We thank Chaniotakis M. and Kounakis K. for video recording and editing. K.P. is funded by a grant from the Hellenic Foundation for Research and Innovation (HFRI) and the General Secretariat for Research and Technology (GSRT). N.T. is funded by grants from the European Research Council (ERC &#8211; GA695190 &#8211; MANNA), the European Commission Framework Programmes, and the Greek Ministry of Education.

1. Necrotic cell death-induced by hyperactive ion channels
NOTE: Gain-of-function mutations in the gene family of degenerins, including mec-4 and deg-3 among others, results in the generation of hyperactive ion channels triggering necrotic cell death of six touch receptor neurons required for mechanosensation in worms3. Necrosis induced by the aberrant stimulation of degenerins displays several mechanistic and morphological similarities to excitotoxicity in mammals. The maintenance of energy metabolism and calcium homeostasis has a crucial role on neuronal survival during necrosis11. The following strains can be used to monitor necrotic cell death triggered by hyperactive ion channels, mec-4(u231)X and deg-3(u662)V.
<ol>
	<li>Maintenance, synchronization and preparation of mutant worms for examination of necrotic cell death
	<ol>
		<li>Day 1: Pick L4 larvae of mec-4(u231) or deg-3(u662) mutant nematodes onto Nematode Growth Media (NGM; Table 1) plates seeded with Escherichia coli (OP50) using a dissecting stereomicroscope.</li>
		<li>Place 10 L4 nematodes per seeded NGM plate and grow them at the standard temperature of 20 &#176;C.</li>
		<li>Day 5: Wash the plates with 1 mL of M9 buffer (Table 1) and collect the animals in a 1.5 mL tube.</li>
		<li>Centrifuge at 10,000 x g for 30 s and remove the supernatant.</li>
		<li>Add 0.5 mL of bleaching solution (7 mL of H2O, 1 mL of 5 N NaOH and 2 mL of bleach). 
		NOTE: Bleaching solution gradually lose its efficiency; hence it should be prepared daily.</li>
		<li>Vortex and monitor periodically until the worms have dissolved. 
		NOTE: Avoid bleaching for periods longer than 5 min because the embryos&#8217; viability will be affected.</li>
		<li>Centrifuge at 10,000 x g for 30 s and remove the supernatant.</li>
		<li>Wash twice the pellet (eggs) with 1 mL of M9 buffer.</li>
		<li>After washing, resuspend the eggs in 200 &#181;L of M9 buffer and incubate them for 25 min at 34 &#176;C in a water bath.</li>
		<li>Maintain a separate group of control sample (eggs) at 20 &#176;C.</li>
		<li>Pipette 100 &#181;L of control or heat shock-treated eggs and place them on unseeded NGM plates. Each plate contains at least 100-200 eggs.</li>
		<li>Incubated the eggs at 20 &#176;C until hatching.</li>
	</ol>
	</li>
	<li>Mounting L1 larvae for examination using differential interference contrast (DIC; Nomarsky) microscopy
	<ol>
		<li>Prepare 2% agarose pads.</li>
		<li>Use 1 mL of M9 buffer to wash the plates and collect L1 larvae nematodes in 1.5 mL tubes.</li>
		<li>Centrifuge at 10,000 x g for 30 s.</li>
		<li>Remove the supernatant and keep the pellet (nematodes).</li>
		<li>Add 100 &#181;L of 20 mM M9/levamisole buffer to anesthetize the nematodes. 
		NOTE: Avoid sodium azide as an anesthetic. Sodium azide triggers mitochondrial damage and oxidative stress leading eventually to cell death induction</li>
		<li>Pipette 10 &#181;L of M9/levamisole buffer containing L1 worms and mount them on 2% agarose pads (Table 1).</li>
		<li>Gently place a coverslip on the top of the sample. 
		NOTE: Seal the coverslip with nail polish to preserve humidity throughout the process of imaging.</li>
		<li>Observe worms using differential interference contrast (DIC; Nomarsky) microscopy.</li>
		<li>Score neurodegeneration of the six touch receptor neurons by counting cells with the characteristic vacuolated appearance per nematode.</li>
	</ol>
	</li>
</ol>
2. Protein aggregate-induced neurodegeneration
NOTE: The following strains can be used to investigated protein aggregates-induced neurotoxicity: (A) overexpression of human &#945;-synuclein in dopaminergic neurons, UA44: Is[baIn1; pdat-1&#945;-syn, pdat-1GFP] and (B) overexpression of human polyglutamine protein (PolyQ) pan-neuronally, AM101: rmsIs110[prgef-1Q40::YFP]6,10.
<ol>
	<li>Maintenance, synchronization and preparation of transgenic nematodes for neurodegeneration assay
	<ol>
		<li>Use a dissecting stereomicroscope to monitor C. elegans development and growth.</li>
		<li>Day 1: Synchronize the population of transgenic nematodes by picking and transferring 15-20 L4 larvae of each strain on freshly OP50-seeded NGM plates. 
		NOTE: Use at least three plates of each strain per condition.</li>
		<li>Incubate and let the nematodes to grow at the standard temperature of 20 &#176;C.</li>
		<li>Day 2: Perform daily preconditioning for 30 minutes by transferring the plates in an incubator set at 34 &#176;C. Then, return the preconditioned nematodes back at the standard temperature of 20 &#176;C. 
		NOTE: Different genetic backgrounds might be sensitive to high temperature for long periods exposure.</li>
		<li>(A) If investigating overexpression of human &#945;-synuclein in dopaminergic neurons, UA44: Is[baIn1; pdat-1&#945;-syn, pdat-1GFP]: on Day 9, monitor 7-days-old transgenic nematodes for dopaminergic neuronal cell death.</li>
		<li>(B) If investigating overexpression of human polyglutamine protein (PolyQ) pan-neuronally, AM101: rmsIs110[prgef-1Q40::YFP]: on Day 5, measure neuronal PolyQ aggregates in the head region of 4-days-old transgenic animals expressing Q40::YFP.</li>
	</ol>
	</li>
	<li>Mounting the samples for microscopic examination
	<ol>
		<li>Prepare 2% agarose pads (Table 1).</li>
		<li>Add 10 &#181;L of 20 mM M9/levamisole buffer drop at the center of the agarose pad.</li>
		<li>Pick the respective transgenic nematodes and transfer them in a M9/levamisole drop. 
		NOTE: Place 20-30 nematodes per drop.</li>
		<li>Place gently a coverslip on the top of the sample. 
		NOTE: Seal the coverslip with nail polish to preserve humidity throughout the process of imaging.</li>
		<li>Proceed to microscopic examination of the respective samples.</li>
	</ol>
	</li>
	<li>Acquisition process and data analysis of transgenic nematodes co-expressing &#945;-synuclein and cytosolic GFP in dopaminergic neurons
	<ol>
		<li>Use an epifluorescence microscope combined with a camera (e.g., EVOS FL Auto 2).</li>
		<li>Detect and capture z-stack images of the head region at 20x magnification.</li>
		<li>Save and collect the maximum intensity projection images.</li>
		<li>Proceed to the analysis of the acquired images.</li>
		<li>Examine the transgenic worms for neurodegeneration by scoring the following cellular characteristics, (i) loss of fluorescence from neurons expressing GFP under the promoter of dat-1, (ii) neurons showing soma and/or axonal blebbing, outgrowths or dendritic loss.</li>
		<li>Import and analyze the data by using a software package (e.g., Excel).</li>
	</ol>
	</li>
</ol>
3. Acquisition process and data analysis of transgenic nematodes expressing pan-neuronally PolyQ40 fused with YFP
<ol>
	<li>Use an epifluorescence microscope combined with a camera (e.g., EVOS FL Auto 2).</li>
	<li>Detect and capture z-stack images of the head region at 20x magnification.</li>
	<li>Save and collect the maximum intensity projection images.</li>
	<li>Proceed to the analysis of the acquired images by using Fiji software.</li>
	<li>Open images with Fiji program14.</li>
	<li>Select Split Channels command via the Image and Color drop-down menu. 
	NOTE: Keep the green channel image.</li>
	<li>Use the freehand selection tool to manually set the fluorescent region of interest (ROI; e.g., head).</li>
	<li>Add the respective ROI in ROI Manager via Analyze and Tools drop-down menu.</li>
	<li>Subtract the background to 50% by selecting Process and Subtract Background.</li>
	<li>Set up and apply threshold values via the menu command Image | Adjust | Threshold. Keep and set the same threshold values throughout image analysis of the entire experiment.</li>
	<li>Select the respective ROI from the ROI Manager.</li>
	<li>Analyze the number of protein aggregates by using the menu command Analyze and Analyze Particles.</li>
	<li>Repeat steps 3.5-3.12 for each acquired image.</li>
	<li>Copy the display values from the separate Results window.</li>
	<li>Paste/Import and analyze the results by using a software package.</li>
</ol>
4. Report statistical analysis
<ol>
	<li>Use at least 30 nematodes for each experimental condition. Perform three biological replicates.</li>
	<li>Use statistical analysis software to either conduct student t-test (comparison between two groups) or ANOVA (comparison among multiple groups) for statistical analysis with p &#60; 0.05 as significant.</li>
</ol>

