This study was supported by the Jane and Aatos Erkko Foundation.

This protocol involves the use of animals and all the procedures were approved by Ethical Committees on the Use and Care of Animals and the Animal Facility at the University of Helsinki.
1. Preparation of the organ culture dish
<ol>
	<li>Perform all procedures in a laminar flow hood. Clean work surfaces with 70% ethanol and use autoclaved glass instruments and solutions. Sterilize scissors and other metal equipment in a glass-bead sterilizer.</li>
	<li>Prepare filters normally stored in 70% ethanol by washing them three times in 1x PBS to remove ethanol (Figure 1). Cut filters into rectangular pieces (3 x 3-5 x 5 mm). 
	NOTE: Washed filter pieces can be stored for several days in 1x PBS at 4 &#176;C.</li>
	<li>Prepare the culture medium (1:1 DMEM:F12 supplemented with 1% [v/v] 200 mM L-alanyl-L-glutamine dipeptide in 0.85% NaCl, 10% [v/v] FBS, 150 &#181;g/mL ascorbic acid, and 0.2% [v/v] penicillin [10,000 I.U./mL] and streptomycin [10,000 &#181;g/mL]). Store at 4 &#176;C.</li>
	<li>Place the 30 mm metal grids (with 1-2 mm diameter holes that enable tissue imaging) in a 35 mm Petri dish. Add sufficient media to reach the grid surface without producing air bubbles. Pre-warm the prepared culture dish at 37 &#176;C until the tissue is isolated and ready for culture (in a standard incubator with 5% CO2 and 90%-95% humidity).</li>
</ol>
2. Incisor dissection and isolation of the proximal end
<ol>
	<li>Sacrifice the animals following an approved animal care protocol.</li>
	<li>Decapitate the mouse and dissect the mandible. To do so, first remove the skin to expose the mandible and cut through the masseter muscles to separate it from the maxilla and the rest of the head.</li>
	<li>Once the mandible is isolated, remove the tongue and as much soft tissue as possible.</li>
	<li>Collect all the mandibles and keep them in a Petri dish containing PBS on ice, as this enhances the viability of the tissues.</li>
	<li>Transfer one mandible to a glass Petri dish and use disposable 20/26 G hypodermic needles to dissect the incisor under a stereomicroscope. Split the mandible at the midline, cutting through the symphysis. Clean the soft and muscle tissue away from the bone surface for better visualization. 
	&#8203;NOTE: A glass Petri dish is essential, as this will not blunt the needles.</li>
	<li>Mandibles obtained from animals younger than 10 days are softer and more fragile, therefore, use disposable 20/26 G hypodermic needles to open each half of the mandible longitudinally to expose the incisor tooth. For mice older than 10 days, use tweezers to grip the mandible and break the bone to expose the tooth.</li>
	<li>Gently detach the incisor from the surrounding bone and cut off the proximal end, which contains the cervical loop.</li>
	<li>Cut the proximal end and remove the mineralized enamel and dentin matrix.</li>
	<li>Keep the collected proximal ends in Dulbecco&#39;s PBS on ice until ready for culture.</li>
</ol>
3. Culture
<ol>
	<li>Carefully place a filter rectangle on the top of a grid in a pre-warmed culture dish.</li>
	<li>Use a stereomicroscope to properly orient the tissue pieces.</li>
	<li>Place in a standard incubator at 37 &#176;C with 5% CO2 and 90%-95% humidity.</li>
	<li>Change the medium every other day and replace with fresh medium, carefully avoiding formation of air bubbles. Monitor tissue growth and photograph daily using a camera attached to the stereomicroscope.</li>
</ol>
4. Adding soluble factors to the culture
<ol>
	<li>Supplement the culture medium with soluble factors and molecules of interest to study their effect on regulation of SCs. 
	&#8203;NOTE: The administration protocol for any molecule (growth factors, signaling molecules, blocking antibodies, pharmacological compounds such as inhibitors or activators, vectors, etc.) depends on its half-life and solubility. These parameters also determine the appropriate control to be used.</li>
</ol>
5. Molecular and histological analyses
<ol>
	<li>Remove the culture medium.</li>
	<li>Carefully add ice-cold methanol to the tissues to prevent detachment from the filters.</li>
	<li>Leave methanol for 5 min.</li>
	<li>Transfer filters carrying tissue explants to sampling tubes.</li>
	<li>Fix the explants in 4% paraformaldehyde in PBS for 10-24 h at 4 &#176;C.</li>
	<li>Proceed with established protocols for histological processing (paraffin, frozen, etc.) or immunostainings.</li>
</ol>
6. Culture of tissue slices
NOTE: There are several variations to this protocol, which are all equally successful and are a matter of personal choice, depending on the speed and the skill of the user. These refer to the buffer used to collect and maintain tissue viability. For this purpose, Krebs buffer, PBS supplemented with 2% glucose and antibiotics, or PBS can be used. If Krebs buffer is used, it should be made 1 day in advance and kept at 4 &#176;C.
<ol>
	<li>Before the experiment, prepare 4%-5% low-melting point agarose by dissolving 2-2.5 g of low-melting point agarose in 50 mL of boiling 2% glucose/PBS, after which the solution should be placed in a 45 &#176;C water bath.</li>
	<li>Set up the vibratome, wash with 70% ethanol, and fill with ice-cold 2% glucose/PBS supplemented with antibiotics (100 U/mL penicillin, 100 mg/mL streptomycin).</li>
	<li>Dissect the proximal ends of the incisor and collect them in the ice-cold 2% glucose/PBS supplemented with antibiotics.</li>
	<li>Place one proximal end of the incisor in the mold containing 4%-5% low-melting point agarose. Under a stereomicroscope, orient the piece in the desired direction and leave on ice for the agarose to harden.</li>
	<li>Trim the hardened agarose block and place it in the vibratome. Cut thick slices (150-300 &#181;m).</li>
	<li>Collect the slices in a Petri dish containing ice-cold 2% glucose/PBS supplemented with antibiotics.</li>
	<li>Use a spatula to transfer the thick slices on a filter rectangle placed on the pre-warmed grid prepared as in section 1.3.</li>
	<li>Incubate the thick slices in the incubator and proceed with imaging (Figure 2).</li>
</ol>

