We thank members of the Ivanov and Anderson labs for their helpful discussion and feedback on this manuscript. This work was supported by the National Institutes of Health [GM111700 and CA168872 to PA, NS094918 to PI], the National Science Centre in Poland [grant UMO-2012/06/M/NZ3/00054 to WS]. WS also acknowledges the Ministry of Science and Higher Education in Poland (Mobility Plus Program) and the Polish-American Fulbright Commission for their financial support of his research in the USA.

1. Cell Preparation
<ol>
	<li>Add autoclaved coverslips to 12 wells of a 24-well plate, as indicated in Figure 1A; this can be done using a sterile Pasteur pipette attached to a vacuum to pick up each coverslip. Gently tap the coverslip on the side of the well to release the suction, allowing the coverslip to fall into the well.</li>
	<li>Plate 1 x 105 U-2 OS (U2OS) osteosarcoma cells per well at a final volume of 500 &#181;L of medium. Move the plate side to side and up and down several times to ensure that the cells are evenly distributed.</li>
	<li>Gently press the coverslips down with a clean P1000 tip to ensure that the coverslip is on the bottom of the well and that there are no bubbles under the coverslip.</li>
</ol>
2. Stressing Cells
<ol>
	<li>The following day, visually check the plate to ensure that the cells are evenly dispersed and evenly confluent across the coverslip, as variations between samples may adversely impact the reproducibility of results. Use a 10X objective on an inverted tissue-culture microscope.</li>
	<li>Preheat the medium to 37 &#176;C. Avoid applying cold or hot media to the cells, as these cause cold shock or heat shock, respectively.</li>
	<li>Dilute drugs in preheated media. For each different drug concentration, prepare 2 wells containing 500 &#181;L of medium. Prepare an additional 500 &#181;L to allow for loss while pipetting. Aliquot 4 tubes, each containing 1.5 mL.
	<ol>
		<li>For sodium arsenite: to each well containing 500 &#181;L, add 1.5 &#181;L of 100 mM sodium arsenite (final concentration: 100 &#181;M) or add 0.75 &#181;L of 100 mM sodium arsenite (final concentration: 50 &#181;M).</li>
		<li>For vinorelbine: to each well containing 500 &#181;L, add 22.5 &#181;L of 10 mM vinorelbine (final concentration: 150 &#181;M) or add 18.75 &#181;L of 10 mM vinorelbine (final concentration: 100 &#181;M). 
		NOTE: Sodium arsenite is a well-characterized and&#160;commonly used stress granule inducer and is therefore classically used as a positive control.</li>
	</ol>
	</li>
	<li>Remove and discard the media from wells B1 - 4 and C1 - 4. Add the media with drugs and wait for 60 min (Figure 1A).
	<ol>
		<li>Add 500 &#181;L of medium with 100 &#181;M sodium arsenite to wells B1 and B2. Add 500 &#181;L of medium with 50 &#181;M sodium arsenite to wells B3 and B4.</li>
		<li>Add 500 &#181;L of medium with 150 &#181;M vinorelbine to wells C1 and C2. Add 500 &#181;L of medium with 125 &#181;M vinorelbine to wells C3 and C4.</li>
	</ol>
	</li>
	<li>30 min prior to fixation, treat the wells in column 2 with 5 &#181;L of cycloheximide (1 mg/mL stock) and the wells in column 4 with 2 &#181;L of puromycin (1.25 mg/mL stock). Gently rock the plate to mix before placing the plate back in the 37 &#176;C incubator.</li>
</ol>
3. Cell Fixation and Immunofluorescence
NOTE: Before the experiment, ensure that the methanol is cooled to -20 &#176;C. Make buffers, including Phosphate-buffered Saline (PBS), 5% Normal Horse Serum (NHS) in PBS, and 4% paraformaldehyde (PFA) in PBS.
<ol>
	<li>Discard the media and wash the wells containing coverslips with PBS. Depending on the drugs used, it might be important to properly discard the media containing drugs; contact the local environmental safety office for specific instructions. To wash efficiently, fill a squeeze bottle with PBS, cut back the tip in order to allow a gentle flow rather than a tight stream, and use this to add PBS to each well after aspirating the original PBS.</li>
	<li>Fix the cells using ~250 &#181;L of 4% PFA for 15 min at RT under gentle agitation. Completely cover the top of the coverslip with PFA; 250 &#181;L should be sufficient, but if not, add more. Always avoid pipetting directly onto the coverslips, as some cells (or stress treatments of cells) can alter attachment, and the force from pipetting can dislodge the cells.</li>
	<li>Remove the PFA and discard properly. Contact the local environmental safety office for details on how to properly discard paraformaldehyde.</li>
	<li>Add ~250 &#181;L of methanol (-20 &#176;C) and incubate for 5 min at RT under gentle rocking; this both permeabilizes and flattens the cells.</li>
	<li>Remove and discard the methanol and block the cells by applying ~250 &#181;L of 5% NHS for 1 h at RT O/N at 4 &#176;C. Contact the local environmental safety office for details on how to properly discard of methanol.</li>
	<li>For primary antibodies, dilute the antibodies in 5% NHS. 
	NOTE: The use of multiple SG markers is key to confirming whether the granules observed are bona fide SGs. The number of SG markers that can be used depends on the filters available in the microscope. If standard green, red, and far-red filter sets are available, use G3BP1, eIF4G, and eIF3b at a 1/250 dilution.
	<ol>
		<li>For this experiment (12 coverslips at 250 &#181;L each-Total: 3 mL of 5% NHS), add 12 &#181;L of each of the following: anti-G3BP1, anti-eIF3b, and anti-eIF4G. Incubate the primary antibodies using gentle agitation for at least 1 h at RT or O/N at 4 &#176;C.</li>
	</ol>
	</li>
	<li>Wash the wells 3x with PBS, and incubate each wash for 5 min.</li>
	<li>For secondary antibodies, dilute all secondary antibodies (1/250 dilution) and Hoechst dye (1/1,000 dilution) in 5% NHS.
	<ol>
		<li>For this experiment (12 coverslips at 250 &#181;L each-Total: 3 mL of 5% NHS), add 12 &#181;L of each of the following: Cy2-Mouse, Cy3-Rabbit, and Cy5-Goat (a 1/250 dilution of each) and add 3 &#181;L of Hoechst dye.</li>
		<li>Incubate the coverslips with the secondary antibodies for 1 h at RT. During this and the following steps, protect the samples from light by covering the plate with a box or by placing foil over the top of the tissue culture dish.</li>
	</ol>
	</li>
	<li>Wash the wells three times with PBS for 5 min each.</li>
	<li>Mount the coverslips onto labeled glass slides using mounting medium. Heat the mounting medium in a 37 &#176;C heat block for 10 min; this decreases the viscosity and makes it easier to pipette. With a cut P200 tip, pipette 25 &#181;L of mounting medium per coverslip onto a glass slide; 4-8 coverslips can fit on one glass slide, assuming that the microscope stage allows this. Using fine forceps, transfer the coverslip from the well to the slide, making sure to put the cell side down on the mounting medium. Using a clean P200 tip, press the coverslip down.</li>
	<li>Once all the coverslips have been mounted, use folded lab tissue to clean up excess mounting medium by pressing the lab tissue very firmly onto the slide. Use a squeeze bottle containing H2O to flush off the excess mounting medium and then repeat the blotting with folded lab tissue to remove the water.</li>
</ol>
4. Fluorescence In Situ Hybridization (FISH)
<ol>
	<li>Plate and treat the cells, using steps 1 and 2.1-4 as a guide; it is only necessary to plate the cells in column 1, as only 3 coverslips are needed in the following experiment.</li>
	<li>Ensure that all buffers are prepared (i.e.&#160;4% PFA in PBS, 70% ethanol in water, 2x Saline-Sodium-Citrate (SSC), and 5% NHS), that the methanol is cooled down to -20 &#176;C, and that the hybridization oven is warmed up to the appropriate temperature.</li>
	<li>Carry out steps 3.1-3.3 to wash and fix the cells.</li>
	<li>Permeabilize cells by adding -20 &#176;C methanol for 10 min.</li>
	<li>Remove the methanol and incubate the coverslips in 70% ethanol. Place the plate at 4 &#176;C overnight. Seal the plate using parafilm to prevent evaporation.</li>