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	<li>Nikoletopoulou, V., Tavernarakis, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Necrotic+cell+death+in+Caenorhabditis+elegans.">Necrotic cell death in Caenorhabditis elegans.</a> Methods in Enzymology. 545, 127-155 (2014).</li><li>Syntichaki, P., Tavernarakis, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+biochemistry+of+neuronal+necrosis:+rogue+biology.">The biochemistry of neuronal necrosis: rogue biology.</a> Nature Reviews Neuroscience. 4 (8), 672-684 (2003).</li><li>Syntichaki, P., Tavernarakis, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Genetic+models+of+mechanotransduction:+the+nematode+Caenorhabditis+elegans.">Genetic models of mechanotransduction: the nematode Caenorhabditis elegans.</a> Physiological Reviews. 84 (4), 1097-1153 (2004).</li><li>Berkowitz, L. 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=Application+of+a+C.+elegans+dopamine+neuron+degeneration+assay+for+the+validation+of+potential+Parkinson's+disease+genes.">Application of a C. elegans dopamine neuron degeneration assay for the validation of potential Parkinson's disease genes.</a> Journal of Visualized Experiments. (17), (2008).</li><li>Brignull, H. R., Moore, F. E., Tang, S. J., Morimoto, R. I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Polyglutamine+proteins+at+the+pathogenic+threshold+display+neuron-specific+aggregation+in+a+pan-neuronal+Caenorhabditis+elegans+model.">Polyglutamine proteins at the pathogenic threshold display neuron-specific aggregation in a pan-neuronal Caenorhabditis elegans model.</a> Journal of Neuroscience. 26 (29), 7597-7606 (2006).</li><li>Gidalevitz, T., Ben-Zvi, A., Ho, K. H., Brignull, H. R., Morimoto, R. I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Progressive+disruption+of+cellular+protein+folding+in+models+of+polyglutamine+diseases.">Progressive disruption of cellular protein folding in models of polyglutamine diseases.</a> Science. 311 (5766), 1471-1474 (2006).</li><li>Gitler, A. D., 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+Parkinson's+disease+protein+alpha-synuclein+disrupts+cellular+Rab+homeostasis.">The Parkinson's disease protein alpha-synuclein disrupts cellular Rab homeostasis.</a> Proceedings of the National Academy of Sciences of the United States of America. 105 (1), 145-150 (2008).</li><li>Klaips, C. L., Jayaraj, G. G., Hartl, F. U. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Pathways+of+cellular+proteostasis+in+aging+and+disease.">Pathways of cellular proteostasis in aging and disease.</a> Journal of Cell Biology. 217 (1), 51-63 (2018).</li><li>Labbadia, J., Morimoto, R. I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+biology+of+proteostasis+in+aging+and+disease.">The biology of proteostasis in aging and disease.</a> Annual Review of Biochemistry. 84, 435-464 (2015).</li><li>Tucci, M. L., Harrington, A. J., Caldwell, G. A., Caldwell, K. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Modeling+dopamine+neuron+degeneration+in+Caenorhabditis+elegans.">Modeling dopamine neuron degeneration in Caenorhabditis elegans.</a> Methods in Molecular Biology. 793, 129-148 (2011).</li><li>Kourtis, N., Nikoletopoulou, V., Tavernarakis, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Small+heat-shock+proteins+protect+from+heat-stroke-associated+neurodegeneration.">Small heat-shock proteins protect from heat-stroke-associated neurodegeneration.</a> Nature. 490 (7419), 213-218 (2012).</li><li>Kourtis, N., Tavernarakis, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Small+heat+shock+proteins+and+neurodegeneration:+recent+developments.">Small heat shock proteins and neurodegeneration: recent developments.</a> BioMolecular Concepts. 9 (1), 94-102 (2018).</li><li>Kumsta, C., Chang, J. T., Schmalz, J., Hansen, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Hormetic+heat+stress+and+HSF-1+induce+autophagy+to+improve+survival+and+proteostasis+in+C.+elegans.">Hormetic heat stress and HSF-1 induce autophagy to improve survival and proteostasis in C. elegans.</a> Nature Communications. 8, 14337 (2017).</li><li>Schindelin, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Fiji:+an+open-source+platform+for+biological-image+analysis.">Fiji: an open-source platform for biological-image analysis.</a> Nature Methods. 9 (7), 676-682 (2012).</li><li>Palikaras, K., Lionaki, E., Tavernarakis, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Coordination+of+mitophagy+and+mitochondrial+biogenesis+during+ageing+in+C.+elegans.">Coordination of mitophagy and mitochondrial biogenesis during ageing in C. elegans.</a> Nature. 521 (7553), 525-528 (2015).</li><li>Samara, C., Syntichaki, P., Tavernarakis, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Autophagy+is+required+for+necrotic+cell+death+in+Caenorhabditis+elegans.">Autophagy is required for necrotic cell death in Caenorhabditis elegans.</a> Cell Death and Differentiation. 15 (1), 105-112 (2008).</li></ol>

