The authors would like to acknowledge the Montpellier Rio Imaging (MRI) platform where the acquisitions were performed. They thank Isabel Cristina Lopez Mejia, Alexandra Metz, Irina Lassot, Solange Desagher, Fabien Loustalot, and Virginie Georget for their help in different parts of the protocol. This work was supported by the Fondation pour la Recherche M&#233;dicale (FRM) (Equipe FRM 2011 -n&#176;DEQ20111223745).

All the animal procedures in this protocol are in strict adherence with the guidelines of the European Community Council Directive of 24 November 1986 (86-609/EEC). House the mice in group, allowing food and water ad libitum. Maintain them in a controlled environment (22 &#177;1 &#176;C, 55 &#177;5% humidity) with a 12 hr:12 hr light:dark cycle (light on at 7:00 am).
1. Culture of Murine Primary Cells: Mouse Embryonic Fibroblasts (MEFs)
<ol>
	<li>Autoclave thin forceps, as well as curved forceps and dissecting scissors. Store in a sterile container. Use sterile D-PBS (Dulbecco&#39;s Phosphate-Buffered Saline). Prepare complete MEFs medium: Dulbecco&#39;s modified Eagle medium (DMEM)/F12 supplemented with 10% fetal calf serum (FBS), 1 mM L-glutamine, 1 mM sodium pyruvate, 1% non-essential amino acids, and 0.5 mM 2-mercaptoethanol and warm at 37 &#176;C.</li>
	<li>Euthanize a pregnant mouse (at 13.5 days post-co&#239;tum (dpc)) by cervical dislocation. Remove the uterine horns from the mouse sanitized with&#160;90% EtOH. Under a sterile and clean hood, place the horns with the embryos in 37 &#176;C prewarmed D-PBS. Open the horns, place the embryos in a 100 mm sterile plastic Petri dish, clean them up from the umbilical cord material and wash them with warm D-PBS to remove blood excess. Under a binocular, remove the embryo&#8217;s limbs, the internal organs and the upper part of the head containing the brain.</li>
	<li>In a new Petri dish, mince the embryos into very small pieces with a sterile surgical blade or scissors (at least for 1 min). In the case of embryos of different genotypes, be careful to put each embryo in individual Petri dishes and keep the tail or the upper head for genotyping.</li>
	<li>Cover the embryo with 1x&#160;trypsin-EDTA (0.25% trypsin, 1 mM EDTA) . Incubate for 30 min to 1 hr in a 37 &#176;C incubator. Add 10 ml of complete MEFs medium to stop trypsin reaction. Pipet up and down to remove all aggregates. Let sit the cell suspension into a 50 ml tube (filled with complete medium) for 10 min, and centrifuge the supernatant for 5 min at 300 x g at room temperature. Resuspend the pellet in complete medium (6 ml for 1 embryo). Viable nucleated cells can be counted using trypan blue (around 5 x 106 cells can be expected from one embryo). Plate 3 ml per 60 mm Petri dish.</li>
	<li>Change the medium the next day and allow the cells to grow until the dishes are confluent. Many cell types can be seen, but only fibroblasts will survive subculture. </li>
	<li>Split the cells and allow them to grow in 35 mm dishes with glass bottom (important for time lapse experiment), until 50-70% confluency for the transfection. Test for Mycoplasma and mouse pathogens. </li>
</ol>
2. Culture Adaptations in the Case of Neurons
<ol>
	<li>The day before the culture, coat 35 mm glass bottom Petri dishes with poly-L-lysine (200 &#181;l of 0.1 mg/ml) under a sterile and clean hood, and leave overnight.</li>
	<li>On the next morning, rinse with sterile pure water, twice for 5 min and once for 45 min to 1 hr. Replace with 2 ml of DMEM plus 10% FBS medium and keep in a 37 &#176;C incubator.</li>
	<li>Dissect embryos at 18.5 dpc. Under a sterile and clean hood, place the horns with the embryos in cold sterile HBSS (Hank&#39;s Balanced Salt Solution) in 100 mm Petri dish. Neonatal pups can also be used instead of embryos in order to preserve the life of the dam and enable it to produce more offspring, especially in the case of transgenic animals which can be difficult to obtain. In individual Petri dishes, take each embryo or newborn and cut the head with scissors. Hold the head by inserting curved forceps into the eyes, cut the skin and carefully open the soft skull from the back of the head until the eyes, on each side of the head. Cut the optic nerves and the brain stem, remove the brain, and put it in a new Petri dish containing HBSS. Under a stereoscope, remove all the meninges using two thin forceps. Separate the hippocampi, the cortex or any other part of the brain depending on the structure to study.</li>
	<li>Immerse the dissected brain structure in 4.5 ml of cold HBSS prepared previously in 15 ml tubes and keep on ice until digestion with trypsin. Add 0.5 ml of 2.5% trypsin and incubate at 37 &#176;C for 15 min to 20 min. Rinse the trypsin 3x&#160;with HBSS, being extremely careful to not discard the digested brain parts.</li>
	<li>Resuspend in 500 &#181;l (hippocampi) to 1 ml (cortex) DMEM plus 10% FBS and pipet up and down several times with a 1 ml micropipette equipped with a 1 ml tip, then equipped with 1 ml plus 200 &#181;l tips, until there is no visible aggregate.</li>