	<li>The following day, remove the ethanol and rehydrate the cells by adding 500 &#181;L of 2x SSC. Incubate the coverslips for 5 min with gentle agitation at RT.</li>
	<li>Remove the 2x SSC and add 500 &#181;L of 2X SSC. Incubate for 5 min under gentle agitation.</li>
	<li>Place a piece of parafilm flat on the bottom of the hybridization oven. Pipette 25 &#181;L of hybridization buffer onto the parafilm for each coverslip. Remove the coverslip from the 24-well dish (at this point, the coverslips are cell-side up) and place the coverslip cell-side down on the hybridization buffer. Do this at 42 &#176;C or optionally at 65 &#176;C for 15 min. 
	NOTE: Completing this step at 65 &#176;C will denature cellular RNAs; this can improve the signal if the polyA is masked by interactions with proteins.</li>
	<li>Dilute the Biotin-Oligo(dT) probe (100 ng/&#181;L) in hybridization buffer to a concentration of 2 ng/&#181;L; 25 &#181;L per coverslip is sufficient.</li>
	<li>For each coverslip, pipette 25 &#181;L of hybridization buffer containing Biotin-Oligo(dT) onto the parafilm. Pick up the coverslip with forceps and gently touch the edge of the coverslip onto a lab tissue to remove excess hybridization buffer. Transfer the coverslip to the hybridization buffer with Biotin-Oligo(dT); remember to keep the cell side down.</li>
	<li>Place the coverslips in a hybridization box to limit evaporation. Incubate the coverslips with Biotin-Oligo(dT) in hybridization buffer for 60 min at 42 &#176;C.</li>
	<li>Place 2x SSC in the hybridization oven to allow it to equilibrate to 42 &#176;C.</li>
	<li>Add ~500 &#181;L of warmed 2x SSC to the wells in the 24-well dish and use forceps to transfer the coverslips to the well. Incubate for 10 min.</li>
	<li>Repeat the above wash step twice&#160;at 42 &#176;C and then twice at RT.</li>
	<li>Complete steps 3.5-3.10, making sure to use a streptavidin fluorochrome to detect the Biotin-Oligo(dT) instead of one conventional antibody.</li>
</ol>
5. Ribopuromycylation Assay to Assess Translational Status
<ol>
	<li>Plate U2OS cells on coverslips, as indicated in step 1, but only plate one coverslip per condition (in this case, 3 coverslips: nontreated, 100 &#181;M sodium arsenite, and 150 &#181;M vinorelbine) (Figure 1A).</li>
	<li>Stress cells using the protocol in step 2, completing steps 2.1-2.4.</li>
	<li>5 min before fixation, add 2 &#181;L of puromycin (stock: 1.25 mg/mL; dilute 2 &#181;L in 500 &#181;L to obtain a final puromycin concentration of 5 &#181;g/mL) and 2.9 &#181;L of emetine (stock: 20 &#181;g/mL; add 2.9 &#181;L to the same solution already containing the puromycin) to each well containing 0.5 mL.</li>
	<li>Complete steps 3.1-3.10 as indicated above, using an anti-puromycin antibody (1/1000 dilution) to detect puromycin. Ideally, use two other SG markers in the remaining channels.</li>
	<li>When quantifying the puromycin signal, take all images using the same exposure. Choose this exposure by using the brightest (unstressed) sample and taking an image as bright as possible without saturation. 
	NOTE: The intensity of the anti-puromycin fluorescent signal represents ongoing translation, as puromycin substitutes for an amino acid, incorporates into the nascent protein, and enforces the premature termination of the protein.</li>
</ol>
6. Image Acquisition and Analysis
<ol>
	<li>Quantifying Stress Granules
	<ol>
		<li>To quantify SGs, acquire 3 - 5 images totaling &#62;100 cells per sample using a 40X objective. Alternatively, acquire images using other objectives, but ensure that &#62;100 cells are counted per coverslip and that the magnification is large enough to clearly visualize the granules. Do this by dividing the coverslip into five roughly equal regions and randomly selecting a field from each region (Figure 1B); images of the same field should include all channels to assess the colocalization of markers.</li>
		<li>Once all images have been acquired, merge the channels. Some camera software will automatically do this, while others require manual merging; this can be done with ImageJ by opening all the images and then selecting [Image | Color | Merge Channels].</li>
		<li>Manually count the total number of cells by counting the number of nuclei, using Hoechst as the nuclei marker. Manually count the number of cells that contain more than two SGs per cell. 
		NOTE: For example, using a merged three-channel image displaying G3BP1 (green), eIF4G (red), and Hoechst (blue), count the nuclei (or number of cells) using the blue channel. Then, count SG-positive cells as those with two or more yellow foci per cell. The granules will appear yellow, as green from G3BP1 and red from eIF4G appear yellow if colocalized.</li>
		<li>Determine the percentage of cells that are SG positive by combining the data from the 3-5 independent regions and then calculate: 
		number of SG positive / number of nuclei) *100 = percent of SG-positive cells</li>
	</ol>
	</li>
	<li>Assessing Colocalization by Line Scan Analysis &#8211; Manual Method
	<ol>
		<li>Open ImageJ. Download it for free from ()</li>
		<li>Open the ROI manager: [Analyze | Tools | ROI manager&#8230;].</li>
		<li>Open the merged image in ImageJ: [File | Open].</li>
		<li>Using the line tool located in the ImageJ toolbar, add a line that goes through an SG, making sure to include before and after the SG. Add this line to the ROI manager by clicking [Add] in the ROI manager window.</li>
		<li>Split the merged image into separate channels to assess the localization of each marker to the granule: [Image | Color | Split Channel]; this will split the merged image into three black-and-white images.</li>
		<li>In the black-and-white image, make sure that the line is selected; the line is selected if it appears in the image. If not, in the ROI manager window, click on the line in the panel; this will highlight the line in blue in the ROI manager window and will make the line visible on the black-and-white image. If the line still does not appear, be sure that &#34;show all&#34; is checked in the ROI manager and then click on the line in the image.</li>
		<li>Analyze the intensity of the line: [Analyze | Plot Profile]; this will bring up the &#34;Plot Profile&#34; window, which plots the intensity of the signal across the line.</li>
		<li>Within the &#34;Plot Profile&#34; window, click [List], which brings up a window containing the raw data from the graph. Copy all the data in this window and paste it into a spreadsheet file. To do this, select all the data in the window: [Edit | Select All]. Copy the date: [Edit | Copy]. Open a spreadsheet file and paste the data: [Edit | Paste].</li>
		<li>Complete steps 6.2.6 - 6.2.8 for each channel separately. Be sure to keep track of the channel being assessed.</li>
		<li>In a spreadsheet, generate a line graph of the results. Select the columns that include data by pressing [control] and clicking on the letter at the top of each column. Then, select line graph: [Insert | Line graph].</li>
		<li>Repeat this analysis for multiple stress granules across multiple independent experiments.</li>
	</ol>
	</li>
	<li>Assessing Colocalization by Line Scan Analysis &#8211; ImageJ Plugin
	<ol>
		<li>Download and install the RGB profile tool from the ImageJ website (https://imagej.nih.gov/ij/macros/tools/RGBProfilesTool.txt); when correctly installed, a red, green, and blue (RGB)-lined icon should appear in the toolbar.</li>
		<li>Open the image (e.g., Tiff, JPG) in ImageJ: [File | Open].</li>
		<li>Click on the RGB icon located in the ImageJ toolbar.</li>
		<li>Click and drag to add a line that extends through an SG, making sure to include adjacent regions; an image of the histogram will appear in a pop-up window.</li>
		<li>Save the data as an image: [File | Save As | Tiff]. Alternatively, export and then graph the data in another graphing program using step 6.2.8 from above.</li>
	</ol>
	</li>
</ol>

