This study was supported by NIH grant DE025014 to JQF.

All protocols were reviewed and approved by the Institutional Animal Care and Use Committee (IACUC) at Texas A&#38;M University College of Dentistry.
1. Animal Breeding
<ol>
	<li>Use three animal models in this study. To investigate the fate of the embryonic chondrocytes in condyle formation, first use Col10a1-Cre15 mice and cross them with Rosa26tdTomato (B6;129S6-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/J) mice to obtain Col10a1-Cre and Rosa26tdTomato mice. Next, cross these mice with 2.3Col1a1-GFP mice16. Use Col10a1-Cre; Rosa26tdTomato; 2.3Col1a1-GFP mice to perform the cell lineage tracing experiments (Figure 1B).</li>
	<li>To study the fate of the postnatal chondrocytes, follow the same procedure as in step 1.1, but use the Aggrecan-creERT2 (Agg-CreERT2)17,18 line and keep the Agg-CreERT2; Rosa26tdTomato; 2.3Col1a1-GFP mice to perform the cell lineage tracing experiments (Figure 1C). Inject tamoxifen on postnatal day 14.</li>
	<li>To combine the cell lineage tracing technique with immunofluorescence, cross Agg-CreERT2 mice and Rosa26tdTomato mice. Use mice that carry both genes in the experiment and inject the tamoxifen on postnatal day 3 (Figure 1D).</li>
</ol>
2. Material Preparation
<ol>
	<li>Dissolve the tamoxifen powder in 10% ethanol and 90% corn oil at a concentration of 10 mg/ml. The dosage for injection is 75 mg/kg.</li>
	<li>Dissolve the paraformaldehyde (PFA) powder in PBS to a concentration of 4%, using 2 M sodium hydrate to adjust the pH value to 7.4. Use 4% PFA solution to fix the tissue (the mandibular condyle and hind leg are used here) after sacrifice. Because of its toxicity, handle PFA in the hood with gloves and a facemask.</li>
	<li>Dissolve the EDTA powder in distilled water to a concentration of 10%, using 2 M sodium hydrate to adjust the pH value to 7.4. Use 10% EDTA to decalcify the mandibular condyle and hind leg.</li>
	<li>Dissolve sucrose powder in PBS at concentrations of 15% and 30%. Use the sucrose solution to dehydrate the tissue after decalcification.</li>
	<li>Dissolve the hyaluronidase powder in PBS at a concentration of 2 mg/ml, pH 5.0. This solution is for immunofluorescence antigen retrieval.</li>
	<li>Use a 1.5-ml tube to prepare a blocking solution that contains 3% bovine serum albumin (BSA) and 20% goat serum in PBS for Runx2 or DMP1 immunofluorescent staining.</li>
	<li>Use a 1.5-ml tube to prepare a primary antibody solution that contains 2% goat serum in PBS for Runx2 or DMP1 immunofluorescent staining. The concentration of the primary antibody is 1:400 for Runx2 and 1:100 for DMP1.</li>
	<li>Use a 1.5-ml tube to prepare the rabbit IgG solution as the control for immunofluorescent staining to avoid false positive results. The solution contains 2% goat serum in PBS. The concentration of the rabbit IgG for Runx2 control is 1:400; for DMP1, 1:100. Perform the experiment and control staining simultaneously.</li>
	<li>Use a 1.5 ml tube to prepare a secondary antibody solution that contains 2% goat serum in PBS for Runx2 or DMP1 immunofluorescent staining. Use the secondary antibody at a dilution of 1:500.</li>
</ol>
3. Slide Preparation for Confocal Microscopy (Cell Lineage Tracing Only, No Combination with Immunofluorescence)
<ol>
	<li>Inject tamoxifen in the Agg-creERT2 mice at a favorable time point.
	<ol>
		<li>First, remove a mouse from its cage. Then, use the left thumb and index finger to grab the skin on the back of the mouse and turn it over, exposing the abdomen. Use the right hand to hold the syringe. The optimal entry point for injection is on the left or right side of hypogastrium, avoiding the liver and bladder.</li>
		<li>Keep the syringe parallel to the hind legs of the mouse and inject intraperitoneally. The dosage for injection is 75 mg/kg. The weights of the mice at the ages of 2 weeks, 3 weeks, and 4 weeks old are approximately 7 - 9 g, 11 - 13 g, and 16 - 18 g, respectively.</li>
	</ol>
	</li>
	<li>Anesthetize the mice with a Xylazine/Ketaset combination.
	<ol>
		<li>To prepare the working solution, first dilute the Xylazine and Ketaset with distilled water to a concentration of 1 mg/ml and 5 mg/ml, respectively. Next, mix the Xylazine and Ketaset in a 1:2 ratio. The dosage for injection is 30 &#181;l/g.</li>
		<li>Inject as in step 3.1. Confirm the anesthetization by pinching the mouse&#39;s ankle. The mouse is unconscious if it has no reaction.</li>
	</ol>
	</li>
	<li>Perfuse the mice with 4% PFA after anesthetization.
	<ol>
		<li>After the mouse loses consciousness, fix the four legs of the mouse on a board to entirely expose the abdomen.</li>
