This work was supported by a grant from CIHR (MOP394808) and a Canada Research Chair to C.M.C. E.W.O. was the recipient of a Post-Graduate Scholarship from NSERC.

Note: This protocol is broadly compatible with various monolayer-plated cell/tissue culture models, drug treatment regimens, and labelling targets. Thus in actual use, many specific parameters will vary based on experimental design. Here, references to these user-defined parameters are generic. Example conditions, as used to obtain the representative results, are included in italics.
1. Solutions
<ol>
	<li>Prepare washing buffer by mixing 0.1M Tris-Buffered Hypertonic (300 mM) Saline and 0.05% Polysorbate 20; pH 7.4 at RT.</li>
	<li>Prepare blocking buffer. To 0.05 M Tris-Buffered Hypertonic (300 mM) Saline add 0.05% Polysorbate 20, 3% Bovine Serum Albumin (BSA) and 0.1% cold fish skin gelatin and adjust the pH to 7.4 at RT.</li>
	<li>Prepare antibody diluent by adding 0.05% Polysorbate 20, 1% BSA, 0.1% cold fish skin gelatin to 0.05 M Tris-Buffered Hypertonic (300 mM) Saline and adjust the pH to 7.4 at 4 oC. &#160; 
	Note: The pH of Tris buffers is temperature-dependent. That is, a change in temperature will change the pH of the solution. For consistency, these buffers should always be pH-adjusted at the temperature at which they will be used.</li>
</ol>
2. Cell Culture
Note: Appropriate cell culture protocols will vary based on cell type(s) used. These procedures must be separately optimized. Detailed cell culture methodologies are readily available, including16. A similar procedure was used to obtain the representative results, with the notable differences:
<ol>
	<li>Culture dorsal root ganglia neurons from adult animals as described 12. Use adult-neuron growth medium to culture the cells. Reduce the glial cell density by preplating, rather than glutamate. This results in a mixed neuron-glial culture grown on 12-round glass coverslips with at least 30-60 neurons per plate and accompanying glial cells grown to approximately 40% confluency. It should be noted that neurons in a primary culture will not replicate and will be pushed off of the plate by co-cultured glia if the glia are allowed to grow excessively. In order to avoid affecting the neurons, physical reduction of glial numbers is preferable to chemical/pharmacological methods. 
	Note: For the purposes of this protocol, we assume that the cells of interest are grown to their experimentally-desired state and monolayer-plated. We find that plating on 12-round glass coverslips in 24 well plates to be most convenient. All volumes and procedures described are appropriate for one coverslip in one well of a 24 well plate.</li>
</ol>
3. Drug Treatment of Cultured Cells
Note: Multiple sequential, or overlapping, drug treatments are possible. The drugs, doses/concentrations, and durations of exposure used will depend on the specific experiment.
<ol>
	<li>Remove the original growth medium16 and replace it with medium containing the drug(s) of interest at the chosen concentration(s). In this case, use 10 &#181;M of Morphine solubilized in saline or use saline as control. 
	Note: It is important that each independent replicate (generally a single 24-well plate culture) contain the same common control condition. This will permit normalization of data across replicates, which corrects for inter-trial variability.</li>
	<li>Incubate the cells in the original growth conditions16&#160;for 48 hr.</li>
	<li>For subsequent drug treatments, repeat steps 3.1 and 3.2 with Deltorphin 1 &#181;M, SNC80 1 &#181;M, or vehicle and incubate for 60 min12. Solubilize deltorphin II in water and solubilize SNC80 at 10 mM in 40 &#181;M HCl and sonicate, diluted to 1 mM in water. 
	Note: This protocol assumes the drug(s) have been solubilized such that they may be dissolved at the desired concentration(s) in the chosen growth medium. Appropriate procedures for such solubilization will vary depending on the drug in question and must be separately optimized.</li>
	<li>Wash the cells gently, three times, with ~ 1 ml of washing buffer per wash. Perform each wash by gently aspirating the liquid from the well, then promptly, and gently, refilling the well with fresh solution, as desired (in this case with washing buffer).</li>
</ol>
4. Fixation and Immunocytochemistry
Note:The specific labeling targets will vary by experiment.&#160;In our use, we labeled delta opioid receptors (DOR) and Rab5, Rab 11, and LAMP1, as discussed. The specific antibodies used will depend on the specific experiment. Optimum labeling conditions are dependent on the specific antibody(ies) used. A much fuller discussion of this topic is below.
<ol>
	<li>Fix the cells by immersion in ~ 300 &#181;l 4% paraformaldehyde in 0.1 M phosphate buffered saline for 10 min at 37 &#186;C. 
	Note: It is important that the 4% paraformaldehyde be freshly prepared due to the autofluorescence caused by the use of previously-frozen paraformaldehyde.</li>