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R., Levine, M., Ward, D. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Immunological+method+for+mapping+genes+on+Drosophila+polytene+chromosomes.">Immunological method for mapping genes on Drosophila polytene chromosomes.</a> Proc Natl Acad Sci U S A. 79 (14), 4381-4385 (1982).</li><li>Schneider, C. A., Rasband, W. S., Eliceiri, K. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=NIH+Image+to+ImageJ:+25+years+of+image+analysis.">NIH Image to ImageJ: 25 years of image analysis.</a> Nat Methods. 9 (7), 671-675 (2012).</li><li>David, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nuclear+translation+visualized+by+ribosome-bound+nascent+chain+puromycylation.">Nuclear translation visualized by ribosome-bound nascent chain puromycylation.</a> J Cell Biol. 197 (1), 45-57 (2012).</li><li>Panas, M. D., Kedersha, N., McInerney, G. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Methods+for+the+characterization+of+stress+granules+in+virus+infected+cells.">Methods for the characterization of stress granules in virus infected cells.</a> Methods. 90, 57-64 (2015).</li><li>David, A., Bennink, J. R., Yewdell, J. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Emetine+optimally+facilitates+nascent+chain+puromycylation+and+potentiates+the+ribopuromycylation+method+(RPM)+applied+to+inert+cells.">Emetine optimally facilitates nascent chain puromycylation and potentiates the ribopuromycylation method (RPM) applied to inert cells.</a> Histochem Cell Biol. 139 (3), 501-504 (2013).</li><li>Dieterich, D. C., 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=In+situ+visualization+and+dynamics+of+newly+synthesized+proteins+in+rat+hippocampal+neurons.">In situ visualization and dynamics of newly synthesized proteins in rat hippocampal neurons.</a> Nat Neurosci. 13 (7), 897-905 (2010).</li><li>Ruggieri, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dynamic+oscillation+of+translation+and+stress+granule+formation+mark+the+cellular+response+to+virus+infection.">Dynamic oscillation of translation and stress granule formation mark the cellular response to virus infection.</a> Cell Host Microbe. 12 (1), 71-85 (2012).</li><li>Ghisolfi, L., Dutt, S., McConkey, M. E., Ebert, B. L., Anderson, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Stress+granules+contribute+to+alpha-globin+homeostasis+in+differentiating+erythroid+cells.">Stress granules contribute to alpha-globin homeostasis in differentiating erythroid cells.</a> Biochem Biophys Res Commun. 420 (4), 768-774 (2012).</li><li>Ohn, T., Kedersha, N., Hickman, T., Tisdale, S., Anderson, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+functional+RNAi+screen+links+O-GlcNAc+modification+of+ribosomal+proteins+to+stress+granule+and+processing+body+assembly.">A functional RNAi screen links O-GlcNAc modification of ribosomal proteins to stress granule and processing body assembly.</a> Nat Cell Biol. 10 (10), 1224-1231 (2008).</li><li>Porter, A. C., Fanger, G. R., Vaillancourt, R. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Signal+transduction+pathways+regulated+by+arsenate+and+arsenite.">Signal transduction pathways regulated by arsenate and arsenite.</a> Oncogene. 18 (54), 7794-7802 (1999).</li><li>Shen, S., Li, X. F., Cullen, W. R., Weinfeld, M., Le, X. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Arsenic+binding+to+proteins.">Arsenic binding to proteins.</a> Chem Rev. 113 (10), 7769-7792 (2013).</li><li>McDonald, K. K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=TAR+DNA-binding+protein+43+(TDP-43)+regulates+stress+granule+dynamics+via+differential+regulation+of+G3BP+and+TIA-1.">TAR DNA-binding protein 43 (TDP-43) regulates stress granule dynamics via differential regulation of G3BP and TIA-1.</a> Hum Mol Genet. 20 (7), 1400-1410 (2011).</li><li>Aulas, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=G3BP1+promotes+stress-induced+RNA+granule+interactions+to+preserve+polyadenylated+mRNA.">G3BP1 promotes stress-induced RNA granule interactions to preserve polyadenylated mRNA.</a> J Cell Biol. 209 (1), 73-84 (2015).</li><li>Martin, S., Tazi, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Visualization+of+G3BP+stress+granules+dynamics+in+live+primary+cells.">Visualization of G3BP stress granules dynamics in live primary cells.</a> J Vis Exp. (87), (2014).</li><li>Wippich, F., 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=Dual+specificity+kinase+DYRK3+couples+stress+granule+condensation/dissolution+to+mTORC1+signaling.">Dual specificity kinase DYRK3 couples stress granule condensation/dissolution to mTORC1 signaling.</a> Cell. 152 (4), 791-805 (2013).</li></ol>

The authors have nothing to disclose.

As evidenced by immunohistological studies in multiple diseases, chronic stress leads to the formation of different intracellular foci. For example, most neurodegenerative diseases are characterized by intracellular aggregates of insoluble proteins. The presence of SG-associated proteins in such aggregates is often the basis for concluding that such foci are SGs. A similar conclusion is also drawn when SG marker-positive cytoplasmic foci are observed in cells treated with new stress stimuli. This protocol provides a simp...