		<li>Saturate the abdomen with 70% ethanol and make an excision from the lower abdomen to the neck along the middle line. Pinch and simultaneously pull the skin to the lateral sides to reveal the peritoneal membrane. Use dissection scissors to make a longitudinal excision.</li>
		<li>Cut off and remove the front ribs to expose the heart. Puncture the heart from the left ventricle with a 22 G syringe, hold the syringe, and simultaneously cut a slot in the right auricle.</li>
		<li>Slowly inject the 4% PFA, which is perfused along the cardiovascular system while the blood flushes out of the cut from the right auricle. The volume of the PFA for perfusion is 1 ml/gram. Perform this step in a Class I biosafety cabinet that is hard-ducted to the building exhaust system.&#160;</li>
	</ol>
	</li>
	<li>Peel off the mouse&#39;s skin and put the whole body into a 50-ml polypropylene centrifuge tube that contains 40 ml of 4% PFA to fix overnight at 4 &#176;C.</li>
	<li>Use dissection scissors and # 3 and # 5 forceps to carefully remove the mandible and hind leg from the body and to remove the muscles and tendons on the surface. Perform this step in a Class I biosafety cabinet&#160;that is hard-ducted to the building exhaust system.</li>
	<li>Cut the mandible into two pieces at the distal region of the third molar.&#160;Similarly, cut the femur and tibia in the midshaft to expose the bone marrow cavity in order to accelerate decalcification. Put the part that includes the condyle and condylar process and along with the hind leg into 40 ml of 10% EDTA to decalcify at 4 &#176;C for 2 - 4 days in a 50-ml polypropylene centrifuge tube.</li>
	<li>Use 50 ml of 15% sucrose to dehydrate the condyle and hind leg overnight at 4 &#176;C in a 50-ml polypropylene centrifuge tube.</li>
	<li>Use 30% sucrose to dehydrate the condyle and hind leg overnight at 4 &#176;C in a 50-ml polypropylene centrifuge tube.</li>
	<li>Along the sagittal plane, embed the sample with OCT on the cutting plate in the cryosection machine.
	<ol>
		<li>Horizontally lay the condyle or the hind leg in the mounting mold. Submerge the tissue in OCT and leave it in the cryosection machine until the OCT freezes.</li>
		<li>Mount the OCT block on the cutting plate. Wait for approximately 15 min before cutting to ensure that the OCT is completely frozen.</li>
	</ol>
	</li>
	<li>Cut the condyle and hind leg into 10-&#181;m sections. Collect the sections on slides and store at -20 &#176;C.</li>
	<li>Incubate the slide in a 37 &#176;C chamber to remove the water before staining.</li>
	<li>Wash the slides twice with distilled water for 5 min.</li>
	<li>Wipe off the water around each section. Use a hydrophobic barrier pen to circle the sections and drop DAPI or non-fluorescing anti-fade mounting solution into the circle. Carefully lay down the cover slip.</li>
</ol>
4. Immunohistochemical Staining for Runx2 and DMP1
NOTE: The IgG control is necessary for immunohistochemical staining to avoid false-positive signals. The staining for the experimental and control groups needs to be performed simultaneously.
<ol>
	<li>Incubate the slides in a 37 &#176;C chamber to remove the water before staining.</li>
	<li>Wash the slides twice with distilled water.</li>
	<li>Use the hydrophobic barrier pen to circle all the sections on the slide. From this step, add all of the prepared solution into the circle to completely cover the sections.</li>
	<li>Treat the sections with hyaluronidase in a humid chamber at 37 &#176;C for 30 min. The volume of the solution (in steps 4.5 - 4.8) depends on the size of the section. Use 50 &#181;l of solution for the condyle and 100 &#181;l for the long bone. Wash with PBST (PBS that contains 0.1% Tween 20) three times.</li>
	<li>Prepare and apply the blocking solution to each section and incubate them in a humid chamber for 1 hr at room temperature.</li>
	<li>Incubate the sections with primary antibody solution (rabbit anti-mouse Runx2, or rabbit anti-mouse DMP1) at 4 &#176;C overnight. Wash with PBS three times.</li>
	<li>Incubate the sections with secondary antibody solution (goat anti-rabbit, Alexa Fluor 488) for 2 hr at room temperature. Wash with PBS three times.</li>
	<li>Wipe off the water around the section and drop DAPI into the circle to cover the section on the slide. Carefully lay down the cover slip.</li>
</ol>
5. Confocal Microscopy
<ol>
	<li>Capture fluorescent cell images using a confocal microscope at wavelengths ranging from 488 &#181;m (green) to 561 &#181;m (red). Take multiple stacked images at 200 Hz (dimensions of 1,024 &#215; 1,024)19 using 10X, 20X, and 63X lenses.</li>
</ol>

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The authors declare that they have no competing financial interests or other conflicts of interest.