The authors declare no competing interests.

Here, we introduce and describe widely accessible methodologies for growth, synchronization and microscopic examination of some versatile C. elegans models investigating age-dependent neurodegeneration. Particularly, we assess and dissect the cellular and molecular underpinnings of age-related neuronal breakdown by using hyperactivated ion channel-induced necrosis and protein aggregate-induced neurotoxicity1,2,3,</...

Over the last two decades, C. elegans has been widely used as a model organism to investigate the molecular mechanisms of necrotic cell death. C. elegans offers an exceptionally well-characterized and mapped nervous system, transparent body structure and a diverse repertoire of genetic and imaging methods to monitor in vivo cellular function and survival throughout ageing. Thus, several C. elegans genetic models of neurodegeneration have been already developed to assess neuronal viability. In particular, well-described and used nematode models include the hyperactive ion channel-induced necrosis1,2,3 and cell death triggered by increased protein aggregation4,5,6,7,8,9,10 and heat stroke11,12, among others.
Short-term exposure to sub-lethal temperatures conferred resistance against necrotic cell death, triggered by a subsequent heat stress both in nematodes and mammalian neurons11. Interestingly, daily preconditioning of nematodes at a mild elevated temperature protects against neurodegeneration, which is inflicted by diverse stimuli, such as ionic imbalance (e.g., mec-4(u231) and/or deg-3(u662)) and protein aggregation (e.g., &#945;-synuclein and polyQ40)11,13.
Here, we describe versatile methodologies using C. elegans to monitor and evaluate age-dependent neurodegeneration in well-established models of human diseases, such as excitotoxicity-triggered cell death, Parkinson&#8217;s and Huntington&#8217;s disease. Moreover, we underline the neuroprotective role of heat preconditioning in several models of neurodegeneration. A combination of these techniques together with genetic and/or pharmacological screens will result in the identification and characterization of novel cell death modulators, with potential therapeutic interest.