Cells employ many mechanisms to respond to stress. Some responses occur at the post-transcriptional level and involve regulating mRNA translation and/or stability1,2. Stress-modulated mRNA translational arrest and degradation are associated with the formation of specific nonmembranous cellular foci, the most well characterized being Stress Granules (SGs)3. SGs are cytoplasmic foci that concentrate nontranslating mRNPs in translationally-arrested cells responding to stress (e.g., oxidation, heat shock, nutrient starvation, and viral infection)4. In addition to nontranslating mRNAs, SGs contain translation initiation factors, RNA-binding proteins, and various signaling proteins5. SGs are biomarkers of inhibited protein translation and altered RNA metabolism and have been linked to cell survival and apoptosis, signaling pathways, and nuclear processes5.
SGs are dynamic entities, and their formation is tightly connected to the status of cellular translation6. Despite their seemingly solid appearance, most SG protein components rapidly shuttle in and out, with a residence time of seconds. While SGs persist for minutes to hours, most of their components are in rapid flux. The inhibition of translation initiation and the consequent disassembly of translating polysomes promote the formation of SGs; thus, SGs are in equilibrium with translating polysomes. This polysome/SG equilibrium is key to distinguishing bona fide SGs from other stress-induced foci6,7.
Arresting translation initiation entails the conversion of translation-competent pre-initiation complexes that contain mRNA, translation initiation factors (eIF), and 40S ribosomal subunits (so-called 48S complexes) into translationally stalled complexes (so-called 48S* complexes) that can coalesce into SGs4,6. SGs are promoted by translational arrest at two different steps upstream of 48S complex formation: interference with the functions of the cap-binding eIF4F complex (e.g., targeting its eIF4A subunit) or phosphorylation of the &#945; subunit of translation initiation factor eIF2, mediated by one or more of the four eIF2 kinases. The presence of stalled 48S complexes (i.e.&#160;40S ribosomal subunits and selected translation initiation factors) is a hallmark of SGs8,9.
SGs have been linked to various pathological states, such as viral infections, neurodegeneration, autoimmunity, and cancer3,10,11,12,13. Mutated forms of several SG components are associated with neurodegenerative diseases (e.g., amyotrophic lateral sclerosis) in which neurons display intracellular pathological inclusions that may play active roles in neuronal death13. Some viruses hijack SG components to inhibit SG formation and to enhance viral replication14. Recent studies also link SGs to cancer15 and to cancer cell survival under chemo- and radiotherapy treatments10,16,17,18,19,20. While such findings have stimulated great interest in SG biology, many of the published reports lack important controls to distinguish the formation of bona fide SGs from other stress-induced foci.
SGs were initially described as nonmembranous cytoplasmic foci composed of selected mRNA-binding Proteins (RBPs), including T-cell ntracellular antigen 1 (TIA-1) and Poly-A-binding Protein (PABP); translation initiation factors; polyadenylated mRNA; and small ribosomal subunits4,6,21,22. Traditionally, their composition has been determined by techniques such as immunostaining and the ectopic expression of fluorescently tagged proteins23,24. Due to their highly dynamic nature, the immunolocalization of SG proteins and/or mRNAs remains the defining methodology for detecting SGs23,24. To date, many RBPs and other proteins (over 120 distinct proteins) are described as SG components11. As many SG-localized proteins change their localization in both a stress-dependent and an independent manner and can accumulate at other intracellular compartments and foci, it is important to choose correct SG markers and to employ functional criteria to distinguish SGs from other types of stress-induced foci. Bona fide SGs contain mRNA, translation initiation factors, and small ribosomal subunits and are in dynamic equilibrium with translation.
This simple workflow is designed to determine whether stress-induced foci are bona fide SGs. This workflow includes several experimental approaches using U2OS cells, cells commonly used to study SGs. These cells are ideal, as they have a large cytoplasm, are relatively flat, and attach strongly to glass coverslips. Other cell types can be used to study SGs, but it is important to be aware that differences in timing, drug concentration, and abundance of SG-nucleating proteins can alter the kinetics and composition. Additionally, some cells respond to paraformaldehyde fixation by forming cell surface blebs, giving then a ruffled appearance that causes the punctate localization of some SG markers; without careful analysis, these can be misclassified as SGs. This highlights the necessity of assessing all criteria required to identify stress-induced foci as bona fide SGs. Vinorelbine (VRB), a cancer therapeutic that promotes SGs20, as well as Sodium Arsenite (SA), a robust and well-characterized SG inducer, are used as stresses for the experiments in this protocol.
Canonical SGs contain multiple SG markers (both proteins and mRNAs) that colocalize in cytoplasmic foci. This protocol uses both immunofluorescence and fluorescence in situ hybridization (FISH) to detect the localization of protein markers and polyadenylated mRNA22, respectively. Briefly, indirect immunofluorescence uses antibodies (i.e.&#160;primary antibodies) specific for a given protein to detect it within the cell. Then, secondary antibodies (usually species-specific) attached to fluorochromes recognize the primary antibody and reveal the target protein localization. Fluorescent microscopy is used to detect the localized signal within the cell. Using antibodies produced in different species and detecting them with differently colored secondary antibodies allows for the detection of the colocalization of multiple antibodies, indicating that their protein targets are found in the same location23. It is important to select markers that have been verified to colocalize at bona fide SGs.
FISH uses a labeled probe that base-pairs to a specific RNA or DNA sequence25. To detect mRNA, this protocol uses a biotinylated oligo(dT)40 probe that hybridizes (or base-pairs) to the polyA tail of mRNA (i.e.&#160;polyA FISH). The biotinylated probe is then detected using fluorescently conjugated streptavidin, as streptavidin has a high affinity for biotin. When assessing SGs, it is important to couple polyA FISH with immunofluorescence detecting an SG marker, as in bona fide SGs, the two signals should colocalize.
Using this protocol, colocalization is assessed in multiple ways. In a multi-channel (i.e.&#160;RGB: red, green, and blue) image, colocalization will alter the color of the overlapped signal (e.g.&#160;colocalized red and green appear yellow)23. Additionally, colocalization is quantified graphically using line scan analysis, where the intensity of each of color is measured across a given line8,20. This protocol describes two line scan analysis procedures using ImageJ26. One procedure is manual and goes through the entire process, while the other uses a macro, or a simple program that automates the manual steps. It is important to go through the manual program to understand the macro procedure.
SGs form in cells where translation is repressed; therefore, cells with SGs should display decreased levels of global translation compared to untreated cells. Experimentally, ribopuromycylation is used. Puromycin and emetine are added to cells for a short duration prior to fixation, allowing the puromycin to incorporate into actively forming polypeptides, causing termination27,28. Treatment with emetine is required to prevent re-initiation29. Puromycin can then be detected using anti-puromycin antibody, giving a snapshot of active translation. This method is used because it is quick, does not require pre-starving with a medium lacking a particular amino acid (and potentially prestressing the cells), and reveals the subcellular localization of protein translation. Other methods, notably using modified amino acid analogs, such as the methionine analog L-azidohomoalaine (AHA), coupled with &#34;click-it&#34; chemistry30, have been used to show that cells containing SGs exhibit much lower translation than neighboring cells31. However, this technique requires methionine starvation followed by pulse-labeling for 15-30 min. Methionine starvation constitutes an additional stress, while the long labeling time (i.e.&#160;15-30 min) results in the measurement of cumulative rather than ongoing translation and also allows the newly-synthesized proteins to move from their site of synthesis to their final destination within the cell. In contrast, ribopuromycylation is much faster and is compatible with any medium, such as the glucose-free medium used to induce SGs via glucose starvation.