Due to technological limitations, it is always difficult to investigate the behavior of cells in vivo. However, the cell lineage tracing technique is proving to be a powerful tool for studying cell biology7-9. In this study, we further improve this protocol by combining it with immunofluorescence. In this way, cell fate can be defined by multiple related markers, which broadens the application of lineage tracing. Moreover, this co-localization of immunofluorescence and tomato signal simultaneously dis...

During development, endochondral bone formation accounts for over 80% of the skeletal volume. It is widely believed that it begins with the apoptosis of hypertrophic chondrocytes. Subsequently, the cells from the underlying bone marrow invade and initiate angiogenesis, followed by new bone deposition by bone marrow- and periosteum-derived cells1,2. The cell fate of hypertrophic chondrocytes (HCs), however, has been an issue of debate for decades3. Initially, HCs were considered to be the end of the chondrocyte differentiation pathway, and apoptosis was generally thought to be the ultimate fate of HCs. Now, some researchers suggest that at least some HCs could survive and contribute to endochondral bone formation. Although they proposed that growth plate chondrocytes had the ability to transdifferentiate into osteoblasts based on ultrastructure, immunohistochemical staining, and in vitro studies46, none of these methods were definitive in demonstrating chondrocyte contribution to the osteoblast lineage.
The cell lineage tracing technique provides a more rigorous way to study cell fate. Briefly speaking, a recombinase enzyme, which is only expressed in a specific type of cell, stimulates the expression of the reporter gene. In this way, this type of cell and their descendants are permanently labeled7. The Cre-loxP system is commonly used in lineage tracing. Cre (the recombinase enzyme) will excise the STOP sequence between the two loxP sites and activate the reporter in a specific cell line (Figure 1A). In some cases, the investigator can choose a favorable time point to activate Cre by using a drug, such as tamoxifen, causing Cre to fuse to a modified form of the estrogen receptor (CreERT2)8. Fluorescent reporters have become the standard in lineage tracing experiments because they dramatically reduce the complexity and improve the accuracy and efficiency of cell fate tracing8,9. tdTomato is becoming the best choice among fluorescent reporters since it has the brightest fluorescent protein and the strongest epifluorescence, making it easily visualized7 (Figure 1A).
By using the Rosa26tdTomato lineage tracing system, our group and other investigators have shown that HCs can change their phenotype into bone cells during development10-14. To accomplish this, we developed two sets of tracing combinations with Rosa26tdtomato (ubiquitous expression in all cells)/Cre (specific to chondrocytes) mice: 2.3Col1a1-GFP (specific to osteoblasts) and immunofluorescence (specific to bone cells). The data demonstrate that both methods are viable ways to study cell fate in vivo.

<table><tbody><tr><td>Tamoxifen&amp;nbsp;</td><td>Sigma</td><td>T5648</td><td>activate the Cre event&amp;nbsp;</td></tr><tr><td>Paraformaldehyde</td><td>Sigma&amp;nbsp;</td><td>P6148</td><td>fix the sample</td></tr><tr><td>Ethylenediaminetetraacetic acid</td><td>Alfa Aesar</td><td>A10713</td><td>decalcify the hard tissue</td></tr><tr><td>Sucrose&amp;nbsp;</td><td>Sigma</td><td>S0389</td><td>dehydrate the tissue</td></tr><tr><td>Hyaluronidase from bovine testes&amp;nbsp;</td><td>Sigma</td><td>H4272</td><td>retrieve antigen for immunochemical staining</td></tr><tr><td>Bovine serum albumin</td><td>Sigma&amp;nbsp;</td><td>A3059</td><td>blocking solution&amp;nbsp;</td></tr><tr><td>primary antibody for Runx2&amp;nbsp;</td><td>Cell Signal</td><td>D1L7F</td><td>primary antibody for immunochemical staining</td></tr><tr><td>primary antibody for DMP1</td><td>provided by Dr. Chunlin Qin</td><td></td><td>primary antibody for immunochemical staining</td></tr><tr><td>anti-rabbit IgG</td><td>Sigma</td><td>18140</td><td>control for immunochemical staining</td></tr><tr><td>secondary antibody&amp;nbsp;</td><td>Invitrogen</td><td>A11008</td><td>second antibody for immunochemical staining</td></tr><tr><td>OCT</td><td>Tissue-Tek</td><td>4583</td><td>embed the sample for frozen section</td></tr><tr><td>Tween 20</td><td>Fisher Scientific</td><td>BP337</td><td>PBST</td></tr><tr><td>non-fluorescing antifade mountant</td><td>Life technologies</td><td>P36934</td><td>mounting slides</td></tr><tr><td>DAPI</td><td>Life technologies</td><td>P36931</td><td>nuclear staining</td></tr><tr><td>Hydrophobic Barrier Pen</td><td>Vector Laboratories</td><td></td><td>circle the section on the slide for for immunochemical staining&amp;nbsp;</td></tr><tr><td>Xylazine</td><td>AnaSed</td><td></td><td>anesthetization&amp;nbsp;</td></tr><tr><td>Ketaset&amp;nbsp;</td><td>Zoetis</td><td></td><td>anesthetization&amp;nbsp;</td></tr><tr><td>cryosection machine</td><td>Leica</td><td>CM1860 UV</td><td></td></tr><tr><td>confocal microscope</td><td>Leica</td><td>DM6000 CFS&amp;nbsp;</td><td></td></tr></tbody></table>