	<li>Distribute 100-200 &#181;l of cell suspension to each 35 mm glass bottom dish containing DMEM plus 10% FBS and let the neurons adhere at 37 &#176;C for at least 3 hr. Replace by prewarmed neuron complete medium (Neurobasal medium supplemented with 250 &#181;M L-glutamine and NS21, prepared as described in Chen et al.19) and leave at 37 &#176;C to allow neuronal growth. Transfect the neurons at 5 to 14 days in vitro (div) (the efficiency of transfection is higher after a couple of div but synaptic connections are better established from 7-10 div).</li>
</ol>
3. Transfection of EGFP-G3BP1 Construct
Transfect the cells with a vector containing the cDNA of your protein of interest (any component of SGs) fused to a fluorescent marker (GFP, YFP, etc.), using 3 &#181;g of purified plasmid per 35 mm dish.
<ol>
	<li>Transfect the MEFs using a commercial method, following the manufacturer&#39;s protocol (See Table of Materials/Reagents).</li>
	<li>Transfect the neurons with a calcium phosphate method adapted from Xia et al.20&#160;Briefly:
	<ol>
		<li>Prepare the solutions: DMEM-wash: DMEM containing 25 mM KCl; transfection solution: DMEM-wash containing 1x&#160;DMKY (HEPES 5 mM, MgCl2 10 mM, phenol red); and shock solution: HeBS 1x, DMKY 1x,&#160;and DMSO 2% (v/v); and keep them at 37 &#176;C.</li>
		<li>Remove the media from the neurons, filtrate, and keep it at 37 &#176;C. Wash with DMEM-wash then replace with transfection medium and keep at 37 &#176;C during the preparation of the calcium phosphate-plasmid DNA precipitates.</li>
		<li>In a 1.5 ml microcentrifuge tube, add (in this order) Braun water (final volume 50 &#181;l), 5 &#181;l of CaCl2 2.5 M, and 3 &#181;g of plasmid DNA. Drop this mix onto 50 &#181;l of HeBS 2x&#160;already introduced in a round bottom polypropylene tube. Mix the tube by rotation along with the dropping. Let the precipitate form at room temperature during 30 min.</li>
		<li>Add the precipitate dropwise onto the neurons and leave at 37 &#176;C during 30 to 50 min.</li>
		<li>Replace with shock solution for 1 min, then rinse with DMEM-wash and finally reintroduce the preconditioned medium. Keep the cells at 37 &#176;C.</li>
	</ol>
	</li>
</ol>
4. Visualization of G3BP Containing SGs Assembly and Dynamics
<ol>
	<li>Replace the medium of the cells which contains phenol red by phenol red-free medium.</li>
	<li>Use a confocal microscope equipped with fluorescence for the acquisitions. Turn on the microscope systems: mercury lamp, computer, and lasers. Warm up the chamber to 37 &#176;C at least 20 min before the beginning of the acquisitions.</li>
	<li>The over expression of G3BP induces the spontaneous formation of a type of SGs. The cells may thus be observed for the assembly of SGs 24 hr right after the transfection without stress induction. Alternatively, stress can be induced to further induce the assembly of SGs. Add 0.5 mM sodium arsenite and start the acquisition right after the addition of the compound (granules will be well formed within 1 hr).</li>
	<li>Add oil to the immersion objective (use 40X or 63X objectives) and install the Petri dish over the objective in the adapted 35 mm microscope holder, stabilized on the stage holder. Check that the dish is flat otherwise the acquisitions will be altered. Turn on the fluorescence light according to the relevant fluorophore and visualize transfected cells. Turn off fluorescence once a cell of interest is in the field in order to minimize bleaching and cytotoxicity.</li>
	<li>In the &#34;acquire tab&#34;, select the lasers depending on the excitation wavelength of the tag fluorophore (488 nm in our protocol which uses EGFP-tagged G3BP) and select the adapted emission length for the PMT (photomultiplier tube). Adjust the laser power (usually not more than 10%) to minimize noise and oversaturation as well as toxicity, and set the gain and offset to modify the signal to noise ratio. Scan fast (1,000 Hz) in order to minimize the duration of laser exposition (line average 2, frame average 1). If desired, set the parameters for the Z stack to be able to reconstruct the image in 3D (a Z step of 1 &#181;m is usually fine with cells). Determine the interval time between each acquisition: smaller intervals permit to obtain a more coherent movie but this may induce photobleaching and toxicity (an interval of 20 sec was used in the described experiments). Duration of total acquisition may vary depending on the stress type. Many G3BP-containing SGs are formed very rapidly under arsenite treatment and are well visible after 1 hr of treatment: in that case, choose rapidly the cells to film and start the acquisitions right after the stress, with a total duration of acquisitions of 15-20 min largely sufficient to observe the assembly of several SGs.</li>
	<li>Save the pictures and reconstruct the stacks and movie using ImageJ software.</li>
</ol>