Canonical SGs are in dynamic equilibrium with actively translating polysomes. This can be assessed experimentally by treating samples with the drugs that stabilize or destabilize polysomes, thus tipping the balance between SGs and polysomes23. Cycloheximide (or emetine, which behaves similarly) blocks elongation by &#34;freezing&#34; ribosomes onto mRNA, thus decreasing the pool of available non-polysomal mRNPs able to form SGs. Experimentally, this can be used in two ways: by adding cycloheximide (or emetine) before stress to prevent SG formation or by adding cycloheximide (or emetine) after the SGs have formed, even without removing the stressing agent, causing SG disassembly, as stalled preinitiation complexes are slowly admitted into the polysome fraction. In contrast, puromycin causes premature termination and promotes polysome disassembly, increasing the pool of initiating mRNAs capable of assembling into SGs. Experimentally, puromycin treatment increases the number of SGs or lowers the threshold at which they form in response to graded stress or drug dosage. When assessing the effect of puromycin, it is important to use a sub-maximal level of the drug of interest, as puromycin is expected to augment the effect of the drug and to increase the percent of cells displaying SGs &#8211; this cannot occur if the drug/stress causes SGs in 100% of the cells initially. This contrasts with cycloheximide treatment, which disassembles SGs and works best when ~95% of the cells initially display SGs so that the largest possible decrease can be observed and accurately quantified.
This protocol provides a framework to study SGs in mammalian cells. Methods include: (1) immunofluorescent staining and ImageJ analysis to assess the colocalization the classic SG-associated markers eIF4G, eIF3b, and Ras GTPase-activating protein-binding protein 1 (G3BP1) in putative SGs; (2) oligo(dT) fluorescence in situ hybridization (polyA FISH) to detect polyadenylated mRNA; (3) cycloheximide and puromycin treatment to determine whether stress-induced foci are in dynamic equilibrium with polysomes; and (4) ribopuromycylation to assess the translational status of cells containing putative SGs. Together, these assays can determine whether stress-induced foci can be classified as bona fide SGs.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>U-2 OS</td>
			<td>ATCC</td>
			<td>ATCC&#174;HTB-96&#8482;</td>
			<td>- commonly written as &#34;U2OS&#34; 
			- culture at 37 &#176;C under 5% CO2 in 10% FBS/DMEM</td>
		</tr>
		<tr>
			<td>Dulbecco&#39;s Modification of Eagle&#39;s Medium</td>
			<td>Corning</td>
			<td>10-013-CV</td>
			<td>- abbreviated DMEM 
			- contains 4.5 g/L glucose, pyruvate, and phenol red 
			- supplemented with 10% FBS, 10 mM HEPES, and penicillin/steptomycin 
			- prewarm prior drug(s) dilution</td>
		</tr>
		<tr>
			<td>Fetal Bovine Serum</td>
			<td>Sigma</td>
			<td>F2442-500ml</td>
			<td>- abbreviated FBS 
			- used to supplement media</td>
		</tr>
		<tr>
			<td>HEPES (1 M)</td>
			<td>Thermo Fisher Scientific</td>
			<td>15630-080</td>
			<td>- used to supplement media</td>
		</tr>
		<tr>
			<td>penicilline streptomycine</td>
			<td>Sigma</td>
			<td>P0781-100ml</td>
			<td>- used to supplement media</td>
		</tr>
		<tr>
			<td>24 well plate</td>
			<td>Costar</td>
			<td>3524</td>
			<td></td>
		</tr>
		<tr>
			<td>lab tissues</td>
			<td>KIMTECH SCIENCE</td>
			<td>34120</td>
			<td>- commonly called &#34;kimwipes&#34;</td>
		</tr>
		<tr>
			<td>Coverglass for Growth Cover Glasses</td>
			<td>Fisher Scientific</td>
			<td>12-545-82</td>
			<td>- autoclaved before used 
			- keep sterile in the tissue culture hood</td>
		</tr>
		<tr>
			<td>Sodium (meta)arsenite &#8805;90%</td>
			<td>Sigma</td>
			<td>S7400-100G</td>
			<td>- commonly called sodium arsenite and abbreviated SA 
			- dissolution in water at 1 M concentration, then dilute to 100 &#181;M as a working stock</td>
		</tr>
		<tr>
			<td>Vinorelbine</td>
			<td>TSZ CHEM</td>
			<td>RS055</td>
			<td>- abbreviated VRB 
			- dissolve in water to 10 mM</td>
		</tr>
		<tr>
			<td>Puromycin</td>
			<td>Sigma</td>
			<td>P9620</td>
			<td>- used to assess translation level (ribopuromycylation) 
			- used to assess SG connection with active translation 
			- dilute in water to 10 mg/mL</td>
		</tr>
		<tr>
			<td>Emetine dihydrochloride hydrate</td>
			<td>Sigma</td>
			<td>E2375</td>
			<td>- used in combination with puro to assess general translation level 
			- used to assess SG connection with active translation 
			- dilute in water to 10 mg/mL</td>
		</tr>
		<tr>
			<td>Cycloheximide</td>
			<td>Sigma</td>
			<td>C4859</td>
			<td>- abbreviated CHX 
			- used to assess SG connection with active translation 
			- dilute in water to 10 mg/mL</td>
		</tr>
		<tr>
			<td>Phosphate Buffered Saline</td>
			<td>Lonza / VWR</td>
			<td>95042-486</td>
			<td>- abbreviated PBS 
			- wash buffer for immunofluorescence</td>
		</tr>
		<tr>
			<td>Paraformaldehyde reagent grade, crystalline</td>
			<td>Sigma</td>
			<td>P6148-500G</td>
			<td>- make a 4% solution in hot PBS in fume hood, stir until dissolved 
			- aliquots can be stored at - 20 &#176;C for several months 
			- hazardous, use ventilation 
			- discard in special waste</td>
		</tr>
		<tr>
			<td>Methanol, ACS</td>
			<td>BDH / VWR</td>
			<td>BDH1135-4LP</td>
			<td>- pre-chilled to -20&#176;C before use 
			- discard in special waste</td>
		</tr>
		<tr>
			<td>Normal Horse Serum</td>
			<td>Thermo Fisher Scientific</td>
			<td>31874</td>
			<td>- abbreviated NHS 
			- dilute to 5% in PBS 
			- add sodium azide for storage at 4&#176;C 
			- blocking solution for immunofluorescence</td>
		</tr>
		<tr>
			<td>Ethanol, Pure, 200 Proof (100%),USP, KOPTEC</td>
			<td>Decon Labs / VWR</td>
			<td>89125-188</td>
			<td>- dilute to 70% with water</td>
		</tr>
		<tr>
			<td>Fisherbrand Superfrost Plus Microscope Slides</td>
			<td>Fisherbrand</td>
			<td>12-550-15</td>
			<td></td>
		</tr>
		<tr>
			<td>mouse anti G3BP1 antibody (TT-Y)</td>
			<td>Santa Cruz</td>
			<td>sc-81940</td>
			<td>- store at 4 &#176;C 
			- use at 1/100 dilution</td>
		</tr>
		<tr>
			<td>rabbit anti eIF4G antibody (H-300)</td>
			<td>Santa Cruz</td>
			<td>sc-11373</td>
			<td>- store at 4 &#176;C 
			- 1/250 dilution</td>
		</tr>
		<tr>
			<td>goat anti eIF3&#951; (N-20) antibody</td>
			<td>Santa Cruz</td>
			<td>sc-16377</td>
			<td>- eIF3&#951; is also known as eIF3b 
			- store at 4 &#176;C 
			- 1/250 dilution</td>
		</tr>
		<tr>
			<td>mouse anti puromycin 12D10 antibody</td>
			<td>Millipore</td>
			<td>MABE343</td>
			<td>- store at 4 &#176;C 
			- 1/1000 dilution</td>
		</tr>
		<tr>
			<td>Cy2 AffiniPure Donkey Anti-Mouse IgG (H+L)</td>
			<td>Jackson Immunoresearch</td>
			<td>715-225-150</td>
			<td>- reconstitute in water as per manufacturer&#8217;s instructions then store at 4&#176;C 
			- 1/250 dilution</td>
		</tr>
		<tr>
			<td>Cy3 AffiniPure Donkey Anti-Rabbit IgG (H+L)</td>
			<td>Jackson Immunoresearch</td>
			<td>711-165-152</td>
			<td>- reconstitute in water as per manufacturer&#8217;s instructions then store at 4&#176;C 
			- 1/2500 dilution</td>
		</tr>
		<tr>
			<td>Cy5 AffiniPure Donkey Anti-Goat IgG (H+L)</td>
			<td>Jackson Immunoresearch</td>
			<td>705-175-147</td>
			<td>- reconstitute in water as per manufacturer&#8217;s instructions then store at 4&#176;C 
			- 1/250 dilution</td>
		</tr>
		<tr>
			<td>Hoechst 33258 solution</td>
			<td>Sigma</td>
			<td>94403-1ML</td>
			<td>- incubate with secondary antibodies 
			-stock solution 0.5 mg/mL in dH20, protect from light 
			- Store at 4 &#176;C</td>
		</tr>
		<tr>
			<td>Cy3 Streptavidin</td>
			<td>Jackson Immunoresearch</td>
			<td>016-160-084</td>
			<td>- reconstitute in water as per manufacturer&#8217;s instructions, then store at 4&#176;C 
			- 1/250 dilution</td>
		</tr>
		<tr>
			<td>oligo-(dT)40x probe biotinilated</td>
			<td>Integrated DNA Technologies (IDT)</td>
			<td>/</td>
			<td>- reconstitute in water to 100 ng/mL, aliquot and store at -20&#176;C 
			- dilute in hybridation buffer 1/50 prior to use 
			- custom order</td>
		</tr>
		<tr>
			<td>hybridation box</td>
			<td>/</td>
			<td>/</td>
			<td>- make a moisture chamber with any storing slide box by adding humidified paper on the bottom 
			- prewarm the box prior use</td>
		</tr>
		<tr>
			<td>20 x SSC buffer</td>
			<td>Thermo fisher Ambion</td>
			<td>AM9763</td>
			<td>- dilute to 2X SSC using RNase Free water (DEPC treated) 
			- store at room temperature 
			- wash buffer for FISH</td>
		</tr>
		<tr>
			<td>PerfectHybPlus Hybridization Buffer</td>
			<td>Sigma</td>
			<td>H7033-50ml</td>
			<td>- block and probe incubation buffer for FISH</td>
		</tr>
		<tr>
			<td>slide mounting media</td>
			<td>home made</td>
			<td>/</td>
			<td>- mix 5 g of &#8220;cold-soluble&#8221; poly(vinyl alcohol) in 20 ml of PBS 
			- mix by sonication, followed by stirring overnight at RT 
			- Add 5 ml of glycerol and 0.2 ml of 20 % sodium azide, and stir for 16 h at RT 
			- centrifugation at 20,000 g for 20 min, discard large pellet 
			- aliquot viscous liquid, long-term storage at -20&#176;C, 1 week at 4&#176;C</td>
		</tr>
		<tr>
			<td>Parafilm &#34;M&#34;</td>
			<td>Sigma</td>
			<td>P7793-1EA</td>
			<td>- usually referred as &#34;parafilm&#34;</td>
		</tr>
		<tr>
			<td>Poly(vinyl alcohol)</td>
			<td>Sigma</td>
			<td>P-8136-250G</td>
			<td>- reagent to make vinol</td>
		</tr>
		<tr>
			<td>Glycerol</td>
			<td>Sigma</td>
			<td>G5516-100ML</td>
			<td>- reagent to make vinol</td>
		</tr>
		<tr>
			<td>sodium azide</td>
			<td>Fisher Scientific</td>
			<td>S2002-5G</td>
			<td>- preservative agent for blocking solution and vinol 
			- make a 20 % dilution in water</td>
		</tr>
	</tbody>
</table>