<ol>
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E., Warshawsky, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cellular+renewal+in+the+enamel+organ+and+the+odontoblast+layer+of+the+rat+incisor+as+followed+by+radioautography+using+3H-thymidine.">Cellular renewal in the enamel organ and the odontoblast layer of the rat incisor as followed by radioautography using 3H-thymidine.</a> The Anatomical Record. 183 (4), 523-561 (1975).</li><li>Balic, A., Thesleff, I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Tissue+interactions+regulating+tooth+development+and+renewal.">Tissue interactions regulating tooth development and renewal.</a> Current Topics in Developmental Biology. 115, 157-186 (2015).</li><li>Scadden, D. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+stem-cell+niche+as+an+entity+of+action.">The stem-cell niche as an entity of action.</a> Nature. 441 (7097), 1075-1079 (2006).</li><li>Juuri, E., 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=Sox2+marks+epithelial+competence+to+generate+teeth+in+mammals+and+reptiles.">Sox2 marks epithelial competence to generate teeth in mammals and reptiles.</a> Development. 140 (7), 1424-1432 (2013).</li><li>Juuri, E., 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=Sox2++stem+cells+contribute+to+all+epithelial+lineages+of+the+tooth+via+Sfrp5++progenitors.">Sox2+ stem cells contribute to all epithelial lineages of the tooth via Sfrp5+ progenitors.</a> Developmental Cell. 23 (2), 317-328 (2012).</li><li>Feng, J., Mantesso, A., De Bari, C., Nishiyama, A., Sharpe, P. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dual+origin+of+mesenchymal+stem+cells+contributing+to+organ+growth+and+repair.">Dual origin of mesenchymal stem cells contributing to organ growth and repair.</a> Proceedings of the National Academy of Sciences of the United States of America. 108 (16), 6503-6508 (2011).</li><li>Kaukua, 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=Glial+origin+of+mesenchymal+stem+cells+in+a+tooth+model+system.">Glial origin of mesenchymal stem cells in a tooth model system.</a> Nature. 513 (7519), 551-554 (2014).</li><li>Zhao, H., 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=Secretion+of+shh+by+a+neurovascular+bundle+niche+supports+mesenchymal+stem+cell+homeostasis+in+the+adult+mouse+incisor.">Secretion of shh by a neurovascular bundle niche supports mesenchymal stem cell homeostasis in the adult mouse incisor.</a> Cell Stem Cell. 14 (2), 160-173 (2014).</li><li>Vidovic, 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=alphaSMA-expressing+perivascular+cells+represent+dental+pulp+progenitors+in+vivo.">alphaSMA-expressing perivascular cells represent dental pulp progenitors in vivo.</a> Journal of Dental Research. 96 (3), 323-330 (2017).</li><li>Trowell, O. 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The authors declare no conflicts of interest.