	<li>Wash the cells gently, 3 times, with ~ 1 ml of washing buffer per wash, as described in 3.3.</li>
	<li>Incubate the cells in 300 &#181;l blocking buffer for 2 hr at RT.</li>
	<li>Incubate the cells with primary antibodies in 300 &#181;l of antibody diluent for 48 hr at 4 &#186;C. In our use, primary antibodies against DOR (rabbit anti-DOR) and one of: Rab5 (mouse anti-Rab5), Rab 11 (mouse anti-Rab11), and LAMP1 (goat anti-LAMP1).</li>
	<li>Wash the cells gently, three times, with ~ 1 ml of washing buffer per wash, as described in 3.3.</li>
	<li>Incubate the cells with secondary antibodies conjugated to different fluorophores (see discussion below) in 300 &#181;l of antibody diluent for 1 hr at RT. In this, and all subsequent steps, protect the cells from light. To obtain the representative results, use green-emitting fluorophore-conjugated anti-rabbit and either a red-emitting fluorophore-conjugated anti-mouse or red-emitting fluorophore-conjugated anti-goat.</li>
	<li>Wash the cells gently, 3 times, with ~ 1 ml of washing buffer per wash, as described in 3.3.</li>
	<li>Remove the 12-round coverslips from 24 well plates by leaving &#160;~ 1 ml of washing buffer in each well, holding the plate at ~ 45&#186;, and lever the coverslip off of the well floor using fine forceps. The coverslip will come to rest against the well wall, from where it can easily be removed using the forceps.</li>
	<li>Mount the coverslips, cell-side-down, on microscope slides with anti-fading mounting medium.</li>
</ol>
5. Microscope Settings
<ol>
	<li>Using a high magnification objective (100X), first locate a representative cell to be imaged using epifluorescence.</li>
	<li>Configure the image capture settings to record 8-bit uncompressed TIFF images of each labeled channel (for detection of each fluorophore used e.g., 488 nm and 594 nm), to image each channel sequentially (either by line or frame), and to average 4 to 6 scans for the final image. Optimal image resolution will be microscope-specific, but 1024 x 1024 typically yields good results.</li>
	<li>Switch to the confocal imaging path and focus to a z-plane through the center of the cell.</li>
	<li>Optimize pinhole (typically 1 Airy unit), laser power, and photomultiplier tube voltage (gain) and offset for each channel. Save/record these settings. Use the same microscope settings for imaging all the cells labelled for any given target pair in the same replicate. 
	Note: This process will usually result in sufficient photobleaching that this cell should not be imaged for analysis.</li>
</ol>
6. Imaging
<ol>
	<li>Using a high magnification objective (e.g., 100X), first locate a cell to be imaged using epifluorescence.</li>
	<li>Switch to the confocal imaging path and focus to a z-plane through the center of the cell. If available, use software zoom/crop to restrict the scan area to the cell of interest.</li>
	<li>Capture images for each labelled channel using the settings previously established. Repeat steps 6.1 to 6.3 to image 15 or more cells per condition per replicate to ensure a sufficient sample.</li>
</ol>
7. Colocalization Analysis
<ol>
	<li>Open the pair of images (e.g., &#8216;green&#8217; and &#8216;red&#8217;) of a cell in ImageJ. Use the Image &#62; Color &#62; Merge Channels&#8230; command to generate an RGB image.</li>
	<li>Draw a selection around the cell of interest. Use the ImageJ plugin &#8220;PSC Colocalization&#8221; (11; available from&#160;https://www.cpib.ac.uk/tools-resources/software/psc-colocalization-plugin/) to quantify colocalization of the targets in the selected cell.</li>
	<li>Record the desired colocalization measure (typically Pearson&#8217;s r&#160;17). Repeat steps 7.1 to 7.3 for each imaged cell.</li>
</ol>
8. Data Normalization
<ol>
	<li>Calculate the mean of the recorded colocalization values of the common control conditions of each replicate of each labeling condition. &#160; 
	Note: For example, the mean of the colocalization values of neurons in the &#8220;48-hr vehicle, 60-min vehicle&#8221; drug condition in each of 3 independent replicates in each of 3 labeling conditions (receptor and each of 3 compartments).</li>
	<li>Multiply the means by (-1) to yield the offset for each replicate in each labeling condition. Add the offset for each replicate in each labelling condition to each colocalization value in that replicate. 
	Note: This will normalize the data such that the mean colocalization measure for the common control condition is 0 in each replicate of each labeling condition.</li>
	<li>Pool the data from all replicates of each labeling condition. 
	Note: Changes in colocalization can now be analyzed across replicates. Statistical analysis&#160;will depend upon experimental design but will typically involve analysis-of-variance (ANOVA) followed by appropriate post-hoc tests (e.g., Tukey). For statistical resources, see e.g.,&#160;18.</li>
</ol>