co-localization of cell lineage markers and the tomato signal

The cell lineage tracing system has been used predominantly in developmental biology studies. The use of Cre recombinase allows for the activation of the reporter in a specific cell line and all progeny. Here, we used the cell lineage tracing technique to demonstrate that chondrocytes directly transform into osteoblasts and osteocytes during long bone and mandibular condyle development using two kinds of Cre, Col10a1-Cre and Aggrecan-CreERT2 (Agg-CreERT2), crossed with Rosa26tdTomato. Both Col10 and aggrecan are well-recognized markers for chondrocytes.
On this basis, we developed a new method-cell lineage tracing in conjunction with fluorescent immunohistochemistry-to define cell fate by analyzing the expression of specific cell markers. Runx2 (a marker for early-stage osteogenic cells) and Dentin matrix protein1 (DMP1; a marker for late-stage osteogenic cells) were used to identify chondrocyte-derived bone cells and their differentiation status. This combination not only broadens the application of cell lineage tracing, but also simplifies the generation of compound mice. More importantly, the number, location, and differentiation statuses of parent cell progeny are displayed simultaneously, providing more information than cell lineage tracing alone. In conclusion, the co-application of cell lineage tracing techniques and immunofluorescence is a powerful tool for investigating cell biology in vivo.

Chondrocytes Directly Transform into Bone Cells (Osteoblasts and Osteocytes) in the Mandibular Condyle and Long Bone.
Aggrecan, a critical gene for chondrogenesis, is mainly expressed in early and mature chondrocytes18. As a result, the injection of tamoxifen at 2 weeks of age in Agg-CreERT2; Rosa26tdTomato mice activated the red-tomato reporter in all ...

Watch this Scientific Journal Video about Co-localization of Cell Lineage Markers and the Tomato Signal at JoVE.com

Co-localization of Cell Lineage Markers and the Tomato Signal

We developed two sets of tracing combinations in Rosa26tdtomato (ubiquitously expressed in all cells)/Cre (specifically expressed in chondrocytes) mice: one with 2.3Col1a1-GFP (specific to osteoblasts) and one with immunofluorescence (specific to bone cells). The data demonstrate the direct transformation of chondrocytes into bone cells.

The cell lineage tracing system has been used predominantly in developmental biology studies. The use of Cre recombinase allows for the activation of the ...

co-localization-of-cell-lineage-markers-and-the-tomato-signal

Research

JoVE Journal

Developmental Biology

12.1K Views.  Texas A&M University College of Dentistry. We developed two sets of tracing combinations in Rosa26tdtomato (ubiquitously expressed in all cells)/Cre (specifically expressed in chondrocytes) mice: one with 2.3Col1a1-GFP (specific to osteoblasts) and one with immunofluorescence (specific to bone cells). The data demonstrate the direct transformation of chondrocytes into bone cells.

Video: Co-localization of Cell Lineage Markers and the Tomato Signal

A Method for Lineage Tracing of Corneal Cells Using Multi-color Fluorescent Reporter Mice

Lineage tracing experiments define the origin, fate and behavior of cells in a specific tissue or organism. This technique has been successfully applied for many decades, revealing seminal findings in developmental biology. More recently, it was adopted by stem cell biologists to identify and track different stem cell populations with minimal experimental intervention. The recent developments in mouse genetics, the availability of a large number of mouse strains, and the advancements in fluorescent microscopy allow the straightforward design of powerful lineage tracing systems for various tissues with basic expertise, using commercially available tools. We have recently taken advantage of this powerful methodology to explore the origin and fate of stem cells at the ocular surface using R26R-Confetti mouse. This model offers a multi-color genetic system, for the expression of 4 fluorescent genes in a random manner. Here we describe the principles of this methodology and provide an adaptable protocol for designing lineage tracing experiments; specifically for the corneal epithelium as well as for other tissues.