In vitro organ culture has been used extensively to study inductive potential and epithelial-mesenchymal interactions that govern organ growth and morphogenesis. The Thesleff laboratory has demonstrated how to adapt the Sax&#233;n modification of the Trowell-type organ culture and use it to study tooth development14. The reproducible conditions and advancements in fluorescent reporters have made this a useful method for monitoring tooth morphogenesis and the distinct cell populations with...

Mouse incisors grow continuously due to life-long preservation of the stem cells (SC) that support the unceasing production of tooth components. These include epithelial SCs, which generate enamel-producing ameloblasts, and mesenchymal stem cells (MSCs), which generate dentin-producing odontoblasts, among other cells1. The epithelial SCs in the continuously growing incisors were initially identified as label-retaining cells2,3 and have since been shown to express a number of well-known stemness genes, including Sox24. These cells share common features with epithelial SCs in other organs and reside within the SC niche called the cervical loop located on the labial side of the incisor. The niche is a dynamic entity composed of cells and extracellular matrix that control SC activity5. Lineage-tracing studies have demonstrated that Sox2+ epithelial SCs can regenerate the whole epithelial compartment of the tooth and that they are crucial for successional tooth formation6,7. MSCs with dentin reparative or regenerative potential are largely recruited from outside the organ through blood vessels and nerves8,9,10,11, therefore, providing a suitable model to study recruitment, migration, and housing of the MSC population.
To study SCs in vivo is not always feasible, since many of the genetic and/or pharmacological manipulations can affect organ homeostasis and/or have lethal consequences. Therefore, organ culture provides an excellent tool to study regulation of SCs and their niches in vitro. The organ culture system that utilizes a metal grid was initially developed by Trowell12 to study organ development and has been further modified by Saxen13&#160;to study inductive signals in kidney development. Since then, this in vitro method of culturing the whole or part of the organ has been successfully applied in different fields. In the field of tooth development, this method has been widely used to study the epithelial-mesenchymal interactions that govern tooth development14&#160;and successional tooth formation15. The work of the Thesleff laboratory has demonstrated the utility of this system for temporal analysis of tooth growth and morphogenesis, for analysis of the effect of various molecules and growth factors on tooth growth, and for time-lapse live imaging of tooth development16,17. More recently, this method has been utilized to study regulation of incisor SCs and their niche18,19, which is described in detail here.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>1-mL plastic syringes</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Disposable 20/26 gauge hypodermic needles</td>
			<td>Terumo</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>DMEM</td>
			<td>Gibco</td>
			<td>61965-026</td>
			<td></td>
		</tr>
		<tr>
			<td>Dulbecco&#39;s Phosphate-Buffered Saline</td>
			<td>Gibco</td>
			<td>14287</td>
			<td></td>
		</tr>
		<tr>
			<td>Extra Fine Bonn Scissors</td>
			<td>F.S.T.</td>
			<td>14084-08</td>
			<td></td>
		</tr>
		<tr>
			<td>F-12</td>
			<td>Gibco</td>
			<td>31765-027</td>
			<td></td>
		</tr>
		<tr>
			<td>FBS South American (CE)</td>
			<td>LifeTechn.</td>
			<td>10270106</td>
			<td>divide in aliquotes, store at -20&#176;C</td>
		</tr>
		<tr>
			<td>Glass bead sterilizer, Steri 250 Seconds-Sterilizer</td>
			<td>Simon Keller Ltd</td>
			<td>4AJ-6285884</td>
			<td></td>
		</tr>
		<tr>
			<td>GlutaMAX-1 (200 mM L-alanyl-L-glutamine dipeptide)</td>
			<td>Gibco</td>
			<td>35050-038</td>
			<td></td>
		</tr>
		<tr>
			<td>Isopore Polycarb.Filters, 0,1 um 25-mm diameter</td>
			<td>MerckMillipore</td>
			<td>VCTP02500</td>
			<td>Store in 70% ethanol at room temperature.</td>
		</tr>
		<tr>
			<td>L-Ascobic Acid</td>
			<td>Sigma</td>
			<td>A4544-25g</td>
			<td>diluted 100 mg/ml in MilliQ, filter strerilized and divided in 20&#956;l aliquotes, store at dark, -20&#176;C</td>
		</tr>
		<tr>
			<td>Low melting agarose</td>
			<td>TopVision</td>
			<td>R0801</td>
			<td></td>
		</tr>
		<tr>
			<td>Metal grids</td>
			<td></td>
			<td></td>
			<td>Commercially available, or self-made from stainless-steel mesh (corrosion resistant, size of mesh 0.7 mm). Cut approximately 30 mm diameter disk and bend the edges to give 3 mm height. Use nails to make holes.</td>
		</tr>
		<tr>
			<td>Micro forceps</td>
			<td>Medicon</td>
			<td>07.60.03</td>
			<td></td>
		</tr>
		<tr>
			<td>Paraformaldehyde</td>
			<td>Sigma-Aldrich</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Penicillin-Streptomycin (10,000U/ml) sol.</td>
			<td>Gibco</td>
			<td>15140-148</td>
			<td></td>
		</tr>
		<tr>
			<td>Petri dishes, Soda-Lime glass</td>
			<td>DWK Life Sciences</td>
			<td>9170442</td>
			<td></td>
		</tr>
		<tr>
			<td>Petridish 35 mm, with vent</td>
			<td>Duran</td>
			<td>237554008</td>
			<td></td>
		</tr>
		<tr>
			<td>Petridish 90 mm, no vent classic</td>
			<td>Thermo Fisher</td>
			<td>101RT/C</td>
			<td></td>
		</tr>
		<tr>
			<td>Small scissors</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
	</tbody>
</table>