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N., von Zastrow, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Role+of+ubiquitination+in+endocytic+trafficking+of+G-protein-coupled+receptors.">Role of ubiquitination in endocytic trafficking of G-protein-coupled receptors.</a> Traffic. 12 (2), 137-148 (2011).</li><li>Nagi, K., Pi&#241;eyro, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Regulation+of+opioid+receptor+signalling:+implications+for+the+development+of+analgesic+tolerance.">Regulation of opioid receptor signalling: implications for the development of analgesic tolerance.</a> Mol. Brain. 4 (1), 25 (2011).</li><li>Whistler, J. L., Enquist, J., 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=Modulation+of+postendocytic+sorting+of+G+protein-coupled+receptors.">Modulation of postendocytic sorting of G protein-coupled receptors.</a> Science. 297 (5581), 615-620 (2002).</li><li>Von Zastrow, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Regulation+of+opioid+receptors+by+endocytic+membrane+traffic:+mechanisms+and+translational+implications.">Regulation of opioid receptors by endocytic membrane traffic: mechanisms and translational implications.</a> Drug Alcohol Depend. 108 (3), 166-171 (2010).</li><li>Milan-Lobo, L., Whistler, J. 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Pharmacol. 172 (2), 615-629 (2014).</li><li>Schnell, U., Dijk, F., Sjollema, K. a. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Immunolabeling+artifacts+and+the+need+for+live-cell+imaging.">Immunolabeling artifacts and the need for live-cell imaging.</a> Nature Methods. 9 (2), 152-158 (2012).</li><li>Rozenfeld, R., Gupta, A., Devi, L. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cell+surface+targeting+of+mu-delta+opioid+receptor+heterodimers+by+RTP4.">Cell surface targeting of mu-delta opioid receptor heterodimers by RTP4.</a> Proc. Natl. Acad. 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The authors have nothing to disclose.

We have optimized this protocol for the analysis of primary cultures of adult dorsal root ganglion neurons (primary sensory neurons). It can also be used, with little or no modification, for monolayer-plated cultured cells broadly. The colocalizational analysis is also possible in tissue slices and other such preparations11, however the drug treatment and tissue fixation/preparation components would not be appropriate.
Of interest, the ICC methods presented here can also be used, wi...

Receptors, especially G protein coupled receptors (GPCRs), are routinely trafficked intracellularly, to and from the cell surface1. These complexly orchestrated and tightly controlled processes dictate cells&#8217; available receptor complements and regulate receptor temporal activity, desensitization, and resensitization2&#8211;4. Importantly, these processes are responsive to cellular environments including drug-induced receptor activity or inactivity. That is, the actions of ligands at receptors can alter intracellular trafficking of those receptors, thereby altering cell responsiveness. In this manner, external ligands exert yet more effects upon cell function, even beyond classical messenger-to-effector cascades5,6.
Examining such changes in induced receptor trafficking is difficult. All available techniques involve limitations. Biotin protection assays have been used to monitor surface receptors populations. These receptors are biotinylated and a timecourse of immunoprecipitations is performed to quantify the reduction in biotinylated receptors over time. This technique essentially monitors the gradual degradation of an initial, labeled, population of receptors7, and is very useful in constructing time courses of this process. Unfortunately, this assay is unable to monitor any process other than degradation of the original pool of receptors, such as internalization, recycling, or new receptors. Also, the addition of an antibody in the 150kDa range to a receptor in the 50kDa range can alter the receptor&#8217;s trafficking8,9, and this technique may be difficult to use with low expression-level receptors.
Other procedures use various methods to identify intracellular trafficking compartments (e.g., endosomes, etc.) and assess their colocalization with the receptors of interest. This includes the use of heterologous systems expressing fluorescent-protein-tagged chimeric constructs of the receptors and compartment markers (e.g., Rab-family GTPases). This potentially enables the use of live-cell imaging, removing issues related to fixation and permeabilization. While powerful, such a strategy suffers from the same limitations of heterologous systems in general: tag and expression level effects on trafficking behavior and incompatibility with more physiologically representative cell types. More popularly, dyes are used to easily label intracellular compartments (e.g., lysosomes, ostensibly)10. Dyes, however, can lack specificity (all acidic organelles in the case of dyes for lysosomes) and do not assess trafficking through other compartments. Still, these techniques allow considerable control over the system and experimental conditions and may benefit from the colocalization analysis methods presented here, below.
The method we present here refines the tracking of receptor trafficking by colocalization. Using immunocytochemistry (ICC) to label appropriate markers, it is possible to identify multiple distinct intracellular compartments. This also allows the use of physiologically-relevant primary cell cultures in place of heterologous systems. This ICC protocol involves fixing the cells of interest prior to labeling; this permits labeling at a specific timepoint following drug treatment(s). This produces a &#8216;snapshot&#8217; of global receptor-compartment associations at that timepoint. With multiple timepoints, a timecourse of trafficking changes can also be constructed.
Briefly, cells are drug-treated, labeled for the receptor and intracellular compartment of interest, confocally imaged, and the photomicrographs are analyzed to mathematically quantify colocalization of the receptor and compartment11. In our use, we examined the colocalization of a receptor with Rab5, Rab11, and Lysosomal-associated membrane protein 1 (LAMP1). These markers identify early endosomes, recycling endosomes, and lysosomes, respectively. These colocalization measures act as proxies for the overarching processes of internalization, recycling, and degradation12.
As with all techniques, some limitations should be considered. Due to the need to image every individual neuron analyzed, this technique can become quite labor-intensive depending on the number of conditions and timepoints involved. All immunolabeling must also contend with the effects on cellular ultrastructure, protein localization, and epitope accessibility caused by fixation and permeabilization13.
Though originally optimized for use with primary cultures of primary sensory neurons, this method is broadly compatible with other monolayer-plated culture models.
The use of a mathematically quantified measure of colocalization is, notably, far more methodologically rigorous than previous techniques used to assess receptor trafficking changes, which have often relied on vague, subjective measures such as visually-inspected multi-channel overlays14.
This technique is particularly useful for its broad compatibility with in vivo interventions (prior to primary culture generation), in vitro interventions (during culture growth), and various labeling targets15. As such, it may be adapted to many different research questions.