In this article we describe the principles for designing and performing a multi-color lineage tracing experiment using R26R-Confetti mice. We provide a specific protocol for tracking corneal epithelial cells which can be modified for other tissues of interest.

Lineage tracing experiments define the origin, fate and behavior of cells in a specific tissue or organism. This technique has been successfully applied ...

Cell Lineage Analyses and Gene Function Studies Using Twin-spot MARCM

Mosaic analysis with a repressible cell marker (MARCM) is a positive mosaic labeling system that has been widely applied in Drosophila neurobiological studies to depict intricate morphologies and to manipulate the function of genes in subsets of neurons within otherwise unmarked and unperturbed organisms. Genetic mosaics generated in the MARCM system are mediated through site-specific recombination between homologous chromosomes within dividing precursor cells to produce both marked (MARCM clones) and unmarked daughter cells during mitosis. An extension of the MARCM method, called twin-spot MARCM (tsMARCM), labels both of the twin cells derived from a common progenitor with two distinct colors. This technique was developed to enable the retrieval of useful information from both hemi-lineages. By comprehensively analyzing different pairs of tsMARCM clones, the tsMARCM system permits high-resolution neural lineage mapping to reveal the exact birth-order of the labeled neurons produced from common progenitor cells. Furthermore, the tsMARCM system also extends gene function studies by permitting the phenotypic analysis of identical neurons of different animals. Here, we describe how to apply the tsMARCM system to facilitate studies of neural development in Drosophila.

Here, we present a protocol for a mosaic labeling technique that permits the visualization of neurons derived from a common progenitor cell in two distinct colors. This facilitates neural lineage analysis with the capability of birth-dating individual neurons and studying gene function in the same neurons of different individuals.

Mosaic analysis with a repressible cell marker (MARCM) is a positive mosaic labeling system that has been widely applied in Drosophila neurobiological ...

Confocal Live Imaging of Shoot Apical Meristems from Different Plant Species

The shoot apical meristem (SAM) functions as a conserved stem cell reservoir and it generates almost all aboveground tissues during the postembryonic development. The activity and morphology of SAMs determine important agronomic traits, such as shoot architecture, size and number of reproductive organs, and most importantly, grain yield. Here, we provide a detailed protocol for analyzing both the surface morphology and the internal cellular structure of the living SAMs from different species through laser scanning confocal microscope. The whole procedure from the sample preparation to the acquisition of high resolution three-dimensional (3D) images can be accomplished within as short as 20 minutes. We demonstrate that this protocol is highly efficient for studying not only the inflorescence SAMs of the model species but also the vegetative meristems from different crops, providing a simple but powerful tool to study the organization and development of meristems across different plant species.

This protocol presents how to live image and analyze the shoot apical meristems from different plant species using laser scanning confocal microscopy.

The shoot apical meristem (SAM) functions as a conserved stem cell reservoir and it generates almost all aboveground tissues during the postembryonic ...

Visualization of IL-22-expressing Lymphocytes Using Reporter Mice

Reporter mice have been widely used to observe the localization of expression of targeted genes. This protocol focuses on a strategy to establish a new transgenic reporter mouse model. We chose to visualize interleukin (IL) 22 gene expression because this cytokine has important activities in the intestine, where it contributes to repair tissues damaged by inflammation. Reporter systems offer considerable advantages over other methods of identifying products in vivo. In the case of IL-22, other studies had first isolated cells from tissues and then re-stimulated the cells in vitro. IL-22, which is normally secreted, was trapped inside cells using a drug, and intracellular staining was used to visualize it. This method identifies cells capable of producing IL-22, but it does not determine whether they were doing so in vivo. The reporter design includes inserting a gene for a fluorescent protein (tdTomato) into the IL-22 gene in such a way that the fluorescent protein cannot be secreted and therefore remains trapped inside the producing cells in vivo. Fluorescent producers can then be visualized in tissue sections or by ex vivo analysis through flow cytometry. The actual construction process for the reporter included recombineering a bacterial artificial chromosome that contained the IL-22 gene. This engineered chromosome was then introduced into the mouse genome. Homeostatic IL-22 reporter expression was observed in different mouse tissues, including the spleen, thymus, lymph nodes, Peyer&#39;s patch, and intestine, by flow cytometry analysis. Colitis was induced by T-cell (CD4+CD45RBhigh) transfer, and reporter expression was visualized. Positive T cells were first present in the mesenteric lymph nodes, and then they accumulated inside the lamina propria of the distal small intestine and colon tissues. The strategy using BACs gave good-fidelity reporter expression compared to IL-22 expression, and it is simpler than knock-in procedures.