methods to classify cytoplasmic foci as mammalian stress granules

Cells are often challenged by sudden environmental changes. Stress Granules (SGs), cytoplasmic ribonucleoprotein complexes that form in cells exposed to stress conditions, are implicated in various aspects of cell metabolism and survival. SGs modulate cellular signaling pathways, post-transcriptional gene expression, and stress response programs. The formation of these mRNA-containing granules is directly connected to cellular translation. SG assembly is triggered by inhibited translation initiation, and SG disassembly is promoted by translation activation or by inhibited translation elongation. This relationship is further highlighted by SG composition. Core SG components are stalled translation pre-initiation complexes, mRNA, and selected RNA-binding Proteins (RBPs). The purpose of SG assembly is to conserve cellular energy by sequestering translationally stalled housekeeping mRNAs, allowing for the enhanced translation of stress-responsive proteins. In addition to the core constituents, such as stalled translation preinitiation complexes, SGs contain a plethora of other proteins and signaling molecules. Defects in SG formation can impair cellular adaptation to stress and can thus promote cell death. SGs and similar RNA-containing granules have been linked to a number of human diseases, including neurodegenerative disorders and cancer, leading to the recent interest in classifying and defining RNA granule subtypes. This protocol describes assays to characterize and quantify mammalian SGs.

Stress-induced foci are not necessarily SGs. SGs are classified as cytoplasmic foci that contain mRNAs, translation initiation factors, and RNA-binding proteins and are in equilibrium with active translation. The above protocol can be used as a template to characterize whether a given stress induces bona fide SGs.
SGs colocalize with other known SG markers, including both proteins and mRNA. SA and VRB induce cytoplasmic...

Watch this Scientific Journal Video about Methods to Classify Cytoplasmic Foci as Mammalian Stress Granules at JoVE.com

Methods to Classify Cytoplasmic Foci as Mammalian Stress Granules

Stress Granules (SGs) are nonmembranous cytoplasmic structures that form in cells exposed to a variety of stresses. SGs contain mRNAs, RNA-binding proteins, small ribosomal subunits, translation-related factors, and various cell signaling proteins. This protocol describes a workflow that uses several experimental approaches to detect, characterize, and quantify bona fide SGs.

Cells are often challenged by sudden environmental changes. Stress Granules (SGs), cytoplasmic ribonucleoprotein complexes that form in cells exposed to ...

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Biology

14.5K Views.  Brigham and Women's Hospital. Stress Granules (SGs) are nonmembranous cytoplasmic structures that form in cells exposed to a variety of stresses. SGs contain mRNAs, RNA-binding proteins, small ribosomal subunits, translation-related factors, and various cell signaling proteins. This protocol describes a workflow that uses several experimental approaches to detect, characterize, and quantify bona fide SGs.

Video: Methods to Classify Cytoplasmic Foci as Mammalian Stress Granules

Trypsinizing and Subculturing Mammalian Cells

As cells reach confluency, they must be subcultured or passaged. Failure to subculture confluent cells results in reduced mitotic index and eventually in cell death. The first step in subculturing is to detach cells from the surface of the primary culture vessel by trypsinization or mechanical means. The resultant cell suspension is then subdivided, or reseeded, into fresh cultures. Secondary cultures are checked for growth and fed periodically, and may be subsequently subcultured to produce tertiary cultures. The time between passaging of cells varies with the cell line and depends on the growth rate.

As cells reach confluency, they must be subcultured or passaged. This video will demonstrate a procedure for subculturing both adherent and suspension cells.

As cells reach confluency, they must be subcultured or passaged. Failure to subculture confluent cells results in reduced mitotic index and eventually in ...

Quantification of &gamma;H2AX Foci in Response to Ionising Radiation

DNA double-strand breaks (DSBs), which are induced by either endogenous metabolic processes or by exogenous sources, are one of the most critical DNA lesions with respect to survival and preservation of genomic integrity. An early response to the induction of DSBs is phosphorylation of the H2A histone variant, H2AX, at the serine-139 residue, in the highly conserved C-terminal SQEY motif, forming &gamma;H2AX1. Following induction of DSBs, H2AX is rapidly phosphorylated by the phosphatidyl-inosito 3-kinase (PIKK) family of proteins, ataxia telangiectasia mutated (ATM), DNA-protein kinase catalytic subunit and ATM and RAD3-related (ATR)2. Typically, only a few base-pairs (bp) are implicated in a DSB, however, there is significant signal amplification, given the importance of chromatin modifications in DNA damage signalling and repair. Phosphorylation of H2AX mediated predominantly by ATM spreads to adjacent areas of chromatin, affecting approximately 0.03% of total cellular H2AX per DSB2,3. This corresponds to phosphorylation of approximately 2000 H2AX molecules spanning ~2 Mbp regions of chromatin surrounding the site of the DSB and results in the formation of discrete &gamma;H2AX foci which can be easily visualized and quantitated by immunofluorescence microscopy2. The loss of &gamma;H2AX at DSB reflects repair, however, there is some controversy as to what defines complete repair of DSBs; it has been proposed that rejoining of both strands of DNA is adequate however, it has also been suggested that re-instatement of the original chromatin state of compaction is necessary4-8. The disappearence of &gamma;H2AX involves at least in part, dephosphorylation by phosphatases, phosphatase 2A and phosphatase 4C5,6. Further, removal of &gamma;H2AX by redistribution involving histone exchange with H2A.Z has been implicated7,8. Importantly, the quantitative analysis of &gamma;H2AX foci has led to a wide range of applications in medical and nuclear research. Here, we demonstrate the most commonly used immunofluorescence method for evaluation of initial DNA damage by detection and quantitation of &gamma;H2AX foci in &gamma;-irradiated adherent human keratinocytes9.