<table border="0" cellpadding="0" cellspacing="0">
	<tbody>
		<tr>
			<td>Trizma Base</td>
			<td>Sigma Aldrich</td>
			<td>T1503-500G</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium Chloride</td>
			<td>Sigma Aldrich</td>
			<td>S9888-500G</td>
			<td></td>
		</tr>
		<tr>
			<td>Tween 20</td>
			<td>Fisher Scientific</td>
			<td>BP337-500</td>
			<td></td>
		</tr>
		<tr>
			<td>Hydrochloric Acid</td>
			<td>Sigma Aldrich</td>
			<td align="right">258148</td>
			<td></td>
		</tr>
		<tr>
			<td>Albumin from Bovine Serum</td>
			<td>Sigma Aldrich</td>
			<td>A7906-100G</td>
			<td></td>
		</tr>
		<tr>
			<td>Gelatin from cold water fish skin</td>
			<td>Sigma Aldrich</td>
			<td>G7041-100G</td>
			<td></td>
		</tr>
		<tr>
			<td>Corning Costar Cell Culture Plates: 24-well</td>
			<td>Fisher Scientific</td>
			<td align="right">720084</td>
			<td></td>
		</tr>
		<tr>
			<td>12 circle Microscope Cover Glass</td>
			<td>Fisher Scientific</td>
			<td align="right">1254580</td>
			<td></td>
		</tr>
		<tr>
			<td>Aqua/Poly-Mount</td>
			<td>Polysciences</td>
			<td>18606-20</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium Phosphate Monobasic</td>
			<td>Sigma Aldrich</td>
			<td>S9638-500G</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium Phosphate Dibasic</td>
			<td>Sigma Aldrich</td>
			<td>S9763-500G</td>
			<td></td>
		</tr>
		<tr>
			<td>Paraformaldehyde</td>
			<td>Polysciences</td>
			<td>00380-1</td>
			<td></td>
		</tr>
		<tr>
			<td>Dumont #5 Forceps - Standard/Dumoxel</td>
			<td>Fine Science Tools</td>
			<td>11251-30</td>
			<td></td>
		</tr>
		<tr>
			<td>Rabbit anti-DOR antibody</td>
			<td>MyBioSource</td>
			<td>MBS316175</td>
			<td>Used at 1:1500</td>
		</tr>
		<tr>
			<td>Mouse anti-Rab5 antibody</td>
			<td>Sigma Aldrich</td>
			<td>R7904</td>
			<td>Used at 1:750</td>
		</tr>
		<tr>
			<td>Mouse anti-Rab11 antibody</td>
			<td>Millipore</td>
			<td>05-853</td>
			<td>Used at 1:500</td>
		</tr>
		<tr>
			<td>Goat anti-LAMP1 antibody</td>
			<td>Santa Cruz</td>
			<td>SC8098</td>
			<td>Used at 1:750</td>
		</tr>
		<tr>
			<td>Donkey anti-rabbit Alexa 488 conjugated antibody</td>
			<td>Life Technologies</td>
			<td>A-21206</td>
			<td>Used at 1:200 to 1:2000</td>
		</tr>
		<tr>
			<td>Goat anti-mouse Alexa 594 conjugated antibody</td>
			<td>Life Technologies</td>
			<td>A-11005</td>
			<td>Used at 1:200 to 1:2000</td>
		</tr>
		<tr>
			<td>Donkey anti-goat Alexa 594 conjugated antibody</td>
			<td>Life Technologies</td>
			<td>A-11058</td>
			<td>Used at 1:200 to 1:2000</td>
		</tr>
	</tbody>
</table>