<ol>
	<li>Thomas, M. G., Loschi, M., Desbats, M. A., Boccaccio, G. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=RNA+granules:+The+good,+the+bad+and+the+ugly.">RNA granules: The good, the bad and the ugly.</a> Cellular Signalling. 23 (2), 324-334 (2011).</li><li>Kedersha, N., 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:+sites+of+mRNA+triage+that+regulate+mRNA+stability+and+translatability.">Stress granules: sites of mRNA triage that regulate mRNA stability and translatability.</a> Biochemical Society transactions. 30 (6), 963-969 (2002).</li><li>Anderson, P., Kedersha, N. <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:+the+Tao+of+RNA+triage.">Stress granules: the Tao of RNA triage.</a> Trends in Biochemical Sciences. 33 (3), 141-150 (2008).</li><li>Gilks, N., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Stress+granule+assembly+is+mediated+by+prion-like+aggregation+of+TIA-1.">Stress granule assembly is mediated by prion-like aggregation of TIA-1.</a> Molecular biology of the cell. 15 (12), 5383-5398 (2004).</li><li>Tourri&#232;re, H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+RasGAP-associated+endoribonuclease+G3BP+assembles+stress+granules.">The RasGAP-associated endoribonuclease G3BP assembles stress granules.</a> The Journal of Cell Biology. 160 (6), 823-831 (2003).</li><li>Parker, 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=A+Ras-GTPase-activating+protein+SH3-domain-binding+protein.">A Ras-GTPase-activating protein SH3-domain-binding protein.</a> Molecular and Cellular Biology. 16 (6), 2561-2569 (1996).</li><li>Annibaldi, A., Dousse, A., Martin, S., Tazi, J., Widmann, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Revisiting+G3BP1+as+a+RasGAP+binding+protein:+sensitization+of+tumor+cells+to+chemotherapy+by+the+RasGAP+317-326+sequence+does+not+involve+G3BP1.">Revisiting G3BP1 as a RasGAP binding protein: sensitization of tumor cells to chemotherapy by the RasGAP 317-326 sequence does not involve G3BP1.</a> PLOS ONE. 6 (12), (2011).</li><li>Kennedy, D., French, J., Guitard, E., Ru, K., Tocque, B., Mattick, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Characterization+of+G3BPs:+tissue+specific+expression,+chromosomal+localisation+and+rasGAP(120)+binding+studies.">Characterization of G3BPs: tissue specific expression, chromosomal localisation and rasGAP(120) binding studies.</a> Journal of Cellular Biochemistry. 84 (1), 173-187 (2001).</li><li>Kobayashi, T., Winslow, S., Sunesson, L., Hellman, U., Larsson, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=PKC&#945;+Binds+G3BP2+and+Regulates+Stress+Granule+Formation+Following+Cellular+Stress.">PKC&#945; Binds G3BP2 and Regulates Stress Granule Formation Following Cellular Stress.</a> PLOS ONE. 7 (4), (2012).</li><li>Tourri&#232;re, H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=RasGAP-associated+endoribonuclease+G3Bp:+selective+RNA+degradation+and+phosphorylation-dependent+localization.">RasGAP-associated endoribonuclease G3Bp: selective RNA degradation and phosphorylation-dependent localization.</a> Molecular and Cellular Biology. 21 (22), 7747-7760 (2001).</li><li>Costa, M., Ochem, A., Staub, A., Falaschi, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Human+DNA+helicase+VIII:+a+DNA+and+RNA+helicase+corresponding+to+the+G3BP+protein,+an+element+of+the+ras+transduction+pathway.">Human DNA helicase VIII: a DNA and RNA helicase corresponding to the G3BP protein, an element of the ras transduction pathway.</a> Nucleic acids research. 27 (3), 817-821 (1999).</li><li>Solomon, S., 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=Distinct+structural+features+of+caprin-1+mediate+its+interaction+with+G3BP-1+and+its+induction+of+phosphorylation+of+eukaryotic+translation+initiation+factor+2alpha,+entry+to+cytoplasmic+stress+granules,+and+selective+interaction+with+a+subset+of+mRNAs.">Distinct structural features of caprin-1 mediate its interaction with G3BP-1 and its induction of phosphorylation of eukaryotic translation initiation factor 2alpha, entry to cytoplasmic stress granules, and selective interaction with a subset of mRNAs.</a> Molecular and Cellular Biology. 27 (6), 2324-2342 (2007).</li><li>Soncini, C., Berdo, I., Draetta, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ras-GAP+SH3+domain+binding+protein+(G3BP)+is+a+modulator+of+USP10,+a+novel+human+ubiquitin+specific+protease.">Ras-GAP SH3 domain binding protein (G3BP) is a modulator of USP10, a novel human ubiquitin specific protease.</a> Oncogene. 20 (29), 3869-3879 (2001).</li><li>Zekri, L., 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=Control+of+fetal+growth+and+neonatal+survival+by+the+RasGAP-associated+endoribonuclease+G3BP.">Control of fetal growth and neonatal survival by the RasGAP-associated endoribonuclease G3BP.</a> Molecular and Cellular Biology. 25 (19), 8703-8716 (2005).</li><li>Martin, S., 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=Deficiency+of+G3BP1,+the+stress+granules+assembly+factor,+results+in+abnormal+synaptic+plasticity+and+calcium+homeostasis+in+neurons.">Deficiency of G3BP1, the stress granules assembly factor, results in abnormal synaptic plasticity and calcium homeostasis in neurons.</a> Journal of neurochemistry. , (2013).</li><li>Mazroui, R., Huot, M. -. E., Tremblay, S., Filion, C., Labelle, Y., Khandjian, E. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Trapping+of+messenger+RNA+by+Fragile+X+Mental+Retardation+protein+into+cytoplasmic+granules+induces+translation+repression.">Trapping of messenger RNA by Fragile X Mental Retardation protein into cytoplasmic granules induces translation repression.</a> Human molecular genetics. 11 (24), 3007-3017 (2002).</li><li>Colombrita, 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=TDP-43+is+recruited+to+stress+granules+in+conditions+of+oxidative+insult.">TDP-43 is recruited to stress granules in conditions of oxidative insult.</a> Journal of neurochemistry. 111 (4), 1051-1061 (2009).</li><li>Thomas, M. G., Tosar, L. J. M., Desbats, M. A., Leishman, C. C., Boccaccio, G. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mammalian+Staufen+1+is+recruited+to+stress+granules+and+impairs+their+assembly.">Mammalian Staufen 1 is recruited to stress granules and impairs their assembly.</a> Journal of Cell Science. 122 (4), 563-573 (2009).</li><li>Chen, Y., Stevens, B., Chang, J., Milbrandt, J., Barres, B. A., Hell, 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=NS21:+re-defined+and+modified+supplement+B27+for+neuronal+cultures.">NS21: re-defined and modified supplement B27 for neuronal cultures.</a> Journal of neuroscience. 171 (2), 239-247 (2008).</li><li>Xia, Z., Dudek, H., Miranti, C. K., Greenberg, M. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Calcium+Influx+via+the+NMDA+Receptor+Induces+Immediate+Early+Gene+Transcription+by+a+MAP+Kinase/ERK-Dependent+Mechanism.">Calcium Influx via the NMDA Receptor Induces Immediate Early Gene Transcription by a MAP Kinase/ERK-Dependent Mechanism.</a> The Journal of Neuroscience. 16 (17), 5425-5436 (1996).</li><li>Dudek, H., Ghosh, A., Greenberg, M. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Calcium+phosphate+transfection+of+DNA+into+neurons+in+primary+culture.">Calcium phosphate transfection of DNA into neurons in primary culture.</a> Current protocols in neuroscience. 3, (2001).</li><li>Reineke, L. C., Dougherty, J. D., Pierre, P., Lloyd, R. 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The authors declare that they have no competing financial interests.