<table>
	<tbody>
		<tr>
			<td>Agar</td>
			<td>Sigma-Aldrich</td>
			<td>5040</td>
			<td></td>
		</tr>
		<tr>
			<td>Agarose</td>
			<td>Biozym</td>
			<td>8,40,004</td>
			<td></td>
		</tr>
		<tr>
			<td>AM101: rmsIs110[prgef-1Q40::YFP]</td>
			<td>Caenorhabditis Genetics Center (CGC)</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Calcium chloride dehydrate (CaCl2&#8729;2H2O)</td>
			<td>Sigma-Aldrich</td>
			<td>C5080</td>
			<td></td>
		</tr>
		<tr>
			<td>Cholesterol</td>
			<td>SERVA Electrophoresis</td>
			<td>17101.01</td>
			<td></td>
		</tr>
		<tr>
			<td>deg-3(u662)V or deg-3(d)</td>
			<td>Caenorhabditis Genetics Center (CGC)</td>
			<td></td>
			<td>Maintain animals at 20 &#176;C</td>
		</tr>
		<tr>
			<td>DIC microscope (Nomarsky)</td>
			<td>Zeiss</td>
			<td></td>
			<td>Axio Vert A1</td>
		</tr>
		<tr>
			<td>Dissecting stereomicroscope</td>
			<td>Nikon Corporation</td>
			<td></td>
			<td>SMZ645</td>
		</tr>
		<tr>
			<td>Epifluorescence microscope</td>
			<td>Thermo Fisher Scientific</td>
			<td></td>
			<td>EVOS Cell Imaging Systems</td>
		</tr>
		<tr>
			<td>Escherichia coli OP50 strain</td>
			<td>Caenorhabditis Genetics Center (CGC)</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Greiner Petri dishes (60 mm x 15 mm)</td>
			<td>Sigma-Aldrich</td>
			<td>P5237</td>
			<td></td>
		</tr>
		<tr>
			<td>image analysis software</td>
			<td>Fiji</td>
			<td></td>
			<td>https://fiji.sc</td>
		</tr>
		<tr>
			<td>KH2PO4</td>
			<td>EMD Millipore</td>
			<td>1,37,010</td>
			<td></td>
		</tr>
		<tr>
			<td>K2HPO4</td>
			<td>EMD Millipore</td>
			<td>1,04,873</td>
			<td></td>
		</tr>
		<tr>
			<td>Magnesium sulfate (MgSO4)</td>
			<td>Sigma-Aldrich</td>
			<td>M7506</td>
			<td></td>
		</tr>
		<tr>
			<td>mec-4(u231)X or mec-4(d)</td>
			<td>Caenorhabditis Genetics Center (CGC)</td>
			<td></td>
			<td>Maintain animals at 20 &#176;C</td>
		</tr>
		<tr>
			<td>Microscope slides (75 mm x 25 mm x 1 mm)</td>
			<td>Marienfeld, Lauda-Koenigshofen</td>
			<td>10 006 12</td>
			<td></td>
		</tr>
		<tr>
			<td>Microscope cover glass (18 mm x 18 mm)</td>
			<td>Marienfeld, Lauda-Koenigshofen</td>
			<td>01 010 30</td>
			<td></td>
		</tr>
		<tr>
			<td>Microsoft Office 2011 Excel software package</td>
			<td>Microsoft Corporation, Redmond, USA</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Na2HPO4</td>
			<td>EMD Millipore</td>
			<td>1,06,586</td>
			<td></td>
		</tr>
		<tr>
			<td>Nematode growth medium (NGM) agar plates</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Nystatin stock solution</td>
			<td>Sigma-Aldrich</td>
			<td>N3503</td>
			<td></td>
		</tr>
		<tr>
			<td>Peptone</td>
			<td>BD, Bacto</td>
			<td>211677</td>
			<td></td>
		</tr>
		<tr>
			<td>Phosphate buffer</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium chloride (NaCl)</td>
			<td>EMD Millipore</td>
			<td>1,06,40,41,000</td>
			<td></td>
		</tr>
		<tr>
			<td>Standard equipment for preparing agar plates (autoclave, Petri dishes, etc.)</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Standard equipment for maintaining worms (platinum wire pick, incubators, etc.)</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>statistical analysis software</td>
			<td>GraphPad Software Inc., San Diego, USA</td>
			<td></td>
			<td>GraphPad Prism software package</td>
		</tr>
		<tr>
			<td>Streptomycin</td>
			<td>Sigma-Aldrich</td>
			<td>S6501</td>
			<td></td>
		</tr>
		<tr>
			<td>Tetramisole hydrochloride</td>
			<td>Sigma-Aldrich</td>
			<td>L9756</td>
			<td></td>
		</tr>
		<tr>
			<td>UA44: Is[baIn1; pdat-1&#945;-syn, pdat-1GFP]</td>
			<td></td>
			<td></td>
			<td>Upon request: G. Caldwell (University of Alabama, Tuscaloosa AL)</td>
		</tr>
	</tbody>
</table>