tracking drug-induced changes in receptor post-internalization trafficking by colocalizational analysis

The intracellular trafficking of receptors is a collection of complex and highly controlled processes. Receptor trafficking modulates signaling and overall cell responsiveness to ligands and is, itself, influenced by intra- and extracellular conditions, including ligand-induced signaling. Optimized for use with monolayer-plated cultured cells, but extendable to free-floating tissue slices, this protocol uses immunolabelling and colocalizational analysis to track changes in intracellular receptor trafficking following both chronic/prolonged and acute interventions, including exogenous drug treatment. After drug treatment, cells are double-immunolabelled for the receptor and for markers for the intracellular compartments of interest. Sequential confocal microscopy is then used to capture two-channel photomicrographs of individual cells, which are subjected to computerized colocalizational analysis to yield quantitative colocalization scores. These scores are normalized to permit pooling of independent replicates prior to statistical analysis. Representative photomicrographs may also be processed to generate illustrative figures. Here, we describe a powerful and flexible technique for quantitatively assessing induced receptor trafficking.

Using this technique, it is possible to quantify changes in receptor post-internalization trafficking following both chronic/prolonged and acute drug treatments. After drug treatments, fixation, and labeling, high-resolution two-channel photomicrographs are captured of each cell of interest. Representative images may be combined with false-color colocalization to generate illustrative figures (Figure 1). Subsequent colocalizational analysis, as described, yield quantitative scores of target-target coloca...

Watch this Scientific Journal Video about Tracking Drug-induced Changes in Receptor Post-internalization Trafficking by Colocalizational Analysis at JoVE.com

Tracking Drug-induced Changes in Receptor Post-internalization Trafficking by Colocalizational Analysis

Receptor trafficking modulates signaling and cell responsiveness to ligands and is, itself, responsive to cell conditions, including ligand-induced signaling. Here, we describe a powerful and flexible technique for quantitatively assessing drug-induced receptor trafficking using immunolabeling and colocalizational analysis.

The intracellular trafficking of receptors is a collection of complex and highly controlled processes. Receptor trafficking modulates signaling and ...

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8.7K Views.  University of California Irvine. Receptor trafficking modulates signaling and cell responsiveness to ligands and is, itself, responsive to cell conditions, including ligand-induced signaling. Here, we describe a powerful and flexible technique for quantitatively assessing drug-induced receptor trafficking using immunolabeling and colocalizational analysis.

Video: Tracking Drug-induced Changes in Receptor Post-internalization Trafficking by Colocalizational Analysis

Tracking Dynamics of Muscle Engraftment in Small Animals by In Vivo Fluorescent Imaging

Muscular dystrophies are a group of degenerative muscle diseases characterized by progressive loss of contractile muscle cells. Currently, there is no curative treatment available. Recent advances in stem cell biology have generated new hopes for the development of effective cell based therapies to treat these diseases. Transplantation of various types of stem cells labeled with fluorescent proteins into muscles of dystrophic animal models has been used broadly in the field. A non-invasive technique with the capability to track the transplanted cell fate longitudinally can further our ability to evaluate muscle engraftment by transplanted cells more accurately and efficiently.
In the present study, we demonstrate that in vivo fluorescence imaging is a sensitive and reliable method for tracking transplanted GFP (Green Fluorescent Protein)-labeled cells in mouse skeletal muscles. Despite the concern about background due to the use of an external light necessary for excitation of fluorescent protein, we found that by using either nude mouse or eliminating hair with hair removal reagents much of this problem is eliminated. Using a CCD camera, the fluorescent signal can be detected in the tibialis anterior (TA) muscle after injection of 5 x 105 cells from either GFP transgenic mice or eGFP transduced myoblast culture. For more superficial muscles such as the extensor digitorum longus (EDL), injection of fewer cells produces a detectable signal. Signal intensity can be measured and quantified as the number of emitted photons per second in a region of interest (ROI). Since the acquired images show clear boundaries demarcating the engrafted area, the size of the ROI can be measured as well. If the legs are positioned consistently every time, the changes in total number of photons per second per muscle and the size of the ROI reflect the changes in the number of engrafted cells and the size of the engrafted area. Therefore the changes in the same muscle over time are quantifiable. In vivo fluorescent imaging technique has been used primarily to track the growth of tumorogenic cells, our study shows that it is a powerful tool that enables us to track the fate of transplanted stem cells.