The most critical steps in the protocol concern the transfection and more particularly the time lapse acquisitions, which have to be carefully monitored in order to lower down the cytotoxicity.
Culture of primary cells is not a difficult part, as long as sterile conditions are maintained and caution is taken in order to prevent damage during the dissection and cell dissociation steps. MEFs can be kept frozen at early passages. Neuron transfection with calcium phosphate has been shown to work w...

Stress granules (SGs) are non-membranous cytoplasmic foci formed as a cellular protective response to environmental stress, such as elevated temperature, oxidative stress, hypoxia, osmotic shock, UV irradiation, glucose deprivation, or viral infection1. They can be induced chemically by treatment with compounds like sodium arsenite, which triggers oxidative stress. SGs accumulate stalled translation arrested messenger ribonucleoprotein (mRNPs) complexes2, sequestering mRNAs from the translational machinery, and their assembly can be triggered by the phosphorylation of eIF2&#945; (eukaryotic initiation factor 2 &#945;). SGs are dynamic structures which exchange components with the polysomes and other granules like the P-bodies. They constitute a &#34;triage center&#34; where mRNAs are sorted and processed for either translation, reinitiation, degradation, or packaging into stable non-polysomal mRNPs3. The assembly of SGs is fast but it is a gradual process with initial numerous small aggregates which coalesce into larger granules. The use of chemical inhibitors that disrupt or stabilize microtubules shows that the microtubule network is required for SG dynamics including assembly, coalescence and disassembly processes.
The dynamic assembly of SGs is also promoted by aggregation of specific RNA-binding proteins (RNA-BP) like TIA-1 (T-cell internal antigen-1) and TIAR (TIA-1-related protein), which are able to dimerize and promote polysome disassembly and the routing of mRNAs into SGs4. G3BP (RasGAP SH3 domain binding protein) is such an RNA-BP that localizes to SGs when cells are stressed with arsenite or high temperature, and overexpression of dephosphorylated G3BP can induce SGs assembly5.
G3BP is an evolutionarily conserved RNA-BP that was initially characterized through its interaction with a Ras-GTPase activating protein (RasGAP p120 6); but this interaction was recently revisited7. The G3BP family includes two members in mammals, G3BP1 (referred to as G3BP) and G3BP2&#160;8. Both proteins colocalize in SGs, when cells are subjected to stress9. G3BPs comprise an N-terminal NTF2 domain suggested to influence their localization and oligomerization, followed by proline rich (PxxP) motifs, then C-terminal motifs associated with RNA binding: the canonical RNA-Recognition Motif (RRM) with conserved RNP1 and RNP2 motifs, followed by an arginine-glycine rich (RGG) box. Interestingly, the analysis of different parts of the protein by constructing different domains fused to EGFP showed that the NTF2-like domain and the RNA-binding domain were the most efficiently recruited to SGs, suggesting the importance of the properties of dimerization and RNA binding in the assembly of SGs. Diverse models have revealed different functions of G3BP proteins in vitro10-13. Disruption of G3BP in mice have shown the importance of this protein in developmental growth and survival14, as well as an important role for G3BP in the Central Nervous System (CNS), characterized by ataxia and defects in spatial working memory15. G3BP deficiency leads to altered neuronal plasticity and calcium homeostasis, establishing a direct link between SG formation and neurodegenerative diseases15. It is thus important to be able to study the dynamics of SGs in primary cells like neurons.
This protocol provides a simple way to observe the assembly of G3BP1-containing SGs in primary cells under arsenite treatment. It can be used to study SGs assembly under different conditions, for example different kinds of stresses. It can also be adapted to other granules or other constituents of SGs. Indeed, this protocol focuses on G3BP1, but there are other stress granules markers like TIA-1/R, TTP (tristetraprolin)2, FMRP (Fragile X Mental Retardation Syndrome protein)16, TDP-43 (transactive response DNA binding protein 43)17 or Staufen18. In particular, proteins like TIA-1/R are, like G3BP, nucleating RNA binding proteins that can induce SGs assembly when overexpressed, even if the different formed SGs can differ in function, regulation and associated transcripts. Transfection of fluorophore-tagged version of any of these key components or nucleators of SGs can be performed to image particular SGs assembly and dynamics.

