture protocol, demonstrating that fluorescent imaging of protein-bound poly(ADP-ribose) (PAR) chains, a rapid and early DDR indicator, effectively reveals DDR dynamics in PCs within these cultures, in response to genotoxic stress.

Author Spotlight: Deciphering the Role of ATM in Ataxia-Telangiectasia and the Associated Cerebellar Degeneration

Cerebellar Purkinje cells (PCs) are particularly sensitive to deficiencies in the DNA damage response. A protocol is presented for the visual evaluation of the dynamics of PC response to DNA damage, which involves staining protein-bound poly(ADP-ribose) chains within cerebellar organotypic cultures.

Methods Article

Detection and Analysis of DNA Damage in Mouse Skeletal Muscle In Situ Using the TUNEL Method