We describe here a transgenic reporter mouse model to visualize the IL-22-producing cells inside different mouse tissues. This method can be used to track the location of other cytokines or secretary proteins in the mouse.

Reporter mice have been widely used to observe the localization of expression of targeted genes. This protocol focuses on a strategy to establish a new ...

Immunology and Infection

Identification of Plasmodesmal Localization Sequences in Proteins In Planta

Plasmodesmata (Pd) are cell-to-cell connections that function as gateways through which small and large molecules are transported between plant cells. Whereas Pd transport of small molecules, such as ions and water, is presumed to occur passively, cell-to-cell transport of biological macromolecules, such proteins, most likely occurs via an active mechanism that involves specific targeting signals on the transported molecule. The scarcity of identified plasmodesmata (Pd) localization signals (PLSs) has severely restricted the understanding of protein-sorting pathways involved in plant cell-to-cell macromolecular transport and communication. From a wealth of plant endogenous and viral proteins known to traffic through Pd, only three PLSs have been reported to date, all of them from endogenous plant proteins. Thus, it is important to develop a reliable and systematic experimental strategy to identify a functional PLS sequence, that is both necessary and sufficient for Pd targeting, directly in the living plant cells. Here, we describe one such strategy using as a paradigm the cell-to-cell movement protein (MP) of the Tobacco mosaic virus (TMV). These experiments, that identified and characterized the first plant viral PLS, can be adapted for discovery of PLS sequences in most Pd-targeted proteins.

Identification of Plasmodesmal Localization Sequences in Proteins In Planta

Plant intercellular connections, the plasmodesmata (Pd), play central roles in plant physiology and plant-virus interactions. Critical to Pd transport are sorting signals that direct proteins to Pd. However, our knowledge about these sequences is still in its infancy. We describe a strategy to identify Pd localization signals in Pd-targeted proteins.

Plasmodesmata (Pd) are cell-to-cell connections that function as gateways through which small and large molecules are transported between plant cells. ...

In Situ Hybridization for the Precise Localization of Transcripts in Plants

With the advances in genomics research of the past decade, plant biology has seen numerous studies presenting large-scale quantitative analyses of gene expression. Microarray and next generation sequencing approaches are being used to investigate developmental, physiological and stress response processes, dissect epigenetic and small RNA pathways, and build large gene regulatory networks1-3. While these techniques facilitate the simultaneous analysis of large gene sets, they typically provide a very limited spatiotemporal resolution of gene expression changes. This limitation can be partially overcome by using either profiling method in conjunction with lasermicrodissection or fluorescence-activated cell sorting4-7. However, to fully understand the biological role of a gene, knowledge of its spatiotemporal pattern of expression at a cellular resolution is essential. Particularly, when studying development or the effects of environmental stimuli and mutants can the detailed analysis of a gene's expression pattern become essential. For instance, subtle quantitative differences in the expression levels of key regulatory genes can lead to dramatic phenotypes when associated with the loss or gain of expression in specific cell types. 
Several methods are routinely used for the detailed examination of gene expression patterns. One is through analysis of transgenic reporter lines. Such analysis can, however, become time-consuming when analyzing multiple genes or working in plants recalcitrant to transformation. Moreover, an independent validation to ensure that the transgene expression pattern mimics that of the endogenous gene is typically required. Immunohistochemical protein localization or mRNA in situ hybridization present relatively fast alternatives for the direct visualization of gene expression within cells and tissues. The latter has the distinct advantage that it can be readily used on any gene of interest. In situ hybridization allows detection of target mRNAs in cells by hybridization with a labeled anti-sense RNA probe obtained by in vitro transcription of the gene of interest. 
Here we outline a protocol for the in situ localization of gene expression in plants that is highly sensitivity and specific. It is optimized for use with paraformaldehyde fixed, paraffin-embedded sections, which give excellent preservation of histology, and DIG-labeled probes that are visualized by immuno-detection and alkaline-phosphatase colorimetric reaction. This protocol has been successfully applied to a number of tissues from a wide range of plant species, and can be used to analyze expression of mRNAs as well as small RNAs8-14.

In Situ Hybridization for the Precise Localization of Transcripts in Plants

The in situ hybridization protocol described here allows a direct localization of mRNA and small RNA expression at the cellular level with high sensitivity and specificity. The procedure is optimized for paraffin-embedded plant tissue sections, is applicable to a wide range of plants and tissues, and can be completed within ten days.

With the advances in genomics research of the past decade, plant biology has seen numerous studies presenting large-scale quantitative analyses of gene ...