<table border="0" cellpadding="0" cellspacing="0" style="width:881px;" width="881">
	<colgroup>
		<col />
		<col />
		<col />
		<col />
	</colgroup>
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:297px;">Name of Material/ Equipment</td>
			<td style="width:153px;">Company</td>
			<td style="width:119px;">Catalog Number</td>
			<td style="width:312px;">Comments/Description</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:297px;"></td>
			<td style="width:153px;"></td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:297px;">DMEM/F12</td>
			<td style="width:153px;">Gibco</td>
			<td style="width:119px;">21331</td>
			<td>Pre-warm at 37 &#176;C</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:297px;">Sodium Pyruvate</td>
			<td style="width:153px;">Gibco</td>
			<td style="width:119px;">11360</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:297px;">Non essential amino acids</td>
			<td style="width:153px;">Gibco</td>
			<td style="width:119px;">11140</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:297px;">L-Glutamine</td>
			<td style="width:153px;">Gibco</td>
			<td style="width:119px;">25030</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:297px;">Trypsin</td>
			<td style="width:153px;">Gibco</td>
			<td style="width:119px;">15096</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:297px;">Glass bottom B-35</td>
			<td style="width:153px;">Greiner</td>
			<td style="width:119px;">627860/627861</td>
			<td>Treated or not (treated: increases attachment of adherent cells)</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:297px;">Poly-L-lysine</td>
			<td style="width:153px;">Sigma-Aldrich</td>
			<td style="width:119px;">P2636</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:297px;">DMEM</td>
			<td style="width:153px;">Gibco</td>
			<td style="width:119px;">31966</td>
			<td>Pre-warm at 37 &#176;C</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:297px;">HeBS</td>
			<td style="width:153px;">Sigma-Aldrich</td>
			<td style="width:119px;">51558</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:297px;">Neurobasal</td>
			<td style="width:153px;">Gibco</td>
			<td style="width:119px;">21103</td>
			<td>Pre-warm at 37 &#176;C</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:297px;">2-mercaptoethanol</td>
			<td style="width:153px;">Gibco</td>
			<td style="width:119px;">31350</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:297px;">Forceps</td>
			<td style="width:153px;">Biotek</td>
			<td style="width:119px;">DU-110-A</td>
			<td>Very thin, tips 0,1 mm (useful to remove meninges)</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:297px;">Curved forceps</td>
			<td style="width:153px;">Biotek</td>
			<td style="width:119px;">P-110-BUF</td>
			<td>Very thin, tips 0,1 mm&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:297px;">Small scissors</td>
			<td style="width:153px;">Biotek</td>
			<td style="width:119px;">CM-85-BS</td>
			<td>Can be useful to remove hippocampi</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Polyplus transfection JetPEI reagent&#160;</td>
			<td style="width:153px;">Ozyme</td>
			<td style="width:119px;">101-10</td>
			<td>MEFs transfection, follow the forward protocol</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Inverted laser scanning confocal microscope</td>
			<td style="width:153px;">Leica&#160;</td>
			<td style="width:119px;">SP5</td>
			<td></td>
		</tr>
	</tbody>
</table>

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 granule&#160;formation is important in the response of cells to stress, permitting a cellular adaptation with stalled translation, until the stress has cleared, associated to prevention of apoptosis. This assay permits to study the SGs in primary cells, by following the localization of key SGs protein components (Figure 1). G3BP, a key factor of SGs assembly, is present rather diffusively in the cytoplasm of cultured MEFs or neurons (Figure 2A a and c</str...