Tracking Dynamics of Muscle Engraftment in Small Animals by In Vivo Fluorescent Imaging

We describe an in vivo fluorescence imaging protocol to monitor muscle regeneration by GFP-labeled myoblasts after transplantation into skeletal muscles of both healthy and dystrophic mice. This protocol can be adapted to study muscle regeneration by transplantation of other types of cells and in other muscular conditions as well.

Muscular dystrophies are a group of degenerative muscle diseases characterized by progressive loss of contractile muscle cells. Currently, there is no ...

Environmentally Induced Heritable Changes in Flax

Some flax varieties respond to nutrient stress by modifying their genome and these modifications can be inherited through many generations. Also associated with these genomic changes are heritable phenotypic variations 1,2. The flax variety Stormont Cirrus (Pl) when grown under three different nutrient conditions can either remain inducible (under the control conditions), or become stably modified to either the large or small genotroph by growth under high or low nutrient conditions respectively. The lines resulting from the initial growth under each of these conditions appear to grow better when grown under the same conditions in subsequent generations, notably the Pl line grows best under the control treatment indicating that the plants growing under both the high and low nutrients are under stress. One of the genomic changes that are associated with the induction of heritable changes is the appearance of an insertion element (LIS-1) 3, 4 while the plants are growing under the nutrient stress. With respect to this insertion event, the flax variety Stormont Cirrus (Pl) when grown under three different nutrient conditions can either remain unchanged (under the control conditions), have the insertion appear in all the plants (under low nutrients) and have this transmitted to the next generation, or have the insertion (or parts of it) appear but not be transmitted through generations (under high nutrients) 4. The frequency of the appearance of this insertion indicates that it is under positive selection, which is also consistent with the growth response in subsequent generations. Leaves or meristems harvested at various stages of growth are used for DNA and RNA isolation. The RNA is used to identify variation in expression associated with the various growth environments and/or t he presence/absence of LIS-1. The isolated DNA is used to identify those plants in which the insertion has occurred.

Growing some flax varieties under nutrient stress results in genomic variation within a subset of the genome and phenotypic variation. A complex insertion at a specific site is associated with growth under various nutrient regimes and with changes in gene expression around this site.

Some flax varieties respond to nutrient stress by modifying their genome and these modifications can be inherited through many generations. Also ...

Monitoring Equilibrium Changes in RNA Structure by 'Peroxidative' and 'Oxidative' Hydroxyl Radical Footprinting

RNA molecules play an essential role in biology. In addition to transmitting genetic information, RNA can fold into unique tertiary structures fulfilling a specific biologic role as regulator, binder or catalyst. Information about tertiary contact formation is essential to understand the function of RNA molecules. Hydroxyl radicals (&bull;OH) are unique probes of the structure of nucleic acids due to their high reactivity and small size.1 When used as a footprinting probe, hydroxyl radicals map the solvent accessible surface of the phosphodiester backbone of DNA1 and RNA2 with as fine as single nucleotide resolution. Hydroxyl radical footprinting can be used to identify the nucleotides within an intermolecular contact surface, e.g. in DNA-protein1 and RNA-protein complexes. Equilibrium3 and kinetic4 transitions can be determined by conducting hydroxyl radical footprinting as a function of a solution variable or time, respectively. A key feature of footprinting is that limited exposure to the probe (e.g., 'single-hit kinetics') results in the uniform sampling of each nucleotide of the polymer.5
In this video article, we use the P4-P6 domain of the Tetrahymena ribozyme to illustrate RNA sample preparation and the determination of a Mg(II)-mediated folding isotherms. We describe the use of the well known hydroxyl radical footprinting protocol that requires H2O2 (we call this the 'peroxidative' protocol) and a valuable, but not widely known, alternative that uses naturally dissolved O2 (we call this the 'oxidative' protocol). An overview of the data reduction, transformation and analysis procedures is presented.

Monitoring Equilibrium Changes in RNA Structure by &#039;Peroxidative&#039; and &#039;Oxidative&#039; Hydroxyl Radical Footprinting

This protocol describes how to quantify the Mg(II)-dependent formation of RNA tertiary structure by two methods of hydroxyl radical footprinting.

RNA molecules play an essential role in biology. In addition to transmitting genetic information, RNA can fold into unique tertiary structures fulfilling ...