use of trowell-type organ culture to study regulation of dental stem cells

Organ development, function, and regeneration depend on stem cells, which reside within discrete anatomical spaces called stem cell niches. The continuously growing mouse incisor provides an excellent model to study tissue-specific stem cells. The epithelial tissue-specific stem cells of the incisor are located at the proximal end of the tooth in a niche called the cervical loop. They provide a continuous influx of cells to counterbalance the constant abrasion of the self-sharpening tip of the tooth. Presented here is a detailed protocol for the isolation and culture of the proximal end of the mouse incisor that houses stem cells and their niche. This is a modified Trowell-type organ culture protocol that enables in vitro culture of tissue pieces (explants), as well as the thick tissue slices at the liquid/air interface on a filter supported by a metal grid. The organ culture protocol described here enables tissue manipulations not feasible in vivo, and when combined with the use of a fluorescent reporter(s), it provides a platform for the identification and tracking of discrete cell populations in live tissues over time, including stem cells. Various regulatory molecules and pharmacological compounds can be tested in this system for their effect on stem cells and their niches. This ultimately provides a valuable tool to study stem cell regulation and maintenance.

The epithelial SCs reside in a niche called the cervical loop, which is located at the proximal end of the incisor (Figure 3A). Cervical loops are morphologically distinct structures composed of inner and outer enamel epithelium that encase the stellate reticulum, a core of loosely arranged epithelial cells (Figure 3B,C). There are two cervical loops in each incisor (Figure 3A), but only the labial cervical loop con...