Watch this Scientific Journal Video about Visualization of G3BP Stress Granules Dynamics in Live Primary Cells at JoVE.com

Visualization of G3BP Stress Granules Dynamics in Live Primary Cells

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 ...

visualization-of-g3bp-stress-granules-dynamics-in-live-primary-cells

Research

JoVE Journal

Biology

18.2K Views.  Institut de Génétique Moléculaire de Montpellier, CNRS UMR 5535. 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.

Video: Visualization of G3BP Stress Granules Dynamics in Live Primary Cells

A Rapid Technique for the Visualization of Live Immobilized Yeast Cells

We present here a simple, rapid, and extremely flexible technique for the immobilization and visualization of growing yeast cells by epifluorescence microscopy. The technique is equally suited for visualization of static yeast populations, or time courses experiments up to ten hours in length. My microscopy investigates epigenetic inheritance at the silent mating loci in S. cerevisiae. There are two silent mating loci, HML and HMR, which are normally not expressed as they are packaged in heterochromatin. In the sir1 mutant background silencing is weakened such that each locus can either be in the expressed or silenced epigenetic state, so in the population as a whole there is a mix of cells of different epigenetic states for both HML and HMR. My microscopy demonstrated that there is no relationship between the epigenetic state of HML and HMR in an individual cell. sir1 cells stochastically switch epigenetic states, establishing silencing at a previously expressed locus or expressing a previously silenced locus. My time course microscopy tracked individual sir1 cells and their offspring to score the frequency of each of the four possible epigenetic switches, and thus the stability of each of the epigenetic states in sir1 cells. See also  Xu et al., Mol. Cell 2006.

A rapid technique for the visualization of growing immobilized yeast cells, here applied to fluorescent reporters at the silent mating loci HML and HMR

We present here a simple, rapid, and extremely flexible technique for the immobilization and visualization of growing yeast cells by epifluorescence ...

Live Imaging of Dense-core Vesicles in Primary Cultured Hippocampal Neurons

Observing and characterizing dynamic cellular processes can yield important information about cellular activity that cannot be gained from static images.  Vital fluorescent probes, particularly green fluorescent protein (GFP) have revolutionized cell biology stemming from the ability to label specific intracellular compartments and cellular structures. For example, the live imaging of GFP (and its spectral variants) chimeras have allowed for a dynamic 
analysis of the cytoskeleton, organelle transport, and membrane dynamics in a multitude of organisms and cell types [1-3].  Although live imaging has become prevalent, this approach still poses many technical challenges, particularly in primary cultured neurons.  One challenge is the expression of GFP-tagged proteins in post-mitotic neurons; the other is the ability to capture fluorescent images while minimizing phototoxicity, photobleaching, 
and maintaining general cell health.  Here we provide a protocol that describes a lipid-based transfection method that yields a relatively low transfection rate (~0.5%), however is ideal for the imaging of fully polarized neurons.  A low transfection rate is essential so that single axons and dendrites can be characterized as to their orientation to the cell body to confirm directionality of transport, i.e., anterograde v. retrograde.  Our approach to imaging 
GFP expressing neurons relies on a standard wide-field fluorescent microscope outfitted with a CCD camera, image capture software, and a heated imaging chamber. We have imaged a wide variety of organelles or structures, for example, dense-core vesicles, mitochondria, growth cones, and actin without any special optics or excitation requirements other than a fluorescent light source. Additionally, spectrally-distinct, fluorescently 
labeled proteins, e.g., GFP and dsRed-tagged proteins, can be visualized near simultaneously to characterize co-transport or other coordinated cellular events.  The imaging approach described here is flexible for a variety of imaging applications and can be adopted by a laboratory for relatively little cost provided a microscope is available.

Live cell imaging is of particular utility when studying the dynamics of organelle trafficking. Here we describe a protocol for live imaging of dense-core vesicles in cultured neurons using wide-field fluorescence microscopy. This protocol is flexible and can be adapted to image other organelles such as mitochondria, endosomes, and peroxisomes.

Observing and characterizing dynamic cellular processes can yield important information about cellular activity that cannot be gained from static images.  ...

Isolation and Primary Culture of Rat Hepatic Cells

Primary hepatocyte culture is a valuable tool that has been extensively used in basic research of liver function, disease, pathophysiology, pharmacology and other related subjects. The method based on two-step collagenase perfusion for isolation of intact hepatocytes was first introduced by Berry and Friend in 1969 1 and, since then, has undergone many modifications. The most commonly used technique was described by Seglenin 1976 2. Essentially, hepatocytes are dissociated from anesthetized adult rats by a non-recirculating collagenase perfusion through the portal vein. The isolated cells are then filtered through a 100 &mu;m pore size mesh nylon filter, and cultured onto plates. After 4-hour culture, the medium is replaced with serum-containing or serum-free medium, e.g. HepatoZYME-SFM, for additional time to culture. These procedures require surgical and sterile culture steps that can be better demonstrated by video than by text. Here, we document the detailed steps for these procedures by both video and written protocol, which allow consistently in the generation of viable hepatocytes in large numbers.