Quantification of &#947;H2AX Foci in Response to Ionising Radiation

Quantification of DNA double-strand streaks using &gamma;H2AX formation as a molecular marker has become an invaluable tool in radiation biology. Here we demonstrate the use of an immunofluorescence assay for quantification of &gamma;H2AX foci after exposure of cells to radiation.

DNA double-strand breaks (DSBs), which are induced by either endogenous metabolic processes or by exogenous sources, are one of the most critical DNA ...

Quantitation of &gamma;H2AX Foci in Tissue Samples

DNA double-strand breaks (DSBs) are particularly lethal and genotoxic lesions, that can arise either by endogenous (physiological or pathological) processes or by exogenous factors, particularly ionizing radiation and radiomimetic compounds. Phosphorylation of the H2A histone variant, H2AX, at the serine-139 residue, in the highly conserved C-terminal SQEY motif, forming &gamma;H2AX, is an early response to DNA double-strand breaks1. This phosphorylation event is mediated by the phosphatidyl-inosito 3-kinase (PI3K) family of proteins, ataxia telangiectasia mutated (ATM), DNA-protein kinase catalytic subunit and ATM and RAD3-related (ATR)2. Overall, DSB induction results in the formation of discrete nuclear &gamma;H2AX foci which can be easily detected and quantitated by immunofluorescence microscopy2. Given the unique specificity and sensitivity of this marker, analysis of &gamma;H2AX foci has led to a wide range of applications in biomedical research, particularly in radiation biology and nuclear medicine. The quantitation of &gamma;H2AX foci has been most widely investigated in cell culture systems in the context of ionizing radiation-induced DSBs. Apart from cellular radiosensitivity, immunofluorescence based assays have also been used to evaluate the efficacy of radiation-modifying compounds. In addition, &gamma;H2AX has been used as a molecular marker to examine the efficacy of various DSB-inducing compounds and is recently being heralded as important marker of ageing and disease, particularly cancer3. Further, immunofluorescence-based methods have been adapted to suit detection and quantitation of &gamma;H2AX foci ex vivo and in vivo4,5. Here, we demonstrate a typical immunofluorescence method for detection and quantitation of &gamma;H2AX foci in mouse tissues.

Quantitation of &#947;H2AX Foci in Tissue Samples

Quantitation of DNA double-strand breaks on the basis of &gamma;H2AX foci has become an invaluable tool, particularly in radiation biology, for the evaluation of tissue radiosensitivity and effects of radiation modifying compounds. Here we demonstrate the use of an immunofluorescence assay for quantitation of &gamma;H2AX foci in tissue samples.

DNA double-strand breaks (DSBs) are particularly lethal and genotoxic lesions, that can arise either by endogenous (physiological or pathological) ...

Activation of Apoptosis by Cytoplasmic Microinjection of Cytochrome c

Apoptosis, or programmed cell death, is a conserved and highly regulated pathway by which cells die1. Apoptosis can be triggered when cells encounter a wide range of cytotoxic stresses. These insults initiate signaling cascades that ultimately cause the release of cytochrome c from the mitochondrial intermembrane space to the cytoplasm2. The release of cytochrome c from mitochondria is a key event that triggers the rapid activation of caspases, the key cellular proteases which ultimately execute cell death3-4.
The pathway of apoptosis is regulated at points upstream and downstream of cytochrome c release from mitochondria5. In order to study the post-mitochondrial regulation of caspase activation, many investigators have turned to direct cytoplasmic microinjection of holocytochrome c (heme-attached) protein into cells6-9. Cytochrome c is normally localized to the mitochondria where attachment of a heme group is necessary to enable it to activate apoptosis10-11. Therefore, to directly activate caspases, it is necessary to inject the holocytochrome c protein instead of its cDNA, because while the expression of cytochrome c from cDNA constructs will result in mitochondrial targeting and heme attachment, it will be sequestered from cytosolic caspases. Thus, the direct cytosolic microinjection of purified heme-attached cytochrome c protein is a useful tool to mimic mitochondrial cytochrome c release and apoptosis without the use of toxic insults which cause cellular and mitochondrial damage.
In this article, we describe a method for the microinjection of cytochrome c protein into cells, using mouse embryonic fibroblasts (MEFs) and primary sympathetic neurons as examples. While this protocol focuses on the injection of cytochrome c for investigations of apoptosis, the techniques shown here can also be easily adapted for microinjection of other proteins of interest.

Activation of Apoptosis by Cytoplasmic Microinjection of Cytochrome c

In this protocol, we describe the direct cytoplasmic microinjection of cytochrome c protein into fibroblasts and primary sympathetic neurons. This technique allows for the introduction of cytochrome c protein into the cytoplasm of cells and mimics the release of cytochrome c from mitochondria, which occurs during apoptosis.

Apoptosis, or programmed cell death, is a conserved and highly regulated pathway by which cells die1.  Apoptosis can be triggered when cells encounter a ...

Visualizing Cytoplasmic Flow During Single-cell Wound Healing in Stentor coeruleus

Although wound-healing is often addressed at the level of whole tissues, in many cases individual cells are able to heal wounds within themselves, repairing broken cell membrane before the cellular contents leak out. The giant unicellular organism Stentor coeruleus, in which cells can be more than one millimeter in size, have been a classical model organism for studying wound healing in single cells. Stentor cells can be cut in half without loss of viability, and can even be cut and grafted together. But this high tolerance to cutting raises the question of why the cytoplasm does not simply flow out from the size of the cut. Here we present a method for cutting Stentor cells while simultaneously imaging the movement of cytoplasm in the vicinity of the cut at high spatial and temporal resolution. The key to our method is to use a &#34;double decker&#34; microscope configuration in which the surgery is performed under a dissecting microscope focused on a chamber that is simultaneously viewed from below at high resolution using an inverted microscope with a high NA lens. This setup allows a high level of control over the surgical procedure while still permitting high resolution tracking of cytoplasm.

Visualizing Cytoplasmic Flow During Single-cell Wound Healing in Stentor coeruleus

The giant ciliate Stentor coeruleus is a classical system for studying regeneration and wound healing in single cells.&#160;By imaging Stentor cells simultaneously at low and high magnification it is possible to measure cytoplasmic flows before, during, and after wounding.

Although wound-healing is often addressed at the level of whole tissues, in many cases individual cells are able to heal wounds within themselves, ...

Visualization of G3BP Stress Granules Dynamics in Live Primary Cells

SGs can be visualized in cells by immunostaining of specific protein components or polyA+ mRNAs. SGs are highly dynamic and the study of their assembly and fate is important to understand the cellular response to stress. The deficiency in key factors of SGs like G3BP (RasGAP SH3 domain Binding Protein) leads to developmental defects in mice&#160;and alterations of the Central Nervous System. To study the dynamics of SGs in cells from an organism, one can culture primary cells and follow the localization of a transfected tagged component of SGs. We describe time-lapse experiment to observe G3BP1-containing SGs in Mouse Embryonic Fibroblasts (MEFs). This technique can also be used to study G3BP-containing SGs in live neurons, which is crucial as it was recently shown that these SGs are formed at the onset of neurodegenerative diseases like Alzheimer&#39;s disease. This approach can be adapted to any other cellular body and granule protein component, and performed with transgenic animals, allowing the live study of granules dynamics for example in the absence of a specific factor of these granules.