Watch this Scientific Journal Video about Use of Trowell-Type Organ Culture to Study Regulation of Dental Stem Cells at JoVE.com

Use of Trowell-Type Organ Culture to Study Regulation of Dental Stem Cells

The Trowell-type organ culture method has been used to unravel complex signaling networks that govern tooth development and, more recently, for studying regulation involved in stem cells of the continuously growing mouse incisor. Fluorescent-reporter animal models and live-imaging methods facilitate in-depth analyses of dental stem cells and their specific niche microenvironment.

Organ development, function, and regeneration depend on stem cells, which reside within discrete anatomical spaces called stem cell niches. The ...

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Developmental Biology

2.0K Views.  University of Helsinki. The Trowell-type organ culture method has been used to unravel complex signaling networks that govern tooth development and, more recently, for studying regulation involved in stem cells of the continuously growing mouse incisor. Fluorescent-reporter animal models and live-imaging methods facilitate in-depth analyses of dental stem cells and their specific niche microenvironment.

Video: Use of Trowell-Type Organ Culture to Study Regulation of Dental Stem Cells

Use of the TetON System to Study Molecular Mechanisms of Zebrafish Regeneration

The zebrafish has become a very important model organism for studying vertebrate development, physiology, disease, and tissue regeneration. A thorough understanding of the molecular and cellular mechanisms involved requires experimental tools that allow for inducible, tissue-specific manipulation of gene expression or signaling pathways. Therefore, we and others have recently adapted the TetON system for use in zebrafish. The TetON system facilitates temporally and spatially-controlled gene expression and we have recently used this tool to probe for tissue-specific functions of Wnt/beta&#8211;catenin signaling during zebrafish tail fin regeneration. Here we describe the workflow for using the TetON system to achieve inducible, tissue-specific gene expression in the adult regenerating zebrafish tail fin. This includes the generation of stable transgenic TetActivator and TetResponder lines, transgene induction and techniques for verification of tissue-specific gene expression in the fin regenerate. Thus, this protocol serves as blueprint for setting up a functional TetON system in zebrafish and its subsequent use, in particular for studying fin regeneration.

Here we outline the workflow for using the TetON system to achieve tissue-specific gene expression in the adult regenerating zebrafish tail fin.

The zebrafish has become a very important model organism for studying vertebrate development, physiology, disease, and tissue regeneration. A thorough ...

Method of Studying Palatal Fusion using Static Organ Culture

Cleft lip and palate are among the most common of all birth defects. The secondary palate forms from mesenchymal shelves covered with epithelium that adheres to form the midline epithelial seam (MES). The theories suggest that MES cells follow an epithelial to mesenchymal transition (EMT), apoptosis and migration, making a fused palate 1. Complete disintegration of the MES is the final essential phase of palatal confluence with surrounding mesenchymal cells. We provide a method for palate organ culture. The developed in vitro protocol allows the study of the biological and molecular processes during fusion. The applications of this technique are numerous, including evaluating responses to exogenous chemical agents, effects of regulatory and growth factors and specific proteins. Palatal organ culture has a number of advantages including manipulation at different stages of development that is not possible using in vivo studies.

Studies of palate development are motivated by the incidence of cleft palate, a birth defect that imposes a tremendous health burden and can leave lasting disfigurement. We demonstrate here a technique to culture palatal shelves that can be used to study different signaling pathways involved in palatal development and fusion.

Cleft lip and palate are among the most common of all birth defects. The secondary palate forms from mesenchymal shelves covered with epithelium that ...

Epigenetic Regulation of Cardiac Differentiation of Embryonic Stem Cells and Tissues

Specific gene transcription is a key biological process that underlies cell fate decision during embryonic development. The biological process is mediated by transcription factors which bind genomic regulatory regions including enhancers and promoters of cardiac constitutive genes. DNA is wrapped around histones that are subjected to chemical modifications. Modifications of histones further lead to repressed, activated or poised gene transcription, thus bringing another level of fine tuning regulation of gene transcription. Embryonic Stem cells (ES cells) recapitulate within embryoid bodies (i.e., cell aggregates) or in 2D culture the early steps of cardiac development. They provide in principle enough material for chromatin immunoprecipitation (ChIP), a technology broadly used to identify gene regulatory regions. Furthermore, human ES cells represent a human cell model of cardiogenesis. At later stages of development, mouse embryonic tissues allow for investigating specific epigenetic landscapes required for determination of cell identity. Herein, we describe protocols of ChIP, sequential ChIP followed by PCR or ChIP-sequencing using ES cells, embryoid bodies and cardiac specific embryonic regions. These protocols allow to investigating the epigenetic regulation of cardiac gene transcription.