Primary hepatocytes provide a valuable tool to evaluate biochemical, molecular, and metabolic functions in a physiologically relevant experimental system. We describe a reliable protocol for rat in situ liver perfusion, which consistently generates viable hepatocytes up to 1.0 &times; 108 cells per preparation with cell viability between 88 ~ 96%.

Primary hepatocyte culture is a valuable tool that has been extensively used in basic research of liver function, disease, pathophysiology, pharmacology ...

Visualization of Endoplasmic Reticulum Localized mRNAs in Mammalian Cells

In eukaryotes, most of the messenger RNAs (mRNAs) that encode secreted and membrane proteins are localized to the surface of the endoplasmic reticulum (ER). However, the visualization of these mRNAs can be challenging. This is especially true when only a fraction of the mRNA is ER-associated and their distribution to this organelle is obstructed by non-targeted (i.e. "free") transcripts. In order to monitor ER-associated mRNAs, we have developed a method in which cells are treated with a short exposure to a digitonin extraction solution that selectively permeabilizes the plasma membrane, and thus removes the cytoplasmic contents, while simultaneously maintaining the integrity of the ER. When this method is coupled with fluorescent in situ hybridization (FISH), one can clearly visualize ER-bound mRNAs by fluorescent microscopy. Using this protocol the degree of ER-association for either bulk poly(A) transcripts or specific mRNAs can be assessed and even quantified. In the process, one can use this assay to investigate the nature of mRNA-ER interactions.

Here we describe a method to visualize endoplasmic reticulum-associated mRNAs in mammalian tissue culture cells. This technique involves the selective permeabilization of the plasma membrane with digitonin to remove cytoplasmic contents followed by fluorescent in situ hybridization to detect either bulk poly(A) mRNA or specific transcripts.

In eukaryotes, most of the messenger RNAs (mRNAs) that encode secreted and membrane proteins are localized to the surface of the endoplasmic reticulum ...

4D Imaging of Protein Aggregation in Live Cells

One of the key tasks of any living cell is maintaining the proper folding of newly synthesized proteins in the face of ever-changing environmental conditions and an intracellular environment that is tightly packed, sticky, and hazardous to protein stability1. The ability to dynamically balance protein production, folding and degradation demands highly-specialized quality control machinery, whose absolute necessity is observed best when it malfunctions. Diseases such as ALS, Alzheimer's, Parkinson's, and certain forms of Cystic Fibrosis have a direct link to protein folding quality control components2, and therefore future therapeutic development requires a basic understanding of underlying processes. Our experimental challenge is to understand how cells integrate damage signals and mount responses that are tailored to diverse circumstances.
The primary reason why protein misfolding represents an existential threat to the cell is the propensity of incorrectly folded proteins to aggregate, thus causing a global perturbation of the crowded and delicate intracellular folding environment1. The folding health, or "proteostasis," of the cellular proteome is maintained, even under the duress of aging, stress and oxidative damage, by the coordinated action of different mechanistic units in an elaborate quality control system3,4. A specialized machinery of molecular chaperones can bind non-native polypeptides and promote their folding into the native state1, target them for degradation by the ubiquitin-proteasome system5, or direct them to protective aggregation inclusions6-9.
In eukaryotes, the cytosolic aggregation quality control load is partitioned between two compartments8-10: the juxtanuclear quality control compartment (JUNQ) and the insoluble protein deposit (IPOD) (Figure 1 - model). Proteins that are ubiquitinated by the protein folding quality control machinery are delivered to the JUNQ, where they are processed for degradation by the proteasome. Misfolded proteins that are not ubiquitinated are diverted to the IPOD, where they are actively aggregated in a protective compartment.
Up until this point, the methodological paradigm of live-cell fluorescence microscopy has largely been to label proteins and track their locations in the cell at specific time-points and usually in two dimensions. As new technologies have begun to grant experimenters unprecedented access to the submicron scale in living cells, the dynamic architecture of the cytosol has come into view as a challenging new frontier for experimental characterization. We present a method for rapidly monitoring the 3D spatial distributions of multiple fluorescently labeled proteins in the yeast cytosol over time. 3D timelapse (4D imaging) is not merely a technical challenge; rather, it also facilitates a dramatic shift in the conceptual framework used to analyze cellular structure.
We utilize a cytosolic folding sensor protein in live yeast to visualize distinct fates for misfolded proteins in cellular aggregation quality control, using rapid 4D fluorescent imaging. The temperature sensitive mutant of the Ubc9 protein10-12 (Ubc9ts) is extremely effective both as a sensor of cellular proteostasis, and a physiological model for tracking aggregation quality control. As with most ts proteins, Ubc9ts is fully folded and functional at permissive temperatures due to active cellular chaperones. Above 30 &deg;C, or when the cell faces misfolding stress, Ubc9ts misfolds and follows the fate of a native globular protein that has been misfolded due to mutation, heat denaturation, or oxidative damage. By fusing it to GFP or other fluorophores, it can be tracked in 3D as it forms Stress Foci, or is directed to JUNQ or IPOD.