modeling age-associated neurodegenerative diseases in caenorhabditis elegans

Battling human neurodegenerative pathologies and managing their pervasive socioeconomic impact is becoming a global priority. Notwithstanding their detrimental effects on the human life quality and the healthcare system, the majority of human neurodegenerative disorders still remain incurable and non-preventable. Therefore, the development of novel therapeutic interventions against such maladies is becoming a pressing urgency. Age-associated deterioration of neuronal circuits and function is evolutionarily conserved in organisms as diverse as the lowly worm Caenorhabditis elegans and humans, signifying similarities in the underlying cellular and molecular mechanisms. C. elegans is a highly malleable genetic model, which offers a well-characterized nervous system, body transparency and a diverse repertoire of genetic and imaging techniques to assess neuronal activity and quality control during ageing. Here, we introduce and describe methodologies utilizing some versatile nematode models, including hyperactivated ion channel-induced necrosis (e.g., deg-3(d) and mec-4(d)) and protein aggregate (e.g., &#945;-syunclein and poly-glutamate)-induced neurotoxicity, to monitor and dissect the cellular and molecular underpinnings of age-related neuronal breakdown. A combination of these animal neurodegeneration models, together with genetic and pharmacological screens for cell death modulators will lead to an unprecedented understanding of age-related breakdown of neuronal function and will provide critical insights with broad relevance to human health and quality of life.

Necrotic cell death-induced by hyperactive ion channels 
Using the procedures presented here, mec-4(u231) and deg-3u662) mutant embryos were either incubated for 25 min at 34 &#176;C or kept at the standard temperature of 20 &#176;C. Upon hatching, the number of neuronal cell corpses was determined at the L1 larval stage of both groups. Necrotic cell death is diminished in nematodes that hatched from heat shock preconditioned eggs (Figure 1A-1B...

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Modeling Age-Associated Neurodegenerative Diseases in Caenorhabditis elegans

Here, we introduce and describe widely accessible methodologies utilizing some versatile nematode models, including hyperactivated ion channel-induced necrosis and protein aggregate-induced neurotoxicity, to monitor and dissect the cellular and molecular underpinnings of age-associated neurodegenerative diseases.

Modeling Age-Associated Neurodegenerative Diseases in Caenorhabditis elegans

Battling human neurodegenerative pathologies and managing their pervasive socioeconomic impact is becoming a global priority. Notwithstanding their ...

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5.3K Views.  Foundation for Research and Technology-Hellas, Greece. Here, we introduce and describe widely accessible methodologies utilizing some versatile nematode models, including hyperactivated ion channel-induced necrosis and protein aggregate-induced neurotoxicity, to monitor and dissect the cellular and molecular underpinnings of age-associated neurodegenerative diseases.

Video: Modeling Age-Associated Neurodegenerative Diseases in Caenorhabditis elegans

Interview: Protein Folding and Studies of Neurodegenerative Diseases

In this interview, Dr. Lindquist describes relationships between protein folding, prion diseases and neurodegenerative disorders. The problem of the protein folding is at the core of the modern biology. In addition to their traditional biochemical functions, proteins can mediate transfer of biological information and therefore can be considered a genetic material. This recently discovered function of proteins has important implications for studies of human disorders. Dr. Lindquist also describes current experimental approaches to investigate the mechanism of neurodegenerative diseases based on genetic studies in model organisms.

In this interview, Dr. Lindquist describes relationships between protein folding, prion diseases and neurodegenerative disorders. The problem of the protein folding is at the core of the modern biology. In addition to their traditional biochemical functions, proteins can mediate transfer of biological information and therefore can be considered a genetic material. This recently discovered function of proteins has important implications for studies of human disorders. Dr. Lindquist also describes current experimental approaches to investigate the mechanism of neurodegenerative diseases based on genetic studies in model organisms.

In this interview, Dr. Lindquist describes relationships between protein folding, prion diseases and neurodegenerative disorders. The problem of the ...

The Production of C. elegans Transgenes via Recombineering with the galK Selectable Marker

The creation of transgenic animals is widely utilized in C. elegans research including the use of GFP fusion proteins to study the regulation and expression pattern of genes of interest or generation of tandem affinity purification (TAP) tagged versions of specific genes to facilitate their purification. Typically transgenes are generated by placing a promoter upstream of a GFP reporter gene or cDNA of interest, and this often produces a representative expression pattern. However, critical elements of gene regulation, such as control elements in the 3' untranslated region or alternative promoters, could be missed by this approach. Further only a single splice variant can be usually studied by this means. In contrast, the use of worm genomic DNA carried by fosmid DNA clones likely includes most if not all elements involved in gene regulation in vivo which permits the greater ability to capture the genuine expression pattern and timing. To facilitate the generation of transgenes using fosmid DNA, we describe an E. coli based recombineering procedure to insert GFP, a TAP-tag, or other sequences of interest into any location in the gene. The procedure uses the galK gene as the selection marker for both the positive and negative selection steps in recombineering which results in obtaining the desired modification with high efficiency. Further, plasmids containing the galK gene flanked by homology arms to commonly used GFP and TAP fusion genes are available which reduce the cost of oligos by 50% when generating a GFP or TAP fusion protein. These plasmids use the R6K replication origin which precludes the need for extensive PCR product purification. Finally, we also demonstrate a technique to integrate the unc-119 marker on to the fosmid backbone which allows the fosmid to be directly injected or bombarded into worms to generate transgenic animals. This video demonstrates the procedures involved in generating a transgene via recombineering using this method.