A fine tuning regulation of gene transcription underlies embryonic cell fate decision. Herein, we describe chromatin immunoprecipitation assays used to investigate epigenetic regulation of both cardiac differentiation of stem cells and cardiac development of mouse embryos.

Specific gene transcription is a key biological process that underlies cell fate decision during embryonic development. The biological process is mediated ...

Large-Scale Production of Cardiomyocytes from Human Pluripotent Stem Cells Using a Highly Reproducible Small Molecule-Based Differentiation Protocol

Maximizing the benefit of human pluripotent stem cells (hPSCs) for research, disease modeling, pharmaceutical and clinical applications requires robust methods for the large-scale production of functional cell types, including cardiomyocytes. Here we demonstrate that the temporal manipulation of WNT, TGF-&#946;, and SHH signaling pathways leads to highly efficient cardiomyocyte differentiation of single-cell passaged hPSC lines in both static suspension and stirred suspension bioreactor systems. Employing this strategy resulted in ~ 100% beating spheroids, consistently containing &#62; 80% cardiac troponin T-positive cells after 15 days of culture, validated in multiple hPSC lines. We also report on a variation of this protocol for use with cell lines not currently adapted to single-cell passaging, the success of which has been verified in 42 hPSC lines. Cardiomyocytes generated using these protocols express lineage-specific markers and show expected electrophysiological functionalities. Our protocol presents a simple, efficient and robust platform for the large-scale production of human cardiomyocytes.

Here, we present a robust, fast and scalable cardiomyocyte differentiation protocol for human pluripotent stem cells (hPSCs). Cardiomyocytes derived using this large-scale method can provide sufficient cell numbers for their effective use in human cardiovascular disease modeling, high-throughput drug screening, and potentially clinical applications.

Maximizing the benefit of human pluripotent stem cells (hPSCs) for research, disease modeling, pharmaceutical and clinical applications requires robust ...

Horizontal Whole Mount: A Novel Processing and Imaging Protocol for Thick, Three-dimensional Tissue Cross-sections of Skin

Processing a tissue of interest to generate a microscopic image that supports a scientific argument can be challenging. The acquisition of high-quality microscopic images is not entirely dependent upon the quality of the microscope, but also upon the methods of tissue processing, which often involve multiple critical actions or steps. Furthermore, mesenchymal cell types in the skin and other tissues represent a new challenge for tissue preparation and imaging. Here, we present a complete process, from tissue harvest to microscopy. Our technique, called &#34;horizontal whole mount,&#34; is one that novices can quickly become proficient in and that allows for antigen preservation and detection in 60-300 &#181;m-thick sections cut with a cryostat. Sections of this thickness provide enhanced visualization of tissue microarchitecture in a three-dimensional environment. In addition, the protocol preserves mesenchymal cells in a manner that enhances image quality when compared to standard cryostat or paraffin sections, thereby increasing the efficacy and reliability of immunostaining. We believe that this protocol will benefit all laboratories that visualize skin, and possibly other tissues and organs.

This work presents a novel processing and imaging protocol for thick, three-dimensional tissue cross-section analysis that enables the full exploitation of confocal imaging modalities. This protocol preserves antigenicity and represents a robust system to analyze skin histology and potentially other tissue types.

Processing a tissue of interest to generate a microscopic image that supports a scientific argument can be challenging. The acquisition of high-quality ...