Stress granules (SGs) are cytoplasmic RNA granules containing stalled ribonucleoprotein particles (RNPs), and important in cellular response to various stresses. Dynamics of SGs can be followed in live cells by visualizing the localization of a tagged component of SGs in transfected primary cells after stress.

SGs can be visualized in cells by immunostaining of specific protein components or polyA+ mRNAs. SGs are highly dynamic and the study of their assembly ...

Stimulation of Cytoplasmic DNA Sensing Pathways In Vitro and In Vivo

In order to efficiently stimulate an innate immune response, DNA must be of sufficient length and purity. We present a method where double stranded DNA (dsDNA) which has the requisite characteristics to stimulate the cytoplasmic DNA sensing pathways can be generated cheaply and with ease. By the concatemerization of short, synthetic oligonucleotides (which lack CpG motifs), dsDNA can be generated to be of sufficient length to activate the cytosolic DNA sensing pathway. This protocol involves blunt end ligation of the oligonucleotides in the presence of polyethylene glycol (PEG), which provides an environment for efficient ligation to occur. The dsDNA concatemers can be used, following purification by phenol/chloroform extraction, to simulate the innate immune response in vitro by standard transfection protocols. This DNA can also be used to stimulate innate immunity in vivo by intradermal injection into the ear pinna of a mouse, for example. By standardizing the concatemerization process and the subsequent stimulation protocols, a reliable and reproducible activation of the innate immune system can be produced.

Stimulation of Cytoplasmic DNA Sensing Pathways In Vitro and In Vivo

The aim of the protocol is to use optimal methods for stimulating the cytoplasmic DNA sensing pathways in cells and in vivo. This is achieved by improving the generation of long, double-stranded DNA during blunt-end ligation. Cells or mice are then transfected using a lipid transfection reagent.

In order to efficiently stimulate an innate immune response, DNA must be of sufficient length and purity. We present a method where double stranded DNA ...

Methods to Assess Subcellular Compartments of Muscle in C. elegans

Muscle is a dynamic tissue that responds to changes in nutrition, exercise, and disease state. The loss of muscle mass and function with disease and age are significant public health burdens. We currently understand little about the genetic regulation of muscle health with disease or age. The nematode C. elegans is an established model for understanding the genomic regulation of biological processes of interest. This worm&#8217;s body wall muscles display a large degree of homology with the muscles of higher metazoan species. Since C. elegans is a transparent organism, the localization of GFP to mitochondria and sarcomeres allows visualization of these structures in vivo. Similarly, feeding animals cationic dyes, which accumulate based on the existence of a mitochondrial membrane potential, allows the assessment of mitochondrial function in vivo. These methods, as well as assessment of muscle protein homeostasis, are combined with assessment of whole animal muscle function, in the form of movement assays, to allow correlation of sub-cellular defects with functional measures of muscle performance. Thus, C. elegans provides a powerful platform with which to assess the impact of mutations, gene knockdown, and/or chemical compounds upon muscle structure and function. Lastly, as GFP, cationic dyes, and movement assays are assessed non-invasively, prospective studies of muscle structure and function can be conducted across the whole life course and this at present cannot be easily investigated in vivo in any other organism.

Methods to Assess Subcellular Compartments of Muscle in C. elegans

Skeletal muscle is essential for locomotion and is the bodies&#8217; main protein store. Muscle health measurements within C. elegans are described. Prospective changes to muscle structure and function are assessed using localized GFP and cationic dyes.

Muscle is a dynamic tissue that responds to changes in nutrition, exercise, and disease state. The loss of muscle mass and function with disease and age ...

Xenopus laevis as a Model to Identify Translation Impairment

Protein synthesis is a fundamental process to gene expression impacting diverse biological processes notably adaptation to environmental conditions. The initiation step, which involves the assembly of the ribosomal subunits at the mRNA initiation codon, involved initiation factor including eIF4G1. Defects in this rate limiting step of translation are linked to diverse disorders. To study the potential consequences of such deregulations, Xenopus laevis oocytes constitute an attractive model with high degrees of conservation of essential cellular and molecular mechanisms with human. In addition, during meiotic maturation, oocytes are transcriptionally repressed and all necessary proteins are translated from preexisting, maternally derived mRNAs. This inexpensive model enables exogenous mRNA to become perfectly integrated with an effective translation. Here is described a protocol for assessing translation with a factor of interest (here eIF4G1) using stored maternal mRNA that are the first to be polyadenylated and translated during oocyte maturation as a physiological readout. At first, mRNA synthetized by in vitro transcription of plasmids of interest (here eIF4G1) are injected in oocytes and kinetics of oocyte maturation by Germinal Vesicle Breakdown detection is determined. The studied maternal mRNA target is the serine/threonine-protein-kinase mos. Its polyadenylation and its subsequent translation are investigated together with the expression and phosphorylation of proteins of the mos signaling cascade involved in oocyte maturation. Variations of the current protocol to put forward translational defects are also proposed to emphasize its general applicability. In light of emerging evidence that aberrant protein synthesis may be involved in the pathogenesis of neurological disorders, such a model provides the opportunity to easily assess this impairment and identify new targets.

Xenopus laevis as a Model to Identify Translation Impairment

Protein synthesis control occurs mainly at the translation initiation step, deficiencies in which are linked to diverse disorders. To better understand their etiology, we described here a protocol using Xenopus laevis oocytes assessing the translation of mos transcript in the presence of a mutant of translation initiation factor eIF4G1.

Protein synthesis is a fundamental process to gene expression impacting diverse biological processes notably adaptation to environmental conditions. The ...

Comet Assay as an Indirect Measure of Systemic Oxidative Stress

Higher eukaryotic organisms cannot live without oxygen; yet, paradoxically, oxygen can be harmful to them. The oxygen molecule is chemically relatively inert because it has two unpaired electrons located in different pi * anti-bonding orbitals. These two electrons have parallel spins, meaning they rotate in the same direction about their own axes. This is why the oxygen molecule is not very reactive. Activation of oxygen may occur by two different mechanisms; either through reduction via one electron at a time (monovalent reduction), or through the absorption of sufficient energy to reverse the spin of one of the unpaired electrons. This results in the production of reactive oxidative species (ROS). There are a number of ways in which the human body eliminates ROS in its physiological state. If ROS production exceeds the repair capacity, oxidative stress results and damages different molecules. There are many different methods by which oxidative stress can be measured. This manuscript focuses on one of the methods named cell gel electrophoresis, also known as &#8220;comet assay&#8221; which allows measurement of DNA breaks. If all factors known to cause DNA damage, other than oxidative stress are kept constant, the amount of DNA damage measured by comet assay is a good parameter of oxidative stress. The principle is simple and relies upon the fact that DNA molecules are negatively charged. An intact DNA molecule has such a large size that it does not migrate during electrophoresis. DNA breaks, however, if present result in smaller fragments which move in the electrical field towards the anode. Smaller fragments migrate faster. As the fragments have different sizes the final result of the electrophoresis is not a distinct line but rather a continuum with the shape of a comet. The system allows a quantification of the resulting &#8220;comet&#8221; and thus of the DNA breaks in the cell.

Comet assay measures DNA breaks, induced by different factors. If all factors (except oxidative stress) causing DNA damage are kept constant, the amount of DNA damage is a good indirect parameter of oxidative stress. The goal of this protocol is to use comet assay for indirect measurement of oxidative stress.

Higher eukaryotic organisms cannot live without oxygen; yet, paradoxically, oxygen can be harmful to them. The oxygen molecule is chemically relatively ...