Biology

Cell Specific Analysis of Arabidopsis Leaves Using Fluorescence Activated Cell Sorting

After initiation of the leaf primordium, biomass accumulation is controlled mainly by cell proliferation and expansion in the leaves1. However, the Arabidopsis leaf is a complex organ made up of many different cell types and several structures. At the same time, the growing leaf contains cells at different stages of development, with the cells furthest from the petiole being the first to stop expanding and undergo senescence1. Different cells within the leaf are therefore dividing, elongating or differentiating; active, stressed or dead; and/or responding to stimuli in sub-sets of their cellular type at any one time. This makes genomic study of the leaf challenging: for example when analyzing expression data from whole leaves, signals from genetic networks operating in distinct cellular response zones or cell types will be confounded, resulting in an inaccurate profile being generated.
To address this, several methods have been described which enable studies of cell specific gene expression. These include laser-capture microdissection (LCM)2 or GFP expressing plants used for protoplast generation and subsequent fluorescence activated cell sorting (FACS)3,4, the recently described INTACT system for nuclear precipitation5 and immunoprecipitation of polysomes6.
FACS has been successfully used for a number of studies, including showing that the cell identity and distance from the root tip had a significant effect on the expression profiles of a large number of genes3,7. FACS of GFP lines have also been used to demonstrate cell-specific transcriptional regulation during root nitrogen responses and lateral root development8, salt stress9 auxin distribution in the root10 and to create a gene expression map of the Arabidopsis shoot apical meristem11. Although FACS has previously been used to sort Arabidopsis leaf derived protoplasts based on autofluorescence12,13, so far the use of FACS on Arabidopsis lines expressing GFP in the leaves has been very limited4. In the following protocol we describe a method for obtaining Arabidopsis leaf protoplasts that are compatible with FACS while minimizing the impact of the protoplast generation regime. We demonstrate the method using the KC464 Arabidopsis line, which express GFP in the adaxial epidermis14, the KC274 line, which express GFP in the vascular tissue14 and the TP382 Arabidopsis line, which express a double GFP construct linked to a nuclear localization signal in the guard cells (data not shown; Figure 2). We are currently using this method to study both cell-type specific expression during development and stress, as well as heterogeneous cell populations at various stages of senescence.

Cell Specific Analysis of Arabidopsis Leaves Using Fluorescence Activated Cell Sorting

A method for producing Arabidopsis leaf protoplasts that are compatible with fluorescence activated cell sorting (FACS), allowing for studies of specific cell populations. This method is compatible with any Arabidopsis line that expresses GFP in a subset of cells.

After initiation of the leaf primordium, biomass accumulation is controlled mainly by cell proliferation and expansion in the leaves1. However, the ...

Lineage Tracing of Inducible Fluorescently-Labeled Stem Cells in the Adult Mouse Brain

A telomerase reverse transcriptase (Tert) lineage-tracing mouse line was developed to investigate the behavior and fate of adult tissue stem cells, by crossing the &#39;Tet-On&#39; system oTet-Cre mouse with a novel reverse tetracycline transactivator (rtTA) transgene linked to the Tert promoter, which we have demonstrated marks a novel population of adult brain stem cells. Here, administration of the tetracycline derivative doxycycline to mTert-rtTA::oTet-Cre mice will indelibly mark a population of cells that express a 4.4 kb fragment of the promoter region of the gene Tert. When combined the Rosa-mTmG reporter, mTert-rtTA::oTet-Cre::Rosa-mTmG mice will express membrane tdTomato (mTomato) until doxycycline treatment induces the replacement of mTomato expression with membrane EGFP (mGFP) in cells that also express Tert. Therefore, when these triple-transgenic lineage tracing mice receive doxycycline (the &#34;pulse&#34; period during which TERT expressing cells are marked), these cells will become indelibly marked mGFP+ cells, which can be tracked for any desirable amount of time after doxycycline removal (the &#34;chase&#34; period), even if Tert expression is subsequently lost. Brains are then perfusion-fixed and processed for immunofluorescence and other downstream applications in order to interpret changes to stem cell activation, proliferation, lineage commitment, migration to various brain niches, and differentiation to mature cell types. Using this system, any rtTA mouse can be mated to oTet-Cre and a Rosa reporter to conduct doxycycline-inducible &#34;pulse-chase&#34; lineage&#160;tracing experiments using markers of stem cells.

The ability to permanently mark stem cells and their progeny with a fluorophore using an inducible transgenic lineage tracing mouse line allows for spatial and temporal analysis of activation, proliferation, migration, and/or differentiation in vivo. Lineage tracing can reveal novel information about lineage commitment, response to intervention(s), and multipotency.