Single-cell Photoconversion in Living Intact Zebrafish

Animal and plant tissue is composed of distinct populations of cells. These cells interact over time to build and maintain the tissue and can cause disease when disrupted. Scientists have developed clever techniques to investigate characteristics and natural dynamics of these cells within intact tissue by expressing fluorescent proteins in subsets of cells. However, at times, experiments require more selected visualization of cells within the tissue, sometimes at the single-cell or population-of-cells manner. To achieve this and visualize single cells within a population of cells, scientists have utilized single-cell photoconversion of fluorescent proteins. To demonstrate this technique, we show here how to direct UV light to an Eos-expressing cell of interest in an intact, living zebrafish. We then image those photoconverted Eos+ cells 24 h later to determine how they changed in the tissue. We describe two techniques: single cell photoconversion and photoconversions of populations of cell. These techniques can be used to visualize cell-cell interactions, cell-fate and differentiation, and cell migrations, making it a technique that is applicable in numerous biological questions.

Here, we present a protocol to show how cell photoconversion is achieved through UV exposure to specific areas expressing the fluorescent protein, Eos, in living animals.

Animal and plant tissue is composed of distinct populations of cells. These cells interact over time to build and maintain the tissue and can cause ...

Identification of Skeletal Muscle Satellite Cells by Immunofluorescence with Pax7 and Laminin Antibodies

Immunofluorescence is an effective method that helps to identify different cell types on tissue sections. In order to study the desired cell population, antibodies for specific cell markers are applied on tissue sections. In adult skeletal muscle, satellite cells (SCs) are stem cells that contribute to muscle repair and regeneration. Therefore, it is important to visualize and trace the satellite cell population under different physiological conditions. In resting skeletal muscle, SCs reside between the basal lamina and myofiber plasma membrane. A commonly used marker for identifying SCs on the myofibers or in cell culture is the paired box protein Pax7. In this article, an optimized Pax7 immunofluorescence protocol on skeletal muscle sections is presented that minimizes non-specific staining and background. Another antibody that recognizes a protein (laminin) of the basal lamina was also added to help identify SCs. Similar protocols can also be used to perform double or triple labeling with Pax7 and antibodies for additional proteins of interest.

The precise identification of satellite cells is essential for studying their functions under various physiological and pathological conditions. This article presents a protocol to identify satellite cells on adult skeletal muscle sections by immunofluorescence-based staining.

Immunofluorescence is an effective method that helps to identify different cell types on tissue sections. In order to study the desired cell population, ...

Computational Analysis of the Caenorhabditis elegans Germline to Study the Distribution of Nuclei, Proteins, and the Cytoskeleton

The Caenorhabditis elegans (C. elegans) germline is used to study several biologically important processes including stem cell development, apoptosis, and chromosome dynamics. While the germline is an excellent model, the analysis is often two dimensional due to the time and labor required for three-dimensional analysis. Major readouts in such studies are the number/position of nuclei and protein distribution within the germline. Here, we present a method to perform automated analysis of the germline using confocal microscopy and computational approaches to determine the number and position of nuclei in each region of the germline. Our method also analyzes germline protein distribution that enables the three-dimensional examination of protein expression in different genetic backgrounds. Further, our study shows variations in cytoskeletal architecture in distinct regions of the germline that may accommodate specific spatial developmental requirements. Finally, our method enables automated counting of the sperm in the spermatheca of each germline. Taken together, our method enables rapid and reproducible phenotypic analysis of the C. elegans germline.

Computational Analysis of the Caenorhabditis elegans Germline to Study the Distribution of Nuclei, Proteins, and the Cytoskeleton

We present an automated method for three-dimensional reconstruction of the Caenorhabditis elegans germline. Our method determines the number and position of each nucleus within the germline and analyses germline protein distribution and cytoskeletal structure.

The Caenorhabditis elegans (C. elegans) germline is used to study several biologically important processes including stem cell development, apoptosis, and ...