The Production of C. elegans Transgenes via Recombineering with the galK Selectable Marker

The ability to produce transgenes for Caenorhabditis elegans using genomic DNA carried by fosmids is particularly attractive as all of the native regulatory elements are retained. Described is a simple and robust procedure for the production of transgenes via recombineering with the galK selectable marker.

The creation of transgenic animals is widely utilized in C. elegans research including the use of GFP fusion proteins to study the regulation and ...

Isolation and In vitro Activation of Caenorhabditis elegans Sperm

Males and hermaphrodites are the two naturally found sexual forms in the nematode C. elegans. The amoeboid sperm are produced by both males and hermaphrodites. In the earlier phase of gametogenesis, the germ cells of hermaphrodites differentiate into limited number of sperm - around 300 - and are stored in a small 'bag' called the spermatheca. Later on, hermaphrodites continually produce oocytes1. In contrast, males produce exclusively sperm throughout their adulthood. The males produce so much sperm that it accounts for &gt;50% of the total cells in a typical adult worm2. Therefore, isolating sperm from males is easier than from that of hermaphrodites.
Only a small proportion of males are naturally generated due to spontaneous non-disjunction of X chromosome3. Crossing hermaphrodites with males or more conveniently, the introduction of mutations to give rise to Him (High Incidence of Males) phenotype are some of strategies through which one can enrich the male population3.
Males can be easily distinguished from hermaphrodites by observing the tail morphology4. Hermaphrodite's tail is pointed, whereas male tail is rounded with mating structures.
Cutting the tail releases vast number of spermatids stored inside the male reproductive tract. Dissection is performed under a stereo microscope using 27 gauge needles. Since spermatids are not physically connected with any other cells, hydraulic pressure expels internal contents of male body, including spermatids2.
Males are directly dissected on a small drop of 'Sperm Medium'. Spermatids are sensitive to alteration in the pH. Hence, HEPES, a compound with good buffering capacity is used in sperm media. Glucose and other salts present in sperm media help maintain osmotic pressure to maintain the integrity of sperm.
Post-meiotic differentiation of spermatids into spermatozoa is termed spermiogenesis or sperm activation. Shakes5, and Nelson6 previously showed that round spermatids can be induced to differentiate into spermatozoa by adding various activating compounds including Pronase E. Here we demonstrate in vitro spermiogenesis of C. elegans spermatids using Pronase E.
Successful spermiogenesis is pre-requisite for fertility and hence the mutants defective in spermiogenesis are sterile. Hitherto several mutants have been shown to be defective specifically in spermiogenesis process7. Abnormality found during in vitro activation of novel Spe (Spermatogenesis defective) mutants would help us discover additional players participating in this event.

Isolation and In vitro Activation of Caenorhabditis elegans Sperm

A protocol for isolating and activating spermatids from male C. elegans is described here. Cutting the posterior end of male releases spermatids. The spermatids can be activated by addition of protease.

Males and hermaphrodites are the two naturally found sexual forms in the nematode C. elegans. The amoeboid sperm are produced by both males and ...

Solid Plate-based Dietary Restriction in Caenorhabditis elegans

Reduction of food intake without malnutrition or starvation is known to increase lifespan and delay the onset of various age-related diseases in a wide range of species, including mammals. It also causes a decrease in body weight and fertility, as well as lower levels of plasma glucose, insulin, and IGF-1 in these animals. This treatment is often referred to as dietary restriction (DR) or caloric restriction (CR). The nematode Caenorhabditis elegans has emerged as an important model organism for studying the biology of aging. Both environmental and genetic manipulations have been used to model DR and have shown to extend lifespan in C. elegans. However, many of the reported DR studies in C. elegans were done by propagating animals in liquid media, while most of the genetic studies in the aging field were done on the standard solid agar in petri plates. Here we present a DR protocol using standard solid NGM agar-based plate with killed bacteria.

Solid Plate-based Dietary Restriction in Caenorhabditis elegans

Here we present a protocol for performing solid plate-based dietary restriction in C. elegans with killed bacteria.

Reduction of food intake without malnutrition or starvation is known to increase lifespan and delay the onset of various age-related diseases in a wide ...

Time-lapse Microscopy of Early Embryogenesis in Caenorhabditis elegans

Caenorhabditis elegans has often been used as a model system in studies of early developmental processes. The transparency of the 
embryos, the genetic resources, and the relative ease of transformation are qualities that make C. elegans an excellent model for early embryogenesis. Laser-based 
confocal microscopy and fluorescently labeled tags allow researchers to follow specific cellular structures and proteins in the developing embryo. For example, 
one can follow specific organelles, such as lysosomes or mitochondria, using fluorescently labeled dyes. These dyes can be delivered to the early embryo by means 
of microinjection into the adult gonad. Also, the localization of specific proteins can be followed using fluorescent protein tags. Examples are presented here 
demonstrating the use of a fluorescent lysosomal dye as well as fluorescently tagged histone and ubiquitin proteins. The labeled histone is used to visualize 
the DNA and thus identify the stage of the cell cycle. GFP-tagged ubiquitin reveals the dynamics of ubiquitinated vesicles in the early embryo. Observations 
of labeled lysosomes and GFP:: ubiquitin can be used to determine if there is colocalization between ubiquitinated vesicles and lysosomes. A technique for 
the microinjection of the lysosomal dye is presented. Techniques for generating transgenenic strains are presented elsewhere (1, 2). For imaging, embryos 
are cut out of adult hermaphrodite nematodes and mounted onto 2% agarose pads followed by time-lapse microscopy on a standard laser scanning confocal 
microscope or a spinning disk confocal microscope. This methodology provides for the high resolution visualization of early embryogenesis.