A telomerase reverse transcriptase (Tert) lineage-tracing mouse line was developed to investigate the behavior and fate of adult tissue stem cells, by ...

Neuroscience

Imaging Spatial Reorganization of a MAPK Signaling Pathway Using the Tobacco Transient Expression System

Visualization of dynamic signaling events in live cells has been a challenge. We expanded an established transient expression system, the biomolecular fluorescent complementation (BiFC) assay in tobacco epidermal cells, from testing protein-protein interaction to monitoring spatial distribution of signal transduction in plant cells. In this protocol, we used the BiFC assay to show that the interaction and the signaling between the Arabidopsis MAPKKK YODA and MAPK6 occur at the plasma membrane. When the scaffold protein BASL was co-expressed, the YODA-MAPK interaction redistributed and spatially co-polarized with CFP-BASL. This modified tobacco expression system allows for quick examination of signaling localization and dynamic changes (less than 4 days) and can accommodate multiple of fluorescent protein colors (at least three). We also presented detailed methods to quantify protein distribution (asymmetric spatial localization, or &#34;polarization&#34;) in tobacco cells. This advanced tobacco expression system has a potential to be used widely for quick testing of dynamic signaling events in live plant cells.

At the subcellular level, signaling events are dynamically modulated by developmental and environmental cues. Here we describe a protocol that employs the tobacco transient expression system to monitor dynamic protein-protein interaction and to disclose spatial organization of signal transduction in plant cells.

Visualization of dynamic signaling events in live cells has been a challenge. We expanded an established transient expression system, the biomolecular ...

Lineage Tracing and Clonal Analysis in Developing Cerebral Cortex Using Mosaic Analysis with Double Markers (MADM)

Beginning from a limited pool of progenitors, the mammalian cerebral cortex forms highly organized functional neural circuits. However, the underlying cellular and molecular mechanisms regulating lineage transitions of neural stem cells (NSCs) and eventual production of neurons and glia in the developing neuroepithelium remains unclear. Methods to trace NSC division patterns and map the lineage of clonally related cells have advanced dramatically. However, many contemporary lineage tracing techniques suffer from the lack of cellular resolution of progeny cell fate, which is essential for deciphering progenitor cell division patterns. Presented is a protocol using mosaic analysis with double markers (MADM) to perform in vivo clonal analysis. MADM concomitantly manipulates individual progenitor cells and visualizes precise division patterns and lineage progression at unprecedented single cell resolution. MADM-based interchromosomal recombination events during the G2-X phase of mitosis, together with temporally inducible CreERT2, provide exact information on the birth dates of clones and their division patterns. Thus, MADM lineage tracing provides unprecedented qualitative and quantitative optical readouts of the proliferation mode of stem cell progenitors at the single cell level. MADM also allows for examination of the mechanisms and functional requirements of candidate genes in NSC lineage progression. This method is unique in that comparative analysis of control and mutant subclones can be performed in the same tissue environment in vivo. Here, the protocol is described in detail, and experimental paradigms to employ MADM for clonal analysis and lineage tracing in the developing cerebral cortex are demonstrated. Importantly, this protocol can be adapted to perform MADM clonal analysis in any murine stem cell niche, as long as the CreERT2 driver is present.

Lineage Tracing and Clonal Analysis in Developing Cerebral Cortex Using Mosaic Analysis with Double Markers MADM

A protocol to perform lineage tracing and functional genetic analysis of candidate genes at a single cell level using mosaic analysis with double markers (MADM) is presented. MADM clonal analysis provides a quantitative framework to measure the proliferative behavior, cellular output, and lineage relationship of individual progenitors and their daughter cells.

Beginning from a limited pool of progenitors, the mammalian cerebral cortex forms highly organized functional neural circuits. However, the underlying ...

Co-localization of Cell Lineage Markers and the Tomato Signal

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A Method for Lineage Tracing of Corneal Cells Using Multi-color Fluorescent Reporter Mice

Cell Lineage Analyses and Gene Function Studies Using Twin-spot MARCM

Confocal Live Imaging of Shoot Apical Meristems from Different Plant Species

Visualization of IL-22-expressing Lymphocytes Using Reporter Mice

Identification of Plasmodesmal Localization Sequences in Proteins In Planta

In Situ Hybridization for the Precise Localization of Transcripts in Plants

Cell Specific Analysis of Arabidopsis Leaves Using Fluorescence Activated Cell Sorting

Lineage Tracing of Inducible Fluorescently-Labeled Stem Cells in the Adult Mouse Brain

Imaging Spatial Reorganization of a MAPK Signaling Pathway Using the Tobacco Transient Expression System

Lineage Tracing and Clonal Analysis in Developing Cerebral Cortex Using Mosaic Analysis with Double Markers (MADM)