Use of Hematopoietic Stem Cell Transplantation to Assess the Origin of Myelodysplastic Syndrome

Myelodysplastic syndromes (MDS) are a diverse group of hematopoietic stem cell disorders that are defined by ineffective hematopoiesis, peripheral blood cytopenias, dysplasia, and a propensity for transformation to acute leukemia. NUP98-HOXD13 (NHD13) transgenic mice recapitulate human MDS in terms of peripheral blood cytopenias, dysplasia, and transformation to acute leukemia. We previously demonstrated that MDS could be transferred from a genetically engineered mouse with MDS to wild-type recipients by transplanting MDS bone marrow nucleated cells (BMNC). To more clearly understand the MDS cell of origin, we have developed approaches to transplant specific, immunophenotypically defined hematopoietic subsets. In this article, we describe the process of isolating and transplanting specific populations of hematopoietic stem and progenitor cells. Following transplantation, we describe approaches to assess the efficiency of transplantation and persistence of the donor MDS cells.

We describe the use of hematopoietic stem cell transplantation (HSCT) to assess the malignant potential of genetically engineered hematopoietic cells. HSCT is useful for evaluating various malignant hematopoietic cells in vivo as well as generating a large cohort of mice with myelodysplastic syndromes (MDS) or leukemia to evaluate novel therapies.

Myelodysplastic syndromes (MDS) are a diverse group of hematopoietic stem cell disorders that are defined by ineffective hematopoiesis, peripheral blood ...

Isolation, Propagation, and Prion Protein Expression During Neuronal Differentiation of Human Dental Pulp Stem Cells

Bioethical issues related to the manipulation of embryonic stem cells have hindered advances in the field of medical research. For this reason, it is very important to obtain adult stem cells from different tissues such as adipose, umbilical cord, bone marrow and blood. Among the possible sources, dental pulp is particularly interesting because it is easy to obtain in respect of bioethical considerations. Indeed, human Dental Pulp Stem Cells (hDPSCs) are a type of adult stem cells able to differentiate in neuronal-like cells and can be obtained from the third molar of healthy patients (13-19 ages). In particular, the dental pulp was removed with an excavator, cut into small slices, treated with collagenase IV and cultured in a flask. To induce the neuronal differentiation, hDPSCs were stimulated with EGF/bFGF for 2 weeks. Previously, we have demonstrated that during the differentiation process the content of cellular prion Protein (PrPC) in hDPSCs increased. The cytofluorimetric analysis showed an early expression of PrPC that increased after neuronal differentiation process. Ablation of PrPC by siRNA PrP prevented neuronal differentiation induced by EGF/bFGF. In this paper, we illustrate that as we enhanced the isolation, separation and in vitro cultivation methods of hDPSCs with several easy procedures, more efficient cell clones were obtained and large-scale expansion of the mesenchymal stem cells (MSCs) was observed. We also show how the hDPSCs, obtained with methods detailed in the protocol, are an excellent experimental model to study the neuronal differentiation process of MSCs and subsequent cellular and molecular processes.

Here we present a protocol for human Dental Pulp Stem Cells isolation and propagation in order to evaluate the prion protein expression during neuronal differentiation process.

Bioethical issues related to the manipulation of embryonic stem cells have hindered advances in the field of medical research. For this reason, it is very ...

Use of Trowell-Type Organ Culture to Study Regulation of Dental Stem Cells

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Use of the TetON System to Study Molecular Mechanisms of Zebrafish Regeneration

Method of Studying Palatal Fusion using Static Organ Culture

Epigenetic Regulation of Cardiac Differentiation of Embryonic Stem Cells and Tissues

Large-Scale Production of Cardiomyocytes from Human Pluripotent Stem Cells Using a Highly Reproducible Small Molecule-Based Differentiation Protocol

Horizontal Whole Mount: A Novel Processing and Imaging Protocol for Thick, Three-dimensional Tissue Cross-sections of Skin

Single-cell Photoconversion in Living Intact Zebrafish

Identification of Skeletal Muscle Satellite Cells by Immunofluorescence with Pax7 and Laminin Antibodies

Computational Analysis of the Caenorhabditis elegans Germline to Study the Distribution of Nuclei, Proteins, and the Cytoskeleton

Use of Hematopoietic Stem Cell Transplantation to Assess the Origin of Myelodysplastic Syndrome

Isolation, Propagation, and Prion Protein Expression During Neuronal Differentiation of Human Dental Pulp Stem Cells