In Vivo 4-Dimensional Tracking of Hematopoietic Stem and Progenitor Cells in Adult Mouse Calvarial Bone Marrow

Through a delicate balance between quiescence and proliferation, self renewal and production of differentiated progeny, hematopoietic stem cells (HSCs) maintain the turnover of all mature blood cell lineages. The coordination of the complex signals leading to specific HSC fates relies upon the interaction between HSCs and the intricate bone marrow microenvironment, which is still poorly understood[1-2].
We describe how by combining a newly developed specimen holder for stable animal positioning with multi-step confocal and two-photon in vivo imaging techniques, it is possible to obtain high-resolution 3D stacks containing HSPCs and their surrounding niches and to monitor them over time through multi-point time-lapse imaging. High definition imaging allows detecting ex vivo labeled hematopoietic stem and progenitor cells (HSPCs) residing within the bone marrow. Moreover, multi-point time-lapse 3D imaging, obtained with faster acquisition settings, provides accurate information about HSPC movement and the reciprocal interactions between HSPCs and stroma cells.
Tracking of HSPCs in relation to GFP positive osteoblastic cells is shown as an exemplary application of this method. This technique can be utilized to track any appropriately labeled hematopoietic or stromal cell of interest within the mouse calvarium bone marrow space.

In Vivo 4-Dimensional Tracking of Hematopoietic Stem and Progenitor Cells in Adult Mouse Calvarial Bone Marrow

The nature of the interactions between hematopoietic stem and progenitor cells (HSPCs) and bone marrow niches is poorly understood. Custom hardware modifications and a multi-step acquisition protocol allow the use of two-photon and confocal microscopy to image ex vivo labeled HSPCs homed within bone marrow areas, tracking interactions and movement.

Through a delicate balance between quiescence and proliferation, self renewal and production of differentiated progeny, hematopoietic stem cells (HSCs) ...

Fecal Glucocorticoid Analysis: Non-invasive Adrenal Monitoring in Equids

Adrenal activity can be assessed in the equine species by analysis of feces for corticosterone metabolites. During a potentially aversive situation, corticotrophin releasing hormone (CRH) is released from the hypothalamus in the brain. This stimulates the release of adrenocorticotrophic hormone (ACTH) from the pituitary gland, which in turn stimulates release of glucocorticoids from the adrenal gland. In horses the glucocorticoid corticosterone is responsible for several adaptations needed to support equine flight behaviour and subsequent removal from the aversive situation. Corticosterone metabolites can be detected in the feces of horses and assessment offers a non-invasive option to evaluate long term patterns of adrenal activity. Fecal assessment offers advantages over other techniques that monitor adrenal activity including blood plasma and saliva analysis. The non-invasive nature of the method avoids sampling stress which can confound results. It also allows the opportunity for repeated sampling over time and is ideal for studies in free ranging horses. This protocol describes the enzyme linked immunoassay (EIA) used to assess feces for corticosterone, in addition to the associated biochemical validation.

Adrenal activity can be assessed in the equine species by analysis of feces for corticosterone metabolites. The method offers a non-invasive option to assess long term patterns in both domestic and free ranging horses. This protocol describes the enzyme linked immunoassay involved and the associated biochemical validation.

Adrenal activity can be assessed in the equine species by analysis of feces for corticosterone metabolites. During a potentially aversive situation, ...

Analysis of SCAP N-glycosylation and Trafficking in Human Cells

Elevated lipogenesis is a common characteristic of cancer and metabolic diseases. Sterol regulatory element-binding proteins (SREBPs), a family of membrane-bound transcription factors controlling the expression of genes important for the synthesis of cholesterol, fatty acids and phospholipids, are frequently upregulated in these diseases. In the process of SREBP nuclear translocation, SREBP-cleavage activating protein (SCAP) plays a central role in the trafficking of SREBP from the endoplasmic reticulum (ER) to the Golgi and in subsequent proteolysis activation. Recently, we uncovered that glucose-mediated N-glycosylation of SCAP is a prerequisite condition for the exit of SCAP/SREBP from the ER and movement to the Golgi. N-glycosylation stabilizes SCAP and directs SCAP/SREBP trafficking. Here, we describe a protocol for the isolation of membrane fractions in human cells and for the preparation of the samples for the detection of SCAP N-glycosylation and total protein by using western blot. We further provide a method to monitor SCAP trafficking by using confocal microscopy. This protocol is appropriate for the investigation of SCAP N-glycosylation and trafficking in mammalian cells.

Analysis of SCAP N-glycosylation and Trafficking in Human Cells

We describe a modified method for membrane fraction isolation from human cells and sample preparation for the detection of SCAP N-glycosylation and total protein by using western blot. We further introduce a GFP-labeling method to monitor SCAP trafficking using confocal microscopy. This protocol can be used in regular biology laboratories.