Time-lapse Microscopy of Early Embryogenesis in Caenorhabditis elegans

This article describes a technique for the visualization of the early events of embryogenesis in the nematode Caenorhabditis elegans.

Caenorhabditis elegans has often been used as a model system in studies of early developmental processes.  The transparency of the 
embryos, the genetic ...

Basic Caenorhabditis elegans Methods: Synchronization and Observation

Research into the molecular and developmental biology of the nematode Caenorhabditis elegans was begun in the early seventies by Sydney Brenner and it has since been used extensively as a model organism 1. C. elegans possesses key attributes such as simplicity, transparency and short life cycle that have made it a suitable experimental system for fundamental biological studies for many years 2. Discoveries in this nematode have broad implications because many cellular and molecular processes that control animal development are evolutionary conserved 3.
C. elegans life cycle goes through an embryonic stage and four larval stages before animals reach adulthood. Development can take 2 to 4 days depending on the temperature. In each of the stages several characteristic traits can be observed. The knowledge of its complete cell lineage 4,5 together with the deep annotation of its genome turn this nematode into a great model in fields as diverse as the neurobiology 6, aging 7,8, stem cell biology 9 and germ line biology 10. 
An additional feature that makes C. elegans an attractive model to work with is the possibility of obtaining populations of worms synchronized at a specific stage through a relatively easy protocol. The ease of maintaining and propagating this nematode added to the possibility of synchronization provide a powerful tool to obtain large amounts of worms, which can be used for a wide variety of small or high-throughput experiments such as RNAi screens, microarrays, massive sequencing, immunoblot or in situ hybridization, among others. 
Because of its transparency, C. elegans structures can be distinguished under the microscope using Differential Interference Contrast microscopy, also known as Nomarski microscopy. The use of a fluorescent DNA binder, DAPI (4',6-diamidino-2-phenylindole), for instance, can lead to the specific identification and localization of individual cells, as well as subcellular structures/defects associated to them.

Basic Caenorhabditis elegans Methods: Synchronization and Observation

The easiness of maintaining and propagating the nematode C. elegans make it a nice model organism to work with. The possibility of synchronizing worms allows the work with a significant amount of subjects at the same developmental stage, what facilitates the study of one particular process in many animals.

Research into the molecular and developmental biology of the nematode Caenorhabditis elegans was begun in the early seventies by Sydney Brenner and it has ...

Prostaglandin Extraction and Analysis in Caenorhabditis elegans

Caenorhabditis elegans is emerging as a powerful animal model to study the biology of lipids1-9. Prostaglandins are an important class of eicosanoids, which are lipid signals derived from polyunsaturated fatty acids (PUFAs)10-14. These signalling molecules are difficult to study because of their low abundance and reactive nature. The characteristic feature of prostaglandins is a cyclopentane ring structure located within the fatty acid backbone. In mammals, prostaglandins can be formed through cyclooxygenase enzyme-dependent and -independent pathways10,15. C. elegans synthesizes a wide array of prostaglandins independent of cyclooxygenases6,16,17. A large class of F-series prostaglandins has been identified, but the study of eicosanoids is at an early stage with ample room for new discoveries. Here we describe a procedure for extracting and analyzing prostaglandins and other eicosanoids. Charged lipids are extracted from mass worm cultures using a liquid-liquid extraction technique and analyzed by liquid chromatography coupled to electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS). The inclusion of deuterated analogs of prostaglandins, such as PGF2 &alpha;-d4 as an internal standard is recommended for quantitative analysis. Multiple reaction monitoring or MRM can be used to quantify and compare specific prostaglandin types between wild-type and mutant animals. Collision-induced decomposition or MS/MS can be used to obtain information on important structural features. Liquid chromatography mass spectrometry (LC-MS) survey scans of a selected mass range, such as m/z 315-360 can be used to evaluate global changes in prostaglandin levels. We provide examples of all three analyses. These methods will provide researchers with a toolset for discovering novel eicosanoids and delineating their metabolic pathways.

Prostaglandin Extraction and Analysis in Caenorhabditis elegans

In this paper, we describe an optimized procedure for extracting and analyzing prostaglandins and other eicosanoids from C. elegans using LC-MS/MS.

Caenorhabditis elegans is emerging as a powerful animal model to study the biology of lipids1-9. Prostaglandins are an important class of eicosanoids, ...