Cellular viability depends on timely and efficient management of protein misfolding. Here we describe a method for visualizing the different potential fates of a misfolded protein: refolding, degradation, or sequestration in inclusions. We demonstrate the use of a folding sensor, Ubc9ts, for monitoring proteostasis and aggregation quality control in live cells using 4D microscopy.

One of the key tasks of any living cell is maintaining the proper folding of newly synthesized proteins in the face of ever-changing environmental ...

Visualization of Endoplasmic Reticulum Subdomains in Cultured Cells

The lipids and proteins in eukaryotic cells are continuously exchanged between cell compartments, although these retain their distinctive composition and functions despite the intense interorganelle molecular traffic. The techniques described in this paper are powerful means of studying protein and lipid mobility and trafficking in vivo and in their physiological environment. Fluorescence recovery after photobleaching (FRAP) and fluorescence loss in photobleaching (FLIP) are widely used live-cell imaging techniques for studying intracellular trafficking through the exo-endocytic pathway, the continuity between organelles or subcompartments, the formation of protein complexes, and protein localization in lipid microdomains, all of which can be observed under physiological and pathological conditions. The limitations of these approaches are mainly due to the use of fluorescent fusion proteins, and their potential drawbacks include artifactual over-expression in cells and the possibility of differences in the folding and localization of tagged and native proteins. Finally, as the limit of resolution of optical microscopy (about 200 nm) does not allow investigation of the fine structure of the ER or the specific subcompartments that can originate in cells under stress (i.e. hypoxia, drug administration, the over-expression of transmembrane ER resident proteins) or under pathological conditions, we combine live-cell imaging of cultured transfected cells with ultrastructural analyses based on transmission electron microscopy.

We describe the imaging approaches we use to investigate the distribution and mobility of the transfected fluorescent proteins resident in the endoplasmic reticulum (ER) by means of the confocal imaging of living cells. We also ultrastructurally analyze the effect of their expression on the architecture of this subcellular compartment.

The lipids and proteins in eukaryotic cells are continuously exchanged between cell compartments, although these retain their distinctive composition and ...

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 ...

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 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 ...

Application of High-speed Super-resolution SPEED Microscopy in Live Primary Cilium

The primary cilium is a microtubule-based protrusion on the surface of many eukaryotic cells and contains a unique complement of proteins that function critically in cell motility and signaling. Since cilia are incapable of synthesizing their own protein, nearly 200 unique ciliary proteins need to be trafficked between the cytosol and primary cilia. However, it is still a technical challenge to map three-dimensional (3D) locations of transport pathways for these proteins in live primary cilia due to the limitations of currently existing techniques. To conquer the challenge, recently we have developed and employed a high-speed virtual 3D super-resolution microscopy, termed single-point edge-excitation sub-diffraction (SPEED) microscopy, to determine the 3D spatial location of transport pathways for both cytosolic and membrane proteins in primary cilia of live cells. In this article, we will demonstrate the detailed setup of SPEED microscopy, the preparation of cells expressing fluorescence-protein-labeled ciliary proteins, the real-time single-molecule tracking of individual proteins in live cilium and the achievement of 3D spatial probability density maps of transport routes for ciliary proteins.

Recently we mapped the three-dimensional (3D) spatial locations of transport routes for various proteins translocating inside primary cilia in live cells. Here this paper details the experimental setup, the process of biological samples and the data analyses for the 3D super-resolution fluorescence imaging approach newly applied in live primary cilia.

The primary cilium is a microtubule-based protrusion on the surface of many eukaryotic cells and contains a unique complement of proteins that function ...

Exploiting Live Imaging to Track Nuclei During Myoblast Differentiation and Fusion

Nuclear positioning within cells is important for multiple cellular processes in development and regeneration. The most intriguing example of nuclear positioning occurs during skeletal muscle differentiation. Muscle fibers (myofibers) are multinucleated cells formed by the fusion of muscle precursor cells (myoblasts) derived from muscle stem cells (satellite cells) that undergo proliferation and differentiation. Correct nuclear positioning within myofibers is required for the proper muscle regeneration and function. The common procedure to assess myoblast differentiation and myofiber formation relies on fixed cells analyzed by immunofluorescence, which impedes the study of nuclear movement and cell behavior over time. Here, we describe a method for the analysis of myoblast differentiation and myofiber formation by live cell imaging. We provide a software for automated nuclear tracking to obtain a high-throughput quantitative characterization of nuclear dynamics and myoblast behavior (i.e., the trajectory) during differentiation and fusion.

Skeletal muscle differentiation is a highly dynamic process, which particularly relies on nuclear positioning. Here, we describe a method to track nuclei movements by live cell imaging during myoblast differentiation and myotube formation and to perform a quantitative characterization of nuclei dynamics by extracting information from automatic tracking.

Nuclear positioning within cells is important for multiple cellular processes in development and regeneration. The most intriguing example of nuclear ...