Elevated lipogenesis is a common characteristic of cancer and metabolic diseases. Sterol regulatory element-binding proteins (SREBPs), a family of ...

Live Cell Imaging and 3D Analysis of Angiotensin Receptor Type 1a Trafficking in Transfected Human Embryonic Kidney Cells Using Confocal Microscopy

Live-cell imaging is used to simultaneously capture time-lapse images of angiotensin type 1a receptors (AT1aR) and intracellular compartments in transfected human embryonic kidney-293 (HEK) cells following stimulation with angiotensin II (Ang II). HEK cells are transiently transfected with plasmid DNA containing AT1aR tagged with enhanced green fluorescent protein (EGFP). Lysosomes are identified with a red fluorescent dye. Live-cell images are captured on a laser scanning confocal microscope after Ang II stimulation and analyzed by software in three dimensions (3D, voxels) over time. Live-cell imaging enables investigations into receptor trafficking and avoids confounds associated with fixation, and in particular, the loss or artefactual displacement of EGFP-tagged membrane receptors. Thus, as individual cells are tracked through time, the subcellular localization of receptors can be imaged and measured. Images must be acquired sufficiently rapidly to capture rapid vesicle movement. Yet, at faster imaging speeds, the number of photons collected is reduced. Compromises must also be made in the selection of imaging parameters like voxel size in order to gain imaging speed. Significant applications of live-cell imaging are to study protein trafficking, migration, proliferation, cell cycle, apoptosis, autophagy and protein-protein interaction and dynamics, to name but a few.

Here we present a protocol to image cells expressing green fluorescent protein-tagged angiotensin type 1a receptors during endocytosis initiated by angiotensin II treatment. This technique includes labeling lysosomes with a second fluorescent marker, and then utilizing software to analyze the co-localization of receptor and lysosome in three dimensions over time.

Live-cell imaging is used to simultaneously capture time-lapse images of angiotensin type 1a receptors (AT1aR) and intracellular compartments in ...

Detection of Ligand-activated G Protein-coupled Receptor Internalization by Confocal Microscopy

Confocal laser scanning microscopy (CLSM) is an optical imaging technique for high-contrast imaging. It is a powerful approach to visualize fluorescent fusion proteins, such as green fluorescent protein (GFP), to determine their expression, localization, and function. The subcellular localization of target proteins is important for identification, characterization, and functional analyses. Internalization is one of the predominant mechanisms controlling G protein-coupled receptor (GPCR) signaling to ensure the appropriate cellular responses to stimuli. Here, we describe an experimental method to detect the subcellular localization and internalization of GPCR in HEK293 cells with confocal microscopy. In addition, this experiment provides some details about cell culture and transfection. This protocol is compatible with a variety of widely available fluorescent markers and is applicable to the visualization of the subcellular localization of a majority of proteins, as well as of the internalization of GPCR. This technique should enable researchers to efficiently manipulate GPCR gene expression in mammalian cell lines and should facilitate studies on GPCR subcellular localization and internalization.

This protocol describes confocal microscopy detection of G protein-coupled receptor (GPCR) internalization in mammalian cells. It includes the basic cell culture, transfection, and confocal microscopy procedure and provides an efficient and easily interpretable method to detect the subcellular localization and internalization of fusion-expressed GPCR.

Confocal laser scanning microscopy (CLSM) is an optical imaging technique for high-contrast imaging. It is a powerful approach to visualize fluorescent ...

A Graphical User Interface for Software-assisted Tracking of Protein Concentration in Dynamic Cellular Protrusions

Filopodia are dynamic, finger-like cellular protrusions associated with migration and cell-cell communication. In order to better understand the complex signaling mechanisms underlying filopodial initiation, elongation and subsequent stabilization or retraction, it is crucial to determine the spatio-temporal protein activity in these dynamic structures. To analyze protein function in filopodia, we recently developed a semi-automated tracking algorithm that adapts to filopodial shape-changes, thus allowing parallel analysis of protrusion dynamics and relative protein concentration along the whole filopodial length. Here, we present a detailed step-by-step protocol for optimized cell handling, image acquisition and software analysis. We further provide instructions for the use of optional features during image analysis and data representation, as well as troubleshooting guidelines for all critical steps along the way. Finally, we also include a comparison of the described image analysis software with other programs available for filopodia quantification. Together, the presented protocol provides a framework for accurate analysis of protein dynamics in filopodial protrusions using image analysis software.

We present a software solution for semi-automated tracking of relative protein concentration along the length of dynamic cellular protrusions.

Filopodia are dynamic, finger-like cellular protrusions associated with migration and cell-cell communication. In order to better understand the complex ...

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

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

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

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

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