Cultivation of Caenorhabditis elegans in Three Dimensions in the Laboratory

The use of genetic model organisms such as Caenorhabditis elegans has led to seminal discoveries in biology over the last five decades. Most of what we know about C. elegans is limited to laboratory cultivation of the nematodes that may not necessarily reflect the environments they normally inhabit in nature. Cultivation of C. elegans in a 3D habitat that is more similar to the 3D matrix that worms encounter in rotten fruits and vegetative compost in nature could reveal novel phenotypes and behaviors not observed in 2D. In addition, experiments in 3D can address how phenotypes we observe in 2D are relevant for the worm in nature. Here, a new method in which C. elegans grows and reproduces normally in three dimensions is presented. Cultivation of C. elegans in Nematode Growth Tube-3D (NGT-3D) can allow us to measure the reproductive fitness of C. elegans strains or different conditions in a 3D environment. We also present a novel method, termed Nematode Growth Bottle-3D (NGB-3D), to cultivate C. elegans in 3D for microscopic analysis. These methods allow scientists to study C. elegans biology in conditions that are more reflective of the environments they encounter in nature. These can help us to understand the overlying evolutionary relevance of the physiology and behavior of C. elegans we observe in the laboratory.

Cultivation of Caenorhabditis elegans in Three Dimensions in the Laboratory

We present a simple method to construct 3D nematode cultivation systems called NGT-3D and NGB-3D. These can be used to study nematode fitness and behaviors in habitats that are more similar to natural Caenorhabditis elegans habitats than the standard 2D laboratory C. elegans culture plates.

The use of genetic model organisms such as Caenorhabditis elegans has led to seminal discoveries in biology over the last five decades. Most of what we ...

Methods to Study Changes in Inherent Protein Aggregation with Age in Caenorhabditis elegans

In the last decades, the prevalence of neurodegenerative disorders, such as Alzheimer's disease (AD) and Parkinson's disease (PD), has grown. These age-associated disorders are characterized by the appearance of protein aggregates with fibrillary structure in the brains of these patients. Exactly why normally soluble proteins undergo an aggregation process remains poorly understood. The discovery that protein aggregation is not limited to disease processes and instead part of the normal aging process enables the study of the molecular and cellular mechanisms that regulate protein aggregation, without using ectopically expressed human disease-associated proteins. Here we describe methodologies to examine inherent protein aggregation in Caenorhabditis elegans through complementary approaches. First, we examine how to grow large numbers of age-synchronized C. elegans to obtain aged animals and we present the biochemical procedures to isolate highly-insoluble-large aggregates. In combination with a targeted genetic knockdown, it is possible to dissect the role of a gene of interest in promoting or preventing age-dependent protein aggregation by using either a comprehensive analysis with quantitative mass spectrometry or a candidate-based analysis with antibodies. These findings are then confirmed by in vivo analysis with transgenic animals expressing fluorescent-tagged aggregation-prone proteins. These methods should help clarify why certain proteins are prone to aggregate with age and ultimately how to keep these proteins fully functional.

Methods to Study Changes in Inherent Protein Aggregation with Age in Caenorhabditis elegans

The goal of the method presented here is to explore protein aggregation during normal aging in the model organism C. elegans. The protocol represents a powerful tool to study the highly insoluble large aggregates that form with age and to determine how changes in proteostasis impact protein aggregation.

In the last decades, the prevalence of neurodegenerative disorders, such as Alzheimer's disease (AD) and Parkinson's disease (PD), has grown. These ...

Measurement of Oxygen Consumption Rates in Intact Caenorhabditis elegans

Optimal mitochondrial function is critical for healthy cellular activity, particularly in cells that have high energy demands like those in the nervous system and muscle. Consistent with this, mitochondrial dysfunction has been associated with a myriad of neurodegenerative diseases and aging in general. Caenorhabditis elegans have been a powerful model system for elucidating the many intricacies of mitochondrial function. Mitochondrial respiration is a strong indicator of mitochondrial function and recently developed respirometers offer a state-of-the-art platform to measure respiration in cells. In this protocol, we provide a technique to analyze live, intact C. elegans. This protocol spans a period of ~7 days and includes steps for (1) growing and synchronization of C. elegans, (2) preparation&#160;of compounds to be injected and hydration of probes, (3) drug loading and cartridge equilibration, (4) preparation of worm assay plate and assay run, and (5) post-experiment data analysis.

Measurement of Oxygen Consumption Rates in Intact Caenorhabditis elegans

Mitochondrial respiration is critical for organismal survival; therefore, oxygen consumption rate is an excellent indicator of mitochondrial health. In this protocol, we describe the use of a commercially available respirometer to measure basal and maximal oxygen consumption rates in live, intact, and freely-motile Caenorhabditis elegans.

Optimal mitochondrial function is critical for healthy cellular activity, particularly in cells that have high energy demands like those in the nervous ...

Modeling Age-Associated Neurodegenerative Diseases in Caenorhabditis elegans

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Interview: Protein Folding and Studies of Neurodegenerative Diseases

The Production of C. elegans Transgenes via Recombineering with the galK Selectable Marker

Isolation and In vitro Activation of Caenorhabditis elegans Sperm

Solid Plate-based Dietary Restriction in Caenorhabditis elegans

Time-lapse Microscopy of Early Embryogenesis in Caenorhabditis elegans

Basic Caenorhabditis elegans Methods: Synchronization and Observation

Prostaglandin Extraction and Analysis in Caenorhabditis elegans

Cultivation of Caenorhabditis elegans in Three Dimensions in the Laboratory

Methods to Study Changes in Inherent Protein Aggregation with Age in Caenorhabditis elegans

Measurement of Oxygen Consumption Rates in Intact Caenorhabditis elegans